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AuthorsAuthor(s) IDTitleYearSource titleVolumeIssueArt. No.Page startPage endPage countCited byDOILinkAffiliationsAuthors with affiliationsAbstractAuthor KeywordsIndex KeywordsMolecular Sequence NumbersChemicals/CASTradenamesManufacturersFunding DetailsFunding Text 1Funding Text 2Funding Text 3Funding Text 4Funding Text 5Funding Text 6Funding Text 7Funding Text 8Funding Text 9Funding Text 10Correspondence AddressEditorsSponsorsPublisherConference nameConference dateConference locationConference codeISSNISBNCODENPubMed IDLanguage of Original DocumentAbbreviated Source TitleDocument TypePublication StageOpen AccessSourceEID
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Ulmer B., Odenthal M., Buettner R., Roth W., Kloth M.57311094800;7004338357;7005353115;7201760493;6603589047;Diffusion kernel-based predictive modeling of KRAS dependency in KRAS wild type cancer cell lines2022npj Systems Biology and Applications81210.1038/s41540-021-00211-8https://www.scopus.com/inward/record.uri?eid=2-s2.0-85123201537&doi=10.1038%2fs41540-021-00211-8&partnerID=40&md5=571597a2475ed9c96b51178f53143fbbInstitute of Pathology, Cologne University Hospital, Cologne, Germany; Institute of Pathology, Mainz University Hospital, Mainz, GermanyUlmer, B., Institute of Pathology, Cologne University Hospital, Cologne, Germany; Odenthal, M., Institute of Pathology, Cologne University Hospital, Cologne, Germany; Buettner, R., Institute of Pathology, Cologne University Hospital, Cologne, Germany; Roth, W., Institute of Pathology, Mainz University Hospital, Mainz, Germany; Kloth, M., Institute of Pathology, Mainz University Hospital, Mainz, GermanyRecent progress in clinical development of KRAS inhibitors has raised interest in predicting the tumor dependency on frequently mutated RAS-pathway oncogenes. However, even without such activating mutations, RAS proteins represent core components in signal integration of several membrane-bound kinases. This raises the question of applications of specific inhibitors independent from the mutational status. Here, we examined CRISPR/RNAi data from over 700 cancer cell lines and identified a subset of cell lines without KRAS gain-of-function mutations (KRASwt) which are dependent on KRAS expression. Combining machine learning-based modeling and whole transcriptome data with prior variable selection through protein-protein interaction network analysis by a diffusion kernel successfully predicted KRAS dependency in the KRASwt subgroup and in all investigated cancer cell lines. In contrast, modeling by RAS activating events (RAE) or previously published RAS RNA-signatures did not provide reliable results, highlighting the heterogeneous distribution of RAE in KRASwt cell lines and the importance of methodological references for expression signature modeling. Furthermore, we show that predictors of KRASwt models contain non-substitutable information signals, indicating a KRAS dependency phenotype in the KRASwt subgroup. Our data suggest that KRAS dependent cancers harboring KRAS wild type status could be targeted by directed therapeutic approaches. RNA-based machine learning models could help in identifying responsive and non-responsive tumors. © 2022, The Author(s).M.K. received grant support from the Else-Kröner-Forschungskolleg.Ulmer, B.; Institute of Pathology, Germany; email: bastian.ulmer@uk-koeln.deNature Research20567189Englishnpj Syst. Bio. Appl.ArticleFinalAll Open Access, GoldScopus2-s2.0-85123201537
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Mercado J.V., Koyama M., Nakasaki K.57393505300;56203883200;35560623900;Short-term changes in the anaerobic digestion microbiome and biochemical pathways with changes in organic load2022Science of the Total Environment81315258510.1016/j.scitotenv.2021.152585https://www.scopus.com/inward/record.uri?eid=2-s2.0-85122074800&doi=10.1016%2fj.scitotenv.2021.152585&partnerID=40&md5=1aa994ca0041cd35a663c47e9865db0fSchool of Environment and Society, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, JapanMercado, J.V., School of Environment and Society, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan; Koyama, M., School of Environment and Society, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan; Nakasaki, K., School of Environment and Society, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, JapanFluctuations in organic loading rate are frequently experienced in practical-scale anaerobic digestion systems. These impose shocks to the microbiome leading to process instability and failure. This study elucidated the short-term changes in biochemical pathways and the contributions of microbial groups involved in anaerobic digestion with varying organic load shocks. A mixture of starch and hipolypeptone corresponding to a carbon-to‑nitrogen ratio of 25 was used as substrate. Batch vial reactors were run using acclimatized sludge fed with organic load varying from 0 to 5 g VS/L. Methane yield decreased with increasing organic load. The microbiome alpha diversity represented as the number of operational taxonomic units (OTUs) and the Shannon index both decreased with organic load indicating microbiome specialization. The biochemical pathways predicted using PICRUSt2 were analyzed along with the corresponding contributions of microbial groups leading to a proposed pathway of substrate utilization. Genus Trichococcus (order Lactobacillales) increased in contribution to starch degradation pathways with increase in organic load while genus Macellibacteroides (order Bacteroidales) was prominent in contribution to bacterial anaerobic digestion pathways. Strictly acetoclastic Methanosaeta increased in prominence over hydrogenotrophic Methanolinea with increase in organic load. Results from this study provide better understanding of how anaerobic digesters respond to organic load shocks. © 2021 Elsevier B.V.Bioinformatics; Biomethane; Metagenome; Organic loading rate; PICRUSt2Batch reactors; Bioinformatics; Sludge digestion; Starch; Biochemical pathway; Biomethane; Load shock; Metagenomes; Microbial groups; Microbiome; Organic load; Organic loading rates; PICRUSt2; Process failure; Anaerobic digestion; carbon; hipolypeptone; methane; nitrogen; peptone; starch; unclassified drug; anaerobic digestion; bacteriology; bioinformatics; genomics; methane; microbial community; organic matter; acclimatization; anaerobic digestion; Article; Bacteroidales; biochemistry; carbon nitrogen ratio; degradation; Lactobacillales; Macellibacteroides; Methanolinea; Methanosaeta; microbial community; microbial diversity; nonhuman; organic loading rate; scoring system; Shannon index; taxonomy; Trichococcus; waste sitecarbon, 7440-44-0; methane, 74-82-8; nitrogen, 7727-37-9; starch, 9005-25-8, 9005-84-9Japan Society for the Promotion of Science, KAKEN: JP21K17906The present study was partially supported by JSPS KAKENHI Grant Number JP21K17906 . We are also grateful to the Hokubu Sludge Treatment Centre located in Yokohama, Kanagawa Prefecture, Japan, for providing the anaerobic digester sludge used as seed sludge for our study.The present study was partially supported by JSPS KAKENHI Grant Number JP21K17906. We are also grateful to the Hokubu Sludge Treatment Centre located in Yokohama, Kanagawa Prefecture, Japan, for providing the anaerobic digester sludge used as seed sludge for our study.Nakasaki, K.; School of Environment and Society, 2-12-1 Ookayama, Meguro-ku, Japan; email: nakasaki.k.aa@m.titech.ac.jpElsevier B.V.489697STEVAEnglishSci. Total Environ.ArticleFinalScopus2-s2.0-85122074800
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Goberna M., Verdú M.12787620100;7006992956;Cautionary notes on the use of co-occurrence networks in soil ecology2022Soil Biology and Biochemistry16610853410.1016/j.soilbio.2021.108534https://www.scopus.com/inward/record.uri?eid=2-s2.0-85122618823&doi=10.1016%2fj.soilbio.2021.108534&partnerID=40&md5=3268b298a45beeba6db6997d4d05d632Department of Environment and Agronomy, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7.5, Madrid, 28040, Spain; Department of Ecology, Centro de Investigaciones sobre Desertificación (CIDE-CSIC), Carretera Moncada-Náquera km 4.5, Moncada, Valencia 46113, SpainGoberna, M., Department of Environment and Agronomy, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7.5, Madrid, 28040, Spain; Verdú, M., Department of Ecology, Centro de Investigaciones sobre Desertificación (CIDE-CSIC), Carretera Moncada-Náquera km 4.5, Moncada, Valencia 46113, SpainSoil ecology is witnessing exponential growth in the number of studies using co-occurrence network analysis. Researchers reconstruct networks based on the co-occurrence of taxa or genes across soil samples at a wide range of geographic scales - from single aggregates to the whole planet - and taxonomic scopes, some studies targeting specific taxa or guilds to others surveying the whole microbiome as well as micro- and mesofauna. Co-occurrence networks can be very useful to extract simple patterns from complex datasets. Applications include the detection of abiotic and biotic factors that determine community structure, the identification of keystone taxa and their relationship to specific soil functions, and the inference of mechanisms of community assembly. However, networks are more and more often misused and serve as mere graphic tools with no attempt at hypothesis testing. In this perspectives article, we first review the main usage of co-occurrence network analysis in soil ecology during the last decade. We then discuss the applications and caveats of network analysis in soil ecology, leaving apart strictly methodological aspects of network reconstruction, which is beyond the focus of this article. Finally, we include recommendation guidelines – such as the possibility of informing networks with geographic, environmental and/or phylogenetic information – with the hope that this will facilitate network analysis to become a useful tool that helps elucidate meaningful patterns in soil ecology. © 2022 The AuthorsCo-occurrence patterns; Ecological interactions; Keystone taxa; Microbial networks; Network analysis; Soil microbiomeEcology; Co-occurrence networks; Co-occurrence pattern; Ecological interactions; Exponential growth; Geographics; Keystone taxon; Microbial network; Microbiome; Soil ecology; Soil microbiome; Soils; ecology; keystone species; methodology; microbial activity; network analysis; phylogenetics; soil emission; targeting; taxonomyCGL2017-8975-R, MCIN/AEI/10.13039/501100011033, PID2020-119634GB-I00; European Regional Development Fund, ERDFCarmen Trasar-Cepeda, as Chief Editor of Soil Biology and Biochemistry, detected an overuse of co-occurrence networks in soil ecology and conceived the idea of a Perspectives manuscript to provide recommendation guidelines. We are most grateful to her for inviting us to contribute to the topic. We also thank Sara Sánchez Moreno for her interesting comments on soil nematode ecology. The original version of this manuscript was significantly improved thanks to the thorough reports by three anonymous referees. The authors received grants CGL2017-8975-R and PID2020-119634GB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ ERDF A way of making Europe”.Carmen Trasar-Cepeda, as Chief Editor of Soil Biology and Biochemistry, detected an overuse of co-occurrence networks in soil ecology and conceived the idea of a Perspectives manuscript to provide recommendation guidelines. We are most grateful to her for inviting us to contribute to the topic. We also thank Sara S?nchez Moreno for her interesting comments on soil nematode ecology. The original version of this manuscript was significantly improved thanks to the thorough reports by three anonymous referees. The authors received grants CGL2017-8975-R and PID2020-119634GB-I00 funded by MCIN/AEI/10.13039/501100011033 and by ?ERDF A way of making Europe?.Goberna, M.; Department of Environment and Agronomy, Carretera de La Coruña km 7.5, Spain; email: marta.goberna@inia.esElsevier Ltd380717SBIOAEnglishSoil Biol. Biochem.Short SurveyFinalScopus2-s2.0-85122618823
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Mauri M.55900943500;Information Visualization for the Construction Industry2022Structural Integrity201852.06E+0210.1007/978-3-030-82430-3_8https://www.scopus.com/inward/record.uri?eid=2-s2.0-85120867173&doi=10.1007%2f978-3-030-82430-3_8&partnerID=40&md5=abe3ac3fdbdb3dc3187caf4aa737a26dPolitecnico di Milano, Via Durando 10, Milano, 20158, ItalyMauri, M., Politecnico di Milano, Via Durando 10, Milano, 20158, ItalyThe chapter introduces the topic by contextualizing, historically and conceptually, the use of visual properties to convey data and information for the built environment. It presents how design affects the visualization process, highlighting the authorial choices that influence how readers perceives information, showing why visualizations are not the result of a mechanical process of data encoding, but rather the outcome of an authorial process of representation. This is done by presenting the elements composing a visualization: the visual variables, the layout elements, and contextual information. Visual variables can be seen as “construction blocks” used to encode data dimensions, and strengths and weaknesses of their usage are exposed. The chapter then discusses visual models as “blueprints” featuring specific mappings of data onto visual variables, presenting a selection of useful ones and highlighting their context of use as well as issues in their usage. Finally, it is highlighted the relevance of contextual elements (such as titles, legends, and annotations) in the process of encoding/decoding of information and their role in providing readers the implicit knowledge needed to understand the subject and to get insights from the visualizations. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.Annotations; Data visualization; Information visualization; Legends; Visual models; Visual variables; Visualization layoutPolitecnico di MilanoThe approach exposed in this publication is the result of the joint experience of the people at DensityDesign Lab (Politecnico di Milano). A special thank goes to Gabriele Colombo and Angeles Briones, who over the years helped the author in identifying and test approaches and sources on the topic.Mauri, M.; Politecnico di Milano, Via Durando 10, Italy; email: michele.mauri@polimi.itSpringer Science and Business Media Deutschland GmbH2522560XEnglishStructur. Integr.Book ChapterFinalScopus2-s2.0-85120867173
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Wang Z., Romat H., Chevalier F., Riche N.H., Murray-Rust D., Bach B.57202051406;57202047152;18834382100;36457833900;14827312400;37103551800;Interactive Data Comics2022IEEE Transactions on Visualization and Computer Graphics28194495410.1109/TVCG.2021.3114849https://www.scopus.com/inward/record.uri?eid=2-s2.0-85118643760&doi=10.1109%2fTVCG.2021.3114849&partnerID=40&md5=ba5ee936f03f41701f323b0c8f6b50aeUniversity of Edinburgh, United Kingdom; ETH Zurich, Switzerland; University of Toronto, Canada; Microsoft Research, United States; Delft, NetherlandsWang, Z., University of Edinburgh, United Kingdom; Romat, H., ETH Zurich, Switzerland; Chevalier, F., University of Toronto, Canada; Riche, N.H., Microsoft Research, United States; Murray-Rust, D., Delft, Netherlands; Bach, B., University of Edinburgh, United KingdomThis paper investigates how to make data comics interactive. Data comics are an effective and versatile means for visual communication, leveraging the power of sequential narration and combined textual and visual content, while providing an overview of the storyline through panels assembled in expressive layouts. While a powerful static storytelling medium that works well on paper support, adding interactivity to data comics can enable non-linear storytelling, personalization, levels of details, explanations, and potentially enriched user experiences. This paper introduces a set of operations tailored to support data comics narrative goals that go beyond the traditional linear, immutable storyline curated by a story author. The goals and operations include adding and removing panels into pre-defined layouts to support branching, change of perspective, or access to detail-on-demand, as well as providing and modifying data, and interacting with data representation, to support personalization and reader-defined data focus. We propose a lightweight specification language, COMICSCRIPT, for designers to add such interactivity to static comics. To assess the viability of our authoring process, we recruited six professional illustrators, designers and data comics enthusiasts and asked them to craft an interactive comic, allowing us to understand authoring workflow and potential of our approach. We present examples of interactive comics in a gallery. This initial step towards understanding the design space of interactive comics can inform the design of creation tools and experiences for interactive storytelling. © 1995-2012 IEEE.Data comics; interactive storytelling; Non-linear narrativeData visualization; Specification languages; Visual communication; Visual languages; Visualization; Data comic; Interactive storytelling; Interactivity; Layout; Medium; Non linear; Non-linear narrative; Personalizations; Space explorations; Storylines; Space research; article; human; human experiment; language; narrative; storytelling; workflowIEEE Computer Society10772626ITVGE34587073EnglishIEEE Trans Visual Comput GraphicsArticleFinalScopus2-s2.0-85118643760
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Kulmann-Leal B., Ellwanger J.H., Chies J.A.B.57212218378;54882232000;6701376655;CCR5Δ32 in Brazil: Impacts of a European Genetic Variant on a Highly Admixed Population2021Frontiers in Immunology1275835810.3389/fimmu.2021.758358https://www.scopus.com/inward/record.uri?eid=2-s2.0-85121726892&doi=10.3389%2ffimmu.2021.758358&partnerID=40&md5=fa5f1ad8d9d2852dfe7426c77cc91896Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, BrazilKulmann-Leal, B., Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Ellwanger, J.H., Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Chies, J.A.B., Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, BrazilThe genetic background of Brazilians encompasses Amerindian, African, and European components as a result of the colonization of an already Amerindian inhabited region by Europeans, associated to a massive influx of Africans. Other migratory flows introduced into the Brazilian population genetic components from Asia and the Middle East. Currently, Brazil has a highly admixed population and, therefore, the study of genetic factors in the context of health or disease in Brazil is a challenging and remarkably interesting subject. This phenomenon is exemplified by the genetic variant CCR5Δ32, a 32 base-pair deletion in the CCR5 gene. CCR5Δ32 originated in Europe, but the time of origin as well as the selective pressures that allowed the maintenance of this variant and the establishment of its current frequencies in the different human populations is still a field of debates. Due to its origin, the CCR5Δ32 allele frequency is high in European-derived populations (~10%) and low in Asian and African native human populations. In Brazil, the CCR5Δ32 allele frequency is intermediate (4-6%) and varies on the Brazilian States, depending on the migratory history of each region. CCR5 is a protein that regulates the activity of several immune cells, also acting as the main HIV-1 co-receptor. The CCR5 expression is influenced by CCR5Δ32 genotypes. No CCR5 expression is observed in CCR5Δ32 homozygous individuals. Thus, the CCR5Δ32 has particular effects on different diseases. At the population level, the effect that CCR5Δ32 has on European populations may be different than that observed in highly admixed populations. Besides less evident due to its low frequency in admixed groups, the effect of the CCR5Δ32 variant may be affected by other genetic traits. Understanding the effects of CCR5Δ32 on Brazilians is essential to predict the potential use of pharmacological CCR5 modulators in Brazil. Therefore, this study reviews the impacts of the CCR5Δ32 on the Brazilian population, considering infectious diseases, inflammatory conditions, and cancer. Finally, this article provides a general discussion concerning the impacts of a European-derived variant, the CCR5Δ32, on a highly admixed population. Copyright © 2021 Kulmann-Leal, Ellwanger and Chies.Brazil; cancer; CCR5; CCR5delta32; infectious disease; inflammation; pathogen; population geneticscenicriviroc; chemokine receptor CCR5; chemokine receptor ccr5 d32; glycoprotein; leronlimab; macrophage inflammatory protein 1alpha; macrophage inflammatory protein 1beta; RANTES; unclassified drug; acute myeloid leukemia; anemia; antiretroviral therapy; autoimmune disease; Brazil; CD4+ T lymphocyte; cell migration; communicable disease; cytokine storm; DNA polymorphism; gene deletion; gene frequency; genetic variability; hematologic malignancy; hematopoietic stem cell; Hodgkin disease; Human immunodeficiency virus; Human immunodeficiency virus 1; Human immunodeficiency virus infection; immune response; immunosuppressive treatment; inflammation; Influenza virus; lymphoblastoma; malignant neoplasm; nervous system inflammation; periodontal disease; preeclampsia; prostate cancer; regulatory T lymphocyte; Review; rheumatoid arthritis; Schistosoma; systemic lupus erythematosus; toxoplasmosiscenicriviroc, 497223-25-3, 497223-28-6; leronlimab, 674782-26-4; macrophage inflammatory protein 1alpha, 155075-84-6; macrophage inflammatory protein 1beta, 122071-81-2Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES; Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq; Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul, FAPERGSBK-L receives a fellowship from Conselho Nacional de Desenvolvimento Cientıfí co e Tecnológico (CNPq, Brazil). JE receives a postdoctoral fellowship from Coordenação de Aperfeiçoamento de Pessoal de Nıveĺ Superior (Programa Nacional de Pós-Doutorado – PNPD/CAPES, Brazil). JC receives a research fellowship from CNPq (Bolsa de Produtividade em Pesquisa - Nı́vel 1A, Brazil) and has research projects funded by Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS, Brazil) and CAPES (Brazil).Chies, J.A.B.; Laboratório de Imunobiologia e Imunogenética, Brazil; email: jabchies@terra.com.brFrontiers Media S.A.1664322434956188EnglishFront. Immunol.ReviewFinalAll Open Access, Gold, GreenScopus2-s2.0-85121726892
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Ribeiro J., Lima P., Nunes F.56103654000;57349397300;35079191400;Trial Monitor: Scaffolding personalised Web dashboards for Human–Computer Interaction field trials2021SoftwareX1610088310.1016/j.softx.2021.100883https://www.scopus.com/inward/record.uri?eid=2-s2.0-85119599570&doi=10.1016%2fj.softx.2021.100883&partnerID=40&md5=d2ebb959274e6b56bc2094d943cd85fdFraunhofer Portugal AICOS, Alfredo Allen 455, Porto, 4200-135, PortugalRibeiro, J., Fraunhofer Portugal AICOS, Alfredo Allen 455, Porto, 4200-135, Portugal; Lima, P., Fraunhofer Portugal AICOS, Alfredo Allen 455, Porto, 4200-135, Portugal; Nunes, F., Fraunhofer Portugal AICOS, Alfredo Allen 455, Porto, 4200-135, PortugalWe developed Trial Monitor, a software tool that scaffolds the creation of personalised Web dashboards for monitoring participants in technology-enabled field trials. The tool supports Human–Computer Interaction researchers, who frequently monitor participants’ usage patterns at a distance, drawing on data from self-report scales, sensors, or application usage logs. Trial Monitor requires researchers or developers to write minimal configuration files, and generates personalised Web dashboards, which save researchers time from implementing or adopting a different dashboard for every system they evaluate in a field trial study. © 2021 The AuthorsData visualisation; Field trials; Remote monitoring; TelemonitoringData visualization; Scaffolds; Configuration files; Field trial; Interaction fields; OR applications; Remote monitoring; Software-tools; Tele-monitoring; Tool support; Usage patterns; Human computer interactionEuropean Commission, EC: POCI-01-0247-FEDER-038400; European Regional Development Fund, ERDF; Programa Operacional Temático Factores de Competitividade, POFCThis work was partially supported by EyeFundusScopeNEO: Demonstration of EyeFundusScope with Non-Expert Ophthalmology Users, cofunded by Portugal 2020, framed under the Operational Program Competitiveness and Internationalization (COMPETE 2020) and European Regional Development Fund from European Union, with operation code POCI-01-0247-FEDER-038400.Nunes, F.; Fraunhofer Portugal AICOS, Alfredo Allen 455, Portugal; email: francisco.nunes@fraunhofer.ptElsevier B.V.23527110EnglishSoftwareXArticleFinalAll Open Access, GoldScopus2-s2.0-85119599570
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Sokolova M., Marshall J.C., Benschop J.57314653600;55247314900;23011764200;Risk factors for hospitalisation amongst leptospirosis patients in new zealand2021Tropical Medicine and Infectious Disease6418810.3390/tropicalmed6040188https://www.scopus.com/inward/record.uri?eid=2-s2.0-85118172437&doi=10.3390%2ftropicalmed6040188&partnerID=40&md5=6535bffc502014a4cb653e86ec03147eEpiCentre, School of Veterinary Science, Massey University, Palmerston North, 4474, New Zealand; School of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand; Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, School of Veterinary Science, Massey University, Palmerston North, 4474, New ZealandSokolova, M., EpiCentre, School of Veterinary Science, Massey University, Palmerston North, 4474, New Zealand; Marshall, J.C., School of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand; Benschop, J., Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, School of Veterinary Science, Massey University, Palmerston North, 4474, New ZealandLeptospirosis is a neglected zoonotic disease that is widespread in tropical and subtropical regions such as Oceania, which includes New Zealand. The incidence rate of leptospirosis in New Zealand remains high in comparison to other high-income countries, with over half of the notified patients hospitalised, and the factors associated with hospitalisation are poorly understood. This study aimed to estimate the risk factors for hospitalisation amongst leptospirosis patients using passive surveillance data: notifications from 1 January 1999 to 31 December 2017 extracted from New Zealand’s notifiable disease database. There were 771 hospitalised and 673 non-hospitalised patients. Multivariable logistic regression was used to identify risk factors. The year of notification was significantly and positively associated with hospitalisation, with adjusted (adj.) OR 1.03 (95% CI:1.01–1.05). Occupation was significantly associated with hospitalisation, with the adjusted odds of hospitalisa-tion amongst dairy farmers notified with leptospirosis at adj. OR 1.44 (95% CI: 1.02–2.02) times the adjusted odds of hospitalisation amongst farmers that worked with other livestock. Seropositivity for Leptospira interrogans Copenhageni (adj. OR 5.96, 95% CI: 1.68–21.17) and Pomona (adj. OR 1.14, 95% CI: 0.74–1.74)) was more likely to result in hospitalisation when compared to Leptospira borgpetersenii Ballum (baseline). Seropositivity for Leptospira borgpetersenii Hardjo (adj. OR 0.71, 95% CI: 0.49–1.01) and Tarassovi (adj. OR 0.39, 95% CI: 0.23–0.66) was less likely to result in hospitalisation when compared to Ballum (baseline). All the estimates were additionally adjusted for the effect of sex, age, ethnicity, reported occupational exposure, geographical location, reported season, and deprivation status Although passive surveillance data has limitations we have been able to identify that the New Zealand dairy farming population may benefit from a targeted awareness campaign. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Hospitalisation; Leptospira spp; Risk factors; Surveillance dataMinisterio de Sanidad, Consumo y Bienestar Social, MISAN; Institute of Environmental Science and Research, ESRWe gratefully acknowledge the assistance given by the ESR in providing and allowing the use of the NZ surveillance data. Parts of this material are based on data and information provided by the Institute of Environmental Science & Research Ltd. on behalf of the Ministry of Health. However, the analyses, conclusions, opinions, and statements expressed herein are those of the authors and not necessarily those of the Institute of Environmental Science & Research Ltd. or the Ministry of Health. We also extend our thanks to all the people involved in the different stages of the data collection process, making this study possible.Sokolova, M.; EpiCentre, New Zealand; email: m.sokolova@massey.ac.nzMDPI24146366EnglishTrop. Med. Infect. Dis.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85118172437
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Malaterre C., Lareau F., Pulizzotto D., St-Onge J.26037162500;57212515294;57197819957;57220816452;Eight journals over eight decades: a computational topic-modeling approach to contemporary philosophy of science2021Synthese1991-228832923110.1007/s11229-020-02915-6https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096913871&doi=10.1007%2fs11229-020-02915-6&partnerID=40&md5=373ec2b8174830bdb585830c53779b38Département de philosophie, Université du Québec à Montréal (UQAM), 455 boulevard René-Lévesque Est, Montreal, QC H3C 3P8, Canada; Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), 1205 rue Saint-Denis, Montreal, QC H3C 3P8, Canada; Département d’informatique, Université du Québec à Montréal (UQAM), 201 avenue Président-Kennedy, Montreal, QC H2X 3Y7, Canada; Département d’études littéraires, Université du Québec à Montréal (UQAM), 405 rue Sainte-Catherine Est, Montreal, QC H3C 3P8, CanadaMalaterre, C., Département de philosophie, Université du Québec à Montréal (UQAM), 455 boulevard René-Lévesque Est, Montreal, QC H3C 3P8, Canada, Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), 1205 rue Saint-Denis, Montreal, QC H3C 3P8, Canada; Lareau, F., Département d’informatique, Université du Québec à Montréal (UQAM), 201 avenue Président-Kennedy, Montreal, QC H2X 3Y7, Canada; Pulizzotto, D., Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), 1205 rue Saint-Denis, Montreal, QC H3C 3P8, Canada, Département d’études littéraires, Université du Québec à Montréal (UQAM), 405 rue Sainte-Catherine Est, Montreal, QC H3C 3P8, Canada; St-Onge, J., Département de philosophie, Université du Québec à Montréal (UQAM), 455 boulevard René-Lévesque Est, Montreal, QC H3C 3P8, Canada, Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), 1205 rue Saint-Denis, Montreal, QC H3C 3P8, CanadaAs a discipline of its own, the philosophy of science can be traced back to the founding of its academic journals, some of which go back to the first half of the twentieth century. While the discipline has been the object of many historical studies, notably focusing on specific schools (e.g., logical empiricism) or major figures of the field (e.g., Carnap, Kuhn), little work has focused on the journals themselves. Here, we investigate contemporary philosophy of science by means of computational text-mining approaches: we apply topic-modeling algorithms to eight major philosophy of science journals, from the 1930s up until 2017. Based on the full-text content of some 15,897 articles, we identified 25 research themes and 8 thematic clusters that show how the research agenda of the philosophy of science has changed in its content over the course of the last eight decades, up to the philosophy of science we now know. We also show how each one of the journals contributed in its own way to this thematic evolution. © 2021, Springer Nature B.V.Digital humanities; Digital philosophy; Philosophy of science journals; Text mining; Topic modelingFonds de Recherche du Québec-Société et Culture, FRQSC: FRQSC-276470; Canada Foundation for Innovation, CFI: 34555; Canada Research Chairs: CRC-950-230795The authors are grateful to JSTOR, Elsevier, Oxford University Press, Springer, Taylor and Francis, and University of Chicago Press for providing access to journal articles for text-mining purposes. They thank Oliver Lean, Charles Pence and Luca Rivelli for comments on an earlier version of the manuscript, as well as the audience of a 2019 TEC seminar at UQAM where this work was presented. They also thank the reviewers at Synthese for their valuable comments. Funding from Canada Foundation for Innovation (Grant 34555) and Canada Research Chairs (CRC-950-230795) is gratefully acknowledged. F.L. acknowledges funding from the Fonds de recherche du Québec - Société et culture (FRQSC-276470).The authors are grateful to JSTOR, Elsevier, Oxford University Press, Springer, Taylor and Francis, and University of Chicago Press for providing access to journal articles for text-mining purposes. They thank Oliver Lean, Charles Pence and Luca Rivelli for comments on an earlier version of the manuscript, as well as the audience of a 2019 TEC seminar at UQAM where this work was presented. They also thank the reviewers at Synthese for their valuable comments. Funding from Canada Foundation for Innovation (Grant 34555) and Canada Research Chairs (CRC-950-230795) is gratefully acknowledged.?F.L. acknowledges funding from the Fonds de recherche du Qu?bec - Soci?t? et culture (FRQSC-276470).Malaterre, C.; Département de philosophie, 455 boulevard René-Lévesque Est, Canada; email: malaterre.christophe@uqam.caSpringer Science and Business Media B.V.397857EnglishSyntheseArticleFinalScopus2-s2.0-85096913871
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Halkos G., Tsilika K.6701440263;6506532108;Visual exploration of energy use in eu 28: Dynamics, patterns, policies2021Energies1422753210.3390/en14227532https://www.scopus.com/inward/record.uri?eid=2-s2.0-85119338865&doi=10.3390%2fen14227532&partnerID=40&md5=328fce389c500a112a6f9fb609e616cdLaboratory of Operations Research, Department of Economics, School of Economics and Business, University of Thessaly, Volos, 38333, Greece; Department of Business Administration, School of Social Sciences, Hellenic Open University, Patras, 26335, GreeceHalkos, G., Laboratory of Operations Research, Department of Economics, School of Economics and Business, University of Thessaly, Volos, 38333, Greece; Tsilika, K., Laboratory of Operations Research, Department of Economics, School of Economics and Business, University of Thessaly, Volos, 38333, Greece, Department of Business Administration, School of Social Sciences, Hellenic Open University, Patras, 26335, GreeceThe paper places emphasis on primary energy resources, their covariation, and their correlation with socioeconomic factors and aims to provide a systematic analysis of their development over time. The analysis uses evidence from European Union (EU) country-level data and is based on visual analytics techniques. Different results from the same territories show that energy consumption does not always reflect or is due to climatological or meteorological conditions. Extensive use of visualization is adopted as a means of contributing to the understanding of energy use, some involved problems and concepts, and energy consumption trends over time. We present an approach that addresses the informatics challenges based on the integration of visualization software, data integration, and cluster analysis. Our cross-sectional energy review advocates that EU energy leaders are moving towards a low-carbon economy. The correlations of energy variables with economic and pollution effects are stronger in greater levels of energy use, which means that energy use has an obvious impact on economic growth and the environment. Visual and automated methods employed for the analysis, reveal the direction, the strength, and the nature of the dependence structure, in clusters covering the range of energy use in EU 28 countries. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Correlation analysis; Energy use; K-means clustering; Trends; Visual data explorationCluster analysis; Data integration; Data visualization; Economics; Energy utilization; K-means clustering; Renewable energy resources; Correlation analysis; Dynamics patterns; Energy; Energy use; Energy-consumption; European union; K-means++ clustering; Trend; Visual data exploration; Visual exploration; VisualizationHalkos, G.; Laboratory of Operations Research, Greece; email: halkos@uth.grMDPI19961073EnglishEnergiesArticleFinalAll Open Access, GoldScopus2-s2.0-85119338865
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Bhatt D.K., Chammas R., Daemen T.57211924674;7004122588;7003605597;Resistance mechanisms influencing oncolytic virotherapy, a systematic analysis2021Vaccines910116610.3390/vaccines9101166https://www.scopus.com/inward/record.uri?eid=2-s2.0-85117813569&doi=10.3390%2fvaccines9101166&partnerID=40&md5=2c4ff9f4e919ce09dadfeb4b335727ddUniversity Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, University of Groningen, Groningen, 9713 AV, Netherlands; Center for Translational Research in Oncology, Instituto do Câncer do Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, 01246-000, BrazilBhatt, D.K., University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, University of Groningen, Groningen, 9713 AV, Netherlands, Center for Translational Research in Oncology, Instituto do Câncer do Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, 01246-000, Brazil; Chammas, R., Center for Translational Research in Oncology, Instituto do Câncer do Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, 01246-000, Brazil; Daemen, T., University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, University of Groningen, Groningen, 9713 AV, NetherlandsResistance to therapy is a frequently observed phenomenon in the treatment of cancer, and as with other cancer therapeutics, therapies based on oncolytic viruses also face the challenges of resistance, such as humoral and cellular antiviral responses, and tumor-associated interferon-mediated resistance. In order to identify additional mechanisms of resistance that may contribute to therapeutic failure, we developed a systematic search strategy for studies published in PubMed. We analyzed 6143 articles on oncolytic virotherapy and found that approximately 8% of these articles use resistance terms in the abstract and/or title. Of these 439 articles, 87 were original research. Most of the findings reported pertain to resistance mediated by tumor-cell-dependent interferon signaling. Yet, mechanisms such as epigenetic modifications, hypoxia-mediated inhibition, APO-BEC-mediated resistance, virus entry barriers, and spatiotemporal restriction to viral spread, alt-hough not frequently assessed, were demonstrated to play a major role in resistance. Similarly, our results suggest that the stromal compartment consisting of, but not limited to, myeloid cells, fibro-blasts, and epithelial cells requires more study in relation to therapy resistance using oncolytic vi-ruses. Thus, our findings emphasize the need to assess the stromal compartment and to identify novel mechanisms that play an important role in conferring resistance to oncolytic virotherapy. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Cancer cells; Oncolytic virotherapy; Resistance mechanisms; Stromal cells; Therapeutic resistanceneutralizing antibody; oncolytic virus; bone marrow cell; breast cancer; cancer cell; cancer therapy; carcinogenesis; cell heterogeneity; efficacy parameters; epigenetic modification; epithelium cell; gene overexpression; gene therapy; human; hypoxia; interferon signaling; meta analysis; oncolytic virotherapy; prostate cancer; Review; stroma cell; systematic review; virus infection; virus replication; Wart virusCoordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES; Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq: 305700/2017-0Funding: The authors’ work was supported by CNPq (Grant Award 305700/2017-0 to R.C.), CAPES (Finance Code 001, to D.B.), and an ATTP-GSMS scholarship (Abel Tasman Talent Program to D.K.B.).Daemen, T.; University Medical Center Groningen, Netherlands; email: c.a.h.h.daemen@umcg.nlMDPI2076393XEnglishVaccinesReviewFinalAll Open Access, GreenScopus2-s2.0-85117813569
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Rutz Voumard R., Dugger K.M., Kiker W.A., Barber J., Borasio G.D., Curtis J.R., Jox R.J., Creutzfeldt C.J.57215705460;57226162191;57226155181;57024424300;7006579334;57218094313;23090806200;8892687400;Goal-Concordant Care After Severe Acute Brain Injury2021Frontiers in Neurology1271078310.3389/fneur.2021.710783https://www.scopus.com/inward/record.uri?eid=2-s2.0-85116327029&doi=10.3389%2ffneur.2021.710783&partnerID=40&md5=1c3c54406762bd7a1b99685a34006165Department of Neurology, Harborview Medical Center, University of Washington, Seattle, WA, United States; Department of Palliative and Supportive Care, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland; Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, United States; Cambia Palliative Care Center of Excellence, University of Washington, Seattle, WA, United States; Department of Neurosurgery, Harborview Medical Center, University of Washington, Seattle, WA, United States; Institute of Humanities in Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, SwitzerlandRutz Voumard, R., Department of Neurology, Harborview Medical Center, University of Washington, Seattle, WA, United States, Department of Palliative and Supportive Care, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland; Dugger, K.M., Department of Neurology, Harborview Medical Center, University of Washington, Seattle, WA, United States; Kiker, W.A., Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, United States, Cambia Palliative Care Center of Excellence, University of Washington, Seattle, WA, United States; Barber, J., Department of Neurosurgery, Harborview Medical Center, University of Washington, Seattle, WA, United States; Borasio, G.D., Department of Palliative and Supportive Care, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland; Curtis, J.R., Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, United States, Cambia Palliative Care Center of Excellence, University of Washington, Seattle, WA, United States; Jox, R.J., Department of Palliative and Supportive Care, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland, Institute of Humanities in Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland; Creutzfeldt, C.J., Department of Neurology, Harborview Medical Center, University of Washington, Seattle, WA, United States, Cambia Palliative Care Center of Excellence, University of Washington, Seattle, WA, United StatesBackground: Patients with severe acute brain injury (SABI) lack decision-making capacity, calling on families and clinicians to make goal-concordant decisions, aligning treatment with patient's presumed goals-of-care. Using the family perspective, this study aimed to (1) compare patient's goals-of-care with the care they were receiving in the acute setting, (2) identify patient and family characteristics associated with goal-concordant care, and (3) assess goals-of-care 6 months after SABI. Methods: Our cohort included patients with SABI in our Neuro-ICU and a Glasgow Coma Scale Score <12 after day 2. Socio-demographic and clinical characteristics were collected through surveys and chart review. At enrollment and again at 6 months, each family was asked if the patient would prefer medical care focused on extending life vs. care focused on comfort and quality of life, and what care the patient is currently receiving. We used multivariate regression to examine the characteristics associated with (a) prioritized goals (comfort/extending life/unsure) and (b) goal concordance. Results: Among 214 patients, families reported patients' goals-of-care to be extending life in 118 cases (55%), comfort in 71 (33%), and unsure for 25 (12%), while care received focused on extending life in 165 cases (77%), on comfort in 23 (11%) and families were unsure in 16 (7%). In a nominal regression model, prioritizing comfort over extending life was significantly associated with being non-Hispanic White and having worse clinical severity. Most patients who prioritized extending life were receiving family-reported goal-concordant care (88%, 104/118), while most of those who prioritized comfort were receiving goal-discordant care (73%, 52/71). The only independent association for goal concordance was having a presumed goal of extending life at enrollment (OR 23.62, 95% CI 10.19–54.77). Among survivors at 6 months, 1 in 4 family members were unsure about the patient's goals-of-care. Conclusion: A substantial proportion of patients are receiving unwanted aggressive care in the acute setting after SABI. In the first days, such aggressive care might be justified by prognostic uncertainty. The high rate of families unsure of patient's goals-of-care at 6 months suggests an important need for periodic re-evaluation of prognosis and goals-of-care in the post-acute setting. © Copyright © 2021 Rutz Voumard, Dugger, Kiker, Barber, Borasio, Curtis, Jox and Creutzfeldt.goal-concordant care; neuropalliative care; palliative care; severe acute brain injury; shared decision-makingNational Institute of Neurological Disorders and Stroke, NINDS: K23 NS099421; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, SNF: P400PM_186732RR was supported by a grant of the Swiss National Science Foundation (P400PM_186732). CC received funding from a career development award from the National Institute of Neurological Disorders and Stroke (K23 NS099421). The researchers’ funders had no role in the design, data analysis, interpretation or writing of the manuscript. All co-authors had full access to all the data in the study and had final responsibility for the decision to submit the publication.Creutzfeldt, C.J.; Department of Neurology, United States; email: clairejc@uw.eduFrontiers Media S.A.16642295EnglishFront. Neurol.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85116327029
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Ahuja S., Lazar I.M.57205732493;7006566883;Systems-Level Proteomics Evaluation of Microglia Response to Tumor-Supportive Anti-Inflammatory Cytokines2021Frontiers in Immunology1264604310.3389/fimmu.2021.646043https://www.scopus.com/inward/record.uri?eid=2-s2.0-85115659827&doi=10.3389%2ffimmu.2021.646043&partnerID=40&md5=10e6cec5a3fcdc6d66ca22a21c0d3fb6Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States; Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, United States; Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United StatesAhuja, S., Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States; Lazar, I.M., Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, United States, Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United StatesBackground: Microglia safeguard the CNS against injuries and pathogens, and in the presence of certain harmful stimuli are capable of inducing a disease-dependent inflammatory response. When exposed to anti-inflammatory cytokines, however, these cells possess the ability to switch from an inflammatory to an immunosuppressive phenotype. Cancer cells exploit this property to evade the immune system, and elicit an anti-inflammatory microenvironment that facilitates tumor attachment and growth. Objective: The tumor-supportive biological processes that are activated in microglia cells in response to anti-inflammatory cytokines released from cancer cells were explored with mass spectrometry and proteomic technologies. Methods: Serum-depleted and non-depleted human microglia cells (HMC3) were treated with a cocktail of IL-4, IL-13, IL-10, TGFβ, and CCL2. The cellular protein extracts were analyzed by LC-MS/MS. Using functional annotation clustering tools, statistically significant proteins that displayed a change in abundance between cytokine-treated and non-treated cells were mapped to their biological networks and pathways. Results: The proteomic analysis of HMC3 cells enabled the identification of ~10,000 proteins. Stimulation with anti-inflammatory cytokines resulted in the activation of distinct, yet integrated clusters of proteins that trigger downstream a number of tumor-promoting biological processes. The observed changes could be classified into four major categories, i.e., mitochondrial gene expression, ECM remodeling, immune response, and impaired cell cycle progression. Intracellular immune activation was mediated mainly by the transducers of MAPK, STAT, TGFβ, NFKB, and integrin signaling pathways. Abundant collagen formation along with the expression of additional receptors, matrix components, growth factors, proteases and protease inhibitors, was indicative of ECM remodeling processes supportive of cell-cell and cell-matrix adhesion. Overexpression of integrins and their modulators was reflective of signaling processes that link ECM reorganization with cytoskeletal re-arrangements supportive of cell migration. Antigen processing/presentation was represented by HLA class I histocompatibility antigens, and correlated with upregulated proteasomal subunits, vesicular/viral transport, and secretory processes. Immunosuppressive and proangiogenic chemokines, as well as anti-angiogenic factors, were detectable in low abundance. Pronounced pro-inflammatory, chemotactic or phagocytic trends were not observed, however, the expression of certain receptors, signaling and ECM proteins indicated the presence of such capabilities. Conclusions: Comprehensive proteomic profiling of HMC3 cells stimulated with anti-inflammatory cytokines revealed a spectrum of microglia phenotypes supportive of cancer development in the brain via microenvironment-dependent biological mechanisms. © Copyright © 2021 Ahuja and Lazar.anti-inflammatory; cytokine; ECM remodeling; microglia; proteomics; tumorhistocompatibility antigen; immunoglobulin enhancer binding protein; interleukin 10; interleukin 13; interleukin 4; mitogen activated protein kinase; monocyte chemotactic protein 1; STAT protein; STAT3 protein; STAT6 protein; transforming growth factor beta; triggering receptor expressed on myeloid cells 2; tumor necrosis factor; cytokine; anti inflammatory cytokine; Article; bioinformatics; brain metastasis; chemotaxis; controlled study; cytoskeleton; data processing; electrospray; gene expression; glioblastoma; human; human cell; immune response; immunofluorescence microscopy; liquid chromatography-mass spectrometry; microglia; mitochondrial gene; protein expression; protein fingerprinting; protein protein interaction; proteomics; brain; cell line; immunology; microglia; procedures; proteomics; tumor escape; tumor microenvironment; Brain; Cell Line; Cytokines; Humans; Microglia; Proteomics; Tumor Escape; Tumor Microenvironmentinterleukin 13, 148157-34-0; mitogen activated protein kinase, 142243-02-5; CytokinesEASY-nLC 1200 UHPLC system; Eclipse TE2000-U, Nikon, United States; hercules, Biorad, United StatesAgilent, United States; Biorad, United States; Nikon, United StatesNational Institute of General Medical Sciences, NIGMS: 1R01GM121920This work was supported by an award from the National Institute of General Medical Sciences (Grant No. 1R01GM121920) to IL.Lazar, I.M.; Department of Biological Sciences, United StatesFrontiers Media S.A.1664322434566949EnglishFront. Immunol.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85115659827
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Howard P.H., Ajena F., Yamaoka M., Clarke A.20733927700;57222293906;57248068700;57247199400;“Protein” Industry Convergence and Its Implications for Resilient and Equitable Food Systems2021Frontiers in Sustainable Food Systems568418110.3389/fsufs.2021.684181https://www.scopus.com/inward/record.uri?eid=2-s2.0-85114340638&doi=10.3389%2ffsufs.2021.684181&partnerID=40&md5=a617b39f968e45d653f69374155020a9Department of Community Sustainability, Michigan State University, East Lansing, MI, United States; Independent Scholar, Rome, Italy; Université Gustave Eiffel, Paris, France; Independent Scholar, London, United KingdomHoward, P.H., Department of Community Sustainability, Michigan State University, East Lansing, MI, United States, Independent Scholar, Rome, Italy; Ajena, F., Independent Scholar, Rome, Italy; Yamaoka, M., Université Gustave Eiffel, Paris, France; Clarke, A., Independent Scholar, London, United KingdomRecent years have seen the convergence of industries that focus on higher protein foods, such as meat processing firms expanding into plant-based substitutes and/or cellular meat production, and fisheries firms expanding into aquaculture. A driving force behind these changes is dominant firms seeking to increase their power relative to close competitors, including by extending beyond boundaries that pose constraints to growth. The broad banner of “protein” offers a promising space to achieve this goal, despite its nutritionally reductionist focus on a single macronutrient. Protein firm strategies to increase their dominance are likely to further diminish equity in food systems by exacerbating power asymmetries. In addition, the resilience of food systems has the potential to be weakened as these strategies tend to reduce organizational diversity, as well as the genetic diversity of livestock and crops. To better understand these changes, we visually characterize firms that are most dominant in higher protein food industries globally and their recent strategic moves. We discuss the likelihood for these trends to further jeopardize food system resilience and equity, and we make recommendations for avoiding these impacts. © Copyright © 2021 Howard, Ajena, Yamaoka and Clarke.consolidation; diversity; equity; political ecology; protein; resilience; visualizationThe authors wish to thank three reviewers for their helpful suggestions. We also wish to thank members of the International Panel of Experts on Sustainable Food Systems and the organization's secretariat for discussions that informed the development of this manuscript.Howard, P.H.; Department of Community Sustainability, United States; email: howardp@msu.eduFrontiers Media S.A.2571581XEnglishFront. Sustain. food Syst.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85114340638
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Tauzin A., Nayrac M., Benlarbi M., Gong S.Y., Gasser R., Beaudoin-Bussières G., Brassard N., Laumaea A., Vézina D., Prévost J., Anand S.P., Bourassa C., Gendron-Lepage G., Medjahed H., Goyette G., Niessl J., Tastet O., Gokool L., Morrisseau C., Arlotto P., Stamatatos L., McGuire A.T., Larochelle C., Uchil P., Lu M., Mothes W., De Serres G., Moreira S., Roger M., Richard J., Martel-Laferrière V., Duerr R., Tremblay C., Kaufmann D.E., Finzi A.57226617222;57210452682;57219699236;57221957835;55893637300;57216826465;25632111500;35743347800;57207981689;57114557100;57204015968;57221946314;57207963631;35234275400;57219403405;56646627300;57214727107;57219401842;57219403641;57209821499;6701424936;55624659200;37054263400;6508099268;57201666616;7004545308;7006630854;55413240600;57207895031;23568696000;36661125300;57194424377;7005236335;57208090961;57203237269;A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses2021Cell Host and Microbe29711371.15E+093010.1016/j.chom.2021.06.001https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108098380&doi=10.1016%2fj.chom.2021.06.001&partnerID=40&md5=6af5d2b22f458a775012a98d23c238bfCentre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2BA, Canada; Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, United States; University of Washington, Department of Global Health, Seattle, WA 98109, United States; Département des Neurosciences, Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, United States; Institut National de Santé Publique du Québec, Quebec, QC H2P 1E2, Canada; Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; Department of Microbiology, New York University School of Medicine, New York, NY 10016, United States; Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Consortium for HIV/AIDS Vaccine Development (CHAVD), La Jolla, CA, United StatesTauzin, A., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Nayrac, M., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Benlarbi, M., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Gong, S.Y., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2BA, Canada; Gasser, R., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Beaudoin-Bussières, G., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Brassard, N., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Laumaea, A., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Vézina, D., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Prévost, J., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Anand, S.P., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2BA, Canada; Bourassa, C., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Gendron-Lepage, G., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Medjahed, H., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Goyette, G., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Niessl, J., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada, Consortium for HIV/AIDS Vaccine Development (CHAVD), La Jolla, CA, United States; Tastet, O., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Gokool, L., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Morrisseau, C., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Arlotto, P., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Stamatatos, L., Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, United States, University of Washington, Department of Global Health, Seattle, WA 98109, United States; McGuire, A.T., Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, United States; Larochelle, C., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département des Neurosciences, Université de Montréal, Montreal, QC H3C 3J7, Canada; Uchil, P., Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, United States; Lu, M., Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, United States; Mothes, W., Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, United States; De Serres, G., Institut National de Santé Publique du Québec, Quebec, QC H2P 1E2, Canada; Moreira, S., Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; Roger, M., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada, Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; Richard, J., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Martel-Laferrière, V., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Duerr, R., Department of Microbiology, New York University School of Medicine, New York, NY 10016, United States; Tremblay, C., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada; Kaufmann, D.E., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada, Consortium for HIV/AIDS Vaccine Development (CHAVD), La Jolla, CA, United States; Finzi, A., Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada, Département de Microbiologie, Université de Montréal, Infectiologie et Immunologie, Montreal, QC H2X 0A9, Canada, Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2BA, CanadaWhile the standard regimen of the BNT162b2 mRNA vaccine for SARS-CoV-2 includes two doses administered 3 weeks apart, some public health authorities are spacing these doses, raising concerns about efficacy. However, data indicate that a single dose can be up to 90% effective starting 14 days post-administration. To assess the mechanisms contributing to protection, we analyzed humoral and T cell responses three weeks after a single BNT162b2 dose. We observed weak neutralizing activity elicited in SARS-CoV-2 naive individuals but strong anti-receptor binding domain and spike antibodies with Fc-mediated effector functions and cellular CD4+ T cell responses. In previously infected individuals, a single dose boosted all humoral and T cell responses, with strong correlations between T helper and antibody immunity. Our results highlight the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support for spacing doses to vaccinate more individuals in conditions of vaccine scarcity. © 2021 Elsevier Inc.ADCC; coronavirus; COVID-19; humoral responses; mRNA vaccine; neutralization; SARS-CoV-2; spike glycoproteins; T cell responses; variantsbnt 162b 2; CD134 antigen; CD4 antigen; CD40 ligand; CD69 antigen; CD8 antigen; comirnaty; coronavirus spike glycoprotein; Fc receptor; gamma interferon; immunoglobulin A antibody; immunoglobulin G antibody; immunoglobulin M antibody; interleukin 10; interleukin 17; interleukin 2; lysosome associated membrane protein 1; neutralizing antibody; SARS-CoV-2 antibody; T lymphocyte receptor; tumor necrosis factor; tumor necrosis factor receptor superfamily member 9; bnt 162 vaccine; carrier protein; immunoglobulin Fc fragment; neutralizing antibody; recombinant vaccine; RNA vaccine; virus antibody; adult; aged; antibody dependent cellular cytotoxicity; antibody response; Article; CD4+ T lymphocyte; CD8+ T lymphocyte; cellular immunity; controlled study; convalescence; coronavirus disease 2019; drug efficacy; effector cell; escape mutation; female; human; human cell; Human coronavirus HKU1; Human coronavirus OC43; humoral immunity; major clinical study; male; Middle East respiratory syndrome coronavirus; nonhuman; peripheral blood mononuclear cell; receptor binding; SARS coronavirus; Severe acute respiratory syndrome coronavirus 2; single drug dose; T lymphocyte; T lymphocyte subpopulation; upregulation; vaccination; virus infectivity; virus neutralization; administration and dosage; Betacoronavirus; chemistry; immunity; immunology; middle aged; prevention and control; T lymphocyte; vaccination; young adult; Adult; Antibodies, Neutralizing; Antibodies, Viral; Betacoronavirus; Carrier Proteins; COVID-19; COVID-19 Vaccines; Female; Humans; Immunity; Immunoglobulin Fc Fragments; Male; Middle Aged; SARS-CoV-2; T-Lymphocytes; Vaccination; Vaccines, Synthetic; Young AdultCD40 ligand, 226713-27-5; comirnaty, 2417899-77-3; gamma interferon, 82115-62-6; interleukin 2, 85898-30-2; carrier protein, 80700-39-6; Antibodies, Neutralizing; Antibodies, Viral; BNT162 vaccine; Carrier Proteins; COVID-19 Vaccines; Immunoglobulin Fc Fragments; mRNA Vaccine; Vaccines, Syntheticbnt 162b 2National Institutes of Health, NIH: AI144462, R01 AI122953-05, RCHS0235 950-232424; Fondation du CHUM; Genome Canada; Canadian Institutes of Health Research, CIHR: 352417; Fonds de Recherche du Québec - Santé, FRQS; Canada Foundation for Innovation, CFI: 41027; MitacsThe authors are grateful to the donors who participated in this study. The authors thank the CRCHUM BSL3 and Flow Cytometry Platforms for technical assistance. We thank Annie Moisan, Gilles Turcotte, and Sclérodermie Québec for their generous support in the acquisition of the FACSymphony. We thank Dr. Stefan Pöhlmann (Georg-August University, Germany) for the plasmid coding for SARS-CoV-2 and SARS-CoV-1 S glycoproteins and Dr. M. Gordon Joyce (US MHRP) for the monoclonal antibody CR3022. The graphical abstract was prepared using images from BioRender.com . This work was supported by le Ministère de l’Économie et de l’Innovation du Québec , Programme de Soutien aux Organismes de Recherche et d’Innovation to A.F. and by the Fondation du CHUM. This work was also supported by CIHR foundation grant 352417 to A.F., and by Exceptional Fund COVID-19 from the Canada Foundation for Innovation (CFI) 41027 to A.F. and D.E.K. Work on variants presented here was supported by the Sentinelle COVID Quebec network led by the LSPQ in collaboration with Fonds de Recherche du Québec Santé (FRQS) to A.F, and Genome Canada – Génome Québec to M.R. Support was also provided by NIH AI144462 CHAVD to D.E.K. (consortium PI: Dennis Burton). A.F. is the recipient of Canada Research Chair on Retroviral Entry no. RCHS0235 950-232424. V.M.-L. is supported by a FRQS Junior 1 salary award. D.E.K. is an FRQS Merit Research scholar. R.D. was supported by NIH grant R01 AI122953-05 . S.P.A., J.P., and G.B.-B. are supported by CIHR fellowships. R.G. is supported by a MITACS Accélération postdoctoral fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our results support the parallel use of both AIM and ICS assays for SARS-CoV-2 vaccine immunomonitoring. While most clinical trials relied on the IFN-? ELISPOT assay and/or ICS to measure T cell responses, our data suggest the notion that BNT162b2 and some other SARS-CoV-2 vaccines in advanced clinical evaluation, including non-mRNA-vaccines, preferentially elicit Th1 responses and may have to be reconsidered (Corbett et al., 2020; van Doremalen et al., 2020; Ewer et al., 2021; Laczk? et al., 2020; Zhang et al., 2020). Indeed, these assays are sensitive for detection of Th1 cytokines and cytotoxic responses, but largely miss other important components of virus-specific cellular immunity. Consistent with this, we found that AIM assays were highly sensitive to detect vaccine-induced CD4+ and CD8+ T cells, consistent with recent findings in natural SARS-CoV-2 infection and vaccination (Dan et al., 2021; Kalimuddin et al., 2021). Still, ICS assays were essential to reveal qualitative differences in cellular responses elicited after vaccination in PI versus naive participants, with more proinflammatory and antiviral CD4+ and CD8+ T cell functional profiles in almost all PI individuals, including IFN-?, TNF-?, and for the CD8+ T cells, cytotoxic functions. Based on current knowledge, we suggest that a balanced humoral and Th1-directed cellular immune response may be important for protection from COVID-19 and the development of effective vaccine-induced immunization.The authors are grateful to the donors who participated in this study. The authors thank the CRCHUM BSL3 and Flow Cytometry Platforms for technical assistance. We thank Annie Moisan, Gilles Turcotte, and Scl?rodermie Qu?bec for their generous support in the acquisition of the FACSymphony. We thank Dr. Stefan P?hlmann (Georg-August University, Germany) for the plasmid coding for SARS-CoV-2 and SARS-CoV-1 S glycoproteins and Dr. M. Gordon Joyce (US MHRP) for the monoclonal antibody CR3022. The graphical abstract was prepared using images from BioRender.com. This work was supported by le Minist?re de l??conomie et de l'Innovation du Qu?bec, Programme de Soutien aux Organismes de Recherche et d'Innovation to A.F. and by the Fondation du CHUM. This work was also supported by CIHR foundation grant 352417 to A.F. and by Exceptional Fund COVID-19 from the Canada Foundation for Innovation (CFI) 41027 to A.F. and D.E.K. Work on variants presented here was supported by the Sentinelle COVID Quebec network led by the LSPQ in collaboration with Fonds de Recherche du Qu?bec Sant? (FRQS) to A.F, and Genome Canada ? G?nome Qu?bec to M.R. Support was also provided by NIH AI144462 CHAVD to D.E.K. (consortium PI: Dennis Burton). A.F. is the recipient of Canada Research Chair on Retroviral Entry no. RCHS0235 950-232424. V.M.-L. is supported by a FRQS Junior 1 salary award. D.E.K. is an FRQS Merit Research scholar. R.D. was supported by NIH grant R01 AI122953-05. S.P.A. J.P. and G.B.-B. are supported by CIHR fellowships. R.G. is supported by a MITACS Acc?l?ration postdoctoral fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. A.T. M.N. D.E.K, and A.F. conceived the study. A.T. M.N. R.G. G.B.B. J.P. S.P.A. J.N. J.R. D.E.K. and A.F. designed experimental approaches. A.T. M.N. M.B. S.Y.G. R.G. G.B.B. N.B. D.V. J.P. S.P.A. C.B. J.R. D.E.K. and A.F. performed, analyzed, and interpreted the experiments. A.T. M.N. R.D. and O.T. performed statistical analysis. S.Y.G. A.L. J.P. H.M. G.G.L. G.G. L.S. A.T.M. P.U. M.L. W.M. J.R. and A.F. contributed unique reagents. L.G. C.M. P.A. V.M.-L. and C.T. collected clinical samples. C.L. G.D.S. S.M. and M.R. provided scientific input related to VOC. A.T. M.N. D.E.K. and A.F. wrote the manuscript with inputs from others. Every author has read, edited, and approved the final manuscript. The authors declare no competing interests.Tremblay, C.; Centre de Recherche du CHUMCanada; email: c.tremblay@umontreal.ca
Kaufmann, D.E.; Centre de Recherche du CHUMCanada; email: daniel.kaufmann@umontreal.ca
Finzi, A.; Centre de Recherche du CHUMCanada; email: andres.finzi@umontreal.ca		Cell Press1931312834133950EnglishCell Host and MicrobeArticleFinalAll Open Access, Bronze, GreenScopus2-s2.0-85108098380
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Sheyholislami H., Connor K.L.57222129132;57208012036;Are probiotics and prebiotics safe for use during pregnancy and lactation? A systematic review and meta-analysis2021Nutrients1372382110.3390/nu13072382https://www.scopus.com/inward/record.uri?eid=2-s2.0-85109543656&doi=10.3390%2fnu13072382&partnerID=40&md5=6acd5bf70d617f40414fee6f87d49826Department of Health Sciences, Carleton University, Ottawa, ON K1S5B6, CanadaSheyholislami, H., Department of Health Sciences, Carleton University, Ottawa, ON K1S5B6, Canada; Connor, K.L., Department of Health Sciences, Carleton University, Ottawa, ON K1S5B6, CanadaProbiotic and prebiotic products have shown potential health benefits, including for the prevention of adverse pregnancy outcomes. The incidence of adverse effects in pregnant people and their infants associated with probiotic/prebiotic/synbiotic intake, however, remains unclear. The objectives of this study were to evaluate the evidence on adverse effects of maternal probiotic, prebiotic, and/or synbiotic supplementation during pregnancy and lactation and interpret the findings to help inform clinical decision-making and care of this population. A systematic review was conducted following PRISMA guidelines. Scientific databases were searched using pre-determined terms, and risk of bias assessments were conducted to determine study quality. Inclusion criteria were English language studies, human studies, access to full-text, and probiotic/prebiotic/synbiotic supplementation to the mother and not the infant. In total, 11/100 eligible studies reported adverse effects and were eligible for inclusion in quantitative analysis, and data were visualised in a GOfER diagram. Probiotic and prebiotic products are safe for use during pregnancy and lactation. One study reported increased risk of vaginal discharge and changes in stool consistency (relative risk [95% CI]: 3.67 [1.04, 13.0]) when administering Lactobacillus rhamnosus and L. reuteri. Adverse effects associated with probiotic and prebiotic use do not pose any serious health concerns to mother or infant. Our findings and knowledge translation visualisations provide healthcare professionals and consumers with information to make evidence-informed decisions about the use of pre-and probiotics. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Adverse effects; Infant; Prebiotics; Pregnancy; Probiotics; Safety; Synbioticsprebiotic agent; probiotic agent; synbiotic agent; female; human; infant; lactation; meta analysis; newborn; pregnancy; prenatal exposure; risk assessment; risk factor; Female; Humans; Infant; Infant, Newborn; Lactation; Prebiotics; Pregnancy; Prenatal Exposure Delayed Effects; Probiotics; Risk Assessment; Risk Factors; SynbioticsPrebioticsConnor, K.L.; Department of Health Sciences, Canada; email: kristin.connor@carleton.caMDPI AG2072664334371892EnglishNutrientsReviewFinalAll Open Access, Gold, GreenScopus2-s2.0-85109543656
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Martinez-Marquez D., Pingali S., Panuwatwanich K., Stewart R.A., Mohamed S.57201631899;57223407367;24921934000;7402716998;7102845249;Application of eye tracking technology in aviation, maritime, and construction industries: A systematic review2021Sensors21134289110.3390/s21134289https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108265859&doi=10.3390%2fs21134289&partnerID=40&md5=918fd56036f93d0b782d04c733e14111School of Engineering and Built Environment, Griffith University, Gold Coast, QLD 4222, Australia; Sirindhorn International Institute of Technology, Thammasat University, Pathum Thani, 12120, ThailandMartinez-Marquez, D., School of Engineering and Built Environment, Griffith University, Gold Coast, QLD 4222, Australia; Pingali, S., School of Engineering and Built Environment, Griffith University, Gold Coast, QLD 4222, Australia; Panuwatwanich, K., Sirindhorn International Institute of Technology, Thammasat University, Pathum Thani, 12120, Thailand; Stewart, R.A., School of Engineering and Built Environment, Griffith University, Gold Coast, QLD 4222, Australia; Mohamed, S., School of Engineering and Built Environment, Griffith University, Gold Coast, QLD 4222, AustraliaMost accidents in the aviation, maritime, and construction industries are caused by human error, which can be traced back to impaired mental performance and attention failure. In 1596, Du Laurens, a French anatomist and medical scientist, said that the eyes are the windows of the mind. Eye tracking research dates back almost 150 years and it has been widely used in different fields for several purposes. Overall, eye tracking technologies provide the means to capture in real time a variety of eye movements that reflect different human cognitive, emotional, and physiological states, which can be used to gain a wider understanding of the human mind in different scenarios. This systematic literature review explored the different applications of eye tracking research in three high-risk industries, namely aviation, maritime, and construction. The results of this research uncovered the demographic distribution and applications of eye tracking research, as well as the different technologies that have been integrated to study the visual, cognitive, and attentional aspects of human mental performance. Moreover, different research gaps and potential future research directions were highlighted in relation to the usage of additional technologies to support, validate, and enhance eye tracking research to better understand human mental performance. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Accidents; Aviation; Construction; Eye tracking; Hazard identification; Human-machine interfaces; Maritime; Mental performance; Training; Visual attentionConstruction industry; Eye movements; Attention failures; Demographic distributions; Eye tracking technologies; Future research directions; Physiological state; Research gaps; Systematic literature review; Systematic Review; Eye tracking; aviation; building industry; eye movement; human; technology; Aviation; Construction Industry; Eye Movements; Eye-Tracking Technology; Humans; TechnologyAcknowledgments: This work was supported and founded by Griffith School of Engineering and Built Environment.Martinez-Marquez, D.; School of Engineering and Built Environment, Australia; email: daniel.martinezmarquez@griffithuni.edu.auMDPI AG1424822034201734EnglishSensorsArticleFinalAll Open Access, GreenScopus2-s2.0-85108265859
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Singh R.K., Singh A., Ksherchokpa L., Rallen O., Taniang B., Lego Y.J., Padung E., Kumar A., Tag H., Mauerhofer V.57203380587;57217562323;57222653254;55314386700;57222659530;57194693496;55314386600;57204150576;24345338600;24171666100;Grassroots Approaches for Sustaining Biocultural Diversity and Livelihood Security: Insights from Indian Eastern Himalaya2021Environmental Management6811737110.1007/s00267-021-01462-1https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103652915&doi=10.1007%2fs00267-021-01462-1&partnerID=40&md5=c8121b72ee708f8fd0942a230b0e9f1fCollege of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh 791102, India; ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh 226101, India; Dirang Bazar, West Kameng DistrictArunachal Pradesh, India; Village Sibut, East Siang, Pasighat, Arunachal Pradesh 791102, India; Village Kurum-Kume, Papum Pare, Kurum-Kume, Arunachal Pradesh, India; GTC Colony, East Siang, Pasighat, Arunachal Pradesh 791102, India; Doying Gumin College, East Siang, Pasighat, Arunachal Pradesh 791102, India; ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India; Department of Botany, Rajiv Gandhi University, Rono Hills, Doimukh, Arunachal Pradesh 791112, India; Environmental Law Centre of the Organization for the Strategic Coordination of Environmental Research, Meiji University, Tokyo, Japan; ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, IndiaSingh, R.K., College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh 791102, India, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India; Singh, A., ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh 226101, India; Ksherchokpa, L., Dirang Bazar, West Kameng DistrictArunachal Pradesh, India; Rallen, O., Village Sibut, East Siang, Pasighat, Arunachal Pradesh 791102, India; Taniang, B., Village Kurum-Kume, Papum Pare, Kurum-Kume, Arunachal Pradesh, India; Lego, Y.J., GTC Colony, East Siang, Pasighat, Arunachal Pradesh 791102, India; Padung, E., Doying Gumin College, East Siang, Pasighat, Arunachal Pradesh 791102, India; Kumar, A., ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India; Tag, H., Department of Botany, Rajiv Gandhi University, Rono Hills, Doimukh, Arunachal Pradesh 791112, India; Mauerhofer, V., Environmental Law Centre of the Organization for the Strategic Coordination of Environmental Research, Meiji University, Tokyo, JapanBioculturally significant plants, which have played a key role in sustaining the livelihoods of tribal communities of Arunachal Pradesh, India, are facing threats from changing land use patterns, climatic aberrations and socioeconomic stressors. This study highlights two unique grassroots approaches to conserving these species and their associated cultural knowledge within the traditional land use systems of Arunachal Pradesh: Community Knowledge Gardens (CKGs) and Clan Reserve Forests (CRFs). Four CKGs and one CRF, transformed from existing traditional land use systems, were investigated in three socio-ecologically diverse landscapes of Nyishi, Adi and Monpa communities. Study participants, including both men and women, played an active role in devising locally compatible criteria and protocols for strengthening the conservation of key plant species within their traditional land use systems, through CKG and CRF approaches. A total of 86 plant species, conserved through the CKGs and 44 from the Adi CRF, were identified as having high food, ethnomedicinal and cultural values. The Shannon-Weaver index of richness of plant species conserved was highest in the Nyishi CKG, with a value of 38; while for Adi and Monpa it was 30 and 18, respectively. The pattern of Shannon-Weaver diversity index was in the order of 2.91, 2.64 and 2.63, respectively for the CKGs of these three communities. In comparison to individual CKGs, relatively higher species diversity (3.18) was found in the Adi CRF. Increased sharing of traditional knowledge among the community members, regular incomes and equitable sharing of the tangible and intangible benefits of using plant species were identified as important success indicators of the CKGs and CRF. In addition to providing valuable insights on biocultural knowledge and enabling the participants to strengthen their existing local land use practices for conserving valued plant biodiversity, the study outcomes have the potential to inform and strengthen the policies on environmental sustainability. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.Biocultural resources; Community Knowledge Gardens; Community Reserve Forests; Conservation; Livelihoods Environmental and Conservation PoliciesBiodiversity; Conservation; Economics; Environmental protection; Forestry; Plants (botany); Sustainable development; Biocultural diversity; Cultural knowledge; Environmental sustainability; Intangible benefits; Land-use systems; Shannon-Weaver diversity index; Success indicators; Traditional knowledge; Land use; ethnic group; grassroots level; land use change; livelihood; participatory approach; socioeconomic conditions; species richness; sustainability; traditional knowledge; adult; article; biodiversity; cultural value; environmental sustainability; female; forest; human; land use; male; outcome assessment; security; species diversity; biodiversity; environmental protection; forest; India; traditional medicine; Arunachal Pradesh; Himalayas; India; Biodiversity; Conservation of Natural Resources; Female; Forests; Humans; India; Male; Medicine, TraditionalKerala Agricultural University, KAUThis study is dedicated to the Monpa, Adi and Nyishi communities. We are grateful to the community leaders, members and knowledge holders for providing the information. The taxonomic help in identifying plant species (including identifying new species from state Arunachal Pradesh) and understanding the basic ecological aspects obtained from Dr R C Srivastava, Botanical Survey of India, Itanagar, Arunachal Pradesh are gratefully acknowledged. College of Horticulture and Forestry, Central Agricultural University, Pasighat and National Innovation Foundation-India, Ahmedabad are acknowledged for their financial help. The logistical support obtained from ICAR-CSSRI, Karnal, Haryana, India for preparing this article is also acknowledged. The valuable comments of two anonymous reviewers are acknowledged that has improved quality of earlier version of this article. RKS conceived the idea. RKS, LK, OR, BT, YJL and EP mobilized the communities, condcuted the required activities and collected the data. RKS and AK analyzed the data. RKS and AMS wrote and revised the paper. HT helped in the checking taxonomic identification, categorizing status of plant species and followed further actions with local stakeholders. LK, OR, BT, YJL and EP assisted in re-collection of data with the required activities to validate the data and assisted in assessing long-term progress of works at local level in contact with RKS. VM contributed in methodological and discussion contents of study. All the authors read the final paper and made critical suggestions for improvement.Singh, R.K.; College of Horticulture and Forestry, India; email: ranjaysingh_jbp@rediffmail.comSpringer0364152XEMNGD33822243EnglishEnviron. Manage.ArticleFinalScopus2-s2.0-85103652915
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Bae S., Yang R., Gyory P., Uhr J., Szafir D.A., Do E.Y.-L.57219109024;57219287205;57203301736;57225996832;57190532886;14824449600;Touching Information with DIY Paper Charts & AR Markers2021Proceedings of Interaction Design and Children, IDC 202143343810.1145/3459990.3465191https://www.scopus.com/inward/record.uri?eid=2-s2.0-85110136952&doi=10.1145%2f3459990.3465191&partnerID=40&md5=c8cb95d8ce3a22ae5d9e61fbe9c2f2ffAtlas Institute, University of Colorado Boulder, United StatesBae, S., Atlas Institute, University of Colorado Boulder, United States; Yang, R., Atlas Institute, University of Colorado Boulder, United States; Gyory, P., Atlas Institute, University of Colorado Boulder, United States; Uhr, J., Atlas Institute, University of Colorado Boulder, United States; Szafir, D.A., Atlas Institute, University of Colorado Boulder, United States; Do, E.Y.-L., Atlas Institute, University of Colorado Boulder, United StatesFostering data literacy has largely been the domain of formal educational systems and export-oriented tools. Informal educational approaches, such as games or family activities, may overcome barriers to engaging with data by fostering data literacy through casual engagement. This work in progress explores how informal learning through creation and play with interactive data representations (physicalizations) can foster increased literacy and engagement with data. We outline a series of DIY paper charts using AR markers and everyday materials to help children interact and explore data through the creative process of making. © 2021 Owner/Author.data literacy; data physicalization; DIYCreative process; Data representations; Educational approach; Educational systems; Informal learning; Paper charts; Work in progress; International tradeNational Science Foundation, NSF: IIS-2040489This research is sponsored in part by the U.S. National Science Foundation through grant IIS-2040489.BRIDGES;EUGAIN;Hellenic Republic - National and Kapodistrian University of Athens;LUMSAssociation for Computing Machinery, Inc2021 ACM Interaction Design and Children, IDC 202124 June 2021 through 30 June 20211698939781450384520EnglishProc. Interact. Des. Child., IDCConference PaperFinalScopus2-s2.0-85110136952
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Anand S.P., Prévost J., Nayrac M., Beaudoin-Bussières G., Benlarbi M., Gasser R., Brassard N., Laumaea A., Gong S.Y., Bourassa C., Brunet-Ratnasingham E., Medjahed H., Gendron-Lepage G., Goyette G., Gokool L., Morrisseau C., Bégin P., Martel-Laferrière V., Tremblay C., Richard J., Bazin R., Duerr R., Kaufmann D.E., Finzi A.57204015968;57114557100;57210452682;57216826465;57219699236;55893637300;25632111500;35743347800;57221957835;57221946314;57204721001;35234275400;57207963631;57219403405;57219401842;57219403641;16416998400;36661125300;7005236335;23568696000;7005169712;57194424377;57208090961;57203237269;Longitudinal analysis of humoral immunity against SARS-CoV-2 Spike in convalescent individuals up to 8 months post-symptom onset2021Cell Reports Medicine261002903410.1016/j.xcrm.2021.100290https://www.scopus.com/inward/record.uri?eid=2-s2.0-85107066823&doi=10.1016%2fj.xcrm.2021.100290&partnerID=40&md5=b76b42f2a5817add4e4da16c347b6638Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Héma-Québec, Affaires Médicales et InnovationQC QC G1V 5C3, Canada; CHU Ste-Justine, Montreal, QC H3T 1C5, Canada; Departments of Pathology and Microbiology, New York University School of Medicine, New York, NY 10016, United States; Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, CanadaAnand, S.P., Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada, Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Prévost, J., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Nayrac, M., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Beaudoin-Bussières, G., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Benlarbi, M., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Gasser, R., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Brassard, N., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Laumaea, A., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Gong, S.Y., Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada, Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Bourassa, C., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Brunet-Ratnasingham, E., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Medjahed, H., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Gendron-Lepage, G., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Goyette, G., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Gokool, L., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Morrisseau, C., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Bégin, P., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, CHU Ste-Justine, Montreal, QC H3T 1C5, Canada; Martel-Laferrière, V., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Tremblay, C., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Richard, J., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Bazin, R., Héma-Québec, Affaires Médicales et InnovationQC QC G1V 5C3, Canada; Duerr, R., Departments of Pathology and Microbiology, New York University School of Medicine, New York, NY 10016, United States; Kaufmann, D.E., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Finzi, A., Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada, Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, CanadaWith the recent approval of highly effective coronavirus disease 2019 (COVID-19) vaccines, functional and lasting immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently under investigation as antibody levels in plasma were shown to decline during convalescence. Since the absence of antibodies does not equate to absence of immune memory, we evaluate the presence of SARS-CoV-2-specific memory B cells in convalescent individuals. Here, we report a longitudinal assessment of humoral immune responses on 32 donors up to 8 months post-symptom onset. Our observations indicate that anti-Spike and anti-receptor binding domain (RBD) immunoglobulin M (IgM) in plasma decay rapidly, whereas the reduction of IgG is less prominent. Neutralizing activity also declines rapidly when compared to Fc-effector functions. Concomitantly, the frequencies of RBD-specific IgM+ B cells wane significantly when compared to RBD-specific IgG+ B cells, which remain stable. Our results add to the current understanding of immune memory following SARS-CoV-2 infection, which is critical for secondary infection prevention and vaccine efficacy. © 2021 The AuthorsADCC; antibodies; coronavirus; COVID-19; humoral responses; memory B cells; neutralization; RBD; SARS-CoV-2; Spike glycoproteinsNational Institutes of Health, NIH: R01 AI122953-05; National Institute of Allergy and Infectious Diseases, NIAID: ARP-4376; American Foundation for Aging Research, AFAR; Fondation du CHUM; Canadian Institutes of Health Research, CIHR: 352417, VR2-173203; Fonds de Recherche du Québec - Santé, FRQS; Canada Foundation for Innovation, CFI: 41027, RCHS0235 950-232424; MitacsThe authors are grateful to the convalescent plasma donors who participated in this study. The authors thank the CRCHUM BSL3 and Flow Cytometry Platforms for technical assistance. We thank Dr. Stefan P?hlmann and Dr. Markus Hoffmann (Georg-August University, Germany) for the plasmid coding for SARS-CoV-2 S glycoproteins and Dr. M. Gordon Joyce (US MHRP) for the monoclonal antibody CR3022. The following reagent was obtained through the NIH HIV Reagent Program, Division of AIDS, NIAID, NIH: CEM.NKR CCR5+ Cells, ARP-4376, contributed by Dr. Alexandra Trkola. The graphical abstract was prepared using images from BioRender.com. This work was supported by le Minist?re de l??conomie et de l'Innovation du Qu?bec, Programme de soutien aux organismes de recherche et d'innovation to A.F. by the Fondation du CHUM, and by the Fondation du CHU Sainte-Justine. This work was also supported by the American Foundation for AIDS Research (amfAR) to A.F. and D.E.K. This work was also supported by Canada's COVID-19 Immunity Task Force (CITF), in collaboration with the Canadian Institutes of Health Research (CIHR) (grant VR2-173203); a CIHR foundation grant no. 352417 to A.F.; CIHR COVID-19 Rapid Research Funding to A.F. R.B. and P.B.; and by an Exceptional Fund COVID-19 from the Canada Foundation for Innovation (CFI) no. 41027 to A.F. and D.E.K. A.F. is the recipient of Canada Research Chair on Retroviral Entry no. RCHS0235 950-232424. V.M.-L. and P.B. are supported by FRQS Junior 1 salary awards. D.E.K. is a FRQS Merit Research Scholar. R.D. was supported by NIH grant R01 AI122953-05. S.P.A. J.P. and G.B.-B. are supported by CIHR fellowships. R.G. is supported by a MITACS Acc?l?ration postdoctoral fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. S.P.A. J.P. J.R. and A.F. conceived the study; S.P.A. J.P. M.N. G.B.-B. E.B.-R. J.R. D.E.K. and A.F. designed experimental approaches; S.P.A. J.P. M.N. G.B.-B. M.B. R.G. N.B. A.L. S.Y.G. C.B. G.G.-L. P.B. J.R. R.B. R.D. D.E.K. and A.F. performed, analyzed, and interpreted the experiments; R.D. performed statistical analyses; S.P.A. J.P. J.R. and G.G. contributed novel reagents; A.L. H.M. G.G.-L. L.G. C.M. V.M.-L. and C.T. collected and processed clinical samples; and S.P.A. J.P. R.D. and A.F. wrote the paper. Every author has read, edited, and approved the final manuscript. The authors declare no competing interests.The authors are grateful to the convalescent plasma donors who participated in this study. The authors thank the CRCHUM BSL3 and Flow Cytometry Platforms for technical assistance. We thank Dr. Stefan Pöhlmann and Dr. Markus Hoffmann (Georg-August University, Germany) for the plasmid coding for SARS-CoV-2 S glycoproteins and Dr. M. Gordon Joyce (US MHRP) for the monoclonal antibody CR3022. The following reagent was obtained through the NIH HIV Reagent Program, Division of AIDS, NIAID, NIH: CEM.NKR CCR5+ Cells, ARP-4376, contributed by Dr. Alexandra Trkola. The graphical abstract was prepared using images from BioRender.com . This work was supported by le Ministère de l’Économie et de l’Innovation du Québec, Programme de soutien aux organismes de recherche et d’innovation to A.F., by the Fondation du CHUM , and by the Fondation du CHU Sainte-Justine . This work was also supported by the American Foundation for AIDS Research (amfAR) to A.F. and D.E.K. This work was also supported by Canada’s COVID-19 Immunity Task Force (CITF), in collaboration with the Canadian Institutes of Health Research (CIHR) (grant VR2-173203 ); a CIHR foundation grant no. 352417 to A.F.; CIHR COVID-19 Rapid Research Funding to A.F., R.B., and P.B.; and by an Exceptional Fund COVID-19 from the Canada Foundation for Innovation (CFI) no. 41027 to A.F. and D.E.K. A.F. is the recipient of Canada Research Chair on Retroviral Entry no. RCHS0235 950-232424. V.M.-L. and P.B. are supported by FRQS Junior 1 salary awards. D.E.K. is a FRQS Merit Research Scholar. R.D. was supported by NIH grant R01 AI122953-05 . S.P.A., J.P., and G.B.-B. are supported by CIHR fellowships. R.G. is supported by a MITACS Accélération postdoctoral fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Duerr, R.; Departments of Pathology and Microbiology, United States; email: ralf.duerr@nyulangone.org
Kaufmann, D.E.; Centre de Recherche du CHUMCanada; email: daniel.kaufmann@umontreal.ca
Finzi, A.; Department of Microbiology and Immunology, Canada; email: andres.finzi@umontreal.ca		Cell Press26663791EnglishCell Rep. Med.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85107066823
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Riskiyev A., Ciobanu A., Hovhannesyan A., Akopyan K., Gadoev J., Parpieva N.57223976964;57188782883;57200314911;57189757256;55912572600;6506093758;Characteristics and treatment outcomes of patients with tuberculosis receiving adjunctive surgery in Uzbekistan2021International Journal of Environmental Research and Public Health1812654110.3390/ijerph18126541https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108097929&doi=10.3390%2fijerph18126541&partnerID=40&md5=6c468b736402a6335bf715ee501bf0feRepublican Specialized Scientific-Practical Medical Centre of Phthisiology and Pulmonology, 1 Alimov street, Tashkent City, 100086, Uzbekistan; World Health Organization Regional Office for Europe, UN City, Marmorvej 51, Copenhagen, DK-2100, Denmark; Tuberculosis Research and Prevention Centre NGO, Yerevan, 0070, Armenia; World Health Organization Country Office in Uzbekistan, 16 Tarobiy Street,, Tashkent City, 100100, UzbekistanRiskiyev, A., Republican Specialized Scientific-Practical Medical Centre of Phthisiology and Pulmonology, 1 Alimov street, Tashkent City, 100086, Uzbekistan; Ciobanu, A., World Health Organization Regional Office for Europe, UN City, Marmorvej 51, Copenhagen, DK-2100, Denmark; Hovhannesyan, A., World Health Organization Regional Office for Europe, UN City, Marmorvej 51, Copenhagen, DK-2100, Denmark; Akopyan, K., World Health Organization Regional Office for Europe, UN City, Marmorvej 51, Copenhagen, DK-2100, Denmark, Tuberculosis Research and Prevention Centre NGO, Yerevan, 0070, Armenia; Gadoev, J., World Health Organization Country Office in Uzbekistan, 16 Tarobiy Street,, Tashkent City, 100100, Uzbekistan; Parpieva, N., Republican Specialized Scientific-Practical Medical Centre of Phthisiology and Pulmonology, 1 Alimov street, Tashkent City, 100086, UzbekistanSurgical interventions are performed as an adjunct to pharmacological treatment in Uzbekistan in 10–12% of diagnosed tuberculosis (TB) patients. In this study among patients with respiratory TB who had surgical interventions in Republican Specialized Scientific-Practical Medical Centre of Phthisiology and Pulmonology of Uzbekistan (RSSPMCPP) from January to May 2017, we describe (i) reasons and types of surgical intervention, (ii) post-surgical complications, (iii) histological diagnosis before and after surgery, and (iv) treatment outcomes. There were 101 patients included in the analysis (mean age 36 years; 51% male; 71% lived in rural areas). The main indications for surgical intervention included pulmonary tuberculoma (40%), fibrocavitary, or cavernous pulmonary TB (23%) and massive hemoptysis (20%). Pulmonary resections were the most frequent surgical procedures: segmentectomy (41%), lobectomy or bilobectomy (19%), and combined resection (17%). Ten patients (9%) suffered post-surgery complications. According to histological examination after surgery, TB was confirmed in 81 (80%) patients. For the other 20 patients, the confirmed diagnoses were: lung cancer (n = 6), echinococcosis (n = 5), post-TB fibrosis (n = 5), non-tuberculous pleurisy (n = 2), hamartoma (n = 1), and pneumonia (n = 1). The majority of patients (94%), who underwent surgery, were considered successfully treated. In conclusion, adjunctive surgical therapy can be an option for TB treatment, especially in cases of complicated TB. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Adjunctive surgical intervention; Operational research; SORT-IT; Tuberculosis; Uzbekistanaminosalicylic acid; capreomycin; cycloserine; ethambutol; kanamycin; ofloxacin; protionamide; pyrazinamide; disease treatment; histology; research work; respiratory disease; tuberculosis; adult; Article; atelectasis; body mass; bronchopleural fistula; bronchus fistula; bronchus obstruction; decortication; diabetes mellitus; drug sensitivity; echinococcosis; empyema; female; fibrosis; hamartoma; heart disease; hematothorax; hemoptysis; hepatitis; human; Human immunodeficiency virus; lobectomy; lung cancer; lung resection; lung tuberculosis; major clinical study; male; pleurectomy; pneumonia; pneumothorax; segmentectomy; thoracocentesis; thoracoplasty; thoracostomy; thoracotomy; treatment outcome; tuberculoma; tuberculosis; Uzbekistan; wedge resection; wound infection; lung tuberculosis; retrospective study; treatment outcome; tuberculosis; Uzbekistan; Uzbekistan; Adult; Female; Humans; Male; Pneumonectomy; Retrospective Studies; Treatment Outcome; Tuberculosis; Tuberculosis, Pulmonary; Uzbekistanaminosalicylic acid, 133-10-8, 133-15-3, 28088-64-4, 51540-64-8, 65-49-6, 80702-32-5, 133-09-5, 6018-19-5, 6059-16-1; capreomycin, 11003-38-6, 1405-37-4; cycloserine, 339-72-0, 68-39-3, 68-41-7; ethambutol, 10054-05-4, 1070-11-7, 3577-94-4, 74-55-5; kanamycin, 11025-66-4, 61230-38-4, 8063-07-8; ofloxacin, 82419-36-1; protionamide, 14222-60-7; pyrazinamide, 98-96-4Funding: This research received no external funding. Funds for open access publication are provided by the World Health Organization Country Office in Uzbekistan and the German KfW Development Bank, the project “TB prevention and control in Uzbekistan”.Acknowledgments: The authors thank the Ministry of Health of Republic of Uzbekistan, Republican Specialized Scientific Practical Medical Centre of Phthisiology and Pulmonology under Ministry of Health of the Republic of Uzbekistan for defining research questions and providing data for this study, and the secretariat of the European TB Research Initiative (ERI-TB) at the World Health Organization Regional Office for Europe and World Health Organization Country Office in Uzbekistan for organizing the Structured Operational Research Training (SORT-TB) supported by the German KfW Development Bank, in line with joint World Health Organization/KfW “TB prevention and control in Uzbekistan” project. The SORT-TB curriculum was an adaptation of the SORT IT course of the UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR) SORT IT course (https://www.who.int/tdr/capacity/strengthening/sort/en/; accessed on 23 October 2020) to the eastern European and central Asian context. The current course was co-facilitated by officers from the World Health Organization Country Office in Uzbekistan; the World Health Organization Regional Office for Europe; the International Union Against Tuberculosis and Lung Disease (the Union) and individual experts in the area of tuberculosis research.Riskiyev, A.; Republican Specialized Scientific-Practical Medical Centre of Phthisiology and Pulmonology, 1 Alimov street, Uzbekistan; email: anvar_6070@list.ruMDPI1661782734204519EnglishInt. J. Environ. Res. Public HealthArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85108097929
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Sulaiman N., Pieroni A., Sõukand R., Whitney C., Polesny Z.57254279600;7004092892;6506885585;57254623400;23029095200;Socio–Cultural Significance of Yerba Maté among Syrian Residents and Diaspora2021Economic Botany75297111110.1007/s12231-021-09523-6https://www.scopus.com/inward/record.uri?eid=2-s2.0-85114703741&doi=10.1007%2fs12231-021-09523-6&partnerID=40&md5=582b75ee4abd393d84001197e9b7b1c8Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha - Suchdol, 165 00, Czech Republic; University of Gastronomic Sciences, Pollenzo, Bra, Italy; Medical Analysis Department, Faculty of Science, Tishk International University, Erbil, Iraq; Department of Environmental Sciences, Informatics and Statistics, Ca’ Foscari University of Venice, Venice, Italy; Institute of Crop Sciences and Resource Conservation (INRES), Horticulture Institute, University of Bonn, Auf Dem Huegel 6, Bonn, 53121, Germany; Center for Development Research (ZEF), University of Bonn, Genscherallee 3, Bonn, 53113, GermanySulaiman, N., Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha - Suchdol, 165 00, Czech Republic; Pieroni, A., University of Gastronomic Sciences, Pollenzo, Bra, Italy, Medical Analysis Department, Faculty of Science, Tishk International University, Erbil, Iraq; Sõukand, R., Department of Environmental Sciences, Informatics and Statistics, Ca’ Foscari University of Venice, Venice, Italy; Whitney, C., Institute of Crop Sciences and Resource Conservation (INRES), Horticulture Institute, University of Bonn, Auf Dem Huegel 6, Bonn, 53121, Germany, Center for Development Research (ZEF), University of Bonn, Genscherallee 3, Bonn, 53113, Germany; Polesny, Z., Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha - Suchdol, 165 00, Czech RepublicSocio–Cultural Significance of Yerba Maté among Syrian Residents and Diaspora. Syria is the world’s second–largest importer of the dried leaves of Ilex paraguariensis A.St.–Hil., commonly known as yerba maté. The unique story of yerba maté in the Syrian beverage culture started at the beginning of the twentieth century when Syrian migrants returning from South America brought the beverage with them. The overall aim of our study is to understand yerba maté use among Syrians and its role as an essential part of the Syrian beverage culture. We compare yerba maté consumption on spatial, gender, and religious bases through semi–structured interviews with 50 respondents, with equal participation among genders, place of residence, and cultural–religious groups (Sunni, Alawite, Christian, Druze, and Ismaili). We found that the Alawite and Druze groups have the highest yerba maté consumption, and that men drink more than women. Yerba maté was the most preferred stimulant drink among participants, followed by coffee and tea, respectively. Interviews reveal social and cultural factors, perceived addiction, perceived pleasure, and perceived health properties as the drivers behind yerba maté consumption in Syria. © 2021, The New York Botanical Garden.Beverages; Conflict area; Cultural migration; Ethnobotany; Ilex paraguariensis; Stimulant plants20213113; Česká Zemědělská Univerzita v PrazeWe would like to thank all study participants who shared with us their time and knowledge and two anonymous reviewers for their helpful comments on the manuscript. The study was funded by the Internal Grant Agency of the Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague (IGA FTZ, Project No. 20213113). The authors declare that they have no conflict of interest. ZP, AP, and NS drafted the narrative. NS, AP, and RS designed the study. NS carried out the data collection, analyzed the data, and drafted the manuscript with major contributions from all the co–authors. AP, RS, CW, and ZP critically revised the manuscript. All authors read and approved the final manuscript version. The data that support the findings of this study are available from the corresponding author, upon reasonable request. The Code of Ethics of the International Society of Ethnobiology was rigorously followed, and informed consent was obtained prior to interviews. Participants were fully informed about the objectives and purpose of the proposed research. The question about religion was asked appropriately, respecting its sensitivity in the Syrian context.Polesny, Z.; Department of Crop Sciences and Agroforestry, Kamýcká 129, Czech Republic; email: polesny@ftz.czu.czSpringer130001ECBOAEnglishEcon. Bot.ArticleFinalAll Open Access, Bronze, GreenScopus2-s2.0-85114703741
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Macieira R.M., Oliveira L.A.S., Cardozo-Ferreira G.C., Pimentel C.R., Andrades R., Gasparini J.L., Sarti F., Chelazzi D., Cincinelli A., Gomes L.C., Giarrizzo T.16022364500;57223146677;57191829334;36155996900;55388609000;6603361579;57217178573;9437463200;6602476805;7103337735;17345581900;Microplastic and artificial cellulose microfibers ingestion by reef fishes in the Guarapari Islands, southwestern Atlantic2021Marine Pollution Bulletin167112371310.1016/j.marpolbul.2021.112371https://www.scopus.com/inward/record.uri?eid=2-s2.0-85105035659&doi=10.1016%2fj.marpolbul.2021.112371&partnerID=40&md5=b2c8cd988c1d6854c5a8a4f6183cd97dLaboratório de Ictiologia, Departamento de Oceanografia e Ecologia, Universidade Federal do Espírito Santo, Goiabeiras, Vitória, Espírito Santo 29.075-910, Brazil; Complexo Biopráticas, Universidade Vila Velha, Rua Comissário José Dantas de Melo 21, Boa Vista, Vila Velha, Espírito Santo 29.102-770, Brazil; Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro 27.910-970, Brazil; Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia, 3, Sesto Fiorentino, Florence 50019, Italy; Núcleo de Ecologia Aquática e Pesca da Amazônia (NEAP), Universidade Federal do Pará, Av. Perimetral 2651, Terra Firme, Belém, Pará 66.077-830, BrazilMacieira, R.M., Laboratório de Ictiologia, Departamento de Oceanografia e Ecologia, Universidade Federal do Espírito Santo, Goiabeiras, Vitória, Espírito Santo 29.075-910, Brazil; Oliveira, L.A.S., Complexo Biopráticas, Universidade Vila Velha, Rua Comissário José Dantas de Melo 21, Boa Vista, Vila Velha, Espírito Santo 29.102-770, Brazil; Cardozo-Ferreira, G.C., Laboratório de Ictiologia, Departamento de Oceanografia e Ecologia, Universidade Federal do Espírito Santo, Goiabeiras, Vitória, Espírito Santo 29.075-910, Brazil; Pimentel, C.R., Laboratório de Ictiologia, Departamento de Oceanografia e Ecologia, Universidade Federal do Espírito Santo, Goiabeiras, Vitória, Espírito Santo 29.075-910, Brazil; Andrades, R., Laboratório de Ictiologia, Departamento de Oceanografia e Ecologia, Universidade Federal do Espírito Santo, Goiabeiras, Vitória, Espírito Santo 29.075-910, Brazil; Gasparini, J.L., Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro 27.910-970, Brazil; Sarti, F., Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia, 3, Sesto Fiorentino, Florence 50019, Italy; Chelazzi, D., Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia, 3, Sesto Fiorentino, Florence 50019, Italy; Cincinelli, A., Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia, 3, Sesto Fiorentino, Florence 50019, Italy; Gomes, L.C., Complexo Biopráticas, Universidade Vila Velha, Rua Comissário José Dantas de Melo 21, Boa Vista, Vila Velha, Espírito Santo 29.102-770, Brazil; Giarrizzo, T., Núcleo de Ecologia Aquática e Pesca da Amazônia (NEAP), Universidade Federal do Pará, Av. Perimetral 2651, Terra Firme, Belém, Pará 66.077-830, BrazilThis study investigated the ingestion of microplastics and artificial cellulose particles by 103 specimens belonging to 21 reef fish species from the southwestern Atlantic. Specimens of six species had ingested microplastics and artificial cellulose particles, while those of another three species had ingested only one type of material. In our samples, man-made cellulose fibers were more common than microplastics. The tomtate grunt, Haemulon aurolineatum, ingested more particles than any of the other species. Overall, transparent particles were predominant, and polyamide was the most common plastic material. Household sewage, fishery activity, and navigation appear to be the principal sources of the artificial particles ingested by the reef fishes. Our results provide an important database on oceanic contamination by microplastics and artificial cellulose particles. Understanding this impact on tropical reef fish will contribute to the development of strategies to mitigate pollution by anthropogenic debris in reef systems. © 2021 Elsevier LtdBrazil; Cellulose-based fibers; Litter; Marine fishes; Plastic; PolymersFish; Microplastic; Reefs; Sewage; Brazil; Cellulose fiber; Cellulose-based fiber; Fish species; Marine fish; Microfibre; Microplastics; Plastic; Reef fishes; Southwestern Atlantic; Cellulose; cellulose; cellulose; plastic; cellulose; fish; ingestion rate; litter; marine pollution; plastic waste; pollution control; pollution effect; polymer; reef; Article; Atlantic Ocean; controlled study; environmental exposure; fish; geographic distribution; ingestion; microplastic pollution; nonhuman; water analysis; water contamination; water quality; animal; eating; environmental monitoring; fish; human; island (geological); water pollutant; Brazil; Cellulose; Fishes; Islands; Particles; Samples; Sewage; Atlantic Ocean; Atlantic Ocean (Southwest); Brazil; Espirito Santo; Guarapari; Haemulon; Haemulon aurolineatum; Pisces; Animals; Cellulose; Eating; Environmental Monitoring; Fishes; Humans; Islands; Microplastics; Plastics; Water Pollutants, Chemicalcellulose, 61991-22-8, 68073-05-2, 9004-34-6; Cellulose; Microplastics; Plastics; Water Pollutants, ChemicalPPP/119/2017; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES: 311078/2019-2 / #312431/2018-0; Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq: 04/2017 – PPP/119/2017; Fundação de Amparo à Pesquisa e Inovação do Espírito Santo, FAPESThis study was funded by Funda??o de Amparo ? Pesquisa e Inova??o do Esp?rito Santo - FAPES (grant FAPES/CNPq N? 04/2017 ? PPP/119/2017). L.A. da S. de O. acknowledges financial support from Nossa Bolsa (FAPES), and R.A., G.C.C.-F., C.R.P. and J.L.G are grateful to the Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - Brazil (CAPES) - Finance Code 001. C.R.P. also thanks the FAPES for a PhD scholarship. T.G. and L.C.G. received a research productivity grant from CNPq (#311078/2019-2 / #312431/2018-0). D.C. and A.C. gratefully acknowledge CSGI (Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase), Florence (Italy) for financial support.This study was funded by Fundação de Amparo à Pesquisa e Inovação do Espírito Santo - FAPES (grant FAPES/CNPq N° 04/2017 – PPP/119/2017 ). L.A. da S. de O. acknowledges financial support from Nossa Bolsa ( FAPES ), and R.A., G.C.C.-F., C.R.P. and J.L.G are grateful to the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brazil ( CAPES ) - Finance Code 001 . C.R.P. also thanks the FAPES for a PhD scholarship. T.G. and L.C.G. received a research productivity grant from CNPq (#311078/2019-2 / #312431/2018-0). D.C. and A.C. gratefully acknowledge CSGI (Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase), Florence (Italy) for financial support.Macieira, R.M.; Laboratório de Ictiologia, Brazil; email: raphaelmacieira@hotmail.comElsevier Ltd0025326XMPNBA33962257EnglishMar. Pollut. Bull.ArticleFinalScopus2-s2.0-85105035659
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Abdul-Hussein A., Kareem A., Tewari S., Bergeron J., Briollais L., Challis J.R.G., Davidge S.T., Delrieux C., Fortier I., Goldowitz D., Nepomnaschy P., Wazana A., Connor K.L.57218600358;57218602052;57220653036;36966222800;6701527302;36012752000;7005933822;55887255100;6602608336;7006144166;6507583093;6602263376;57208012036;Early life risk and resiliency factors and their influences on developmental outcomes and disease pathways: A rapid evidence review of systematic reviews and meta-analyses2021Journal of Developmental Origins of Health and Disease123357372210.1017/S2040174420000689https://www.scopus.com/inward/record.uri?eid=2-s2.0-85089729719&doi=10.1017%2fS2040174420000689&partnerID=40&md5=bc38fca56f06ca7936656826b86fe84aDepartment of Health Sciences, Carleton University, Ottawa, ON, Canada; Research Institute of the McGill University Health Centre, Montreal, QC, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Simon Fraser University, Burnaby, BC, Canada; Women and Children's Health Research Institute and Obstetrics and Gynaecology, University of Alberta, Edmonton, AB, Canada; Universidad Nacional Del sur Argentina, Bahiá Blanca, Argentina; Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Psychiatry, McGill University, Montreal, CanadaAbdul-Hussein, A., Department of Health Sciences, Carleton University, Ottawa, ON, Canada; Kareem, A., Department of Health Sciences, Carleton University, Ottawa, ON, Canada; Tewari, S., Department of Health Sciences, Carleton University, Ottawa, ON, Canada; Bergeron, J., Research Institute of the McGill University Health Centre, Montreal, QC, Canada; Briollais, L., Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada; Challis, J.R.G., University of Toronto, Toronto, ON, Canada, Simon Fraser University, Burnaby, BC, Canada; Davidge, S.T., Women and Children's Health Research Institute and Obstetrics and Gynaecology, University of Alberta, Edmonton, AB, Canada; Delrieux, C., Universidad Nacional Del sur Argentina, Bahiá Blanca, Argentina; Fortier, I., Research Institute of the McGill University Health Centre, Montreal, QC, Canada; Goldowitz, D., Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Nepomnaschy, P., Simon Fraser University, Burnaby, BC, Canada; Wazana, A., Psychiatry, McGill University, Montreal, Canada; Connor, K.L., Department of Health Sciences, Carleton University, Ottawa, ON, CanadaThe Developmental Origins of Health and Disease (DOHaD) framework aims to understand how environmental exposures in early life shape lifecycle health. Our understanding and the ability to prevent poor health outcomes and enrich for resiliency remain limited, in part, because exposure-outcome relationships are complex and poorly defined. We, therefore, aimed to determine the major DOHaD risk and resilience factors. A systematic approach with a 3-level screening process was used to conduct our Rapid Evidence Review following the established guidelines. Scientific databases using DOHaD-related keywords were searched to capture articles between January 1, 2009 and April 19, 2019. A final total of 56 systematic reviews/meta-analyses were obtained. Studies were categorized into domains based on primary exposures and outcomes investigated. Primary summary statistics and extracted data from the studies are presented in Graphical Overview for Evidence Reviews diagrams. There was substantial heterogeneity within and between studies. While global trends showed an increase in DOHaD publications over the last decade, the majority of data reported were from high-income countries. Articles were categorized under six exposure domains: Early Life Nutrition, Maternal/Paternal Health, Maternal/Paternal Psychological Exposure, Toxicants/Environment, Social Determinants, and Others. Studies examining social determinants of health and paternal influences were underrepresented. Only 23% of the articles explored resiliency factors. We synthesized major evidence on relationships between early life exposures and developmental and health outcomes, identifying risk and resiliency factors that influence later life health. Our findings provide insight into important trends and gaps in knowledge within many exposures and outcome domains. ©Development; exposure; health determinants; lifecourse health; riskConnor, K.L.; Department of Health Sciences, 1125 Colonel By Drive, 3310 Health Sciences Building, Canada; email: kristin.connor@carleton.caCambridge University Press2040174432746960EnglishJ. Dev. Orig. Health Dis.ReviewFinalScopus2-s2.0-85089729719
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Ferreira V., Pié L., Terceño A.57220962976;23570054900;6506440940;Economic impact of the bioeconomy in Spain: Multiplier effects with a bio social accounting matrix2021Journal of Cleaner Production298126752210.1016/j.jclepro.2021.126752https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103584865&doi=10.1016%2fj.jclepro.2021.126752&partnerID=40&md5=48d300469bcad7d89310c3609b77b19fMarkets and Financial Analysis Research Group, Department of Business Management, Faculty of Business and Economics, Universitat Rovira i Virgili, Av. Universitat No 1, Reus, 43204, SpainFerreira, V., Markets and Financial Analysis Research Group, Department of Business Management, Faculty of Business and Economics, Universitat Rovira i Virgili, Av. Universitat No 1, Reus, 43204, Spain; Pié, L., Markets and Financial Analysis Research Group, Department of Business Management, Faculty of Business and Economics, Universitat Rovira i Virgili, Av. Universitat No 1, Reus, 43204, Spain; Terceño, A., Markets and Financial Analysis Research Group, Department of Business Management, Faculty of Business and Economics, Universitat Rovira i Virgili, Av. Universitat No 1, Reus, 43204, SpainThe bioeconomy emerges as a new economic model to help address issues related to environmental care and focus on a more sustainable economy. In the last decade, it has become a global priority and many countries have published their own strategies that clearly refer to the development of the bioeconomy. The symmetric social accounting matrix with basic prices was constructed, including the breakdown of biobased accounts belonging to the bioeconomy to determine which sectors of the bioeconomy are most strategic to promote sustainable economic growth. This constructed matrix was used to analyse the economic influence of the bioeconomy products and their impact on job creation. The analysis was carried out using the diffusion and absorption multipliers, which enabled the interpretation of the linkages between the different economic agents. The results were analysed in depth and the multipliers decomposed into their different effects, own, open and circular, and complemented with the calculation of the employment multiplier to evaluate the most important sectors for employment generation. The analysis was applied to the case of Spain. The results of this research enabled the identification of the strategic sectors where economic policies can be applied since these are the ones that increase economic growth and activities within the bioeconomy and create jobs. The conclusions indicated that the Spanish bioeconomy is still focused on traditional sectors and has not yet developed its potential in more innovative biobased products, demonstrating that the bioeconomy in Spain still has a long way to go. © 2021 Elsevier LtdBioeconomy; Impact analyses; Multipliers; Multisectoral models; Social accounting matrix; SpainEconomic and social effects; Sustainable development; Economic impacts; Economic models; Impact analysis; matrix; Multiplier; Multiplier effects; Multisectoral model; Social accounting matrix; Spain; Sustainable economy; Economic analysisHorizon 2020 Framework Programme, H2020: 713679; Universitat Rovira i Virgili; Horizon 2020This project received funding from the European Union's Horizon 2020 research and innovation programme under Marie Sk?odowska-Curie grant agreement No. 713679 and from the Universitat Rovira i Virgili (URV).This project received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement No. 713679 and from the Universitat Rovira i Virgili (URV).Pié, L.; Markets and Financial Analysis Research Group, Av. Universitat No 1, Spain; email: laia.pie@urv.catElsevier Ltd9596526JCROEEnglishJ. Clean. Prod.ArticleFinalScopus2-s2.0-85103584865
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McNutt A., Chugh R.57218768101;25824628800;Integrated visualization editing via parameterized declarative templates2021Conference on Human Factors in Computing Systems - Proceedings110.1145/3411764.3445356https://www.scopus.com/inward/record.uri?eid=2-s2.0-85106679213&doi=10.1145%2f3411764.3445356&partnerID=40&md5=17686afea89f869334aee6131353406bUniversity of Chicago, Chicago, IL, United StatesMcNutt, A., University of Chicago, Chicago, IL, United States; Chugh, R., University of Chicago, Chicago, IL, United StatesInterfaces for creating visualizations typically embrace one of sev- eral common forms. Textual specifcation enables fne-grained control, shelf building facilitates rapid exploration, while chart choosing promotes immediacy and simplicity. Ideally these approaches could be unifed to integrate the user- and usage-dependent benefts found in each modality, yet these forms remain distinct. We propose parameterized declarative templates, a simple abstraction mechanism over JSON-based visualization grammars, as a foundation for multimodal visualization editors. We demonstrate how templates can facilitate organization and reuse by factoring the more than 160 charts that constitute Vega-Lite's example gallery into approximately 40 templates. We exemplify the pliability of abstracting over charting grammars by implementing-as a template-the functionality of the shelf builder Polestar (a simulacra of Tableau) and a set of templates that emulate the Google Sheets chart chooser. We show how templates support multimodal visualization editing by implementing a prototype and evaluating it through an approachability study. © 2021 ACM.Declarative grammars; Information visualization; Ivy; Systems; Templates; User interfacesHuman engineering; Software engineering; Abstraction mechanism; Multi-modal visualization; Parameterized; VisualizationAssociation for Computing Machinery10th International Conference on Materials Processing and Characterisation, ICMPC 202021 February 2020 through 23 February 20201687909781450380966EnglishConf Hum Fact Comput Syst ProcConference PaperFinalAll Open Access, GreenScopus2-s2.0-85106679213
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Jahn L.J., Simon D., Jensen M., Bradshaw C., Ellabaan M.M.H., Sommer M.O.A.57194342764;57201979663;57223714640;57223717611;19638246900;23994698200;Compatibility of Evolutionary Responses to Constituent Antibiotics Drive Resistance Evolution to Drug Pairs2021Molecular Biology and Evolution38520572069310.1093/molbev/msab006https://www.scopus.com/inward/record.uri?eid=2-s2.0-85105154227&doi=10.1093%2fmolbev%2fmsab006&partnerID=40&md5=858930f2d98f4ba00552025deb7dc11cNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, DenmarkJahn, L.J., Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; Simon, D., Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; Jensen, M., Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; Bradshaw, C., Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; Ellabaan, M.M.H., Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; Sommer, M.O.A., Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, DenmarkAntibiotic combinations are considered a relevant strategy to tackle the global antibiotic resistance crisis since they are believed to increase treatment efficacy and reduce resistance evolution (WHO treatment guidelines for drug-resistant tuberculosis: 2016 update.). However, studies of the evolution of bacterial resistance to combination therapy have focused on a limited number of drugs and have provided contradictory results (Lipsitch, Levin BR. 1997; Hegreness et al. 2008; Munck et al. 2014). To address this gap in our understanding, we performed a large-scale laboratory evolution experiment, adapting eight replicate lineages of Escherichia coli to a diverse set of 22 different antibiotics and 33 antibiotic pairs. We found that combination therapy significantly limits the evolution of de novode novo resistance in E. coli, yet different drug combinations vary substantially in their propensity to select for resistance. In contrast to current theories, the phenotypic features of drug pairs are weak predictors of resistance evolution. Instead, the resistance evolution is driven by the relationship between the evolutionary trajectories that lead to resistance to a drug combination and those that lead to resistance to the component drugs. Drug combinations requiring a novel genetic response from target bacteria compared with the individual component drugs significantly reduce resistance evolution. These data support combination therapy as a treatment option to decelerate resistance evolution and provide a novel framework for selecting optimized drug combinations based on bacterial evolutionary responses. © 2021 The Author(s).adaptive evolution; antimicrobial resistance; combination therapyaminoglycoside; antibiotic agent; beta lactam; chloramphenicol; cotrimoxazole; erythromycin; fosfomycin; macrolide; polypeptide antibiotic agent; quinolone derivative; sulfamethoxazole; tetracycline derivative; trimethoprim; antiinfective agent; antibiotic resistance; antibiotic therapy; Article; combination drug therapy; controlled study; Escherichia coli; Escherichia coli infection; nonhuman; treatment response; biological model; evolution; genetics; multidrug resistance; Anti-Bacterial Agents; Biological Evolution; Drug Resistance, Multiple, Bacterial; Drug Therapy, Combination; Escherichia coli; Models, Geneticchloramphenicol, 134-90-7, 2787-09-9, 56-75-7; cotrimoxazole, 8064-90-2; erythromycin, 114-07-8, 70536-18-4; fosfomycin, 23155-02-4; sulfamethoxazole, 723-46-6; trimethoprim, 738-70-5; Anti-Bacterial Agents4004- 00213; 638902; H2020 Marie Skłodowska-Curie Actions, MSCA: 642738; National Forest Foundation, NFF: NNF10CC1016517; European Commission, EC; Horizon 2020; Novo Nordisk Fonden, NNFThis study was supported by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 642738, MetaRNA as well from the European Union's Horizon 2020 (ERC-2014-StG) under grant agreement 638902, LimitMDR. In addition, funding was received from Danish Council for Independent Research, Sapere Aude Program DFF 4004- 00213 and from The Novo Nordisk Foundation under NFF grant number: NNF10CC1016517.Sommer, M.O.A.; Novo Nordisk Foundation Center for Biosustainability, Denmark; email: msom@bio.dtu.dkOxford University Press7374038MBEVE33480997EnglishMol. Biol. Evol.ArticleFinalAll Open Access, Hybrid Gold, GreenScopus2-s2.0-85105154227
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Engström A.57203502586;Conceptualizing Lifestyle and Routine Activities in the Early 21st Century: A Systematic Review of Self-Report Measures in Studies on Direct-Contact Offenses in Young Populations2021Crime and Delinquency675737782410.1177/0011128720937640https://www.scopus.com/inward/record.uri?eid=2-s2.0-85086905253&doi=10.1177%2f0011128720937640&partnerID=40&md5=f0ecb0fc95d9ee24c999b686f06b8568Malmö University, SwedenEngström, A., Malmö University, SwedenCriticism is commonly directed at research based on lifestyle-exposure theory and routine activity theory for the use of imprecise measures. To examine this issue further, this systematic review maps activities used as indicators of lifestyle and routine activities in studies on direct-contact crime among young individuals (mean age of 24 or younger). The results indicate that a broad range of activities are used as measures of lifestyle and routine activities in the 101 included studies. Studies on victimization often use illegal activities and substance use as measures of lifestyle or routine activities while studies on offending mainly rely on measures of unstructured and peer-oriented leisure activities. Overall, most studies seem more concerned with specific activities rather than routines or lifestyles. © The Author(s) 2020.lifestyle-exposure theory; measurement; operationalization; routine activity theory; violenceEngström, A.; Malmö UniversitySweden; email: alexander.engstrom@mau.seSAGE Publications Inc.111287CRDLAEnglishCrime Delinq.ArticleFinalScopus2-s2.0-85086905253
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Trubnikov A., Hovhannesyan A., Akopyan K., Ciobanu A., Sadirova D., Kalandarova L., Parpieva N., Gadoev J.57222759272;57200314911;57189757256;57188782883;57222759500;57222761759;6506093758;55912572600;Effectiveness and safety of a shorter treatment regimen in a setting with a high burden of multidrug-resistant tuberculosis2021International Journal of Environmental Research and Public Health1884121210.3390/ijerph18084121https://www.scopus.com/inward/record.uri?eid=2-s2.0-85104006113&doi=10.3390%2fijerph18084121&partnerID=40&md5=5ff7a56d50e1e395f0cd4efb4adb23b0Abt Associates, Rashidov Street C-4, 20A, Yunosobod District, Tashkent, 100093, Uzbekistan; Republican Specialized Scientific Practical Medical Centre of Phthisiology and Pulmonology under Ministry of Health of the Republic of Uzbekistan, Sh. Alimov 1, Little Ring Road, Tashkent, 100086, Uzbekistan; World Health Organization Regional Office for Europe, UN City, Marmorvej 51, Copenhagen, DK-2100, Denmark; Tuberculosis Research and Prevention Center NGO, Yerevan, 0023, Armenia; Tashkent City Center of Phthisiology and Pulmonology, Lutfi Street 33/1, 7th District, Chilonzor District, Tashkent, 100043, Uzbekistan; World Health Organization Uzbekistan Country Office, 16, Tarobiy Street, Tashkent, 100100, UzbekistanTrubnikov, A., Abt Associates, Rashidov Street C-4, 20A, Yunosobod District, Tashkent, 100093, Uzbekistan, Republican Specialized Scientific Practical Medical Centre of Phthisiology and Pulmonology under Ministry of Health of the Republic of Uzbekistan, Sh. Alimov 1, Little Ring Road, Tashkent, 100086, Uzbekistan; Hovhannesyan, A., World Health Organization Regional Office for Europe, UN City, Marmorvej 51, Copenhagen, DK-2100, Denmark; Akopyan, K., World Health Organization Regional Office for Europe, UN City, Marmorvej 51, Copenhagen, DK-2100, Denmark, Tuberculosis Research and Prevention Center NGO, Yerevan, 0023, Armenia; Ciobanu, A., World Health Organization Regional Office for Europe, UN City, Marmorvej 51, Copenhagen, DK-2100, Denmark; Sadirova, D., Tashkent City Center of Phthisiology and Pulmonology, Lutfi Street 33/1, 7th District, Chilonzor District, Tashkent, 100043, Uzbekistan; Kalandarova, L., Tashkent City Center of Phthisiology and Pulmonology, Lutfi Street 33/1, 7th District, Chilonzor District, Tashkent, 100043, Uzbekistan; Parpieva, N., Republican Specialized Scientific Practical Medical Centre of Phthisiology and Pulmonology under Ministry of Health of the Republic of Uzbekistan, Sh. Alimov 1, Little Ring Road, Tashkent, 100086, Uzbekistan; Gadoev, J., World Health Organization Uzbekistan Country Office, 16, Tarobiy Street, Tashkent, 100100, UzbekistanTreatment of drug-resistant tuberculosis is lengthy, insufficiently effective, and toxic. Since 2016, the World Health Organization has recommended shorter treatment regimens (STR). We assessed effectiveness and predictors of drug adverse events (DAE) among patients treated with STR. There were 95 consecutive rifampicin-resistant patients enrolled in STR in Tashkent between June 2018 and September 2019. Of these, 66.3% were successfully treated, 17.9% suffered failed treatment, 7.4% died, 5.3% were lost to follow-up and 3.2% were not evaluated. No recurrence was identified in 54 patients after 12 months of successful treatment completion. There were 47 reported DAE: the incidence rate was 6.15 DAE per 100 person-months-of-treatment. Any DAE was reported in 38 (40%) patients and grade 3/4 DAE were recorded in 21 (22.1%) patients. Median time to DAE was 101 (interquartile range 64–139) days. The most frequently encountered DAE were gastro-intestinal disorders, followed by hepatotoxicity and ototoxicity. The most commonly offending drug inducing DAE was protionamide. The dose was temporarily interrupted in 55.3% of DAE, reduced in 8.5% of DAE and permanently withdrawn in another 8.5% of DAE. HIV status was the only predictor associated with increased hazard of DAE. In Uzbekistan STR showed moderate effectiveness and safety, although treatment failure was high. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Drug adverse event; Operational research; RR-TB treatment outcome; Shorter treatment regimen; SORT IT; Uzbekistanantiretrovirus agent; capreomycin; clofazimine; ethambutol; isoniazid; kanamycin; moxifloxacin; protionamide; pyrazinamide; quinolone derivative; rifampicin; rifampicin; tuberculostatic agent; antibiotic resistance; disease treatment; research; safety; toxicity; tuberculosis; acute psychosis; adult; Article; ataxia; cardiotoxicity; central nervous system disease; cohort analysis; controlled study; disease burden; disease severity; drug dose regimen; drug efficacy; drug megadose; drug safety; female; follow up; hearing impairment; human; Human immunodeficiency virus infection; incidence; liver toxicity; major clinical study; male; middle aged; multidrug resistant tuberculosis; multiple organ failure; nausea; nephrotoxicity; optic neuritis; patient monitoring; population structure; prediction; risk factor; short course therapy; skin disease; tinnitus; treatment duration; treatment failure; treatment outcome; Uzbekistan; vomiting; clinical protocol; multidrug resistant tuberculosis; Tashkent; Uzbekistan; Antitubercular Agents; Clinical Protocols; Humans; Rifampin; Treatment Outcome; Tuberculosis, Multidrug-Resistant; Uzbekistancapreomycin, 11003-38-6, 1405-37-4; clofazimine, 2030-63-9; ethambutol, 10054-05-4, 1070-11-7, 3577-94-4, 74-55-5; isoniazid, 54-85-3, 62229-51-0, 65979-32-0; kanamycin, 11025-66-4, 61230-38-4, 8063-07-8; moxifloxacin, 151096-09-2; protionamide, 14222-60-7; pyrazinamide, 98-96-4; rifampicin, 13292-46-1; Antitubercular Agents; RifampinAcknowledgments: The authors thank the Ministry of Health of Republic of Uzbekistan, Republican Specialized Scientific Practical Medical Centre of Phthisiology and Pulmonology under Ministry of Health of the Republic of Uzbekistan for defining research questions and providing data for this study, and the secretariat of the European TB Research Initiative (ERI-TB) at the World Health Organization Regional Office for Europe and World Health Organization Country Office in Uzbekistan for organizing the Structured Operational Research Training (SORT-TB) supported by the German KfW Development Bank, in line with joint World Health Organization/KfW “TB prevention and control in Uzbekistan” project. The SORT-TB curriculum was an adaptation of the SORT IT course of the UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR) SORT IT course (https://www.who.int/tdr/capacity/strengthening/sort/en/ (accessed on 12 March 2021)) to the eastern European and central Asian context. The current course was co-facilitated by officers from the World Health Organization Country Office in Uzbekistan; the World Health Organization Regional Office for Europe; the International Union Against Tuberculosis and Lung Disease (the Union) and individual experts in the area of tuberculosis research.World Health Organization Country Office in Uzbekistan and the German KfW Development Bank, the project ?TB prevention and control in Uzbekistan?.Trubnikov, A.; Abt Associates, Rashidov Street C-4, 20A, Yunosobod District, Uzbekistan; email: Aleksandr_Trubnikov@abtassoc.com
Trubnikov, A.; Republican Specialized Scientific Practical Medical Centre of Phthisiology and Pulmonology under Ministry of Health of the Republic of Uzbekistan, Sh. Alimov 1, Little Ring Road, Uzbekistan; email: Aleksandr_Trubnikov@abtassoc.com
Hovhannesyan, A.; World Health Organization Regional Office for Europe, Marmorvej 51, Denmark; email: hovhannesyana@who.int		MDPI AG1661782733924701EnglishInt. J. Environ. Res. Public HealthArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85104006113
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Saud V., Thomopoulos N.57196425381;55399574600;Towards inclusive transport landscapes: Re-visualising a Bicycle Sharing Scheme in Santiago Metropolitan Region2021Journal of Transport Geography92103004210.1016/j.jtrangeo.2021.103004https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103100061&doi=10.1016%2fj.jtrangeo.2021.103004&partnerID=40&md5=8e4d6a219637cadf6f1df701c694fd02The Bartlett Development Planning Unit, University College London, United Kingdom; Department of Tourism and Transport, School of Hospitality and Tourism Management, University of Surrey, United KingdomSaud, V., The Bartlett Development Planning Unit, University College London, United Kingdom; Thomopoulos, N., Department of Tourism and Transport, School of Hospitality and Tourism Management, University of Surrey, United KingdomBicycle Sharing Schemes (BSS) are re-emerging as promising components of urban mobility solutions worldwide. However, the lack of consistent collaboration strategies between different actors and institutions, which have been tested in a wide range of cities and contexts regarding their design, tender, operation and expansion, raises significant social and governance implications. Urban transport features as a melting pot for diverse policy objectives, ranging from business model innovation, public tendering, and accessibility increase to the equity and social justice agenda. By employing a Multi-Level Perspective (MLP) framework and by introducing alluvial diagrams and circular dendrograms to BSS planning through a mixed-methods approach, this article illustrates an innovative tool in managing BSS in the context of the Global South. The strength of such diagrams has been underestimated to date since they can be particularly useful for public and private urban transport planners and policy-makers. Visualising user flows in such a manner, particularly in near-live time, may offer valuable insight on the operational challenges of BSS. Findings of the cross-sectional survey in Santiago de Chile confirm that maintenance is significant for user satisfaction levels. Furthermore, decisions regarding BSS expansion and modification could be based on such analysis and diagrams due to the precise identification of both the busiest and those under-represented BSS stations based on revealed preferences. © 2021 Elsevier LtdBicycle Sharing System; Data Visualisation; Global South; Public Tendering; Urban Transport Equalitycycle transport; landscape; urban transport; visualization; Chile; Metropolitana; Santiago [Metropolitana]CA16222-43582; University College London, UCL; Comisión Nacional de Investigación Científica y Tecnológica, CONICYT: 72160366; University of SurreyThe authors would like to thank Prof. Jenny Mindell, Prof. Julio Davila and Prof. Waleska Caiaffa for the invitation to participate in the Newton Fund & CONFAP “Indicators for a Healthy City: A Brazil-UK knowledge-sharing” international workshop, CONICYT / Becas Chile scholarship (72160366) awarded to the first author as well as the WISE-ACT COST Action (CA16222-43582) for supporting a Short-Term Scientific Mission hosted by Dr. Karel Martens at the Chair of Urban and Regional Planning of Technion University. Additionally, the authors are grateful to three anonymous referees of this article and to Dr. Matthew Hardy who contributed in its significant improvement, along with all suggestions by the panellists and participants on an earlier draft of this article presented at the 2019 “Micro-mobility in Transition: Challenges for Urban Transport Governance” workshop co-organised by University College London and the University of Surrey.The authors would like to thank Prof. Jenny Mindell, Prof. Julio Davila and Prof. Waleska Caiaffa for the invitation to participate in the Newton Fund & CONFAP ?Indicators for a Healthy City: A Brazil-UK knowledge-sharing? international workshop, CONICYT / Becas Chile scholarship (72160366) awarded to the first author as well as the WISE-ACT COST Action (CA16222-43582) for supporting a Short-Term Scientific Mission hosted by Dr. Karel Martens at the Chair of Urban and Regional Planning of Technion University. Additionally, the authors are grateful to three anonymous referees of this article and to Dr. Matthew Hardy who contributed in its significant improvement, along with all suggestions by the panellists and participants on an earlier draft of this article presented at the 2019 ?Micro-mobility in Transition: Challenges for Urban Transport Governance? workshop co-organised by University College London and the University of Surrey.Saud, V.; The Bartlett Development Planning Unit, United Kingdom; email: veronica.saud.15@ucl.ac.ukElsevier Ltd9666923EnglishJ. Transp. Geogr.ArticleFinalScopus2-s2.0-85103100061
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Obermeier M.M., Wicaksono W.A., Taffner J., Bergna A., Poehlein A., Cernava T., Lindstaedt S., Lovric M., Müller Bogotá C.A., Berg G.57189842028;57191587082;57195378474;56308393300;49962165300;56289016300;14022897900;57207734125;56719019700;7201431307;Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance2021ISME Journal153921937410.1038/s41396-020-00822-9https://www.scopus.com/inward/record.uri?eid=2-s2.0-85095826156&doi=10.1038%2fs41396-020-00822-9&partnerID=40&md5=3c55701acc302157e220d04b22063b8aInstitute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz, 8010, Austria; ACIB GmbH, Krenngasse 37/II, Graz, 8010, Austria; Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstrasse 8, Göttingen, 37077, Germany; Know-Center GmbH, Research Center for Data-Driven Business & Big Data Analytics, Infeldgasse 13/VI, Graz, 8010, AustriaObermeier, M.M., Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz, 8010, Austria, ACIB GmbH, Krenngasse 37/II, Graz, 8010, Austria; Wicaksono, W.A., Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz, 8010, Austria; Taffner, J., Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz, 8010, Austria; Bergna, A., Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz, 8010, Austria, ACIB GmbH, Krenngasse 37/II, Graz, 8010, Austria; Poehlein, A., Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstrasse 8, Göttingen, 37077, Germany; Cernava, T., Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz, 8010, Austria; Lindstaedt, S., Know-Center GmbH, Research Center for Data-Driven Business & Big Data Analytics, Infeldgasse 13/VI, Graz, 8010, Austria; Lovric, M., Know-Center GmbH, Research Center for Data-Driven Business & Big Data Analytics, Infeldgasse 13/VI, Graz, 8010, Austria; Müller Bogotá, C.A., Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz, 8010, Austria, ACIB GmbH, Krenngasse 37/II, Graz, 8010, Austria; Berg, G., Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz, 8010, Austria, ACIB GmbH, Krenngasse 37/II, Graz, 8010, AustriaThe expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiome associated with Sphagnum moss forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of culture collections, metagenomic data and a fosmid library from different geographic sites in Europe, we identified a low abundant but highly diverse pool of resistance determinants, which targets an unexpectedly broad range of 29 antibiotics including natural and synthetic compounds. This derives both, from the extraordinarily high abundance of efflux pumps (up to 96%), and the unexpectedly versatile set of ARGs underlying all major resistance mechanisms. Multi-resistance was frequently observed among bacterial isolates, e.g. in Serratia, Rouxiella, Pandoraea, Paraburkholderia and Pseudomonas. In a search for novel ARGs, we identified the new class A β-lactamase Mm3. The native Sphagnum resistome comprising a highly diversified and partially novel set of ARGs contributes to the bog ecosystem´s plasticity. Our results reinforce the ecological link between natural and clinically relevant resistomes and thereby shed light onto this link from the aspect of pristine plants. Moreover, they underline that diverse resistomes are an intrinsic characteristic of plant-associated microbial communities, they naturally harbour many resistances including genes with potential clinical relevance. © 2020, The Author(s).bacterium; gene; grass; microbial community; moss; protein; Bacteria (microorganisms); Pandoraea; Pseudomonas; Serratia; Sphagnum; antiinfective agent; antibiotic resistance; bacterial gene; Europe; metagenome; wetland; Anti-Bacterial Agents; Drug Resistance, Microbial; Europe; Genes, Bacterial; Metagenome; WetlandsAnti-Bacterial AgentsBundesministerium für Wissenschaft, Forschung und Wirtschaft, BMWFW; Bundesministerium für Verkehr, Innovation und Technologie, BMVIT; Standortagentur TirolAcknowledgements We thank Christian Berg for sampling design, Stephanie Hollauf, Franz Stocker and Angelika Schäfer for helping with the preparation of moss samples for downstream processing, Harald Blasl and Bettina Semler for their help with the screenings and Silvia Ferrario for helping with subcloning and protein expression. Special thanks go to Isabella Wrolli for her indispensable technical help in the lab, to Henry Müller for his technical guidance, as well as to Christian Partl and Kristina Pavlovic (all Graz) for the support with data visualisation. We thank the reviewers for relevant remarks and suggestions that increased the value of the study. This work was supported by the Federal Ministry of Science, Research and Economy (BMWFW), the Federal Ministry of Traffic, Innovation and Technology (bmvit), the Styrian Business Promotion Agency SFG, the Standortagentur Tirol, the Government of Lower Austria and ZIT - Technology Agency of the City of Vienna through the COMET-Funding Program managed by the Austrian Research Promotion Agency FFG. Supported by TU Graz Open Access Publishing Fund.Müller Bogotá, C.A.; Institute of Environmental Biotechnology, Petersgasse 12/I, Austria; email: christina.mueller@tugraz.atSpringer Nature1751736233177608EnglishISME J.ArticleFinalAll Open Access, Hybrid GoldScopus2-s2.0-85095826156
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Vinci-Booher S., James T.W., James K.H.35249382800;57212072372;7202538701;Visual-motor contingency during symbol production contributes to short-term changes in the functional connectivity during symbol perception and long-term gains in symbol recognition2021NeuroImage227117554210.1016/j.neuroimage.2020.117554https://www.scopus.com/inward/record.uri?eid=2-s2.0-85098193822&doi=10.1016%2fj.neuroimage.2020.117554&partnerID=40&md5=0ce7b5fd71c669ac74ad4d6dfa90af30Department of Psychological and Brain Sciences at Indiana University in BloomingtonIN, United StatesVinci-Booher, S., Department of Psychological and Brain Sciences at Indiana University in BloomingtonIN, United States; James, T.W., Department of Psychological and Brain Sciences at Indiana University in BloomingtonIN, United States; James, K.H., Department of Psychological and Brain Sciences at Indiana University in BloomingtonIN, United StatesLetter production relies on a tight coupling between motor movements and visual feedback—each stroke of the letter is visually experienced as it is produced. Experience with letter production leads to increases in functional connectivity, a measure of neural communication, among visual and motor brain systems and leads to gains in letter recognition in preliterate children. We hypothesized that the contingency between the motor and visual experiences of the written form during production would result in both effects. Twenty literate adults were trained on four sets of novel symbols over the course of one week. Each symbol set was trained through one of four training conditions: drawing with ink, drawing without ink, watching a handwritten symbol unfold as if being drawn, and watching a static handwritten symbol. Contingency of motor and visual experiences occurred in the drawing with ink condition. The motor and visual experiences were rendered non-contingent in each of the other three conditions by controlling for visual or motor experience. Participants were presented with the trained symbols during fMRI scanning at three time points: one pre-training, one post-training, and one after a week-long no-training delay. Recognition was tested after each training session and after the third scan. We found that the contingency between visual and motor experiences during production changed the pattern of functional connectivity among visual, motor, and auditory neural communities and resulted in better recognition performance at post-training than at pre-training. Recognition gains were maintained after the no-training delay, but the functional connections observed immediately after training returned to their pre-training baselines. Our results suggest that behaviors that couple sensory and motor systems result in temporary changes in neural communication during perception that may not directly support changes in recognition. © 2021fMRI; Functional connectivity; Handwriting; Learning; Letters; Perception; Recognitionadult; article; drawing; female; functional connectivity; functional magnetic resonance imaging; handwriting; human; human experiment; learning; male; molecular recognition; motor system; perception; sensory system; brain; diagnostic imaging; functional neuroimaging; nerve cell network; nuclear magnetic resonance imaging; pattern recognition; photostimulation; physiology; psychomotor performance; young adult; Adult; Brain; Female; Functional Neuroimaging; Humans; Magnetic Resonance Imaging; Male; Nerve Net; Pattern Recognition, Visual; Photic Stimulation; Psychomotor Performance; Recognition, Psychology; Young AdultHD 07475This research was funded by the Indiana University Office of the Vice Provost for Research Emerging Areas of Research Initiative, Learning: Brains, Machines, and Children and by the National Institute of Health , T32 Grant # HD 07475 . The authors would like to thank Anastasia Nikoulina and Richard Betzel for their help in implementing the community detection algorithms. The authors would also like to thank Courtney DelaCuesta, Sarah Harris, and Hannah Marotta for their help with data collection.Vinci-Booher, S.; Department of Psychological and Brain Sciences at Indiana University in BloomingtonUnited States; email: svincibo@iu.eduAcademic Press Inc.10538119NEIME33359354EnglishNeuroImageArticleFinalAll Open Access, GoldScopus2-s2.0-85098193822
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Belichenko O., Kolosova V., Melnikov D., Kalle R., Sõukand R.57197704690;55582081200;57193073504;35799950700;6506885585;Language of administration as a border: Wild food plants used by setos and russians in pechorsky district of pskov oblast, NW Russia2021Foods102367110.3390/foods10020367https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103024042&doi=10.3390%2ffoods10020367&partnerID=40&md5=f93cb75e7433ef1fe41a6e8e9d972ee7Department of Environmental Sciences, Informatics and Statistics, Ca’Foscari University of Venice, Via Torino 155, Mestre, Venice, 30172, Italy; Institute for Linguistic Studies, Russian Academy of Sciences, Tuchkov Pereulok 9, St Petersburg, 199004, Russian Federation; Komarov Botanical Institute, Russian Academy of Sciences, Professor Popov St. 2, St Petersburg, 197376, Russian Federation; University of Gastronomic Sciences, Piazza Vittorio Emanuele 9, Pollenzo, Bra (Cn), 12042, ItalyBelichenko, O., Department of Environmental Sciences, Informatics and Statistics, Ca’Foscari University of Venice, Via Torino 155, Mestre, Venice, 30172, Italy; Kolosova, V., Department of Environmental Sciences, Informatics and Statistics, Ca’Foscari University of Venice, Via Torino 155, Mestre, Venice, 30172, Italy, Institute for Linguistic Studies, Russian Academy of Sciences, Tuchkov Pereulok 9, St Petersburg, 199004, Russian Federation; Melnikov, D., Komarov Botanical Institute, Russian Academy of Sciences, Professor Popov St. 2, St Petersburg, 197376, Russian Federation; Kalle, R., University of Gastronomic Sciences, Piazza Vittorio Emanuele 9, Pollenzo, Bra (Cn), 12042, Italy; Sõukand, R., Department of Environmental Sciences, Informatics and Statistics, Ca’Foscari University of Venice, Via Torino 155, Mestre, Venice, 30172, ItalySocio-economic changes impact local ethnobotanical knowledge as much as the ecological ones. During an ethnobotanical field study in 2018–2019, we interviewed 25 Setos and 38 Russians in the Pechorsky District of Pskov Oblast to document changes in wild plant use within the last 70 years according to the current and remembered practices. Of the 71 botanical taxa reported, the most popular were Vaccinium vitis-idaea, Vaccinium oxycoccos, Vaccinium myrtillus, Betula spp., and Rumex acetosa. The obtained data was compared with that of 37 Setos and 35 Estonians interviewed at the same time on the other side of the border. Our data revealed a substantial level of homogeneity within the plants used by three or more people with 30 of 56 plants overlapping across all four groups. However, Seto groups are ethnobotanically closer to the dominant ethnic groups immediately surrounding them than they are to Setos across the border. Further study of minor ethnic groups in a post-Soviet context is needed, paying attention to knowledge transmission patterns. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Ethnic minority; Local ecological knowledge; Post-Soviet ethnobotany; Seto; Wild food plantsHorizon 2020 Framework Programme, H2020: 714874; European Research Council, ERCFunding: This research was financed by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (DiGe, grant agreement No 714874).Belichenko, O.; Department of Environmental Sciences, Via Torino 155, Italy; email: olga.belichenko@unive.itMDPI AG23048158EnglishFoodsArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85103024042
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Zong J., Barnwal D., Neogy R., Satyanarayan A.57221141785;57219620410;57221147705;55193351500;Lyra 2: Designing interactive visualizations by demonstration2021IEEE Transactions on Visualization and Computer Graphics2729222289304314110.1109/TVCG.2020.3030367https://www.scopus.com/inward/record.uri?eid=2-s2.0-85100385281&doi=10.1109%2fTVCG.2020.3030367&partnerID=40&md5=5421c67bbcb8408b7db13934d552d56cMassachusetts Institute of Technology, United States; Indian Institute of Technology Kharagpur, IndiaZong, J., Massachusetts Institute of Technology, United States; Barnwal, D., Indian Institute of Technology Kharagpur, India; Neogy, R., Massachusetts Institute of Technology, United States; Satyanarayan, A., Massachusetts Institute of Technology, United StatesRecent graphical interfaces offer direct manipulation mechanisms for authoring visualizations, but are largely restricted to static output. To author interactive visualizations, users must instead turn to textual specification, but such approaches impose a higher technical burden. To bridge this gap, we introduce Lyra 2, a system that extends a prior visualization design environment with novel methods for authoring interaction techniques by demonstration. Users perform an interaction (e.g., button clicks, drags, or key presses) directly on the visualization they are editing. The system interprets this performance using a set of heuristics and enumerates suggestions of possible interaction designs. These heuristics account for the properties of the interaction (e.g., target and event type) as well as the visualization (e.g., mark and scale types, and multiple views). Interaction design suggestions are displayed as thumbnails; users can preview and test these suggestions, iteratively refine them through additional demonstrations, and finally apply and customize them via property inspectors. We evaluate our approach through a gallery of diverse examples, and evaluate its usability through a first-use study and via an analysis of its cognitive dimensions. We find that, in Lyra 2, interaction design by demonstration enables users to rapidly express a wide range of interactive visualizations. © 1995-2012 IEEE.Direct manipulation; interaction design by demonstration; interactive visualizationDemonstrations; Iterative methods; Cognitive dimensions; Direct manipulation; Graphical interface; Interaction design; Interaction techniques; Interactive visualizations; Multiple views; Visualization designs; Visualization; article; heuristics; human; human experiment; inspectorNational Science Foundation, NSF: 1942659IEEE Computer Society10772626ITVGE33048697EnglishIEEE Trans Visual Comput GraphicsArticleFinalAll Open Access, GreenScopus2-s2.0-85100385281
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Namin S., Zhou Y., Neuner J., Beyer K.57212527028;57131631100;6701746026;35758557300;The role of residential history in cancer research: A scoping review2021Social Science and Medicine270113657310.1016/j.socscimed.2020.113657https://www.scopus.com/inward/record.uri?eid=2-s2.0-85098596638&doi=10.1016%2fj.socscimed.2020.113657&partnerID=40&md5=1c578fe700d01801c2ae17972c81fca2Institute for Health & Equity, Medical College of Wisconsin, Milwaukee, WI, United States; General Internal Medicine, Medical College of Wisconsin, Milwaukee, WI, United StatesNamin, S., Institute for Health & Equity, Medical College of Wisconsin, Milwaukee, WI, United States; Zhou, Y., Institute for Health & Equity, Medical College of Wisconsin, Milwaukee, WI, United States; Neuner, J., General Internal Medicine, Medical College of Wisconsin, Milwaukee, WI, United States; Beyer, K., Institute for Health & Equity, Medical College of Wisconsin, Milwaukee, WI, United StatesThe role of residential history in cancer prevention, diagnosis, treatment, and survivorship is garnering increasing attention in cancer research. To our knowledge, there is no comprehensive synthesis of the current state of knowledge in the field. We reviewed the extant literature on this topic and conducted a scoping analysis to examine two main research questions: (a) To what degree, and how, have researchers accounted for residential history/mobility in cancer research? and (b) What are the gaps in the literature based on a knowledge synthesis using scoping review and concept mapping? To answer these questions, this scoping analysis focuses on how researchers compile, analyze and discuss residential history/mobility in studies on cancer. The study is focused on peer-reviewed articles from 6 different datasets (PubMed, Cinahl, Scopus, Web of Science and JSTOR, ERIC) from 1990 to August 2020. The review captured 1951 results in total, which was scoped to 281 relevant peer-reviewed journal articles. First, we examined these articles based on cancer continuum, cancer type and the main theme. Second, we identified 21 main themes and an additional 16 sub-themes in the pool of the selected articles. We utilized concept mapping to provide a conceptual framework and to highlight the underlying socioecological assumptions and paradigms. Results show that cancer research incorporating residential histories is primarily focused on incidence and estimating cumulative exposure, with little consideration across the cancer continuum. Additionally, our review suggests that although the social environment plays an important role across the cancer continuum, a small number of articles were focused on such factors and this area remains relatively unexplored. Additionally, the expansion of interdisciplinary research on residential mobility before and after cancer diagnosis will enhance understanding of the role of environmental and socioeconomic characteristics and exposures on cancer continuum. © 2020 Elsevier LtdCancer; Cancer continuum; Environmental exposure; Residence characteristics; Residential history; Residential mobilitycancer; disease treatment; environmental effect; interdisciplinary approach; research; residential mobility; socioeconomic status; cancer diagnosis; cancer research; Cinahl; concept mapping; conceptual framework; demography; environmental exposure; human; incidence; interdisciplinary research; Medline; migration; review; Scopus; social environment; Web of Science; health care delivery; neoplasm; population dynamics; research; Scopus; Delivery of Health Care; Humans; Neoplasms; Population Dynamics; ResearchU.S. Department of Health and Human Services, HHS; Health Resources and Services Administration, HRSAThis work was partly supported by grant T32HP10030 from the Health Resources and Services Administration (HRSA), an operating division of the Department of Health and Human Services . These contents are solely the responsibility of the authors and do not necessarily represent the official views of the HRSA or the U.S. Department of Health and Human Services.Namin, S.; Institute for Health & Equity, 8701 Watertown Plank Rd., United States; email: snamin@mcw.eduElsevier Ltd2779536SSMDE33388619EnglishSoc. Sci. Med.ReviewFinalScopus2-s2.0-85098596638
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Kalle R., Sõukand R.35799950700;6506885585;The name to remember: Flexibility and contextuality of preliterate folk plant categorization from the 1830s, in Pernau, Livonia, historical region on the eastern coast of the Baltic Sea2021Journal of Ethnopharmacology264113254410.1016/j.jep.2020.113254https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090587950&doi=10.1016%2fj.jep.2020.113254&partnerID=40&md5=d26d2fdec96eaf9bb290eda53d601637University of Gastronomic Sciences, Piazza Vittorio Emanuele II 9, Pollenzo, Italy; Ca’ Foscari University of Venice, Via Torino 155, Mestre, Venice, ItalyKalle, R., University of Gastronomic Sciences, Piazza Vittorio Emanuele II 9, Pollenzo, Italy; Sõukand, R., Ca’ Foscari University of Venice, Via Torino 155, Mestre, Venice, ItalyEthnopharmacological relevance: Research on the folk categorization of nature in preliterate societies in Europe is complicated due to the fragmentation of the information available and is rarely undertaken. Yet the data is valuable and may provide, in certain circumstances, important insights, if not into novel medicines, then into the historical logic of selection and memorisation of plants useful from a medicinal perspective. Aims of the study: We aim to understand the ethnobotany of a preliterate society by analysing the emic (derived from people) perspective on nature-related culture of one of Europe's smaller nations, whose written language and culture was shaped in the 18th-19th centuries by other, larger nations of Europe, and thus from the etic (academic) perspective. We attempt to identify how folk categorization is reflected in the relationships between plant names and uses and to map the structure of those relationships. Data and methods: We base our analysis on one of the oldest ethnobotanical manuscripts and herbaria of the Baltic governorates, compiled in 1831 by an amateur botanist, Baltic German Pastor Johann Heinrich Rosenplänter (1782–1846), which was derived from conversations with his parishioners from the tiny Pärnu parish. The historical dataset was critically analysed from an ethnobotanical perspective in light of recent identifications of the herbarium specimens. Results: Although the Rosenplänter collection is fragmentary, the logic of plant categorization by non-literate peasants at that time is clearly seen in the data. Plants preserved in the herbarium were predominantly used for ethno-medicinal, food or ethno-veterinary purposes, such as treating chronic skin and joint diseases as well as severe acute diseases in humans and animals. Among 129 folk taxa analysed, more than one third had apparent purpose-related plant names providing clear links to their use, whereas a few multifunctional plants had several names reflecting diverse uses. For example, Hypericum spp., which was used in three different ways, had three semantically distinct names. However, among the plants that Rosenplänter collected, there were also some that were simply named and described by people but lacked any usability data (e.g., Trollius europaeus), meaning that use as such was not the primary criterion for recognising a plant. The web-like structure of preliterate thinking in plant-related knowledge reveals a deep relationship with the environment and the interpretation of new elements through familiar natural objects. Conclusion: Our findings demonstrate that historical ethnobotanical data, if thoughtfully analysed, can be used not only for comparative purposes, but also for understanding the logic of preliterate thinking. We encourage future in-depth studies of historical ethnobotanical data in Europe in order to understand the relationship between nature and culture of native European populations. © 2020 The Author(s)19th century; Ethnopharmacology; Ethnoveterinary; Europe; Historical ethnobotany; Nature and cultureArticle; Asteraceae; Baltic Sea; Brassicaceae; Caryophyllaceae; Ericaceae; ethnobotany; Fabaceae; human; Hypericum; Lamiaceae; nonhuman; Orobanchaceae; plant; Poaceae; Rosaceae; seashore; traditional medicine; Baltic States; ethnobotany; ethnology; ethnopharmacology; history; medicinal plant; publication; Baltic States; Ethnobotany; Ethnopharmacology; History, 18th Century; History, 19th Century; Humans; Manuscripts, Medical as Topic; Medicine, Traditional; Plants, MedicinalHorizon 2020 Framework Programme, H2020: 714874; European Research Council, ERC; Horizon 2020Research was partially supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Starting Grant project “Ethnobotany of divided generations in the context of centralization”, grant agreement No. 714874 ).Research was partially supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Starting Grant project ?Ethnobotany of divided generations in the context of centralization?, grant agreement No. 714874).Sõukand, R.; Ca’ Foscari University of Venice, Via Torino 155, Mestre, Italy; email: renata.soukand@unive.itElsevier Ireland Ltd3788741JOETD32798616EnglishJ. Ethnopharmacol.ArticleFinalAll Open Access, Hybrid GoldScopus2-s2.0-85090587950
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Yarasca-Aybar C.57209908627;The tambos of the peruvian rural territory: A systematic catalog proposal as design strategy2021Journal of Architecture and Urbanism451809410.3846/jau.2021.13944https://www.scopus.com/inward/record.uri?eid=2-s2.0-85106966637&doi=10.3846%2fjau.2021.13944&partnerID=40&md5=2cfd7f65c97a99c6951277d1a4cdaeacMaestría en Arquitectura y Procesos Proyectuales, Pontificia Universidad Católica del Perú, Lima, Peru; Escuela Profesional de Arquitectura, Universidad Peruana Unión, Lima, PeruYarasca-Aybar, C., Maestría en Arquitectura y Procesos Proyectuales, Pontificia Universidad Católica del Perú, Lima, Peru, Escuela Profesional de Arquitectura, Universidad Peruana Unión, Lima, PeruThe tambos are small buildings that function as social platforms in Peruvian rural areas to provide essential services to the entire vulnerable and dispersed rural population. The Peruvian government intends to implement more than a thousand new tambos in the national territory. However, this social infrastructure program faces heterogeneous conditions and demands according to Peru’s geographical and population complexity. This article proposes developing a systematic catalog of modular components as a design strategy for the architectural approach of future tambos. Georeferenced data and climate design guidelines were used to conduct this study. As a result, the systematic catalog synthesizes critical variables such as natural regions and programmatic requirements to generate diverse architectural configurations of the new tambos. Therefore, these future buildings would be optimally articulated in different areas of influence under a systematic vision of the Peruvian rural territory. © 2021 The Author(s). Published by Vilnius Gediminas Technical University.Architectural design; Design strategy; Problem solving; Rural; Sustainabilityarchitectural design; building; record; rural area; strategic approach; sustainability; PeruYarasca-Aybar, C.; Maestría en Arquitectura y Procesos Proyectuales, Peru; email: cristianyarasca@upeu.edu.peVGTU20297955EnglishJ. Archit. Urban.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85106966637
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Singh R.K., Bhardwaj R., Sureja A.K., Kumar A., Singh A., Hazarika B.N., Hussain S.M., Singh A., Lego Y.J., Rallen O.57203380587;57189644333;11939479500;57204150576;57217562323;55901798900;57191439653;55726472600;57194693496;55314386700;Livelihood resilience in the face of multiple stressors: biocultural resource-based adaptive strategies among the vulnerable communities2021Sustainability Science10.1007/s11625-021-01057-zhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85118305671&doi=10.1007%2fs11625-021-01057-z&partnerID=40&md5=6df22c6c247483dbd1dbfa5c9e3d5515College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh 791102, India; ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India; ICAR-National Bureau of Plant Genetic Resources, New Delhi, India; ICAR-Indian Agricultural Research Institute, New Delhi, India; ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, Lucknow, Uttar Pradesh 226101, India; ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India; GTC Colony, East Siang, Pasighat, Arunachal Pradesh 791102, India; Village Sibut, East Siang, Pasighat, Arunachal Pradesh 791102, IndiaSingh, R.K., College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh 791102, India, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India; Bhardwaj, R., College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh 791102, India, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India; Sureja, A.K., College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh 791102, India, ICAR-Indian Agricultural Research Institute, New Delhi, India; Kumar, A., ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India; Singh, A., ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, Lucknow, Uttar Pradesh 226101, India; Hazarika, B.N., College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh 791102, India; Hussain, S.M., College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh 791102, India; Singh, A., College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh 791102, India, ICAR-National Dairy Research Institute, Karnal, Haryana 132001, India; Lego, Y.J., GTC Colony, East Siang, Pasighat, Arunachal Pradesh 791102, India; Rallen, O., Village Sibut, East Siang, Pasighat, Arunachal Pradesh 791102, IndiaMarginalized communities across the world are increasingly faced with a suit of social-ecological stressors, taking a huge toll on their biocultural resources and livelihoods. Collaborative learning is considered to be a feasible strategy for livelihood resilience among vulnerable communities experiencing such stressors. Taking insights from social-ecological resilience theory, this study discusses how Adi community, living in the ecologically fragile ecosystems of Arunachal Pradesh, India, has developed a location-specific biocultural resource-based adaptive strategy to enhance their livelihood resilience. A novel participatory approach—‘recipe contest’—was used to mobilize Adi women from 11 villages of the state’s East Siang district with overall aim of developing nutritious and culturally relevant food products based entirely on local resources and knowledge. A total of 43 women (winners of the recipe contests) and 33 other knowledgeable community members (total 76 participants), by participating in focus group discussions and personal interviews, shared their knowledge and experiences relating to local foods and sustainability. We found that a range of climatic, ecological, socioeconomic and political stressors were adversely impacting Adi women’s subsistence livelihoods. Through community mobilization, these women formed Self-Help Groups (SHGs) and together they developed a marketable product, ‘Adi Siang Nutri’, with ingredients provided by 12 local species. This value-added product, integrated with local livelihood trajectories, helped diversify and increase the Adi women’s income, allowing them to better safeguard themselves from aforementioned risks. The local species used as the ingredients are being conserved, and have several perceived socio-cultural, ecological and ethnomedicinal benefits. This participatory action research promises to make a significant change in the social-ecological resilience and associated biocultural resources of Adi women. Our findings provide valuable insights for several food, nutritional security and environmental policies to improve social-ecological resilience using biocultural resources. © 2021, The Author(s), under exclusive licence to Springer Japan KK, part of Springer Nature.Adi tribe; Arunachal Pradesh; Biocultural diversity; Collaborative learning; India; Livelihoods; Multiple stressors; Social-ecological resilienceASFRM-14; Kerala Agricultural University, KAU: CAU/DR/BCS/06/01-08-2007, CHF/CAU/CRAC/2021/205The authors are grateful to the Adi women who provided their knowledge and local support for this study. The funding support obtained from College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh through projects on traditional foods and women?s knowledge system (CAU/DR/BCS/06/01-08-2007) and indigenous natural resources management by tribal communities of Arunachal Pradesh (CHF/CAU/CRAC/2021/205) through National-Innovation Foundation-India, Ahmedabad are gratefully acknowledged. The authors also acknowledge Dr. RC Srivastava, Botanical Survey of India, Itanagar, Arunachal Pradesh for his taxonomic identification of plant species. Dr. Prapasri Puwastien and Dr. Kunchi Judprasong from Institute of Nutrition, Mahidol University, Thailand also are acknowledged for providing ASFRM-6 (fish meal) and ASFRM-14 (Rice flour) food reference materials.Singh, R.K.; College of Horticulture and Forestry, India; email: ranjaysingh_jbp@rediffmail.comSpringer Japan18624065EnglishSustainability Sci.ArticleArticle in PressScopus2-s2.0-85118305671
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Conroy M.57287752900;Networks, maps, and time: Visualizing historical networks using palladio2021Digital Humanities Quarterly1531 Decemberhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85116524883&partnerID=40&md5=ee79c49dc9b7baacd9cbd07f029e6af9The University of Memphis, United StatesConroy, M., The University of Memphis, United StatesMany tools can produce maps, graphs, and charts that may differ in seemingly minor ways. Data visualization tools are one type of “middleware” that can be all but forgotten when one is presented with final products such as papers and presentations containing visualizations [Drucker and Svensson 2016]. Since the output of various software packages is sometimes similar, it is easy to forget the assumptions that went into the diagram, the dataset, and the software when looking at the final product — or even while using the tool if one becomes sufficiently accustomed to the interface. In this review, I revisit the visualization suite Palladio – which Miriam Posner has called a “Swiss Army knife for humanities data” [Posner 2014] – and the many projects that have made use of Palladio’s core features in the years since its launch. I examine the strengths and limitations of Palladio, as a network and map-making tool for exploring data and for rapidly prototyping diagrams, designed with an iterative process in mind. I contrast this iterative mentality with the analytic sensibility of tools like Gephi and Cytoscape, and review the primary features of Palladio with one primary case study (my own visualizations of the French Enlightenment network) and examples of how the features have been used in other digital humanities projects. Palladio is very useful for qualitative studies of data that include geospatial and chronological dimensions, especially when the data are tagged with different types of qualitative metadata, but it also tends to impose a historical geographical view on the data by foregrounding geospatial relationships, time, and other historical considerations. © 2021, Alliance of Digital Humanities Organisations. All rights reserved.Conroy, M.; The University of MemphisUnited States; email: mrconroy@memphis.eduAlliance of Digital Humanities Organisations19384122EnglishDigit. Humanit. Q.ArticleFinalScopus2-s2.0-85116524883
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Li Q., Lin H., Tang C., Wei X., Peng Z., Ma X., Chen T.57211753995;57219115547;57218165673;57211743975;57202799508;56242668800;57205699805;Exploring the âDouble-Edged Swordâ? Effect of Auto-Insight Recommendation in Exploratory Data Analysis2021CEUR Workshop Proceedings2903https://www.scopus.com/inward/record.uri?eid=2-s2.0-85110540862&partnerID=40&md5=ffa87b684be5ffaf343e2d166733322aSchool of Information Science and Technology, ShanghaiTech University; Ai Group; Ai Department, Shenzhen Semacare Medical Technology Co.; Department of Computer Science and Engineering, Hong Kong University of Science and TechnologyLi, Q., School of Information Science and Technology, ShanghaiTech University; Lin, H., Ai Group; Tang, C., Ai Group; Wei, X., Ai Department, Shenzhen Semacare Medical Technology Co.; Peng, Z., Department of Computer Science and Engineering, Hong Kong University of Science and Technology; Ma, X., Department of Computer Science and Engineering, Hong Kong University of Science and Technology; Chen, T., Department of Computer Science and Engineering, Hong Kong University of Science and TechnologyModern data analytics tools often provide visualizations as an accessible data window to users in exploratory data analysis (EDA). Still, many analysts feel lost in this process due to issues such as the high complexity of data. Auto-insight recommendations offer a promising alternative by suggesting possible interpretations of the data to users during EDA but might impose undesirable effects on users. In this study, we systematically explore the "double-edged sword"effect of auto-insight recommendations on EDA in terms of exploration assistance, message reliability, and interference. Particularly, we design and develop two versions of a Tableau-like visualization system termed TurboVis: One supports auto-insight recommendations while the other does not. We first demonstrate how typical visualization specification tools can be augmented by incorporating auto-insight recommendations and then conduct a within-subjects user study with 18 participants during which they experience both versions in EDA tasks. We find that although auto-insight recommendations encourage more visualization inspections, they also introduce biases to data exploration. The perceived level of message reliability and interference of auto-insight recommendations depend on data familiarity and task structures. Our work elicits design implications for embedding auto-insight recommendations into the EDA process. © 2021 Copyright for this paper by its authors.Auto-insight; Exploratory data analysis; Visualization recommendationsData Analytics; Data handling; Information analysis; User interfaces; Visualization; Analytics tools; Data exploration; Design implications; Exploratory data analysis; High complexity; Specification tools; Undesirable effects; Visualization system; Data visualizationGlowacka D.Krishnamurthy V.CEUR-WS2021 Joint ACM Conference on Intelligent User Interfaces Workshops, ACMIUI-WS 202113 April 2021 through 17 April 202117000516130073EnglishCEUR Workshop Proc.Conference PaperFinalScopus2-s2.0-85110540862
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Miranda B.P., Queiroz V.F., Araújo T.D.O., Santos C.G.R., Meiguins B.S.57125740300;57224936837;57125731200;35180344300;57126167600;A low-cost multi-user augmented reality application for data visualization2021Multimedia Tools and Applications10.1007/s11042-021-11141-2https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108609475&doi=10.1007%2fs11042-021-11141-2&partnerID=40&md5=8d86611c7abcba617fe3503ab0f78e7bUniversidade Federal do Pará, Belém, Pará, BrazilMiranda, B.P., Universidade Federal do Pará, Belém, Pará, Brazil; Queiroz, V.F., Universidade Federal do Pará, Belém, Pará, Brazil; Araújo, T.D.O., Universidade Federal do Pará, Belém, Pará, Brazil; Santos, C.G.R., Universidade Federal do Pará, Belém, Pará, Brazil; Meiguins, B.S., Universidade Federal do Pará, Belém, Pará, BrazilAmong the existing platforms, the mobile platform provides most of the augmented reality experiences for users. Augmented reality solutions have been applied in several contexts due to technological advances in this area. However, many of these advances are still out of reach of more massive access by regular users due to access limitations or the cost of these new technologies. After conducting a literature review considering the application of data visualization in augmented reality environments, we have identified an evolution of equipment used in this context with a decrease of low-cost proposals. Hence, the works related to these two areas showed high use of technologies not yet accessible to the vast majority of users. Thus, we propose a low-cost augmented reality application that can be used on mobile devices for data visualization. We developed a hybrid proposal of an augmented reality prototype to interacting with cards through the mobile device to support the process of creating data visualization. The tangible cards have a design that helps the user in the visualization creation process, indicating each card’s role in the interaction process. The proposed application supports a multi-user environment, allowing multiple users to interact simultaneously with data visualizations in the AR environment. The visualizations are generated on a dedicated server for this function, providing a set of seven different types of visualization. To validate the developed prototype we performed two tests, the first being a stress assessment on the server that generates data visualizations to analyze the proposed application’s scalability. The second was a remote usability test with twelve participants, to evaluate the interaction and design of the cards, and the viability of this solution for augmented reality applications. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.Card-based interaction; Information visualization; Mobile augmented realityAugmented reality; Costs; Software prototyping; Technology transfer; User experience; Visualization; Augmented reality applications; Dedicated servers; Interaction process; Literature reviews; Multiuser environments; Remote usability; Stress assessment; Technological advances; Data visualizationMiranda, B.P.; Universidade Federal do ParáBrazil; email: brunelli@ufpa.brSpringer13807501MTAPFEnglishMultimedia Tools ApplArticleArticle in PressScopus2-s2.0-85108609475
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Pozzi C., Ladio A.H.55427683800;6603227336;The southern river otter (Lontra provocax): insights from the perspective of Andean Patagonian ethnozoology2021Ethnobiology and Conservation1011910.15451/ec2021-04-10.20-1-19https://www.scopus.com/inward/record.uri?eid=2-s2.0-85106652619&doi=10.15451%2fec2021-04-10.20-1-19&partnerID=40&md5=9eea03acf87b5df15126312f7cf08455Departamento de Conservación y Educación Ambiental, Parque Nacional Nahuel Huapi., Av. San Martin 24, Bariloche, Rio Negro 8400, Argentina; INIBIOMA, CONICET-Universidad Nacional del Comahue, Quintral 1250, San Carlos de Bariloche, Río Negro 8400, ArgentinaPozzi, C., Departamento de Conservación y Educación Ambiental, Parque Nacional Nahuel Huapi., Av. San Martin 24, Bariloche, Rio Negro 8400, Argentina, INIBIOMA, CONICET-Universidad Nacional del Comahue, Quintral 1250, San Carlos de Bariloche, Río Negro 8400, Argentina; Ladio, A.H., Departamento de Conservación y Educación Ambiental, Parque Nacional Nahuel Huapi., Av. San Martin 24, Bariloche, Rio Negro 8400, Argentina, INIBIOMA, CONICET-Universidad Nacional del Comahue, Quintral 1250, San Carlos de Bariloche, Río Negro 8400, ArgentinaAnimals play a significant role in many cultures around the world. The southern river otter Lontra provocax (known locally as the “huillín”) is endemic to southern Argentina and Chile, and is currently in danger of extinction. Mapuche communities have always lived closely alongside their animal resources, generating unique bonds with them. The objective of this work is to obtain an overview of the importance given to this species in the literature of the region with regard to the nature-culture connection. A systematic bibliographical review was carried out using reference libraries and web browsers. From all the sources analysed, 110 were selected which held biocultural information. The main approach used was ecological; however, the ethnohistorical texts provided the richest information on the bond between this otter and humans. The Mapuche name “huillín” appears in all the publications analysed, showing its continuity over time. Of all the zootoponyms found, 87.5% were Chilean and 12.5% were Argentine. The Argentine case is found in Nahuel Huapi lake, and is worthy of note as its name could involve the huillín. The results of this work increase our knowledge of the biocultural heritage of our region, and enable us to reflect on the associated historical and political processes. © 2021Ethnohistory; Fauna; Mapuche; Name; OriginConsejo Nacional de Investigaciones Científicas y Técnicas, CONICET: PIP 0723We would especially like to thank Lorenzo Loncon and Kalfu Rayen for their substantive contribution to the manuscript. Also Dr. Marisa Malvestitti and Dr. Pablo Arias. From the Patagonia Museum a special thanks to Dr. Eduardo Bessera, Mr. Eduardo Perez, Marta Romero and Eduardo Morgenstein. Thank to Erik M?ller for the final version of Figure3. The authors also acknowledge with gratitude the comments made by the anonymous reviewer on the earlier version of this paper. This investigation was supported by the Consejo Nacional de Investigaciones Cient?ficas y T?cnicas (CONICET) of Argentina (PIP 0723).We would especially like to thank Lorenzo Loncon and Kalfu Rayen for their substantive contribution to the manuscript. Also Dr. Marisa Malvestitti and Dr. Pablo Arias. From the Patagonia Museum a special thanks to Dr. Eduardo Bessera, Mr. Eduardo Perez, Marta Romero and Eduardo Morgenstein. Thank to Erik Müller for the final version of Figure 3. The authors also acknowledge with gratitude the comments made by the anonymous reviewer on the earlier version of this paper. This investigation was supported by the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) of Argentina (PIP 0723).Ladio, A.H.; Departamento de Conservación y Educación Ambiental, Av. San Martin 24, Argentina; email: ahladio@gmail.comUniversidade Federal Rural de Pernambuco22384782EnglishEthnobiol. Conserv.ArticleFinalAll Open Access, BronzeScopus2-s2.0-85106652619
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Ciomborowska‐basheer J., Staszak K., Kubiak M.R., Makałowska I.57200339016;57211939690;56656175500;6701670159;Not so dead genes—retrocopies as regulators of their disease‐related progenitors and hosts2021Cells10491210.3390/cells10040912https://www.scopus.com/inward/record.uri?eid=2-s2.0-85105222692&doi=10.3390%2fcells10040912&partnerID=40&md5=aa16747a622f8bb2a4f1883225500f73Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University Poznań, Poznań, 61‐614, PolandCiomborowska‐basheer, J., Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University Poznań, Poznań, 61‐614, Poland; Staszak, K., Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University Poznań, Poznań, 61‐614, Poland; Kubiak, M.R., Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University Poznań, Poznań, 61‐614, Poland; Makałowska, I., Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University Poznań, Poznań, 61‐614, PolandRetroposition is RNA‐based gene duplication leading to the creation of single exon nonfunctional copies. Nevertheless, over time, many of these duplicates acquire transcriptional capabilities. In human in most cases, these so‐called retrogenes do not code for proteins but function as regulatory long noncoding RNAs (lncRNAs). The mechanisms by which they can regulate other genes include microRNA sponging, modulation of alternative splicing, epigenetic regulation and competition for stabilizing factors, among others. Here, we summarize recent findings related to lncRNAs originating from retrocopies that are involved in human diseases such as cancer and neurodegenerative, mental or cardiovascular disorders. Special attention is given to retrocopies that regulate their progenitors or host genes. Presented evidence from the literature and our bio-informatics analyses demonstrates that these retrocopies, often described as unimportant pseudogenes, are significant players in the cell’s molecular machinery. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Disease; Host gene; LncRNA; Parental gene; Regulation; Retrocopies; Retropositionhigh mobility group B protein; long untranslated RNA; microRNA; microRNA 34a; Wnt protein; long untranslated RNA; acute myeloid leukemia; alternative RNA splicing; Alzheimer disease; amyotrophic lateral sclerosis; apoptosis; atrial fibrillation; autism; bile duct atresia; bioinformatics; bone metabolism; brain development; CAMK2N2 gene; cancer growth; cancer stem cell; cardiovascular disease; cell proliferation; degenerative disease; epigenetics; exon; gene; gene dosage; gene duplication; gene overexpression; genetic transcription; glioblastoma; glucose blood level; HMGA1 gene; HMGB1P10 gene; HMGB1P5 gene; host; human; Huntington chorea; insulin resistance; liver cirrhosis; liver transplantation; lung cancer; malignant neoplasm; maternal death; mental disease; nervous system inflammation; non insulin dependent diabetes mellitus; Parkinson disease; preeclampsia; prostate cancer; proteinuria; pseudogene; Review; schizophrenia; signal transduction; synaptic transmission; transcription termination; upregulation; animal; diseases; genetics; metabolism; open reading frame; retroposon; Animals; Disease; Humans; Neurodegenerative Diseases; Open Reading Frames; Retroelements; RNA, Long Noncodinghigh mobility group B protein, 431548-19-5; Retroelements; RNA, Long NoncodingMakałowska, I.; Institute of Human Biology and Evolution, Poland; email: izabel@amu.edu.plMDPI2073440933921034EnglishCellsReviewFinalAll Open Access, Gold, GreenScopus2-s2.0-85105222692
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Takahashi Y., Park K.J., Natori Y., Dublin D., Dasgupta R., Miwa K.57211800251;57222187638;57222180619;55353230100;55752585700;57222178583;Enhancing synergies in nature’s contributions to people in socio-ecological production landscapes and seascapes: lessons learnt from ten site-based projects in biodiversity hotspots2021Sustainability Science310.1007/s11625-021-00927-whttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85101808566&doi=10.1007%2fs11625-021-00927-w&partnerID=40&md5=d0156263735b2465eb89177f10dadf81Institute for Global Environmental Strategies, 2108-11, Kamiyamaguchi, Hayama, Kanagawa 240-0115, Japan; Tonkin & Taylor Limited, Victoria Street West, PO Box 5271, Auckland, 1142, New Zealand; Conservation International Japan, MEISTER YOTSUYA 201, 1-17 Yotsuya, Shinjuku, Tokyo 160-0004, Japan; Akita International University, Yuwa, Akita, Akita 010-1292, Japan; Hokkaido University of Education, 1-15-55 Shiroyama, Kushiro, Hokkaido 085-8580, JapanTakahashi, Y., Institute for Global Environmental Strategies, 2108-11, Kamiyamaguchi, Hayama, Kanagawa 240-0115, Japan; Park, K.J., Tonkin & Taylor Limited, Victoria Street West, PO Box 5271, Auckland, 1142, New Zealand; Natori, Y., Conservation International Japan, MEISTER YOTSUYA 201, 1-17 Yotsuya, Shinjuku, Tokyo 160-0004, Japan, Akita International University, Yuwa, Akita, Akita 010-1292, Japan; Dublin, D., Conservation International Japan, MEISTER YOTSUYA 201, 1-17 Yotsuya, Shinjuku, Tokyo 160-0004, Japan, Hokkaido University of Education, 1-15-55 Shiroyama, Kushiro, Hokkaido 085-8580, Japan; Dasgupta, R., Institute for Global Environmental Strategies, 2108-11, Kamiyamaguchi, Hayama, Kanagawa 240-0115, Japan; Miwa, K., Institute for Global Environmental Strategies, 2108-11, Kamiyamaguchi, Hayama, Kanagawa 240-0115, JapanTrade-offs in nature’s contributions to people (NCP), particularly in material NCP versus regulating and non-material NCP, continue to rise. Socio-ecological production landscapes and seascapes (SEPLS) represent harmonious human–nature interactions resulting in positive outcomes for both biodiversity and human well-being, thus implying synergies among multiple NCP are possible. In case studies of ten projects selected from biodiversity hotspots under the GEF-Satoyama Project, we investigated whether and how synergies in NCP exist within SEPLS and explored management interventions that enhanced these synergies. Using the responses to an online survey completed by project managers from each project and drawing on project reports, we identified a wide array of NCP deriving from various ecosystems within the project SEPLS. Habitat and food provisions, both attributed to multiple ecosystem types, were key components of the NCP bundles present in the project SEPLS. Among the management options that enhanced NCP in SEPLS were food-centred approaches entailing organic agriculture, eco-labelling, branding and improved agricultural practices. Habitat-centred approaches included participatory biodiversity monitoring, ecosystem restoration, co-management and conservation agreements with landowners. Synergies in NCP were generated by integrating these interventions with enabling governance structures and through community empowerment. If combined with mapping and modelling techniques, identifying NCP bundles in SEPLS from local people’s perspectives as we outlined in this study, would help to better contextualise the analysis of NCP bundles. Such contextualised NCP bundle analyses will help field practitioners understand how to enhance synergies between multiple NCP and the broader conservation community could access untapped NCP knowledge. © 2021, The Author(s).Ecosystem services; Equality; Impact evaluation; Landscape approach; Satoumi; SatoyamaMinistry of the Environment, Government of Japan, MOE: JPMEERF16S11504We thank the Global Environment Facility (GEF) for its support to the GEF-Satoyama project (Project ID: 5784). This research was also supported by the Environment Research and Technology Development Fund (S-15-1(4) Predicting and Assessing Natural Capital and Ecosystem Services (PANCES) of the Ministry of the Environment, Japan (JPMEERF16S11504). We thank the organizations which implemented the sub-grant projects (Table ) for their generous cooperation to this research.Takahashi, Y.; Institute for Global Environmental Strategies, 2108-11, Kamiyamaguchi, Japan; email: yasuo.takahashi@iges.or.jpSpringer Japan18624065EnglishSustainability Sci.ArticleArticle in PressAll Open Access, Hybrid GoldScopus2-s2.0-85101808566
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Halkos G., Nomikos S., Tsilika K.6701440263;57218377827;6506532108;Evidence for Novel Structures Relating CSR Reporting and Economic Welfare: Environmental Sustainability—A Continent-Level Analysis2021Computational Economics210.1007/s10614-020-10091-5https://www.scopus.com/inward/record.uri?eid=2-s2.0-85100208179&doi=10.1007%2fs10614-020-10091-5&partnerID=40&md5=b9b582cc6caefd63f9a285a46dda4ab9Laboratory of Operations Research, Department of Economics, University of Thessaly, Volos, Greece; Hellenic Open University, Patras, GreeceHalkos, G., Laboratory of Operations Research, Department of Economics, University of Thessaly, Volos, Greece; Nomikos, S., Laboratory of Operations Research, Department of Economics, University of Thessaly, Volos, Greece; Tsilika, K., Laboratory of Operations Research, Department of Economics, University of Thessaly, Volos, Greece, Hellenic Open University, Patras, GreeceThis paper aims to work towards a factual framework to substantiate the linkage between corporate social responsibility (CSR) reporting and economic activity and between CSR reporting and CO2 pollution, continent-wide. The document summarizes the conclusions of the dynamic analysis of CSR reports and the correlation analysis between CSR reports and economic—environmental variables, always using evidence from continent-level data. We draw on growth—environmental data and CSR reports from 1999 to 2017 to perform an analysis that quantifies the direction, the strength and the nature of the dependence structure between the two variables. Continents’ position according to their CSR reporting performance, CSR report trends over time, comparative schemes among continents, compose a global view on continents’ differentiation on CSR practices and strategies. Overall, the paper contributes to the understanding of how the CSR policies have been integrated and evolved worldwide. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC part of Springer Nature.Continent levels; Corporate social responsibility; Correlation measures; Exploratory data analysis; TrendsHalkos, G.; Laboratory of Operations Research, Greece; email: halkos@uth.grSpringer9277099EnglishComput. Econ.ArticleArticle in PressScopus2-s2.0-85100208179
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Ferreira V., Pié L., Terceño A.57220962976;23570054900;6506440940;The role of the foreign sector in the Spanish bioeconomy: Two approaches based on sam linear models2020International Journal of Environmental Research and Public Health17249381126110.3390/ijerph17249381https://www.scopus.com/inward/record.uri?eid=2-s2.0-85097924630&doi=10.3390%2fijerph17249381&partnerID=40&md5=77b822d38835eba47cd67996f780757eMarkets and Financial Analysis Research Group, Department of Business Management, Universitat Rovira i Virgili, Reus, 43204, SpainFerreira, V., Markets and Financial Analysis Research Group, Department of Business Management, Universitat Rovira i Virgili, Reus, 43204, Spain; Pié, L., Markets and Financial Analysis Research Group, Department of Business Management, Universitat Rovira i Virgili, Reus, 43204, Spain; Terceño, A., Markets and Financial Analysis Research Group, Department of Business Management, Universitat Rovira i Virgili, Reus, 43204, SpainThe bioeconomy emerges as an opportunity to focus on a more sustainable economy, avoid dependence on non-renewable resources and help to mitigate negative environmental impacts. The bioeconomy is considered a priority for the European Union and for Spain, which launched its strategy in 2016. To promote the Spanish bioeconomy, the impact and variables that may influence its development must be known. While previous works have analyzed the domestic sectors, this paper focuses on analyzing the economic importance of Spanish bioeconomy products and on the influence of and the existing links between the foreign sector and the rest of the economy. For this purpose, we apply two different methodologies based on linear social accounting matrix (SAM) models. The linkages show that many bioeconomy products have the potential to promote the rest of the economy and the values of some product multipliers become more significant due to their import dependence. These results enable us to know the structure of the Spanish bioeconomy and the relationships within its account. This analysis is a useful tool for developing policies focused on fostering the bioeconomy and economic growth. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.Bioeconomy; Foreign sector; Linear multipliers; Social accounting matrix; Spaineconomic development; economic growth; environmental economics; environmental impact; European Union; foreign policy; sustainable development; article; economic development; human; Spain; biotechnology; economic development; European Union; Spain; statistical model; Spain; Biotechnology; Economic Development; European Union; Linear Models; Spain713679; Horizon 2020 Framework Programme, H2020; Universitat Rovira i VirgiliThis research has received funding from the European Union?s Horizon 2020 research and innovation program under the Marie Sk?odowska-Curie grant agreement No. 713679 and from the Universitat Rovira i Virgili (URV).Funding: This research has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 713679 and from the Universitat Rovira i Virgili (URV).Pié, L.; Markets and Financial Analysis Research Group, Spain; email: laia.pie@urv.catMDPI AG1661782733333837EnglishInt. J. Environ. Res. Public HealthArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85097924630
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Langle-Flores A., Quijas S.57194653568;6503954796;A systematic review of ecosystem services of Islas Marietas National Park, Mexico, an insular marine protected area2020Ecosystem Services4610121410.1016/j.ecoser.2020.101214https://www.scopus.com/inward/record.uri?eid=2-s2.0-85094577334&doi=10.1016%2fj.ecoser.2020.101214&partnerID=40&md5=423e70c20379a829567cad73c6d45706Centro Universitario de la Costa, Universidad de Guadalajara, Puerto Vallarta, Jalisco 48280, MexicoLangle-Flores, A., Centro Universitario de la Costa, Universidad de Guadalajara, Puerto Vallarta, Jalisco 48280, Mexico; Quijas, S., Centro Universitario de la Costa, Universidad de Guadalajara, Puerto Vallarta, Jalisco 48280, MexicoIslands are good models to conceptualize how ecosystem services are part of interactions in social-ecological systems. However, efforts have been insufficient to synthesize and integrate the accumulated knowledge of islands’ ecosystem services. Holistic islands’ ecosystem services assessments are key to achieve an effective translation of research into decision making, in contexts such as loss of biodiversity and climate change. Using a systematic review of 58 studies published from 1964 to 2019, we identified associations between environments, habitats, ecosystem services, their components and beneficiaries in Islas Marietas National Park (IMNP), marine protected area and international tourist destination in western Mexico. Analysis of occurrence and data visualization were applied to synthesize the information. We identified 12 ecosystem services, the most quantified services being migratory and nursery habitat for species, followed by gene pool protection, recreation and tourism in marine ecosystems, especially in coral reefs. The most quantified component was “supply” for eight services. Main beneficiaries of knowledge of services were information brokers. We highlighted substantial knowledge gaps and identified constraints to advance knowledge of ecosystem services in IMNP. We proposed steps to incorporate the islands’ ecosystem services into decision making, and visualized pathways for future social-ecological synthesis research in marine protected areas. © 2020 Elsevier B.V.Demand; Economic value; Ecosystems service cascades; Social value; Social-ecological system; Supply241257, 511-6/18-9453; Universidad de Guadalajara, UDG: UDG-CA-940We thank Patricia Balvanera, Alma P. Rodríguez-Troncoso and Fabio G. Cupul-Magaña for their valuable and fruitful observations. The authors would like to thank Ginette Morrisseau and Brian O’Malley for English language edition. We also thank the editor and anonymous reviewer for their very useful comments helping us improve the paper. This work was supported by Programa para el Desarrollo Profesional Docente (PRODEP) [projects no. 511-6/18-9453 (AL) and 241257 (SQ), respectively]; and Universidad de Guadalajara’s academic group “Biodiversidad y Servicios Ecosistémicos” [UDG-CA-940].Quijas, S.; Centro Universitario de la Costa, Mexico; email: sandra.quijas@cuc.udg.mxElsevier B.V.22120416EnglishEcosyst. Serv.ReviewFinalScopus2-s2.0-85094577334
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Singh S., Geeta R., Das S.57214304639;6506015319;55597087353;Comparative sequence analysis across Brassicaceae, regulatory diversity in KCS5 and KCS6 homologs from Arabidopsis thaliana and Brassica juncea, and intronic fragment as a negative transcriptional regulator2020Gene Expression Patterns3811914610.1016/j.gep.2020.119146https://www.scopus.com/inward/record.uri?eid=2-s2.0-85091768289&doi=10.1016%2fj.gep.2020.119146&partnerID=40&md5=72e58ee4e985a92b4bf87d170aafb9cbDepartment of Botany, University of Delhi, Delhi, 110007, IndiaSingh, S., Department of Botany, University of Delhi, Delhi, 110007, India; Geeta, R., Department of Botany, University of Delhi, Delhi, 110007, India; Das, S., Department of Botany, University of Delhi, Delhi, 110007, IndiaIntra- and epicuticular-waxes primarily comprising of very long chain aliphatic lipid (VLCFA), terpenoids and secondary metabolites such as sterol and flavonoids played a major role in successful colonization of terrestrial ecosystem by aquatic plants and are thus considered as a key evolutionary innovation. The key rate limiting step of Fatty Acid (FA) biosynthesis of condensation/elongation are catalyzed by the enzyme, β-ketoacyl coenzyme A synthase (KCS), part of FAE (Fatty Acid Elongase) complex. KCS6 has been shown to be responsible for elongation using C22 fatty acid as substrate and is considered essential for synthesis of VLCFA for cuticular waxes. Earlier studies have established KCS5 as a close paralog of KCS6 in Arabidopsis thaliana, albeit with non-redundant function. We subsequently established segmental duplication responsible for origin of KCS6-KCS5 paralogy which is exclusive to Brassicaceae. In the present study, we aim to understand impact of duplication on regulatory diversification and evolution, through sequence and functional analysis of cis-regulatory element of KCS5 and KCS6. High level of sequence variation leading to conservation of only the proximal end of the promoter corresponding to the core promoter was observed among Brassicaceae members; such high diversity was also revealed when sliding window analysis revealed only two to three phylogenetic footprints. Profiling of transcription factor binding sites (TFBS) across Brassicaceae shows presence of light, hormone and stress responsive motifs; a few motifs involved in tissue specific expression (Skn-1; endosperm) were also detected. Functional characterization using transcriptional fusion constructs revealed regulatory diversification when promoter activity of homologs from A. thaliana and Brassica juncea were compared. When subjected to 5-Azacytidine, altered promoter activity was observed, implying role of DNA methylation in transcriptional regulation. Finally, investigation of the role of an 87 bp fragment from first intron that is retained in a splice variant, revealed it to be a transcriptional repressor. This is a first report on comparative sequence and functional analysis of transcriptional regulation of KCS5 and KCS6; further studies are required before manipulation of cuticular waxes as a strategy for mitigating stress. © 2020 Elsevier B.V.Arabidopsis; Brassica; Cuticle; KCS5; KCS6; Regulatory diversityazacitidine; transcription factor; 3 oxoacyl acyl carrier protein synthase; plant protein; Arabidopsis thaliana; Article; binding site; Brassica juncea; Brassicaceae; comparative study; DNA methylation; endosperm; gene duplication; gene sequence; intron; nonhuman; priority journal; promoter region; sequence analysis; transcription regulation; aerial plant part; Brassica; classification; gene expression regulation; genetic polymorphism; genetics; metabolism; molecular evolution; phylogeny; sequence homology; 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase; Brassica; Evolution, Molecular; Gene Expression Regulation, Plant; Introns; Phylogeny; Plant Components, Aerial; Plant Proteins; Polymorphism, Genetic; Promoter Regions, Genetic; Sequence Homologyazacitidine, 320-67-2, 52934-49-3; 3 oxoacyl acyl carrier protein synthase, 9077-10-5; 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase; Plant ProteinsJoseph Rowntree Foundation, JRF; University Grants Committee, UGC; Smoking Research Foundation, SRF; University of Delhi, DUThe study was supported by R&D grants, and DST-PURSE grant from Delhi University, Delhi, India to RG and SD. SS is grateful to UGC, India for award of JRF/SRF .The study was supported by R&D grants, and DST-PURSE grant from Delhi University, Delhi, India to RG and SD. SS is grateful to UGC, India for award of JRF/SRF.Das, S.; Department of Botany, India; email: sdas@botany.du.ac.inElsevier B.V.1567133XGEPEA32947048EnglishGene Expr. PatternsArticleFinalScopus2-s2.0-85091768289
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Villamor A., Signorini L.F., Costantini F., Terzin M., Abbiati M.36057455100;57218462006;13612499300;57216361255;6602994861;Evidence of genetic isolation between two Mediterranean morphotypes of Parazoanthus axinellae2020Scientific Reports10113938110.1038/s41598-020-70770-zhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85089518997&doi=10.1038%2fs41598-020-70770-z&partnerID=40&md5=895fbb6ea7a0e817c40681be6a5e8245Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, Ravenna, 48123, Italy; International Council for the Exploration of the Sea, HC Andersen 22-24, Copenhagen, 1553, Denmark; Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Israel; CoNISMa, Piazzale Flaminio 9, Rome, 00196, Italy; Consiglio Nazionale Delle Ricerche, Istituto di Scienze Marine, ISMAR, Bologna, Italy; Dipartimento di Beni Culturali, Università di Bologna, Via degli Ariani, 1, Ravenna, RA 48121, ItalyVillamor, A., Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, Ravenna, 48123, Italy, International Council for the Exploration of the Sea, HC Andersen 22-24, Copenhagen, 1553, Denmark; Signorini, L.F., Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, Ravenna, 48123, Italy, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Israel; Costantini, F., Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, Ravenna, 48123, Italy, CoNISMa, Piazzale Flaminio 9, Rome, 00196, Italy; Terzin, M., Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, Ravenna, 48123, Italy; Abbiati, M., Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, Ravenna, 48123, Italy, Consiglio Nazionale Delle Ricerche, Istituto di Scienze Marine, ISMAR, Bologna, Italy, Dipartimento di Beni Culturali, Università di Bologna, Via degli Ariani, 1, Ravenna, RA 48121, ItalyCoralligenous assemblages are among the most species-rich and vulnerable habitats of the Mediterranean Sea. Nevertheless, data on connectivity patterns on species inhabiting these habitats, crucial to define management and protection priorities, are largely lacking. Moreover, unreliable species-level taxonomy can confound ecological studies and mislead management strategies. In the northwestern Mediterranean two Parazoanthus axinellae morphotypes differing in size, color and preferred substrate are found in sympatry. In this study, we used COI and ITS sequence polymorphism to assess (1) the genetic divergence between the two morphotypes, (2) their connectivity patterns and (3) their phylogenetic position within the Parazoanthidae. Specimens of P. axinellae were sampled in 11 locations along the northwestern Mediterranean; in 6 locations, samples of the two morphotypes were collected in sympatry. Small genetic diversity and structure were found within morphotypes, while marked and consistent differentiation was detected between them. Moreover, the less widespread morphotype appeared to be closer to Pacific species as P. juanfernandezii and P. elongatus. Our findings confirmed the limited knowledge on Parazoanthus species complex, and how this gap can have important implication for the conservation strategies of this widespread and valuable genus in the Mediterranean Sea. © 2020, The Author(s).article; genetic variability; Mediterranean Sea; morphotype; species complex; sympatry; animal; Anthozoa; biodiversity; ecosystem; genetic variation; genetics; phylogeny; population genetics; procedures; reproductive isolation; sea anemone; Southern Europe; Animals; Anthozoa; Biodiversity; Ecosystem; Genetic Variation; Genetics, Population; Mediterranean Region; Mediterranean Sea; Phylogeny; Reproductive Isolation; Sea AnemonesMinistero dell’Istruzione, dell’Università e della Ricerca, MIUR: Prin 2015 (MIUR) prot. 2015J922E4Costantini, F.; Dipartimento di Scienze Biologiche, Via S. Alberto 163, Italy; email: federica.costantini@unibo.itNature Research2045232232811877EnglishSci. Rep.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85089518997
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Riley N.M., Malaker S.A., Bertozzi C.R.56161765800;55904715300;7102715711;Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis2020Analytical Chemistry92221487814884610.1021/acs.analchem.0c02950https://www.scopus.com/inward/record.uri?eid=2-s2.0-85095833292&doi=10.1021%2facs.analchem.0c02950&partnerID=40&md5=cf9a064adc6bca280b1edb1ee6e0498bDepartment of Chemistry and Stanford ChEM-H, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, Stanford, CA, United StatesRiley, N.M., Department of Chemistry and Stanford ChEM-H, Stanford University, Stanford, CA, United States; Malaker, S.A., Department of Chemistry and Stanford ChEM-H, Stanford University, Stanford, CA, United States; Bertozzi, C.R., Department of Chemistry and Stanford ChEM-H, Stanford University, Stanford, CA, United States, Howard Hughes Medical Institute, Stanford, CA, United StatesThe recently described O-glycoprotease OpeRATOR presents exciting opportunities for O-glycoproteomics. This bacterial enzyme purified from Akkermansia muciniphila cleaves N-terminally to serine and threonine residues that are modified with (preferably asialylated) O-glycans. This provides orthogonal cleavage relative to canonical proteases (e.g., trypsin) for improved O-glycopeptide characterization with tandem mass spectrometry (MS/MS). O-glycopeptides with a modified N-terminal residue, such as those generated by OpeRATOR, present several potential benefits, perhaps the most notable being de facto O-glycosite localization without the need of glycan-retaining fragments in MS/MS spectra. Indeed, O-glycopeptides modified exclusively at the N-terminus would enable O-glycoproteomic methods to rely solely on collision-based fragmentation rather than electron-driven dissociation because glycan-retaining peptide fragments would not be required for localization. The caveat is that modified peptides would need to reliably contain only a single O-glycosite. Here, we use methods that combine collision- and electron-based fragmentation to characterize the number of O-glycosites that are present in O-glycopeptides derived from the OpeRATOR digestion of four known O-glycoproteins. Our data show that over 50% of O-glycopeptides in our sample generated from combined digestion using OpeRATOR and trypsin contain multiple O-glycosites, indicating that collision-based fragmentation alone is not sufficient. Electron-based dissociation methods are necessary to capture the O-glycopeptide diversity present in OpeRATOR digestions. ©Amino acids; Dissociation; Electrons; Mass spectrometry; Polysaccharides; Bacterial enzymes; Dissociation methods; Electron-driven; Glycoproteomics; Peptide fragments; Potential benefits; Tandem mass spectrometry; Threonine residues; PeptidesNational Institutes of Health, NIH: F32-GM126663-01, K00 CA212454, R01 CA200423; Howard Hughes Medical Institute, HHMIThe authors gratefully acknowledge support from Howard Hughes Medical Institute and National Institute of Health (NIH) Grant R01 CA200423 awarded to C.R.B. NMR was funded through an NIH Predoctoral to Postdoctoral Transition Award (Grant K00 CA212454). S.A.M. was supported by an NIH F32 Postdoctoral Fellowship (F32-GM126663-01).Bertozzi, C.R.; Department of Chemistry and Stanford ChEM-H, United States; email: bertozzi@stanford.eduAmerican Chemical Society32700ANCHAEnglishAnal. Chem.ArticleFinalAll Open Access, GreenScopus2-s2.0-85095833292
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Maitland V.C., Robinson C.V., Porter T.M., Hajibabaei M.57219984667;57201682743;23489970400;12240029000;Freshwater diatom biomonitoring through benthic kick-net metabarcoding2020PLoS ONE1511 Novembere0242143310.1371/journal.pone.0242143https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096406901&doi=10.1371%2fjournal.pone.0242143&partnerID=40&md5=ee78affce19a83b5742e42fd66815d3dCentre for Biodiversity Genomics &, Department of Integrative Biology, University of Guelph, Guelph, ON, CanadaMaitland, V.C., Centre for Biodiversity Genomics &, Department of Integrative Biology, University of Guelph, Guelph, ON, Canada; Robinson, C.V., Centre for Biodiversity Genomics &, Department of Integrative Biology, University of Guelph, Guelph, ON, Canada; Porter, T.M., Centre for Biodiversity Genomics &, Department of Integrative Biology, University of Guelph, Guelph, ON, Canada; Hajibabaei, M., Centre for Biodiversity Genomics &, Department of Integrative Biology, University of Guelph, Guelph, ON, CanadaBiomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, multi-substrate periphyton collection, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional multi-substrate microhabitat periphyton collections and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton collection and kick-net methodologies or site status, but there was significant difference between diatom communities depending on site (P = 0.042). These results show the diatom taxonomic coverage achieved through DNA metabarcoding of kick-net is suitable for ecological biomonitoring applications. The shift to a more robust sampling approach and capturing diatoms as well as macroinvertebrates in a single sampling event has the potential to significantly improve efficiency of biomonitoring programmes that currently only use the kick-net technique to sample macroinvertebrates. © 2020 Maitland et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.fresh water; DNA; fresh water; Article; benthic kick net metabarcoding; bioinformatics; biological monitoring; community; community assemblage; controlled study; diatom; DNA barcoding; DNA library; DNA sequencing; ecology; environmental monitoring; gene amplification; habitat; intermethod comparison; macroinvertebrate; nonhuman; periphyton; sampling; species diversity; taxonomy; animal; biodiversity; biofilm; biological monitoring; biology; diatom; ecosystem; genetics; high throughput sequencing; invertebrate; physiology; procedures; river; water quality; Animals; Biodiversity; Biofilms; Biological Monitoring; Computational Biology; Diatoms; DNA; DNA Barcoding, Taxonomic; Ecosystem; Environmental Monitoring; Fresh Water; High-Throughput Nucleotide Sequencing; Invertebrates; Periphyton; Rivers; Water QualityDNA, 9007-49-2; DNAGovernment of CanadaThis study is funded by the Government of Canada through Genome Canada and Ontario Genomics. Teresita Porter was funded by the Government of Canada through the Genomics Research and Development Initiative (GRDI) Metagenomics-Based Ecosystem Biomonitoring Project (Ecobiomics).The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We would like to extend thanks to Michael Wright for providing advice on laboratory procedures and sequencing the samples, Josip Rudar for assistance with bioinformatics and Genevieve Johnson for help collecting samples. We would also like to acknowledge Jessica Robinson, Jaclyn McKeown, Allison Brown and Monica Young from the Centre for Biodiversity Genomics? Collections department for assisting with imaging and use of equipment.Hajibabaei, M.; Centre for Biodiversity Genomics &, Canada; email: mhajibab@uoguelph.caPublic Library of Science19326203POLNC33206700EnglishPLoS ONEArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85096406901
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Prévost J., Gasser R., Beaudoin-Bussières G., Richard J., Duerr R., Laumaea A., Anand S.P., Goyette G., Benlarbi M., Ding S., Medjahed H., Lewin A., Perreault J., Tremblay T., Gendron-Lepage G., Gauthier N., Carrier M., Marcoux D., Piché A., Lavoie M., Benoit A., Loungnarath V., Brochu G., Haddad E., Stacey H.D., Miller M.S., Desforges M., Talbot P.J., Maule G.T.G., Côté M., Therrien C., Serhir B., Bazin R., Roger M., Finzi A.57114557100;55893637300;57216826465;23568696000;57194424377;35743347800;57204015968;57219403405;57219699236;57114118800;35234275400;55599953300;16245687800;6701657173;57207963631;57220037925;57220023349;57200585115;7004356236;57220034894;57220035632;37079329100;57220039935;36610073300;57201898242;56600989200;6701643379;7102670281;57220032509;16644586400;36958020200;6603347137;7005169712;57207895031;57203237269;Cross-Sectional Evaluation of Humoral Responses against SARS-CoV-2 Spike2020Cell Reports Medicine171001268910.1016/j.xcrm.2020.100126https://www.scopus.com/inward/record.uri?eid=2-s2.0-85092582125&doi=10.1016%2fj.xcrm.2020.100126&partnerID=40&md5=c6114f806a7a40d075fb9dc705035faaCentre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Pathology, New York University School of Medicine, New York, NY 10016, United States; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Héma-Québec, Affaires Médicales et Innovation, Québec, QC G1V 5C3, Canada; Hôpital Sacré-Cœur de Montréal, Montreal, QC H4J 1C5, Canada; Hôpital Cité-de-la-Santé, Laval, QC H7M 3L9, Canada; Hôtel-Dieu de Lévis, Lévis, QC G6V 3Z1, Canada; Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5H4, Canada; CIUSSS du Saguenay-Lac-Saint-Jean, Hôpital de Chicoutimi, Chicoutimi, QC G7H 5H6, Canada; Hôpital de Verdun, Montreal, QC H4G 2A3, Canada; CHU de Québec, Hôpital Enfant-Jésus, Quebec, QC G1J 1Z4, Canada; CIUSSS de la Mauricie-et-du-Centre-du-Québec, Trois-Rivières, QC G9A 5C5, Canada; INRS-Institut Armand Frappier, Laval, QC H7V 1B7, Canada; CHU Ste-Justine, Montreal, QC H3T 1C5, Canada; Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Laboratoire de Santé Publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; Département de Pédiatrie, Université de Montréal, Montreal, QC H3T 1C5, Canada; Micheal G. DeGroote Institute for Infectious Disease Research, Master Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, CanadaPrévost, J., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Gasser, R., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Beaudoin-Bussières, G., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Richard, J., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Duerr, R., Department of Pathology, New York University School of Medicine, New York, NY 10016, United States; Laumaea, A., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Anand, S.P., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Goyette, G., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Benlarbi, M., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Ding, S., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Medjahed, H., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Lewin, A., Héma-Québec, Affaires Médicales et Innovation, Québec, QC G1V 5C3, Canada; Perreault, J., Héma-Québec, Affaires Médicales et Innovation, Québec, QC G1V 5C3, Canada; Tremblay, T., Héma-Québec, Affaires Médicales et Innovation, Québec, QC G1V 5C3, Canada; Gendron-Lepage, G., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Gauthier, N., Hôpital Sacré-Cœur de Montréal, Montreal, QC H4J 1C5, Canada; Carrier, M., Hôpital Cité-de-la-Santé, Laval, QC H7M 3L9, Canada; Marcoux, D., Hôtel-Dieu de Lévis, Lévis, QC G6V 3Z1, Canada; Piché, A., Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5H4, Canada; Lavoie, M., CIUSSS du Saguenay-Lac-Saint-Jean, Hôpital de Chicoutimi, Chicoutimi, QC G7H 5H6, Canada; Benoit, A., Hôpital de Verdun, Montreal, QC H4G 2A3, Canada; Loungnarath, V., CHU de Québec, Hôpital Enfant-Jésus, Quebec, QC G1J 1Z4, Canada; Brochu, G., CIUSSS de la Mauricie-et-du-Centre-du-Québec, Trois-Rivières, QC G9A 5C5, Canada; Haddad, E., Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada, CHU Ste-Justine, Montreal, QC H3T 1C5, Canada, Département de Pédiatrie, Université de Montréal, Montreal, QC H3T 1C5, Canada; Stacey, H.D., Micheal G. DeGroote Institute for Infectious Disease Research, Master Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Miller, M.S., Micheal G. DeGroote Institute for Infectious Disease Research, Master Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Desforges, M., INRS-Institut Armand Frappier, Laval, QC H7V 1B7, Canada, CHU Ste-Justine, Montreal, QC H3T 1C5, Canada; Talbot, P.J., INRS-Institut Armand Frappier, Laval, QC H7V 1B7, Canada; Maule, G.T.G., Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Côté, M., Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Therrien, C., Laboratoire de Santé Publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; Serhir, B., Laboratoire de Santé Publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; Bazin, R., Héma-Québec, Affaires Médicales et Innovation, Québec, QC G1V 5C3, Canada; Roger, M., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada, Laboratoire de Santé Publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; Finzi, A., Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada, Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, CanadaPrévost et al. report a cross-sectional study on a cohort of 106 COVID-19 patients and show that most infected individuals are able to elicit a sustained antibody response over time. However, plasma neutralizing capacity wanes after infection resolution, but its implication on protection from re-infection remains unknown. © 2020 The Author(s)SARS-CoV-2 is responsible for the coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The Spike glycoproteins of SARS-CoV-2 mediate viral entry and are the main targets for neutralizing antibodies. Understanding the antibody response directed against SARS-CoV-2 is crucial for the development of vaccine, therapeutic, and public health interventions. Here, we perform a cross-sectional study on 106 SARS-CoV-2-infected individuals to evaluate humoral responses against SARS-CoV-2 Spike. Most infected individuals elicit anti-Spike antibodies within 2 weeks of the onset of symptoms. The levels of receptor binding domain (RBD)-specific immunoglobulin G (IgG) persist over time, and the levels of anti-RBD IgM decrease after symptom resolution. Although most individuals develop neutralizing antibodies within 2 weeks of infection, the level of neutralizing activity is significantly decreased over time. Our results highlight the importance of studying the persistence of neutralizing activity upon natural SARS-CoV-2 infection. © 2020 The Author(s)coronavirus; COVID-19; cross-reactivity, IgA; IgG; IgM; neutralization; RBD; SARS-CoV-2; Spike glycoproteinsHHSN272201400008C; National Institutes of Health, NIH; National Institute of Allergy and Infectious Diseases, NIAID: R01AI122953; Fondation du CHUM; Ministère de l'Économie, de l’Innovation et des Exportations du Québec, MEIE; Canadian Institutes of Health Research, CIHR: 352417; W. Garfield Weston Foundation; Mitacs; Stichting A.F. Deutman Oogheelkunde Researchfonds, SAFDORThe authors thank the CRCHUM BSL3 and Flow Cytometry Platforms for technical assistance. We thank Dr. Florian Krammer (Icahn School of Medicine at Mount Sinai, NY) for the plasmid expressing the SARS-CoV-2 RBD domain, Dr. Stefan Pöhlmann (Georg-August University, Germany) for the plasmids coding SARS-CoV S, SARS-CoV-2 S, and HCoV 229E and NL63 S glycoproteins, and Dr. M. Gordon Joyce (U.S. MHRP) for the monoclonal antibody CR3022. We also thank Danka K. Shank and Melina Bélanger Collard from the Laboratoire de Santé Publique du Québec for their help in preparing the specimens. The graphical abstract was prepared using images from BioRender.com . This work was supported by le Ministère de l’Économie et de l’Innovation du Québec , Programme de soutien aux organismes de recherche et d’innovation to A.F. and by the Fondation du CHUM . This work was also supported by Canada’s COVID-19 Immunity Task Force (CITF), in collaboration with the Canadian Institutes of Health Research (CIHR) and a CIHR foundation grant #352417 to A.F. Development of SARS-CoV-2 reagents was partially supported by the NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS) contract HHSN272201400008C . A.F. is the recipient of Canada Research Chair on Retroviral Entry no. RCHS0235 950-232424 . R.D. was supported by NIH grant R01 AI122953-05 . M.C. is the recipient of a Tier II Canada Research Chair in Molecular Virology and Antiviral Therapeutics and an Ontario’s Early Researcher Award . J. Prévost, G.B.-B., and S.P.A are supported by CIHR fellowships . R.G. is supported by a MITACS Accélération postdoctoral fellowship . M.S.M. was supported in part by a CIHR New Investigator Award , Ontario Early Researcher Award , CIHR COVID Rapid Response Funding , and the W. Garfield Weston Foundation Weston Family Microbiome Initiative . The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.The authors thank the CRCHUM BSL3 and Flow Cytometry Platforms for technical assistance. We thank Dr. Florian Krammer (Icahn School of Medicine at Mount Sinai, NY) for the plasmid expressing the SARS-CoV-2 RBD domain, Dr. Stefan P?hlmann (Georg-August University, Germany) for the plasmids coding SARS-CoV S, SARS-CoV-2 S, and HCoV 229E and NL63 S glycoproteins, and Dr. M. Gordon Joyce (U.S. MHRP) for the monoclonal antibody CR3022. We also thank Danka K. Shank and Melina B?langer Collard from the Laboratoire de Sant? Publique du Qu?bec for their help in preparing the specimens. The graphical abstract was prepared using images from BioRender.com. This work was supported by le Minist?re de l??conomie et de l'Innovation du Qu?bec, Programme de soutien aux organismes de recherche et d'innovation to A.F. and by the Fondation du CHUM. This work was also supported by Canada's COVID-19 Immunity Task Force (CITF), in collaboration with the Canadian Institutes of Health Research (CIHR) and a CIHR foundation grant #352417 to A.F. Development of SARS-CoV-2 reagents was partially supported by the NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS) contract HHSN272201400008C. A.F. is the recipient of Canada Research Chair on Retroviral Entry no. RCHS0235 950-232424. R.D. was supported by NIH grant R01 AI122953-05. M.C. is the recipient of a Tier II Canada Research Chair in Molecular Virology and Antiviral Therapeutics and an Ontario's Early Researcher Award. J. Pr?vost, G.B.-B. and S.P.A are supported by CIHR fellowships. R.G. is supported by a MITACS Acc?l?ration postdoctoral fellowship. M.S.M. was supported in part by a CIHR New Investigator Award, Ontario Early Researcher Award, CIHR COVID Rapid Response Funding, and the W. Garfield Weston Foundation Weston Family Microbiome Initiative. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. J. Pr?vost, J.R. B.S. R.B. M.R. and A.F. conceived the study. J. Pr?vost, J.R. and A.F. designed experimental approaches; J. Pr?vost, G.B.-B. R.G. A. Laumaea, J.R. S.P.A. G.G. M.B. S.D. T.T. J. Perreault, A. Lewin, R.D. R.B. M.R. and A.F. performed, analyzed, and interpreted the experiments; J. Pr?vost, G.B.-B. J.R. H.M. G.G.-L. H.D.S. M.S.M. M.D. P.J.T. G.T.G.M. M. C?t?, and A.F. contributed novel reagents; N.G. M. Carrier, D.M. A.P. M.L. A.B. V.L. G.B. E.H. C.T. R.B. and M.R. collected clinical samples; J. Pr?vost, J.R. and A.F. wrote the paper. Every author has read, edited, and approved the final manuscript. The authors declare no competing interests.Finzi, A.; Centre de Recherche du CHUMCanada; email: andres.finzi@umontreal.caCell Press26663791EnglishCell Rep. Med.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85092582125
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Losev T., Storteboom S., Carpendale S., Knudsen S.57221148519;57024218600;6507907377;55537385900;Distributed Synchronous Visualization Design: Challenges and Strategies2020Proceedings - 8th Evaluation and Beyond: Methodological Approaches for Visualization, BELIV 20209307756110210.1109/BELIV51497.2020.00008https://www.scopus.com/inward/record.uri?eid=2-s2.0-85100129413&doi=10.1109%2fBELIV51497.2020.00008&partnerID=40&md5=f8c3913d869d3e4bd54db4ec6d56a662Simon Fraser University, Canada; University of Calgary, CanadaLosev, T., Simon Fraser University, Canada; Storteboom, S., University of Calgary, Canada; Carpendale, S., Simon Fraser University, Canada; Knudsen, S., University of Calgary, CanadaWe reflect on our experiences as designers of COVID-19 data visualizations working in a distributed synchronous design space during the pandemic. This is especially relevant as the pandemic posed new challenges to distributed collaboration amidst civic lockdown measures and an increased dependency on spatially distributed teamwork across almost all sectors. Working from home being 'the new normal', we explored potential solutions for collaborating and prototyping remotely from our own homes using the existing tools at our disposal. Since members of our cross-disciplinary team had different technical skills, we used a range of synchronous remote design tools and methods. We aimed to preserve the richness of co-located collaboration such as face-to-face physical presence, body gestures, facial expressions, and the making and sharing of physical artifacts. While meeting over Zoom, we sketched on paper and used digital collaboration tools, such as Miro and Google Docs. Using an auto-ethnographic approach, we articulate our challenges and strategies throughout the process, providing useful insights about synchronous distributed collaboration. © 2020 IEEE.visualization design distributed synchronous collaboration information visualization computer supported collaborative workVisualization; Co-located collaboration; Cross-disciplinary teams; Design tools and methods; Digital collaborations; Distributed collaboration; Ethnographic approaches; Synchronous designs; Visualization designs; DesignHorizon 2020 Framework Programme, H2020; H2020 Marie Skłodowska-Curie Actions, MSCA: 753816; Natural Sciences and Engineering Research Council of Canada, NSERC; Horizon 2020The authors would like to thank Jackie Yu, Neil Chulpongsatorn and the Centre for Health Informatics, Cumming School of Medicine at the University of Calgary for their contributions to the process. This research was supported in part by the Natural Sciences and Engineering Research Council of Canada (NSERC) and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 753816.The authors would like to thank Jackie Yu, Neil Chulpongsatorn and the Centre for Health Informatics, Cumming School of Medicine at the University of Calgary for their contributions to the process. This research was supported in part by the Natural Sciences and Engineering Research Council of Canada (NSERC) and the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 753816.Losev, T.; Simon Fraser UniversityCanada; email: tatiana_losev@sfu.caBezerianos A.Hall K.Huron S.Kay M.Meyer M.Sedlmair M.Institute of Electrical and Electronics Engineers Inc.8th IEEE Workshop on Evaluation and Beyond: Methodological Approaches for Visualization, BELIV 202025 October 20201669739781728196428EnglishProc. - Eval. Beyond: Methodol. Approaches Vis., BELIVConference PaperFinalAll Open Access, Bronze, GreenScopus2-s2.0-85100129413
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Elli T., Hinrichs U., Bradley A., Hills Z., Collins C., Kelsky K.57197775451;24477337100;56749446400;57205427958;56760469700;6507706443;Tied in Knots: A Case Study on Anthropographic Data Visualization about Sexual Harassment in the Academy2020Proceedings - 2020 IEEE VIS Arts Program, VISAP 202093079652944110.1109/VISAP51628.2020.00010https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099729180&doi=10.1109%2fVISAP51628.2020.00010&partnerID=40&md5=955d46bb86bafe7b4dd0da67dcbc3ae1Ontario Tech University, Politecnico di Milano, Italy; University of St Andrews, United KingdomElli, T., Ontario Tech University, Politecnico di Milano, Italy; Hinrichs, U., University of St Andrews, United Kingdom; Bradley, A., Ontario Tech University, Politecnico di Milano, Italy; Hills, Z., Ontario Tech University, Politecnico di Milano, Italy; Collins, C., Ontario Tech University, Politecnico di Milano, Italy; Kelsky, K.With this pictorial we present the design process of 'The Academia is Tied in Knots', an interactive visualization based on sensitive and qualitative data, namely personal stories reported by people who have experienced sexual harassment in academia. We discuss how we approached the task of visualizing sensitive, uncomfortable, yet important topics in terms of data-mapping and visual representation, including the appropriateness of computational vs. manual approaches to help foreground relevant themes. We also describe the design process behind the visualization and we discuss it from a feminist data visualization perspective. © 2020 IEEE.antropographic data visualization; data curation; qualitative data; Sexual harassment; tailored visual modelsBrunvand E.Han Y.C.Hull C.Lantin M.Institute of Electrical and Electronics Engineers Inc.2020 IEEE VIS Arts Program, VISAP 202027 October 2020 through 29 October 20201663659781728185538EnglishProc. - IEEE VIS Arts Program, VISAPConference PaperFinalAll Open Access, GreenScopus2-s2.0-85099729180
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Zhu S., Sun G., Jiang Q., Zha M., Liang R.57218543448;55750131400;57218549465;57218546306;55622054000;A survey on automatic infographics and visualization recommendations2020Visual Informatics4324401210.1016/j.visinf.2020.07.002https://www.scopus.com/inward/record.uri?eid=2-s2.0-85089487325&doi=10.1016%2fj.visinf.2020.07.002&partnerID=40&md5=965ec56cc9ed6649a083536f6d7e2f47College of Computer Science and Technology, Zhejiang University of Technology, ChinaZhu, S., College of Computer Science and Technology, Zhejiang University of Technology, China; Sun, G., College of Computer Science and Technology, Zhejiang University of Technology, China; Jiang, Q., College of Computer Science and Technology, Zhejiang University of Technology, China; Zha, M., College of Computer Science and Technology, Zhejiang University of Technology, China; Liang, R., College of Computer Science and Technology, Zhejiang University of Technology, ChinaAutomatic infographics generators employ machine learning algorithms/user-defined rules and visual embellishments into the creation of infographics. It is an emerging topic in the field of information visualization that has requirements in many sectors, such as dashboard design, data analysis, and visualization recommendation. The growing popularity of visual analytics in recent years brings increased attention to automatic infographics. This creates the need for a broad survey that reviews and assesses the significant advances in this field. Automatic tools aim to lower the barrier for visually analyzing data by automatically generating visualizations for analysts to search and make a choice, instead of manually specifying. This survey reviews and classifies automatic tools and papers of visualization recommendations into a set of application categories including network-graph visualizations, annotation visualizations, and storytelling visualization. More importantly, this report presents several challenges and promising directions for future work in the field of automatic infographics and visualization recommendations. © 2020 The Author(s)Automatic visualization; Data-driven; Knowledge-based; Machine learning; Visual embellishmentsData visualization; Information analysis; Information systems; Learning algorithms; Machine learning; Surveys; Automatic tools; Emerging topics; Infographics; Information visualization; Network graph; Visual analytics; Visual embellishments; VisualizationNO.LY19F020026; Key Technology Research and Development Program of Shandong: 2019C01009; National Natural Science Foundation of China, NSFC: 61902350, 61972356; Natural Science Foundation of Zhejiang Province, ZJNSF: LY19F020026; Fundamental Research Funds for the Central Universities: RF-C2019001This work is partly supported by National Natural Science Foundation of China (No. 61972356 , 61902350 ), Zhejiang Provincial Natural Science Foundation of China (NO. LY19F020026 ), Zhejiang Provincial Key Research and Development Program of China (No. 2019C01009 ), and Fundamental Research Funds for the Provincial Universities of Zhejiang (NO. RF-C2019001 ).This work is partly supported by National Natural Science Foundation of China (No. 61972356, 61902350), Zhejiang Provincial Natural Science Foundation of China (NO.LY19F020026), Zhejiang Provincial Key Research and Development Program of China (No. 2019C01009), and Fundamental Research Funds for the Provincial Universities of Zhejiang (NO. RF-C2019001).Sun, G.; College of Computer Science and Technology, China; email: guodao@zjut.edu.cnElsevier B.V.25432656EnglishVis. Inform.ArticleFinalAll Open Access, GoldScopus2-s2.0-85089487325
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Kolosova V., Belichenko O., Rodionova A., Melnikov D., Sõukand R.55582081200;57197704690;57213581207;57193073504;6506885585;Foraging in boreal forest: Wild food plants of the republic of Karelia, NW Russia2020Foods981015910.3390/foods9081015https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090667841&doi=10.3390%2ffoods9081015&partnerID=40&md5=5739eca920a0019d8177faa533658699Department of Environmental Sciences, Informatics and Statistics, Ca Foscari University of Venice, Via Torino 155, Venice, 30172, Italy; Institute for Linguistic Studies, Russian Academy of Sciences, Tuchkov pereulok 9, St Petersburg, 199004, Russian Federation; Institute of Linguistics, Literature and History of the Karelian Research Centre, Russian Academy of Sciences, Pushkinskaya St. 11, Petrozavodsk, 185910, Russian Federation; Komarov Botanical Institute, Russian Academy of Sciences, Professor Popov St. 2, St Petersburg, 197376, Russian FederationKolosova, V., Department of Environmental Sciences, Informatics and Statistics, Ca Foscari University of Venice, Via Torino 155, Venice, 30172, Italy, Institute for Linguistic Studies, Russian Academy of Sciences, Tuchkov pereulok 9, St Petersburg, 199004, Russian Federation; Belichenko, O., Department of Environmental Sciences, Informatics and Statistics, Ca Foscari University of Venice, Via Torino 155, Venice, 30172, Italy; Rodionova, A., Institute of Linguistics, Literature and History of the Karelian Research Centre, Russian Academy of Sciences, Pushkinskaya St. 11, Petrozavodsk, 185910, Russian Federation; Melnikov, D., Komarov Botanical Institute, Russian Academy of Sciences, Professor Popov St. 2, St Petersburg, 197376, Russian Federation; Sõukand, R., Department of Environmental Sciences, Informatics and Statistics, Ca Foscari University of Venice, Via Torino 155, Venice, 30172, ItalyWhile the current consumption of wild food plants in the taiga of the American continent is a relatively well-researched phenomenon, the European taiga area is heavily underrepresented in the scientific literature. The region is important due to its distinctive ecological conditions with restricted seasonal availability of wild plants. During an ethnobotanical field study conducted in 2018-2019, 73 people from ten settlements in the Republic of Karelia were interviewed. In addition, we conducted historical data analysis and ethnographical source analysis. The most widely consumed wild food plants are forest berries (three Vaccinium species, and Rubus chamaemorus), sapyielding Betula and acidic Rumex. While throughout the lifetime of the interviewees the list of used plants did not change considerably, the ways in which they are processed and stored underwent several stages in function of centrally available goods, people s welfare, technical progress, and ideas about the harm and benefit of various products and technological processes. Differences in the food use of wild plants among different ethnic groups living in the region were on the individual level, while all groups exhibited high variability in the methods of preparation of most used berries. The sustainability of berry use over time has both ecological and economical factors. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.E=thnobotany; Karelia; wild food plants; Local Ecological Knowledge; Nordic studies; boreal forestHorizon 2020 Framework Programme, H2020: 714874; European Research Council, ERCFunding: This research was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant number 714874.Belichenko, O.; Department of Environmental Sciences, Via Torino 155, Italy; email: olga.belichenko@unive.it(O.B.)
Sõukand, R.; Department of Environmental Sciences, Via Torino 155, Italy; email: renata.soukand@unive.it(R.S.)		MDPI Multidisciplinary Digital Publishing Institute23048158EnglishFoodsArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85090667841
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Stelzenmüller V., Coll M., Cormier R., Mazaris A.D., Pascual M., Loiseau C., Claudet J., Katsanevakis S., Gissi E., Evagelopoulos A., Rumes B., Degraer S., Ojaveer H., Moller T., Giménez J., Piroddi C., Markantonatou V., Dimitriadis C.6504770762;57200581637;7005448876;9736304600;57211432208;57211666287;8275355900;55879579300;56507383300;24447903600;8600095900;6507073835;6603176466;23398024400;37032586500;24482197600;56166393500;24447868900;Operationalizing risk-based cumulative effect assessments in the marine environment2020Science of the Total Environment7241381182010.1016/j.scitotenv.2020.138118https://www.scopus.com/inward/record.uri?eid=2-s2.0-85082657138&doi=10.1016%2fj.scitotenv.2020.138118&partnerID=40&md5=f87e10bfc3a37bd0d52b371419de75dbThünen Institute of Sea Fisheries, Bremerhaven, Germany; Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, n° 37-49, Barcelona, 08003, Spain; Helmholtz-Zentrum Geesthacht, Institute for Coastal Research, Max-Planck-Straße 1, Geesthacht, 21502, Germany; Department of Ecology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece; Basque Centre for Climate Change (BC3), Parque Científico UPV/EHU, Edificio Sede 1, Planta 1, Barrio Sarriena, s/n, Leioa, 48940, Spain; National Center for Scientific Research, PSL Université Paris, CRIOBE, USR 3278 CNRS-EPHE-UPVD, Maison des Océans, 195 rue Saint-Jacques, Paris, 75005, France; Laboratoire d'Excellence CORAIL, Moorea, French Polynesia; University of the Aegean, Department of Marine Sciences, Mytilene, Greece; University Iuav of Venice, Tolentini, Santa Croce 191, Venezia, 30135, Italy; Royal Belgian Institute of Natural Sciences (RBINS), Operational Directorate Natural Environment (OD Nature), Marine Ecology and Management (MARECO), Vautierstraat 29, Brussels, 1000, Belgium; University of Tartu, Ringi 35, Pärnu, 80012, Estonia; National Institute of Aquatic Resources, Technical University of Denmark, Kemitorvet Building 201, Kgs. Lyngby, 2800, Denmark; Estonian Marine Institute, University of Tartu, Mäealuse 14, Tallinn, 12618, Estonia; European Commission, Joint Research Centre, Institute for Environment and Sustainability, Via Fermi 2749, Ispra, 21027, Italy; National Marine Park of Zakynthos, El. Venizelou 1, Zakynthos, 29100, GreeceStelzenmüller, V., Thünen Institute of Sea Fisheries, Bremerhaven, Germany; Coll, M., Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, n° 37-49, Barcelona, 08003, Spain; Cormier, R., Helmholtz-Zentrum Geesthacht, Institute for Coastal Research, Max-Planck-Straße 1, Geesthacht, 21502, Germany; Mazaris, A.D., Department of Ecology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece; Pascual, M., Basque Centre for Climate Change (BC3), Parque Científico UPV/EHU, Edificio Sede 1, Planta 1, Barrio Sarriena, s/n, Leioa, 48940, Spain; Loiseau, C., National Center for Scientific Research, PSL Université Paris, CRIOBE, USR 3278 CNRS-EPHE-UPVD, Maison des Océans, 195 rue Saint-Jacques, Paris, 75005, France, Laboratoire d'Excellence CORAIL, Moorea, French Polynesia; Claudet, J., National Center for Scientific Research, PSL Université Paris, CRIOBE, USR 3278 CNRS-EPHE-UPVD, Maison des Océans, 195 rue Saint-Jacques, Paris, 75005, France, Laboratoire d'Excellence CORAIL, Moorea, French Polynesia; Katsanevakis, S., University of the Aegean, Department of Marine Sciences, Mytilene, Greece; Gissi, E., University Iuav of Venice, Tolentini, Santa Croce 191, Venezia, 30135, Italy; Evagelopoulos, A., University of the Aegean, Department of Marine Sciences, Mytilene, Greece; Rumes, B., Royal Belgian Institute of Natural Sciences (RBINS), Operational Directorate Natural Environment (OD Nature), Marine Ecology and Management (MARECO), Vautierstraat 29, Brussels, 1000, Belgium; Degraer, S., Royal Belgian Institute of Natural Sciences (RBINS), Operational Directorate Natural Environment (OD Nature), Marine Ecology and Management (MARECO), Vautierstraat 29, Brussels, 1000, Belgium; Ojaveer, H., University of Tartu, Ringi 35, Pärnu, 80012, Estonia, National Institute of Aquatic Resources, Technical University of Denmark, Kemitorvet Building 201, Kgs. Lyngby, 2800, Denmark; Moller, T., Estonian Marine Institute, University of Tartu, Mäealuse 14, Tallinn, 12618, Estonia; Giménez, J., Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, n° 37-49, Barcelona, 08003, Spain; Piroddi, C., European Commission, Joint Research Centre, Institute for Environment and Sustainability, Via Fermi 2749, Ispra, 21027, Italy; Markantonatou, V., University of the Aegean, Department of Marine Sciences, Mytilene, Greece; Dimitriadis, C., National Marine Park of Zakynthos, El. Venizelou 1, Zakynthos, 29100, GreeceEcosystem-based management requires an assessment of the cumulative effects of human pressures and environmental change. The operationalization and integration of cumulative effects assessments (CEA) into decision-making processes often lacks a comprehensive and transparent framework. A risk-based CEA framework that divides a CEA in risk identification, risk analysis and risk evaluation, could structure such complex analyses and facilitate the establishment of direct science-policy links. Here, we examine carefully the operationalization of such a risk-based CEA framework with the help of eleven contrasting case studies located in Europe, French Polynesia, and Canada. We show that the CEA framework used at local, sub-regional, and regional scales allowed for a consistent, coherent, and transparent comparison of complex assessments. From our analysis, we pinpoint four emerging issues that, if accurately addressed, can improve the take up of CEA outcomes by management: 1) framing of the CEA context and defining risk criteria; 2) describing the roles of scientists and decision-makers; 3) reducing and structuring complexity; and 4) communicating uncertainty. Moreover, with a set of customized tools we describe and analyze for each case study the nature and location of uncertainty as well as trade-offs regarding available knowledge and data used for the CEA. Ultimately, these tools aid decision-makers to recognize potential caveats and repercussions of management decisions. One key recommendation is to differentiate CEA processes and their context in relation to governance advice, marine spatial planning or regulatory advice. We conclude that future research needs to evaluate how effective management measures are in reducing the risk of cumulative effects. Changing governance structures takes time and is often difficult, but we postulate that well-framed and structured CEA can function as a strategic tool to integrate ecosystem considerations across multiple sectorial policies. © 2020Decision-making process; Ecosystem-based management; Effects assessment; Risk criteria and management; Science-policy interfaceConcrete pavements; Economic and social effects; Ecosystems; Risk analysis; Risk assessment; Uncertainty analysis; Decision making process; Ecosystem-based management; Effects assessment; Risk criteria; Science - policy interfaces; Decision making; anthropogenic effect; decision making; ecosystem management; environmental change; marine ecosystem; marine environment; risk assessment; Canada; decision making; Europe; French Polynesia; human; marine environment; review; risk assessment; uncertainty; Canada; Europe; French PolynesiaEuropean Cooperation in Science and Technology, COST: CA15121This article is a product of the working group on cumulative effects assessment under the framework of COST Action 15121 ?Advancing marine conservation in the European and contiguous seas? (MarCons; http://www.marcons-cost.eu; (Katsanevakis et al. 2017)?supported by COST (European Cooperation in Science and Technology, CA15121). Special thanks to Nicole Stollberg who helped to develop high quality figures. Further, we thank two anonymous reviewers for their helpful comments.Stelzenmüller, V.; Thünen Institute of Sea FisheriesGermany; email: vanessa.stelzenmueller@thuenen.deElsevier B.V.489697STEVA32247136EnglishSci. Total Environ.ReviewFinalAll Open Access, Hybrid Gold, GreenScopus2-s2.0-85082657138
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Weisleitner K., Perras A.K., Unterberger S.H., Moissl-Eichinger C., Andersen D.T., Sattler B.56160248600;56239175600;56026580900;26640624300;7202231963;7005258886;Cryoconite Hole Location in East-Antarctic Untersee Oasis Shapes Physical and Biological Diversity2020Frontiers in Microbiology111165810.3389/fmicb.2020.01165https://www.scopus.com/inward/record.uri?eid=2-s2.0-85086658419&doi=10.3389%2ffmicb.2020.01165&partnerID=40&md5=143a3e7e307682338f45fc1291b85dd8Institute of Ecology, University of Innsbruck, Innsbruck, Austria; Austrian Polar Research Institute, Vienna, Austria; Center for Medical Research, Medical University of Graz, Graz, Austria; Unit of Material Technology, University of Innsbruck, Innsbruck, Austria; SETI Institute, Mountain View, CA, United StatesWeisleitner, K., Institute of Ecology, University of Innsbruck, Innsbruck, Austria, Austrian Polar Research Institute, Vienna, Austria; Perras, A.K., Center for Medical Research, Medical University of Graz, Graz, Austria; Unterberger, S.H., Unit of Material Technology, University of Innsbruck, Innsbruck, Austria; Moissl-Eichinger, C., Center for Medical Research, Medical University of Graz, Graz, Austria; Andersen, D.T., SETI Institute, Mountain View, CA, United States; Sattler, B., Institute of Ecology, University of Innsbruck, Innsbruck, Austria, Austrian Polar Research Institute, Vienna, AustriaAntarctic cryoconite holes (CHs) are mostly perennially ice-lidded and sediment-filled depressions that constitute important features on glaciers and ice sheets. Once being hydrologically connected, these microbially dominated mini-ecosystems provide nutrients and biota for downstream environments. For example, the East Antarctic Anuchin Glacier gradually melts into the adjacent perennially ice-covered Lake Untersee, and CH biota from this glacier contribute up to one third of the community composition in benthic microbial mats within the lake. However, biogeochemical features of these CHs and associated spatial patterns across the glacier are still unknown. Here we hypothesized about the CH minerogenic composition between the different sources such as the medial moraine and other zones. Further, we intended to investigate if the depth of the CH mirrors the CH community composition, organic matter (OM) content and would support productivity. In this study we show that both microbial communities and biogeochemical parameters in CHs were significantly different between the zones medial moraine and the glacier terminus. Variations in microbial community composition are the result of factors such as depth, diameter, organic matter, total carbon, particle size, and mineral diversity. More than 90% of all ribosomal sequence variants (RSV) reads were classified as Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria. Archaea were detected in 85% of all samples and exclusively belonged to the classes Halobacteria, Methanomicrobia, and Thermoplasmata. The most abundant genus was Halorubrum (Halobacteria) and was identified in nine RSVs. The core microbiome for bacteria comprised 30 RSVs that were affiliated with Cyanobacteria, Bacteroidetes, Actinobacteria, and Proteobacteria. The archaeal fraction of the core microbiome consisted of three RSVs belonging to unknown genera of Methanomicrobiales and Thermoplasmatales and the genus Rice_Cluster_I (Methanocellales). Further, mean bacterial carbon production in cryoconite was exceptionally low and similar rates have not been reported elsewhere. However, bacterial carbon production insignificantly trended toward higher rates in shallow CHs and did not seem to be supported by accumulation of OM and nutrients, respectively, in deeper holes. OM fractions were significantly different between shallower CHs along the medial moraine and deeper CHs at the glacier terminus. Overall, our findings suggest that wind-blown material originating south and southeast of the Anuchin Glacier and deposits from a nunatak are assumed to be local inoculation sources. High sequence similarities between samples from the Untersee Oasis and other Antarctic sites further indicate long-range atmospheric transport mechanisms that complement local inoculation sources. © Copyright © 2020 Weisleitner, Perras, Unterberger, Moissl-Eichinger, Andersen and Sattler.16S rRNA; Anuchin Glacier; archaea; bacterial activity; biogeochemistry; cryoconite holes; mineralogycarbon; nitrogen; organic matter; phosphorus; algal bloom; aquatic environment; archaeon; Article; Betaproteobacteria; biodiversity; biogeochemistry; cryoconite hole; cyanobacterium; cyanophage; DNA extraction; gene sequence; Halobacteria; high throughput sequencing; marine environment; Methanomicrobia; Methanomicrobiales; Methanosarcinales; microbial community; microbial diversity; microbiome; nested polymerase chain reaction; particle size; particulate matter; Planctomycetes; principal component analysis; scanning electron microscopy; sea surface temperature; sediment; solar radiation; stoichiometry; thermogravimetry; Thermoplasmata; X ray diffraction; X ray powder diffractioncarbon, 7440-44-0; nitrogen, 7727-37-9; phosphorus, 7723-14-0Tawani FoundationPrimary support for this research was provided by the Tawani Foundation and the Trottier Family Foundation. Logistics support was provided by Antarctic Logistics Centre International (ALCI), Cape Town, South Africa and the Von Braun Center for Science Innovation. We are especially thankful to Colonel (IL) J. N. Pritzker, IL ARNG (retired), of the Tawani Foundation, Lorne Trottier, and fellow field team members for their support during the expedition. We also thank Elias Dechent, Gry Larsen, and Salvador Morales-Gomez for help with chemical analyses. Willi Salvenmoser provided sample coating prior scanning electron microscopy. We are grateful for the improvement of the manuscript which was provided by the reviewers. Funding. This study was supported by the Tawani Foundation of Chicago, the Trottier Family Foundation, NASA?s Exobiology and Astrobiology Programs, and the Arctic and Antarctic Research Institute.Sattler, B.; Institute of Ecology, Austria; email: Birgit.Sattler@uibk.ac.at
Sattler, B.; Austrian Polar Research InstituteAustria; email: Birgit.Sattler@uibk.ac.at		Frontiers Media S.A.1664302XEnglishFront. Microbiol.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85086658419
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Blumenschein M., Debbeler L.J., Lages N.C., Renner B., Keim D.A., El-Assady M.57202108253;57199740922;57218161982;24399780000;34769953100;57190300096;v-plots: Designing Hybrid Charts for the Comparative Analysis of Data Distributions2020Computer Graphics Forum393565577410.1111/cgf.14002https://www.scopus.com/inward/record.uri?eid=2-s2.0-85088092294&doi=10.1111%2fcgf.14002&partnerID=40&md5=639949d659cab0a404b87fb4fef71de0University of Konstanz, GermanyBlumenschein, M., University of Konstanz, Germany; Debbeler, L.J., University of Konstanz, Germany; Lages, N.C., University of Konstanz, Germany; Renner, B., University of Konstanz, Germany; Keim, D.A., University of Konstanz, Germany; El-Assady, M., University of Konstanz, GermanyComparing data distributions is a core focus in descriptive statistics, and part of most data analysis processes across disciplines. In particular, comparing distributions entails numerous tasks, ranging from identifying global distribution properties, comparing aggregated statistics (e.g., mean values), to the local inspection of single cases. While various specialized visualizations have been proposed (e.g., box plots, histograms, or violin plots), they are not usually designed to support more than a few tasks, unless they are combined. In this paper, we present the v-plot designer; a technique for authoring custom hybrid charts, combining mirrored bar charts, difference encodings, and violin-style plots. v-plots are customizable and enable the simultaneous comparison of data distributions on global, local, and aggregation levels. Our system design is grounded in an expert survey that compares and evaluates 20 common visualization techniques to derive guidelines for the task-driven selection of appropriate visualizations. This knowledge externalization step allowed us to develop a guiding wizard that can tailor v-plots to individual tasks and particular distribution properties. Finally, we confirm the usefulness of our system design and the user-guiding process by measuring the fitness for purpose and applicability in a second study with four domain and statistic experts. © 2020 The Author(s) Computer Graphics Forum © 2020 The Eurographics Association and John Wiley & Sons Ltd. Published by John Wiley & Sons Ltd.CCS Concepts; • Human-centered computing → Visualization design and evaluation methodsInformation analysis; Systems analysis; Visualization; Aggregation level; Comparative analysis; Data distribution; Descriptive statistics; Fitness for purpose; Global distribution; Particular distribution; Visualization technique; DesignHorizon 2020 Framework Programme, H2020: 825041; Deutsche Forschungsgemeinschaft, DFG: FOR 2374, Project‐ID 251654672, Project‐ID 422037984; Bundesministerium für Bildung und Forschung, BMBF: 01EL1420A; Horizon 2020We thank the anonymous reviewers for their valuable feedback and Tony Arthur for his linguistic revision. Our work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) within the projects TRR 161 (Project-ID 251654672), DFG Grant FOR 2374 ?RiskDynamics?, and project A3 of the Centre of Excellence 2117 (Project-ID 422037984). Furthermore, our research was supported by the Federal Ministry of Education and Research (BMBF) within the Project SmartAct (Grant 01EL1420A) and by the European Union's Horizon 2020 research and innovation programme under grant agreement No 825041.We thank the anonymous reviewers for their valuable feedback and Tony Arthur for his linguistic revision. Our work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) within the projects TRR 161 (Project‐ID 251654672), DFG Grant FOR 2374 “RiskDynamics”, and project A3 of the Centre of Excellence 2117 (Project‐ID 422037984). Furthermore, our research was supported by the Federal Ministry of Education and Research (BMBF) within the Project SmartAct (Grant 01EL1420A) and by the European Union's Horizon 2020 research and innovation programme under grant agreement No 825041.Blumenschein, M.; University of KonstanzGermany; email: michael.blumenschein@uni-konstanz.deBlackwell Publishing Ltd1677055CGFODEnglishComput Graphics ForumArticleFinalAll Open Access, GreenScopus2-s2.0-85088092294
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Badhwar R., Upadhyay A.56453196000;57189335137;Modulation of cellular protein quality control pathways using small natural molecules2020Bioactive Natural Products in Drug Discovery609641310.1007/978-981-15-1394-7_22https://www.scopus.com/inward/record.uri?eid=2-s2.0-85088436781&doi=10.1007%2f978-981-15-1394-7_22&partnerID=40&md5=36b335ca2d90c86f7e44bab6c5fa6d9dDepartment of Bioinformatics, School of Bioengineering and Bioscience, Lovely Professional University, Phagwara, India; Department of Biochemistry, Central University of Rajasthan, Ajmer, IndiaBadhwar, R., Department of Bioinformatics, School of Bioengineering and Bioscience, Lovely Professional University, Phagwara, India; Upadhyay, A., Department of Biochemistry, Central University of Rajasthan, Ajmer, IndiaEukaryotic cellular system is an extremely successful biological model that has evolved over a very long period of time with a higher success rate and utmost efficiency in its structural arrangement and functioning. It consists of a number of processes that monitor and regulate the intracellular signaling and metabolism. The presence of well-developed subsystems for the maintenance of genomic and proteomic repertoire is one major hallmark that the eukaryotes have achieved. Protein quality control (PQC) system represents a group of subsystems, consisting of molecular chaperones, autophagy, and ubiquitin proteasome system (UPS) that helps in folding, maintenance, and degradation of cellular proteins. Deregulation of these pathways under various kinds of unwanted conditions may cause disruption of natively folded proteins, and accumulation of these aberrant proteins may lead to different types of conformational disorders and sometimes speed up the process of ageing. In the past few years, several types of therapeutic strategies have been proposed and worked out by multiple research groups to modulate the efficiency of the PQC pathways, in order to reduce the cellular burden of proteotoxicity. Using small molecules to reestablish the folding efficiency of molecular chaperones and for the upregulation of proteolytic abilities of the UPS and autophagic pathways is one highly worked out and effective approach to provide symptomatic relief in many disease conditions. These small molecules have also shown beneficial effects in interfering with the aggregation pathways of proteins and hence could be used as a possible therapeutic strategy to prevent and cure neurodegeneration and several ageing-associated problems. © Springer Nature Singapore Pte Ltd. 2020.Autophagy; Cancer; Chaperones; Natural molecules; Neurodegeneration; Proteostasis; Ubiquitin proteasome systemUpadhyay, A.; Department of Biochemistry, IndiaSpringer Singapore9789811513947; 9789811513930EnglishBioact. Nat. Prod. in Drug Discov.Book ChapterFinalScopus2-s2.0-85088436781
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Fernandes M.L., Sousa L.P., Quintela A., Marques M., Reis J., Simão A.P., Castro A.T., Marques J.M., Alves F.L.57372363100;55851275800;36716599700;57212649143;57214333950;57214716123;57199670057;57211344855;36130953500;Mapping the future: Pressures and impacts in the Portuguese maritime spatial planning2020Science of the Total Environment715136863410.1016/j.scitotenv.2020.136863https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078671669&doi=10.1016%2fj.scitotenv.2020.136863&partnerID=40&md5=228999ab2e8dda94fecf4cbdf59a6aaeDepartment of Environment and Planning & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus de Santiago, Aveiro, 3810-193, Portugal; Direção-Geral de Recursos Naturais, Segurança e Serviços Marítimos, Avenida Brasília, Lisboa, 1449-030, PortugalFernandes, M.L., Department of Environment and Planning & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus de Santiago, Aveiro, 3810-193, Portugal; Sousa, L.P., Department of Environment and Planning & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus de Santiago, Aveiro, 3810-193, Portugal; Quintela, A., Department of Environment and Planning & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus de Santiago, Aveiro, 3810-193, Portugal; Marques, M., Department of Environment and Planning & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus de Santiago, Aveiro, 3810-193, Portugal; Reis, J., Department of Environment and Planning & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus de Santiago, Aveiro, 3810-193, Portugal; Simão, A.P., Direção-Geral de Recursos Naturais, Segurança e Serviços Marítimos, Avenida Brasília, Lisboa, 1449-030, Portugal; Castro, A.T., Direção-Geral de Recursos Naturais, Segurança e Serviços Marítimos, Avenida Brasília, Lisboa, 1449-030, Portugal; Marques, J.M., Direção-Geral de Recursos Naturais, Segurança e Serviços Marítimos, Avenida Brasília, Lisboa, 1449-030, Portugal; Alves, F.L., Department of Environment and Planning & CESAM-Centre for Environmental and Marine Studies, University of Aveiro, Campus de Santiago, Aveiro, 3810-193, PortugalMaritime Spatial Planning (MSP) is bringing new challenges to planning and management in the marine realm, namely on the environmental assessment of the new plans and projects. Portugal is developing its first MSP instrument, PSOEM (Plano de Situação do Ordenamento do Espaço Marítimo), since 2015 and published it on December 2019. This paper focuses on a particular stage of the Strategic Environmental Assessment (SEA) of PSOEM regarding the assessment of the activities/uses that may significantly affect Natura 2000 marine network during the Plan's implementation in the Mainland subdivision. Over the years, progress has been made in researching and assessing the environmental impacts of maritime activities/uses. However, its application to practice raised several challenges and limitations. The methodological approach presented in this paper was developed to overcome knowledge, data and time constraints. Some of the limitations are a consequence of the MSP approach itself adopted in Portugal, namely the low technical detail on future uses and activities, which is required and desirable at this level of planning. Others relate with the lack of spatially explicit data on marine habitats and species distribution preserved under Natura 2000 network, which is not fully established in the marine environment. The adopted methodology started with the characterization and mapping of the conservation values and the pressures arising from the potential activities/uses. It followed with the assessment of their impacts and finally with the identification of mitigation measures, which were then adopted by the PSOEM as good practices. As new knowledge is generated and more information is collected, this tailor-made approach can be easily adapted and improved to keep supporting decision-making throughout PSOEM's implementation. The method can be easily adapted and transferred to other contexts, not only within the Portuguese maritime area, and could be made available to stakeholders that wish to invest in blue growth. © 2020 Elsevier B.V.Activities and uses; Environmental assessment; MSP; Natura 2000; Portugal; SEAConservation; Decision making; Environmental impact assessments; Mapping; Activities and uses; Environmental assessment; Methodological approach; Natura 2000; Natura 2000 networks; Portugal; Species distributions; Strategic environmental assessments; Environmental impact; decision making; maritime transportation; policy implementation; spatial planning; strategic environmental assessment; transportation development; transportation planning; article; decision making; environmental impact; habitat; marine environment; Portugal; species distribution; PortugalBTI/PSOEM/DAO/2017; Centro de Estudos Ambientais e Marinhos, Universidade de Aveiro, CESAM: UID/AMB/50017/2019; Fundação para a Ciência e a Tecnologia, FCT: DGRM / UA ( BTI/PSOEM/DAO/2017, PD/BD/113485/2015, SFRH/BD/138422/2018; Ministério da Ciência, Tecnologia e Ensino Superior, MCTES; European Regional Development Fund, FEDERThis work was financed by the Directorate General for Natural Resources, Safety and Maritime Services (DGRM) and has been developed under the consortium DGRM/UA ? for development of the Strategic Environmental Assessment of the Portuguese Maritime Spatial Plan. MLF was supported by Portuguese Foundation for Science and Technology ? FCT, with a Do*Mar programme PhD grant (PD/BD/113485/2015). LS and AQ were financed through Project SIMNORAT (EASME/&EMFF/2015/1.2.1.3/03/SI2.742089). MM was supported by the Portuguese Foundation for Science and Technology (FCT), with a PhD grant (SFRH/BD/138422/2018). JR was supported under consortium DGRM/UA (BTI/PSOEM/DAO/2017). Thanks are due for the financial support to CESAM (UID/AMB/50017/2019), to FCT/MCTES through national funds, and the co-funding by the FEDER, within the PT2020 Partnership Agreement and Compete 2020.This work was financed by the Directorate General for Natural Resources, Safety and Maritime Services (DGRM) and has been developed under the consortium DGRM/UA – for development of the Strategic Environmental Assessment of the Portuguese Maritime Spatial Plan. MLF was supported by Portuguese Foundation for Science and Technology – FCT, with a Do*Mar programme PhD grant ( PD/BD/113485/2015 ). LS and AQ were financed through Project SIMNORAT ( EASME/&EMFF/2015/1.2.1.3/03/SI2.742089 ). MM was supported by the Portuguese Foundation for Science and Technology (FCT), with a PhD grant ( SFRH/BD/138422/2018 ). JR was supported under consortium DGRM / UA ( BTI/PSOEM/DAO/2017 ). Thanks are due for the financial support to CESAM ( UID/AMB/50017/2019 ), to FCT / MCTES through national funds, and the co-funding by the FEDER , within the PT2020 Partnership Agreement and Compete 2020.Fernandes, M.L.; Department of Environment and Planning & CESAM-Centre for Environmental and Marine Studies, Campus de Santiago, Portugal; email: maria.luz@ua.ptElsevier B.V.489697STEVA32018101EnglishSci. Total Environ.ArticleFinalScopus2-s2.0-85078671669
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Veira-González X., Cairo A.57207955871;55820343400;From artisans to engineers: How technology transformed formats, workflows, teams and the craft of infographics and data visualization in the news2020Information Visualization in The Era of Innovative Journalism134153https://www.scopus.com/inward/record.uri?eid=2-s2.0-85106089566&partnerID=40&md5=f89d5521d3a574aebf5588cd38faf994Universitat de Girona, Spain; University of Miami, United StatesVeira-González, X., Universitat de Girona, Spain; Cairo, A., University of Miami, United States[No abstract available]Veira-González, X.; Universitat de GironaSpainTaylor and Francis9780367809638; 9780367360498EnglishInf. Vis. in The Era of Innov. Journal.Book ChapterFinalScopus2-s2.0-85106089566
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Maurer G.D., Brucker D.P., Stoffels G., Filipski K., Filss C.P., Mottaghy F.M., Galldiks N., Steinbach J.P., Hattingen E., Langen K.-J.16043361500;26657829900;11440988400;57204859388;55293674200;55173093500;8057355400;7103123774;6505923786;24383825000;18F-FET PET imaging in differentiating glioma progression from treatment-related changes: A single-center experience2020Journal of Nuclear Medicine6145065111010.2967/jnumed.119.234757https://www.scopus.com/inward/record.uri?eid=2-s2.0-85076920792&doi=10.2967%2fjnumed.119.234757&partnerID=40&md5=ea368fa20a0a00b17b1e39977f52717fDr. Senckenberg Institute of Neurooncology, Goethe University Hospital, Frankfurt am Main, Germany; University Cancer Center Frankfurt, Goethe University Hospital, Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/ Mainz, Heidelberg, Germany; Institute of Neuroscience and Medicine (INM-3 and INM-4), Research Center Juelich, Juelich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Neurology (Edinger Institute), Goethe University Hospital, Frankfurt am Main, Germany; Department of Nuclear Medicine, RWTH University Hospital, Aachen, Germany; Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, Maastricht, Netherlands; Center of Integrated Oncology, Universities of Aachen, Cologne, Duesseldorf, Bonn, Germany; Department of Neurology, University Hospital Cologne, Cologne, Germany; Institute of Neuroradiology, Goethe University Hospital, Frankfurt am Main, GermanyMaurer, G.D., University Cancer Center Frankfurt, Goethe University Hospital, Frankfurt am Main, Germany, German Cancer Consortium (DKTK), Partner Site Frankfurt/ Mainz, Heidelberg, Germany; Brucker, D.P., University Cancer Center Frankfurt, Goethe University Hospital, Frankfurt am Main, Germany, German Cancer Consortium (DKTK), Partner Site Frankfurt/ Mainz, Heidelberg, Germany; Stoffels, G., Institute of Neuroscience and Medicine (INM-3 and INM-4), Research Center Juelich, Juelich, Germany; Filipski, K., German Cancer Consortium (DKTK), Partner Site Frankfurt/ Mainz, Heidelberg, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany, Institute of Neurology (Edinger Institute), Goethe University Hospital, Frankfurt am Main, Germany; Filss, C.P., Institute of Neuroscience and Medicine (INM-3 and INM-4), Research Center Juelich, Juelich, Germany, Department of Nuclear Medicine, RWTH University Hospital, Aachen, Germany; Mottaghy, F.M., Department of Nuclear Medicine, RWTH University Hospital, Aachen, Germany, Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, Maastricht, Netherlands, Center of Integrated Oncology, Universities of Aachen, Cologne, Duesseldorf, Bonn, Germany; Galldiks, N., Institute of Neuroscience and Medicine (INM-3 and INM-4), Research Center Juelich, Juelich, Germany, Center of Integrated Oncology, Universities of Aachen, Cologne, Duesseldorf, Bonn, Germany, Department of Neurology, University Hospital Cologne, Cologne, Germany; Steinbach, J.P., Dr. Senckenberg Institute of Neurooncology, Goethe University Hospital, Frankfurt am Main, Germany, University Cancer Center Frankfurt, Goethe University Hospital, Frankfurt am Main, Germany, German Cancer Consortium (DKTK), Partner Site Frankfurt/ Mainz, Heidelberg, Germany; Hattingen, E., Institute of Neuroradiology, Goethe University Hospital, Frankfurt am Main, Germany; Langen, K.-J., Institute of Neuroscience and Medicine (INM-3 and INM-4), Research Center Juelich, Juelich, Germany, Department of Nuclear Medicine, RWTH University Hospital, Aachen, Germany, Center of Integrated Oncology, Universities of Aachen, Cologne, Duesseldorf, Bonn, GermanyIn glioma patients, differentiation between tumor progression (TP) and treatment-related changes (TRCs) remains challenging. Difficulties in classifying imaging alterations may result in a delay or an unnecessary discontinuation of treatment. PET using O-(2-18F-fluoroethyl)-L-tyrosine (18F-FET) has been shown to be a useful tool for detecting TP and TRCs. Methods: We retrospectively evaluated 127 consecutive patients with World Health Organization grade II-IV glioma who underwent 18F-FET PET imaging to distinguish between TP and TRCs. 18F-FET PET findings were verified by neuropathology (40 patients) or clinicoradiologic follow-up (87 patients). Maximum tumor-to-brain ratios (TBRmax) of 18F-FET uptake and the slope of the time-activity curves (20-50 min after injection) were determined. The diagnostic accuracy of 18F-FET PET parameters was evaluated by receiver-operating-characteristic analysis and χ2 testing. The prognostic value of 18F-FET PET was estimated using the Kaplan-Meier method. Results: TP was diagnosed in 94 patients (74%) and TRCs in 33 (26%). For differentiating TP from TRCs, receiver-operating-characteristic analysis yielded an optimal 18F-FET TBRmax cutoff of 1.95 (sensitivity, 70%; specificity, 71%; accuracy, 70%; area under the curve, 0.75 ± 0.05). The highest accuracy was achieved by a combination of TBRmax and slope (sensitivity, 86%; specificity, 67%; accuracy, 81%). However, accuracy was poorer when tumors harbored isocitrate dehydrogenase (IDH) mutations (91% in IDH-wild-type tumors, 67% in IDH-mutant tumors, P, 0.001). 18F-FET PET results correlated with overall survival (P, 0.001). Conclusion: In our neurooncology department, the diagnostic performance of 18F-FET PET was convincing but slightly inferior to that of previous reports. COPYRIGHT © 2020 by the Society of Nuclear Medicine and Molecular Imaging.18F-FET PET; Glioma; Pseudoprogression; Treatment-related changes; Tumor progressionO-(2-fluoroethyl)tyrosine; tyrosine; adult; aged; diagnostic imaging; disease exacerbation; female; glioma; human; male; middle aged; pathology; positron emission tomography; retrospective study; young adult; Adult; Aged; Disease Progression; Female; Glioma; Humans; Male; Middle Aged; Positron-Emission Tomography; Retrospective Studies; Tyrosine; Young Adulttyrosine, 16870-43-2, 55520-40-6, 60-18-4; O-(2-fluoroethyl)tyrosine; Tyrosine2014/SIN-02The Dr. Senckenberg Institute of Neurooncology is supported by the Dr. Senckenberg foundation (grant 2014/SIN-02). Joachim Steinbach has received a grant from Merck, as well as honoraria for lectures, travel, or advisory board participation from Roche, Medac, Bristol-Myers Squibb, and Abbvie. No other potential conflict of interest relevant to this article was reported.Maurer, G.D.; Dr. Senckenberg Institute of Neurooncology, Schleusenweg 2-16, Germany; email: gabriele.maurer@kgu.deSociety of Nuclear Medicine Inc.1615505JNMEA31519802EnglishJ. Nucl. Med.ArticleFinalAll Open Access, BronzeScopus2-s2.0-85076920792
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Degbelo A., Sarfraz S., Kray C.36655652400;57202648017;8399247700;Data scale as cartography: a semi-automatic approach for thematic web map creation2020Cartography and Geographic Information Science472153170210.1080/15230406.2019.1677176https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074813363&doi=10.1080%2f15230406.2019.1677176&partnerID=40&md5=53fd977ce596fd84ed2737f4de8c7f19Institute for Geoinformatics, University of Münster, Münster, GermanyDegbelo, A., Institute for Geoinformatics, University of Münster, Münster, Germany; Sarfraz, S., Institute for Geoinformatics, University of Münster, Münster, Germany; Kray, C., Institute for Geoinformatics, University of Münster, Münster, GermanyOpen government promises increased transparency by providing its citizens datasets about city processes. Open data portals have been emerging all over the world as mines of open geographic datasets. Thematic web maps are key to understanding these open geographic datasets. Current thematic web maps are created by programmers and/or cartographers, and thus are not designed to be easily reused with new geographic datasets. As a result, they pose several challenges to non-experts wanting to adapt them to new scenarios. This article introduces a semi-automatic approach for the creation of thematic web maps by and for users with no prior training in cartography. The approach relies on the mapping between Stevens’ data types and Bertin’s visual variables, to suggest (meaningful) thematic map visualizations for a given input geographic dataset. It was implemented as a web prototype in AngularJS and evaluated with 19 participants. Results from the user study suggest that despite facing a few challenges in accurately identifying Stevens’ data types, participants managed to successfully create web maps and correctly answer spatial questions. The prototype and insights gathered from the user study are relevant to making cartographic products more accessible to a broader population, and open geographic data more usable in the context of an open government. © 2019, © 2019 Cartography and Geographic Information Society.adaptive maps; Geographic visualization; human computation; open government; thematic cartography; visual variables; web mapsMaps; Population statistics; Visualization; Geographic visualization; Human computation; open government; Thematic cartography; Visual variables; Open Data; adaptive management; automation; cartography; data set; government; visualization; World Wide Web64233, H2020-MSCA-ITN-2014; European Commission, ECThis work was supported by the European Commission through the GEO-C project (http://www.geo-c.eu/); H2020 Marie Sk?odowska-Curie Actions [H2020-MSCA-ITN-2014, Grant Agreement Number: 64233]. We thank the editor and the anonymous reviewers for their very constructive feedback.Degbelo, A.; Institute for Geoinformatics, Germany; email: auriol.degbelo@uni-osnabrueck.deTaylor and Francis Inc.15230406CGSCFEnglishCartogr. Geogr. Inf. SciArticleFinalScopus2-s2.0-85074813363
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Elmassry M.M., Mudaliar N.S., Colmer-Hamood J.A., San Francisco M.J., Griswold J.A., Dissanaike S., Hamood A.N.57209335581;57208205532;6506923357;6603754632;7006687979;8540945700;7004207829;New markers for sepsis caused by Pseudomonas aeruginosa during burn infection2020Metabolomics16340710.1007/s11306-020-01658-2https://www.scopus.com/inward/record.uri?eid=2-s2.0-85081730811&doi=10.1007%2fs11306-020-01658-2&partnerID=40&md5=157777f69eeb8853c634492135dac6b0Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States; Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, United States; Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street STOP 6591, Lubbock, TX 79430-6591, United States; Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, TX, United States; Honors College, Texas Tech University, Lubbock, TX, United States; Caris Life Sciences, Phoenix, AZ, United StatesElmassry, M.M., Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States; Mudaliar, N.S., Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, United States, Caris Life Sciences, Phoenix, AZ, United States; Colmer-Hamood, J.A., Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street STOP 6591, Lubbock, TX 79430-6591, United States, Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, TX, United States; San Francisco, M.J., Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States, Honors College, Texas Tech University, Lubbock, TX, United States; Griswold, J.A., Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, United States; Dissanaike, S., Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, United States; Hamood, A.N., Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, United States, Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street STOP 6591, Lubbock, TX 79430-6591, United StatesIntroduction: Sepsis is a leading cause of mortality in burn patients. One of the major causes of sepsis in burn patients is Pseudomonas aeruginosa. We hypothesized that during dissemination from infected burn wounds and subsequent sepsis, P. aeruginosa affects the metabolome of the blood resulting in changes to specific metabolites that would serve as biomarkers for early diagnosis of sepsis caused by P. aeruginosa. Objectives: To identify specific biomarkers in the blood after sepsis caused by P. aeruginosa infection of burns. Methods: Gas chromatography with time-of-flight mass spectrometry was used to compare the serum metabolome of mice that were thermally injured and infected with P. aeruginosa (B–I) to that of mice that were neither injured nor infected, mice that were injured but not infected, and mice that were infected but not injured. Results: Serum levels of 19 metabolites were significantly increased in the B–I group compared to controls while levels of eight metabolites were significantly decreased. Thymidine, thymine, uridine, and uracil (related to pyrimidine metabolism), malate and succinate (a possible sign of imbalance in the tricarboxylic acid cycle), 5-oxoproline (related to glutamine and glutathione metabolism), and trans-4-hydroxyproline (a major component of the protein collagen) were increased. Products of amino acid metabolism were significantly decreased in the B–I group, including methionine, tyrosine, indole-3-acetate, and indole-3-propionate. Conclusion: In all, 26 metabolites were identified, including a unique combination of five metabolites (trans-4-hydroxyproline, 5-oxoproline, glycerol-3-galactoside, indole-3-acetate, and indole-3-propionate) that could serve as a set of biomarkers for early diagnosis of sepsis caused by P. aeruginosa in burn patients. © 2020, Springer Science+Business Media, LLC, part of Springer Nature.Burn; Gas chromatography with time-of-flight mass spectrometry; Infection; Metabolomics; Pseudomonas aeruginosa; Sepsis3 phosphoglycerate; 3,6 anhydro dextro galactose; 4 methylbenzenesulfonamide; alpha tocopherol; biological marker; cholesterol; conduritol beta epoxide; creatinine; fructose 6 phosphate; glucose; glucose 6 phosphate; glycolic acid; hexuronic acid; hippuric acid; hydroxyproline; indoleacetic acid; indolepropionic acid; lactic acid; malic acid; mannose; methionine; nonadecanoic acid; oxalic acid; pyroglutamic acid; succinic acid; thymidine; thymine; tyrosine; unclassified drug; uracil; uridine; biological marker; abnormal value; adult; amino acid metabolism; animal experiment; animal model; animal tissue; Article; blood level; burn infection; burn patient; comparative study; controlled study; early diagnosis; female; gas chromatography; metabolic fingerprinting; metabolome; metabolomics; mouse; nonhuman; Pseudomonas aeruginosa; Pseudomonas infection; sepsis; thermal injury; time of flight mass spectrometry; animal; blood; burn; disease model; mass spectrometry; metabolism; microbiology; sepsis; wound infection; Animals; Biomarkers; Burns; Chromatography, Gas; Disease Models, Animal; Female; Mass Spectrometry; Metabolomics; Mice; Pseudomonas aeruginosa; Sepsis; Wound Infectionalpha tocopherol, 1406-18-4, 1406-70-8, 52225-20-4, 58-95-7, 59-02-9; cholesterol, 57-88-5; creatinine, 19230-81-0, 60-27-5; fructose 6 phosphate, 56-83-7, 643-13-0; glucose, 50-99-7, 84778-64-3; glucose 6 phosphate, 56-73-5; glycolic acid, 79-14-1; hippuric acid, 495-69-2, 532-94-5; hydroxyproline, 51-35-4, 6912-67-0; indoleacetic acid, 32536-43-9, 87-51-4; indolepropionic acid, 830-96-6; lactic acid, 113-21-3, 50-21-5; malic acid, 149-61-1, 6915-15-7; mannose, 31103-86-3, 3458-28-4; methionine, 59-51-8, 63-68-3, 7005-18-7; oxalic acid, 144-62-7; pyroglutamic acid, 16891-48-8, 28874-51-3, 98-79-3; succinic acid, 110-15-6; thymidine, 50-89-5; thymine, 65-71-4; tyrosine, 16870-43-2, 55520-40-6, 60-18-4; uracil, 66-22-8; uridine, 58-96-8; BiomarkersTexas Tech University, TTUThis study was funded in part by the Burn Center of Research Excellence (BCoRE) in the Department of Surgery at TTUHSC, Lubbock, TX, USA. MME was funded by a grant-in-aid from the Texas Tech University Association of Biologists and a summer dissertation research award, and a graduate student research support award from the Texas Tech University Graduate School.Hamood, A.N.; Department of Surgery, United States; email: abdul.hamood@ttuhsc.eduSpringer1573388232170472EnglishMetabolomicsArticleFinalAll Open Access, Bronze, GreenScopus2-s2.0-85081730811
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Lauerburg R.A.M., Diekmann R., Blanz B., Gee K., Held H., Kannen A., Möllmann C., Probst W.N., Rambo H., Cormier R., Stelzenmüller V.55968733400;16635524800;57000179100;26643898100;7005187754;34972851500;6603955209;36835011700;56572731200;7005448876;6504770762;Socio-ecological vulnerability to tipping points: A review of empirical approaches and their use for marine management2020Science of the Total Environment7051358381510.1016/j.scitotenv.2019.135838https://www.scopus.com/inward/record.uri?eid=2-s2.0-85076420100&doi=10.1016%2fj.scitotenv.2019.135838&partnerID=40&md5=51164762b70dd981552ec780b61f730fThünen-Institute of Sea Fisheries, Herwigstraße 31, Bremerhaven, 27572, Germany; Thünen-Institute of Fisheries Ecology, Herwigstraße 31, Bremerhaven, 27572, Germany; Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research, Max-Planck-Straße 1, Geesthacht, 21502, Germany; University of Hamburg, Research Unit Sustainability and Global Change, Grindelberg 5, Hamburg, 20144, Germany; University of Hamburg, Institute for Marine Ecosystem and Fisheries Science, Olbersweg 24, Hamburg, 22767, GermanyLauerburg, R.A.M., Thünen-Institute of Sea Fisheries, Herwigstraße 31, Bremerhaven, 27572, Germany, University of Hamburg, Institute for Marine Ecosystem and Fisheries Science, Olbersweg 24, Hamburg, 22767, Germany; Diekmann, R., Thünen-Institute of Fisheries Ecology, Herwigstraße 31, Bremerhaven, 27572, Germany; Blanz, B., University of Hamburg, Research Unit Sustainability and Global Change, Grindelberg 5, Hamburg, 20144, Germany; Gee, K., Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research, Max-Planck-Straße 1, Geesthacht, 21502, Germany; Held, H., University of Hamburg, Research Unit Sustainability and Global Change, Grindelberg 5, Hamburg, 20144, Germany; Kannen, A., Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research, Max-Planck-Straße 1, Geesthacht, 21502, Germany; Möllmann, C., University of Hamburg, Institute for Marine Ecosystem and Fisheries Science, Olbersweg 24, Hamburg, 22767, Germany; Probst, W.N., Thünen-Institute of Sea Fisheries, Herwigstraße 31, Bremerhaven, 27572, Germany; Rambo, H., Thünen-Institute of Sea Fisheries, Herwigstraße 31, Bremerhaven, 27572, Germany; Cormier, R., Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research, Max-Planck-Straße 1, Geesthacht, 21502, Germany; Stelzenmüller, V., Thünen-Institute of Sea Fisheries, Herwigstraße 31, Bremerhaven, 27572, GermanySustainability in the provision of ecosystem services requires understanding of the vulnerability of social-ecological systems (SES) to tipping points (TPs). Assessing SES vulnerability to abrupt ecosystem state changes remains challenging, however, because frameworks do not operationally link ecological, socio-economic and cultural elements of the SES. We conducted a targeted literature review on empirical assessments of SES and TPs in the marine realm and their use in ecosystem-based management. Our results revealed a plurality of terminologies, definitions and concepts that hampers practical operationalisation of these concepts. Furthermore, we found a striking lack of socio-cultural aspects in SES vulnerability assessments, possibly because of a lack of involvement of stakeholders and interest groups. We propose guiding principles for assessing vulnerability to TPs that build on participative approaches and prioritise the connectivity between SES components by accounting for component linkages, cascading effects and feedback processes. © 2019 Elsevier B.V.Ecosystem-based management; Socio-ecological systems; Stakeholders; Tipping points; Transdisciplinary research; Vulnerability assessmentsEnvironmental engineering; Pollution; Ecosystem-based management; Socio-ecological systems; Stakeholders; Tipping point; Vulnerability assessments; Ecosystems; ecosystem management; ecosystem service; empirical analysis; marine environment; research; stakeholder; sustainability; vulnerability; ecosystem; human; interdisciplinary research; nomenclature; reviewBundesministerium für Bildung und Forschung, BMBF: 01LC1720AThis article is based on work carried out under the SeaUseTip project (Spatial and temporal analysis of tipping points of the socio-ecological system of the North Sea (German EEZ) under different management scenarios) funded by the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF) (grant number: 01LC1720A ) under the Tipping Points, Dynamics and Interactions Between Social and Ecological Systems (BioTip) call. We thank three anonymous reviewers for their helpful feedback on the manuscript.This article is based on work carried out under the SeaUseTip project (Spatial and temporal analysis of tipping points of the socio-ecological system of the North Sea (German EEZ) under different management scenarios) funded by the German Federal Ministry of Education and Research (Bundesministerium f?r Bildung und Forschung, BMBF) (grant number: 01LC1720A) under the Tipping Points, Dynamics and Interactions Between Social and Ecological Systems (BioTip) call. We thank three anonymous reviewers for their helpful feedback on the manuscript.Lauerburg, R.A.M.; University of Hamburg, Olbersweg 24, Germany; email: Rebecca.lauerburg@uni-hamburg.deElsevier B.V.489697STEVA31855803EnglishSci. Total Environ.ReviewFinalScopus2-s2.0-85076420100
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Rodriguez Espinosa P., Chen Y.-C., Sun C.-A., You S.-L., Lin J.-T., Chen K.-H., Hsing A.W., Heaney C.A.57204069512;57211191540;35275967000;7201516961;37054022700;15844994000;57216192346;7004288559;Exploring health and well-being in Taiwan: What we can learn from individuals' narratives2020BMC Public Health201159210.1186/s12889-020-8201-3https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078886952&doi=10.1186%2fs12889-020-8201-3&partnerID=40&md5=ca258f5d822c79ef6cbc31a66f37b751Stanford Prevention Research Center, Stanford University School of Medicine, 3300 Hillview Ave (Mail code: 5537), Palo Alto, CA 94304, United States; School of Medicine, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan; Big Data Research Center, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan; Department of Public Health, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan; Department of Clinical Psychology, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan; Stanford Cancer Institute, Stanford University, School of Medicine, CJ Huang Building, 780 Welch Road, Palo Alto, CA 94305, United States; Department of Epidemiology, Stanford University, Palo Alto, CA, United States; Department of Psychology, Stanford University, 450 Serra Mall, Palo Alto, CA 94305, United StatesRodriguez Espinosa, P., Stanford Prevention Research Center, Stanford University School of Medicine, 3300 Hillview Ave (Mail code: 5537), Palo Alto, CA 94304, United States; Chen, Y.-C., School of Medicine, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan, Big Data Research Center, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan; Sun, C.-A., Big Data Research Center, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan, Department of Public Health, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan; You, S.-L., School of Medicine, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan; Lin, J.-T., School of Medicine, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan; Chen, K.-H., Department of Clinical Psychology, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang District, New Taipei City, Taiwan; Hsing, A.W., Stanford Prevention Research Center, Stanford University School of Medicine, 3300 Hillview Ave (Mail code: 5537), Palo Alto, CA 94304, United States, Stanford Cancer Institute, Stanford University, School of Medicine, CJ Huang Building, 780 Welch Road, Palo Alto, CA 94305, United States, Department of Epidemiology, Stanford University, Palo Alto, CA, United States; Heaney, C.A., Stanford Prevention Research Center, Stanford University School of Medicine, 3300 Hillview Ave (Mail code: 5537), Palo Alto, CA 94304, United States, Department of Psychology, Stanford University, 450 Serra Mall, Palo Alto, CA 94305, United StatesBackground: Our aim was to explore the concepts of health and well-being from the point of view of the people experiencing them. Most of the efforts to understand these concepts have focused on disease prevention and treatment. Less is known about how individuals achieve health and well-being, and their roles in the pursuit of a good life. We hoped to identify important components of these concepts that may provide new targets and messages to strengthen existing public health programs. An improved understanding of health and well-being - or what it means to be well - can guide interventions that help people lead healthier, more fulfilling lives. Methods: Using a grounded qualitative approach drawing from narrative inquiry, we interviewed 24 Taiwanese adults. Thematic inductive coding was employed to explore the nature of health and well-being. Results: Eight constituent domains emerged regarding well-being and health. While the same domains were found for both constructs, important frequency differences were found when participants discussed health versus well-being. Physical health and lifestyle behaviors emerged as key domains for health. Disease-related comments were the most frequently mentioned sub-category within the physical health domain, along with health care use and aging-related changes. For well-being, family and finances emerged as key domains. Family appears to be a cornerstone element of well-being in this sample, with participants often describing their personal well-being as closely tied to - and often indistinguishable from - their family. Other domains included work-life, sense of self, resilience, and religion/spirituality. Conclusions: Health and well-being are complex and multifaceted constructs, with participants discussing their constituent domains in a very interconnected manner. Programs and policies intended to promote health and well-being may benefit from considering these domains as culturally-appropriate leverage points to bring about change. Additionally, while the domains identified in this study are person-centered (i.e., reflecting the personal experiences of participants), the stories that participants offered provided insights into how well-being and health are influenced by structural, societal and cultural factors. Our findings also offer an opportunity for future refinement and rethinking of existing measurement tools surrounding these constructs. © 2020 The Author(s).(3-10 for indexing purposes): Well-being; Family; Health; Health behaviors; Qualitative inquiry; Taiwanadult; aged; female; health status; human; male; mental health; middle aged; Taiwan; verbal communication; Adult; Aged; Female; Health Status; Humans; Male; Mental Health; Middle Aged; Narration; TaiwanRodriguez Espinosa, P.; Stanford Prevention Research Center, 3300 Hillview Ave (Mail code: 5537), United States; email: prespinosa@stanford.eduBioMed Central Ltd.1471245832013898EnglishBMC Public HealthArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85078886952
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Malaterre C., Pulizzotto D., Lareau F.26037162500;57197819957;57212515294;Revisiting three decades of Biology and Philosophy: a computational topic-modeling perspective2020Biology and Philosophy3515210.1007/s10539-019-9729-4https://www.scopus.com/inward/record.uri?eid=2-s2.0-85076915332&doi=10.1007%2fs10539-019-9729-4&partnerID=40&md5=98f72aa665982587b9bd6c0b2bbab4ebDépartement de philosophie, Université du Québec à Montréal (UQAM), 455 Boulevard René-Lévesque Est, Montréal, QC H3C 3P8, Canada; Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), 1205 rue Saint-Denis, Montréal, QC H3C 3P8, Canada; Département d’études littéraires, Université du Québec à Montréal (UQAM), 405 rue Sainte-Catherine Est, Montréal, QC H3C 3P8, Canada; Département d’informatique, Université du Québec à Montréal (UQAM), 201, av. Président-Kennedy, Montréal, QC H3C 3P8, CanadaMalaterre, C., Département de philosophie, Université du Québec à Montréal (UQAM), 455 Boulevard René-Lévesque Est, Montréal, QC H3C 3P8, Canada, Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), 1205 rue Saint-Denis, Montréal, QC H3C 3P8, Canada; Pulizzotto, D., Département d’études littéraires, Université du Québec à Montréal (UQAM), 405 rue Sainte-Catherine Est, Montréal, QC H3C 3P8, Canada; Lareau, F., Département d’informatique, Université du Québec à Montréal (UQAM), 201, av. Président-Kennedy, Montréal, QC H3C 3P8, CanadaThough only established as a discipline since the 1970s, philosophy of biology has already triggered investigations about its own history (e.g., Grene and Depew in The philosophy of biology: an episodic history, Cambridge University Press, Cambridge, 2004. https://doi.org/10.1017/CBO9780511819018; Hull, in: Ruse (ed) The Oxford handbook of philosophy of biology, Oxford University Press, New York, pp 11–33, 2008). When it comes to assessing the road since travelled—the research questions that have been pursued—manuals and ontologies also offer specific viewpoints, highlighting dedicated domains of inquiry and select work. In this article, we propose to approach the history of the philosophy of biology with a complementary data-driven perspective that makes use of statistical algorithms applied to the complete full-text corpus of one major journal of the field—Biology and Philosophy—from its launch in 1986 up until 2017. By running text-mining and topic-modeling algorithms, we identified 67 key research topics that span across these 32 years. We also investigated the evolution of these topics over time and their fluctuating significance in the journal articles. Our results concur with known episodes or traits of the discipline—for instance, the significance of evolution-related topics or the decrease of articles with a marked historical dimension—but also highlight a diversity of topics that is much richer than what is usually acknowledged. © 2019, Springer Nature B.V.Biology and Philosophy journal; Digital history; Digital philosophy; History of philosophy of science; Text mining; Topic modelingalgorithm; biology; data mining; historical perspective; philosophySocial Sciences and Humanities Research Council of Canada, SSHRC: 435-2014-0943; Fonds de Recherche du Québec - Santé, FRQS: 276470; Canada Foundation for Innovation, CFI; Canada Research Chairs: CRC-950-230795; Canada Foundation for Innovation: 34555The authors are grateful to Springer for kindly providing access to Biology and Philosophy. The authors also thank Michael Ruse, Phillip Honenberger and Charles Pence for valuable insights on the history of the philosophy of biology as well as Jean-François Chartier for text-mining expertise. Funding from Canada Foundation for Innovation (Grant 34555), Canada Social Sciences and Humanities Research Council (Grant 435-2014-0943) and Canada Research Chair (CRC-950-230795) is gratefully acknowledged. FL acknowledges support from the Fonds de recherche du Québec - Société et culture (Grant 276470)The authors are grateful to Springer for kindly providing access to Biology and Philosophy. The authors also thank Michael Ruse, Phillip Honenberger and Charles Pence for valuable insights on the history of the philosophy of biology as well as Jean-Fran?ois Chartier for text-mining expertise. Funding from Canada Foundation for Innovation (Grant 34555), Canada Social Sciences and Humanities Research Council (Grant 435-2014-0943) and Canada Research Chair (CRC-950-230795) is gratefully acknowledged.?FL acknowledges support from the Fonds de recherche du Qu?bec - Soci?t? et culture (Grant 276470)Malaterre, C.; Centre interuniversitaire de recherche sur la science et la technologie (CIRST), 1205 rue Saint-Denis, Canada; email: malaterre.christophe@uqam.caSpringer1693867BIOPEEnglishBiol. Philos.ArticleFinalScopus2-s2.0-85076915332
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Llopis J.C., Diebold C.L., Schneider F., Harimalala P.C., Patrick L., Messerli P., Zaehringer J.G.57201384958;57211374411;26635946800;57209414570;57214750884;21743398900;56784239400;Capabilities Under Telecoupling: Human Well-Being Between Cash Crops and Protected Areas in North-Eastern Madagascar2020Frontiers in Sustainable Food Systems3126910.3389/fsufs.2019.00126https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079043534&doi=10.3389%2ffsufs.2019.00126&partnerID=40&md5=ad02aefa02f4fe7db97c448594bb11c8Centre for Development and Environment, University of Bern, Bern, Switzerland; Institute of Geography, University of Bern, Bern, Switzerland; Ecole Supérieure des Sciences Agronomiques, Département des Eaux et Forêts, Université d'Antananarivo, Antananarivo, Madagascar; Ecole Doctorale de Gestion des Ressources Naturelles et Développement, Université d'Antananarivo, Antananarivo, MadagascarLlopis, J.C., Centre for Development and Environment, University of Bern, Bern, Switzerland, Institute of Geography, University of Bern, Bern, Switzerland; Diebold, C.L., Centre for Development and Environment, University of Bern, Bern, Switzerland; Schneider, F., Centre for Development and Environment, University of Bern, Bern, Switzerland; Harimalala, P.C., Ecole Supérieure des Sciences Agronomiques, Département des Eaux et Forêts, Université d'Antananarivo, Antananarivo, Madagascar; Patrick, L., Ecole Doctorale de Gestion des Ressources Naturelles et Développement, Université d'Antananarivo, Antananarivo, Madagascar; Messerli, P., Centre for Development and Environment, University of Bern, Bern, Switzerland, Institute of Geography, University of Bern, Bern, Switzerland; Zaehringer, J.G., Centre for Development and Environment, University of Bern, Bern, SwitzerlandGlobal change processes are increasing their pace and reach, leading to telecoupled situations, where distant factors come to outpace local determinants of land use change. Often, these dynamics drive agricultural intensification processes, with as yet unclear implications for the well-being of human populations living in the areas affected. This study explores how two key telecoupling dynamics affect local well-being in the biodiversity hotspot of Madagascar. It focuses on forest frontier landscapes, which are undergoing processes of agricultural intensification as a consequence of distant factors. Concretely, we look at how the recent establishment of two, largely externally funded, terrestrial protected areas, Masoala National Park and Makira Natural Park, and the ongoing price boom for two export cash crops, vanilla and clove, have influenced the well-being of local populations in the country's north-east. We present data from eight focus group discussions conducted in four villages located on the periphery of the two protected areas. Drawing on the “capabilities approach,” we identify the key components of the local understanding of well-being, lay out the interconnections between these components, and explore how the two telecoupling processes affect well-being dynamics. Our findings reveal that well-being components present bundle characteristics, where increases or decreases in one component lead to parallel increases, or decreases in a set of them. We further ascertain that telecoupling processes might lead to trade-offs between well-being components. These findings highlight the need for a holistic understanding of human well-being when planning protected areas, and when designing governance mechanisms to steer local landscapes under intense cash crop price fluctuations toward sustainable outcomes. © Copyright © 2020 Llopis, Diebold, Schneider, Harimalala, Patrick, Messerli and Zaehringer.agricultural commodities trade; agricultural intensification; capabilities approach; conservation; human well-being; shifting cultivationUnited States Agency for International Development, USAID; Direktion für Entwicklung und Zusammenarbeit, DEZA: 400440 152167; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, SNFThis research was supported by the Swiss Programme for Research on Global Issues for Development (r4d programme) supported by the Swiss National Science Foundation (SNSF) and the Swiss Agency for Development and Cooperation (SDC), grant number 400440 152167.The authors warmly thank all participants in this study, and the local authorities for the help provided. We are grateful to research assistant Venat Raelison for his help in conducting the focus group discussions, and to the School of Agronomic Sciences, Department of Water and Forests, University of Antananarivo, for their logistic support. We thank Tina Hirschbuehl for editing the language of the manuscript. We also appreciate the two reviewers' comments, which helped to improve the quality of the manuscript substantially. Funding. This research was supported by the Swiss Programme for Research on Global Issues for Development (r4d programme) supported by the Swiss National Science Foundation (SNSF) and the Swiss Agency for Development and Cooperation (SDC), grant number 400440 152167.The Makira Forest Project was initiated in the early 2000s by WCS and the Ministry of Water and Forest, supported by USAID, to develop carbon financing options for sustainable funding of conservation interventions in the area (Meyers, 2001). Makira received temporary protection status in 2005 and was eventually granted definitive protection as a Natural Park (IUCN category II) managed by WCS in 2012, with the first international sales of its REDD+ emission reduction credits taking place in 2013 (WCS, 2015). In 2014, the management rights of the forests in the buffer zone of Makira PA that fell within Beanana’s village boundaries were transferred to local communities there.Llopis, J.C.; Centre for Development and Environment, Switzerland; email: jorge.llopis@cde.unibe.chFrontiers Media S.A.2571581XEnglishFront. Sustain. food Syst.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85079043534
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Al-Ahmadi H.H.57220061705;Hospital-scale chest X-ray database visualization using RAWGraph technique2020Computer Science Journal of Moldova282123139https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108510261&partnerID=40&md5=94ed7e6f2a055ae153b92b15472fd6f9Department of Software Engineering, College of Computer Science and Engineering, University of Jeddah, Saudi ArabiaAl-Ahmadi, H.H., Department of Software Engineering, College of Computer Science and Engineering, University of Jeddah, Saudi ArabiaFor identification and screening of several lung diseases, the chest X-ray is just one of the very most often obtainable radiological tests. Most modern-day hospitals’ Photo Archiving and Communication Systems (PACS) collect thousands of X-ray imaging scientific studies, followed by radiological stories that are collected and saved. In this paper, we employ the graph strategy to collect and store the dataset of those X-ray pictures. The RAWGraph can be an open source web tool for its production of inactive information visualizations, which can be changed to become further altered. Initially designed for picture artists to extend a succession of responsibilities, maybe not available in combination with different applications, it has developed into a stage that offers easy tactics to map information measurements on visual factors. That poses a more chart-based way of information visualization; every visual version will be an unaffiliated module displaying distinct visual factors that may be utilized to map information measurements. Thus, end-users may develop complex information visualizations. We assess the correlation and relationship among different aspects of this data set. We now provide a chest X-ray database, particularly”ChestX-ray8”, that contains 108,948 frontal perspective X-rays of 32,717 specific and distinct patients, with all containing a written text created from eight disorder image tags (where just about every image could have multi-labels), in the related reports utilizing standard language processing. In this paper, we use diverse methods for visualization, which can be Circle Packing, Bee Swarm Plot, Convex Hull, Boxplot, and Circular Dendrogram. We image the dataset more accurately and examine the terms of these various arrangements of features precisely. ©2021 by CSJM.Data visualization; Graphs; Visual interface; Visualization tools; X-raysAl-Ahmadi, H.H.; Department of Software Engineering, Saudi Arabia; email: hhalahamade@uj.edu.saInstitute of Mathematics and Computer Science15614042EnglishComput. Sci. J. Mold.ArticleFinalScopus2-s2.0-85108510261
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Mann A.E., Fellows Yates J.A., Fagernäs Z., Austin R.M., Nelson E.A., Hofman C.A.56957707700;57195555643;57216493111;57205611894;57202789769;55086645000;Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus2020Quaternary International410.1016/j.quaint.2020.11.019https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096930788&doi=10.1016%2fj.quaint.2020.11.019&partnerID=40&md5=a913d9761ee9ce5dc5ed191569473106Department of Biological Sciences, Clemson University, Clemson, SC, United States; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany; Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig Maximilian University, Munich, Germany; Department of Anthropology, Smithsonian National Museum of Natural History, Washington, DC, United States; Department of Anthropology, University of Oklahoma, Norman, OK, United States; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, United States; Department of Anthropology, University of Texas at Arlington, Arlington, TX, United States; Institut für Naturwissenschaftliche Archäologie, Eberhard Karls Universität Tübingen, Tübingen, 72074, Germany; Natural History Museum Oslo, University of Oslo, Oslo, NorwayMann, A.E., Department of Biological Sciences, Clemson University, Clemson, SC, United States; Fellows Yates, J.A., Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany, Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig Maximilian University, Munich, Germany; Fagernäs, Z., Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany; Austin, R.M., Department of Anthropology, Smithsonian National Museum of Natural History, Washington, DC, United States, Department of Anthropology, University of Oklahoma, Norman, OK, United States, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, United States, Natural History Museum Oslo, University of Oslo, Oslo, Norway; Nelson, E.A., Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany, Department of Anthropology, University of Texas at Arlington, Arlington, TX, United States, Institut für Naturwissenschaftliche Archäologie, Eberhard Karls Universität Tübingen, Tübingen, 72074, Germany; Hofman, C.A., Department of Anthropology, University of Oklahoma, Norman, OK, United States, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, United StatesDental calculus and other preserved microbiome substrates are an attractive target for dietary reconstruction in past populations through a variety of physical, chemical, and molecular means. Recently, studies have attempted to reconstruct diet from archaeological dental calculus using archaeogenetic techniques. While dental calculus may provide a relatively stable environment for DNA preservation, the detection of plants and animals possibly consumed by an individual through DNA analysis is primarily hindered by microbial richness and incomplete reference databases. Moreover, high genomic similarity within eukaryotic groups - such as mammals - can obfuscate precise taxonomic identification. In the current study we demonstrate the challenges associated with accurate taxonomic identification and authentication of dietary taxa in ancient DNA data using both synthetic and ancient dental calculus datasets. We highlight common errors and sources of contamination across ancient DNA datasets, provide recommendations for dietary DNA validation, and call for caution in the interpretation of diet from dental calculus and other archaeological microbiome substrates. © 2020Ancient DNA; Dental calculus; Diet; Metagenomics678901; Horizon 2020 Framework Programme, H2020; European Research Council, ERC; Max-Planck-Institut für Menschheitsgeschichte, MPI-SHHJ.A.F.Y. was partially funded by the European Research Council (ERC) under the European Union's Horizon 2020 research innovation programme (ERC-2015-StG 678901-FoodTransforms to Philipp W. Stockhammer, Ludwig Maximilian University Munich, Germany). Z.F. was supported by the Werner Siemens Stiftung through Dr. Christina Warinner. This research was supported in part through computational resources provided by the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History (J.A.F.Y). We thank Stephanie Schnorr for comments on an early version of this manuscript and two anonymous reviewers who improved this work.J.A.F.Y. was partially funded by the European Research Council (ERC) under the European Union's Horizon 2020 research innovation programme ( ERC-2015-StG 678901 -FoodTransforms to Philipp W. Stockhammer, Ludwig Maximilian University Munich, Germany). Z.F. was supported by the Werner Siemens Stiftung through Dr. Christina Warinner. This research was supported in part through computational resources provided by the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History (J.A.F.Y). We thank Stephanie Schnorr for comments on an early version of this manuscript and two anonymous reviewers who improved this work.Mann, A.E.; Clemson University Department of Biological Sciences, 111 Jordan Hall, United States; email: amann3@g.clemson.eduElsevier Ltd10406182EnglishQuat. Int.ArticleArticle in PressAll Open Access, Hybrid Gold, GreenScopus2-s2.0-85096930788
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González-Alcaide G., González-Teruel A.16066904100;9635890400;Supervision of doctoral dissertations as a reflection of library and information science in spain: Actors and topics [Dirección de tesis doctorales como reflejo de la biblioteconomía y documentación académica española: Actores y temas]2020Profesional de la Informacion294e290441118210.3145/epi.2020.jul.41https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090227459&doi=10.3145%2fepi.2020.jul.41&partnerID=40&md5=97d2324acd3514655e7c2d155c02f0e7Universitat de València, Departamento de Historia de la Ciencia y Documentación, Avda. Blasco Ibáñez, 15, Valencia, 46010, SpainGonzález-Alcaide, G., Universitat de València, Departamento de Historia de la Ciencia y Documentación, Avda. Blasco Ibáñez, 15, Valencia, 46010, Spain; González-Teruel, A., Universitat de València, Departamento de Historia de la Ciencia y Documentación, Avda. Blasco Ibáñez, 15, Valencia, 46010, SpainDoctoral dissertations enable the transfer of research skills and capacities to future generations and the consolidation of lines of research in a given area of knowledge. The field of Library and Information Science in public universities in Spain is characterized by the supervision of doctoral theses by academics in the area. We identified active professors during the 2019–2020 academic year, their date of appointment as civil servants within the public university system, the dissertations that they supervised, and their participation in papers published in scientific journals. The analysis included 644 theses. About a quarter (23%) of university faculty have never supervised a doctoral thesis, and most faculty members and tenured professors (60%) show a lower than average rate of adviserships per year since their academic appoint-ment. There is a high concentration of PhD advisers in just a few institutions and academics (8% of university professors have supervised 42% of the dissertations), with an important gender imbalance: women supervised an average of 1.8 dissertations, compared with 2.6 for men. Information units and services, study metrics and scientific publications, and information sources are the topics of 47% of the dissertations. Many of the professors with 10 or more adviserships (n/N = 12/18) lack a subject area specialization, and their role in PhD supervision was not related to their participation in research activities oriented toward publishing in scientific journals. Our results suggest that considering supervision of doctoral theses as an important academic merit could contribute to a further concentration of power and social capital among a small group of advisers. This phenomenon could reduce the plurality of topics addressed and favor suboptimal adviserships. The imbalances described emerge as another threat, exacerbating the epistemological crisis in the discipli-ne and in the university studies in this area of knowledge. © 2020, El Profesional de la Informacion. All rights reserved.Academic merit; Concentration of power; Doctoral dissertations; Gender gap; Gender inequality; Library and Information Science; Research; Research topics; Scientific production; Social capital; Spain; Subject specialization; University profes-sorsGonzález-Alcaide, G.; Universitat de València, Avda. Blasco Ibáñez, 15, Spain; email: gregorio.gonzalez@uv.esEl Profesional de la Informacion13866710SpanishProf. Inf.ArticleFinalAll Open Access, GreenScopus2-s2.0-85090227459
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Kuhail M.A.A., Lauesen S.37055610700;6602878279;Uvis: A Formula-Based End-User Tool for Data Visualization2020IEEE Access89117123110264110278210.1109/ACCESS.2020.3002591https://www.scopus.com/inward/record.uri?eid=2-s2.0-85087402232&doi=10.1109%2fACCESS.2020.3002591&partnerID=40&md5=abff268cd09440ac1edd93affcd90d81College of Technological Innovation, Zayed University, Abu Dhabi, United Arab Emirates; Computer Science Department, IT University of Copenhagen, Copenhagen, DenmarkKuhail, M.A.A., College of Technological Innovation, Zayed University, Abu Dhabi, United Arab Emirates; Lauesen, S., Computer Science Department, IT University of Copenhagen, Copenhagen, DenmarkExisting approaches to data visualization are one of these two: accessible to end-user developers but limited in customizability, or inaccessible and expressive. For instance, commercial charting tools are easy to use, but support only predefined visualizations, while programmatic visualization tools support custom visualizations, but require advanced programming skills. We show that it is possible to combine the learnability of charting tools and the expressiveness of visualization tools. Uvis is an interactive visualization and user interface design tool that targets end-user developers with skills comparable to spreadsheet formulas. With Uvis, designers drag and drop visual objects, set visual properties to formulas, and see the result immediately. The formulas are declarative and similar to spreadsheet formulas. The formulas compute the property values and can refer to data from database, visual objects, and end-user input. To substantiate our claim, we compared Uvis with popular visualization tools. Further, we conducted usability studies that test the ability of designers to customize visualizations with our approach. Our results show that end-user developers can learn the basics of Uvis relatively fast. © 2013 IEEE.End-user development; formulas; information visualization; visualization toolsSpreadsheets; User interfaces; Visualization; Customizability; End-user developers; Interactive visualizations; Programming skills; Usability studies; User interface designs; Visual properties; Visualization tools; Data visualizationZayed University, ZUThis work was supported in part by the Danish Research Council’s Nabiit Programme, and in part by the Zayed University, United Arab Emirates.Kuhail, M.A.A.; College of Technological Innovation, United Arab Emirates; email: mohammad.kuhail@zu.ac.aeInstitute of Electrical and Electronics Engineers Inc.21693536EnglishIEEE AccessArticleFinalAll Open Access, GoldScopus2-s2.0-85087402232
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Cidrás D.57203995064;Eucalypt-free-zone' municipalities: Analysis of the local political actors in Galicia, Spain [Municipios "libres de eucaliptos": Análisis de los actores políticos locales en Galicia]2020Boletin de la Asociacion de Geografos Espanoles842785210.21138/bage.2785https://www.scopus.com/inward/record.uri?eid=2-s2.0-85082812154&doi=10.21138%2fbage.2785&partnerID=40&md5=c44d436781373175929ae80dadbfcb44Departamento de Xeografía, Universidade de Santiago de Compostela, SpainCidrás, D., Departamento de Xeografía, Universidade de Santiago de Compostela, SpainThe controversy around the eucalypt plantations transcends in Galicia its forest policy and encompasses today the less-studied social and political contexts. Whilst none of its species have been catalogued by the Spanish Government as invasive species, many local governments are assembling together to influence and reverse the situation. Taking this into account, this work studies the values, attitudes and political behaviors inherent in the fight against the expansion of eucalypts. Specifically, we examine at the local scale and through the cognitive hierarchy theory and discourse analysis, 20 cases of local governments that debate its own "Eucalypt-Free-Zone" declaration. Our analysis reveals that the conventional left-right spectrum is reproduced within the parties along their valuation of eucalypt plantations. Namely, those arguments based on the economic and social values adopt greater importance compared to the ecological and environmental ones. This hierarchy generates political isolation and motivates the absence of consensus. Therefore, we conclude that only an eventual decrease in wood price would motivate a relevant turn of political attitudes towards its management. Furthermore, the improvised inclusion of political debates perpetuates or even emphasizes the divergences of sectoral interests in the management of eucalypts. © 2020 Asociacion de Geografos Espanoles. All rights reserved.Cognitive hierarchy theory; Discourse analysis; Eucalyptus, forest policy; Invasive speciesdicotyledon; management practice; plantation; valuation; Galicia [Spain]Cidrás, D.; Departamento de Xeografía, Spain; email: diego.cidras.fernandez@usc.esAsociacion Espanola de Geografia2129426SpanishBol. Asoc. Geogr. Esp.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85082812154
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Goedhart J.6602537873;Plottwist: A web app for plotting and annotating continuous data2020PLoS Biology181e3000581910.1371/journal.pbio.3000581https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078560094&doi=10.1371%2fjournal.pbio.3000581&partnerID=40&md5=871a82049a1fb09f593fa0b8d2ca9fc1Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, NetherlandsGoedhart, J., Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, NetherlandsExperimental data can broadly be divided in discrete or continuous data. Continuous data are obtained from measurements that are performed as a function of another quantitative variable, e.g., time, length, concentration, or wavelength. The results from these types of experiments are often used to generate plots that visualize the measured variable on a continuous, quantitative scale. To simplify state-of-the-art data visualization and annotation of data from such experiments, an open-source tool was created with R/shiny that does not require coding skills to operate it. The freely available web app accepts wide (spreadsheet) and tidy data and offers a range of options to normalize the data. The data from individual objects can be shown in 3 different ways: (1) lines with unique colors, (2) small multiples, and (3) heatmap-style display. Next to this, the mean can be displayed with a 95% confidence interval for the visual comparison of different conditions. Several color-blind-friendly palettes are available to label the data and/or statistics. The plots can be annotated with graphical features and/or text to indicate any perturbations that are relevant. All user-defined settings can be stored for reproducibility of the data visualization. The app is dubbed PlotTwist and runs locally or online: https://huygens.science.uva.nl/PlotTwist Copyright: © 2020 Joachim Goedhart. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.article; data visualization; quantitative analysis; reproducibility; skill; biology; color; computer graphics; computer interface; human; information processing; Internet; longitudinal study; medical record; mobile application; procedures; software; time factor; Color; Computational Biology; Computer Graphics; Data Aggregation; Data Curation; Forms and Records Control; Humans; Internet; Longitudinal Studies; Mobile Applications; Software; Time Factors; User-Computer InterfaceSome of the PlotTwist code is taken from PlotsofData, and it is partially inspired by ggplotGUI (https://github.com/gertstulp/ggplotgui/) by Gert Stulp. The color-blind-safe palettes were developed by Paul Tol (https://personal.sron.nl/~pault/) and Masataka Okabe and Kei Ito (https://jfly.uni-koeln.de/color/). I am grateful to Marten Postma and all other colleagues at Molecular Cytology (UvA) for helpful discussions and Auke Folkerts (UvA, the Netherlands) for help with the server that runs shiny. Finally, the feedback, suggestions, enthusiastic responses, and example plots that are shared on Twitter are highly appreciated.Goedhart, J.; Swammerdam Institute for Life Sciences, Netherlands; email: j.goedhart@uva.nlPublic Library of Science15449173PBLIB31929523EnglishPloS Biol.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85078560094
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Satyanarayan A., Lee B., Ren D., Heer J., Stasko J., Thompson J., Brehmer M., Liu Z.55193351500;8705619100;55907202100;6603794736;7006755495;57202616180;35730813800;55714445500;Critical reflections on visualization authoring systems2020IEEE Transactions on Visualization and Computer Graphics26188072264614712710.1109/TVCG.2019.2934281https://www.scopus.com/inward/record.uri?eid=2-s2.0-85075735773&doi=10.1109%2fTVCG.2019.2934281&partnerID=40&md5=9f4408d1f3071567e4c6649e234b2964Massachusetts Institute of Technology, United States; Microsoft Research, United States; University of California, Santa Barbara, United States; University of Washington, United States; Georgia Institute of Technology, United States; Adobe ResearchSatyanarayan, A., Massachusetts Institute of Technology, United States; Lee, B., Microsoft Research, United States; Ren, D., University of California, Santa Barbara, United States; Heer, J., University of Washington, United States; Stasko, J., Georgia Institute of Technology, United States; Thompson, J., Georgia Institute of Technology, United States; Brehmer, M., Microsoft Research, United States; Liu, Z., Adobe ResearchAn emerging generation of visualization authoring systems support expressive information visualization without textual programming. As they vary in their visualization models, system architectures, and user interfaces, it is challenging to directly compare these systems using traditional evaluative methods. Recognizing the value of contextualizing our decisions in the broader design space, we present critical reflections on three systems we developed-Lyra, Data Illustrator, and Charticulator. This paper surfaces knowledge that would have been daunting within the constituent papers of these three systems. We compare and contrast their (previously unmentioned) limitations and trade-offs between expressivity and learnability. We also reflect on common assumptions that we made during the development of our systems, thereby informing future research directions in visualization authoring systems. © 1995-2012 IEEE.Critical reflection; Expressivity; Learnability; Reusability; Visualization authoringEconomic and social effects; Information systems; Reusability; User interfaces; Critical reflections; Evaluative methods; Expressivity; Future research directions; Information visualization; Learnability; System architectures; Visualization models; Visualization; articleIEEE Computer Society10772626ITVGE31442976EnglishIEEE Trans Visual Comput GraphicsArticleFinalAll Open Access, GreenScopus2-s2.0-85075735773
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Walny J., Frisson C., West M., Kosminsky D., Knudsen S., Carpendale S., Willett W.23398999400;35104875400;57203513982;57203517760;55537385900;6507907377;22958981500;Data Changes Everything: Challenges and Opportunities in Data Visualization Design Handoff2020IEEE Transactions on Visualization and Computer Graphics261881669512221410.1109/TVCG.2019.2934538https://www.scopus.com/inward/record.uri?eid=2-s2.0-85075637644&doi=10.1109%2fTVCG.2019.2934538&partnerID=40&md5=4a8517eac1051348646723dd1784e213University of Calgary, Calgary, CanadaWalny, J., University of Calgary, Calgary, Canada; Frisson, C., University of Calgary, Calgary, Canada; West, M., University of Calgary, Calgary, Canada; Kosminsky, D., University of Calgary, Calgary, Canada; Knudsen, S., University of Calgary, Calgary, Canada; Carpendale, S., University of Calgary, Calgary, Canada; Willett, W., University of Calgary, Calgary, CanadaComplex data visualization design projects often entail collaboration between people with different visualization-related skills. For example, many teams include both designers who create new visualization designs and developers who implement the resulting visualization software. We identify gaps between data characterization tools, visualization design tools, and development platforms that pose challenges for designer-developer teams working to create new data visualizations. While it is common for commercial interaction design tools to support collaboration between designers and developers, creating data visualizations poses several unique challenges that are not supported by current tools. In particular, visualization designers must characterize and build an understanding of the underlying data, then specify layouts, data encodings, and other data-driven parameters that will be robust across many different data values. In larger teams, designers must also clearly communicate these mappings and their dependencies to developers, clients, and other collaborators. We report observations and reflections from five large multidisciplinary visualization design projects and highlight six data-specific visualization challenges for design specification and handoff. These challenges include adapting to changing data, anticipating edge cases in data, understanding technical challenges, articulating data-dependent interactions, communicating data mappings, and preserving the integrity of data mappings across iterations. Based on these observations, we identify opportunities for future tools for prototyping, testing, and communicating data-driven designs, which might contribute to more successful and collaborative data visualization design. © 1995-2012 IEEE.data mapping; design handoff; design process; Information visualizationInformation systems; Mapping; Security of data; Visualization; Data characterization; Data mappings; Design process; Design specification; Development platform; Information visualization; Visualization designs; Visualization software; Data visualization; article; data visualization; humanHorizon 2020 Framework Programme, H2020: 753816; Natural Sciences and Engineering Research Council of Canada, NSERC; Alberta Innovates - Technology Futures, AITF; Singapore-MIT Alliance for Research and Technology Centre, SMARTThis project was funded in part by The National Energy Board of Canada, the National Sciences and Engineering Research Council of Canada, Alberta Innovates Technology Futures, SMART Technologies, and the European Union s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 753816.This project was funded in part by The National Energy Board of Canada, the National Sciences and Engineering Research Council of Canada, Alberta Innovates Technology Futures, SMART Technologies, and the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 753816.IEEE Computer Society10772626ITVGE31478857EnglishIEEE Trans Visual Comput GraphicsArticleFinalAll Open Access, GreenScopus2-s2.0-85075637644
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Kosminsky D., Walny J., Vermeulen J., Knudsen S., Willett W., Carpendale S.57203517760;23398999400;25723878600;55537385900;22958981500;6507907377;Belief at first sight: Data visualization and the rationalization of seeing2019Information Design Journal2514355310.1075/idj.25.1.04koshttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85082743855&doi=10.1075%2fidj.25.1.04kos&partnerID=40&md5=b7d4beeb05f61ce491e4790f3e3b43b8School of Fine Arts, Federal University of Rio de Janeiro, Brazil; National Energy Board of Canada, Canada; Department of Computer Science, Aarhus University, Denmark; Department of Computer Science, University of Calgary, Canada; University of Calgary, Canada; Simon Fraser University, CanadaKosminsky, D., School of Fine Arts, Federal University of Rio de Janeiro, Brazil; Walny, J., National Energy Board of Canada, Canada; Vermeulen, J., Department of Computer Science, Aarhus University, Denmark; Knudsen, S., Department of Computer Science, University of Calgary, Canada; Willett, W., University of Calgary, Canada; Carpendale, S., Simon Fraser University, CanadaData visualizations are often represented in public discourse as objective proof of facts. However, a visualization is only a single translation of reality, just like any other media, representation devices, or modes of representation. If we wish to encourage thoughtful, informed, and literate consumption of data visualizations, it is crucial that we consider why they are often presented and interpreted as objective. We reflect theoretically on data visualization as a system of representation historically anchored in science, rationalism, and notions of objectivity. It establishes itself within a lineage of conventions for visual representations which extends from the Renaissance to the present and includes perspective drawing, photography, cinema and television, as well as computer graphics. By examining our tendency to see credibility in data visualizations and grounding that predisposition in a historical context, we hope to encourage more critical and nuanced production and interpretation of data visualizations in the public discourse. © 2019 John Benjamins Publishing CompanyData visualization; Historical context; Objectivity; RepresentationHorizon 2020 Framework Programme, H2020; H2020 Marie Skłodowska-Curie Actions, MSCA: 753816The theme for this paper emerged from a 3-year project on visualizing open government data at the University of Calgary. During that time, we had many fruitful conversations over the implications of visualizing data for the public, and the implied trust in the data that this would or would not bring. This paper is a result of some of these conversations. We thank Sarah Storteboom and Annette Hester for their insightful comments on drafts of this article. This project was funded in part by The National Energy Board of Canada, the National Sciences and Engineering Research Council of Canada, Alberta Innovates Technology Futures, SMART Technologies, the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 753816, and Information Plus Conference.Kosminsky, D.; School of Fine Arts, Brazil; email: doriskos@eba.ufrj.brJohn Benjamins Publishing Company1425471EnglishInf. Des. J.ArticleFinalAll Open Access, Hybrid Gold, GreenScopus2-s2.0-85082743855
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Luque-Chipana M., Vanhulst P., Verma H., Lalanne D., Evéquoz F.57194155683;57202337890;55505866600;36962970800;8280934700;Vasco: Interactive tool for early-exploration of data2019IHM 2019 - Annexes des Actes de la 31e Conference Francophone sur l'Interaction Homme-Machinea410.1145/3366551.3370343https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078449798&doi=10.1145%2f3366551.3370343&partnerID=40&md5=88799e85cf27475f0abd84860936dcfeUniv. of Fribourg, Fribourg, Switzerland; HES-SO Valais-Wallis, Sierre, SwitzerlandLuque-Chipana, M., Univ. of Fribourg, Fribourg, Switzerland; Vanhulst, P., Univ. of Fribourg, Fribourg, Switzerland; Verma, H., HES-SO Valais-Wallis, Sierre, Switzerland; Lalanne, D., Univ. of Fribourg, Fribourg, Switzerland; Evéquoz, F., HES-SO Valais-Wallis, Sierre, SwitzerlandWe describe Vasco, a data visualization tool for inexperienced users. Vasco is designed to allow and promote early exploration of data, targeting users without experience in the design of visualizations and data analysis. Vasco structures the interface to select easily data and create visualizations, using panels and cards. Vasco automatically generates the best graphics according to the selection of variables and data morphology. In addition, Vasco helps give the user control and organization with multiple workspaces. Finally, a controlled study, that compares the usability of Vasco with Voyager 2, shows that users find helpful the presence of the dimensions data, plus the iterative nature of the exploration, help users understand the data visualization process, make them feel more confident and more performant. © 2019 Copyright held by the owner/author(s).Data visualization; Early exploration; Visualization toolsHuman computer interaction; Visualization; Data visualization tools; Data-visualization process; Interactive tool; Selection of variables; User control; Visualization tools; Data visualizationACM Special Interest Group on Computer-Human Interaction (SIGCHI)Association for Computing Machinery, Inc31e Conference Francophone sur l'Interaction Homme-Machine, IHM 2019 - 31st French-speaking Conference on Human-Computer Interaction, IHM 201910 December 2019 through 13 December 20191561339781450370271EnglishIHM - Annex. Actes Conf. Francoph. Interact. Homme-Mach.Conference PaperFinalAll Open Access, GreenScopus2-s2.0-85078449798
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da Silva Ferrette B.L., Domingues R.R., Ussami L.H.F., Moraes L., de Oliveira Magalhães C., de Amorim A.F., Hilsdorf A.W.S., Oliveira C., Foresti F., Mendonça F.F.57204062760;55507606000;55191321700;57211604187;57211598323;7006426797;6602641594;57216243712;57201511236;26632214800;DNA-based species identification of shark finning seizures in Southwest Atlantic: implications for wildlife trade surveillance and law enforcement2019Biodiversity and Conservation281440074025910.1007/s10531-019-01862-0https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074600318&doi=10.1007%2fs10531-019-01862-0&partnerID=40&md5=8d9fdea1217f5113edd1c077fc3802dfLaboratório de Genética e Conservação, Universidade Santa Cecília (UNISANTA), 277 Oswaldo Cruz Street, Santos, São Paulo 11045-907, Brazil; Laboratório de Genética Pesqueira e Conservação (GenPesC), Instituto do Mar (IMar), Universidade Federal de São Paulo (UNIFESP), 144 Dr. Carvalho de Mendonça Street, Santos, São Paulo 11070-102, Brazil; Laboratório de Biologia e Genética de Peixes (LBGP), Instituto de Biociências de Botucatu (IBB), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 250 Prof. Dr. Antonio Celso Wagner Zanin Street, Botucatu, São Paulo 18618-689, Brazil; Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, 200 Dr. Cândido Xavier de Almeida e Souza Avenue, Mogi das Cruzes, São Paulo 08780-911, Brazil; Fisheries Institute (IP), 192 Bartolomeu de Gusmão Avenue, Santos, São Paulo 11045-401, Brazilda Silva Ferrette, B.L., Laboratório de Genética e Conservação, Universidade Santa Cecília (UNISANTA), 277 Oswaldo Cruz Street, Santos, São Paulo 11045-907, Brazil, Laboratório de Genética Pesqueira e Conservação (GenPesC), Instituto do Mar (IMar), Universidade Federal de São Paulo (UNIFESP), 144 Dr. Carvalho de Mendonça Street, Santos, São Paulo 11070-102, Brazil; Domingues, R.R., Laboratório de Genética Pesqueira e Conservação (GenPesC), Instituto do Mar (IMar), Universidade Federal de São Paulo (UNIFESP), 144 Dr. Carvalho de Mendonça Street, Santos, São Paulo 11070-102, Brazil; Ussami, L.H.F., Laboratório de Biologia e Genética de Peixes (LBGP), Instituto de Biociências de Botucatu (IBB), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 250 Prof. Dr. Antonio Celso Wagner Zanin Street, Botucatu, São Paulo 18618-689, Brazil; Moraes, L., Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, 200 Dr. Cândido Xavier de Almeida e Souza Avenue, Mogi das Cruzes, São Paulo 08780-911, Brazil; de Oliveira Magalhães, C., Laboratório de Genética Pesqueira e Conservação (GenPesC), Instituto do Mar (IMar), Universidade Federal de São Paulo (UNIFESP), 144 Dr. Carvalho de Mendonça Street, Santos, São Paulo 11070-102, Brazil, Laboratório de Biologia e Genética de Peixes (LBGP), Instituto de Biociências de Botucatu (IBB), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 250 Prof. Dr. Antonio Celso Wagner Zanin Street, Botucatu, São Paulo 18618-689, Brazil; de Amorim, A.F., Fisheries Institute (IP), 192 Bartolomeu de Gusmão Avenue, Santos, São Paulo 11045-401, Brazil; Hilsdorf, A.W.S., Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, 200 Dr. Cândido Xavier de Almeida e Souza Avenue, Mogi das Cruzes, São Paulo 08780-911, Brazil; Oliveira, C., Laboratório de Biologia e Genética de Peixes (LBGP), Instituto de Biociências de Botucatu (IBB), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 250 Prof. Dr. Antonio Celso Wagner Zanin Street, Botucatu, São Paulo 18618-689, Brazil; Foresti, F., Laboratório de Biologia e Genética de Peixes (LBGP), Instituto de Biociências de Botucatu (IBB), Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 250 Prof. Dr. Antonio Celso Wagner Zanin Street, Botucatu, São Paulo 18618-689, Brazil; Mendonça, F.F., Laboratório de Genética Pesqueira e Conservação (GenPesC), Instituto do Mar (IMar), Universidade Federal de São Paulo (UNIFESP), 144 Dr. Carvalho de Mendonça Street, Santos, São Paulo 11070-102, BrazilSharks developed life history traits that make them susceptible to overfishing. This is, in turn, a risk for extinction, and several species are affected. The high price of shark fins in the international trade has triggered the widespread capture of sharks at unsustainable levels, prompting illegal and unethical practices, such as finning. To address these concerns, the present study aimed to identify species composition using molecular techniques based on DNA barcoding and DNA polymorphism on samples taken from illegal shark fin seizures conducted by the Federal Environmental Agency of Brazil. A species-specific DNA-based identification from three finning seizures in Brazil found at least 20 species from 747 shark fins, some of which were identified as endangered and protected under Brazilian legislation, while others were representative of restricted catches, according to Appendix II of CITES. In the seizure from Belém, 338 fins were identified as belonging to at least 19 different species, while in the seizure from Natal 211, fins belonging to at least 8 different species were identified. Furthermore, 198 fins from Cananéia were identified through PCR-Multiplex as belonging to Isurus oxyrinchus. These results raise concerns about the environmental and socioeconomic effects of finning on developing countries. Furthermore, this study represents the first finning evaluation from Brazil in the Southwest Atlantic, highlighting the importance of developing policies aimed toward restricting and regulating the shark trade and detecting IUU fisheries and illegal trade of endangered species, mainly in developing countries, where fisheries management, surveillance, and species-specific fisheries catch data are often sporatic. © 2019, Springer Nature B.V.Conservation; DNA barcoding; Elasmobranchs; Fisheries management; Genetic identification; Threatened speciescatch statistics; DNA; endangered species; extinction risk; fish; fishery management; genetic analysis; identification method; international trade; law enforcement; life history trait; overfishing; polymorphism; Brazil; Chondrichthyes; ElasmobranchiiFundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP: 2009/54660-6, 2011/23787-0, 2017/02420-8Funding was provided by the S?o Paulo Research Foundation (FAPESP) (Grant Numbers 2009/54660-6; 2011/23787-0; 2017/02420-8).Funding was provided by the São Paulo Research Foundation (FAPESP) (Grant Numbers 2009/54660-6; 2011/23787-0; 2017/02420-8).Domingues, R.R.; Laboratório de Genética Pesqueira e Conservação (GenPesC), 144 Dr. Carvalho de Mendonça Street, Brazil; email: domingues.pesca@gmail.comSpringer Netherlands9603115BONSEEnglishBiodiversity Conserv.ArticleFinalScopus2-s2.0-85074600318
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López L.-A., Cadarso M.-Á., Zafrilla J., Arce G.23100482700;14044623200;55363057200;57193236444;The carbon footprint of the U.S. multinationals’ foreign affiliates2019Nature Communications10116722110.1038/s41467-019-09473-7https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064244134&doi=10.1038%2fs41467-019-09473-7&partnerID=40&md5=19285fddb1f158d3df615e6c093206c9Faculty of Economics and Business, University of Castilla-La Mancha, Plaza de la Universidad 1, Albacete, 02071, Spain; Faculty of Economics and Business, Complutense University of Madrid, Campus de Somosaguas, Pozuelo de Alarcón, Madrid, 28223, SpainLópez, L.-A., Faculty of Economics and Business, University of Castilla-La Mancha, Plaza de la Universidad 1, Albacete, 02071, Spain; Cadarso, M.-Á., Faculty of Economics and Business, University of Castilla-La Mancha, Plaza de la Universidad 1, Albacete, 02071, Spain; Zafrilla, J., Faculty of Economics and Business, University of Castilla-La Mancha, Plaza de la Universidad 1, Albacete, 02071, Spain; Arce, G., Faculty of Economics and Business, Complutense University of Madrid, Campus de Somosaguas, Pozuelo de Alarcón, Madrid, 28223, SpainMultinational enterprises (MNE) need to be a part of the solution in the fight against climate change, as claimed by investors and consumers, reducing emissions within their operations and supply chains. This paper measures the carbon footprint of U.S. MNE foreign affiliates (US-MNE) operating beyond the U.S. borders. Using a multiregional input-output model and information about US-MNE activities, the US-MNE carbon footprint ranks US-MNE as the 12th top emitter of the world. In relative terms, one dollar of value added generated by US-MNE affiliates operating abroad requires higher emissions than the domestic average and the ratio increases when only developing host countries are considered. Only 8% of total carbon footprint returns to the U.S. as virtual carbon embodied in the U.S. final consumption. Potential technology transfers between the U.S. parent company and affiliates to reduce US-MNE carbon footprint have been performed to evaluate potential rippled effects of mitigation actions. © 2019, The Author(s).carbon footprint; climate change; emission control; environmental economics; input-output analysis; multinational enterprise; Article; carbon footprint; economic aspect; human; United StatesMinisterio de Economía y Competitividad, MINECO: ECO2016–78938-R; Universidad de Castilla-La Mancha, UCLMThis work was supported by Ministerio de Economía y Competitividad (ECO2016–78938-R) and by the University of Castilla-La Mancha (UCLM).López, L.-A.; Faculty of Economics and Business, Plaza de la Universidad 1, Spain; email: Luis.LSantiago@uclm.esNature Publishing Group2041172330976001EnglishNat. Commun.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85064244134
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Pfefferle A., Jacobs B., Netskar H., Ask E.H., Lorenz S., Clancy T., Goodridge J.P., Sohlberg E., Malmberg K.-J.56690284100;16679183400;57211788925;56606106900;55266491400;36054460400;6701366126;26041144400;35488587600;Intra-lineage Plasticity and Functional Reprogramming Maintain Natural Killer Cell Repertoire Diversity2019Cell Reports29822842.29E+071510.1016/j.celrep.2019.10.058https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074973086&doi=10.1016%2fj.celrep.2019.10.058&partnerID=40&md5=8b4cddde683691cf5bb7b781722124baCenter for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden; Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Fate Therapeutics, Inc., San Diego, CA, United StatesPfefferle, A., Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden; Jacobs, B., Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Netskar, H., Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Ask, E.H., Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Lorenz, S., Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Clancy, T., Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Goodridge, J.P., Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, Fate Therapeutics, Inc., San Diego, CA, United States; Sohlberg, E., Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden; Malmberg, K.-J., Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden, Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, NorwayNatural killer (NK) cell repertoires are made up of phenotypically distinct subsets with different functional properties. The molecular programs involved in maintaining NK cell repertoire diversity under homeostatic conditions remain elusive. Here, we show that subset-specific NK cell proliferation kinetics correlate with mTOR activation, and global repertoire diversity is maintained through a high degree of intra-lineage subset plasticity during interleukin (IL)-15-driven homeostatic proliferation in vitro. Slowly cycling sorted KIR+CD56dim NK cells with an induced CD57 phenotype display increased functional potential associated with increased transcription of genes involved in adhesion and immune synapse formation. Rapidly cycling cells upregulate NKG2A, display a general loss of functionality, and a transcriptional signature associated with increased apoptosis/cellular stress, actin-remodeling, and nuclear factor κB (NF-κB) activation. These results shed light on the role of intra-lineage plasticity during NK cell homeostasis and suggest that the functional fate of the cell is tightly linked to the acquired phenotype and transcriptional reprogramming. Unique and genetically hard-wired NK cell repertoires are well-maintained over time despite the rapid turnover of NK cells. Pfefferle et al. identify the role of intra-lineage plasticity during NK cell homeostasis and suggest that a cell's functional fate is tightly linked to its acquired phenotype as determined by transcriptional reprogramming. © 2019 The Author(s)differentiation; education; homeostasis; IL-15; killer cell immunoglobulin-like receptors; natural killer cells; plasticity; single-cell RNA sequencingactin; CD56 antigen; CD57 antigen; immunoglobulin enhancer binding protein; interleukin 15; mammalian target of rapamycin; natural killer cell receptor NKG2A; CD56 antigen; CD57 antigen; IL15 protein, human; immunoglobulin enhancer binding protein; interleukin 15; KLRC1 protein, human; natural killer cell lectin like receptor subfamily C; apoptosis; Article; cell fate; cell lineage; cell plasticity; cell proliferation; cell selection; cell stress; controlled study; genetic transcription; homeostasis; in vitro study; natural killer cell; nuclear reprogramming; phenotype; priority journal; synapse; upregulation; genetics; human; kinetics; metabolism; natural killer cell; physiology; sequence analysis; Apoptosis; CD56 Antigen; CD57 Antigens; Humans; Interleukin-15; Killer Cells, Natural; Kinetics; NF-kappa B; NK Cell Lectin-Like Receptor Subfamily C; Phenotype; Sequence Analysis, RNA; SynapsesCD56 Antigen; CD57 Antigens; IL15 protein, human; Interleukin-15; KLRC1 protein, human; NF-kappa B; NK Cell Lectin-Like Receptor Subfamily CKreftforeningen, NCS; Cancerfonden; Karolinska Institutet, KI; Vetenskapsrådet, VR; Norges Forskningsråd; Helse Sør-Øst RHF, sorostThis work was supported by grants from the Swedish Research Council, the Swedish Children's Cancer Society, the Swedish Cancer Society, the Tobias Foundation, the Karolinska Institutet, the Norwegian Cancer Society, the Norwegian Research Council, the South-Eastern Norway Regional Health Authority, and the KG Jebsen Center for Cancer Immunotherapy. B.J. was funded by a Mildred Scheel postdoctoral scholarship from the Dr. Mildred Scheel Foundation for Cancer Research of the German Cancer Aid Organization. A.P. and B.J. conducted experiments. A.P. analyzed the data. S.L. performed RNA sequencing and generated the libraries. H.N. analyzed the RNA-seq data. E.H.A. generated the t-SNE plots. J.P.G. T.C. E.S. and K.-J.M. provided scientific input. A.P. wrote the original draft. E.S. and K.-J.M. designed research and reviewed and edited the manuscript. K.-J.M. is a scientific advisor and consultant at FATE Therapeutics. J.P.G. is an employee at FATE Therapeutics. The current work is non-related to the research activities at FATE and has been conducted without any financial support from FATE Therapeutics.K.-J.M. is a scientific advisor and consultant at FATE Therapeutics. J.P.G. is an employee at FATE Therapeutics. The current work is non-related to the research activities at FATE and has been conducted without any financial support from FATE Therapeutics.This work was supported by grants from the Swedish Research Council , the Swedish Children’s Cancer Society , the Swedish Cancer Society , the Tobias Foundation , the Karolinska Institutet , the Norwegian Cancer Society , the Norwegian Research Council , the South-Eastern Norway Regional Health Authority , and the KG Jebsen Center for Cancer Immunotherapy . B.J. was funded by a Mildred Scheel postdoctoral scholarship from the Dr. Mildred Scheel Foundation for Cancer Research of the German Cancer Aid Organization .Malmberg, K.-J.; Center for Infectious Medicine, Sweden; email: kalle.malmberg@ki.seElsevier B.V.2211124731747601EnglishCell Rep.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85074973086
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Cespedes-Lopez M.-F., Mora-Garcia R.-T., Perez-Sanchez V.R., Perez-Sanchez J.-C.56951238300;56951143700;57196042109;56368638800;Meta-analysis of price premiums in housing with energy performance certificates (EPC)2019Sustainability (Switzerland)11226303510.3390/su11226303https://www.scopus.com/inward/record.uri?eid=2-s2.0-85075876748&doi=10.3390%2fsu11226303&partnerID=40&md5=2c9e047cea4d122710f8899bcf9e8daaBuilding Sciences and Urbanism Department, University of Alicante, San Vicente del Raspeig, Alicante, 03690, SpainCespedes-Lopez, M.-F., Building Sciences and Urbanism Department, University of Alicante, San Vicente del Raspeig, Alicante, 03690, Spain; Mora-Garcia, R.-T., Building Sciences and Urbanism Department, University of Alicante, San Vicente del Raspeig, Alicante, 03690, Spain; Perez-Sanchez, V.R., Building Sciences and Urbanism Department, University of Alicante, San Vicente del Raspeig, Alicante, 03690, Spain; Perez-Sanchez, J.-C., Building Sciences and Urbanism Department, University of Alicante, San Vicente del Raspeig, Alicante, 03690, SpainStudies have found that housing with energy performance certificates have a positive premium in sales price. However, other studies have obtained negative or unexpected results. The objective of this study is to determine whether or not housing with energy performance certificates (EPC) have positive premiums in the sales price. For this purpose, a systematic review, meta-analysis, and meta-regression of prior studies were conducted in order to determine whether the existence of an EPC influences sales price. A total of 66 documents were examined, with a total of 173 sales registers. The impact of having or not having an EPC was analyzed for housing sales price premiums on a global level, as well as the premiums in Europe for each of the ABCDEFG qualification letters. The results suggest that: 1) Globally speaking, it is estimated that housing with an EPC has an overall price premium of 4.20%, on a continent level, with premiums of 5.36% being obtained in North America, 4.81% in Asia, and 2.32% in Europe; 2) in Europe, the results are not conclusive with regards to the ABCDEFG qualification, since there is no consensus as to the letter base to be used as a reference for comparisons, thereby generating small comparable samples. © 2019 by the authors.Energy efficiency; Energy performance certificate (EPC); Meta-analysis; Meta-regression; Price premiums; Systematic reviewcertification; energy efficiency; housing; literature review; meta-analysis; price determination; regression analysis; residential energy; Asia; Europe; North AmericaUniversidad de AlicanteFunding: The author, M.-F.C.-L., received funding from the Doctorate School of the Universidad de Alicante (UA, https://edua.ua.es/) and from the Spanish General Council of Technical Architecture. The author, R.-T.M.-G., received funding from the UA in order to complete a research stay in Chile, resulting in this study.Mora-Garcia, R.-T.; Building Sciences and Urbanism Department, Spain; email: rtmg@ua.esMDPI20711050EnglishSustainabilityArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85075876748
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Alabdullah A.K., Borrill P., Martin A.C., Ramirez-Gonzalez R.H., Hassani-Pak K., Uauy C., Shaw P., Moore G.57212507557;50761021800;20734821900;52264324400;36056395200;9732865400;57200818168;7403282659;A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization2019Frontiers in Plant Science1013251410.3389/fpls.2019.01325https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074658575&doi=10.3389%2ffpls.2019.01325&partnerID=40&md5=b850e68798a7e58cbdcef12860db8bc6John Innes Centre, Norwich Research Park, Norwich, United Kingdom; School of Biosciences, University of Birmingham, Birmingham, United Kingdom; Computational and Analytical Sciences, Rothamsted Research, Harpenden, United KingdomAlabdullah, A.K., John Innes Centre, Norwich Research Park, Norwich, United Kingdom; Borrill, P., School of Biosciences, University of Birmingham, Birmingham, United Kingdom; Martin, A.C., John Innes Centre, Norwich Research Park, Norwich, United Kingdom; Ramirez-Gonzalez, R.H., John Innes Centre, Norwich Research Park, Norwich, United Kingdom; Hassani-Pak, K., Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom; Uauy, C., John Innes Centre, Norwich Research Park, Norwich, United Kingdom; Shaw, P., John Innes Centre, Norwich Research Park, Norwich, United Kingdom; Moore, G., John Innes Centre, Norwich Research Park, Norwich, United KingdomPolyploidization has played an important role in plant evolution. However, upon polyploidization, the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to stabilize the polyploid genome. Therefore, upon the polyploidization of wheat, a hexaploid species with three related (homeologous) genomes, the stabilization process may have involved rapid changes in content and expression of MGs on homeologous chromosomes (homeologs). To examine this hypothesis, sets of candidate MGs were identified in wheat using co-expression network analysis and orthology informed approaches. In total, 130 RNA-Seq samples from a range of tissues including wheat meiotic anthers were used to define co-expressed modules of genes. Three modules were significantly correlated with meiotic tissue samples but not with other tissue types. These modules were enriched for GO terms related to cell cycle, DNA replication, and chromatin modification and contained orthologs of known MGs. Overall, 74.4% of genes within these meiosis-related modules had three homeologous copies which was similar to other tissue-related modules. Amongst wheat MGs identified by orthology, rather than co-expression, the majority (93.7%) were either retained in hexaploid wheat at the same number of copies (78.4%) or increased in copy number (15.3%) compared to ancestral wheat species. Furthermore, genes within meiosis-related modules showed more balanced expression levels between homeologs than genes in non-meiosis-related modules. Taken together, our results do not support extensive gene loss nor changes in homeolog expression of MGs upon wheat polyploidization. The construction of the MG co-expression network allowed identification of hub genes and provided key targets for future studies. © Copyright © 2019 Alabdullah, Borrill, Martin, Ramirez-Gonzalez, Hassani-Pak, Uauy, Shaw and Moore.co-expression; hexaploid; meiosis; network; polyploidization; wheatBiotechnology and Biological Sciences Research Council, BBSRC: BB/J007188/1, BB/N002628/1, BB/R007233/1, BBS/E/C/000I0210, BBS/E/J/000PR9779, BBS/E/J/000PR9788This manuscript has been released as a pre-print at https://www.biorxiv.org/ (Alabdullah et al., 2019). The authors would like to acknowledge the UK biotechnology and Biological Sciences Research Council (BBSRC; www.bbsrc.ukri.org) for supporting this work.Alabdullah, A.K.; John Innes Centre, United Kingdom; email: AbdulKader.Alabdullah@jic.ac.ukFrontiers Media S.A.1664462XEnglishFront. Plant Sci.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85074658575
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Wray A.J.D., Minaker L.M.57201009997;15045215900;Is cancer prevention influenced by the built environment? A multidisciplinary scoping review2019Cancer12519329933111210.1002/cncr.32376https://www.scopus.com/inward/record.uri?eid=2-s2.0-85068648160&doi=10.1002%2fcncr.32376&partnerID=40&md5=adb53696202258f7d7bd60e5823106d1School of Planning, University of Waterloo, Waterloo, ON, Canada; Human Environments Analysis Laboratory, University of Western Ontario, London, ON, CanadaWray, A.J.D., School of Planning, University of Waterloo, Waterloo, ON, Canada, Human Environments Analysis Laboratory, University of Western Ontario, London, ON, Canada; Minaker, L.M., School of Planning, University of Waterloo, Waterloo, ON, CanadaThe built environment is a significant determinant of human health. Globally, the growing prevalence of preventable cancers suggests a need to understand how features of the built environment shape exposure to cancer development and distribution within a population. This scoping review examines how researchers across disparate fields understand and discuss the built environment in primary and secondary cancer prevention. It is focused exclusively on peer-reviewed sources published from research conducted in Australia, Canada, Ireland, New Zealand, the United Kingdom, and the United States from 1990 to 2017. The review captured 9958 potential results in the academic literature, and this body of results was scoped to 268 relevant peer-reviewed journal articles indexed across 13 subject databases. Spatial proximity, transportation, land use, and housing are well-understood features of the built environment that shape cancer risk. Built-environment features predominantly influence air quality, substance use, diet, physical activity, and screening adherence, with impacts on breast cancer, lung cancer, colorectal cancer, and overall cancer risk. The majority of the evidence fails to provide direct recommendations for advancing cancer prevention policy and program objectives for municipalities. The expansion of interdisciplinary work in this area would serve to create a significant population health impact. © 2019 American Cancer Societycancer; cities; environment; geography; housing; neighborhood; policy; public health; screening; transportationair quality; breast cancer; built environment; cancer prevention; cancer risk; colorectal cancer; geography; health care policy; health care quality; health program; human; land use; lung cancer; nutrition; physical activity; population research; prevalence; priority journal; Review; substance use; traffic and transport; adverse event; Australia; Canada; demography; environmental exposure; environmental planning; female; global disease burden; interdisciplinary communication; Ireland; neoplasm; risk assessment; United Kingdom; United States; Australia; Built Environment; Canada; Environment Design; Environmental Exposure; Female; Global Burden of Disease; Humans; Interdisciplinary Communication; Ireland; Neoplasms; Residence Characteristics; Risk Assessment; United Kingdom; United StatesCanadian Cancer Society, CBCF: 704744; University of WaterlooThis work was supported by the Canadian Cancer Society (grant 704744) and a University of Waterloo Undergraduate Research Initiative award.Minaker, L.M.; School of Planning, Canada; email: lminaker@uwaterloo.caJohn Wiley and Sons Inc.0008543XCANCA31287585EnglishCancerReviewFinalAll Open Access, GreenScopus2-s2.0-85068648160
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Sottorff I., Wiese J., Imhoff J.F.55745639400;24336939300;7005354833;High diversity and novelty of Actinobacteria isolated from the coastal zone of the geographically remote young volcanic Easter Island, Chile2019International Microbiology223377390410.1007/s10123-019-00061-9https://www.scopus.com/inward/record.uri?eid=2-s2.0-85071628039&doi=10.1007%2fs10123-019-00061-9&partnerID=40&md5=52e39a8db6cd78b3e64b4da99698dcacGEOMAR Centre for Ocean Research Kiel, Marine Microbiology, Düsternbrooker Weg 20, Kiel, 24105, Germany; Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, ChileSottorff, I., GEOMAR Centre for Ocean Research Kiel, Marine Microbiology, Düsternbrooker Weg 20, Kiel, 24105, Germany, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile; Wiese, J., GEOMAR Centre for Ocean Research Kiel, Marine Microbiology, Düsternbrooker Weg 20, Kiel, 24105, Germany; Imhoff, J.F., GEOMAR Centre for Ocean Research Kiel, Marine Microbiology, Düsternbrooker Weg 20, Kiel, 24105, GermanyEaster Island is an isolated volcanic island in the Pacific Ocean. Despite the extended knowledge about its origin, flora, and fauna, little is known about the bacterial diversity inhabiting this territory. Due to its isolation, Easter Island can be considered as a suitable place to evaluate microbial diversity in a geographically isolated context, what could shed light on actinobacterial occurrence, distribution, and potential novelty. In the present study, we performed a comprehensive analysis of marine Actinobacteria diversity of Easter Island by studying a large number of coastal sampling sites, which were inoculated into a broad spectrum of different culture media, where most important variations in composition included carbon and nitrogen substrates, in addition to salinity. The isolates were characterized on the basis of 16S ribosomal RNA gene sequencing and phylogenetic analysis. High actinobacterial diversity was recovered with a total of 163 pure cultures of Actinobacteria representing 72 phylotypes and 20 genera, which were unevenly distributed in different locations of the island and sample sources. The phylogenetic evaluation indicated a high degree of novelty showing that 45% of the isolates might represent new taxa. The most abundant genera in the different samples were Micromonospora, Streptomyces, Salinispora, and Dietzia. Two aspects appear of primary importance in regard to the high degree of novelty and diversity of Actinobacteria found. First, the application of various culture media significantly increased the number of species and genera obtained. Second, the geographical isolation is considered to be of importance regarding the actinobacterial novelty found. © 2019, Springer Nature Switzerland AG.Actinobacteria; Easter Island; New taxa; Pacific Ocean; Polynesiabacterial DNA; ribosome DNA; RNA 16S; Actinobacteria; biodiversity; chemistry; Chile; classification; cluster analysis; DNA sequence; environmental microbiology; genetics; isolation and purification; microbiological examination; phylogeny; Polynesia; Actinobacteria; Bacteriological Techniques; Biodiversity; Chile; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Environmental Microbiology; Phylogeny; Polynesia; RNA, Ribosomal, 16S; Sequence Analysis, DNADNA, Bacterial; DNA, Ribosomal; RNA, Ribosomal, 16SDeutscher Akademischer Austauschdienst, DAAD; Helmholtz AssociationWe thank the Deutscher Akademischer Austauschdienst (DAAD) and Helmholtz association for the financial support.Imhoff, J.F.; GEOMAR Centre for Ocean Research Kiel, Düsternbrooker Weg 20, Germany; email: jimhoff@geomar.deSpringer1139670930811004EnglishInt. Microbiol.ArticleFinalScopus2-s2.0-85071628039
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Chande S.V.36571448300;Database query optimization using genetic algorithms: A systematic literature review2019International Journal of Advanced Trends in Computer Science and Engineering8519031913110.30534/ijatcse/2019/14852019https://www.scopus.com/inward/record.uri?eid=2-s2.0-85076513643&doi=10.30534%2fijatcse%2f2019%2f14852019&partnerID=40&md5=2dc536e7310c434b4f38f497b4512927International School of Informatics and Management, Jaipur, IndiaChande, S.V., International School of Informatics and Management, Jaipur, IndiaAs data is escalating exponentially efficient storage and fast retrieval of data are increasingly becoming areas of significance for researchers. Query optimization is probably the most researched problem in the database domain. Among the solutions to this problem, Genetic Algorithms have proved to be a viable alternative. This systematic literature review explores work done on the application of Genetic Algorithm to optimization of database queries to understand how its use for database query optimization has taken shape and to identify the open questions. It could be inferred that Join-Order, Distributed databases and Hybrids with Genetic Algorithm are sustaining researchers’ interest. © 2019, World Academy of Research in Science and Engineering. All rights reserved.Data Management Optimization; Genetic AlgorithmsChande, S.V.; International School of Informatics and ManagementIndia; email: swatichande@rediffmail.comWorld Academy of Research in Science and Engineering22783091EnglishInt. J. Adv. Trends Comput. Sci. Eng.ArticleFinalAll Open Access, BronzeScopus2-s2.0-85076513643
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Malaterre C., Chartier J.-F., Pulizzotto D.26037162500;48360928400;57197819957;What is this thing called philosophy of science? A computational topic-modeling perspective, 1934–20152019HOPOS92215249710.1086/704372https://www.scopus.com/inward/record.uri?eid=2-s2.0-85071910592&doi=10.1086%2f704372&partnerID=40&md5=9281b543f1dac6073804b9408f08d49dDépartement de philosophie, Centre interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal, 455 Boulevard René-Lévesque Est, Montréal, QC H3C 3P8, Canada; Université du Québec à Montréal, CanadaMalaterre, C., Département de philosophie, Centre interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal, 455 Boulevard René-Lévesque Est, Montréal, QC H3C 3P8, Canada; Chartier, J.-F., Université du Québec à Montréal, Canada; Pulizzotto, D., Université du Québec à Montréal, CanadaWhat is philosophy of science? Numerous manuals, anthologies, and essays provide carefully reconstructed vantage points on the discipline that have been gained through expert and piecemeal historical analyses. In this article, we address the question from a complementary perspective: we target the content of one major journal in the field— Philosophy of Science—and apply unsupervised text-mining methods to its complete corpus, from its start in 1934 until 2015. By running topic-modeling algorithms over the full-text corpus, we identified 126 key research topics that span 82 years. We also tracked those topics’ evolution and fluctuating significance over time in the journal articles. Our results concur with and document known and lesser-known episodes in the philosophy of science, including the rise and fall of logic and language-related topics, the relative stability of a metaphysical and ontological questioning (space and time, causation, natural kinds, realism), the significance of epistemological issues about the nature of scientific knowledge, and the rise of a recent philosophy of biology and other trends. These analyses exemplify how computational text-mining methods can be used to provide an empirical large-scale and data-driven perspective on the history of philosophy of science that is complementary to other current historical approaches. © 2019 by the International Society for the History of Philosophy of Science.Université du Québec à Montréal, UQAM: CRC-950-230795; Social Sciences and Humanities Research Council of Canada, SSHRC: 435-2014-0943; Canada Foundation for Innovation: 34555We thank JSTOR for kindly providing access to the complete numerical corpus of Philosophy of Science. We also thank Heather Douglas and three anonymous referees for very helpful comments and bibliographical references, as well as the audiences at the 2018 Canadian Philosophical Association meeting (Montreal) and the 2018 Philosophy of Science Association meeting (Seattle), at which earlier versions of the article were presented. Funding from the Canada Foundation for Innovation (grant 34555), the Canada Social Sciences and Humanities Research Council (grant 435-2014-0943), and the Canada Research Chair in Philosophy of the Life Sciences at UQAM (CRC-950-230795) is gratefully acknowledged.Malaterre, C.; Département de philosophie, 455 Boulevard René-Lévesque Est, Canada; email: malaterre.christophe@uqam.caUniversity of Chicago Press21525188EnglishHOPOSArticleFinalAll Open Access, BronzeScopus2-s2.0-85071910592
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Driscoll K.P., Richard Hauer F.57209509526;6508097287;Seasonal flooding affects habitat and landscape dynamics of a gravel-bed river floodplain2019Freshwater Science383510526310.1086/704826https://www.scopus.com/inward/record.uri?eid=2-s2.0-85069436818&doi=10.1086%2f704826&partnerID=40&md5=01befcceffd70d0589bd0eaa92731004Systems Ecology Graduate Program, University of Montana, Missoula, MT 59812, United States; Rocky Mountain Research Station, Albuquerque, NM 87102, United States; Flathead Lake Biological Station, University of Montana, Polson, MT 59806, United States; Montana Institute on Ecosystems, University of Montana, Missoula, MT 59812, United StatesDriscoll, K.P., Systems Ecology Graduate Program, University of Montana, Missoula, MT 59812, United States, Rocky Mountain Research Station, Albuquerque, NM 87102, United States; Richard Hauer, F., Systems Ecology Graduate Program, University of Montana, Missoula, MT 59812, United States, Flathead Lake Biological Station, University of Montana, Polson, MT 59806, United States, Montana Institute on Ecosystems, University of Montana, Missoula, MT 59812, United StatesFloodplains are comprised of aquatic and terrestrial habitats that are reshaped frequently by hydrologic processes that operate at multiple spatial and temporal scales. It is well established that hydrologic and geomorphic dynamics are the primary drivers of habitat change in river floodplains over extended time periods. However, the effect of fluctuating discharge on floodplain habitat structure during seasonal flooding is less well understood. We collected ultra-high resolution digital multispectral imagery of a gravel-bed river floodplain in western Montana on 6 dates during a typical seasonal flood pulse and used it to quantify changes in habitat abundance and diversity associated with annual flooding. We observed significant changes in areal abundance of many habitat types, such as riffles, runs, shallow shorelines, and overbank flow. However, the relative abundance of some habitats, such as backwaters, springbrooks, pools, and ponds, changed very little. We also examined habitat transition patterns throughout the flood pulse. Few habitat transitions occurred in the main channel, which was dominated by riffle and run habitat. In contrast, in the near-channel, scoured habitats of the floodplain were dominated by cobble bars at low flows but transitioned to isolated flood channels at moderate discharge. The areal abundance of habitat types in near-channel floodplain areas varied as discharge fluctuated. These areas were most diverse and dissimilar in habitat composition at intermediate flows during both the rising and falling limbs of the hydrograph. The geomorphically stable areas of the floodplain were dominated by herbaceous habitat, and we observed fewer transitions from one habitat type to another during the seasonal flood pulse. However, the largest habitat diversity occurred during peak flow, which highlights the influence of flooding on the development and expansion of a broad array of aquatic habitats during the annual cycle of flooding. We conclude that the response of floodplain habitat abundance and diversity is strongly influenced by location on the riverscape. © 2019 by The Society for Freshwater Science.Flooding disturbance; Floodplains; Gravel-bed river; Habitat diversitydischarge; disturbance; flooding; floodplain; gravel bed stream; habitat availability; habitat structure; habitat type; landscape change; spatiotemporal analysisNSF-IIA-1443108; Montana Institute on Ecosystems, IoEThis research was supported by the National Science Foundation EPSCoR program award NSF-IIA-1443108 to the State of Montana and through the Montana Institute on Ecosystems. We thank Diane Whited for her expertise on classification and poten- tial sources of error. We are grateful to the anonymous reviewers and the Associate Editor for their very helpful reviews and comments on the original draft of this manuscript.Richard Hauer, F.; Systems Ecology Graduate Program, United States; email: ric.hauer@umontana.eduUniversity of Chicago Press21619549EnglishFreshwater Sci.ArticleFinalScopus2-s2.0-85069436818
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Zajchowski C.A.B., Brownlee M.T.J., Rose J.57126383400;54418569000;55455103100;Air quality and the visitor experience in parks and protected areas2019Tourism Geographies2146136341210.1080/14616688.2018.1522546https://www.scopus.com/inward/record.uri?eid=2-s2.0-85057529056&doi=10.1080%2f14616688.2018.1522546&partnerID=40&md5=1678753aec62cd2c79e7591e78971651Department of Human Movement Sciences, Old Dominion University, Norfolk, VA, United States; Department of Parks, Recreation, and Tourism Management, Clemson University, Clemson, SC, United States; Department of Health, Kinesiology, and Recreation, University of Utah, Salt Lake City, UT, United StatesZajchowski, C.A.B., Department of Human Movement Sciences, Old Dominion University, Norfolk, VA, United States; Brownlee, M.T.J., Department of Parks, Recreation, and Tourism Management, Clemson University, Clemson, SC, United States; Rose, J., Department of Health, Kinesiology, and Recreation, University of Utah, Salt Lake City, UT, United StatesAir pollution is one of the greatest environmental health risks facing people worldwide. The transboundary nature of air pollution may place park and protected area (PPA) resources, as well as visitors, at risk of exposure to the same harmful pollutants that plague urban populations. Despite our knowledge of the various impacts of air pollution on endemic species, ecosystem functions, and human health, there exists a gap in our understanding of the affective, behavioral, and cognitive role of air pollution in the visitor experience in PPAs. We reduced this deficit by conducting a scoping review of existing empirical social science literature focused on the social and psychological effects of degraded air quality in and around PPAs. Using a systematic scoping process, we assessed peer-reviewed, empirical social science articles (n = 458), for evidence of human dimensions of air quality scholarship in International Union for Conservation of Nature (IUCN) protected area sites. Results suggest a relative dearth of peer-reviewed social science scholarship explicitly focused on the visitor experience of air quality in PPAs worldwide. Descriptive analyses illustrate a consolidation of scholarship in specific publications, as well as geographic concentration of scholarship in North American protected areas and IUCN Category II (National Parks). Subsequent inductive analyses yielded five emergent themes—ecosystem services, visitor impacts, transit, measurement of behavior, and variable importance—evident in human dimensions of air quality literature, as well as variety of implications for future human dimensions of air quality scholarship and PPA management. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.air pollution; Air quality; ecosystem services; ecotourism; national parks; parks and protected areas; visitor experienceair quality; atmospheric pollution; ecosystem service; ecotourism; national park; protected area; psychology; social impact; tourist behavior; North AmericaZajchowski, C.A.B.; Department of Human Movement Sciences, United States; email: czajchow@odu.eduRoutledge14616688EnglishTour. Geogr.ArticleFinalScopus2-s2.0-85057529056
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Lepawsky J., Davis J.-M., Akese G., Persaud D.9637533700;57203643861;56685593900;57205490742;Cooking with Controversies: How Geographers Might Use Controversy Mapping as a Research Tool2019Professional Geographer713437448210.1080/00330124.2018.1531243https://www.scopus.com/inward/record.uri?eid=2-s2.0-85060242315&doi=10.1080%2f00330124.2018.1531243&partnerID=40&md5=74bd9dc6db6ae95630de12711eba6db9Memorial University, Canada; University of Illinois at Urbana-Champaign, United StatesLepawsky, J., Memorial University, Canada; Davis, J.-M., University of Illinois at Urbana-Champaign, United States; Akese, G., Memorial University, Canada; Persaud, D., Memorial University, CanadaThe purpose of this article is twofold. The first is to suggest that techniques for mapping public disagreements over claims to knowledge, or controversies, can act as assistive devices for researchers in geography to move from research topics to research questions. A second purpose is to offer a recipe or “how-to” guide of specific approaches and free scholarly software that researchers without specialized coding skills can use to achieve their own controversy mapping goals. We use a case of creating a controversy map covering the issue of transboundary movements of electronic waste (e-waste) to illustrate how these approaches and software can be associated together so that other researchers may put them to use for their own controversy mapping purposes. © 2019, © 2019 American Association of Geographers.controversy mapping; e-desechos; e-waste; issue mapping; mapeo de controversias; mapeo de problemas; techniques; técnicaselectronic waste; knowledge; mapping; research method; softwareRoutledge330124EnglishProf. Geogr.ArticleFinalScopus2-s2.0-85060242315
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Eily A.N., Pryer K.M., Li F.-W.57202855451;6603530921;35210611500;A first glimpse at genes important to the Azolla–Nostoc symbiosis2019Symbiosis782149162510.1007/s13199-019-00599-2https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061006467&doi=10.1007%2fs13199-019-00599-2&partnerID=40&md5=4fc991a955c7911b01dc387d7d0bad9dDepartment of Biology, Duke University, Durham, NC 27708, United States; Boyce Thompson Institute & Plant Biology Section, Cornell University, Ithaca, NY 14853, United StatesEily, A.N., Department of Biology, Duke University, Durham, NC 27708, United States; Pryer, K.M., Department of Biology, Duke University, Durham, NC 27708, United States; Li, F.-W., Boyce Thompson Institute & Plant Biology Section, Cornell University, Ithaca, NY 14853, United StatesAzolla is a small genus of diminutive aquatic ferns with a surprisingly vast potential to benefit the environment and agriculture, as well as to provide insight into the evolution of plant-cyanobacterial symbioses. This capability is derived from the unique relationship Azolla spp. have with their obligate, nitrogen-fixing cyanobacterial symbiont, Nostoc azollae, that resides in their leaves. Although previous work has specified the importance of the exchange of ammonium and sucrose metabolites between these two partners, we have yet to determine the underlying molecular mechanisms that make this symbiosis so successful. The newly sequenced and annotated reference genome of Azolla filiculoides has allowed us to investigate gene expression profiles of A. filiculoides—both with and without its obligate cyanobiont, N. azollae—revealing genes potentially essential to the Azolla-Nostoc symbiosis. We observed the absence of differentially expressed glutamine synthetase (GS) and glutamate synthase (GOGAT) genes, leading to questions about how A. filiculoides regulates the machinery it uses for nitrogen assimilation. Ushering A. filiculoides into the era of transcriptomics sets the stage to truly begin to understand the uniqueness of the Azolla-Nostoc symbiosis. © 2019, Springer Nature B.V.Ferns; Nitrogen-assimilation; Nitrogen-fixation; RNA-sequencing; Symbiosisammonium; aquatic plant; cyanobacterium; fern; gene expression; genetic analysis; genomics; metabolite; molecular analysis; RNA; sucrose; symbiosis; Azolla; Azolla filiculoides; Cyanobacteria; Filicophyta; NostocNational Science Foundation, NSF; Duke University; Sigma XiAcknowledgements The authors thank Kathryn Picard, Karla Sosa, Layne Huiet, Tzu-Tong Kao, Deb Greene, the two anonymous reviewers, and the editor of Symbiosis for their support and feedback on the earlier versions of this manuscript. We are also grateful to Henriette Schluepmann for sending us whole plants of Azolla filiculoides, Eric Monson for expertise in data visualization, David Corcoran for consultation on the transcription factor enrichment analysis, Joseph Jackson and Daniel Higginbotham for computational troubleshooting, and Daniele Armaleo for help and resources with qPCR. The first author is especially grateful to these funding sources: National Science Foundation Graduate Research Fellowship Program, Sigma Xi grant-in-aid of research, Duke Biology grant-in-aid of research, and the Botanical Society of America for conferring the Edgar T. Wherry award to the first author’s presentation of this as a contributed paper in the Pteridological section of Botany 2018. This paper is part of a doctoral dissertation completed at Duke University by ANE under the direction of KMP.The authors thank Kathryn Picard, Karla Sosa, Layne Huiet, Tzu-Tong Kao, Deb Greene, the two anonymous reviewers, and the editor of Symbiosis for their support and feedback on the earlier versions of this manuscript. We are also grateful to Henriette Schluepmann for sending us whole plants of Azolla filiculoides , Eric Monson for expertise in data visualization, David Corcoran for consultation on the transcription factor enrichment analysis, Joseph Jackson and Daniel Higginbotham for computational troubleshooting, and Daniele Armaleo for help and resources with qPCR. The first author is especially grateful to these funding sources: National Science Foundation Graduate Research Fellowship Program, Sigma Xi grant-in-aid of research, Duke Biology grant-in-aid of research, and the Botanical Society of America for conferring the Edgar T. Wherry award to the first author?s presentation of this as a contributed paper in the Pteridological section of Botany 2018. This paper is part of a doctoral dissertation completed at Duke University by ANE under the direction of KMP.Eily, A.N.; Department of Biology, United States; email: ariana.eily@duke.eduSpringer Netherlands3345114SYMBEEnglishSymbiosisArticleFinalScopus2-s2.0-85061006467
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Kun P., Mulder I., De Götzen A., Kortuem G.57205027320;57220362850;24724148200;6602781855;Creative data work in the design process2019C and C 2019 - Proceedings of the 2019 Creativity and Cognition346358510.1145/3325480.3325500https://www.scopus.com/inward/record.uri?eid=2-s2.0-85068705750&doi=10.1145%2f3325480.3325500&partnerID=40&md5=cc03490a3af928724b114f0e7329c613Delft University of Technology, Landbergstraat 15, Delft, 2628CE, Netherlands; Aalborg University Copenhagen, A.C. Meyers Vaenge 15, Copenhagen, 2450, DenmarkKun, P., Delft University of Technology, Landbergstraat 15, Delft, 2628CE, Netherlands; Mulder, I., Delft University of Technology, Landbergstraat 15, Delft, 2628CE, Netherlands; De Götzen, A., Aalborg University Copenhagen, A.C. Meyers Vaenge 15, Copenhagen, 2450, Denmark; Kortuem, G., Delft University of Technology, Landbergstraat 15, Delft, 2628CE, NetherlandsThe current work investigates how creativity manifests when designers use data work in the early phase of design. Designers are increasingly interested in utilizing the massive amounts of data surrounding our everyday lives. However, data work is still challenging to incorporate into the design process. In this paper, we present a case study with three novice design teams who were tasked to integrate data work into their design process. During the study, we observed how creativity took place in framing a design problem. We present and discuss their actions from a creativity process perspective, highlighting how they used and rationalized data-inspired inquiries creatively in the early phase of design. The current results inform the development of a design framework to structure data work methodologically and coherently into design processes. We coin this design framework Exploratory Data Inquiry. © 2019 ACM.Creative data work; Data science; Design inquiry; Design methodology; Exploratory data analysisData Science; Creative data work; Creativity process; Design frameworks; Design Methodology; Design problems; Design process; Exploratory data analysis; Structure data; DesignEuropean Commission, EC: H2020-ICT-2015-687818 Open4CitizensThe authors would like to express their appreciations for Mi-lene Goncalves for the fruitful discussions leading up to the presented work and to the students participating in the study. The presented research is partially funded by the European Commission under grant agreement H2020-ICT-2015-687818 Open4Citizens.ACM SIGCHIAssociation for Computing Machinery, Inc12th ACM Creativity and Cognition Conference, C and C 201923 June 2019 through 26 June 20191487529781450359177EnglishC C - Proc. Creativity CognConference PaperFinalScopus2-s2.0-85068705750
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Guebila M.B., Thiele I.57203845512;9037011100;Predicting gastrointestinal drug effects using contextualized metabolic models2019PLoS Computational Biology156e1007100610.1371/journal.pcbi.1007100https://www.scopus.com/inward/record.uri?eid=2-s2.0-85068901758&doi=10.1371%2fjournal.pcbi.1007100&partnerID=40&md5=c99a7a7819a7c4e74e112d64b76b3bd8Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland; Discipline of Microbiology, School of Natural Sciences, National University of Ireland, Galway, University RoadGalway, IrelandGuebila, M.B., Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Thiele, I., Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg, School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland, Discipline of Microbiology, School of Natural Sciences, National University of Ireland, Galway, University RoadGalway, IrelandGastrointestinal side effects are among the most common classes of adverse reactions associated with orally absorbed drugs. These effects decrease patient compliance with the treatment and induce undesirable physiological effects. The prediction of drug action on the gut wall based on in vitro data solely can improve the safety of marketed drugs and first-in-human trials of new chemical entities. We used publicly available data of drug-induced gene expression changes to build drug-specific small intestine epithelial cell metabolic models. The combination of measured in vitro gene expression and in silico predicted metabolic rates in the gut wall was used as features for a multilabel support vector machine to predict the occurrence of side effects. We showed that combining local gut wall-specific metabolism with gene expression performs better than gene expression alone, which indicates the role of small intestine metabolism in the development of adverse reactions. Furthermore, we reclassified FDA-labeled drugs with respect to their genetic and metabolic profiles to show hidden similarities between seemingly different drugs. The linkage of xenobiotics to their transcriptomic and metabolic profiles could take pharmacology far beyond the usual indica-tion-based classifications. © 2019 Ben Guebila.Article; computer model; controlled study; Food and Drug Administration; gastrointestinal symptom; gene expression; in vitro study; intestine epithelium cell; intestine wall; metabolism; prediction; receiver operating characteristic; small intestine; support vector machine; transcriptomics; xenobiotic metabolism; adverse drug reaction; biological model; biology; drug effect; human; metabolism; metabolome; oral drug administration; small intestine; xenobiotic agent; Administration, Oral; Computational Biology; Drug-Related Side Effects and Adverse Reactions; Humans; Intestine, Small; Metabolome; Models, Biological; Support Vector Machine; XenobioticsXenobioticsHorizon 2020 Framework Programme, H2020: 757922; Fonds National de la Recherche Luxembourg, FNR: FNR/A12/ 01This study received funding from the Luxembourg National Research Fund 519 (FNR), 522 through the ATTRACT programme (FNR/A12/ 01) and the European Research 520 523 Council (ERC) under the European Union?s Horizon 2020 research and innovation 521 524 programme (grant agreement No 757922). The funders had no role in study design, 525 data collection and analysis, decision to publish, or preparation of the manuscript.Thiele, I.; Luxembourg Centre for Systems Biomedicine, Luxembourg; email: ines.thiele@nuigalway.iePublic Library of Science1553734X31242176EnglishPLoS Comput. Biol.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85068901758
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Wang Z., Bach B., Dingwall H.57202051406;37103551800;57209312158;Teaching data visualization and storytelling with data comic workshops2019Conference on Human Factors in Computing Systems - Proceedings3299043510.1145/3290607.3299043https://www.scopus.com/inward/record.uri?eid=2-s2.0-85067272993&doi=10.1145%2f3290607.3299043&partnerID=40&md5=1d13a12b0171b05e0ebc2a826b804338University of Edinburgh, Edinburgh, United KingdomWang, Z., University of Edinburgh, Edinburgh, United Kingdom; Bach, B., University of Edinburgh, Edinburgh, United Kingdom; Dingwall, H., University of Edinburgh, Edinburgh, United KingdomThis paper presents a method for hands-on creation of data comics in a workshop context and includes a description of the results, lessons learned and future improvements. Data comics is a promising format for data-driven storytelling, leveraging the power of data visualization and visual storytelling with comics. However, authoring data comics requires a diverse range of skills that are both creative and analytical. The workshop was developed to refine a blue-print for future workshops; building in reflections on challenges and potential improvements. Within a 3-week assignment for an illustration class, we ran three 3-hour sessions. Our design was informed by the experiences of previous datacomics workshops. Results show the creative potential of data comics. Challenges to learn from the workshop include the stages to introduce data visualizations and journalistic narratives, the structuring of stories and the method of developing iterations of comic drafts. We close by reflecting on these challenges and how they can inform future improvements and adaptations. © 2019 Copyright held by the owner/author(s). ACMCreative workshop; Data Comics; Data Visualization; Data-driven StorytellingHuman computer interaction; Human engineering; Visualization; Creative potentials; Creative workshops; Data Comics; Data driven; Diverse range; Future improvements; Visual storytellings; Data visualizationACM SIGCHIAssociation for Computing Machinery2019 CHI Conference on Human Factors in Computing Systems, CHI EA 20194 May 2019 through 9 May 20191477719781450359719EnglishConf Hum Fact Comput Syst ProcConference PaperFinalScopus2-s2.0-85067272993
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Caffrey A.R., Babcock Z.R., Lopes V.V., Timbrook T.T., LaPlante K.L.35323937900;57195326636;37021553300;55630261300;13409111500;Heterogeneity in the treatment of bloodstream infections identified from antibiotic exposure mapping2019Pharmacoepidemiology and Drug Safety285707715210.1002/pds.4761https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064910825&doi=10.1002%2fpds.4761&partnerID=40&md5=bcfdaca651615fa1f5540e451427927bInfectious Diseases Research Program and Center of Innovation in Long-term Services and Supports, Veterans Affairs Medical Center, Providence, RI, United States; College of Pharmacy, University of Rhode Island, Kingston, RI, United States; Department of Health Services, Policy and Practice, Brown University School of Public Health, Providence, RI, United States; Department of Pharmacy, University of Utah Health, Salt Lake City, UT, United StatesCaffrey, A.R., Infectious Diseases Research Program and Center of Innovation in Long-term Services and Supports, Veterans Affairs Medical Center, Providence, RI, United States, College of Pharmacy, University of Rhode Island, Kingston, RI, United States, Department of Health Services, Policy and Practice, Brown University School of Public Health, Providence, RI, United States; Babcock, Z.R., College of Pharmacy, University of Rhode Island, Kingston, RI, United States; Lopes, V.V., Infectious Diseases Research Program and Center of Innovation in Long-term Services and Supports, Veterans Affairs Medical Center, Providence, RI, United States; Timbrook, T.T., Department of Pharmacy, University of Utah Health, Salt Lake City, UT, United States; LaPlante, K.L., Infectious Diseases Research Program and Center of Innovation in Long-term Services and Supports, Veterans Affairs Medical Center, Providence, RI, United States, College of Pharmacy, University of Rhode Island, Kingston, RI, United StatesPurpose: As changes in antibiotic therapy are common, intent-to-treat and definitive therapy exposure definitions in infectious disease clinical trials and observational studies may not accurately reflect all antibiotics received over the course of the infection. Therefore, we sought to describe changes in antibiotic therapy and unique treatment patterns among patients with bacteremia. Methods: We conducted a retrospective cohort study of hospitalizations from Veterans Affairs (VA) Medical Centers (January 2002-September 2015) and community hospitals (de-identified Optum Clinformatics DataMart with matched Premier Hospital data; October 2009-March 2013). In the VA population, antibiotic exposures were mapped from the culture collection date among those with positive Staphylococcus aureus cultures. In the Optum-Premier population, exposures were mapped from the admission date among those with a primary diagnosis of bacteremia. Results: Our study included 50 467 bacteremia admissions, with only 14% of admissions having the same treatment pattern as another admission. For every 100 bacteremia admissions, 89 had changes in antibiotic therapy. For every 100 bacteremia admissions with changes in therapy, 95 had unique antibiotic treatment patterns. These findings were consistent in both populations, over time, and among different facilities within study populations. The median time to first therapy change was 2 days after initial therapy, with a median of three changes. Conclusions: Changes in antibiotic therapy for bloodstream infections were nearly universal regardless of hospital setting. Based on our findings, common antibiotic exposure definitions of intent-to-treat and definitive therapy would misclassify exposure in 86% of admissions, which highlights the need for better operational definitions of exposure in infectious diseases research. © 2019 The Authors. Pharmacoepidemiology & Drug Safety Published by John Wiley & Sons Ltdantibiotics; bacteremia; exposure mapping; pharmacoepidemiology; Staphylococcus aureus; treatment patternsantibiotic agent; azithromycin; cefazolin; cefepime; ceftriaxone; ciprofloxacin; gentamicin; levofloxacin; metronidazole; nafcillin; piperacillin plus tazobactam; vancomycin; antiinfective agent; adult; aged; antibiotic therapy; Article; bacteremia; bacterium culture; bloodstream infection; community hospital; female; health care facility; hospital admission; hospitalization; human; major clinical study; male; priority journal; public hospital; retrospective study; Staphylococcus aureus; treatment planning; bacteremia; cohort analysis; comorbidity; drug effect; length of stay; methicillin resistant Staphylococcus aureus; microbiology; middle aged; mortality; Staphylococcus infection; treatment duration; treatment outcome; Aged; Anti-Bacterial Agents; Bacteremia; Cohort Studies; Comorbidity; Duration of Therapy; Female; Hospitals, Veterans; Humans; Length of Stay; Male; Methicillin-Resistant Staphylococcus aureus; Middle Aged; Retrospective Studies; Staphylococcal Infections; Treatment Outcomeazithromycin, 83905-01-5, 117772-70-0, 121470-24-4; cefazolin, 25953-19-9, 27164-46-1; cefepime, 88040-23-7; ceftriaxone, 73384-59-5, 74578-69-1; ciprofloxacin, 85721-33-1; gentamicin, 1392-48-9, 1403-66-3, 1405-41-0; levofloxacin, 100986-85-4, 138199-71-0; metronidazole, 39322-38-8, 443-48-1; nafcillin, 147-52-4, 985-16-0; vancomycin, 1404-90-6, 1404-93-9; Anti-Bacterial AgentsU.S. Department of Veterans Affairs, VA; Pfizer; Merck; Research and Development; Office of Research and Development, ORDThe views expressed are those of the authors and do not necessarily reflect the position or policy of the United States Department of Veterans Affairs. This material is based upon work supported, in part, by the Office of Research and Development, Department of Veterans Affairs. This work was unfunded, and the authors received no specific funding for this work.This study was approved by the Institutional Review Board and Research and Development Committee of the Providence VAMC and approved as exempt by the University of Rhode Island's Institutional Review Board.Aisling Caffrey has received research funding from Pfizer, Merck (Cubist), and The Medicines Company. Zachary Babcock and Vrishali Lopes have no conflicts to disclose. Tristan Timbrook has received honoraria for speaking and/or consulting from BioFire Diagnostics, GenMark Diagnostics, and Roche Diagnostics. Kerry LaPlante has received research funding or acted as a scientific advisor for Allergan, Bard, Merck (Cubist), Pfizer, and The Medicines Company.Caffrey, A.R.; Infectious Diseases Research Program and Center of Innovation in Long-term Services and Supports, United States; email: aisling_caffrey@uri.eduJohn Wiley and Sons Ltd10538569PDSAE30916833EnglishPharmacoepidemiol. Drug Saf.ArticleFinalAll Open Access, Hybrid Gold, GreenScopus2-s2.0-85064910825
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Bae J., Havsol J., Karpefors M., Karlsson A., Mathiason G.36615208900;57207849309;6602148805;25655035500;24450494500;Short text topic modeling to identify trends on wearable bio-sensors in different media type2019Proceedings - 6th International Symposium on Computational and Business Intelligence, ISCBI 201886383078993110.1109/ISCBI.2018.00027https://www.scopus.com/inward/record.uri?eid=2-s2.0-85063041846&doi=10.1109%2fISCBI.2018.00027&partnerID=40&md5=9ea4c900480b6c18e3ff0cd9917091e8School of Informatics, University of Skövde, Skövde, Sweden; AstraZeneca, Gothenburg, SwedenBae, J., School of Informatics, University of Skövde, Skövde, Sweden; Havsol, J., AstraZeneca, Gothenburg, Sweden; Karpefors, M., AstraZeneca, Gothenburg, Sweden; Karlsson, A., School of Informatics, University of Skövde, Skövde, Sweden; Mathiason, G., School of Informatics, University of Skövde, Skövde, SwedenThe technology and techniques for bio-sensors are rapidly evolving. Accordingly, there is significant business interest to identify upcoming technologies and new targets for the near future. Text information from internet reflects much of the recent information and public interests that help to understand the trend of a certain field. Thus, we utilize Dirichlet process topic modeling on different media sources containing short text (e.g., blogs, news) which is able to self-adapt the learned topic space to the data. We share the observations from the domain experts on the results derived from topic modeling on wearable biosensors from multiple media sources over more than eight years. We analyze the topics on wearable devices, forecast and market analysis, and bio-sensing techniques found from our method. © 2018 IEEE.Bayesian non-parametrics; Bio-sensor; short text; topic modeling; wearableBiosensors; Information analysis; Bayesian nonparametrics; Dirichlet process; Market analysis; Short texts; Text information; Topic Modeling; wearable; Wearable devices; Wearable sensorsStiftelsen för Kunskaps- och Kompetensutveckling, KKS: 2105/23ACKNOWLEDGMENTS We thank our collaboration partner Recorded Future for the support with their system. This work was performed under the project “Picking the Winners: Forecasting Emergent Technology through Bibliometrics/Altmetrics, Topic Modeling and Information Fusion” funded by the Swedish Knowledge Foundation under grant 2105/23.Institute of Electrical and Electronics Engineers Inc.6th International Symposium on Computational and Business Intelligence, ISCBI 201827 August 2018 through 29 August 20181450229781538694503EnglishProc. - Int. Symp. Comput. Bus. Intell., ISCBIConference PaperFinalScopus2-s2.0-85063041846
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Martínez-García M., Vallejo M., Hernández-Lemus E., Álvarez-Díaz J.A.57200414115;7004446142;56000877400;22937134400;Novel methods of qualitative analysis for health policy research2019Health Research Policy and Systems1716310.1186/s12961-018-0404-zhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85059954444&doi=10.1186%2fs12961-018-0404-z&partnerID=40&md5=25aa15fa2b153c11ef7a3c9c4123587aSociomedical Research Department, National Institute of Cardiology, Juan Badiano 1, Mexico City, 14080, Mexico; Computational Genomics Division, National Institute of Genomic Medicine, Periférico Sur 4809, Mexico City, 14610, Mexico; Medical School, Autonomous Metropolitan University, Calzada del Hueso 1100, Mexico City, 04960, MexicoMartínez-García, M., Sociomedical Research Department, National Institute of Cardiology, Juan Badiano 1, Mexico City, 14080, Mexico; Vallejo, M., Sociomedical Research Department, National Institute of Cardiology, Juan Badiano 1, Mexico City, 14080, Mexico; Hernández-Lemus, E., Computational Genomics Division, National Institute of Genomic Medicine, Periférico Sur 4809, Mexico City, 14610, Mexico; Álvarez-Díaz, J.A., Medical School, Autonomous Metropolitan University, Calzada del Hueso 1100, Mexico City, 04960, MexicoBackground: Currently, thanks to the growing number of public database resources, most evidence on planning and management, healthcare institutions, policies and practices is becoming available to everyone. However, one of the limitations for the advancement of data and literature-driven research has been the lack of flexibility of the methodological resources used in qualitative research. There is a need to incorporate friendly, cheaper and faster tools for the systematic, unbiased analysis of large data corpora, in particular regarding the qualitative aspects of the information (often overlooked). Methods: This article proposes a series of novel techniques, exemplified by the case of the role of Institutional Committees of Bioethics to (1) massively identify the documents relevant to a given issue, (2) extract the fundamental content, focusing on qualitative analysis, (3) synthesize the findings in the published literature, (4) categorize and visualize the evidence, and (5) analyse and report the results. Results: A critical study of the institutional role of public health policies and practices in Institutional Committees of Bioethics was used as an example application of the method. Interactive strategies were helpful to define and conceptualise variables, propose research questions and refine research interpretation. These methods are additional aids to systematic reviews, pre-coding schemes and construction of a priori diagrams to survey and analyse social science literature. Conclusions: These novel methods have proven to facilitate the formulation and testing of hypotheses on the subjects to be studied. Such tools may allow important advances going from descriptive approaches to decision-making and even institutional assessment and policy redesign, by pragmatic reason of time and costs. © 2019 The Author(s).Algorithms; Complex networks; Data mining; Health policy; Healthcare economics and organisations; Social control policiesadult; article; bioethics; data mining; female; health care cost; health care policy; human; male; organization; qualitative analysis; social control; sociology; systematic review; data analysis; decision making; health care delivery; information dissemination; methodology; public health; qualitative research; research; Bioethics; Data Analysis; Decision Making; Delivery of Health Care; Health Policy; Humans; Information Dissemination; Public Health; Qualitative Research; Research; Research Design; Social SciencesConsejo Nacional de Ciencia y Tecnología, CONACYT: 179431/2012This work was supported by CONACYT (grant no.179431/2012) [EHL], as well as by federal funding from the National Institute of Cardiology (Mexico) [MV] and the National Institute of Genomic Medicine (Mexico) [EHL]. [EHL] acknowledges additional support from the 2016 Marcos Moshinsky Chair in the Physical Sciences.Martínez-García, M.; Sociomedical Research Department, Juan Badiano 1, Mexico; email: mireya.martinez@cardiologia.org.mxBioMed Central Ltd.1478450530642358EnglishHealth Res. Policy Syst.ArticleFinalAll Open Access, Gold, GreenScopus2-s2.0-85059954444
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Hogräfer M., Schulz H.-J.57203549091;24367269700;ReVize: A library for visualization toolchaining with vega-lite2019Italian Chapter Conference 2019 - Smart Tools and Apps in computer Graphics, STAG 2019129139310.2312/stag.20191375https://www.scopus.com/inward/record.uri?eid=2-s2.0-85081615547&doi=10.2312%2fstag.20191375&partnerID=40&md5=6f356afd5265d239392efb435d36d63aDepartment of Computer Science, Aarhus University, DenmarkHogräfer, M., Department of Computer Science, Aarhus University, Denmark; Schulz, H.-J., Department of Computer Science, Aarhus University, DenmarkThe field of tools for data visualization has been growing in recent years, with each tool contributing new ways to create and work with visualizations, and each offering a specialized set of features, interaction metaphors and user interfaces. This means on one hand that users have a wide choice in visualization tools. On the other hand, though, this choice might also lock-in the user: Once made, it becomes difficult and sometimes even impossible to switch to another tool - e.g., to further refine a visualization made in one tool inside another. In turn, users are forced to work around any shortcomings of the chosen tool, as switching to another tool is even more cumbersome. In this paper, we introduce ReVize, an open-source library for visualization toolchaining. ReVize makes use of Vega-Lite as a common exchange format to be able to add toolchain support to web-based tools. In contrast to existing approaches, this solution to visualization toolchaining allows for authoring a visualization with multiple tools in a back-and-forth fashion, without a preset order in which tools are to be used. We demonstrate ReVize by adding toolchain support to three existing tools - KNIME, ColorBrewer, and VisFlow - for using them in concert to author visualizations. © 2019 The Author(s) Eurographics Proceedings © 2019 The Eurographics Association.User interfaces; Visualization; Exchange format; Interaction metaphors; Lock-in; Multiple tools; Open-source libraries; Visualization tools; Web-based tools; Data visualizationDeutsche Forschungsgemeinschaft, DFGThe authors would like to thank Jo Vermeulen, Henrik Korsgaard, and the anonymous reviewers for their valuable input to this paper. The idea for this paper originated in part from the UniVA research project funded by the German Research Foundation (DFG).Agus M.Corsini M.Pintus R.Eurographics Association2019 Italian Chapter Conference - Smart Tools and Apps in Computer Graphics, STAG 201914 November 2019 through 15 November 20191599829783038681007EnglishItal. Chapter Conf. - Smart Tools Apps Comput. Graph., STAGConference PaperFinalScopus2-s2.0-85081615547