51
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Zhuang H, Huang TY, Acuna DE. Graphical integrity issues in open access publications: Detection and patterns of proportional ink violations. PLoS Comput Biol 2021; 17:e1009650. [PMID: 34898598 PMCID: PMC8700024 DOI: 10.1371/journal.pcbi.1009650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/23/2021] [Accepted: 11/16/2021] [Indexed: 11/19/2022] Open
Abstract
Academic graphs are essential for communicating complex scientific ideas and results. To ensure that these graphs truthfully reflect underlying data and relationships, visualization researchers have proposed several principles to guide the graph creation process. However, the extent of violations of these principles in academic publications is unknown. In this work, we develop a deep learning-based method to accurately measure violations of the proportional ink principle (AUC = 0.917), which states that the size of shaded areas in graphs should be consistent with their corresponding quantities. We apply our method to analyze a large sample of bar charts contained in 300K figures from open access publications. Our results estimate that 5% of bar charts contain proportional ink violations. Further analysis reveals that these graphical integrity issues are significantly more prevalent in some research fields, such as psychology and computer science, and some regions of the globe. Additionally, we find no temporal and seniority trends in violations. Finally, apart from openly releasing our large annotated dataset and method, we discuss how computational research integrity could be part of peer-review and the publication processes.
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Affiliation(s)
- Han Zhuang
- School of Information Studies, Syracuse University, Syracuse, New York, United States of America
| | - Tzu-Yang Huang
- School of Information Studies, Syracuse University, Syracuse, New York, United States of America
| | - Daniel E. Acuna
- School of Information Studies, Syracuse University, Syracuse, New York, United States of America
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52
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Rebeaud ME, Cova F, Ruggeri V, Rochoy M. Raising public awareness about the misuse of predatory journals: One year after the "hydroxychloroquine and push-scooters accidents" hoax. Therapie 2021; 77:373-375. [PMID: 34819237 DOI: 10.1016/j.therap.2021.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Mathieu E Rebeaud
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Florian Cova
- Philosophy Department, University of Geneva, 1211 Geneva, Switzerland
| | - Valentin Ruggeri
- Nuclear Medicine Department, Grenoble-Alpes University Hospital, 38000 Grenoble, France
| | - Michaël Rochoy
- Collectif Du Côté de la Science, 62230 Outreau France; ULR 2694 - METRICS, CERIM, Département de Médecine Générale, University Lille, CHU Lille, 59000 Lille, France.
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53
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Asymptomatic infection is the pandemic's dark matter. Proc Natl Acad Sci U S A 2021; 118:2114054118. [PMID: 34526404 PMCID: PMC8463787 DOI: 10.1073/pnas.2114054118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 01/02/2023] Open
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54
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Dombrowski SC, J. McGill R, Farmer RL, Kranzler JH, Canivez GL. Beyond the Rhetoric of Evidence-Based Assessment: A Framework for Critical Thinking in Clinical Practice. SCHOOL PSYCHOLOGY REVIEW 2021. [DOI: 10.1080/2372966x.2021.1960126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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55
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Teodoro D, Ferdowsi S, Borissov N, Kashani E, Vicente Alvarez D, Copara J, Gouareb R, Naderi N, Amini P. Information retrieval in an infodemic: the case of COVID-19 publications. J Med Internet Res 2021; 23:e30161. [PMID: 34375298 PMCID: PMC8451964 DOI: 10.2196/30161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/22/2021] [Accepted: 08/05/2021] [Indexed: 12/31/2022] Open
Abstract
Background The COVID-19 global health crisis has led to an exponential surge in published scientific literature. In an attempt to tackle the pandemic, extremely large COVID-19–related corpora are being created, sometimes with inaccurate information, which is no longer at scale of human analyses. Objective In the context of searching for scientific evidence in the deluge of COVID-19–related literature, we present an information retrieval methodology for effective identification of relevant sources to answer biomedical queries posed using natural language. Methods Our multistage retrieval methodology combines probabilistic weighting models and reranking algorithms based on deep neural architectures to boost the ranking of relevant documents. Similarity of COVID-19 queries is compared to documents, and a series of postprocessing methods is applied to the initial ranking list to improve the match between the query and the biomedical information source and boost the position of relevant documents. Results The methodology was evaluated in the context of the TREC-COVID challenge, achieving competitive results with the top-ranking teams participating in the competition. Particularly, the combination of bag-of-words and deep neural language models significantly outperformed an Okapi Best Match 25–based baseline, retrieving on average, 83% of relevant documents in the top 20. Conclusions These results indicate that multistage retrieval supported by deep learning could enhance identification of literature for COVID-19–related questions posed using natural language.
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Affiliation(s)
- Douglas Teodoro
- HES-SO University of Applied Arts and Sciences of Western Switzerland, Rue de la Tambourine 17, Carouge, CH.,SIB Swiss Institute of Bioinformatics, Lausanne, CH
| | - Sohrab Ferdowsi
- HES-SO University of Applied Arts and Sciences of Western Switzerland, Rue de la Tambourine 17, Carouge, CH
| | | | - Elham Kashani
- Institute of Pathology, University of Bern, Bern, CH
| | - David Vicente Alvarez
- HES-SO University of Applied Arts and Sciences of Western Switzerland, Rue de la Tambourine 17, Carouge, CH
| | - Jenny Copara
- HES-SO University of Applied Arts and Sciences of Western Switzerland, Rue de la Tambourine 17, Carouge, CH.,SIB Swiss Institute of Bioinformatics, Lausanne, CH.,University of Geneva, Geneva, CH
| | - Racha Gouareb
- HES-SO University of Applied Arts and Sciences of Western Switzerland, Rue de la Tambourine 17, Carouge, CH
| | - Nona Naderi
- HES-SO University of Applied Arts and Sciences of Western Switzerland, Rue de la Tambourine 17, Carouge, CH.,SIB Swiss Institute of Bioinformatics, Lausanne, CH
| | - Poorya Amini
- Risklick AG, Bern, CH.,Clinical Trials Unit Bern, Bern, CH
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56
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Baveye PC. Objectivity of the peer‐review process: Enduring myth, reality, and possible remedies. LEARNED PUBLISHING 2021. [DOI: 10.1002/leap.1414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Philippe C. Baveye
- Université Paris‐Saclay avenue Lucien Brétignières Thiverval‐Grignon 78850 France
- Saint Loup Research Institute 7 rue des chênes, La Grande Romelière Saint Loup Lamairé 79600 France
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57
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Ferraro PJ, Agrawal A. Synthesizing evidence in sustainability science through harmonized experiments: Community monitoring in common pool resources. Proc Natl Acad Sci U S A 2021; 118:e2106489118. [PMID: 34257156 PMCID: PMC8307536 DOI: 10.1073/pnas.2106489118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Paul J Ferraro
- Carey Business School, The Johns Hopkins University, Baltimore, MD 21202;
- Department of Environmental Health and Engineering, a joint department of the Bloomberg School of Public Health and the Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD 21212
| | - Arun Agrawal
- School for Environment and Sustainability, Gerald R. Ford School of Public Policy, University of Michigan, Ann Arbor, MI 48109
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58
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Malpica‐Cruz L, Abadía‐Cardoso A, Aquino‐Baleytó M, Beas‐Luna R, Becerril‐García EE, Castillo‐Géniz JL, Galván‐Magaña F, García‐Rodríguez E, Herzka SZ, Hoyos‐Padilla EM, Lara‐Mendoza RE, Lorda J, Oñate‐González EC, Pérez‐Weil RJ, Saavedra‐Sotelo NC, Santana‐Morales O, Towns V, Zepeda‐Domínguez JA. Empowering fishers for Great White Shark stewardship: Reply to Madigan et al. 2021. Conserv Lett 2021. [DOI: 10.1111/conl.12828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Luis Malpica‐Cruz
- Universidad Autónoma de Baja California Instituto de Investigaciones Oceanológicas Carretera Ensenada‐Tijuana 3917, Fraccionamiento Playitas Ensenada Baja California 22860 México
- ECOCIMATI A.C., Av. del Puerto 2270 Colonia Hidalgo Ensenada Baja California 22880 México
| | - Alicia Abadía‐Cardoso
- Universidad Autónoma de Baja California Facultad de Ciencias Marinas Carretera Ensenada‐Tijuana 3917, Fraccionamiento Playitas Ensenada Baja California 22860 México
| | - Marc Aquino‐Baleytó
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas Av. Instituto Politécnico Nacional S/N La Paz Baja California Sur 23096 México
| | - Rodrigo Beas‐Luna
- Universidad Autónoma de Baja California Facultad de Ciencias Marinas Carretera Ensenada‐Tijuana 3917, Fraccionamiento Playitas Ensenada Baja California 22860 México
| | - Edgar E. Becerril‐García
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas Av. Instituto Politécnico Nacional S/N La Paz Baja California Sur 23096 México
- Pelagios Kakunjá A.C. Sinaloa 1540 La Paz Baja California Sur 23070 México
| | - José L. Castillo‐Géniz
- Centro Regional de Investigación Acuícola y Pesquera de Ensenada Instituto Nacional de Pesca y Acuacultura Carr. Tijuana‐Ensenada km 97.5 Ensenada Baja California 22760 México
| | - Felipe Galván‐Magaña
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas Av. Instituto Politécnico Nacional S/N La Paz Baja California Sur 23096 México
| | - Emiliano García‐Rodríguez
- Departamento de Oceanografía Biológica Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE) Carretera Ensenada‐Tijuana 3918, Zona Playitas Ensenada Baja California 22860 México
| | - Sharon Z. Herzka
- Departamento de Oceanografía Biológica Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE) Carretera Ensenada‐Tijuana 3918, Zona Playitas Ensenada Baja California 22860 México
| | | | - Raúl E. Lara‐Mendoza
- Dirección General Adjunta de Investigación Pesquera en el Atlántico Instituto Nacional de Pesca y Acuacultura. SADER. Ciudad de México México
| | - Julio Lorda
- Universidad Autónoma de Baja California Facultad de Ciencias Carretera Ensenada‐Tijuana 3917, Fraccionamiento Playitas Ensenada Baja California 22860 México
| | - Erick C. Oñate‐González
- Universidad Autónoma de Nuevo León Facultad de Ciencias Biológicas Av. Pedro de Alba y Manuel L. Barragán s/n. Cd. Universitaria San Nicolás de los Garza Nuevo León 66455 México
| | - Rodrigo J. Pérez‐Weil
- Comisión Nacional de Áreas Naturales Protegidas. Avenida Ejército Nacional 223 Anahuac I Sección Miguel Hidalgo Ciudad de México 11320 México
| | - Nancy C. Saavedra‐Sotelo
- Universidad Autónoma de Sinaloa Facultad de Ciencias del Mar Paseo Claussen S/N, Los Pinos Mazatlán Sinaloa 82040 México
| | - Omar Santana‐Morales
- ECOCIMATI A.C., Av. del Puerto 2270 Colonia Hidalgo Ensenada Baja California 22880 México
- Universidad Autónoma de Baja California Facultad de Ciencias Marinas Carretera Ensenada‐Tijuana 3917, Fraccionamiento Playitas Ensenada Baja California 22860 México
| | - Valeria Towns
- Instituto de Ecología, Universidad Nacional Autónoma de México. Circuito Universitario Ciudad Universitaria Ciudad de México 04510 México
| | - José A. Zepeda‐Domínguez
- Universidad Autónoma de Baja California Facultad de Ciencias Marinas Carretera Ensenada‐Tijuana 3917, Fraccionamiento Playitas Ensenada Baja California 22860 México
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59
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Bak-Coleman JB, Alfano M, Barfuss W, Bergstrom CT, Centeno MA, Couzin ID, Donges JF, Galesic M, Gersick AS, Jacquet J, Kao AB, Moran RE, Romanczuk P, Rubenstein DI, Tombak KJ, Van Bavel JJ, Weber EU. Stewardship of global collective behavior. Proc Natl Acad Sci U S A 2021; 118:e2025764118. [PMID: 34155097 PMCID: PMC8271675 DOI: 10.1073/pnas.2025764118] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Collective behavior provides a framework for understanding how the actions and properties of groups emerge from the way individuals generate and share information. In humans, information flows were initially shaped by natural selection yet are increasingly structured by emerging communication technologies. Our larger, more complex social networks now transfer high-fidelity information over vast distances at low cost. The digital age and the rise of social media have accelerated changes to our social systems, with poorly understood functional consequences. This gap in our knowledge represents a principal challenge to scientific progress, democracy, and actions to address global crises. We argue that the study of collective behavior must rise to a "crisis discipline" just as medicine, conservation, and climate science have, with a focus on providing actionable insight to policymakers and regulators for the stewardship of social systems.
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Affiliation(s)
- Joseph B Bak-Coleman
- Center for an Informed Public, University of Washington, Seattle, WA 98195;
- eScience Institute, University of Washington, Seattle, WA 98195
| | - Mark Alfano
- Ethics & Philosophy of Technology, Delft University of Technology, 2628 CD Delft, The Netherlands
- Institute of Philosophy, Australian Catholic University, Banyo Queensland 4014, Australia
| | - Wolfram Barfuss
- Earth System Analysis, Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, 14473 Potsdam, Germany
- Tübingen AI Center, University of Tübingen, 72074 Tübingen, Germany
| | - Carl T Bergstrom
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Miguel A Centeno
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08544
| | - Iain D Couzin
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78315 Radolfzell am Bodensee, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Jonathan F Donges
- Earth System Analysis, Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, 14473 Potsdam, Germany
- Stockholm Resilience Centre, Stockholm University, 11419 Stockholm, Sweden
| | | | - Andrew S Gersick
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Jennifer Jacquet
- Department of Environmental Studies, New York University, New York, NY 10012
| | | | - Rachel E Moran
- Center for an Informed Public, University of Washington, Seattle, WA 98195
| | - Pawel Romanczuk
- Institute for Theoretical Biology, Department of Biology, Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Daniel I Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Kaia J Tombak
- Department of Anthropology, Hunter College of the City University of New York, New York, NY 10065
| | - Jay J Van Bavel
- Department of Psychology, New York University, New York, NY 10003
- Center for Neural Science, New York University, New York, NY 10003
| | - Elke U Weber
- Department of Psychology, Princeton University, Princeton, NJ 08544
- Andlinger Center for Energy and Environment, School of Engineering and Applied Science, Princeton University, Princeton, NJ 08544
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60
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Scheufele DA, Hoffman AJ, Neeley L, Reid CM. Misinformation about science in the public sphere. Proc Natl Acad Sci U S A 2021; 118:e2104068118. [PMID: 33837156 PMCID: PMC8054008 DOI: 10.1073/pnas.2104068118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dietram A Scheufele
- Life Sciences Communication, University of Wisconsin-Madison, Madison, WI 53706;
| | - Andrew J Hoffman
- Ross School of Business, University of Michigan, Ann Arbor, MI 48109
| | | | - Czerne M Reid
- Department of Psychiatry, University of Florida, Gainesville, FL 32610
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