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Comment lire un article scientifique en sciences biomédicales
(2025) El-Hage, Jinane; Alarcón, Emilio I.
Naviguer dans la littérature scientifique est difficile, en particulier pour les étudiants qui ne sont pas familiers avec les termes techniques, le jargon et le contenu dense. Beaucoup ont du mal à distiller les messages essentiels ou à relier les résultats à des discussions scientifiques plus larges. Au-delà de la complexité inhérente des articles eux-mêmes, le domaine scientifique ne prend souvent pas en compte d'autres défis importants affectant la compréhension. Ceux-ci incluent un jargon excessif, des limitations linguistiques, des variations culturelles dans la cognition, la neurodivergence et d'autres facteurs liés à la lisibilité. Malgré l'abondance d'informations, le manque d'instruction formelle en lecture et en interprétation des articles de recherche laisse les étudiants mal équipés pour s'engager de manière critique avec la littérature scientifique. Il n'existe pas de solution universelle pour aborder ce problème. Ce livre traite de ces défis en offrant un guide structuré pour lire, résumer et analyser les articles scientifiques. Testés dans un cours obligatoire de communication scientifique à l'Université d'Ottawa, les outils et stratégies présentés ont été conçus pour améliorer la compréhension et la pensée critique. Ici, nous nous appuyons sur des études de cas et des publications en libre accès évaluées par des pairs de notre équipe pour guider les étudiants à travers des stratégies clés pour identifier avec précision les sections critiques des articles de recherche, préparer des résumés significatifs et formuler des questions pertinentes pour une discussion approfondie. Contrairement à d'autres ressources qui se concentrent uniquement sur les revues médicales, ce livre propose des stratégies applicables à travers les disciplines, reflétant la nature interdisciplinaire des enquêtes scientifiques d'aujourd'hui. De plus, ce livre compare les résumés générés par les étudiants avec les résultats de ChatGPT, mettant en évidence les limites de l'IA et la valeur de l'intuition humaine dans l'interprétation scientifique. Cette ressource éducative ouverte permet aux étudiants de naviguer et de communiquer efficacement la science. Dans ce livre, nous proposons quatre outils interactifs pour guider et simplifier la lecture et la compréhension de la littérature scientifique. Une page web dédiée héberge ces outils, ainsi que deux fichiers séparés présentant des exemples réels d'étudiants ayant utilisé la feuille de rapport de résumé pour construire leurs résumés de deux articles différents. Ces exemples sont comparés aux résumés générés par ChatGPT en utilisant les mêmes feuilles. Tous les documents sont disponibles sous forme de PDF interactifs et de fichiers Word, organisés dans l'ordre où ils apparaissent dans le livre. Pour une meilleure expérience, nous recommandons d'ouvrir les versions PDF avec un lecteur PDF tel qu'Adobe Acrobat ou Adobe Reader. Le premier outil est le modèle de définitions de mots/concepts, qui permet aux étudiants d'enregistrer des termes ou concepts inconnus et de les définir avec leurs propres mots. Le deuxième outil, la liste de contrôle, sert de guide de lecture pour aider les lecteurs à évaluer de manière critique et active la lisibilité et la qualité d'un article lors de la première lecture. Le système de score s'appuie sur la liste de contrôle et fournit un cadre plus avancé pour évaluer objectivement diverses sections d'un article, aboutissant à un score global. L'outil final et principal est la feuille de rapport de résumé, conçue pour aider les utilisateurs à créer un résumé structuré de l'article. Cet outil solidifie les concepts clés et minimise le besoin de revenir à l'article original, car le résumé servira de référence autonome. Enfin, nous avons inclus deux fichiers présentant des exemples de feuilles de résumé complétées par deux étudiants différents—chaque fichier comprend des feuilles de résumé de deux articles remplies par des étudiants et les mêmes remplies par ChatGPT—pour illustrer la comparaison.
How to Read a Scientific Paper in Biomedical Sciences
(2025) El-Hage, Jinane; Alarcón, Emilio I.
Navigating scientific literature is challenging, particularly for students unfamiliar with technical terms, jargon, and dense content. Many struggle to distill core messages or connect findings to broader scientific discussions. Beyond the built-in complexity of the papers themselves, the field of science often fails to consider other important challenges affecting comprehension. These include excessive jargon, language limitations, cultural variations in cognition, neurodivergence, and other factors related to readability. Despite abundant information, the lack of formal instruction in reading and interpreting research papers leaves students ill-equipped to engage critically with scientific literature. There is no one size-fits-all approach to tackle this issue. This book addresses these challenges by offering a structured guide to reading, summarizing, and analyzing scientific papers. Piloted in a mandatory science communication course at the University of Ottawa, the tools and strategies presented have been designed to enhance comprehension and critical thinking. Here, we build on case studies and open-access peer-reviewed publications from our team to guide students through key strategies for accurately identifying critical sections of research papers, preparing meaningful summaries, and articulating insightful questions for further discussion. Unlike other resources that focus solely on medical journals, this book provides strategies applicable across disciplines, reflecting on the interdisciplinary nature of today’s scientific inquiries. Additionally, this book compares student-generated summaries with ChatGPT outputs, highlighting the limitations of AI and the value of human insight in scientific interpretation. This Open Educational Resource empowers students to navigate and communicate science effectively. In this book, we offer four interactive tools to guide and simplify the reading and comprehension of scientific literature. A dedicated repository web page hosts these tools, along with two separate files showcasing real examples of students who used the summary report sheet to build their summaries of two different papers. These examples are compared with summaries generated by ChatGPT using the same sheets. All documents are available as interactive PDFs and Word files, organized in the order they appear in the book. For the best experience, we recommend opening the PDF versions with a PDF reader such as Adobe Acrobat or Adobe Reader. The first tool is the Words/Concepts Definitions Template, which allows students to record unfamiliar terms or concepts and define them in their own words. The second tool, the Checklist, serves as a reading guide to help readers critically and actively evaluate a paper’s readability and quality during the initial reading. The Score System builds on the checklist and provides a more advanced framework to objectively assess various sections of a paper, culminating in an overall score. The final and primary tool is the Summary Report Sheet, designed to help users create a structured summary of the paper. This tool solidifies key concepts and minimizes the need to revisit the original paper, as the summary will serve as a standalone reference. Finally, we included two files featuring examples of completed summary sheets by two different students—each file includes summary sheets of two papers filled by students and the same ones filled by ChatGPT—to illustrate the comparison.
Systematic review of validated case definitions to identify hypertensive disorders of pregnancy in administrative healthcare databases
(2023) Johnston, Amy; Dancey, Sonia R; Tseung, Victrine; Skidmore, Becky; Tanuseputro, Peter; Smith, Graeme N; Coutinho, Thais; Edwards, Jodi D
Background Administrative data are frequently used to study cardiovascular disease (CVD) risk in women with hypertensive disorders of pregnancy (HDP). Little is known about the validity of case-finding definitions (CFDs, eg, disease classification codes/algorithms) designed to identify HDP in administrative databases. Methods A systematic review of the literature. We searched MEDLINE, Embase, CINAHL, Web of Science and grey literature sources for eligible studies. Two independent reviewers screened articles for eligibility and extracted data. Quality of reporting was assessed using checklists; risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool, adapted for administrative studies. Findings were summarised descriptively. Results Twenty-six studies were included; most (62%) validated CFDs for a variety of maternal and/or neonatal outcomes. Six studies (24%) reported reference standard definitions for all HDP definitions validated; seven reported all 2×2 table values for ≥1 CFD or they were calculable. Most CFDs (n=83; 58%) identified HDP with high specificity (ie, ≥98%); however, sensitivity varied widely (3%–100%). CFDs validated for any maternal hypertensive disorder had the highest median sensitivity (91%, range: 15%–97%). Quality of reporting was generally poor, and all studies were at unclear or high risk of bias on ≥1 QUADAS-2 domain. Conclusions Even validated CFDs are subject to bias. Researchers should choose the CFD(s) that best align with their research objective, while considering the relative importance of high sensitivity, specificity, negative predictive value and/or positive predictive value, and important characteristics of the validation studies from which they were derived (eg, study prevalence of HDP, spectrum of disease studied, methodological rigour, quality of reporting and risk of bias). Higher quality validation studies on this topic are urgently needed. PROSPERO registration number CRD42021239113.
Systematic reviews of clinical practice guidelines: a methodological guide
(2018) Johnston, Amy; Kelly, Shannon E.; Hsieh, Shu-Ching; Skidmore, Becky; Wells, George A.
Systematic reviews (SRs) of clinical practice guidelines (CPGs) are unique knowledge syntheses that require tailored approaches to, and greater subjectivity in, design and execution compared to other SRs in clinical epidemiology. We provide review authors structured direction on how to design and conduct methodologically rigorous SRs of CPGs.
A systematic review of clinical practice guidelines on the use of low molecular weight heparin and fondaparinux for the treatment and prevention of venous thromboembolism: Implications for research and policy decision-making
(2018) Johnston, Amy; Hsieh, Shu-Ching; Carrier, Marc; Kelly, Shannon E.; Bai, Zemin; Skidmore, Becky; Wells, George A.
Background Venous thromboembolism (VTE) is a major global cause of morbidity and mortality. Low molecular weight heparin (LMWH) and fondaparinux (FDP) are frequently used to treat and prevent VTE and have a variety of safety and practical advantages over other anticoagulants, including use in outpatient settings. These medications are commonly listed on drug formularies, which act as a gateway for health plan prescription coverage by outlining the circumstances under which patients will be covered for specific drugs and drug products. Because patient access to medications is impacted by the nature of their listing on formularies, they must be rigorously reviewed and modernized as new evidence emerges. Methods As part of a broader drug class review team, we completed a systematic review of clinical practice guidelines to determine whether the recommendations they reported aligned with the indications listed for the coverage of LMWH and FDP in an outpatient drug formulary. Guideline quality was assessed using the Appraisal of Guidelines for Research & Evaluation (AGREE) II tool. Recommendation matrices were used to systematically compare, categorize, and summarize included recommendations. Results Twenty-seven guidelines were included from which 168 eligible recommendations were identified. Generally, AGREE II domains were adequately addressed; however, domain five (applicability) was poorly addressed. Most recommendations were based on moderate- to low-quality/limited evidence and reported on the use of LMWHs generally; few reported on specific agents. Conclusions Our findings contributed to the recommendation that the formulary listing for LMWH and FDP be streamlined to include coverage for specific outpatient indications. The paucity of available evidence on the comparative efficacy of specific LMWH agents against each other and FDP limited agent-specific listing recommendations, highlighting the need for high-quality comparative studies on this topic.
Accelerated induction regimens of TNFalpha inhibitors in patients with inflammatory bowel disease: a scoping review protocol
(2018-01-19) Johnston, Amy; Natarajan, Sabrina; Hayes, Meghan; MacDonald, Erika; Shorr, Risa
Introduction Tumour necrosis factor (TNF)-alpha inhibitors are commonly used to treat inflammatory bowel disease (IBD). In patients with IBD who are unresponsive to their first induction dose, the implementation of an ‘accelerated’ induction dose schedule (doses more frequent than recommended in product monographs) is becoming increasingly common. It is unclear whether this practice results in favourable patient outcomes, such as avoidance of surgery and disease remission. As such, there is a need to identify and map the current evidence base on accelerated induction schedules of these medications in the treatment of IBD. Methods and analysis A scoping review will be employed to systematically identify and characterise the nature of scientific literature on accelerated induction regimens of TNF-alpha inhibitors. MEDLINE, Embase, International Pharmaceutical Abstracts and grey literature will be searched to identify relevant studies. The titles/ abstracts of all records and full text of potentially relevant articles will be independently screened for inclusion by two reviewers. Data will be abstracted from included studies by one reviewer and verified for accuracy by another. The findings will be synthesised descriptively. Ethics and dissemination We intend to report the findings of this scoping review in a peer-reviewed journal and a scientific conference. Trial registration This research was registered prospectively with the Open Science Framework (https:// osf. io/ z7n2d/).
Tissue photo-bonding using biopolymer crosslinked with rose bengal
(2016) Pupkaite, Justina; Temkit, Maha; Kochevar, Irene; Suuronen, Erik; Alarcon, Emilio; Griffith, May
Visible light-activated photobonding of tissues presents an attractive alternative to surgical suturing for closing of dermal wounds. The advantages of photo-bonding include reduced inflammation and less scarring. However, the materials currently used for light-activated wound closure allow for only a limited, if any, ability to modulate the biological and mechanical properties of the resulting bonded tissue. Particularly, the micrometric void within dermal wounds presents another obstacle for the photo-bonding materials, since collagen structures are required for the photobonding to occur. Therefore, developing a light-activated biomaterial glue that can overcome these limitations would represent an important advance in translational potential. To this end, we have developed a new generation of photo-bonding materials based on vinyl-modified collagen and rose Bengal that are crosslinkable using visible light.
Brain Natriuretic Peptide Production and Secretion in Inflammation
(2012) Ogawa, Tsuneo; de Bold, Adolfo J
Gene expression and secretion of the cardiac polypeptide hormones atrial natriuretic factor (ANF) and brain natriuretic peptide (BNP) are simultaneously upregulated in various cardiac disorders such as congestive heart failure, ischemic heart disease, and hypertensive heart disease, in which hemodynamic or neuroendocrine changes are key components in the progression of disease. However, during acute cardiac allograft rejection, plasma BNP levels are increased but not those of ANF. Successful treatment of the rejection episode decreases the elevated plasma BNP to prerejection values suggesting that substances related to inflammation may selectively influence BNP gene expression. Indeed, cytokines such as TNFα and IL-1β selectively stimulate cardiac BNP at the transcriptional and translational levels in cardiomyocyte cultures without affecting ANF. This selective BNP increase is seen in vivo, in addition to acute cardiac allograft rejection, in several circumstances where inflammation significantly contributes to the pathogenesis of disease such as in sepsis and in acute myocarditis.
Radionuclide Imaging of Viable Myocardium: Is it Underutilized?
(2011) Mylonas, Ilias; Beanlands, Rob S. B.
Coronary artery disease is the major cause of heart failure in North America. Viability assessment is important as it aims to identify patients who stand to benefit from coronary revascularization. Radionuclide modalities currently used in the assessment of viability include 201Tl SPECT, 99mTc-based SPECT imaging, and 18F-fluorodexoyglucose (18F-FDG)-PET imaging. Different advances have been made in the last year to improve the sensitivity and specificity of these modalities. In addition, the optimum amount of viable (yet dysfunctional) myocardium is important to identify in patients, as a risk–benefit ratio must be considered. Patients with predominantly viable/hibernating myocardium can benefit from revascularization from a mortality and morbidity standpoint. However, in patients with minimal viability (predominantly scarred myocardium), revascularization risk may certainly be too high to justify revascularization without expected benefit. Understanding different radionuclide modalities and new developments in the assessment of viability in ischemic heart failure patients is the focus of this discussion.

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