RESUMO
This study uses National Institutes of Health RePORTER data for mentored K awards and R01-equivalent grants to all departments in US schools of medicine to characterize K-award distribution and K-to-R transition by gender and department between 1997 and 2021.
Assuntos
Distinções e Prêmios , Pesquisa Biomédica , Financiamento Governamental , Mentores , Humanos , Pesquisa Biomédica/classificação , Pesquisa Biomédica/economia , Financiamento Governamental/economia , National Institutes of Health (U.S.) , Estados Unidos , Fatores SexuaisRESUMO
The term "biobanking" is often misapplied to any collection of human biological materials (biospecimens) regardless of requirements related to ethical and legal issues or the standardization of different processes involved in tissue collection. A proper definition of biobanks is large collections of biospecimens linked to relevant personal and health information (health records, family history, lifestyle, genetic information) that are held predominantly for use in health and medical research. In addition, the International Organization for Standardization, in illustrating the requirements for biobanking (ISO 20387:2018), stresses the concept of biobanks being legal entities driving the process of acquisition and storage together with some or all of the activities related to collection, preparation, preservation, testing, analysing and distributing defined biological material as well as related information and data. In this review article, we aim to discuss the basic principles of biobanking, spanning from definitions to classification systems, standardization processes and documents, sustainability and ethical and legal requirements. We also deal with emerging specimens that are currently being generated and shaping the so-called next-generation biobanking, and we provide pragmatic examples of cancer-associated biobanking by discussing the process behind the construction of a biobank and the infrastructures supporting the implementation of biobanking in scientific research.
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Bancos de Espécimes Biológicos , Pesquisa Biomédica , Medicina de Precisão , Manejo de Espécimes , Acreditação , Bancos de Espécimes Biológicos/classificação , Bancos de Espécimes Biológicos/ética , Bancos de Espécimes Biológicos/legislação & jurisprudência , Bancos de Espécimes Biológicos/normas , Pesquisa Biomédica/classificação , Pesquisa Biomédica/ética , Pesquisa Biomédica/legislação & jurisprudência , Pesquisa Biomédica/normas , Guias como Assunto , Humanos , Formulação de Políticas , Medicina de Precisão/classificação , Medicina de Precisão/ética , Medicina de Precisão/normas , Manejo de Espécimes/classificação , Manejo de Espécimes/ética , Manejo de Espécimes/normas , Participação dos Interessados , Terminologia como AssuntoAssuntos
Bibliometria , Pesquisa Biomédica/classificação , COVID-19/epidemiologia , COVID-19/metabolismo , Publicações Periódicas como Assunto/classificação , SARS-CoV-2/metabolismo , Antivirais/administração & dosagem , Antivirais/metabolismo , Pesquisa Biomédica/tendências , COVID-19/terapia , Humanos , Publicações Periódicas como Assunto/tendências , SARS-CoV-2/efeitos dos fármacosRESUMO
Racial disparities in cardiovascular and cerebrovascular health outcomes are well described, and recent research has shed light on the mechanistic underpinnings of those disparities. However, "race" is a social construct that is poorly defined and continually evolving and is historically based on faulty premises. The continued categorization by race in physiological research suggests that there are inherent differences between races, rather than addressing the specific underlying factors that result in health disparities between groups. The purpose of this Perspectives article is to provide a brief history of the genesis of categorization by race, why such categorization should be reconsidered in physiology research, and offer recommendations to more directly investigate the underlying factors that result in group disparities in cardiovascular and cerebrovascular health.
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Pesquisa Biomédica , Doenças Cardiovasculares/etnologia , Doenças Cardiovasculares/fisiopatologia , Sistema Cardiovascular/fisiopatologia , Disparidades nos Níveis de Saúde , Fisiologia , Grupos Raciais , Determinantes Sociais da Saúde/etnologia , Pesquisa Biomédica/classificação , Doenças Cardiovasculares/classificação , Humanos , Fisiologia/classificação , Fatores Raciais , Grupos Raciais/classificaçãoRESUMO
Gathering information from the scientific literature is essential for biomedical research, as much knowledge is conveyed through publications. However, the large and rapidly increasing publication rate makes it impractical for researchers to quickly identify all and only those documents related to their interest. As such, automated biomedical document classification attracts much interest. Such classification is critical in the curation of biological databases, because biocurators must scan through a vast number of articles to identify pertinent information within documents most relevant to the database. This is a slow, labor-intensive process that can benefit from effective automation.We present a document classification scheme aiming to identify papers containing information relevant to a specific topic, among a large collection of articles, for supporting the biocuration classification task. Our framework is based on a meta-classification scheme we have introduced before; here we incorporate into it features gathered from figure captions, in addition to those obtained from titles and abstracts. We trained and tested our classifier over a large imbalanced dataset, originally curated by the Gene Expression Database (GXD). GXD collects all the gene expression information in the Mouse Genome Informatics (MGI) resource. As part of the MGI literature classification pipeline, GXD curators identify MGI-selected papers that are relevant for GXD. The dataset consists of ~60 000 documents (5469 labeled as relevant; 52 866 as irrelevant), gathered throughout 2012-2016, in which each document is represented by the text of its title, abstract and figure captions. Our classifier attains precision 0.698, recall 0.784, f-measure 0.738 and Matthews correlation coefficient 0.711, demonstrating that the proposed framework effectively addresses the high imbalance in the GXD classification task. Moreover, our classifier's performance is significantly improved by utilizing information from image captions compared to using titles and abstracts alone; this observation clearly demonstrates that image captions provide substantial information for supporting biomedical document classification and curation.Database URL.
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Pesquisa Biomédica/estatística & dados numéricos , Biologia Computacional/métodos , Curadoria de Dados/métodos , Bases de Dados Factuais , Animais , Pesquisa Biomédica/classificação , Pesquisa Biomédica/métodos , Biologia Computacional/classificação , Mineração de Dados/métodos , Humanos , InternetRESUMO
Finding small homogeneous subgroup cohorts in large heterogeneous populations is a critical process for hypothesis development in biomedical research. Concurrent computational approaches are still lacking in robust answers to the question "what hypotheses are likely to be novel and to produce clinically relevant results with well thought-out study designs?" We have developed a novel subgroup discovery method which employs a deep exploratory mining process to slice and dice thousands of potential subpopulations and prioritize potential cohorts based on their explainable contrast patterns and which may provide interventionable insights. We conducted computational experiments on both synthesized data and a clinical autism data set to assess performance quantitatively for coverage of pre-defined cohorts and qualitatively for novel knowledge discovery, respectively. We also conducted a scaling analysis using a distributed computing environment to suggest computational resource needs for when the subpopulation number increases. This work will provide a robust data-driven framework to automatically tailor potential interventions for precision health.
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Pesquisa Biomédica/classificação , Estudos de Coortes , Mineração de Dados/métodos , Feminino , Humanos , Masculino , Aprendizado de Máquina não SupervisionadoRESUMO
Biomedical event extraction plays an important role in the extraction of biological information from large-scale scientific publications. However, most state-of-the-art systems separate this task into several steps, which leads to cascading errors. In addition, it is complicated to generate features from syntactic and dependency analysis separately. Therefore, in this paper, we propose an end-to-end model based on long short-term memory (LSTM) to optimize biomedical event extraction. Experimental results demonstrate that our approach improves the performance of biomedical event extraction. We achieve average F1-scores of 59.68, 58.23, and 57.39 percent on the BioNLP09, BioNLP11, and BioNLP13's Genia event datasets, respectively. The experimental study has shown our proposed model's potential in biomedical event extraction.
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Pesquisa Biomédica/classificação , Biologia Computacional/métodos , Mineração de Dados/métodos , Redes Neurais de ComputaçãoRESUMO
BACKGROUND: A standard or consensus definition of a systematic review does not exist. Therefore, if there is no definition about a systematic review in secondary studies that analyse them or the definition is too broad, inappropriate studies might be included in such evidence synthesis. The aim of this study was to analyse the definition of a systematic review (SR) in health care literature, elements of the definitions that are used and to propose a starting point for an explicit and non-ambiguous SR definition. METHODS: We included overviews of systematic reviews (OSRs), meta-epidemiological studies and epidemiology textbooks. We extracted the definitions of SRs, as well as the inclusion and exclusion criteria that could indicate which definition of a SR the authors used. We extracted individual elements of SR definitions, categorised and quantified them. RESULTS: Among the 535 analysed sources of information, 188 (35%) provided a definition of a SR. The most commonly used reference points for the definitions of SRs were Cochrane and the PRISMA statement. We found 188 different elements of SR definitions and divided them into 14 categories. The highest number of SR definition elements was found in categories related to searching (N = 51), analysis/synthesis (N = 23), overall methods (N = 22), quality/bias/appraisal/validity (N = 22) and aim/question (N = 13). The same five categories were also the most commonly used combination of categories in the SR definitions. CONCLUSION: Currently used definitions of SRs are vague and ambiguous, often using terms such as clear, explicit and systematic, without further elaboration. In this manuscript we propose a more specific definition of a systematic review, with the ultimate aim of motivating the research community to establish a clear and unambiguous definition of this type of research.
Assuntos
Metanálise como Assunto , Literatura de Revisão como Assunto , Revisões Sistemáticas como Assunto , Humanos , Pesquisa Biomédica/classificação , Pesquisa Biomédica/métodos , Estudos Epidemiológicos , Medicina Baseada em Evidências/classificação , Medicina Baseada em Evidências/métodos , Reprodutibilidade dos Testes , Livros de Texto como AssuntoRESUMO
BACKGROUND: Current methods for assessing strength of evidence prioritize the contributions of randomized controlled trials (RCTs). The objective of this study was to characterize strength of evidence (SOE) tools in recent use, identify their application to lifestyle interventions for improved longevity, vitality, or successful aging, and to assess implications of the findings. METHODS: The search strategy was created in PubMed and modified as needed for four additional databases: Embase, AnthropologyPlus, PsycINFO, and Ageline, supplemented by manual searching. Systematic reviews and meta-analyses of intervention trials or observational studies relevant to lifestyle intervention were included if they used a specified SOE tool. Data was collected for each SOE tool. Conditions necessary for assigning the highest SOE grading and treatment of prospective cohort studies within each SOE rating framework were summarized. The expert panel convened to discuss the implications of findings for assessing evidence in the domain of lifestyle medicine. RESULTS AND CONCLUSIONS: A total of 15 unique tools were identified. Ten were tools developed and used by governmental agencies or other equivalent professional bodies and were applicable in a variety of settings. Of these 10, four require consistent results from RCTs of high quality to award the highest rating of evidence. Most SOE tools include prospective cohort studies only to note their secondary contribution to overall SOE as compared to RCTs. We developed a new construct, Hierarchies of Evidence Applied to Lifestyle Medicine (HEALM), to illustrate the feasibility of a tool based on the specific contributions of diverse research methods to understanding lifetime effects of health behaviors. Assessment of evidence relevant to lifestyle medicine requires a potential adaptation of SOE approaches when outcomes and/or exposures obviate exclusive or preferential reliance on RCTs. This systematic review was registered with the International Prospective Register of Systematic Reviews, PROSPERO [CRD42018082148].
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Pesquisa Biomédica/métodos , Medicina Baseada em Evidências/métodos , Comportamentos Relacionados com a Saúde , Estilo de Vida , Ensaios Clínicos Controlados Aleatórios como Assunto/métodos , Projetos de Pesquisa , Idoso , Envelhecimento , Pesquisa Biomédica/classificação , Medicina Baseada em Evidências/classificação , Humanos , Ensaios Clínicos Controlados Aleatórios como Assunto/classificaçãoRESUMO
In France, the so-called "Jardé law" (named for its proposer) on human research, implemented since 2016, defines the regulatory and legal framework for "prospective" studies, formerly known as "biomedical research" or "common care". Three categories are distinguished: type 1 is at-risk drug or non-drug interventional research, type 2 is low-risk, low-burden interventional research, and type 3 is non-interventional research. The decrees of April 12, 2018 precisely define a list of research categories for types 2 and 3, thereby clarifying the regulatory procedures. The Sponsor registers the trial on the database of the National Drug Safety Agency (ANSM), or the European EudraCT database for drug studies, to obtain an identification number. Regulatory procedures are undertaken with the IRB and ANSM and then the Data Protection Commission (CNIL). Retrospective research on previously collected data (other than genetic) does not come under the Jardé law, and is governed by the 1978 data protection law, updated by the application decree of December 2016 and the law No. 2018-493 of June 20, 2018 on protection of personal data. This article presents a clarification of the key methodologic and regulatory steps.
Assuntos
Estudos Clínicos como Assunto/legislação & jurisprudência , Equipamentos e Provisões , Legislação de Medicamentos , Estudos Prospectivos , Estudos Retrospectivos , Experimentação Humana Terapêutica/legislação & jurisprudência , Pesquisa Biomédica/classificação , Pesquisa Biomédica/legislação & jurisprudência , França , HumanosRESUMO
In Brazil, the CNPq (National Council for Scientific and Technological Development) provides grants, funds and fellowships to productive scientists to support their investigations. They are ranked and categorized into four hierarchical levels ranging from PQ 1A (the highest) to PQ 1D (the lowest). Few studies, however, report and analyse scientific productivity in different sub-fields of Biomedical Sciences (BS), e.g., Biochemistry, Pharmacology, Biophysics and Physiology. In fact, systematic comparisons of productivity among the PQ 1 categories within the above sub-fields are lacking in the literature. Here, the scientific productivity of 323 investigators receiving PQ 1 fellowships (A to D levels) in these sub-fields of BS was investigated. The Scopus database was used to compile the total number of articles, citations, h-index values and authorship positions (first-, co- or last-listed author) in the most cited papers by researchers granted CNPq fellowships. We found that researchers from Pharmacology had the best performance for all of the parameters analysed, followed by those in Biochemistry. There was great variability in scientific productivity within the PQ 1A level in all of the sub-fields of BS, but not within the other levels (1B, 1C and 1D). Analysis of the most cited papers of PQ 1(A-D) researchers in Pharmacology revealed that the citations of researchers in the 1C and 1D levels were associated with publications with their senior supervisors, whereas those in the 1B level were less connected with their supervisors in comparison to those in 1A. Taken together, these findings suggest that the scientific performance of PQ 1A researchers in BS is not homogenous. In our opinion, parameters such as the most cited papers without the involvement of Ph.D. and/or post-doctoral supervisors should be used to make decisions regarding any given researcher's fellowship award level.
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Bibliometria , Disciplinas das Ciências Biológicas/classificação , Pesquisa Biomédica/classificação , Pesquisa Biomédica/economia , Pesquisa Biomédica/normas , Pesquisadores/classificação , Apoio à Pesquisa como Assunto , Autoria/normas , Disciplinas das Ciências Biológicas/economia , Brasil , Bases de Dados Bibliográficas , Eficiência , Feminino , Humanos , Masculino , Pesquisadores/economia , Pesquisadores/normasAssuntos
Alergia e Imunologia/organização & administração , Anticorpos , Pesquisa Biomédica/organização & administração , Sociedades Científicas/organização & administração , Alergia e Imunologia/economia , Anticorpos/isolamento & purificação , Anticorpos/uso terapêutico , Pesquisa Biomédica/classificação , Pesquisa Biomédica/economia , França , Humanos , Sociedades Científicas/economiaRESUMO
The classification of knowledge is essential for understanding between researchers and the advancement of science. In this article a brief classification of clinical research methods is presented. The advantages that researchers use the same nomenclature are recalled, which enables improved communication among researchers, facilitates replication of studies and searches in databases, and helps to establish the aspects that can affect the different research models. They are grouped into four broad categories: epidemiological articles, articles of qualitative methodology, mixed methodology articles and review articles.
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Andrologia , Pesquisa Biomédica/estatística & dados numéricos , Publicações Periódicas como Assunto/estatística & dados numéricos , Pesquisa Biomédica/classificação , Estudos Epidemiológicos , Humanos , Projetos de PesquisaRESUMO
Countries, research institutions, and scholars are interested in identifying and promoting high-impact and transformative scientific research. This paper presents a novel set of text- and citation-based metrics that can be used to identify high-impact and transformative works. The 11 metrics can be grouped into seven types: Radical-Generative, Radical-Destructive, Risky, Multidisciplinary, Wide Impact, Growing Impact, and Impact (overall). The metrics are exemplified, validated, and compared using a set of 10,778,696 MEDLINE articles matched to the Science Citation Index ExpandedTM. Articles are grouped into six 5-year periods (spanning 1983-2012) using publication year and into 6,159 fields constructed using comparable MeSH terms, with which each article is tagged. The analysis is conducted at the level of a field-period pair, of which 15,051 have articles and are used in this study. A factor analysis shows that transformativeness and impact are positively related (ρ = .402), but represent distinct phenomena. Looking at the subcomponents of transformativeness, there is no evidence that transformative work is adopted slowly or that the generation of important new concepts coincides with the obsolescence of existing concepts. We also find that the generation of important new concepts and highly cited work is more risky. Finally, supporting the validity of our metrics, we show that work that draws on a wider range of research fields is used more widely.
Assuntos
Algoritmos , Biologia Computacional/métodos , Fator de Impacto de Revistas , Publicações Periódicas como Assunto/estatística & dados numéricos , Ciência/estatística & dados numéricos , Pesquisa Biomédica/classificação , Pesquisa Biomédica/normas , Pesquisa Biomédica/estatística & dados numéricos , Humanos , Publicações Periódicas como Assunto/classificação , Publicações Periódicas como Assunto/normas , Editoração/classificação , Editoração/normas , Editoração/estatística & dados numéricos , Reprodutibilidade dos Testes , Ciência/classificação , Ciência/normasRESUMO
Today, research is seen as an investment to promote innovation and maintain sustainable social-economic development in all societies. The growth of scientific products and the expansion of knowledge in different scientific fields have entailed more attention to assessments and the impact evaluation of both outcome and process of researchers in all fields. In light of this need, policymakers in the medical field have paid more attention to evaluating the outcomes of research in terms of its impact on the society using many different indicators. In this short communication, the performance of scholarly published scientific products are discussed and the indicators that measure such impacts are evaluated and recommendation is given to APJCP' editorial board on how to align its activities toward achieving better impact and scientometric measures for the journal.
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Pesquisa Biomédica/classificação , Pesquisa Biomédica/normas , Guias como Assunto , Fator de Impacto de Revistas , Revisão por Pares/normas , Comunicação , Humanos , PesquisadoresRESUMO
This article presents a classifier that leverages Wikipedia knowledge to represent documents as vectors of concepts weights, and analyses its suitability for classifying biomedical documents written in any language when it is trained only with English documents. We propose the cross-language concept matching technique, which relies on Wikipedia interlanguage links to convert concept vectors between languages. The performance of the classifier is compared to a classifier based on machine translation, and two classifiers based on MetaMap. To perform the experiments, we created two multilingual corpus. The first one, Multi-Lingual UVigoMED (ML-UVigoMED) is composed of 23,647 Wikipedia documents about biomedical topics written in English, German, French, Spanish, Italian, Galician, Romanian, and Icelandic. The second one, English-French-Spanish-German UVigoMED (EFSG-UVigoMED) is composed of 19,210 biomedical abstract extracted from MEDLINE written in English, French, Spanish, and German. The performance of the approach proposed is superior to any of the state-of-the art classifier in the benchmark. We conclude that leveraging Wikipedia knowledge is of great advantage in tasks of multilingual classification of biomedical documents.
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Pesquisa Biomédica/classificação , Mineração de Dados/métodos , Documentação/classificação , Enciclopédias como Assunto , Bases de Conhecimento , Multilinguismo , Processamento de Linguagem Natural , Semântica , HumanosRESUMO
Diagnostic Test Accuracy (DTA) describes a field of research that aims to assess how well a test is able to detect or exclude a condition of interest. Although geriatric medicine is not as reliant on investigations as other medical disciplines, almost all patient encounters with older adults will involve some form of diagnostic assessment. Thus, understanding the terminology and methods of DTA is essential for any clinician. In this review we use examples based around the diagnosis of dementia to highlight issues in DTA research. Some of these are generic to any DTA research and some are particularly pertinent to older adults. One can apply a test accuracy framework to a clinical question by defining four key components: the condition of interest; the index test(s) (i.e. the assessment(s) of interest); the reference standard (the best available method for assessing the condition of interest) and the population or healthcare setting in which testing takes place. Test accuracy is often described using complementary measures of sensitivity and specificity. However, many other metrics to describe test accuracy are available; in clinical practice predictive values may have greater utility. These and other descriptive statistics can be derived from a two by two table that cross-classifies the index test results with the reference standard results. Test performance and utility is not only determined by accuracy, other measures such as feasibility and acceptability should be considered and may be of particular importance when describing test performance in older adults with physical and cognitive impairments.