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2.
World Neurosurg ; 161: 350-353, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-35505554

RESUMO

OBJECTIVE: To investigate whether financial bias exists in hydrocephalus and vertebral augmentation literature. METHODS: A systematic literature search was performed in PubMed of studies concerning vertebral augmentation and cerebrospinal fluid valves. The relationship between reported conflicts of interest and the nature of the conclusion (positive vs. neutral and negative) was analyzed. RESULTS: Having a conflict of interest was significantly associated with reporting a positive conclusion in studies investigating valves for hydrocephalus (92.3% positive conclusion vs. 36.4%; P = 0.001), but not for cement augmentation studies (80.5% positive conclusion vs. 65.7%; P = 0.087). As studies concerning vertebral augmentation implants had only positive conclusions, no analysis could be performed. CONCLUSIONS: Our findings suggest a positive relationship between reported conflict of interest and positive outcome in neurosurgical literature concerning cerebrospinal fluid valves.


Assuntos
Conflito de Interesses , Hidrocefalia , Humanos , Hidrocefalia/cirurgia , Indústrias , PubMed , Publicações
3.
World Neurosurg ; 161: 418-423, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-35505562

RESUMO

BACKGROUND: Classic randomized controlled trials (RCTs) form the cornerstone for medical guidelines and protocols. However, in neurosurgery, RCTs are not always applicable to everyday clinical practice. Pragmatic controlled trials aim to incorporate real-life data with the preservation of the methodologic quality. This study is a systematic literature review of all pediatric neurosurgical RCTs published between 2000 and 2020 and an analysis of their pragmatism. METHODS: An electronic database search was performed in PubMed, EMBASE, and the Cochrane Library to identify all relevant trials. Pragmatism was evaluated retrospectively on 9 domains: eligibility, recruitment, setting, organization, flexibility (delivery and adherence), follow-up, primary outcome, and primary analysis. RESULTS: Of the 1862 studies included, 15 met the inclusion criteria. On average, studies scored between equally pragmatic/explanatory and rather pragmatic (M = 3.59, standard deviation [SD] = 0.56). Lowest ratings were seen for setting (M = 2.80, SD = 1.66) and eligibility (M = 3.20, SD = 1.66). Highest scores of pragmatism were given to analysis (M = 4.67, SD = 0.82) and intervention organization (M = 4.60, SD = 1.06). There was no significant difference between studies based on number of patients included, main subject, or publication year. CONCLUSIONS: Pediatric neurosurgical RCTs scored reasonably well on overall pragmatism. In the future, there will be a greater need for pragmatic controlled trials in pediatric neurosurgery to bridge the divide between real-life data and reliable methodological quality. There is an opportunity to develop further applications of pragmatism tailored to surgical interventions.


Assuntos
Neurocirurgia , Criança , Bases de Dados Factuais , Humanos , Procedimentos Neurocirúrgicos , PubMed
4.
World Neurosurg ; 161: 450-458.e2, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-35505565

RESUMO

OBJECTIVE: Our goal was to investigate the presence of surveys to assess neurosurgical educational content and to propose a novel standardized Neurosurgical Education Outcomes Survey (NEOS) with compatible statistical analyses. METHODS: Google Scholar and PubMed were used to conduct a structured literature review for articles published between January 2000 and July 2021 and containing standardized methodology for assessing neurosurgical educational content. RESULTS: Fifteen studies identified during the search assessed virtual and in-person educational content; however, the literature lacked a standardized assessment. A standardized NEOS was proposed before a comprehensive discussion of compatible statistical analyses. CONCLUSIONS: The NEOS may offer a viable option for comparing in-person and virtual content with respect to learner preferences and subjective and objective feedback. Future studies are needed to explore practical utility in enhancing the quality of neurosurgical educational content.


Assuntos
Internet , Escolaridade , Retroalimentação , Humanos , PubMed
5.
Biomolecules ; 12(4)2022 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-35454109

RESUMO

Finding, exploring and filtering frequent sentence-based associations between a disease and a biomedical entity, co-mentioned in disease-related PubMed literature, is a challenge, as the volume of publications increases. Darling is a web application, which utilizes Name Entity Recognition to identify human-related biomedical terms in PubMed articles, mentioned in OMIM, DisGeNET and Human Phenotype Ontology (HPO) disease records, and generates an interactive biomedical entity association network. Nodes in this network represent genes, proteins, chemicals, functions, tissues, diseases, environments and phenotypes. Users can search by identifiers, terms/entities or free text and explore the relevant abstracts in an annotated format.


Assuntos
Proteínas , Software , Mineração de Dados , Fenótipo , PubMed
6.
Medicina (Kaunas) ; 58(4)2022 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-35454298

RESUMO

Background and Objectives: The advancement of artificial intelligence (AI) based technologies in medicine is progressing rapidly, but the majority of its real-world applications has not been implemented. The establishment of an accurate diagnosis with treatment has now transitioned into an artificial intelligence era, which has continued to provide an amplified understanding of liver cancer as a disease and helped to proceed better with the method of procurement. This article focuses on reviewing the AI in liver-associated diseases and surgical procedures, highlighting its development, use, and related counterparts. Materials and Methods: We searched for articles regarding AI in liver-related ailments and surgery, using the keywords (mentioned below) on PubMed, Google Scholar, Scopus, MEDLINE, and Cochrane Library. Choosing only the common studies suggested by these libraries, we segregated the matter based on disease. Finally, we compiled the essence of these articles under the various sub-headings. Results: After thorough review of articles, it was observed that there was a surge in the occurrence of liver-related surgeries, diagnoses, and treatments. Parallelly, advanced computer technologies governed by AI continue to prove their efficacy in the accurate screening, analysis, prediction, treatment, and recuperation of liver-related cases. Conclusions: The continual developments and high-order precision of AI is expanding its roots in all directions of applications. Despite being novel and lacking research, AI has shown its intrinsic worth for procedures in liver surgery while providing enhanced healing opportunities and personalized treatment for liver surgery patients.


Assuntos
Inteligência Artificial , Programas de Rastreamento , Humanos , Fígado/cirurgia , PubMed
7.
BMC Bioinformatics ; 23(1): 144, 2022 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-35448946

RESUMO

BACKGROUND: The abundance of biomedical text data coupled with advances in natural language processing (NLP) is resulting in novel biomedical NLP (BioNLP) applications. These NLP applications, or tasks, are reliant on the availability of domain-specific language models (LMs) that are trained on a massive amount of data. Most of the existing domain-specific LMs adopted bidirectional encoder representations from transformers (BERT) architecture which has limitations, and their generalizability is unproven as there is an absence of baseline results among common BioNLP tasks. RESULTS: We present 8 variants of BioALBERT, a domain-specific adaptation of a lite bidirectional encoder representations from transformers (ALBERT), trained on biomedical (PubMed and PubMed Central) and clinical (MIMIC-III) corpora and fine-tuned for 6 different tasks across 20 benchmark datasets. Experiments show that a large variant of BioALBERT trained on PubMed outperforms the state-of-the-art on named-entity recognition (+ 11.09% BLURB score improvement), relation extraction (+ 0.80% BLURB score), sentence similarity (+ 1.05% BLURB score), document classification (+ 0.62% F1-score), and question answering (+ 2.83% BLURB score). It represents a new state-of-the-art in 5 out of 6 benchmark BioNLP tasks. CONCLUSIONS: The large variant of BioALBERT trained on PubMed achieved a higher BLURB score than previous state-of-the-art models on 5 of the 6 benchmark BioNLP tasks. Depending on the task, 5 different variants of BioALBERT outperformed previous state-of-the-art models on 17 of the 20 benchmark datasets, showing that our model is robust and generalizable in the common BioNLP tasks. We have made BioALBERT freely available which will help the BioNLP community avoid computational cost of training and establish a new set of baselines for future efforts across a broad range of BioNLP tasks.


Assuntos
Benchmarking , Processamento de Linguagem Natural , Fontes de Energia Elétrica , Idioma , PubMed
8.
J Med Libr Assoc ; 110(2): 185-204, 2022 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-35440905

RESUMO

Introduction: Poor indexing and inconsistent use of terms and keywords may prevent efficient retrieval of studies on the patient-based benefit-risk assessment (BRA) of medicines. We aimed to develop and validate an objectively derived content search strategy containing generic search terms that can be adapted for any search for evidence on patient-based BRA of medicines for any therapeutic area. Methods: We used a robust multistep process to develop and validate the content search strategy: (1) we developed a bank of search terms derived from screening studies on patient-based BRA of medicines in various therapeutic areas, (2) we refined the proposed content search strategy through an iterative process of testing sensitivity and precision of search terms, and (3) we validated the final search strategy in PubMed by firstly using multiple sclerosis as a case condition and secondly computing its relative performance versus a published systematic review on patient-based BRA of medicines in rheumatoid arthritis. Results: We conceptualized a final search strategy to retrieve studies on patient-based BRA containing generic search terms grouped into two domains, namely the patient and the BRA of medicines (sensitivity 84%, specificity 99.4%, precision 20.7%). The relative performance of the content search strategy was 85.7% compared with a search from a published systematic review of patient preferences in the treatment of rheumatoid arthritis. We also developed a more extended filter, with a relative performance of 93.3% when compared with a search from a published systematic review of patient preferences in lung cancer.


Assuntos
Artrite Reumatoide , Artrite Reumatoide/tratamento farmacológico , Humanos , MEDLINE , PubMed , Medição de Risco
9.
BMC Med Inform Decis Mak ; 22(1): 83, 2022 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-35351120

RESUMO

BACKGROUND: Analyzing the unstructured textual data contained in electronic health records (EHRs) has always been a challenging task. Word embedding methods have become an essential foundation for neural network-based approaches in natural language processing (NLP), to learn dense and low-dimensional word representations from large unlabeled corpora that capture the implicit semantics of words. Models like Word2Vec, GloVe or FastText have been broadly applied and reviewed in the bioinformatics and healthcare fields, most often to embed clinical notes or activity and diagnostic codes. Visualization of the learned embeddings has been used in a subset of these works, whether for exploratory or evaluation purposes. However, visualization practices tend to be heterogeneous, and lack overall guidelines. OBJECTIVE: This scoping review aims to describe the methods and strategies used to visualize medical concepts represented using word embedding methods. We aim to understand the objectives of the visualizations and their limits. METHODS: This scoping review summarizes different methods used to visualize word embeddings in healthcare. We followed the methodology proposed by Arksey and O'Malley (Int J Soc Res Methodol 8:19-32, 2005) and by Levac et al. (Implement Sci 5:69, 2010) to better analyze the data and provide a synthesis of the literature on the matter. RESULTS: We first obtained 471 unique articles from a search conducted in PubMed, MedRxiv and arXiv databases. 30 of these were effectively reviewed, based on our inclusion and exclusion criteria. 23 articles were excluded in the full review stage, resulting in the analysis of 7 papers that fully correspond to our inclusion criteria. Included papers pursued a variety of objectives and used distinct methods to evaluate their embeddings and to visualize them. Visualization also served heterogeneous purposes, being alternatively used as a way to explore the embeddings, to evaluate them or to merely illustrate properties otherwise formally assessed. CONCLUSIONS: Visualization helps to explore embedding results (further dimensionality reduction, synthetic representation). However, it does not exhaust the information conveyed by the embeddings nor constitute a self-sustaining evaluation method of their pertinence.


Assuntos
Processamento de Linguagem Natural , Semântica , Bases de Dados Factuais , Registros Eletrônicos de Saúde , Humanos , PubMed
11.
Artigo em Inglês | MEDLINE | ID: mdl-35329058

RESUMO

Human biomonitoring (HBM) is a rapidly developing field that is emphasized as an important approach for the assessment of health risks. However, its value for health risk assessment (HRA) remains to be clarified. We performed a review of publications concerned with applications of HBM in the assessment of health risks. The selection of publications for this review was limited by the search engines used (only PubMed and Scopus) and a timeframe of the last five years. The review focused on the clarity of 10 HRA elements, which influence the quality of HRA. We show that the usage of HBM data in HRA is limited and unclear. Primarily, the key HRA elements are not consistently applied or followed when using HBM in such assessments, and secondly, there are inconsistencies regarding the understanding of fundamental risk analysis principles and good practices in risk analysis. Our recommendations are as follows: (i) potential usage of HBM data in HRA should not be non-critically overestimated but rather limited and aligned to a specific value for exposure assessment or for the interpretation of health damage; (ii) improvements to HRA approaches, using HBM information or not, are needed and should strictly follow theoretical foundations of risk analysis.


Assuntos
Monitoramento Biológico , Publicações Periódicas como Assunto , Bibliometria , Monitoramento Ambiental , Humanos , PubMed , Medição de Risco
12.
Clin Imaging ; 85: 43-47, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-35240478

RESUMO

PURPOSE: To evaluate interventional radiology (IR) research over time based on the study type of published articles and the visibility of articles to non-radiology clinicians. METHODS: We performed a search of all PubMed-indexed literature from January 1, 1991, through November 11, 2020, for clinical IR articles classified by their study type, categorized as: 1) meta-analyses/systematic reviews/practice guidelines; 2) randomized controlled trials; 3) non-randomized controlled trials; and 4) longitudinal/observational studies. Clinical IR articles were defined as those that met keyword criteria constructed from Society of Interventional Radiology procedure guides. Data were also collected on medical specialty journal categories that published IR-related articles. RESULTS: When we examined the first vs. the last decade of our study period, the number of IR articles published increased across all study types: randomized controlled trials (374 to 2620; 601% change), longitudinal/observational studies (2324 to 12,447; 436%), meta-analyses/systematic reviews/practice guidelines (1179 to 6135; 420%), non-randomized controlled trials (471 to 2161; 359%). The journal categories with the highest mean percentage increase of IR articles across all study types were obstetrics and gynecology (659%), peripheral vascular disease (342%), and emergency medicine (221%). We found a decrease of IR articles published in surgery (-6.0%), pediatrics (-14%), and pulmonary (-21%) journals. CONCLUSION: The number of IR articles grew quickly and at a similar rate compared with all PubMed-indexed articles and increased as a proportion of articles published in non-imaging specialty journals. This indicates greater visibility of IR studies for all clinicians and is encouraging towards the advancement of IR techniques.


Assuntos
Obstetrícia , Radiologia Intervencionista , Bibliometria , Criança , Feminino , Humanos , Gravidez , PubMed
13.
J Biomed Inform ; 128: 104047, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35257868

RESUMO

The co-occurrence analysis of Medical Subject Heading (MeSH) terms extracted from the PubMed database is popularly used in bibliometrics. Practically for making the result interpretable, it is necessary to apply a certain filter procedure of co-occurrence matrix for removing the low-frequency items due to their low representativeness. Unfortunately, there is rare research referring to determine a critical threshold to remove the noise of co-occurrence matrix. Here, we proposed a probabilistic model for co-occurrence analysis that can provide statistical inferences about whether the paired items co-occur randomly. With help of this model, the dimensionality of co-occurrence matrix could be reduced according to the selected threshold. The conceptual model framework, simulation and practical applications are illustrated in the manuscript. Further details (including all reproducible codes) can be downloaded from the project website: https://github.com/xizhou/co-occurrence-analysis.git.


Assuntos
Bibliometria , Medical Subject Headings , Análise por Conglomerados , Modelos Estatísticos , PubMed
14.
J Integr Complement Med ; 28(3): 202-217, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-35294303

RESUMO

Objective: This systematic review aimed to document and describe how and when to assess patients' expectancies to acupuncture and the relationship between patients' expectancies and clinical effects. Materials and Methods: Three English databases, including PubMed, Cochrane Central Register of Controlled Trials, and EMBASE, and four Chinese databases, including the Chinese Biomedicine Literature Database, Chinese Journal Full-text Database, Chinese Scientific Journal Full-text Database, and Wanfang Database, were searched up to February 2020. Studies involving patients' expectancies to acupuncture were included. Based on the detailed situations of patients' expectancies, we made a standardized data extraction table that included the basic information of articles, study design details, and measurement of expectations. Based on the data, a descriptive analysis was performed, covering the characteristics of studies, measuring methods of expectations and the relationship between patients' expectancies and clinical effects. Methodology quality assessment was also performed by the risk of bias and the standards for reporting interventions in controlled trials of acupuncture. Results: There were 61 randomized controlled trials included in our analysis. The number of articles increased gradually over time and grew significantly after 2008. About half of trials focused on pain alleviation. Expectancies were measured before the treatment (N = 43), after the treatment (N = 3), and both before and after the treatment (N = 10), and five studies did not mention it. The measurement of expectancies used self-made questionnaires or scales (N = 27), the Acupuncture Expectations Scale (N = 6), and other scales (N = 11), while 17 studies did not describe what scale they used. The used questionnaires or scales mostly tried to ascertain the strength of confidence that acupuncture would help. Patients' expectancies and clinical effects were relevant in 19 studies, irrelevant in 21 studies, and were not mentioned in 21 studies. Conclusions: Patients' expectations to acupuncture have received increasing attention in recent years, but there is still no recognized measurement time and methods. It is critical to develop questions and answers regarding patients' expectations with better discrimination and reliability to accurately assess expectations and to explore the relationship between patients' expectations and acupuncture outcomes in future trials.


Assuntos
Terapia por Acupuntura , Terapia por Acupuntura/métodos , Humanos , PubMed , Publicações , Reprodutibilidade dos Testes , Projetos de Pesquisa
15.
J Med Libr Assoc ; 110(1): 43-46, 2022 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-35210961

RESUMO

OBJECTIVE: The National Library of Medicine (NLM) inaugurated a "publication type" concept to facilitate searches for systematic reviews (SRs). On the other hand, clinical queries (CQs) are validated search strategies designed to retrieve scientifically sound, clinically relevant original and review articles from biomedical literature databases. We compared the retrieval performance of the SR publication type (SR[pt]) against the most sensitive CQ for systematic review articles (CQrs) in PubMed. METHODS: We ran date-limited searches of SR[pt] and CQrs to compare the relative yield of articles and SRs, focusing on the differences in retrieval of SRs by SR[pt] but not CQrs (SR[pt] NOT CQrs) and CQrs NOT SR[pt]. Random samples of articles retrieved in each of these comparisons were examined for SRs until a consistent pattern became evident. RESULTS: For SR[pt] NOT CQrs, the yield was relatively low in quantity but rich in quality, with 79% of the articles being SRs. For CQrs NOT SR[pt], the yield was high in quantity but low in quality, with only 8% being SRs. For CQrs AND SR[pt], the quality was highest, with 92% being SRs. CONCLUSIONS: We found that SR[pt] had high precision and specificity for SRs but low recall (sensitivity), whereas CQrs had much higher recall. SR[pt] OR CQrs added valid SRs to the CQrs yield at low cost (i.e., added few non-SRs). For searches that are intended to be exhaustive for SRs, SR[pt] can be added to existing sensitive search filters.


Assuntos
National Library of Medicine (U.S.) , PubMed , Revisões Sistemáticas como Assunto , Estados Unidos
16.
J Med Libr Assoc ; 110(1): 103-108, 2022 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-35210969

RESUMO

BACKGROUND: An article's citations are useful for finding related articles that may not be readily found by keyword searches or textual similarity. Citation analysis is also important for analyzing scientific innovation and the structure of the biomedical literature. We wanted to facilitate citation analysis for the broad community by providing a user-friendly interface for accessing and analyzing citation data for biomedical articles. CASE PRESENTATION: We seeded the Citation Cloud dataset with over 465 million open access citations culled from six different sources: PubMed Central, Microsoft Academic Graph, ArnetMiner, Semantic Scholar, Open Citations, and the NIH iCite dataset. We implemented a free, public extension to PubMed that allows any user to visualize and analyze the entire citation cloud around any paper of interest A: the set of articles cited by A, those which cite A, those which are co-cited with A, and those which are bibliographically coupled to A. CONCLUSIONS: Citation Cloud greatly enables the study of citations by the scientific community, including relatively advanced analyses (co-citations and bibliographic coupling) that cannot be undertaken using other available tools. The tool can be accessed by running any PubMed query on the Anne O'Tate value-added search interface and clicking on the Citations button next to any retrieved article.


Assuntos
Bibliometria , Publicações , Internet , PubMed
17.
Braz J Phys Ther ; 26(1): 100392, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35158222

RESUMO

BACKGROUND: Access to full-text articles is an essential element of evidence-based practice. OBJECTIVE: Estimate the percentage of articles in the Physiotherapy Evidence Database (PEDro) that have free full-text access and compare free access between PEDro and PubMed. Secondary objectives for access via PEDro: determine if publication year and geographic location impact on free access; determine if adding a link to a portable document format (PDF) locator website would improve free access; and evaluate the association between article characteristics and free access. METHODS: This observational study used a random sample of 200 articles published in 2000-2019 and indexed in PEDro. Data collectors in Australia, Brazil, Nepal, and Spain attempted to access free full text for each article via PEDro. One data collector attempted to access free full text via PubMed. One data collector attempted to access full text via a PDF locator (http://www.pdfsearchengine.net/). The percentage (95% confidence interval [CI]) of articles with free full-text access from PEDro, PubMed, and the PDF locator website were calculated. Logistic regression was used to evaluate the association between free full-text access and article characteristics. RESULTS: Free full text could be accessed via PEDro for 51% of the articles (95% CI: 44, 58). PEDro had 4% higher free access than PubMed (95% CI: 1, 7). Access via PEDro did not vary systematically with time, geographic location, or article characteristics. Access improved by 9% (95% CI: 6, 14) by adding a PDF locator website. CONCLUSIONS: PEDro is a good source of free full-text articles for physical therapists and other rehabilitation professionals. Evidence resources, professional organisations, employers, researchers, and research agencies could all help to increase access to free full text.


Assuntos
Fisioterapeutas , Modalidades de Fisioterapia , Brasil , Bases de Dados Factuais , Humanos , PubMed
18.
PLoS One ; 17(2): e0263001, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35139089

RESUMO

The COVID-19 outbreak has posed an unprecedented challenge to humanity and science. On the one side, public and private incentives have been put in place to promptly allocate resources toward research areas strictly related to the COVID-19 emergency. However, research in many fields not directly related to the pandemic has been displaced. In this paper, we assess the impact of COVID-19 on world scientific production in the life sciences and find indications that the usage of medical subject headings (MeSH) has changed following the outbreak. We estimate through a difference-in-differences approach the impact of the start of the COVID-19 pandemic on scientific production using the PubMed database (3.6 Million research papers). We find that COVID-19-related MeSH terms have experienced a 6.5 fold increase in output on average, while publications on unrelated MeSH terms dropped by 10 to 12%. The publication weighted impact has an even more pronounced negative effect (-16% to -19%). Moreover, COVID-19 has displaced clinical trial publications (-24%) and diverted grants from research areas not closely related to COVID-19. Note that since COVID-19 publications may have been fast-tracked, the sudden surge in COVID-19 publications might be driven by editorial policy.


Assuntos
Pesquisa Biomédica , COVID-19 , Bibliometria , Disciplinas das Ciências Biológicas , COVID-19/epidemiologia , Humanos , Medical Subject Headings , PubMed
19.
Med Ref Serv Q ; 41(1): 86-94, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35225742

RESUMO

Searching the athletic training literature can be confusing and overwhelming with many possible databases for locating relevant peer-reviewed scholarship. Finding evidence-based literature from respected publications is helpful in clinical decision-making for athletic training practitioners. This column details recommended databases and search tips to help students, staff, clinicians, and faculty in the field of athletic training find the literature they need to help make evidence-based decisions and to stay current with the published literature. Databases discussed include Cochrane, PubMed, SPORTDiscus, CINAHL, PEDro, Sports Medicine, and Education Index (formerly Physical Education Index), and Google Scholar.


Assuntos
Esportes , Docentes , Humanos , Educação Física e Treinamento , PubMed , Esportes/educação , Estudantes
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