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1.
Genes (Basel) ; 12(3)2021 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-33809949

RESUMO

The coronavirus disease 2019 (COVID-19) pandemic has caused more than 2.3 million casualties worldwide and the lack of effective treatments is a major health concern. The development of targeted drugs is held back due to a limited understanding of the molecular mechanisms underlying the perturbation of cell physiology observed after viral infection. Recently, several approaches, aimed at identifying cellular proteins that may contribute to COVID-19 pathology, have been reported. Albeit valuable, this information offers limited mechanistic insight as these efforts have produced long lists of cellular proteins, the majority of which are not annotated to any cellular pathway. We have embarked in a project aimed at bridging this mechanistic gap by developing a new bioinformatic approach to estimate the functional distance between a subset of proteins and a list of pathways. A comprehensive literature search allowed us to annotate, in the SIGNOR 2.0 resource, causal information underlying the main molecular mechanisms through which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related coronaviruses affect the host-cell physiology. Next, we developed a new strategy that enabled us to link SARS-CoV-2 interacting proteins to cellular phenotypes via paths of causal relationships. Remarkably, the extensive information about inhibitors of signaling proteins annotated in SIGNOR 2.0 makes it possible to formulate new potential therapeutic strategies. The proposed approach, which is generally applicable, generated a literature-based causal network that can be used as a framework to formulate informed mechanistic hypotheses on COVID-19 etiology and pathology.


Assuntos
Autofagia/genética , /virologia , Interações entre Hospedeiro e Microrganismos/genética , Transdução de Sinais , /genética , Ontologia Genética , Redes Reguladoras de Genes , Humanos , Inflamação/genética , Inflamação/metabolismo , Inflamação/virologia , Proteoma , PubMed , /patogenicidade , Transdução de Sinais/genética
2.
Brief Bioinform ; 22(2): 800-811, 2021 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-33757278

RESUMO

OBJECTIVE: This study aims at reviewing novel coronavirus disease (COVID-19) datasets extracted from PubMed Central articles, thus providing quantitative analysis to answer questions related to dataset contents, accessibility and citations. METHODS: We downloaded COVID-19-related full-text articles published until 31 May 2020 from PubMed Central. Dataset URL links mentioned in full-text articles were extracted, and each dataset was manually reviewed to provide information on 10 variables: (1) type of the dataset, (2) geographic region where the data were collected, (3) whether the dataset was immediately downloadable, (4) format of the dataset files, (5) where the dataset was hosted, (6) whether the dataset was updated regularly, (7) the type of license used, (8) whether the metadata were explicitly provided, (9) whether there was a PubMed Central paper describing the dataset and (10) the number of times the dataset was cited by PubMed Central articles. Descriptive statistics about these seven variables were reported for all extracted datasets. RESULTS: We found that 28.5% of 12 324 COVID-19 full-text articles in PubMed Central provided at least one dataset link. In total, 128 unique dataset links were mentioned in 12 324 COVID-19 full text articles in PubMed Central. Further analysis showed that epidemiological datasets accounted for the largest portion (53.9%) in the dataset collection, and most datasets (84.4%) were available for immediate download. GitHub was the most popular repository for hosting COVID-19 datasets. CSV, XLSX and JSON were the most popular data formats. Additionally, citation patterns of COVID-19 datasets varied depending on specific datasets. CONCLUSION: PubMed Central articles are an important source of COVID-19 datasets, but there is significant heterogeneity in the way these datasets are mentioned, shared, updated and cited.


Assuntos
/epidemiologia , Conjuntos de Dados como Assunto , Disseminação de Informação/métodos , PubMed , /isolamento & purificação , Humanos
3.
Nat Methods ; 18(3): 262-271, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33649586

RESUMO

Single-cell technologies have made it possible to profile millions of cells, but for these resources to be useful they must be easy to query and access. To facilitate interactive and intuitive access to single-cell data we have developed scfind, a single-cell analysis tool that facilitates fast search of biologically or clinically relevant marker genes in cell atlases. Using transcriptome data from six mouse cell atlases, we show how scfind can be used to evaluate marker genes, perform in silico gating, and identify both cell-type-specific and housekeeping genes. Moreover, we have developed a subquery optimization routine to ensure that long and complex queries return meaningful results. To make scfind more user friendly, we use indices of PubMed abstracts and techniques from natural language processing to allow for arbitrary queries. Finally, we show how scfind can be used for multi-omics analyses by combining single-cell ATAC-seq data with transcriptome data.


Assuntos
Gerenciamento de Dados/métodos , Armazenamento e Recuperação da Informação/métodos , Análise de Célula Única/métodos , Transcriptoma/genética , Algoritmos , Animais , Análise de Dados , Bases de Dados Genéticas , Regulação da Expressão Gênica , Camundongos , Processamento de Linguagem Natural , PubMed , Interface Usuário-Computador
4.
Pac Symp Biocomput ; 26: 107-118, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33691009

RESUMO

How has the focus of research papers on a given disease changed over time? Identifying the papers at the cusps of change can help highlight the emergence of a new topic or a change in the direction of research. We present a generally applicable unsupervised approach to this question based on semantic changepoints within a given collection of research papers. We illustrate the approach by a range of examples based on a nascent corpus of literature on COVID-19 as well as subsets of papers from PubMed on the World Health Organization list of neglected tropical diseases. The software is freely available at: https://github.com/pdddinakar/SemanticChangepointDetection.


Assuntos
Semântica , Biologia Computacional , Humanos , PubMed
5.
Zhongguo Zhen Jiu ; 41(1): 111-4, 2021 Jan 12.
Artigo em Chinês | MEDLINE | ID: mdl-33559454

RESUMO

OBJECTIVE: To analyze the literature characteristics of the clinical researches on tumor treatment with acupuncture-moxibustion in PubMed database so as to provide the references for the study of acupuncture-moxibusion in intervention of tumor. METHODS: The articles on the clinical researches of acupuncture-moxibusion in treatment of tumor were retrieved from PubMed database listed till December 31, 2018. Using bibliometric methodology, the analysis was conducted on publication year, publication journal, author, country or region, research institution, disease spectrum and therapeutic regimen. RESULTS: A total of 143 articles are included. The publications are increased steadily since 2004. The articles are published in 64 international journals, of which, Acupuncture in Medicine (12 articles) and Integrative Cancer Therapies (10 articles) occupy the the largest number of publications. They are distributed in 18 countries and regions, of which, the top two countries are America (44 articles) and China (34 articles. The involved types of cancer include breast cancer, prostate cancer, gastric cancer, etc. Acupuncture-moxibustion is mainly for complication and the comorbid disorders after treatment, such as pain, nausea and vomiting and fatigue at most. The regimen of acupuncture-moxibustion is determined by the symptoms and electroacupuncture is the main measure of treatment. CONCLUSION: Acupuncture-moxibustion is quite extensively involved in the treatment of tumor in the field of nervous (mental) system and digestive system. But the regimen of acupuncture- moxibustion needs to be further optimized and promoted.


Assuntos
Terapia por Acupuntura , Moxibustão , Bibliometria , China , Humanos , PubMed
6.
Med Ref Serv Q ; 40(1): 103-109, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33625331

RESUMO

LitCovid is a curated literature hub with more than 60,000 articles about the novel coronavirus and the disease it causes-COVID-19. It is updated daily with scientific information from new PubMed articles that are relevant to COVID-19. Relevant articles are manually assigned to eight broad categories for ease of searching: general, mechanism, transmission, diagnosis, treatment, prevention, case report, and forecasting. Users can filter by location and what clinical trials are happening. As a centralized location curated daily with the most authoritative information on coronavirus and COVID-19, LitCovid is an effective source of credible up-to-date research.


Assuntos
Pesquisa Biomédica , Bases de Dados Factuais , Disseminação de Informação/métodos , PubMed/organização & administração , Relatório de Pesquisa , Humanos , National Library of Medicine (U.S.) , Estados Unidos
7.
Artigo em Inglês | MEDLINE | ID: mdl-33419178

RESUMO

The main purpose of this systematic review and meta-analysis was to compare the effects of strength training (ST) and plyometric training (PT) on vertical jump, linear sprint and change of direction (COD) performance in female soccer players. A systematic search of the PubMed, Web of Science, Google Scholar and SportDiscus databases revealed 12 studies satisfying the inclusion criteria. The inverse-variance random-effects model for meta-analyses was used. Effect sizes (ES) were represented by the standardized mean difference and presented alongside 95% confidence intervals (CI). The magnitude of the main effect was small to moderate (vertical jump (ES 0.53 (95% CI-0.11, 0.95), Z = 2.47 (p = 0.01); linear sprint (ES -0.66 (95% CI-2.03, -0.21), Z = 2.20 (p = 0.03); COD (ES -0.36 (95% CI-0.68, -0.03), Z = 2.17 (p = 0.03)). Subgroup analyses were performed (i.e., ST and PT duration, frequency, session duration and total number of sessions), revealing no significant subgroup differences (p = 0.12-0.88). In conclusion, PT provides better benefits than ST to improve vertical jump, linear sprint and COD performance in female soccer players. However, significant limitations in the current literature prevent assured PT and ST prescription recommendations being made.


Assuntos
Desempenho Atlético , Exercício Pliométrico , Treinamento de Resistência , Futebol , Feminino , Humanos , PubMed
8.
Otol Neurotol ; 42(2): 341-344, 2021 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-33443361

RESUMO

OBJECTIVE: PubMed is the world's largest online collection of biomedical literature citations. A PubMed search (October 11, 2019) using the medical subject heading terms "history" and "mastoidectomy" was conducted. The heading "best matches" listed as first article "A brief history of mastoidectomy," a very relevant free full text. The aim of this study is to validate or not the relevance attributed to this study as the first article listed in best matches. METHODOLOGY: All the references of the article mentioned before 1860 were checked, further completed with other original sources, and studied again, with particular attention to their extracted quotes. RESULTS: Surprisingly, this article contains many inaccuracies, notably concerning Galen, Lucas van Leyden, Paré, Riolan the Younger, Justus von Berger, Jasser, Dezeimeris, Wilde and Toynbee. This was most certainly related to blind trust of some secondary references. CONCLUSION: Never trust secondary references. This article also raises questions on the validity and the relevance of the best matches algorithm in PubMed.


Assuntos
Algoritmos , Mastoidectomia , Humanos , PubMed
9.
Artigo em Inglês | MEDLINE | ID: mdl-33513981

RESUMO

Background: Nowadays the use of intraoral scanners has become a routine practice in orthodontics. It allows the introduction of many treatment innovations. One should consider to what extent intraoral scanners have influenced the everyday orthodontic practice and in what direction should the further research in this field be conducted. This study is aimed to systematically review and synthesize available controlled trials investigating the accuracy and efficacy of intraoral scanners for orthodontic purpose to provide clinically useful information and to direct further research in this field. Methods: A literature search of free text and MeSH terms was performed by using MedLine (PubMed), Scopus, Web of Science and Embase. The search engines were used to find studies on application of intraoral scanners in orthodontics (from 1950 to 30 September 2020). The following keywords were used: "intraoral scanners AND efficiency AND accuracy AND orthodontics". Results: The number of potential identified articles was 71, including 61 from PubMed, two from Scopus, three from Web of Science and five from Embase. After removal of duplicates, 67 full-text articles were analyzed for inclusion criteria, 16 of them were selected and finally included in the qualitative synthesis. Conclusions: There are plenty of data available on accuracy and efficacy of different scanners. Scanners of the same generation from different manufacturers have almost identical accuracy. This is the reason why future similar research will not introduce much to the orthodontics. The challenge for the coming years is to find new applications of digital impressions in the orthodontic practice.


Assuntos
Ortodontia , Bibliometria , Assistência Odontológica , Humanos , PubMed , Ferramenta de Busca
10.
Trials ; 22(1): 59, 2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-33451350

RESUMO

BACKGROUND: Several drugs are being repurposed for the treatment of the coronavirus disease 2019 (COVID-19) pandemic based on in vitro or early clinical findings. As these drugs are being used in varied regimens and dosages, it is important to enable synthesis of existing safety data from clinical trials. However, availability of safety information is limited by a lack of timely reporting of overall clinical trial results on public registries or through academic publication. We aimed to analyse the evidence gap in this data by conducting a rapid review of results posting on ClinicalTrials.gov and in academic publications to quantify the number of trials missing results for drugs potentially being repurposed for COVID-19. METHODS: ClinicalTrials.gov was searched for 19 drugs that have been identified as potential treatments for COVID-19. Relevant clinical trials for any prior indication were listed by identifier (NCT number) and checked for results and for timely result reporting (within 395 days of the primary completion date). Additionally, PubMed and Google Scholar were searched to identify publications of results not listed on the registry. A second, blinded search of 10% of trials was conducted to assess reviewer concordance. RESULTS: Of 3754 completed trials, 1516 (40.4%) did not post results on ClinicalTrials.gov or in the academic literature. Tabular results were available on ClinicalTrials.gov for 1172 (31.2%) completed trials. A further 1066 (28.4%) had published results in the academic literature, but did not report results on ClinicalTrials.gov . Key drugs missing clinical trial results include hydroxychloroquine (37.0% completed trials unreported), favipiravir (77.8%) and lopinavir (40.5%). CONCLUSIONS: There is an important evidence gap for the safety of drugs being repurposed for COVID-19. This uncertainty could cause unnecessary additional morbidity and mortality during the pandemic. We recommend caution in experimental drug use for non-severe disease and urge clinical trial sponsors to report missing results retrospectively.


Assuntos
Antivirais/uso terapêutico , Ensaios Clínicos como Assunto , Inibidores Enzimáticos/uso terapêutico , Sistema de Registros , Relatório de Pesquisa , Amidas/uso terapêutico , Combinação de Medicamentos , Reposicionamento de Medicamentos , Medicina Baseada em Evidências , Humanos , Hidroxicloroquina/uso terapêutico , Lopinavir/uso terapêutico , PubMed , Pirazinas/uso terapêutico , Projetos de Pesquisa , Ritonavir/uso terapêutico
11.
Methods Mol Biol ; 2231: 261-295, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33289898

RESUMO

The book chapter introduces the National Center for Biotechnology Information (NCBI) Genome Workbench, a desktop GUI software package to manipulate and visualize complex molecular biology models provided in many data formats. Genome Workbench integrates graphical views and computational tools in a single package to facilitate discoveries. In this chapter we provide a step-by-step protocol guidance on how to do comparative analysis of sequences using NCBI BLAST and multiple sequence alignment algorithms, build phylogenetic trees, and use graphical views for sequences, alignments, and trees to validate the findings. The software package can be used to prepare high-quality whole genome submissions to NCBI. The software package is user-friendly and includes validation and editing tools to fix errors as part of preparing the submission.


Assuntos
Biologia Computacional/métodos , Bases de Dados de Ácidos Nucleicos/organização & administração , Genômica/métodos , Alinhamento de Sequência/métodos , Software , Algoritmos , Genoma/genética , Filogenia , PubMed/organização & administração
13.
Cytokine ; 137: 155312, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33128927

RESUMO

BACKGROUND: COVID-19, as a newly-emerged viral infection has now spread all over the world after originating in Wuhan, China. Pneumonia is the hallmark of the disease, with dyspnea in half of the patients and acute respiratory distress syndrome (ARDS) in up to one -third of the cases. Pulmonary edema, neutrophilic infiltration, and inflammatory cytokine release are the pathologic signs of this disease. The anti-inflammatory effect of the photobiomodulation (PBM) has been confirmed in many previous studies. Therefore, this review study was conducted to evaluate the direct effect of PBM on the acute lung inflammation or ARDS and also accelerating the regeneration of the damaged tissues. The indirect effects of PBM on modulation of the immune system, increasing the blood flow and oxygenation in other tissues were also considered. METHODOLOGY: The databases of PubMed, Cochrane library, and Google Scholar were searched to find the relevant studies. Keywords included the PBM and related terms, lung inflammation, and COVID-19 -related signs. Studies were categorized with respect to the target tissue, laser parameters, and their results. RESULTS: Seventeen related papers were included in this review. All of them were in animal models. They showed that the PBM could significantly decrease the pulmonary edema, neutrophil influx, and generation of pro-inflammatory cytokines (tumor necrosis factor-α (TNF-α), interleukin 1 beta (IL-1ß), interleukin 6 (IL-6), intracellular adhesion molecule (ICAM), reactive oxygen species (ROS), isoform of nitric oxide synthase (iNOS), and macrophage inflammatory protein 2 (MIP-2)). CONCLUSION: Our findings revealed that the PBM could be helpful in reducing the lung inflammation and promoting the regeneration of the damaged tissue. PBM can increase the oxygenation indirectly in order to rehabilitate the affected organs. Thus, the infra-red lasers or light-emitting diodes (LEDs) are recommended in this regard.


Assuntos
/radioterapia , Terapia com Luz de Baixa Intensidade , Pulmão/efeitos da radiação , Pneumonia/radioterapia , /sangue , Citocinas/metabolismo , Humanos , Pulmão/fisiopatologia , Macrófagos/efeitos dos fármacos , Macrófagos/imunologia , Neutrófilos/efeitos dos fármacos , Neutrófilos/imunologia , Pneumonia/imunologia , Pneumonia/fisiopatologia , PubMed , Edema Pulmonar/imunologia , Edema Pulmonar/fisiopatologia , Edema Pulmonar/radioterapia , Espécies Reativas de Oxigênio/metabolismo , /radioterapia
14.
BMC Med Inform Decis Mak ; 20(Suppl 11): 322, 2020 12 30.
Artigo em Inglês | MEDLINE | ID: mdl-33380331

RESUMO

BACKGROUND: Natural language processing (NLP) tools can facilitate the extraction of biomedical concepts from unstructured free texts, such as research articles or clinical notes. The NLP software tools CLAMP, cTAKES, and MetaMap are among the most widely used tools to extract biomedical concept entities. However, their performance in extracting disease-specific terminology from literature has not been compared extensively, especially for complex neuropsychiatric disorders with a diverse set of phenotypic and clinical manifestations. METHODS: We comparatively evaluated these NLP tools using autism spectrum disorder (ASD) as a case study. We collected 827 ASD-related terms based on previous literature as the benchmark list for performance evaluation. Then, we applied CLAMP, cTAKES, and MetaMap on 544 full-text articles and 20,408 abstracts from PubMed to extract ASD-related terms. We evaluated the predictive performance using precision, recall, and F1 score. RESULTS: We found that CLAMP has the best performance in terms of F1 score followed by cTAKES and then MetaMap. Our results show that CLAMP has much higher precision than cTAKES and MetaMap, while cTAKES and MetaMap have higher recall than CLAMP. CONCLUSION: The analysis protocols used in this study can be applied to other neuropsychiatric or neurodevelopmental disorders that lack well-defined terminology sets to describe their phenotypic presentations.


Assuntos
Transtorno do Espectro Autista , Processamento de Linguagem Natural , Benchmarking , Humanos , PubMed , Software
15.
Sci Data ; 7(1): 408, 2020 11 20.
Artigo em Inglês | MEDLINE | ID: mdl-33219227

RESUMO

Portfolio analysis is a fundamental practice of organizational leadership and is a necessary precursor of strategic planning. Successful application requires a highly detailed model of research options. We have constructed a model, the first of its kind, that accurately characterizes these options for the biomedical literature. The model comprises over 18 million PubMed documents from 1996-2019. Document relatedness was measured using a hybrid citation analysis + text similarity approach. The resulting 606.6 million document-to-document links were used to create 28,743 document clusters and an associated visual map. Clusters are characterized using metadata (e.g., phrases, MeSH) and over 20 indicators (e.g., funding, patent activity). The map and cluster-level data are embedded in Tableau to provide an interactive model enabling in-depth exploration of a research portfolio. Two example usage cases are provided, one to identify specific research opportunities related to coronavirus, and the second to identify research strengths of a large cohort of African American and Native American researchers at the University of Michigan Medical School.


Assuntos
Pesquisa Biomédica/tendências , PubMed , Acesso à Informação , Metadados
16.
J Perinat Med ; 48(9): 900-911, 2020 Nov 26.
Artigo em Inglês | MEDLINE | ID: mdl-33001856

RESUMO

The objective of this review was to identify the most significant studies reporting on COVID-19 during pregnancy and to provide an overview of SARS-CoV-2 infection in pregnant women and perinatal outcomes. Eligibility criteria included all reports, reviews; case series with more than 100 individuals and that reported at least three of the following: maternal characteristics, maternal COVID-19 clinical presentation, pregnancy outcomes, maternal outcomes and/or neonatal/perinatal outcomes. We included eight studies that met the inclusion criteria, representing 10,966 cases distributed in 15 countries around the world until July 20, 2020. The results of our review demonstrate that the maternal characteristics, clinical symptoms, maternal and neonatal outcomes almost 11,000 cases of COVID-19 and pregnancy described in 15 different countries are not worse or different from the general population. We suggest that pregnant women are not more affected by the respiratory complications of COVID-19, when compared to the outcomes described in the general population. We also suggest that the important gestational shift Th1-Th2 immune response, known as a potential contributor to the severity in cases of viral infections during pregnancy, are counter-regulated by the enhanced-pregnancy-induced ACE2-Ang-(1-7) axis. Moreover, the relatively small number of reported cases during pregnancy does not allow us to affirm that COVID-19 is more aggressive during pregnancy. Conversely, we also suggest, that down-regulation of ACE2 receptors induced by SARS-CoV-2 cell entry might have been detrimental in subjects with pre-existing ACE2 deficiency associated with pregnancy. This association might explain the worse perinatal outcomes described in the literature.


Assuntos
Betacoronavirus , Infecções por Coronavirus/epidemiologia , Pandemias , Pneumonia Viral/epidemiologia , Complicações Infecciosas na Gravidez/epidemiologia , Complicações Infecciosas na Gravidez/virologia , Resultado da Gravidez/epidemiologia , Comorbidade , Infecções por Coronavirus/complicações , Infecções por Coronavirus/diagnóstico , Grupos Étnicos , Feminino , Humanos , Recém-Nascido , Transmissão Vertical de Doença Infecciosa/estatística & dados numéricos , Terapia Intensiva Neonatal/estatística & dados numéricos , Masculino , Pneumonia Viral/complicações , Pneumonia Viral/diagnóstico , Gravidez , Nascimento Prematuro/epidemiologia , PubMed
17.
PLoS One ; 15(10): e0240123, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33022014

RESUMO

The COVID-19 pandemic has unleashed a deluge of publications. For this cross-sectional study we compared the amount and reporting characteristics of COVID-19-related academic articles and preprints and the number of ongoing clinical trials and systematic reviews. To do this, we searched the PubMed database of citations and abstracts for published life science journals by using appropriate combinations of medical subject headings (MeSH terms), and the COVID-19 section of the MedRxiv and BioRxiv archives up to 20 May 2020 (21 weeks). In addition, we searched Clinicaltrial.gov, Chinese Clinical Trial Registry, EU Clinical Trials Register, and 15 other trial registers, as well as PROSPERO, the international prospective register of systematic reviews. The characteristics of each publication were extracted. Regression analyses and Z tests were used to detect publication trends and their relative proportions. A total of 3635 academic publications and 3805 preprints were retrieved. Only 8.6% (n = 329) of the preprints were already published in indexed journals. The number of academic and preprint publications increased significantly over time (p<0.001). Case reports (6% academic vs 0.9% preprints; p<0.001) and letters (17.4% academic vs 0.5% preprints; p<0.001) accounted for a greater share of academic compared to preprint publications. Differently, randomized controlled trials (0.22% vs 0.63%; p<0.001) and systematic reviews (0.08% vs 5%) made up a greater share of the preprints. The relative proportion of clinical studies registered at Clinicaltrials.gov, Chinese Clinical Trial Registry, and EU Clinical Trials Register was 57.9%, 49.5%, and 98.9%, respectively, most of which were still "recruiting". PROSPERO listed 962 systematic review protocols. Preprints were slightly more prevalent than academic articles but both were increasing in number. The void left by the lack of primary studies was filled by an outpour of immediate opinions (i.e., letters to the editor) published in PubMed-indexed journals. Summarizing, preprints have gained traction as a publishing response to the demand for prompt access to empirical, albeit not peer-reviewed, findings during the present pandemic.


Assuntos
Betacoronavirus , Infecções por Coronavirus/epidemiologia , Pneumonia Viral/epidemiologia , Pré-Publicações como Assunto , Editoração , Ensaios Clínicos Controlados Aleatórios como Assunto , Sistema de Registros , Revisões Sistemáticas como Assunto , Arquivos , Bibliometria , Disciplinas das Ciências Biológicas , Infecções por Coronavirus/virologia , Estudos Transversais , Bases de Dados Factuais , Humanos , Pandemias , Revisão por Pares , Pneumonia Viral/virologia , PubMed
18.
Medicine (Baltimore) ; 99(44): e22885, 2020 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-33126338

RESUMO

BACKGROUND: Publications regarding the 100 top-cited articles in a given discipline are common, but studies reporting the association between article topics and their citations are lacking. Whether or not reviews and original articles have a higher impact factor than case reports is a point for verification in this study. In addition, article topics that can be used for predicting citations have not been analyzed. Thus, this study aims to METHODS:: We searched PubMed Central and downloaded 100 top-cited abstracts in the journal Medicine (Baltimore) since 2011. Four article types and 7 topic categories (denoted by MeSH terms) were extracted from abstracts. Contributors to these 100 top-cited articles were analyzed. Social network analysis and Sankey diagram analysis were performed to identify influential article types and topic categories. MeSH terms were applied to predict the number of article citations. We then examined the prediction power with the correlation coefficients between MeSH weights and article citations. RESULTS: The citation counts for the 100 articles ranged from 24 to 127, with an average of 39.1 citations. The most frequent article types were journal articles (82%) and comparative studies (10%), and the most frequent topics were epidemiology (48%) and blood and immunology (36%). The most productive countries were the United States (24%) and China (23%). The most cited article (PDID = 27258521) with a count of 135 was written by Dr Shang from Shandong Provincial Hospital Affiliated to Shandong University (China) in 2016. MeSH terms were evident in the prediction power of the number of article citations (correlation coefficients  = 0.49, t = 5.62). CONCLUSION: The breakthrough was made by developing dashboards showing the overall concept of the 100 top-cited articles using the Sankey diagram. MeSH terms can be used for predicting article citations. Analyzing the 100 top-cited articles could help future academic pursuits and applications in other academic disciplines.


Assuntos
Bibliometria , Fator de Impacto de Revistas , Medical Subject Headings , Publicações Periódicas como Assunto/tendências , Publicações , Previsões , Humanos , Redes Sociais Online , PubMed , Publicações/classificação , Publicações/normas , Publicações/estatística & dados numéricos
19.
Stud Health Technol Inform ; 273: 228-233, 2020 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-33087617

RESUMO

Mobile health applications for diabetes are developed like never before and many patients use them for their personalized health needs. With increased use, an increased number of usability evaluations are performed to assure that the applications function as intended. In this review the goal was to determine what usability methods are currently used in the evaluation of mobile health applications for diabetes and how these are used. METHODS: A literature review was conducted to identify applicable studies in the databases ACM Digital Library, Cinahl and Pubmed between the years 2015 and 2020. After the inclusion and exclusion criteria were applied, 32 articles remained that were included in the final review. RESULTS: Most of the studies included one established usability engineering method such as an expert-based and/or user-based method or a validated questionnaire/instrument. Some also included a combination of these. Others used methods of their own design; commonly questionnaires and interviews either on their own or in combination. CONCLUSION: To achieve an adequate level of evidence and quality in the evaluation, it is important that at least one is an established usability engineering method or a validated instrument. This to assure and continue to build the evidence base in this area.


Assuntos
Diabetes Mellitus , Aplicativos Móveis , Telemedicina , Diabetes Mellitus/diagnóstico , Diabetes Mellitus/terapia , Humanos , PubMed , Inquéritos e Questionários
20.
BMC Bioinformatics ; 21(Suppl 5): 250, 2020 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-33106154

RESUMO

Biological contextual information helps understand various phenomena occurring in the biological systems consisting of complex molecular relations. The construction of context-specific relational resources vastly relies on laborious manual extraction from unstructured literature. In this paper, we propose COMMODAR, a machine learning-based literature mining framework for context-specific molecular relations using multimodal representations. The main idea of COMMODAR is the feature augmentation by the cooperation of multimodal representations for relation extraction. We leveraged biomedical domain knowledge as well as canonical linguistic information for more comprehensive representations of textual sources. The models based on multiple modalities outperformed those solely based on the linguistic modality. We applied COMMODAR to the 14 million PubMed abstracts and extracted 9214 context-specific molecular relations. All corpora, extracted data, evaluation results, and the implementation code are downloadable at https://github.com/jae-hyun-lee/commodar . CCS CONCEPTS: • Computing methodologies~Information extraction • Computing methodologies~Neural networks • Applied computing~Biological networks.


Assuntos
Mineração de Dados/métodos , Aprendizado de Máquina , PubMed , Publicações
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