Online First Publication: A Resource for Authors.
Ontology highlight
ABSTRACT:
SUBMITTER: Cornell CN
PROVIDER: S-EPMC9096989 | biostudies-literature | 2022 May
REPOSITORIES: biostudies-literature
Publications
Online First Publication: A Resource for Authors.
HSS journal : the musculoskeletal journal of Hospital for Special Surgery 20220309 2
Similar Datasets
Project description: Not available
| S-EPMC9239854 | biostudies-literature
Project description:ObjectiveThe extent to which biomedical authors have received training in publication ethics, and their attitudes and opinions about the ethical aspects of specific behaviours, have been understudied. We sought to characterise the knowledge and attitudes of biomedical authors about common issues in publication ethics.DesignCross-sectional online survey.Setting and participantsCorresponding authors of research submissions to 20 journals.Main outcome measuresPerceived level of unethical behaviour (rated 0 to 10) presented in five vignettes containing key variables that were experimentally manipulated on entry to the survey and perceived level of knowledge of seven ethical topics related to publishing (prior publication, author omission, self-plagiarism, honorary authorship, conflicts of interest, image manipulation and plagiarism).Results4043/10 582 (38%) researchers responded. Respondents worked in 100 countries and reported varying levels of publishing experience. 67% (n=2700) had received some publication ethics training from a mentor, 41% (n=1677) a partial course, 28% (n=1130) a full course and 55% (n=2206) an online course; only a small proportion rated training received as excellent. There was a full range (0 to 10 points) in ratings of the extent of unethical behaviour within each vignette, illustrating a broad range of opinion about the ethical acceptability of the behaviours evaluated, but these opinions were little altered by the context in which it occurred. Participants reported substantial variability in their perceived knowledge of seven publication ethics topics; one-third perceived their knowledge to be less than 'some knowledge' for the sum of the seven ethical topics and only 9% perceived 'substantial knowledge' of all topics.ConclusionsWe found a large degree of variability in espoused training and perceived knowledge, and variability in views about how ethical or unethical scenarios were. Ethical standards need to be better articulated and taught to improve consistency of training across institutions and countries.
| S-EPMC6254423 | biostudies-literature
Project description:IntroductionCochrane Africa (https://africa.cochrane.org/) aims to increase Cochrane reviews addressing high priority questions in sub-Saharan Africa (SSA). Researchers residing in SSA, despite often drawing on Cochrane methods, training or resources, conduct and publish systematic reviews outside of Cochrane. Our objective was to investigate the extent to which Cochrane authors from SSA publish Cochrane and non-Cochrane reviews.MethodsWe conducted a bibliometric study of systematic reviews and overviews of systematic reviews from SSA, first by identifying SSA Cochrane authors, then retrieving their first and last author systematic reviews and overviews from PubMed (2008 to April 2019) and using descriptive analyses to investigate the country of origin, types of reviews and trends in publishing Cochrane and non-Cochrane systematic reviews over time. To be eligible, a review had to have predetermined objectives, eligibility criteria, at least two databases searched, data extraction, quality assessment and a first or last author with a SSA affiliation.ResultsWe identified 657 Cochrane authors and 757 eligible systematic reviews. Most authors were from South Africa (n=332; 51%), followed by Nigeria (n=126; 19%). Three-quarters of the reviews (71%) were systematic reviews of interventions. The intervention reviews were more likely to be Cochrane reviews (60.3% vs 39.7%). Conversely, the overviews (23.8% vs 76.2%), qualitative reviews (14.8% vs 85.2%), diagnostic test accuracy reviews (16.1% vs 83.9%) and the 'other' reviews (11.1% vs 88.9%) were more likely to be non-Cochrane reviews. During the study period, the number of non-Cochrane reviews increased more than the number of Cochrane reviews. About a quarter of the reviews covered infectious disease topics.ConclusionCochrane authors from SSA are increasingly publishing a diverse variety of systematic reviews and overviews of systematic reviews, often opting for non-Cochrane journals.
| S-EPMC8479947 | biostudies-literature
Project description:The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids. The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
2016-07-26 | GSE84767 | GEO
Project description:The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids. The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section. Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
2016-07-26 | E-GEOD-84767 | biostudies-arrayexpress
Project description:Title: Gene Expression in Ara-C Resistance in AML A microarray study of altered gene expression in acute myeloid leukemia cell lines Keywords: cell type comparison Keywords: Expression profiling by array
2005-09-01 | GSE2788 | GEO
Project description:Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR) that collects and integrates imaging data acquired across many different imaging modalities. IDR links data from several imaging modalities, including high-content screening, super-resolution and time-lapse microscopy, digital pathology, public genetic or chemical databases, and cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable re-analysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open source platform that others can use to publish their own image data. Thus IDR provides both a novel on-line resource and a software infrastructure that promotes and extends publication and re-analysis of scientific image data.
| S-EPMC5536224 | biostudies-literature
Project description:BACKGROUND:A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences. DESCRIPTION:PineappleDB is an online, curated database providing integrated access to annotated expressed sequence tag (EST) data for cDNA clones isolated from pineapple fruit, root, and nematode infected root gall vascular cylinder tissues. The database currently houses over 5600 EST sequences, 3383 contig consensus sequences, and associated bioinformatic data including splice variants, Arabidopsis homologues, both MIPS based and Gene Ontology functional classifications, and clone distributions. The online resource can be searched by text or by BLAST sequence homology. The data outputs provide comprehensive sequence, bioinformatic and functional classification information. CONCLUSION:The online pineapple bioinformatic resource provides the research community with access to pineapple fruit and root/gall sequence and bioinformatic data in a user-friendly format. The search tools enable efficient data mining and present a wide spectrum of bioinformatic and functional classification information. PineappleDB will be of broad appeal to researchers investigating pineapple genetics, non-climacteric fruit ripening, root-knot nematode infection, crassulacean acid metabolism and alternative RNA splicing in plants.
| S-EPMC1260026 | biostudies-literature
Project description:ObjectiveWorldwide, the respiratory syncytial virus (RSV) represents the predominant viral agent causing bronchiolitis and pneumonia in children. To conduct research and tackle existing healthcare disparities, RSV-related research activities around the globe need to be described. Hence, we assessed the associated scientific output (represented by research articles) by geographical, chronological and socioeconomic criteria and analysed the authors publishing in the field by gender. Also, the 15 most cited articles and the most prolific journals were identified for RSV research.DesignRetrospective, descriptive study.SettingThe NewQIS (New Quality and Quantity Indices in Science) platform was employed to identify RSV-related articles published in the Web of Science until 2013. We performed a numerical analysis of all articles, and examined citation-based aspects (eg, citation rates); results were visualised by density equalising mapping tools.ResultsWe identified 4600 RSV-related articles. The USA led the field; US-American authors published 2139 articles (46.5%% of all identified articles), which have been cited 83 000 times. When output was related to socioeconomic benchmarks such as gross domestic product or Research and Development expenditures, Guinea-Bissau, The Gambia and Chile were ranked in leading positions. A total of 614 articles on RSV (13.34% of all articles) were attributed to scientific collaborations. These were primarily established between high-income countries. The gender analysis indicated that male scientists dominated in all countries except Brazil.ConclusionsThe majority of RSV-related research articles originated from high-income countries whereas developing nations showed only minimal publication productivity and were barely part of any collaborative networks. Hence, research capacity in these nations should be increased in order to assist in addressing inequities in resource allocation and the clinical burden of RSV in these countries.
| S-EPMC5577886 | biostudies-literature
Project description:The COVID-19 pandemic has resulted in school closures and distancing requirements that have disrupted both work and family life for many. Concerns exist that these disruptions caused by the pandemic may not have influenced men and women researchers equally. Many medical journals have published papers on the pandemic, which were generated by researchers facing the challenges of these disruptions. Here we report the results of an analysis that compared the gender distribution of authors on 1893 medical papers related to the pandemic with that on papers published in the same journals in 2019, for papers with first authors and last authors from the United States. Using mixed-effects regression models, we estimated that the proportion of COVID-19 papers with a woman first author was 19% lower than that for papers published in the same journals in 2019, while our comparisons for last authors and overall proportion of women authors per paper were inconclusive. A closer examination suggested that women's representation as first authors of COVID-19 research was particularly low for papers published in March and April 2020. Our findings are consistent with the idea that the research productivity of women, especially early-career women, has been affected more than the research productivity of men.
| S-EPMC7304994 | biostudies-literature