AuthorArranger automates formatting title pages and author affiliations for manuscript submissions.
Ontology highlight
ABSTRACT:
SUBMITTER: Machiela MJ
PROVIDER: S-EPMC9240033 | biostudies-literature | 2022 Jun
REPOSITORIES: biostudies-literature
Publications
AuthorArranger automates formatting title pages and author affiliations for manuscript submissions.
Machiela Mitchell J MJ Tobias Geoffrey G
Communications biology 20220628 1
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Project description:Author affiliations are essential in bibliometric studies, requiring relevant information extraction from free-text affiliations. Precisely determining an author's location from their affiliation is crucial for understanding research networks, collaborations, and geographic distribution. Existing geoparsing tools using regular expressions have limitations due to unstructured and ambiguous affiliations, resulting in erroneous location identification, especially for unconventional variations or misspellings. Moreover, their inefficient handling of big datasets hampers large-scale bibliometric studies. Though machine learning-based geoparsers exist, they depend on explicit location information, creating challenges when detailed geographic data is absent. To address these issues, we developed and evaluated a natural language processing model to predict the city, state, and country from an author's free-text affiliation. Our model automates location inference, overcoming drawbacks of existing methods. Trained and tested with MapAffil, a publicly available geoparsed dataset of PubMed affiliations up to 2018, our model accurately retrieves high-resolution locations, even without explicit mentions of a city, state, or even country. Leveraging NLP techniques and the LinearSVC algorithm, our machine learning model achieves superior accuracy based on several validation datasets. This research demonstrates a practical application of text classification for inferring specific geographical locations from free-text affiliations, benefiting researchers and institutions in analyzing research output distribution.
| S-EPMC11484971 | biostudies-literature
Project description:BackgroundObstructive sleep apnea syndrome (OSAS) is a common chronic sleep disorder. OSAS is closely related to cardiovascular disease, metabolic disorders, cancer risk, and sudden death. This association has special significance in young people. Although it is known that OSAS has a great impact on physical health, it is estimated that 70-80% of patients with moderate-to-severe OSAS remain undiagnosed. Therefore, a new method for early diagnosis of the disease, the therapeutic effect of OSAS and prevention of complications to important.MethodsA total of 110 patients with moderate-to-severe OSAS diagnosed in the Sleep Disorders Diagnosis and Treatment Center of Peking University Shenzhen Hospital were selected. After excluding other diseases, 59 patients were finally selected as the OSAS group. In addition, 60 healthy people were selected as the control group. Serum RNA was then extracted. Eight RNA samples were randomly selected from the two groups for high-throughput miRNA sequencing. The 10 miRNAs with the greatest differences were selected as preselected markers from the results. Then, qRT-PCR was performed on the remaining RNA samples of the two groups to extract and verify the 10 miRNAs, and statistical analysis was performed between groups.ResultsA diagnostic panel was constructed by a stepwise logistic regression model combined with the expression data of miRNAs in the validation phase. A four-miRNA panel was identified to better predict OSAS, and the model was calculated using the following formula: Logit (P)= 0.77-1.65 × miR-486-5p - 4.56 × miR-148a-3p + 1.79 × miR-744-5p + 1.13 × let-7d-3p. The AUC for the four-miRNA panel was 0.955 (95% CI: 0.899 to 0.985; sensitivity = 91.38%, specificity = 91.38%). Gene Ontology (GO) annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis was included in bioinformatic analysis.ConclusionA 4-miRNAs panel as a diagnostic biomarker for OSAS screening is feasible.
| S-EPMC9656345 | biostudies-literature
Project description:IntroductionUniversity ranking systems and the publish-or-perish dictum, among other factors, are driving universities and researchers around the world to increase their research productivity. Authors frequently report multiple affiliations in published articles. It is not known if the reported institutional affiliations are real affiliations, which is when the universities have contributed substantially to the research conducted and to the published manuscript. This study aims to establish whether there is an empirical basis for author affiliation misrepresentation in authors with multiple institutional affiliations.Methods and analysisThis individual secondary data exploratory analysis on Scopus-indexed articles for 2016 will search all authors who report multiple institutional affiliations in which at least one of the affiliations is to a Chilean university. We will consider that misrepresentation of an affiliation is more likely when it is not possible to verify objectively a link between the author and the mentioned institution through institutional websites. If we cannot corroborate the author affiliation, we will consider this a finding of potential misrepresentation of the affiliation. We will summarise results with descriptive statistics.Ethics and disseminationThe study protocol was approved by the institutional ethics committee of Universidad de Santiago de Chile, Resolution No. 261, and dated January 15, 2018. Results will be submitted to the World Conference on Research Integrity, among other meetings on publication ethics and research integrity, and will be published in scientific, peer-reviewed journals.
| S-EPMC6398759 | biostudies-literature
Project description:BackgroundBy assessing the changes in concentration of soluble receptor activator of nuclear factor κ B ligand (RANKL) and osteoprotegrin (OPG) after initiation of combination antiretroviral therapy (cART) in treatment-naïve HIV-infected patients we aimed to evaluate whether the initial accelerated bone loss could be mediated by increased soluble RANKL (sRANKL) levels associated with CD4+ T cell recovery.MethodsWe used multiplex immunoassays to determine sRANKL and OPG concentrations in plasma from 48 HIV patients at baseline and 12, 24, 48 and 96 weeks after cART initiation.ResultsSoluble RANKL changed significantly over time (overall p = 0.02) with 25% decrease (95% CI: -42 to -5) at week 24 compared to baseline and stabilized at a lower level thereafter. We found no correlation between CD4+ T cell count increment and changes in sRANKL or between percentage change in BMD and changes in sRANKL.ConclusionIn this study there was no indication that the accelerated bone loss after cART initiation was mediated by early changes in sRANKL due to CD4+ T cell recovery. Future studies should focus on the initial weeks after initiation of cART.Trial registrationClinical-Trial.gov . id NCT00135460 , August 25, 2005. The study was approved by the Danish Data Protection Agency, Danish Medicines Agency and Regional Ethics Committee.
| S-EPMC5387326 | biostudies-literature
Project description:ObjectiveTo determine whether researchers are submitting manuscripts and peer reviews to BMJ journals out of hours and whether this has changed over time.DesignObservational study of research manuscripts and peer reviews submitted between 2012 and 2019 for which an author's address could be geocoded.SettingOnline BMJ submission systems for two large general medical journals.Main outcome measuresManuscript and peer review submissions on weekends, on national holidays, and by hour of day (to determine early mornings and late nights). Logistic regression was used to estimate the probability of manuscript and peer review submissions on weekends or holidays.ResultsThe analyses included more than 49 000 manuscript submissions and 76 000 peer reviews. Little change over time was seen in the average probability of manuscript or peer review submissions occurring on weekends or holidays. The levels of out of hours work were high, with average probabilities of 0.14 to 0.18 for work on the weekends and 0.08 to 0.13 for work on holidays compared with days in the same week. Clear and consistent differences were seen between countries. Chinese researchers most often worked at weekends and at midnight, whereas researchers in Scandinavian countries were among the most likely to submit during the week and the middle of the day.ConclusionThe differences between countries that are persistent over time show that a "culture of overwork" is a literal thing, not just a figure of speech.
| S-EPMC7222960 | biostudies-literature
Project description:Background Environmental health and other researchers can benefit from automated or semi-automated summaries of data within published studies as summarizing study methods and results is time and resource intensive. Automated summaries can be designed to identify and extract details of interest pertaining to the study design, population, testing agent/intervention, or outcome (etc.). Much of the data reported across existing publications lack unified structure, standardization and machine-readable formats or may be presented in complex tables which serve as barriers that impede the development of automated data extraction methodologies. As full automation of data extraction seems unlikely soon, encouraging investigators to submit structured summaries of methods and results in standardized formats with meta-data tagging of content may be of value during the publication process. This would produce machine-readable content to facilitate automated data extraction, establish sharable data repositories, help make research data FAIR, and could improve reporting quality. Objectives A pilot study was conducted to assess the feasibility of asking participants to summarize study methods and results using a structured, web-based data extraction model as a potential workflow that could be implemented during the manuscript submission process. Methods Eight participants entered study details and data into the Health Assessment Workplace Collaborative (HAWC). Participants were surveyed after the extraction exercise to ascertain 1) whether this extraction exercise will impact their conducting and reporting of future research, 2) the ease of data extraction, including which fields were easiest and relatively more problematic to extract and 3) the amount of time taken to perform data extractions and other related tasks. Investigators then presented participants the potential benefits of providing structured data in the format they were extracting. After this, participants were surveyed about 1) their willingness to provide structured data during the publication process and 2) whether they felt the potential application of structured data entry approaches and their implementation during the journal submission process should continue to be further explored. Conclusions Routine provision of structured data that summarizes key information from research studies could reduce the amount of effort required for reusing that data in the future, such as in systematic reviews or agency scientific assessments. Our pilot study suggests that directly asking authors to provide that data, via structured templates, may be a viable approach to achieving this: participants were willing to do so, and the overall process was not prohibitively arduous. We also found some support for the hypothesis that use of study templates may have halo benefits in improving the conduct and completeness of reporting of future research. While limitations in the generalizability of our findings mean that the conditions of success of templates cannot be assumed, further research into how such templates might be designed and implemented does seem to have enough chance of success that it ought to be undertaken. Data extraction; Automated data extraction; Electronic data extraction manuscript submission; Structured data; Data sharing; Natural language processing (NLP); Semantic authoring; Author opinion; Author feedback; Author willingness; Data summary; Systematic review; Study quality; Study quality reporting; Risk of bias reporting; Study evaluation; Data extraction tool; Data extraction software; Standardized data; Data templates; Author submission requirements; Machine readable; Knowledge translation; Science translation.
| S-EPMC9280381 | biostudies-literature
Project description:C/EBPα is an essential transcription factor involved in regulating the expression or function of certain cell-cycle regulators. However, little is known about the role of methylation in regulating the antiproliferation activity of C/EBPα. Here, we report that knockdown of protein arginine methyltransferases 1 (PRMT1) leads to cellular growth arrest accompanied by a decrease in Cyclin D1 gene expression in breast cancer cells. Furthermore, we reveal that C/EBPα is methylated by PRMT1 at three arginine residues (R35, R156, and R165), which impairs the interaction of C/EBPα with HDAC3 and modulates the transcription activity of C/EBPα and Cyclin D1 gene expression. PRMT1 is upregulated in human breast cancer, and elevated PRMT1 is correlated with cancer malignancy. Most importantly, a specific inhibitor of PRMT1 significantly impedes the growth of cancer cells from triple-negative breast cancer patients. Our data demonstrate that high expression of PRMT1 promotes the expression of Cyclin D1 through methylation of C/EBPα to interfere with the repressive function of HDAC3, which leads to rapid growth of tumor cells during the pathogenesis of breast cancer. This evidence that PRMT1 mediates C/EBPα methylation sheds light on a novel therapeutic pathway for breast cancer.
2020-04-05 | GSE121168 | GEO
Project description: Not available
| S-EPMC5934772 | biostudies-literature
Project description:Animals capable of complex behaviors tend to have more distinct brain areas than simpler organisms, and artificial networks that perform many tasks tend to self-organize into modules (1-3). This suggests that different brain areas serve distinct functions supporting complex behavior. However, a common observation is that essentially anything that an animal senses, knows, or does can be decoded from neural activity in any brain area (4-6). If everything is everywhere, why have distinct areas? Here we show that the function of a brain area is more related to how different types of information are combined (formatted) in neural representations than merely whether that information is present. We compared two brain areas: the middle temporal area (MT), which is important for visual motion perception (7, 8), and the dorsolateral prefrontal cortex (dlPFC), which is linked to decision-making and reward expectation (9, 10)). When monkeys based decisions on a combination of motion and reward information, both types of information were present in both areas. However, they were formatted differently: in MT, they were encoded separably, while in dlPFC, they were represented jointly in ways that reflected the monkeys' decision-making. A recurrent neural network (RNN) model that mirrored the information formatting in MT and dlPFC predicted that manipulating activity in these areas would differently affect decision-making. Consistent with model predictions, electrically stimulating MT biased choices midway between the visual motion stimulus and the preferred direction of the stimulated units (11), while stimulating dlPFC produced 'winner-take-all' decisions that sometimes reflected the visual motion stimulus and sometimes reflected the preference of the stimulated units, but never in between. These results are consistent with the tantalizing possibility that a modular structure enables complex behavior by flexibly reformatting information to accomplish behavioral goals.
| S-EPMC11722384 | biostudies-literature