PaperPlayer biorxiv scientific communication and education

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.248369v1?rss=1

Authors: Wren, J. D., Georgescu, C.

Abstract:

Although citations are used as a quantifiable, objective metric of academic influence, cases have been documented whereby references were added to a paper solely to inflate the perceived influence of a body of research. This reference list manipulation (RLM) could take place during the peer-review process (e.g., coercive citation from editors or reviewers), or prior to it (e.g., a quid-pro-quo between authors). Surveys have estimated how many people may have been affected by coercive RLM at one time or another, but it is not known how many authors engage in RLM, nor to what degree. Examining a subset of active, highly published authors (n=20,803) in PubMed, we find the frequency of non-self citations (NSC) to one author coming from one paper approximates Zipf's law. We propose the Gini Index as a simple means of quantifying skew in this distribution and test it against a series of "red flag" metrics that are expected to result from RLM attempts. We estimate between 81 (FDR <0.05) and 231 (FDR<0.10) authors are outliers on the curve, suggestive of chronic, repeated RLM. Based upon the distribution, we estimate approximately 3,284 (16%) of all authors may have engaged in RLM to some degree, possibly opportunistically. Finally, we find authors who use 18% or more of their references for self-citation are significantly more likely to have NSC Gini distortions, suggesting their desire to see their work cited carries over into their peer-review activity.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.246637v1?rss=1

Authors: Candal-Pedreira, C., Ruano-Ravina, A., Fernandez, E., Ramos, J., Campos-Varela, I., Perez-Rios, M.

Abstract:

Background: Retracted articles continue to be cited after retraction, and this could have consequences for the scientific community and general population alike. This study was conducted to analyze the impact of retraction on citations received by retracted papers in two-time frames: during a post-retraction period equivalent to the time the article had been in print before retraction; and during the total post-retraction period. Results: The results indicated an increase in post-retraction citations when compared with citations received pre-retraction. There were some exceptions however: first, citations received by articles published in first-quartile journals decreased immediately after retraction (p<0.05), only to increase again after some time had elapsed; and second, post-retraction citations decreased significantly in the case of articles that had received many citations before their retraction (p<0.05). Conclusions: The results indicate that retraction of articles has no impact on citations in the long term, since the retracted articles continue to be cited, thus circumventing their retraction. More effective mechanisms should be established to prevent the citation of retracted articles in scientific papers. Methods: Quasi-experimental, pre-post evaluation study. A total of 304 retracted original articles and literature reviews indexed in Medline fulfilled the exclusion criteria. Articles were required to have been published in Pubmed from January 2013 through December 2016 and been retracted between January 2014 and December 2016. The main outcome was the number of citations received before and after retraction. Results were broken down by journal quartile according to impact factor and the most cited papers (pre-retraction) were specifically analyzed.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.240879v1?rss=1

Authors: Mishra, P., Prasad, A., Babu, S., Yadav, G.

Abstract:

Extraction and analysis of useful knowledge from the vast amount of relevant published literature can add valuable insights to any research theme or area of interest. We introduce a simplified bibliometric data analysis protocol for gaining substantial insights into research thematics, which can also serve as a handy practical skill for researchers, while working from home. In this paper, we provide ways of developing a holistic research strategy using bibliometric-data driven approaches that integrate network analysis and information management, without the need of full paper access. This protocol is a comprehensive multi-modular pathway for analysis of metadata obtained from major scientific publishing houses by use of a Decision Support System (DSS). A simple case study on the invasive species Lantana camara has been presented as a proof-of-concept to show how one can implement this DSS based protocol. Some perspectives are also provided on how the outcomes can be used directly or scaled up for long term research interventions. We hope that this work will simplify exploratory literature review, and enable rational design of research objectives for scholars, as well as development of comprehensive grant proposals that address gaps in research.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.05.237313v1?rss=1

Authors: Sarkar, B., Munshi, A., Ghosh, B., Ganesh, T., Manikandan, A., Biswal, S. S., Sahid, T., B, R., Sengupta, S., Roychaowdhary, S., Bhattacharya, J., Gazi, M., De, A., George, K., Ghosh, T., Akhter, J., Mandal, S., Gupta, R., Roy, S., Jassal, K., Rastogi, K., Bansal, K., Chaterjee, P., Biswas, L. N., Bondopadhay, S., Pradhan, A., Mohanti, B. K.

Abstract:

Background: This study aims to analyze the dynamics of the published articles and preprints of Covid 19 related literature from different scientific databases and sharing platforms. Methods: The PubMed, Elsevier, and Research Gate (RG) databases were under consideration in this study over a specific time. Analyses were carried out on the number of publications as (a) function of time (day), (b) journals and (c) authors. Doubling time of the number of publications was analyzed for PubMed all articles and Elsevier published articles. Analyzed databases were (1A) PubMed all articles (01/12/2019 to 12/06/2020) (1B) PubMed Review articles (01/12/2019 to 2/5/2020) and (1C) PubMed Clinical Trials (01/01/2020-30/06/2020) (2) Elsevier all publications (01/12/2019 to 25/05/2020) (3) RG (Article, Pre Print, Technical Report) (15/04/2020 to 30/4/2020). Findings: Total publications in the observation period for PubMed, Elsevier, and RG were 23000, 5898 and 5393 respectively. The average number of publications/day for PubMed, Elsevier and RG were 70.0 {+/-}128.6, 77.6{+/-}125.3 and 255.6{+/-}205.8 respectively. PubMed shows an avalanche in the number of publication around May 10, number of publications jumped from 6.0{+/-}8.4/day to 282.5{+/-}110.3/day. The average doubling time for PubMed, Elsevier, and RG was 10.3{+/-}4 days, 20.6 days, and 2.3{+/-}2.0 days respectively. In PubMed average articles/journal was 5.2{+/-}10.3 and top 20 authors representing 935 articles are of Chinese descent. The average number of publications per author for PubMed, Elsevier, and RG was 1.2{+/-}1.4, 1.3{+/-}0.9, and 1.1{+/-}0.4 respectively. Subgroup analysis, PubMed review articles mean and median review time for each article were <0|17{+/-}17|77> and 13.9 days respectively; and reducing at a rate of -0.21 days (count)/day. Interpretation: Although the disease has been known for around 6 months, the number of publications related to the Covid-19 until now is huge and growing very fast with time. It is essential to rationalize the publications scientifically by the researchers, authors, reviewers, and publishing houses.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.04.235879v1?rss=1

Authors: Wu, H., Eungpinichpong, W., Ruan, H., Zhang, X., Dong, X.

Abstract:

This study investigates motor fitness (MF), fundamental movement skills (FMS), and functional movement screen (FMS) in 7-10-year-old children, and evaluates the relationship between FMS?MF and FMS combination with Seefeldt`s model for empirical research, thus to present effective strategies of physical development in children. A class was randomly selected in four school grades (1-4) along with 30 students from each to take the Test of Gross Motor Development-2 (TGMD-2). A total of 117 children (42 girls, aged 7-10) participated in three tests: TGMD-2, MF tests, and FMS. MF levels (good, fair, and poor) and FMS levels (high, moderate, and low) were classified according to specific percentile ranges. A multiple (RxC) chi-square test analysis of the relationship between MF, FMS, and FMS was applied and post hoc testing estimated the possibility of FMS and FMS predicting MF. The results showed that only 43% of children were rated "good" on MF. Most fourth-grade students exhibited a certain gap with mature FMS (TGMD-2 score 70.13{+/-}9.68< 96 full scores). Boys scored significantly higher on the object control subtest and the TGMD-2 total score compared to girls (p<0.001), while girls had a significantly greater score than boys on the FMS ( p =0.001). The results of multiple chi-square demonstrated FMS to be weakly correlated with MF, {chi} 2 (4,N=117) =14.605, p =0.006< 0.01, Cramers V = 0.25. Both 60.5% of "excellent" FMS and 59.6% of "high" FMS children were categorized as having a "good" MF level. On the other hand, only 23.1% of the "worst" FMS and 24.3% of "low" FMS individuals were classified as having a "good" MF level. Our results suggest that MF, FMS, FMS are relatively independent systems linking with each other, generating mutual interaction in childrens motor development. At different stages or different advantages of them motor development, we may emphasize training one or a few parts.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.225979v1?rss=1

Authors: Araujo, G. S.

Abstract:

Teaching computer programming is not a simple task and it is challenging to introduce the concepts of programming in graduate programs of other fields. Little efforts have been made on engaging students in computational development after programming trainings. An emerging need is to establish subjects of bioinformatics and programming languages in genetics and molecular biology graduate programs, when students in these degree programs are immersed in a sea of genomic and transcriptomic data, which demands proficient computational treatment. I report an empirical guideline to introduce programming languages and recommend Python as first language for graduate programs in which students were from genetics and molecular biology backgrounds. Including the development of programming solutions related to graduate students' research activities may improve programming skills and better engagement. These results suggest that the applied approach leads to enhanced learning of introductory to autonomy in highly advanced programming concepts by graduate students. This guide should be extended for other research programs.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.30.228916v1?rss=1

Authors: Yanai, I., Lercher, M.

Abstract:

When analyzing the results of an experiment, the mental focus on a specific hypothesis might prevent the exploration of other aspects of the data, effectively blinding one to new ideas. To test this notion, we performed an experiment in which we asked undergraduate students to analyze a fictitious dataset. In addition to being asked what they could conclude from the dataset, half of the students were asked to also test specific hypotheses. In line with our notion, students in the hypothesis-free group were almost 5 times more likely to observe an image of a gorilla when simply plotting the data, a proxy for an initial step towards data analysis. If these findings are representative also of scientific research as a whole, they warrant concern about the current emphasis on hypothesis-driven research, especially in the context of information-rich datasets such as those now routinely created in the biological sciences. Our work provides evidence for a link between the psychological effect of selective attention and hypothesis-driven data analysis, and suggests a hidden cost to having a hypothesis when analyzing a dataset.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.30.228643v1?rss=1

Authors: Shiina, A., Niitsu, T., Kobori, O., Idemoto, K., Hashimoto, T., Sasaki, T., Igarashi, Y., Shimizu, E., Nakazato, M., Hashimoto, K., Iyo, M.

Abstract:

To control the spread of the newly developed corona viral infection diseases (COVID-19), peoples appropriate precautionary behaviors should be promoted. We conducted a series of online questionnaire survey, to gather a total of 8,000 citizens responses on March 27-28, 2020 in Japan and April 17-21 in the UK and Spain. Compared to Japan, the knowledge and anxiety level and the frequency of precautionary behaviors were higher in the UK and Spain. Participants with infected acquaintances were more concerned about COVID-19. However, participants in the UK rarely wore a medical mask. Participants in the UK and Spain were eager to get information about COVID-19 compared to those in Japan. The participants in Spain tended not to trust official information and to believe specialists' comments instead. The urgency of the spread of COVID-19, cultural backgrounds, and recent political situations appear to contribute to the differences among countries revealed herein.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.29.226464v1?rss=1

Authors: Gompo, T. R., Jyoti, S., Pandit, S., Sapkota, R. C., Pandey, A.

Abstract:

Nepal has an agrarian-based economy where the livestock sector contributes about 12 percent to the national GDP. Rupandehi district is one of the largest dairy pocket areas in the nation, but the disease, such as leptospirosis, posed a negative impact on their production and productivity. Despite the economic importance of cattle leptospirosis, the disease is concerned for the people's occupational risk and food safety. Although leptospirosis is a priority zoonosis in Nepal, the effective implementation of the control program lacks both in animal and human health. A cross-sectional study was conducted to estimate the prevalence and identify associated risk factors of cattle leptospirosis from March 2019 to April 2020. Altogether, 206 cattle herds located in all the sixteen local levels of the district were visited. The owners were interviewed to record the cattle management system's information and their knowledge of the zoonotic diseases. A total of 383 cattle serum samples were collected, and an indirect antibody ELISA was performed to estimate the infection status of leptospirosis in the cattle herds. All the data were analyzed by Open epi and R software for the descriptive and analytical study. Bivariate and multivariable logistic regression was applied to assess the potential herd level and animal level risk factors. Out of seven potential herd-level risk factors, the purchased cattle herds (OR: 7.2, 95% CI: 1.24-136.5, p=0.025) and cattle with herd size >10 (OR: 14.92, 95% CI: 2.61-283.38, p=0.025) were identified as significant risk factors for leptospirosis. At the animal level, the cattle taken for grazing in pastureland accessed by the community dog was a significant risk factor (OR: 4.16, 95% CI: 1.13- 14.06, p=0.034). Surprisingly, none of the farmers had heard about leptospirosis before. The outcome of this research could be an epidemiological insight in control of priority zoonosis to protect the livestock economy and reduce their negative impact on public health.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.28.225953v1?rss=1

Authors: Huang, A., Hancock, D., Clemson, M., Yeo, G., Harney, D. J., Denny, P., Denyer, G.

Abstract:

Production of high-quality multiple-choice questions (MCQs) for both formative and summative assessment is a time-consuming task requiring great skill, creativity, and insight. The transition to online examinations, with the concomitant exposure of previously tried-and-tested MCQs, exacerbates the challenges of question production, and highlights the need for innovative solutions. Several groups have shown that it is practical to leverage the student cohort to produce a very large number of syllabus-aligned MCQs for study banks. Although student-generated questions are well suited for formative feedback and practice activities, they are generally not thought to be suitable for high-stakes assessments. In this study, we aimed to demonstrate that training can be provided to students in a scalable fashion to generate questions of similar quality to those produced by experts, and that identification of suitable questions can be achieved with minimal academic review and editing. Biochemistry and Molecular Biology students were assigned a series of activities designed to coach them in the art of writing and critiquing MCQs. This training resulted in the production of over one thousand MCQs that were then gauged for potential by either expert academic judgement, or via a data-driven approach in which the questions were trialled objectively in a low-stakes test. Questions selected by either method were then deployed in a high-stakes in-semester assessment alongside questions from two academically authored sources: textbook-derived MCQs, and past paper questions. A total of 120 MCQs from these four sources were deployed in assessments attempted by over 600 students. Each question was subjected to rigorous performance analysis, including the calculation of standard metrics from classical test theory and more sophisticated Item Response Theory (IRT) measures. The results showed that MCQs authored by students and selected at low cost performed as well as questions authored by academics, illustrating the potential of this strategy for the efficient creation of large numbers of high quality MCQs for summative assessment.

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