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bioRxiv2020

Measuring the quality of scientific references in Wikipedia: an analysis of more than 80M citations to over 800,000 scientific articles

Wikipedia is a widely used online reference work which cites hundreds of thousands of scientific articles across its entries. The quality of these citations has not been previously measured, and such measurements have a bearing on the reliability and quality of the scientific portions of this reference work. Using a novel technique, a massive database of qualitatively described citations, and machine learning algorithms, we analyzed 1,923,575 Wikipedia articles which cited a total of 841,821 scientific articles, and found that most cited articles (58%) are uncited or untested by subsequent studies, while the remainder show a wide variability in contradicting or supporting evidence (2-40%).View Full Text

scientific communication and education↗

bioRxiv2020

Patterns of discursive interactions between students and teachers in the biology learning process in High school: the use of social media

Increasingly, blending teaching has become a reality in a generation where the digital language is present in virtually every activity. In addition to allowing greater independence and encouraging students to learn at their own pace, blending teaching allows the student to easily access reliable information quickly. Therefore, new studies related to active learning methodology are fundamental. In this study we analyzed 69 interactions between high school students and their teachers in a biology learning activity using a social networking site and the methodology proposed by Mortimer and Scott. The results showed that the prior knowledge of students as well as questions posing challenges and problems to be solved, a very important approach in learning Science Methodology, were barely explored by teachers and mediators (17% and 1%, respectively). Our data demonstrated that the use of digital technology alone does not guarantee interactions that contribute to the learning process in the field of natural sciences. Proposals were also discussed so that these interactions become more diversified and interesting for students, arousing interest in research and promoting the knowledge of scientific methodology.Competing Interest StatementThe authors have declared no competing interest.View Full Text

scientific communication and education↗

bioRxiv2020

BIP4COVID19: Releasing impact metrics data for articles relevant to COVID-19

Since the beginning of the 2019-20 coronavirus pandemic, a large number of relevant articles has been published or become available in preprint servers. These articles, along with earlier related literature, compose a valuable knowledge base affecting contemporary research studies, or even government actions to limit the spread of the disease and treatment decisions taken by physicians. However, the number of such articles is increasing at an intense rate making the exploration of the relevant literature and the identification of useful knowledge in it challenging. In this work, we describe BIP4COVID19, an open dataset compiled to facilitate the coronavirus-related literature exploration, by providing various indicators of scientific impact for the relevant articles. Additionally, we provide a publicly accessible Web interface on top of our data, allowing the exploration of the publications based on the computed indicators.

scientific communication and education↗

bioRxiv2020

Assessment of whether published non-Cochrane systematic reviews of nursing follow the review protocols registered in the International Prospective Register of Systematic Reviews (PROSPERO): A comparative study

Purpose We compare published non-Cochrane reviews of nursing with their pre-registered protocols on PROSPERO to quantify the prevalence of differences and the extent to which the differences were explained.Methods We searched for protocols and their corresponding reviews in PROSPERO’s nursing group that were “completed and published” from inception to September 8th, 2019. Two authors independently identified differences and classified the difference as none, partial, or complete, and determined if the existed differences had been explained. Frequency (n), percentage (%), median, and inter-quartile ranges were used to analyze the extent of differences and explanations.Results We identified 22 pre-registered protocols and their reviews. All 22 pairs (100%) exhibited differences. Eighteen pairs (82%) showed differences in at least six methodological sections, while 21 pairs (95%) involved completed difference in at least one section. The median number of differences per review was 8.00 (upper quartile = 6.00, lower quartile = 9.75). The differences involved all 13 compared methodology-related sections. Only 5 (3%) of all differences were explained in the systematic reviews.Conclusions We observed widespread differences between non-Cochrane reviews of nursing and their protocols recorded in PROSPERO, with relatively few explanations for the changes. Measures including establishing a new item in the reporting guideline of systematic reviews to guide reporting and explaining the reasons for differences between protocols and systematic reviews or even requiring authors to do so at the Journal’s author guideline are recommended to improve transparency.View Full Text

scientific communication and education↗

bioRxiv2020

Residual-matching: An efficient alternative to random sampling in human subjects research recruitment

ABSTRACTGiven the time- and resource-intense nature of human subjects research, we have developed a more intelligent approach to participant recruitment above and beyond random sampling that leverages pilot or preliminary results to reduce the overall number of participants needed for recruitment from an existing electronic cohort or database. Using open-access data from the General Social Survey (GSS) of the National Opinion Research Center, we generated pilot and validation datasets through a simulation to establish moderate and weak relationships based on linear regression. We then compared the performance of our residual-matching method against random sampling in their probabilities of achieving a given level of statistical power as well as their prediction accuracies. Results showed that the residual-matching method was superior to random sampling, yielding smaller sample sizes with equivalent mean square error. We therefore advocate the use of residual matching when scaling up pilot studies to conserve time and resources in larger follow-up studies.Competing Interest StatementThe authors have declared no competing interest.View Full Text

scientific communication and education↗

bioRxiv2020

Pandemic Publishing: Medical journals drastically speed up their publication process for Covid-19

In times of public crises, including the current Covid-19 pandemic, rapid dissemination of relevant scientific knowledge is of paramount importance. The duration of scholarly journals’ publication process is one of the main factors hindering quick delivery of new information. While proper editorial assessment and peer review obviously require some time, turnaround times for medical journals can be up to several months, which is undesirable in the era of a crisis. Following initiatives of medical journals and scholarly publishers to accelerate their publication process, this study assesses whether medical journals have indeed managed to speed up their publication process for Covid-19 related articles. It studies the duration of 14 medical journals’ publication process both during and prior to the current pandemic. Assessing a total of 669 articles, the study concludes that medical journals have indeed drastically accelerated the publication process for Covid-19 related articles since the outbreak of the pandemic. Compared to articles published in the same journals before the pandemic, turnaround times have decreased on average by 49%. The largest decrease in number of days between submission and publication of articles was due to a decrease in the number of days required for peer review. For articles not related to Covid-19, no acceleration of the publication process is found. While the acceleration of journals’ publication process is laudable from the perspective of quick information dissemination, it also raises concerns relating to the quality of the peer review process and the quality of the resulting publications.Competing Interest StatementThe authors have declared no competing interest.View Full Text

scientific communication and education↗

bioRxiv2020

A scientometric overview of CORD-19

As the COVID-19 pandemic unfolds, researchers from all disciplines are coming together and contributing their expertise. CORD-19, a dataset of COVID-19 and coronavirus publications, has been made available along-side calls to help mine the information it contains and to create tools to search it more effectively. We analyse the delineation of the publications included in CORD-19 from a scientometric perspective. Based on a comparison to the Web of Science database, we find that CORD-19 provides an almost complete coverage of research on COVID-19 and coronaviruses. CORD-19 contains not only research that deals directly with COVID-19 and coronaviruses, but also research on viruses in general. Publications from CORD-19 focus mostly on a few well-defined research areas, in particular: coronaviruses (primarily SARS-CoV, MERS-CoV and SARS-CoV-2); public health and viral epidemics; molecular biology of viruses; influenza and other families of viruses; immunology and antivirals; clinical medicine. CORD-19 publications that appeared in 2020, especially editorials and letters, are disproportionately popular on social media. While we fully endorse the CORD-19 initiative, it is important to be aware that CORD-19 extends beyond research on COVID-19 and coronaviruses.

scientific communication and education↗

bioRxiv2020

Antibiotic-resistant Salmonella species and Escherichia coli in broiler chickens from farms, abattoirs and open markets in selected districts of Zambia

Salmonella species and Escherichia coli are major bacterial enteropathogens of global public health importance that cause foodborne diseases, thereby contributing to increased human morbidity and mortality. Both pathogens have also been found to contribute towards the spread of antimicrobial resistance through the food chain, especially in poultry. The aim of this study was to determine the occurrence of antibiotic-resistant Salmonella sp. and E. coli in broiler chickens at farm level, abattoirs and open markets in selected districts of Zambia. A cross-sectional study was undertaken in seven districts of Zambia to determine the resistance profiles of Salmonella sp. and E. coli obtained from broiler chickens at farms, abattoirs and open markets. A total of 470 samples were collected, including litter, cloacal swabs and carcass swabs. Samples were inoculated into buffered peptone water, sub-cultured onto MacConkey and Xylose Lysine Deoxycholate agar plates. Identification of Salmonella sp. and E. coli was done using the API-20E kit and confirmation by 16S rDNA sequencing. Confirmed isolates were tested against a panel of 10 antibiotics using the Kirby-Bauer disc-diffusion method and interpreted according to the Clinical Laboratory Standards Institute guidelines. Analysis of the antibiotic susceptibility test results was done using WHONET 2018 software. Overall, 4 Salmonella spp. and 280 E. coli were isolated. One of the Salmonella sp. was resistant to ampicillin (25%), amoxicillin/clavulanic acid (25%) and cefotaxime (25%). E. coli antibiotic resistance was highest to tetracycline (81.4%) and lowest to imipenem (0.7%). The antibiotic susceptibility profile revealed 55% (154/280) multidrug resistant E. coli, with the highest multidrug resistance profile (20.7%) in the ampicillin-tetracycline-trimethoprim/sulfamethoxazole drug combination. Furthermore, 4.3% (12/280) of the isolates showed Extensive Drug resistance. The levels of antimicrobial resistance to E. coli and Salmonella observed in market-ready chickens is of public health concern.View Full Text

scientific communication and education↗

bioRxiv2020

Open Access and Altmetrics in the pandemic age: Forescast analysis on COVID-19 related literature

We present an analysis on the uptake of open access on COVID-19 related literature as well as the social media attention they gather when compared with non OA papers. We use a dataset of publications curated by Dimensions and analyze articles and preprints. Our sample includes 11,686 publications of which 67.5% are openly accessible. OA publications tend to receive the largest share of social media attention as measured by the Altmetric Attention Score. 37.6% of OA publications are bronze, which means toll journals are providing free access. MedRxiv contributes to 36.3% of documents in repositories but papers in BiorXiv exhibit on average higher AAS. We predict the growth of COVID-19 literature in the following 30 days estimating ARIMA models for the overall publications set, OA vs. non OA and by location of the document (repository vs. journal). We estimate that COVID-19 publications will double in the next 20 days, but non OA publications will grow at a higher rate than OA publications. We conclude by discussing the implications of such findings on the dissemination and communication of research findings to mitigate the coronavirus outbreak.Competing Interest StatementThe authors have declared no competing interest.View Full Text

scientific communication and education↗

bioRxiv2020

Impacts of the 1918 Flu on survivors ' nutritional status:a double quasi-natural experiment

ABSTRACTA unique set of events that took place in Puerto Rico during 1918-1919 generated conditions of a “double “quasi-natural experiment. We exploit these conditions to empirically identify effects of exposure to the 1918 flu pandemic, those of the devastation left by an earthquake-tsunami that struck the island in 1918, and those associated with the joint occurrence of these events. We use geographic variation to identify the effects of the quake and timing of birth variation to identify those of the flu. In addition, we use markers of nutritional status gathered in a nationally representative sample of individuals aged 75 and older in 2002. This unique data set enables to make two distinct contributions. First, unlike most fetal-origins research that singles out early nutritional status as a determinant of adult health, we test the hypothesis that the 1918 flu had deleterious effects on the nutritional status on adult survivors who at the time of the flu were in utero or infants. Second, and unlike most research on the effects of the flu, we focus on markers of nutritional status set when the adult survivors were children or adolescents. We find that estimates of effects of the pandemic are sizeable primarily among females and among those who, in addition to the flu, were exposed to the earthquake-tsunami. We argue that these findings constitute empirical evidence supporting the conjecture that effects of the 1918 flu alone and the combined effects of the flu and the earthquake are associated not just with damage experienced during the fetal period but also postnatally.View Full Text

scientific communication and education↗

bioRxiv2020

International authorship and collaboration in bioRxiv preprints

As preprints become integrated into conventional avenues of scientific communication, its critical to understand who is included and who is not. However, little is known about which countries are participating or how they collaborate with each other. Here, we present an analysis of all 67,885 preprints posted on bioRxiv (through 2019) using the first comprehensive dataset of country-level preprint author affiliations. We find the plurality of preprints (39%) come from the United States, and that countries such as the U.S. and U.K. are overrepresented on bioRxiv relative to their overall scientific output, while countries including China, Russia, and Turkey show lower bioRxiv adoption. We describe a set of "contributor countries" including Uganda, Croatia and Thailand that appear almost exclusively as non-senior authors on international collaborations. Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the U.S.

scientific communication and education↗

bioRxiv2020

The case for formal methodology in scientific reform

Current attempts at methodological reform in sciences come in response to an overall lack of rigor in methodological and scientific practices in experimental sciences. However, most methodological reform attempts suffer from similar mistakes and over-generalizations to the ones they aim to address. We argue that this can be attributed in part to lack of formalism and first principles. Considering the costs of allowing false claims to become canonized, we argue for formal statistical rigor and scientific nuance in methodological reform. To attain this rigor and nuance, we propose a five-step formal approach for solving methodological problems. To illustrate the use and benefits of such formalism, we present a formal statistical analysis of three popular claims in the metascientific literature: (a) that reproducibility is the cornerstone of science; (b) that data must not be used twice in any analysis; and (c) that exploratory projects imply poor statistical practice. We show how our formal approach can inform and shape debates about such methodological claims.

scientific communication and education↗

bioRxiv2020

A systematic examination of preprint platforms for use in the medical and biomedical sciences setting

ABSTRACTObjectives The objective of this review is to identify all preprint platforms with biomedical and medical scope and to compare and contrast the key characteristics and policies of these platforms. We also aim to provide a searchable database to enable relevant stakeholders to compare between platforms.Study Design and Setting Preprint platforms that were launched up to 25th June 2019 and have a biomedical and medical scope according to MEDLINE’s journal selection criteria were identified using existing lists, web-based searches and the expertise of both academic and non-academic publication scientists. A data extraction form was developed, pilot-tested and used to collect data from each preprint platform’s webpage(s). Data collected were in relation to scope and ownership; content-specific characteristics and information relating to submission, journal transfer options, and external discoverability; screening, moderation, and permanence of content; usage metrics and metadata. Where possible, all online data were verified by the platform owner or representative by correspondence.Results A total of 44 preprint platforms were identified as having biomedical and medical scope, 17 (39%) were hosted by the Open Science Framework preprint infrastructure, six (14%) were provided by F1000 Research Ltd (the Open Research Central infrastructure) and 21 (48%) were other independent preprint platforms. Preprint platforms were either owned by non-profit academic groups, scientific societies or funding organisations (n=28; 64%), owned/partly owned by for-profit publishers or companies (n=14; 32%) or owned by individuals/small communities (n=2; 5%). Twenty-four (55%) preprint platforms accepted content from all scientific fields although some of these had restrictions relating to funding source, geographical region or an affiliated journal’s remit. Thirty-three (75%) preprint platforms provided details about article screening (basic checks) and 14 (32%) of these actively involved researchers with context expertise in the screening process. The three most common screening checks related to the scope of the article, plagiarism and legal/ethical/societal issues and compliance. Almost all preprint platforms allow submission to any peer-reviewed journal following publication, have a preservation plan for read-access, and most have a policy regarding reasons for retraction and the sustainability of the service. Forty-one (93%) platforms currently have usage metrics, with the most common metric being the number of downloads presented on the abstract page.Conclusion A large number of preprint platforms exist for use in biomedical and medical sciences, all of which offer researchers an opportunity to rapidly disseminate their research findings onto an open-access public server, subject to scope and eligibility. However, the process by which content is screened before online posting and withdrawn or removed after posting varies between platforms, which may be associated with platform operation, ownership, governance and financing.In concurrence with an increase in the number of preprint servers and platforms supporting biomedical and medical sciences research since 2013, there has been substantial growth in the number of preprints posted in this research area.The significant benefits of accelerated dissemination of research that preprints offer has attracted the support of many major funders.The raised profile of preprints has led to their wider acceptance in institutional and individual level assessment.This is the first full examination of the characteristics and policies of 44 preprint platforms with biomedical and medical scope. We use a robust methodological approach to extract relevant information from web-based material with input from preprint platform owners.Despite concerns regarding the permanence and quality of preprints, most preprint platforms have long-term preservation strategies and many have screening checks (for example, a basic check for the relevance of content) in place. For some platforms, these checks are performed by researchers with content expertise.We provide a searchable database as a valuable resource for researchers, funders and policymakers in the biomedical and medical science field to determine which preprint platforms are relevant to their research scope and which have the functionality and policies that they value most.Competing Interest StatementJessica Polka is Executive Director of ASAPbio.View Full Text

scientific communication and education↗

bioRxiv2020

Media representation of spiders may exacerbate arachnophobic sentiments by framing a distorted perception of risk

ABSTRACTSpiders are able to arouse strong emotional reactions in humans. While spider bites are statistically rare events, our perception is skewed towards the potential harm spiders can cause to humans. We examined the human dimension of spiders through the lens of traditional media, by analysing more than 300 spider-related news published online in Italian newspapers between 2010 and 2020. We observed a recent, exponential increase in the frequency of the news, particularly those focused on medically important spiders – the Mediterranean black widow (Latrodectus tredecimguttatus) and the Mediterranean recluse (Loxosceles refescens). The news quality was generally poor: 70% contained different types of error, 32% were exaggerated, and in virtually none was an expert consulted. Overstated news referring to spider bites were significantly more shared on social media, thus contributing to frame a distorted perception of the risk associated with a spider bite and possibly reducing general public tolerance of spiders.Competing Interest StatementThe authors have declared no competing interest.View Full Text

scientific communication and education↗

bioRxiv2020

A Multi-perspective Analysis of Retractions in Life Sciences

The aim of this study is to explore trends in retracted publications in life sciences and biomedical sciences over axes like time, countries, journals and impact factors, and topics. Nearly seven thousand publications, which comprise the entirety of retractions visible through PubMed as of August 2019, were used. This work involved sophisticated data collection and analysis techniques to use data from PubMed, Wikipedia, and WikiData, and study it with respect to the above mentioned axes. Importantly, I employ state-of-the-art analysis and visualization techniques from natural language processing (NLP) to understand the topics in retracted literature. To highlight a few results, the analyses demonstrate an increasing rate of retraction over time and noticeable differences in the publication quality (as measured by journal impact factor) among top countries. Moreover, while molecular biology and cancer dominate retractions, we also see a number of retractions not related to biology. The methods and results of this study can be applied to continuously understand the nature and evolution of retractions in life sciences, thus contributing to the health of this research ecosystem.

scientific communication and education↗

bioRxiv2020

A study's got to know its limitations

Background All research has room for improvement, but authors do not always clearly acknowledge the limitations of their work. In this brief report, we sought to identify the prevalence of limitations statements in the medRxiv COVID-19 SARS-CoV-2 dataset.Methods We combined automated methods with manual review to analyse manuscripts for the presence, or absence, either of a defined limitations section in the text, or as part of the general discussion.Results We identified a structured limitations statement in 28% of the manuscripts, and overall 52% contained at least one mention of a study limitation. Over one-third of manuscripts contained none of the terms that might typically be associated with reporting of limitations. Overall our method performed with precision of 0.97 and recall of 0.91.Conclusion The presence or absence of limitations statements can be identified with reasonable confidence using automated tools. We suggest that it might be beneficial to require a defined, structured statement about study limitations, either as part of the submission process, or clearly delineated within the manuscript.Competing Interest StatementThe authors are the founders and shareholders of Scholarcy Limited. Scholarcy technology was used to extract the information from the manuscripts used in this study.View Full Text

scientific communication and education↗

bioRxiv2020

Navigating the Valley of Death: Perceptions of Industry and Academia on Production Platforms and Opportunities

Rational lifestyle engineering using computational methods and synthetic biology has made it possible to genetically improve industrial performance of microbial cell factories for the production of a range of biobased chemicals. However, only an estimated 1 in 5,000 to 10,000 innovations make it through the Valley of Death to market implementation.To gain in-depth insights into the views of industry and academia on key bottlenecks and opportunities to reach market implementation, a qualitative and exploratory study was performed by conducting 12 in depth interviews with 8 industrial and 4 academic participants. The characteristics that any cell factory must have were schematically listed, and commonly recognised opportunities were identified.We found that academics are limited by only technical factors in their research, while industry is restricted in their research choices and flexibility by a series of technical, sector dependent and social factors. This leads to a misalignment of interest of academics and funding industrial partners, often resulting in miscommunication. Although both are of the opinion that academia must perform curiosity-driven research to find innovative solutions, there is a certain pressure to aim for short-term industrial applications. All these factors add up to the Valley of Death; the gap between development and market implementation.A third party, in the form of start-up companies, could be the answer to bridging the Valley of Death.View Full Text

scientific communication and education↗

bioRxiv2020

Dexmedetomidine attenuates the injury of H9C2 cardiomyocytes under Hypoxia/reoxygenation condition partly through the inhibition of endoplasmic reticulum stress

Background Myocardial ischemia-reperfusion injury (MIRI) has been confirmed to induce endoplasmic reticulum stress(ERS) during downstream cascade reaction when myocardial cell function keep deteriorating to a certain degree. The fact of matter is the clinical inconsistence with experimental outcomes still exist due to the mechanism has not been entirely clarified. Dexmedetomidine (DEX), a new generation anti-inflammatory and organ protector, has been testified can attenuate the IRI of heart. This study aimed to find out if DEX had the capacity to protect the injured cardiomyocytes under in vitro hypoxia/reoxygenation circumstance and if the ERS was totally or partly intervened.Methods H9C2 cells were subjected to cytotoxicity detection for 24h with DEX normally cultivated in several different concentrations. The proper hypoxia/reoxygenation (H/R) model parameter were concluded by the cell viability and injuries by cell counting kit-8(CCK8) and lactate dehydrogenase (LDH) release, when undergoing hypoxic condition for 3 h and reoxygenated for 3h, 6h,12h, and 24h, respectively. Also, the above index was assessed for H/R cardiomyocytes cultivated by various concentrations of DEX. The apoptosis, expression of) Glucose-regulated protein 78(GRP78), C/EBP homologous protein (CHOP), and caspase-12 were also examined in all groups.Results 1, 5 and 10 μM DEX in normal culture could significantly promote the proliferation of H9C2 (> 80%); the activity of H9c2 cells decreased to 62.67% (P < 0.05) at 3h of reoxygenation and to 36% at 6h of reoxygenation followed by 3h anoxic treatment; The cell viability of H9c2 cells in H/R groups incubated with 1 μM DEX increased 61.3%, and the LDH concentration in the supernatant was effectively lowered (−13.7, P < 0.05); H/R dramatically decreased the proportion of flow cytometry apoptosis and increased the expression of GRP78, CHOP and caspase-12, while both DEX and 4-phenyl butyric acid (4-PBA) could significantly reverse those above indicators. Additionally, DEX could induce deeper alterations than 4-PBA on the basis of H/R.Conclusion 1 μM DEX can dramatically attended the cell injuries, apoptosis, the expression of GRP78, CHOP and caspase-12 of H9C2 induced by 3h’ hypoxia and 3h’s reoxygenation. moreover, the functions of DEX went beyond the inhibition of ERS under this situation.View Full Text

scientific communication and education↗