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bioRxiv2020

Decision Support Systems based on Scientific Evidence: Bibliometric Networks of Invasive Lantana camara.

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.

scientific communication and education↗

bioRxiv2020

Does retraction after misconduct have an impact on citations? A pre-post study.

BackgroundRetracted 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. ResultsThe 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). ConclusionsThe 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. MethodsQuasi-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.

scientific communication and education↗

bioRxiv2020

Detecting potential reference list manipulation within a citation network

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 Zipfs 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.

scientific communication and education↗

bioRxiv2020

Open Science Saves Lives: Lessons from the COVID-19 Pandemic

In the last decade Open Science principles have been successfully advocated for and are being slowly adopted in different research communities. In response to the COVID-19 pandemic many publishers and researchers have sped up their adoption of Open Science practices, sometimes embracing them fully and sometimes partially or in a sub-optimal manner. In this article, we express concerns about the violation of some of the Open Science principles and its potential impact on the quality of research output. We provide evidence of the misuses of these principles at different stages of the scientific process. We call for a wider adoption of Open Science practices in the hope that this work will encourage a broader endorsement of Open Science principles and serve as a reminder that science should always be a rigorous process, reliable and transparent, especially in the context of a pandemic where research findings are being translated into practice even more rapidly. We provide all data and scripts at https://osf.io/renxy/.

scientific communication and education↗

bioRxiv2020

A lesson from COVID-19 on inaccessibility of web-based information for disabled populations worldwide

Many government websites and mobile content are inaccessible for people with vision, hearing, and cognitive disabilities. The COVID-19 pandemic highlighted these disparities when health authority website information, critical in providing resources for curbing the spread of the virus, remained inaccessible for disabled populations. The Web Content Accessibility Guidelines provide comparatively universally accepted guidelines for website accessibility. We utilized these parameters to examine the number of countries with or without accessible health authority websites. The resulting data indicate a dearth of countries with websites accessible for persons with disabilities. Methods of information dissemination must take into consideration individuals with disabilities, particularly in times of global health crises.

scientific communication and education↗

bioRxiv2020

The Species Awareness Index (SAI): a Wikipedia-derived conservation culturomics metric for public biodiversity awareness

Threats to global biodiversity are well-known, but slowing currents rates of biodiversity loss remains an ongoing challenge. The Aichi Targets set out 20 goals on which the international community should act to alleviate biodiversity decline, one of which (Target 1) aimed to raise public awareness of the importance of biodiversity. Whilst conventional indicators for Target 1 are of low spatial and temporal coverage, conservation culturomics has demonstrated how biodiversity awareness can be quantified at the global scale. Following the Living Planet Index methodology, here we introduced the Species Awareness Index (SAI), an index of changing species awareness on Wikipedia. We calculated this index at the page level for 41,197 IUCN species across 10 Wikipedia languages, incorporating over 2 billion views. Bootstrapped indices for the page level SAI show that overall awareness of biodiversity is marginally increasing, although there are differences among taxonomic classes and languages. Among taxonomic classes, overall awareness of reptiles is increasing fastest, and amphibians slowest. Among languages, overall species awareness for the Japanese Wikipedias is increasing fastest, and the Chinese and German Wikipedias slowest. Although awareness of species on Wikipedia as a whole is increasing, and is significantly higher in traded species, over the period 2016-2020 change in interest appears not to be strongly related to the trade of species or animal pollinators. As a data source for public biodiversity awareness Wikipedia could be integrated into the Biodiversity Engagement Indicator, thereby incorporating a more direct link to biodiversity itself.

scientific communication and education↗

bioRxiv2020

Survey of Core Facilities shows the importance of communication and management for optimal research quality

Recently, it has become evident that academic research faces issues with the reproducibility of research data. It is critical to understand the underlying causes in order to remedy this situation. Core Facilities (CFs) have a central position in the research infrastructure and therefore they are ideally suited to promote and disseminate good research standards through their users. However, there are currently no clear guidelines directly applicable to academic CFs. To identify the most important factors for research quality, we polled 253 CFs across Europe about their practices and analysed in detail the interaction process between CFs and their users, from the first contact to the publication of the results. Although the survey showed that CFs are dedicated to train and advise their users, it highlighted the following areas, the improvement of which would directly increase research quality: 1) motivating users to follow the advice and procedures for best research practice, 2) providing clear guidance on data management practices, 3) improving communication along the whole research process and 4) clearly defining the responsibilities of each party.

scientific communication and education↗

bioRxiv2020

Gender (im)balance in citation practices in cognitive neuroscience

In the field of neuroscience, despite the fact that the proportion of peer-reviewed publications authored by women has increased in recent decades, the proportion of citations of women-led publications has not seen a commensurate increase: In five broad-scope journals, citations of papers first- and/or last-authored by women have been shown to be fewer than would be expected if gender was not a factor in citation decisions (Dworkin et al., 2020). Given the important implications that such underrepresentation may have on the careers of women researchers, it is important to determine whether this same trend is true in subdisciplines of the field, where interventions might be more effective. Here, we report the results of an extension of the analyses carried out by Dworkin et al. (2020) to citation patterns in the Journal of Cognitive Neuroscience (JoCN). The results indicate that the underrepresentation of women-led publications in reference sections is also characteristic of papers published in JoCN over the past decade. Furthermore, this pattern of citation imbalances is present for all gender classes of authors, implicating systemic factors. These results contribute to the growing body of evidence that intentional action is needed to address inequities in the way that we carry out and communicate our science.

scientific communication and education↗

bioRxiv2020

Specialized terminology limits the reach of new scientific knowledge

Words are the building blocks of science. As our understanding of the world progresses, scientific disciplines naturally enrich their specialized vocabulary (jargon). However, in the era of interdisciplinarity, the use of jargon may hinder effective communication amongst scientists that do not share a common linguistic background. The question of how jargon limits the transmission of scientific knowledge has long been debated, but rarely addressed quantitatively. We explored the relationship between the use of jargon and citations using 21,486 articles focusing on cave research, a multidisciplinary field particularly prone to terminological specialization and where linguistic disagreement among peers is frequent. We demonstrate that the use of jargon in the title and abstract significantly reduces the number of citations a paper receives. Given that these elements are the hook to readers, we urge scientists to restrict jargon to sections of the paper where its use is unavoidable.

scientific communication and education↗

bioRxiv2020

Nutrients: trace metals, micronutrients, oestrogen and B-vitamin content of Osun River: A River that runs southwestern Nigeria into the Atlantic Gulf of Guinea

Osun-Osogbo Grove has a long history of healing and therapeutic claims by adherent believers, in spite of advancement in medicine. Scientists made attempts at investigating the biodiversity of the Grove, till date, there has not been convergence point between science and these indigenous beliefs. This study identified the presence of therapeutic agents in the water of Osun-Osogbo River, paying attention to at least six parameters; vitamin, phosphate, nitrate, amino acid, hormone and trace metal. Water samples were taken from two different sites during pre, during and post raining sessions (April 2017 - September 2019) were analysed using High Performance Liquid Chromatography (HPLC), Gas Chromatography Mass Spectroscopy (GC-MS) and Atomic Absorption Spectrometer (AAS). Trace metal analysis revealed an average of 0.009-0.079 mg/Kg Zinc from site one and lower in site two. The mean value of manganese at both sites was virtually the same at 0.018-0.313 mg/kg, aluminum content was 0.045-0.179mg/Kg at site one, 0.050-0.192mg/kg at site two, cobalt was 0.024 mg/kg at site one, 0.026 mg/kg at site two while nickel was 0.006 mg/kg and 0.004 mg/kg for site one and two respectively. HPLC analysis shows mean Methionine content at both sites is higher than the FDA (56.6 ug/mL); site one had 74.41 ug/mL while site two had 57.11 ug/mL The mean values of two water-soluble vitamins; Thiamine (B1) was 3.758 mg/Kg and 2.355 mg/Kg while Pyridoxine (B6) was 0.108 mg/Kg and 0.072 mg/Kg at site one and two. GCMS analysis of steroidal content revealed values below lowest observed effect level (LOEL), testosterone (4.8 ng/L) and estrogen (2.4 ng/L) were still elevated while ethinylestradiol and estriol were [≥]1.5 ng/L. Summarily, site one the major part for spiritual activities showed higher essential nutrient contents than site two which support the enrichment and potential therapeutic properties of the Osun river water. However, further scientific research is required to ensure that these therapeutic potentials supersede the toxicological effect.

scientific communication and education↗

bioRxiv2020

The Wooden Skull: An Innovation Through The Use Of Local Materials And Technology To Promote The Teaching And Learning Of Human Anatomy

Skeleton models are important in facilitating students easy retention and recollection of information in the future. These may assist students carry out hands-on practice in order to acquire and practice new skills that are relevant to first aid. The increasing number of medical institutions and medical students attracts the challenge of inadequate facilitation of the teaching and learning processes. This warrants a study and/or an exploration of an alternative solution such as wooden models in order to solve the problem of scarce and ethically restricted human teaching aids. Wooden pieces (50cm length x 20cm diameter) from a Jacaranda mimosifolia tree were prepared for the carving process and wooden replicas of human skulls were made. Two experimental groups of randomly selected medical students (60: Active and 60: Control) were separately taught using wooden and natural skull models respectively. The two groups were assessed and evaluated using the natural skull models to compare their understanding of the Anatomy of the skull. Additionally, opinion statements were collected from participants in the active group during the oral examination. Six (6) wooden skull models were produced and used for experimental study. Comparisons of academic scores (mean and median) between Active (students using the wooden skull) and control (students using natural skull) groups showed no statistical significant difference (P [≥] 0.05). Concerning the enhancement of learning skills; the wooden model was constructed in a way that would be able to enhance learning as it would be the natural skull. The wooden skull model, with more improvement in structural formation, can adequately facilitate the teaching and learning of anatomy of the Human skull. This project and the experimental study about utilization of the wooden skull model provides a good potential of using the wooden models to supplement the use of the natural human skull.

scientific communication and education↗

bioRxiv2020

Knowledge and attitude regarding stem cell research and its application among medical students in Pakistan

BackgroundThe utilization of stem cells (SCs) has led the way into a new era of therapeutics known as regenerative medicine. Their renewal property offers exciting possibilities in reversing tissue damage caused by metabolic and degenerative changes. Research should be conducted increasingly to explore the possibilities of SC utilization in Pakistan. ObjectivesTo assess the level of knowledge, perception, and attitude of medical students regarding stem cell research (SCR) and its application, to obtain a better insight into the future of stem cell therapy in Pakistan as it is a rapidly emerging field in medicine. Materials and MethodsThis cross-sectional study was carried out using a self-administered questionnaire filled by 206 medical students from different medical colleges in Pakistan. A convenience sampling method was used. Knowledge and attitude scores were calculated based on answers to 28 well-structured questions. Data was analyzed using SPSS. ResultsThe mean values of the answers showed that 60.2% (n=124) of the students had a good knowledge and 39.8% (n=82) had poor knowledge of stem cells. Whereas, 56.8% (n=117) expressed a positive attitude and 43.2% (n=89) expressed a negative attitude towards SCR. Independent t-test applied on knowledge score and attitude showed that the mean knowledge score of people with a positive attitude is higher i.e. 21.25 as compared to the mean knowledge score of people with negative attitude i.e. 19.21. And the difference of the means is significant at p=0.007. Thus, the attitude of students was observed to be significantly dependent on their knowledge about SCR. ConclusionThe results show that medical students have baseline knowledge about SC therapy and a positive attitude towards it. Seminars, workshops should be conducted and this topic should be added to their syllabus so that they obtain proper information about SCR and encourage further research.

scientific communication and education↗

bioRxiv2020

FAIR sharing of molecular visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments

Motivated by the current Covid-19 pandemic that has spurred a substantial flow of structural data we describe how molecular visualization experiences can be used to make these datasets accessible to a broad audience. Using a variety of technology vectors related to the cloud, 3D- and virtual reality gear, we examine how to share curated visualizations of structural biology, modeling and/or bioinformatics datasets for interactive and collaborative exploration. We discuss F.A.I.R. as overarching principle for sharing such visualizations. We provide four initial example scenes related to recent Covid-19 structural data together with a ready-to-use (and share) implementation in the UnityMol software. SynopsisVisualization renders structural molecular data accessible to a broad audience. We describe an approach to share molecular visualization experiences based on FAIR principles. Our workflow is exemplified with recent Covid-19 related data.

scientific communication and education↗

bioRxiv2020

Reporting to the Convention on Biology Diversity: How are countries assessing and protecting their genetic diversity?

Genetic diversity is critically important for all species-domesticated and wild- to adapt to environmental change, and for ecosystem resilience to extreme events. International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve and sustainably and equitably use all levels of biodiversity-genes, species and ecosystems-globally. However, assessment and monitoring of genetic diversity are often overlooked, and there are large knowledge and policy gaps regarding genetic diversity conservation. In this study, we present the first quantitative analysis of genetic diversity assessments conducted by Parties to the CBD. We conducted a detailed, systematic analysis of 114 CBD 5th (submitted 2014) and 6th (submitted 2018) National Reports to quantitatively assess actions, progress on targets, values and indicators related to genetic diversity. First, we found that the importance of genetic diversity is recognised by most Parties to the CBD, and that recognition increased over time. However, genetic targets mainly addressed genetic diversity within cultivated plants, farm animals, and crop wild relatives, with little focus on other wild species. Also, actions for conserving genetic diversity primarily concerned ex-situ facilities and policy, rather than monitoring and intervention for maintaining genetic diversity in situ. The most commonly used indicators of genetic diversity status were the number of genetic resources in conservation facilities, number of threatened breeds, and Red List Index, which are not well correlated to genetic erosion in most species -- highlighting that genetic change is poorly monitored by current indicators. Lastly, analyses of genetic data observations, indigenous use and knowledge of genetic diversity, and strategies being developed and implemented to conserve genetic diversity are highly under-reported. We make several recommendations for the post-2020 CBD Biodiversity Framework to improve awareness, assessment, and monitoring, and facilitate consistent and complete reporting of progress of genetic diversity in future National Reports. Article Impact StatementAn analysis of genetic diversity in CBD National Reports neglects non-domesticated species and demonstrates need for sufficient indicators.

scientific communication and education↗

bioRxiv2020

SuperPlotsOfData - a web app for the transparent display and quantitative comparison of continuous data from discrete conditions

Plots and charts are graphical tools that make data intelligible and digestible by humans. But the oversimplification of data by only plotting the statistical summaries conflicts with the transparent communication of results. Therefore, plotting of all data is generally encouraged and this can be achieved by using a dotplot for discrete conditions. Dotplots, however, often fail to communicate whether the data are from different technical or biological replicates. The superplot has been proposed to improve the communication of experimental design and results. To simplify the plotting of data from discrete conditions as a superplot, the SuperPlotsOfData web app was generated. The tool offers easy and open access to state-of-the-art data visualization. In addition, it incorporates recent innovations in data visualization and analysis, including raindcloud plots and estimation statistics. The free, open-source webtool can be accessed at: https://huygens.science.uva.nl/SuperPlotsOfData/ O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/276881v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1f7462aorg.highwire.dtl.DTLVardef@11fa09eorg.highwire.dtl.DTLVardef@16a17e9org.highwire.dtl.DTLVardef@47db57_HPS_FORMAT_FIGEXP M_FIG C_FIG

scientific communication and education↗

bioRxiv2020

A Mental Health Paradox: Mental health was both a motivator and barrier to physical activity during the COVID-19 pandemic

The COVID-19 pandemic has impacted the mental health, physical activity, and sedentary behavior of citizens worldwide. Using an online survey with 1669 respondents, we sought to understand why and how by querying about perceived barriers and motivators to physical activity that changed because of the pandemic, and how those changes impacted mental health. Consistent with prior reports, our respondents were less physically active (aerobic activity, -11%, p <0.05; strength-based activity, -30%, p<0.01) and more sedentary (+11%, p<0.01) during the pandemic as compared to 6-months before. The pandemic also increased psychological stress (+22%, p <0.01) and brought on moderate symptoms of anxiety and depression. Respondents whose mental health deteriorated the most were also the ones who were least active (depression r = -.21, p<0.01; anxiety r = -.12, p<0.01). The majority of respondents were unmotivated to exercise because they were too anxious (+8%, p <0.01), lacked social support (+6%, p =<0.01), or had limited access to equipment (+23%, p <0.01) or space (+41%, p <0.01). The respondents who were able to stay active reported feeling less motivated by physical health outcomes such as weight loss (-7%, p<0.01) or strength (-14%, p<0.01) and instead more motivated by mental health outcomes such as anxiety relief (+14%, p <0.01). Coupled with previous work demonstrating a direct relationship between mental health and physical activity, these results highlight the potential protective effect of physical activity on mental health and point to the need for psychological support to overcome perceived barriers so that people can continue to be physically active during stressful times like the pandemic.

scientific communication and education↗

bioRxiv2020

Cooperative efforts on developing vaccines and therapies for COVID-19

Health organizations have always sought partnership to join competencies in innovation, even with fierce competition in this sector. In this pandemic moment it is relevant to observe how organizations behave to seek quick and safe answers. The present research analyzes how the cooperation networks were set off considering the clinical trials on therapies and vaccines that were developed specifically to treat or prevent COVID-19. Social Network Analysis technique was used to build cooperation networks and apply metrics that characterize these connections. There was an evaluation of statistics of Strength of cooperation and Unilateral dependence of cooperation that identify the cooperation strength between two organizations, and the dependence of this relations. A total of 415 clinical trial were identified, of which 42% are in cooperation. From organizations that have partnership, firms are the first, followed by universities. We extracted the main categories that concentrate 74% of partnerships in the trials of antibody, and vaccine. Several organizations cooperate in multiple categories of trials, evidencing the efforts to focus on different strategies to treat the disease. We found high strength of cooperation and an assimetryc dependency between partners, which can be assigned to specialized models of partnership and it occurs in competitive enviroments like this pandemic moment. Cooperation were not limited to geographical proximity and the advent of Chinese players can represent a new change in the biotechnological development axis. Finally, the challenge of finding therapeutic or immunological solutions for COVID-19 demonstrates a clear composition of cooperation groups that complement their skills to manage organizational strategies to beat the pandemic. In this new paradigm, there can be partnerships not only in clinical trial but also in pre-competitive technologies development. This experience is expected to change the way of organizations define their R&D strategies and start to adopt more a collaborative innovation model.

scientific communication and education↗

bioRxiv2020

The role of Anti-Mullerian hormone in predicting fertilization and pregnancy rates following in vitro fertilization-embryo transfer (IVF-ET) and intracytoplasmic sperm injection (ICSI) cycles at a public fertility centre in Nigeria

ObjectiveTo determine the role of Anti-Mullerian Hormone (AMH) in predicting fertilization and pregnancy rates following in vitro fertilization-embryo transfer (IVF-ET) and intracytoplasmic sperm injection (ICSI) treatment cycles. MethodsThis was a prospective cohort study of one hundred and fifty consecutive women undergoing IVF-ET/ICSI that were recruited from February 1, 2017 to October 31, 2018 at the Fertility centre of the National Hospital, Abuja, Nigeria. Participants plasma AMH were assayed and were followed up till achieving fertilization and pregnancy. Association between AMH levels, fertilization and pregnancy rates was assessed using univariable and multivariable logistic regression modelling to adjust for confounding variables. ResultsThe mean age and mean AMH level of the participants were 36 {+/-} 4.2 years and 1.74 {+/-} 2.35ng/ml respectively. There was a statistically significant association between AMH level and age (P <0.001), duration of infertility (P =0.026), cause of infertility (P =0.035), number of oocytes retrieved (P =<0.001), number of embryos generated (P =<0.001) and type of treatment (P =<0.001). However, there was no significant difference in the fertilization rates (adjusted odds ratio [AdjOR] 0.36, 95% confidence interval [CI] 0.23-4.30; P =0.533) and pregnancy rates (AdjOR 0.26, 95% CI 0.04-2.00; P =0.210) at different plasma levels of AMH. ConclusionPlasma AMH level was not a predictor of fertilization and pregnancy rates among our cohort of patients who had IVF/ICSI treatment cycles.

scientific communication and education↗