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bioRxiv2020

PeskAAS: A near-real-time, open-source monitoring and analytics system for small-scale fisheries

Small-scale fisheries are responsible for landing half of worlds fish catch, yet there are very sparse data on these fishing activities and associated fisheries production in time and space. Fisheries-dependent data underpin scientific guidance of management and conservation of fisheries systems, but it is inherently difficult to generate robust and comprehensive data for small-scale fisheries, particularly given their dispersed and diverse nature. In tackling this challenge, we use open source software components including the Shiny R package to build PeskAAS; an adaptable and scalable digital application that enables the collation, classification, analysis and visualisation of small-scale fisheries catch and effort data. We piloted and refined this system in Timor-Leste; a small island developing nation. The features that make PeskAAS fit-for-purpose are that it is: (i) fully open-source and free to use (ii) component-based, flexible and able to integrate vessel tracking data with catch records; (iii) able to perform spatial and temporal filtering of fishing productivity by fishing method and habitat; (iv) integrated with species-specific length-weight parameters from FishBase; (v) controlled through a click-button dashboard, that was co-designed with fisheries scientists and government managers, that enables easy to read data summaries and interpretation of context-specific fisheries data. With limited training and code adaptation, the PeskAAS workflow has been used as a framework on which to build and adapt systematic, standardised data collection for small-scale fisheries in other contexts. Automated analytics of these data can provide fishers, managers and researchers with insights into a fishers experience of fishing efforts, fisheries status, catch rates, economic efficiency and geographic preferences and limits that can potentially guide management and livelihood investments.

scientific communication and education↗

bioRxiv2020

HYPERTRIGLICERIDEMIC WAIST, PHYSICAL ACTIVITY AND CARDIOVASCULAR RISK FACTORS IN SCHOOLCHILDREN

The present study aimed to analyze the prevalence of the Hypertriglyceridemic Waist (HTW) and its rates with levels of physical activity, nutritional status and lipid profile of students from public schools. A sample consisted of 448 schoolchildren between 10 and 18 years old, who are assessed by body mass, height, BMI (waist circumference), triglycerides, total cholesterol, HDL-C, LDL-C, non-HDL cholesterol, fasting blood glucose and weekly physical activity time. The survey results showed a high prevalence of the HTW phenotype in schoolchildren (n = 125; 27.9%). The group diagnosed with phenotype has higher body mass, BMI, total cholesterol, LDL-C and non-HDL cholesterol and a lower level of HDL-C about the group without a diagnosis of the phenotype. However, for fasting blood glucose measurements and time of physical activity, the groups are no different. An association analysis using logistic regression showed the HTW phenotype associated with sex, nutritional status, and total cholesterol, where boys presented 2.0 (95% CI 1.3 - 3.2); obese 6.2 (95% CI 2.7 - 17.2) and cholesterol levels above 150 mg / dL 3.5 (95% CI 2.1 - 5.7) times more likely to have the phenotype. In this way, the present research showed a high prevalence of HTW in schoolchildren from public schools, with boys, obese and schoolchildren with total cholesterol levels, the individuals most likely to have the phenotype. However, it is worth emphasizing the importance of monitoring these variables throughout the year in all courses, given the period of strong, biological, behavioral and psychological changes, as they can quickly change the values of the analyzed variables.

scientific communication and education↗

bioRxiv2020

Amount of fiction reading correlates with higher connectivity between cortical areas for language and mentalizing

Behavioral evidence suggests that engaging with fiction is positively correlated with social abilities. The rationale behind this link is that engaging with fiction and fictional characters may offer a training mode for mentalizing and empathizing with sentient agents in the real world, analogous to a flight simulator for pilots. In this study, we explored the relationship between reading fiction and mentalizing by looking at brain network dynamics in 57 participants who varied on how much fiction they read in their daily lives. The hypothesis was that if reading fiction indeed trains mentalizing, a task that requires mentalizing -Like immersing in a fictional story and engaging with a protagonist-should elicit differences in brain network dynamics depending on how much people read. More specifically, more frequent readers should show increased connectivity within the theory of mind network (ToM) or between the ToM network and other brain networks. While brain activation was measured with fMRI, participants listened to two literary narratives. We computed time-course correlations between brain regions and compared the correlation values from listening to narratives to listening to an auditory baseline condition. The between-region correlations were then related to individual differences measures including the amount of fiction that participants consume in their daily lives. Our results show that there is a linear relationship between how much people read and the functional connectivity in areas known to be involved in language and mentalizing. This adds neurobiological credibility to the fiction influences mentalizing abilities hypothesis as suggested on the basis of conceptual analysis.

scientific communication and education↗

bioRxiv2020

FastTrack, A Strategy to Shorten Time to Degree

Recent reports express concern about the sustainability of the biomedical research enterprise in its current form. Recurring concerns include the predictability and sustainability of funding for research, regulatory burden and training the next generation in the biomedical workforce. One specific concern is the duration of training periods during pre-doctoral and post-doctoral studies. This article addresses the issue of time-to-degree (TTD) for doctorates. Many reports stress the importance of shortening the TTD, but provide no recommendations to achieve this goal. Herein, factors potentially affecting TTD are discussed and one mechanism that harmonizes undergraduate and graduate programs is proposed as a strategy to reduce the TTD.

scientific communication and education↗

bioRxiv2020

Forecasting virus diffusion with simple Bayesian forecast combination

There are various diffusion models for S shaped processes like virus diffusion and these models are typically not nested. In this note it is proposed to combine the forecasts using a simple Bayesian forecast combination algorithm. An illustration to daily data on cumulative Covid-19 cases in the Netherlands shows the ease of use of the algorithm and the accuracy of the thus combined forecasts.

scientific communication and education↗

bioRxiv2020

Does the Freeze-all strategy improve the cumulative live birth rate and the time to become pregnant in IVF cycles?

IntroductionFreezing of all good quality embryos and their transfer in subsequent cycles, named the freeze-all strategy (FAS), is widely used for ovarian hyperstimulation syndrome (OHSS) prevention. Indeed, it increases live birth rates among high responders and prevents preterm birth and small for gestational age. Consequently, why shouldnt we extend it to all? Materials and methodsA retrospective and monocentric study was conducted between January 2008 and January 2018 comparing the cumulative live birth rates (CLBR) between patients having undergone FAS and a control group using fresh embryo transfer (FET) and having at least one frozen embryo available. Analyses were made for the entire cohort (population 1) and for different subgroups according to confounding factors selected by a logistic regression (population 3), and to the BELRAP (Belgian Register for Assisted Procreation) criteria (population 2). Results2216 patients were divided into two groups: Freeze all (FA), 233 patients and control (C), 1983 patients. The CLBR was 50.2% vs 58.1% P=0.021 for population 1 and 53.2% vs 63.3% P=0.023 for population 2, including 124 cases and 1241 controls. The CLBR stayed in favour of the C group: 70.1% vs 55.9% P=0.03 even when confounding variables were excluded (FA and C group respectively 109 and 770 patients). The median time to become pregnant was equally in favour of the C group with a median of 5 days against 61 days. ConclusionsCLBR is significantly lower in the FA group compared to the C group with a longer time to become pregnant. Nevertheless, the CLBR in the FA group remains excellent and superior to that observed in previous studies with similar procedures and population. These results confirm the high efficiency of FAS but underline the necessity to restrict the strategy to selected cases.

scientific communication and education↗

bioRxiv2020

Machine Learning Maps Research Needs in COVID-19 Literature

SummaryManually assessing the scope of the thousands of publications on the COVID-19 (coronavirus disease 2019) pandemic is an overwhelming task. Shortcuts through metadata analysis (e.g., keywords) assume that studies are properly tagged. However, machine learning approaches can rapidly survey the actual text of coronavirus abstracts to identify research overlap between COVID-19 and other coronavirus diseases, research hotspots, and areas warranting exploration. We propose a fast, scalable, and reusable framework to parse novel disease literature. When applied to the COVID-19 Open Research Dataset (CORD-19), dimensionality reduction suggested that COVID-19 studies to date are primarily clinical-, modeling- or field-based, in contrast to the vast quantity of laboratory-driven research for other (non-COVID-19) coronavirus diseases. Topic modeling also indicated that COVID-19 publications have thus far focused primarily on public health, outbreak reporting, clinical care, and testing for coronaviruses, as opposed to the more limited number focused on basic microbiology, including pathogenesis and transmission.

scientific communication and education↗

bioRxiv2020

Campaign-Based Citizen Science for Environmental Mycology: the "Science Solstice" and "Summer Soil-stice" Projects to Assess Drug Resistance in Air and Soilborne Aspergillus fumigatus

Citizen science projects are often undertaken for ecological and environmental research purposes but also have great potential for use in microbiology research to track the emergence and spread of pathogens in the environment. Science Solstice and Summer Soil-stice are mycology citizen science projects aimed at assessing drug resistance in Aspergillus fumigatus fungal spores found in air and soil, respectively, in the United Kingdom (UK). A. fumigatus plays an important role in the environment as a decomposer of plant material, but is also an opportunistic human lung pathogen. Infection with drug-resistant spores can lead to a worse clinical outcome for the patient. On the first four solstice and equinox days between June 2018 and June 2019, volunteers were asked to collect air samples from their homes and workplaces and return them to our lab in Freepost envelopes. An additional round of samples was requested from volunteers gardens and/or compost on the June 2019 solstice. In total, 787 volunteers returned 2,132 air samples and 509 soil samples, which grew a total of 7,991 A. fumigatus colonies. The estimated total cost of the study was {pound}2,650; the equivalent of 33 pence per A. fumigatus colony grown. Incorporating citizen science into the environmental surveillance of drug-resistant A. fumigatus allowed for the simultaneous collection of hundreds of environmental samples across the entire UK on the same day. The insights generated from this study would not be practical in the absence of public participation and offers opportunities to ask scientific questions that were previously unaskable.

scientific communication and education↗

bioRxiv2020

Advancing science or advancing careers? Researchers' opinions on success indicators

The way in which we assess researchers has been under the radar in the past few years. Critics argue that current research assessments focus on productivity and that they increase unhealthy pressures on scientists. Yet, the precise ways in which assessments should change is still open for debate. We circulated a survey with Flemish researchers to understand how they work, and how they would rate the relevance of specific indicators used in research assessments. We found that most researchers worked far beyond their expected working schedule. We also found that, although they spent most of their time doing research, respondents wished they could dedicate more time to it and spend less time writing grants and performing other activities such as administrative duties and meetings. When looking at success indicators, we found that indicators related to openness, transparency, quality, and innovation were perceived as highly important in advancing science, but as relatively overlooked in career advancement. Conversely, indicators which denoted of prestige and competition were generally rated as important to career advancement, but irrelevant or even detrimental in advancing science. Open comments from respondents further revealed that, although indicators which indicate openness, transparency, and quality (e.g., publishing open access, publishing negative findings, sharing data, etc.) should ultimately be valued more in research assessments, the resources and support currently in place were insufficient to allow researchers to endorse such practices. In other words, current research assessments are inadequate and ignore practices which are essential in contributing to the advancement of science. Yet, before we change the way in which researchers are being assessed, supporting infrastructures must be put in place to ensure that researchers are able to commit to the activities that may benefit the advancement of science. Submission historyThe first version of this manuscript was submitted to PLOS ONE on 27th June 2020. Revisions after peer-review were submitted on 4th October 2020 and 20th November 2020.

scientific communication and education↗

bioRxiv2020

Only two out of five articles by New Zealand researchers are free-to-access: a multiple API study of access, its impact on open citation advantage, cost of Article Processing Charges (APC), and the potential to increase the proportion of open access

We studied journal articles published by researchers at all eight of New Zealand universities in 2017 to determine how many were freely accessible on the web. We wrote software code to harvest data from multiple sources, code that we now share to enable others to reproduce our work on their own sample set. In May 2019, we ran our code to determine which of the 2017 articles were open at that time and by what method; where those articles would have incurred an Article Processing Charge (APC) we calculated the cost if those charges had been paid. Where articles were not freely available we determined whether the policies of publishers in each case would have allowed deposit in a non-commercial repository (Green open access). We also examined citation rates for different types of access. We found that, of our 2017 sample set, about two out of every five articles were freely accessible without payment or subscription (41%). Where research was explicitly said to be funded by New Zealands major research funding agencies, the proportion was slightly higher at 45%. Where open articles would have incurred an APC we estimated an average cost per article of USD1,682 (for publications where all articles require an APC, that is, Gold open access) and USD2,558 (where APC payment is optional, Hybrid open access) at a total estimated cost of USD1.45m. Of the paid options, Gold is by far more common for New Zealand researchers (82% Gold, 18% Hybrid). In terms of citations, our analysis aligned with previous studies that suggest a correlation between publications being freely accessible and, on balance, slightly higher rates of citation. This is not seen across all types of open access, however, with Diamond OA achieving the lowest rates. Where articles were not freely accessible we found that a very large majority of them (88% or 3089 publications) could have been legally deposited in an institutional repository. Similarly, only in a very small number of cases had a version deposited in the repository of a New Zealand university made the difference between the publication being freely accessible or not (125 publications). Given that most New Zealand researchers support research being open, there is clearly a large gap between belief and practice in New Zealands research ecosystem.

scientific communication and education↗

bioRxiv2020

Transparency and open science reporting guidelines in sleep research and chronobiology journals

"Open science" is an umbrella term describing various aspects of transparent and open science principles. The adoption of open science principles at different levels of the scientific process (e.g., individual researchers, laboratories, institutions) has been rapidly changing the scientific research landscape in the past years, but uptake of these principles differ from discipline to discipline. Here, we asked to what extent journals in the field of sleep and chronobiology research encourage or even require following transparent and open science principles in their author guidelines. To this end, we scored the author guidelines of a comprehensive set of 28 sleep and chronobiology journals, including the major outlets in the field, using the standardised Transparency and Openness (TOP) Factor. This instrument rates the extent to which journals encourage or require following various aspects of open science, including data citation, data transparency, analysis code transparency, materials transparency, design and analysis guidelines, study pre-registration, analysis plan pre-registration, replication, registered reports, and the use of open science badges. Across the 28 journals, we find low values on the TOP Factor (median [25th, 75th percentile] 2.5 [1, 3], min. 0, max. 9, out of a total possible score of 28). This suggests an opportunity for sleep and chronobiology journals to further support the recent developments by implementing transparency and openness principles in their guidelines and making adherence to them mandatory.

scientific communication and education↗

bioRxiv2020

QuoVidi : a open-source web application for the organisation of large scale biological treasure hunts

Learning biology, and in particular systematics, requires learning a substantial amount of specific vocabulary, both for botanical and zoological studies. While crucial, the precise identification of structures serving as evolutionary traits and systematic criteria is not per se a highly motivating task for students. Teaching this in a traditional teaching setting is quite challenging especially with a large crowd of students to be kept engaged. This is even more difficult if, as during the COVID-19 crisis, students are not allowed to access laboratories for hands-on observation on fresh specimens and sometimes restricted to short-range movements outside their home. Here we present QuoVidi, a new open-source web platform for the organisation of large scale treasure hunts. The platform works as follows: students, organised in teams, receive a list of quests that contain morphologic, ecologic or systematic terms. They have to first understand the meaning of the quests, then go and find them in the environment. Once they find the organism corresponding to a quest, they upload a geotagged picture of their finding and submit this on the platform. The correctness of each submission is evaluated by the staff. During the COVID-19 lockdown, previously validated pictures were also submitted for evaluation to students that were locked in low-biodiversity areas. From a research perspective, the system enables the creation of large image databases by the students, similar to citizen-science projects. Beside the enhanced motivation of students to learn the vocabulary and perform observations on self-found specimens, this system allows faculties to remotely follow and assess the work performed by large numbers of students. The interface is freely available, open-source and customizable. It can be used in other disciplines with adapted quests and we expect it to be of interest in many classroom settings.

scientific communication and education↗

bioRxiv2020

Task specialization and its effects on research careers

Scientific careers are conceived as one unique pathway which scientists must follow to succeed. We report the diversity of profiles scientists exhibit based on their contributorship and look into biases in their career trajectory. We use Bayesian networks to train a prediction model based on a dataset of 70,694 publications from PLoS journals representing 347,136 distinct authors and their associated contribution statements. This model is used to predict the contributions of 222,925 authors in 6,236,239 publications, and apply a robust archetypal analysis to profile scientists by career stage. We divide scientific careers into four stages: junior, early-career, mid-career and late-career. Three scientific archetypes are found throughout the four career stages: leader, specialized, and supporting. All three archetypes are encountered for the early- and mid-career stages, whereas for junior and late-career stages only two archetypes are found. Scientists assigned to the leader and specialized archetypes tend to have longer careers than researchers who belong to the supporting archetype. There is consistent gender bias at all stages: the majority of male scientists belong to the leader archetype, while the larger proportion of women belong to the specialized archetype, especially for early and mid-career researchers.

scientific communication and education↗

bioRxiv2020

Authentic field experiences for STEM teachers: Collecting Florida fossils

The extensive sedimentary sequence of Florida preserves evidence of prehistoric life spanning some 40 million years into the past. This paper describes the results of a three-pronged professional development (PD) program conducted in November 2019 in which Florida teachers from eight counties gained knowledge and experience about the process and content of paleontology at an active field research site in northern Florida. Working alongside scientists, 15 elementary, middle, and high school teachers collected 5-million-year-old fossil vertebrates and made scientifically important discoveries that advance understanding of Floridas prehistoric life. The PD included three components: (1) a pre-trip webinar; (2) a morning tour of our museum exhibits to scaffold teachers understanding of the kinds of fossils they would find; and (3) the actual day-long field experience collecting fossils. A post-PD evaluation revealed gains in knowledge about, and experience with, fossils and paleontology. We also found that overall satisfaction with the PD underscored the importance of each of the three components supporting one-another--resulting in a more informative and rewarding learning experience for the participants. Fossils and the science of paleontology are a gateway for STEM learning and this subject and its extensions are applicable to existing standards in earth and life sciences at many grade levels.

scientific communication and education↗

bioRxiv2020

Moistube ™ Irrigation (MTI) Discharge Under Variable Evaporative Demand

We investigated the conceptual capability of Moistube irrigation to discharge under zero applied positive pressure under varied climatic conditions by inducing an artificial evaporative demand (Ed) or negative pressure around moistube tubing. This was premised on the null hypothesis that an artificially induced Ed or negative pressure does not impact moistube discharge. Moistube tubing was enclosed in a 1 m long PVC conduit. A 20 l water reservoir placed on an electronic balance provided a continuous supply of water whilst a three-speed hot air blower facilitated the radiative factor and advection process. The procedure was conducted under varied climatic conditions of air velocities (ua) 1.2 m.s-1, 2.5 m.s-1, and 3.0 m.s-1 and the experiment run times were 159 h, 134 h and 10 h, respectively. The average temperature (Tave) and relative humidity (RH) data for ua = 1.2 m.s-1 were 53{degrees}C and 7.31%, whilst for ua = 2.5 m.s-1, Tave was 56{degrees}C and RH = 7.19%, and for ua = 3.0 m.s-1, Tave was 63{degrees}C and RH = 6.16%. The experimental data was input into the four variable Penman-Monteith method to compute the evaporative demand (Ed). For each of the air velocities, the respective Ed values obtained were 0.16, 0.31 and 0.36 mm.d-1. The Bowen ratios (r) were well below 1 (r < 1), which suggested a sufficient supply of moisture to evaporate. For Ed = 0.16 mm.d-1 the vapour pressure deficit (VPD) was 113.08 mbars, whilst for Ed = 0.31 mm.d-1 and for Ed = 0.36 mm.d-1 the VPD were 129.93 mbars and 150.14 mbars, respectively. The recorded discharges (q) at t = 10 hrs for Ed= 0.16 mm.d-1 was 7.67*10-3 l.hr-1.m-1, whilst for Ed = 0.31 mm.d-1 q = 14.5*10-3 l.hr-1.m-1, and for Ed = 0.36 mm.d-1 q = 20.8*10-3 l.hr-1.m-1. The imposed negative pressure causes an exponential increase in moistube discharge, thus disproving the null hypothesis. The higher the evaporative demand the higher the discharge. This phenomenon allows moistube irrigation to be used for deficit irrigation purposes and allows irrigators to capitalize on realistic soil matric potential irrigation scheduling approach.

scientific communication and education↗

bioRxiv2020

Gender, race and parenthood impact academic productivity during the COVID-19 pandemic: from survey to action.

While the Coronavirus disease 2019 (COVID-19) pandemic is altering academia dynamics, those juggling remote work and domestic demands - including childcare - have already felt the impacts on productivity. Female authors are facing a decrease in papers submission rates since the beginning of the pandemic period. The reasons for this decline in women productivity need to be further investigated. Here we show the influence of gender, parenthood and race in academics productivity during the pandemic period, based on a survey answered by 3,345 Brazilian academics from various knowledge areas and research institutions. Findings revealed that male academics - especially childless ones - were the least affected group, whereas female academics, especially Black women and mothers, were the most impacted group. This scenario will leave long-term effects on the career progression of the most affected groups. The results presented here are crucial for the development of actions and policies that aim to avoid further deepening the gender gap in science. This particular situation we are facing during the pandemic demands institutional flexibility and academia should foster the discussion about actions to benefit Black scientists and academics with families in the post-pandemic scenario.

scientific communication and education↗

bioRxiv2020

QUALIS: The journal ranking system undermining the impact of Brazilian science

A system called QUALIS was implemented in Brazil in 2009, intended to rank graduate programs from different subject areas and promote selected national journals. Since this system uses a complicated suit of criteria (differing among subject areas) to group journals into discrete categories, it could potentially create incentives to publish in low-impact journals ranked highly by QUALIS. Here I assess the influence of the QUALIS journal ranking system on the global impact of Brazilian science. Brazil shows a steeper decrease in the number of citations per document since the implementation of this QUALIS system, compared to the top Latin American countries publishing more scientific articles. All subject areas showed some degree of bias, with social sciences being usually more biased than natural sciences. Lastly, the decrease in the number of citations over time proved steeper in a more biased subject area, suggesting a faster shift towards low-impact journals. Overall, the findings documented here suggest that the QUALIS system has undermined the global impact of Brazilian science, and reinforce a recent recommendation from an official committee evaluating graduate programs to eliminate QUALIS. A system based on impact metrics could avoid introducing distorted incentives, and thereby boost the global impact of Brazilian science.

scientific communication and education↗

bioRxiv2020

Using Metacognitive Strategies to Improve Academic Performance in Biochemistry

Growing evidence suggests that students self-beliefs about the ability to alter their academic abilities can directly influence long-term achievement. These self-beliefs or mindsets can either be fixed (unchangeable) or growth oriented. Students with growth mindsets believe their academic abilities can change, which leads to higher grades and academic persistence in contrast to students with fixed mindsets. However, less is known about how these attributes affect student learning, particularly in college level biochemistry courses. In this study, we utilized social-psychological interventions to promote growth mindset among third and fourth year undergraduate students enrolled in a one semester Biochemistry survey course. Using a mixed-methods study design we evaluated student mindset, attitudes towards learning, and academic performance over four semesters. Our results suggest that although students mindsets did not change as a result of metacognitive interventions, their positive perceptions about learning vs performance did increase. Furthermore, students receiving growth mindset interventions significantly outperformed students who did not receive interventions on the final cumulative exam that assessed critical thinking skills. These results suggest that metacognitive interventions can be an effective tool to improve student academic performance in a biochemistry course.

scientific communication and education↗