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bioRxiv2018

A common statistical misunderstanding in Psychology and Neuroscience: Do we need normally distributed independent or dependent variables for linear regression to work?

Our ability to draw conclusions from experiments often relies on the application of inferential statistics, such as those included within the general-linear-modeling framework. The purpose of this commentary is to direct attention a common fallacy that can be observed in paper reviews and professional exchanges in the field of Psychology and Neuroscience pertaining to multiple regression analysis. The fallacy concerns the confusion of the requirements on the residuals of a linear-regression model with requirements on the dependent or independent variables themselves. A simple thought experiment, algebraic demonstration, and simulation study can demonstrate this misconception. It is our hope that consideration of the fallacy may help clarify distinctions between technical statistical issues and conceptual interpretation of research findings.

scientific communication and education↗

bioRxiv2018

High impact journals in ecology cover proportionally more statistically significant findings

Unbiased scientific reporting is crucial for data and research synthesis. Previous studies suggest that statistically significant results are more likely to be published and more likely to be submitted to high impact journals. However, the most recent research on statistical significance in relation to journal impact factors in ecological research was published more than two decades ago or addressed a small subset of the literature. Here, we extract p-values from all articles published in 11 journals in 2012 and 2014 across a wide range of impact factors with six journals sampled in both years. Our results indicate that the proportion of statistically significant results increases with rising impact factor. Such a trend can have important consequences for syntheses of ecological data and it highlights the importance of covering a wide range of impact factors when identifying published studies for data syntheses. This trend can also lead to a biased understanding of the probability of true effects in ecology and conservation. We caution against the possible downplaying of non-significant results by either journals or authors.

scientific communication and education↗

bioRxiv2018

Beyond the traditional simulation design for evaluating type 1 error rate: from ‘theoretical’ to ‘empirical’ null

When evaluating a newly developed statistical test, the first step is to check its type 1 error (TIE) control using simulations. This is often achieved by the standard simulation design S0 under the so-called theoretical null of no association. In practice, whole-genome association analyses scan through a large number of genetic markers (Gs) for the ones associated with an outcome of interest (Y), where Y comes from an unknown alternative while the majority of Gs are not associated with Y, that is under the empirical null. This reality can be better represented by two other simulation designs, where design S1.1 simulates Y from an alternative model based on G then evaluates its association with independently generated Gnew, while design S1.2 evaluates the association between permutated Yperm and G. More than a decade ago, Efron (2004) has noted the important distinction between the theoretical and empirical null in false discovery rate control. Using scale tests for variance heterogeneity and location tests of interaction effect as two examples, here we show that not all null simulation designs are equal. In examining the accuracy of a likelihood ratio test, while simulation design S0 shows the method has the correct T1E control, designs S1.1 and S1.2 suggest otherwise with empirical T1E values of 0.07 for the 0.05 nominal level. And the inflation becomes more severe at the tail and does not diminish as sample size increases. This is an important observation that calls for new practices for methods evaluation and interpretation of T1E control.

scientific communication and education↗

bioRxiv2018

Intellectual contributions meriting authorship:Survey results from the top cited authors across all science categories

Authorship is the currency of an academic career for which the number of papers researchers publish demonstrates creativity, productivity, and impact. To discourage coercive authorship practices and inflated publication records, journals require authors to affirm and detail their intellectual contributions but this strategy has been unsuccessful as authorship lists continue to grow. Here, we surveyed close to 6000 of the top cited authors in all science categories with a list of 25 research activities that we adapted from the National Institutes of Health (NIH) authorship guidelines. Responses varied widely from individuals in the same discipline, same level of experience, and the same geographic region. Most researchers agreed with the NIH criteria and grant authorship to individuals that draft the manuscript, analyze and interpret data, and propose ideas. However, thousands of the researchers also value supervision and contributing comments to the manuscript whereas the NIH recommends discounting these activities when attributing authorship. People value the minutiae of research beyond writing and data reduction: researchers in the humanities value it less than those in pure and applied sciences; individuals from Far East Asia and Middle East and Northern Africa value these activities more than anglophones and northern Europeans. While developing national and international collaborations, researchers must recognize differences in peoples values while assigning authorship.

scientific communication and education↗

bioRxiv2018

Is there a problem with methods skills in cognitive neuroscience? Evidence from an online survey.

Cognitive neuroscience increasingly relies on complex data analysis methods. Researchers in this field come from highly diverse scientific backgrounds, such as psychology, engineering and medicine. This poses challenges with respect to acquisition of appropriate scientific computing and data analysis skills, as well as communication among researchers with different knowledge and skills sets. Are researchers in cognitive neuroscience adequately equipped to address these challenges? Here, we present evidence from an online survey of methods skills. Respondents (n=305) mainly comprised students and post-doctoral researchers working in the cognitive neurosciences. Multiple choice questions addressed a variety of basic and fundamental aspects of neuroimaging data analysis, such as signal analysis, linear algebra, and statistics. We analysed performance with respect to the following factors: undergraduate degree (grouped into Psychology, Methods, Biology), current researcher status (undergraduate student, PhD student, post-doctoral researcher), gender, and self-rated expertise levels. Overall accuracy was 72%. Not surprisingly, the Methods group performed best (87%), followed by Biology (73%) and Psychology (66%). Accuracy increased from undergraduate (59%) to PhD (74%) level, but not from PhD to post-doctoral (74%) level. The difference in performance for the Methods versus non-methods (Psychology/Biology) groups was particularly striking for questions related to signal analysis and linear algebra, two areas especially relevant to neuroimaging research. Self-rated methods expertise was not strongly predictive of performance. The majority of respondents (93%) indicated they would like to receive at least some additional training on the topics covered in this survey. In conclusion, methods skills among junior researchers in cognitive neuroscience can be improved, researchers are aware of this, and there is strong demand for more skills-oriented training opportunities. We hope that this survey will provide an empirical basis for the development of bespoke skills-oriented training programmes in cognitive neuroscience institutions.

scientific communication and education↗

bioRxiv2018

Evaluation of a guideline developed to reduce HIV-related stigma and discrimination in healthcare settings and establishing consensus

BackgroundDeveloping guidelines and policies is critical to address HIV-related stigma and discrimination (SAD) in healthcare settings. To this end, a multidisciplinary panel developed a guideline to reduce SAD. This project evaluated the appropriateness of implementing the guideline in the Ethiopian context.\n\nMethodsA consensus of the expert panel was established through a Delphi technique which was followed by a panel meeting. Initial tentative recommendations were distributed to experts through e-mails to be evaluated using the modified guideline implementability appraisal (GLIA) v.2.0 checklist.\n\nResultsIn the first round of the Delphi survey, all (13) panel members evaluated the guideline. The overall score for the general domain of the modified GLIA checklist was 96.56%. The scores for individual recommendations ranged from 68.33% to 92.76%. Maximum and minimum scores were attained for measurability (97.71%) and flexibility (59.77%) domains respectively. Percentages mean score lower than 75% was obtained for flexibility and validity domains. Participants suggested that additional tools and training should be added to the guideline. In the second round of the survey, all the recommendations received endorsement with scores above 75%. Maximum and minimum scores were attained for measurability (100%) and flexibility (86.88%) domains respectively. During the panel meeting, issues of responsibility for implementing the guideline were discussed.\n\nConclusionThe project evaluated implementability of a guideline developed to reduce HIV-related SAD in healthcare settings. The Delphi survey was followed by a half-day meeting that helped in further clarification of points.

scientific communication and education↗

bioRxiv2018

Opinions of 12 to 13-year-olds in Austria and Australia on the worry, cause and imminence of Climate Change

Although we are in the third decade of climate science communication as a discipline, and there is overwhelming scientific consensus and physical evidence for climate change, the general public continues to wrestle with climate change policy and advocacy. Early adolescence (12 to 13 years old) is a critical but under-researched demographic for the formation of attitudes related to climate change. This paper presents opinions on the worry, cause, and imminence of climate change that were collected from n=463 1st year secondary school students (12-13 years old) in public secondary schools in inner-urban centres in Austria and Australia. Overall, 86.83% of eligible respondents agreed that climate change was probably or definitely something we should worry about, 80.33% agreed that climate change was probably or definitely caused by humans, and 83.17% agreed that climate change was probably or definitely something that was happening now. The respondents opinions were also compared to their respective adult population, with Australian 12-13 year olds showing strong positive climate-friendly attitudes, both in comparison to their adult population, and to their Austrian peers. In addition, although the opinions of Austrian 12-13 year olds were quite high, they did not reflect the higher climate-friendly opinions of their adult community. Our results suggest that socio-cultural worldview or socio-cultural cognition theory may not have the influence on this age group as it does on the respective adult population - and, if they are affected, there are attitudes or factors in this age group which resist the opinion-influence from their mature community. These findings are significant as early adolescents may be pivotal in the climate science communication arena and investigating their opinions with regard to climate change may offer an unexplored and under-utilised target for future communication efforts and climate literacy programmes.

scientific communication and education↗

bioRxiv2018

SciReader*: A Cloud-based Recommender System for Biomedical Literature

With the growing number of biomedical papers published each year, keeping up with relevant literature has become increasingly important, and yet more challenging. SciReader (www.scireader.com) is a cloud-based personalized recommender system that specifically aims to assist biomedical researchers and clinicians identify publications of interest to them. SciReader uses topic modeling and other machine learning algorithms to provide users with recommendations that are recent, relevant, and of high quality1.

scientific communication and education↗

bioRxiv2018

Does being a grateful person increase one’s level of well-being? The mediating role of indebtedness

In this work, we define gratitude, paying attention to interpersonal gratitude and its relationship with dispositional debt. We examined the disposition to feel indebted through analysis of convergence and divergence, exploratory and confirmatory analysis of the most used measurement instrument. The Revised Indebtedness Scale depicted a four factor solution interrelated with a high consistency of content, which allows their labeling and describing. To do this, two samples of university students were selected; one of the sample sizes had 229 Spanish participants and the other 200 participants. Subsequently, a mediation model was tested in which the \"Self-sufficiency and discomfort in receiving help\" factor mediates the relationship between interpersonal gratitude and the \"Positive relations with others\" dimension of the Wellbeing scale. The results are discussed in relation to the need for conceptual definition of the constructs in Positive Psychology.

scientific communication and education↗

bioRxiv2018

Researchers preferentially collaborate with same-gendered colleagues across the life sciences

Evidence suggests that women in academia are hindered by conscious and unconscious biases, and often feel excluded from formal and informal opportunities for research collaboration. In addition to ensuring fairness and helping to redress gender imbalance in the academic workforce, increasing womens access to collaboration could help scientific progress by drawing on more of the available human capital. Here, we test whether researchers tend to collaborate with same-gendered colleagues, using more stringent methods and a larger dataset than in past work. Our results reaffirm that researchers co-publish with colleagues of the same gender more often than expected by chance, and show that this gender homophily is slightly stronger today than it was 10 years ago. Contrary to our expectations, we found no evidence that homophily is driven mostly by senior academics, and no evidence that homophily is stronger in fields where women are in the minority. Interestingly, journals with a high impact factor for their discipline tended to have comparatively low homophily, as predicted if mixed-gender teams produce better research. We discuss some potential causes of gender homophily in science.

scientific communication and education↗

bioRxiv2018

Outcomes of early NIH-funded investigators: Experience of the National Institute of Allergy and Infectious Diseases

Survival of junior scientists in academic biomedical research is difficult in todays highly competitive funding climate. National Institute of Health (NIH) data on first-time R01 grantees indicate the rate at which early investigators drop out from a NIH-supported research career is most rapid 4 to 5 years from the first R01 award. The factors associated with a high risk of dropping out, and whether these factors impact all junior investigators equally, are unclear. We identified a cohort of 1,496 investigators who received their first R01-equivalent (R01-e) awards from the National Institute of Allergy and Infectious Diseases between 2003 and 2010, and studied all their subsequent NIH grant applications through 2016. Ultimately, 57% of the cohort were successful in obtaining new R01-e funding, despite highly competitive conditions. Among those investigators who failed to compete successfully for new funding (43%), the average time to dropping out was 5 years. Investigators who successfully obtained new grants showed remarkable within-person consistency across multiple grant submission behaviors, including submitting more applications per year, more renewal applications, and more applications to multiple NIH Institutes. Funded investigators appeared to have two advantages over their unfunded peers at the outset: they had better scores on their first R01-e grants and they demonstrated an early ability to write applications that would be scored, not triaged. The cohort rapidly segregated into two very different groups on the basis of PI consistency in the quality and frequency of applications submitted after their first R01-e award. Lastly, we identified a number of specific demographic factors, intitutional characteristics, and grant submission behaviors that were associated with successful outcomes, and assessed their predictive value and relative importance for the likelihood of obtaining additional NIH funding.

scientific communication and education↗

bioRxiv2018

Attitudes, Perceptions and Barriers to Research and Publishing among Research and Teaching Staff: A Case Study

BackgroundThe economic development of any nation is centered on research. Unfortunately, research activities had suffered serious setback in tertiary research institutions in Nigeria. This study explores the attitudes, perceptions and barriers to research and publishing among academic staff in Nigerian Institute of Leather and Science Technology, (NILEST) Zaria Nigeria.\n\nMethodA structured self-administered questionnaire was distributed among 130 research and teaching staff at the various Directorates in NILEST. Data are presented in frequencies and percentages for questionnaire responses.\n\nResultExactly 93.85%of the questionnaires were validated for the study which included 81.15% male and 18.85% female. The participant were researchers (26.23%), lecturers (31.15%), Technologist (20.49%) and Instructors (22.13%). The majority of participant agreed that research is important for the institute (90.98%). A total of 81.15% believed that conducting research should be mandatory for all academic staff. Only 44.26% was self-reported to have ongoing research. Some of the obstacles reported to have prevented research activities included: lack of funding (72.13%), lack of professional mentorship (84.43%) and inadequate research facilities (89.34%). Participants without a single published paper were 54.545%. Some of the reasons given for not having published papers were \"no writing experience (95.65%), high publishing fee (79.71%) and long waiting period for peer review (97.10%)\". The suggestions to improve research status by respondents included\" provision of research grants/funds (92.62%), provision of internet facilities (95.10%), mandatory publication (26.23%) and appropriate mentorship (34.43%).\n\nConclusionMajority of the respondents believed that research is relevant, only a few were engaged in active research and published articles as evidence. It is therefore recommended that policy makers should devise strategies to focus on active research activities in order to achieve the desire research mandate and goal of institutions in the development of the nations economy.

scientific communication and education↗

bioRxiv2018

Evaluation of the capacity of Pediatricians in Nigeria to conduct of research: A nationwide Survey.

BackgroundQuality health care service delivery to children and adolescents is enhanced by continuous research into the health challenges of this subpopulation led by paediatricians with tremendous capacity to investigate and proffer solutions to the myriads of childhood illnesses. Understanding the health issues therefore is the foundation for implementation of viable interventions that assure optimum service delivery. In view of this background, the Paediatric Association of Nigeria (PAN) directed that research into childrens health challenges in Nigeria should be brought to the front burner in the country. Pursuant to this laudable goal this study was conceived to evaluate the research capacity and capability of paediatricians in Nigeria and the institutions they represent. In view of above needs, this study aimed at evaluating the research capacities and challenges among paediatricians.\n\nMethodsThe survey used a cross-sectional nationwide design to enroll paediatricians into the study. The study was a combination of both online and face-to-face survey using questionnaire developed from Research Capacity Assessment Framework. Information on previous research work, challenges encountered, existing capacity and utilization of research outcome were obtained. The SPSS version 20 was used for data entry and analysis. For qualitative variables, similar responses were grouped under thematic heading.\n\nResultsThe response rates for online (via email survey, group-administered in a conference and individual face-to-face (at workshops) were 32 (3.2%), 75 (13.6%) and 15 (60%) respectively. The majority, 87(85.5%) of the participants had conducted prevalence studies, compared to 9 (8.8%) that had done experimental studies. Those who have ever received grant funding for their studies were 21 (19.4%), while the proportion whose research outcome had informed policy update and practice were policy 20 (18.2%). More than 55% of the participants had challenges on some of the seven aspects of research: research topic, proposal, funding, fieldwork, analysis, utilizing findings and collaboration. Less than 40% of the participants had received training on some of the tested 14 research capacity areas except for the area of ethics where 78 (70.9%) reported having received training. For 51 (46.4%) this ethics training included the Good Clinical Practice Guidelines.\n\nConclusionNigerian Academic Paediatricians need to be stimulated to develop interest in research by building their presently low research capacity if future paediatric practice is to be driven significantly by evidence.

scientific communication and education↗

bioRxiv2018

Commitments by the biopharmaceutical industry to clinical trials transparency: the evolving environment

BackgroundSponsors of clinical trials have ethical obligations to register protocols, to report study results and to comply with applicable legal requirements.\n\nObjectiveTo evaluate public commitments to trial disclosure and rates of disclosure by members and non-members of the European Federation of Pharmaceutical Industries and Associations (EFPIA) and/or the Pharmaceutical Research and Manufacturers of America (PhRMA).\n\nStudy selectionWebsites of the top 50 biopharmaceutical companies by 2015 sales were searched for statements relating to trial data disclosure. Disclosure of trial results completed by biopharmaceutical industry and non-industry sponsors of at least 30 trials (2006-2015) was assessed using TrialsTracker.\n\nFindingsAmong the top 50 companies, 30 were EFPIA/PhRMA members and 20 were non-members, of which 26 and none, respectively, had a statement on their website committing to the disclosure of trials data. Of 29 377 trials in TrialsTracker, 9511 were industry-sponsored (69 companies) and 19 866 were non-industry-sponsored (254 institutions). The overall mean disclosure rate was 55%, with higher rates for industry (74%) than for non-industry sponsors (46%). Of the 30 companies within the top 50 with data in TrialsTracker, the mean disclosure rate was 76% (77% for EFPIA/PhRMA members [n = 25] versus 67% for non-members [n = 5]).\n\nConclusionsMost of the top 50 biopharmaceutical companies have publicly committed to the disclosure of trial data. Industry sponsors have responded to the ethical and legal demands of trial disclosure to a greater extent than non-industry sponsors, and now disclose three quarters of their trials.

scientific communication and education↗

bioRxiv2018

Teachers’ approaches to genetics teaching mirror their perceptions of teaching controversial, societal and sensitive issues

The skills required to understand genetic phenomena and transfer knowledge to real world situations are an important part of 21st century scientific literacy. While socio-scientific issues (SSI) are increasingly emphasised in science curricula, teachers have low interest in adopting SSI in teaching. Little is known about how teachers choose content for their teaching, although this process translates curricula to teaching practice. We explored how teachers choose content and contexts for biology courses on cells, heredity, and biotechnology by interviewing ten Finnish upper-secondary school teachers. We studied how the teachers described teaching on genetically modified organisms, hereditary disorders, and human traits. Teachers perceptions on genetics teaching were classified to Developmental, Structural and Hereditary approaches. The approaches were connected not only to the teachers perceptions of the more important content, but also teacher inclinations towards teaching genetics in the human context and perceptions of students interest in different topics. Teachers justified their choices by national, local school, and teachers personal-level factors. While teachers mentioned that SSI are important, they were never mentioned among the important contexts. Nevertheless, some teachers embraced teaching genetics in the human context while others avoided them. Teachers justified their avoidance for personal and pedagogical factors, such as their competence in dealing with these contexts. Experience played a part in the approach that teachers had, and contrary to the results of previous research, the less experienced teachers were more open to discussing human genetics. We conclude that curriculum development is important to encourage teachers to adopt more SSI-oriented teaching. Disclosure statementTuomas Aivelo has participated in writing biology textbooks for upper-secondary school biology for eOppi Oy. None of the teachers involved in this study used biology textbooks from eOppi Oy.

scientific communication and education↗

bioRxiv2018

Options for calibrating CERES-maize genotype specific parameters under data-scarce environments

Most crop simulation models require the use of Genotype Specific Parameters (GSPs) which provide the Genotype component of GxExM interactions. Estimation of GSPs is the most difficult aspect of most modelling exercises because it requires expensive and time-consuming field experiments. GSPs could also be estimated using multi-year and multi locational data from breeder evaluation experiments. This research was set up with the following objectives: i) to determine GSPs of 10 newly released maize varieties for the Nigerian Savannas using data from both calibration experiments and by using existing data from breeder varietal evaluation trials; ii) to compare the accuracy of the GSPs generated using experimental and breeder data; and iii) to evaluate CERES-Maize model to simulate grain and tissue nitrogen contents. For experimental evaluation, 8 different experiments were conducted during the rainy and dry seasons of 2016 across the Nigerian Savanna. Breeder evaluation data was also collected for 2 years and 7 locations. The calibrated GSPs were evaluated using data from a 4 year experiment conducted under varying nitrogen rates (0, 60 and 120kg N ha-1). For the model calibration using experimental data, calculated model efficiency (EF) values ranged between 0.86-0.92 and coefficient of determination (d-index) between 0.92-0.98. Calibration of time-series data produced nRMSE below 7% while all prediction deviations were below 10% of the mean. For breeder experiments, EF (0.52-0.81) and d-index (0.46-0.83) ranges were lower. Prediction deviations were below 17% of the means for all measured variables. Model evaluation using both experimental and breeder trials resulted in good agreement (low RMSE, high EF and d-index values) between observed and simulated grain yields, and tissue and grain nitrogen contents. We conclude that higher calibration accuracy of CERES-Maize model is achieved from detailed experiments. If unavailable, data from breeder experimental trials collected from many locations and planting dates can be used with lower but acceptable accuracy.

scientific communication and education↗

bioRxiv2018

Nucleotides inclusion in pet food: effect of thermic treatment and shelf-life

A growing trend of nucleotides supplementation in pets is occurring in recent years with the final goal of reinforcing the immune system and promoting intestinal function. Despite that, data evaluating possible alterations of nucleotides during pet food processing are lacking. The aim of the study was to evaluate the recovery percentage of nucleotides in dry and canned food after processing and storage. Selected dry and canned feed were supplemented with 0.4/100 g dry matter basis of Prosol petMOD. Recovery percentage in dry food was 75% and 74% at the end of technological process and a 12-month shelf-life, while in canned food it was 43% and 41%, respectively. These results support the hypothesis that N could be included during pet food process but industries have to increase the awareness about possible losses, especially in canned food.

scientific communication and education↗

bioRxiv2018

Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience

The present study analyzed 960 papers published in Molecular and Cellular Biology (MCB) from 2009-2016 and found 59 (6.1%) to contain inappropriately duplicated images. The 59 instances of inappropriate image duplication led to 42 corrections, 5 retractions and 12 instances in which no action was taken. Our experience suggests that the majority of inappropriate image duplications result from errors during figure preparation that can be remedied by correction. Nevertheless, ~10% of papers with inappropriate image duplications in MCB were retracted. If this proportion is representative, then as many as 35,000 papers in the literature are candidates for retraction due to image duplication. The resolution of inappropriate image duplication concerns after publication required an average of 6 h of journal staff time per published paper. MCB instituted a pilot program to screen images of accepted papers prior to publication that identified 12 manuscripts (14.5% out of 83) with image concerns in two months. The screening and correction of papers before publication required an average of 30 min of staff time per problematic paper. Image screening can identify papers with problematic images prior to publication, reduces post-publication problems and requires significantly less staff time than the correction of problems after publication.

scientific communication and education↗