ResearchPad - careers Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Predicting the impact of patient and private provider behavior on diagnostic delay for pulmonary tuberculosis patients in India: A simulation modeling study]]> India contributes more than a quarter of the 10 million global tuberculosis (TB) cases every year.Several studies capture long, circuitous care pathways followed by TB patients until their diagnosis. However, these studies do not quantify the link between diagnostic delay and underlying patient and provider behavior characteristics.What did the researchers do and find?We developed a quantitative simulation model to estimate the impact of behavioral characteristics of patients and providers on diagnostic delay and estimated the parameters of this model using data from detailed interviews of 76 patients from Mumbai and 64 patients from Patna.We found that earlier test ordering by providers would yield a much larger reduction in diagnostic delay than increasing their diagnostic accuracy.What do these findings mean?Policy-makers and implementing agencies should encourage early test ordering behavior by providers to reduce diagnostic delay, and, consequently, to reduce disease transmission. ]]> <![CDATA[Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles]]> <![CDATA[What makes an effective grants peer reviewer? An exploratory study of the necessary skills]]> This exploratory mixed methods study describes skills required to be an effective peer reviewer as a member of review panels conducted for federal agencies that fund research, and examines how reviewer experience and the use of technology within such panels impacts reviewer skill development. Two specific review panel formats are considered: in-person face-to-face and virtual video conference. Data were collected through interviews with seven program officers and five expert peer review panelists, and surveys from 51 respondents. Results include the skills reviewers’ consider necessary for effective review panel participation, their assessment of the relative importance of these skills, how they are learned, and how review format affects skill development and improvement. Results are discussed relative to the peer review literature and with consideration of the importance of professional skills needed by successful scientists and peer reviewers.

<![CDATA[The early experiences of Physician Associate students in the UK: A regional cross-sectional study investigating factors associated with engagement]]> The number of physician associates (PAs) training and working in the UK has increased over the last few years following the proliferation of postgraduate courses. Understanding early experiences and what impacts on engagement is important if we are to appropriately support this relatively new professional group.MethodsThis paper reports on a cross-sectional analysis of the first year of data from a prospective 10-year longitudinal cohort study. First year PA students (n = 89) were enrolled from five universities in one UK region where the training programmes were less than 2 years old. Data collected were: demographic information, wellbeing, burnout and engagement, expectations, placement experience, performance and caring responsibilities. Pearson’s correlations were used to examine relationships between variables and to select variables for a hierarchical regression analysis to understand which factors were associated with engagement. Descriptive statistics were calculated for questions relating to experience.ResultsThe experiences of PA students during their first 3–6 months were mixed. For example, 78.7% of students felt that there were staff on placement they could go to for support, however, 44.8% reported that staff did not know about the role and 61.3% reported that staff did not know what clinical work they should undertake. Regression analysis found that their level of engagement was associated with their perceived career satisfaction, overall well-being, and caring responsibilities.ConclusionsThe support systems required for PAs may need to be examined as results showed that the PA student demographic is different to that of medical students and caring responsibilities are highly associated with engagement. A lack of understanding around the PA role in clinical settings may also need to be addressed in order to better support and develop this workforce. ]]> <![CDATA[‘In search of lost time’: Identifying the causative role of cumulative competition load and competition time-loss in professional tennis using a structural nested mean model]]>

Injury prevention is critical to the achievement of peak performance in elite sport. For professional tennis players, the topic of injury prevention has gained even greater importance in recent years as multiple of the best male players have been sidelined owing to injury. Identifying potential causative factors of injury is essential for the development of effective prevention strategies, yet such research is hampered by incomplete data, the complexity of injury etiology, and observational study biases. The present study attempts to address these challenges by focusing on competition load and time-loss to competition—a completely observable risk factor and outcome—and using a structural nested mean model (SNMM) to identify the potential causal role of cumulative competition load on the risk of time-loss. Using inverse probability of treatment weights to balance exposure histories with respect to player ability, past injury, and consecutive competition weeks at each time point; the SNMM analysis of 389 professional male players and 55,773 weeks of competition found that total load significantly increases the risk of time-loss (HR = 1.05 per 1,000 games of additional load 95% CI 1.01-1.10) and this effect becomes magnified with age. Standard regression showed a protective effect of load, highlighting the value of more robust causal methods in the study of dynamic exposures and injury in sport and the need for further applications of these methods for understanding how time-loss and injuries of elite athletes might be prevented in the future.

<![CDATA[Beware of vested interests: Epistemic vigilance improves reasoning about scientific evidence (for some people)]]>

In public disputes, stakeholders sometimes misrepresent statistics or other types of scientific evidence to support their claims. One of the reasons this is problematic is that citizens often do not have the motivation nor the cognitive skills to accurately judge the meaning of statistics and thus run the risk of being misinformed. This study reports an experiment investigating the conditions under which people become vigilant towards a source’s claim and thus reason more carefully about the supporting evidence. For this, participants were presented with a claim by a vested-interest or a neutral source and with statistical evidence which was cited by the source as being in support of the claim. However, this statistical evidence actually contradicted the source’s claim but was presented as a contingency table, which are typically difficult for people to interpret correctly. When the source was a lobbyist arguing for his company’s product people were better at interpreting the evidence compared to when the same source argued against the product. This was not the case for a different vested-interests source nor for the neutral source. Further, while all sources were rated as less trustworthy when participants realized that the source had misrepresented the evidence, only for the lobbyist source was this seen as a deliberate attempt at deception. Implications for research on epistemic trust, source credibility effects and science communication are discussed.

<![CDATA[Prevalence of depressive symptoms among Italian medical students: The multicentre cross-sectional “PRIMES” study]]>


Four percent of the world’s population suffers from depression, which is a major public health issue. Medical students are at risk, as their depressive symptoms (DS) prevalence is reported to be approximately 27% worldwide. Since few data on Italian medical students exist, this study aimed to estimate their DS prevalence and assess risk and protective factors.


The PRIMES was a multicentre cross-sectional study performed in 12 Italian medical schools. Questionnaires were self-reported and included 30 sociodemographic items and the Beck Depression Inventory-II (BDI-II). The primary outcome was the presence of DS (BDI-II score≥14). The main analyses were chi-squared tests and multivariable logistic regressions with a p-value<0.05 considered significant.


The number of collected questionnaires was 2,513 (117 BDI-II incomplete). Females accounted for 61.3% of the respondents, and the median age was 22 years (IQR = 4). The prevalence of DS was 29.5%. Specifically, 14.0% had mild depression, 11.1% had moderate depression, and 4.5% had severe depression. The main risk factors for DS were age, being female, bisexual/asexual orientation, living with partner/housemates, poor economic status (worsened by living far from home), less than 90 min of weekly exercise, relatives with psychiatric disorders, personal chronic disease, judging medical school choice negatively, unsatisfying friendships with classmates, competitive and hostile climate among classmates, thinking that medical school hinders specific activities and being worried about not measuring up to the profession. Protective factors included family cohesion, hobbies, intellectual curiosity as a career motivation and no worries about the future.


Italian medical students are at high risk of reporting DS, similar to the global population of medical students’. Medical schools must make efforts to implement preventive and treatment interventions by offering counselling and working on modifiable factors, such as lifestyle and learning climate.

<![CDATA[Will COVID-19 become the next neglected tropical disease?]]> ]]> <![CDATA[Height of overburden fracture based on key strata theory in longwall face]]>

Among the three overburden zones (the caving zone, the fracture zone, and the continuous deformation zone) in longwall coal mining, the continuous deformation zone is often considered to be continuous without cracks, so continuum mechanics can be used to calculate the subsidence of overburden strata. Longwall coal mining, however, will induce the generation of wide cracks in the surface and thus may cause the continuous deformation zone to fracture. In this paper, whether there are cracks in the continuous deformation zone as well as the height of overburden fracture in longwall face and the subsidence and deformation of strata of different fracture penetration ratios were studied by means of physical simulation, theoretical analysis and numerical simulation. The results show that: (1) Rock stratum starts to fracture as long as it has slightly subsided for only tens of millimeters, and the height of fracture development is the height of working face overburden. (2) With the increase of fracture penetration ratio, the subsidence of key strata remains basically unchanged; the surface deformation range and the maximum compression deformation decrease, while the maximum horizontal movement and maximum horizontal tensile deformation increase. Therefore, the subsidence of overburden strata which have fractured but have not broken can be calculated through the continuum mechanics method.

<![CDATA[On the value of preprints: An early career researcher perspective]]>

Peer-reviewed journal publication is the main means for academic researchers in the life sciences to create a permanent public record of their work. These publications are also the de facto currency for career progress, with a strong link between journal brand recognition and perceived value. The current peer-review process can lead to long delays between submission and publication, with cycles of rejection, revision, and resubmission causing redundant peer review. This situation creates unique challenges for early career researchers (ECRs), who rely heavily on timely publication of their work to gain recognition for their efforts. Today, ECRs face a changing academic landscape, including the increased interdisciplinarity of life sciences research, expansion of the researcher population, and consequent shifts in employer and funding demands. The publication of preprints, publicly available scientific manuscripts posted on dedicated preprint servers prior to journal-managed peer review, can play a key role in addressing these ECR challenges. Preprinting benefits include rapid dissemination of academic work, open access, establishing priority or concurrence, receiving feedback, and facilitating collaborations. Although there is a growing appreciation for and adoption of preprints, a minority of all articles in life sciences and medicine are preprinted. The current low rate of preprint submissions in life sciences and ECR concerns regarding preprinting need to be addressed. We provide a perspective from an interdisciplinary group of ECRs on the value of preprints and advocate their wide adoption to advance knowledge and facilitate career development.

<![CDATA[DeephESC 2.0: Deep Generative Multi Adversarial Networks for improving the classification of hESC]]>

Human embryonic stem cells (hESC), derived from the blastocysts, provide unique cellular models for numerous potential applications. They have great promise in the treatment of diseases such as Parkinson’s, Huntington’s, diabetes mellitus, etc. hESC are a reliable developmental model for early embryonic growth because of their ability to divide indefinitely (pluripotency), and differentiate, or functionally change, into any adult cell type. Their adaptation to toxicological studies is particularly attractive as pluripotent stem cells can be used to model various stages of prenatal development. Automated detection and classification of human embryonic stem cell in videos is of great interest among biologists for quantified analysis of various states of hESC in experimental work. Currently video annotation is done by hand, a process which is very time consuming and exhaustive. To solve this problem, this paper introduces DeephESC 2.0 an automated machine learning approach consisting of two parts: (a) Generative Multi Adversarial Networks (GMAN) for generating synthetic images of hESC, (b) a hierarchical classification system consisting of Convolution Neural Networks (CNN) and Triplet CNNs to classify phase contrast hESC images into six different classes namely: Cell clusters, Debris, Unattached cells, Attached cells, Dynamically Blebbing cells and Apoptically Blebbing cells. The approach is totally non-invasive and does not require any chemical or staining of hESC. DeephESC 2.0 is able to classify hESC images with an accuracy of 93.23% out performing state-of-the-art approaches by at least 20%. Furthermore, DeephESC 2.0 is able to generate large number of synthetic images which can be used for augmenting the dataset. Experimental results show that training DeephESC 2.0 exclusively on a large amount of synthetic images helps to improve the performance of the classifier on original images from 93.23% to 94.46%. This paper also evaluates the quality of the generated synthetic images using the Structural SIMilarity (SSIM) index, Peak Signal to Noise ratio (PSNR) and statistical p-value metrics and compares them with state-of-the-art approaches for generating synthetic images. DeephESC 2.0 saves hundreds of hours of manual labor which would otherwise be spent on manually/semi-manually annotating more and more videos.

<![CDATA[Late-life mortality is underestimated because of data errors]]>

Knowledge of true mortality trajectory at extreme old ages is important for biologists who test their theories of aging with demographic data. Studies using both simulation and direct age validation found that longevity records for ages 105 years and older are often incorrect and may lead to spurious mortality deceleration and mortality plateau. After age 105 years, longevity claims should be considered as extraordinary claims that require extraordinary evidence. Traditional methods of data cleaning and data quality control are just not sufficient. New, more strict methodologies of data quality control need to be developed and tested. Before this happens, all mortality estimates for ages above 105 years should be treated with caution.

<![CDATA[Is there an association between working conditions and health? An analysis of the Sixth European Working Conditions Survey data]]>

This paper analyses the association between working conditions and physical health using data from the Sixth European Working Conditions Survey (EWCS6) released in 2017. The econometric analysis uses two indicators to describe health status: self-assessed health (SAH), which is a subjective indicator of health; and an objective indicator of health (SICK), which is based on the occurrence of any illness or health problem that has lasted or is expected to last for more than 6 months. The theoretical hypotheses concerning the association between working conditions and SAH and the association between working conditions and SICK are tested using a standard ordered probit model and a standard probit model, respectively. The results show that encouraging working conditions, work environment, and job support are associated with both better self-assessed health and better objective health.

<![CDATA[Reliable novelty: New should not trump true]]>

Although a case can be made for rewarding scientists for risky, novel science rather than for incremental, reliable science, novelty without reliability ceases to be science. The currently available evidence suggests that the most prestigious journals are no better at detecting unreliable science than other journals. In fact, some of the most convincing studies show a negative correlation, with the most prestigious journals publishing the least reliable science. With the credibility of science increasingly under siege, how much longer can we afford to reward novelty at the expense of reliability? Here, I argue for replacing the legacy journals with a modern information infrastructure that is governed by scholars. This infrastructure would allow renewed focus on scientific reliability, with improved sort, filter, and discovery functionalities, at massive cost savings. If these savings were invested in additional infrastructure for research data and scientific code and/or software, scientific reliability would receive additional support, and funding woes—for, e.g., biological databases—would be a concern of the past.

<![CDATA[A proposal for the future of scientific publishing in the life sciences]]>

Science advances through rich, scholarly discussion. More than ever before, digital tools allow us to take that dialogue online. To chart a new future for open publishing, we must consider alternatives to the core features of the legacy print publishing system, such as an access paywall and editorial selection before publication. Although journals have their strengths, the traditional approach of selecting articles before publication (“curate first, publish second”) forces a focus on “getting into the right journals,” which can delay dissemination of scientific work, create opportunity costs for pushing science forward, and promote undesirable behaviors among scientists and the institutions that evaluate them. We believe that a “publish first, curate second” approach with the following features would be a strong alternative: authors decide when and what to publish; peer review reports are published, either anonymously or with attribution; and curation occurs after publication, incorporating community feedback and expert judgment to select articles for target audiences and to evaluate whether scientific work has stood the test of time. These proposed changes could optimize publishing practices for the digital age, emphasizing transparency, peer-mediated improvement, and post-publication appraisal of scientific articles.

<![CDATA[Gender and cultural bias in student evaluations: Why representation matters]]>

Gendered and racial inequalities persist in even the most progressive of workplaces. There is increasing evidence to suggest that all aspects of employment, from hiring to performance evaluation to promotion, are affected by gender and cultural background. In higher education, bias in performance evaluation has been posited as one of the reasons why few women make it to the upper echelons of the academic hierarchy. With unprecedented access to institution-wide student survey data from a large public university in Australia, we investigated the role of conscious or unconscious bias in terms of gender and cultural background. We found potential bias against women and teachers with non-English speaking backgrounds. Our findings suggest that bias may decrease with better representation of minority groups in the university workforce. Our findings have implications for society beyond the academy, as over 40% of the Australian population now go to university, and graduates may carry these biases with them into the workforce.

<![CDATA[Developing a modern data workflow for regularly updated data]]>

Over the past decade, biology has undergone a data revolution in how researchers collect data and the amount of data being collected. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. Regularly updated data present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow leverages tools from software development, including version control and continuous integration, to create a modern data management system that automates the pipeline.

<![CDATA[Open notebook science can maximize impact for rare disease projects]]>

Transparency lies at the heart of the open lab notebook movement. Open notebook scientists publish laboratory experiments and findings in the public domain in real time, without restrictions or omissions. Research on rare diseases is especially amenable to the open notebook model because it can both increase scientific impact and serve as a mechanism to engage patient groups in the scientific process. Here, I outline and describe my own success with my open notebook project, LabScribbles, as well as other efforts included in the initiative.

<![CDATA[Evidence that nonsignificant results are sometimes preferred: Reverse P-hacking or selective reporting?]]>

There is increased concern about poor scientific practices arising from an excessive focus on P-values. Two particularly worrisome practices are selective reporting of significant results and ‘P-hacking’. The latter is the manipulation of data collection, usage, or analyses to obtain statistically significant outcomes. Here, we introduce the novel, to our knowledge, concepts of selective reporting of nonsignificant results and ‘reverse P-hacking’ whereby researchers ensure that tests produce a nonsignificant result. We test whether these practices occur in experiments in which researchers randomly assign subjects to treatment and control groups to minimise differences in confounding variables that might affect the focal outcome. By chance alone, 5% of tests for a group difference in confounding variables should yield a significant result (P < 0.05). If researchers less often report significant findings and/or reverse P-hack to avoid significant outcomes that undermine the ethos that experimental and control groups only differ with respect to actively manipulated variables, we expect significant results from tests for group differences to be under-represented in the literature. We surveyed the behavioural ecology literature and found significantly more nonsignificant P-values reported for tests of group differences in potentially confounding variables than the expected 95% (P = 0.005; N = 250 studies). This novel, to our knowledge, publication bias could result from selective reporting of nonsignificant results and/or from reverse P-hacking. We encourage others to test for a bias toward publishing nonsignificant results in the equivalent context in their own research discipline.

<![CDATA[Maintenance and inspection as risk factors in helicopter accidents: Analysis and recommendations]]>

In this work, we establish that maintenance and inspection are a risk factor in helicopter accidents. Between 2005 and 2015, flawed maintenance and inspection were causal factors in 14% to 21% of helicopter accidents in the U.S. civil fleet. For these maintenance-related accidents, we examined the incubation time from when the maintenance error was committed to the time when it resulted in an accident. We found a significant clustering of maintenance accidents within a short number of flight-hours after maintenance was performed. Of these accidents, 31% of these accidents occurred within the first 10 flight-hours. This is reminiscent of infant mortality in reliability engineering, and we characterized it as maintenance error infant mortality. The last quartile of maintenance-related accidents occurred after 60 flight-hours following maintenance and inspection. We then examined the “physics of failures” underlying maintenance-related accidents and analyzed the prevalence of different types of maintenance errors in helicopter accidents. We found, for instance, that the improper or incomplete (re)assembly or installation of a part category accounted for the majority of maintenance errors with 57% of such cases, and within this category, the incorrect torquing of the B-nut and incomplete assembly of critical linkages were the most prevalent maintenance errors. We also found that within the failure to perform a required preventive maintenance and inspection task category, the majority of the maintenance programs were not executed in compliance with federal regulations, nor with the manufacturer maintenance plan. Maintenance-related accidents are particularly hurtful for the rotorcraft community, and they can be eliminated. This is a reachable objective when technical competence meets organizational proficiency and the collective will of all the stakeholders in this community. We conclude with a set of recommendations based on our findings, which borrow from the ideas underlying the defense-in-depth safety principle to address this disquieting problem.