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bioRxiv2018

Beyond financial conflicts of interest: Institutional oversight of faculty consulting agreements at schools of medicine and public health

ImportanceApproximately one-third of U.S. life sciences faculty engage in industry consulting. Despite reports that consulting contracts often impinge on faculty and university interests, institutional approaches to regulating consulting agreements are largely unknown.\n\nObjectiveTo investigate the nature of institutional oversight of faculty consulting contracts at U.S. schools of medicine and public health.\n\nDesignStructured telephone interviews with institutional administrators. Questions included the nature of oversight for faculty consulting agreements, if any, and views about consulting as a private versus institutional matter. Interviews were analyzed using a structured coding scheme.\n\nSettingAll accredited schools of medicine and public health in the U.S.\n\nParticipantsAdministrators responsible for faculty affairs were identified via internet searches and telephone and email follow-up. The 118 administrators interviewed represented 73% of U.S. schools of medicine and public health, and 75% of those invited to participate.\n\nInterventionStructured, 15-30 minute telephone interviews.\n\nMain outcomes and measuresPrevalence and type of institutional oversight; responses to concerning provisions in consulting agreements; perceptions of institutional oversight.\n\nResultsOne third of institutions (36%) required faculty to submit at least some agreements for institutional review and 36% reviewed contracts upon request, while 35% refused to review contracts. Among institutions with review, there was wide variation the issues covered. The most common topic was intellectual property rights (64%), while only 23% looked at publication rights and 19% for inappropriately broad confidentiality provisions. Six in ten administrators reported they had no power to prevent faculty from signing consulting agreements. Although most respondents identified institutional risks from consulting relationships, many maintained that consulting agreements are \"private.\"\n\nConclusions and relevanceOversight of faculty consulting agreements at U.S. schools of medicine and public health is inconsistent across institutions and usually not robust. The interests at stake suggest the need for stronger oversight.

scientific communication and education↗

bioRxiv2018

Spatio-temporal variability of soil nutrients and the responses of growth during growth stages of winter wheat in the north of China

Study on soil nutrient variability and its effect on the growth and development of crop under traditional tillage mode is the foundation to comprehensively implement the precision agriculture policy on the field scale and crop excellent management. In this paper, a winter wheat field of 28.5 hm2 under traditional cultivation model in Tianzhuang town of Huantai county was selected as the research area. Sampling by mesh point method (60x60m), the variation characteristics of soil available nitrogen (AN), available phosphorus (AP) and available potassium (AK) in the before sowing, reviving stage, jointing stage, filling stage of winter wheat were analyzed by the method of geostatistics and GIS. At the same time, Pearson correlation analysis was used to study the response of wheat growth and development to soil nutrient variation. As the growth period goes by, 1) each nutrient showed low-high-low and moderate variability. AN and AK had the highest content at reviving stage, while AP at jointing stage, as turning point. The order of variability of each nutrient was AN>AP>AK. 2) The difference of nutrient variation first increased and then decreased, and showed medium to strong spatial correlation.\n\nThree nutrients in the before sowing stage were strong spatial correlation, and the reviving stage was medium spatial correlation, to the jointing and filling stages, AN was medium spatial correlation, AP and AK were strong spatial correlation. The spatial correlation of each nutrients was the weakest in the reviving stage, and AN was the strongest in the before sowing stage, while AP and AK were strongest in the jointing stage. The spatial correlation of each soil nutrients decreased from before sowing to reviving stage, jointing stage to filling stage, and the spatial correlation increased from reviving stage to jointing stage. 3) Soil nutrient content first increased and then decreased, and the grade of nutrient gradually decreased. 4) The correlation between soil nutrients and wheat growth was gradually increasing. AN had the highest correlation with wheat growth, followed by AK and AP lowest. The effect of soil nutrients on the growth of wheat at the reviving stage was higher than that of the current nutrient, and the growth of wheat at jointing stage was mainly influenced by the current nutrient, while the growth of wheat at the filling period was both influenced by the nutrient content of the last and the current period; the date to supplement fertilizer should be postponed properly. In this study, the soil nutrient dynamics and its influence on the growth of wheat during the winter wheat growth period under the traditional field model were well understood, which could provide a theoretical basis for the precision management of soil nutrients in the northern winter wheat area with relatively uniform planting environment and cultivation management.

scientific communication and education↗

bioRxiv2018

Improvement of arthroscopic surgical performance using a new wide-angle arthroscope

BackgroundWe have developed a new arthroscope with a field of view of 150{degrees}. This requires less motion to maneuver, and the optical error is decreased. It also improves how novices learn arthroscopy. We hypothesized that surgical performance using this arthroscope is superior to a conventional arthroscope. This study tested the hypothesis using motion analysis and a new validated parameter, \"dimensionless squared jolt\" (DSJ).\n\nMethodsWe compared the surgical performance using between the wide-angle and the conventional arthroscope among 14 novice orthopedic residents who performed three standardized tasks three times with each arthroscope. The tasks simulated arthroscopic rotator cuff repair surgical skills. Their motion was analyzed using an optical tracking system. The differences in performance parameters, such as time taken, average acceleration of the hands (m/s2), the number of movements, and the total path length (m) including DSJ between the two arthroscopes, were investigated using paired t-tests.\n\nResultsAll the estimated values for the tasks using the 150{degrees} arthroscope were lower than those for the 105{degrees} arthroscope. There were statistically significant differences in performance between the two arthroscopes only for DSJ (p = 0.014) and average acceleration (p = 0.039).\n\nConclusionsDSJ and average acceleration are reliable parameters for representing hand-eye coordination. The surgical performance of novice arthroscopists was better with the new wide-angle arthroscope than with the conventional arthroscope.

scientific communication and education↗

bioRxiv2018

Gender and international diversity improves equity in peer review

The fairness of scholarly peer review has been challenged by evidence of disparities in publication outcomes based on author demographic characteristics. To assess this, we conducted an exploratory analysis of peer review outcomes of 23,876 initial submissions and 7,192 full submissions that were submitted to the biosciences journal eLife between 2012 and 2017. Women and authors from nations outside of North America and Europe were underrepresented both as gatekeepers (editors and peer reviewers) and authors. We found evidence of a homophilic relationship between the demographics of the gatekeepers and authors and the outcome of peer review; that is, there were higher rates of acceptance in the case of gender and country homophily. The acceptance rate for manuscripts with male last authors was seven percent, or 3.5 percentage points, greater than for female last authors (95% CI = [0.5, 6.4]); this gender inequity was greatest, at nine percent or about 4.8 percentage points (95% CI = [0.3, 9.1]), when the team of reviewers was all male; this difference was smaller and not significantly different for mixed-gender reviewer teams. Homogeny between countries of the gatekeeper and the corresponding author was also associated with higher acceptance rates for many countries. To test for the persistence of these effects after controlling for potentially confounding variables, we conducted a logistic regression including document and author metadata. Disparities in acceptance rates associated with gender and country of affiliation and the homophilic associations remained. We conclude with a discussion of mechanisms that could contribute to this effect, directions for future research, and policy implications. Code and anonymized data have been made available at https://github.com/murrayds/elife-analysis\n\nAuthor summaryPeer review, the primary method by which scientific work is evaluated, is ideally a fair and equitable process in which scientific work is judged solely on its own merit. However, the integrity of peer review has been called into question based on evidence that outcomes often differ between male and female authors, and for authors in different countries. We investigated such disparities at the biosciences journal eLife by analyzing the demographics of authors and gatekeepers (editors and peer reviewers), and peer review outcomes of all submissions between 2012 and 2017. Outcomes were more favorable for male authors and those affiliated with institutions in North America and Europe; these groups were also over-represented among gatekeepers. There was evidence that peer review outcomes were influenced by homophily --a preference of gatekeepers for manuscripts from authors with shared characteristics. We discuss mechanisms that could contribute to this effect, directions for future research, and policy implications.

scientific communication and education↗

bioRxiv2018

Gridlock from Diagnosis to Treatment of Multidrug Resistant Tuberculosis in Tanzania: Patients Perspectives from the Focus Group Discussion

IntroductionMolecular diagnostics have revolutionized the diagnosis of multidrug resistant tuberculosis (MDR-TB). Yet in Tanzania we found delay in diagnosis with more than 70% of MDR-TB patients having history of several previous treatment courses for TB signaling complications of prior missed diagnosis. We aimed to explore patients viewpoints and experiences with personal and socio-behavioral obstacles from MDR-TB diagnosis to treatment in an attempt to understand these prior findings.\n\nMethodsThe study was conducted in December 2016 with MDR-TB patients admitted at Kibongoto Infectious Diseases Hospital. We used semi-structured interviews and focus group discussion to examine patients views and experiences during MDR-TB diagnosis. Groups were sex aggregated to allow free interaction and to gauge gender specific issues in the social and behavioral contexts. The discussion - explored patients delivery factors that were impacting delay from MDR-TB diagnosis to treatment. Iterative data collection and analysis was applied with data, codes and categories being compared and refined.\n\nResultsForty-five MDR-TB patients participated in 6 focus group discussions. Challenges and barriers contributing to the delay from MDR-TB diagnosis to treatment were as follows: 1) The general population had differing understanding of MDR-TB that led to seeking services from traditional healers; 2) Also socio-economic adversity made health-seeking behavior difficult and often unproductive; 3) In the health system, challenges included inadequacy of MDR-TB diagnostic centers, lack of knowledge on behalf of health care providers to consider MDR-TB and order appropriate diagnostics; 4) Insufficiency in the specimen referral system for early diagnosis of MDR-TB. Non-adherence of TB patients to first-line anti-TB drugs prior to MDR-TB diagnosis given the multitude of barriers discussed was coupled with both intentional and unintentional non-adherence of health care providers to international standards of TB care.\n\nConclusionPatient-centered strategies bridging communities and the health system are urgently required for optimum MDR-TB control in Tanzania.

scientific communication and education↗

bioRxiv2018

Overview of biomedical and public health reviews in Ethiopia from 1970 to 2018: trends, methodological qualities, gaps and future directions

IntroductionGlobally, there has been a dramatic increment of narrative reviews, systematic reviews and overview publication rates. In Ethiopia, only small number of reviews are published and no overviews conducted in biomedical and public health disciplines. Therefore, we aimed to (1) assess the trend of narrative and systematic reviews in Ethiopia, (2) examine their methodological quality and (3) suggest future directions for improvement.\n\nMethodsPubMed, EMBASE, Web of Science, SCOPUS, CINHAL, WHO Global Index Medicus, Cochrane Library and PsycINFO electronic databases were searched and supplemented by hand searching as well. All narrative reviews and systematic reviews with or without a meta-analysis from 1970 to April 2018 were included. The International Narrative Systematic assessment (INSA) for narrative reviews and A MeaSurement Tool to Assess Systematic Reviews (AMSTAR-2) for systematic reviews with or without a meta-analysis were used for quality appraisal. Fishers exact test at the p-value threshold of 0.05 was used to compare the differences in methodological quality.\n\nResultsOf the 2,201 initially identified articles, 106 articles published from 1970 to 2018 were eligible for full-text review. Among included reviews, 50.9% were narrative reviews, 16% were systematic reviews and 33.1% were systematic reviews with meta-analyses. Twenty-nine percent were published in Ethiopia and 43.4% were published after 2015. 85.1% of narrative reviews poorly described the characteristics of included studies and 63.8% did not report a conflict of interest. In systematic reviews, 89.6%, 91.7%, and 100% did not register/publish the protocol, justifying the selection of the study designs for inclusion and report sources of funding for the primary studies respectively. Overall, 55.3% of narrative reviews and 75% of systematic reviews with or without meta-analysis had poor methodological quality.\n\nConclusionsAlthough publication rate of narrative and systematic reviews have risen in Ethiopia, half of the narrative reviews and three-quarters of the systematic reviews had poor methodological quality. We recommend authors to strictly follow standardized quality assessment tools during conducting reviews. Moreover, immediate interventions such as providing methodological training and employers, editors and peer-reviewers should carefully evaluate all reviews before submission or publication.\n\nWhat is new?O_ST_ABSKey findingsC_ST_ABSO_LIThe publication rate of narrative and systematic reviews have risen in Ethiopia.\nC_LIO_LIAlmost half of narrative reviews and three-fourths of systematic reviews with or without meta-analysis had poor scientific methodological quality.\nC_LI\n\nWhat this adds to what is knownO_LITo our knowledge, this is the first overview of its kind providing insight into the publication trend of narrative and systematic reviews, and their methodological rigor in Ethiopia.\nC_LI\n\nWhat is the implication, what should change nowO_LIOur review shows that the methodological quality of reviews in biomedical and public health discipline in Ethiopia is substantially low and urges immediate intervention.\nC_LIO_LIWe recommended authors to strictly follow standardized quality assessment tools during designing, conducting and reporting (systematic)reviews.\nC_LI

scientific communication and education↗

bioRxiv2018

Soil health pilot study in England: outcomes from an on-farm earthworm survey

Earthworms are primary candidates for national soil health monitoring as they are ecosystem engineers that benefit both food production and ecosystem services associated with soil security. Supporting farmers to monitor soil health could help to achieve the policy aspiration of sustainable soils by 2030 in England; however, little is known about how to overcome participation barriers, appropriate methodologies (practical, cost-effective, usefulness) or training needs. This paper presents the results from a pilot #60minworms study which mobilised farmers to assess over >1300 ha farmland soils in spring 2018. The results interpretation framework is based on the presence of earthworms from each of the three ecological groups at each observation (20cm3pit) and spatially across a field (10 soil pits). Results showed that most fields have basic earthworm biodiversity, but 42 % fields may be at risk of over-cultivation as indicated by absence/rarity of epigeic and/or anecic earthworms; and earthworm counting is not a reliable indicator of earthworm biodiversity. Tillage had a negative impact (p < 0.05) on earthworm populations and organic matter management did not mitigate tillage impacts. In terms of farmer participation, Twitter and Farmers Weekly magazine were highly effective channels for recruitment. Direct feedback from participants included excellent scores in trust, value and satisfaction of the protocol (e.g. 100 % would do the test again) and 57 % would use their worm survey results to change their soil management practices. A key training need in terms of earthworm identification skills was reported. The trade-off between data quality, participation rates and fieldwork costs suggests there is potential to streamline the protocol further to #30minuteworms (5 pits), incurring farmer fieldwork costs of approximately {pound}1.48 ha-1. At national scales, {pound}14 million pounds across 4.7 M ha-1 in fieldwork costs per survey could be saved by farmer participation.

scientific communication and education↗

bioRxiv2018

Relationships of trainee dentists’ empathy and communication characteristics with simulated patients’ assessment in medical interviews

ObjectivesWe aimed to clarify the characteristics of communication between trainee dentists and simulated patients (SPs) and to examine how the level of trainee dentists self-reported empathy influences assessment by SPs in medical interviews.\n\nMaterials and methodsThe study involved 100 trainee dentists at Okayama University Hospital and eight SPs. The trainee dentists conducted initial interviews with the SPs after completing the Japanese version of the Jefferson Scale of Empathy. Their interviews were recorded and analyzed using the Roter Interaction Analysis System. The SPs assessed the trainees communication immediately after each interview. The trainee dentists were classified into two groups (more positive and less positive groups) according to SP assessment scores.\n\nResultsCompared with the less positive trainees, the more positive trainees scored higher on the [Emotional expression] and lower on the [Medical data gathering] Roter Interaction Analysis System categories. There was no difference in [Dental data gathering] between the two groups. The SPs of more positive trainees had higher rates of [Positive talk] and [Emotional expression] and lower rates of [Medical information giving] and [Dental information giving]. The trainees with more positive ratings from SPs had significantly higher Jefferson Scale of Empathy total scores.\n\nConclusionThe results of this study suggest that responding to the SPs emotions is a relevant characteristic of dentist-SP communication to SPs positive assessment in medical interviews. Further, trainees self-reported empathy was related with the SPs assessment of trainees communication, which indicated that patient satisfaction can be improved by increasing the dentists empathy. Thus, an empathic attitude among dentists is a significant determinant of patient satisfaction.

scientific communication and education↗

bioRxiv2018

Taxonomic revision of Leopold and Rudolf Blaschka Glass Models of Invertebrates 1888 Catalogue, with correction of authorities

The glass models of invertebrates crafted by Leopold and Rudolf Blaschka were made between 1863 and 1889. Production ceased when the glassmakers turned their attention to what is now known as the Ware Collection of Blaschka Glass Models of Plants, created for the Harvard Museum of Natural History. Nearly 130 years have passed since their last published catalogue of species in 1888 and the nomenclature they applied is now a confusing mix that includes many junior synonyms and unavailable names. This is an issue for many museums and universities which owns Blaschka models as uncertain identifications may compromised interpretation of this rediscovered legacy. Nowadays, many museums and universities hold collections of those glass invertebrates but misspelled, mislabelled or simply apply the century old taxonomy of 1888. Here, we provide a valuable resource for curators and enthusiasts alike. We studied and updated the final catalogue 1888 from the Blaschkas Dresden-based workshop. We first focused on major taxonomical changes from taxa to species, as well as on an analysis of the acknowledged authorities. We found that only 35.3% of the models retain their original names, while 3.7% lack any known synonym and their identity remains open to interpretation. Finally, two of the authorities listed in the catalogue, Ernst Haeckel and Philip Henry Gosse, were incorrectly acknowledged for an extensive range of models. This study is the first of its kind on the Blaschka collection, and it will help in the identification and naming of Blaschka models worldwide.

scientific communication and education↗

bioRxiv2018

Involving patients and publics in medical and health care research studies: an exploratory survey on participant recruiting and representativeness from the perspective of study authors

Research on patient and public involvement so far concentrates on defining involvement, describing involvement methods, and analyzing involvement practice in various individual research disciplines. There is little empirical data on the process of and aims for selecting participants, and to what extend lay people involved in research can and should be representative of the population at large. To explore practices and perceptions on these issues and on future PPI conduct more generally, we sent an electronic survey to authors who published involvement activities as part of their studies in medical and social science journals. We identified such authors with a systematic search of five databases and applied descriptive statistics for analysis. Of those who returned the survey (n=127 of 315; 40%), most had previously conducted involvement activities (73%). 45% reported more than one type of involvement, e.g. consultation and deliberation and participation (14%) and to have recruited more than one type of participant for their PPI activity (56%), e.g. lay publics and expert publics (33% of 71). Representativeness was seen by most respondents as a crucial objective when recruiting participants, while less than half found the recruitment of suitable participants very easy (9%) or rather easy (34%). Many respondents found it generally difficult (52%) or very difficult (17%) to achieve good representativeness. They identified significant respective challenges and desired more guidance on various aspects of planning and conducting PPI (56%). 55% thought that the concept of \"involvement\" should be changed or improved. We conclude that participant recruitment and representativeness are controversial in current PPI practice given the manifold challenges mentioned by the survey respondents. Our findings may inform further research particularly regarding- the potentially large number of - unpublished PPI activities.

scientific communication and education↗

bioRxiv2018

The PCR Simulator: an on-line application for teaching Design of Experiments and the polymerase chain reaction

Our PCR Simulator is a web-based application designed to introduce concepts of multi-factorial experimental design and support teaching of the polymerase chain reaction. Learners select experimental settings and receive results of their simulated reactions quickly, allowing rapid iteration between data generation and analysis. This enables the student to perform complex iterative experimental design strategies within a short teaching session. Here we provide a short overview of the user interface and underpinning model, and describe our experience using this tool in a teaching environment.

scientific communication and education↗

bioRxiv2018

Evaluating FAIR-Compliance Through an Objective, Automated, Community-Governed Framework

With the increased adoption of the FAIR Principles, a wide range of stakeholders, from scientists to publishers, funding agencies and policy makers, are seeking ways to transparently evaluate resource FAIRness. We describe the FAIR Evaluator, a software infrastructure to register and execute tests of compliance with the recently published FAIR Metrics. The Evaluator enables digital resources to be assessed objectively and transparently. We illustrate its application to three widely used generalist repositories - Dataverse, Dryad, and Zenodo - and report their feedback. Evaluations allow communities to select relevant Metric subsets to deliver FAIRness measurements in diverse and specialized applications. Evaluations are executed in a semi-automated manner through Web Forms filled-in by a user, or through a JSON-based API. A comparison of manual vs automated evaluation reveals that automated evaluations are generally stricter, resulting in lower, though more accurate, FAIRness scores. Finally, we highlight the need for enhanced infrastructure such as standards registries, like FAIRsharing, as well as additional community involvement in domain-specific data infrastructure creation.

scientific communication and education↗

bioRxiv2018

Mind the Gap: Identifying What Is Missed When Searching Only the Broad Scope with PubMed Clinical Queries

ObjectivePubMed Clinical Queries are subdivided into \"Broad\" and \"Narrow\" versions. These versions are tuned to maximize either retrieval or sensitivity using two different sets of keywords and MeSH headings. While a searcher might assume that all items retrieved by Filter name/Narrow would also be found in the set Filter name/Broad, this is not explicitly guaranteed. It is the purpose of this study to quantify the overlap between these two sets and confirm whether Filter/Narrow is always a subset of Filter/Broad.\n\nMethodsFor each of the five PubMed Clinical Queries, PubMed was searched for citations matching the query Filter/Narrow NOT Filter/Broad. This number was compared with that for Filter/Broad to compute a \"degree of discordance\" between the two sets. This process was then repeated for the MeSH headings for \"Medicine\" and \"Diseases\" as well as for a set of test searches.\n\nResultsFour of the five Clinical Queries returned citations using Filter/Narrow that were not found with Filter/Broad. Discordances between the sets Broad and Narrow were generally modest for \"Etiology\", \"Diagnosis\" and \"Clinical prediction guides\". \"Prognosis\" was notably more discordant - a searcher could easily miss one Prognosis/Narrow citation for every ten citations she retrieves when using Prognosis/Broad alone for a given search.\n\nConclusionsUsers of the Clinical Queries apart from \"Therapy\" who are interested in retrieving as many relevant citations as possible should consider combining Filter/Narrow together with Filter/Broad in their search strategy. This is particularly true for \"Prognosis\", as otherwise the risk of missing relevant citations is substantial.

scientific communication and education↗

bioRxiv2018

Facilitating Patient and Public Involvement in basic and preclinical health research.

Involving patients in research broadens a researchers field of influence and may generate novel ideas. Preclinical research is integral to the progression of innovative healthcare. These are not patient-facing disciplines and implementing meaningful PPI can be a challenge. A discussion forum and thematic analysis identified key challenges of implementing PPI for preclinical researchers. In response we developed a \"PPI Ready\" planning canvas. For contemporaneous evaluation of PPI, a psychometric questionnaire and an open source tool for its evaluation were developed. The questionnaire measures information, procedural and quality assessment. Combined with the open source evaluation tool, researchers are notified if PPI is unsatisfactory in any of these areas. The tool is easy to use and adapts a psychometric test into a format familiar to preclinical scientists. Designed to be used iteratively across a research project, it provides a simple reporting grade to document satisfaction trend over the research lifecycle.

scientific communication and education↗

bioRxiv2018

A data-driven approach to reduce gender disparity in invited speaker programs at scientific meetings

We present a data-driven approach that uses established metrics of scientific quality to select invited speakers; this approach enables gender parity in conference programs while ensuring high scientific standards. Gender disparity continues to be an issue in STEM, with progress requiring consistent and focused efforts. Here, we present a data-driven approach to promote high quality, gender balanced invited speaker selection for neuroscience conferences. We have targeted invited speaker opportunities because underrepresentation of female speakers at international neuroscience conferences remains a major problem, and such opportunities are critical for career development. First, we audited the top ten neuroscience journals (indexed by SCImago Journal and Country Rank; SJR), identifying (1) highly cited papers, (2) gender of first and last authors, and (3) field-weighted citation impact and total publications of first and last authors. Second, we used these data to establish a database of high quality scientists that could be used to select speakers for conferences. We found that research quality (as indexed by field-weighted citation impact and total publications) of authors of highly cited publications in the top 10 neuroscience journals did not differ significantly for females and males. The comparison between the gender base rate in neuroscience and authors publishing highly cited papers in high-quality neuroscience journals shows that female representation, particularly at last author level, is less than the estimated base rate for neuroscience. In summary, we present a data-driven approach to invited speaker selection that would facilitate gender balanced conference programs while maintaining the highest of scientific standards. This approach minimizes the influence of implicit gender bias in speaker selection decisions by using scientific quality metrics that STEM researchers are familiar with, and indeed use to evaluate their own performance. Having an immediate effect on reducing gender disparity in conference programs, our approach would generate a positive spiral for more long-term reduction of gender disparity in STEM.

scientific communication and education↗

bioRxiv2018

PlotsOfData - a web app for visualizing data together with its summaries

Reporting of the actual data in graphs and plots increases transparency and enables independent evaluation. On the other hand, data summaries are often used in graphs since they aid interpretation. State-of-the art data visualizations can be made with the ggplot2 package, which uses the ideas of a grammar of graphics to generate a graphic from multiple layers of data. However, ggplot2 requires coding skills and an understanding of the tidy data structure. To democratize state-of-the-art data visualization of raw data with a selection of statistical summaries, a web app was written using R/shiny that uses the ggplot2 package for generating plots. A multilayered approach together with adjustable transparency offers a unique flexibility, enabling users can to choose how to display the data and which of the data summaries to add. Four data summaries are provided, mean, median, boxplot, violinplot, to accommodate several types of data distributions. In addition, 95% confidence intervals can be added for visual inferences. By adjusting the transparency of the layers, the visualization of the raw data together with the summary can be tuned for optimal presentation and interpretation. The app is dubbed PlotsOfData and is available at: https://huygens.science.uva.nl/PlotsOfData/\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/426767v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (21K):\norg.highwire.dtl.DTLVardef@1f8a09eorg.highwire.dtl.DTLVardef@1f8feb3org.highwire.dtl.DTLVardef@19b781org.highwire.dtl.DTLVardef@5e7b55_HPS_FORMAT_FIGEXP M_FIG C_FIG

scientific communication and education↗

bioRxiv2018

Adherence to the iDSI reference case among published cost-per-DALY averted studies

BackgroundThe iDSI reference case, originally published in 2014, aims to improve the quality and comparability of cost-effectiveness analyses (CEAs). This study assesses whether the development of the guideline has improved the reporting and methodology for CEAs using disability-adjusted life-years (DALYs).\n\nMethodsWe analyzed the Tufts Medical Center Global Health CEA Registry to identify cost-per-DALY averted studies published from 2011 to 2017. Among each of 11 principles in the iDSI reference case, we translated all reporting standards and methodological specifications into quantifiable yes/no questions and awarded articles one point for each item satisfied. We then separately calculated reporting and methods scores, measured as percent adherence (0%=no adherence, 100%=full adherence). Using the year 2014 as the dissemination period, we conducted a pre-post analysis. Additionally, we conducted an analysis stratified by the 11 principles and examined different scoring strategies and dissemination periods in sensitivity analyses.\n\nResultsArticles averaged 74% adherence to reporting standards and 60% adherence to methodological specifications. Adherence to reporting standards increased slightly over time (72% pre-2014 vs. 75% post-2014, p<0.01), but methodological adherence did not significantly improve (59% pre-2014 vs. 60% post-2014, p=0.53). Overall, reporting adherence scores exceeded methodology adherence scores (74% vs. 60%, p<0.001). Articles seldom addressed budget impact (9% reporting, 10% methodology) or equity (7% reporting, 7% methodology).\n\nConclusionsThe iDSI reference case has substantial potential to serve as a useful resource for researchers and policy-makers in global health settings, but greater effort to promote adherence and awareness is needed to achieve its potential.

scientific communication and education↗

bioRxiv2018

Risk Factors Associated with Dengue Virus Infection in Guangdong Province: a Community-based Case-control Study

BackgroundDengue fever is a mosquito-borne infectious disease, and it is now still epidemic in China, especially in Guangdong Province. Owing to the absence of dengue vaccination, effective preventive measure is critical for controlling of dengue fever. This study aimed to explore the individual risk factors of dengue virus infection in Guangdong Province, as well as to provide a scientific basis for prevention and supervision of dengue fever in future.\n\nMethodsA case-control study including 237 cases and 237 controls was performed. The data was collected from the epidemiological questionnaires. Univariate analysis was used for preliminary screening of 28 variables potentially related to dengue virus infection, and an unconditioned logistic regression analysis was used for multivariate analysis to analysis those statistically significant variables.\n\nResultsMultivariate analysis of the result showed three independent risk factors: activities in the park (odd ratio [OR]= 1.70, 95%CI 1.03 to 2.83), outdoor sports (OR= 1.67, 95%CI 1.07 to 2.62), and poor indoor daylight quality (OR= 2.27, 95%CI 1.00 to 5.15); and two protective factors: two persons per room (OR=0.43, 95%CI 0.28 to 0.67), three persons and above per room (OR=0.43, 95%CI 0.22 to 0.86), using air-condition (OR=0.43, 95%CI 0.20 to 0.93).\n\nConclusionThese results are conducive to learn the risk factors for dengue virus infection in Guangdong Province. It is crucial to provide effective and efficient strategy to improve environmental protection and anti-mosquito measures. In addition, more systematic studies are needed to explore the other potential risk factors for dengue fever infection.\n\nAuthor summaryDengue fever, one of the mosquito-borne infectious diseases, is mainly transmitted by Aedes aegypti in Asia and Southeast Asia countries. Since 1978, the incidence of dengue fever has markedly increased in China especially in Guangdong province. In order to formulate the effective prevention and control measures, we explored the risk factors of dengue virus infection in Guangdong Province by conducting a case-control study. In this study, 237 patients with dengue virus infection and 237 participants without dengue virus infection were included. Then through these questionnaires and data analysis, we found that activities in the park, outdoor sports, and poor indoor daylight quality significantly contributed to the residents risk of dengue virus infection. On the other hand, we observed that using air-condition and using anti-mosquito measures were effective personal prevention interventions.

scientific communication and education↗