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Peer review is the gold standard for scientific communication, but its ability to guarantee the quality of published research remains difficult to verify. Recent modeling studies suggest that peer review is sensitive to reviewer misbehavior, and it has been claimed that referees who sabotage work they perceive as competition may severely undermine the quality of publications. Here we examine which aspects of suboptimal reviewing practices most strongly impact quality, and test different mitigating strategies that editors may employ to counter them. We find that the biggest hazard to the quality of published literature is not selfish rejection of high-quality manuscripts but indifferent acceptance of low-quality ones. Bypassing or blacklisting bad reviewers and consulting additional reviewers to settle disagreements can reduce but not eliminate the impact. The other editorial strategies we tested do not significantly improve quality, but pairing manuscripts to reviewers unlikely to selfishly reject them and allowing revision of rejected manuscripts minimize rejection of above-average manuscripts. In its current form, peer review offers few incentives for impartial reviewing efforts. Editors can help, but structural changes are more likely to have a stronger impact. [ABSTRACT FROM AUTHOR]

This paper introduces a bibliometric, citation network-based method for assessing the social validation of novel research, and applies this method to the development of high-throughput toxicology research at the US Environmental Protection Agency. Social validation refers to the acceptance of novel research methods by a relevant scientific community; it is formally independent of the technical validation of methods, and is frequently studied in history, philosophy, and social studies of science using qualitative methods. The quantitative methods introduced here find that high-throughput toxicology methods are spread throughout a large and well-connected research community, which suggests high social validation. Further assessment of social validation involving mixed qualitative and quantitative methods are discussed in the conclusion. [ABSTRACT FROM AUTHOR]

Background: Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with—and potential exchange of—microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills. Results: Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency. Conclusions: We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes. [ABSTRACT FROM AUTHOR]

Background: Based on single cross-sectional data, prior research finds evidence of “transportation assimilation” among U.S. immigrants: the length of stay in the U.S. is negatively correlated with public transit use. This paper revisits this question by using repeated cross-sectional data, and examines the trend of transportation assimilation over time. Methods and results: Using 1980, 1990, 2000 1% census and 2010 (1%) American Community Survey, I examine the relationship between the length of stay in the U.S. and public transit ridership among immigrants. I first run regressions separately in four data sets: I regress public transit ridership on the length of stay, controlling for other individual and geographic variables. I then compare the magnitudes of the relationship in four regressions. To study how the rate of transportation assimilation changes over time, I pool the data set and regress public transit ridership on the length of stay and its interactions with year dummies to compare the coefficients across surveys. Results confirm the conclusion of transportation assimilation: as the length of stay in the U.S. increases, an immigrant’s public transit use decreases. However, the repeated cross-section analysis suggests the assimilation rate has been decreasing in the past few decades. Conclusions: This paper finds evidence of transportation assimilation: immigrants become less likely to ride public transit as the length of stay in the U.S. increases. The assimilation rate, however, has been decreasing over time. This paper finds that the rate of public transit ridership among new immigrants upon arrival, the geographic distribution of immigrants, and the changing demographics of the U.S. immigrants play roles in affecting the trend of transportation assimilation. [ABSTRACT FROM AUTHOR]

Visual design, learning sciences, and nanotechnology may be strange bedfellows; yet, as this paper highlights, peer interaction between a designer and a scientist is an effective method for helping scientists acquire visual design skills. We describe our findings from observing twelve sessions at the Design Help Desk, a tutoring center at the University of Washington. At each session, a scientist (who is expert in his own domain but a novice in design) consulted a designer (who is expert in design but a novice in science) in order to receive advice and guidance on how to improve a scientific visualization. At the Design Help Desk, this pairing consistently produced a momentary disequilibrium in the scientist’s thought process: a disequilibrium that led to agency (where the scientist gained ownership of his/her own learning) and conceptual change in the scientist’s understanding of visual design. Scientists who visited the Design Help Desk were satisfied with their experience, and their published work demonstrated an improved ability to visually communicate research findings—a skill critical to the advancement of science. To our knowledge, the Design Help Desk is a unique effort to educate scientists in visual design; we are not aware of any other design-advice/tutoring centers at public or private universities in the United States or abroad. [ABSTRACT FROM AUTHOR]

Although substantial attention has focused on efforts by the new Administration to block environmental policies, climate politics have been contentious in the US since well before the election of Donald Trump. In this paper, we extend previous work on empirical examinations of echo chambers in US climate politics using new data collected on the federal climate policy network in summer 2016. We test for the similarity and differences at two points in time in homophily and echo chambers using Exponential Random Graph Models (ERGM) to compare new findings from 2016 to previous work on data from 2010. We show that echo chambers continue to play a significant role in the network of information exchange among policy elites working on the issue of climate change. In contrast to previous findings where echo chambers centered on a binding international commitment to emission reductions, we find that the pre-existing echo chambers have almost completely disappeared and new structures have formed around one of the main components of the Obama Administration’s national climate policy: the Clean Power Plan. These results provide empirical evidence that science communication and policymaking at the elite level shift in relation to the policy instruments under consideration. [ABSTRACT FROM AUTHOR]

Encouraging knowledge flow between mutually relevant disciplines is a worthy aim of research policy makers. Yet, it is less clear what types of research promote cross-disciplinary knowledge flow and whether such research generates particularly influential knowledge. Empirical questions remain as to how to identify knowledge-flow mediating research and how to provide support for this research. This study contributes to addressing these gaps by proposing a new way to identify knowledge-flow mediating research at the individual research article level, instead of at more aggregated levels. We identify journal articles that link two mutually relevant disciplines in three ways—aggregating, bridging, and diffusing. We then examine the likelihood that these papers receive subsequent citations or have funding acknowledgments. Our case study of cognitive science and educational research knowledge flow suggests that articles that aggregate knowledge from multiple disciplines are cited significantly more often than are those whose references are drawn primarily from a single discipline. Interestingly, the articles that meet the criteria for being considered knowledge-flow mediators are less likely to reflect funding, based on reported acknowledgements, than were those that did not meet these criteria. Based on these findings, we draw implications for research policymakers. [ABSTRACT FROM AUTHOR]

While basic access to clean water is critical, another important issue is the affordability of water access for people around the globe. Prior international work has highlighted that a large proportion of consumers could not afford water if priced at full cost recovery levels. Given growing concern about affordability issues due to rising water rates, and a comparative lack of work on affordability in the developed world, as compared to the developing world, more work is needed in developed countries to understand the extent of this issue in terms of the number of households and persons impacted. To address this need, this paper assesses potential affordability issues for households in the United States using the U.S. EPA’s 4.5% affordability criteria for combined water and wastewater services. Analytical results from this paper highlight high-risk and at-risk households for water poverty or unaffordable water services. Many of these households are clustered in pockets of water poverty within counties, which is a concern for individual utility providers servicing a large proportion of customers with a financial inability to pay for water services. Results also highlight that while water rates remain comparatively affordable for many U.S. households, this trend will not continue in the future. If water rates rise at projected amounts over the next five years, conservative projections estimate that the percentage of U.S. households who will find water bills unaffordable could triple from 11.9% to 35.6%. This is a concern due to the cascading economic impacts associated with widespread affordability issues; these issues mean that utility providers could have fewer customers over which to spread the large fixed costs of water service. Unaffordable water bills also impact customers for whom water services are affordable via higher water rates to recover the costs of services that go unpaid by lower income households. [ABSTRACT FROM AUTHOR]

Lung cancer, primarily non-small-cell lung cancer (NSCLC), is the leading cause of cancer deaths in the United States and worldwide. While early detection significantly improves five-year survival, there are no reliable diagnostic tools for early detection. Several exosomal microRNAs (miRs) are overexpressed in NSCLC, and have been suggested as potential biomarkers for early detection. The present paper develops a mathematical model for early stage of NSCLC with emphasis on the role of the three highest overexpressed miRs, namely miR-21, miR-205 and miR-155. Simulations of the model provide quantitative relationships between the tumor volume and the total mass of each of the above miRs in the tumor. Because of the positive correlation between these miRs in the tumor tissue and in the blood, the results of the paper may be viewed as a first step toward establishing a combination of miRs 21, 205, 155 and possibly other miRs as serum biomarkers for early detection of NSCLC. [ABSTRACT FROM AUTHOR]

Background: There have been growing recommendations to include education in multi-disciplinary interventions targeting chronic pain management. However, effects of this strategy on short- and long-term self-management of chronic pain, remain largely unexplored. Objectives: 1. To provide an updated overview of studies that report on the impact of patient education in multi-disciplinary interventions, on self-management of chronic pain; 2. To explore associations between education and chronic pain self-management techniques; and 3. To identify the format and duration of suitable chronic pain interventions targeted at patient self-management. Methods: Design: Narrative systematic literature review of randomised or controlled study designs. Data Sources: PubMed, CINAHL, EMBASE, PsycINFO. Participants: Adult patients with chronic pain of any aetiology participating in multi-disciplinary programs that included education. Main outcome measures: Assessments of level of pain, function, quality of life, self-efficacy, self-management, and any other relevant assessments. Study Appraisal and Synthesis Methods: PRISMA guidelines, Cochrane Risk of Bias tool, and TIDieR model. Results: Database searching identified 485 potential papers. After removal of duplicates, and irrelevant articles by title and abstract, 120 full-text articles were reviewed and 27 studies were included in this systematic review. Studies were predominantly from the United States (n = 8; 29.6%). Over one hundred outcome measures were identified across all studies, with significant variation also observed in terms of how chronic pain duration was defined, and how education was delivered to participants. Overall, positive benefits of education were reported. Conclusions: Education, as part of multi-disciplinary programs, is likely to improve self-management and self-efficacy in people with chronic pain of any aetiology. Heterogeneity in terms of: chronic pain duration; educational resources; healthcare professionals; and outcome measures, were identified as limitations. Further research, in the form of Randomised Controlled Trials addressing these limitations, is recommended. [ABSTRACT FROM AUTHOR]

BACKGROUND: The assessment of bone age and skeletal maturity and its comparison to chronological age is an important task in the medical environment for the diagnosis of pediatric endocrinology, orthodontics and orthopedic disorders, and legal environment in what concerns if an individual is a minor or not when there is a lack of documents. Being a time-consuming activity that can be prone to inter- and intra-rater variability, the use of methods which can automate it, like Machine Learning techniques, is of value. OBJECTIVE: The goal of this paper is to present the state of the art evidence, trends and gaps in the research related to bone age assessment studies that make use of Machine Learning techniques. METHOD: A systematic literature review was carried out, starting with the writing of the protocol, followed by searches on three databases: Pubmed, Scopus and Web of Science to identify the relevant evidence related to bone age assessment using Machine Learning techniques. One round of backward snowballing was performed to find additional studies. A quality assessment was performed on the selected studies to check for bias and low quality studies, which were removed. Data was extracted from the included studies to build summary tables. Lastly, a meta-analysis was performed on the performances of the selected studies. RESULTS: 26 studies constituted the final set of included studies. Most of them proposed automatic systems for bone age assessment and investigated methods for bone age assessment based on hand and wrist radiographs. The samples used in the studies were mostly comprehensive or bordered the age of 18, and the data origin was in most of cases from United States and West Europe. Few studies explored ethnic differences. CONCLUSIONS: There is a clear focus of the research on bone age assessment methods based on radiographs whilst other types of medical imaging without radiation exposure (e.g. magnetic resonance imaging) are not much explored in the literature. Also, socioeconomic and other aspects that could influence in bone age were not addressed in the literature. Finally, studies that make use of more than one region of interest for bone age assessment are scarce. [ABSTRACT FROM AUTHOR]

This paper calculates the distribution of an adjusted measure of income that deducts damages due to exposure to air pollution from reported market income in the United States from 2011 to 2014. The Gini coefficient for this measure of adjusted income is 0.682 in 2011, as compared to 0.482 for market income. By 2014, we estimate that the Gini for adjusted income fell to 0.646, while the market income Gini did not appreciably change. The inclusion of air pollution damage acts like a regressive tax: with air pollution, the bottom 20% of households lose roughly 10% of the share of income, while the top 20% of households gain 10%. We find that, unlike the case for market income, New England is not the most unequal division with respect to adjusted income. Further, the difference between adjusted income for white and Hispanics is smaller than expected. However, the gap in augmented income between whites and African-Americans is widening. [ABSTRACT FROM AUTHOR]

Introduction: Concerns about reproducibility and impact of research urge improvement initiatives. Current university ranking systems evaluate and compare universities on measures of academic and research performance. Although often useful for marketing purposes, the value of ranking systems when examining quality and outcomes is unclear. The purpose of this study was to evaluate usefulness of ranking systems and identify opportunities to support research quality and performance improvement. Methods: A systematic review of university ranking systems was conducted to investigate research performance and academic quality measures. Eligibility requirements included: inclusion of at least 100 doctoral granting institutions, be currently produced on an ongoing basis and include both global and US universities, publish rank calculation methodology in English and independently calculate ranks. Ranking systems must also include some measures of research outcomes. Indicators were abstracted and contrasted with basic quality improvement requirements. Exploration of aggregation methods, validity of research and academic quality indicators, and suitability for quality improvement within ranking systems were also conducted. Results: A total of 24 ranking systems were identified and 13 eligible ranking systems were evaluated. Six of the 13 rankings are 100% focused on research performance. For those reporting weighting, 76% of the total ranks are attributed to research indicators, with 24% attributed to academic or teaching quality. Seven systems rely on reputation surveys and/or faculty and alumni awards. Rankings influence academic choice yet research performance measures are the most weighted indicators. There are no generally accepted academic quality indicators in ranking systems. Discussion: No single ranking system provides a comprehensive evaluation of research and academic quality. Utilizing a combined approach of the Leiden, Thomson Reuters Most Innovative Universities, and the SCImago ranking systems may provide institutions with a more effective feedback for research improvement. Rankings which extensively rely on subjective reputation and “luxury” indicators, such as award winning faculty or alumni who are high ranking executives, are not well suited for academic or research performance improvement initiatives. Future efforts should better explore measurement of the university research performance through comprehensive and standardized indicators. This paper could serve as a general literature citation when one or more of university ranking systems are used in efforts to improve academic prominence and research performance. [ABSTRACT FROM AUTHOR]

Objectives: As gentrification continues in New York City as well as other urban areas, residents of lower socioeconomic status maybe at higher risk for residential displacement. Yet, there have been few quantitative assessments of the health impacts of displacement. The objective of this paper is to assess the association between displacement and healthcare access and mental health among the original residents of gentrifying neighborhoods in New York City. Methods: We used 2 data sources: 1) 2005–2014 American Community Surveys to identify gentrifying neighborhoods in New York City, and 2) 2006–2014 Statewide Planning and Research Cooperative System. Our cohort included 12,882 residents of gentrifying neighborhoods in 2006 who had records of emergency department visits or hospitalization at least once every 2 years in 2006–2014. Rates of emergency department visits and hospitalizations post-baseline were compared between residents who were displaced and those who remained. Results: During 2006–2014, 23% were displaced. Compared with those who remained, displaced residents were more likely to make emergency department visits and experience hospitalizations, mainly due to mental health (Rate Ratio = 1.8, 95% confidence interval = 1.5, 2.2), after controlling for baseline demographics, health status, healthcare utilization, residential movement, and the neighborhood of residence in 2006. Conclusions: These findings suggest negative impacts of displacement on healthcare access and mental health, particularly among adults living in urban areas and with a history of frequent emergency department visits or hospitalizations. [ABSTRACT FROM AUTHOR]

The social functions of urbanized areas are highly dependent on and supported by the convenient access to public transportation systems, particularly for the less privileged populations who have restrained auto ownership. To accurately evaluate the public transit accessibility, it is critical to capture the spatiotemporal variation of transit services. This can be achieved by measuring the shortest paths or minimum travel time between origin-destination (OD) pairs at each time-of-day (e.g. every minute). In recent years, General Transit Feed Specification (GTFS) data has been gaining popularity for between-station travel time estimation due to its interoperability in spatiotemporal analytics. Many software packages, such as ArcGIS, have developed toolbox to enable the travel time estimation with GTFS. They perform reasonably well in calculating travel time between OD pairs for a specific time-of-day (e.g. 8:00 AM), yet can become computational inefficient and unpractical with the increase of data dimensions (e.g. all times-of-day and large network). In this paper, we introduce a new algorithm that is computationally elegant and mathematically efficient to address this issue. An open-source toolbox written in C++ is developed to implement the algorithm. We implemented the algorithm on City of St. George’s transit network to showcase the accessibility analysis enabled by the toolbox. The experimental evidence shows significant reduction on computational time. The proposed algorithm and toolbox presented is easily transferable to other transit networks to allow transit agencies and researchers perform high resolution transit performance analysis. [ABSTRACT FROM AUTHOR]

This paper forecasts the 2016 canine Anaplasma spp. seroprevalence in the United States from eight climate, geographic and societal factors. The forecast’s construction and an assessment of its performance are described. The forecast is based on a spatial-temporal conditional autoregressive model fitted to over 11 million Anaplasma spp. seroprevalence test results for dogs conducted in the 48 contiguous United States during 2011–2015. The forecast uses county-level data on eight predictive factors, including annual temperature, precipitation, relative humidity, county elevation, forestation coverage, surface water coverage, population density and median household income. Non-static factors are extrapolated into the forthcoming year with various statistical methods. The fitted model and factor extrapolations are used to estimate next year’s regional prevalence. The correlation between the observed and model-estimated county-by-county Anaplasma spp. seroprevalence for the five-year period 2011–2015 is 0.902, demonstrating reasonable model accuracy. The weighted correlation (accounting for different sample sizes) between 2015 observed and forecasted county-by-county Anaplasma spp. seroprevalence is 0.987, exhibiting that the proposed approach can be used to accurately forecast Anaplasma spp. seroprevalence. The forecast presented herein can a priori alert veterinarians to areas expected to see Anaplasma spp. seroprevalence beyond the accepted endemic range. The proposed methods may prove useful for forecasting other diseases. [ABSTRACT FROM AUTHOR]

Many US biomedical PhD programs receive more applications for admissions than they can accept each year, necessitating a selective admissions process. Typical selection criteria include standardized test scores, undergraduate grade point average, letters of recommendation, a resume and/or personal statement highlighting relevant research or professional experience, and feedback from interviews with training faculty. Admissions decisions are often founded on assumptions that these application components correlate with research success in graduate school, but these assumptions have not been rigorously tested. We sought to determine if any application components were predictive of student productivity measured by first-author student publications and time to degree completion. We collected productivity metrics for graduate students who entered the umbrella first-year biomedical PhD program at the University of North Carolina at Chapel Hill from 2008–2010 and analyzed components of their admissions applications. We found no correlations of test scores, grades, amount of previous research experience, or faculty interview ratings with high or low productivity among those applicants who were admitted and chose to matriculate at UNC. In contrast, ratings from recommendation letter writers were significantly stronger for students who published multiple first-author papers in graduate school than for those who published no first-author papers during the same timeframe. We conclude that the most commonly used standardized test (the general GRE) is a particularly ineffective predictive tool, but that qualitative assessments by previous mentors are more likely to identify students who will succeed in biomedical graduate research. Based on these results, we conclude that admissions committees should avoid over-reliance on any single component of the application and de-emphasize metrics that are minimally predictive of student productivity. We recommend continual tracking of desired training outcomes combined with retrospective analysis of admissions practices to guide both application requirements and holistic application review. [ABSTRACT FROM AUTHOR]

How did post-socialist transition and a parallel shift in international labor division restructure regional innovation systems in Central and Eastern Europe? This question is increasingly important, because current EU innovation policy is combined with regional development in Smart Specialization Strategies; however, spatial trends of innovation in Central and Eastern Europe are not fully understood which might lead to less than perfectly efficient policy. In this paper we describe the spatial dynamics of inventor activity in the Czech Republic, Hungary, Poland and Slovakia between 1981 and 2010 –a period that covers both the late socialist era and the post-socialist transition. Cleaning and analyzing the publicly available data from the United States Patent and Trademark Office we illustrate that Central and Eastern European patents made in international co-operations with partners outside the region receive more citations than those Central and Eastern European patents that lack international co-operation. Furthermore, the technological portfolio of the former patents has become increasingly independent from the technological portfolio of the latter class. A town-level analysis of the applicant-inventor ties reveals that inventors have started to work for foreign assignees in those towns where no innovation activity had been recorded before. However, the positive effect does not last long and patenting seems to be only periodic in the majority of these towns. Therefore, innovation policy in Central and Eastern European countries, as well as in other less developed regions, shall foster synergies between international and domestic collaborations in order to decrease regional disparities in patenting. [ABSTRACT FROM AUTHOR]

Background: Policies designed to restrict marketing, access to, and public use of electronic cigarettes (e-cigarettes) are increasingly under debate in various jurisdictions in the US. Little is known about public perceptions of these policies and factors that predict their support or opposition. Methods: Using a sample of US adults from Amazon Mechanical Turk in May 2015, this paper identifies beliefs about the benefits and costs of regulating e-cigarettes and identifies which of these beliefs predict support for e-cigarette restricting policies. Results: A higher proportion of respondents agreed with 8 different reasons to regulate e-cigarettes (48.5% to 83.3% agreement) versus 7 reasons not to regulate e-cigarettes (11.5% to 18.9%). The majority of participants agreed with 7 out of 8 reasons for regulation. When all reasons to regulate or not were included in a final multivariable model, beliefs about protecting people from secondhand vapor and protecting youth from trying e-cigarettes significantly predicted stronger support for e-cigarette restricting policies, whereas concern about government intrusion into individual choices was associated with reduced support. Discussion: This research identifies key beliefs that may underlie public support or opposition to policies designed to regulate the marketing and use of e-cigarettes. Advocates on both sides of the issue may find this research valuable in developing strategic campaigns related to the issue. Implications: Specific beliefs of potential benefits and costs of e-cigarette regulation (protecting youth, preventing exposure to secondhand vapor, and government intrusion into individual choices) may be effectively deployed by policy makers or health advocates in communicating with the public. [ABSTRACT FROM AUTHOR]

The goal of this paper is to estimate peer influence in video gaming time among adolescents. Using a nationally representative sample of the U.S. school-aged adolescents in 2009–2010, we estimate a structural model that accounts for the potential biases in the estimate of the peer effect. Our peer group is exogenously assigned and includes one year older adolescents in the same school grade as the respondent. The peer measure is based on peers’ own reports of video gaming time. We find that an additional one hour of playing video games per week by older grade-mates results in .47 hours increase in video gaming time by male responders. We do not find significant peer effect among female responders. Effective policies aimed at influencing the time that adolescents spend video gaming should take these findings into account. [ABSTRACT FROM AUTHOR]

The spatial distribution of income shapes the structure and organisation of cities and its understanding has broad societal implications. Despite an abundant literature, many issues remain unclear. In particular, all definitions of segregation are implicitely tied to a single indicator, usually rely on an ambiguous definition of income classes, without any consensus on how to define neighbourhoods and to deal with the polycentric organization of large cities. In this paper, we address all these questions within a unique conceptual framework. We avoid the challenge of providing a direct definition of segregation and instead start from a definition of what segregation is not. This naturally leads to the measure of representation that is able to identify locations where categories are over- or underrepresented. From there, we provide a new measure of exposure that discriminates between situations where categories co-locate or repel one another. We then use this feature to provide an unambiguous, parameter-free method to find meaningful breaks in the income distribution, thus defining classes. Applied to the 2014 American Community Survey, we find 3 emerging classes—low, middle and higher income—out of the original 16 income categories. The higher-income households are proportionally more present in larger cities, while lower-income households are not, invalidating the idea of an increased social polarisation. Finally, using the density—and not the distance to a center which is meaningless in polycentric cities—we find that the richer class is overrepresented in high density zones, especially for larger cities. This suggests that density is a relevant factor for understanding the income structure of cities and might explain some of the differences observed between US and European cities. [ABSTRACT FROM AUTHOR]

A common policy approach to reducing childhood obesity aims to shape the environment in which children spend most of their time: neighborhoods and schools. This paper uses richly detailed data on the body mass index (BMI) of all New York City public school students in grades K-8 to assess the potential for place-based approaches to reduce child obesity. We document variation in the prevalence of obesity across NYC public schools and census tracts, and then estimate the extent to which this variation can be explained by differences in individual-level predictors (such as race and household income). Both unadjusted and adjusted variability across neighborhoods and schools suggest place-based policies have the potential to meaningfully reduce child obesity, but under most realistic scenarios the improvement would be modest. [ABSTRACT FROM AUTHOR]

The “fetal origins” hypothesis suggests that fetal conditions not only affect birth characteristics such as birth weight and gestational age, but also have lifelong health implications. Despite widespread interest in this hypothesis, few methodological advances have been proposed to improve the measurement and modeling of fetal conditions. A Statistics in Medicine paper by Bollen, Noble, and Adair examined favorable fetal growth conditions (FFGC) as a latent variable. Their study of Filipino children from Cebu provided evidence consistent with treating FFGC as a latent variable that largely mediates the effects of mother’s characteristics on birth weight, birth length, and gestational age. This innovative method may have widespread utility, but only if the model applies equally well across diverse settings. Our study assesses whether the FFGC model of Cebu replicates and generalizes to a very different population of children from North Carolina (N = 705) and Pennsylvania (N = 494). Using a series of structural equation models, we find that key features of the Cebu analysis replicate and generalize while we also highlight differences between these studies. Our results support treating fetal conditions as a latent variable when researchers test the fetal origins hypothesis. In addition to contributing to the substantive literature on measuring fetal conditions, we also discuss the meaning and challenges involved in replicating prior research. [ABSTRACT FROM AUTHOR]

A survey in the United States revealed that an alarmingly large percentage of university psychologists admitted having used questionable research practices that can contaminate the research literature with false positive and biased findings. We conducted a replication of this study among Italian research psychologists to investigate whether these findings generalize to other countries. All the original materials were translated into Italian, and members of the Italian Association of Psychology were invited to participate via an online survey. The percentages of Italian psychologists who admitted to having used ten questionable research practices were similar to the results obtained in the United States although there were small but significant differences in self-admission rates for some QRPs. Nearly all researchers (88%) admitted using at least one of the practices, and researchers generally considered a practice possibly defensible if they admitted using it, but Italian researchers were much less likely than US researchers to consider a practice defensible. Participants’ estimates of the percentage of researchers who have used these practices were greater than the self-admission rates, and participants estimated that researchers would be unlikely to admit it. In written responses, participants argued that some of these practices are not questionable and they have used some practices because reviewers and journals demand it. The similarity of results obtained in the United States, this study, and a related study conducted in Germany suggest that adoption of these practices is an international phenomenon and is likely due to systemic features of the international research and publication processes. [ABSTRACT FROM AUTHOR]

In this study, university-industry collaborations in China and the USA are analyzed in terms of co-authored publications indexed in the Web of Science (WoS). Results show a wide gap between China and the USA: Chinese universities are much less active in collaborations with industry in terms of either publication productivity or collaboration intensity. In selecting local and foreign industrial partners, however, more variation exists among Chinese universities than among US universities. The US system is domestically oriented more than that of China. In the USA, the intensity of university-industry collaboration is determined by research quality, whereas in China this is not the case. In both China and the USA, distance is not critical for the establishment of domestic university-industry collaboration. A high correlation is found between productivity indicators including total publications and university-industry co-authored publications. However, the productivity indicators are less correlated with the intensity of university-industry collaboration. Large research universities with strong ties to domestic industry play critical roles in both national publication systems. [ABSTRACT FROM AUTHOR]

There is strong epidemiological evidence that poor diet is associated with depression. The reverse has also been shown, namely that eating a healthy diet rich in fruit, vegetables, fish and lean meat, is associated with reduced risk of depression. To date, only one randomised controlled trial (RCT) has been conducted with elevated depression symptoms being an inclusion criterion, with results showing that a diet intervention can reduce clinical levels of depression. No such RCTs have been performed in young adults. Young adults with elevated levels of depression symptoms and who habitually consume a poor diet were randomly allocated to a brief 3-week diet intervention (Diet Group) or a habitual diet control group (Control Group). The primary and secondary outcome measures assessed at baseline and after the intervention included symptoms of depression (Centre for Epidemiological Studies Depression Scale; CESD-R; and Depression Anxiety and Stress Scale– 21 depression subscale; DASS-21-D), current mood (Profile of Mood States), self-efficacy (New General Self-Efficacy Scale) and memory (Hopkins Verbal Learning Test). Diet compliance was measured via self-report questionnaires and spectrophotometry. One-hundred-and-one individuals were enrolled in the study and randomly assigned to the Diet Group or the Control Group. Upon completion of the study, there was complete data for 38 individuals in each group. There was good compliance with the diet intervention recommendations assessed using self-report and spectrophotometry. The Diet group had significantly lower self-reported depression symptoms than the Control Group on the CESD-R (p = 0.007, Cohen’s d = 0.65) and DASS-21 depression subscale (p = 0.002, Cohen’s d = 0.75) controlling for baseline scores on these scales. Reduced DASS-21 depression subscale scores were maintained on follow up phone call 3 months later (p = .009). These results are the first to show that young adults with elevated depression symptoms can engage in and adhere to a diet intervention, and that this can reduce symptoms of depression. The findings provide justification for future research into the duration of these benefits, the impacts of varying diet composition, and their biological basis. [ABSTRACT FROM AUTHOR]

Context: An estimated 21% of non-U.S.-born persons in the United States have a reactive tuberculin skin test (TST) and are at risk of progressing to TB disease. The effectiveness of strategies by healthcare facilities to improve targeted TB infection testing and linkage to care among this population is unclear. Evidence acquisition: Following Cochrane guidelines, we searched several sources to identify studies that assessed strategies directed at healthcare providers and/or non-U.S.–born patients in U.S. healthcare facilities. Evidence synthesis: Seven studies were eligible. In a randomized controlled trial (RCT), patients with reactive TST who received reminders for follow-up appointments were more likely to attend appointments (risk ratio, RR = 1.05, 95% confidence interval 1.00–1.10), but rates of return in a quasi-RCT study using patient reminders did not significantly differ between study arms (P = 0.520). Patient-provider language concordance in a retrospective cohort study did not increase provider referrals for testing (P = 0.121) or patient testing uptake (P = 0.159). Of three studies evaluating pre and post multifaceted interventions, two increased TB infection testing (from 0% to 77%, p < .001 and RR 2.28, 1.08–4.80) and one increased provider referrals for TST (RR 24.6, 3.5–174). In another pre-post study, electronic reminders to providers increased reading of TSTs (RR 2.84, 1.53–5.25), but only to 25%. All seven studies were at high risk of bias. Conclusions: Multifaceted strategies targeting providers may improve targeted TB infection testing in non-U.S.-born populations visiting U.S. healthcare facilities; uncertainties exist due to low-quality evidence. Additional high-quality studies on this topic are needed. [ABSTRACT FROM AUTHOR]

Objective: The Centers for Disease Control and Prevention (CDC) coordinates a labor-intensive process to measure the prevalence of autism spectrum disorder (ASD) among children in the United States. Random forests methods have shown promise in speeding up this process, but they lag behind human classification accuracy by about 5%. We explore whether more recently available document classification algorithms can close this gap. Materials and methods: Using data gathered from a single surveillance site, we applied 8 supervised learning algorithms to predict whether children meet the case definition for ASD based solely on the words in their evaluations. We compared the algorithms’ performance across 10 random train-test splits of the data, using classification accuracy, F1 score, and number of positive calls to evaluate their potential use for surveillance. Results: Across the 10 train-test cycles, the random forest and support vector machine with Naive Bayes features (NB-SVM) each achieved slightly more than 87% mean accuracy. The NB-SVM produced significantly more false negatives than false positives (P = 0.027), but the random forest did not, making its prevalence estimates very close to the true prevalence in the data. The best-performing neural network performed similarly to the random forest on both measures. Discussion: The random forest performed as well as more recently available models like the NB-SVM and the neural network, and it also produced good prevalence estimates. NB-SVM may not be a good candidate for use in a fully-automated surveillance workflow due to increased false negatives. More sophisticated algorithms, like hierarchical convolutional neural networks, may not be feasible to train due to characteristics of the data. Current algorithms might perform better if the data are abstracted and processed differently and if they take into account information about the children in addition to their evaluations. Conclusion: Deep learning models performed similarly to traditional machine learning methods at predicting the clinician-assigned case status for CDC’s autism surveillance system. While deep learning methods had limited benefit in this task, they may have applications in other surveillance systems. [ABSTRACT FROM AUTHOR]

Annual soil moisture estimates are useful to characterize trends in the climate system, in the capacity of soils to retain water and for predicting land and atmosphere interactions. The main source of soil moisture spatial information across large areas (e.g., continents) is satellite-based microwave remote sensing. However, satellite soil moisture datasets have coarse spatial resolution (e.g., 25–50 km grids); and large areas from regional-to-global scales have spatial information gaps. We provide an alternative approach to predict soil moisture spatial patterns (and associated uncertainty) with higher spatial resolution across areas where no information is otherwise available. This approach relies on geomorphometry derived terrain parameters and machine learning models to improve the statistical accuracy and the spatial resolution (from 27km to 1km grids) of satellite soil moisture information across the conterminous United States on an annual basis (1991–2016). We derived 15 primary and secondary terrain parameters from a digital elevation model. We trained a machine learning algorithm (i.e., kernel weighted nearest neighbors) for each year. Terrain parameters were used as predictors and annual satellite soil moisture estimates were used to train the models. The explained variance for all models-years was >70% (10-fold cross-validation). The 1km soil moisture grids (compared to the original satellite soil moisture estimates) had higher correlations (improving from r2 = 0.1 to r2 = 0.46) and lower bias (improving from 0.062 to 0.057 m3/m3) with field soil moisture observations from the North American Soil Moisture Database (n = 668 locations with available data between 1991–2013; 0-5cm depth). We conclude that the fusion of geomorphometry methods and satellite soil moisture estimates is useful to increase the spatial resolution and accuracy of satellite-derived soil moisture. This approach can be applied to other satellite-derived soil moisture estimates and regions across the world. [ABSTRACT FROM AUTHOR]

The jasmonic acid cascade plays a pivotal role in induced plant resistance to herbivores. There have been a number of investigations into the potential uses of derivatives of this hormone for pest management. Understanding the phenotypic plasticity of plant defense traits interactions in agricultural systems may facilitate the development of novel and improved management practices, which is desirable as management of insects in most agricultural systems is currently heavily reliant on insecticides. The rice water weevil (RWW), Lissorhoptrus oryzophilus Kuschel, is a pest of rice, Oryza sativa, in the southern U.S. and globally. The effects of the jasmonic acid derivative, methyl jasmonate (MJ), on induced defenses to RWW in rice, and the potential costs of MJ-induced resistance to plant growth and fitness, were tested in a series of field and greenhouse trials. It was hypothesized that seed treatments with MJ would reduce densities of larval RWW. A second hypothesis was that MJ seed treatments would alter emergence, biomass accumulation, and yield of rice. The final hypothesis was that induction of plant resistance to the RWW would diminish as the time from seed treatment increased. In order to investigate these hypotheses, RWW densities were determined in greenhouse and field trials. Plant growth was measured in the field by assessing plant emergence, root and shoot biomass, time of heading, and yield (grain mass). Results indicated that MJ seed treatments induced resistance to RWW, although this effect decayed over time. Additionally, there were costs to plant growth and fitness; emergence and heading were delayed and biomass was reduced. Importantly, however, yields on a per-plant were not significantly reduced by MJ treatment. Overall, these results are promising and show the potential for the use of jasmonate elicitors as part of a pest management program in rice. [ABSTRACT FROM AUTHOR]

Introduction: Reproducible research is increasingly gaining interest in the research community. Automating the production of research manuscript tables from statistical software can help increase the reproducibility of findings. Logistic regression is used in studying disease prevalence and associated factors in epidemiological studies and can be easily performed using widely available software including SAS, SUDAAN, Stata or R. However, output from these software must be processed further to make it readily presentable. There exists a number of procedures developed to organize regression output, though many of them suffer limitations of flexibility, complexity, lack of validation checks for input parameters, as well as inability to incorporate survey design. Methods: We developed a SAS macro, %svy_logistic_regression, for fitting simple and multiple logistic regression models. The macro also creates quality publication-ready tables using survey or non-survey data which aims to increase transparency of data analyses. It further significantly reduces turn-around time for conducting analysis and preparing output tables while also addressing the limitations of existing procedures. In addition, the macro allows for user-specific actions to handle missing data as well as use of replication-based variance estimation methods. Results: We demonstrate the use of the macro in the analysis of the 2013–2014 National Health and Nutrition Examination Survey (NHANES), a complex survey designed to assess the health and nutritional status of adults and children in the United States. The output presented here is directly from the macro and is consistent with how regression results are often presented in the epidemiological and biomedical literature, with unadjusted and adjusted model results presented side by side. Conclusions: The SAS code presented in this macro is comprehensive, easy to follow, manipulate and to extend to other areas of interest. It can also be incorporated quickly by the statistician for immediate use. It is an especially valuable tool for generating quality, easy to review tables which can be incorporated directly in a publication. [ABSTRACT FROM AUTHOR]

Non-typhoidal Salmonella (NTS) infection is one of the major causes of diarrheal disease throughout the world. In recent years, an increase in human S. Javiana infection has been reported from the southern part of the United States. However, the sources and routes of transmission of this Salmonella serotype are not well understood. The objective of this study was to perform a systematic review of the literature to identify risk factors for human S. Javiana infection. Using PRISMA guidelines, we conducted a systematic search in Web of Science, PubMed, and the Morbidity and Mortality Weekly Report (MMWR). Searches returned 63 potential articles, of which 12 articles met all eligibility criteria and were included in this review. A review of the literature indicated that both food and non-food (such as animal contact) exposures are responsible for the transmission of S. Javiana infection to humans. Consumption of fresh produce (tomatoes and watermelons), herbs (paprika-spice), dairy products (cheese), drinking contaminated well water and animal contact were associated with human S. Javiana infections. Based on the findings of this study, control of human S. Javiana infection should include three factors, (a) consumption of drinking water after treatment, (b) safe animal contact, and (c) safe food processing and handling procedures. The risk factors of S. Javiana infections identified in the current study provide helpful insight into the major vehicles of transmission of S. Javiana. Eventually, this will help to improve the risk management of this Salmonella serotype to reduce the overall burden of NTS infection in humans. [ABSTRACT FROM AUTHOR]

Not much is known about the fleet level total seabird bycatch from pelagic longlines of United States vessels in the western North Atlantic or other fleets of the Atlantic or other oceans. Onboard observers generally only record seabird bycatch during line hauling. Seabirds are predominantly caught during the line setting stage, and, due to predation or mechanical action, those caught prior to the haul can drop off the hook and be lost to the onboard observer. We developed a model to gauge the size of this bycatch loss problem and provide a first approximation of its impact on estimates of total fleet bycatch. We started with a traditional loss-free bycatch model, which assumes that birds recorded were the only birds captured, and integrated into it two crucial components of the bycatch process: capture origin (set or haul) and bycatch loss of set-captures. We extracted count data on seabird bycatch loss and bycatch mortality from the literature on other longline fisheries and used these data to simulate potential total seabird bycatch in the western North Atlantic. Simulations revealed the shortcomings of both the traditional bycatch model and the current haul-only observer protocol, each of which contributed to biologically significant underestimation of total bycatch and estimation uncertainty. Based on our results, we recommend a loss-corrected modeling approach to provide a more accurate estimate of seabird mortalities in pelagic longline fisheries. Where possible, fishery-specific seabird bycatch loss rates need to be ascertained via specific set and haul observing protocols. But, even where fishery-specific estimates for a region are not available, the methodology developed here is applicable to other pelagic longline fisheries to approximate fleet-level loss-corrected bycatch. [ABSTRACT FROM AUTHOR]

The Medical Monitoring Project (MMP) is an HIV surveillance system that provides national estimates of HIV-related behaviors and clinical outcomes. When first implemented, MMP excluded persons living with HIV not receiving HIV care. This analysis will describe new case-surveillance-based methods to identify and recruit persons living with HIV who are out of care and at elevated risk for mortality and ongoing HIV transmission. Stratified random samples of all persons living with HIV were selected from the National HIV Surveillance System in five public health jurisdictions from 2012–2014. Sampled persons were located and contacted through seven different data sources and five methods of contact to collect interviews and medical record abstractions. Data were weighted for non-response and case reporting delay. The modified sampling methodology yielded 1159 interviews (adjusted response rate, 44.5%) and matching medical record abstractions for 1087 (93.8%). Of persons with both interview and medical record data, 264 (24.3%) would not have been included using prior MMP methods. Significant predictors were identified for successful contact (e.g., retention in care, adjusted Odds Ratio [aOR] 5.02; 95% Confidence Interval [CI] 1.98–12.73), interview (e.g. moving out of jurisdiction, aOR 0.24; 95% CI: 0.12–0.46) and case reporting delay (e.g. rural residence, aOR 3.18; 95% CI: 2.09–4.85). Case-surveillance-based sampling resulted in a comparable response rate to existing MMP methods while providing information on an important new population. These methods have since been adopted by the nationally representative MMP surveillance system, offering a model for public health program, research and surveillance endeavors seeking inclusion of all persons living with HIV. [ABSTRACT FROM AUTHOR]

Downscaled climate projections need to be linked to downscaled projections of population and economic growth to fully develop implications for land, natural resources, and ecosystems for future scenarios. We develop an empirical spatiotemporal approach for jointly projecting population and income at the county scale in the United States that is consistent with neoclassical economic growth theory and overlapping labor markets and that accounts for labor migration and spatial spillovers. Downscaled projections generated for the five Shared Socioeconomic Pathways used to support global scenario analysis generally show growth focused around relatively few centers especially in the southeast and western regions, with some areas in the Midwest and northeast experiencing population declines. Results are consistent with economic growth theory and with historical trends in population change and convergence of per capita personal income across US counties. [ABSTRACT FROM AUTHOR]

Latinos are the largest and fastest-growing minority group in the U.S., and Latina women represent the largest portion of minority births, having the highest birth rate in the U.S. for over 20 years. In addition, Latina women are at increased risk of entering pregnancy being overweight or having obesity and gaining excess gestational weight. Excess gestational weight gain (GWG) has short- and long-term adverse health outcomes for the woman and her child. Although culturally tailored interventions show promise toward promoting healthy GWG among Latina women, findings from current interventions have had mixed results, suggesting the need for further tailoring to meet the needs of this heterogeneous population group. This qualitative study was designed to explore first-time pregnant, low-income Latina women’s beliefs, attitudes, and experiences with GWG. The study employed qualitative research using semi-structured interviews conducted with 23 first-time pregnant Latina women between 22 and 36 weeks of gestation. Interviews were conducted by trained bilingual staff, transcribed verbatim, and analyzed using thematic analysis. Results showed that participants were uncertain if their GWG was within a healthy range. Although the majority of participants knew that GWG should be limited, they were not sure what the amount should be. In addition, the majority of participants reported attitudes of acceptance of and resignation to excessive GWG as being part of pregnancy. Several women appeared to believe that they did not have control over their weight gain during pregnancy. Moreover, analysis identified that sociocultural and interpersonal factors such as social support influence the beliefs, attitudes, and experiences with GWG of the low-income, majority immigrant Latina women who participated in this study. Study findings can be used to further tailor prenatal care practices and interventions aimed at altering modifiable risk factors associated with excess GWG among Latinas. Future interventions designed for low-income, immigrant Latina women that consider sociocultural influences on women’s beliefs and attitudes related to GWG, as well as the influence of social support networks on women’s health behaviors during pregnancy, will likely be more effective in preventing excessive GWG. [ABSTRACT FROM AUTHOR]

Acute abdominal pain (colic) is the most common reason for emergency veterinary treatment in the horse. Consolidation of data through a systematic review is important to inform evidence-based medicine and clinical guidelines, but there are currently no published systematic reviews on colic in the horse. The aim of this study was to identify, categorize and appraise the evidence on factors associated with increased risk of developing abdominal pain (colic) due to gastrointestinal disease in the adult horse. A scoping review was performed to identify and categorize evidence on all risk factors for colic. A systematic review of management-related risk factors was then performed following PRISMA guidelines. Both searches were conducted in Medline, CAB Abstracts and Web of Science databases, and publications were assessed against inclusion and exclusion criteria. For the scoping review, study and participant characteristics of included publications and key results were extracted and tabulated. For the systematic review, cohort, case-control or cross-sectional studies investigating acute abdominal pain in horses within two weeks of management changes were assessed. Study characteristics, participant characteristics and study results of included publications for the systematic review were extracted and tabulated. Included publications were appraised using the Joanna Briggs Institute Critical Appraisal Tools for cohort, case-control and cross-sectional studies. The scoping review search identified 3,756 publications. Fifty eight studies met final inclusion criteria, and 22 categories of risk factors were identified. These were grouped into three broad areas: horse-related factors, management-related factors and environment-related factors. The largest body of evidence related to management change. The systematic review of management change identified 410 publications: 14 met inclusion criteria for analysis. These consisted of one cohort, eight case-control and five cross-sectional studies. The studies were conducted between 1990–2008, and the majority of studies were located in the USA (8/14) or UK (3/14). The risk factors related to management change that were assessed were feed, carer, exercise, pasture, water and housing. The largest bodies of evidence for increased risk of colic associated with management change were changes in feed (5/14 publications) and recent change in housing (3/14). Most studies (8/14) did not meet the JBI criterion on confounding factors. There was marked heterogeneity of study methodologies and measures. This is the first study to use a combined scoping and systematic review to analyse evidence for modifiable risk factors for a common condition in the horse. It provides a comprehensive review that will be a key resource for researchers, veterinary practitioners and horse owners. It identified modifiable risk factors associated with an increased risk of colic which should be a key target for preventative health programmes. The findings from the critical appraisal were used to develop recommendations for future research to improve the quality of evidence-based veterinary medicine. [ABSTRACT FROM AUTHOR]

Given limited resources for managing invasive species, traditional survey methods may not be feasible to implement at a regional scale. Environmental DNA (eDNA) sampling has proven to be an effective method for detecting some invasive species, but comparisons between the detection probability of eDNA and traditional survey methods using modern occupancy modeling methods are rare. We developed a qPCR assay to detect two species of watersnake (Nerodia fasciata and Nerodia sipedon) introduced to California, USA, and we compared the efficacy of eDNA and aquatic trapping. We tested 3–9 water samples each from 30 sites near the known range of N. fasciata, and 61 sites near the known range of N. sipedon. We also deployed aquatic funnel traps at a subset of sites for each species. We detected N. fasciata eDNA in three of nine water samples from just one site, but captured N. fasciata in traps at three of ten sites. We detected N. sipedon eDNA in five of six water samples from one site, which was also the only site of nine at which this species was captured in traps. Traditional trapping surveys had a higher probability of detecting watersnakes than eDNA surveys, and both survey methods had higher detection probability for N. sipedon than N. fasciata. Occupancy models that integrated both trapping and eDNA surveys estimated that 5 sites (95% Credible Interval: 4–10) of 91 were occupied by watersnakes (both species combined), although snakes were only detected at four sites (three for N. fasciata, one for N. sipedon). Our study shows that despite the many successes of eDNA surveys, traditional sampling methods can have higher detection probability for some species. We recommend those tasked with managing species invasions explicitly compare eDNA and traditional survey methods in an occupancy framework to inform their choice of the best method for detecting nascent populations. [ABSTRACT FROM AUTHOR]

High-quality genotypic data is a requirement for many genetic analyses. For any crop, errors in genotype calls, phasing of markers, linkage maps, pedigree records, and unnoticed variation in ploidy levels can lead to spurious marker-locus-trait associations and incorrect origin assignment of alleles to individuals. High-throughput genotyping requires automated scoring, as manual inspection of thousands of scored loci is too time-consuming. However, automated SNP scoring can result in errors that should be corrected to ensure recorded genotypic data are accurate and thereby ensure confidence in downstream genetic analyses. To enable quick identification of errors in a large genotypic data set, we have developed a comprehensive workflow. This multiple-step workflow is based on inheritance principles and on removal of markers and individuals that do not follow these principles, as demonstrated here for apple, peach, and sweet cherry. Genotypic data was obtained on pedigreed germplasm using 6-9K SNP arrays for each crop and a subset of well-performing SNPs was created using ASSIsT. Use of correct (and corrected) pedigree records readily identified violations of simple inheritance principles in the genotypic data, streamlined with FlexQTL software. Retained SNPs were grouped into haploblocks to increase the information content of single alleles and reduce computational power needed in downstream genetic analyses. Haploblock borders were defined by recombination locations detected in ancestral generations of cultivars and selections. Another round of inheritance-checking was conducted, for haploblock alleles (i.e., haplotypes). High-quality genotypic data sets were created using this workflow for pedigreed collections representing the U.S. breeding germplasm of apple, peach, and sweet cherry evaluated within the RosBREED project. These data sets contain 3855, 4005, and 1617 SNPs spread over 932, 103, and 196 haploblocks in apple, peach, and sweet cherry, respectively. The highly curated phased SNP and haplotype data sets, as well as the raw iScan data, of germplasm in the apple, peach, and sweet cherry Crop Reference Sets is available through the Genome Database for Rosaceae. [ABSTRACT FROM AUTHOR]

Past research has documented myriad pernicious psychological effects of high economic inequality, prompting interest into how people perceive, evaluate, and react to inequality. Here we propose, refine, and validate the Support for Economic Inequality Scale (SEIS)–a novel measure of attitudes towards economic inequality. In Study 1, we distill eighteen items down to five, providing evidence for unidimensionality and reliability. In Study 2, we replicate the scale’s unidimensionality and reliability and demonstrate its validity. In Study 3, we evaluate a United States version of the SEIS. Finally, in Studies 4–5, we demonstrate the SEIS’s convergent and predictive validity, as well as evidence for the SEIS being distinct from other conceptually similar measures. The SEIS is a valid and reliable instrument for assessing perceptions of and reactions to economic inequality and provides a useful tool for researchers investigating the psychological underpinnings of economic inequality. [ABSTRACT FROM AUTHOR]

Representation of women in science drops substantially at each career stage, from early student to senior investigator. Disparities in opportunities for women to contribute to research metrics, such as distinguished speaker events and authorship, have been reported in many fields in the U.S.A. and Europe. However, whether female representation in scientific contributions differs in other regions, such as Latin America, is not well understood. In this study, in order to determine whether female authorship is influenced by gender or institutional location of the last (senior) author or by subfield within ecology, we gathered author information from 6849 articles in ten ecological and zoological journals that publish research articles either in or out of Latin America. We found that female authorship has risen marginally since 2002 (27 to 31%), and varies among Latin American countries, but not between Latin America and other regions. Last author gender predicted female co-authorship across all journals and regions, as research groups led by women published with over 60% female co-authors whereas those led by men published with less than 20% female co-authors. Our findings suggest that implicit biases and stereotype threats that women face in male-led laboratories could be sources of female withdrawal and leaky pipelines in ecology and zoology. Accordingly, we encourage every PI to self-evaluate their lifetime percentage of female co-authors. Female role models and cultural shifts–especially by male senior authors–are crucial for female retention and unbiased participation in science. [ABSTRACT FROM AUTHOR]

Background: Physician Orders for Life-Sustaining Treatment (POLST) programs have expanded rapidly, but evaluating their impact on hospital care is challenging. Objectives: To demonstrate how careful study design can reveal POLST’s impact at hospital admission and why analyses of state registry data are unlikely to capture POLST’s effects. Design: Prospective cohort study. Setting and participants: Adult in-patients with Do Not Intubate and/or Do Not Resuscitate (DNR/I) orders in the electronic medical record at the time of discharge from Johns Hopkins Hospital over 18 months. For patients with unplanned readmissions within 30 days, records were reviewed to determine if a Maryland Medical Order for Life-Sustaining Treatment (MOLST) form was presented and for the time from readmission to a DNR/I order in the EMR. Analyses were stratified by whether patients could communicate or were accompanied by a proxy at readmission. Results: Among 1,507 patients with DNR/I orders at discharge, 124 (8%) had unplanned readmissions, 112 (90%) could communicate or were accompanied by a proxy at readmission, and 12 (10%) could not communicate and were unaccompanied. For patients who were unaccompanied and could not communicate, MOLST significantly decreased the median time from readmission to DNR/I order (1.2 vs 27.1 hours, P = .001), but this association was greatly attenuated among patients who could communicate or were accompanied by a proxy (16.4 vs 25.4 hours P = .10). Conclusion: Among patients who wanted to avoid intubation and/or CPR, MOLST forms were protective when the patient was unaccompanied by a healthcare proxy at admission and could not communicate. Fewer than 10% of patients met these criteria during unplanned readmissions, and state registry data does not allow this sub-population to be identified. [ABSTRACT FROM AUTHOR]

Motion triggered camera traps are an increasingly popular tool for wildlife research and can be used to survey for multiple species simultaneously. As with all survey techniques, it is crucial to conduct camera trapping research following study designs that include adequate spatial and temporal replication, and sufficient probability of detecting species presence. The use and configuration of multiple camera traps within a single survey site are understudied considerations that could have a substantial impact on detection probability. Our objective was to test the role that camera number (one, two or three units), and spacing along a linear transect (100 m or 150 m), have on the probability of detecting a species given it is present. From January to March, 2017 we collected data on six mammal species in Maine, USA: coyote (Canis latrans), fisher (Pekania pennanti), American marten (Martes americana), short-tailed weasel (Mustela erminea), snowshoe hare (Lepus americanus), and American red squirrel (Tamiasciurus hudsonicus). We used multi-scale occupancy modelling to compare pooled detection histories of different configuration of five cameras deployed at the same survey site (n = 32), and how the configuration would influence the probability of detecting a species given it was available at the site. Across all six species, we found substantial increases in probability of detection as the number of cameras increased from one to two (22 to 400 percent increase), regardless of the spacing between cameras. For most species the magnitude of the increase was less substantial when adding a third camera (4 to 85 percent increase), with coyote and snowshoe hare showing a pronounced effect. The influence of survey station features also varied by species. We suggest that using pooled data from two or three cameras at a survey site is a cost effective approach to increase detection success over a single camera. [ABSTRACT FROM AUTHOR]

Fecal pollution management remains one of the biggest challenges for water quality authorities worldwide. Advanced fecal pollution source identification technologies are now available that can provide quantitative information from many animal groups. As public interest in these methodologies grows, it is vital to use standardized procedures with clearly defined data acceptance metrics and conduct field studies demonstrating the use of these techniques to help resolve real-world water quality challenges. Here we apply recently standardized human-associated qPCR methods with custom data acceptance metrics (HF183/BacR287 and HumM2), along with established procedures for ruminant (Rum2Bac), cattle (CowM2 and CowM3), canine (DG3 and DG37), and avian (GFD) fecal pollution sources to (i) demonstrate the feasibility of implementing standardized qPCR procedures in a large-scale field study, and (ii) characterize trends in fecal pollution sources in the research area. A total of 602 water samples were collected over a one-year period at 29 sites along the Trask, Kilchis, and Tillamook rivers and tributaries in the Tillamook Bay Watershed (OR, USA). Host-associated qPCR results were combined with high-resolution geographic information system (GIS) land use and general indicator bacteria (E. coli) measurements to elucidate water quality fecal pollution trends. Results demonstrate the feasibility of implementing standardized fecal source identification qPCR methods with established data acceptance metrics in a large-scale field study leading to new investigative leads suggesting that elevated E. coli levels may be linked to specific pollution sources and land use activities in the Tillamook Bay Watershed. [ABSTRACT FROM AUTHOR]

Since January 1, 2017, the United States Food and Drug Administration (FDA) has fully implemented the Veterinary Feed Directive (VFD) final rule aimed at facilitating the judicious use of medically important antimicrobials in food-producing animals. The objective of this study was to identify the common perceptions of Tennessee (TN) cattle producers regarding the VFD. We used a combination of focus groups and survey questionnaires to explore TN cattle producers’ perceptions regarding the VFD. Preliminary findings from seven focus groups of 62 producers were used in the development of the questionnaire sent both online and in-print to rest of cattle producers in TN. The beef focus group participants perceived the VFD: to be a top-down policy; to have led to unregulated access to in-feed antimicrobials; a regulation that has limited the producers’ ability to prevent disease and leading to economic losses; to negatively affect small producers; and to be affected by challenges related to prescription writing and disposal of un-used medicines. The dairy focus group participants perceived the VFD as unnecessary and burdensome, to have affected small producers, and introduced additional costs. Among the survey questionnaire respondents, 35 (15.4%) beef producers and 6 (13.6%) dairy producers respectively were not familiar at all with the VFD. Forty-eight (21.1%) beef producers and 11 (25%) dairy producers were slightly familiar with VFD. Gender was significantly associated (P = 0.02) with the beef producers’ belief in the usefulness of the VFD. Similarly, for dairy producers, herd size was significantly associated (P = 0.002) with their perceptions regarding the usefulness of the VFD. The findings of this study could inform future VFD policy review processes. More awareness regarding the VFD and its benefits is needed among both beef and dairy producers in TN. [ABSTRACT FROM AUTHOR]

Objectives: Reviews of violence against children in disaster settings focus on armed conflict. Little is understood about natural disasters which has implications in planning humanitarian response. We examined the magnitude and direction of the association between exposure to natural disasters and physical, emotional, and sexual violence against children, and assessed the quality of the evidence. Methods: We searched 15 health and social science databases from first record until May 16, 2018. Publications describing all types of quantitative study design were eligible for inclusion. We presented study characteristics and quality in a narrative form and generated pooled estimates using a three-level random effects model. We evaluated Cochrane’s Q with p-values below 0.10 and radial plots to assess heterogeneity. Planned subgroup analyses explored differential results by violence form, study design, and analysis method. Results: 11 publications met inclusion criteria. The majority were cross-sectional studies examining physical or sexual violence in the United States. We found no evidence of a consistent association or directional influence between natural disasters and violence against children. Combined categorical violence outcomes had substantial heterogeneity [Q (df = 66) = 252.83, p < 0.001]. Subgroups without evidence of heterogeneity had confidence intervals that included a possible null effect. Our findings were mainly limited by inconsistencies in operational definitions of violence, a lack of representative sampling, and unclear establishment of temporal order between natural disaster exposure and violence outcomes. Conclusions: Based on the available evidence, we cannot confidently conclude that natural disasters increase the level or severity of violence against children above non-disaster settings, however heterogeneity and study quality hamper our ability to draw firm conclusions. More nuanced and rigorous research is needed to inform practice and policy as natural disasters increasingly affect human populations. [ABSTRACT FROM AUTHOR]

Commercial captive breeding and trade in body parts of threatened wild carnivores is an issue of significant concern to conservation scientists and policy-makers. Following a 2016 decision by Parties to the Convention on International Trade in Endangered Species of Wild Fauna and Flora, South Africa must establish an annual export quota for lion skeletons from captive sources, such that threats to wild lions are mitigated. As input to the quota-setting process, South Africa’s Scientific Authority initiated interdisciplinary collaborative research on the captive lion industry and its potential links to wild lion conservation. A National Captive Lion Survey was conducted as one of the inputs to this research; the survey was launched in August 2017 and completed in May 2018. The structured semi-quantitative questionnaire elicited 117 usable responses, representing a substantial proportion of the industry. The survey results clearly illustrate the impact of a USA suspension on trophy imports from captive-bred South African lions, which affected 82% of respondents and economically destabilised the industry. Respondents are adapting in various ways, with many euthanizing lions and becoming increasingly reliant on income from skeleton export sales. With rising consumer demand for lion body parts, notably skulls, the export quota presents a further challenge to the industry, regulators and conservationists alike, with 52% of respondents indicating they would adapt by seeking ‘alternative markets’ for lion bones if the export quota allocation restricted their business. Recognizing that trade policy toward large carnivores represents a ‘wicked problem’, we anticipate that these results will inform future deliberations, which must nonetheless also be informed by challenging inclusive engagements with all relevant stakeholders. [ABSTRACT FROM AUTHOR]

Poor reporting quality may contribute to irreproducibility of results and failed ‘bench-to-bedside’ translation. Consequently, guidelines have been developed to improve the complete and transparent reporting of in vivo preclinical studies. To examine the impact of such guidelines on core methodological and analytical reporting items in the preclinical anesthesiology literature, we sampled a cohort of studies. Preclinical in vivo studies published in Anesthesiology, Anesthesia & Analgesia, Anaesthesia, and the British Journal of Anaesthesia (2008–2009, 2014–2016) were identified. Data was extracted independently and in duplicate. Reporting completeness was assessed using the National Institutes of Health Principles and Guidelines for Reporting Preclinical Research. Risk ratios were used for comparative analyses. Of 7615 screened articles, 604 met our inclusion criteria and included experiments reporting on 52 490 animals. The most common topic of investigation was pain and analgesia (30%), rodents were most frequently used (77%), and studies were most commonly conducted in the United States (36%). Use of preclinical reporting guidelines was listed in 10% of applicable articles. A minority of studies fully reported on replicates (0.3%), randomization (10%), blinding (12%), sample-size estimation (3%), and inclusion/exclusion criteria (5%). Statistics were well reported (81%). Comparative analysis demonstrated few differences in reporting rigor between journals, including those that endorsed reporting guidelines. Principal items of study design were infrequently reported, with few differences between journals. Methods to improve implementation and adherence to community-based reporting guidelines may be necessary to increase transparent and consistent reporting in the preclinical anesthesiology literature. [ABSTRACT FROM AUTHOR]

Evidence suggests that suicide rates can increase following the suicide of a prominent celebrity or peer, sometimes known as ‘suicide contagion’. The risk of contagion is especially high when media coverage is detailed and sensational. A recent study reported a 10% increase in U.S. suicides in the months following the suicide of comedian Robin Williams, who died in August 2014. The authors tentatively linked this increase to sensational media coverage; however, no content analysis of U.S. media was performed. As such, the aim of the present study is to formally examine the tone and content of U.S. newspaper coverage of Williams’ suicide. The primary objective is to assess adherence to suicide reporting guidelines in U.S. newspapers after his suicide. The secondary objective is to identify common emerging themes discussed in these articles. The tertiary objective is to compare patterns of results in the U.S media with those in the Canadian media. Articles about Williams’ suicide were collected from 10 U.S. newspapers in the 30-day period following his death using systematic retrieval software, which were then examined for adherence to suicide reporting recommendations. An inductive thematic analysis was also undertaken. A total of 63 articles were included in the study. We found that 100% of articles did not call it a ‘successful’ suicide, 96.8% did not use pejorative phrases and 71% did not say ‘commit’ suicide. However, only 11% included information about help-seeking, 27% tended to romanticize his suicide and 46% went into detail about the method. The most prominent emerging theme was Williams’ struggles with mental illness and addiction. These findings suggest that U.S. newspapers moderately adhered to best practice recommendations when reporting Williams’ suicide. Key recommendations were underapplied, which may have contributed to suicide contagion. New interventions targeting U.S. journalists and media may be needed to improve suicide reporting. [ABSTRACT FROM AUTHOR]

Background: Health literacy (HL) skills are essential to enable self-management and shared decision-making in patients with type 2 diabetes mellitus (T2DM). Limited HL in these patients is associated with poorer outcomes. It is not clear what the burden of limited HL in patients with T2DM across countries and what factors influence it. Methods: A systematic review was conducted according to the PRISMA guidelines. The study protocol was registered with PROSPERO (CRD42017056150). We searched MEDLINE, EMBASE, PsycINFO, CINAHL and ERIC for articles published up to January 2017. Articles that measured HL levels in adult patients with T2DM; that used validated HL tools; and that were reported in English were included. Two reviewers assessed studies for eligibility and quality, and extracted the data. Prevalence of limited HL is calculated from the number of patients with less than adequate HL over the total number of patients with T2DM in the study. Meta-analysis and meta-regression analysis were conducted using the Open Meta-analyst software. Results: Twenty-nine studies involving 13,457 patients with T2DM from seven countries were included. In total, seven different HL measurement tools were used. The prevalence of limited HL ranged from 7.3% to 82%, lowest in Switzerland and the highest in Taiwan. Meta-regression analysis of all included studies showed the country of study (p<0.001), HL tool used (p = 0.002), and the country’s region (p<0.001) contributed to the variation findings. Thirteen studies in the USA measured functional HL. The pooled prevalence of inadequate functional HL among patients with T2DM in the USA was 28.9% (95% CI: 20.4–37.3), with high heterogeneity (I2 = 97.9%, p <0.001). Studies were done in the community as opposed to a hospital or primary care (p = 0.005) and populations with education level lower than high school education (p = 0.009) reported a higher prevalence of limited HL. Conclusion: The prevalence of limited HL in patients with T2DM varied widely between countries, HL tools used and the country’s region. Pooled prevalence showed nearly one in three patients with T2DM in the USA had limited functional HL. Interactions with healthcare providers and educational attainment were associated with reported of prevalence in the USA. [ABSTRACT FROM AUTHOR]