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The U.S. art museum sector is grappling with diversity. While previous work has investigated the demographic diversity of museum staffs and visitors, the diversity of artists in their collections has remained unreported. We conduct the first large-scale study of artist diversity in museums. By scraping the public online catalogs of 18 major U.S. museums, deploying a sample of 10,000 artist records comprising over 9,000 unique artists to crowdsourcing, and analyzing 45,000 responses, we infer artist genders, ethnicities, geographic origins, and birth decades. Our results are threefold. First, we provide estimates of gender and ethnic diversity at each museum, and overall, we find that 85% of artists are white and 87% are men. Second, we identify museums that are outliers, having significantly higher or lower representation of certain demographic groups than the rest of the pool. Third, we find that the relationship between museum collection mission and artist diversity is weak, suggesting that a museum wishing to increase diversity might do so without changing its emphases on specific time periods and regions. Our methodology can be used to broadly and efficiently assess diversity in other fields. [ABSTRACT FROM AUTHOR]

Introduction: Measles remains a major public health problem in many developing countries in which vaccination coverage is poor, as is the case in the Central African Republic (CAR). At the beginning of the 2000s, a surveillance system was established in the country, and samples from suspected cases are regularly tested in the laboratory for serological confirmation. Since 2007, when case-by-case monitoring with standardized laboratory databases and monitoring, was set up, no assessment have been performed. Therfore, 9 years later it seemed appropriate to make a first assessment. The aim of the study reported here was to describe the epidemiology of measles in the CAR on the basis of surveillance and laboratory data. Method: A descriptive retrospective study was conducted, based on the databases of the measles surveillance programme and of the Institut Pasteur laboratory in Bangui during the period 2007–2015. Results: During this study period, the surveillance programme notified 3767 cases. Of these, 2795 (75%) were sent for laboratory confirmation, and 24.6% (687/2795) were confirmed serologically. Of the 1797 cases of measles declared during this period by the surveillance programme, 1110 (61.8%) were confirmed clinically or by epidemiological linkage. The majority of confirmed cases (83.7%; 575/687) occurred in children under 10 years, over half of whom (44.2%; 304/687) were aged 1–4 years. Epidemics occurred regularly between 2011 and 2015, with > 10% of laboratory-confirmed cases. The rate of laboratory investigation was < 80% between 2011 and 2013 but nearly 100% in the other years. Conclusion: Measles remains a common, endemic illness in the CAR. Improved detection will require better measles surveillance, increased vaccination coverage, revision of the investigation forms to include the WHO case definition and training of the health personnel involved in case-finding in the field. [ABSTRACT FROM AUTHOR]

Background: Influenza-like Illness (ILI) is a medical diagnosis of possible influenza or another respiratory illness with a common set of symptoms. The deaths of four schoolchildren, during a pandemic influenza outbreak in December 2017 in Ghana, raised doubts about the ILI surveillance system’s performance. We evaluated the ILI surveillance system in the Greater Accra region, Ghana, to assess the system’s attributes and its performance on set objectives. Methods: CDC guidelines were used to evaluate the data of the ILI surveillance system between 2013 and 2017. We interviewed the surveillance personnel on the system’s description and operation. Additionally, routinely entered ILI data from the National Influenza Center provided by the six sentinel sites in Accra was extracted. We sampled and reviewed 120 ILI case-investigation forms from these sites. Surveillance activities were examined on system’s performance indicators, each being scored on a scale of 1 to 3 (poorest to best performance). Results: All population and age groups were under ILI surveillance over the period evaluated. Overall, 2948 suspected case-patients, including 392 (13.3%) children under-five were reported, with 219 being positive for influenza virus (Predictive value positive = 7.4%). The predominant influenza subtype was H3N2, recorded in 90 (41.1%) of positive case-patients. The system only met two out of its four objectives. None of the six sentinel sites consistently met their annual 260 suspected case-detection quota. Samples reached the laboratory on average 48 hours after collection and results were disseminated within 7 days. Of 120 case-investigation forms sampled, 91 (76.3%) were completely filled in. Conclusions: The ILI surveillance system in the Greater Accra region is only partially meeting its objectives. While it is found to be sensitive, representative and timely, the data quality was sub-optimal. We recommend the determination of thresholds for alert and outbreak detection and ensuring that sentinel sites meet their weekly case-detection targets. [ABSTRACT FROM AUTHOR]

The triglyceride glucose (TyG) index, a product of triglyceride and fasting glucose, is a reliable marker for insulin resistance (IR). Obesity is also known to be closely related with IR. Recently, the efficiency of TyG-related markers that combine obesity markers with TyG index has been studied; however, earlier studies were limited in number and the results were inconsistent. Therefore, in this study, we investigated the efficiency of several combinations of TyG index and obesity indices, namely, body mass index (BMI), waist circumference (WC), and waist-to-height ratio (WHtR), in reflecting IR. Data were obtained from the Korean National Health and Nutrition Examination Survey from 2007–2010. A total of 11,149 subjects (4,777 men and 6,372 women) were included. IR was defined as the homeostasis model assessment for IR (HOMA-IR) of above the 75th percentile for each gender. Logistic regression analysis was performed after adjusting for confounding factors, to compare and identify the associations of the 4 parameters (TyG index, TyG-BMI, TyG-WC, and TyG-WHtR) with IR. For each parameter, odds ratios (OR) and 95% confidence intervals (CIs) of quartiles 2–4 were calculated and compared with quartile 1 as a reference. A receiver operating characteristic (ROC) curve analysis was conducted to evaluate the ability of each parameter to predict IR. The adjusted ORs of quartile 4 in comparison with quartile 1 (95% CIs) for IR were 7.60 (6.52–8.87) for TyG index, 12.82 (10.89–15.10) for TyG-BMI, 16.29 (13.70–19.38) for TyG-WC, and 14.86 (12.53–17.62) for TyG-WHtR. The areas under the ROC curve for each parameter were 0.690 for TyG index, 0.748 for TyG-BMI, 0.731 for TyG-WC, and 0.733 for TyG-WHtR. In conclusion, TyG-BMI was found to be superior to other parameters for IR prediction. We propose TyG-BMI as an alternative marker for assessing IR in clinical settings. [ABSTRACT FROM AUTHOR]

The observation that exerting self-control in an initial task impairs subsequent self-control performance in a following task has been used to explain a wide range of phenomena. If evidence for this “ego-depletion” effect was initially believed to be strong, it is now questioned. Recent meta-analyses indicated that this effect was sensitive to publication bias and that it was greatly reduced after control for this bias. In a pre-registered replication attempt where an ego-depletion protocol was conducted in multiple independent laboratories, the effect was not distinguishable from zero. Here, a different approach is adopted to examine the validity of this effect by improving the experimental protocol with the addition of important methodological precautions: 1) a pre-test measurement, 2) a learning period, 3) a prolonged depleting task, 4) a similar control condition, and 5) valid indexes of self-control. Accordingly, a well-learned Simon task was done before and after 1h of continuous practice of a Stroop task in a high inhibition demands condition (75% of incongruent trials) or in a control condition (0% of incongruent trials). Datasets from between-subjects (Study 1, N = 82) and within-subjects (Study 2, N = 52) experiments were analyzed using generalized linear mixed models. A significant ego-depletion effect was found in Study 1 (greater interference effect and accuracy decline in high inhibition demands than in control condition) but not in Study 2. Because it is difficult to explain this difference in results, the findings suggest that, even in a context chosen to optimize the observation of an ego-depletion effect, it seems difficult to be conclusive about the existence of this effect. [ABSTRACT FROM AUTHOR]

Background: In lymphangioleiomyomatosis (LAM), tuberous sclerosis gene mutations activate the mechanistic target of the rapamycin pathway, resulting in vascular endothelial growth factor-D (VEGF-D) overproduction. While the utility of serum VEGF-D testing for the diagnosis of LAM is outlined in ATS/JRS LAM Guidelines, the assay has not been fully validated for Asian populations. Our aims were to validate serum VEGF-D testing in Japan, by directly comparing measurements in Japan and the U.S., determining the diagnostic cut-off for serum VEGF-D levels among the Japanese women with typical thin walled cystic change on CT, and determining the performance of VEGF-D as a prognostic biomarker. Subjects and methods: We determined serum VEGF-D levels from 108 LAM patients, 14 disease controls, and 51 healthy volunteers from the Japanese population. Measurements of 61 LAM patients were compared to those from the principal VEGF-D laboratory in the U.S at Cincinnati Children’s Hospital Medical Center. We correlated baseline serum VEGF-D levels with baseline and longitudinal clinical data to determine how pregnancy, sirolimus or gonadotrophin-releasing hormone (GnRH) agonists influence serum VEGF-D levels. Results: Serum VEGF-D measurements in Japan and the U.S. were very similar. Baseline serum VEGF-D levels effectively distinguished LAM from other diseases and healthy volunteers at a cut-off level of 645 pg/ml and were diagnostically specific at 800 pg/ml, consistent with the recommendations of the ATS/JRS LAM Guidelines. Baseline serum VEGF-D correlated negatively with the DLco baseline % predicted and with the annual decrease in DLco % predicted. There was no significant association between baseline serum VEGF-D level and the outcomes of death or transplant. Serum VEGF-D levels markedly decreased during treatment with sirolimus, but not with GnRH analogues. Serum VEGF-D levels of most LAM patients did not increase over time, and neither pregnancy nor menopause significantly modulated serum VEGF-D levels. Conclusions: Serum VEGF-D is a useful diagnostic and therapeutic biomarker for LAM. Satisfactory precision and international inter-laboratory agreement of the clinical assay support VEGF-D recommendations in the ATS/JRS LAM Guidelines for the Japanese population. [ABSTRACT FROM AUTHOR]

Surface incoming shortwave (solar) radiation data are an important component of many scientific analyses, but direct measurements are not commonly available. Estimates can be obtained from gridded meteorological analysis or reanalysis systems, such as the Global Data Assimilation Systems (GDAS) and Modern Era Retrospective Reanalysis System (MERRA-2), or calculated using empirical models dependent on meteorological variables such as air temperature. The purpose of this analysis was to compare multiple methods for estimating daily shortwave radiation in a tropical highland environment in Ethiopia. Direct solar radiation outputs of GDAS and MERRA-2, topographically corrected outputs of the two analysis systems, and empirically estimated solar radiation values calculated with the systems’ air temperature data were compared to see which produced the most reliable radiation values. GDAS appeared to underestimate the seasonal variability, resulting in low correlation (R2) with in situ data and large mean bias error (MBE). In comparison, MERRA-2 did not underestimate variability, but produced larger bias than the empirical model estimates. There was an improvement in correlation and reduction in MBE when using the GDAS air temperature predictions in the empirical model, but the opposite was true for MERRA-2. The empirical model using station air temperature data (stationT) produced the highest correlation across all four stations, with best performance at the lower elevation sites. The direct shortwave radiation outputs of MERRA-2 produced comparable correlation values, with larger R2 at stations at higher elevation. Topography possibly influenced these results, as MERRA-2 performed comparably to stationT at the stations in moderate terrain, but not in steeper terrain. This work can serve as a starting point for analyses in other tropical highland regions, where continuous in situ solar radiation data are rarely available. [ABSTRACT FROM AUTHOR]

Drought stress has been identified as the major environmental factor limiting soybean [Glycine max (L.) Merr.] yield worldwide. Current breeding efforts in soybean largely focus on identifying genotypes with high seed yield and drought tolerance. Water use efficiency (WUE) that results in greater yield per unit rainfall is an important parameter in determining crop yields in many production systems, and is often related with crop drought tolerance. Even though roots are major plant organs that perceive and respond to drought stress, their utility in improving soybean yield and WUE under different environmental and management conditions are largely unclear. The objectives of this research was to evaluate soybean cultivars and breeding and germplasm lines for yield, WUE, root penetrability of hardpan, and root morphology. Field experiments were conducted at two locations in South Carolina (southeastern United States) during the 2017 cropping season to test the genotypes for yield and root morphology under irrigated and non-irrigated conditions. Two independent controlled-environmental experiments were conducted to test the genotypes for WUE and root penetrability of synthetic hardpans. The slow wilting lines NTCPR94-5157 and N09-13890 had equal or greater yield than the checks- cultivar NC-Raleigh and the elite South Carolina breeding line SC07-1518RR, under irrigated and non-irrigated conditions. The high yielding genotypes NTCPR94-5157, N09-13890, and SC07-1518RR exhibited root parsimony (reduced root development). This supported the recent hypothesis in literature that root parsimony would have adaptational advantage to improve yield under high input field conditions. The high yielding genotypes NTCPR94-5157, N09-13890, NC-Raleigh, and SC07-1518RR and a cultivar Boggs (intermediate in yield) possessed high WUE and had increased root penetrability of hardpans. These genotypes offer useful genetic materials for soybean breeding programs for improving yield, drought tolerance, and/or hardpan penetrability. [ABSTRACT FROM AUTHOR]

Open biomedical repositories, such as PubMed Central (PMC), are a means to make research discoverable and permanently accessible. Assessing the potential interest of key stakeholders in an Australasia PubMed Central was the objective of this research. The investigation is novel, assisting in the development of open science infrastructure through its systematic analysis of the potential interest in, and viability of a biomedical repository for managing openly accessible research outputs for the Australasia region. The research adopted a qualitative approach based on semi-structured interviews and a focus group. Forty-four stakeholders located throughout Australia and New Zealand participated in the research. Participants expanded upon their experience of PubMed, MEDLINE, PMC and their use of information resources for research and clinical practice. The Evidence Based Healthcare (EBHC) pyramid was the theoretical model adopted to explain open biomedical repository processes. A strengths, weaknesses, opportunities and threats (SWOT) analysis identified support for exploring membership of an international PMC system, in particular Europe PMC. Lessons learnt from PMC US, Europe PMC and PMC Canada (collectively known as PubMed Central International) informed the investigation. A major strength identified was that PubMed Central International has been able to achieve high levels of compliance way beyond that of most institutional repositories. A great threat faced is overcoming the difficulties of working together with other major world bodies and financially sustaining an Australasia PMC. Improving Australasian biomedical knowledge management processes may be possible from adopting a PMC for retrieving and transferring research, linked to the data underlying the research. This in turn could help put regional research under a brighter spotlight, potentially leading to improvements in research quality. There is an opportunity for a potential Australasia PMC to harvest biomedical research from the National Library of Australia’s aggregator database, Trove and work closely with Europe PMC to avoid duplication of effort. Overall, establishment of an Australasia permanent biomedical digital open repository is perceived as important, with significant potential flow-on benefits to healthcare, industry and society. [ABSTRACT FROM AUTHOR]

This paper proposes a weighted generalization of the recently developed Euclidean Index. The weighting mechanism is designed to reflect the reputation of the journal within which an article appears. The weights are constructed using the Eigenfactor Article Influence percentiles scores. The rationale for assigning weights is that citations in more prestigious journals should be adjusted to logically reflect higher costs of production and higher vetting standards, and to partially counter several pragmatic issues surrounding truncated citation counts. Simulated and empirical demonstrations of the proposed approaches are included, which emphasize the flexibility and efficacy of the proposed generalization. [ABSTRACT FROM AUTHOR]

Background: Routine surveillance is required to monitor the performance of tuberculosis diagnostic programme and is essential for the rapid detection of drug resistance. The main objective of this study was to explore the effectiveness and stakeholder perception of the current routine surveillance system for previously treated tuberculosis cases in Tanzania with a view to identify interventions to improve and accelerate positive patient outcomes. Methods: A study using quantitative and qualitative methods of data collection including in-depth interviews and focus group discussions with health care service providers was conducted in four regions. Quantitative data were extracted from the routine databases to assess performance. Results: Quantitative findings from 2011 to 2013 showed 2,750 specimens from previously treated TB cases were received at the reference laboratory. The number increased year on year, but even in the most recent year was only 61% of that expected. The median and interquartile range of turnaround time in days from specimen reception to results reported for smear microscopy, culture and drug susceptibility testing were 1(1, 1), 61(43, 71) and 129(72, 170) respectively. Contaminated specimens were reported in 3.6% of cases. The qualitative analysis showed the system of sending specimens using postal services was seen to be efficient by participants. However, there were many challenges and significant delays in specimens reaching the reference laboratory associated with lack of funds to transfer specimens, weak form completion, inadequate training and poor supervision. These all adversely affected the implementation of the routine surveillance system. Conclusions: Many issues limit the effectiveness of the routine surveillance system in Tanzania. Priority areas for strengthening are; specimen transportation, supervision and availability of commodities. A pilot study of a revised routine surveillance system that takes into account the observations from this study alongside improved access to drug susceptibility testing using Xpert MTB/RIF should be considered. [ABSTRACT FROM AUTHOR]

A Partial Least Squares (PLS) carbonate (CO3) prediction model was developed for soils throughout the contiguous United States using mid-infrared (MIR) spectroscopy. Excellent performance was achieved over an extensive geographic and chemical diversity of soils. A single model for all soil types performed very well with a root mean square error of prediction (RMSEP) of 12.6 g kg-1 and was further improved if Histosols were excluded (RMSEP 11.1 g kg-1). Exclusion of Histosols was particularly beneficial for accurate prediction of CO3 values when the national model was applied to an independent regional dataset. Little advantage was found in further narrowing the taxonomic breadth of the calibration dataset, but higher precision was obtained by running models for a restricted range of CO3. A model calibrated using only on the independent regional dataset, was unable to accurately predict CO3 content for the more chemically diverse national dataset. Ten absorbance peaks enabling CO3 prediction by mid-infrared (MIR) spectroscopy were identified and evaluated for individual and combined predictive power. A single-band model derived from an absorbance peak centered at 1796 cm-yielded the lowest RMSEP of 13.5 g kg-1 for carbonate prediction compared to other single-band models. This predictive power is attributed to the strength and sharpness of the peak, and an apparent minimal overlap with confounding co-occurring spectral features of other soil components. Drawing from the 10 identified bands, multiple combinations of 3 or 4 peaks were able to predict CO3 content as well as the full-spectrum national models. Soil CO3 is an excellent example of a soil parameter that can be predicted with great effectiveness and generality, and MIR models could replace direct laboratory measurement as a lower cost, high quality alternative. [ABSTRACT FROM AUTHOR]

Mobilization of trace metals from soils to surface waters can impact both human and ecosystem health. This study resamples a water sample archive to explore the spatial pattern of streamwater total concentrations of arsenic, cadmium, copper, lead, and zinc and their associations with biogeochemical controls in northern New England. Road deicing appears to result in elevated trace metal concentrations, as trace metal concentrations are strongly related to sodium concentrations and are most elevated when the sodium: chloride ratio is near 1.0 (~halite). Our results are consistent with previous laboratory and field studies that indicate cation exchange as a metal mobilization mechanism when road salt is applied to soils containing metals. This study also documents associations among sodium, chloride, dissolved organic carbon, iron, and metal concentrations, suggesting cation exchange mechanisms related to road deicing are not the only mechanisms that increase trace metal concentrations in surface waters. In addition to cation exchange, this study considers dissolved organic carbon complexation and oxidation-reduction conditions affecting metal mobility from soils in a salt-rich environment. These observations demonstrate that road deicing has the potential to increase streamwater trace metal concentrations across broad spatial scales and increase risks to human and ecosystem health. [ABSTRACT FROM AUTHOR]

In the era of big science, countries allocate big research and development budgets to large scientific facilities that boost collaboration and research capability. A nuclear fusion device called the “tokamak” is a source of great interest for many countries because it ideally generates sustainable energy expected to solve the energy crisis in the future. Here, to explore the scientific effects of tokamaks, we map a country’s research capability in nuclear fusion research with normalized revealed comparative advantage on five topical clusters—material, plasma, device, diagnostics, and simulation—detected through a dynamic topic model. Our approach captures not only the growth of China, India, and the Republic of Korea but also the decline of Canada, Japan, Sweden, and the Netherlands. Time points of their rise and fall are related to tokamak operation, highlighting the importance of large facilities in big science. The gravity model points out that two countries collaborate less in device, diagnostics, and plasma research if they have comparative advantages in different topics. This relation is a unique feature of nuclear fusion compared to other science fields. Our results can be used and extended when building national policies for big science. [ABSTRACT FROM AUTHOR]

Dengue is a national priority disease in Cambodia. The Cambodian National Dengue Surveillance System is based on passive surveillance of dengue-like inpatients reported by public hospitals and on a sentinel, pediatric hospital-based active surveillance system. This system works well to assess trends but the sensitivity of the early warning and time-lag to usefully inform hospitals can be improved. During The ECOnomic development, ECOsystem MOdifications, and emerging infectious diseases Risk Evaluation (ECOMORE) project’s knowledge translation platforms, Cambodian hospital staff requested an early warning tool to prepare for major outbreaks. Our objective was therefore to find adapted tools to improve the early warning system and preparedness. Dengue data was provided by the National Dengue Control Program (NDCP) and are routinely obtained through passive surveillance. The data were analyzed at the provincial level for eight Cambodian provinces during 2008–2015. The R surveillance package was used for the analysis. We evaluated the effectiveness of Bayesian algorithms to detect outbreaks using count data series, comparing the current count to an expected distribution obtained from observations of past years. The analyses bore on 78,759 patients with dengue-like syndromes. The algorithm maximizing sensitivity and specificity for the detection of major dengue outbreaks was selected in each province. The overall sensitivity and specificity were 73% and 97%, respectively, for the detection of significant outbreaks during 2008–2015. Depending on the province, sensitivity and specificity ranged from 50% to 100% and 75% to 100%, respectively. The final algorithm meets clinicians’ and decisionmakers’ needs, is cost-free and is easy to implement at the provincial level. [ABSTRACT FROM AUTHOR]

Mobile, vehicle-installed road weather sensors are becoming ubiquitous. While mobile sensors are often capable of making observations on a high frequency, their reliability and accuracy may vary. Large-scale road weather observation and forecasting are still mostly based on stationary road weather stations (RWS). Though expensive, sparsely located and making observations on a relatively low frequency, RWS’ reliability and accuracy are well-known and accommodated for in the road weather forecasting models. Statistical analysis revealed that road weather conditions indeed have a great effect on how the observations of mobile and stationary road weather temperature sensors differ from each other. Consequently, we calibrated the observations of mobile sensors with a linear mixed model. The mixed model was fitted fusing ca. 20 000 pairs of mobile and RWS observations of the same location at the same time, following a rendezvous model of sensor calibration. The calibration nearly halved the MSE between the observations of the mobile and the RWS sensor types. Computationally very light, the calibration can be embedded directly in the sensors. [ABSTRACT FROM AUTHOR]

Background: Cystic echinococcosis (CE) is a globally occurring zoonosis, whereas alveolar echinococcosis (AE) is endemic only in certain parts of the Northern Hemisphere. The socioeconomic impact of human echinococcosis has been shown to be considerable in highly endemic regions. However, detailed data on direct healthcare-related costs associated with CE and AE are scarce for high income countries. The aim of this study was to evaluate direct costs of human disease caused by CE and AE in Austria. Methods: Clinical data from a registry maintained at a national reference center for echinococcosis at the Medical University of Vienna were obtained for the years 2012–2014. These data were used in conjunction with epidemiological data from Austria’s national disease reporting system and diagnostic reference laboratory for echinococcosis to assess nationwide costs attributable to CE and AE. Results: In Austria, total modelled direct costs were 486,598€ (95%CI 341,825€ – 631,372€) per year for CE, and 683,824€ (95%CI 469,161€ - 898,486€) for AE. Median costs per patient with AE from diagnosis until the end of a 10-year follow-up period were 30,832€ (25th– 75th percentile: 23,197€ - 31,220€) and 62,777€ (25th– 75th percentile: 60,806€ - 67,867€) for inoperable and operable patients, respectively. Median costs per patients with CE from diagnosis until end of follow-up after 10 years were 16,253€ (25th– 75th percentile: 8,555€ - 24,832€) and 1,786€ (25th– 75th percentile: 736€ - 2,146€) for patients with active and inactive cyst stages, respectively. The first year after inclusion was the most cost-intense year in the observed period, with hospitalizations and albendazole therapy the main contributors to direct costs. Conclusions: This study provides detailed information on direct healthcare-related costs associated with CE and AE in Austria, which may reflect trends for other high-income countries. Surgery and albendazole therapy, due to surprisingly high drug prices, were identified as important cost-drivers. These data will be important for cost-effectiveness analyses of possible prevention programs. [ABSTRACT FROM AUTHOR]

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

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

Salivary alpha-amylase (sAA) activity has been widely used in psychological and medical research as a surrogate marker of sympathetic nervous system activation, though its utility remains controversial. The aim of this work was to compare alternative intensive longitudinal models of sAA data: (a) a traditional model, where sAA is a function of hour (hr) and hr squared (sAAj , t = f(hr, hr2), and (b) an autoregressive model, where values of sAA are a function of previous values (sAAj , t = f(sAA j , t-1, sAA j , t-2, …, sAA j , t-p). Nineteen normal subjects (9 males and 10 females) participated in the experiments and measurements were performed every hr between 9:00 and 21:00 hr. Thus, a total of 13 measurements were obtained per participant. The Napierian logarithm of the enzymatic activity of sAA was analysed. Data showed that a second-order autoregressive (AR(2)) model was more parsimonious and fitted better than the traditional multilevel quadratic model. Therefore, sAA follows a process whereby, to forecast its value at any given time, sAA values one and two hr prior to that time (sAA j , t = f(SAAj , t-1, SAAj , t-2) are most predictive, thus indicating that sAA has its own inertia, with a “memory” of the two previous hr. These novel findings highlight the relevance of intensive longitudinal models in physiological data analysis and have considerable implications for physiological and biobehavioural research involving sAA measurements and other stress-related biomarkers. [ABSTRACT FROM AUTHOR]

Previous studies have found a positive effect of cosmetics on certain behavioral measures, such as the tip given to waitresses by male patrons. These studies have employed confederates who usually wear cosmetics. We therefore sought to examine whether the positive effect found in these studies could, in part, be explained by a change in behavior. In order to test the possibility of a ‘cosmetics placebo effect’, we employed a confederate to solicit donations from passersby. On some days our confederate would not have any cosmetics applied to her face (i.e., no cosmetics condition), on some days cosmetics were pretended to be applied to her face (i.e., placebo cosmetics condition), and on other days cosmetics were actually applied to her face (i.e., cosmetics condition). In line with previous research, we found that across conditions men donated significantly more than women to our female solicitor, providing support for the ‘showoff hypothesis’, in which male generosity serves as a mating tactic. When investigating men’s donations in more detail, we found that the highest percentage of donations came in the cosmetics condition, followed by the placebo cosmetics condition, and then by no cosmetics condition. The effect of condition on donation rates, however, was not statistically significant. Our study was limited to one solicitor and one dependent variable (i.e., percentage of people approached who donated) and therefore future research would benefit from using more confederates as well as examining other behavioral measures. Given the influence of cosmetics use on so many real-world outcomes, we believe that further exploration into a possible ‘cosmetics placebo effect’ would be valuable. [ABSTRACT FROM AUTHOR]

Despite of an extensive statistical literature showing that discretizing continuous variables results in substantial loss of information, categorization of continuous variables has been a common practice in clinical research and in cancer dose finding (phase I) clinical trials. The objective of this study is to quantify the loss of information incurred by using a discrete set of doses to estimate the maximum tolerated dose (MTD) in phase I trials, instead of a continuous dose support. Escalation With Overdose Control and Continuous Reassessment Method were used because they are model-based designs where dose can be specified either as continuous or as a set of discrete levels. Five equally spaced sets of doses with different interval lengths and three sample sizes with sixteen scenarios were evaluated to compare the operating characteristics between continuous and discrete dose designs by Monte Carlo simulation. Loss of information was quantified by safety and efficiency measures. We conclude that if there is insufficient knowledge about the true MTD value, as commonly happens in phase I clinical trials, a continuous dose scheme minimizes information loss. If one is required to implement a design using discrete doses, then a scheme with 9 to 11 doses may yield similar results to the continuous dose scheme. [ABSTRACT FROM AUTHOR]

The wind- and rainfall areas of tropical cyclones (TCs) making landfall over South Korea were examined for the period 1998–2013 by using the Modern Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2) and Tropical Rainfall Measuring Mission (TRMM) 3B42 data. Here, the wind- and rainfall areas were defined as the regions where wind speeds and precipitation rates exceed 14 m s-1 and 80 mm day-1 within 1000 km from the TC center, respectively. In general, TCs show significantly asymmetric wind and rainfall structures, with strong vertical wind shear appearing over South Korea during the landfall period. The rainfall area significantly increases with environmental vertical wind shear while the wind area is not sensitive to it. Composite analyses of the cases of strong and weak vertical wind shear confirm that the increase of rainfall area is related to the asymmetric convection (rising/sinking motion in the downshear-left/upshear-right side) induced by the vertical wind shear. This work highlights the importance of local atmospheric environment in determining the area primarily affected by strong winds or heavy rainfall during TC landfalls. [ABSTRACT FROM AUTHOR]

The British Library and STFC are working together to connect metadata relating to PhD theses to use of research facilities provided by STFC. Through the creation of a graph which connects metadata across EThOS, the UK national e-theses repository, the STFC insitutional repository ePubs and the Diamond Light Source repository, links between the theses, authors and instiutions have been made. This pilot work has the potential to be extended to enhance the metadata stored within EThOS which is administered by The British Library. This work presents an exciting possibility for other institutions as this graph will present a method to enable the bi-directional updating of metadata held across different systems. [ABSTRACT FROM AUTHOR]

Introduction: Internal and external quality control (QC) of rapid diagnostic tests (RDTs) is important to increase reliability of RDTs currently used to diagnose malaria. However, cross-checking of used RDTs as part of quality assurance can rarely be done by off-site personnel because there is no guarantee of retaining visible test lines after manufacturers’ recommended reading time. Therefore, this study examined the potential of using Fionet™ technology for remote RDT quality monitoring at seven clinics, identifying reasons for making RDT processing and interpretation errors, and taking corrective actions for improvement of diagnosis and consequently improved management of febrile patients Methods: The study was conducted at seven military health facilities in Mainland Tanzania and utilized RDTs capable of detecting Plasmodium falciparum specific Histidine-rich protein 2 (Pf-HRP2) and the genus specific Plasmodium lactate dehydrogenase (pLDH) for other species of plasmodium (P. vivax, P. malariae or P. ovale; pan-pLDH). Patients’ data and images of processed RDTs from seven clinics were uploaded on a Fionet web portal and reviewed regularly to monitor preparation procedures and visual interpretation of test results compared to automated analysis using the Deki reader of RDT. Problems detected were rapidly communicated to remote laboratory personnel at the clinic for corrective action and follow-up of patients who were falsely diagnosed as negative and missed treatment. Factors contributing to making errors in visual interpretation of RDT results were analyzed during visits to the health facilities. Results: A total of 1,367 (1.6%) out of 83,294 RDT test images uploaded to the Fionet portal had discordant test results of which 822 (60.1%) and 545 (39.9%) were falsely reported as negative and positive, respectively. False negative and false positive test results were common for a single test line in 515 (62.7%) and 741 (54.2%) tests, respectively. Out of 1,367 RDT images assessed, 98 (7.2%) had quality problems related to preparation procedures of which 95(96.9%) errors were due to putting too much blood on the sample well or insufficient buffer in the respective wells. The reasons for discrepant results included, false reporting of none existent lines in 526 (38.5%) tests, missing a faint positive line in 493 (36.1%), missing a strong positive line in 248(18.1%) and errors caused by poorly processed RDTs in 96 (7.2%) tests. Among the false negative tests (n = 822), 669 (48.9%) patients were eligible for follow–up and only 339 (48.5%) were reached and 291 (85.8%) received appropriate anti-malaria therapy. Conclusion: Fionet technology enabled remote monitoring of RDT quality issues, identifying reasons contributing to laboratory personnel making errors and provided a rapid method to implement corrective actions at remote sites to improve malaria diagnosis and consequently improved health care management of febrile patients infected with malaria. [ABSTRACT FROM AUTHOR]

The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, . The purpose of the BRCA Exchange is to provide the community with a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype. More than 20,000 variants have been aggregated, three times the number found in the next-largest public database at the project’s outset, of which approximately 6,150 have expert classifications. The data set is based on shared information from existing clinical databases—Breast Cancer Information Core (BIC), ClinVar, and the Leiden Open Variation Database (LOVD)—as well as population databases, all linked to a single point of access. The BRCA Challenge has brought together the existing international Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium expert panel, along with expert clinicians, diagnosticians, researchers, and database providers, all with a common goal of advancing our understanding of BRCA1 and BRCA2 variation. Ongoing work includes direct contact with national centers with access to BRCA1 and BRCA2 diagnostic data to encourage data sharing, development of methods suitable for extraction of genetic variation at the level of individual laboratory reports, and engagement with participant communities to enable a more comprehensive understanding of the clinical significance of genetic variation in BRCA1 and BRCA2. [ABSTRACT FROM AUTHOR]

Recent changes in institutional cyberinfrastructure and collections data storage methods have dramatically improved accessibility of specimen-based data through the use of digital databases and data aggregators. This analysis of digitized fish collections in the U.S. demonstrates how information from data aggregators, in this case iDigBio, can be extracted and analyzed. Data from U.S. institutional fish collections in iDigBio were explored through a strictly programmatic approach using the ridigbio package and fishfindR web application. iDigBio facilitates the aggregation of collections data on a purely voluntary fashion that requires collection staff to consent to sharing of their data. Not all collections are sharing their data with iDigBio, but the data harvested from 38 of the 143 known fish collections in the U.S. that are in iDigBio account for the majority of fish specimens housed in U.S. collections. In the 22 years since publication of the last survey providing information on these 38 collections, 1,219,168 specimen records (lots), 15,225,744 specimens, 3,192 primary types, and 32,868 records of secondary types have been added. This is an increase of 65.1% in the number of cataloged records and an increase of 56.1% in the number of specimens. In addition to providing specimen-based data for research, education, and various outreach activities, data that are accessible via data aggregators can be used to develop accurate, up-to-date reports of information on institutional collections. Such reports present collections data in an organized and accessible fashion and can guide targeted efforts by collections personnel to meet discipline-specific needs and make data more transparent to downstream users. Data from this survey will be updated and published regularly in a dynamic web application that will aid collections staff in communicating collections value while simultaneously giving stakeholders a way to explore collections holdings as they relate to the institutions in which they are housed. It is through this resource that collections will be able to leverage their data against those of similar collections to aid in the procurement of financial and institutional support. [ABSTRACT FROM AUTHOR]

Background: To enable incremental optimization of screening, regular reporting of quality indicators is required. Aim: To report key quality indicators and basic statistics about cervical screening in Sweden. Methods: We collected individual level data on all cervical cytologies, histopathologies, human papillomavirus tests and all invitations for cervical screening in Sweden during 2013–2016. Results: There were over 2,278,000 cervical samples collected in Sweden in 2014–2016. Organized samples (resulting from an invitation) constituted 69% of samples. The screening test coverage of all resident women aged 23–60 was 82%. The coverage has slowly increased for >10 years. There is large variability between counties (from 71% to 92%) over time. There were 25,725 women with high-grade lesions in cytology during 2013–2015. Only 96% of these women had a follow-up histopathology within a year. Cervical cancer incidence showed an increasing trend. Conclusion: Key quality indicators such as population coverage and follow-up rates were stable or improving, but there was nevertheless an unexplained cervical cancer increase. [ABSTRACT FROM AUTHOR]

Introduction: Shared decision making (SDM) is a process whereby decisions are made together by patients and/or families and clinicians. Nevertheless, few patients are aware of its proven benefits. This study investigated the feasibility, acceptability and impact of an intervention to raise public awareness of SDM in public libraries. Materials and methods: A 1.5 hour interactive workshop to be presented in public libraries was co-designed with Quebec City public library network officials, a science communication specialist and physicians. A clinical topic of maximum reach was chosen: antibiotic overuse in treatment of acute respiratory tract infections. The workshop content was designed and a format, whereby a physician presents the information and the science communication specialist invites questions and participation, was devised. The event was advertised to the general public. An evaluation form was used to collect data on participants’ sociodemographics, feasibility and acceptability components and assess a potential impact of the intervention. Facilitators held a post-workshop focus group to qualitatively assess feasibility, acceptability and impact. Results: All 10 planned workshops were held. Out of 106 eligible public participants, 89 were included in the analysis. Most participants were women (77.6%), retired (46.1%) and over 45 (59.5%). Over 90% of participants considered the workshop content to be relevant, accessible, and clear. They reported substantial average knowledge gain about antibiotics (2.4, 95% Confidence Interval (CI): 2.0–2.8; P < .001) and about SDM (4.0, 95% CI: 3.4–4.5; P < .001). Self-reported knowledge gain about SDM was significantly higher than about antibiotics (4.0 versus 2.4; P < .001). Knowledge gain did not vary by sociodemographic characteristics. The focus group confirmed feasibility and suggested improvements. Conclusions: A public library intervention is feasible and effective way to increase public awareness of SDM and could be a new approach to implementing SDM by preparing potential patients to ask for it in the consulting room. [ABSTRACT FROM AUTHOR]

Laboratory science requires careful maintenance of sterile reagents and tools as well as the sterilization of waste prior to disposal. However, steam autoclaves typically used for this purpose may not be readily accessible to everyone in the scientific community, such as K-12 teachers, researchers in the field, students in under-funded laboratories, or persons in the developing world who lack funding and resources. This work examines the use of commercial electric pressure cookers as an alternative method for the sterilization of media, instruments, and waste. Four commonly available brands of pressure cooker were tested for their ability to sterilize microbiological media, a variety of metal instruments, and high-titer microbial cultures. All four pressure cookers were able to sterilize these starting materials as well as a range of microbial types, including Gram-positive bacteria, Gram-negative bacteria, filamentous fungi, unicellular fungi, and mixed environmental samples. Only the Instant Pot, however, was able to sterilize autoclave tester ampoules of Geobacillus stearothermophilus spores. These results suggest that, depending on the nature of the work undertaken, store-bought pressure cookers can be an appropriate substitute for commercial autoclaves. Their adoption may also help increase the accessibility of science to a broader range of investigators. [ABSTRACT FROM AUTHOR]

Bias accusations have eroded trust in journalism to impartially check facts. Traditionally journalists have avoided responding to such accusations, resulting in an imbalanced flow of arguments about the news media. This study tests what would happen if journalists spoke up more in defense of their profession, while simultaneously also testing effects of doing more fact checking. A five-day field experiment manipulated whether an online news portal included fact check stories and opinion pieces defending journalism. Fact checking was beneficial in terms of three democratically desirable outcomes–media trust, epistemic political efficacy, and future news use intent–only when defense of journalism stories were also present. No partisan differences were found in effects: Republicans, Democrats, and Independents were all affected alike. These results have important implications for journalistic practice as well as for theories and methods of news effects. [ABSTRACT FROM AUTHOR]

Quantum++ is a modern general-purpose multi-threaded quantum computing library written in C++11 and composed solely of header files. The library is not restricted to qubit systems or specific quantum information processing tasks, being capable of simulating arbitrary quantum processes. The main design factors taken in consideration were the ease of use, portability, and performance. The library’s simulation capabilities are only restricted by the amount of available physical memory. On a typical machine (Intel i5 8Gb RAM) Quantum++ can successfully simulate the evolution of 25 qubits in a pure state or of 12 qubits in a mixed state reasonably fast. The library also includes support for classical reversible logic, being able to simulate classical reversible operations on billions of bits. This latter feature may be useful in testing quantum circuits composed solely of Toffoli gates, such as certain arithmetic circuits. [ABSTRACT FROM AUTHOR]

Lakes are a key geographical feature in Canada and have an impact on the regional climate. In the winter, they are important for recreational activities such as snowmobiling and ice fishing and act as part of an important supply route for northern communities. The ability to accurately report lake ice characteristics such as thickness is vital, however, it is underreported in Canada and there is a lack of lake ice thickness records for temperate latitude areas such as Central Ontario. Here, we evaluate the application of previously developed temperature models and RADARSAT-2 for estimating lake ice thickness in Central Ontario and provide insight into the regions long term ice thickness variability. The ALS Environmental Science Shallow Water Ice Profiler (SWIP) was used for validation of both temperature and radar-based models. Results indicate that the traditional approach that uses temperatures to predict ice thickness during ice growth has low RMSE values of 2.3 cm and correlations of greater than 0.9. For ice decay, similar low RMSE values of 2.1 cm and high correlations of 0.97 were found. Using RADARSAT-2 to estimate ice thickness results in R2 values of 0.6 (p < 0.01) but high RMSE values of 11.7 cm. Uncertainty in the RADARSAT-2 approach may be linked to unexplored questions about scattering mechanisms and the interaction of radar signal with mid-latitude lake ice. The application of optimized temperature models to a long-term temperature record revealed a thinning of ice cover by 0.81 cm per decade. [ABSTRACT FROM AUTHOR]

Background: The knowledge of circulating HCV genotypes and subtypes in a country is crucial to guide antiviral therapy and to understand local epidemiology. Studies investigating circulating HCV genotypes and their trends have been conducted in Belgium. However they are outdated, lack nationwide representativeness or were not conducted in the general population. Methods: In order to determine the distribution of different circulating HCV genotypes in Belgium, we conducted a multicentre study with all the 19 Belgian laboratories performing reimbursed HCV genotyping assays. Available genotype and subtype data were collected for the period from 2008 till 2015. Furthermore, a limited number of other variables were collected: some demographic characteristics from the patients and the laboratory technique used for the determination of the HCV genotype. Results: For the study period, 11,033 unique records collected by the participating laboratories were used for further investigation. HCV genotype 1 was the most prevalent (53.6%) genotype in Belgium, with G1a and G1b representing 19.7% and 31.6%, respectively. Genotype 3 was the next most prevalent (22.0%). Further, genotype 4, 2, and 5 were responsible for respectively 16.1%, 6.2%, and 1.9% of HCV infections. Genotype 6 and 7 comprise the remaining <1%. Throughout the years, a stable distribution was observed for most genotypes. Only for genotype 5, a decrease as a function of the year of analysis was observed, with respectively 3.6% for 2008, 2.3% for 2009 and 1.6% for the remaining years. The overall M:F ratio was 1.59 and was mainly driven by the high M:F ratio of 3.03 for patients infected with genotype 3. Patients infected with genotype 3 are also younger (mean age 41.7 years) than patients infected with other genotypes (mean age above 50 years for all genotypes). The patients for whom a genotyping assay was performed in 2008 were younger than those from 2015. Geographical distribution demonstrates that an important number of genotyped HCV patients live outside the Belgian metropolitan cities. Conclusion: This national monitoring study allowed a clear and objective view of the circulating HCV genotypes in Belgium and will help health authorities in the establishment of cost effectiveness determinations before implementation of new treatment strategies. This baseline characterization of the circulating genotypes is indispensable for a continuous surveillance, especially for the investigation of the possible impact of migration from endemic regions and prior to the increasing use of highly potent direct-acting antiviral (DAA) agents. [ABSTRACT FROM AUTHOR]

The discovery of the life-threatening zoonotic infection Plasmodium knowlesi has added to the challenges of prompt and accurate malaria diagnosis and surveillance. In this study from Aceh Province, Indonesia, a malaria elimination setting where P. knowlesi endemicity was not previously known, we report the laboratory investigation and difficulties encountered when using molecular detection methods for quality assurance of microscopically identified clinical cases. From 2014 to 2015, 20 (49%) P. falciparum, 16 (39%) P. vivax, 3 (7%) P. malariae, and 2 (5%) indeterminate species were identified by microscopy from four sentinel health facilities. At a provincial-level reference laboratory, loop-mediated isothermal amplification (LAMP), a field-friendly molecular method, was performed and confirmed Plasmodium in all samples though further species-identification was limited by the unavailability of non-falciparum species-specific testing with the platform used. At a national reference laboratory, several molecular methods including nested PCR (nPCR) targeting the 18 small sub-unit (18S) ribosomal RNA, nPCR targeting the cytochrome-b (cytb) gene, a P. knowlesi-specific nPCR, and finally sequencing, were necessary to ultimately classify the samples as: 19 (46%) P. knowlesi, 8 (20%) P. falciparum, 14 (34%) P. vivax. Microscopy was unable to identify or mis-classified up to 56% of confirmed cases, including all cases of P. knowlesi. With the nPCR methods targeting the four human-only species, P. knowlesi was missed (18S rRNA method) or showed cross-reactivity for P. vivax (cytb method). To facilitate diagnosis and management of potentially fatal P. knowlesi infection and surveillance for elimination of human-only malaria in Indonesia and other affected settings, new detection methods are needed for testing at the point-of-care and in local reference laboratories. [ABSTRACT FROM AUTHOR]

In addition to high vaccination coverage, timely and accurate laboratory confirmation of measles cases is critical to interrupt measles transmission. To evaluate the role of real-time reverse transcription-polymerase chain reaction (RT-PCR) in the diagnosis of measles cases, 46,363 suspected measles cases with rash and 395 suspected measles cases without rash were analyzed in this study; the cases were obtained from the Chinese measles surveillance system (MSS) during 2014–2017 and simultaneously detected by measles-specific IgM enzyme-linked immunosorbent assay (ELISA) and real-time RT-PCR. However, some IgM-negative measles cases were identified by real-time RT-PCR. The proportion of these IgM-negative and viral nucleic acid-positive measles cases was high among measles cases with measles vaccination history, cases without rash symptoms, and cases within 3 days of specimen collection after onset. The proportion of IgM-negative and viral nucleic acid-positive measles cases in the 0–3 day group was up to 14.4% for measles cases with rash and 40% for measles cases without rash. Moreover, the proportions of IgM-negative and nucleic acid-positive measles cases gradually increased with the increase in the measles vaccination dose. Therefore, integrated with IgM ELISA, real-time RT-PCR would greatly improve the accurate diagnosis of measles cases and avoid missing the measles cases, especially for measles cases during the first few days after onset when the patients were highly contagious and for measles cases with secondary vaccine failure. In conclusion, our study reconfirmed that IgM ELISA is the gold-standard detection assay for measles cases confirmation. However, real-time RT-PCR should be introduced and used to supplement the laboratory diagnosis, especially in the setting of pre-elimination and/or elimination wherever appropriate. [ABSTRACT FROM AUTHOR]

Genetic testing availability in the health care system is rapidly increasing, along with the diffusion of next-generation sequencing (NGS) into diagnostics. These issues make imperative the knowledge-drive optimization of testing in the clinical setting. Time estimations of wet laboratory procedure in Italian molecular laboratories offering genetic diagnosis were evaluated to provide data suitable to adjust efficiency and optimize health policies and costs. A survey was undertaken by the Italian Society of Human Genetics (SIGU). Forty-two laboratories participated. For most molecular techniques, the most time-consuming steps are those requiring an intensive manual intervention or in which the human bias can affect the global process time-performances. For NGS, for which the study surveyed also the interpretation time, the latter represented the step that requiring longer times. We report the first survey describing the hands-on times requested for different molecular diagnostics procedures, including NGS. The analysis of this survey suggests the need of some improvements to optimize some analytical processes, such as the implementation of laboratory information management systems to minimize manual procedures in pre-analytical steps which may affect accuracy that represents the major challenge to be faced in the future setting of molecular genetics laboratory. [ABSTRACT FROM AUTHOR]

The use of human neuroimaging technology provides knowledge about several emotional and cognitive processes at the neural level of organization. In particular, electroencephalographic (EEG) techniques allow researchers to explore high-temporal resolution of the neural activity that underlie the dynamics of cognitive processes. Although EEG research has been mostly applied in laboratory settings, recently a low-cost, portable EEG apparatus was released, which allows exploration of different emotional and cognitive processes during every-day activities. We compared a wide range of EEG measures using both a low-cost portable and a high-quality laboratory system. EEG recordings were done with both systems while participants performed an active task (Go/NoGo) and during their resting-state. Results showed similar waveforms in terms of morphology and amplitude of the ERPs, and comparable effects between conditions of the applied Go/NoGo paradigm. In addition, the contribution of each frequency to the entire EEG was not significantly different during resting-state, and fluctuations in amplitude of oscillations showed long-range temporal correlations. These results showed that low-cost, portable EEG technology can provide an alternative of enough quality for measuring brain activity outside a laboratory setting, which could contribute to the study of different populations in more ecological contexts. [ABSTRACT FROM AUTHOR]

Background: Currently, molecular xenomonitoring efforts for lymphatic filariasis rely on PCR or real-time PCR-based detection of Brugia malayi, Brugia timori and Wuchereria bancrofti in mosquito vectors. Most commonly, extraction of DNA from mosquitoes is performed using silica column-based technologies. However, such extractions are both time consuming and costly, and the diagnostic testing which follows typically requires expensive thermal cyclers or real-time PCR instruments. These expenses present significant challenges for laboratories in many endemic areas. Accordingly, in such locations, there exists a need for inexpensive, equipment-minimizing diagnostic options that can be transported to the field and implemented in minimal resource settings. Here we present a novel diagnostic approach for molecular xenomonitoring of filarial parasites in mosquitoes that uses a rapid, NaOH-based DNA extraction methodology coupled with a portable, battery powered PCR platform and a test strip-based DNA detection assay. While the research reported here serves as a proof-of-concept for the backpack PCR methodology for the detection of filarial parasites in mosquitoes, the platform should be easily adaptable to the detection of W. bancrofti and other mosquito-transmitted pathogens. Methodology/Principal findings: Through comparisons with standard silica column-based DNA extraction techniques, we evaluated the performance of a rapid, NaOH-based methodology for the extraction of total DNA from pools of parasite-spiked vector mosquitoes. We also compared our novel test strip-based detection assay to real-time PCR and conventional PCR coupled with gel electrophoresis, and demonstrated that this method provides sensitive and genus-specific detection of parasite DNA from extracted mosquito pools. Finally, by comparing laboratory-based thermal cycling with a field-friendly miniaturized PCR approach, we have demonstrated the potential for the point-of-collection-based use of this entire diagnostic platform that is compact enough to fit into a small backpack. Conclusions/Significance: Because this point-of-collection diagnostic platform eliminates reliance on expensive and bulky instrumentation without compromising sensitivity or specificity of detection, it provides an alternative to cost-prohibitive column-dependent DNA extractions that are typically coupled to detection methodologies requiring advanced laboratory infrastructure. In doing so, this field-ready system should increase the feasibility of molecular xenomonitoring within B. malayi-endemic locations. Of greater importance, this backpack PCR system also provides the proof-of-concept framework for the development of a parallel assay for the detection of W. bancrofti. [ABSTRACT FROM AUTHOR]

The rates of pulmonary colonization and disease due to nontuberculous mycobacteria (NTM) appear to be increasing globally, but diversity of species recovered as well as clinical relevance of NTM isolates differ considerably by geographic region. The first nationwide study of isolation frequency and clinical significance of NTM in Serbia included all patients with respiratory specimens yielding a positive NTM culture over the six-year period, 2010–2015. We analyzed trends in annual NTM isolation and NTM pulmonary disease (PD) incidence rates, with NTM PD cases defined in accordance with microbiological criteria established by the American Thoracic Society/Infectious Diseases Society of America (ATS/IDSA). 777 pulmonary NTM isolates were collected from 565 patients, of whom 126 (22.3%) met the ATS/IDSA criteria. The annual NTM isolation and NTM PD incidence rates per 100,000 changed over 2010–2015 from 0.9 to 1.6 (p = 0.1746) and from 0.18 to 0.48 (p = f0.0040), respectively. Both isolation and disease rates increased considerably with age, while higher NTM PD rates were also associated with residence in urbanized areas. Diversity of NTM species isolated was shown to be region-specific, with M. xenopi as the most prevalent species (17.3%), and increasing isolation rates of rapid growing mycobacteria (RGM) (p = 0.0072). M. xenopi was also the most common cause of NTM PD (28.6%), followed by RGM (27.8%). With 73% clinically relevant isolates, M. abscessus was identified as the most clinically relevant NTM species. While NTM PD obviously remains a rare disease in Serbia, the overall results justify recognition of NTM as pathogens of rising importance, and require further characterization of their epidemiology in the country. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhizal fungi (AMF) have been shown to influence plant community structure and diversity. Studies based on single plant–single AMF isolate experiments show that within AMF species variation leads to large differential growth responses of different plant species. Because of these differential effects, genetic differences among isolates of an AMF species could potentially have strong effects on the structure of plant communities. We tested the hypothesis that within species variation in the AMF Rhizophagus irregularis significantly affects plant community structure and plant co-existence. We took advantage of a recent genetic characterization of several isolates using double-digest restriction-site associated DNA sequencing (ddRADseq). This allowed us to test not only for the impact of within AMF species variation on plant community structure but also for the role of the R. irregularis phylogeny on plant community metrics. Nine isolates of R. irregularis, belonging to three different genetic groups (Gp1, Gp3 and Gp4), were used as either single inoculum or as mixed diversity inoculum. Plants in a mesocosm representing common species that naturally co-exist in European grasslands were inoculated with the different AMF treatments. We found that within-species differences in R. irregularis did not strongly influence the performance of individual plants or the structure of the overall plant community. However, the evenness of the plant community was affected by the phylogeny of the fungal isolates, where more closely-related AMF isolates were more likely to affect plant community evenness in a similar way compared to more genetically distant isolates. This study underlines the effect of within AMF species variability on plant community structure. While differential effects of the AMF isolates were not strong, a single AMF species had enough functional variability to change the equilibrium of a plant community in a way that is associated with the evolutionary history of the fungus. [ABSTRACT FROM AUTHOR]

The abundance of skeletal remains of cave bears in Pleistocene deposits can offer crucial information on the biology and life history of this megafaunal element. The histological study of 62 femora from 23 different European localities and comparisons with specimens of five extant ursid species revealed novel data on tissue types and growth patterns. Cave bear’s femoral bone microstructure is characterized by a fibrolamellar complex with increasing amounts of parallel-fibered and lamellar bone towards the outer cortex. Remodelling of the primary bone tissue initially occurs close to the perimedullary margin of the bone cortex around the linea aspera. Although similar histological traits can be observed in many extant bear species, the composition of the fibrolamellar complex can vary greatly. Cave bears reached skeletal maturity between the ages of 10 and 14, which is late compared to other bear species. There is a significant correlation between altitude and growth, which reflects the different body sizes of cave bears from different altitudes. [ABSTRACT FROM AUTHOR]

Measurement of pH in IVF-media using the blood gas analyzer (BGA) requires validation, because IVF-media is outside the intended scope of the BGA. To determine whether the Siemens Rapidpoint 500 BGA is suitable for pH measurements in IVF-media this study will validate the BGA and assess its accuracy. In this method comparison study, the pH of over three hundred IVF-media samples was measured with the BGA and a pH electrode (Hanna pH checker). The precision of both the BGA and the pH electrode were excellent (coefficient variation <1.4%). However, the closeness of agreement between measured values of both devices were not equivalent to each other in the tested IVF-media, showing 15% to 85% accordance between devices. The pH measured with the blood gas analyzer was also significantly higher in the tested media, compared to that measured by the pH electrode. One of the tested media did not reach its target pH when it was measured with the BGA, even at 9% CO2. The results show that the validated blood gas analyzer produces excellent results in terms of precision but not in terms of accuracy. Inaccurate measurement may lead to misinterpretation of results and consequently to suboptimal culture conditions. Therefore, each laboratory is encouraged to perform a validation of their BGA. [ABSTRACT FROM AUTHOR]

Cryptic species are a challenge for systematics, but their elucidation also may leave critical information gaps about the distribution, conservation status, and behavior of affected species. We use the leopard frogs of the eastern U.S. as a case study of this issue. We refined the known range of the recently described Rana kauffeldi, the Atlantic Coast Leopard Frog, relative to the region’s two other leopard frog species, conducted assessments of conservation status, and improved methods for separating the three species using morphological field characters. We conducted over 2,000 call and visual surveys and took photographs of and tissue samples from hundreds of frogs. Genetic analysis supported a three-species taxonomy and provided determinations for 220 individual photographed frogs. Rana kauffeldi was confirmed in eight U.S. states, from North Carolina to southern Connecticut, hewing closely to the Atlantic Coastal Plain. It can be reliably differentiated in life from R. pipiens, and from R. sphenocephala 90% of the time, based on such characters as the femoral reticulum patterning, dorsal spot size and number, and presence of a snout spot. However, the only diagnostic character separating R. kauffeldi from R. sphenocephala remains the breeding call described in 2014. Based on our field study, museum specimens, and prior survey data, we suggest that R. kauffeldi has declined substantially in the northern part of its range, but is more secure in the core of its range. We also report, for the first time, apparent extirpations of R. pipiens from the southeastern portion of its range, previously overlooked because of confusion with R. kauffeldi. We conclude with a generalized ecological research agenda for cryptic species. For R. kauffeldi, needs include descriptions of earlier life stages, studies of niche partitioning with sympatric congeners and the potential for hybridization, and identification of conservation actions to prevent further declines. [ABSTRACT FROM AUTHOR]

Backgrounds: The characteristics and conditions of growth and development have made adolescence one of the most vital and influential ages for prevention and health promotion, especially in the area of high-risk behaviors. Accordingly, the aim of this study was to determine adolescent health information seeking behavior related to high-risk behaviors in a selected educational district in Isfahan (Iran). Methodology: The present study was of an applied type, which was conducted using the survey research method. The statistical population consisted of adolescent students at public schools in Isfahan (6519 subjects), and the sample size was determined to be 364 based on Cochran's formula. The sampling method was of a cluster sampling type, and the data collection tool was a researcher-made questionnaire. The validity of the questionnaire was approved by medical librarians, and using the Cronbach's alpha method, the reliability was obtained to be 0.85. SPSS 16 software was used for data analysis at two statistical levels: descriptive and inferential (independent t-test, one-sample t-test, chi-square, Pearson correlation coefficient and Mann-Whitney). Findings: "Lack of mobility" was the most important health information need related to adolescent high-risk behaviors. The most important sources to obtain health information related to high-risk behaviors were "the Internet" with a mean score of 3.69 and "virtual social media" with a mean score of 3.49 out of 5. Adolescents had a positive attitude towards health information. The most important barriers to seeking health information were mentioned as follows: "difficulty in determining the quality of information found", "absence of appropriate information", and "concerns about the disclosure of their problems or illness to others". From the perspective of adolescents, the most important criterion for the evaluation of information quality was "the trueness and correctness of the information" and the need for health information related to high-risk behaviors was higher in girls than in boys. Conclusions/Significance: Considering adolescents’ positive attitude towards use of health information, it is necessary to put valid information at their disposal through different information resources, taking into account their level of information literacy. Accordingly, medical librarians’ abilities are suggested to be used for the production, evaluation, and introduction of health-related reading materials in the field of high-risk behaviors in easy language and suitable for adolescents. [ABSTRACT FROM AUTHOR]

Significance: Protocols for testing and reporting emissions of Harmful and Potentially Harmful Constituents (HPHCs) from electronic cigarettes (e-cigs) are lacking. The premise of this study is that multi-path relationships may be developed to describe interactions between product characteristics, use behavior and emissions to develop appropriate protocols for tobacco product regulatory compliance testing. Methods: This study proposes a framework consisting of three component terms: HPHC mass concentration, HPHC mass ratio and total particulate mass (TPM) concentration. The framework informs experiments to investigate dependence of aerosol emissions from five electronic cigarettes spanning several design generations and three e-liquids for six repeated trials at each of ten flow conditions. Results: Results are reported for TPM concentration as a function of flow conditions spanning the range of natural environment topography observed in prior studies. An empirical correlation describing TPM concentration as a function of flow conditions and coil power setting (6, 7.5 and 10 watts) for the Innokin iTaste MVP 2.0 vaporizer with Innokin iClear 30 dual coil tank is presented. Additional results document the impact of flow conditions and wick and coil design on TPM concentration through comparison of the Innokin iClear 30 (upper coil, capillary action wick) and the Innokin iClear X.I (lower coil, gravity fed wick) operated at 7.5 watts. The impact of e-liquid on TPM concentration is illustrated by comparing emissions from an NJOY Vape Pen filled with AVAIL Arctic Blast, Tobacco Row, and Mardi Gras e-liquids. TPM concentration is shown to depend upon flow conditions across a range of e-cigarette product designs including cig-a-like, pen-style, box-mod and emergent disposable-cartridge style devices. Conclusions: A framework provides a foundation for reporting emissions across a variety of e-cigs, e-liquids and research laboratories. The study demonstrates TPM concentration is a function of topography behavior (i.e. puff flow rate and puff duration) for varying device operating power and product characteristics. [ABSTRACT FROM AUTHOR]

Indo-Pacific red lionfish (Pterois volitans) have invaded the western Atlantic, and most recently the northern Gulf of Mexico (nGOM), at a rapid pace. Given their generalist habitat affinities and diet, and strong ecological overlap with members of the commercially valuable snapper-grouper complex, increased density and abundance of lionfish could result in significant competitive interactions with nGOM commercially important species. We experimentally investigated the intensity of behavioral interactions between lionfish and indigenous, abundant and economically important juvenile nGOM red snapper (Lutjanus campechanus), and other increasingly abundant juvenile tropical snapper species (gray snapper—L. griseus and lane snapper—L. synagris) in large outdoor mesocosms to examine snapper vulnerabilities to lionfish competition. When paired with lionfish, red snapper swimming activity (i.e., time swimming and roving around experimental tank or at structure habitat during experiments) was significantly lower than in intraspecific control trials, but gray and lane snapper swimming activities in the presence of lionfish did not significantly differ from their intraspecific controls. Additionally in paired trials, red and lane snapper swimming activities were significantly lower than those of lionfish, while no significant difference in swimming activities was observed between lionfish and gray snapper. We found that red snapper prey consumption rates in the presence of lionfish were significantly lower than in their intraspecific 3-individual control trials, but when paired together no significant differences in prey consumption rates between red snapper and lionfish were observed. When paired with lane or gray snapper, lionfish were observed having comparatively higher prey consumption than snappers, or as observed in lionfish intraspecific 1-individual controls. However, lane and gray snapper consumption rates in the presence of lionfish did not significantly differ from those in intraspecific controls. These findings suggest that competition between juvenile snappers and invasive lionfish may be variable, with lionfish exhibiting differing degrees of competitive dominance and snappers exhibiting partial competitive vulnerability and resistance to lionfish. While the degree of intensity at which these interactions may occur in nGOM reefs may differ from those observed in our findings, this study enables greater understanding of the potential ecological effects of red lionfish on native reef fishes. [ABSTRACT FROM AUTHOR]

The University of British Columbia Nepal Expedition took place over several months in the fall of 2016 and was comprised of an international team of 37 researchers. This paper describes the objectives, study characteristics, organization and management of this expedition, and presents novel blood gas data during acclimatization in both lowlanders and Sherpa. An overview and framework for the forthcoming publications is provided. The expedition conducted 17 major studies with two principal goals—to identify physiological differences in: 1) acclimatization; and 2) responses to sustained high-altitude exposure between lowland natives and people of Tibetan descent. We performed observational cohort studies of human responses to progressive hypobaric hypoxia (during ascent), and to sustained exposure to 5050 m over 3 weeks comparing lowlander adults (n = 30) with Sherpa adults (n = 24). Sherpa were tested both with (n = 12) and without (n = 12) descent to Kathmandu. Data collected from lowlander children (n = 30) in Canada were compared with those collected from Sherpa children (n = 57; 3400–3900m). Studies were conducted in Canada (344m) and the following locations in Nepal: Kathmandu (1400m), Namche Bazaar (3440m), Kunde Hospital (3480m), Pheriche (4371m) and the Ev-K2-CNR Research Pyramid Laboratory (5050m). The core studies focused on the mechanisms of cerebral blood flow regulation, the role of iron in cardiopulmonary regulation, pulmonary pressures, intra-ocular pressures, cardiac function, neuromuscular fatigue and function, blood volume regulation, autonomic control, and micro and macro vascular function. A total of 335 study sessions were conducted over three weeks at 5050m. In addition to an overview of this expedition and arterial blood gas data from Sherpa, suggestions for scientists aiming to perform field-based altitude research are also presented. Together, these findings will contribute to our understanding of human acclimatization and adaptation to the stress of residence at high-altitude. [ABSTRACT FROM AUTHOR]

Estimates of spatial patterns of broad-scale species richness are central to major questions in ecology, evolution and conservation. Yet, they are scarce due to incomplete information on species distributions. Often the only germane data derives from museum specimens collected during non-standardized sampling. Rarefaction, a promising approach to estimate broad-scale richness with these data, estimates the expected number of species represented in subsets of n specimens drawn from N specimens collected in a sampling unit. One version of rarefaction, known as individual-based rarefaction, assumes that the N specimens collected in a sampling unit constitute a random sample of individuals in that sampling unit. Another version, known as spatially explicit rarefaction, assumes that the N specimens collected in a sampling unit are spatially aggregated. We examined the working hypothesis that, when applied to museum specimen data, spatially explicit rarefaction is less biased than individual-based rarefaction because it reduces overestimation due to spatially aggregated sampling. We derived five predictions from this working hypothesis and tested them using computer simulation experiments based on a database of 129,782 plant specimens from Nicaragua, and sampling units of 5 x 5, 50 x 50, and 100 x 100 km. One experiment was a negative control, whereby we simulated collection of randomly chosen individuals from each sampling unit. In contrast, three other experiments included spatially aggregated sampling. In all experiments we applied individual-based and spatially explicit rarefaction to estimate richness, with n = 200 and n = 500 specimens. As expected, the experiment designed as a negative control did not support the working hypothesis. The other three experiments supported the working hypothesis in analyses of larger sampling units, but not in 5 x 5 km sampling units. The predictions we derived from the working hypothesis can be used to assess which rarefaction version is best in particular systems. [ABSTRACT FROM AUTHOR]

Effective video monitoring systems require optimization of camera and road network coverage, to exploit fully the hardware and software solutions in smart city traffic applications. Monitoring requirements have grown increasingly diverse as scenes are becoming increasingly complex, thereby transforming the camera and road network coverage optimization issue into a nonlinear, high-dimension, and multi-objective problem. Previous research on this topic however, has focused on a single, specific optimization objective, which may result in invalid optimization results in actual applications. To extend this research, we propose a multi-objective scheduling optimization algorithm for a camera network that addresses the problem of directional road network coverage. In this solution, we incorporate an expanding parameter of main optical axes into particle swarm optimization algorithm. Our new strategy divides the range of main optical axes of all the cameras to control the scheduling number, achieving collaborative optimization of multiple objectives. In a simulated camera and road network, an experiment was designed for evaluating the effectiveness of the proposed method, comparing the distribution of optimization results with the global and local optimal solutions of the true value. A second experiment compared the distribution, performance and running time of the optimization results with different values of expanding parameter of main optical axes. A third experiment compared the performance of the optimization solutions with different values of camera parameters. The results showed that the proposed method can adapt to user application preference, and is effective and robust to schedule and allocate monitoring resources in different scenarios. [ABSTRACT FROM AUTHOR]