Simulation of Hyperspectral Images

A software package generates simulated hyperspectral imagery for use in validating algorithms that generate estimates of Earth-surface spectral reflectance from hyperspectral images acquired by airborne and spaceborne instruments. This software is based on a direct simulation Monte Carlo approach for modeling three-dimensional atmospheric radiative transport, as well as reflections from surfaces characterized by spatially inhomogeneous bidirectional reflectance distribution functions. In this approach, "ground truth" is accurately known through input specification of surface and atmospheric properties, and it is practical to consider wide variations of these properties. The software can treat both land and ocean surfaces, as well as the effects of finite clouds with surface shadowing. The spectral/spatial data cubes computed by use of this software can serve both as a substitute for, and a supplement to, field validation data

Challenges in Monitoring Regional Trail

This study reports traffic monitoring results at 30 locations on a 972-mi shared-use trail network across the east-central United States. We illustrate challenges in adapting the principles in the Federal Highway Administration’s Traffic Monitoring Guide to a regional trail network. We make four contributions: 1) we use factor analysis and k-means clustering to implement a stratified random process for selecting monitoring sites; 2) we illustrate quality assurance procedures and the challenges of obtaining valid results from a multi-state monitoring system; 3) we describe variation in trail traffic volumes across five land use classes in response to daily weather and seasons; and 4) we report two performance measures for the network: annual average daily trail traffic and trail miles traveled. The Rails to Trails Conservancy deployed passive infrared traffic monitors in 2015 through 2017. Site-specific regression models were used to impute missing daily traffic volumes. The effects of weather were consistent across land use classes but the effects of temporal variables, including weekend and season of year, varied. A plan for short-duration monitoring is presented. Results confirm the FHWA monitoring principles and the difficulties of implementing them regionally

Determinants of penetrance and variable expressivity in monogenic metabolic conditions across 77,184 exomes

Hundreds of thousands of genetic variants have been reported to cause severe monogenic diseases, but the probability that a variant carrier develops the disease (termed penetrance) is unknown for virtually all of them. Additionally, the clinical utility of common polygenetic variation remains uncertain. Using exome sequencing from 77,184 adult individuals (38,618 multi-ancestral individuals from a type 2 diabetes case-control study and 38,566 participants from the UK Biobank, for whom genotype array data were also available), we apply clinical standard-of-care gene variant curation for eight monogenic metabolic conditions. Rare variants causing monogenic diabetes and dyslipidemias display effect sizes significantly larger than the top 1% of the corresponding polygenic scores. Nevertheless, penetrance estimates for monogenic variant carriers average 60% or lower for most conditions. We assess epidemiologic and genetic factors contributing to risk prediction in monogenic variant carriers, demonstrating that inclusion of polygenic variation significantly improves biomarker estimation for two monogenic dyslipidemias

Traffic Impacts of Bicycle Facilities

Engineers need information about interactions between vehicles and bicyclists to design efficient, safe transportation systems. This study involved a review of design guidelines for bicycle facilities, observation of bicycle-vehicle interactions at nine roadways with different types of bicycle facilities, analysis of results, and description of design implications. Facilities observed included buffered and striped bicycle lanes, sharrows, signed shared lanes, and shoulders of various widths. Driver behaviors were categorized as no change in trajectory, deviation within lane, encroachment into adjacent lane, completion of a passing maneuver, and queuing behind cyclists. Drivers on roadways with bicycle lanes were less likely to encroach into adjacent lanes, pass, or queue when interacting with cyclists than drivers on roadways with sharrows, signs designating shared lanes, or no bicycle facilities. Queueing behind cyclists, the most significant impact on vehicular traffic flows, generally was highest on roads with no facilities or shared facilities without marked lanes. Statistical modeling confirmed the descriptive results. Given an objective of increasing predictability of driver behavior, buffered or striped bicycle lanes offer advantages over other facilities. Sharrows may alert drivers to the presence of cyclists, but traffic impacts on roadways with sharrows may not differ significantly from roadways with no facilities. Signs indicating bicyclists may occupy lanes also may alert drivers to the presence of cyclists, but this study provided no evidence that interactions on roadways marked only with signs differ from roadways with no facilities. From the perspective of reducing potential traffic impacts, bicycle lanes are to be preferred over sharrows or signage

Low specificity of determine HIV1/2 RDT using whole blood in south west Tanzania

Objective: To evaluate the diagnostic performance of two rapid detection tests (RDTs) for HIV 1/2 in plasma and in whole blood samples. Methods: More than 15,000 study subjects above the age of two years participated in two rounds of a cohort study to determine the prevalence of HIV. HIV testing was performed using the Determine HIV 1/2 test (Abbott) in the first (2006/2007) and the HIV 1/2 STAT-PAK Dipstick Assay (Chembio) in the second round (2007/2008) of the survey. Positive results were classified into faint and strong bands depending on the visual appearance of the test strip and confirmed by ELISA and Western blot. Results: The sensitivity and specificity of the Determine RDT were 100% (95% confidence interval = 86.8 to 100%) and 96.8% (95.9 to 97.6%) in whole blood and 100% (99.7 to 100%) and 97.9% (97.6 to 98.1%) in plasma respectively. Specificity was highly dependent on the tested sample type: when using whole blood, 67.1% of positive results were false positive, as opposed to 17.4% in plasma. Test strips with only faint positive bands were more often false positive than strips showing strong bands and were more common in whole blood than in plasma. Evaluation of the STAT-PAK RDT in plasma during the second year resulted in a sensitivity of 99.7% (99.1 to 99.9%) and a specificity of 99.3% (99.1 to 99.4%) with 6.9% of the positive results being false. Conclusions: Our study shows that the Determine HIV 1/2 strip test with its high sensitivity is an excellent tool to screen for HIV infection, but that – at least in our setting – it can not be recommended as a confirmatory test in VCT campaigns where whole blood is used

How do self-assessment of alexithymia and sensitivity to bodily sensations relate to alcohol consumption?

Background Alexithymia describes an abnormality of emotional experience that is commonly expressed among individuals with addiction and alcohol abuse disorders. Alexithymic individuals are characterized by difficulties in identifying and describing their emotions. This impairment is linked to the development and maintenance of addiction. Moreover, an emergent theory suggests alexithymia is itself secondary to a failure of interoception (sensitivity to internal bodily signals, including physiological arousal states). Methods The present study tested for hypothesized contributory roles of alexithymia and dysfunctional interoception in the expression of binge drinking. Alexithymia, subjective sensitivity to bodily sensations, and alcohol consumption scores were quantified using the Toronto Alexithymia Scale, the Body Perception Questionnaire and the Alcohol Use Questionnaire respectively, in a normative sample (N=600). Regression and bootstrapping mediation analyses were used to test the hypothesis that alexithymia mediated the association between sensitivity to bodily sensations and alcohol consumption. Results Alexithymia was positively correlated with sensitivity to bodily sensations and with alcohol consumption. Mediation analysis revealed that alexithymia, and more precisely, difficulty in identifying feelings, mediated the relationship between sensitivity to bodily sensations and alcohol consumption, such that the predictive effect of sensitivity to bodily sensations on alcohol intake became non-significant when controlling for alexithymia. Conclusions These results indicate that alexithymia is associated with subjective hypersensitivity to bodily sensations. Moreover, our findings support the theoretical proposal that alexithymia is an expression of impaired processing of bodily sensations including physiological arousal, which underpin the development of maladaptive coping strategies, including alcohol use disorders. Our observations extend a growing literature emphasizing the importance of interoception and alexithymia in addiction, which can inform the development of new therapeutic strategies

Three Novel Downstream Promoter Elements Regulate MHC Class I Promoter Activity in Mammalian Cells

BACKGROUND: MHC CLASS I TRANSCRIPTION IS REGULATED BY TWO DISTINCT TYPES OF REGULATORY PATHWAYS: 1) tissue-specific pathways that establish constitutive levels of expression within a given tissue and 2) dynamically modulated pathways that increase or decrease expression within that tissue in response to hormonal or cytokine mediated stimuli. These sets of pathways target distinct upstream regulatory elements, have distinct basal transcription factor requirements, and utilize discrete sets of transcription start sites within an extended core promoter. METHODOLOGY/PRINCIPAL FINDINGS: We studied regulatory elements within the MHC class I promoter by cellular transfection and in vitro transcription assays in HeLa, HeLa/CIITA, and tsBN462 of various promoter constructs. We have identified three novel MHC class I regulatory elements (GLE, DPE-L1 and DPE-L2), located downstream of the major transcription start sites, that contribute to the regulation of both constitutive and activated MHC class I expression. These elements located at the 3' end of the core promoter preferentially regulate the multiple transcription start sites clustered at the 5' end of the core promoter. CONCLUSIONS/SIGNIFICANCE: Three novel downstream elements (GLE, DPE-L1, DPE-L2), located between +1 and +32 bp, regulate both constitutive and activated MHC class I gene expression by selectively increasing usage of transcription start sites clustered at the 5' end of the core promoter upstream of +1 bp. Results indicate that the downstream elements preferentially regulate TAF1-dependent, relative to TAF1-independent, transcription

Acute wound management: revisiting the approach to assessment, irrigation, and closure considerations

Abstract Background As millions of emergency department (ED) visits each year include wound care, emergency care providers must remain experts in acute wound management. The variety of acute wounds presenting to the ED challenge the physician to select the most appropriate management to facilitate healing. A complete wound history along with anatomic and specific medical considerations for each patient provides the basis of decision making for wound management. It is essential to apply an evidence‐based approach and consider each wound individually in order to create the optimal conditions for wound healing. Aims A comprehensive evidence‐based approach to acute wound management is an essential skill set for any emergency physician or acute care practitioner. This review provides an overview of current evidence and addresses frequent pitfalls. Methods A systematic review of the literature for acute wound management was performed. Results A structured MEDLINE search was performed regarding acute wound management including established wound care guidelines. The data obtained provided the framework for evidence‐based recommendations and current best practices for wound care. Conclusion Acute wound management varies based on the wound location and characteristics. No single approach can be applied to all wounds; however, a systematic approach to acute wound care integrated with current best practices provides the framework for exceptional wound management

Recommendations for clinical interpretation of variants found in non-coding regions of the genome

Background The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts. Methods We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups. Results We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants. Conclusions These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms