cssi/SciSciGPT-SciSciNet huggingface dataset:
Clinical evidence and bioinformatics characterization of potential hepatitis C virus resistance pathways for sofosbuvir

Sofosbuvir (Sovaldi, SOF) is a nucleotide analog prodrug that targets the hepatitis C virus (HCV) nonstructural protein 5B (NS5B) polymerase and inhibits viral replication. High sustained virological response rates are achieved when SOF is used in combination with ribavirin with or without pegylated interferon in subjects with chronic HCV infection. Potential mechanisms of HCV resistance to SOF and other nucleos(t)ide analog NS5B polymerase inhibitors are not well understood. SOF was the first U.S. Food and Drug Administration (FDA)-approved antiviral drug for which genotypic resistance analyses were based almost entirely on next-generation sequencing (NGS), an emerging technology that lacks a standard data analysis pipeline. The FDA Division of Antiviral Products developed an NGS analysis pipeline and performed independent analyses of NGS data from five SOF clinical trials. Additionally, structural bioinformatics approaches were used to characterize potential resistance-associated substitutions. Using protocols we developed, independent analyses of the NGS data reproduced results that were comparable to those reported by Gilead Sciences, Inc. Low-frequency, treatment-emergent substitutions occurring at conserved NS5B amino acid positions in subjects who experienced virological failure were also noted and further evaluated. The NS5B substitutions, L159F (sometimes in combination with L320F or C316N) and V321A, emerged in 2.2%-4.4% of subjects who failed SOF treatment across clinical trials. Moreover, baseline polymorphisms at position 316 were potentially associated with reduced response rates in HCV genotype 1b subjects. Analyses of these variants modeled in NS5B crystal structures indicated that all four substitutions could feasibly affect SOF anti-HCV activity. Conclusion: SOF has a high barrier to resistance; however, low-frequency NS5B substitutions associated with treatment failure were identified that may contribute to resistance of this important drug for chronic HCV infection. (Hepatology 2015;61:56–65)
Quantification of agricultural drought occurrence as an estimate for insurance programs

Temporal irregularities of rainfall and drought have major impacts on rainfed cropping systems. The main goal of this study was to develop an approach for realizing drought occurrence based on local winter wheat yield loss and rainfall. The domain study included 11 counties in the state of Washington that actively grow rainfed winter wheat and an uncertainty rainfall evaluation model using daily rainfall values from 1985 to 2007. An application was developed that calculates a rainfall index for insurance that was then used to determine the drought intensity for each study year and for each study site. Evaluation of the drought intensity showed that both the 1999–2000 and 2000–2001 growing seasons were stressful years for most of the study locations, while the 2005–2006 and the 2006–2007 growing seasons experienced the lowest drought intensity for all locations. Our results are consistent with local extension reports of drought occurrences. Quantification of drought intensity based on this application could provide a convenient index for insurance companies for determining the effect of rainfall and drought on crop yield loss under the varying weather conditions of semi-arid regions.
Persistence of the vernacular: A minority shaping urban form

Abstract This paper presents the emerging expression of architectural identity in Dekaokto, a refugee neighbourhood built by the Greek government in the northern Aegean port of Kavala. Ever since the refugees occupied Dekaokto in the mid‐1920s, houses and neighbourhood space have been gradually appropriated and modified to restore a way of life left behind in Asia Minor. Refugee culture was created and re‐created throughout decades despite official attempts to purge the new Greek state of its Turkish‐oriental influence. By examining the refugee experience, we witness the invention of a ‘high’, or national culture, through its inherent opposition to the ‘low’, or local culture. High culture is traced here through the neoclassicist national programme officially adopted and promoted by the Greek state in public architecture. Evidence of refugee ‘low‐culture’, on the other hand, is to be found in the living testimony of its domestic architecture.
Evidence for a low dimension strange attractor for temperature variations inside helium-II counter-flow jets

Abstract Time series measurements of the temperature of liquid helium inside the chamber of thermal counterflow jets driven by a constant heat source show four distinct regions of fluid flow as a function of heater power. Detailed analysis suggests that the temperature variations for the lowest power oscillatory region may be characterized by a strange attractor of fractal dimension, ∼4.
Cuprizone neurotoxicity in the rat: Morphologic observations

Abstract Weanling male Wistar rats fed a diet containing 0.5–2% cuprizone developed intramyelinic edema of the cerebellar white matter, hilum of the dentate nucleus and superior cerebellar peduncle. Oligodendrocytes in these regions showed hyperchromatic nuclei and abnormally dense cytoplasm, with an increase in the number of free ribosomes and enlargement of mitochondria. Unlike the lesions produced by cuprizone in weanling mice, those in the rat did not lead to demyelination. Cuprizone caused a distal peripheral axonopathy, with degeneration of myelinated axons in the sciatic nerve but preservation of the spinal nerve roots, dorsal root ganglia, posterior spinal funiculi and anterior horn cells. Unmyelinated fibers were largely spared. Some axonal regeneration occurred despite the continued administration of cuprizone. The intramyelinic edema and the nuclear and cytoplasmic abnormalities of the oligodendrocytes disappeared after the resumption of a normal diet.
Abrasion resistance of nanostructured and conventional cemented carbides

Abstract The abrasion resistance of nanostructured WCCo composites, synthesized by a novel spray conversion method, is determined and compared with that of conventional materials. Scratching by diamond indenter and abrasion by hard (diamond), soft (zirconia) and intermediate (SiC) abrasives was investigated. The size of the scratch formed by the diamond is simply related to the hardness of the composite. Plastic deformation, fracture and fragmentation of the WC grains increase with their size. Nanoscale composites show purely ductile scratch formation. Nanocomposites possess an abrasion resistance approximately double that of the most resistant conventional material: this is a higher gain than the increase in hardness which is at most 23%. This large gain is due to a specific grain size effect on abrasion resistance in the case of diamond and SiC abrasive and to a very rapid increase of abrasion resistance with hardness in the case of the softer (SiC and ZrO2) abrasives. The observation of the abraded surfaces of conventional composites reproduced the known mechanisms: plastic deformation and fracture of WC grains by hard abrasives; removal of binder phase and fall-out of WC by soft abrasives. Magnetic fields from the ferromagnetic Co prevent the observation of abrasion mechanisms in the very fine-structured nanocomposites.
Positioning the Morbidly Obese Patient for Anesthesia

Each of the different positions employed during surgery can compromise cardiopulmonary function in the morbidly obese patient. An understanding of the physiologic changes that can occur is essential for the successful management of these patients.
From AAPC algorithms to high performance permutation routing and sorting

Several recent papers have proposed or analyzed optimal algorithms to route all-to-all personalized communication (AAPC) over communication networks such as meshes, hypercubes and omega switches. However, the constant factors of these algorithms are often an obscure function of system parameters such as link speed, processor clock rate, and memory access time. In this paper we investigate these architectural factors, showing the impact of the communication style, the network routing table, and most importantly, the local memory system, on AAPC performance and permutation routing on the Cray T3D. The fast hardware barriers on the T3D permit a straightforward AAPC implementation using routing phases separated by barriers, which improve performance by controlling congestion. However, we found that a practical implementation was difficult, and the resulting AAPC performance was less than expected. After detailed analysis, several corrections were made to the AAPC algorithm and to the machine’s routing table, raising the performance from 41% to 74% of the nominal bisection bandwidth of the network. Most AAPC performance measurements are for permuting large, contiguous blocks of data (i.e., every processor has an array of P contiguous elements to be sent to every other processor). In practice, sorting and true h h permutation routing require data elements to be gathered from their source location into a buffer, transferred over the network, and scattered into their final location in a destination array. We obtain an optimal T3D implementation by chaining local and remote memory operations together. We quantify the implementation’s efficiency both experimentally and theoretically, using the recently-introduced copy transfer model, and present results for a counting sort based on this AAPC implementation.
NC-stat as a screening tool for carpal tunnel syndrome in industrial workers.

Objective The initial purpose of this study was to establish a normal data set for median nerve studies in industrial workers using NC-stat technology. Methods Sixteen hundred ninety-five persons applying for employment at a single heavy industry plant without symptoms of carpal tunnel syndrome (CTS) were studied. Results Values for median distal motor latency (DML), amplitude, and F-waves were recorded in the dominant limbs. The DML was 3.81 +/- 0.57 milliseconds, with a 95% cut-off value of 4.75 milliseconds. Amplitude of the compound muscle action potential was 0.95 +/- 0.46 mV, reflecting the use of volume conduction by this technology. Most of the workers who were characterized as having borderline, prolonged, or very prolonged distal motor latencies according to NeuroMetrix automated report actually fell below the 95% cut-off of this independent data analysis. Conclusion NC-stat technology using DML appears to be no more sensitive or specific than a traditionally performed DML for the diagnosis of CTS. Until recently promoted sensory studies using NC-stat technology are better defined, this technology cannot be recommended for screening or diagnosis of CTS in an industrial population.
Pharmacologic effects of intravenously administered aminophylline in asthmatic children

The effects of intravenously administered aminophylline were studied in 49 asthmatic children while they were symptomatic. The drug was administered in a dose of 4 mg. per kilogram of body weight either rapidly over a 4 to 5 minute period or slowly over an 8 hour period. Blood theophylline concentrations and FEV 1 were determined at 15 and 30 minutes and 1, 2, 4, 6, and 8 hours after administration of the drug was begun. The safety of both methods of intravenous administration of aminophylline was documented by absence of adverse effects. The superiority of giving aminophylline relatively rapidly was clearly demonstrated on clinical grounds, by rapid improvement in FEV 1 , and by prompt attainment of therapeutic plasma concentrations of theophylline. A control group of 10 patients who were treated with bed rest and intravenous fluids alone showed only minimal transient improvement in FEV 1 .
Implementing a mathematical model for locating EMS vehicles in Fayetteville, NC

Emergency medical services (EMS) aims to reduce the elapsed time to respond to an emergency. The number and location of vehicles within the service area, directly affect the attainment of this goal. In this paper, we focus on a mathematical modeling approach for locating/allocating emergency vehicles and facilities in a manner that increases the number of calls that are answered within the 8-min national average. This model was applied to the EMS system in the city of Fayetteville, North Carolina, and results indicate that the average response time can be significantly improved through strategically allocating vehicles throughout the service area.
Timing of peak oil uncertain

According to the Hubbert peak theory, oil production in any geographic area will follow a bellshaped curve. The timing of the ‘peak’ in global oil production is important because after that point, there will be less and less oil available for consumption. A new report from the U.S. Government Accountability Office found that most studies estimate that peak oil production will occur sometime between now and 2040. The uncertainty in these estimates could be reduced with better information about worldwide supply and demand, and alternative fuels and transportation technologies could mitigate the effects of a global decline in oil production. However, the report found no coordinated U.S. federal strategy to address these issues. The report, “Uncertainty about Future Oil Supply Makes It Important to Develop a Strategy for Addressing a Peak and Decline in Oil Production,” is available at http://www.gao.gov/cgi-bin/getrpt?GAO-07-283
Whole genome comparison of six Crocosphaera watsonii strains with differing phenotypes

Crocosphaera watsonii, a unicellular nitrogen-fixing cyanobacterium found in oligotrophic oceans, is important in marine carbon and nitrogen cycles. Isolates of C. watsonii can be separated into at least two phenotypes with environmentally important differences, indicating possibly distinct ecological roles and niches. To better understand the evolutionary history and variation in metabolic capabilities among strains and phenotypes, this study compared the genomes of six C. watsonii strains, three from each phenotypic group, which had been isolated over several decades from multiple ocean basins. While a substantial portion of each genome was nearly identical to sequences in the other strains, a few regions were identified as specific to each strain and phenotype, some of which help explain observed phenotypic features. Overall, the small-cell type strains had smaller genomes and a relative loss of genetic capabilities, while the large-cell type strains were characterized by larger genomes, some genetic redundancy, and potentially increased adaptations to iron and phosphorus limitation. As such, strains with shared phenotypes were evolutionarily more closely related than those with the opposite phenotype, regardless of isolation location or date. Unexpectedly, the genome of the type-strain for the species, C. watsonii WH8501, was quite unusual even among strains with a shared phenotype, indicating it may not be an ideal representative of the species. The genome sequences and analyses reported in this study will be important for future investigations of the proposed differences in adaptation of the two phenotypes to nutrient limitation, and to identify phenotype-specific distributions in natural Crocosphaera populations.
Microtechnologies for Neurobiology

Oscillatory activity in cortical networks is thought to provide the foundation for many high-level processes including working memory and attention. It has been shown that spatial information propagation delay and connectivity density can determine the innate properties of local network activity. The initial formation of neuronal networks in the central nervous system occurs due to the interaction of the genetic programming of the cells and the presentation of external molecular cues. The activity-driven refinement that occurs later, giving rise to the highly complex networks within the brain, are dependent on the initial anatomical formation and structural connectivity which occurs without external activity cues. We describe technologies used to (1) modulate the genetic programming of neurons and (2) precisely control temporal and spatial presentation of environmental cues in vitro. We are exploring the ability to define simple oscillatory networks using these experimental techniques.Copyright © 2010 by ASME
Effects of anelastic deformation on high-temperature stress relaxation of polycrystalline MgO and Al2O3

High-temperature (1160 to 1450‡ C) deformation of dense polycrystalline (10 to 90 Μm) Al2O3 and MgO doped with Fe (up to 2.65 cation %) was studied by stress relaxation, dead-load creep and creep recovery. In some cases, all three deformation tests were conducted on a single specimen. A comparison of strain rate-stress data calculated from both stress relaxation and dead-load creep experiments revealed discrepancies in both the magnitude of the strain rates and the dependence between the strain rate and stress. These differences were attributed to the existence of anelastic deformation effects. The correction of stress relaxation data in the low stress regime for linear anelasticity led to strain rate-stress data in reasonably close agreement with results obtained from dead-load creep tests conducted in the viscous creep regime. Creep recovery experiments indicated that anelastic deformation in these ceramic materials was relatively insensitive to changes in temperature and grain size over the range of variables studied.
Betwixt and Between: Ethnoarchaeology, Women, Susan Kent

The gilded Marshalltown traditionally went to the guy dressed in faded khakis, eyes squinting in a weather-beaten face, pipe in hand, trowel in the belt (Flannery 1982:267). He dug square holes to ...
Calibration of the Weibull stress scale parameter, σu, using the Master Curve

Abstract This work proposes that the Weibull stress scale parameter, σu, increases with temperature to reflect the increasing microscale toughness of ferritic steels caused by local events that include plastic shielding of microcracks, microcrack blunting, and microcrack arrest. The Weibull modulus, m, then characterizes the temperature invariant, random distribution of microcrack sizes in the material. Direct calibration of σu values at temperatures over the DBT region requires extensive sets of fracture toughness values. A more practical approach developed here utilizes the so-called Master Curve standardized in ASTM Test Method E1921-02 to provide the needed temperature vs. toughness dependence for a material using a minimum number of fracture tests conducted at one temperature. The calibration procedure then selects σu values that force the Weibull stress model to predict the Master Curve temperature dependence of KJc values for the material. At temperatures in mid-to-upper transition, the process becomes more complex as fracture test specimens undergo gradual constraint loss and the idealized conditions of high-constraint, small-scale yielding assumed in E1921-02 gradually degenerate. The paper develops the σu calibration process to incorporate these effects in addition to consideration of threshold toughness effects and the testing of fracture specimens with varying crack-front lengths. Initial illustrations of the calibration process for simpler conditions, i.e. 1T crack-front lengths, use the temperature dependent flow properties and a range of toughness levels for an A533B pressure vessel steel. Then using the extensive fracture toughness data sets for an A508 pressure vessel steel generated recently by Faleskog et al. [Engng. Fract. Mech., in press], the paper concludes with calibrations of both m and σu over the DBT region and assessments of the Master Curve calibration approach developed here.
Modeling clustered non-stationary Poisson processes for stochastic simulation inputs

A validated simulation model primarily requires performing an appropriate input analysis mainly by determining the behavior of real-world processes using probability distributions. In many practical cases, probability distributions of the random inputs vary over time in such a way that the functional forms of the distributions and/or their parameters depend on time. This paper answers the question whether a sequence of observations from a process follow the same statistical distribution, and if not, where the exact change points are, so that observations within two consecutive change points follow the same distribution. We propose two different methods based on likelihood ratio test and cluster analysis to detect multiple change points when observations follow non-stationary Poisson process with diverse occurrence rates over time. Results from a comprehensive Monte Carlo study indicate satisfactory performance for the proposed methods. A well-known example is also considered to show the application of our findings in real world cases.
Comparison of finite differences and finite elements on a parabolic problem

Numerical solutions to the diffusion equation are examined on a smooth, nearly orthogonal mesh. (AIP)
Abstract 220: BRCA1 regulates p53 target expression via DNp73

Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL In response to cellular stresses, the tumor suppressor gene p53 is stabilized and transactivates several categories of target genes, including cell cycle arrest genes and pro-apoptotic genes. These sets of genes are not activated simultaneously and how the differential expression of these targets occurs has been the subject of intense scrutiny. We have previously shown that overexpression of BRCA1 stabilizes p53 but fails to activate the expression of its proapoptotic targets. When BRCA1 is overexpressed, the posttranslational modifications of p53 are the same as those that occur in response to stress and p53 is still able to bind to the promoters of the proapoptotic targets. In order to determine how BRCA1 regulates p53 gene expression, we've explored the role of the p53 family members. We find that BRCA1 is able to induce DNp73, a dominant negative acting isoform of p73. Unexpectedly, we found that BRCA1 upregulates DNp73 expression, an isoform of the p53 family member p73 lacking the transactivation domain, which has been previously implicated in cell survival. This observation has important implications for understanding the selectivity of p53-dependent transcription as well as the tumor suppressive action of BRCA1 that favors DNA repair over cell death. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 220. doi:10.1158/1538-7445.AM2011-220
Smoking and symptom effects on the curves of lung function growth and decline

Numerous studies have examined the natural time course of human lung function growth and decline throughout life. In most of these studies the investigators used statistical models that required a priori assumptions concerning the underlying form or structure of the lung function data, thus introducing possible biases. In this study we used recently developed nonparametric regression (spline) techniques to describe the evolution of lung function measures with age. This procedure yields an optimally fitted smooth curve through the data and estimates of the process velocity and does not require assumptions concerning the underlying shape of the data curves. The lung function growth-velocity curves are used to estimate the age of growth cessation. This technique was applied to the FVC, FEV1, and the FEV1/FVC ratios of 1,295 females and 1,230 males who were tested in at least one of the first nine surveys of the Tucson epidemiologic study of airway obstructive diseases. Data were analyzed stratified according to gender, smoking status, and respiratory symptoms or diseases. The results indicate large differences between the fitted FEV1 and FEV1/FVC smoothed curves of the various subgroups compared with asymptomatic nonsmokers. These differences were most pronounced in the adult symptomatic smokers, who had higher rates of lung function loss that also began at earlier ages, for both sexes. No significant differences were observed between asymptomatic and symptomatic nonsmokers, most likely because of the reduced number of symptomatic nonsmokers, particularly among the males.
Real-time block matching motion estimation onto GPGPU

This work presents an efficient method to map Motion Estimation (ME) algorithms onto General Purpose Graphic Processing Unit (GPGPU) architectures using CUDA programming model. Our method jointly exploits the massive parallelism available in current GPGPU devices and the parallelization potential of ME algorithms: Full Search (FS) and Diamond Search (DS). Our main goal is to evaluate the feasibility of achieving real-time high-definition video encoding performance running on GPUs. For comparison reasons, multi-core parallel and distributed versions of these algorithms were developed using OpenMP and MPI (Message Passing Interface) libraries, respectively. The CUDA-based solutions achieve the highest speed-up in comparison with OpenMP and MPI versions for both algorithms and, when compared to the state-of-the-art, our FS and DS solutions reach up to 18x and 11x speed-up, respectively.
Hyperspectral imaging for safety inspection of food and agricultural products

Development of effective food inspection systems is critical in successful implementation of the hazard analysis and critical control points (HACCP) program. Hyperspectral imaging or imaging spectroscopy, which combines techniques of imaging and spectroscopy to acquire spatial and spectral information simultaneously, has great potential in food quality and safety inspection. This paper reviewed the basic principle and features of hyperspectral imaging and its hardware and software implementation. The potential areas of application for hyperspectral imaging in food quality and safety inspection were identified and its limitations were discussed. A hyperspectral imaging system developed for research in food quality and safety inspection was described. Experiments were performed to acquire hyperspectral images from four classes of poultry carcasses: normal, cadaver, septicemia, and tumor. Noticeable differences in the spectra of the relative reflectance and its second difference in the wavelengths between 430 nm and 900 nm were observed between wholesome and unwholesome carcasses. Differences among the three classes of unwholesome carcasses were also observed from their respective spectra. These results showed that hyperspectral imaging can be an effective tool for safety inspection of poultry carcasses.
Resolvability Analysis For Rock Property Inversions of Multicomponent Seismic Data

A Singular Value Decomposition (SVD) technique has been used to investigate the resolvability and reliability of rock property parameters from linearized inversions of multicomponent pre-stack reflection seismic data. Resolution maps of rock property parameters have been generated and plotted as functions of maximum incident angle and background shear-to-compressional wave velocity ratio for different components of the seismic data: pure compressional wave PP, compressional-to-shear converted wave PSv, and pure shear wave SvSv. The sensitivity to noises of each parameter has been illustrated by the variation of the resolution matrix with the damping factor used in the SVD. Our analyses have shown that Pand S-impedance can be resolved reliably from separate inversions of PP and PSv (or SvSv) data, respectively. The S-impedance from PP data is much more sensitive to noises than that from PSv (or SvSv). Density should be able to be resolved reliably from SvSv data. Density from either PP or PSv data is likely to be unreliable on real seismic data. In order to resolve velocity and density or Lame constants and density reliably, joint inversion of PP with PSv and SvSv, especially with the inclusion of SvSv data, is needed.
Granulometry of Non-colloidal Particulate Matter Transported by Urban Runoff

This study examined the granulometry of non-colloidal particulate matter (PM) from four urban transportation land use catchments (source areas) in Baton Rouge, Little Rock, North Little Rock, and New Orleans. Particle gradations ranging from 1 to greater than 10,000 μm were separated into dissolved (less than 1 μm), suspended (1–25 μm), settleable (25–75 μm), and sediment (75–4750 μm) fractions. In Baton Rouge, the primary site, results indicate a suspended mass-based d 50m of 10.8, 5.0 μm [mean ( $$\bar x$$ ), standard deviation (s)], a particle density (ρ s) of 2.40, 0.19 g/cm3 based on 12 events with complete runoff volume capture. On an event-basis, the suspended fraction ranged from 5–25% of the entire gradation mass and correlated to turbidity. The Baton Rouge d 50m excluding grit-size material from all events was 356, 69 μm as compared to 421, 219 μm for accumulated PM including grit from all sites. Size gradations were successfully modeled with a gamma distribution. Particle density generally varied from 2.1 to 2.6 g/cm3 across gradations. While specific surface area generally increased with decreasing particle size, over 50% of total surface area was associated with gradations greater than 250 μm. The point of zero charge (pzc-pH) ranges from 7.5 to 9 for settleable and sediment fractions. Results from these sites support published results for fully captured rainfall–runoff events at a Cincinnati site of the same land use, and provide properties/indices for monitoring, regulatory guidance, treatability studies, source control, and design of in situ unit operations targeting particle separation mechanisms.
Reducing Undesirable Actions of Motor Vehicle Drivers at Railroad-Highway Grade Crossings

This paper reports on unsafe actions of motor vehicle drivers at gated railroad-highway grade crossings and behavioral modifications in response to installation of a centerline barrier that prevented drivers from going through the gates. A comparison of driver behavior in the pre- and post-barrier periods indicated the effectiveness of the barrier in reducing unsafe actions. A major concern of the Nebraska Department of Roads is the potential for crashes at railroad-highway grade crossings that result from unsafe actions of motorists such as rushing the gates to beat an oncoming train and playing "chicken" with an approaching train (i.e., intentionally standing a motor vehicle on the tracks and moving only when the train brakes). Some driver actions at crossings (e.g., backing up, U-turns) may result in crashes involving motor vehicles only. The railroad crossing at North 141st Street in Waverly, Nebraska, was studied for about 4 months with the help of a night vision camera and a digital video recorder. ...
Bone mineral density and fractures among alcohol-dependent women in treatment and in recovery.

Women are at higher risk for osteoporosis, but most of the literature examining the effect of alcohol abuse on bone mineral density (BMD) has been in men. The aim of this study was to determine differences in BMD and fracture prevalence among women in treatment for alcohol abuse, in recovery and non-alcohol-dependent women. This cross-sectional study was completed at two residential substance abuse centers in Iowa (USA). The patients were Caucasian women, aged 18–70 years, in treatment for alcohol abuse and dependence (n=228); in recovery and abstaining from alcohol (n=156); and women with no history of alcohol abuse (n=447). The main outcome measures were femoral neck and lumbar spine BMD measured by dual-energy X-ray absorptiometry (DXA); self-reported lifetime fracture prevalence. After adjusting for age and menopausal status, women in treatment had BMDs that were 7.7% (p<0.01) and 6.3% (p<0.01) lower at the femoral neck and lumbar spine, respectively, than non-alcohol-abusing women, and 4.8% lower at both bone sites (p<0.01) than women in recovery. Femoral neck BMD of women in recovery was 3.1% lower (p<0.01) than in non-alcohol-dependent women; however, the difference was not significant following multivariate analysis. Women in treatment and recovery reported more fractures during childhood and early adolescence than non-alcohol-dependent women (p<0.01). Women in recovery also reported significantly greater numbers of fractures following sobriety than their paired non-alcohol-dependent counterparts. Alcohol abuse and dependence was associated with lower femoral neck and lumbar spine BMD. Women with histories of alcohol dependence had a higher lifetime prevalence of fractures, including time periods before the onset of problem drinking and following abstinence, suggesting that factors other than acute intoxication contributed to the greater fracture prevalence.
Identification of the Ah-Receptor Structural Determinants for Ligand Preferences

The aryl hydrocarbon receptor (AHR) is a transcription factor that responds to diverse ligands and plays a critical role in toxicology, immune function, and cardiovascular physiology. The structural basis of the AHR for ligand promiscuity and preferences is critical for understanding AHR function. Based on the structure of a closely related protein HIF2α, we modeled the AHR ligand binding domain (LBD) bound to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and benzo(a)pyrene (BaP) and identified residues that control ligand preferences by shape and H-bond potential. Mutations to these residues, particularly Q377 and G298, resulted in robust and opposite changes in the potency of TCDD and BaP and up to a 20-fold change in the ratio of TCDD/BaP efficacy. The model also revealed a flexible "belt" structure; molecular dynamic (MD) simulation suggested that the "belt" and several other structural elements in the AHR-LBD are more flexible than HIF2α and likely contribute to ligand promiscuity. Molecular docking of TCDD congeners to a model of human AHR-LBD ranks their binding affinity similar to experimental ranking of their toxicity. Our study reveals key structural basis for prediction of toxicity and understanding the AHR signaling through diverse ligands.
Isolation of the saddle and crown conformers of cyclotriveratrylene (CTV) oxime

Abstract The oxime of cyclotriveratrylene (CTV) has been prepared and the individual crown and saddle conformers were isolated and characterized. The equilibrium constant was measured in CDCl3 and in DMSO-d6 and was shown to favor the crown conformer by an order of magnitude in DMSO-d6, relative to an approximately equal mixture at equilibrium in CDCl3. The time course for interconversion of the saddle to the crown was measured by 1H NMR and the t1/2 of the saddle was determined to be 2.45 h in CDCl3 at 25 °C, and 3.71 h in DMSO-d6.
How Party Affiliation Conditions the Experience of Dissonance and Explains Polarization and Selective Exposure

Objectives Dissonance theory has been widely studied in the social sciences, especially given its implications for polarization and selective exposure. This study expands previous research by investigating how this process may differ when a foundational political identity such as party affiliation is at stake. Methods This study adapts a classic dissonance paradigm—writing a counterattitudinal essay under conditions of high versus low choice—to a political context by manipulating the topic of the essay to advocating membership in the opposing political party. Results In this context, party affiliation conditions response to writing a counterattitudinal essay: only Republican respondents demonstrate heightened dissonance, selective exposure, and polarization as a result of this task, particularly when the essay is political. Conclusions Dissonance may not be a universal response to potentially arousing tasks, but if only some groups experience dissonance and polarization after enumerating the benefits of an opposing party, it may bias democratic functioning.
Bayesian latent variable models for mixed discrete outcomes

SUMMARY In studies of complex health conditions, mixtures of discrete outcomes (event time, count, binary, ordered categorical) are commonly collected. For example, studies of skin tumorigenesis record latency time prior to the first tumor, increases in the number of tumors at each week, and the occurrence of internal tumors at the time of death. Motivated by this application, we propose a general underlying Poisson variable framework for mixed discrete outcomes, accommodating dependency through an additive gamma frailty model for the Poisson means. The model has log-linear, complementary log-log, and proportional hazards forms for count, binary and discrete event time outcomes, respectively. Simple closed form expressions can be derived for the marginal expectations, variances, and correlations. Following a Bayesian approach to inference, conditionally-conjugate prior distributions are chosen that facilitate posterior computation via an MCMC algorithm. The methods are illustrated using data from a Tg.AC mouse bioassay study.
Ontologies and tools for analysing and composing simulation confederations for the training and testing domains

Military training and testing events integrate a diverse set of live and simulated systems, most of which were built independently and weren’t specifically designed to work together. Data interoperability and service-oriented architecture approaches, while essential, do not provide a complete solution to ensuring that systems will be fully compatible in their interactions. We describe a complementary approach that uses Web Ontology Language and Semantic Web Rule Language to capture information about the roles and capabilities required to complete a task, and the detailed attributes of candidate resources. Our toolset applies automated reasoning to determine whether each candidate resource has the requisite capabilities and is compatible with other resources. If there are multiple candidates for a role, the reasoner ranks the relative goodness of each with respect to constraints and metrics that are appropriate for the specific task needs of the exercise or deployment. We include worked examples illustrating the kinds of information we capture about resources and how rules and constraints are applied to provide a nuanced assessment of their compatibility in a specific context.
Circulating estrogens and estrogens within the breast among postmenopausal BRCA1/2 mutation carriers.

Accurately quantifying parent estrogens (PE) estrone (E1) and estradiol (E2) and their metabolites (EM) within breast tissue and serum may permit detailed investigations of their contributions to breast carcinogenesis among BRCA1/2 mutation carriers. We conducted a study of PE/EM in serum, nipple aspirate fluid (NAF), and ductal lavage supernatant (DLS) among postmenopausal BRCA1/2 mutation carriers. PE/EM (conjugated and unconjugated) were measured in paired serum/NAF (n = 22 women) and paired serum/DLS samples (n = 24 women) using quantitative liquid chromatography–tandem mass spectrometry (LC/MS/MS). The relationships between serum and tissue-specific PE/EM were measured using Pearson’s correlation coefficients. Conjugated forms of PE/EM constituted the majority of estrogen in serum (88 %), NAF (59 %) and DLS (69 %). PE/EM in NAF and serum were highly correlated [E1 (r = 0.97, p < 0.0001), E2 (r = 0.90, p < 0.0001) and estriol (E3) (r = 0.74, p < 0.0001)] as they were in DLS and serum [E1 (r = 0.92, p < 0.0001; E2 (r = 0.70, p = 0.0001; E3 (r = 0.67, p = 0.0004)]. Analyses of paired total estrogen values for NAF and serum, and DLS and serum yielded ratios of 0.22 (95 % CI 0.19–0.25) and 0.28 (95 % CI 0.24–0.32), respectively. This report is the first to employ LC/MS/MS to quantify PE/EM in novel breast tissue-derived biospecimens (i.e., NAF and DLS). We demonstrate that circulating PE and EM are strongly and positively correlated with tissue-specific PE and EM measured in NAF and DLS among postmenopausal BRCA1/2 mutation carriers. If confirmed, future etiologic studies could utilize the more readily obtainable serum hormone levels as a reliable surrogate measure of exposure at the tissue level.
The Effect of Perimeter Geometry on FBAR Resonator Electrical Performance

We describe the first four Lamb-Rayleigh modes seen in an FBAR resonator. We also describe the effect of apodization (non parallel edges) have on the kx-ky space as compared to square resonators.
SMSI effects on CO adsorption and hydrogenation on Pt catalysts: I. Infrared spectra of adsorbed CO prior to and during reaction conditions

Infrared spectroscopy has been employed to characterize adsorbed CO species under steadystate reaction conditions in the presence of H2 and also under equilibrium adsorption conditions in the presence of He. During reaction, kinetic data were obtained simultaneously with ir spectra using a special ir reactor cell. Turnover frequencies on Pt were found to vary more than 100-fold as the support material varied, and the activity ranking of these catalysts was: PtTiO2(SMSI)>PtTiO2(LT) ≥ Ptη-Al2O3 − PtSiO2-Al2O3>PtSiO2. Two principal ir bands were observed on Pt—a high-frequency band between 2050 and 2080 cm−1 and a low-frequency band between 1780 and 1860 cm−1. Except for TiO2-supported Pt, very similar behavior was observed, i.e., intense ir bands occurred which were nearly insensitive to temperature and the presence of H2, and these catalysts exhibited strong bands under reaction conditions. In contrast, the PtTiO2(SMSI) catalyst showed almost no ir-detectable CO during reaction and, even more surprising, CO band intensities were also markedly reduced at 300 K by the presence of H2. No obvious correlation was found between detectable CO species and specific activity; however, this study strongly infers that only a very small fraction of surface Pt atoms constitute active sites, and the higher activity occurring on the SMSI PtTiO2 catalyst is attributed to a weakened CO-metal bond resulting in more competitive H2 chemisorption and higher surface concentrations of hydrogen under reaction conditions.
Evaluation of the waxy endosperm trait in proso millet (Panicum miliaceum).

The entire USDA-ARS maintained collection of 650 accessions of proso millet (Panicum miliaceum L.) was evaluated for the presence of accessions with waxy (amylose-free) endosperm starch. Six accessions, five of which derived from mainland China, were identified. Segregation ratios for waxy endosperm were evaluated in F 2 and F 3 populations derived from crosses between two waxy accessions, PI 436625 (Lung Shu 16) and PI 436626 (Lung Shu 18), and several wild-type accessions. The waxy trait was found to be under the control of duplicate recessive alleles at two loci, herein designated Wx-1 and Wx-2. Wild-type alleles at these loci were designated Wx-1 and Wx-2. Iodine-binding revealed a mean grain-starch amylose concentration of 3.5% in waxy lines and 25.3% in wild-type proso. Expression of the granule-bound starch synthase (waxy protein) in waxy lines was reduced to approximately one-tenth that of wild-type accessions. The waxy accessions identified now are available for the introgression of this trait into breeding lines adapted to the Great Plains of North America.
Quo vadis, PUF?: trends and challenges of emerging physical-disorder based security

The physical unclonable function (PUF) has emerged as a popular and widely studied security primitive based on the randomness of the underlying physical medium. To date, most of the research emphasis has been placed on finding new ways to measure randomness, hardware realization and analysis of a few initially proposed structures, and conventional secret-key based protocols. In this work, we present our subjective analysis of the emerging and future trends in this area that aim to change the scope, widen the application domain, and make a lasting impact. We emphasize on the development of new PUF-based primitives and paradigms, robust protocols, public-key protocols, digital PUFs, new technologies, implementations, metrics and tests for evaluation/validation, as well as relevant attacks and countermeasures.
The Role of Brothels in Reducing HIV Risk in Sonagachi, India

High rates of empowerment, HIV-related knowledge, and condom use among sex workers in Sonagachi, India have been attributed to a community-led intervention called the Sonagachi HIV/AIDS Intervention Program (SHIP). In this research we examined the crucial role of brothels in the success of the intervention. In-depth, semistructured interviews were conducted with 55 participants of SHIP. The results indicate that brothels help sex workers reduce HIV risk by (a) serving as targeted sites for SHIP's HIV intervention efforts, (b) being operated by madams (women managers of brothels) who participate in SHIP's intervention efforts and promote healthy regimes, (c) structuring the economic transactions and sexual performances related to sex work, thus standardizing sex-related behavior, and (d) promoting community empowerment among brothel residents. Implications of these results are discussed for future efforts to replicate SHIP's success in other sex work communities.
Using clinical decision support as a means of implementing a universal postpartum depression screening program

A major barrier to the diagnosis of postpartum depression (PPD) includes symptom detection. The lack of awareness and understanding of PPD among new mothers, the variability in clinical presentation, and the various diagnostic strategies can increase this further. The purpose of this study was to test the feasibility of adding clinical decision support (CDS) to the electronic health record (EHR) as a means of implementing a universal standardized PPD screening program within a large, at high risk, population. All women returning to the Mount Sinai Hospital OB/GYN Ambulatory Practice for postpartum care between 2010 and 2013 were presented with the Edinburgh Postnatal Depression Scale (EPDS) in response to a CDS “hard stop” built into the EHR. Of the 2102 women who presented for postpartum care, 2092 women (99.5 %) were screened for PPD in response to a CDS hard stop module. Screens were missing on ten records (0.5 %) secondary to refusal, language barrier, or lack of clarity in the EHR. Technology is becoming increasingly important in addressing the challenges faced by health care providers. While the identification of PPD has become the recent focus of public health concerns secondary to the significant social burden, numerous barriers to screening still exist within the clinical setting. The utility of adding CDS in the form of a hard stop, requiring clinicians to enter a standardized PPD mood assessment score to the patient EHR, offers a sufficient way to address a primary barrier to PPD symptom identification at the practitioner level.
Web survey of foster youth advisory boards in the United States

Abstract This study administered a web survey of foster youth advisory boards (YAB) in the United States. The survey was emailed to state or private agency representatives in 50 states and the District of Columbia. A total of 49 valid surveys were completed for an overall response rate of 96%. Respondents in 47 states (96%) reported having a foster youth advisory board. There was variation in the type of boards that operated. Just under half reported relying on a single source of funding (47%). The most common features of a YAB were: 1) foster youth issues and concerns, 2) advising a state agency director, 3) youth advocacy, and 4) a youth adult partnership model of decision-making. Opportunities to discuss foster youth issues and concerns and make youth-informed policy and practice decisions were rated by respondents as representing the most beneficial aspects of facilitating a YAB. Recruitment of members and high member turnover were rated as the most challenging aspects of YAB facilitation. Study findings are discussed in the context of participatory practices in child welfare systems and the features of youth advisory boards that facilitate youth voice and representation.