Miracle-dz/UniFAR-FTUs huggingface dataset:
OP2: An active library framework for solving unstructured mesh-based applications on multi-core and many-core architectures

OP2 is an “active” library framework for the solution of unstructured mesh-based applications. It utilizes source-to-source translation and compilation so that a single application code written using the OP2 API can be transformed into different parallel implementations for execution on different back-end hardware platforms. In this paper we present the design of the current OP2 library, and investigate its capabilities in achieving performance portability, near-optimal performance, and scaling on modern multi-core and many-core processor based systems. A key feature of this work is OP2's recent extension facilitating the development and execution of applications on a distributed memory cluster of GPUs. We discuss the main design issues in parallelizing unstructured mesh based applications on heterogeneous platforms. These include handling data dependencies in accessing indirectly referenced data, the impact of unstructured mesh data layouts (array of structs vs. struct of arrays) and design considerations in generating code for execution on a cluster of GPUs. A representative CFD application written using the OP2 framework is utilized to provide a contrasting benchmarking and performance analysis study on a range of multi-core/many-core systems. These include multi-core CPUs from Intel (Westmere and Sandy Bridge) and AMD (Magny-Cours), GPUs from NVIDIA (GTX560Ti, Tesla C2070), a distributed memory CPU cluster (Cray XE6) and a distributed memory GPU cluster (Tesla C2050 GPUs with InfiniBand). OP2's design choices are explored with quantitative insights into their contributions to performance. We demonstrate that an application written once at a high-level using the OP2 API can be easily portable across a wide range of contrasting platforms and is capable of achieving near-optimal performance without the intervention of the domain application programmer.
Mining significant substructure-substructure pairs in structural associations

Biological and chemical objects in bioinformatics are often linked to structures: proteins and DNAs to their sequences, small-molecule compounds to their chemical structures, and pathways to their network structures. Associations among these objects, such as interactions between proteins and compounds, are of particular interest in the field, and these associations are often given as a graph: the objects are represented as nodes, and the associated pairs are connected by edges. To analyze these associations through relationships between the local substructures of individual objects, we propose a general framework for exactly enumerating substructure-substructure pairs significantly overrepresented in the “associated” pairs with edges rather than in all other “control” pairs with no edges. Analyzing relationships between local information have been successfully applied to sequences, table-form data, and texts. For example, co-evolution is a key biological concept for understanding protein interactions in terms of their sequences [1], co-modules which describe coherent patterns across paired data sets are developed to analyze the gene-expression and drug-response data [2], and co-occurrence of the words is one of fundamental tools for mining biomedical texts [3]. Thus, using our framework, applying this concept to the associations between more complicated structures such as trees and graphs would also give insights to understand underlying biological problems. The proposed framework can be applied to various types of association datasets with structures (sequences, trees, and graphs): interaction between compounds and proteins, and side-effect associations between compounds. In this work, we analyze the interactions between drugs and targets, i.e., the structural associations between chemical structures of drug compounds and amino-acid sequences of target proteins.
Spontaneous R-Symmetry Breaking in O'Raifeartaigh Models

We study the question of whether spontaneous U(1)R breaking can occur in O'Raifeartaigh-type models of spontaneous supersymmetry breaking. We show that in order for it to occur, there must be a field in the theory with R-charge different from 0 or 2. We construct the simplest O'Raifeartaigh model with this property, and we find that for a wide range of parameters, it has a meta-stable vacuum where U(1)R is spontaneously broken. This suggests that spontaneous U(1)R breaking actually occurs in generic O'Raifeartaigh models.
Paediatric normative values of the incremental shuttle walking test

Incremental Shuttle Walking Test; Paediatric Population; Reference value; Statistical regression Background: Reference values for the incremental shuttle walking test (ISWT) which is applicable in the paediatric population to prescribe exercise need to be solidly established. This study aimed to contribute for establishing paediatric reference values of the ISWT and a reference equation for predicting ISWT. Methods: In a cross-sectional study, 55 healthy children performed two ISWT in a 10-m long corridor. The anthropometric and demographic data, physical activity, spirometry and quadriceps muscle strength (QMS) were measured using standardized protocols. Results: In general, healthy children walked 1233.82±348.86 meters in the ISWT, presenting large variability (range 340-2250 m). There were significant correlations between the distance walked in the ISWT with gender (r=0.274; p=.043), age (r=0.659; p<0.001), weight (r=0.310; p=.021), height (r=0.646; p<.001), PAS (r=0.284; p=.035), quadriceps muscle strength (r=0.535; p<.001), but not with BMI (r=-0.026; p=.852) or with FEV1 % predicted (r=0.152; p=.267). A model of stepwise multiple regression showed that gender, age, weight and QMS were independent contributors to the ISWT in healthy subjects, explaining 70% (p<0.001) of the variability. The derived reference equation was: ISWTpredicted= 699.69+(239.329*gender)+(134.616*age)-(9.941*weight)+(12.107*QMS), where male gender = 1 and female gender = 0. Conclusion: In conclusion, the variability of the paediatric ISWT was explained largely by gender, age, weight and QMS. The reference equation could be useful for interpreting the walking performance of paediatric population.
Religion and youth educational aspirations: a multilevel approach

ABSTRACT Previous research has demonstrated that individual religious beliefs and practices are associated with educational outcomes. However, less is known about the manner in which the overall religious cultural influence of a religion can affect an individual’s educational aspirations. Using multilevel analyses on two waves of the National Study of Youth and Religion (NSYR) merged with county-level variables from the US Census, and the Religious Congregations and Membership Study (RCMS), the study shows that a county’s higher Jewish population share is associated with a higher level of educational aspirations for the youth, regardless of being Jewish or not. This Jewish contextual effect remains robust even after controlling a wide range of individual and county-level variables, such as individual academic achievement and religious identity. Consistent with the relevant theory and literature, the negative main effect of county-level conservative Protestant population share on educational aspirations is explained by county-level socioeconomic characteristics. The same mechanism is used in part to explain the initially positive relationship between Catholic population share and educational aspirations. Finally, the study highlights the importance of using a multilevel approach to examine and provide understanding of the relationship between religious influence and educational outcomes.
SIGN: similarity identification in gene expression

MOTIVATION High-throughput molecular profiles of human cells have been used in predictive computational approaches for stratification of healthy and malignant phenotypes and identification of their biological states. In this regard, pathway activities have been used as biological features in unsupervised and supervised learning schemes. RESULTS We developed SIGN (Similarity Identification in Gene expressioN), a flexible open source R package facilitating the use of pathway activities and their expression patterns to identify similarities between biological samples. We defined a new measure, the transcriptional similarity coefficient, which captures similarity of gene expression patterns, instead of quantifying overall activity, in biological pathways between the samples. To demonstrate the utility of SIGN in biomedical research, we establish that SIGN discriminates subtypes of breast tumors and patients with good or poor overall survival. SIGN outperforms the best models in DREAM challenge in predicting survival of breast cancer patients using the data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC). In summary, SIGN can be used as a new tool for interrogating pathway activity and gene expression patterns in unsupervised and supervised learning schemes to improve prognostic risk estimation for cancer patients by the biomedical research community. AVAILABILITY AND IMPLEMENTATION An open source R package is available (https://cran.r-project.org/web/packages/SIGN/). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Intensive support to improve clinical decision making in cardiovascular care: a randomised controlled trial in general practice

Objective: To evaluate the effects of feedback reports combined with outreach visits from trained non-physicians on the clinical decision making of general practitioners (GPs) in cardiovascular care. Design: Pragmatic cluster controlled trial with randomisation of practices to support (intervention group) or no special attention (control group); analysis after 2 years. Setting: 124 general practices in The Netherlands. Participants: 185 GPs. Main outcome measures: Compliance rates for 12 evidence-based indicators for the management of patients with hypertension, hypercholesterolaemia, angina pectoris, or heart failure. The evaluation relied on the prospective recording of patient encounters by the participating GPs. Results: The GPs reported 30 101 clinical decisions at baseline and 22 454 decisions after the intervention. A significant improvement was seen for five of the 12 indicators: assessment of risk factors in patients with hypercholesterolaemia (odds ratio 2.04; 95% CI 1.44 to 2.88) or angina pectoris (3.07; 1.08 to 8.79), provision of information and advice to patients with hypercholesterolaemia (1.58, 1.17 to 2.13) or hypertension (1.55, 1.35 to 1.77), and checking for clinical signs of deterioration in patients with heart failure (4.11, 2.17 to 7.77). Single handed practices, non-training practices, and practices with older GPs gained particular benefit from the intervention. Conclusions: Intensive support from trained non-physicians can alter certain aspects of the clinical decision making of GPs in cardiovascular care. The effect is small and the strategy needs further development.
Multimodel approach for pedestrian detection

Good performance of pedestrian detection in an automatic driving system is a necessary task. Many pedestrian detection algorithm use Histogram Oriented Gradient (HOG) for feature extraction and Support Vector Machine (SVM) for classification. Some papers use additional features with HOG, such as Local Binary Pattern (HOG-LBP), to improve the performance. Neural Network and Extreme Learning Machine (ELM) are also used for classification like SVM, but SVM always finds global optimum for classification. This paper adds algorithm to this HOG, SVM system for improving the detection performance. This paper proposes a new method which uses pose of pedestrian. The proposed model outperforms conventional method in SDL dataset.
Molecular insights into cell toxicity of a novel familial amyloidogenic variant of β2‐microglobulin

The first genetic variant of β2‐microglobulin (b2M) associated with a familial form of systemic amyloidosis has been recently described. The mutated protein, carrying a substitution of Asp at position 76 with an Asn (D76N b2M), exhibits a strongly enhanced amyloidogenic tendency to aggregate with respect to the wild‐type protein. In this study, we characterized the D76N b2M aggregation path and performed an unprecedented analysis of the biochemical mechanisms underlying aggregate cytotoxicity. We showed that, contrarily to what expected from other amyloid studies, early aggregates of the mutant are not the most toxic species, despite their higher surface hydrophobicity. By modulating ganglioside GM1 content in cell membrane or synthetic lipid bilayers, we confirmed the pivotal role of this lipid as aggregate recruiter favouring their cytotoxicity. We finally observed that the aggregates bind to the cell membrane inducing an alteration of its elasticity (with possible functional unbalance and cytotoxicity) in GM1‐enriched domains only, thus establishing a link between aggregate‐membrane contact and cell damage.
Mediterranean diet, Alzheimer disease, and vascular mediation.

OBJECTIVES To examine the association between the Mediterranean diet (MeDi) and Alzheimer disease (AD) in a different AD population and to investigate possible mediation by vascular pathways. Design, Setting, Patients, and MAIN OUTCOME MEASURES A case-control study nested within a community-based cohort in New York, NY. Adherence to the MeDi (0- to 9-point scale with higher scores indicating higher adherence) was the main predictor of AD status (194 patients with AD vs 1790 nondemented subjects) in logistic regression models that were adjusted for cohort, age, sex, ethnicity, education, apolipoprotein E genotype, caloric intake, smoking, medical comorbidity index, and body mass index (calculated as weight in kilograms divided by height in meters squared). We investigated whether there was attenuation of the association between MeDi and AD when vascular variables (stroke, diabetes mellitus, hypertension, heart disease, lipid levels) were simultaneously introduced in the models (which would constitute evidence of mediation). RESULTS Higher adherence to the MeDi was associated with lower risk for AD (odds ratio, 0.76; 95% confidence interval, 0.67-0.87; P<.001). Compared with subjects in the lowest MeDi tertile, subjects in the middle MeDi tertile had an odds ratio of 0.47 (95% confidence interval, 0.29-0.76) and those at the highest tertile an odds ratio of 0.32 (95% confidence interval, 0.17-0.59) for AD (P for trend <.001). Introduction of the vascular variables in the model did not change the magnitude of the association. CONCLUSIONS We note once more that higher adherence to the MeDi is associated with a reduced risk for AD. The association does not seem to be mediated by vascular comorbidity. This could be the result of either other biological mechanisms (oxidative or inflammatory) being implicated or measurement error of the vascular variables.
Nanowire GMR Thin Films for Magnetic Sensors

We present an appealing technique for the fabrication of nanowire-GMR thin films for magnetic sensors. Using this technique, magnetic sensors can be created that are transparent, flexible, and can have a size from square microns to square meters with no exponeitial cost increases. The electrical sheet resistance of these sensors are between 100-100k Ω/ , with a %GMR on the scale of 10%. A electrodeposition technique is used to create current perpendicular to plane (CPP) multilayer GMR nanowires inside of aluminum oxide templates. After fabrication, the nanowires can be transferred to substrates using a variety of techniques including vacuum filtration, metering rod, and spray coating methods. The operational parameters of the magnetic sensors are determined by the characteristics of the nanowires, which include their chemical makeup, length, density, amount of oxidation removal and annealing.
A RF Low Power 0.18-µm based CMOS Differential Ring Oscillator

A voltage controlled ring oscillator is implemented using the 1P6M 0. 18μm CMOS process provided by TSMC with 1.8 volts power supply. Differential delay cell stages are used to reduce noise. The output frequency range is 3.125-5.26 GHz with control voltages range 1 V to 1.8 V. The simulated result of the circuit draws 0.621 mW of power from the 1.8 V supply. Keywords— CMOS, low power, phase noised, differential delay cell, voltage controlled oscillator (VCO).
Factors to consider in evaluating the appropriateness of restraints during forensic evaluations

Forensic examiners frequently conduct evaluations with individuals who may be regarded as dangerous. To manage this situation, forensic examiners may prefer examinees to wear restraints. Available literature indicates that the use of restraints may be both physically and psychologically detrimental and thus possibly both reduces the yield and limits the utility of psychological test data. Although there is a lack of research addressing this concern, one must use the available information to inform the decision on utilization of restraints during forensic evaluations. In addition, professional ethics, test standards and norms, the reported adverse effects of restraints on both psychiatric patients and inmates, and the concept of forced medication are reviewed to help assess the appropriateness of restraints during forensic evaluations. This analysis provides forensic examiners with insight and recommendations to determine if the use of restraints is best practice during forensic evaluations, particularly within the United States.
Anti-obesity efficacy of nanoemulsion oleoresin capsicum in obese rats fed a high-fat diet

Purpose This study determined the effects of oleoresin capsicum (OC) and nanoemulsion OC (NOC) on obesity in obese rats fed a high-fat diet. Methods The rats were randomly separated into three groups: a high-fat (HF) diet group, HF + OC diet group, and HF + NOC diet group. All groups were fed the diet and water ad libitum for 14 weeks. Results NOC reduced the body weight and adipose tissue mass, whereas OC did not. OC and NOC reduced mRNA levels of adipogenic genes, including peroxisome proliferator-activated receptor (PPAR)-γ, sterol regulatory element-binding protein-1c, and fatty acid-binding protein in white adipose tissue. The mRNA levels of genes related to β-oxidation or thermogenesis including PPAR-α, palmitoyltransferase-1α, and uncoupling protein-2 were increased by the OC and NOC relative to the HF group. Both OC and NOC clearly stimulated AMP-activated protein kinase (AMPK) activity. In particular, PPAR-α, palmitoyltransferase-1α, uncoupling protein-2 expression, and AMPK activity were significantly increased in the NOC group compared to in the OC group. NOC decreased glycerol-3-phosphate dehydrogenase activity whereas OC did not. Conclusion From these results, NOC could be suggested as a potential anti-obesity agent in obese rats fed a HF diet. The effects of the NOC on obesity were associated with changes of multiple gene expression, activation of AMPK, and inhibition of glycerol-3-phosphate dehydrogenase in white adipose tissue.
Nutrition among men and household food security in an internally displaced persons camp in Kenya

Abstract Objective To determine the nutritional status of men and the food security status of their households in an internally displaced persons (IDP) camp in Kenya. Design A descriptive, cross-sectional study using a questionnaire and biometric measurements was completed in June 2013. Setting IDP camp, Rongai, Kenya. Subjects A total of 267 men aged ≥18 years residing within the camp were recruited via respondent-driven sampling. Statistical associations between categorical variables were analysed using Pearson’s χ 2 tests, while independent t tests were used for continuous variables. Results Among the men surveyed, we found a mean BMI of 20·3 (sd 2·5) kg/m2, with 23·9 % of participants in the underweight category (BMI<18·5 kg/m2). The mean Individual Dietary Diversity Score was 6 out of a maximum score of 9. The mean Household Food Insecurity Access Scale score was 11·6 (sd 6·8), with 180 participants (71·7 %) residing in households categorised as severely food insecure. Low monthly household income (<2000 Kenyan Shillings, or $US 25) was associated with a higher food insecurity score (P<0·001), greater likelihood of residing in a severely food-insecure household (P<0·001), low dietary diversity score (P<0·05) and being underweight (P<0·01). Conclusions While the nutritional status of men in the IDP camp is comparable to non-displaced men in Kenya, household food insecurity is relatively high. Efforts to improve food security for the future are essential to minimise the impact of severe food insecurity on mental health, disease profiles and family well-being reported in other IDP settings.
Rank-selection criterion for Krylov-subspace-based adaptive filtering techniques

We propose a novel rank-selection criterion for the Krylov-subspace-based filtering techniques such as the well-known multistage Wiener filter. We provide two necessary and sufficient conditions for the low-dimensional Krylov subspace to contain the optimal filter. The first condition is that the subspace is invariant under the transformation by the autocorrelation matrix associated with the subspace itself, and the second condition is its reverse inclusion. We derive two criteria based on the conditions; the criterion based on the first condition coincides with the conventional one, and the one based on the second is the proposed one. Simulation results indicate that the proposed criterion induces a natural relation between the threshold parameter and the average rank.
Profiling and Improving I/O Performance of a Large-Scale Climate Scientific Application

Exascale computing systems are soon to emerge, which will pose great challenges on the huge gap between computing and I/O performance. Many large-scale scientific applications play an important role in our daily life. The huge amounts of data generated by such applications require highly parallel and efficient I/O management policies. In this paper, we adopt a mission-critical scientific application, GEOS-5, as a case to profile and analyze the communication and I/O issues that are preventing applications from fully utilizing the underlying parallel storage systems. Through in-detail architectural and experimental characterization, we observe that current legacy I/O schemes incur significant network communication overheads and are unable to fully parallelize the data access, thus degrading applications' I/O performance and scalability. To address these inefficiencies, we redesign its I/O framework along with a set of parallel I/O techniques to achieve high scalability and performance. Evaluation results on the NASA discover cluster show that our optimization of GEOS- 5 with ADIOS has led to significant performance improvements compared to the original GEOS-5 implementation.