bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting turbulence small-scale behavior using velocity gradient triple decomposition
Authors: Das Rishita , Girimaji Sharath S 
Published: April 2020

Abstract
Turbulence small-scale behavior has been commonly investigated in literature by decomposing the velocity-gradient tensor (A

ij
) into the symmetric strain-rate (S

ij
) and anti-symmetric rotation-rate (W

ij
) tensors. To develop further insight, we revisit some of the key studies using a triple decomposition of the velocity-gradient tensor. The additive triple decomposition formally segregates the contributions of normal-strain-rate (N

ij
), pure-shear (H

ij
) and rigid-body-rotation-rate (R

ij
). The decomposition not only highlights the key role of shear, but it also provides a more accurate account of the influence of normal-strain and pure rotation on important small-scale features. First, the local streamline topology and geometry are described in terms of the three constituent tensors in velocity-gradient invariants’ space. Using direct numerical simulation (DNS) data sets of forced isotropic turbulence, the velocity-gradient and pressure field fluctuations are examined at different Reynolds numbers. At all Reynolds numbers, shear contributes the most and rigid-body-rotation the least toward the velocity-gradient magnitude (A
2 ≡ A

ij

A

ij
). Especially, shear contribution is dominant in regions of high values of A
2 (intermittency). It is shown that the high-degree of enstrophy intermittency reported in literature is due to the shear contribution toward vorticity rather than that of rigid-body-rotation. The study also provides an explanation for the non-intermittent nature of pressure-Laplacian, despite the strong intermittency of enstrophy and dissipation fields. The study further investigates the alignment of the rotation axis with normal strain-rate and pressure Hessian eigenvectors. Overall, it is demonstrated that triple decomposition offers unique and deeper understanding of velocity-gradient behavior in turbulence.
A comprehensive neural networks study of the phase transitions of Potts model
Authors: Tan D-R , Li C-D , Zhu W-P , Jiang F-J 
Published: April 2020

Abstract
Using the techniques of neural networks (NN), we study the three-dimensional (3D) five-state ferromagnetic Potts model on the cubic lattice as well as the two-dimensional (2D) three-state antiferromagnetic Potts model on the square lattice. Unlike the conventional approach, here we follow the idea employed by Li et al (2018 Ann. Phys., NY
391 312–331). Specifically, instead of numerically generating numerous objects for the training, the whole or part of the theoretical ground state configurations of the studied models are considered as the training sets. Remarkably, our investigation of these two models provides convincing evidence for the effectiveness of the method of preparing training sets used in this study. In particular, the results of the 3D model obtained here imply that the NN approach is as efficient as the traditional method since the signal of a first order phase transition, namely tunneling between two channels, determined by the NN method is as strong as that calculated with the Monte Carlo technique. Furthermore, the outcomes associated with the considered 2D system indicate even little partial information of the ground states can lead to conclusive results regarding the studied phase transition. The achievements reached in our investigation demonstrate that the performance of NN, using certain amount of the theoretical ground state configurations as the training sets, is impressive.
Quantum secure direct communication based on single-photon Bell-state measurement
Authors: Li Tao , Long Gui-Lu 
Published: April 2020

Abstract
Security loopholes exploiting the flaws of practical apparatus, especially non-ideal photon detectors, are pressing issues in practical quantum communication. We propose a simple quantum secure direct communication protocol based on single-photon Bell-state measurement and remove side-channel attacks on photon detectors. This quantum communication protocol in principle works in a deterministic way, and it does not require the two-photon interference of photons from independent sources. The single-photon Bell-state measurement with a unity efficiency can be constructed with only linear optics, which significantly simplifies its experimental implementation. Furthermore, we prove that our quantum secure direct communication protocol is immune to general detector-side-channel attacks.
ATLAS muon trigger performance
Authors: Ventura Andrea 
Published: April 2020

Abstract
Muons in the final state represent an important signature for many physics studies performed at the Large Hadron Collider (LHC), involving analyses on Standard Model measurements and on new physics searches. An optimized selection of such events requires an efficient and deeply understood muon trigger system. The present work describes the ATLAS muon trigger, consisting of a hardware-based system (Level-1) followed by a software-based reconstruction (High-Level Trigger). To handle the increase of luminosity in Run 2, several upgrades have been implemented to reduce the trigger rate, while still maintaining high values for the efficiency. Such improvements include the request of a coincidence of hits in the muon spectrometer and the hadronic tile calorimeter, an optimised muon isolation and a better estimation of transverse momentum. An overview will be presented on the most recent improvements of the ATLAS muon trigger and on its performance during Run 2. Finally an outlook for the most relevant upgrades planned for Run 3 will be reported.
Viscous dissipation effect on Williamson nanofluid over stretching/shrinking wedge with thermal radiation and chemical reaction
Authors: Ibrahim Wubshet , Negera Mekonnen 
Published: April 2020

Abstract
This paper scrutinizes the effect of viscous dissipation on unsteady two-dimensional boundary layer flow of Williamson nanofluid over a stretching/Shrinking wedge. To express the boundary condition in concentration problem the passive control concept used. The governing PDEs are converted to ODEs by means of a similarity transformation before being solved numerically by finite difference scheme called Keller-Box method. The equations were numerically solved by using Matlab software 2013a. The characteristics of parameters such as wedge angle, unsteadiness, Williamson, slip, Brownian motion, thermophoresis, chemical reaction parameters, Prandtl number, Biot-number, Eckert number and Lewis number on velocity, concentration and temperature profiles and skin friction coefficient, Nusselt number and Sherwood number are presented in graphs and tables. The result of the study designates that the velocity profiles increased with an upsurge of wedge angle, unsteady parameter and suction parameter while it is diminished with an increase of Williamson and injection parameter. The temperature profiles upsurges with the distended Williamson parameter, Biot number and injection parameter, while it is declined for large values of wedge angle, unsteady and suction parameter. With an increase of Williamson, unsteady and suction parameter the concentration profiles upsurges, while it is decreased with an increase of wedge angle and injection parameter. The numerical results are compared with available literature and obtained a good agreement.
Low oxygen pressure synthesis of NdNiO3-δ nanowires by electrospinning
Authors: Medina M S , Ramirez B N , Ferreira P M G L , Huang H P , Zenatti A , Lanfredi A J C , Escote M T 
Published: April 2020

Abstract
Synthesis of RNiO3 (R = rare earth) nanowires can be interesting as building blocks with potential applications in optoelectronic devices. Here, we describe the synthesis and characterization of NdNiO3-δ
(NNO) nanowires produced by electrospinning technique via polymeric precursor solution at relatively low temperature and oxygen pressure. These NNO nanowires were characterized by x-ray diffraction (XRD), x-ray photodetection spectroscopy (XPS), Field Emission Scanning Electron Microscopy (Fe-SEM), Magnetization (M(T)) and electrical resistance (R(T)) measurements. SEM images revealed a granular nanowire microstructure of NNO nanostructures, with a distribution of nanowire diameters ranging from 50 to 150 nm. The NNO nanowires also exhibit granular characteristics with an average grain diameter of 40 nm. The x-ray diffraction patterns of the NNO nanowires indicated that these samples exhibited a high degree of crystallinity and their Bragg reflections can be indexed to an orthorhombic-distorted (Pbnm symmetry) perovskite structure. The crystalline structure seems to be slightly texturized in some Bragg directions and with a slightly strained crystallite. M(T) and R(T) measurement as a function of temperature curves show that these NNO samples present a metal-insulator (MI) transition close to T

MI
∼ 198 K, which is usually observed in NNO thin films and bulk samples. The nanostructured shape and these experimental observations can be promising in designing new electronic devices using this strongly correlated oxide.
COVID-19 outbreak: organisation of a geriatric assessment and coordination unit. A French example
Authors: Koeberle Séverine , Tannou Thomas , Bouiller Kévin , Becoulet Nicolas , Outrey Justin , Chirouze Catherine , Aubry Régis 
Published: April 2020

Abstract
Older people are particularly affected by the COVID-19 outbreak because of their vulnerability as well as the complexity of health organisations, particularly in the often-compartmentalised interactions between community, hospital and nursing home actors. In this endemic situation, with massive flows of patients requiring holistic management including specific and intensive care, the appropriate assessment of each patient’s level of care and the organisation of specific networks is essential.
To that end, we propose here a territorial organisation of health care, favouring communication between all actors. This organisation of care is based on three key points:
To use the basis of territorial organisation of health by facilitating the link between hospital settings and geriatric sectors at the regional level. To connect private, medico-social and hospital actors through a dedicated centralised unit for evaluation, geriatric coordination of care and decision support. A geriatrician coordinates this multidisciplinary unit. It includes an emergency room doctor, a supervisor from the medical regulation centre (Centre 15), an infectious disease physician, a medical hygienist and a palliative care specialist. To organise an ad hoc follow-up channel, including the necessary resources for the different levels of care required, according to the resources of the territorial network, and the creation of a specific COVID geriatric palliative care service.
This organisation meets the urgent health needs of all stakeholders, facilitating its deployment and allows the sustainable implementation of a coordinated geriatric management dynamic between the stakeholders on the territory.
Cardiotoxicity of Use of Sequential Aromatase Inhibitors in Women With Breast Cancer
Authors: Khosrow-Khavar Farzin , Bouganim Nathaniel , Filion Kristian B , Suissa Samy , Azoulay Laurent 
Published: April 2020

Abstract
The association between use of aromatase inhibitors (AIs) and cardiovascular outcomes is controversial. While some observational studies have assessed the cardiovascular safety of AIs as upfront treatments, their cardiotoxicity as sequential treatments with tamoxifen remains unknown. Thus, we conducted a population-based cohort study using data from the United Kingdom Clinical Practice Research Datalink linked to the Hospital Episode Statistics and Office for National Statistics databases. We employed a prevalent new-user design to propensity-score match, in a 1:2 ratio, patients switching from tamoxifen to AIs with patients continuing tamoxifen between 1998 and 2016. Cox proportional hazards models were used to estimate hazard ratios and 95% confidence intervals for the study outcomes (myocardial infarction, ischemic stroke, heart failure, and cardiovascular mortality). Overall, 1,962 patients switching to AIs were matched to 3,874 patients continuing tamoxifen. Compared with tamoxifen, AIs were associated with an increased risk of myocardial infarction (hazard ratio (HR) = 2.08, 95% confidence interval (CI): 1.02, 4.27). The hazard ratios were elevated for ischemic stroke (HR = 1.58, 95% CI: 0.85, 2.93) and heart failure (HR = 1.69, 95% CI: 0.79, 3.62) but not cardiovascular mortality (HR = 0.87, 95% CI: 0.49, 1.54), with confidence intervals including the null value. The elevated hazard ratios observed for the cardiovascular outcomes should be corroborated in future large observational studies.
Novel sources of (co)variation in nestling begging behavior and hunger at different biological levels of analysis
Authors: Wetzel Daniel P , Mutzel Ariane , Wright Jonathan , Dingemanse Niels J 
Published: April 2020

Abstract
Biological hypotheses predicting patterns of offspring begging typically concern the covariance with hunger and/or development at specific hierarchical levels. For example, hunger drives within-individual patterns of begging, but begging also drives food intake among individuals within broods, and begging and food intake can covary positively or negatively among genotypes or broods. Testing biological phenomena that occur at multiple levels, therefore, requires the partitioning of covariance between traits of interest to ensure that each level-specific relationship is appropriately assessed. We performed a partial cross-fostering study on a wild population of great tits (Parus major), then used multivariate mixed models to partition variation and covariation in nestling begging effort and two metrics of nestling hunger within versus among individual nestlings and broods. At the within-individual level, we found that nestlings begged more intensely when hungrier (positive correlation between begging and hunger). However, among individuals, nestlings that were fed more frequently also begged more intensely on average (negative correlation between begging and hunger). Variation in nestling mass did not give rise to the negative correlation between begging and hunger among nestlings, but we did find that lighter nestlings begged more intensely than their heavier biological siblings, suggesting that this effect may be driven by a genetic component linked to offspring size. Our study illustrates how patterns of covariance can differ across biological levels of analysis and addresses biological mechanisms that could produce these previously obscured patterns.
Predicting target genes of non-coding regulatory variants with IRT
Authors: Wu Zhenqin , Ioannidis Nilah M , Zou James 
Published: April 2020

Abstract

Summary
Interpreting genetic variants of unknown significance (VUS) is essential in clinical applications of genome sequencing for diagnosis and personalized care. Non-coding variants remain particularly difficult to interpret, despite making up a large majority of trait associations identified in genome-wide association studies (GWAS) analyses. Predicting the regulatory effects of non-coding variants on candidate genes is a key step in evaluating their clinical significance. Here, we develop a machine-learning algorithm, Inference of Connected expression quantitative trait loci (eQTLs) (IRT), to predict the regulatory targets of non-coding variants identified in studies of eQTLs. We assemble datasets using eQTL results from the Genotype-Tissue Expression (GTEx) project and learn to separate positive and negative pairs based on annotations characterizing the variant, gene and the intermediate sequence. IRT achieves an area under the receiver operating characteristic curve (ROC-AUC) of 0.799 using random cross-validation, and 0.700 for a more stringent position-based cross-validation. Further evaluation on rare variants and experimentally validated regulatory variants shows a significant enrichment in IRT identifying the true target genes versus negative controls. In gene-ranking experiments, IRT achieves a top-1 accuracy of 50% and top-3 accuracy of 90%. Salient features, including GC-content, histone modifications and Hi-C interactions are further analyzed and visualized to illustrate their influences on predictions. IRT can be applied to any VUS of interest and each candidate nearby gene to output a score reflecting the likelihood of regulatory effect on the expression level. These scores can be used to prioritize variants and genes to assist in patient diagnosis and GWAS follow-up studies.

Availability and implementation
Codes and data used in this work are available at https://github.com/miaecle/eQTL_Trees.

Supplementary information
Supplementary data are available at Bioinformatics online.
scHLAcount: allele-specific HLA expression from single-cell gene expression data
Authors: Darby Charlotte A , Stubbington Michael J T , Marks Patrick J , Martínez Barrio Álvaro , Fiddes Ian T 
Published: April 2020

Abstract

Summary
Bulk RNA sequencing studies have demonstrated that human leukocyte antigen (HLA) genes may be expressed in a cell type-specific and allele-specific fashion. Single-cell gene expression assays have the potential to further resolve these expression patterns, but currently available methods do not perform allele-specific quantification at the molecule level. Here, we present scHLAcount, a post-processing workflow for single-cell RNA-seq data that computes allele-specific molecule counts of the HLA genes based on a personalized reference constructed from the sample’s HLA genotypes.

Availability and implementation
scHLAcount is available under the MIT license at https://github.com/10XGenomics/scHLAcount.

Supplementary information
Supplementary data are available at Bioinformatics online.
‘ISIS is not Islam’: Epistemic Injustice, Everyday Religion, and Young Muslims’ Narrative Resistance
Authors: Sandberg Sveinung , Colvin Sarah 
Published: April 2020

AbstractPowerful narratives that invoke religious concepts—jihad, Sharia, shahid, Caliphate, kuffar, and al-Qiyāmah—have accompanied jihadi violence but also inspired robust counter-narratives from Muslims. Taking a narrative criminological approach, we explore the rejection of religious extremism that emerges in everyday interactions in a religious community under intense pressure in Western societies. Drawing on qualitative interviews with 90 young Muslims in Norway, we argue that young Muslims suffer epistemic injustice in their narrative exclusion from the mainstream and assess the narrative credibility they try to maintain in the face of marginalization. We suggest that young Muslims’ religious narratives reject a mainstream characterization of Islam as essentially a religion of aggression and simultaneously join forces with that mainstream in seeking the narrative exclusion of the jihadi extremists.
Population Movement, City Closure in Wuhan, and Geographical Expansion of the COVID-19 Infection in China in January 2020
Authors: Liu Kun , Ai Siqi , Song Shuxuan , Zhu Guanghu , Tian Fei , Li Huan , Gao Yuan , Wu Yinglin , Zhang Shiyu , Shao Zhongjun , Liu Qiyong , Lin Hualiang 
Published: April 2020

Abstract

Background
The unprecedented outbreak of corona virus disease 2019 (COVID-19) infection in Wuhan City has caused global concern; the outflow of the population from Wuhan was believed to be a main reason for the rapid and large-scale spread of the disease, so the government implemented a city-closure measure to prevent its transmission considering the large amount of travel before the Chinese New Year.

Methods
Based on the daily reported new cases and the population-movement data between 1 and 31 January, we examined the effects of population outflow from Wuhan on the geographical expansion of the infection in other provinces and cities of China, as well as the impacts of the city closure in Wuhan using different closing-date scenarios.

Results
We observed a significantly positive association between population movement and the number of the COVID-19 cases. The spatial distribution of cases per unit of outflow population indicated that the infection in some areas with a large outflow of population might have been underestimated, such as Henan and Hunan provinces. Further analysis revealed that if the city-closure policy had been implemented 2 days earlier, 1420 (95% confidence interval, 1059–1833) cases could have been prevented, and if 2 days later, 1462 (1090–1886) more cases would have been possible.

Conclusions
Our findings suggest that population movement might be one important trigger for the transmission of COVID-19 infection in China, and the policy of city closure is effective in controlling the epidemic.
Antibody Detection and Dynamic Characteristics in Patients With Coronavirus Disease 2019
Authors: Xiang Fei , Wang Xiaorong , He Xinliang , Peng Zhenghong , Yang Bohan , Zhang Jianchu , Zhou Qiong , Ye Hong , Ma Yanling , Li Hui , Wei Xiaoshan , Cai Pengcheng , Ma Wan-Li 
Published: April 2020

Abstract

Background
The coronavirus disease 2019 (COVID-19), caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been rapidly spreading nationwide and abroad. A serologic test to identify antibody dynamics and response to SARS-CoV-2 was developed.

Methods
The antibodies against SARS-CoV-2 were detected by an enzyme-linked immunosorbent assay based on the recombinant nucleocapsid protein of SARS-CoV-2 in patients with confirmed or suspected COVID-19 at 3–40 days after symptom onset. The gold standard for COVID-19 diagnosis was nucleic acid testing for SARS-CoV-2 by real-time reverse-transcription polymerase chain reaction (rRT-PCR). The serodiagnostic power of the specific immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies against SARS-CoV-2 was investigated in terms of sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and consistency rate.

Results
The seroconversion of specific IgM and IgG antibodies were observed as early as the fourth day after symptom onset. In the patients with confirmed COVID-19, sensitivity, specificity, PPV, NPV, and consistency rate of IgM were 77.3% (51/66), 100%, 100%, 80.0%, and 88.1%, respectively, and those of IgG were 83.3% (55/66), 95.0%, 94.8%, 83.8%, and 88.9%. In patients with suspected COVID-19, sensitivity, specificity, PPV, NPV, and consistency rate of IgM were 87.5% (21/24), 100%, 100%, 95.2%, and 96.4%, respectively, and those of IgG were 70.8% (17/24), 96.6%, 85.0%, 89.1%, and 88.1%. Both antibodies performed well in serodiagnosis for COVID-19 and rely on great specificity.

Conclusions
The antibodies against SARS-CoV-2 can be detected in the middle and later stages of the illness. Antibody detection may play an important role in the diagnosis of COVID-19 as a complementary approach to viral nucleic acid assays.