bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generating synthetic magnetism via Floquet engineering auxiliary qubits in phonon-cavity-based lattice
Authors: Wang Xin , Li Hong-Rong , Li Fu-Li 
Published: February 2020

Abstract
Gauge magnetic fields have a close relation to breaking time-reversal symmetry in condensed matter. In the presence of the gauge fields, we might observe nonreciprocal and topological transport. Inspired by these, there is a growing effort to realize exotic transport phenomena in optical and acoustic systems. However, due to charge neutrality, realizing analog magnetic flux for phonons in nanoscale systems is still challenging in both theoretical and experimental studies. Here we propose a novel mechanism to generate synthetic magnetic field for phonon lattice by Floquet engineering auxiliary qubits. We find that, a longitudinal Floquet drive on the qubit will produce a resonant coupling between two detuned acoustic cavities. Specially, the phase encoded into the longitudinal drive can exactly be transformed into the phonon–phonon hopping. Our proposal is general and can be realized in various types of artificial hybrid quantum systems. Moreover, by taking surface-acoustic-wave (SAW) cavities for example, we propose how to generate synthetic magnetic flux for phonon transport. In the presence of synthetic magnetic flux, the time-reversal symmetry will be broken, which allows one to realize the circulator transport and analog Aharonov–Bohm effects for acoustic waves. Last, we demonstrate that our proposal can be scaled to simulate topological states of matter in quantum acoustodynamics system.
Protein–ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data
Authors: Xia Chun-Qiu , Pan Xiaoyong , Shen Hong-Bin 
Published: February 2020

Abstract

Motivation
Knowledge of protein–ligand binding residues is important for understanding the functions of proteins and their interaction mechanisms. From experimentally solved protein structures, how to accurately identify its potential binding sites of a specific ligand on the protein is still a challenging problem. Compared with structure-alignment-based methods, machine learning algorithms provide an alternative flexible solution which is less dependent on annotated homogeneous protein structures. Several factors are important for an efficient protein–ligand prediction model, e.g. discriminative feature representation and effective learning architecture to deal with both the large-scale and severely imbalanced data.

Results
In this study, we propose a novel deep-learning-based method called DELIA for protein–ligand binding residue prediction. In DELIA, a hybrid deep neural network is designed to integrate 1D sequence-based features with 2D structure-based amino acid distance matrices. To overcome the problem of severe data imbalance between the binding and nonbinding residues, strategies of oversampling in mini-batch, random undersampling and stacking ensemble are designed to enhance the model. Experimental results on five benchmark datasets demonstrate the effectiveness of proposed DELIA pipeline.

Availability and implementation
The web server of DELIA is available at www.csbio.sjtu.edu.cn/bioinf/delia/.

Supplementary information
Supplementary data are available at Bioinformatics online.
MUM&Co: accurate detection of all SV types through whole-genome alignment
Authors: O’Donnell Samuel , Fischer Gilles 
Published: February 2020

Abstract

Summary
MUM&Co is a single bash script to detect structural variations (SVs) utilizing whole-genome alignment (WGA). Using MUMmer’s nucmer alignment, MUM&Co can detect insertions, deletions, tandem duplications, inversions and translocations greater than 50 bp. Its versatility depends upon the WGA and therefore benefits from contiguous de-novo assemblies generated by third generation sequencing technologies. Benchmarked against five WGA SV-calling tools, MUM&Co outperforms all tools on simulated SVs in yeast, plant and human genomes and performs similarly in two real human datasets. Additionally, MUM&Co is particularly unique in its ability to find inversions in both simulated and real datasets. Lastly, MUM&Co’s primary output is an intuitive tabulated file containing a list of SVs with only necessary genomic details.

Availability and implementation
https://github.com/SAMtoBAM/MUMandCo.

Supplementary information
Supplementary data are available at Bioinformatics online.
High-throughput and efficient multilocus genome-wide association study on longitudinal outcomes
Authors: Xu Huang , Li Xiang , Yang Yaning , Li Yi , Pinheiro Jose , Sasser Kate , Hamadeh Hisham , Steven Xu , Yuan Min ,   and for the Alzheimer’s Disease Neuroimaging Initiative
Published: February 2020

Abstract

Motivation
With the emerging of high-dimensional genomic data, genetic analysis such as genome-wide association studies (GWAS) have played an important role in identifying disease-related genetic variants and novel treatments. Complex longitudinal phenotypes are commonly collected in medical studies. However, since limited analytical approaches are available for longitudinal traits, these data are often underutilized. In this article, we develop a high-throughput machine learning approach for multilocus GWAS using longitudinal traits by coupling Empirical Bayesian Estimates from mixed-effects modeling with a novel ℓ0-norm algorithm.

Results
Extensive simulations demonstrated that the proposed approach not only provided accurate selection of single nucleotide polymorphisms (SNPs) with comparable or higher power but also robust control of false positives. More importantly, this novel approach is highly scalable and could be approximately &gt;1000 times faster than recently published approaches, making genome-wide multilocus analysis of longitudinal traits possible. In addition, our proposed approach can simultaneously analyze millions of SNPs if the computer memory allows, thereby potentially allowing a true multilocus analysis for high-dimensional genomic data. With application to the data from Alzheimer's Disease Neuroimaging Initiative, we confirmed that our approach can identify well-known SNPs associated with AD and were much faster than recently published approaches (≥6000 times).

Availability and implementation
The source code and the testing datasets are available at https://github.com/Myuan2019/EBE_APML0.

Supplementary information
Supplementary data are available at Bioinformatics online.
Estimation and inference for the indirect effect in high-dimensional linear mediation models
Authors: Zhou Ruixuan Rachel , Wang Liewei , Zhao Sihai Dave 
Published: February 2020

Summary
Mediation analysis is difficult when the number of potential mediators is larger than the sample size. In this paper we propose new inference procedures for the indirect effect in the presence of high-dimensional mediators for linear mediation models. We develop methods for both incomplete mediation, where a direct effect may exist, and complete mediation, where the direct effect is known to be absent. We prove consistency and asymptotic normality of our indirect effect estimators. Under complete mediation, where the indirect effect is equivalent to the total effect, we further prove that our approach gives a more powerful test compared to directly testing for the total effect. We confirm our theoretical results in simulations, as well as in an integrative analysis of gene expression and genotype data from a pharmacogenomic study of drug response. We present a novel analysis of gene sets to understand the molecular mechanisms of drug response, and also identify a genome-wide significant noncoding genetic variant that cannot be detected using standard analysis methods.
Antibiotic Prescribing Choices and Their Comparative C. Difficile Infection Risks: A Longitudinal Case-Cohort Study
Authors: Brown Kevin Antoine , Langford Bradley , Schwartz Kevin L , Diong Christina , Garber Gary , Daneman Nick 
Published: February 2020

Abstract

Background
Antibiotic use is the strongest modifiable risk factor for the development of Clostridioides difficile infection, but prescribers lack quantitative information on comparative risks of specific antibiotic courses. Our objective was to estimate risks of C. difficile infection associated with receipt of specific antibiotic courses.

Methods
We conducted a longitudinal case-cohort analysis representing over 90% of Ontario nursing home residents, between 2012 and 2017. Our primary exposure was days of antibiotic receipt in the prior 90 days. Adjustment covariates included: age, sex, prior emergency department or acute care stay, Charlson comorbidity index, prior C. difficile infection, acid suppressant use, device use, and functional status. We examined incident C. difficile infection, including cases identified within the nursing home, and those identified during subsequent hospital admissions. Adjusted and unadjusted regression models were used to measure risk associated with 5- to 14-day courses of 18 different antibiotics.

Results
We identified 1708 cases of C. difficile infection (1.27 per 100 000 resident-days). Longer antibiotic duration was associated with increased risk: 10- and 14-day courses incurred 12% (adjusted relative risk [ARR] = 1.12, 95% confidence interval [CI]: 1.09, 1.14) and 27% (ARR = 1.27, 95% CI: 1.21,1.30) more risk compared to 7-day courses. Among 7-day courses with similar indications: moxifloxacin resulted in 121% more risk than amoxicillin (ARR = 2.21, 95% CI: 1.67, 3.08), ciprofloxacin engendered 89% more risk than nitrofurantoin (ARR = 1.89, 95% CI: 1.45, 2.68), and clindamycin resulted in 112% (ARR = 2.12, 95% CI: 1.32, 3.78) more risk than cloxacillin.

Conclusions
C. difficile infection risk increases with antibiotic duration, and there are wide disparities in risks associated with antibiotic courses used for similar indications.
Plasma S100A8/A9 Concentrations and Clinical Outcomes of Ischemic Stroke in 2 Independent Multicenter Cohorts
Authors: Guo Daoxia , Zhu Zhengbao , Xu Tan , Zhong Chongke , Wang Aili , Xie Xuewei , Peng Yanbo , Peng Hao , Li Qunwei , Ju Zhong , Geng Deqin , Chen Jing , Liu Liping , Wang Yilong , Zhang Yonghong , He Jiang 
Published: February 2020

Abstract

Background
S100A8/A9 is implicated in inflammation mechanisms related to atherosclerosis and plaque vulnerability, but it remains unclear whether S100A8/A9 is associated with the prognosis of ischemic stroke. The aim of this study was to investigate these associations in 2 independent multicenter cohorts.

Methods
Plasma S100A8/A9 concentrations at baseline were measured among 4785 patients with ischemic stroke from 2 independent cohorts: Infectious Factors, Inflammatory Markers, and Prognosis of Acute Ischemic Stroke (IIPAIS) and China Antihypertensive Trial in Acute Ischemic Stroke (CATIS). The primary outcome was a composite outcome of death or major disability at 3 months after ischemic stroke. Secondary outcomes were major disability, death, and a composite outcome of death or vascular events.

Results
Among the combined participants of IIPAIS and CATIS, the adjusted odds ratios associated with the highest quartile of plasma S100A8/A9 were 2.11 (95% CI, 1.66–2.68) for the primary outcome and 1.62 (95% CI, 1.27–2.07) for the secondary outcome of major disability; adjusted hazard ratios were 4.14 (95% CI, 2.10–8.15) for the secondary outcome of death and 2.08 (95% CI, 1.38–3.13) for the composite outcome of death or vascular events. Each SD increase of log-transformed S100A8/A9 was associated with 28% (95% CI, 18%–39%; P &lt; 0.001) increased risk of the primary outcome. Multivariable-adjusted spline regression analyses showed a linear association between plasma S100A8/A9 concentrations and primary outcome (P &lt; 0.001 for linearity). Subgroup analyses further confirmed these associations.

Conclusions
High plasma S100A8/A9 concentrations at baseline were independently associated with increased risks of adverse clinical outcomes at 3 months after ischemic stroke, suggesting that S100A8/A9 might have a role as a prognostic marker of ischemic stroke.
Teacher interaction strategies and situated willingness to communicate
Authors: Peng Jian-E 
Published: February 2020

Abstract
This study explores variation in willingness to communicate (WTC) in English between whole-class interaction and dyadic and group interaction, and teacher interaction strategies identified to sustain students’ WTC in whole-class interaction that primarily followed the initiation–response–feedback (IRF) pattern. Data were collected from a regular English class at a university in China through audio-recording of a lesson, classroom observation, self-rating of WTC by 23 students, and stimulated recall interviews with four focal students. The results indicate that WTC in whole-class interaction did not significantly differ from WTC in dyadic and group interaction. Teacher interaction strategies, including the use of open or referential questions in the I-move and F-move, manipulation of wait time following prompts, and monitoring private speech and contextual or multimodal clues of students’ WTC, functioned to sustain classroom WTC. Implications for adopting teacher interaction strategies in line with lesson plans within the framework of IRF pedagogic discourse are discussed.
Constraining landslide characteristics with Bayesian inversion of field and seismic data
Authors: Moretti L , Mangeney A , Walter F , Capdeville Y , Bodin T , Stutzmann E , Le Friant A 
Published: February 2020

SUMMARYUsing a fully nonlinear Bayesian approach based on forward modelling of granular flow, we invert for landslide parameters (volume, release geometry and rheology) from different kinds of observations. Synthetic tests show that the runout distance and the deposit area by themselves do not constrain landslide parameters. Better constraints on landslide parameters are obtained from the thickness distribution of the landslide deposits, as well as from the force history applied by the landslide to the ground, which contains information on the landslide dynamics. Therefore, inverting force histories calculated from seismic broad-band records is an important alternative to inverting thickness distributions of landslide deposits, which are usually difficult to obtain. We test the method on the 1997 Boxing Day debris avalanche on Montserrat Island, which involved 40 − 50 Mm3. The Bayesian inversion and granular flow model provide good estimates for volume, release geometry and effective friction coefficient. This study thus underlines the value of broad-band seismic records as observations to monitor landslides and validation for their numerical flow models.
Co-participation in physical activity: perspectives from Australian parents of pre-schoolers
Authors: Hnatiuk Jill A , Dwyer Genevieve , George Emma S , Bennie Andrew 
Published: February 2020

Abstract
Co-participation in physical activity may be important for helping families with young children meet physical activity recommendations. Yet, little is known about what families perceive to be the benefits, barriers and facilitators of co-participation. This study explored (i) parents’ perceptions about physical activity and possible benefits of family-based co-participation in physical activity, (ii) their perceived facilitators and barriers to co-participation and (iii) their recommendations for improving co-participation within their community. Fifteen parents (14 mothers, 1 father) of 2- to 4-year-old children residing in Western Sydney, Australia, participated in one-on-one interviews between September 2016 and January 2017. Interviews were audio-recorded and transcribed verbatim. Four main themes and seven sub-themes emerged from the thematic analysis of the interview data. When parents were asked to reflect on their understanding of physical activity, they discussed a range of well-known activities (e.g. active play, active transport) and also reported ‘anything but screen time’. The major benefits parents reported about co-participation were spending quality time together, improving children’s general health and well-being and the development of physical skills. Social (e.g. social networks, negative stereotypes) and environmental (e.g. home space, neighbourhood design, shading) facilitators and barriers were identified, yet their impact on co-participation often varied depending on the presence (or lack thereof) of other factors in the physical or social environment. Key recommendations suggested by parents included improvements to home outdoor spaces, neighbourhood design and play spaces and community services.
Study of the time-relationship of the mechano-electrical interaction in an animal model of tetralogy of Fallot: implications for the risk assessment of ventricular arrhythmias
Authors: Bove Thierry , Alipour Symakani Rahi , Verbeke Jonas , Vral Anne , El Haddad Milad , De Wilde Hans , Stroobandt Roland , De Pooter Jan 
Published: February 2020

Abstract

OBJECTIVES
The long-term outcome of tetralogy of Fallot (TOF) is determined by progressive right ventricular (RV) dysfunction through pulmonary regurgitation (PR) and the risk of malignant arrhythmia. Although mechano-electrical coupling in TOF is well-known, its time effect on the inducibility of arrhythmia remains ill-defined. The goal of this study was to investigate the mechano-electrical properties at different times in animals with chronic PR.

METHODS
PR was induced by a transannular patch with limited RV scarring in infant pigs. Haemodynamic assessment included biventricular pressure–volume loops after 3 (n = 8) and 6 months (n = 7) compared to controls (n = 5). The electrophysiological study included endocardial monophasic action potential registration, intraventricular conduction velocity and induction of ventricular arrhythmia by burst pacing.

RESULTS
Progressive RV dilation was achieved at 6 months (RV end-diastolic volume 143 ± 13 ml/m2—RV end-systolic volume 96 ± 7 ml/m2; P &lt; 0.001), in association with depressed RV contractility (preload recruitable stroke work-slope: 19 ± 1 and 11 ± 3 Mw.ml−1.s−1 for control and 6 m; P &lt; 0.001) and left ventricular contractility (preload recruitable stroke work-slope: 60 ± 13 and 40 ± 11 Mw.ml−1.s−1 for control and 6 m; P = 0.005). Concomitant to QRS prolongation, monophasic action potential90-duration and dispersion at the RV and left ventricle were increased at 6 months. Intraventricular conduction was delayed only in the RV at 6 months (1.8 ± 0.2 and 2.4 ± 0.6 m/s for group 6M and the control group; P = 0.035). Sustained ventricular arrhythmias were not inducible.

CONCLUSIONS
In animals yielding the sequelae of a contemporary operation for TOF, mechano-electrical alterations are progressive and affect predominantly the RV after midterm exposure of PR. Because ventricular arrhythmias were not inducible despite significant RV dilation, the data suggest that the haemodynamic RV deterioration effectively precedes the risk of inducing sustained arrhythmia after TOF repair and opens a window for renewed stratification of contemporary risk factors of ventricular arrhythmias in patients operated on with currently used pulmonary valve- and RV-related techniques.
Treat bronchopleural fistula after right lower lobectomy by extra right middle lobectomy—a neglected approach
Authors: Wang Yan-Qing , Zhuang Wei 
Published: February 2020

Abstract

OBJECTIVES
Bronchopleural fistula (BPF) after right lower lobectomy (RLL), although uncommon, is associated with high mortality rates. This study was aimed at evaluating the therapeutic effect of extra right middle lobectomy (ERML) in the management of BPF after RLL.

METHODS
We investigated 12 consecutive patients who were treated at our hospital for BPF occurring after RLL. The diagnosis of BPF was established by bronchoscopy in all cases and BPFs were treated by ERML. All patients were followed up for at least 1 year after ERML to assess treatment outcomes.

RESULTS
The severity of infection and malnutrition after BPF was different for different patients. All patients agreed to undergo ERML. The procedure was uneventful in all cases, and there were no cases of perioperative complications or death. The median duration of hospitalization after ERML was 10.5 (range 6–21) days. Postoperative pathological examination showed the presence of hyperaemia and oedema in the BPF stump, and inflammatory cell infiltration in the stroma. The fresh stump of the bronchus intermedius was well structured. Patients were followed up for a median duration of 27 (range 12–41) months. The BPFs were successfully treated in all patients, and a new BPF did not develop in the new fresh stump in any of the cases.

CONCLUSIONS
ERML aimed at creating a fresh stump for quick healing could be alternative for treating BPF after RLL.
Kaposi Sarcoma-Associated Herpesvirus Infection and Endemic Burkitt Lymphoma
Authors: Oluoch Peter O , Oduor Cliff I , Forconi Catherine S , Ong’echa John M , Münz Christian , Dittmer Dirk P , Bailey Jeffrey A , Moormann Ann M 
Published: February 2020

Abstract

Background
Endemic Burkitt lymphoma (eBL) is associated with Epstein-Barr virus (EBV) and Plasmodium falciparum malaria coinfections. However, the role of Kaposi sarcoma-associated herpesvirus (KSHV), also endemic in Africa, has not been evaluated as a cofactor in eBL pathogenesis.

Methods
Multiplexed seroprofiles for EBV, malaria, and KSHV were generated for 266 eBL patients, 78 non-eBL cancers, and 202 healthy children. KSHV and EBV loads were quantified by PCR.

Results
KSHV seroprevalence did not differ by study group but was associated with age. Seropositivity, defined by K8.1/LANA or in combination with 5 other KSHV antigens (ORF59, ORF65, ORF61, ORF38, and K5) was associated with antimalarial antibody levels to AMA1 (odds ratio [OR], 2.41, P &lt; .001; OR, 2.07, P &lt; .001) and MSP1 (OR, 2.41, P = .0006; OR, 5.78, P &lt; .001), respectively. KSHV loads did not correlate with antibody levels nor differ across groups but were significantly lower in children with detectable EBV viremia (P = .014).

Conclusions
Although KSHV-EBV dual infection does not increase eBL risk, EBV appears to suppress reactivation of KSHV while malaria exposure is associated with KSHV infection and/or reactivation. Both EBV and malaria should, therefore, be considered as potential effect modifiers for KSHV-associated cancers in sub-Saharan Africa.