bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Foraging Mandala for Aquatic Microorganisms
Authors: Fernandez Vicente I , Yawata Yutaka , Stocker Roman 
Published: November 2018

Abstract
Aquatic environments harbor a great diversity of microorganisms, which interact with the same patchy, particulate, or diffuse resources by means of a broad array of physiological and behavioral adaptations, resulting in substantially different life histories and ecological success. To date, efforts to uncover and understand this diversity have not been matched by equivalent efforts to identify unifying frameworks that can provide a degree of generality and thus serve as a stepping stone to scale up microscale dynamics to predict their ecosystem-level consequences. In particular, evaluating the ecological consequences of different resource landscapes and of different microbial adaptations has remained a major challenge in aquatic microbial ecology. Here, inspired by Ramon Margalef’s mandala for phytoplankton, we propose a foraging mandala for microorganisms in aquatic environments, which accounts for both the local environment and individual adaptations. This biophysical framework distills resource acquisition into two fundamental parameters: the search time for a new resource and the growth return obtained from encounter with a resource. We illustrate the foraging mandala by considering a broad range of microbial adaptations and environmental characteristics. The broad applicability of the foraging mandala suggests that it could be a useful framework to compare disparate microbial strategies in aquatic environments and to reduce the vast complexity of microbe-environment interactions into a minimal number of fundamental parameters.
A high-throughput data analysis and materials discovery tool for strongly correlated materials
Authors: Hafiz Hasnain , Khair Adnan Ibne , Choi Hongchul , Mueen Abdullah , Bansil Arun , Eidenbenz Stephan , Wills John , Zhu Jian-Xin , Balatsky Alexander V. , Ahmed Towfiq 
Published: November 2018

AbstractModeling off-electron systems is challenging due to the complex interplay of the effects of spin–orbit coupling, electron–electron interactions, and the hybridization of the localizedf-electrons with itinerant conduction electrons. This complexity drives not only the richness of electronic properties but also makes these materials suitable for diverse technological applications. In this context, we propose and implement a data-driven approach to aid the materials discovery process. By deploying state-of-the-art algorithms and query tools, we train our learning models using a large, simulated dataset based on existing actinide and lanthanide compounds. The machine-learned models so obtained can then be used to search for new classes of stable materials with desired electronic and physical properties. We discuss the basic structure of ourf-electron database, and our approach towards cleaning and correcting the structure data files. Illustrative examples of the applications of our database include successful prediction of stable superstructures of double perovskites and identification of a number of physically-relevant trends in strongly correlated features off-electron based materials.
Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis
Authors: Qin Shao-Wei , Jiang Ren-Jun , Zhang Na , Liu Zhan-Wen , Li Cai-Lin , Guo Zhong-Zhong , Bao Liang-Hong , Zhao Li-Feng 
Published: November 2018

AbstractThe desert plant Populus euphratica Oliv. has typical heterophylly; linear (Li), lanceolate (La), ovate (Ov) and broad-ovate (Bo) leaves grow in turn as trees develop to maturity. P. euphratica is therefore a potential model organism for leaf development. To investigate the roles of RNAs (including mRNAs, miRNAs, lncRNAs and circRNAs) in the morphogenesis of P. euphratica heterophylls, juvenile heterophylls were sampled individually, and then, the expression patterns of miRNAs, mRNAs, lncRNAs and circRNAs were analysed by small RNA sequencing and strand-specific RNA sequencing. We found that 1374 mRNAs, 19 miRNAs, 71 lncRNAs and 2 circRNAs were P. euphratica heterophyll morphogenesis–associated (PHMA) RNAs; among them, 17 PHMA miRNAs could alter the expression of 46 PHMA mRNAs. Furthermore, 11 lncRNAs and 2 circRNAs interacted with 27 PHMA mRNAs according to the ceRNA hypothesis. According to GO and KEGG pathway analysis, PHMA RNAs were mainly involved in metabolism, response to stimulus and developmental processes. Our results indicated that external environmental factors and genetic factors in P. euphratica co-regulated the expression of PHMA RNAs, repressed cell division, reinforced cell growth, and ultimately resulted in the morphogenesis of P. euphratica heterophylls.
Foxi3 transcription factor activity is mediated by a C-terminal transactivation domain and regulated by the Protein Phosphatase 2A (PP2A) complex
Authors: Singh Sunita , Jangid Rahul K. , Crowder Alyssa , Groves Andrew K. 
Published: November 2018

AbstractThe Forkhead box (FOX) family consists of at least 19 subgroups of transcription factors which are characterized by the presence of an evolutionary conserved ‘forkhead’ or ‘winged-helix’ DNA-binding domain. Despite having a conserved core DNA binding domain, FOX proteins display remarkable functional diversity and are involved in many developmental and cell specific processes. In the present study, we focus on a poorly characterized member of the Forkhead family, Foxi3, which plays a critical role in the development of the inner ear and jaw. We show that Foxi3 contains at least two important functional domains, a nuclear localization sequence (NLS) and a C-terminal transactivation domain (TAD), and that it directly binds its targets in a sequence specific manner. We also show that the transcriptional activity of Foxi3 is regulated by phosphorylation, and that the activity of Foxi3 can be attenuated by its physical interaction with the protein phosphatase 2A (PP2A) complex.
Grail attenuates influenza A virus infection and pathogenesis by inhibiting viral nucleoprotein
Authors: Lin Hui-Tsu , Chen Cheng-Cheung , Liu Pei-Yao , Wu Hsueh-Ling , Wu Ti-Hui , Huang Chih-Heng , Chen Ying-Chuan 
Published: November 2018

AbstractGrail is a well-characterized mediator of metabolic disease, tumour progression, and immune response. However, its role in influenza A virus (IAV) infection remains poorly understood. In this study, we demonstrated that Grail knockdown potentiates IAV infection, whereas Grail overexpression blocks IAV replication. The intranasal administration of IAV to Grail KO mice led to a lower survival rate than in similarly infected wild-type mice. Additionally, IAV-infected Grail KO mice had higher viral titres, greater immune cell infiltration, and increased expression of inflammatory cytokines in the lungs. Mechanistically, we showed that Grail interacts with viral nucleoprotein (NP), targeting it for degradation and inhibiting IAV replication. NP expression was increased in Grail knockdown cells and reduced in cells overexpressing Grail. Collectively, our results demonstrate that Grail acts as a negative regulator of IAV infection and replication by degrading viral NP. These data increase our understanding of the host antiviral response to infection with IAV.
Quantitative assessment of the association between GRIA1 polymorphisms and migraine risk
Authors: Gao Xueren , Wang Jianguo 
Published: November 2018

Purpose: The association between GRIA1 rs548294 G&gt;A and rs2195450 C&gt;T polymorphisms and migraine risk has been reported in several case–control studies. However, the results of studies are inconsistent. Thus, we conducted a meta-analysis to more precisely estimate the association of the two polymorphisms with migraine risk.
Methods: Eligible studies were retrieved and screened from the online databases (EMBASE, PubMed, Web of Science, Wanfang, and Chinese National Knowledge Infrastructure). The pooled odds ratio (OR) with corresponding 95.0% confidence intervals (CIs) was assessed using random- or fixed-effects model.
Results: A total of 1233 cases and 1374 controls from four eligible studies were included. The pooled analysis showed that GRIA1 rs548294 G&gt;A polymorphism was not significantly associated with migraine risk. GRIA1 rs2195450 C&gt;T polymorphism was significantly associated with migraine risk under heterozygous model (CT vs. CC, OR = 1.23, 95%CI = 1.02–1.48, PZ = 0.03). Further subgroup analysis based on ethnicity showed a significant association of GRIA1 rs2195450 C&gt;T polymorphism with migraine risk in Asian population, but not in Caucasian population.
Conclusions: Our results indicates that GRIA1 rs2195450 C&gt;T polymorphism is significantly associated with migraine risk. However, the number of studies included in the meta-analysis was small. Thus, more high quality case–control studies with a large sample size are still required to confirm these findings.
Experimental research on insulation properties of C6F12O/N2 and C6F12O/CO2 gas mixtures
Authors: Tian Shuangshuang , Zhang Xiaoxing , Xiao Song , Deng Zaitao , Li Yi , Tang Ju 
Published: November 2018

This study investigates the insulation performance of the new environmental friendly insulation gas C6F12O mixed with N2 and CO2 under the AC frequency voltage under 0.10–0.30 MPa. Firstly, the mixing ratio of C6F12O in the mixed gas is discussed by the gas phase state equation. The breakdown voltage of C6F12O gas mixtures under quasi‐uniform electric field and the initial voltage of partial discharge in the highly non‐uniform field are measured by the experimental method, and the insulation characteristics of SF6 gas mixtures are compared. The self‐recovery performance of the gas mixture is analysed as well. Experimental results show that the mixing ratio of C6F12O is lower than 7% under 0.10 MPa, such that the operation requirements of the equipment can be satisfied. The breakdown voltage of 3% C6F12O gas mixtures is the same as that of 10% SF6 gas mixtures. The partial discharge inception voltage of 6% C6F12O gas mixtures is close to that of 10% SF6 gas mixtures. After 100 times of breakdown, the breakdown voltage of C6F12O gas mixtures does not decrease. Compared with N2, the breakdown voltage of C6F12O mixed with CO2 shows a more dispersive trend.
Asynchronous fault location scheme for half‐wavelength transmission lines based on propagation characteristics of voltage travelling waves
Authors: Nan Peng , Menghan Cheng , Rui Liang , Zare Firuz 
Published: November 2018

Due to prominent attenuation of travelling waves, double‐end fault location method produces considerable errors when applied to ultra‐high voltage AC half‐wavelength transmission (UAHT) lines. In order to address this problem, this study presents a novel fault location scheme based on the attenuation, refraction and reflection principles of aerial‐mode voltage travelling waves (AVTWs). In the scheme, the faulted section of an UAHT line is first determined according to the accumulated amplitude ratio of the pre‐determined frequency components of AVTWs asynchronously sampled at both terminals of the line. Then, the Teager energy of the first two wavefronts of the AVTW – measured at the terminal in the faulted section – is used to define two factors for selecting the appropriate accurate fault location method. Finally, the single‐end travelling wave method is adopted for locating the faults near the line terminal. The presented double‐end method utilises the amplitude ratio of AVTWs to locate the faults far from the line terminal. A 1000 kV UAHT line model is considered with various fault conditions in PSCAD/EMTDC simulations. The simulation results and analysis demonstrate that the proposed fault location scheme is accurate and immune to fault distances, fault types, fault impedances and fault inception angles.
LC–CLC compensation topology for capacitive power transfer system to improve misalignment performance
Authors: Luo Bo , Mai Ruikun , Guo Limou , Wu Dong , He Zhengyou 
Published: November 2018

To improve the coupler misalignment performance, this study proposes an LC–CLC compensation topology for high‐power and long‐distance capacitive power transfer system. The LC circuit in the transmitter and the CLC circuit in the receiver are adopted as the resonant tank for the capacitive coupler. The fundamental harmonics approximation method is employed to analyse the system working principle. Considering the misalignment of coupler, the characteristic of output power is provided against the variation of coupler capacitance. A 1 kW CPT system with 150 mm transfer distance is set up to validate the proposed compensation circuit under various misalignment conditions. The experiment results show that the system can transfer 1009 W output power with 90.56% DC–DC efficiency at 150 mm transfer distance when the coupler is well aligned. When the misalignment is 325 mm, the variation of the output power is only 10.6% in X‐direction and 15.2% in Y‐direction. The proposed system can achieve high anti‐misalignment performance.
Effectiveness of the new integrated strategy to control the transmission of Schistosoma japonicum in China: a systematic review and meta-analysis
Authors: Qian Chunyan , Zhang Yuefeng , Zhang Xinyan , Yuan Chao , Gao Zhichao , Yuan Hong , Zhong Jiang 
Published: November 2018

Since 2004, the national schistosomiasis control strategy in China has shifted from the morbidity control strategy (conventional strategy) to an integrated strategy (new strategy). We investigated the effectiveness of the new strategy and compared it against the conventional strategy. We retrieved from electronic databases the literature regarding the new strategy published from 2000 to 2017. The effect of the new or conventional strategy on infection by Schistosoma japonicum of humans and snails (Oncomelania hupensis) was evaluated with pooled log relative risk (logRR). A total of only eight eligible publications were included in the final meta-analysis. The results showed that implementation of the new strategy reduced the infection risk by 3–4 times relative to the conventional strategy. More specifically, the conventional strategy caused a reduction in both human (logRR = 0.56, 95% CI: 0.12–0.99) and snail infections (logRR = 0.34, 95% CI: −0.69–1.37), while the new strategy also significantly reduced both human (logRR = 1.89, 95% CI: 1.33–2.46) and snail infections (logRR = 1.61, 95% CI: 1.06–2.15). In contrast to the conventional strategy, the new strategy appeared more effective to control both human (logRR difference = 1.32, 95% CI: 0.78–1.86) and snail infections (logRR difference = 1.53, 95% CI: 0.76–2.31). Our data demonstrate that the new integrated strategy is highly effective to control the transmission of S. japonicum in China, and this strategy is recommended for schistosomiasis elimination in other affected regions across the world, with adaptation to local conditions.
Generalizability of heterogeneous treatment effect estimates across samples
Authors: Coppock Alexander , Leeper Thomas J. , Mullinix Kevin J. 
Published: November 2018

Significance
In experiments, the degree to which results generalize to other populations depends critically on the degree of treatment effect heterogeneity. We replicated 27 survey experiments (encompassing 101,745 individual survey responses) originally conducted on nationally representative samples using online convenience samples, finding very high correspondence despite obvious differences in sample composition. We contend this pattern is due to low treatment effect heterogeneity in these types of standard social science survey experiments.
Nanomagnetic properties of the meteorite cloudy zone
Authors: Einsle Joshua F. , Eggeman Alexander S. , Martineau Ben H. , Saghi Zineb , Collins Sean M. , Blukis Roberts , Bagot Paul A. J. , Midgley Paul A. , Harrison Richard J. 
Published: November 2018

Significance
The cloudy zone is naturally occurring nanocomposite found in Fe–Ni metal-bearing meteorites. It not only is a potent carrier of paleomagnetic information from the early solar system but also shows promise as a sustainable alternative to rare earth-based permanent magnets. Here we explain how the remarkable magnetic properties of the cloudy zone are linked to its 3D chemical, crystallographic, and magnetic architecture, using a state-of-the-art combination of nanometer to subnanometer resolution tomography and micromagnetic simulations. We discover the mechanism by which paleomagnetic information becomes encoded into the cloudy zone and, inspired by our findings, point toward potential pathways to optimize synthetic analogues of the cloudy zone for industrial applications.
HPV Testing With 16, 18, and 45 Genotyping Stratifies Cancer Risk for Women With Normal Cytology
Authors: Stoler Mark H , Wright Thomas C , Parvu Valentin , Yanson Karen , Eckert Karen , Kodsi Salma , Cooper Charles 
Published: November 2018

ABSTRACT

Objectives
To determine the BD Onclarity human papillomavirus (HPV) assay performance and risk values for cervical intraepithelial neoplasia grade 2 (CIN2) or higher and cervical intraepithelial neoplasia grade 3 (CIN3) or higher during Papanicolaou/HPV cotesting in a negative for intraepithelial lesions or malignancies (NILM) population.

Methods
In total, 22,383 of the 33,858 enrolled women were 30 years or older with NILM cytology. HPV+ and a subset of HPV– patients (3,219/33,858 combined; 9.5%) were referred to colposcopy/biopsy.

Results
Overall, 7.9% of women were Onclarity positive; HPV 16 had the highest prevalence (1.5%). Verification bias-adjusted (VBA) CIN2 or higher and CIN3 or higher prevalences were 0.9% and 0.3%, respectively. Onclarity had VBA CIN2 or higher (44.1%) and CIN3 or higher (69.5%) sensitivities, as well as CIN2 or higher (92.4%) and CIN3 or higher (92.3%) specificities—all similar to Hybrid Capture 2. HPV 16, 18, 45, and the other 11 genotypes had CIN3 or higher risks of 6.9%, 2.6%, 1.1%, and 2.2%, respectively.

Conclusions
Onclarity is clinically validated for cotesting in NILM women. Genotyping actionably stratifies women at greater CIN3 or higher risk.
The Association between the Montreal Cognitive Assessment and Functional Activity Questionnaire in the Systolic Blood Pressure Intervention Trial (SPRINT)
Authors: Still Carolyn H , Pajewski Nicholas M , Chelune Gordon J , Rapp Stephen R , Sink Kaycee M , Wadley Virginia G , Williamson Jeff D , Lerner Alan J 
Published: November 2018

Abstract

Objective
To examine the association of global cognitive function assessed via the Montreal Cognitive Assessment (MoCA) and deficiencies in instrumental activities of daily living (IADL) on the Functional Activity Questionnaire (FAQ) in hypertensive older adults in the Systolic Blood Pressure Intervention Trial (SPRINT).

Methods
In cross-sectional analysis, 9,296 SPRINT participants completed the MoCA at baseline. The FAQ was obtained from 2,705 informants for SPRINT participants scoring <21 or <22 on the MoCA, depending on education. FAQ severity ranged from no dysfunction (Score = 0) to moderate/severe dysfunction (Score = 5+).

Results
Participants who triggered FAQ administration were older, less educated, and more likely to be Black or Hispanic (p < 0.001). Sixty-one percent (n = 1,661) of participants’ informants reported no functional difficulties in IADLs. An informant report, however, of any difficulty on the FAQ was associated with lower MoCA scores after controlling for age, sex, race/ethnicity, and education (p < 0.05). Partial proportional odds regression indicates that participants scoring lower on the MoCA (in the 10th to <25th, fifth to <10th, and <fifth percentiles) had higher adjusted odds of their informant indicating dysfunction on the FAQ, relative to participants scoring at or above the 25th percentile on the MoCA (p < 0.001).

Conclusions
While lower global cognitive function was strongly associated with IADL deficits on FAQ, informants indicated no functional difficulties for the majority of SPRINT participants, despite low MoCA scores. These findings can help with designing future studies which aim to detect mild cognitive impairment and/or dementia in large, community-dwelling populations.
pyNVR: investigating factors affecting feature selection from scRNA-seq data for lineage reconstruction
Authors: Chen Bob , Herring Charles A , Lau Ken S 
Published: November 2018

Abstract

Motivation
The emergence of single-cell RNA-sequencing has enabled analyses that leverage transitioning cell states to reconstruct pseudotemporal trajectories. Multidimensional data sparsity, zero inflation and technical variation necessitate the selection of high-quality features that feed downstream analyses. Despite the development of numerous algorithms for the unsupervised selection of biologically relevant features, their differential performance remains largely unaddressed.

Results
We implemented the neighborhood variance ratio (NVR) feature selection approach as a Python package with substantial improvements in performance. In comparing NVR with multiple unsupervised algorithms such as dpFeature, we observed striking differences in features selected. We present evidence that quantifiable dataset properties have observable and predictable effects on the performance of these algorithms.

Availability and implementation
pyNVR is freely available at https://github.com/KenLauLab/NVR.

Supplementary information
Supplementary data are available at Bioinformatics online.
Severe Morbidity and Mortality Associated With Respiratory Syncytial Virus Versus Influenza Infection in Hospitalized Older Adults
Authors: Ackerson Bradley , Tseng Hung Fu , Sy Lina S , Solano Zendi , Slezak Jeff , Luo Yi , Fischetti Christine A , Shinde Vivek 
Published: November 2018

AbstractBackgroundRespiratory syncytial virus (RSV) is an important cause of serious respiratory illness in older adults. Comparison of RSV and influenza infection in hospitalized older adults may increase awareness of adult RSV disease burden.MethodsHospitalized adults aged ≥60 years who tested positive for RSV or influenza between 1 January 2011 and 30 June 2015 were identified from Kaiser Permanente Southern California electronic medical records. Baseline characteristics, comorbidities, utilization, and outcomes were compared.ResultsThe study included 645 RSV- and 1878 influenza-infected hospitalized adults. Patients with RSV were older than those with influenza (mean, 78.5 vs 77.4 years; P = .035) and more likely to have congestive heart failure (35.3% vs 24.5%; P < .001) and chronic obstructive pulmonary disease (COPD) (29.8% vs 24.3%; P = .006) at baseline. In adjusted analyses, RSV infection was associated with greater odds of length of stay ≥7 days (odds ratio [OR] = 1.5; 95% confidence interval [CI], 1.2–1.8; P < .001); pneumonia (OR = 2.7; 95% CI, 2.2–3.2; P < .001); intensive care unit admission (OR = 1.3; 95% CI, 1.0–1.7; P = .023); exacerbation of COPD (OR = 1.7; 95% CI, 1.3–2.4; P = .001); and greater mortality within 1 year of admission (OR = 1.3; 95% CI, 1.0–1.6; P = .019).ConclusionsRSV infection may result in greater morbidity and mortality among older hospitalized adults than influenza. Increased recognition of adult RSV disease burden will be important in the evaluation and use of new RSV vaccines and antivirals.