bluuebunny/crossref_metadata_2025_split huggingface dataset:
VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants
Authors: Ip Eddie , Chapman Gavin , Winlaw David , Dunwoodie Sally L. , Giannoulatou Eleni 
Published: November 2019

Abstract
Next-generation sequencing (NGS) technologies generate thousands to millions of genetic variants per sample. Identification of potential disease-causal variants is labor intensive as it relies on filtering using various annotation metrics and consideration of multiple pathogenicity prediction scores. We have developed VPOT (variant prioritization ordering tool), a python-based command line tool that allows researchers to create a single fully customizable pathogenicity ranking score from any number of annotation values, each with a user-defined weighting. The use of VPOT can be informative when analyzing entire cohorts, as variants in a cohort can be prioritized. VPOT also provides additional functions to allow variant filtering based on a candidate gene list or by affected status in a family pedigree. VPOT outperforms similar tools in terms of efficacy, flexibility, scalability, and computational performance. VPOT is freely available for public use at GitHub (https://github.com/VCCRI/VPOT/). Documentation for installation along with a user tutorial, a default parameter file, and test data are provided.
Institutional complementarity, firm behavior, and firm heterogeneity: A cross-national analysis
Authors: Camyar Isa , Ulupinar Bahar 
Published: November 2019

AbstractHow do political economic institutions and different types of institutional complementarity in particular influence firm behavior? Existing studies do not offer much help in answering this question. In this research, we systematically connect institutional complementarity and its two distinct logics (the logic of reinforcement and the logic of compensation) to firm performance. Using a sample of more than fourteen thousand firms from twenty advanced industrial democracies, our empirical analysis finds that institutional complementarity is related to firm performance in a distinct way. That is, the different logics of institutional complementarity apply only to specific segments of the economy. While the logic of reinforcement works for small firms and labor-intensive firms, the logic of compensation favors large firms and capital-intensive firms. The empirical novelty of our research lies in offering a cross-national, firm-level and large-n analysis of institutional complementarity. Theoretically, our finding of firm heterogeneity helps in establishing the boundary conditions of institutional complementarity and hence advances the general understanding of the subject.
Association of maternal prenatal psychological stressors and distress with maternal and early infant faecal bacterial profile
Authors: Naudé Petrus J.W. , Claassen-Weitz Shantelle , Gardner-Lubbe Sugnet , Botha Gerrit , Kaba Mamadou , Zar Heather J. , Nicol Mark P. , Stein Dan J. 
Published: November 2019

AbstractObjective:Findings from animal studies indicate that the early gut bacteriome is a potential mechanism linking maternal prenatal stress with health trajectories in offspring. However, clinical studies are scarce and the associations of maternal psychological profiles with the early infant faecal bacteriome are unknown. This study aimed to investigate the associations of prenatal stressors and distress with early infant faecal bacterial profiles in a South African birth cohort study.Methods:Associations between prenatal symptoms of depression, distress, intimate partner violence (IPV) and posttraumatic stress disorder (PTSD) and faecal bacterial profiles were evaluated in meconium and subsequent stool specimens from 84 mothers and 101 infants at birth, and longitudinally from a subset of 69 and 36 infants at 4–12 and 20–28 weeks of age, respectively, in a South African birth cohort study.Results:Infants born to mothers that were exposed to high levels of IPV had significantly higher proportions ofCitrobacterand three unclassified genera, all of which belonging to the family Enterobacteriaceae detected at birth. Proportions of these Enterobacteriaceae remained significantly increased over time (birth to 20–28 weeks of life) in infants born to mothers with high levels of IPV exposure compared to infants from mothers with no/low IPV exposure. Infants born to mothers exposed to IPV also had higher proportions of the genusWeissellaat 4–12 weeks compared to infants from mothers with no/low IPV exposure. Faecal specimens from mothers exposed to IPV had higher proportions of the family Lactobacillaceae and lower proportions of Peptostreptococcaceae at birth. Maternal psychological distress was associated with decreased proportions of the family Veillonellaceae in infants at 20–28 weeks and a slower decline in Gammaproteobacteria over time. No changes in beta diversity were apparent for maternal or infant faecal bacterial profiles in relation to any of the prenatal measures for psychological adversities.Conclusion:Maternal lifetime IPV and antenatal psychological distress are associated with altered bacterial profiles in infant and maternal faecal bacteria. These findings may provide insights in the involvement of the gut bacteria linking maternal psychological adversity and the maturing infant brain.
LEARNING FORMULAIC SEQUENCES THROUGH VIEWING L2 TELEVISION AND FACTORS THAT AFFECT LEARNING
Authors: Puimège Eva , Peters Elke 
Published: November 2019

AbstractThe present study explores the incidental learning of formulaic sequences (FS) from audio-visual input and factors affecting the learning of FS. A pretest-posttest, within-participant design was adopted. English-as-a-foreign-language learners (L1 = Dutch; n = 42) watched a one-hour English-language documentary without subtitles. Learning gains were measured at the level of form recall and meaning recall. Significant learning gains were found in both the form recall and meaning recall tests, indicating that several knowledge aspects of FS can be learned incidentally from audio-visual input. The findings also revealed a positive relationship between learners’ prior vocabulary knowledge and the learning gains. Further, several item-related factors affected the learning gains (e.g., collocate-node relationship, frequency). Finally, the findings showed the incremental nature of learning FS, as preknowledge of the meaning of the FS prior to the TV viewing was the strongest predictor of learning the form of FS.
Beresford Hope, the Church of England, and the Elementary Education Act of 1870
Authors: Turner Michael J. 
Published: November 2019

AbstractHistorians have used a number of political, social, and other factors to explain the controversy surrounding elementary education in Victorian Britain. This article underscores the importance of religious motivations. The Act of 1870 – a significant extension of state responsibility – did not end debates about the purpose of education and the pros and cons of government involvement and religious instruction. Prominent among voluntaryists and anti-secularists was A. J. Beresford Hope, whose position offers useful insights into the educational agencies of the Church and the manner in which churchmen responded to new circumstances. This article explains Hope’s attitude and uses it to explore some of the causes and consequences of the Act of 1870. What type of schooling best suited the British people? Should it have a basis in something other than religion? How could the Church and its supporters meet the challenges posed by education reform?
A wideband dielectric resonator antenna with switchable diversity patterns
Authors: Abdalrazik Ahmad , Abdel-Rahman Adel B. , Allam Ahmed , Abo-Zahhad Mohammed 
Published: November 2019

AbstractIn this paper, a reduced-size dielectric resonator antenna with switchable diversity patterns is proposed. Ring- and linear-shaped slots are etched in the ground plane of the antenna so as to generate two modes $TE_{\delta 11}^x$ and $TE_{\delta 12}^x$ at a center frequency of 19 GHz. Moreover, two groups of PIN diodes are integrated into these slots to short one group of slots, and let the other group generates the required mode. Thus, the antenna is able to generate two switchable patterns with an envelope correlation coefficient of 0.4. Furthermore, the antenna size is reduced to half of its original size by placing a copper sheet over certain plane of the antenna structure. The antenna achieves wide bandwidths of 17.6–20.9 GHz (17.1$\percnt $) and 18.3–21.6 GHz (13.8$\percnt $) in cases of exciting $TE_{\delta 11}^x$ and $TE_{\delta 12}^x$ modes, respectively. The antenna also attainsa high gain of 7.1 and 3.2 dB at the center frequency.
DNA methylation at LRP1 gene locus mediates the association between maternal total cholesterol changes in pregnancy and cord blood leptin levels
Authors: Guay Simon-Pierre , Houde Andrée-Anne , Breton Edith , Baillargeon Jean-Patrice , Perron Patrice , Gaudet Daniel , Hivert Marie-France , Brisson Diane , Bouchard Luigi 
Published: November 2019

AbstractPlacental lipids transfer is essential for optimal fetal development, and alterations of these mechanisms could lead to a higher risk of adverse birth outcomes. Low-density lipoprotein receptor (LDLR), LDL receptor-related protein 1 (LRP1), and scavenger receptor class B type 1 (SCARB1) genes are encoding lipoprotein receptors expressed in the placenta where they participate in cholesterol exchange from maternal to fetal circulation. The aim of this study was thus to investigate the association between maternal lipid changes occurring in pregnancy, placental DNA methylation (DNAm) variations at LDLR, LRP1, and SCARB1 gene loci, and newborn’s anthropometric profile at birth. Sixty-nine normoglycemic women were followed from the first trimester of pregnancy until delivery. Placental DNAm was quantified at 43 Cytosine-phosphate-Guanines (CpGs) at LDLR, LRP1, and SCARB1 gene loci using pyrosequencing: 4 CpGs were retained for further analysis. Maternal clinical data were collected at each trimester of pregnancy. Newborns’ data were collected from medical records. Statistical models included minimally newborn sex and gestational and maternal age. Maternal total cholesterol changes during pregnancy (ΔT3-T1) were correlated with DNAm variations at LDLR (r = −0.32, p = 0.01) and LRP1 (r = 0.34, p = 0.007). DNAm at these loci was also correlated with newborns’ cord blood triglyceride and leptin levels. Mediation analysis supports a causal relationship between maternal cholesterol changes, DNAm levels at LRP1 locus, and cord blood leptin concentration (pmediation = 0.02). These results suggest that LRP1 DNAm link maternal blood cholesterol changes in pregnancy and offspring adiposity at birth, which provide support for a better follow-up of blood lipids in pregnancy.
A Scaling for Wave Dispersion Relationships in Ice‐Covered Waters
Authors: Yu Jie , Rogers W. Erick , Wang David W. 
Published: November 2019

AbstractWe consider the scaling of dispersion relationships for wave propagation on ice‐covered waters, aiming to identify a set of parameters that are physically meaningful and can be used in various continuum‐based theories. These parameters characterize the relative importance of the effects of ice inertia, effective viscosity, and elasticity, hence can be used to guide the dynamic similarity between different scales. Application to laboratory and field measurements shows scale collapse of data sets toward a general trend. From the dimensionless parameters of the theoretical prediction, the effective ice properties can be estimated more consistently.
Assessment of CMIP5 GCM Simulation Performance for Temperature Projection in the Tibetan Plateau
Authors: Jia Kun , Ruan Yunfeng , Yang Yanzhao , You Zhen 
Published: November 2019

AbstractThe performance of 33 Coupled Model Intercomparison Project 5 (CMIP5) general circulation models (GCMs) in temperature simulations in the Tibetan Plateau (TP) was comprehensively assessed by an improved score‐based and multiple‐criteria method using data collected from 1961 to 2005. Future temperatures were also simulated based on a multimodel ensemble coupled with the Delta downscaling method for near‐term (2006–2050) and long‐term (2051–2095) projections under Representative Concentration Pathways (RCP, scenarios RCP4.5 and RCP8.5). Our results demonstrated that all the GCMs evaluated in our study could capture the seasonal temperature patterns. However, most GCMs tended to underestimate temperatures by an average of −2.0°C. All the GCMs could effectively simulate temporal distribution, with a mean correlation coefficient of 0.997. However, they did not perform well in reproducing spatial distribution. Different assessment criteria lead to inconsistent results; however, the improved rank score method with multiple criteria provided a robust assessment of GCMs performance. MPI‐ESM‐LR, CMCC‐CMS, and GFDL‐ESM 2M showed a better temperature simulation performance compared to the other GCMs that we have assessed. Topographic correction could effectively enhance spatial distribution simulation; however, this increased temperature underestimation. Future temperatures were projected to increase by 1.4°C and 1.6°C in near‐term, and by 2.4°C and 4.0°C in long‐term under RCP4.5 and RCP8.5 scenarios, respectively. High temperatures mainly occurring in the southeastern end of the Himalayas, as well as the northern and southeastern margins of the TP. The results are expected to provide valuable information on climate change and its impact on hydrology, ecology, and socioeconomics of the TP.
Age of the Canada Basin, Arctic Ocean: Indications From High‐Resolution Magnetic Data
Authors: Zhang T. , Dyment J. , Gao J.Y. 
Published: November 2019

AbstractThe origin and history of the Amerasia basin are long‐running debates, which hinder our knowledge of the Mesozoic tectonic configurations and geodynamic processes in the Arctic. This lack of knowledge is due in part to the paucity of accurate magnetic data in the ice‐covered basin. Here, we identify the crustal age of the Canada Basin, a major part of the Amerasia Basin, through high‐resolution deep‐tow and sea‐surface magnetic data. The best fit of the four pairs of magnetic lineations revealed by the high‐resolution magnetic data is 139.5–128.6 Ma (or 142.4–132.8 Ma, depending on the geomagnetic polarity timescale). The crustal age provides crucial constraints on the evolution of the circum‐Arctic tectonic features and generally supports the hypothesis that the opening of the Amerasia Basin is related to the subductions during the closure of the South Anyui Ocean.
Reconstruction of Local Magnetic Structures by a Modified Radial Basis Function Method
Authors: Chen Wenming , Wang Xiaogang , Tsyganenko N. A. , Andreeva V. A. , Semenov V. S. 
Published: November 2019

AbstractLocal magnetic structures in space environments, in particular, those in the diffusion region such as magnetic nulls or separators, are very difficult to identify by satellite measurements but important for understanding of magnetic reconnection. Multi‐spacecraft missions such as Cluster or MMS, however, provide an opportunity to reconstruct the fine structures using vector data of space magnetometers. In this paper, we introduce a method for such a local reconstruction, based on the modified radial basis functions (Andreeva & Tsyganenko, 2016, https://doi.org/10.1002/2016JA023217), used previously for the global magnetic field modeling. A principal advantage of this method is its freedom from a priori assumptions on the magnetic field topology. The method has been tested on 21/2 and 3D reconnection geometries and provided a good agreement with preset models. The relative errors of null positions, γ‐line directions, and ∑‐surface normal directions are found to be below 6% even with 20% random errors added to the target magnetic field vectors in reconstruction of 3D separator model geometry. Applications of the method to the field reconstruction based on Cluster measurements are also presented and discussed.
Seismicity, Fault Slip Rates, and Fault Interactions in a Fault System
Authors: Gao Yajing , Luo Gang , Sun Yunqiang 
Published: November 2019

AbstractSeismicity and the partitioning of slip rates in interacting and mechanically coupled fault systems are poorly understood. We developed and used three‐dimensional viscoelastoplastic finite element models to simulate earthquakes, earthquake cycles, and synthetic seismicity in single and bifurcated fault systems and investigate seismicity, fault slip rates, and interactions and mechanical coupling between faults in fault systems. The modeled interseismic velocities and coseismic displacements are consistent with those from analytical and quasi‐analytical solutions. We found that the modeled frequency‐magnitude relation satisfies the Gutenberg‐Richter relation and the b value is inversely related to differential stress. We observed that the seismicity on two parallel faults is often interdependent and complementary: high seismic moment release rates on a fault are usually accompanied by low ones on the other fault and vice versa; the two faults collectively accommodate far‐field tectonic loading and crustal relative motion. Model results showed that when two parallel faults have the same or similar strength, they have similar seismicity and long‐term slip rates, but when one of the two faults has lower strength, it has more active seismicity and a faster slip rate than the other; the sum of their slip rates equals the far‐field crustal relative motion in both cases. The results in this study provide scientific insights into the spatiotemporal migration of seismicity and partitioning of fault slip rates in an interacting and mechanically coupled fault system and help to qualify b values and to evaluate the earthquake hazard and risk on each of the faults in such a system.
Total Variation Regularization of Geodetically Constrained Block Models in Southwest Taiwan
Authors: Huang Mong‐Han , Evans Eileen L. 
Published: November 2019

AbstractRapid convergence between the Eurasian plate and the Philippine Sea Plate makes Taiwan one of the most active tectonic regions in the world, and this strain is accommodated on a complex network of thrust and strike‐slip faulting. Here, we use ascending and descending Interferometric Synthetic Aperture Radar (InSAR) data integrated with continuous GPS measurements to monitor interseismic deformation in southwest Taiwan. Geodetic observations show rapid (20–40 mm/year) southwestward motion in the Pingtung plain in south Taiwan and more than 10 mm/year uplift in the southern part of the Western Foothills. We use combined InSAR and CGPS measurements from 2004 to 2010 to constrain a block model of horizontal interseismic crustal deformation. Total variation regularization (TVR) serves as a tool for block model selection to algorithmically assess the block model geometry based on geodetic observations, simultaneously estimating block rotations and fault slip rates on block‐bounding faults. The block model results suggest that the margins of the Western Foothills accommodate most of the interseismic deformation in southwestern Taiwan. Thirty‐five independent blocks are required to explain interseismic crustal deformation with a mean residual velocity of 3.6 mm/year. Based on this horizontal model, we then forward predict vertical displacement and find good consistency between the predicted uplift and the geodetic observations. Our approach shows an efficient and objective way to estimate fault activities and seismic hazards in the interseismic period based on dense geodetic measurements and their uncertainties.
Effect of Water on the Thermal Properties of Olivine With Implications for Lunar Internal Temperature
Authors: Zhang Baohua , Ge Jianhua , Xiong Zili , Zhai Shuangmeng 
Published: November 2019

AbstractHow water could affect thermal transport properties is a key question that needs to be quantified experimentally when it is incorporated as structurally bound hydroxyl groups in the lattice of mantle minerals. In this study, thermal diffusivity (D) and thermal conductivity (κ) of San Carlos olivine aggregates with various water contents (up to 0.2 wt.% H2O) were measured simultaneously using transient plane‐source method up to 873 K and 3 GPa. Experimental results demonstrate that water content can significantly reduce the thermal diffusivity (D) and thermal conductivity (κ) of olivine aggregate. With the increase of H2O content from 0.08 to 0.2 wt.%, the absolute values of D and κ for olivine samples decrease by 5–13% and 17–33% and by 3–8% and 14–21%, respectively. D and κ of olivine aggregate decrease with temperature but increase with pressure. Heat capacity is influenced by pressure negatively. Combining the present data with surface heat flow of the Moon as well as heat production, the calculated temperature profiles provide new constraints on the lunar geotherm and possible H2O content in the lunar interior.
Heteroepitaxial vertical perovskite hot-electron transistors down to the monolayer limit
Authors: Kim Brian S. Y. , Hikita Yasuyuki , Yajima Takeaki , Hwang Harold Y. 
Published: November 2019

AbstractTwo-dimensional heterostructures combined with vertical geometries are candidates to probe and utilize the physical properties of atomically-thin materials. The vertical configuration enables a unique form of hot-carrier spectroscopy as well as atomic-scale devices. Here, we present the room-temperature evolution of heteroepitaxial perovskite hot-electron transistors using a SrRuO3 base down to the monolayer limit (∼4 Å). As a fundamental electronic probe, we observe an abrupt transition in the hot-electron mean free path as a function of base thickness, coinciding with the thickness-dependent resistive transition. As a path towards devices, we demonstrate the integrated synthesis of perovskite one-dimensional electrical edge contacts using water-soluble and growth-compatible Sr3Al2O6 hard masks. Edge-contacted monolayer-base transistors exhibit on/off ratios reaching ∼108, complete electrostatic screening by the base manifesting pure hot-electron injection, and excellent scaling of the output current density with device dimensions. These results open new avenues for incorporating emergent phenomena at oxide interfaces and in heterostructures.