bluuebunny/crossref_metadata_2025_split huggingface dataset:
Random Force Perturbations: A New Extension of the Cell Perturbation Method for Turbulence Generation in Multiscale Atmospheric Boundary Layer Simulations
Authors: Mazzaro L. J. , Koo E. , Muñoz‐Esparza D. , Lundquist J. K. , Linn R. R. 
Published: June 2019

AbstractCoupling between mesoscale and large eddy simulation (LES) is critically important for many atmospheric model applications, from predictions of wind energy to fire propagation. The grid‐nesting technique enables bridging between vastly different scales without incurring prohibitive computational costs. However, the transition from coarser to finer resolutions often requires a large number of grid points from inflow boundaries for the development of fine‐scale turbulence features in the LES domain. Recently, the cell perturbation method (CPM) was developed to reduce the turbulence development region with high computational efficiency. Herein, we explore a new method based on the CPM that uses force perturbations in both the horizontal and vertical directions (Force Cell Perturbation Method) instead of the potential temperature perturbations in the original CPM, as an attempt to further explore the performance of the random perturbation techniques. This approach is tested for a neutral and a convective atmospheric boundary layer under idealized conditions. Overall, similar performance is found between the optimal configurations of the CPM and the Force Cell Perturbation Method pointing to the robustness of this family of perturbation methods in accelerating turbulence generation in nested domains. Vertical force perturbations performed better than horizontal force perturbations for both atmospheric stability conditions. The CPM performed best under convective stability conditions. The combination of the force and potential temperature perturbations is found to provide no additional performance improvement over the stand‐alone application of the individual methods.
Polygenic risk associated with post-traumatic stress disorder onset and severity
Authors: Misganaw Burook , Guffanti Guia , Lori Adriana , Abu-Amara Duna , Flory Janine D. ,   SBPBC, Hammamieh Rasha , Gautam Aarti , Yang Ruoting , Daigle Bernie J. , Hood Leroy , Wang Kai , Lee Inyoul , Mellon Synthia H. , Wolkowitz Owen M. , Mueller Susanne , Yehuda Rachel , Jett Marti , Marmar Charles R. , Ressler Kerry J. , Doyle Francis J. 
Published: June 2019

AbstractPost-traumatic stress disorder (PTSD) is a psychiatric illness with a highly polygenic architecture without large effect-size common single-nucleotide polymorphisms (SNPs). Thus, to capture a substantial portion of the genetic contribution, effects from many variants need to be aggregated. We investigated various aspects of one such approach that has been successfully applied to many traits, polygenic risk score (PRS) for PTSD. Theoretical analyses indicate the potential prediction ability of PRS. We used the latest summary statistics from the largest published genome-wide association study (GWAS) conducted by Psychiatric Genomics Consortium for PTSD (PGC-PTSD). We found that the PRS constructed for a cohort comprising veterans of recent wars (n = 244) explains a considerable proportion of PTSD onset (Nagelkerke R2 = 4.68%, P = 0.003) and severity (R2 = 4.35%, P = 0.0008) variances. However, the performance on an African ancestry sub-cohort was minimal. A PRS constructed with schizophrenia GWAS also explained a significant fraction of PTSD diagnosis variance (Nagelkerke R2 = 2.96%, P = 0.0175), confirming previously reported genetic correlation between the two psychiatric ailments. Overall, these findings demonstrate the important role polygenic analyses of PTSD will play in risk prediction models as well as in elucidating the biology of the disorder.
Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity
Authors: Penvose Ashley , Keenan Jessica L. , Bray David , Ramlall Vijendra , Siggers Trevor 
Published: June 2019

AbstractThe type II nuclear receptors (NRs) function as heterodimeric transcription factors with the retinoid X receptor (RXR) to regulate diverse biological processes in response to endogenous ligands and therapeutic drugs. DNA-binding specificity has been proposed as a primary mechanism for NR gene regulatory specificity. Here we use protein-binding microarrays (PBMs) to comprehensively analyze the DNA binding of 12 NR:RXRα dimers. We find more promiscuous NR-DNA binding than has been reported, challenging the view that NR binding specificity is defined by half-site spacing. We show that NRs bind DNA using two distinct modes, explaining widespread NR binding to half-sites in vivo. Finally, we show that the current models of NR specificity better reflect binding-site activity rather than binding-site affinity. Our rich dataset and revised NR binding models provide a framework for understanding NR regulatory specificity and will facilitate more accurate analyses of genomic datasets.
In vivo nuclear capture and molecular profiling identifies Gmeb1 as a transcriptional regulator essential for dopamine neuron function
Authors: Tuesta Luis M. , Djekidel Mohamed N. , Chen Renchao , Lu Falong , Wang Wengang , Sabatini Bernardo L. , Zhang Yi 
Published: June 2019

AbstractMidbrain dopamine (mDA) neurons play a central role in reward signaling and are widely implicated in psychiatric and neurodegenerative disorders. To understand how mDA neurons perform these functions, it is important to understand how mDA-specific genes are regulated. However, cellular heterogeneity in the mammalian brain presents a major challenge to obtaining this understanding. To this end, we developed a virus-based approach to label and capture mDA nuclei for transcriptome (RNA-Seq), and low-input chromatin accessibility (liDNase-Seq) profiling, followed by predictive modeling to identify putative transcriptional regulators of mDA neurons. Using this method, we identified Gmeb1, a transcription factor predicted to regulate expression of Th and Dat, genes critical for dopamine synthesis and reuptake, respectively. Gmeb1 knockdown in mDA neurons resulted in downregulation of Th and Dat, as well as in severe motor deficits. This study thus identifies Gmeb1 as a master regulator of mDA gene expression and function, and provides a general method for identifying cell type-specific transcriptional regulators.
APC/CCDH1 synchronizes ribose-5-phosphate levels and DNA synthesis to cell cycle progression
Authors: Li Yang , Yao Cui-Fang , Xu Fu-Jiang , Qu Yuan-Yuan , Li Jia-Tao , Lin Yan , Cao Zhong-Lian , Lin Peng-Cheng , Xu Wei , Zhao Shi-Min , Zhao Jian-Yuan 
Published: June 2019

AbstractAccumulation of nucleotide building blocks prior to and during S phase facilitates DNA duplication. Herein, we find that the anaphase-promoting complex/cyclosome (APC/C) synchronizes ribose-5-phosphate levels and DNA synthesis during the cell cycle. In late G1 and S phases, transketolase-like 1 (TKTL1) is overexpressed and forms stable TKTL1-transketolase heterodimers that accumulate ribose-5-phosphate. This accumulation occurs by asymmetric production of ribose-5-phosphate from the non-oxidative pentose phosphate pathway and prevention of ribose-5-phosphate removal by depleting transketolase homodimers. In the G2 and M phases after DNA synthesis, expression of the APC/C adaptor CDH1 allows APC/CCDH1 to degrade D-box-containing TKTL1, abrogating ribose-5-phosphate accumulation by TKTL1. TKTL1-overexpressing cancer cells exhibit elevated ribose-5-phosphate levels. The low CDH1 or high TKTL1-induced accumulation of ribose-5-phosphate facilitates nucleotide and DNA synthesis as well as cell cycle progression in a ribose-5-phosphate-saturable manner. Here we reveal that the cell cycle control machinery regulates DNA synthesis by mediating ribose-5-phosphate sufficiency.
Enantioselective synthesis of cis-hydrobenzofurans bearing all-carbon quaternary stereocenters and application to total synthesis of (‒)-morphine
Authors: Zhang Qing , Zhang Fu-Min , Zhang Chang-Sheng , Liu Si-Zhan , Tian Jin-Miao , Wang Shao-Hua , Zhang Xiao-Ming , Tu Yong-Qiang 
Published: June 2019

Abstract(‒)-Morphine, which is selected as an essential medicine by World Health Organization, is widely applied in the treatment of the pain-related diseases. Due to its synthetically challenging molecular architecture and important clinical role, extensive synthetic studies of morphine-type alkaloids have been conducted. However, catalytic asymmetric total synthesis of (‒)-morphine remains a long-standing challenge. Here, we disclose an efficient enantioselective total synthesis of (‒)-morphine in a longest linear sequence of 16 steps. The key transformation features a highly enantioselective Robinson annulation enabled by our spiro-pyrrolidine catalyst to rapidly construct the densely functionalized cis-hydrodibenzofuran framework containing vicinal stereocenters with an all-carbon quaternary center. This asymmetric approach provides an alternative strategy for the synthesis of (‒)-morphine and its analogues.
Anatomy of the energetic driving force for charge generation in organic solar cells
Authors: Nakano Kyohei , Chen Yujiao , Xiao Bo , Han Weining , Huang Jianming , Yoshida Hiroyuki , Zhou Erjun , Tajima Keisuke 
Published: June 2019

AbstractEliminating the excess energetic driving force in organic solar cells leads to a smaller energy loss and higher device performance; hence, it is vital to understand the relation between the interfacial energetics and the photoelectric conversion efficiency. In this study, we systematically investigate 16 combinations of four donor polymers and four acceptors in planar heterojunction. The charge generation efficiency and its electric field dependence correlate with the energy difference between the singlet excited state and the interfacial charge transfer state. The threshold energy difference is 0.2 to 0.3 eV, below which the efficiency starts dropping and the charge generation becomes electric field-dependent. In contrast, the charge generation efficiency does not correlate with the energy difference between the charge transfer and the charge-separated states, indicating that the binding of the charge pairs in the charge transfer state is not the determining factor for the charge generation.
Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy
Authors: Takata Atsushi , Nakashima Mitsuko , Saitsu Hirotomo , Mizuguchi Takeshi , Mitsuhashi Satomi , Takahashi Yukitoshi , Okamoto Nobuhiko , Osaka Hitoshi , Nakamura Kazuyuki , Tohyama Jun , Haginoya Kazuhiro , Takeshita Saoko , Kuki Ichiro , Okanishi Tohru , Goto Tomohide , Sasaki Masayuki , Sakai Yasunari , Miyake Noriko , Miyatake Satoko , Tsuchida Naomi , Iwama Kazuhiro , Minase Gaku , Sekiguchi Futoshi , Fujita Atsushi , Imagawa Eri , Koshimizu Eriko , Uchiyama Yuri , Hamanaka Kohei , Ohba Chihiro , Itai Toshiyuki , Aoi Hiromi , Saida Ken , Sakaguchi Tomohiro , Den Kouhei , Takahashi Rina , Ikeda Hiroko , Yamaguchi Tokito , Tsukamoto Kazuki , Yoshitomi Shinsaku , Oboshi Taikan , Imai Katsumi , Kimizu Tomokazu , Kobayashi Yu , Kubota Masaya , Kashii Hirofumi , Baba Shimpei , Iai Mizue , Kira Ryutaro , Hara Munetsugu , Ohta Masayasu , Miyata Yohane , Miyata Rie , Takanashi Jun-ichi , Matsui Jun , Yokochi Kenji , Shimono Masayuki , Amamoto Masano , Takayama Rumiko , Hirabayashi Shinichi , Aiba Kaori , Matsumoto Hiroshi , Nabatame Shin , Shiihara Takashi , Kato Mitsuhiro , Matsumoto Naomichi 
Published: June 2019

AbstractAlthough there are many known Mendelian genes linked to epileptic or developmental and epileptic encephalopathy (EE/DEE), its genetic architecture is not fully explained. Here, we address this incompleteness by analyzing exomes of 743 EE/DEE cases and 2366 controls. We observe that damaging ultra-rare variants (dURVs) unique to an individual are significantly overrepresented in EE/DEE, both in known EE/DEE genes and the other non-EE/DEE genes. Importantly, enrichment of dURVs in non-EE/DEE genes is significant, even in the subset of cases with diagnostic dURVs (P = 0.000215), suggesting oligogenic contribution of non-EE/DEE gene dURVs. Gene-based analysis identifies exome-wide significant (P = 2.04 × 10−6) enrichment of damaging de novo mutations in NF1, a gene primarily linked to neurofibromatosis, in infantile spasm. Together with accumulating evidence for roles of oligogenic or modifier variants in severe neurodevelopmental disorders, our results highlight genetic complexity in EE/DEE, and indicate that EE/DEE is not an aggregate of simple Mendelian disorders.
Accounting for corner flow unifies the understanding of droplet formation in microfluidic channels
Authors: Korczyk Piotr M. , van Steijn Volkert , Blonski Slawomir , Zaremba Damian , Beattie David A. , Garstecki Piotr 
Published: June 2019

AbstractWhile shear emulsification is a well understood industrial process, geometrical confinement in microfluidic systems introduces fascinating complexity, so far prohibiting complete understanding of droplet formation. The size of confined droplets is controlled by the ratio between shear and capillary forces when both are of the same order, in a regime known as jetting, while being surprisingly insensitive to this ratio when shear is orders of magnitude smaller than capillary forces, in a regime known as squeezing. Here, we reveal that further reduction of—already negligibly small—shear unexpectedly re-introduces the dependence of droplet size on shear/capillary-force ratio. For the first time we formally account for the flow around forming droplets, to predict and discover experimentally an additional regime—leaking. Our model predicts droplet size and characterizes the transitions from leaking into squeezing and from squeezing into jetting, unifying the description for confined droplet generation, and offering a practical guide for applications.
Diffusing wave paradox of phototactic particles in traveling light pulses
Authors: Lozano Celia , Bechinger Clemens 
Published: June 2019

AbstractCells navigate through complex surroundings by following cues from their environment. A prominent example is Dictyostelium, which is directed by chemotaxis towards regions with higher concentrations. In the presence of traveling chemical waves, however, amoebae migrate counter to the running wave. Such behavior, referred to as diffusing wave paradox, suggests the existence of adaptation and directional memory. Here we experimentally investigate the response of phototactic self-propelled microparticles to traveling light-pulses. Despite their entirely memory-less (i.e., strictly local) response to the environment, we observe the same phenomenological behavior, i.e., particle motion counter to the pulse direction. Our findings are supported by a minimal model which considers active particle reorientations within local light gradients. The complex and robust behavior of synthetic active particles to spatially and temporally varying stimuli enables new strategies for achieving collective behavior and can be used for the design of micro-robotic systems with limited signal-processing capabilities.
Microstructure arrays of DNA using topographic control
Authors: Cha Yun Jeong , Park Soon Mo , You Ra , Kim Hyoungsoo , Yoon Dong Ki 
Published: June 2019

AbstractDNA is a common biomaterial in nature as well as a good building block for producing useful structures, due to its fine feature size and liquid crystalline phase. Here, we demonstrate that a combination of shear-induced flow and microposts can be used to create various kinds of interesting microstructure DNA arrays. Our facile method provides a platform for forming multi-scale hierarchical orientations of soft- and biomaterials, using a process of simple shearing and controlled evaporation on a patterned substrate. This approach enables potential patterning applications using DNA or other anisotropic biomaterials based on their unique structural characteristics.
The mechanism of tidal triggering of earthquakes at mid-ocean ridges
Authors: Scholz Christopher H. , Tan Yen Joe , Albino Fabien 
Published: June 2019

AbstractThe strong tidal triggering of mid-ocean ridge earthquakes has remained unexplained because the earthquakes occur preferentially during low tide, when normal faulting earthquakes should be inhibited. Using Axial Volcano on the Juan de Fuca ridge as an example, we show that the axial magma chamber inflates/deflates in response to tidal stresses, producing Coulomb stresses on the faults that are opposite in sign to those produced by the tides. When the magma chamber’s bulk modulus is sufficiently low, the phase of tidal triggering is inverted. We find that the stress dependence of seismicity rate conforms to triggering theory over the entire tidal stress range. There is no triggering stress threshold and stress shadowing is just a continuous function of stress decrease. We find the viscous friction parameter A to be an order of magnitude smaller than laboratory measurements. The high tidal sensitivity at Axial Volcano results from the shallow earthquake depths.
Boost multi‐level NPC‐fed VS large rated asynchronous pumped storage hydro‐generating unit
Authors: Joseph Anto , Kim Seok‐Min , Sing Lee Sze , Dominic Arun , Lee Kyo‐Beum 
Published: June 2019

The authors intent using a boost multi‐level converter for the doubly fed induction machine (DFIM) used in variable‐speed pumped storage plants (VS‐PSP). Voltage‐source converters connected on the rotor side of the machine control the active and reactive powers of the unit. The proposed boost neutral point clamped (NPC) converter topology provides a voltage output two times larger than a conventional three‐level NPC (3L‐NPC) with similar DC‐link voltage and equal number of switches. Hence, it increases the speed variation of the unit, which improves the efficiency during generation and pumping modes. Moreover, it reduces the starting period of the unit at the pumping mode, which is significant during mode changeover time. Furthermore, it reduces switching and conduction losses in the converter. It also reduces the total harmonic distortion in the output current, as it provides five output voltage levels. These improvements show that the boost NPC converter topology is better among VS‐PSP project authorities. In addition, the reliability of the proposed topology is investigated, where converter redundancy is a challenging issue in asynchronous VS‐PSP units. The proposed boost NPC was compared with the conventional 3L‐NPC system by examining a 250 MW DFIM hydro‐generating unit.
Wind turbines robust fault reconstruction using adaptive sliding mode observer
Authors: Taherkhani Ashkan , Bayat Farhad 
Published: June 2019

This study addresses the problem of reliable power generation in wind turbines subject to actuator and sensor faults in the presence of disturbances and uncertainties. For this purpose, an adaptive sliding mode observer is proposed and shown that it is able to reconstruct the faults without even knowing the exact magnitude of the faults, disturbances and uncertainties. Rather, it is only assumed that these signals are bounded. For evaluation purpose, a 5 MW wind turbine system is utilised and a set of simulation results are provided, which verify the accuracy, effectiveness and robust performance of the proposed approach.
Load and mutual inductance estimation based on phase‐differences for electric vehicle wireless charging system
Authors: Zhang Yuwang , Guo Yanjie , Zhu Qingwei , Wang Lifang 
Published: June 2019

In this study, a new method to estimate the load and mutual inductance for a wireless charging system (WCS) is presented. Instead of simultaneously using the root mean square and phase angles of related voltages and currents, accurate estimations can be obtained through the phase differences in the primary side. Firstly, the WCS model with dual‐side inductor–capacitor–capacitor compensation networks is established, and the reflected impedance is analysed based on the phase differences in the primary side. Then, the estimation calculation of load and mutual inductance is derived according to the reflected impedance. Meanwhile, the output voltage estimation in the primary side is realised based on the estimated values of the load and mutual inductance. Finally, experiments are conducted to verify the effectiveness of the proposed method in the 3.3 kW electric vehicle wireless charging experiment platform. Experimental results show that the estimation errors of the load and mutual inductance are <5 and 3.5%, respectively, and the system output voltage can be effectively estimated based on their estimated results.
Impact of interface traps/defects and self‐heating on the degradation of performance of a 4H‐SiC VDMOSFET
Authors: Alqaysi Mustafa H. , Martinez Antonio , Ahmeda Khaled , Ubochi Brendan , Kalna Karol 
Published: June 2019

The reliability of silicon carbide metal oxide semiconductor field‐effect transistors remains a challenge in power applications and relates to the SiO2–SiC interface. The presence of unwanted interface traps/defects degrades the device performance. The impact of acceptor traps/defects on the performance of a 4H‐SiC vertical Diffused Metal Oxide Semiconductor Field Effect Transistor (DMOSFET) with a breakdown voltage of 1700 V is investigated. ‐ and ‐ characteristics were simulated, using a drift‐diffusion model coupled to Fourier heat equations, and are in a good agreement with experimental results. The presence of interface traps/defects were shown to produce degradation of threshold voltage, but the impact diminishes as temperature increases. A threshold voltage shift of 3.5 V occurs for a trap concentration of 2 × 1013 cm–2/eV at room temperature. The transfer characteristics obtained from electro‐thermal modelling show a larger degradation than those at a constant temperature. This degradation increases with the drain bias increase. The threshold voltage from the electro‐thermal simulations is 5 V compared to 4 V observed in constant 423 K temperature simulations at. Finally, the interface traps/defects increases breakdown voltage exhibiting a strong dependency on the trap density and their energy decay characteristics.
Soft‐switching DC–DC converter with controllable resonant tank featuring high efficiency and wide voltage gain range
Authors: Wang Yifeng , Liu Ruixin , Han Fuqiang , Yang Liang , Meng Zhun 
Published: June 2019

A two‐mode resonant DC–DC converter with auxiliary switch (named as sLLC‐C) has been presented. Two simple structural circuits (namely LLC and LLCC) are integrated into one topology with only two magnetic cores, through the topological transformation method. The proposed converter successfully inherits the advantages of the above two circuits, while avoiding their drawbacks as well. At the rating condition, it functions as an LLC circuit, and thus high conversion efficiency is easily obtained. The LLCC working mode is called automatically once the input voltage increases. In such a way, within a limited frequency range, the voltage gain range is effectively extended. A detailed parameter design is given to help achieve desirable performances. Finally, experiments are carried out to validate the feasibility and correctness of the proposed sLLC‐C converter. The output voltage is maintained at 400 V, even if the input voltage varies in the range of 150–400 V. Besides, the preferable soft‐switching characteristics are ensured for both the power switches and secondary‐side diodes. The maximum efficiency of 97.3% is achieved. Thus, wide voltage gain range and high conversion efficiency are acquired simultaneously. These performances make the proposed converter well appropriate for the fuel cell generation applications.