bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum chemistry and charge transport in biomolecules with superconducting circuits
Authors: García-Álvarez L. , Las Heras U. , Mezzacapo A. , Sanz M. , Solano E. , Lamata L. 
Published: June 2016

AbstractWe propose an efficient protocol for digital quantum simulation of quantum chemistry problems and enhanced digital-analog quantum simulation of transport phenomena in biomolecules with superconducting circuits. Along these lines, we optimally digitize fermionic models of molecular structure with single-qubit and two-qubit gates, by means of Trotter-Suzuki decomposition and Jordan-Wigner transformation. Furthermore, we address the modelling of system-environment interactions of biomolecules involving bosonic degrees of freedom with a digital-analog approach. Finally, we consider gate-truncated quantum algorithms to allow the study of environmental effects.
Effect of experimental laser imperfections on laser wakefield acceleration and betatron source
Authors: Ferri J. , Davoine X. , Fourmaux S. , Kieffer J. C. , Corde S. , Ta Phuoc K. , Lifschitz A. 
Published: June 2016

AbstractLaser pulses in current ultra-short TW systems are far from being ideal Gaussian beams. The influence of the presence of non-Gaussian features of the laser pulse is investigated here from experiments and 3D Particle-in-Cell simulations. Both the experimental intensity distribution and wavefront are used as input in the simulations. It is shown that a quantitative agreement between experimental data and simulations requires to use realistic pulse features. Moreover, some trends found in the experiments, such as the growing of the X-ray signal with the plasma length, can only be retrieved in simulations with realistic pulses. The performances on the electron acceleration and the synchrotron X-ray emission are strongly degraded by these non-Gaussian features, even keeping constant the total laser energy. A drop on the X-ray photon number by one order of magnitude was found. This clearly put forward the limitation of using a Gaussian beam in the simulations.
Pure electronic metal-insulator transition at the interface of complex oxides
Authors: Meyers D. , Liu Jian , Freeland J. W. , Middey S. , Kareev M. , Kwon Jihwan , Zuo J. M. , Chuang Yi-De , Kim J. W. , Ryan P. J. , Chakhalian J. 
Published: June 2016

AbstractIn complex materials observed electronic phases and transitions between them often involve coupling between many degrees of freedom whose entanglement convolutes understanding of the instigating mechanism. Metal-insulator transitions are one such problem where coupling to the structural, orbital, charge and magnetic order parameters frequently obscures the underlying physics. Here, we demonstrate a way to unravel this conundrum by heterostructuring a prototypical multi-ordered complex oxide NdNiO3 in ultra thin geometry, which preserves the metal-to-insulator transition and bulk-like magnetic order parameter, but entirely suppresses the symmetry lowering and long-range charge order parameter. These findings illustrate the utility of heterointerfaces as a powerful method for removing competing order parameters to gain greater insight into the nature of the transition, here revealing that the magnetic order generates the transition independently, leading to an exceptionally rare purely electronic metal-insulator transition with no symmetry change.
Multimodal Correlative Preclinical Whole Body Imaging and Segmentation
Authors: Akselrod-Ballin Ayelet , Dafni Hagit , Addadi Yoseph , Biton Inbal , Avni Reut , Brenner Yafit , Neeman Michal 
Published: June 2016

AbstractSegmentation of anatomical structures and particularly abdominal organs is a fundamental problem for quantitative image analysis in preclinical research. This paper presents a novel approach for whole body segmentation of small animals in a multimodal setting of MR, CT and optical imaging. The algorithm integrates multiple imaging sequences into a machine learning framework, which generates supervoxels by an efficient hierarchical agglomerative strategy and utilizes multiple SVM-kNN classifiers each constrained by a heatmap prior region to compose the segmentation. We demonstrate results showing segmentation of mice images into several structures including the heart, lungs, liver, kidneys, stomach, vena cava, bladder, tumor, and skeleton structures. Experimental validation on a large set of mice and organs, indicated that our system outperforms alternative state of the art approaches. The system proposed can be generalized to various tissues and imaging modalities to produce automatic atlas-free segmentation, thereby enabling a wide range of applications in preclinical studies of small animal imaging.
Suppression of compensating native defect formation during semiconductor processing via excess carriers
Authors: Alberi K. , Scarpulla M. A. 
Published: June 2016

AbstractIn many semiconductors, compensating defects set doping limits, decrease carrier mobility and reduce minority carrier lifetime thus limiting their utility in devices. Native defects are often responsible. Suppressing the concentrations of compensating defects during processing close to thermal equilibrium is difficult because formation enthalpies are lowered as the Fermi level moves towards the majority band edge. Excess carriers, introduced for example by photogeneration, modify the formation enthalpy of semiconductor defects and thus can be harnessed during crystal growth or annealing to suppress defect populations. Herein we develop a rigorous and general model for defect formation in the presence of steady-state excess carrier concentrations by combining the standard quasi-chemical formalism with a detailed-balance description that is applicable for any defect state in the bandgap. Considering the quasi-Fermi levels as chemical potentials, we demonstrate that increasing the minority carrier concentration increases the formation enthalpy for typical compensating centers, thus suppressing their formation. This effect is illustrated for the specific example of GaSb. While our treatment is generalized for excess carrier injection or generation in semiconductors by any means, we provide a set of guidelines for applying the concept in photoassisted physical vapor deposition.
Quantifying and predicting Drosophila larvae crawling phenotypes
Authors: Günther Maximilian N. , Nettesheim Guilherme , Shubeita George T. 
Published: June 2016

AbstractThe fruit fly Drosophila melanogaster is a widely used model for cell biology, development, disease, and neuroscience. The fly’s power as a genetic model for disease and neuroscience can be augmented by a quantitative description of its behavior. Here we show that we can accurately account for the complex and unique crawling patterns exhibited by individual Drosophila larvae using a small set of four parameters obtained from the trajectories of a few crawling larvae. The values of these parameters change for larvae from different genetic mutants, as we demonstrate for fly models of Alzheimer’s disease and the Fragile X syndrome, allowing applications such as genetic or drug screens. Using the quantitative model of larval crawling developed here we use the mutant-specific parameters to robustly simulate larval crawling, which allows estimating the feasibility of laborious experimental assays and aids in their design.
Thermodynamic power of non-Markovianity
Authors: Bylicka Bogna , Tukiainen Mikko , Chruściński Dariusz , Piilo Jyrki , Maniscalco Sabrina 
Published: June 2016

AbstractThe natural framework to discuss thermodynamics at the quantum level is the theory of open quantum systems. Memory effects arising from strong system-environment correlations may lead to information back-flow, that is non-Markovian behaviour. The relation between non-Markovianity and quantum thermodynamics has been until now largely unexplored. Here we show by means of Landauer’s principle that memory effects control the amount of work extraction by erasure in presence of realistic environments.
Combining operando synchrotron X-ray tomographic microscopy and scanning X-ray diffraction to study lithium ion batteries
Authors: Pietsch Patrick , Hess Michael , Ludwig Wolfgang , Eller Jens , Wood Vanessa 
Published: June 2016

AbstractWe present an operando study of a lithium ion battery combining scanning X-ray diffraction (SXRD) and synchrotron radiation X-ray tomographic microscopy (SRXTM) simultaneously for the first time. This combination of techniques facilitates the investigation of dynamic processes in lithium ion batteries containing amorphous and/or weakly attenuating active materials. While amorphous materials pose a challenge for diffraction techniques, weakly attenuating material systems pose a challenge for attenuation-contrast tomography. Furthermore, combining SXRD and SRXTM can be used to correlate processes occurring at the atomic level in the crystal lattices of the active materials with those at the scale of electrode microstructure. To demonstrate the benefits of this approach, we investigate a silicon powder electrode in lithium metal half-cell configuration. Combining SXRD and SRXTM, we are able to (i) quantify the dissolution of the metallic lithium electrode and the expansion of the silicon electrode, (ii) better understand the formation of the Li15Si4 phase and (iii) non-invasively probe kinetic limitations within the silicon electrode. A simple model based on the 1D diffusion equation allows us to qualitatively understand the observed kinetics and demonstrates why high-capacity electrodes are more prone to inhomogeneous lithiation reactions.
Mortality among People Living with HIV and AIDS in China: Implications for Enhancing Linkage
Authors: Li Meng , Tang Weiming , Bu Kai , Mahapatra Tanmay , Zhang Xiayan , Feng Yibing , Chen Fangfang , Guo Wei , Wang Liyan , Ding Zhengwei , Qin Qianqian , Liu Shiliang , Tucker Joseph D. , Wang Lu , Wang Ning 
Published: June 2016

AbstractTo assess the patterns and predictors of AIDS-related mortality and identify its correlates among adult people living with HIV/AIDS (PLWHA) in China, a retrospective record-based cohort study was conducted among 18 years or older PLWHA, who had at least one follow up reported to the national database between January-1989 and June-2012. Cumulative Incidence Function was used to calculate AIDS-related mortality rate. Gray’s test was used to determine the variation in cumulative incidence across strata. The Fine and Gray model was used to measure the burden of cumulative incidence of AIDS-related mortality and strength of its association with potential correlates. Among 375,629 patients, 107,634 died during study period, of which 54,759 (50.87%) deaths were AIDS-related. Cumulative mortality rates of AIDS-related death at one, two, five, 10 and 15 years post-diagnosis were 5.7%, 8.2%, 14.3%, 22.9% and 30.9%, respectively. Among PLWHA, male gender, ethnic minority and having AIDS were associated with significantly higher mortality. Further, homosexual transmission, being on ART and increasing CD4-testing frequency were associated with lower mortality. To reduce mortality among PLWHA, efficient interventions targeting males, ethnic minority, heterosexually infected and AIDS patients should be combined with immunologic monitoring, enhancement of coverage of HIV-testing and ART.
Raman scattering and anomalous Stokes–anti-Stokes ratio in MoTe2 atomic layers
Authors: Goldstein Thomas , Chen Shao-Yu , Tong Jiayue , Xiao Di , Ramasubramaniam Ashwin , Yan Jun 
Published: June 2016

AbstractStokes and anti-Stokes Raman scattering are performed on atomic layers of hexagonal molybdenum ditelluride (MoTe2), a prototypical transition metal dichalcogenide (TMDC) semiconductor. The data reveal all six types of zone center optical phonons, along with their corresponding Davydov splittings, which have been challenging to see in other TMDCs. We discover that the anti-Stokes Raman intensity of the low energy layer-breathing mode becomes more intense than the Stokes peak under certain experimental conditions and find the effect to be tunable by excitation frequency and number of atomic layers. These observations are interpreted as a result of resonance effects arising from the C excitons in the vicinity of the Brillouin zone center in the photon-electron-phonon interaction process.
Control efficacy of complex networks
Authors: Gao Xin-Dong , Wang Wen-Xu , Lai Ying-Cheng 
Published: June 2016

AbstractControlling complex networks has become a forefront research area in network science and engineering. Recent efforts have led to theoretical frameworks of controllability to fully control a network through steering a minimum set of driver nodes. However, in realistic situations not every node is accessible or can be externally driven, raising the fundamental issue of control efficacy: if driving signals are applied to an arbitrary subset of nodes, how many other nodes can be controlled? We develop a framework to determine the control efficacy for undirected networks of arbitrary topology. Mathematically, based on non-singular transformation, we prove a theorem to determine rigorously the control efficacy of the network and to identify the nodes that can be controlled for any given driver nodes. Physically, we develop the picture of diffusion that views the control process as a signal diffused from input signals to the set of controllable nodes. The combination of mathematical theory and physical reasoning allows us not only to determine the control efficacy for model complex networks and a large number of empirical networks, but also to uncover phenomena in network control, e.g., hub nodes in general possess lower control centrality than an average node in undirected networks.
Melamine Impairs Renal and Vascular Function in Rats
Authors: Tian Xiao Yu , Wong Wing Tak , Lau Chi Wai , Wang Yi-Xiang , Cheang Wai San , Liu Jian , Lu Ye , Huang Huihui , Xia Yin , Chen Zhen Yu , Mok Chuen-Shing , Lau Chau-Ming , Huang Yu 
Published: June 2016

AbstractMelamine incident, linked to nephrotoxicity and kidney stone in infants previously exposed to melamine-contaminated milk products, was unprecedentedly grave in China in 2008 as little was known about the mechanistic process leading to renal dysfunction in affected children. This study investigates whether neonatal ingestion of melamine leads to renal and vascular dysfunction in adulthood; and whether ingestion of melamine in pregnant rats leads to renal dysfunction in their offspring. A combination of approaches employed includes functional studies in rat renal arteries, renal blood flow measurement by functional magnetic resonance imaging, assay for pro-inflammatory and fibrotic biomarkers, immunohistochemistry and detection of plasma and renal melamine. We provide mechanistic evidence showing for the first time that melamine reduces renal blood flow and impairs renal and vascular function associated with overexpression of inflammatory markers, transforming growth factor-β1, bone morphogenic protein 4 and cyclooxygenase-2 in kidney and renal vasculature. Melamine also induces renal inflammation and fibrosis. More importantly, melamine causes nephropathies in offsprings from pregnant rat exposed to melamine during pregnancy, as well as in neonatal rat exposed to melamine afterbirth, thus supporting the clinical observations of kidney stone and acute renal failure in infants consuming melamine-contaminated milk products.
Homotopy-Theoretic Study & Atomic-Scale Observation of Vortex Domains in Hexagonal Manganites
Authors: Li Jun , Chiang Fu-Kuo , Chen Zhen , Ma Chao , Chu Ming-Wen , Chen Cheng-Hsuan , Tian Huanfang , Yang Huaixin , Li Jianqi 
Published: June 2016

AbstractEssential structural properties of the non-trivial “string-wall-bounded” topological defects in hexagonal manganites are studied through homotopy group theory and spherical aberration-corrected scanning transmission electron microscopy. The appearance of a “string-wall-bounded” configuration in RMnO3 is shown to be strongly linked with the transformation of the degeneracy space. The defect core regions (~50 Å) mainly adopt the continuous U(1) symmetry of the high-temperature phase, which is essential for the formation and proliferation of vortices. Direct visualization of vortex strings at atomic scale provides insight into the mechanisms and macro-behavior of topological defects in crystalline materials.
Effect of ionic radii on the Curie temperature in Ba1-x-ySrxCayTiO3 compounds
Authors: Berenov A. , Le Goupil F. , Alford N. 
Published: June 2016

AbstractA series of Ba1-x-ySrxCayTiO3 compounds were prepared with varying average ionic radii and cation disorder on A-site. All samples showed typical ferroelectric behavior. A simple empirical equation correlated Curie temperature, TC, with the values of ionic radii of A-site cations. This correlation was related to the distortion of TiO6 octahedra observed during neutron diffraction studies. The equation was used for the selection of compounds with predetermined values of TC. The effects of A-site ionic radii on the temperatures of phase transitions in Ba1-x-ySrxCayTiO3 were discussed.
Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors
Authors: Chan Alfred A. , Bashir Mina , Rivas Magali N. , Duvall Karen , Sieling Peter A. , Pieber Thomas R. , Vaishampayan Parag A. , Love Susan M. , Lee Delphine J. 
Published: June 2016

AbstractThe microbiome impacts human health and disease. Until recently, human breast tissue and milk were presumed to be sterile. Here, we investigated the presence of microbes in the nipple aspirate fluid (NAF) and their potential association with breast cancer. We compared the NAF microbiome between women with a history of breast cancer (BC) and healthy control women (HC) using 16S rRNA gene amplicon sequencing. The NAF microbiome from BC and HC showed significant differences in community composition. Two Operational Taxonomic Units (OTUs) showed differences in relative abundances between NAF collected from BC and HC. In NAF collected from BC, there was relatively higher incidence of the genus Alistipes. By contrast, an unclassified genus from the Sphingomonadaceae family was relatively more abundant in NAF from HC. These findings reflect the ductal source DNA since there were no differences between areolar skin samples collected from BC and HC. Furthermore, the microbes associated with BC share an enzymatic activity, Beta-Glucuronidase, which may promote breast cancer. This is the first report of bacterial DNA in human breast ductal fluid and the differences between NAF from HC and BC. Further investigation of the ductal microbiome and its potential role in breast cancer are warranted.
High salt promotes autoimmunity by TET2-induced DNA demethylation and driving the differentiation of Tfh cells
Authors: Wu Haijing , Huang Xin , Qiu Hong , Zhao Ming , Liao Wei , Yuan Shuguang , Xie Yubing , Dai Yong , Chang Christopher , Yoshimura Akihiko , Lu Qianjin 
Published: June 2016

AbstractFollicular helper T cells (Tfh) have been well documented to play a critical role in autoimmunity, such as systemic lupus erythematosus (SLE), by helping B cells. In this study, high salt (sodium chloride, NaCl), under physiological conditions, was demonstrated to increase the differentiation of Tfh. A high-salt diet markedly increased lupus features in MRL/lpr mice. The mechanism is NaCl-induced DNA demethylation via the recruitment of the hydroxytransferase Ten-Eleven Translocation 2 (TET2). Gene silencing of TET2 obviously diminished NaCl-induced Tfh cell polarization in vitro. In addition, the gene expression of sh2d1a, map3k1, spn and stat5b was enhanced after NaCl treatment, consistent with the findings in lupus CD4+T cells. However, only spn was directly regulated by TET2 and spn was not the sole target for NaCl. Our findings not only explain the epigenetic mechanisms of high-salt induced autoimmunity but also provide an attractive molecular target for intervention strategies of patients.
A Local Learning Rule for Independent Component Analysis
Authors: Isomura Takuya , Toyoizumi Taro 
Published: June 2016

AbstractHumans can separately recognize independent sources when they sense their superposition. This decomposition is mathematically formulated as independent component analysis (ICA). While a few biologically plausible learning rules, so-called local learning rules, have been proposed to achieve ICA, their performance varies depending on the parameters characterizing the mixed signals. Here, we propose a new learning rule that is both easy to implement and reliable. Both mathematical and numerical analyses confirm that the proposed rule outperforms other local learning rules over a wide range of parameters. Notably, unlike other rules, the proposed rule can separate independent sources without any preprocessing, even if the number of sources is unknown. The successful performance of the proposed rule is then demonstrated using natural images and movies. We discuss the implications of this finding for our understanding of neuronal information processing and its promising applications to neuromorphic engineering.
Human Protein Subcellular Localization with Integrated Source and Multi-label Ensemble Classifier
Authors: Guo Xiaotong , Liu Fulin , Ju Ying , Wang Zhen , Wang Chunyu 
Published: June 2016

AbstractPredicting protein subcellular location is necessary for understanding cell function. Several machine learning methods have been developed for computational prediction of primary protein sequences because wet experiments are costly and time consuming. However, two problems still exist in state-of-the-art methods. First, several proteins appear in different subcellular structures simultaneously, whereas current methods only predict one protein sequence in one subcellular structure. Second, most software tools are trained with obsolete data and the latest new databases are missed. We proposed a novel multi-label classification algorithm to solve the first problem and integrated several latest databases to improve prediction performance. Experiments proved the effectiveness of the proposed method. The present study would facilitate research on cellular proteomics.
Circulating miRNAs are generic and versatile therapeutic monitoring biomarkers in muscular dystrophies
Authors: Israeli David , Poupiot Jérôme , Amor Fatima , Charton Karine , Lostal William , Jeanson-Leh Laurence , Richard Isabelle 
Published: June 2016

AbstractThe development of medical approaches requires preclinical and clinical trials for assessment of therapeutic efficacy. Such evaluation entails the use of biomarkers, which provide information on the response to the therapeutic intervention. One newly-proposed class of biomarkers is the microRNA (miRNA) molecules. In muscular dystrophies (MD), the dysregulation of miRNAs was initially observed in muscle biopsy and later extended to plasma samples, suggesting that they may be of interest as biomarkers. First, we demonstrated that dystromiRs dysregulation occurs in MD with either preserved or disrupted expression of the dystrophin-associated glycoprotein complex, supporting the utilization of dystromiRs as generic biomarkers in MD. Then, we aimed at evaluation of the capacity of miRNAs as monitoring biomarkers for experimental therapeutic approach in MD. To this end, we took advantage of our previously characterized gene therapy approach in a mouse model for α-sarcoglycanopathy. We identified a dose-response correlation between the expression of miRNAs on both muscle tissue and blood serum and the therapeutic benefit as evaluated by a set of new and classically-used evaluation methods. This study supports the utility of profiling circulating miRNAs for the evaluation of therapeutic outcome in medical approaches for MD.