bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation of the TGFβ pathway impairs endothelial to haematopoietic transition
Authors: Vargel Özge , Zhang Yang , Kosim Kinga , Ganter Kerstin , Foehr Sophia , Mardenborough Yannicka , Shvartsman Maya , Enright Anton J. , Krijgsveld Jeroen , Lancrin Christophe 
Published: February 2016

AbstractThe endothelial to haematopoietic transition (EHT) is a key developmental process where a drastic change of endothelial cell morphology leads to the formation of blood stem and progenitor cells during embryogenesis. As TGFβ signalling triggers a similar event during embryonic development called epithelial to mesenchymal transition (EMT), we hypothesised that TGFβ activity could play a similar role in EHT as well. We used the mouse embryonic stem cell differentiation system for in vitro recapitulation of EHT and performed gain and loss of function analyses of the TGFβ pathway. Quantitative proteomics analysis showed that TGFβ treatment during EHT increased the secretion of several proteins linked to the vascular lineage. Live cell imaging showed that TGFβ blocked the formation of round blood cells. Using gene expression profiling we demonstrated that the TGFβ signalling activation decreased haematopoietic genes expression and increased the transcription of endothelial and extracellular matrix genes as well as EMT markers. Finally we found that the expression of the transcription factor Sox17 was up-regulated upon TGFβ signalling activation and showed that its overexpression was enough to block blood cell formation. In conclusion we showed that triggering the TGFβ pathway does not enhance EHT as we hypothesised but instead impairs it.
The nature of hydrogen-bonding interaction in the prototypic hybrid halide perovskite, tetragonal CH3NH3PbI3
Authors: Lee June Ho , Lee Jung-Hoon , Kong Eui-Hyun , Jang Hyun Myung 
Published: February 2016

AbstractIn spite of the key role of hydrogen bonding in the structural stabilization of the prototypic hybrid halide perovskite, CH3NH3PbI3(MAPbI3), little progress has been made in our in-depth understanding of the hydrogen-bonding interaction between the MA+-ion and the iodide ions in the PbI6-octahedron network. Herein, we show that there exist two distinct types of the hydrogen-bonding interaction, namingα- andβ-modes, in the tetragonal MAPbI3on the basis of symmetry argument and density-functional theory calculations. The computed Kohn-Sham (K-S) energy difference between these two interaction modes is 45.14 meV per MA-site with theα-interaction mode being responsible for the stable hydrogen-bonding network. The computed bandgap (Eg) is also affected by the hydrogen-bonding mode, withEgof theα-interaction mode (1.73 eV) being significantly narrower than that of theβ-interaction mode (2.03 eV). We have further estimated the individual bonding strength for the ten relevant hydrogen bonds having a bond critical point.
Relation between detection rate and inappropriate shocks in single versus dual chamber cardioverter-defibrillator – an analysis from the OPTION trial
Authors: Kolb Christof , Sturmer Marcio , Babuty Dominique , Sick Peter , Davy Jean Marc , Molon Giulio , Schwab Jörg Otto , Mantovani Giuseppe , Wickliffe Andrew , Lennerz Carsten , Semmler Verena , Siot Pierre-Henri , Reif Sebastian 
Published: February 2016

AbstractThe programming of implantable cardioverter-defibrillators (ICDs) influences inappropriate shock rates. The aim of the study is to analyse rates of patients with appropriate and inappropriate shocks according to detection zones in the OPTION trial. All patients received dual chamber (DC) ICDs randomly assigned to be programmed either to single chamber (SC) or to DC settings including PARAD+ algorithm. In a post-hoc analysis, rates of patients with inappropriate and appropriate shocks were calculated for shocks triggered at heart rates ≥170 bpm (ventricular tachycardia zone) and at rates ≥200 bpm (ventricular fibrillation zone). In the SC group, higher rates of patients with total and inappropriate shocks were delivered at heart rates ≥170 bpm than at rates ≥200 bpm (total shocks: 21.1% vs. 16.6%; p = 0.002; inappropriate shocks: 7.6% vs. 4.5%, p = 0.016; appropriate shocks: 15.2% vs. 13.5%; p = n.s.). No such differences were observed in the DC group (total shocks: 14.3% vs. 12.6%; p = n.s.; inappropriate shocks: 3.9% vs. 3.6%; p = n.s.; appropriate shocks: 12.2% vs. 10.4%; p = n.s.). The higher frequency of patients with total shocks with SC settings than with DC settings that benefit from PARAD+ was driven by a higher percentage of patients with inappropriate shocks in the VT zone (170–200 bpm) in the SC population.
Surface damage and structure evolution of recrystallized tungsten exposed to ELM-like transient loads
Authors: Yuan Y. , Du J. , Wirtz M. , Luo G.-N. , Lu G.-H. , Liu W. 
Published: February 2016

Abstract
Surface damage and structure evolution of the full tungsten ITER divertor under transient heat loads is a key concern for component lifetime and plasma operations. Recrystallization caused by transients and steady-state heat loads can lead to degradation of the material properties and is therefore one of the most serious issues for tungsten armor. In order to investigate the thermal response of the recrystallized tungsten under edge localized mode-like transient thermal loads, fully recrystallized tungsten samples with different average grain sizes are exposed to cyclic thermal shocks in the electron beam facility JUDITH 1. The results indicate that not only does the microstructure change due to recrystallization, but that the surface residual stress induced by mechanical polishing strongly influences the surface cracking behavior. The stress-free surface prepared by electro-polishing is shown to be more resistant to cracking than the mechanically polished one. The resulting surface roughness depends largely on the loading conditions instead of the recrystallized-grain size. As the base temperature increases from room temperature to 400 °C, surface roughening mainly due to the shear bands in each grain becomes more pronounced, and sub-grains (up to 3 μm) are simultaneously formed in the sub-surface. The directions of the shear bands exhibit strong grain-orientation dependence, and they are generally aligned with the traces of {1 1 2} twin habit planes. The results suggest that twinning deformation and dynamic recrystallization represent the predominant mechanism for surface roughening and related microstructure evolution.
Optimization of ICRH for core impurity control in JET-ILW
Authors: Lerche E. , Goniche M. , Jacquet P. , Van Eester D. , Bobkov V. , Colas L. , Giroud C. , Monakhov I. , Casson F.J. , Rimini F. , Angioni C. , Baruzzo M. , Blackman T. , Brezinsek S. , Brix M. , Czarnecka A. , Crombé K. , Challis C. , Dumont R. , Eriksson J. , Fedorczak N. , Graham M. , Graves J.P. , Gorini G. , Hobirk J. , Joffrin E. , Johnson T. , Kazakov Y. , Kiptily V. , Krivska A. , Lennholm M. , Lomas P. , Maggi C. , Mantica P. , Mathews G. , Mayoral M.-L. , Meneses L. , Mlynar J. , Monier-Garbet P. , Nave M.F. , Noble C. , Nocente M. , Nunes I. , Ongena J. , Petravich G. , Petrzilka V. , Pütterich T. , Reich M. , Santala M. , Solano E.R. , Shaw A. , Sips G. , Stamp M. , Tardocchi M. , Tsalas M. , Valisa M. 
Published: February 2016

Abstract
Ion cyclotron resonance frequency (ICRF) heating has been an essential component in the development of high power H-mode scenarios in the Jet European Torus ITER-like wall (JET-ILW). The ICRF performance was improved by enhancing the antenna-plasma coupling with dedicated main chamber gas injection, including the preliminary minimization of RF-induced plasma-wall interactions, while the RF heating scenarios where optimized for core impurity screening in terms of the ion cyclotron resonance position and the minority hydrogen concentration. The impact of ICRF heating on core impurity content in a variety of 2.5 MA JET-ILW H-mode plasmas will be presented, and the steps that were taken for optimizing ICRF heating in these experiments will be reviewed.
Non-resonant fishbone-like modes in tokamak plasmas with reversed magnetic shear
Authors: Wang Xian-Qu , Wang Xiao-Gang 
Published: February 2016

Abstract
Energetic ion excited non-resonant fishbone-like modes (FLMs) of m / n  >  1 is investigated for reversed magnetic shear configurations. It is found that the mode can be destabilized by trapped fast ions with a similar excitation mechanism as m / n  =  1 fishbones but with a local interchange-like mode structure, which is in agreement with previous experiments (Toi et al 1999 Nucl. Fusion
39 1929). The dispersion relation of the mode is derived for m / n  >  1. The radial mode structure is then studied by numerically solving the eigenvalue equation. Effects of on/off-axis heating, the width of the particle distribution, the beam energy and the energy distribution on the mode are discussed in detail. Nonlinear analysis of the mode is also carried out by a modified predator–prey model.
Applying high-performance computing in drug discovery and molecular simulation
Authors: Liu Tingting , Lu Dong , Zhang Hao , Zheng Mingyue , Yang Huaiyu , Xu Yechun , Luo Cheng , Zhu Weiliang , Yu Kunqian , Jiang Hualiang 
Published: February 2016

Abstract
In recent decades, high-performance computing (HPC) technologies and supercomputers in China have significantly advanced, resulting in remarkable achievements. Computational drug discovery and design, which is based on HPC and combines pharmaceutical chemistry and computational biology, has become a critical approach in drug research and development and is financially supported by the Chinese government. This approach has yielded a series of new algorithms in drug design, as well as new software and databases. This review mainly focuses on the application of HPC to the fields of drug discovery and molecular simulation at the Chinese Academy of Sciences, including virtual drug screening, molecular dynamics simulation, and protein folding. In addition, the potential future application of HPC in precision medicine is briefly discussed.
Correlation Between UpToDate Searches and Reported Cases of Middle East Respiratory Syndrome During Outbreaks in Saudi Arabia
Authors: Thorner Anna R. , Cao Bin , Jiang Terrence , Warner Amy J. , Bonis Peter A. 
Published: February 2016

Abstract
Background.  UpToDate is an online clinical decision support resource that is used extensively by clinicians around the world. Digital surveillance techniques have shown promise to aid with the detection and monitoring of infectious disease outbreaks. We sought to determine whether UpToDate searches for Middle East respiratory syndrome (MERS) could be used to detect and monitor MERS outbreaks in Saudi Arabia.
Methods.  We analyzed daily searches related to MERS in Jeddah and Riyadh, Saudi Arabia during 3 outbreaks in these cities in 2014 and 2015 and compared them with reported cases during the same periods. We also compared UpToDate MERS searches in the affected cities to those in a composite of 4 negative control cities for the 2 outbreaks in 2014.
Results.  UpToDate MERS searches during all 3 MERS outbreaks in Saudi Arabia showed a correlation to reported cases. In addition, UpToDate MERS search volume in Jeddah and Riyadh during the outbreak periods in 2014 was significantly higher than the concurrent search volume in the 4 negative control cities. In contrast, during the baseline periods, there was no difference between UpToDate searches for MERS in the affected cities compared with the negative control cities.
Conclusions.  UpToDate search activity seems to be useful for detecting and monitoring outbreaks of MERS in Saudi Arabia.
Percutaneous Lumbopelvic Fixation for Reduction and Stabilization of Sacral Fractures With Spinopelvic Dissociation Patterns
Authors: Williams Seth K. , Quinnan Stephen M. 
Published: February 2016

Summary:
Sacral fractures that result in spinopelvic dissociation are unstable injuries that are often treated surgically, with iliosacral screw fixation and/or lumbopelvic fixation from L4 to the pelvis. Open lumbopelvic fixation allows for direct fracture reduction and immediate postoperative weight bearing, but is associated with a relatively high wound complication rate. Open surgery often takes several hours and can be associated with significant blood loss, and therefore may not be well tolerated physiologically in these patients who often have multiple injuries. We developed a percutaneous lumbopelvic reduction and fixation technique to address these issues.
Hepatoblastoma in Explanted Livers of Patients With Biliary Atresia
Authors: Amir Achiya Z. , Sharma Ajay , Cutz Ernest , Avitzur Yaron , Shaikh Furqan , Kamath Binita M. , Ling Simon C. , Ghanekar Anand , Ng Vicky L. 
Published: February 2016

ABSTRACTObjectives:Surveillance of hepatic nodules for malignant transformation to hepatocellular carcinoma is important in the monitoring of patients with biliary atresia (BA). To date, only 2 published case reports describe the finding of hepatoblastoma (HB) in this setting. The present study aimed to investigate this association of HB and BA, and to assess the utility of alpha‐fetoprotein (aFP) as a marker in the diagnosis.Methods:A retrospective study of all patients who underwent isolated liver transplantation (LTx) for the primary diagnosis of BA at a single center, between January 1999 and June 2014, was conducted. Patient demographics, pre‐LTx aFP levels, and histologic examination of native liver explants were reviewed.Results:One hundred two (44% men, median age 11 months) patients underwent LTx for BA. Two (2%) explants examinations were confirmatory for concomitant HB; both patients had abnormally elevated aFP. Overall, 56 (55%) patients had available pre‐LTx aFP levels. Recipients with persistently abnormal aFP levels (n = 20, 36%) were older at hepatoportoenterostomy (107 vs 68 days, P = 0.02) and younger at LTx surgery (359 vs 1713 days, P < 0.01), compared to patients with constantly normal levels (n = 24, 43%).Conclusions:In our cohort, HB was found to coexist in approximately 2% of patients with BA undergoing LTx, far exceeding the hypothetical anticipated incidence of 1:10 billion for the concomitant diagnoses. Elevated serum aFP levels may be sensitive but not specific for HB in this context. Further research is required to identify specific mechanisms and risk factors.
Religion as a Risk Factor for Suicide Attempt and Suicide Ideation Among Depressed Patients
Authors: Lawrence Ryan E. , Brent David , Mann J. John , Burke Ainsley K. , Grunebaum Michael F. , Galfalvy Hanga C. , Oquendo Maria A. 
Published: February 2016

Abstract
We aimed to examine the relationship between religion and suicide attempt and ideation. Three hundred twenty-one depressed patients were recruited from mood-disorder research studies at the New York State Psychiatric Institute. Participants were interviewed using the Structured Clinical Interview for DSM Disorders, Columbia University Suicide History form, Scale for Suicide Ideation, and Reasons for Living Inventory. Participants were asked about their religious affiliation, importance of religion, and religious service attendance. We found that past suicide attempts were more common among depressed patients with a religious affiliation (odds ratio, 2.25; p = 0.007). Suicide ideation was greater among depressed patients who considered religion more important (coefficient, 1.18; p = 0.026) and those who attended services more frequently (coefficient, 1.99; p = 0.001). We conclude that the relationship between religion and suicide risk factors is complex and can vary among different patient populations. Physicians should seek deeper understanding of the role of religion in an individual patient’s life in order to understand the person’s suicide risk factors more fully.
Mortality After Bereavement: The Role of Cardiovascular Disease and Depression
Authors: Stahl Sarah T. , Arnold Alice M. , Chen Jia-Yuh , Anderson Stewart , Schulz Richard 
Published: February 2016

ABSTRACT

Objectives
Late-life bereavement is associated with an increased risk of mortality. This study assesses the associations among bereavement, cardiovascular disease (CVD), and depressive symptoms on mortality in older men and women.

Methods
We examined data from the Cardiovascular Health Study, a prospective population-based cohort study of older adults. We compared mortality in those who became bereaved from 1989 to 1999 (n = 593) to an age- and sex-matched sample of individuals who remained married (n = 593). Cox regression was used to examine the association between bereavement and 3-year all-cause mortality and whether or not the association differed by sex, presence of CVD, or postbereavement depressive symptoms.

Results
One hundred ninety-nine (16.8%) individuals died. There was no association of bereavement with mortality (hazard ratio [HR] = 0.98 [0.74–1.30]). However, there were significant interaction effects of bereavement with participant sex (p < .001) and CVD (p = .010). Bereavement decreased the risk of mortality in women (HR = 0.67 [0.46–0.97]) and increased the risk of mortality in men (HR = 1.77 [1.14–2.75]). Within sex, the association of bereavement with mortality differed according to CVD status. The reduced risk of mortality associated with bereavement in women was only observed in women with CVD, and the increased risk in men was only observed in men without CVD. High levels of depressive symptoms attenuated the relation between bereavement and mortality in men without CVD.

Conclusions
The relation between bereavement and mortality was different in men and women and varied by CVD status. Bereavement decreased mortality in women with CVD and increased mortality in men without CVD.
Initial Results of a Single-Source Dual-Energy Computed Tomography Technique Using a Split-Filter
Authors: Euler André , Parakh Anushri , Falkowski Anna L. , Manneck Sebastian , Dashti David , Krauss Bernhard , Szucs-Farkas Zsolt , Schindera Sebastian T. 
Published: February 2016

Objective
The aim of this study was to investigate the image quality, radiation dose, and accuracy of virtual noncontrast images and iodine quantification of split-filter dual-energy computed tomography (CT) using a single x-ray source in a phantom and patient study.

Materials and Methods
In a phantom study, objective image quality and accuracy of iodine quantification were evaluated for the split-filter dual-energy mode using a tin and gold filter. In a patient study, objective image quality and radiation dose were compared in thoracoabdominal CT of 50 patients between the standard single-energy and split-filter dual-energy mode. The radiation dose was estimated by size-specific dose estimate. To evaluate the accuracy of virtual noncontrast imaging, attenuation measurements in the liver, spleen, and muscle were compared between a true noncontrast premonitoring scan and the virtual noncontrast images of the dual-energy scans. Descriptive statistics and the Mann-Whitney U test were used.

Results
In the phantom study, differences between the real and measured iodine concentration ranged from 2.2% to 21.4%. In the patient study, the single-energy and dual-energy protocols resulted in similar image noise (7.4 vs 7.1 HU, respectively; P = 0.43) and parenchymal contrast-to-noise ratio (CNR) values for the liver (29.2 vs 28.5, respectively; P = 0.88). However, the vascular CNR value for the single-energy protocol was significantly higher than for the dual-energy protocol (10.0 vs 7.1, respectively; P = 0.006). The difference in the measured attenuation between the true and the virtual noncontrast images ranged from 3.1 to 6.7 HU. The size-specific dose estimate of the dual-energy protocol was, on average, 17% lower than that of the single-energy protocol (11.7 vs 9.7 mGy, respectively; P = 0.008).

Conclusions
Split-filter dual-energy compared with single-energy CT results in similar objective image noise in addition to dual-energy capabilities at 17% lower radiation dose. Because of beam hardening, split-filter dual-energy can lead to decreased CNR values of iodinated structures.
Semi-Supervised Learning of the Electronic Health Record for Phenotype Stratification
Authors: Beaulieu-Jones Brett K. , Greene Casey S. ,   the Pooled Resource Open-Access ALS Clinical Trials Consortium
Published: February 2016

AbstractPatient interactions with health care providers result in entries to electronic health records (EHRs). EHRs were built for clinical and billing purposes but contain many data points about an individual. Mining these records provides opportunities to extract electronic phenotypes, which can be paired with genetic data to identify genes underlying common human diseases. This task remains challenging: high quality phenotyping is costly and requires physician review; many fields in the records are sparsely filled; and our definitions of diseases are continuing to improve over time. Here we develop and evaluate a semi-supervised learning method for EHR phenotype extraction using denoising autoencoders for phenotype stratification. By combining denoising autoencoders with random forests we find classification improvements across multiple simulation models and improved survival prediction in ALS clinical trial data. This is particularly evident in cases where only a small number of patients have high quality phenotypes, a common scenario in EHR-based research. Denoising autoencoders perform dimensionality reduction enabling visualization and clustering for the discovery of new subtypes of disease. This method represents a promising approach to clarify disease subtypes and improve genotype-phenotype association studies that leverage EHRs.GRAPHICAL ABSTRACTHIGHLIGHTSDenoising autoencoders (DAs) can model electronic health records.Semi-supervised learning with DAs improves ALS patient survival predictions.DAs improve patient cluster visualization through dimensionality reduction.
A Central Limit Theorem for Punctuated Equilibrium
Authors: Bartoszek K. 
Published: February 2016

AbstractCurrent evolutionary biology models usually assume that a phenotype undergoes gradual change. This is in stark contrast to biological intuition, which indicates that change can also be punctuated-the phenotype can jump. Such a jump can especially occur at speciation, i.e. dramatic change occurs that drives the species apart. Here we derive a Central Limit Theorem for punctuated equilibrium. We show that, if adaptation is fast, for weak convergence to hold, dramatic change has to be a rare event.AMS subject classification: 60F05, 60J70, 60J85, 62P10, 92B99
Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap
Authors: Gandal Michael J. , Haney Jillian R. , Parikshak Neelroop N. , Leppa Virpi , Horvath Steve , Daniel Geschwind H. 
Published: February 2016

AbstractRecent large-scale studies have identified multiple genetic risk factors for mental illness and indicate a complex, polygenic, and pleiotropic genetic architecture for neuropsychiatric disease. However, little is known about how genetic variants yield brain dysfunction or pathology. We use transcriptomic profiling as an unbiased, quantitative readout of molecular phenotypes across 5 major psychiatric disorders, including autism (ASD), schizophrenia (SCZ), bipolar disorder (BD), depression (MDD), and alcoholism (AAD), compared with carefully matched controls. We identify a clear pattern of shared and distinct gene-expression perturbations across these conditions, identifying neuronal gene co-expression modules downregulated across ASD, SCZ, and BD, and astrocyte related modules most prominently upregulated in ASD and SCZ. Remarkably, the degree of sharing of transcriptional dysregulation was strongly related to polygenic (SNP-based) overlap across disorders, indicating a significant genetic component. These findings provide a systems-level view of the neurobiological architecture of major neuropsychiatric illness and demonstrate pathways of molecular convergence and specificity.One Sentence SummaryAutism, schizophrenia, and bipolar disorder share global gene expression patterns, characterized by astrocyte activation and disrupted synaptic processes.