bluuebunny/crossref_metadata_2025 huggingface dataset:
Switch fault diagnosis and capacitor lifetime monitoring technique for DC–DC converters using a single sensor
Authors: Givi Hadi , Farjah Ebrahim , Ghanbari Teymoor
Published: February 2016

Owing to the key role of the power electronic converters in various applications, their reliability is an important issue. The electrolytic capacitor and the power switch are the most vulnerable components of the converters. On fault occurrence in these components, a suitable remedial strategy should be employed to prevent further damages. The first step in any remedial strategy is fault diagnosis including fault detection and identification. This study proposes a technique for switch fault diagnosis and capacitor lifetime monitoring in non‐isolated single‐switch DC–DC converters. The proposed cost‐effective method could be easily implemented using a printed circuit board Rogowski coil (PCBRC) on the capacitor terminals. The derivative of the capacitor current is captured by the PCBRC. The captured signal contains suitable signatures for detection of switch open‐circuit and short‐circuit faults. In addition to switch fault detection, lifetime of the converter capacitor is also monitored by the PCBRC via calculation of the capacitor equivalent series resistance. The proposed technique is implemented for a buck converter. The experimental results confirm the capability of the proposed technique for switch fault diagnosis and capacitor lifetime monitoring in non‐isolated single‐switch DC–DC converters.
Preliminary Report on the Safety and Efficacy of Staged versus Complete Revascularization in Patients with Multivessel Disease at the Time of Primary Percutaneous Coronary Intervention
Authors: Rashed Ahmed , El-kilany Wael , El-Haddad Mohamed , Elgendy Islam , Saad Marwan
Published: February 2016

This study aims to determine the safety and efficacy of complete versus staged-percutaneous coronary intervention (PCI) of nonculprit lesions at the time of primary PCI in patients with multivessel disease. Recent trials had suggested that revascularization of nonculprit lesions at the time of primary PCI is associated with better outcomes, however; the optimum timing and overall safety of this approach is not well known. An observational prospective study was conducted, including 50 patients who presented with ST-segment elevation myocardial infarction and found to have at least an additional nonculprit significant (> 70%) type A or B lesion. According to the operator's discretion, patients either underwent complete revascularization of nonculprit significant lesions during primary PCI procedure or within 60 days of primary PCI (staged-PCI). Safety outcomes evaluated were contrast-induced nephropathy (CIN), the amount of contrast used, and fluoroscopy time. Efficacy outcome assessed was major adverse events (MACE) at 1 year. The fluoroscopy time and amount of contrast used were increased in complete revascularization group (35.3 ± 9.6 vs. 26.3 ± 6.7 minutes, p < 0.001, and 219.5 ± 35.1 vs. 187.5 ± 45.5 mL, p = 0.01, respectively); while incidence of CIN remained similar (p = 0.73). The incidence of MACE at 1 year was similar in both groups (23% in the complete revascularization group vs. 25% in the staged-PCI group, p = 0.43). Complete revascularization and staged-PCI of nonculprit type A or B lesions at the time of primary PCI were associated with similar long-term outcomes and safety profile. Larger studies are needed to further validate these results.
Stabilization of Rayleigh–Taylor instability in the presence of viscosity and compressibility: A critical analysis
Authors: Mitra A. , Roychoudhury R. , Khan M.
Published: February 2016

The stabilization of the Rayleigh–Taylor instability growth rate due to the combined effect of viscosity and compressibility has been studied. A detailed explanation of the observed results has been made from theoretical point of view. The numerical results have been compared qualitatively with those of Plesset and Whipple [Phys. Fluids 17, 1 (1974)] and Bernstein and Book [Phys. Fluids 26, 453 (1983)].
The effect of radial inhomogeneity on the collisional power absorption in helicon plasma sources
Authors: Soltani B. , Habibi M. , Zakeri-khatir H.
Published: February 2016

The paper reports on the effects of plasma radial inhomogeneity on the power absorption in a helicon plasma source, which are computationally investigated by the CST Microwave Studio code. RF (13.56 MHz) power deposition was studied using three designs of antennas, namely, the Nagoya type-III, the fractional helix, and the single loop. Argon was used as the plasma working gas at the operating pressure of 15 mTorr. We have focused on the collisional power absorption utilizing WKB approximation to describe the plasma inhomogeneity. The obtained results show that the radial inhomogeneity has different effects on the power absorption at the low and the high magnetic fields. It is found that at low magnetic fields (i.e., B0=0.01 T), there is a specific density (nc) ranging from 5×1018 m−3  to 1×1019 m−3, before and after which the radial inhomogeneity decreases and increases the absorbed power, respectively. On the other hand, at high magnetic fields (i.e., B0=0.1 T), the inhomogeneity has no regular effect on the power absorption in various plasma densities. In addition, for a given plasma density (e.g., n=1018 m−3), as the magnetic field increases, the radial inhomogeneity effect on the power absorption would decrease for the Nagoya type-III and the fractional helix designs. However, for the single loop antenna design, this effect is negligible.
Enhanced sensitivity of the Z-scan technique on saturable absorbers using radially polarized beams
Authors: Liu Dahui , Gu Bing , Ren Boxiao , Lu Changgui , He Jun , Zhan Qiwen , Cui Yiping
Published: February 2016

We develop the Z-scan technique on a saturable absorber under the excitation of radially polarized beams. It is shown that the sensitivity of the Z-scan measurements on a saturable absorber using radially polarized beams has the great improvement compared with those using the scalar light beams such as Gaussian beams, Laguerre-Gaussian beams, and top-hat beams. As the experimental evidence, we investigate the saturable absorption properties of layered WS2 nanosheets in aqueous suspension by performing the radially polarized-beam Z-scan measurements with femtosecond laser pulses in the near infrared region.
Highly efficient and gentle trapping of single cells in large microfluidic arrays for time-lapse experiments
Authors: Yesilkoy F. , Ueno R. , Desbiolles B. X. E. , Grisi M. , Sakai Y. , Kim B. J. , Brugger J.
Published: February 2016

The isolation of single biological cells and their further cultivation in dedicated arrayed chambers are key to the collection of statistically reliable temporal data in cell-based biological experiments. In this work, we present a hydrodynamic single cell trapping and culturing platform that facilitates cell observation and experimentation using standard bio-lab equipment. The proposed design leverages the stochastic position of the cells as they flow into the structured microfluidic channels, where hundreds of single cells are then arrayed in nanoliter chambers for simultaneous cell specific data collection. Numerical simulation tools are used to devise and implement a hydrodynamic cell trapping mechanism that is minimally detrimental to the cell cycle and retains high overall trapping efficiency (∼70%) with the capability of reaching high fill factors (>90%) in short loading times (1–4 min) in a 400-trap device. A Monte Carlo model is developed using the design parameters to estimate the system trapping efficiencies, which show strong agreement with the experimentally acquired data. As proof of concept, arrayed mammalian tissue cells (MIA PaCa-2) are cultured in the microfluidic chambers for two days without viability problems.
Role of magnesium in ZnS structure: Experimental and theoretical investigation
Authors: Shahid M. Y. , Asghar M. , Arbi H. M. , Zafar M. , Ilyas S. Z.
Published: February 2016

Wide band gap semiconductor materials are extending significant applications in electronics and optoelectronics industry. They are showing continued advancement in ultraviolet to infrared LEDs and laser diodes. Likewise the band gap tunability of ZnS with intentional impurities such as Mg and Mn are found useful for optoelectronic devices. Information from literature indicates slight blue shift in the band gap energy of ZnS by Mg doping but nevertheless, we report a reasonable red shift (3.48 eV/356 nm to 2.58 eV/480 nm) in ZnS band gap energy in Mg-ZnS structure. Theoretical model based on first principle theory using local density approximation revealed consistent results on Mg-ZnS structure. Similarly, structural, morphological, optical and electrical properties of the as grown Mg-ZnS were studied by XRD, SEM, FTIR, EDS, UV-Vis Spectrophotometer and Hall measurement techniques.
Perpendicular magnetic anisotropy in CoxMn4−xN (x = 0 and 0.2) epitaxial films and possibility of tetragonal Mn4N phase
Authors: Ito Keita , Yasutomi Yoko , Kabara Kazuki , Gushi Toshiki , Higashikozono Soma , Toko Kaoru , Tsunoda Masakiyo , Suemasu Takashi
Published: February 2016

We grow 25-nm-thick Mn4N and Co0.2Mn3.8N epitaxial films on SrTiO3(001) by molecular beam epitaxy. These films show the tetragonal structure with a tetragonal axial ratio c/a of approximately 0.99. Their magnetic properties are measured at 300 K, and perpendicular magnetic anisotropy is confirmed in both films. There is a tendency that as the Co composition increases, an anisotropy field increases, whereas saturation magnetization and uniaxial magnetic anisotropy energy decrease. First-principles calculation predicts the existence of tetragonal Mn4N phase. This explains the c/a ∼ 0.99 in the Mn4N films regardless of their film thickness and lattice mismatch with substrates used.
Crystal structure and magnetism of the MnxGa (1.15 ≤x ≤ 2.0) rare-earth-free permanent magnet system
Authors: Rejali Rasa , Ryan D. H. , Altounian Z. , Boyer C.B. , Lu Qingmei , Wang Manli , Zhang Hongguo , Yue Ming
Published: February 2016

Room temperature neutron powder diffraction has been used to investigate the chemical structure and magnetic ordering of a series of tetragonal (I4/mmm #139) MnxGa (1.15 ≤ x ≤ 2.0) alloys. Initially (x < 1.5) the excess Mn goes on the 2b site with vacancies appearing at the 2a site. For x > 1.5 Mn also appears on the 2a site. The manganese atoms on the 4d site carry an almost constant moment of 2.16(6) μB/Mn. The loss of magnetisation seen with increasing Mn content is shown to be the result of large (∼3 μB/Mn), antiparallel Mn moments on the 2b, and later 2a sites, and not to a reduction of the Mn moment on the 4d sites.
Electrical resistivity anomaly in (Pr1−yMy)1−xCaxCoO3 epitaxial films (M=Y, Gd) fabricated by pulsed laser deposition
Authors: Noda Y. , Fujishiro H. , Naito T. , Ito A. , Goto T. , Hejtmanek J. , Jirak Z.
Published: February 2016

(Pr1−yMy)1−xCaxCoO3 epitaxial films (M=Y, Gd) have been successfully fabricated by pulsed laser deposition on the single crystal substrates with different lattice constant. The polycrystalline bulk of this material shows a first-order metal-insulator (MI) transition below the critical temperature. Although ρ(T) of all the as-grown films shows a semiconducting behavior at entire temperature range, an anomalous ρ(T) upturn with wide hysteresis can be clearly seen for the film grown on the SrLaAlO4 (SLAO) substrate, which applied the in-plane compressive stress to the film. Such anomaly in ρ(T) is interpreted as a sign of the first-order phase transition related with the spin-state (SS) transition, which was observed in the polycrystalline bulk.
Polyaniline-Supported Bacterial Biofilms as Active Matrices for Platinum Nanoparticles: Enhancement of Electroreduction of Carbon Dioxide
Authors: Seta Ewelina , Lotowska Weronika A. , Rutkowska Iwona A. , Wadas Anna , Raczkowska Adrianna , Nieckarz Marta , Brzostek Katarzyna , Kulesza Pawel J.
Published: February 2016

A hybrid matrix composed of a porous polyaniline underlayer, a robust bacterial biofilm and a multiwalled carbon nanotube overlayer has been demonstrated to function as highly active support for dispersed Pt catalytic nanoparticles during the electroreduction of carbon dioxide in neutral medium (phosphate buffer at pH 6.1). In contrast with bare Pt nanoparticles (deposited at a glassy carbon substrate), application of the hybrid system produces sizeable CO2-reduction currents in comparison to those originating from hydrogen evolution. The result is consistent with an enhancement in the reduction of carbon dioxide. However, the biofilm-based matrix tends to inhibit the catalytic properties of platinum towards proton discharge (competitive reaction) or even oxygen reduction. The hydrated structure permits easy unimpeded flow of aqueous electrolyte at the electrocatalytic interface. Although application of the polyaniline underlayer can be interpreted in terms of stabilization and improvement of the biofilm adherence, the use of carbon nanotubes facilitates electron transfer to Pt catalytic sites. It is apparent from the voltammetric stripping-type analytical experiments that, although formation of some methanol and methanoic acid cannot be excluded, carbon monoxide seems to be the main CO2-reduction product.
Assessing the xanthophyll cycle in natural beech leaves with hyperspectral reflectance
Authors: Sonobe Rei , Wang Quan
Published: February 2016

The xanthophyll cycle is critical for protecting the photosynthetic apparatus from light-induced oxidative stress. A clear view of the xanthophyll cycle is thus important for understanding abiotic stresses that are closely related to plant growth and reproduction. The epoxidation state (EPS) is well correlated with the photosynthetic radiation use efficiency, and is widely used for assessing the xanthophyll cycle. The hyperspectral index, photochemical reflectance index (PRI), has been claimed to be closely related with the EPS, and offers instantaneous information of photosynthetic activity: its applications are, however, largely limited to herbaceous and coniferous species, and few studies have ever focussed on both sunlit and shaded leaves of deciduous plants. In the present study, we examined the possibility of applying PRI for tracing the xanthophyll cycle in a typical deciduous species (Fagus crenata Blume) as well as other species in a cold-temperate mountainous area. This is based on a series of experiments with only light stress and other inhibited treatments. Furthermore, searching for new hyperspectral indices has also been attempted based on both original and first derivative spectra. Results revealed that PRI had low correlations with the EPS of deciduous leaves, especially for sunlit leaves. As a comparison, the newly identified dD677, 803, a differential type of index using reflectance derivatives at 677 and 803 nm, had a much better performance. The robustness of the newly identified index has been confirmed from both inhibitor-treatments and an additional dataset from other deciduous species. The proposed index is hence applicable for tracing the xanthophyll cycle in deciduous species.
Englishness in German translations of Alice in Wonderland
Authors: O’Sulliva Emer
Published: February 2016

In order to explain away the peculiarity of Alice in Wonderland to a German audience, peritexts in many translations construct nonsense, the author Dodgson/Carroll and the novel itself as particularly English phenomena. Examining forewords and afterwords and some German translations, especially two post-war translations from 1922 and 1949 with clear and distinctive Anglo-German cultural agendas, this article will reveal a central paradox: while Englishness is evoked in these peritexts so that the familiarity of the national tropes may supposedly serve to counterbalance the strangeness of the novel, the translations themselves may, in contrast, actually neutralise or domesticate this purported Englishness. Combining imagology and translation studies, this analysis reveals strangely hybrid translations which peritextually proclaim one thing but in practice do another.
Total Reduplication as a category of expressives
Authors: Kallergi Haritini
Published: February 2016

Total Reduplication (henceforth TR) of the type exemplified by Modern Greek aspros aspros ‘white white’ “very white” and vima vima ‘step step’ “step by step” has an expressive dimension, mainly in that it is an optional strategy and it almost always has pragmatic connotations and effects (e.g. making a narration more vivid) (see, e.g., Zwicky & Pullum 1987; Beard & Volpe 2005). This paper poses the question whether TR can be viewed as a category of constructions that exclusively serve as expressive markers in Modern Greek (MG). I discuss the arguments and counterarguments to the idea that TR in MG can be described as a process of “expressive morphosyntax”, in parallel to Zwicky & Pullum’s (1987) notion of “expressive morphology” (which mainly refers to processes such as play languages, ideophones, and schm-reduplication). I also refer to a wide range of criteria of expressivity (involving functional as well as formal characteristics of expressives) in the relevant literature. The discussion points to an incomplete overlap between typical categories of expressives and TR. It also clarifies the senses in which TR is “expressive” and touches on issues of the status of TR in the grammar.
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

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

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

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

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

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

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

Objectives:

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

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

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.
Requirements for the formal representation of pathophysiology mechanisms by clinicians
Authors: de Bono B. , Helvensteijn M. , Kokash N. , Martorelli I. , Sarwar D. , Islam S. , Grenon P. , Hunter P.
Published: February 2016

Knowledge of multiscale mechanisms in pathophysiology is the bedrock of clinical practice. If quantitative methods, predicting patient-specific behaviour of these pathophysiology mechanisms, are to be brought to bear on clinical decision-making, the Human Physiome community and Clinical community must share a common computational blueprint for pathophysiology mechanisms. A number of obstacles stand in the way of this sharing—not least the technical and operational challenges that must be overcome to ensure that (i) the explicit biological meanings of the Physiome's quantitative methods to represent mechanisms are open to articulation, verification and study by clinicians, and that (ii) clinicians are given the tools and training to explicitly express disease manifestations in direct contribution to modelling. To this end, the Physiome and Clinical communities must co-develop a common computational toolkit, based on this blueprint, to bridge the representation of knowledge of pathophysiology mechanisms (a) that is implicitly depicted in electronic health records and the literature, with (b) that found in mathematical models explicitly describing mechanisms. In particular, this paper makes use of a step-wise description of a specific disease mechanism as a means to elicit the requirements of representing pathophysiological meaning explicitly. The computational blueprint developed from these requirements addresses the Clinical community goals to (i) organize and manage healthcare resources in terms of relevant disease-related knowledge of mechanisms and (ii) train the next generation of physicians in the application of quantitative methods relevant to their research and practice.
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable
Authors: Nickerson David , Atalag Koray , de Bono Bernard , Geiger Jörg , Goble Carole , Hollmann Susanne , Lonien Joachim , Müller Wolfgang , Regierer Babette , Stanford Natalie J. , Golebiewski Martin , Hunter Peter
Published: February 2016

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome.
Moramonas marocensis
gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome
Authors: Strassert Jürgen F. H. , Tikhonenkov Denis V. , Pombert Jean-François , Kolisko Martin , Tai Vera , Mylnikov Alexander P. , Keeling Patrick J.
Published: February 2016

A new jakobid genus has been isolated from Moroccan desert soil. The cyst-forming protist
Moramonas marocensis
gen. nov., sp. nov. has two anteriorly inserted flagella of which one points to the posterior cell pole accompanying the ventral feeding groove and is equipped with a dorsal vane—a feature typical for the Jakobida. It further shows a flagellar root system consisting of singlet microtubular root, left root (R1), right root (R2) and typical fibres associated with R1 and R2. The affiliation of
M. marocensis
to the Jakobida was confirmed by molecular phylogenetic analyses of the SSU rRNA gene, five nuclear genes and 66 mitochondrial protein-coding genes. The mitochondrial genome has the high number of genes typical for jakobids, and bacterial features, such as the four-subunit RNA polymerase and Shine–Dalgarno sequences upstream of the coding regions of several genes. The
M. marocensis
mitochondrial genome encodes a similar number of genes as other jakobids, but is unique in its very large genome size (greater than 264 kbp), which is three to four times higher than that of any other jakobid species investigated yet. This increase seems to be due to a massive expansion in non-coding DNA, creating a bloated genome like those of plant mitochondria.
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

Patient 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 ABSTRACT

HIGHLIGHTS

Denoising 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

Current 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

Recent 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 Summary

Autism, schizophrenia, and bipolar disorder share global gene expression patterns, characterized by astrocyte activation and disrupted synaptic processes.
Working with Zika and Usutu Viruses in Vitro
Authors: Barr Kelli L. , Anderson Benjamin D. , Long Maureen T.
Published: February 2016

Usutu and Zika viruses are emerging arboviruses of significant medical and veterinary importance. These viruses have not been studied as well as other medically important arboviruses such as West Nile, dengue, or chikungunya viruses. As such, information regarding the behavior of Zika and Usutu viruses in the laboratory is dated. Usutu virus re-emerged in Austria in 2001 and has since spread throughout the European and Asian continents causing significant mortality among birds. Zika virus has recently appeared in the Americas and has exhibited unique characteristics of pathogenesis, including birth defects, and transmission. Information about the characteristics of Usutu and Zika viruses are needed to better understand the transmission, dispersal, and adaptation of these viruses in new environments. Since their initial characterization in the middle of last century, technologies and reagents have been developed that could enhance our abilities to study these pathogens. Currently, standard laboratory methods for these viruses are limited to 2-3 cell lines and many assays take several days to generate meaningful data. The goal of this study was to characterize these viruses in cell culture to provide some basic parameters to further their study. Cell lines from 17 species were permissive to both Zika and Usutu viruses. These viruses were able to replicate to significant titers in most of the cell lines tested. Moreover, cytopathic effects were observed in 8 of the cell lines tested. The data show that, unlike other flaviviruses, neither Zika nor Usutu viruses require an acidic environment to fuse with a host cell. This may provide a tool to help characterize events or components in the flavivirus fusion process. These data indicate that a variety of cell lines can be used to study Zika and Usutu viruses and may provide an updated foundation for the study of host-pathogen interactions, model development, and the development of therapeutics.

Author Summary

Usutu and Zika viruses are arboviruses of identified in significant medical and veterinary outbreaks in recent years. Currently, standard laboratory methods for these viruses are limited to 2-3 cell lines and basic viral characterization has not been performed since the mid-20thcentury. Zika and Usutu viruses were characterized in cell culture. The data show that a variety of cell lines can be used to study the viruses. Neither Zika nor Usutu viruses require an acidic environment for host cell infection.
Non-homologous DNA increases gene disruption efficiency by altering DNA repair outcomes
Authors: Richardson CD , Ray GJ , Corn JE
Published: February 2016

Cas9 endonuclease can be targeted to genomic sequences by varying the sequence of the single guide RNA (sgRNA). The activity of these Cas9-sgRNA combinations varies widely at different genomic loci and in different cell types. Thus, disrupting genes in polyploid cell lines, or using inefficient sgRNAs, can require extensive downstream screening to identify homozygous clones. We have found that linear, non-homologous oligonucleotide DNA greatly stimulates Cas9-mediated gene disruption in the absence of homology-directed repair. This stimulation greatly increases the frequency of clones with homozygous gene disruptions, even in polyploid cell lines, and rescues otherwise ineffective sgRNAs. The mechanism of enhanced gene disruption differs between human cell lines, stimulating deletion of genomic sequence and/or insertion of non-homologous oligonucleotide DNA at the edited locus in a cell line specific manner. Thus, the addition of non-homologous DNA appears to drive cells towards error-prone instead of error-free repair pathways, dramatically increasing the frequency of gene disruption.
Crystallization and X-ray diffraction analysis of the CH domain of the cotton kinesin GhKCH2
Authors: Qin Xinghua , Chen Ziwei , Li Ping , Liu Guoqin
Published: February 2016

GhKCH2 belongs to a group of plant-specific kinesins (KCHs) containing an actin-binding calponin homology (CH) domain in the N-terminus. Previous studies revealed that the GhKCH2 CH domain (GhKCH2-CH) had a higher affinity for F-actin (Kd= 0.42 ± 0.02 µM) than most other CH-domain-containing proteins. To understand the underlying mechanism, prokaryotically expressed GhKCH2-CH (amino acids 30–166) was purified and crystallized. Crystals were grown by the sitting-drop vapour-diffusion method using 0.1 MTris–HCl pH 7.0, 20%(w/v) PEG 8000 as a precipitant. The crystals diffracted to a resolution of 2.5 Å and belonged to space groupP21, with unit-cell parametersa= 41.57,b= 81.92,c= 83.00 Å, α = 90.00, β = 97.31, γ = 90.00°. Four molecules were found in the asymmetric unit with a Matthews coefficient of 2.22 Å3 Da−1, corresponding to a solvent content of 44.8%.
Crystal structure of recombinant tyrosinase-binding protein MtaL at 1.35 Å resolution
Authors: Lai Xuelei , Soler-Lopez Montserrat , Ismaya Wangsa T. , Wichers Harry J. , Dijkstra Bauke W.
Published: February 2016

Mushroom tyrosinase-associated lectin-like protein (MtaL) binds to matureAgaricus bisporustyrosinasein vivo, but the exact physiological function of MtaL is unknown. In this study, the crystal structure of recombinant MtaL is reported at 1.35 Å resolution. Comparison of its structure with that of the truncated and cleaved MtaL present in the complex with tyrosinase directly isolated from mushroom shows that the general β-trefoil fold is conserved. However, differences are detected in the loop regions, particularly in the β2–β3 loop, which is intact and not cleaved in the recombinant MtaL. Furthermore, the N-terminal tail is rotated inwards, covering the tyrosinase-binding interface. Thus, MtaL must undergo conformational changes in order to bind mature mushroom tyrosinase. Very interestingly, the β-trefoil fold has been identified to be essential for carbohydrate interaction in other lectin-like proteins. Comparison of the structures of MtaL and a ricin-B-like lectin with a bound disaccharide shows that MtaL may have a similar carbohydrate-binding site that might be involved in glycoreceptor activity.