bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of an alpha1A/D‐adrenoceptor antagonist, naftopidil, and a phosphodiesterase type 5 inhibitor, tadalafil, on urinary bladder remodeling in rats with spinal cord injury
Authors: Kadekawa Katsumi , Majima Tsuyoshi , Kawamorita Naoki , Okada Hiroki , Yoshizawa Tsuyoshi , Mori Kenichi , Tyagi Pradeep , Sugaya Kimio , Yoshimura Naoki 
Published: October 2016

AimsIn order to clarify whether an alpha1A/D‐adrenoceptor (α1A/D‐AR) antagonist, naftopidil, or a phosphodiesterase type 5 (PDE5) inhibitor, tadalafil, prevents bladder wall remodeling after spinal cord injury (SCI), we examined the bladder and urethral activity as well as ischemic and fibrotic changes in the bladder using SCI rats with or without naftopidil or tadalafil treatment.MethodsAdult female Sprague‐Dawley rats were divided into four groups: (1) normal (spinal cord intact); (2) vehicle SCI; (3) naftopidil SCI; and (4) tadalafil SCI groups. In SCI groups, rats underwent Th9‐10 spinal cord transection followed by oral application of vehicle, naftopidil (20 mg/kg/day) or tadalafil (2 mg/kg/day) for 1, 2, 4, 8, and 12 weeks. Bladder and urethral pressures, mRNA levels of fibrosis‐related molecules and ischemia markers and the composition of bladder collagen and elastin were evaluated.ResultsNaftopidil treatment reduced the upregulation of mRNA levels of ischemia and fibrosis markers at the early phase of SCI, and ameliorated the decrease of bladder compliance and voiding efficiency, and the increase of urethral pressure and collagen concentration in the bladder wall at the late phase of SCI. Tadalafil treatment reduced the upregulation of mRNA levels of fibrosis markers, the decrease of bladder compliance and the increase of collagen concentration at the late phase of SCI.ConclusionsThese results suggest that naftopidil and tadalafil treatments improved the bladder remodeling shown by increased bladder collagen contents after SCI in a different time course. Thus, these treatments could be effective for reducing the SCI‐related tissue remodeling in the bladder. Neurourol. Urodynam. 9999:XX–XX, 2016. © 2016 Wiley Periodicals, Inc.
Free‐slip boundary conditions for simulating free‐surface incompressible flows through the particle finite element method
Authors: Cerquaglia Marco Lucio , Deliége Geoffrey , Boman Romain , Terrapon Vincent , Ponthot Jean‐Philippe 
Published: October 2016

SummaryThe possibility of using free‐slip conditions within the context of the particle finite element method (PFEM) is investigated. For high Reynolds number engineering applications in which tangential effects at the fluid–solid boundaries are not of primary interest, the use of free‐slip conditions can alleviate the need for very fine boundary layer meshes. Two novel ways for the imposition of free‐slip conditions in the framework of the PFEM are presented. The proposed approach emphasizes robustness and simplicity, while retaining a sufficient level of generality. These two methods are then tested in the case of dam break and sloshing problems, and their respective advantages and drawbacks are discussed. It is also shown how the use of free‐slip conditions can indirectly improve mass conservation properties of the PFEM, even when coarse meshes are employed. Copyright © 2016 John Wiley & Sons, Ltd.
Oncostatin m impairs brown adipose tissue thermogenic function and the browning of subcutaneous white adipose tissue
Authors: Sánchez‐Infantes David , Cereijo Rubén , Peyrou Marion , Piquer‐Garcia Irene , Stephens Jacqueline M. , Villarroya Francesc 
Published: October 2016

ObjectiveSince oncostatin m (OSM) is elevated in adipose tissue in conditions of obesity and type 2 diabetes in mice and humans, the aim of this study was to determine whether this cytokine plays a crucial role in the impairment of brown adipose tissue (BAT) activity and browning capacity that has been observed in people with obesity.MethodsC57BL/6J mice rendered obese by high‐fat diet, their lean controls, and C57BL/6J mice fed a standard diet and implanted subcutaneously with a mini pump through a surgical procedure to deliver OSM or placebo were used. Preadipocytes or fully differentiated brown adipocytes were treated with OSM or vehicle with or without norepinephrine before harvesting. RNA was extracted and processed for qPCR analysis. Media from mature adipocytes was also collected to measure glycerol levels.ResultsStudies demonstrated that OSM gene expression was increased in BAT of mice fed a high‐fat diet. In addition, exogenous OSM impaired BAT activity and the browning capacity of white adipose tissue in vitro and in vivo.ConclusionsOverall, the results reveal a negative role for OSM on BAT and on the browning of white adipose tissue. Therefore, further studies are necessary to demonstrate whether OSM inhibition is a potential treatment for metabolic disorders.
Molecular pathology of paediatric central nervous system tumours
Authors: Chiang Jason CH , Ellison David W 
Published: October 2016

AbstractAdvances in our understanding of the biology of paediatric central nervous system (CNS) tumours have encouraged pathologists to use molecular markers alongside histopathological analysis for disease classification or prognostication and treatment stratification. In this article, we review molecular genetic alterations in paediatric CNS tumours, including those in low‐grade and high‐grade gliomas, ependymomas, and embryonal tumours. Some of these molecular changes with clinicopathological utility have been used for the first time in the most recent edition of the World Health Organization (WHO) classification of CNS tumours to define entities like ependymoma, RELA fusion‐positive or diffuse midline glioma, H3 K27M‐mutant. The classification of paediatric CNS tumours is entering a new era when histopathologists must work with molecular genetic data and their molecular pathology colleagues to provide an optimal diagnostic evaluation for their patients and clinical colleagues. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Interleukin‐33 regulates tissue remodelling and inhibits angiogenesis in the eye
Authors: Theodoropoulou Sofia , Copland David A , Liu Jian , Wu Jiahui , Gardner Peter J , Ozaki Ema , Doyle Sarah L , Campbell Matthew , Dick Andrew D 
Published: October 2016

AbstractAge‐related macular degeneration (AMD) is the leading cause of central vision loss worldwide. Loss of retinal pigment epithelium (RPE) is a major pathological hallmark in AMD with or without pathological neovascularization. Although activation of the immune system is implicated in disease progression, pathological pathways remain diverse and unclear. Here, we report an unexpected protective role of a pro‐inflammatory cytokine, interleukin‐33 (IL‐33), in ocular angiogenesis. IL‐33 and its receptor (ST2) are expressed constitutively in human and murine retina and choroid. When RPE was activated, IL‐33 expression was markedly elevated in vitro. We found that IL‐33 regulated tissue remodelling by attenuating wound‐healing responses, including reduction in the migration of choroidal fibroblasts and retinal microvascular endothelial cells, and inhibition of collagen gel contraction. In vivo, local administration of recombinant IL‐33 inhibited murine choroidal neovascularization (CNV) formation, a surrogate of human neovascular AMD, and this effect was ST2‐dependent. Collectively, these data demonstrate IL‐33 as a potential immunotherapy and distinguishes pathways for subverting AMD pathology. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Glucose oxidase deoxygenation−redox initiation for RAFT polymerization in air
Authors: Lv Yue , Liu Zhifen , Zhu Anqi , An Zesheng 
Published: October 2016

ABSTRACTA new methodology based on glucose oxidase (GOx) deoxygenation and hydrogen peroxide/vitamin C (H2O2/Vc) redox initiation for conducting RAFT polymerization at low temperature in air is reported. GOx catalyzes reduction of oxygen in the presence of glucose to generate hydrogen peroxide, which is directly used to constitute a redox pair with Vc for the efficient generation of hydroxyl radicals to initiate RAFT polymerization in air. Various experimental parameters including temperature, stirring speed, prepolymerization incubation time, and concentrations of Vc, glucose, and GOx were evaluated with respect to monomer conversion, molecular weight, and dispersity. Efficient removal of oxygen is typically realized within 10 min before polymerization is initiated by addition of Vc, and high conversions are achieved within 5 h. Well‐defined homopolymers and block copolymers have been efficiently synthesized with high monomer conversions and low dispersities (< 1.2). Using this new methodology, it is possible to conduct controlled RAFT polymerizations in both open and sealed vessels, though lower conversions but less termination by oxygen are typically observed for the sealed systems. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017, 55, 164–174
A multicenter study on the validation of the Burnout Battery: a new visual analog scale to screen job burnout in oncology professionals
Authors: Deng Yao‐tiao , Liu Jie , Zhang Jie , Huang Bo‐yan , Yi Ting‐wu , Wang Yu‐qing , Zheng Bo , Luo Di , Du Pei‐xin , Jiang Yu 
Published: October 2016

AbstractObjectivesThe objective of the study is to develop a novel tool—the Burnout Battery—for briefly screening burnout among oncology professionals in China and assessing its validity.MethodsA multicenter study was conducted in doctors and nurses of the oncology departments in China from November 2014 to May 2015. The Burnout Battery was administered with the Maslach Burnout Inventory‐Human Services Survey (MBI‐HSS) and the Doctors' Job Burnout Questionnaire.ResultsOf 538 oncology doctors and nurses who completed all the survey, using MBI‐HSS as the standard tool for measuring burnout, 52% had emotional exhaustion, 39.4% had depersonalization, and 59.3% had a low sense of personal accomplishment. Receiver operating characteristic curve analyses showed that the best cut‐off of the Burnout Battery was the battery with 3 bars, which yielded best sensitivity and specificity against all the 3 subscales of MBI‐HSS. With this cut‐off, nearly half of Chinese oncology professionals (46.8%) had burnout. The Burnout Battery correlated significantly with subscales of the MBI‐HSS and the Doctors' Job Burnout Questionnaire. In multiple logistic regression analysis, those who worked more than 60 hours per week and who thought clinical work was the most stressful part of their job were more likely to experience burnout.ConclusionChinese oncology professionals exhibit high levels of burnout. The Burnout Battery appears to be a simple and useful tool for screening burnout. Working long hours and perceiving clinical work as the most stressful part of the job were the main factors associated with burnout.
On the interpretation of electron microscopic maps of biological macromolecules
Authors: Wang Jimin , Moore Peter B. 
Published: October 2016

AbstractThe images of flash‐frozen biological macromolecules produced by cryo‐electron microscopy (EM) can be used to generate accurate, three‐dimensional, electric potential maps for these molecules that resemble X‐ray‐derived electron density maps. However, unlike electron density maps, electric potential maps can include negative features that might for example represent the negatively charged, backbone phosphate groups of nucleic acids or protein carboxylate side chains, which can complicate their interpretation. This study examines the images of groups that include charged atoms that appear in recently‐published, high‐resolution EM potential maps of the ribosome and β‐galactosidase. Comparisons of simulated maps of these same groups with their experimental counterparts highlight the impact that charge has on the appearance of electric potential maps.
pyDock scoring for the new modeling challenges in docking: Protein–peptide, homo‐multimers, and domain–domain interactions
Authors: Pallara Chiara , Jiménez‐García Brian , Romero Miguel , Moal Iain H. , Fernández‐Recio Juan 
Published: October 2016

ABSTRACTThe sixth CAPRI edition included new modeling challenges, such as the prediction of protein–peptide complexes, and the modeling of homo‐oligomers and domain–domain interactions as part of the first joint CASP–CAPRI experiment. Other non‐standard targets included the prediction of interfacial water positions and the modeling of the interactions between proteins and nucleic acids. We have participated in all proposed targets of this CAPRI edition both as predictors and as scorers, with new protocols to efficiently use our docking and scoring scheme pyDock in a large variety of scenarios. In addition, we have participated for the first time in the servers section, with our recently developed webserver, pyDockWeb. Excluding the CASP–CAPRI cases, we submitted acceptable models (or better) for 7 out of the 18 evaluated targets as predictors, 4 out of the 11 targets as scorers, and 6 out of the 18 targets as servers. The overall success rates were below those in past CAPRI editions. This shows the challenging nature of this last edition, with many difficult targets for which no participant submitted a single acceptable model. Interestingly, we submitted acceptable models for 83% of the evaluated protein–peptide targets. As for the 25 cases of the CASP–CAPRI experiment, in which we used a larger variety of modeling techniques (template‐based, symmetry restraints, literature information, etc.), we submitted acceptable models for 56% of the targets. In summary, this CAPRI edition showed that pyDock scheme can be efficiently adapted to the increasing variety of problems that the protein interactions field is currently facing. Proteins 2017; 85:487–496. © 2016 Wiley Periodicals, Inc.
Growth parameter enhancement for MoS2 thin films synthesized by pulsed laser deposition
Authors: Serna Martha I. , Moreno Salvador , Higgins Marissa , Choi Hyunjoo , Minary‐Jolandan Majid , Quevedo‐Lopez Manuel A. 
Published: October 2016

AbstractTwo‐dimensional materials such as graphene and MoS2 have been the main focus of intense research efforts over the past few years. The most common method of exfoliating these materials, although efficient for lab‐scale experiments, is not acceptable for large area and practical applications. Here, we report the deposition of MoS2 layered films on amorphous (SiO2) and crystalline substrates (sapphire) using a pulsed laser deposition (PLD) method. Increased substrate temperature (∼700 °C) and laser energy density (>530 mJ /cm2) promotes crystalline MoS2 films < 20 nm, as demonstrated by fast Fourier transform (FFT) and transmission electron microscopy (TEM). The method reported here opens the possibility for large area layered MoS2 films by using a laser ablation processes. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Towards process‐level representation of model uncertainties: stochastically perturbed parametrizations in the ECMWF ensemble
Authors: Ollinaho Pirkka , Lock Sarah‐Jane , Leutbecher Martin , Bechtold Peter , Beljaars Anton , Bozzo Alessio , Forbes Richard M. , Haiden Thomas , Hogan Robin J. , Sandu Irina 
Published: October 2016

Ensemble forecasts depend on representations of model uncertainties. Here, we introduce a model uncertainty representation where a novel approach is taken to the established methodology of perturbing model parameters. The Stochastically Perturbed Parametrizations (SPP) scheme applies spatially and temporally varying perturbations to 20 parameters and variables in the ECMWF IFS model. The perturbed quantities are chosen from the IFS parametrizations of (a) turbulent diffusion and subgrid orography, (b) convection, (c) clouds and large‐scale precipitation, and (d) radiation. The perturbations are drawn from prescribed distributions.Numerous configurations of SPP are compared in experiments with the ECMWF ensemble forecasts at TL399 resolution up to 15 day lead times. Halving the standard deviations of the perturbations considerably reduces the ensemble spread. Smaller variations of the standard deviations lead to minor changes to the ensemble spread. Experiments with different space and time correlations for the perturbations suggest optimal correlation scales of 2000 km and 72 h. SPP displays a lower skill for upper‐air variables in the medium range than the current operational model uncertainty scheme Stochastically Perturbed Parametrization Tendencies (SPPT) for a given set of fixed initial‐state perturbations. However, in short ranges the two schemes display similar skill. Moreover, verification against surface observations shows SPP is more skilful than SPPT in 2 m temperature for the first couple of forecast days. We show that the direct perturbation of cloud (and radiation) processes in SPP has a greater impact on radiative fluxes than the indirect perturbation via SPPT. SPP also produces a better model climate for a range of variables when comparing long model integrations with the two schemes, indicating the potential advantage of a physically consistent model uncertainty representation. A comparison of the tendency perturbations introduced by SPP and SPPT suggests that the two schemes represent different aspects of model uncertainty.
A unified view of tropical cyclogenesis and intensification
Authors: Kilroy Gerard , Smith Roger K. , Montgomery Michael T. 
Published: October 2016

Idealized high‐resolution numerical simulations of tropical cyclogenesis are presented in a model that represents deep convection by a warm rain process only. Starting with an initially weak, cloud‐free, axisymmetric warm‐cored vortex (maximum wind speed 5 m s−1 at a radius of 100 km), rapid vortex intensification begins after a gestation period on the order of 2 days. From a three‐dimensional perspective, the genesis process is similar to that in the rotating convection paradigm for vortex intensification starting with a much stronger initial vortex (Vmax = 15 m s−1). The patterns of deep convection and convectively amplified cyclonic relative vorticity are far from axisymmetric during the genesis period. Moreover, the organization of the cyclonic relative vorticity into a monopole structure occurs at relatively low wind speeds, before the maximum local wind speed has increased appreciably. Barotropic processes are shown to play an important role in helping to consolidate a single‐signed vorticity monopole within a few hours near the intensification begin time.The rotating convection paradigm appears adequate to explain the basic genesis process within the weak initial vortex, providing strong support for a hypothesis of Montgomery and Smith that the genesis process is not fundamentally different from that of vortex intensification. In particular, genesis does not require a ‘trigger’ and does not depend on the prior existence of a mid‐level vortex.
Fragmentation pathways and structural characterization of organophosphorus compounds related to the Chemical Weapons Convention by electron ionization and electrospray ionization tandem mass spectrometry
Authors: Hosseini Seyed Esmaeil , Saeidian Hamid , Amozadeh Ali , Naseri Mohammad Taghi , Babri Mehran 
Published: October 2016

RationaleFor unambiguous identification of Chemical Weapons Convention (CWC)‐related chemicals in environmental samples, the availability of mass spectra, interpretation skills and rapid microsynthesis of suspected chemicals are essential requirements. For the first time, the electron ionization single quadrupole and electrospray ionization tandem mass spectra of a series of O‐alkyl N‐[bis(dimethylamino)methylidene]‐P‐methylphosphonamidates (Scheme 1, cpd 4) were studied for CWC verification purposes.MethodsO‐Alkyl N‐[bis(dimethylamino)methylidene]‐P‐methylphosphonamidates were prepared through a microsynthetic method and were analyzed using electron ionization and electrospray ionization mass spectrometry with gas and liquid chromatography, respectively, as MS‐inlet systems. General EI and ESI fragmentation pathways were proposed and discussed, and collision‐induced dissociation studies of the protonated derivatives of these compounds were performed to confirm proposed fragment ion structures by analyzing mass spectra of deuterated analogs.ResultsMass spectrometric studies revealed some interesting fragmentation pathways during the ionization process, such as McLafferty rearrangement, hydrogen rearrangement and a previously unknown intramolecular electrophilic aromatic substitution reaction.ConclusionsThe EI and ESI fragmentation routes of the synthesized compounds 4 were investigated with the aim of detecting and identifying CWC‐related chemicals during on‐site inspection and/or off‐site analysis and toxic chemical destruction monitoring. Copyright © 2016 John Wiley & Sons, Ltd.
The effect of lipid extraction on carbon and nitrogen stable isotope ratios in oyster tissues: Implications for glycogen‐rich species
Authors: Patterson H. K. , Carmichael R. H. 
Published: October 2016

RationaleExtraction of lipids from tissues prior to carbon stable isotope analysis (SIA) has become a common practice, despite a lack of species‐specific data to indicate when lipid extraction is needed. Marine invertebrates, including bivalves, are known to store carbon as glycogen and less in the form of lipids than other species, potentially reducing the need for lipid extraction even when C:N values are above 3.5, a value that previous studies suggest indicates a need for lipid extraction of animal tissues.MethodsWe investigated the need for lipid extraction on individual tissues (adductor muscle, gut gland, gill) and whole tissue of a glycogen‐storing species, the oyster Crassostrea virginica. Bulk and lipid‐extracted samples were analyzed for their C and N stable isotope ratios by continuous flow isotope ratio mass spectrometry (IRMS). Samples were analyzed on a 20–20 isotope ratio mass spectrometer (PDZ Europa) after combustion in an elemental analyzer (PDZ Europa Automatic Analyzer‐Gas Solid Liquid).ResultsAlthough the C:N values for most bulk (unextracted) tissue samples were greater than 3.5, the lipid‐extracted δ13C values did not differ from the bulk values. Lipid extraction, however, affected δ15N values in all tissue types except adductor muscle, indicating that separate SIA may be required when tissues are lipid extracted.ConclusionsThese data demonstrate that it is not necessary to lipid extract oyster tissues in all cases, and that C:N thresholds for lipid extraction in other species may not be reliable for organisms such as oysters that store glycogen. Our data indicate that minimizing unnecessary lipid extraction through preliminary testing will save researchers time and expense by avoiding superfluous sample handling, reducing concern over secondary effects on data quality, and reducing the costs of reagents and additional separate stable isotope analysis to ensure analytical accuracy. Copyright © 2016 John Wiley & Sons, Ltd.