bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genome-wide association study of fetal response to type 2 porcine reproductive and respiratory syndrome virus challenge
Authors: Yang Tianfu , Wilkinson James , Wang Zhiquan , Ladinig Andrea , Harding John , Plastow Graham 
Published: February 2016

AbstractControl of porcine reproductive and respiratory syndrome (PRRS) is economically important for the swine industry worldwide. As current PRRS vaccines do not completely protect against heterologous challenge, alternative means of control, including enhanced genetic resilience, are needed. For reproductive PRRS, the genetic basis of fetal response to PRRS virus (PRRSV) infection is poorly understood. Genome-wide association studies (GWAS) were done here using data from 928 fetuses from pregnant gilts experimentally challenged with type 2 PRRSV. Fetuses were assessed for viral load in thymus (VLT), viral load in endometrium (VLE), fetal death (FD) and fetal viability (FV) and genotyped at a medium density. Collectively, 21 candidate genomic regions were found associated with these traits, seven of which overlap with previously reported QTLs for pig health and reproduction. A comparison with ongoing and related transcriptomic analyses of fetal response to PRRSV infection found differentially expressed genes within 18 candidate regions. Some of these genes have immune system functions and have been reported to contribute to host response to PRRSV infection. The results provide new evidence about the genetic basis of fetal response to PRRSV challenge and may ultimately lead to alternative control strategies to reduce the impact of reproductive PRRS.
Comparative transcriptomic profiling of hydrogen peroxide signaling networks in zebrafish and human keratinocytes: Implications toward conservation, migration and wound healing
Authors: Lisse Thomas S. , King Benjamin L. , Rieger Sandra 
Published: February 2016

AbstractSkin wounds need to be repaired rapidly after injury to restore proper skin barrier function. Hydrogen peroxide (H2O2) is a conserved signaling factor that has been shown to promote a variety of skin wound repair processes, including immune cell migration, angiogenesis and sensory axon repair. Despite growing research on H2O2functions in wound repair, the downstream signaling pathways activated by this reactive oxygen species in the context of injury remain largely unknown. The goal of this study was to provide a comprehensive analysis of gene expression changes in the epidermis upon exposure to H2O2concentrations known to promote wound repair. Comparative transcriptome analysis using RNA-seq data from larval zebrafish and previously reported microarray data from a human epidermal keratinocyte line shows that H2O2activates conserved cell migration, adhesion, cytoprotective and anti-apoptotic programs in both zebrafish and human keratinocytes. Further assessment of expression characteristics and signaling pathways revealed the activation of three major H2O2–dependent pathways, EGF, FOXO1 and IKKα. This study expands on our current understanding of the clinical potential of low-level H2O2for the promotion of epidermal wound repair and provides potential candidates in the treatment of wound healing deficits.
Negative regulation of initial steps in skeletal myogenesis by mTOR and other kinases
Authors: Wilson Raphael A. , Liu Jing , Xu Lin , Annis James , Helmig Sara , Moore Gregory , Timmerman Casey , Grandori Carla , Zheng Yanbin , Skapek Stephen X. 
Published: February 2016

AbstractThe transition from a committed progenitor cell to one that is actively differentiating represents a process that is fundamentally important in skeletal myogenesis. Although the expression and functional activation of myogenic regulatory transcription factors (MRFs) are well known to govern lineage commitment and differentiation, exactly how the first steps in differentiation are suppressed in a proliferating myoblast is much less clear. We used cultured mammalian myoblasts and an RNA interference library targeting 571 kinases to identify those that may repress muscle differentiation in proliferating myoblasts in the presence or absence of a sensitizing agent directed toward CDK4/6, a kinase previously established to impede muscle gene expression. We identified 55 kinases whose knockdown promoted myoblast differentiation, either independently or in conjunction with the sensitizer. A number of the hit kinases could be connected to known MRFs, directly or through one interaction node. Focusing on one hit, Mtor, we validated its role to impede differentiation in proliferating myoblasts and carried out mechanistic studies to show that it acts, in part, by a rapamycin-sensitive complex that involves Raptor. Our findings inform our understanding of kinases that can block the transition from lineage commitment to a differentiating state in myoblasts and offer a useful resource for others studying myogenic differentiation.
Invasive floating macrophytes reduce greenhouse gas emissions from a small tropical lake
Authors: Attermeyer K. , Flury S. , Jayakumar R. , Fiener P. , Steger K. , Arya V. , Wilken F. , van Geldern R. , Premke K. 
Published: February 2016

AbstractFloating macrophytes, including water hyacinth (Eichhornia crassipes), are dominant invasive organisms in tropical aquatic systems and they may play an important role in modifying the gas exchange between water and the atmosphere. However, these systems are underrepresented in global datasets of greenhouse gas (GHG) emissions. This study investigated the carbon (C) turnover and GHG emissions from a small (0.6 km2) water-harvesting lake in South India and analysed the effect of floating macrophytes on these emissions. We measured carbon dioxide (CO2) and methane (CH4) emissions with gas chambers in the field as well as water C mineralization rates and physicochemical variables in both the open water and in water within stands of water hyacinths. The CO2 and CH4 emissions from areas covered by water hyacinths were reduced by 57% compared with that of open water. However, the C mineralization rates were not significantly different in the water between the two areas. We conclude that the increased invasion of water hyacinths and other floating macrophytes has the potential to change GHG emissions, a process that might be relevant in regional C budgets.
The memory effect of magnetoelectric coupling in FeGaB/NiTi/PMN-PT multiferroic heterostructure
Authors: Zhou Ziyao , Zhao Shishun , Gao Yuan , Wang Xinjun , Nan Tianxiang , Sun Nian X. , Yang Xi , Liu Ming 
Published: February 2016

AbstractMagnetoelectric coupling effect has provided a power efficient approach in controlling the magnetic properties of ferromagnetic materials. However, one remaining issue of ferromagnetic/ferroelectric magnetoelectric bilayer composite is that the induced effective anisotropy disappears with the removal of the electric field. The introducing of the shape memory alloys may prevent such problem by taking the advantage of its shape memory effect. Additionally, the shape memory alloy can also “store” the magnetoelectric coupling before heat release, which introduces more functionality to the system. In this paper, we study a FeGaB/NiTi/PMN-PT multiferroic heterostructure, which can be operating in different states with electric field and temperature manipulation. Such phenomenon is promising for tunable multiferroic devices with multi-functionalities.
Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control
Authors: Satoh Tadashi , Toshimori Takayasu , Yan Gengwei , Yamaguchi Takumi , Kato Koichi 
Published: February 2016

AbstractThe endoplasmic reticulum (ER) has a sophisticated protein quality control system for the efficient folding of newly synthesized proteins. In this system, a variety of N-linked oligosaccharides displayed on proteins serve as signals recognized by series of intracellular lectins. Glucosidase II catalyzes two-step hydrolysis at α1,3-linked glucose–glucose and glucose–mannose residues of high-mannose-type glycans to generate a quality control protein tag that is transiently expressed on glycoproteins and recognized by ER chaperones. Here we determined the crystal structures of the catalytic α subunit of glucosidase II (GIIα) complexed with two different glucosyl ligands containing the scissile bonds of first- and second-step reactions. Our structural data revealed that the nonreducing terminal disaccharide moieties of the two kinds of substrates can be accommodated in a gourd-shaped bilocular pocket, thereby providing a structural basis for substrate-binding specificity in the two-step deglucosylation catalyzed by this enzyme.
Branched-chain and aromatic amino acid profiles and diabetes risk in Chinese populations
Authors: Chen Tianlu , Ni Yan , Ma Xiaojing , Bao Yuqian , Liu Jiajian , Huang Fengjie , Hu Cheng , Xie Guoxiang , Zhao Aihua , Jia Weiping , Jia Wei 
Published: February 2016

AbstractRecent studies revealed strong evidence that branched-chain and aromatic amino acids (BCAAs and AAAs) are closely associated with the risk of developing type 2 diabetes in several Western countries. The aim of this study was to evaluate the potential role of BCAAs and AAAs in predicting the diabetes development in Chinese populations. The serum levels of valine, leucine, isoleucine, tyrosine, and phenylalanine were measured in a longitudinal and a cross sectional studies with a total of 429 Chinese participants at different stages of diabetes development, using an ultra-performance liquid chromatography triple quadruple mass spectrometry platform. The alterations of the five AAs in Chinese populations are well in accordance with previous reports. Early elevation of the five AAs and their combined score was closely associated with future development of diabetes, suggesting an important role of these metabolites as early markers of diabetes. On the other hand, the five AAs were not as good as existing clinical markers in differentiating diabetic patients from their healthy counterparts. Our findings verified the close correlation of BCAAs and AAAs with insulin resistance and future development of diabetes in Chinese populations and highlighted the predictive value of these markers for future development of diabetes.
Demonstration of enhancement of x-ray flux with foam gold compared to solid gold
Authors: Zhang Lu , Ding Yongkun , Lin Zhiwei , Li Hang , Jing Longfei , Yuan Zheng , Yang Zhiwen , Tan Xiulan , Kuang Longyu , Zhang Wenhai , Li Liling , Li Ping , Yuan Guanghui , Jiang Shaoen , Zhang Baohan 
Published: February 2016

Abstract
Experiments have been conducted to compare the re-emission from foam gold with a 0.3 g cc−1 density and solid gold in a SGIII prototype laser facility. Measurements of the re-emission x-ray flux demonstrate that emission is enhanced by the low density foam gold compared to the solid gold under the same conditions. The emission fraction increases with time and is concentrated on soft x-ray flux between 0.1–1 keV. The simulation results with Multi 1D agree with the experimental results. There are potential advantages to using foam walls for improving the emission and soft x-ray flux in hohlraums.
Dependence of neoclassical toroidal viscosity on the poloidal spectrum of applied nonaxisymmetric fields
Authors: Logan N.C. , Park J.-K. , Paz-Soldan C. , Lanctot M.J. , Smith S.P. , Burrell K.H. 
Published: February 2016

Abstract
This paper presents a single mode model that accurately predicts the coupling of applied nonaxisymmetric fields to the plasma response that induces neoclassical toroidal viscosity (NTV) torque in DIII-D H-mode plasmas. The torque is measured and modeled to have a sinusoidal dependence on the relative phase of multiple nonaxisymmetric field sources, including a minimum in which large amounts of nonaxisymmetric drive is decoupled from the NTV torque. This corresponds to the coupling and decoupling of the applied field to a NTV-driving mode spectrum. Modeling using the perturbed equilibrium nonambipolar transport (PENT) code confirms an effective single mode coupling between the applied field and the resultant torque, despite its inherent nonlinearity. The coupling to the NTV mode is shown to have a similar dependence on the relative phasing as that of the IPEC dominant mode, providing a physical basis for the efficacy of this linear metric in predicting error field correction optima in NTV dominated regimes.
Clear Cell Atypical Fibroxanthoma: Clinicopathological Study of 6 Cases and Review of the Literature With Special Emphasis on the Differential Diagnosis
Authors: Tardío Juan C. , Pinedo Fernando , Aramburu José Antonio , Martínez-González Miguel Á. , Arias Dolores , Khedaoui Radia , Suárez-Massa Dolores , Santonja Carlos 
Published: February 2016

Abstract:
Atypical fibroxanthoma (AFX) is an uncommon dermal-based neoplasm arising on the sun-damaged skin of elderly people. Clear cell AFX is a rare variant with only 12 cases reported until the present date, all of them as case reports, except for 1 small series of 3 cases. The authors report 6 new cases and review the literature with special emphasis on the differential diagnosis. The clear cell variant represents 5% of AFX from their files. Histopathologically, it consists of sheets of epithelioid, pleomorphic cells, intermixed with a varying number of giant multinucleated and spindle cells, the latter arranged in a fascicular pattern. All cell types predominantly exhibit a clear, microvacuolated cytoplasm with well-demarcated cell borders. The clinical and immunohistochemical features of this variant are similar to those of the classic type. Clear cell AFX must be differentiated from other cutaneous clear cell neoplasms, some of them with an aggressive clinical behavior, including clear cell melanoma, primary cutaneous and metastatic clear cell carcinomas, clear cell sarcoma, pleomorphic liposarcoma, tumor of perivascular epithelioid cells, and distinctive dermal clear cell mesenchymal neoplasm. The clinical presentation and immunohistochemical profile play a key role in the differential diagnosis.
Serological screening for celiac disease in a northern Italian child and adolescent population after the onset of type 1 diabetes: a retrospective longitudinal study of a 7-year period
Authors: Bianchi Marina , Cartabia Massimo , Clavenna Antonio , Fortino Ida , Bortolotti Angela , Merlino Luca , Bonati Maurizio 
Published: February 2016

Aim
To evaluate the temporal trend and extent of screening for celiac disease in an Italian pediatric population of incident type 1 diabetes in the period 2006–2011, providing information on adherence to guidelines in primary care.

Methods
Using the Lombardy region’s administrative database, 1–17-year-old children and adolescents diagnosed with type 1 diabetes during the 2006–2011 period were identified. Among these patients, the number screened for celiac disease was calculated on the basis of specific antibodies.

Results
Of the 1563 children and adolescents receiving a diagnosis of type 1 diabetes during the observational period, 53% were tested for celiac disease compared with 12% of individuals without diabetes. The extent to which screening was performed increased two-fold from the 2006–2008 to the 2009–2011 period (P<0.0001). Among the screened population, 1.8 of the non-type 1 diabetes population and 9.4% of the new cases of type 1 diabetes received a diagnosis of celiac disease (90% after type1 diabetes diagnosis and 10% before). Being female and less than 4 years old were factors associated with an increased risk of receiving both diagnoses.

Conclusion
In conclusion, to the best of our knowledge, this is the first report in which celiac disease screening is measured in a type 1 diabetes population from the time of diagnosis up to at least 12 months afterwards. The results provide evidence that, although the rate of screening increased over time, nearly half of children with type 1 diabetes were not screened after diagnosis during the observed period, suggesting scarce adherence to guidelines in primary care.
Chemerin: a new biomarker to predict postendoscopic retrograde cholangiopancreatography pancreatitis
Authors: Koksal Ali R. , Boga Salih , Alkim Huseyin , Sen Ilker , Neijmann Sebnem T. , Alkim Canan 
Published: February 2016

Introduction
Individuals with increased visceral adiposity are considered to be more sensitive and more prone to severe acute pancreatitis because of the inflammatory microenvironment they have. We hypothesized that insulin resistance, adipokines, and proinflammatory cytokines that markedly affect the course of pancreatitis can contribute toward development of postendoscopic retrograde cholangiopancreatography (post-ERCP) pancreatitis (PEP) and aimed to investigate the association between PEP risk and preprocedural serum vaspin, chemerin, tumor necrosis factor α, interleukin-6 (IL-6) levels, and homeostasis model assessment of insulin resistance.

Patients and methods
Eighty-two patients with a diagnosis of choledocholithiasis and 30 controls were enrolled. Preprocedural chemerin, vaspin, IL-6, and well-known PEP risk factors were compared between PEP and non-PEP groups.

Results
The mean age of the patients was 56.3±14.4 years; 52 patients were women. Adipocytokine levels, BMIs, and waist circumferences of the patient group were found to be higher than those of the controls. Total cannulation success and the mean procedure time were 82.9% and 28.7±8.8 min, respectively. PEP developed in 12 (14.6%) patients. Chemerin levels in the PEP group were higher than those in the non-PEP group (580.2±172.5 vs. 392.2±168.2 ng/ml, P<0.01). Insulin resistance was higher in the PEP group than the non-PEP group (P=0.001), but there was no significant difference between PEP and non-PEP groups in terms of preprocedural vaspin, tumor necrosis factor α, IL-6, and C-reactive protein levels. According to logistic regression analysis, increased chemerin levels, homeostasis model assessment of insulin resistance 2.5 or greater, and pancreatic duct cannulation were found to be independent risk factors for PEP [odds ratio (OR)=1.006, P=0.006; OR=4.57, P=0.05; OR=6.54, P=0.02].

Conclusion
Elevated serum chemerin levels and insulin resistance are independent risk factors of PEP development.
An Extended Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction and Cladogenesis
Authors: Beeravolu Champak R. , Condamine Fabien L. 
Published: February 2016

AbstractThe origin and evolution of species’ ranges remains a central focus of historical biogeography and the advent of likelihood methods based on phylogenies has revolutionized the way in which range evolution has been studied. A decade ago, the first elements of what turned out to be a popular inference approach of ancestral ranges based on the processes of Dispersal, local Extinction and Cladogenesis (DEC) was proposed. The success of theDECmodel lies in its use of a flexible statistical framework known as a Continuous Time Markov Chain and since, several conceptual and computational improvements have been proposed using this as a baseline approach. In the spirit of the original version ofDEC, we introduceDEC eXtended(DECX) by accounting for rapid expansion and local extinction as possible anagenetic events on the phylogeny but without increasing model complexity (i.e. in the number of free parameters). Classical vicariance as a cladogenetic event is also incorporated by making use of temporally flexible constraints on the connectivity between any two given areas in accordance with the movement of landmasses and dispersal opportunity over time.DECXis built upon a previous implementation in C/C++ and can analyze phylogenies on the order of several thousand tips in a few minutes. We test our model extensively on Pseudo Observed Datasets and on well-curated and recently published data from various island clades and a worldwide phylogeny of Amphibians (3309 species). We also propose the very first implementation of theDECmodel that can specifically account for trees with fossil tips (i.e. non-ultrametric) using the phylogeny of palpimanoid spiders as a case study. In this paper, we argue in favour of the proposed improvements, which have the advantage of being computationally efficient while toeing the line of increased biological realism.
Domain theory and method theory revisited: a reply to Lowe, De Loo and Nama
Authors: Lukka Kari , Vinnari Eija 
Published: February 2016

Purpose– The purpose of this paper is to provide a response to the commentary of Lowe, De Loo and Nama concerning the authors’ previous article, which was published inAccounting, Auditing & Accountability Journal, Volume 27 Number 8.Design/methodology/approach– The authors address the main points of the commentary by Loweet al.Findings– In addressing each of these issues, the authors point out a few misunderstandings included in the critique as well as make an attempt to further clarify the previous argument.Originality/value– The authors maintain that distinguishing between domain theory and method theory in accounting research will be of help to researchers in several ways.
Implementing IFRSs in the UK devolved administrations
Authors: Wall Anthony , Connolly Ciaran 
Published: February 2016

Purpose
– Utilising concepts drawn from the governmentality literature, the purpose of this paper is to examine the adoption of International Financial Reporting Standards (IFRSs) in the UK’s devolved administrations of Northern Ireland, Scotland and Wales in order to assess why they were adopted and how their introduction has been governed.

Design/methodology/approach
– This research applies a combination of three different approaches, namely: a content analysis; an anonymous online questionnaire; and semi-structured interviews.

Findings
– These include: the transition has had minimal impact upon policy setting and the information produced to aid budgeting and decision making; IFRSs are not entirely appropriate for the public sector; the time, cost and effort involved outweighed the benefits; public sector accounting has become overly-complicated; and the transition is not perceived as part of a wider privatisation programme.

Research limitations/implications
– As this study focuses upon the three UK devolved administrations, the findings may not be applicable in a wider setting.

Practical/implications
– Public sector change must be adequately resourced, carefully planned, with appropriate systems, trained staff and interdisciplinary project teams; accounting change should be based on value for money; and a single, coherent financial regime for the way in which government uses budgets, presents estimates to Parliament and publishes its resource accounts should be implemented.

Originality/value
– This study highlights that accounting change is not just a technical issue and, while it can facilitate a more business-like environment and enhance accountability, all those affected by the changes may not have the requisite skills to fully utilise the (new) information available.