bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic variations in STAT4,C2,HLA-DRB1 and HLA-DQ associated with risk of hepatitis B virus-related liver cirrhosis
Authors: Jiang De-Ke , Ma Xiao-Pin , Wu Xiaopan , Peng Lijun , Yin Jianhua , Dan Yunjie , Huang Hui-Xing , Ding Dong-Lin , Zhang Lu-Yao , Shi Zhuqing , Zhang Pengyin , Yu Hongjie , Sun Jielin , Lilly Zheng S. , Deng Guohong , Xu Jianfeng , Liu Ying , Guo Jinsheng , Cao Guangwen , Yu Long 
Published: November 2015

AbstractRecent genome-wide associated studies (GWASs) have revealed several common loci associated with the risk of hepatitis B virus (HBV)- or hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC). We selected 15 single nucleotide polymorphisms (SNPs) identified through GWASs on HBV- or HCV-related HCC and genotyped them in two independent Chinese cohorts of chronic HBV carriers, including 712 LC cases and 2601 controls. The association of each SNP with the risk of HBV-related LC was assessed by meta-analysis of the two cohorts. Of the 12 SNPs reported in HBV-related HCC GWASs, five SNPs (rs7574865 in STAT4, rs9267673 near C2, rs2647073 and rs3997872 near HLA-DRB1 and rs9275319 near HLA-DQ), were found to be significantly associated with the risk of HBV-related LC (rs7574865: P = 1.79 × 10−2, OR = 1.17, 95% CI = 1.03–1.34; rs9267673: P = 4.91 × 10−4, OR = 1.37, 95% CI = 1.15–1.63; rs2647073: P = 3.53 × 10−5, OR = 1.63, 95% CI = 1.29–2.06; rs3997872: P = 4.22 × 10−4, OR = 1.86, 95% CI = 1.32–2.62; rs9275319: P = 1.30 × 10−2, OR = 1.32, 95% CI = 1.06–1.64). However, among the three SNPs associated with the risk of HCV-related HCC in previous GWASs, none of them showed significant association with the risk of HBV-related LC. Our results suggested that genetic variants associated with HBV-related hepatocarcinogenesis may already play an important role in the progression from CHB to LC.
Inhibition of actin polymerization in the NAc shell inhibits morphine-induced CPP by disrupting its reconsolidation
Authors: Li Gongying , Wang Yanmei , Yan Min , Xu Yunshuai , Song Xiuli , Li Qingqing , Zhang Jinxiang , Ma Hongxia , Wu Yili 
Published: November 2015

AbstractDrug-associated contextual cues contribute to drug craving and relapse after abstinence, which is a major challenge to drug addiction treatment. Previous studies showed that disrupting memory reconsolidation impairs drug reward memory. However, the underlying mechanisms remain elusive. Although actin polymerization is involved in memory formation, its role in the reconsolidation of drug reward memory is unknown. In addition, the specific brain areas responsible for drug memory have not been fully identified. In the present study, we found that inhibiting actin polymerization in the nucleus accumbens (NAc) shell, but not the NAc core, abolishes morphine-induced conditioned place preference (CPP) by disrupting its reconsolidation in rats. Moreover, this effect persists for more than 2 weeks by a single injection of the actin polymerization inhibitor, which is not reversed by a morphine-priming injection. Furthermore, the application of actin polymerization inhibitor outside the reconsolidation window has no effect on morphine-associated contextual memory. Taken together, our findings first demonstrate that inhibiting actin polymerization erases morphine-induced CPP by disrupting its reconsolidation. Our study suggests that inhibition of actin polymerization during drug memory reconsolidation may be a potential approach to prevent drug relapse.
Bacterial and plant HAD enzymes catalyse a missing phosphatase step in thiamin diphosphate biosynthesis
Authors: Hasnain Ghulam , Roje Sanja , Sa Na , Zallot Rémi , Ziemak Michael J. , de Crécy-Lagard Valérie , Gregory Jesse F. , Hanson Andrew D. 
Published: November 2015

The penultimate step of thiamin diphosphate (ThDP) synthesis in plants and many bacteria is dephosphorylation of thiamin monophosphate (ThMP). Non-specific phosphatases have been thought to mediate this step and no genes encoding specific ThMP phosphatases (ThMPases) are known. Comparative genomic analysis uncovered bacterial haloacid dehalogenase (HAD) phosphatase family genes (from subfamilies IA and IB) that cluster on the chromosome with, or are fused to, thiamin synthesis genes and are thus candidates for the missing phosphatase (ThMPase). Three typical candidates (from Anaerotruncus colihominis, Dorea longicatena and Syntrophomonas wolfei) were shown to have efficient in vivo ThMPase activity by expressing them in an Escherichia coli strain engineered to require an active ThMPase for growth. In vitro assays confirmed that these candidates all preferred ThMP to any of 45 other phosphate ester substrates tested. An Arabidopsis thaliana ThMPase homologue (At4g29530) of unknown function whose expression pattern and compartmentation fit with a role in ThDP synthesis was shown to have in vivo ThMPase activity in E. coli and to prefer ThMP to any other substrate tested. However, insertional inactivation of the At4g29530 gene did not affect growth or the levels of thiamin or its phosphates, indicating that Arabidopsis has at least one other ThMPase gene. The Zea mays orthologue of At4g29530 (GRMZM2G035134) was also shown to have ThMPase activity. These data identify HAD genes specifying the elusive ThMPase activity, indicate that ThMPases are substrate-specific rather than general phosphatases and suggest that different evolutionary lineages have recruited ThMPases independently from different branches of the HAD family.
Siglec-9 modulated IL-4 responses in the macrophage cell line RAW264
Authors: Higuchi Hiroshi , Shoji Toru , Murase Yusuke , Iijima Shinji , Nishijima Ken-ichi 
Published: November 2015

Abstract
Siglecs, an immunoglobulin-like lectin family that recognizes the sialic acid moiety, regulate various aspects of immune responses. In the present study, we investigated the effects of Siglecs on the macrophage cell line RAW264, which was stimulated with interleukin-4 (IL-4). The induction of arginase-1 (Arg1) by IL-4 was stronger in Siglec-9-expressing cells than in mock cells. Mutations in the cytoplasmic tyrosine-based inhibitory motifs in Siglec-9 markedly reduced the expression of Arg1. The phosphorylation of Akt by IL-4 and extracellular signal-regulated kinase (ERK) without IL-4 was stronger in Siglec-9-expressing cells, indicating the enhanced activation of the phosphatidylinositol 3 kinase (PI-3K) and mitogen-activated protein kinase kinase (MEK)/ERK pathways, respectively. The enhanced expression of Arg1 was inhibited by MEK inhibitors, but not by PI-3K inhibitor. These results indicate that Siglec-9 affects several different signaling pathways in IL-4-stimulated macrophages, which resulted in enhanced induction of Arg1 in Siglec-9-expressing RAW264 cells.
Fingers-of-God effect of infalling satellite galaxies
Authors: Hikage Chiaki , Yamamoto Kazuhiro 
Published: November 2015

Abstract
Non-linear redshift-space distortion known as the Fingers-of-God (FoG) effect is a major systematic uncertainty in redshift-space distortion studies conducted to test gravity models. The FoG effect has been usually attributed to the random motion of galaxies inside their clusters. When the internal galaxy motion is not well virialized, however, the coherent infalling motion towards the cluster centre generates the FoG effect. Here, we derive an analytical model of the satellite velocity distribution due to the infall motion combined with the random motion. We show that the velocity distribution becomes far from Maxwellian when the infalling motion is dominant. We use simulated subhalo catalogues to find that the contribution of infall motion is important to massive subhaloes and that the velocity distribution has a top-hat like shape as expected from our analytic model. We also study the FoG effect due to infall motion on the redshift-space power spectrum. Using simulated mock samples of luminous red galaxies constructed from haloes and massive subhaloes in N-body simulations, we show that the redshift-space power spectra can differ from expectations when the infall motion is ignored.
Suzaku monitoring of the Wolf–Rayet binary WR 140 around periastron passage: An approach for quantifying the wind parameters
Authors: Sugawara Yasuharu , Maeda Yoshitomo , Tsuboi Yohko , Hamaguchi Kenji , Corcoran Michael , Pollock Andy M. T. , Moffat Anthony F. J. , Williams Peredur M. , Dougherty Sean , Pittard Julian 
Published: November 2015

Abstract
Suzaku observations of the Wolf–Rayet (W–R) binary WR 140 (WC7pd+O5.5fc) were made at four different times around periastron passage in 2009 January. The spectra changed in shape and flux with the phase. As periastron approached, the column density of the low-energy absorption increased, which indicates that the emission from the wind–wind collision plasma was absorbed by the dense W–R wind. The spectra can be mostly fitted with two different components: a warm component with kBT = 0.3–0.6 keV and a dominant hot component with kBT ∼ 3 keV. The emission measure of the dominant, hot component is not inversely proportional to the distance between the two stars. This can be explained by the O star wind colliding before it has reached its terminal velocity, leading to a reduction in its wind momentum flux. At phases closer to periastron, we discovered a cool plasma component in a recombining phase, which is less absorbed. This component may be a relic of the wind–wind collision plasma, which was cooled down by radiation, and may represent a transitional stage in dust formation.
Sub-tomogram averaging in RELION
Authors: Bharat Tanmay A.M. , Scheres Sjors H.W. 
Published: November 2015

AbstractElectron cryo-tomography (cryo-ET) and sub-tomogram averaging allow structure determination of macromoleculesin situ,and are gaining in popularity for initial model generation for single-particle analysis. We describe herein, a protocol for sub-tomogram averaging from cryo-ET data using the RELION software. We describe how to calculate newly developed three-dimensional models for the contrast transfer function and the missing wedge of each sub-tomogram, and how to use these models for regularized-likelihood refinement. This approach has been implemented in the existing workflow for single-particle analysis, so that users may conveniently tap into existing capabilities of the RELION software. As example applications, we present analyses of purified hepatitis B capsid particles andS. cerevisiae80S ribosomes. In both cases, we show that following initial classification, sub-tomogram averaging in RELION allowsde novogeneration of initial models, and provides high-resolution maps where secondary structure elements are resolved.
The impact of irrelevant auditory facial descriptions on memory for target faces: implications for eyewitness memory
Authors: Marsh John E. , Demaine Jack , Bell Raoul , Skelton Faye C. , Frowd Charlie D. , Röer Jan P. , Buchner Axel 
Published: November 2015

Purpose
– The purpose of this paper is to investigate the potential susceptibility of eyewitness memory to the presence of extraneous background speech that comprises a description consistent with, or at odds with, a target face.

Design/methodology/approach
– A between-participants design was deployed whereby participants viewed an unfamiliar target face in the presence of quiet, or extraneous to-be-ignored speech comprising a verbal description that was either congruent or incongruent with the target face. After a short distractor task, participants were asked to describe the target face and construct a composite of the face using PRO-fit software. Further participants rated the likeness of the composites to the target.

Findings
– Recall of correct facial descriptors was facilitated by congruent to-be-ignored speech and inhibited by incongruent to-be-ignored speech compared to quiet. Moreover, incorrect facial descriptors were reported more often in the incongruent speech condition compared with the congruent speech and quiet conditions. Composites constructed after exposure to incongruent speech were rated as worse likenesses to the target than those created after exposure to congruent speech and quiet. Whether congruent speech facilitated or impaired composite construction was found to depend on the distinctiveness of the target face.

Practical implications
– The results suggest that the nature of to-be-ignored background speech has powerful effects on the accuracy of information verbally reported from having witnessed a face. Incongruent speech appears to disrupt the recognition processes that underpin face construction while congruent speech may have facilitative or detrimental effects on this process, depending on the distinctiveness of the target face.

Originality/value
– This is one of the first studies to demonstrate that extraneous speech can produce adverse effects on the recall and recognition of complex visual information: in this case, the appearance of a human face.
The peridynamic model of viscoelastic creep and recovery
Authors: bin Azizi Muhammad Azim , bin Mohd Ihsan Ahmad Kamal Ariffin , bin Nik Mohamed Nik Abdullah 
Published: November 2015

Purpose
– The purpose of this paper is to establish a peridynamic method in predicting viscoelastic creep behaviour with recovery stage and to find the suitable numerical parameters of peridynamic method.

Design/methodology/approach
– A rheological viscoelastic creep constitutive equation including recovery and an elastic peridynamic equation (with integral basis) are examined and used. The elasticity equation within the peridynamic equation is replaced by the viscoelastic equation. A new peridynamic method with two time parameters, i.e. numerical time and viscoelastic real time is designed. The two parameters of peridynamic method, horizon radius and number of nodes per unit volume are studied to get their optimal values. In validating this peridynamic method, comparisons are made between numerical and analytical result and between numerical and experimental data.

Findings
– The new peridynamic method for viscoelastic creep behaviour is approved by the good matching in numerical-analytical data comparison with difference of
<
0.1 per cent and in numerical-experimental data comparison with difference of 4-6 per cent. It can be used for further creep test which may include non-linear viscoelastic behaviour and creep rupture. From this paper, the variation of constants in Burger’s viscoelastic model is also studied and groups of constants values that can simulate solid, fluid and solid-fluid viscoelastic behaviours were obtained. In addition, the numerical peridynamic parameters were also manipulated and examined to achieve the optimal values of the parameters.

Research limitations/implications
– The peridynamic model of viscoelastic creep behaviour preferably should have only one time parameter. This can only be done by solving the unstable fluctuation of dynamic results, which is not discussed in this paper. Another limitation is the tertiary region and creep rupture are not included in this paper.

Practical implications
– The viscoelastic peridynamic model in this paper can serve as an alternative for conventional numerical simulations in viscoelastic area. This model also is the initial step of developing peridynamic model of viscoelastic creep rupture properties (crack initiation, crack propagation, crack branching, etc.), where this future model has high potential in predicting failure behaviours of any components, tools or structures, and hence increase safety and reduce loss.

Originality/value
– The application of viscoelastic creep constitutive model on peridynamic formulation, effect of peridynamic parameters manipulation on numerical result, and optimization of constants of viscoelastic model in simulating three types of viscoelastic creep behaviours.
Statistical simulation of pattern formation by ion-beam sputtering
Authors: Kudryashov Nikolay A. , Skachkov Mikhail V. 
Published: November 2015

Purpose
– The purpose of this paper is to investigate the influence of ion-flow parameters on surface topography and making numerical simulation at the times when the process of surface erosion becomes strongly nonlinear.

Design/methodology/approach
– The base of the mathematical model of target ion-sputtering is nonlinear evolutionary equation in which the erosion velocity dependence on ion flux is evaluated by means of a Monte Carlo method. The difference between this equation and the one of continuum theory is that the ion flux is not smooth function. Instead, it is a set of separate incident ions.

Findings
– Some simulations with using independent random points of arrival for the incident ions leads to results uncorrelated with the continuum model at early times. The ripples are not quite developed or observed. This phenomenon is explained by random fluctuations of the target sputtering depth. Sufficiently big values of the random fluctuations destroy the ripple structure on target surface. The simulation with using equally distributed sequence (Holton sequence) of points of arrival for the incident ions leads to results well correlated with the continuum model.

Originality/value
– The discrete model which goes into the equation of continuum theory within the appropriate asymptotic limit has been proposed. The discretization parameters influence on surface morphology formation has been studied. This paper may be interesting to researchers making the theoretical and numerical analysis of pattern formation on plane target surfaces undergoing ion-beam sputtering.
Optimization of response parameters for polarity in submerged arc welding
Authors: Singh Ravinder Pal , Garg R. K. , Shukla D. K. 
Published: November 2015

Purpose
– Optimization of response parameter is essential in any process .The purpose of this paper is to focus at achieving the optimized parameter for submerged arc welding to furnish the quality welds at direct current electrode positive (DCEP) polarity and direct current electrode negative (DCEN) polarity.

Design/methodology/approach
– This paper achieves the parameter after extensive trial runs and finally parameters are optimized to acquire the cost effective and quality welds in submerged arc welding using the response surface methodology.

Findings
– Apart from effect of parameters on weld bead geometry has been identified but optimized parameters has also been achieved for submerged arc welding process for DCEP and DCEN polarities.

Practical implications
– As this study is related to practical work it may be useful for any relevant application.

Social implications
– The process parameters used in this experimental work will be basis for job work/industry for submerged arc welding.

Originality/value
– This paper identifies the effect of polarity in submerged arc welding.
Quality identification methodology applied to wall-elements based on modal analysis
Authors: Zóltowski Mariusz , Martinod Ronald M. 
Published: November 2015

Purpose– The recommendation of structural standards, e.g. PN-B-03002, shows a need to control the production quality of wall-elements; the quality control demands suitable guidelines to fit the requirements of the current mass-production of the wall-elements, then, the structural standard recognizes the need of improving the methods to identify the real elements quality. The paper aims to discuss these issues.Design/methodology/approach– The proposed inspection methodology corresponds to assessment models that combine the numerical and symptomatic models to evaluate the critical levels of wall-elements, based on non-intrusive tests through the measurement of a set of signals, using the Experimental Modal Analysis (EMA)-based techniques.Findings– The presented work is developed with an approach that applies advanced calculating techniques used for the structural analysis in civil engineering focused on the technical state assessment.Originality/value– The paper proposes a diagnostic methodology that can be added to the current regulations and standards based on EMA techniques.
A systematic review of the methodologies used in research related to adult drug and alcohol rehabilitation in therapeutic communities published 2000-2013
Authors: Perryman Cassandra , Dingle Genevieve 
Published: November 2015

Purpose
– The purpose of this paper is to summarize research conducted in long-term residential rehabilitation centers, including therapeutic communities (TCs), in order to further clarify the effectiveness of this treatment approach and to evaluate the quality of TC research conducted in the period 2000-2013.

Design/methodology/approach
– The composite search engine UQ database Summon were used to find articles with “Therapeutic Community” as title words, and the search was limited to adult participants, peer-reviewed articles, published between January 2000 and June 2013 in the English language. The review was conducted using Cochrane Collaboration methods and reported under the Preferred Reporting Items for Systematic Review and Meta-analyses guidelines.

Findings
– In total, 25 studies met inclusion criteria for the review and represented data from n=5,923 participants in the USA, Australia, Spain, England, and Belgium. Evidence supports the TC approach for a diverse range of individuals who misuse a range of substances. Several studies reported a relationship between retention and outcomes however dropout from treatment is a widespread issue. A paucity of research using multiple time points precludes any firm conclusions regarding the optimal length of treatment in a TC. There is a lack of research on the interplay between individual and community-level factors on client well-being, retention, and longer term outcomes.

Research limitations/implications
– This review highlights the need for TC research that includes multiple time points and follow-up assessments, and measures of change in theoretically meaningful constructs alongside standard measures of demographics, substance use, and psychiatric symptoms.

Practical implications
– The reporting format of TC research should be better standardized in order to create a better basis for research comparison. More standardized reporting would also allow for effect size analysis, and create a more efficacious evidence base.

Originality/value
– This updates the systematic review body of research.