bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of Some Low Temperature Gas‐Generating Compositions
Authors: Mei Xinliang , Yang Hongtao , Li Xiangyu , Li Yanchun , Cheng Yi 
Published: December 2014

AbstractSome low temperature gas‐generating compositions, comprised of guanidine nitrate (GN), basic cupric nitrate (BCN), and ferric oxide (Fe2O3), were studied herein. The thermal decomposition properties and burning characteristics of GN/BCN/Fe2O3 mixtures were investigated by thermogravimetry/differential scanning calorimetry (TG/DSC), burning temperature measurements, automatic calorimetry, and X‐ray diffraction (XRD). This study showed that the maximum burning temperature of GN/BCN/Fe2O3 mixture (613 °C) was 31 % lower than that of GN/BCN mixture and the corresponding heat of combustion (2647 J g−1) decreased by 15 %. When the GN/BCN/Fe2O3 mixtures were burning, Fe2O3 did not directly react with GN but with Cu (or CuO), which was produced by reaction between GN and BCN. The combustion process of GN/BCN/Fe2O3 grains could be divided into four stages: pre‐heated, condensed, combustion, and cooling.
Dimensional approach to symptom factors of major depressive disorder in Koreans, using the Brief Psychiatric Rating Scale: The Clinical Research Center for Depression of South Korea Study
Authors: Park Seon‐Cheol , Jang Eun Young , Kim Daeho , Jun Tae‐Youn , Lee Min‐Soo , Kim Jae‐Min , Kim Jung‐Bum , Jo Sun‐Jin , Park Yong Chon 
Published: December 2014

AbstractAlthough major depressive disorder (MDD) has a variety of symptoms beyond the affective dimensions, the factor structure and contents of comprehensive psychiatric symptoms of this disorder have rarely been explored using the 18‐item Brief Psychiatric Rating Scale (BPRS). We aimed to identify the factor structure of the 18‐item BPRS in Korean MDD patients. A total of 258 MDD patients were recruited from a multicenter sample of the Clinical Research Center for Depression of South Korea study. Psychometric scales were used to assess overall psychiatric symptoms (BPRS), depression (Hamilton Depression Rating Scale), anxiety (Hamilton Anxiety Rating Scale), global severity (Clinical Global Impression of Severity Scale), suicidal ideation (Scale for Suicide Ideation), functioning (Social and Occupational Functioning Assessment Scale), and quality of life (World Health Organization Quality of Life Assessment‐abbreviated version). Common factor analysis with oblique rotation was used to yield factor structure. A four‐factor structure was designed and interpreted by the symptom dimensions to reflect mood disturbance, positive symptoms/apathy, bipolarity, and thought distortion/mannerism. These individual factors were also significantly correlated with clinical variables. The findings of this study support the view that the BPRS may be a promising measuring tool for the initial assessment of MDD patients. In addition, the four‐factor structure of the BPRS may be useful in understanding the mood and psychotic characteristics of these patients.
On Semi-Primary Self-Injective Rings and Faith's Quasi-Frobenius Conjecture
Authors: Iovanov M. C. 
Published: December 2014

AbstractA long-standing conjecture of Faith in ring theory states that a left self-injective semi-primary ring A is necessarily a quasi-Frobenius ring. We propose a new method for approaching this conjecture, and prove it under some mild conditions; we show that if the simple A-modules are at most countably generated over a subring of the centre of A, then the conjecture holds. Also, the conjecture holds for algebras A over sufficiently large fields, i.e. if the cardinality of is larger than the dimension of the simple A-modules (or of A/Jac(A)). This effectively proves the conjecture in many situations, and we obtain several previously known results on this problem as a consequence.
Active travel to work in NSW: trends over time and the effect of social advantage
Authors: Zander Alexis , Rissel Chris , Rogers Kris , Bauman Adrian 
Published: December 2014

Issues addressedActive travel can increase population levels of physical activity, but should be promoted equitably. Socioeconomic advantage, housing location and/or car ownership influence walking and cycling (active travel) for transport. We examined active commuting over time in the Sydney Greater Metropolitan Region, and associations between active commuting and socioeconomic advantage, urban/rural location and car ownership at a Local Government Area (LGA) level across New South Wales (NSW).MethodsJourney to work data from the 2001, 2006 and 2011 Australian Census were examined. Associations between levels of active commuting in each LGA in NSW and the Socio‐Economic Index for Areas (SEIFA), Accessibility/Remoteness Index of Australia (ARIA) and car ownership were examined using negative binomial regression modelling.ResultsBetween 2001 and 2011, active commuting increased in inner Sydney (relative increase of 24%), decreased slightly in outer Sydney (declined 5.1%) and declined in the Greater Metropolitan Region (down 15%). Overall, active commuting increased slightly (6.8% relative increase). After adjusting for the LGA age and sex profile and all other LGA variables, people living in NSW LGAs with high socioeconomic status, more rural areas and low car ownership were more likely to cycle or walk to work.ConclusionsMore needs to be done in NSW to increase levels of active commuting consistently across regions and sociodemographic groups.So what?Despite small increases in active travel in the Sydney region, active travel patterns are not evenly distributed across locations or populations.
Emergence of antibiotic resistance from multinucleated bacterial filaments
Authors: Bos Julia , Zhang Qiucen , Vyawahare Saurabh , Rogers Elizabeth , Rosenberg Susan M. , Austin Robert H. 
Published: December 2014

Significance
Understanding how bacteria rapidly evolve under antibiotic selective pressure is crucial to controlling the development of resistant organisms. We show that initial resistance emerges from successful segregation of mutant chromosomes at the tips of filaments followed by budding of resistant progeny. We propose that the first stages of emergence of resistance occur via the generation of multiple chromosomes within the filament and are achieved by mutation and possibly recombination between the chromosomes.
Correspondence between Scale Morphometrics and Scale and Otolith Chemistry for Interpreting Juvenile Salmon Life Histories
Authors: Campbell Lance A. , Bottom Daniel L. , Volk Eric C. , Fleming Ian A. 
Published: December 2014

AbstractFish scales have long been used to reconstruct fine‐scale habitat transitions such as the movement of juvenile fish from freshwater, estuary, and ocean environments. Despite the importance of life history information to fisheries management and conservation, few studies have validated that scale morphology accurately describes fish movement between these habitats. Therefore, we tested the accuracy of using scale morphometric criteria to identify the movement of juvenile Chinook Salmon Oncorhynchus tshawytscha from freshwater to marine portions of the Columbia River estuary by comparing scale morphometric classification, scale chemistry, and otolith chemistry. Nearly one‐half of all fish collected in the saline portion of the estuary and approximately one‐quarter in the freshwater portion exhibited morphometric patterns (i.e., scale checks and intermediate growth) often associated with periods of estuary rearing. Depending upon the criteria used to define scale checks, otolith chemical results indicated that 33–53% of fish would have been misclassified as estuary residents based solely on their scale patterns. Moreover, many individuals who had resided in strontium‐rich estuary water did not form a visible check (37%) on their scales to coincide with estuary entry. We estimated from otolith chemistry that these fish had either entered at or near the size at which scale formation occurs (35–42 mm) or had recently migrated to the saline portion of the estuary (<30 d) before new scale material could be formed and calcified. Scale chemistry alone was a good indicator of entrance into the saline portion of the estuary. Scale chemistry responded to the strontium‐enriched salt water, and explained 86% of the variation found in otolith chemistry. Scale morphometric classification did not provide the fine‐scale resolution that scale and, even more so, otolith chemistry provided for describing the proportion of juvenile Chinook salmon using the saline portion of the Columbia River estuary.Received December 26, 2013; accepted August 28, 2014
Diverse galactooligosaccharides consumption by bifidobacteria: implications of β-galactosidase—LacS operon
Authors: Akiyama Takuya , Kimura Kazumasa , Hatano Hiroshi 
Published: December 2014

Abstract
Galactooligosaccharides (GOS) possess prebiotic properties that specifically increase the number of bifidobacteria in the human intestine, thus giving health benefits to the host. Although the bifidogenic effect of GOS has been demonstrated in numerous studies, the utilization of GOS by specific bifidobacteria remains unclear. The goal of our study was to elucidate GOS consumption by specific bifidobacteria and gain insights into the mechanism. First, we examined GOS consumption by 14 bifidobacterial strains belonging to seven different species by comparing growth rate, carbohydrate consumption, and acid production. We then performed a transcription analysis in the case of one strong GOS consumer, Bifidobacterium adolescentis YIT 4011T, to predict the operon contributing to GOS use. The study indicated the contribution of an operon consisted of LacS symporter and β-galactosidase to bifidobacterial GOS consumption.
Crystal structure of the catalytic domain of a GH16 β-agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94
Authors: Takagi Emiko , Hatada Yuji , Akita Masatake , Ohta Yukari , Yokoi Gaku , Miyazaki Takatsugu , Nishikawa Atsushi , Tonozuka Takashi 
Published: December 2014

Abstract
A deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94, has a β-agarase (MtAgaA) belonging to the glycoside hydrolase family (GH) 16. The optimal temperature of this bacterium for growth is 43–49 °C, and MtAgaA is stable at 60 °C, which is one of the most thermostable enzymes among GH16 β-agarases. Here, we determined the catalytic domain structure of MtAgaA. MtAgaA consists of a β-jelly roll fold, as observed in other GH16 enzymes. The structure of MtAgaA was most similar to two β-agarases from Zobellia galactanivorans, ZgAgaA, and ZgAgaB. Although the catalytic cleft structure of MtAgaA was similar to ZgAgaA and ZgAgaB, residues at subsite −4 of MtAgaA were not conserved between them. Also, an α-helix, designated as α4′, was uniquely located near the catalytic cleft of MtAgaA. A comparison of the structures of the three enzymes suggested that multiple factors, including increased numbers of arginine and proline residues, could contribute to the thermostability of MtAgaA.
SNPlice: variants that modulate Intron retention from RNA-sequencing data
Authors: Mudvari Prakriti , Movassagh Mercedeh , Kowsari Kamran , Seyfi Ali , Kokkinaki Maria , Edwards Nathan J. , Golestaneh Nady , Horvath Anelia 
Published: December 2014

AbstractRationale: The growing recognition of the importance of splicing, together with rapidly accumulating RNA-sequencing data, demand robust high-throughput approaches, which efficiently analyze experimentally derived whole-transcriptome splice profiles.Results: We have developed a computational approach, called SNPlice, for identifying cis-acting, splice-modulating variants from RNA-seq datasets. SNPlice mines RNA-seq datasets to find reads that span single-nucleotide variant (SNV) loci and nearby splice junctions, assessing the co-occurrence of variants and molecules that remain unspliced at nearby exon–intron boundaries. Hence, SNPlice highlights variants preferentially occurring on intron-containing molecules, possibly resulting from altered splicing. To illustrate co-occurrence of variant nucleotide and exon–intron boundary, allele-specific sequencing was used. SNPlice results are generally consistent with splice-prediction tools, but also indicate splice-modulating elements missed by other algorithms. SNPlice can be applied to identify variants that correlate with unexpected splicing events, and to measure the splice-modulating potential of canonical splice-site SNVs.Availability and implementation: SNPlice is freely available for download from https://code.google.com/p/snplice/ as a self-contained binary package for 64-bit Linux computers and as python source-code.Contact: pmudvari@gwu.edu or horvatha@gwu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Improved gene tree error correction in the presence of horizontal gene transfer
Authors: Bansal Mukul S. , Wu Yi-Chieh , Alm Eric J. , Kellis Manolis 
Published: December 2014

AbstractMotivation: The accurate inference of gene trees is a necessary step in many evolutionary studies. Although the problem of accurate gene tree inference has received considerable attention, most existing methods are only applicable to gene families unaffected by horizontal gene transfer. As a result, the accurate inference of gene trees affected by horizontal gene transfer remains a largely unaddressed problem.Results: In this study, we introduce a new and highly effective method for gene tree error correction in the presence of horizontal gene transfer. Our method efficiently models horizontal gene transfers, gene duplications and losses, and uses a statistical hypothesis testing framework [Shimodaira–Hasegawa (SH) test] to balance sequence likelihood with topological information from a known species tree. Using a thorough simulation study, we show that existing phylogenetic methods yield inaccurate gene trees when applied to horizontally transferred gene families and that our method dramatically improves gene tree accuracy. We apply our method to a dataset of 11 cyanobacterial species and demonstrate the large impact of gene tree accuracy on downstream evolutionary analyses.Availability and implementation: An implementation of our method is available at http://compbio.mit.edu/treefix-dtl/Contact: mukul@engr.uconn.edu or manoli@mit.eduSupplementary information: Supplementary data are available at Bioinformatics online.
flowCL: ontology-based cell population labelling in flow cytometry
Authors: Courtot Mélanie , Meskas Justin , Diehl Alexander D. , Droumeva Radina , Gottardo Raphael , Jalali Adrin , Taghiyar Mohammad Jafar , Maecker Holden T. , McCoy J. Philip , Ruttenberg Alan , Scheuermann Richard H. , Brinkman Ryan R. 
Published: December 2014

Abstract
Motivation: Finding one or more cell populations of interest, such as those correlating to a specific disease, is critical when analysing flow cytometry data. However, labelling of cell populations is not well defined, making it difficult to integrate the output of algorithms to external knowledge sources.
Results: We developed flowCL, a software package that performs semantic labelling of cell populations based on their surface markers and applied it to labelling of the Federation of Clinical Immunology Societies Human Immunology Project Consortium lyoplate populations as a use case.
Conclusion: By providing automated labelling of cell populations based on their immunophenotype, flowCL allows for unambiguous and reproducible identification of standardized cell types.
Availability and implementation: Code, R script and documentation are available under the Artistic 2.0 license through Bioconductor (http://www.bioconductor.org/packages/devel/bioc/html/flowCL.html).
Contact: rbrinkman@bccrc.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
ICMA: an integrated cardiac modeling and analysis platform
Authors: Hussan Jagir R. , Hunter Peter J. , Gladding Patrick A. , Greenberg Neil , Christie Richard , Wu Alan , Sorby Hugh , Thomas James D. 
Published: December 2014

Abstract
Summary: ICMA, a software framework to create 3D finite element models of the left ventricle from cardiac ultrasound or magnetic resonance imaging (MRI) data, has been made available as an open-source code. The framework is hardware vendor independent and uses speckle tracking (endocardial border detection) on ultrasound (MRI) imaging data in the form of DICOM. Standard American Heart Association segment-based strain analysis can be performed using a browser-based interface. The speckle tracking, border detection and model fitting methods are implemented in C++ using open-source tools. They are wrapped as web services and orchestrated via a JBOSS-based application server.
Availability and implementation: The source code for ICMA is freely available under MPL 1.1 or GPL 2.0 or LGPL 2.1 license at https://github.com/ABI-Software-Laboratory/ICMA and a standalone virtual machine at http://goo.gl/M4lJKH for download.
Contact: r.jagir@auckland.ac.nz
Supplementary information: Supplementary materials are available at Bioinformatics online.
The Geography of Interstate Resource Wars *
Authors: Caselli Francesco , Morelli Massimo , Rohner Dominic 
Published: December 2014

AbstractWe establish a theoretical and empirical framework to assess the role of resource endowments and their geographic location in interstate conflict. The main predictions of the theory are that conflict is more likely when at least one country has natural resources, when the resources in the resource-endowed country are closer to the border, and, in the case where both countries have natural resources, when the resources are located asymmetrically vis-à-vis the border. We test these predictions on a novel data set featuring oilfield distances from bilateral borders. The empirical analysis shows that the presence and location of oil are significant and quantitatively important predictors of interstate conflicts after World War II.
Up-regulation of CX3CL1 via Nuclear Factor-κB–dependent Histone Acetylation Is Involved in Paclitaxel-induced Peripheral Neuropathy
Authors: Li Dai , Huang Zhen-Zhen , Ling Yun-Zhi , Wei Jia-You , Cui Yu , Zhang Xiang-Zhong , Zhu He-Quan , Xin Wen-Jun 
Published: December 2014

AbstractAbstract
Using a rat model of paclitaxel-induced neuropathy, both pharmacological and small interfering RNA–based techniques showed that CX3CL1 supports allodynia in this model. Chromatin immunoprecipitation experiments demonstrated that an epigenetic mechanism controls CX3CL1 expression in the spinal neurons of neuropathic rats.

Background:
Up-regulation of CX3CL1 has been revealed to be involved in the neuropathic pain induced by nerve injury. However, whether CX3CL1 participates in the paclitaxel-induced painful peripheral neuropathy remains unknown. The aim of the current study was to elucidate the involvement of transcriptional factors nuclear factor-κB (NF-κB) and its causal interaction with CX3CL1 signaling in the paclitaxel-induced painful peripheral neuropathy.

Methods:
Painful peripheral neuropathy induced by paclitaxel treatment was established in adult male Sprague-Dawley rats. The von Frey test were performed to evaluate neuropathic pain behavior, and real-time quantitative reverse transcription polymerase chain reaction, chromatin immunoprecipitation, Western blot, immunohistochemistry, and small interfering RNA were performed to understand the molecular mechanisms.

Results:
The application of paclitaxel induced an up-regulation of CX3CL1 expression in the spinal neurons, which is reduced significantly by NF-κB inhibitor ammonium pyrrolidinedithiocarbamate or p65 small interfering RNA. Blockade of either CX3CL1 (n = 12 each) or NF-κB (n = 12 each) signaling pathway attenuated mechanical allodynia induced by paclitaxel. Chromatin immunoprecipitation further found that paclitaxel induced an increased recruitment of nuclear factor-κB (NF-κB)p65 to the Cx3cl1 promoter region. Furthermore, an increased acetylation level of H4, but not H3, in Cx3cl1 promoter region in spinal neurons was detected after paclitaxel treatment, which was reversed by inhibition of NF-κB with ammonium pyrrolidinedithiocarbamate or p65 small interfering RNA.

Conclusions:
These findings suggest that up-regulation of CX3CL1 via NF-κB–dependent H4 acetylation might be critical for paclitaxel-induced mechanical allodynia.
Pepper Heat Shock Protein 70a Interacts with the Type III Effector AvrBsT and Triggers Plant Cell Death and Immunity
Authors: Kim Nak Hyun , Hwang Byung Kook 
Published: December 2014

Abstract
Heat shock proteins (HSPs) function as molecular chaperones and are essential for the maintenance and/or restoration of protein homeostasis. The genus Xanthomonas type III effector protein AvrBsT induces hypersensitive cell death in pepper (Capsicum annuum). Here, we report the identification of the pepper CaHSP70a as an AvrBsT-interacting protein. Bimolecular fluorescence complementation and coimmunoprecipitation assays confirm the specific interaction between CaHSP70a and AvrBsT in planta. The CaHSP70a peptide-binding domain is essential for its interaction with AvrBsT. Heat stress (37°C) and Xanthomonas campestris pv vesicatoria (Xcv) infection distinctly induce CaHSP70a in pepper leaves. Cytoplasmic CaHSP70a proteins significantly accumulate in pepper leaves to induce the hypersensitive cell death response by Xcv (avrBsT) infection. Transient CaHSP70a overexpression induces hypersensitive cell death under heat stress, which is accompanied by strong induction of defense- and cell death-related genes. The CaHSP70a peptide-binding domain and ATPase-binding domain are required to trigger cell death under heat stress. Transient coexpression of CaHSP70a and avrBsT leads to cytoplasmic localization of the CaHSP70a-AvrBsT complex and significantly enhances avrBsT-triggered cell death in Nicotiana benthamiana. CaHSP70a silencing in pepper enhances Xcv growth but disrupts the reactive oxygen species burst and cell death response during Xcv infection. Expression of some defense marker genes is significantly reduced in CaHSP70a-silenced leaves, with lower levels of the defense hormones salicylic acid and jasmonic acid. Together, these results suggest that CaHSP70a interacts with the type III effector AvrBsT and is required for cell death and immunity in plants.
The Arabidopsis Cellulose Synthase Complex: A Proposed Hexamer of CESA Trimers in an Equimolar Stoichiometry
Authors: Hill Joseph L. , Hammudi Mustafa B. , Tien Ming 
Published: December 2014

Abstract
Cellulose is the most abundant renewable polymer on Earth and a major component of the plant cell wall. In vascular plants, cellulose synthesis is catalyzed by a large, plasma membrane-localized cellulose synthase complex (CSC), visualized as a hexameric rosette structure. Three unique cellulose synthase (CESA) isoforms are required for CSC assembly and function. However, elucidation of either the number or stoichiometry of CESAs within the CSC has remained elusive. In this study, we show a 1:1:1 stoichiometry between the three Arabidopsis thaliana secondary cell wall isozymes: CESA4, CESA7, and CESA8. This ratio was determined utilizing a simple but elegant method of quantitative immunoblotting using isoform-specific antibodies and 35S-labeled protein standards for each CESA. Additionally, the observed equimolar stoichiometry was found to be fixed along the axis of the stem, which represents a developmental gradient. Our results complement recent spectroscopic analyses pointing toward an 18-chain cellulose microfibril. Taken together, we propose that the CSC is composed of a hexamer of catalytically active CESA trimers, with each CESA in equimolar amounts. This finding is a crucial advance in understanding how CESAs integrate to form higher order complexes, which is a key determinate of cellulose microfibril and cell wall properties.