bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative local L2‐gain and Reachability analysis for nonlinear systems
Authors: Summers Erin , Chakraborty Abhijit , Tan Weehong , Topcu Ufuk , Seiler Pete , Balas Gary , Packard Andrew 
Published: January 2013

SUMMARYThis paper develops theoretical and numerical tools for quantitative local analysis of nonlinear systems. Specifically, sufficient conditions are provided for bounds on the reachable set and L2 gain of the nonlinear system subject to norm‐bounded disturbance inputs. The main theoretical results are extensions of classical dissipation inequalities but enforced only on local regions of the state and input space. Computational algorithms are derived from these local results by restricting to polynomial systems, using convex relaxations, for example the S‐procedure, and applying sum‐of‐squares optimizations. Several pedagogical and realistic examples are provided to illustrate the proposed approach. Copyright © 2013 John Wiley & Sons, Ltd.
Random non‐crossing plane configurations: A conditioned Galton‐Watson tree approach
Authors: Curien Nicolas , Kortchemski Igor 
Published: December 2012

ABSTRACTWe study various models of random non‐crossing configurations consisting of diagonals of convex polygons, and focus in particular on uniform dissections and non‐crossing trees. For both these models, we prove convergence in distribution towards Aldous’ Brownian triangulation of the disk. In the case of dissections, we also refine the study of the maximal vertex degree and validate a conjecture of Bernasconi, Panagiotou and Steger. Our main tool is the use of an underlying Galton‐Watson tree structure. © 2014 Wiley Periodicals, Inc. Random Struct. Alg., 45, 236–260, 2014
Gestational protein restriction induces CA3 dendritic atrophy in dorsal hippocampal neurons but does not alter learning and memory performance in adult offspring
Authors: Lopes A. , Torres D.B. , Rodrigues A.J. , Cerqueira J.J. , Pêgo J.M. , Sousa N. , Gontijo J.A.R. , Boer P.A. 
Published: December 2012

AbstractStudies have demonstrated that nutrient deficiency during pregnancy or in early postnatal life results in structural abnormalities in the offspring hippocampus and in cognitive impairment. In an attempt to analyze whether gestational protein restriction might induce learning and memory impairments associated with structural changes in the hippocampus, we carried out a detailed morphometric analysis of the hippocampus of male adult rats together with the behavioral characterization of these animals in the Morris water maze (MWM). Our results demonstrate that gestational protein restriction leads to a decrease in total basal dendritic length and in the number of intersections of CA3 pyramidal neurons whereas the cytoarchitecture of CA1 and dentate gyrus remained unchanged. Despite presenting significant structural rearrangements, we did not observe impairments in the MWM test. Considering the clear dissociation between the behavioral profile and the hippocampus neuronal changes, the functional significance of dendritic remodeling in fetal processing remains undisclosed.
Neonatal treatment with lipopolysaccharide differentially affects adult anxiety responses in the light–dark test and taste neophobia test in male and female rats
Authors: Tenk Christine M. , Kavaliers Martin , Ossenkopp Klaus‐Peter 
Published: December 2012

AbstractNeonatal administration of the bacterial cell wall component, lipopolysaccharide (LPS) has been shown to alter a variety of behavioural and physiological processes in the adult rat, including altering adult anxiety‐like behaviour. Research conducted to date, however, has produced conflicting findings with some results demonstrating increases in adult anxiety‐like behaviour while others report decreases or no changes in anxiety‐like behaviour. Thus, the current study conducted additional evaluation of the effects of neonatal LPS exposure on adult anxiety‐like behaviours by comparing the behavioural outcomes in the more traditional light–dark test, together with the less common hyponeophagia to sucrose solution paradigm. Male and female Long–Evans rats were treated systemically with either LPS (50 μg/kg) or saline (0.9%) on postnatal days 3 and 5. Animals were then tested in the light–dark apparatus on postnatal day 90 for 30 min. Next, following 5 days of habituation to distilled water delivery in Lickometer drinking boxes, animal were tested for neophagia to a 10% sucrose solution (0.3 M) for 30 min daily on postnatal days 96 and 97. In the light–dark test, neonatal LPS treatment decreased adult anxiety‐like behaviour in females, but not males. In contrast, neonatal exposure to LPS did not influence adult anxiety‐like behaviour as measured by hyponeophagia, but altered the licking patterns of drinking displayed towards a novel, palatable sucrose solution in adult males and females, in a manner that may reflect a decrease in situational anxiety. The current study supports the idea that neonatal LPS treatment results in highly specific alterations of adult anxiety‐like behaviour, the nature of which seems to depend not only on the measure of anxiety behaviour used, but also possibly, on the degree of anxiety experienced during the behavioural test.
Fewer adults add salt at the table after initiation of a national salt campaign in the UK: a repeated cross-sectional analysis
Authors: Sutherland Jennifer , Edwards Phil , Shankar Bhavani , Dangour Alan D. 
Published: January 2013

In 2003, the UK Food Standards Agency and the Department of Health began attempts to reduce national salt intakes via reformulation of processed foods and a consumer awareness campaign on the negative impacts of salt on health. The present study uses large nationally representative samples of households in England to assess whether discretionary salt use was affected by the national salt reduction campaign. Large cross-sectional datasets from the Health Survey for England were used to analyse trends in adults adding salt at the table between 1997 and 2007. Since 1997, there has been a steady decline in salt use at the table. Ordinal logistic regression analysis controlling for age, sex, total household income, region, ethnicity and background trends revealed that the reduction in salt use was significantly greater after the campaign (OR 0·58; 95 % CI 0·54, 0·63). Women (OR 0·71; 95 % CI 0·68, 0·74), non-white ethnic groups (OR 0·69; 95 % CI 0·62, 0·77), high-income households (OR 0·75; 95 % CI 0·69, 0·82), middle-income households (OR 0·79; 95 % CI 0·75, 0·84) and households in central (OR 0·90; 95 % CI 0·84, 0·98) or the south of England (OR 0·82; 95 % CI 0·77, 0·88) were less likely to add salt at the table. The results extend previous evidence of a beneficial response to the salt campaign by demonstrating the effect on salt use at the table. Future programmatic and research efforts may benefit from targeting specific population groups and improving the evidence base for evaluating the impact of the campaign.
Memories, identity and homeliness: the social construction of mealtimes in residential care homes in South Wales
Authors: PHILPIN SUSAN , MERRELL JOY , WARRING JOANNE , HOBBY DEBRA , GREGORY VIC 
Published: January 2013

ABSTRACTMealtimes in residential care homes are fundamentally social occasions, providing temporal structure to the day and opportunities for conversation and companionship. Food and drink are imbued with social meanings and used to express and create relationships between people. There is a dearth of research exploring care home residents' mealtime experiences in the United Kingdom. This paper reports on particular findings from a qualitative study which investigated factors influencing nutritional care provided to residents in two different types of residential care settings in South Wales, UK. Data were generated through focus group interviews with relevant staff members (N = 15), individual interviews with managers (N = 4) and residents (N = 16) of the care homes and their informal carers (N = 10), observation of food preparation and mealtimes throughout the day, and analysis of appropriate documents. Data were analysed using thematic analysis. This paper's focus is on the ways in which care home residents' experiences and understandings of mealtimes were influenced by various environmental factors, such as the home's geographical location, physical lay-out and ambience. Moreover, the shared meaning of mealtimes for residents, informal carers and staff was constructed from each group's socio-cultural background, family experiences and memories, and was integral to residents' sense of normality, community and identity.
Time-resolved metabolomics analysis of β-cells implicates the pentose phosphate pathway in the control of insulin release
Authors: Spégel Peter , Sharoyko Vladimir V. , Goehring Isabel , Danielsson Anders P. H. , Malmgren Siri , Nagorny Cecilia L. F. , Andersson Lotta E. , Koeck Thomas , Sharp Geoffrey W. G. , Straub Susanne G. , Wollheim Claes B. , Mulder Hindrik 
Published: January 2013

Insulin secretion is coupled with changes in β-cell metabolism. To define this process, 195 putative metabolites, mitochondrial respiration, NADP+, NADPH and insulin secretion were measured within 15 min of stimulation of clonal INS-1 832/13 β-cells with glucose. Rapid responses in the major metabolic pathways of glucose occurred, involving several previously suggested metabolic coupling factors. The complexity of metabolite changes observed disagreed with the concept of one single metabolite controlling insulin secretion. The complex alterations in metabolite levels suggest that a coupling signal should reflect large parts of the β-cell metabolic response. This was fulfilled by the NADPH/NADP+ ratio, which was elevated (8-fold; P&lt;0.01) at 6 min after glucose stimulation. The NADPH/NADP+ ratio paralleled an increase in ribose 5-phosphate (&gt;2.5-fold; P&lt;0.001). Inhibition of the pentose phosphate pathway by trans-dehydroepiandrosterone (DHEA) suppressed ribose 5-phosphate levels and production of reduced glutathione, as well as insulin secretion in INS-1 832/13 β-cells and rat islets without affecting ATP production. Metabolite profiling of rat islets confirmed the glucose-induced rise in ribose 5-phosphate, which was prevented by DHEA. These findings implicate the pentose phosphate pathway, and support a role for NADPH and glutathione, in β-cell stimulus-secretion coupling.
Mechanistic studies of FosB: a divalent-metal-dependent bacillithiol-S-transferase that mediates fosfomycin resistance in Staphylococcus aureus
Authors: Roberts Alexandra A. , Sharma Sunil V. , Strankman Andrew W. , Duran Shayla R. , Rawat Mamta , Hamilton Chris J. 
Published: January 2013

FosB is a divalent-metal-dependent thiol-S-transferase implicated in fosfomycin resistance among many pathogenic Gram-positive bacteria. In the present paper, we describe detailed kinetic studies of FosB from Staphylococcus aureus (SaFosB) that confirm that bacillithiol (BSH) is its preferred physiological thiol substrate. SaFosB is the first to be characterized among a new class of enzyme (bacillithiol-S-transferases), which, unlike glutathione transferases, are distributed among many low-G+C Gram-positive bacteria that use BSH instead of glutathione as their major low-molecular-mass thiol. The Km values for BSH and fosfomycin are 4.2 and 17.8 mM respectively. Substrate specificity assays revealed that the thiol and amino groups of BSH are essential for activity, whereas malate is important for SaFosB recognition and catalytic efficiency. Metal activity assays indicated that Mn2+ and Mg2+ are likely to be the relevant cofactors under physiological conditions. The serine analogue of BSH (BOH) is an effective competitive inhibitor of SaFosB with respect to BSH, but uncompetitive with respect to fosfomycin. Coupled with NMR characterization of the reaction product (BS–fosfomycin), this demonstrates that the SaFosB-catalysed reaction pathway involves a compulsory ordered binding mechanism with fosfomycin binding first followed by BSH which then attacks the more sterically hindered C-1 carbon of the fosfomycin epoxide. Disruption of BSH biosynthesis in S. aureus increases sensitivity to fosfomycin. Together, these results indicate that SaFosB is a divalent-metal-dependent bacillithiol-S-transferase that confers fosfomycin resistance on S. aureus.
Ribosomal protein S19 is a novel therapeutic agent in inflammatory kidney disease
Authors: Lv Jun , Huang Xiao Ru , Klug Jörg , Fröhlich Suada , Lacher Philipp , Xu Anping , Meinhardt Andreas , Lan Hui Yao 
Published: January 2013

RPS19 (ribosomal protein S19), a component of the 40S small ribosomal subunit, has recently been identified to bind the pro-inflammatory cytokine macrophage MIF (migration inhibitory factor). In vitro experiments identify RPS19 as the first endogenous MIF inhibitor by blocking the binding of MIF to its receptor CD74 and MIF functions on monocyte adherence to endothelial cells. In the present study, we sought to establish whether recombinant RPS19 can exert anti-inflammatory effects in a mouse model of anti-GBM (glomerular basement membrane) GN (glomerulonephritis) in which MIF is known to play an important role. Accelerated anti-GBM GN was induced in C57BL/6J mice by immunization with sheep IgG followed 5 days later by administration of sheep anti-mouse GBM serum. Groups of eight mice were treated once daily by intraperitoneal injection with 6 mg of RPS19/kg of body weight or an irrelevant control protein (human secretoglobin 2A1), or received no treatment, from day 0 until being killed on day 10. Mice that received control or no treatment developed severe crescentic anti-GBM disease on day 10 with increased serum creatinine, declined creatinine clearance and increased proteinuria. These changes were associated with up-regulation of MIF and its receptor CD74 activation of ERK (extracellular-signal-regulated kinase) and NF-κB (nuclear factor κB) signalling, prominent macrophage and T-cell infiltration, as well as up-regulation of Th1 [T-bet and IFNγ (interferon γ)] and Th17 [STAT3 (signal transducer and activator of transcription 3) and IL (interleukin)-17A] as well as IL-1β and TNFα (tumour necrosis factor α). In contrast, RPS19 treatment largely prevented the development of glomerular crescents and glomerular necrosis, and prevented renal dysfunction and proteinuria (all P&lt;0.001). Of note, RPS19 blocked up-regulation of MIF and CD74 and inactivated ERK and NF-κB signalling, thereby inhibiting macrophage and T-cell infiltration, Th1 and Th17 responses and up-regulation of pro-inflammatory cytokines (all P&lt;0.01). These results demonstrate that RPS19 is a potent anti-inflammatory agent, which appears to work primarily by inhibiting MIF signalling.
Absolute hypoxic exercise training enhancesin vitrothrombin generation by increasing procoagulant platelet-derived microparticles under high shear stress in sedentary men
Authors: Chen Yu-Wen , Chen Yi-Ching , Wang Jong-Shyan 
Published: January 2013

HS (high shear) stress associated with artery stenosis facilitates TG (thrombin generation) by increasing the release of procoagulant PDMPs (platelet-derived microparticles). Physical exercise and hypoxia may paradoxically modulate vascular thrombotic risks. The aim of the present study was to investigate how exercise training with/without hypoxia affected TG mediated by PDMPs under physio-pathological shear flows. A total of 75 sedentary males were randomly divided into five groups (n=15 in each group): 21% O2 [NC (normoxic control)] or 15% O2 [HC (hypoxic control)] at rest or were trained at 50% of peak work rate under 21% O2 [NT (normoxic training)] or 15% O2 [HAT (hypoxic-absolute training)], or 50% of HR (heart rate) reserve under 15% O2 [HRT (hypoxic-relative training)] for 30 min/day, 5 days/week for 4 weeks. The PDMP characteristics and dynamic TG were measured by flow cytometry and thrombinography respectively. Before the intervention, strenuous exercise markedly increased the PDMP count (14.8%) and TG rate (19.5%) in PDMP-rich plasma at 100 dynes/cm2 of shear stress (P&lt;0.05). After the interventions, both NT and HRT significantly attenuated the enhancement of HS-induced PDMPs (4.7 and 4.9%) and TG rate (3.8 and 3.0%) (P&lt;0.05) by severe exercise. Conversely, HAT notably promoted the PDMP count (37.3%) and TG rate (38.9%) induced by HS (P&lt;0.05), concurrent with increasing plasma TF (tissue factor) and coagulation factor V levels at rest or following exercise. We conclude that both HRT and NT depress similarly HS-mediated TG during exercise, but HAT accelerates the prothrombotic response to vigorous exercise. These findings provide new insights into how exercise training under a hypoxic condition influences the risk of thrombosis associated with stenotic arteries.
We need integrated publishing
Authors: FUND Sven 
Published: December 2012

ABSTRACTScholarly publishing has seen a decade of rapid proliferation of business models and emerging technologies. Together with globalization of the publishing market and new challenges, this evolution has also led to rapid advancements in management tasks even within small publishing houses. The outcome of this change for the stakeholders, including researchers, authors, and shareholders, is unclear, and a return to a more cohesive, integrated approach is desirable. One major obstacle must be overcome: organizational inertia.
rBiopaxParser—an R package to parse, modify and visualize BioPAX data
Authors: Kramer Frank , Bayerlová Michaela , Klemm Florian , Bleckmann Annalen , Beißbarth Tim 
Published: December 2012

Abstract
Motivation: Biological pathway data, stored in structured databases, is a useful source of knowledge for a wide range of bioinformatics algorithms and tools. The Biological Pathway Exchange (BioPAX) language has been established as a standard to store and annotate pathway information. However, use of these data within statistical analyses can be tedious. On the other hand, the statistical computing environment R has become the standard for bioinformatics analysis of large-scale genomics data. With this package, we hope to enable R users to work with BioPAX data and make use of the always increasing amount of biological pathway knowledge within data analysis methods.
Results: rBiopaxParser is a software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. These functions enable the user to access and modify specific parts of the BioPAX model. Furthermore, it allows to generate and layout regulatory graphs of controlling interactions and to visualize BioPAX pathways.
Availability: rBiopaxParser is an open-source R package and has been submitted to Bioconductor.
Contact: frank.kramer@med.uni-goettingen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
SCARPA: scaffolding reads with practical algorithms
Authors: Donmez Nilgun , Brudno Michael 
Published: December 2012

Abstract
Motivation: Scaffolding is the process of ordering and orienting contigs produced during genome assembly. Accurate scaffolding is essential for finishing draft assemblies, as it facilitates the costly and laborious procedures needed to fill in the gaps between contigs. Conventional formulations of the scaffolding problem are intractable, and most scaffolding programs rely on heuristic or approximate solutions, with potentially exponential running time.
Results: We present SCARPA, a novel scaffolder, which combines fixed-parameter tractable and bounded algorithms with Linear Programming to produce near-optimal scaffolds. We test SCARPA on real datasets in addition to a simulated diploid genome and compare its performance with several state-of-the-art scaffolders. We show that SCARPA produces longer or similar length scaffolds that are highly accurate compared with other scaffolders. SCARPA is also capable of detecting misassembled contigs and reports them during scaffolding.
Availability: SCARPA is open source and available from http://compbio.cs.toronto.edu/scarpa.
Contact: nild@cs.toronto.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Research on the film‐forming characteristics of octadecylamine at high temperatures
Authors: Cao Shun'an , Hu Jiayuan , Xie Jianli , Liang Qinqin , Yin Li 
Published: January 2013

PurposeThe purpose of this paper is to set out a study of the film‐forming characteristics of octadecylamine (ODA), estimate the feasibility of shutdown protection using ODA at high temperatures, and determine the optimum process condition of shutdown protection for units under full load if ODA has a good film‐forming effect at high temperatures.Design/methodology/approachAn autoclave was used to simulate the water‐vapor environments at 350‐560°C in the water‐steam system of power plants. The decomposition test of ODA was investigated and the ODA film‐forming characteristics were studied for furnace tube materials used in gas‐fired power plants.FindingsResults showed that ODA had a decomposition equilibrium and the decomposition products did not contain harmful organic substances such as low molecular organic acids. ODA would form a satisfactory protective film in the range of 350‐560°C with the best film at 480°C. The protection effect of the film formed by ODA at 560°C was much stronger than was that of its oxide film, which showed the feasibility of shutdown protection using ODA for gas‐fired power plants operating under full load. The optimal conditions of shutdown protection under full load were as follows: the temperature was 560°C, the concentration of ODA was 80 mg/L, the pH was 9.5 and the exposure time was 2 h. From the experimental results of X‐ray photoelectron spectroscopy, it was known that the surface film on the specimens was composed of a compound of ferroferric oxide and ODA, and the film‐forming mechanism was chemical adsorption between N in the ODA and Fe.Originality/valueIt was found that ODA has a good film‐forming effect at high temperatures and it is practicable to implement shutdown protection for base‐load units. The research results can provide theoretical guidelines for shutdown protection of gas‐fired power plants.
Risk assessment in a multinational company (MNC) operating in Vietnam: a case study approach
Authors: Muthuveloo Rajendran , Pulenthiran Ruben , Ping Teoh Ai 
Published: January 2013

PurposeThe purpose of this paper is to study on the risk and preparedness for emergency of a multinational company (MNC) based in Vietnam. This research can assist other MNCs to understand the risk they may face and formulate the necessary emergency preparation to do business in Vietnam.Design/methodology/approachThis study uses the risk management model as a guideline and risk matrix table as a tool of analysis. This research is an exploratory study base and relevant primary data are gathered through structured interviews and secondary data through the MNC web site and published financial reports.FindingsThe findings of this research indicate that there were many risk areas that were not covered by the company. It categorizes risk areas accordingly from high‐risk, medium‐risk to low risk using risk matrix. The results of the finding were based on pure estimation.Research limitations/implicationsThis study is based on a single company and there could be many other risk areas that were not covered.Originality/valueThe data for this research were collected through direct structured interviews among relevant personnel in a MNC based in Vietnam, thus the findings provide the true value of current risk scenario in Vietnam.