bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lex2B, a Phase-Variable Glycosyltransferase, Adds either a Glucose or a Galactose to
Haemophilus influenzae
Lipopolysaccharide
Authors: Deadman M. E. , Hermant P. , Engskog M. , Makepeace K. , Moxon E. R. , Schweda E. K. H. , Hood D. W. 
Published: March 2009

ABSTRACT

Nontypeable
Haemophilus influenzae
is a commensal that frequently causes otitis media and respiratory tract infections. The
lex2
locus encodes a glycosyltransferase that is phase variably expressed and contributes to the significant intrastrain heterogeneity of lipopolysaccharide (LPS) composition in
H. influenzae
. In serotype b strains, Lex2B adds the second β-glucose in the oligosaccharide extension from the proximal heptose of the triheptose inner core backbone; this extension includes a digalactoside that plays a role in resistance of the bacteria to the killing effect of serum. As part of our studies of the structure and genetics of LPS in nontypeable
H. influenzae
, we show here that there are allelic polymorphisms in the
lex2B
sequence that correlate with addition of either a glucose or a galactose to the same position in the LPS molecule across strains. Through exchange of
lex2
alleles between strains we show that alteration of a single amino acid at position 157 in Lex2B appears to be sufficient to direct the alternative glucosyl- or galactosyltransferase activities. Allelic exchange strains express LPS with altered structure and biological properties compared to the wild-type LPS. Thus, Lex2B contributes to both inter- and intrastrain LPS heterogeneity through its polymorphic sequences and phase-variable expression.
Morphological and biochemical changes inPseudomonas fluorescensbiofilms induced by sub-inhibitory exposure to antimicrobial agents
Authors: Dynes James J. , Lawrence John R. , Korber Darren R. , Swerhone George D.W. , Leppard Gary G. , Hitchcock Adam P. 
Published: March 2009

Confocal laser scanning microscopy (CLSM) and scanning transmission X-ray microscopy (STXM) were used to examine the morphological and biochemical changes in Pseudomonas fluorescens biofilms grown in the presence of subinhibitory concentrations of 4 antimicrobial agents: triclosan, benzalkonium chloride, chlorhexidine dihydrochloride, and trisodium phosphate. CLSM analyses using the stains SYTO9 and propidium iodide indicated that the antimicrobial agents affected cell membrane integrity and cellular density to differing degrees. However, fluorescein diacetate assays and plate counts demonstrated that the cells remained metabolically active. Fluorescent lectin binding assays showed that changes in the arrangement and composition of the exopolymer matrix of the biofilms also occurred and that these changes depended on the antimicrobial agent. Detailed single cell analyses using STXM provided evidence that the cell morphology, and the spatial distribution and relative amounts of protein, lipids and polysaccharides in the biofilms and within the cells were different for each antimicrobial. The distribution of chlorhexidine in the biofilm, determined from its distinct spectral signature, was localized mainly inside the bacterial cells. Each antimicrobial agent elicited a unique response; P. fluorescens cells and biofilms changed their morphology and architecture, as well as the distribution and abundance of biomacromolecules, in particular the exopolymer matrix. Pseudomonas fluorescens also exhibited adaptation to benzalkonium chloride at 10 µg/mL. Our observations point to the importance of changes in the quantity and chemistry of the exopolymeric matrix in the response to antimicrobial agents and suggest their importance as targets for control.
Reduced in vivo phosphodiesterase-4 response to acute noradrenaline challenge in diet-induced obese rats
Authors: Greene Michael , Thackeray James T. , Kenk Miran , Thorn Stephanie L. , Bevilacqua Lisa , Harper Mary-Ellen , Beanlands Rob S. , DaSilva Jean N. 
Published: March 2009

Altered sympathetic nervous activity has been linked to the development and persistence of obesity, partly relating to overfeeding. Binding of the selective, positron-emitting phosphodiesterase-4 (PDE4) inhibitor (R)-[11C]rolipram provides a direct index of the cAMP-hydrolyzing enzyme PDE4. This study examines progressive alterations in PDE4 in a high-fat-fed obese animal model. (R)-[11C]Rolipram was injected into diet-induced obese (DIO) and diet-resistant (DR) rats; the animals were killed after 45 min, tissues were extracted, and radioactivity was quantified. Responsiveness of PDE4 to acute noradrenaline (NA) stimulation was determined by 3 h pretreatment with the NA reuptake inhibitor desipramine. There was minimal variance in caloric intake, weight gain, fasting glucose, insulin, and energy expenditure (indirect calorimetry) measures. Basal (R)-[11C]rolipram binding was comparable between DIO and DR rats at 2 or 8 weeks of feeding. The normal increase of PDE4 levels in response to elevated NA by desipramine pretreatment was ablated in PDE4-rich tissues, including brain, heart, and skeletal muscle, of DIO animals after 8 weeks of high-fat diet. Lean DR rats maintained PDE4 responsiveness indicative of a normal NA signal transduction.
Role of protein kinase C β2activation in TNF-α-induced human vascular endothelial cell apoptosis
Authors: Wang Fang , Liu Hui-min , Irwin Michael G. , Xia Zhong-yuan , Huang Zhiyong , Ouyang Jingping , Xia Zhengyuan 
Published: March 2009

The circulatory inflammatory cytokine tumor necrosis factor alpha (TNF-α) is increased in pathologic conditions that initiate or exacerbate vascular endothelial injury, such as diabetes. Protein kinase C (PKC) has been shown to play a critical role in TNF-α-induced human endothelial cell apoptosis. However, the relative roles played by specific isoforms of PKC in TNF-α-induced human endothelial cell apoptosis have not been addressed. We investigated the effects of a selective PKCβ2inhibitor (CGP53353) on TNF-α-induced apoptosis in human vascular endothelial cells (cell line ECV304) and on the production of reactive oxygen species and nitric oxide, and compared its effects with rottlerin, a reagent that has been shown to reduce PKCδ protein levels. Cultured human vascular endothelial cells (ECV304) were treated for 24 h with one of 4 regimes: 40 ng/mL TNF-α alone (TNF-α), TNF-α with 10 µmol/L rottlerin (T+rottlerin), TNF-α with 1 µmol/L CGP53353 (T+CGP), or untreated (control). Cell viability was measured by MTT assay, and cell apoptosis was assessed by flow cytometry. TNF-α-induced endothelial cell apoptosis was associated with dramatic increases in production of intracellular hydrogen peroxide (approximately 20 times greater than control) and superoxide (approximately 16 times greater than control), as measured by dichlorofluorescein and dihydroethidium fluorescent staining, respectively. This increase was accompanied by reduced activity of superoxide dismutase and glutathione peroxidase and, subsequently, an increase in the lipid peroxidation product malondialdehyde. CGP53353, but not rottlerin, abolished or attenuated all these changes. We conclude that PKCβ2plays a major role in TNF-α-induced human vascular endothelial cell apoptosis.
NovelLPLmutations associated with lipoprotein lipase deficiency: two case reports and a literature review
Authors: Rahalkar Amit R. , Giffen Fiona , Har Bryan , Ho Josephine , Morrison Katherine M. , Hill John , Wang Jian , Hegele Robert A. , Joy Tisha 
Published: March 2009

Lipoprotein lipase (LPL) is a key enzyme involved with hydrolysis and removal of triglycerides from plasma. LPL deficiency is a rare condition with an estimated prevalence of 1 in 106. It is characterized biochemically by elevated triglycerides and lowered HDL in the plasma and clinically by a constellation of signs and symptoms during childhood including failure to thrive, lipemia retinalis, eruptive xanthomas, hepatosplenomegaly, and acute pancreatitis. Nearly 100 mutations in the LPL gene have been associated with LPL deficiency. Here we report 2 unrelated pedigrees with LPL deficiency from 2 novel disease-causing LPL mutations: a Gly159Glu missense mutation in exon 5 and a 4-bp ACGG deletion at the 3′ boundary of exon 2. We present molecular findings of these 2 cases and review the biochemical, clinical, and genetic features of LPL deficiency.
Growth and ionoregulatory ontogeny of wild and hatchery-raised juvenile pink salmon (Oncorhynchus gorbuscha)
Authors: Grant A. , Gardner M. , Nendick L. , Sackville M. , Farrell A. P. , Brauner C. J. 
Published: March 2009

Juvenile pink salmon ( Oncorhynchus gorbuscha (Walbaum, 1792)) enter seawater (SW) shortly following emergence. Little is known about growth and development during this life-history stage when sensitivity to sea louse exposure may be high, an issue that is of current concern in British Columbia. We tested the hypothesis that growth and ionoregulatory development were similar in hatchery-raised (Quinsam) and wild (Glendale and One’s Point) juvenile pink salmon (measured over 22 weeks) following SW entry. Fish body mass increased from 0.20 ± 0.01 to 6.47 ± 0.37 g, with mean specific growth rates of 2.74% to 3.05% body mass·day–1among the three groups. In all three groups, gill Na+–K+-ATPase (NKA) activity peaked at 12 µmol ADP·mg protein–1·h–1following 8 weeks post-transfer to SW. Whole body Na+and Cl–concentrations, which again did not differ among groups, were highest upon initial exposure to SW (~70 mmol·kg wet mass–1) and declined over time as gill NKA activity increased, indicating that the hypo-osmoregulatory capacity was not fully developed following emergence and initial entry into SW. Thus, consistent with our hypothesis, few differences were observed between hatchery-raised and wild juvenile pink salmon reared under laboratory conditions. These baseline data may be important for future studies in determining the effects of sea lice on wild juvenile pink salmon.
Ambient temperature and annual timing affect torpor bouts and euthermic phases of hibernating European ground squirrels (Spermophilus citellus)
Authors: Németh István , Nyitrai Viktor , Altbäcker Vilmos 
Published: March 2009

The low body temperature state of hibernating mammals is interrupted regularly by short euthermic phases. The frequency of these euthermic phases changes according to the phase of hibernation. This typical pattern, common among ground squirrels (genus Spermophilus F. Cuvier, 1825), can be regulated by internal factors and affected by outside temperature. To evaluate the effects of internal annual timing and ambient temperature, we monitored nest temperatures of overwintering European ground squirrels ( Spermophilus citellus (L., 1766)) under three temperature conditions during late hibernation (9, 5, 0 °C). Our results showed that in spite of constant thermal conditions, an annual timing effect changed torpor-bout length (TBL) at 9 and 5 °C but not at 0 °C. Ambient temperature had an independent influence on TBL and euthermic phases. The loss in body mass was higher at higher ambient temperatures and was affected by TBL and euthermic phases. Thus, the hibernation pattern of European ground squirrels is regulated by both an annual timing pattern and the ambient temperature in the hibernacula.
Molecular systematics of the genus Sigmodon: results from mitochondrial and nuclear gene sequences
Authors: Henson Dallas D. , Bradley Robert D. 
Published: March 2009

Phylogenetic relationships within the genus Sigmodon Say and Ord, 1825 were examined using sequence data from multiple gene regions, including exon 1 of the nuclear-encoded interphotoreceptor retinoid binding protein, intron 7 of the nuclear beta-fibrinogen gene, and the mitochondrial cytochrome b gene from 27 individuals representing 11 species of Sigmodon. Nuclear genes were analyzed independently, combined with each other, and combined with the mitochondrial data. Topologies were constructed using parsimony and Bayesian methods, with nodal support provided by bootstrap and posterior probability values. All analyses recovered four independent clades (I–IV), each representing unique species groups: hispidus , fulviventer , peruanus , and alstoni . The analyses from the combined data also provided support for relationships previously proposed within those species groups.
CESÀRO–VOLTERRA PATH INTEGRAL FORMULA ON A SURFACE
Authors: CIARLET PHILIPPE G. , GRATIE LILIANA , SERPILLI MICHELE 
Published: March 2009

If a symmetric matrix field e = (eij) of order three satisfies the Saint-Venant compatibility relations in a simply-connected open subset Ω of ℝ3, then e is the linearized strain tensor field of a displacement field v of Ω, i.e. [Formula: see text] in Ω. A classical result, due to Cesàro and Volterra, asserts that, if the field e is smooth, the unknown displacement field v(x) at any point x ∈ Ω can be explicitly written as a path integral inside Ω with endpoint x, and whose integrand is an explicit function of the functions eij and their derivatives. Now let ω be a simply-connected open subset in ℝ2 and let θ : ω → ℝ3 be a smooth immersion. If two symmetric matrix fields (γαβ) and (ραβ) of order two satisfy appropriate compatibility relations in ω, then (γαβ) and (ραβ) are the linearized change of metric and change of curvature tensor field corresponding to a displacement vector field η of the surface θ(ω). We show here that a "Cesàro–Volterra path integral formula on a surface" likewise holds when the fields (γαβ) and (ραβ) are smooth. This means that the displacement vector η(y) at any point θ(y), y ∈ ω, of the surface θ(ω) can be explicitly computed as a path integral inside ω with endpoint y, and whose integrand is an explicit function of the functions γαβ and ραβ and their covariant derivatives. Such a formula has potential applications to the mathematical analysis and numerical simulation of linear "intrinsic" shell models.
Identifying and applying psychological theory to setting and achieving rehabilitation goals
Authors: Scobbie Lesley , Wyke Sally , Dixon Diane 
Published: March 2009

Background: Goal setting is considered to be a fundamental part of rehabilitation; however, theories of behaviour change relevant to goal-setting practice have not been comprehensively reviewed. Objectives: (i) To identify and discuss specific theories of behaviour change relevant to goal-setting practice in the rehabilitation setting. (ii) To identify `candidate' theories that that offer most potential to inform clinical practice. Methods: The rehabilitation and self-management literature was systematically searched to identify review papers or empirical studies that proposed a specific theory of behaviour change relevant to setting and/or achieving goals in a clinical context. Data from included papers were extracted under the headings of: key constructs, clinical application and empirical support. Results: Twenty-four papers were included in the review which proposed a total of five theories: (i) social cognitive theory, (ii) goal setting theory, (iii) health action process approach, (iv) proactive coping theory, and (v) the self-regulatory model of illness behaviour. The first three of these theories demonstrated most potential to inform clinical practice, on the basis of their capacity to inform interventions that resulted in improved patient outcomes. Conclusions: Social cognitive theory, goal setting theory and the health action process approach are theories of behaviour change that can inform clinicians in the process of setting and achieving goals in the rehabilitation setting. Overlapping constructs within these theories have been identified, and can be applied in clinical practice through the development and evaluation of a goal-setting practice framework.
Matrix metalloprotease polymorphisms are associated with gas transfer in alpha 1 antitrypsin deficiency
Authors: McAloon Christopher J. , Wood Alice M. , Gough Stephen C. , Stockley Robert A. 
Published: March 2009

Alpha-1-antitrypsin deficiency (AATD) is associated with variable development of emphysema and other features of chronic obstructive pulmonary disease (COPD). Matrix metalloproteinases (MMPs) are believed to be important in the pathophysiology of COPD, and may therefore confer susceptibility to this phenotype in patients with AATD. Objectives: to assess the role of polymorphism of MMP1, MMP3 and MMP12 in AATD phenotypes. Methods: 424 PiZZ subjects from the UK AATD Registry were assessed for history of chronic bronchitis (CB), post-bronchodilator lung function impairment and decline of lung function. Tag single nucleotide polymorphisms (SNPs) for MMP1, MMP3 and MMP12 were chosen using HapMap (r2>0.8, MAF>0.05) and were genotyped using TaqMan® genotyping technologies. Quantitative genetic association was assessed using regression modelling to correct for covariates. Results: in patients with AATD, carriers of the G allele of rs678815 ( MMP3) had lower gas transfer (KCO) ( P = 0.025, B =-7.766) than the homozygous wild type, while carriers of the T allele of rs470358 ( MMP1) had higher KCO ( P = 0.025, B = 6.130). Conclusions: variations in MMP1 and MMP3 are associated with gas transfer in AATD, supporting a previous family study showing linkage of KCO to this gene region. Replication of these preliminary data is now required particularly if MMP inhibitors are to be considered as a therapeutic option.
Imatinib mesylate as salvage therapy for refractory sclerotic chronic graft-versus-host disease
Authors: Magro Leonardo , Mohty Mohamad , Catteau Benoit , Coiteux Valérie , Chevallier Patrice , Terriou Louis , Jouet Jean-Pierre , Yakoub-Agha Ibrahim 
Published: March 2009

Abstract
Imatinib is a promising candidate for the treatment of fibrotic diseases. This retrospective study evaluated the use of imatinib for the treatment of refractory sclerotic chronic graft-versus-host disease in 14 patients with different hematologic malignancies. Imatinib was started at a median of 44 months after transplantation (range, 16-119 months after transplantation) and was administered for a median of 5.9 months from time of initiation (range, 2.1-74 months from time of initiation). With a median overall follow-up of 11.6 months from time of initiation (range, 4.1-74 months from time of initiation) of imatinib, 4 patients (29%) had to stop imatinib because of drug intolerance. All other adverse reactions were of mild-to-moderate grade and could be managed symptomatically. Overall, 7 patients responded to imatinib (50%; 95% confidence interval, 24%-76%) with 4 patients improving their Rodman score more than or equal to 90%. In addition, imatinib therapy allowed for a significant reduction of corticosteroid dosage. Despite its limited size, this cohort suggests some beneficial activity of imatinib in sclerotic chronic graft-versus-host disease, warranting further prospective investigations.
Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data
Authors: Jaitly Navdeep , Mayampurath Anoop , Littlefield Kyle , Adkins Joshua N , Anderson Gordon A , Smith Richard D 
Published: March 2009

Abstract

Background
Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting this data involves inferring the masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as reading raw data, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls.

Results
With a variety of options that include peak processing, deisotoping, isotope composition, etc, Decon2LS supports processing of multiple raw data formats. Deisotoping can be performed on an individual scan, an individual dataset, or on multiple datasets using batch processing. Other processing options include creating a two dimensional view of mass and liquid chromatography (LC) elution time features, generating spectrum files for tandem MS data, creating total intensity chromatograms, and visualizing theoretical peptide profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample.

Conclusion
Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, Decon2LS is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs.
Decon2LS source code, installer, and tutorials may be downloaded free of charge at http://http:/ncrr.pnl.gov/software/.
Analyses of domains and domain fusions in human proto-oncogenes
Authors: Liu Qi , Huang Jinling , Liu Huiqing , Wan Ping , Ye Xiuzi , Xu Ying 
Published: March 2009

AbstractBackgroundUnderstanding the constituent domains of oncogenes, their origins and their fusions may shed new light about the initiation and the development of cancers.ResultsWe have developed a computational pipeline for identification of functional domains of human genes, prediction of the origins of these domains and their major fusion events during evolution through integration of existing and new tools of our own. An application of the pipeline to 124 well-characterized human oncogenes has led to the identification of a collection of domains and domain pairs that occur substantially more frequently in oncogenes than in human genes on average. Most of these enriched domains and domain pairs are related to tyrosine kinase activities. In addition, our analyses indicate that a substantial portion of the domain-fusion events of oncogenes took place in metazoans during evolution.ConclusionWe expect that the computational pipeline for domain identification, domain origin and domain fusion prediction will prove to be useful for studying other groups of genes.