bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of lipoprotein-associated phospholipase A2 deficiency on pulmonary allergic responses in aspergillus fumigatus sensitized mice
Authors: Jiang Zhilong , Fehrenbach Melane L , Ravaioli Giulia , Kokalari Blerina , Redai Imre G , Sheardown Steven A , Wilson Stephen , Macphee Colin , Haczku Angela 
Published: November 2012

AbstractBackgroundLipoprotein-associated phospholipase A2(Lp-PLA2)/platelet-activating factor acetylhydrolase (PAF-AH) has been implicated in the pathogenesis of cardiovascular disease. A therapeutic targeting of this enzyme was challenged by the concern that increased circulating platelet activating factor (PAF) may predispose to or increase the severity of the allergic airway response. The aim of this study was to investigate whether Lp-PLA2gene deficiency increases the risk of PAF and IgE-mediated inflammatory responsesin vitroandin vivousing mouse models.MethodsLp-PLA2-/- mice were generated and back crossed to the C57BL/6 background. PAF-AH activity was measured using a hydrolysis assay in serum and bronchoalveolar lavage (BAL) samples obtained from mice.Aspergillus fumigatus(Af)-specific serum was prepared for passive allergic sensitization of micein vivoand mast cellsin vitro. β- hexosaminidase release was studied in bone marrow derived mast cells sensitized withAf-specific serum or DNP-IgE and challenged withAfor DNP, respectively. Mice were treated with lipopolysaccharide (LPS) and PAF intratracheally and studied 24 hours later. Mice were sensitized either passively or actively againstAfand were studied 48 hours after a single intranasalAfchallenge. Airway responsiveness to methacholine, inflammatory cell influx in the lung tissue and BAL, immunoglobulin (ELISA) and cytokine (Luminex) profiles were compared between the wild type (WT) and Lp-PLA2-/- mice.ResultsPAF-AH activity was reduced but not completely abolished in Lp-PLA2-/- serum or byin vitrotreatment of serum samples with a high saturating concentration of the selective Lp-PLA2inhibitor, SB-435495. PAF inhalation significantly enhanced airway inflammation of LPS treated WT and Lp-PLA2-/- mice to a similar extent. Sensitized WT and Lp-PLA2-/- bone-marrow derived mast cells released β-hexosaminidase following stimulation by allergen or IgE crosslinking to equivalent levels. Wild type and Lp-PLA2-/- mice responded to passive or active allergic sensitization by significant IgE production, airway inflammation and hyperresponsiveness afterAfchallenge. BAL cell influx was not different between these strains while IL-4, IL-5, IL-6 and eotaxin release was attenuated in Lp-PLA2-/- mice. There were no differences in the amount of total IgE levels in theAfsensitized WT and Lp-PLA2-/- mice.ConclusionsWe conclude that Lp-PLA2deficiency in C57BL/6 mice did not result in a heightened airway inflammation or hyperresponsiveness after PAF/LPS treatment or passive or active allergic sensitization and challenge.
Effective inter-residue contact definitions for accurate protein fold recognition
Authors: Yuan Chao , Chen Hao , Kihara Daisuke 
Published: November 2012

Abstract

Background
Effective encoding of residue contact information is crucial for protein structure prediction since it has a unique role to capture long-range residue interactions compared to other commonly used scoring terms. The residue contact information can be incorporated in structure prediction in several different ways: It can be incorporated as statistical potentials or it can be also used as constraints in ab initio structure prediction. To seek the most effective definition of residue contacts for template-based protein structure prediction, we evaluated 45 different contact definitions, varying bases of contacts and distance cutoffs, in terms of their ability to identify proteins of the same fold.

Results
We found that overall the residue contact pattern can distinguish protein folds best when contacts are defined for residue pairs whose Cβ atoms are at 7.0 Å or closer to each other. Lower fold recognition accuracy was observed when inaccurate threading alignments were used to identify common residue contacts between protein pairs. In the case of threading, alignment accuracy strongly influences the fraction of common contacts identified among proteins of the same fold, which eventually affects the fold recognition accuracy. The largest deterioration of the fold recognition was observed for β-class proteins when the threading methods were used because the average alignment accuracy was worst for this fold class. When results of fold recognition were examined for individual proteins, we found that the effective contact definition depends on the fold of the proteins. A larger distance cutoff is often advantageous for capturing spatial arrangement of the secondary structures which are not physically in contact. For capturing contacts between neighboring β strands, considering the distance between Cα atoms is better than the Cβ−based distance because the side-chain of interacting residues on β strands sometimes point to opposite directions.

Conclusion
Residue contacts defined by Cβ−Cβ distance of 7.0 Å work best overall among tested to identify proteins of the same fold. We also found that effective contact definitions differ from fold to fold, suggesting that using different residue contact definition specific for each template will lead to improvement of the performance of threading.
Distribution and diversity of mycoplasma plasmids: lessons from cryptic genetic elements
Authors: Breton Marc , Tardy Florence , Dordet-Frisoni Emilie , Sagne Eveline , Mick Virginie , Renaudin Joël , Sirand-Pugnet Pascal , Citti Christine , Blanchard Alain 
Published: November 2012

Abstract

Background
The evolution of mycoplasmas from a common ancestor with Firmicutes has been characterized not only by genome down-sizing but also by horizontal gene transfer between mycoplasma species sharing a common host. The mechanisms of these gene transfers remain unclear because our knowledge of the mycoplasma mobile genetic elements is limited. In particular, only a few plasmids have been described within the Mycoplasma genus.

Results
We have shown that several species of ruminant mycoplasmas carry plasmids that are members of a large family of elements and replicate via a rolling-circle mechanism. All plasmids were isolated from species that either belonged or were closely related to the Mycoplasma mycoides cluster; none was from the Mycoplasma bovis-Mycoplasma agalactiae group. Twenty one plasmids were completely sequenced, named and compared with each other and with the five mycoplasma plasmids previously reported. All plasmids share similar size and genetic organization, and present a mosaic structure. A peculiar case is that of the plasmid pMyBK1 from M. yeatsii; it is larger in size and is predicted to be mobilizable. Its origin of replication and replication protein were identified. In addition, pMyBK1 derivatives were shown to replicate in various species of the M. mycoides cluster, and therefore hold considerable promise for developing gene vectors. The phylogenetic analysis of these plasmids confirms the uniqueness of pMyBK1 and indicates that the other mycoplasma plasmids cluster together, apart from the related replicons found in phytoplasmas and in species of the clade Firmicutes.

Conclusions
Our results unraveled a totally new picture of mycoplasma plasmids. Although they probably play a limited role in the gene exchanges that participate in mycoplasma evolution, they are abundant in some species. Evidence for the occurrence of frequent genetic recombination strongly suggests they are transmitted between species sharing a common host or niche.
Case control study to identify risk factors for acute hepatitis C virus infection in Egypt
Authors: Kandeel Amr M , Talaat Maha , Afifi Salma A , El-Sayed Nasr M , Fadeel Moustafa A Abdel , Hajjeh Rana A , Mahoney Frank J 
Published: November 2012

Abstract

Background
Identification of risk factors of acute hepatitis C virus (HCV) infection in Egypt is crucial to develop appropriate prevention strategies.

Methods
We conducted a case–control study, June 2007-September 2008, to investigate risk factors for acute HCV infection in Egypt among 86 patients and 287 age and gender matched controls identified in two infectious disease hospitals in Cairo and Alexandria. Case-patients were defined as: any patient with symptoms of acute hepatitis; lab tested positive for HCV antibodies and negative for HBsAg, HBc IgM, HAV IgM; and 7-fold increase in the upper limit of transaminase levels. Controls were selected from patients’ visitors with negative viral hepatitis markers. Subjects were interviewed about previous exposures within six months, including community-acquired and health-care associated practices.

Results
Case-patients were more likely than controls to have received injection with a reused syringe (OR=23.1, CI 4.7-153), to have been in prison (OR=21.5, CI 2.5-479.6), to have received IV fluids in a hospital (OR=13.8, CI 5.3-37.2), to have been an IV drug user (OR=12.1, CI 4.6-33.1), to have had minimal surgical procedures (OR=9.7, CI 4.2-22.4), to have received IV fluid as an outpatient (OR=8, CI 4–16.2), or to have been admitted to hospital (OR=7.9, CI 4.2-15) within the last 6 months. Multivariate analysis indicated that unsafe health facility practices are the main risk factors associated with transmission of HCV infection in Egypt.

Conclusion
In Egypt, focusing acute HCV prevention measures on health-care settings would have a beneficial impact.
PDGFRα/β and VEGFR2 polymorphisms in colorectal cancer: incidence and implications in clinical outcome
Authors: Estevez-Garcia Purificacion , Castaño Angel , Martin Ana C , Lopez-Rios Fernando , Iglesias Joaquin , Muñoz-Galván Sandra , Lopez-Calderero Iker , Molina-Pinelo Sonia , Pastor Maria D , Carnero Amancio , Paz-Ares Luis , Garcia-Carbonero Rocio 
Published: November 2012

AbstractBackgroundAngiogenesis plays an essential role in tumor growth and metastasis, and is a major target in cancer therapy. VEGFR and PDGFR are key players involved in this process. The purpose of this study was to assess the incidence of genetic variants in these receptors and its potential clinical implications in colorectal cancer (CRC).MethodsVEGFR2, PDGFRα and PDGFRβ mutations were evaluated by sequencing their tyrosine kinase domains in 8 CRC cell lines and in 92 samples of patients with CRC. Correlations with clinicopathological features and survival were analyzed.ResultsFour SNPs were identified, three in PDGFRα [exon 12 (A12): c.1701A>G; exon 13 (A13): c.1809G>A; and exon 17 (A17): c.2439+58C>A] and one in PDGFRβ [exon 19 (B19): c.2601A>G]. SNP B19, identified in 58% of tumor samples and in 4 cell lines (LS174T, LS180, SW48, COLO205), was associated with higher PDGFR and pPDGFR protein levels. Consistent with this observation, 5-year survival was greater for patients with PDGFR B19 wild type tumors (AA) than for those harboring the G-allele genotype (GA or GG) (51% vs 17%; p=0.073). Multivariate analysis confirmed SNP B19 (p=0.029) was a significant prognostic factor for survival, independent of age (p=0.060) or TNM stage (p<0.001).ConclusionsPDGFRβ exon 19 c.2601A>G SNP is commonly encountered in CRC patients and is associated with increased pathway activation and poorer survival. Implications regarding its potential influence in response to PDGFR-targeted agents remain to be elucidated.
Hydroxypropyl methylcellulose, a viscous soluble fiber, reduces insulin resistance and decreases fatty liver in Zucker Diabetic Fatty rats
Authors: Brockman David A , Chen Xiaoli , Gallaher Daniel D 
Published: November 2012

Abstract

Background
Diets producing a high glycemic response result in exaggerated insulin secretion which induces hepatic lipogenesis, contributing to development of insulin resistance and fatty liver. Viscous dietary fibers blunt the postprandial rise in blood glucose, however their effect on type 2 diabetes and obesity are not entirely known. This study examined the effect of chronic consumption of the viscous, non-fermentable dietary fiber, hydroxypropyl methylcellulose (HPMC), on glucose control, insulin resistance and liver lipids in an obese diabetic rat model.

Methods
Three groups of Zucker Diabetic Fatty (ZDF) rats were fed diets containing either 5% non-viscous cellulose (control), low viscosity HPMC (LV-HPMC) or high viscosity HPMC (HV- HPMC) for six weeks. Zucker lean littermates consuming cellulose served as a negative control. Markers of glucose control, including oral glucose tolerance test, glycated hemoglobin and urinary glucose, were measured as well as adiposity and the accumulation of liver lipids.

Results
The HPMC diets increased the viscosity of the small intestinal contents and reduced the postprandial rise in blood glucose. The food efficiency ratio was greater with HPMC feeding compared to the obese control and urinary excretion of glucose and ketone bodies was reduced. The two HPMC groups had lower glycated hemoglobin and kidney weights and a reduced area under the curve during a glucose tolerance test, indicating improved glucose control. Epididymal fat pad weight as percent of body weight was reduced in the HV-HPMC group compared to the obese control group. The HV-HPMC group also had lower concentrations of liver lipid and cholesterol and reduced liver weight. However, HV-HPMC feeding did not affect hepatic gene expression of SREBP-1c or FAS. Muscle concentration of acylcarnitines, a lipid intermediate in fatty acid β-oxidation, was not different between the HPMC groups and obese control, suggesting no change in muscle fatty acid oxidation by HPMC.

Conclusions
Consumption of the viscous non-fermentable fiber HPMC decreased diabetic wasting, improved glucose control and reduced insulin resistance and fatty liver in a model of obesity with diabetes.
Intact skin and not stripped skin is crucial for the safety and efficacy of peanut epicutaneous immunotherapy (EPIT) in mice
Authors: Mondoulet Lucie , Dioszeghy Vincent , Puteaux Emilie , Ligouis Mélanie , Dhelft Véronique , Letourneur Franck , Dupont Christophe , Benhamou Pierre‐Henri 
Published: November 2012

AbstractBackgroundEpicutaneous immunotherapy (EPIT) on intact skin with an epicutaneous delivery system has already been used in preclinical and clinical studies. In epicutaneous vaccination and immunotherapy, the stripping of skin before application of the allergen is suggested to facilitate the passage of allergen through immune cells.ObjectivesThe aim of this study was to compare the immunological response induced by EPIT performed on intact and stripped skin in a mouse model of peanut allergy.MethodsAfter oral sensitization with peanut and cholera toxin, BALB/c mice were epicutaneously treated using an epicutaneous delivery system (Viaskin® (DBV Technologies, Paris) applied either on intact skin or on stripped skin. Following EPIT, mice received an exclusive oral peanut regimen, aimed at triggering esophageal and jejunal lesions. We assessed eosinophil infiltration by histology, mRNA expression in the esophagus, antibody levels and peripheral T‐cell response.ResultsEPIT on intact skin significantly reduced Th2 immunological response (IgE response and splenocyte secretion of Th2 cytokines) as well as esophageal eosinophilia (2.7 ± 0.9, compared to Sham 19.9 ± 1.5, p < 0.01), mRNA expression of Th2 cytokines in tissue and intestinal villus sub‐atrophia (2.9 ± 0.2 vs Sham, 2.1 ± 0.2, p < 0.05). By contrast, EPIT on stripped skin reinforced Th2 systemic immunological response as well as eosinophil infiltration (26.8 ± 15.1), mRNA expression of Th2 cytokines and duodenal villus/crypt‐ratio (2.4 ± 0.3).ConclusionsEpicutaneous allergen‐specific immunotherapy needs the integrity of superficial layers of the stratum corneum to warranty safety of treatment and to induce a tolerogenic profile of the immune response.
Volume Oscillation in Macroporous Gel
Authors: Maeda Shingo , Oda Wahei 
Published: November 2012

Abstract
We succeeded in synthesizing microphase-separated self-oscillating gel and realized volume oscillation of the gel driven by chemical energy. The novel polymer gels were composed of a non-thermoresponsive polyacrylamide main chain covalently bonded to a ruthenium catalyst for the Belousov–Zhabotinsky (BZ) reaction. By changing the temperature, the displacement and frequency of the volume oscillation in gels were changed. Moreover, we showed that the displacement of the gel has a trade-off relationship with the frequency of the volume oscillation.
Assembly of a Small DNA Rectangular Parallelepiped Block into Higher Order Nanostructures
Authors: Nakagawa Hiroyuki , Toda Mariko , Atsumi Hiroshi , Hagihara Masaki , Hayashi-Nishino Mitsuko , Dohno Chikara , Nakatani Kazuhiko 
Published: November 2012

Abstract
A small DNA rectangular parallelepiped block was prepared from a single stranded scaffold strand of 1152 nt long and 28 staple strands by DNA origami method. The scaffold strand, which was obtained by PCR using a phosphorylated primer followed by λ exonuclease digestion, was folded into the designed structure. Subsequent assembly of the DNA block into higher order DNA nanostructures was achieved by slow annealing conditions in the presence of linker strands, giving both the tail-to-tail dimer and the tail-to-head one-dimensional oligomer with a choice of appropriate linker strands.
The Therapeutic Alliance Between Clinicians and Patients Predicts Outcome in Chronic Low Back Pain
Authors: Ferreira Paulo H. , Ferreira Manuela L. , Maher Christopher G. , Refshauge Kathryn M. , Latimer Jane , Adams Roger D. 
Published: November 2012

Background
The impact of the relationship (therapeutic alliance) between patients and physical therapists on treatment outcome in the rehabilitation of patients with chronic low back pain (LBP) has not been previously investigated.

Objective
The purpose of this study was to investigate whether the therapeutic alliance between physical therapists and patients with chronic LBP predicts clinical outcomes.

Design
This was a retrospective observational study nested within a randomized controlled trial.

Methods
One hundred eighty-two patients with chronic LBP who volunteered for a randomized controlled trial that compared the efficacy of exercises and spinal manipulative therapy rated their alliance with physical therapists by completing the Working Alliance Inventory at the second treatment session. The primary outcomes of function, global perceived effect of treatment, pain, and disability were assessed before and after 8 weeks of treatment. Linear regression models were used to investigate whether the alliance was a predictor of outcome or moderated the effect of treatment.

Results
The therapeutic alliance was consistently a predictor of outcome for all the measures of treatment outcome. The therapeutic alliance moderated the effect of treatment on global perceived effect for 2 of 3 treatment contrasts (general exercise versus motor control exercise, spinal manipulative therapy versus motor control exercise). There was no treatment effect modification when outcome was measured with function, pain, and disability measures.

Limitations
Therapeutic alliance was measured at the second treatment session, which might have biased the interaction during initial stages of treatment. Data analysis was restricted to primary outcomes at 8 weeks.

Conclusions
Positive therapeutic alliance ratings between physical therapists and patients are associated with improvements of outcomes in LBP. Future research should investigate the factors explaining this relationship and the impact of training interventions aimed at optimizing the alliance.
What Characterizes People Who Have an Unclear Classification Using a Treatment-Based Classification Algorithm for Low Back Pain? A Cross-Sectional Study
Authors: Stanton Tasha R. , Hancock Mark J. , Apeldoorn Adri T. , Wand Benedict M. , Fritz Julie M. 
Published: November 2012

Background
A treatment-based classification algorithm for low back pain (LBP) was created to help clinicians select treatments to which people are most likely to respond. To allow the algorithm to classify all people with LBP, additional criteria can help therapists make decisions for people who do not clearly fit into a subgroup (ie, unclear classifications). Recent studies indicated that classifications are unclear for approximately 34% of people with LBP.

Objective
To guide improvements in the algorithm, it is imperative to determine whether people with unclear classifications are different from those with clear classifications.

Design
This study was a secondary analysis of data from 3 previous studies investigating the algorithm.

Methods
Baseline data from 529 people who had LBP were used (3 discrete cohorts). The primary outcome was type of classification, that is, clear or unclear. Univariate logistic regression was used to determine which participant variables were related to having an unclear classification.

Results
People with unclear classifications had greater odds of being older (odds ratio [OR]=1.01, 95% confidence interval [CI]=1.003–1.033), having a longer duration of LBP (OR=1.001, 95% CI=1.000–1.001), having had a previous episode(s) of LBP (OR=1.61, 95% CI=1.04–2.49), having fewer fear-avoidance beliefs related to both work (OR=0.98, 95% CI=0.96–0.99) and physical activity (OR=0.98, 95% CI=0.96–0.996), and having less LBP-related disability (OR=0.98, 95% CI=0.96–0.99) than people with clear classifications.

Limitations
Studies from which participant data were drawn had different inclusion criteria and clinical settings.

Conclusions
People with unclear classifications appeared to be less affected by LBP (less disability and fewer fear avoidance beliefs), despite typically having a longer duration of LBP. Future studies should investigate whether modifying the algorithm to exclude such people or provide them with different interventions improves outcomes.
Les deux tournants, ou la religion dans l'œuvre de Durkheim avant Les formes élémentaires
Authors: Paoletti Giovanni 
Published: November 2012

Résumé Durkheim développa son intérêt pour l’étude de la religion très tôt, sans plus le délaisser par la suite. Son programme de recherche, formulé dès ses premiers textes (1886-1887), consiste en quelques questions fondamentales, qui reviennent dans toute son œuvre : la définition de la religion, ses fonctions sociales, son rapport à la morale, son avenir dans les sociétés modernes. Si les questions restent les mêmes, les réponses de Durkheim se modifient au fil des ans. À deux occasions, autour de 1897 et de 1907, on est en présence d’un véritable tournant dans sa conception des phénomènes religieux. Réexaminer ce parcours complexe et laborieux peut aider à jeter une lumière nouvelle sur les enjeux des Formes élémentaires de la vie religieuse et sur les problèmes que Durkheim s’efforça de résoudre dans son dernier chef-d’œuvre.
Peine de mort menace dissuasive ou effet pervers ?
Authors: Demont Vincent , Sayah Ali 
Published: November 2012

Résumé La peine de mort vise notamment à dissuader les potentiels meurtres, mais est-ce réellement efficace ? Cet article survole les études consacrées à cette question pour montrer l’absence de consensus. Il enchaîne avec une approche théorique sur l’impact dissuasif de la peine de mort en prenant en compte des mécanismes mis en avant par la psychologie sociale, comme la rationalité limitée, l’usage d’heuristiques, la motivation, les dimensions culturelles, etc. Et en particulier la psychologie de la menace avec la théorie du management de la terreur et le modèle de maintien de signification. L’article conclut que la peine de mort doit faire face à de nombreux mécanismes psychiques et à des contraintes de cohérences culturelles qui minimisent son potentiel dissuasif.