bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic study of the response of chicken to highly pathogenic avian influenza virus
Authors: Sironi Laura , Williams John L , Stella Alessandra , Minozzi Giulietta , Moreno Ana , Ramelli Paola , Han Jianlin , Weigend Steffen , Wan Junxing , Lombardi Guerino , Cordioli Paolo , Mariani Paola 
Published: June 2011

Abstract

Background
The host mounts an immune response to pathogens, but few data are currently available on the role of host genetics in variation in response to avian influenza (AI). The study presented here investigated the role of the host genetic background in response to in vivo infection with AI virus (AIV).

Methods
Experimental lines of chicken and commercial crosses were experimentally infected intratracheally with 103 EID50/bird of A/Chicken/Italy/13474/99 H7N1 highly pathogenic avian influenza virus (HPAIV). Chickens were genotyped for the Mx polymorphism causing the S631N mutation, and for the Major Histocompatibility Complex (MHC). Whole-genome genotyping was carried out using 60 k Single Nucleotide Polymorphism (SNP) array developed by the poultry Genome-Wide Marker-Assisted Selection Consortium (GWMASC).

Results
Variability in response of different chicken lines to the HPAIV infections and some degree of resistance to AI were observed: a statistically significant effect of chicken line on the response to infection was found. There was no association between survival in healthy conditions and polymorphisms at the Mx gene and the MHC-B region. The analysis based on the 60 k SNPs provided a good clustering of the chicken lines, but no specific genetic cluster associated with response to AIV was identified.

Conclusions
Neither the genotype at the Mx gene or MHC-B locus, nor for SNP spanning the whole-genome identified loci involved in variations to response to AIV infection. These results point towards the possibility that either the genetic factors affecting the response of chickens to the H7N1 HPAIV are weak, or relevant alleles were not segregating in the studied populations.
Toll-Like Receptor 6 differential expression in two pig genetic groups vaccinated against Mycoplasma hyopneumoniae
Authors: Régia Silva Sousa Katiene , Mauric Frossard Ribeiro André , Roberto Nunes Goes Paulo , Eliza Facioni Guimarães Simone , Lopes Paulo Sávio , Veroneze Renata , Gasparino Eliane 
Published: June 2011

Abstract

Background

Mycoplasma hyopneumoniae is the etiologic agent of enzootic pneumonia, which causes important economic losses to swine industry. The Toll-like receptors (TLRs) are pattern-recognition receptors which detect microbial presence and initiate the innate as well as the adaptative immune defense. Toll-like receptor 6 is a type I transmembrane protein that recognizes bacterial components. The aim of this study was to compare mRNA expression pattern of TLR6 gene in two genetically distinct groups of pigs vaccinated against Mycoplasma hyopneumoniae.

Methods
For each genetic group, peripheral blood was collected just before and 10 days after vaccination from 10 Naturalized Brazilian Piau breed and 10 Commercial White Line serum-negative female piglets. RNA was extracted from peripheral blood mononuclear cells (PBMCs), reverse transcripted and the qRT-PCR performed using SYBR green fluorescence system, using GAPDH gene as endogenous control. Analyses were performed by UNIVARIATE (Shapiro-Wilk test) and MIXED procedures of SAS software (version 9.0).

Results
It was observed significant interaction between breed and vaccination, being the TLR6 mRNA expression higher in the Commercial White line than in the Piau breed after vaccination. Furthermore, there was differential expression before and after vaccination in the Commercial White line.

Conclusions
Analysis of in TLR6 gene expression showed difference between the two distinct genetic groups, however, other TLRs gene expression must be evaluated for a better understanding of innate resistance in the pig concerning Mycoplasma hyopneumoniae infection.
Aiming for the complete utilization of sugar-beet pulp: Examination of the effects of mild acid and hydrothermal pretreatment followed by enzymatic digestion
Authors: Kühnel Stefan , Schols Henk A , Gruppen Harry 
Published: May 2011

Abstract

Background
Biomass use for the production of bioethanol or platform chemicals requires efficient breakdown of biomass to fermentable monosaccharides. Lignocellulosic feedstocks often require physicochemical pretreatment before enzymatic hydrolysis can begin. The optimal pretreatment can be different for different feedstocks, and should not lead to biomass destruction or formation of toxic products.

Methods
We examined the influence of six mild sulfuric acid or water pretreatments at different temperatures on the enzymatic degradability of sugar-beet pulp (SBP).

Results
We found that optimal pretreatment at 140°C of 15 minutes in water was able to solubilize 60% w/w of the total carbohydrates present, mainly pectins. More severe treatments led to the destruction of the solubilized sugars, and the subsequent production of the sugar-degradation products furfural, hydroxymethylfurfural, acetic acid and formic acid. The pretreated samples were successfully degraded enzymatically with an experimental cellulase preparation.

Conclusions
In this study, we found that pretreatment of SBP greatly facilitated the subsequent enzymatic degradation within economically feasible time ranges and enzyme levels. In addition, pretreatment of SBP can be useful to fractionate functional ingredients such as arabinans and pectins from cellulose. We found that the optimal combined severity factor to enhance the enzymatic degradation of SBP was between log R'0 = -2.0 and log R'0 = -1.5. The optimal pretreatment and enzyme treatment solubilized up to 80% of all sugars present in the SBP, including ≥90% of the cellulose.
Promising cytotoxic activity profile of fermented wheat germ extract (Avemar®) in human cancer cell lines
Authors: Mueller Thomas , Jordan Karin , Voigt Wieland 
Published: May 2011

Abstract
Fermented wheat germ extract (FWGE) is currently used as nutrition supplement for cancer patients. Limited recent data suggest antiproliferative, antimetastatic and immunological effects which were at least in part exerted by two quinones, 2-methoxy benzoquinone and 2,6-dimethoxybenzquinone as ingredients of FWGE. These activity data prompted us to further evaluate the in vitro antiproliferative activity of FWGE alone or in combination with the commonly used cytotoxic drugs 5-FU, oxaliplatin or irinotecan in a broad spectrum of human tumor cell lines. We used the sulforhodamine B assay to determine dose response relationships and IC50-values were calculated using the Hill equation. Drug interaction of simultaneous and sequential drug exposure was estimated using the model of Drewinko and potential clinical activity was assessed by the model of relative antitumor activity (RAA). Apoptosis was detected by DNA gel electrophoresis.
FWGE induced apoptosis and exerted significant antitumor activity in a broad spectrum of 32 human cancer cell lines. The highest activity was found in neuroblastoma cell lines with an average IC50 of 0.042 mg/ml. Furthermore, IC50-range was very narrow ranging from 0.3 mg/ml to 0.54 mg/ml in 8 colon cancer cell lines. At combination experiments in colon cancer cell lines when FWGE was simultaneously applied with either 5-FU, oxaliplatin or irinotecan we observed additive to synergistic drug interaction, particularly for 5-FU. At sequential drug exposure with 5-FU and FWGE the observed synergism was abolished.
Taken together, FWGE exerts significant antitumor activity in our tumor model. Simultaneous drug exposure with FWGE and 5-FU, oxaliplatin or irinotecan yielded in additive to synergistic drug interaction. However, sequential drug exposure of 5-FU and FWGE in colon cancer cell lines appeared to be schedule-dependent (5-FU may precede FWGE).
Further evaluation of FWGE as a candidate for clinical combination drug regimens appeared to be warranted.
An upper limit for macromolecular crowding effects
Authors: Miklos Andrew C , Li Conggang , Sorrell Courtney D , Lyon L Andrew , Pielak Gary J 
Published: May 2011

Abstract

Background
Solutions containing high macromolecule concentrations are predicted to affect a number of protein properties compared to those properties in dilute solution. In cells, these macromolecular crowders have a large range of sizes and can occupy 30% or more of the available volume. We chose to study the stability and ps-ns internal dynamics of a globular protein whose radius is ~2 nm when crowded by a synthetic microgel composed of poly(N-isopropylacrylamide-co-acrylic acid) with particle radii of ~300 nm.

Results
Our studies revealed no change in protein rotational or ps-ns backbone dynamics and only mild (~0.5 kcal/mol at 37°C, pH 5.4) stabilization at a volume occupancy of 70%, which approaches the occupancy of closely packing spheres. The lack of change in rotational dynamics indicates the absence of strong crowder-protein interactions.

Conclusions
Our observations are explained by the large size discrepancy between the protein and crowders and by the internal structure of the microgels, which provide interstitial spaces and internal pores where the protein can exist in a dilute solution-like environment. In summary, microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.
Development of butanol-tolerant Bacillus subtilis strain GRSW2-B1 as a potential bioproduction host
Authors: Kataoka Naoya , Tajima Takahisa , Kato Junichi , Rachadech Wanitcha , Vangnai Alisa S 
Published: May 2011

Abstract
As alternative microbial hosts for butanol production with organic-solvent tolerant trait are in high demands, a butanol-tolerant bacterium, Bacillus subtilis GRSW2-B1, was thus isolated. Its tolerance covered a range of organic solvents at high concentration (5%v/v), with remarkable tolerance in particular to butanol and alcohol groups. It was susceptible for butanol acclimatization, which resulted in significant tolerance improvement. It has versatility for application in a variety of fermentation process because it has superior tolerance when cells were exposed to butanol either as high-density, late-exponential grown cells (up to 5%v/v) or under growing conditions (up to 2.25%v/v). Genetic transformation procedure was optimized, yielding the highest efficiency at 5.17 × 103 colony forming unit (μg DNA)-1. Gene expression could be effectively driven by several promoters with different levels, where as the highest expression was observed with a xylose promoter. The constructed vector was stably maintained in the transformants, in the presence or absence of butanol stress. Adverse effect of efflux-mediated tetracycline resistance determinant (TetL) to bacterial organic-solvent tolerance property was unexpectedly observed and thus discussed. Overall results indicate that B. subtilis GRSW2-B1 has potential to be engineered and further established as a genetic host for bioproduction of butanol.
Cis-regulation of IRF5expression is unable to fully account for systemic lupus erythematosus association: analysis of multiple experiments with lymphoblastoid cell lines
Authors: Alonso-Perez Elisa , Suarez-Gestal Marian , Calaza Manuel , Kwan Tony , Majewski Jacek , Gomez-Reino Juan J , Gonzalez Antonio 
Published: May 2011

Abstract
Introduction
Interferon regulatory factor 5 gene (IRF5) polymorphisms are strongly associated with several diseases, including systemic lupus erythematosus (SLE). The association includes risk and protective components. They could be due to combinations of functional polymorphisms and related to cis-regulation of IRF5 expression, but their mechanisms are still uncertain. We hypothesised that thorough testing of the relationships between IRF5 polymorphisms, expression data from multiple experiments and SLE-associated haplotypes might provide useful new information.

Methods
Expression data from four published microarray hybridisation experiments with lymphoblastoid cell lines (57 to 181 cell lines) were retrieved. Genotypes of 109 IRF5 polymorphisms, including four known functional polymorphisms, were considered. The best linear regression models accounting for the IRF5 expression data were selected by using a forward entry procedure. SLE-associated IRF5 haplotypes were correlated with the expression data and with the best cis-regulatory models.

Results
A large fraction of variability in IRF5 expression was accounted for by linear regression models with IRF5 polymorphisms, but at a different level in each expression data set. Also, the best models from each expression data set were different, although there was overlap between them. The SNP introducing an early polyadenylation signal, rs10954213, was included in the best models for two of the expression data sets and in good models for the other two data sets. The SLE risk haplotype was associated with high IRF5 expression in the four expression data sets. However, there was also a trend towards high IRF5 expression with some protective and neutral haplotypes, and the protective haplotypes were not associated with IRF5 expression. As a consequence, correlation between the cis-regulatory best models and SLE-associated haplotypes, regarding either the risk or protective component, was poor.

Conclusions
Our analysis indicates that although the SLE risk haplotype of IRF5 is associated with high expression of the gene, cis-regulation of IRF5 expression is not enough to fully account for IRF5 association with SLE susceptibility, which indicates the need to identify additional functional changes in this gene.
Infliximab in ankylosing spondylitis: alone or in combination with methotrexate? A pharmacokinetic comparative study
Authors: Mulleman Denis , Lauféron Francine , Wendling Daniel , Ternant David , Ducourau Emilie , Paintaud Gilles , Goupille Philippe 
Published: June 2011

Abstract
Introduction
Methotrexate (MTX) has been shown to modify infliximab pharmacokinetics in rheumatoid arthritis. However, its combination with infliximab in the treatment of ankylosing spondylitis (AS) is not recommended. The objective of this study was to examine the influence of MTX on infliximab exposure in patients with AS.

Methods
Patients with AS patients who had predominantly axial symptoms were randomised to receive infliximab alone (infusions of 5 mg/kg at weeks 0, 2, 6, 12 and 18) or infliximab combined with MTX (10 mg/week). Infliximab concentrations were measured before and 2 hours after each infusion and at 1, 3, 4, 5, 8, 10, 14 and 18 weeks. We estimated individual cumulative area under the concentration versus time curves (AUC) for infliximab concentration between baseline and week 18 (AUC0-18). Clinical and laboratory evaluations were performed at each visit. The Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) score was the primary end point for clinical response.

Results
Twenty-six patients were included (infliximab group: n = 12, infliximab + MTX group: n = 14), and 507 serum samples were available for measurement of infliximab concentration. The two groups did not differ with regard to AUC0-18 or evolution of BASDAI scores and biomarkers of inflammation.

Conclusions
The combination of MTX and infliximab does not increase the exposure to infliximab over infliximab alone in patients with AS.

Trial registration
ClinicalTrials.gov: NCT00507403
Moving pictures of the human microbiome
Authors: Caporaso J Gregory , Lauber Christian L , Costello Elizabeth K , Berg-Lyons Donna , Gonzalez Antonio , Stombaugh Jesse , Knights Dan , Gajer Pawel , Ravel Jacques , Fierer Noah , Gordon Jeffrey I , Knight Rob 
Published: May 2011

Abstract
Background
Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.

Results
We find that despite stable differences between body sites and individuals, there is pronounced variability in an individual's microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members.

Conclusions
DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions.
Cannabis use before age 15 and subsequent executive
functioning
Authors: Fontes Maria Alice , Bolla Karen I. , Cunha Paulo Jannuzzi , Almeida Priscila Previato , Jungerman Flávia , Laranjeira Ronaldo Ramos , Bressan Rodrigo A. , Lacerda Acioly L. T. 
Published: May 2011

BackgroundMany studies have suggested that adolescence is a period of particular
vulnerability to neurocognitive effects associated with substance misuse.
However, few large studies have measured differences in cognitive
performance between chronic cannabis users who started in early
adolescence (before age 15) with those who started later.AimsTo examine the executive functioning of individuals who started chronic
cannabis use before age 15 compared with those who started chronic
cannabis use after 15 and controls.MethodWe evaluated the performance of 104 chronic cannabis users (49
early-onset users and 55 late-onset users) and 44 controls who undertook
neuropsychological tasks, with a focus on executive functioning.
Comparisons involving neuropsychological measures were performed using
generalised linear model analysis of variance (ANOVA).ResultsThe early-onset group showed significantly poorer performance compared
with the controls and the late-onset group on tasks assessing sustained
attention, impulse control and executive functioning.ConclusionsEarly-onset chronic cannabis users exhibited poorer cognitive performance
than controls and late-onset users in executive functioning. Chronic
cannabis use, when started before age 15, may have more deleterious
effects on neurocognitive functioning.
Age and birth cohort differences in the prevalence of common
mental disorder in England: National Psychiatric Morbidity Surveys
1993–2007
Authors: Spiers Nicola , Bebbington Paul , McManus Sally , Brugha Traolach S. , Jenkins Rachel , Meltzer Howard 
Published: May 2011

BackgroundThere are concerns that the prevalence of mental disorder is
increasing.AimsTo determine whether the prevalence of common adult mental disorders has
increased over time, using age–period–cohort analysis.MethodThe study consisted of a pseudocohort analysis of a sequence of three
cross-sectional surveys of the English household population. The main
outcome was common mental disorder, indicated by a score of 12 or above
on the Revised Clinical Interview Schedule (CIS-R). Secondary outcomes
were neurotic symptoms likely to require treatment, indicated by a CIS-R
score of 18 or over, and individual subscale scores for fatigue, sleep
problems, irritability and worry.ResultsThere were 8670 participants in the 1993 survey, 6977 in the 2000 survey
and 6815 in the 2007 survey. In men a significant increase in common
mental disorder occurred between the cohort born in 1943–9 and that born
in 1950–6 (odds ratio 1.4, 95% CI 1.1–1.9) but prevalence in subsequent
cohorts remained largely stable. More extended increases in prevalence of
sleep problems and mental disorders were observed in women, but not
consistently across cohorts or measures.ConclusionsWe found little evidence that the prevalence of common mental disorder is
increasing.
Psychological treatments in intellectual disability: the
challenges of building a good evidence base
Authors: Bhaumik Sabyasachi , Gangadharan Satheesh , Hiremath Avinash , Russell Paul Swamidhas Sudhakar 
Published: May 2011

SummaryPsychological treatments are widely used for the management of mental health
and behavioural problems in people with intellectual disabilities. The
evidence base, including the cost-effectiveness of such interventions, is
limited. This editorial explores the current evidence base and analyses its
strengths and limitations. The editorial also highlights current problems in
conducting randomised controlled trials in this area and suggests a way
forward.
The truth about genetic variation in the serotonin transporter
gene and response to stress and medication
Authors: McGuffin Peter , Alsabban Shaza , Uher Rudolf 
Published: May 2011

SummaryThe question of whether a functional variant in the promoter of the
serotonin transporter gene (5-HTTLPR) influences response to adversity
and/or antidepressants has generated great interest and controversy. A
review of the literature suggests that the issue is complicated by
differences in methodology and sample ethnicity. When these confounders are
accounted for, there probably is a real, if small, effect of 5-HTTLPR on
response to both serotonin reuptake inhibitors and environmental
adversity.
MAOA, abuse exposure and antisocial behaviour: 30-year
longitudinal study
Authors: Fergusson David M. , Boden Joseph M. , Horwood L. John , Miller Allison L. , Kennedy Martin A. 
Published: May 2011

BackgroundRecent studies have raised issues concerning the replicability of gene ×
environment (G × E) interactions involving the monoamine oxidase A
(MAOA) gene in moderating the associations between
abuse or maltreatment exposure and antisocial behaviour. This study
attempted to replicate the findings in this area using a 30-year
longitudinal study that has strong resemblance to the original research
cohort.AimsTo test the hypothesis that the presence of the low-activity
MAOA genotype was associated with an increased
response to abuse exposure.MethodParticipants were 398 males from the Christchurch Health and Development
Study who had complete data on: MAOA promoter region
variable number tandem repeat genotype; antisocial behaviour to age 30;
and exposure to childhood sexual and physical abuse.ResultsRegression models were fitted to five antisocial behaviour outcomes
(self-reported property offending; self-reported violent offending;
convictions for property/violent offending; conduct problems; hostility)
observed from age 16 to 30, using measures of childhood exposure to
sexual and physical abuse. The analyses revealed consistent evidence of G
× E interactions, with those having the low-activity
MAOA variant and who were exposed to abuse in
childhood being significantly more likely to report later offending,
conduct problems and hostility. These interactions remained statistically
significant after control for a range of potentially confounding factors.
Findings for convictions data were somewhat weaker.ConclusionsThe present findings add to the evidence suggesting that there is a
stable G × E interaction involving MAOA, abuse exposure
and antisocial behaviour across the life course.