bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome sequencing (RNA-Seq) of human endobronchial biopsies: asthmaversuscontrols
Authors: Yick Ching Yong , Zwinderman Aeilko H. , Kunst Peter W. , Grünberg Katrien , Mauad Thais , Dijkhuis Annemiek , Bel Elisabeth H. , Baas Frank , Lutter René , Sterk Peter J. 
Published: January 2013

The cellular and molecular pathways in asthma are highly complex. Increased understanding can be obtained by unbiased transcriptomic analysis (RNA-Seq). We hypothesised that the transcriptomic profile of whole human endobronchial biopsies differs between asthma patients and controls.First, we investigated the feasibility of obtaining RNA from whole endobronchial biopsies suitable for RNA-Seq. Secondly, we examined the difference in transcriptomic profiles between asthma and controls. This cross-sectional study compared four steroid-free atopic asthma patients and five healthy nonatopic controls. Total RNA from four biopsies per subject was prepared for RNA-Seq. Comparison of the numbers of reads per gene in asthma and controls was based on the Poisson distribution.46 genes were differentially expressed between asthma and controls, including pendrin, periostin and BCL2. 10 gene networks were found to be involved in cellular morphology, movement and development.RNA isolated from whole human endobronchial biopsies is suitable for RNA-Seq, showing different transcriptomic profiles between asthma and controls. Novel and confirmative genes were found to be linked to asthma. These results indicate that biological processes in the airways of asthma patients are regulated differently when compared to controls, which may be relevant for the pathogenesis and treatment of the disease.
Toll-like receptor-4 agonist in post-haemorrhage pneumonia: role of dendritic and natural killer cells
Authors: Roquilly Antoine , Broquet Alexis , Jacqueline Cedric , Gautreau Laetitia , Segain Jean Pierre , de Coppet Pierre , Caillon Jocelyne , Altare Frédéric , Josien Regis , Asehnoune Karim 
Published: January 2013

Haemorrhage-induced immunosuppression has been linked to nosocomial infections. We assessed the impact of monophosphoryl lipid A, a Toll/interleukin-1 receptor-domain-containing adaptor protein inducing interferon-biased Toll-like receptor-4 agonist currently used as a vaccine adjuvant in humans, on post-haemorrhage susceptibility to infection.We used a mouse model of post-haemorrhage pneumonia induced by methicillin-susceptibleStaphylococcus aureus. Monophosphoryl lipid A was administered intravenously after haemorrhage and before pneumonia onset.Haemorrhage altered survival rate, increased lung damage (neutrophil accumulation, oedema and cytokine release) and altered the functions of dendritic and natural killer cells. Here, we show that monophosphoryl lipid A decreased systemic dissemination ofS. aureusand dampened inflammatory lung lesions. Monophosphoryl lipid A partially restored the capacity for antigen presentation and the transcriptional activity in dendritic cells. Monophosphoryl lipid A did not restore the interferon-γ mRNA but prevented interleukin-10 mRNA overexpression in natural killer cells compared with untreated mice.Ex vivomonophosphoryl lipid A-stimulated dendritic cells or natural killer cells harvested from haemorrhaged animals were adoptively transferred into mice undergoing post-haemorrhage pneumonia. Stimulated dendritic cells (but not stimulated natural killer cells) improved the survival rate compared with mice left untreated.In vivodepletion of natural killer cells decreased survival rate of monophosphoryl lipid A-treated mice.Dendritic and natural killer cells are critically involved in the beneficial effects of monophosphoryl lipid A within post-haemorrhage pneumonia.
Fixed-dose combination antituberculosis therapy: a systematic review and meta-analysis
Authors: Albanna Amr S. , Smith Benjamin M. , Cowan Deanna , Menzies Dick 
Published: January 2013

Fixed-dose combination (FDC) formulations are currently recommended for the treatment of active tuberculosis (TB). We have conducted a systematic review to evaluate the risk of treatment failure or disease relapse, acquired drug resistance, bacterial conversion after 2 months of treatment, adverse events, adherence and treatment satisfaction associated with treatment of active TB using FDC or separate drug formulations.We searched four electronic databases for randomised controlled trials and cohort studies. Results from trials that directly compared FDC to separate drug formulations were pooled. Results from other studies were reported separately.We identified 2450 citations from which 15 controlled trials and four additional relevant studies were included. In the 15 trials there were no differences in acquired drug resistance, bacterial conversion after 2 months of treatment or adverse drug reactions with FDC or separate drug formulations. There was a trend toward higher risk of failure or relapse with FDC (pooled relative risk 1.28 (95% CI 0.99–1.7)). Based on individual study results, only one of two trials that assessed treatment satisfaction, and none of five that assessed patient adherence, favoured FDCs.Although FDC formulations simplify TB therapy, the current evidence does not indicate that these formulations improve treatment outcomes among patients with active TB.
mTOR direct interactions with Rheb-GTPase and raptor: sub-cellular localization using fluorescence lifetime imaging
Authors: Yadav Rahul B , Burgos Pierre , Parker Anthony W , Iadevaia Valentina , Proud Christopher G , Allen Rodger A , O'Connell James P , Jeshtadi Ananya , Stubbs Christopher D , Botchway Stanley W 
Published: January 2013

Abstract

Background
The mammalian target of rapamycin (mTOR) signalling pathway has a key role in cellular regulation and several diseases. While it is thought that Rheb GTPase regulates mTOR, acting immediately upstream, while raptor is immediately downstream of mTOR, direct interactions have yet to be verified in living cells, furthermore the localisation of Rheb has been reported to have only a cytoplasmic cellular localization.

Results
In this study a cytoplasmic as well as a significant sub-cellular nuclear mTOR localization was shown , utilizing green and red fluorescent protein (GFP and DsRed) fusion and highly sensitive single photon counting fluorescence lifetime imaging microscopy (FLIM) of live cells. The interaction of the mTORC1 components Rheb, mTOR and raptor, tagged with EGFP/DsRed was determined using fluorescence energy transfer-FLIM. The excited-state lifetime of EGFP-mTOR of ~2400 ps was reduced by energy transfer to ~2200 ps in the cytoplasm and to 2000 ps in the nucleus when co-expressed with DsRed-Rheb, similar results being obtained for co-expressed EGFP-mTOR and DsRed-raptor. The localization and distribution of mTOR was modified by amino acid withdrawal and re-addition but not by rapamycin.

Conclusions
The results illustrate the power of GFP-technology combined with FRET-FLIM imaging in the study of the interaction of signalling components in living cells, here providing evidence for a direct physical interaction between mTOR and Rheb and between mTOR and raptor in living cells for the first time.
Derangements of liver tissue bioenergetics in Concanavalin A-induced hepatitis
Authors: Al-Shamsi Mariam , Shahin Allen , Mensah-Brown Eric PK , Souid Abdul-Kader 
Published: January 2013

AbstractBackgroundA novelin vitrosystem was employed to investigate liver tissue respiration (mitochondrial O2consumption) in mice treated with concanavalin A (Con A). This study aimed to investigate hepatocyte bioenergetics in this well-studied hepatitis model.MethodsC57Bl/6 and C57Bl/6IFN-γ−/−mice were injected intravenously with 12 mg ConA/kg. Liver specimens were collected at various timepoints after injection and analyzed for cellular respiration and caspase activation. Serum was analyzed for interferon-gamma (IFN-γ) and aminotransferases. Fluorescence activated cell sorting analysis was used to determine the phenotype of infiltrating cells, and light and electron microscopy were used to monitor morphological changes. Phosphorescence analyzer that measured dissolved O2as function of time was used to evaluate respiration.ResultsIn sealed vials, O2concentrations in solutions containing liver specimen and glucose declined linearly with time, confirming zero-order kinetics of hepatocyte respiration. O2consumption was inhibited by cyanide, confirming the oxidation occurred in the respiratory chain. Enhanced liver respiration (by ≈68%, p<0.02) was noted 3 hr after ConA treatment, and occurred in conjunction with limited cellular infiltrations around the blood vessels. Diminished respiration (by ≈30%,p=0.005) was noted 12 hr after ConA treatment, and occurred in conjunction with deranged mitochondria, areas of necrosis, and prominent infiltrations with immune cells, most significantly, CD3+NKT+cells. Increases in intracellular caspase activity and serum IFN-γ and aminotransferase levels were noted 3 hr after ConA treatment and progressed with time. The above-noted changes were less pronounced in C57Bl/6 IFN-γ−/−mice treated with ConA.ConclusionsBased on these results, liver tissue bioenergetics is increased 3 hr after ConA exposure. This effect is driven by the pathogenesis of the disease, in which IFN-γ and other cytokines contribute to. Subsequent declines in liver bioenergetics appear to be a result of necrosis and active caspases targeting the mitochondria within hepatocytes.
Meta-analysis of associations between TCF7L2 polymorphisms and risk of type 2 diabetes mellitus in the Chinese population
Authors: Wang Jinjin , Hu Fulan , Feng Tianping , Zhao Jingzhi , Yin Lei , Li Linlin , Wang Yan , Wang Qian , Hu Dongsheng 
Published: January 2013

AbstractBackgroundAssociations between transcription factor 7-like 2 (TCF7L2) polymorphisms and type 2 diabetes mellitus (T2DM) have been evaluated extensively in multiple ethnic groups.TCF7L2has emerged as the strongest T2DM susceptibility gene in Europeans, but the findings have been inconsistent in the Chinese population. The purpose of this meta-analysis was to evaluate the associations betweenTCF7L2single nucleotide polymorphisms (SNPs) and T2DM risk in the Chinese population.MethodsWe performed searches in the PubMed, EMBASE, Cochrane, and Chinese databases (CNKI, CQVIP and Wanfang databases) for literature published from January 2007 to February 2012. We reviewed all relevant articles onTCF7L2polymorphisms and susceptibility to T2DM in the Chinese population written in English and Chinese. Two reviewers extracted data independently using a standardized protocol, and any discrepancies were adjudicated by a third reviewer. Fixed-effects and random-effects meta-analyses were performed to pool the odds ratios (ORs). Publication bias and heterogeneity were examined.ResultsA total of 21 articles were confirmed to be eligible for and included in this meta-analysis: 7 (with 3942 cases and 3502 controls) concerning rs11196218 (IVS−/+4G>A), 8 (with 3377 cases and 2975 controls) concerning rs290487 (IVS3−/+C>T), and 14 (with 7902 cases and 7436 controls) concerning rs7903146 (IVS3−/+C>T). Overall, the results showed a significant association between rs7903146 and T2DM risk. The pooled ORs were 1.54 for the comparison of T and C alleles (95% CI [confidence interval]: 1.37–1.74,p= 1.47 × 10-12,I2= 25.20%) and 1.56 for TC heterozygotes and CC homozygotes (95% CI : 1.38–1.76,p= 8.25 × 10-9,I2= 21.00%). The rs11196218(IVS4G>A) and rs290487 (IVS3C>T) SNPs were not associated with T2DM risk.ConclusionsThe rs7903146 SNP of theTCF7L2gene is associated with increased susceptibility to T2DM in the Chinese population as a whole as well as northern Chinese and southern Chinese as subgroups.
Association of the 5HTR2A gene with suicidal behavior: CASE-control study and updated meta-analysis
Authors: González-Castro Thelma Beatriz , Tovilla-Zárate Carlos , Juárez-Rojop Isela , Pool García Sherezada , Velázquez-Sánchez Martha Patricia , Genis Alma , Nicolini Humberto , López Narváez Lilia 
Published: January 2013

AbstractBackgroundThe polymorphism rs6313 (T102C) has been associated with suicidal behavior in case–control and meta-analysis studies, but results and conclusions remain controversial. The aim of the present study was to examine the association between T102C with suicidal behavior in a case–control study and, to assess the combined evidence – this case–control study and available data from other related studies – we carried out a meta-analysis.MethodsWe conducted a case–control study that included 161 patients with suicide attempts and 244 controls; we then performed a meta-analysis. The following models were evaluated in the meta-analysis: A) C allele vs T allele; B) T allele vs C allele; C) Caucasian population, D) Asian population, and E) suicide attempters with schizophrenia.ResultsWe found an association between attempted suicide and control participants for genotype (χ2=6.28, p=0.04, df=2) and allele (χ2=6.17, p=0.01, df=1, OR 1.48 95% IC: 1.08-2.03) frequencies in the case–control study. The meta-analysis, comprising 23 association studies (including the present one), showed that the rs6313 polymorphism is not associated with suicidal behavior for the following comparisons:T allele vs C allele (OR: 1.03; 95% CI 0.93-1.13; p(Z)=0.44); C allele vs T allele: (OR:0.99; 95% CI: 0.90-1.08; p(Z)=0.22); Caucasians (OR:1.09; 95% CI: 0.96-1.23), and Asians (OR:0.96; 95% CI: 0.84-1.09).ConclusionOur results showed association between the rs6313 (T102C) polymorphism and suicidal behavior in the case–control study. However, the meta-analysis showed no evidence of association. Therefore, more studies are necessary to determine conclusively an association between T102C and suicidal behavior.
Age at menarche and its relationship to body mass index among adolescent girls in Kuwait
Authors: Al-Awadhi Nora , Al-Kandari Nouf , Al-Hasan Teebah , AlMurjan Daliah , Ali Salhah , Al-Taiar Abdullah 
Published: January 2013

Abstract

Background
Despite the increasing rates of childhood obesity and rapid change in socio-economic status, the mean age at menarche remains mostly unknown among contemporary girls in Kuwait and other countries in the Gulf region. This study aimed to estimate the mean age at menarche among schoolgirls in Kuwait and investigate the association between age at menarche and obesity.

Methods
A cross-sectional study was conducted on 1,273 randomly selected female high school students from all governorates in Kuwait. Overweight was defined as higher than or equal to the 85th percentile and obesity as higher than or equal to the 95th percentile using growth charts provided by the Centres for Disease Control and Prevention (CDC, 2000). Data on menarche, socio-demographic status, physical activity and diet were collected using confidential self-administered questionnaire.

Results
Out of 1,273 students, 23 (1.8%) were absent or refused to participate. The mean age at menarche was 12.41 years (95% CI: 12.35-12.48). The prevalence of early menarche, defined as less than 11 years of age, was 8.5% (95% CI: 7.0-10.2%). The prevalence of obesity and overweight was 18.3% (95% CI: 16.2-20.6%) and 25.8% (95% CI: 23.42-28.30%), respectively. Age at menarche was inversely and significantly associated with odds of overweight and obesity after adjusting for potential confounders, odds ratio 0.84 (0.77-0.93); (p = 0.001).

Conclusion
Age at menarche among contemporary girls in Kuwait is similar to that in industrialized countries. There is an inverse association between age at menarche and obesity or overweight. Trends in menarcheal age should be monitored and time of sexual maturation and its related factors should be taken into account in strategies that aim to combat obesity.
Lipopolysaccharide-induced expression of surfactant proteins A1 and A2 in human renal tubular epithelial cells
Authors: Liu Jiao , Hu Fengqi , Wang Guirong , Zhou Qingshan , Ding Guohua 
Published: January 2013

Abstract

Background
Surfactant protein A (SP-A), encoded by two functional genes, SP-A1 and SP-A2, is essential for the inflammatory process and host defence in the lungs. Recent studies have demonstrated the extrapulmonary expression of SP-A. Similar to the lungs, the kidneys are organs exposed to external pathogens. The present study evaluated the expression and location of SP-A in the kidneys. The effect of lipopolysaccharide (LPS) on the expression of SP-A subtypes was also studied in renal tubular epithelial (HK-2) cells.

Methods
Immunohistochemical staining was performed using polyclonal antibody against SP-A. RT-PCR was also performed using mRNA from normal human renal tissues and HK-2 cells. The expressions of the SP-A1 and SP-A2 genes were determined by PCR-based RFLP analysis, gene-specific amplification, and direct sequencing of RT-PCR products. Western blot was conducted to analyse the SP-A protein. HK-2 cells were treated with LPS at various concentrations (0, 0.1, 1, 2, 5, and 10 μg/mL) for 8 h and at 5 μg/mL at various time points (0, 2, 4, 8, 16, and 24 h). The LPS-induced expressions of SP-A1 and SP-A2 mRNA and protein were analysed by RT-PCR and Western blot.

Results
SP-A was localised in the renal tubular epithelial cells in the proximal and distal convoluted tubules. SP-A1 and SP-A2 mRNA and protein were expressed in HK-2 cells and human renal tissues, which were significantly increased in time- and dose-dependent manners after LPS treatment (P < 0.05).

Conclusions
Human renal tubular epithelial cells can express both SP-A1 and SP-A2 genes, which may play important roles in the inflammatory modulation of the kidney.
p-Type hydrogen sensing with Al- and V-doped TiO2 nanostructures
Authors: Li Zhaohui , Ding Dongyan , Ning Congqin 
Published: January 2013

Abstract
Doping with other elements is one of the efficient ways to modify the physical and chemical properties of TiO2 nanomaterials. In the present work, anatase TiO2 nanofilms doped with Al and V elements were fabricated through anodic oxidation of Ti6Al4V alloy and further annealing treatment. Hydrogen sensing behavior of the crystallized Ti-Al-V-O nanofilms at various working temperatures was investigated through exposure to 1,000 ppm H2. Different from n-type hydrogen sensing characteristics of undoped TiO2 nanotubes, the Al- and V-doped nanofilms presented a p-type hydrogen sensing behavior by showing increased resistance upon exposure to the hydrogen-containing atmosphere. The Ti-Al-V-O nanofilm annealed at 450°C was mainly composed of anatase phase, which was sensitive to hydrogen-containing atmosphere only at elevated temperatures. Annealing of the Ti-Al-V-O nanofilm at 550°C could increase the content of anatase phase in the oxide nanofilm and thus resulted in a good sensitivity and resistance recovery at both room temperature and elevated temperatures. The TiO2 nanofilms doped with Al and V elements shows great potential for use as a robust semiconducting hydrogen sensor.
Colloidal crystals by electrospraying polystyrene nanofluids
Authors: Coll Arnau , Bermejo Sandra , Hernández David , Castañer Luis 
Published: January 2013

Abstract
This work introduces the electrospray technique as a suitable option to fabricate large-scale colloidal nanostructures, including colloidal crystals, in just a few minutes. It is shown that by changing the deposition conditions, different metamaterials can be fabricated: from scattered monolayers of polystyrene nanospheres to self-assembled three-dimensional ordered nanolayers having colloidal crystal properties. The electrospray technique overcomes the main problems encountered by top-down fabrication approaches, largely simplifying the experimental setup. Polystyrene nanospheres, with 360-nm diameter, were typically electrosprayed using off-the-shelf nanofluids. Several parameters of the setup and deposition conditions were explored, namely the distance between electrodes, nanofluid conductivity, applied voltage, and deposition rate. Layers thicker than 20 μm and area of 1 cm2 were typically produced, showing several domains of tens of microns wide with dislocations in between, but no cracks. The applied voltage was in the range of 10 kV, and the conductivity of the colloidal solution was in the range of 3 to 4 mS. Besides the morphology of the layers, the quality was also assessed by means of optical reflectance measurements showing an 80% reflectivity peak in the vicinity of 950-nm wavelength.
Improved monaural speech segregation based on computational auditory scene analysis
Authors: Yu Wang , Jiajun Lin , Ning Chen , Wenhao Yuan 
Published: January 2013

Abstract
A lot of effort has been made in Computational Auditory Scene Analysis (CASA) to segregate target speech from monaural mixtures. Based on the principle of CASA, this article proposes an improved algorithm for monaural speech segregation. To extract the energy feature more accurately, the proposed algorithm improves the threshold selection for response energy in initial segmentation stage. Since the resulting mask map often contains broken auditory element groups after grouping stage, a smoothing stage is proposed based on morphological image processing. Through the combination of erosion and dilation operations, we suppress the intrusions by removing the unwanted particles and enhance the segregated speech by complementing the broken auditory elements. Systematic evaluation shows that the proposed segregation algorithm improves the output signal-to-noise ratio by an average of 8.55 dB and cuts the percentage of noise residue by an average of 25.36% compared with the mixture, yielding a significant improvement for speech segregation.
Monitoring of some pesticides residue in consumed tea in Tehran market
Authors: Amirahmadi Maryam , Shoeibi Shahram , Abdollahi Mehdi , Rastegar Hossein , Khosrokhavar Roya , Hamedani Morteza Pirali 
Published: January 2013

Abstract
Tea is an agricultural product of the leaves, leaf buds, and internodes of various cultivars and sub-varieties of the Camellia sinensis plant, processed and vulcanized using various methods. Tea is a main beverage in Iranian food basket so should be free from toxic elements such as pesticides residue. There is no data bank on the residue of pesticides in the consumed black tea in Iran. The present study is the first attempt for monitoring of 25 pesticide residues from different chemical groups in tea samples obtained from local markets in Tehran, I.R. Iran during the period 2011. A reliable and accurate method based on spiked calibration curve and QuEChERS sample preparation was developed for determination of pesticide residues in tea by gas chromatography–mass spectrometry (GC/MS). The using of spiked calibration standards for constructing the calibration curve substantially reduced adverse matrix-related effects and negative recovery affected by GCB on pesticides. The recovery of pesticides at 3 concentration levels (n = 3) was in range of 81.4 - 99.4%. The method was proved to be repeatable with RSDr lower than 20%. The limits of quantification for all pesticides were ≤20 ng/g. 53 samples from 17 imported and manufactured brand were analyzed. Detectable pesticides residues were found in 28.3% (15 samples) of the samples. All of the positive samples were contaminated with unregulated pesticides (Endosulfan Sulfate or Bifenthrin) which are established by ISIRI. None of the samples had contamination higher than maximum residue limit set by EU and India.