bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional adaptations following exercise in Thoroughbred horse skeletal muscle highlights molecular mechanisms that lead to muscle hypertrophy
Authors: McGivney Beatrice A , Eivers Suzanne S , MacHugh David E , MacLeod James N , O'Gorman Grace M , Park Stephen DE , Katz Lisa M , Hill Emmeline W 
Published: December 2009

AbstractBackgroundSelection for exercise-adapted phenotypes in the Thoroughbred racehorse has provided a valuable model system to understand molecular responses to exercise in skeletal muscle. Exercise stimulates immediate early molecular responses as well as delayed responses during recovery, resulting in a return to homeostasis and enabling long term adaptation. Global mRNA expression during the immediate-response period has not previously been reported in skeletal muscle following exercise in any species. Also, global gene expression changes in equine skeletal muscle following exercise have not been reported. Therefore, to identify novel genes and key regulatory pathways responsible for exercise adaptation we have used equine-specific cDNA microarrays to examine global mRNA expression in skeletal muscle from a cohort of Thoroughbred horses (n =8) at three time points (before exercise, immediately post-exercise, and four hours post-exercise) following a single bout of treadmill exercise.ResultsSkeletal muscle biopsies were taken from thegluteus mediusbefore (T0), immediately after (T1) and four hours after (T2) exercise. Statistically significant differences in mRNA abundance between time points (T0vsT1and T0vsT2) were determined using the empirical Bayes moderatedt-test in the Bioconductor package Linear Models for Microarray Data (LIMMA) and the expression of a select panel of genes was validated using real time quantitative reverse transcription PCR (qRT-PCR). While only two genes had increased expression at T1(P< 0.05), by T2932 genes had increased (P< 0.05) and 562 genes had decreased expression (P< 0.05). Functional analysis of genes differentially expressed during the recovery phase (T2) revealed an over-representation of genes localized to the actin cytoskeleton and with functions in the MAPK signalling, focal adhesion, insulin signalling, mTOR signaling, p53 signaling and Type II diabetes mellitus pathways. At T1, using a less stringent statistical approach, we observed an over-representation of genes involved in the stress response, metabolism and intracellular signaling. These findings suggest that protein synthesis, mechanosensation and muscle remodeling contribute to skeletal muscle adaptation towards improved integrity and hypertrophy.ConclusionsThis is the first study to characterize global mRNA expression profiles in equine skeletal muscle using an equine-specific microarray platform. Here we reveal novel genes and mechanisms that are temporally expressed following exercise providing new knowledge about the early and late molecular responses to exercise in the equine skeletal muscle transcriptome.
Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
Authors: Oliver Haley F , Orsi Renato H , Ponnala Lalit , Keich Uri , Wang Wei , Sun Qi , Cartinhour Samuel W , Filiatrault Melanie J , Wiedmann Martin , Boor Kathryn J 
Published: December 2009

AbstractBackgroundIdentification of specific genes and gene expression patterns important for bacterial survival, transmission and pathogenesis is critically needed to enable development of more effective pathogen control strategies. The stationary phase stress response transcriptome, including many σB-dependent genes, was defined for the human bacterial pathogenListeria monocytogenesusing RNA sequencing (RNA-Seq) with the Illumina Genome Analyzer. Specifically, bacterial transcriptomes were compared between stationary phase cells ofL. monocytogenes10403S and an otherwise isogenic ΔsigBmutant, which does not express the alternative σ factor σB, a major regulator of genes contributing to stress response, including stresses encountered upon entry into stationary phase.ResultsOverall, 83% of allL. monocytogenesgenes were transcribed in stationary phase cells; 42% of currently annotatedL. monocytogenesgenes showed medium to high transcript levels under these conditions. A total of 96 genes had significantly higher transcript levels in 10403S than in ΔsigB, indicating σB-dependent transcription of these genes. RNA-Seq analyses indicate that a total of 67 noncoding RNA molecules (ncRNAs) are transcribed in stationary phaseL. monocytogenes, including 7 previously unrecognized putative ncRNAs. Application of a dynamically trained Hidden Markov Model, in combination with RNA-Seq data, identified 65 putative σBpromoters upstream of 82 of the 96 σB-dependent genes and upstream of the one σB-dependent ncRNA. The RNA-Seq data also enabled annotation of putative operons as well as visualization of 5'- and 3'-UTR regions.ConclusionsThe results from these studies provide powerful evidence that RNA-Seq data combined with appropriate bioinformatics tools allow quantitative characterization of prokaryotic transcriptomes, thus providing exciting new strategies for exploring transcriptional regulatory networks in bacteria.See minireivewhttp://jbiol.com/content/8/12/107.
Virus infection elevates transcriptional activity of miR164a promoter in plants
Authors: Bazzini Ariel A , Almasia Natalia I , Manacorda Carlos A , Mongelli Vanesa C , Conti Gabriela , Maroniche Guillermo A , Rodriguez María C , Distéfano Ana J , Hopp H Esteban , del Vas Mariana , Asurmendi Sebastian 
Published: December 2009

Abstract

Background
Micro RNAs (miRs) constitute a large group of endogenous small RNAs that have crucial roles in many important plant functions. Virus infection and transgenic expression of viral proteins alter accumulation and activity of miRs and so far, most of the published evidence involves post-transcriptional regulations.

Results
Using transgenic plants expressing a reporter gene under the promoter region of a characterized miR (P-miR164a), we monitored the reporter gene expression in different tissues and during Arabidopsis development. Strong expression was detected in both vascular tissues and hydathodes. P-miR164a activity was developmentally regulated in plants with a maximum expression at stages 1.12 to 5.1 (according to Boyes, 2001) along the transition from vegetative to reproductive growth. Upon quantification of P-miR164a-derived GUS activity after Tobacco mosaic virus Cg or Oilseed rape mosaic virus (ORMV) infection and after hormone treatments, we demonstrated that ORMV and gibberellic acid elevated P-miR164a activity. Accordingly, total mature miR164, precursor of miR164a and CUC1 mRNA (a miR164 target) levels increased after virus infection and interestingly the most severe virus (ORMV) produced the strongest promoter induction.

Conclusion
This work shows for the first time that the alteration of miR pathways produced by viral infections possesses a transcriptional component. In addition, the degree of miR alteration correlates with virus severity since a more severe virus produces a stronger P-miR164a induction.
Design and methods for testing a simple dietary message to improve weight loss and dietary quality
Authors: Merriam Philip A , Ma Yunsheng , Olendzki Barbara C , Schneider Kristin L , Li Wenjun , Ockene Ira S , Pagoto Sherry L 
Published: December 2009

Abstract

Background
The current food pyramid guidelines have been criticized because of their complexity and the knowledge required for users to understand the recommendations. Simplification of a dietary message to focus on a single key aspect of dietary quality, e.g., fiber intake, may make the message much easier to comprehend and adhere, such that respondents can achieve greater weight loss, better dietary quality and overall metabolic health.

Methods and design
This is a randomized controlled clinical trial with two equal sized arms. In total, 240 obese adults who meet diagnostic criteria for the metabolic syndrome will be randomized to one of the two conditions: 1) a high fiber diet and 2) the American Heart Association (AHA) diet. In the high fiber diet condition, patients will be given instruction only on achieving daily dietary fiber intake of 30 g or more. In the AHA diet condition, patients will be instructed to make the several dietary changes recommended by the AHA 2006 guidelines. The trial examines participant weight loss and dietary quality as well as changes in components of the metabolic syndrome, inflammatory biomarkers, low-density lipoprotein cholesterol levels, insulin levels, and glycosolated hemoglobin. Potential mediators, i.e., diet adherence and perceived ease of the diet, and the intervention effect on weight change will also be examined.

Discussions
The purpose of this paper is to outline the study design and methods for testing the simple message of increasing dietary fiber. If the simple dietary approach is found efficacious for weight loss; and, improves dietary quality, metabolic health, and adherence, it might then be used to develop a simple public health message.

Trial registration
NCT00911885
A novel scoring system for prognostic prediction in d-galactosamine/lipopolysaccharide-induced fulminant hepatic failure BALB/c mice
Authors: Feng Bo , Wu Sheng Ming , Lv Sa , Liu Feng , Chen Hong Song , Gao Yan , Dong Fang Ting , Wei Lai 
Published: December 2009

Abstract

Background
It is frequently important to identify the prognosis of fulminant hepatic failure (FHF) patients as this will influence patient management and candidacy for liver transplantation. Therefore, a novel scoring system based on metabonomics combining with multivariate logistic regression was developed to predict the prognosis of FHF mouse model.

Methods
BALB/c mice were used to construct FHF model. Parts of plasma were collected at 4, 5, and 6-h time points after treatment, respectively, and detected using gas chromatography/time-of-flight mass spectrometry (GC/TOFMS). The acquired data were processed using partial least square discriminant analysis (PLS-DA). The metabolic markers identified were used to construct a scoring system by multivariate regression analysis.

Results
28 mice of survival group and 28 of dead group were randomly selected and analyzed. PLS regression analysis showed that both the PLS models of 5 h and 6 h after d-galactosamine/lipopolysaccharide treatment demonstrated good performances. Loadings plot suggested that phosphate, beta-hydroxybutyrate (HB), urea, glucose and lactate concentrations in plasma had the highest weightings on the clustering differences at the three time points. By the multivariate logistic regression analysis, the death/survival index (DSI) was constructed based on relative concentrations of HB, urea and phosphate. It provided general accurate rate of prediction of 93.3% in the independent samples.

Conclusions
The novel scoring system based on metabonomics combining with multivariate logistic regression is accurate in predicting the prognosis of FHF mouse model and may be referred in clinical practice as a more useful prognostic tool with other available information.
Incarceration experiences among a community-recruited sample of injection drug users in Bangkok, Thailand
Authors: Hayashi Kanna , Milloy M-J , Fairbairn Nadia , Kaplan Karyn , Suwannawong Paisan , Lai Calvin , Wood Evan , Kerr Thomas 
Published: December 2009

Abstract

Background
Since 2003 Thailand has waged an aggressive "war on drugs" campaign focused on arresting and incarcerating suspected drug users and dealers. However, little is known about incarceration experiences among IDU in the wake of the recent war on drugs. Therefore, we sought to examine incarceration experiences among IDU in Bangkok, Thailand.

Methods
We examined the prevalence of incarceration among community-recruited IDU participating in the Mitsampan Community Research Project. Multivariate logistic regression was used to identify factors associated with a self-reported history of incarceration. We also examined the prevalence of injection drug use and syringe sharing within prisons.

Results
252 IDU were recruited in August 2008; 66 (26.2%) were female and the median age was 36.5 years. In total, 197 (78.2%) participants reported a history of incarceration. In multivariate analyses, reporting a history of incarceration was associated with a history of compulsory drug treatment (adjusted odds ratio [AOR] = 4.93; 95% confidence interval [CI]: 1.95 - 12.48), non-fatal overdose (AOR = 3.69; 95%CI: 1.45 - 9.39), syringe sharing (AOR = 2.20; 95%CI: 1.12 - 4.32), and female gender (AOR = 0.41; 95%CI: 0.20 - 0.82). Among those who reported a history of incarceration, 59 (29.9%) reported injection drug use in prison, and 48 (81.4%) of these individuals reported sharing syringes in prison. Incarceration was not associated with the number of injections performed in the previous week (p = 0.202).

Conclusion
Over three-quarters of the IDU participating in this study reported a history of incarceration, and 30% of these individuals reported injection drug use within prison. Further, an alarmingly high level of syringe sharing within prison was reported, and incarceration was not associated with reductions in drug use. These findings provide further evidence of the need for community diversion strategies, as well as harm reduction programs, in Thai prisons.
Aminoguanidine inhibits aortic hydrogen peroxide production, VSMC NOX activity and hypercontractility in diabetic mice
Authors: Oak Jeong-Ho , Youn Ji-Youn , Cai Hua 
Published: December 2009

AbstractBackgroundDysfunctionally uncoupled endothelial nitric oxide synthase (eNOS) is involved in producing reactive oxygen species (ROS) in the diabetic endothelium. The present study investigated whether anti-diabetes drug Aminoguanidine (AG) has any effect on eNOS function and vascular oxidant stress.Methods and ResultsBlood glucose levels were increased to 452.0 ± 15.1 mg/dl in STZ-treated male C57BL/6J mice (148.4 ± 3.2 mg/dl in untreated controls). Aortic productions of NO•and O2•-were measured specifically and sensitively using electron spin resonance. Diabetic mice had a marked increase in aortic O2•-production. Aortic hydrogen peroxide (H2O2) production was also increased in diabetic aortas and significantly attenuated by AG. AG however had only a marginal effect in reducing aortic O2•-production, which corresponded to a minimal effect in improving aortic nitric oxide (NO•) bioavailability. The endothelium-dependent vasodilatation however was modestly but significantly improved by AG, likely consequent to AG-induced reduction in hyper-contractility.NAD(P)Hoxidase (NOX)-dependent O2•-production was completely attenuated by AG in endothelium-denuded diabetic aortas.ConclusionIn summary, despite that AG is not an effective eNOS recoupling agent presumably consequent to its ineffectiveness in preventing endothelial NOX activation, it is inhibitory of aortic H2O2production, VSMC NOX activity, and hypercontractility in diabetes.
Tuning microbial hosts for membrane protein production
Authors: Freigassner Maria , Pichler Harald , Glieder Anton 
Published: December 2009

AbstractThe last four years have brought exciting progress in membrane protein research. Finally those many efforts that have been put into expression of eukaryotic membrane proteins are coming to fruition and enable to solve an ever-growing number of high resolution structures. In the past, many skilful optimization steps were required to achieve sufficient expression of functional membrane proteins. Optimization was performed individually for every membrane protein, but provided insight about commonly encountered bottlenecks and, more importantly, general guidelines how to alleviate cellular limitations during microbial membrane protein expression. Lately, system-wide analyses are emerging as powerful means to decipher cellular bottlenecks during heterologous protein production and their use in microbial membrane protein expression has grown in popularity during the past months.This review covers the most prominent solutions and pitfalls in expression of eukaryotic membrane proteins using microbial hosts (prokaryotes, yeasts), highlights skilful applications of our basic understanding to improve membrane protein production. Omics technologies provide new concepts to engineer microbial hosts for membrane protein production.
Effects of hydrogen sulfide on inflammation in caerulein-induced acute pancreatitis
Authors: Sidhapuriwala Jenab N , Ng Siaw Wei , Bhatia Madhav 
Published: December 2009

Abstract

Background
Hydrogen sulfide (H2S), a gaseous mediator plays an important role in a wide range of physiological and pathological processes. H2S has been extensively studied for its various roles in cardiovascular and neurological disorders. However, the role of H2S in inflammation is still controversial. The current study was aimed to investigate the therapeutic potential of sodium hydrosulfide (NaHS), an H2S donor in in vivo model of acute pancreatitis in mice.

Methods
Acute pancreatitis was induced in mice by hourly caerulein injections (50 μg/kg) for 10 hours. Mice were treated with different dosages of NaHS (5 mg/kg, 10 mg/kg or 15 mg/kg) or with vehicle, distilled water (DW). NaHS or DW was administered 1 h before induction of pancreatitis. Mice were sacrificed 1 h after the last caerulein injection. Blood, pancreas and lung tissues were collected and were processed to measure the plasma amylase, myeloperoxidase (MPO) activities in pancreas and lung and chemokines and adhesion molecules in pancreas and lung.

Results
It was revealed that significant reduction of inflammation, both in pancreas and lung was associated with NaHS 10 mg/kg. Further the anti-inflammatory effects of NaHS 10 mg/kg were associated with reduction of pancreatic and pulmonary inflammatory chemokines and adhesion molecules. NaHS 5 mg/kg did not cause significant improvement on inflammation in pancreas and associated lung injury and NaHS 15 mg/kg did not further enhance the beneficial effects seen with NaHS 10 mg/kg.

Conclusion
In conclusion, these data provide evidence for anti-inflammatory effects of H2S based on its dosage used.
Tyrosine Phosphorylation of the N-Methyl-D-Aspartate Receptor 2B Subunit in Spinal Cord Contributes to Remifentanil-Induced Postoperative Hyperalgesia: the Preventive Effect of Ketamine
Authors: Gu Xiaoping , Wu Xiaoli , Liu Yue , Cui Songqin , Ma Zhengliang 
Published: December 2009

Background Experimental and clinical studies showed that intraoperative infusionof remifentanil has been associated with postoperative hyperalgesia. Previous reports suggested that spinal N-methyl-D-aspartate (NMDA) receptors may contribute to the development and maintenance of opioid-induced hyperalgesia. In the present study, we used a rat model of postoperative pain to investigate the role of tyrosine phosphorylation of NMDA receptor 2B (NR2B) subunit in spinal cord in the postoperative hyperalgesia induced by remifentanil and the intervention of pretreatment with ketamine. Results Intraoperative infusion of remifentanil (0.04 mg/kg, subcutaneous) significantly enhanced mechanical allodynia and thermal hyperalgesia induced by the plantar incision during the postoperative period (each lasting between 2 h and 48 h), which was attenuated by pretreatment with ketamine (10 mg/kg, subcutaneous). Correlated with the pain behavior changes, immunocytochemical and western blotting experiments in our study revealed that there was a marked increase in NR2B phosphorylation at Tyr1472 in the superficial dorsal horn after intraoperative infusion of remifentanil, which was attenuated by pretreatment with ketamine. Conclusions This study provides direct evidence that tyrosine phosphorylation of the NR2B at Tyr1472 in spinal dosal horn contributes to postoperative hyperalgesia induced by remifentanil and supports the potential therapeutic value of ketamine for improving postoperative hyperalgesia induced by remifentanil.
Cancer patients' attitudes towards Chinese medicine: a Hong Kong survey
Authors: Lam Yuen-chi , Cheng Chung-wah , Peng Heng , Law Chun-key , Huang Xianzhang , Bian Zhaoxiang 
Published: December 2009

Abstract

Background
This article reports a survey conducted in Hong Kong on the cancer patients' attitudes towards Chinese medicine treatment.

Methods
Cancer patients from three Chinese medicine clinics and one oncology clinic were interviewed with a structured questionnaire.

Results
Of a total of 786 participants included in the study, 42.9% used Western medicine only; 57.1% used at least one form of Chinese medicine; 5 participants used Chinese medicine only; and 56.5% used Chinese medicine before/during/after Western medicine treatment. Commonly used Western medicine and Chinese medicine treatments included chemotherapy (63.7%), radiotherapy (62.0%), surgery (57.6%), Chinese herbal medicine (53.9%) and Chinese dietary therapy (9.5%). Participants receiving chemotherapy used Chinese medicine (63.3%) more than those receiving any other Western medicine treatments. Spearman correlation coefficients showed that the selection of Chinese medicine was associated with the cancer type (rs = -1.36; P < 0.001), stage (rs = 0.178; P < 0.001), duration (rs = -0.074; P = 0.037), whether receiving chemotherapy (rs = 0.165; P < 0.001) and palliative therapy (rs = 0.087; P = 0.015). Nearly two-thirds of the participants (N = 274) did not tell their physicians about using Chinese medicine. Over two-thirds of all participants (68.2%) believed that integrated Chinese and Western medicine was effective.

Conclusion
Chinese medicine is commonly used among Hong Kong cancer patients. The interviewed cancer patients in Hong Kong considered integrative Chinese and Western medicine is an effective cancer treatment.
Transplantation and innate immunity: the lesson of natural killer cells
Authors: Bertaina Alice , Locatelli Franco , Moretta Lorenzo 
Published: December 2009

Abstract
Natural killer cells have been demonstrated to play a major role in mediating an anti-leukemia effect in patients given a T-cell depleted allogeneic hematopoietic stem cell transplantation from an HLA-haploidentical family donor. In particular, donor-derived natural killer cells, which are alloreactive (i.e. KIR/HLA mismatched) towards recipient cells, significantly contribute to the eradication of leukemia blasts escaping the preparative regimen to transplantation. A recent study on high-risk pediatric acute lymphoblastic leukemia refractory to chemotherapy further highlighted the importance of donors with alloreactive natural killer cells in haploidentical hematopoietic stem cell transplantation, as it demonstrated that these cells can emerge starting from the fourth-fifth month after the allograft and persist for many months. This study represents a major breakthrough in the cure of otherwise fatal leukemias, providing information on the best criteria for choosing the optimal donor.
Correlating measurements across samples improves accuracy of large-scale expression profile experiments
Authors: Alvarez Mariano Javier , Sumazin Pavel , Rajbhandari Presha , Califano Andrea 
Published: December 2009

AbstractGene expression profiling technologies suffer from poor reproducibility across replicate experiments. However, when analyzing large datasets, probe-level expression profile correlation can help identify flawed probes and lead to the construction of truer probe sets with improved reproducibility. We describe methods to eliminate uninformative and flawed probes, account for dependence between probes, and address variability due to transcript-isoform mixtures. We test and validate our approach on Affymetrix microarrays and outline their future adaptation to other technologies.