bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of miR-1 and miR-133a in myocardial ischemic postconditioning
Authors: He Bin , Xiao Jian , Ren An-Jing , Zhang Yu-Feng , Zhang Hao , Chen Min , Xie Bing , Gao Xiao-Gang , Wang Ying-Wei 
Published: March 2011

Abstract

Background
Ischemic postconditioning (IPost) has aroused much attention since 2003 when it was firstly reported. The role of microRNAs (miRNAs or miRs) in IPost has rarely been reported. The present study was undertaken to investigate whether miRNAs were involved in the protective effect of IPost against myocardial ischemia-reperfusion (IR) injury and the probable mechanisms involved.

Methods
Thirty SD rats weighing 250-300 g were equally randomized to three groups: Control group, where the rats were treated with thoracotomy only; IR group, where the rats were treated with ischemia for 60 min and reperfusion for 180 min; and IPost group, where the rats were treated with 3 cycles of transient IR just before reperfusion. The extent of myocardial infarction, LDH and CK activities were measured immediately after treatment. Myocardial apoptosis was detected by TUNEL assay. The myocardial tissue was collected after IR or IPost stimulation to evaluate the miRNAs expression level by miRNA-microarray and quantitative real-time RT-PCR. Real-time PCR was conducted to identify changes in mRNA expression of apoptosis-related genes such as Bcl-2, Bax and Caspase-9 (CASP9), and Western blot was used to compare the protein expression level of CASP9 in the three groups. The miRNA mimics and anti-miRNA oligonucleotides (AMO) were transferred into the cultured neonatal cardiomyocytes and myocardium before they were treated with IR. The effect of miRNAs on apoptosis was determined by flow cytometry and TUNEL assay. CASP9, as one of the candidate target of miR-133a, was compared during IR after the miR-133a mimic or AMO-133a was transferred into the myocardium.

Results
IPost reduced the IR-induced infarct size of the left ventricle, and decreased CK and LDH levels. TUNEL assay showed that myocardial apoptosis was attenuated by IPost compared with IR. MiRNA-microarray and RT-PCR showed that myocardial-specific miR-1 and miR-133a were down-regulated by IR, and up-regulated by IPost compared with IR. Furthermore, IPost up-regulated the mRNA expression of Bcl-2, down-regulated that of Bax and CASP9. Western blot showed that IPost also down-regulated the CASP9 protein expression compared with IR. The results of flow cytometry and TUNEL assay showed that up-regulation of miR-1 and miR-133a decreased apoptosis of cardiomyocytes. MiR-133a mimic down-regulated CASP9 protein expression and attenuated IR-induced apoptosis.

Conclusion
MiRNAs are associated with the protective effect of IPost against myocardial IR injury. IPost can up-regulate miR-1 and miR-133a, and decrease apoptosis of cardiomyocyte. Myocardial-specific miR-1 and miR-133a may play an important role in IPost protection by regulating apoptosis-related genes. MiR-133a may attenuate apoptosis of myocardiocytes by targeting CASP9.
AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm
Authors: Kim Jihoon , Patel Kiltesh , Jung Hyunchul , Kuo Winston P , Ohno-Machado Lucila 
Published: March 2011

Abstract

Background
Cross-platform analysis of gene express data requires multiple, intricate processes at different layers with various platforms. However, existing tools handle only a single platform and are not flexible enough to support custom changes, which arise from the new statistical methods, updated versions of reference data, and better platforms released every month or year. Current tools are so tightly coupled with reference information, such as reference genome, transcriptome database, and SNP, which are often erroneous or outdated, that the output results are incorrect and misleading.

Results
We developed AnyExpress, a software package that combines cross-platform gene expression data using a fast interval-matching algorithm. Supported platforms include next-generation-sequencing technology, microarray, SAGE, MPSS, and more. Users can define custom target transcriptome database references for probe/read mapping in any species, as well as criteria to remove undesirable probes/reads.
AnyExpress offers scalable processing features such as binding, normalization, and summarization that are not present in existing software tools.
As a case study, we applied AnyExpress to published Affymetrix microarray and Illumina NGS RNA-Seq data from human kidney and liver. The mean of within-platform correlation coefficient was 0.98 for within-platform samples in kidney and liver, respectively. The mean of cross-platform correlation coefficients was 0.73. These results confirmed those of the original and secondary studies. Applying filtering produced higher agreement between microarray and NGS, according to an agreement index calculated from differentially expressed genes.

Conclusion
AnyExpress can combine cross-platform gene expression data, process data from both open- and closed-platforms, select a custom target reference, filter out undesirable probes or reads based on custom-defined biological features, and perform quantile-normalization with a large number of microarray samples. AnyExpress is fast, comprehensive, flexible, and freely available at http://anyexpress.sourceforge.net.
A proteomics approach to decipher the molecular nature of planarian stem cells
Authors: Fernández-Taboada Enrique , Rodríguez-Esteban Gustavo , Saló Emili , Abril Josep F 
Published: March 2011

Abstract
Background
In recent years, planaria have emerged as an important model system for research into stem cells and regeneration. Attention is focused on their unique stem cells, the neoblasts, which can differentiate into any cell type present in the adult organism. Sequencing of the Schmidtea mediterranea genome and some expressed sequence tag projects have generated extensive data on the genetic profile of these cells. However, little information is available on their protein dynamics.

Results
We developed a proteomic strategy to identify neoblast-specific proteins. Here we describe the method and discuss the results in comparison to the genomic high-throughput analyses carried out in planaria and to proteomic studies using other stem cell systems. We also show functional data for some of the candidate genes selected in our proteomic approach.

Conclusions
We have developed an accurate and reliable mass-spectra-based proteomics approach to complement previous genomic studies and to further achieve a more accurate understanding and description of the molecular and cellular processes related to the neoblasts.
Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites
Authors: Schmidt Søren F , Jørgensen Mette , Chen Yun , Nielsen Ronni , Sandelin Albin , Mandrup Susanne 
Published: March 2011

AbstractBackgroundThe transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and others have previously shown that binding sites of these two transcription factors show a high degree of overlap and are associated with the majority of genes upregulated during differentiation of murine 3T3-L1 adipocytes.ResultsHere we have mapped all binding sites of C/EBPα and PPARγ in human SGBS adipocytes and compared these with the genome-wide profiles from mouse adipocytes to systematically investigate what biological features correlate with retention of sites in orthologous regions between mouse and human. Despite a limited interspecies retention of binding sites, several biological features make sites more likely to be retained. First, co-binding of PPARγ and C/EBPα in mouse is the most powerful predictor of retention of the corresponding binding sites in human. Second, vicinity to genes highly upregulated during adipogenesis significantly increases retention. Third, the presence of C/EBPα consensus sites correlate with retention of both factors, indicating that C/EBPα facilitates recruitment of PPARγ. Fourth, retention correlates with overall sequence conservation within the binding regions independent of C/EBPα and PPARγ sequence patterns, indicating that other transcription factors work cooperatively with these two key transcription factors.ConclusionsThis study provides a comprehensive and systematic analysis of what biological features impact on retention of binding sites between human and mouse. Specifically, we show that the binding of C/EBPα and PPARγ in adipocytes have evolved in a highly interdependent manner, indicating a significant cooperativity between these two transcription factors.
Distinct roles for nitric oxide in resistant C57BL/6 and susceptible BALB/c mice to control Burkholderia pseudomallei infection
Authors: Breitbach Katrin , Wongprompitak Patimaporn , Steinmetz Ivo 
Published: March 2011

AbstractBackgroundBurkholderia pseudomalleiis the causative agent of melioidosis, an emerging bacterial infectious disease in tropical and subtropical areas. We recently showed that NADPH oxidase but not nitric oxide (NO) contributes to resistance in innately resistant C57BL/6 mice in aB. pseudomalleirespiratory infection model. However, the function of NO for resistance was shown to differ among distinct strains of mice and proved also to be stage dependent in various infection models. The present study therefore aimed to examine the role of NO in a systemic infection model of melioidosis and to test whether the function of NO differs among innately resistant C57BL/6 and susceptible BALB/c mice afterB. pseudomalleiinfection.ResultsC57BL/6iNOS-/-mice that were intravenously infected withB. pseudomalleisurvived several weeks, whereas most of the wild type animals succumbed during this period. The bacterial burden in liver and spleen was significantly higher in wild type animals compared toiNOS-/-mice 13 days after challenge. In contrast, BALB/c mice that were treated with amminoguanidine to inhibit NO expression in vivo showed significantly enhanced mortality rates and higher bacterial loads in liver and spleen compared to control animals. The bactericidal function of IFN-γ stimulated C57BL/6iNOS-/-macrophages were not altered afterB. pseudomalleiinfection, but BALB/c macrophages exhibited reduced killing activity against the pathogen when NO was inhibited.ConclusionOur present data indicate a dual role of NO among resistant and susceptible mouse strains afterB. pseudomalleiinfection. NO mediated mechanisms are an essential component to control the infection in susceptible BALB/c mice. In contrast, NO production inB. pseudomalleiinfected C57BL/6 mice rather harmed the host likely due to its detrimental effects.
Psychometric properties of two physical activity questionnaires, the AQuAA and the PASE, in cancer patients
Authors: Liu Roberto DK , Buffart Laurien M , Kersten Marie José , Spiering Marjolein , Brug Johannes , van Mechelen Willem , Chinapaw Mai JM 
Published: March 2011

Abstract

Background
This study aimed to evaluate the reliability and validity of two self-report physical activity (PA) questionnaires - the AQuAA (Activity Questionnaire for Adults and Adolescents) and PASE (Physical Activity Scale for the Elderly) - in cancer patients.

Methods
Test-retest reliability was determined by administering the questionnaires twice within 5 days. Intraclass correlation coefficient (ICC), standard error of measurement (SEM) and smallest detectable difference (SDD) were calculated. Construct validity was determined by comparing the questionnaire results with ActiGraph accelerometer scores using Spearman correlation coefficients (rs) and ICCs. Content validity was examined using the Three-Step Test-Interview (TSTI).

Results
Reliability for the AQuAA scores were fair to excellent (ICC = 0.57 to 0.78). Reliability for the PASE scores ranged from good to excellent (ICC = 0.67 to 0.90). Correlations between the ActiGraph and the AQuAA and the PASE were low (rs = 0.05 and 0.16 respectively, and ICC = -0.001 to 0.44). The TSTI showed that participants experienced difficulties with the examples provided with the questions, the perceptions of intensity level of PA, and with recalling the time spent on PA.

Conclusions
Both questionnaires showed good to excellent test-retest reliability for most scores. Construct validity of both questionnaires was low, as indicated by the low correlations with the ActiGraph. Except for a few difficulties that participants perceived when filling out the questionnaires, the content validity of both questionnaires was good.
Development and implementation of the quality control panel of RT-PCR and real-time RT-PCR for avian influenza A (H5N1) surveillance network in mainland China
Authors: Gao Rongbao , Gao Yan , Wen Leying , Shao Ming , Zou Shumei , Li Changgui , Yang Lei , Li Xiyan , Wang Wei , Shu Yuelong 
Published: March 2011

Abstract

Background
Reverse transcription PCR (RT-PCR) and real time RT-PCR (rRT-PCR) have been indispensable methods for influenza surveillance, especially for determination of avian influenza. The movement of testing beyond reference lab introduced the need of quality control, including the implementation of an evaluation system for validating personal training and sample proficiency testing.

Methods
We developed a panel with lysates of seasonal influenza virus (H1N1, H3N2 and B), serials of diluted H5N1 virus lysates, and in-vitro transcribed H5 hemaglutinin (HA) and an artificial gene RNAs for RT-PCR and rRT-PCR quality control assessment. The validations of stability and reproducibility were performed on the panel. Additionally, the panel was implemented to assess the detection capability of Chinese human avian influenza networks.

Results
The panel has relatively high stability and good reproducibility demonstrated by kappa's tests. In the implementation of panel on Chinese human avian influenza networks, the results suggested that there were a relatively low number of discrepancies for both concise and reproducibility in Chinese avian influenza virus net works.

Conclusions
A quality control panel of RT-PCR and real-time RT-PCR for avian influenza A (H5N1) surveillance network was developed. An availably statistical data, which are used to assess the detection capability of networks on avian influenza virus (H5N1), can be obtained relatively easily through implementation of the panel on networks.
Phase II study of preoperative radiation plus concurrent daily tegafur-uracil (UFT) with leucovorin for locally advanced rectal cancer
Authors: Cellier Patrice , Leduc Bernard , Martin Laurent , Vié Brigitte , Chevelle Christian , Vendrely Véronique , Salemkour Augustin , Carrie Christian , Calais Gilles , Burtin Pascal , Campion Loïc , Boisdron-Celle Michèle , Morel Alain , Berger Virginie , Gamelin Erick 
Published: March 2011

Abstract

Background
Considerable variation in intravenous 5-fluorouracil (5-FU) metabolism can occur due to the wide range of dihydropyrimidine dehydrogenase (DPD) enzyme activity, which can affect both tolerability and efficacy. The oral fluoropyrimidine tegafur-uracil (UFT) is an effective, well-tolerated and convenient alternative to intravenous 5-FU. We undertook this study in patients with locally advanced rectal cancer to evaluate the efficacy and tolerability of UFT with leucovorin (LV) and preoperative radiotherapy and to evaluate the utility and limitations of multicenter staging using pre- and post-chemoradiotherapy ultrasound. We also performed a validated pretherapy assessment of DPD activity and assessed its potential influence on the tolerability of UFT treatment.

Methods
This phase II study assessed preoperative UFT with LV and radiotherapy in 85 patients with locally advanced T3 rectal cancer. Patients with potentially resectable tumors received UFT (300 mg/m/2/day), LV (75 mg/day), and pelvic radiotherapy (1.8 Gy/day, 45 Gy total) 5 days/week for 5 weeks then surgery 4-6 weeks later. The primary endpoints included tumor downstaging and the pathologic complete response (pCR) rate.

Results
Most adverse events were mild to moderate in nature. Preoperative grade 3/4 adverse events included diarrhea (n = 18, 21%) and nausea/vomiting (n = 5, 6%). Two patients heterozygous for dihydropyrimidine dehydrogenase gene (DPYD) experienced early grade 4 neutropenia (variant IVS14+1G > A) and diarrhea (variant 2846A > T). Pretreatment ultrasound TNM staging was compared with postchemoradiotherapy pathology TN staging and a significant shift towards earlier TNM stages was observed (p < 0.001). The overall downstaging rate was 42% for primary tumors and 44% for lymph nodes. The pCR rate was 8%. The sensitivity and specificity of ultrasound for staging was poor. Anal sphincter function was preserved in 55 patients (65%). Overall and recurrence-free survival at 3 years was 86.1% and 66.7%, respectively. Adjuvant chemotherapy was administered to 36 node-positive patients (mean duration 118 days).

Conclusion
Preoperative chemoradiotherapy using UFT with LV plus radiotherapy was well tolerated and effective and represents a convenient alternative to 5-FU-based chemoradiotherapy for the treatment of resectable rectal cancer. Pretreatment detection of DPD deficiency should be performed to avoid severe adverse events.
The DUNDRUM-1 structured professional judgment for triage to appropriate levels of therapeutic security: retrospective-cohort validation study
Authors: Flynn Grainne , O'Neill Conor , McInerney Clare , Kennedy Harry G 
Published: March 2011

Abstract

Background
The assessment of those presenting to prison in-reach and court diversion services and those referred for admission to mental health services is a triage decision, allocating the patient to the appropriate level of therapeutic security. This is a critical clinical decision. We set out to improve on unstructured clinical judgement. We collated qualitative information and devised an 11 item structured professional judgment instrument for this purpose then tested for validity.

Methods
All those assessed following screening over a three month period at a busy remand committals prison (n = 246) were rated in a retrospective cohort design blind to outcome. Similarly, all those admitted to a mental health service from the same prison in-reach service over an overlapping two year period were rated blind to outcome (n = 100).

Results
The 11 item scale had good internal consistency (Cronbach's alpha = 0.95) and inter-rater reliability. The scale score did not correlate with the HCR-20 'historical' score. For the three month sample, the receiver operating characteristic area under the curve (AUC) for those admitted to hospital was 0.893 (95% confidence interval 0.843 to 0.943). For the two year sample, AUC distinguished at each level between those admitted to open wards, low secure units or a medium/high secure service. Open wards v low secure units AUC = 0.805 (95% CI 0.680 to 0.930); low secure v medium/high secure AUC = 0.866, (95% CI 0.784 to 0.949). Item to outcome correlations were significant for all 11 items.

Conclusions
The DUNDRUM-1 triage security scale and its items performed to criterion levels when tested against the real world outcome. This instrument can be used to ensure consistency in decision making when deciding who to admit to secure forensic hospitals. It can also be used to benchmark admission thresholds between services and jurisdictions. In this study we found some divergence between assessed need and actual placement. This provides fertile ground for future research as well as practical assistance in assessing unmet need, auditing case mix and planning care pathways.
Dichrostachys cinerea (L.) Wight et Arn (Mimosaceae) hydro-alcoholic extract action on the contractility of tracheal smooth muscle isolated from guinea-pig
Authors: Aworet-Samseny Raissa RR , Souza Alain , Kpahé Fidele , Konaté Kiessoun , Datté Jacques Y 
Published: March 2011

Abstract

Background

Dichrostachys cinerea (L.) Wight et Arn. (Mimosaceae) is largely used in ethno-medically across Africa, and mainly employed for the treatment of asthma in Ivory Coast and Gabon. The paper analyses the relaxation induced by the methanolic extract of D. cinerea (Edici) in the guinea-pig trachea preparations (GPTPs). Purpose: This study aimed to bring out the scientific basis to the use of this plant leading to the validation of this phytomedicine.

Method
The aorta obtained from guinea-pigs was immediately placed in a Mac Ewen solution. Experiments were performed in preparations suspended between two L-shaped stainless steel hooks in a 10 ml organ bath containing Mac Ewen solution. The isometric contractile force of the aorta strips of guinea-pig were recorded by using a strain gauge. The different drugs were directly administered into the organ bath and the magnitude of GPTPs was evaluated.

Results
Phytochemical analysis of the methanolic extract of Dichrostachys cinerea (Edici) using chemical methods revealed the presence of flavenoids, tannins, sterols, triterpenes and polyphenols. Pharmacological studies performed in GPTPs show that of Dichrostachys cinerea (0.1 mg/ml - 2 mg/ml) evoked a broncho-constriction in GPTPs. Whereas, at concentration up to 2 mg/ml, Edici induced a significant dose-dependent relaxation in the GPTPs. KCl-, ACh- or histamine-evoked contractions of isolated trachea was significantly inhibited by increasing concentrations of Edici (3.5-10 mg/ml). Edici (10 mg/ml) as well as promethazine (0.25 mg/ml) significantly inhibited contractions induced by increasing concentrations of histamine (1×10-7-1×10-4mg/ml). In the presence of atropine at a concentration of 10-6mg/ml, contractile response curve (CRC) evoked by ACh (1×10-5-1×10-2 mg/ml) was significantly abolished in concentration-dependent manner. Edici did not significantly reduced ACh evoked contraction (10-5-10-2mg/ml).

Conclusion
These observations suggest that Edici could act through two mechanisms: firstly by activation of β-adrenergic or histaminergic receptors; and secondly muscarinic receptors may not be greatly involved, that justifying the use of the extract in traditional Medicine in Africa.
Preparation of stable magnetic nanofluids containing Fe3O4@PPy nanoparticles by a novel one-pot route
Authors: Zhao Baobao , Nan Zhaodong 
Published: March 2011

AbstractStable magnetic nanofluids containing Fe3O4@Polypyrrole (PPy) nanoparticles (NPs) were prepared by using a facile and novel method, in which one-pot route was used. FeCl3·6H2O was applied as the iron source, and the oxidizing agent to produce PPy. Trisodium citrate (Na3cit) was used as the reducing reagent to form Fe3O4 NPs. The as-prepared nanofluid can keep long-term stability. The Fe3O4@PPy NPs can still keep dispersing well after the nanofluid has been standing for 1 month and no sedimentation is found. The polymerization reaction of the pyrrole monomers took place with Fe3+ ions as the initiator, in which these Fe3+ ions remained in the solution adsorbed on the surface of the Fe3O4 NPs. Thus, the core-shell NPs of Fe3O4@PPy were obtained. The particle size of the as-prepared Fe3O4@PPy can be easily controlled from 7 to 30 nm by the polymerization reaction of the pyrrole monomers. The steric stabilization and weight of the NPs affect the stability of the nanofluids. The as-prepared Fe3O4@PPy NPs exhibit superparamagnetic behavior.