PrepMS: TOF MS data graphical preprocessing tool

We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings, experimentally determined to work well in most situations. These values, if desired, can be changed by the user. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection and visual data quality assessment. AVAILABILITY: Stand-alone executable files and Matlab toolbox are available for download at: http://sourceforge.net/projects/prepms     

FoxO1在胰岛β细胞代谢灵活性受损及失代偿进程中的作用

葡萄糖及脂肪酸是胰岛β细胞的关键代谢底物,葡萄糖刺激胰岛β细胞分泌胰岛素是维持机体血糖稳态平衡的关键。胰岛素抵抗发生时,β细胞对能量代谢底物的选择失调,加速胰岛β细胞由代偿到胰岛β细胞失代偿的进程,是肥胖胰岛素抵抗最终发展为2型糖尿病的始动因素。核转录因子FoxO1属于Fox家族成员,在胰腺内广泛表达,在β细胞的代谢,发育,增殖过程中发挥着重要的调节作用。鉴于FoxO1在维持胰岛β细胞功能中的关键作用,现着重对FoxO1在胰岛β细胞代谢灵活性受损及失代偿过程发生中的作用调节进行阐述。为其作为调控胰岛β细胞功能的关键靶点提供参考。     

促性腺激素释放激素Buserelin 稳定性的研究

目的:研究Buserelin原料药的性质在温度、湿度、光线等条件的影响下随时间变化的规律,为该原料药的生产、包装、储存、运输及有效期的制定提供依据。方法:根据中国药典2005版二部附录XIX C药物稳定性试验指导原则及化学药物稳定性研究技术指导原则进行强光照射、高温(60℃、40℃)、高湿(RH92.5%±5%、RH75%±5%)影响因素试验,加速试验(40℃±2℃、RH75%±5%;25℃±2℃、RH60%±10%);按Buserelin原料药标准规定的质量指标及相关的检验方法对产品在试验条件下的主要质量指标进行检测。结果:强光照射、高温、高湿等影响因素对Buserelin的稳定性有明显影响,故应密封、于干燥、阴凉处保存。在加速试验中,Buserelin原料药的各项质量指标发生了小的变化,但均在质量标准规定的范围内。结论:强光照射、高温、高湿等影响因素对Buserelin的稳定性有明显影响,应在阴凉干燥处避光密封保存和运输。加速试验结果证明:在此条件下,它的各项质量指标变化均在质量标准范围内,符合Buserelin原料药质量标准规定的要求;故将其保质期暂定为两年。     

Metabolomics Data Normalization with EigenMS

Liquid chromatography mass spectrometry has become one of the analytical platforms of choice for metabolomics studies. However, LC-MS metabolomics data can suffer from the effects of various systematic biases. These include batch effects, day-to-day variations in instrument performance, signal intensity loss due to time-dependent effects of the LC column performance, accumulation of contaminants in the MS ion source and MS sensitivity among others. In this study we aimed to test a singular value decomposition-based method, called EigenMS, for normalization of metabolomics data. We analyzed a clinical human dataset where LC-MS serum metabolomics data and physiological measurements were collected from thirty nine healthy subjects and forty with type 2 diabetes and applied EigenMS to detect and correct for any systematic bias. EigenMS works in several stages. First, EigenMS preserves the treatment group differences in the metabolomics data by estimating treatment effects with an ANOVA model (multiple fixed effects can be estimated). Singular value decomposition of the residuals matrix is then used to determine bias trends in the data. The number of bias trends is then estimated via a permutation test and the effects of the bias trends are eliminated. EigenMS removed bias of unknown complexity from the LC-MS metabolomics data, allowing for increased sensitivity in differential analysis. Moreover, normalized samples better correlated with both other normalized samples and corresponding physiological data, such as blood glucose level, glycated haemoglobin, exercise central augmentation pressure normalized to heart rate of 75, and total cholesterol. We were able to report 2578 discriminatory metabolite peaks in the normalized data (p<0.05) as compared to only 1840 metabolite signals in the raw data. Our results support the use of singular value decomposition-based normalization for metabolomics data.     

Treatment outcomes in locally advanced colorectal carcinoma

BACKGROUND: Locally advanced colorectal cancers form a distinct subgroup where contiguous organs could be involved without distant metastases and so may be amenable to curative surgical resection. It was our objective to report our experience in treating six such patients with operable locally advanced colorectal carcinomas. METHODS: We retrospectively reviewed the case notes of 47 patients who were diagnosed with colorectal cancers at M S Ramaiah Medical Teaching Hospital between the years 1996 - 2001. Six patients were identified with T4 lesions, adjacent organ involvement and with no nodal involvement. The treatments and outcomes for these patients were then reviewed. RESULTS: Two of three patients with rectal malignancies who underwent pelvic exenteration succumbed to disease recurrence within the first 18 months. One of the three patients with colonic cancers died of non malignant causes. The other two are disease free till date. CONCLUSIONS: Aggressive multivisceral resections for locally advanced colonic cancers might be appropriate. Rectal cancers when locally advanced may be considered for pelvic exenteration, but a more guarded prognosis may apply.     

mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code

Background  

Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke.     

从茶尺蠖中分离到一株微小RNA病毒

从核型多角体病毒(PV)感染致死的茶尺蠖幼虫尸体中分离到一株微小RNA病毒(oPV)透射电镜观察纯化的病毒粒子为无囊膜、无表面特征、直径约26nm的球状颗粒.16%的SDS-PAGE显示它有两个分子量为31.5 kDa和28.8 kDa的衣壳蛋白,后者的含量是前者的2.5倍.3′端克隆序列分析表明EoPV基因组3′有poly(A)尾,编码RNA聚合酶(dRp)含有微小RNA病毒RNA聚合酶的八个保守基序,同源性分析表明它与榕透翅毒蛾微小RNA病毒(nPV)亲缘关系最近.这些特点表明该病毒为一株新的微小RNA病毒.