基于支持向量机的siRNA降解效率预测

为了辅助siRNA的设计,从已发表文献中共收集到573个siRNA的实验数据,使用基于统计学习理论的支持向量机(SVM)方法,提取了siRNA序列的碱基对关联性(BBC)特征,然后使用十倍交叉验证方法,对siRNA沉默目标基因的效率进行了预测.结果表明,基于支持向量机,选用多项式核作为核函数的算法具有最高的AUC值(0.73,ROC曲线图)和最高的r值(0.43,Pearson相关系数分析),优于以前基于打分的算法.结果说明,在以后的siRNA的设计中应该更多关注碱基之间的关联信息.     

ALV-J感染鸡骨髓细胞瘤中差异基因编码蛋白的互作网络分析

禽白血病病毒感染后可以引起宿主发生肿瘤.研究肿瘤组织中差异表达基因编码蛋白的相互作用,对理解禽白血病病毒的致病机制具有重要意义.基于文献中J亚群禽白血病病毒感染鸡骨髓瘤组织中差异表达基因编码蛋白进行了网络互作在线分析.结果表明:差异表达基因编码蛋白之间存在着复杂的相互作用,其中SRC网络、FYN网络、MYC网络和ERBB4网络对J亚群禽白血病病毒的致瘤机制可能具有重要作用.     

引导学生在统计中学习“统计”

“统计与概率”是《数学课程标准(实验稿)》规定的四个学习领域之一。北师大版课程标准实验教材从一年级上册开始,就编排了相应的内容引导学生由浅入深地在生活中学习“统计与概率”,并应用于生活之中。教学一年级下册中的“统计”(第84页),应借助日常生活中的例子,让学生经历简单的数据统计过程,在统计中学习“统计”,在做数学中学习数学。简单的数据统计过程包括:问题的提出——收集、整理数据——制成相应的统计图(或表)——根据统计图(或表)的数据作出解释或判断。因此,教学时可以围绕以下几方面展开。1.创设情境,提出问题“。统计”教…     

家族性肥厚型心肌病相关cTnI基因突变检测芯片的应用

基于基因芯片技术对心肌钙蛋白(cTnI)基因上的突变进行了分析.针对外显子上的突变特征设计了特异性探针,制备了可以同时检测cTnI基因上第3,5,7,8外显子突变的低密度基因芯片.对每一个外显子,设计了2条5'端标记荧光的寡核苷酸链,一条模拟野生型序列,另一条模拟突变型序列,将二者混合起来模拟杂合子序列.经过实验条件的优化,制作的芯片可以灵敏、特异地检测cTnI基因外显子上的突变.结果表明,该芯片检测突变正配错配区别明显,荧光强度比值符合理论估计(正中碱基错配的信号强度是完全正配信号强度的50%左右).经进一步对芯片优化后,该芯片有望在家族性肥厚型心肌病的研究和诊断中得到应用.     

一类低秩矩阵填充问题的快速优化算法

低秩矩阵填充问题是一个秩最小化问题,通常凸松弛为核范数最小化问题来求解.该问题针对有无噪声或有无约束的情形需要分开求解,这使得求解过程变得繁琐.本文建立了一个基于核范数最小化的低秩矩阵填充统一模型,借助临近算子,设计了一种有效且具有收敛性保证的不动点凸优化算法求解该模型.通过对仿真数据和真实数据的数值实验,本文提出的算法与经典的算法相比,在计算效率和精度上都展现出较好的效果.     

基于张量低秩加稀疏模型的MRI重建方法

传统的基于压缩感知的磁共振(MRI)重建方法处理动态MRI数据时,需要将其向量化,但这种操作会在一定程度破坏数据内部的结构信息,从而有可能会降低重建质量.本文直接面向张量数据,建立了动态MRI重建的张量稀疏加低秩模型框架,并设计了一个基于交替方向乘子法(ADMM)的求解算法.实验结果表明,本文提出的模型和算法是有效的.     

人脑分类机理的构造性学习方法

构造性学习(CML)算法训练分类器对有些样本会有“拒认状态”,构造性学习算法中对这一状况的处理使用就近原则,然而,这种方法无法体现数据之间的联系.为了能更好地体现数据间的联系,提出了人脑分类机理的构造性学习方法(HB-CML).在测试阶段,把测试样本、训练样本都考虑进来,利用人脑对数据的自动分类机理,对“拒认状态”样本进行分类标记.同时,选取UCI数据集进行实验.结果表明:与CML算法相比,该方法的分类更为有效.     

46例白血病细胞免疫表型分析

目的:探讨白细胞免疫表型在白血病诊断中的临床价值及意义.方法:用23种单克隆抗体(CD),用流式细胞仪对46例白血病患者骨髓单个核细胞进行测定.结果:各型白血病主要表达本系列特异抗原,B-ALL可见表达髓系抗原,髓系也可见表达淋系抗原,M3较少表达CD34和HLA-DR;2例混合型白血病(HAL)表达CD+34,CD+13,CD+33,CD+19,CD+10,CD+20,CD+38.1例M0患者.结论:白血病细胞具有高度异质性;FAB与免疫分型同时结合可互相补充,提高诊断率.淋巴细胞增殖性疾病进行免疫表型分析有准确诊断的重要意义.     

关于脑卒中发病环境因素的分析及干预

文章针对2012年“高教社杯”全国大学生数学建模竞赛(CUMCM)专科组C题所给的数据和提出的问题,结合数理统计原理分析并处理了所给的数据,并结合脑卒中的诱发与环境因素的关系,建立了统计回归模型,利用regress回归分析算法,运用Matlab软件进行求解,得出脑卒中发病率与气温、气压、相对湿度间的关系;且通过考虑气温、气压、相对湿度间的相关性对发病率影响问题,利用数理统计原理对它们之间的相关性进行分析,对所提出的统计回归模型进行多次模型改进,最后对高危人群提出预警和干预的建议方案.     

采用单次快拍数据实现MIMO雷达目标角度估计

通过深入研究多输入多输出(MIMO)雷达的角度估计算法,针对MIMO雷达角度估计中的实时性和相干目标源问题,基于双基地MIMO雷达的信号模型,提出了一种采用单次快拍数据的估计算法.算法采用MIMO雷达接收的单次快拍数据,构造出块Hankel矩阵,并证明该矩阵的秩等于总目标个数,且不受信号相关性的影响,通过奇异值分解获得对应的信号子空间,结合ESPRIT算法实现了对相干和非相干目标的收发角度估计.该算法减少了数据量和计算量,具有更好的实时处理性;通过矩阵的重构,能够准确地估计相干信源对应的信号或噪声子空间.由于采用了同一信号子空间,实现了参数的自动配对,更利于在实际中应用.计算机仿真结果证实了算法的有效性和可行性.     

A robust statistical procedure to discover expression biomarkers using microarray genomic expression data

INTRODUCTION Microarray technique is a powerful laboratory tool for simultaneously monitoring genome-wide expression in different conditions. One of the most important applications of microarray technique is the classification of tumor subtypes or different disease states to facilitate clinical researchers in diagnostic, therapeutic or prognostic decisions for patients (Golub et al., 1999; Alizadeh et al., 2000; Spindler, 2006). The generally used approaches, such as cluster analysis and…     

Pure total flavonoids from Citrus paradisi Macfadyen actmsynergistically with arsenic trioxide in inducingmapoptosis of Kasumi-1 leukemia cells in vitro

To investigate the potential effects of pure total flavonoid compounds (PTFCs) from Citrus paradisi Macfadyen separately or combined with arsenic trioxide on the proliferation of human myeloid leukemia cells and the mechanisms underlying the action of PTFCs. The effects of PTFCs separately or combined with arsenic trioxide on the proliferation and apoptosis of leukemia cells were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), fluorescence microscopy, and flow cytometry. Their effects on the expression levels of apoptosis-related regulators were determined by Western blot assay. PTFCs combined with arsenic trioxide significantly inhibited the growth of Kasumi-1 cells, and apoptosis was confirmed by flow cytometry analysis. Hoechst 33258 staining showed more significant morphological changes and more apoptosis following the combined treatment. Western blots showed changes in the expression of genes for poly ADP-ribose polymerase (PARP), caspase 3/9, and P65. The results indicated that PTFCs separately or combined with arsenic trioxide inhibited proliferation of leukemia cells in vitro and induced their apoptosis by modulating the expression of apoptosis-related regulator genes.     

Quantitative analysis of a panel of gene expression in prostate cancer——with emphasis on NPY expression analysis

Objective: To investigate molecular alterations associating with prostate carcinoma progression and potentially provide information toward more accurate prognosis/diagnosis. Methods: A set of laser captured microdissected (LCM) specimens from 300 prostate cancer (PCa) patients undergoing radical prostatectomy (RP) were defined. Ten patients representing "aggressive" PCa, and 10 representing "non-aggressive" PCa were selected based on prostate-specific antigen (PSA) recurrence,Gleason score, pathological stage and tumor cell differentiation, with matched patient age and race between the two groups.Normal and neoplastic prostate epithelial cells were collected with LCM from frozen tissue slides obtained from the RP specimens.The expressions of a panel of genes, including NPY, PTEN, AR,AMACR, DD3, and GSTP1, were measured by quantitative real-time RT-PCR (TaqMan), and correlation was analyzed with clinicopathological features. Results: The expressions of AMACR and DD3 were consistently up-regulated in cancer cells compared to benign prostate epithelial cells in all PCa patients, whereas GSTP1 expression was down regulated in each patient. NPY, PTEN and AR exhibited a striking difference in their expression patterns between aggressive and non-aggressive PCas (P=0.0203, 0.0284, and 0.0378, respectively, Wilcoxon rank sum test). The lower expression of NPY showed association with "aggressive" PCas based on a larger PCa patient cohort analysis (P=0.0037,univariate generalized linear model (GLM) analysis). Conclusion: Despite widely noted heterogeneous nature of PCa, gene expression alterations of AMACR, DD3, and GSTP1 in LCM-derived PCa epithelial cells suggest for common underlying mechanisms in the initiation of PCa. Lower NPY expression level is significantly associated with more aggressive clinical behavior of PCa; PTEN and AR may have potential in defining PCa with aggressive clinical behavior. Studies along these lines have potential to define PCa-associated gene expression alterations and likely co-regulation of genes/pathways critical in the biology of PCa onset/progression.     

SEREX技术筛选EID3及其表达的实验研究

[目的]新的大肠癌相关性抗原EID3的基因克隆及其诊断价值研究.[方法]利用大肠癌病人体内血清中所含的对肿瘤抗原产生的特异性抗体筛选睾丸组织cDNA噬菌体表达文库和大肠癌组织cDNA噬菌体表达文库(SEREX),并用RT-PCR技术研究EID3 mRNA在正常组织和大肠癌传代细胞表达.[结果]睾丸组织cDNA噬菌体表达文库筛选得到了可以诱导大肠癌病人抗体免疫应答的新抗原EID3基因(Gen-bank NM_001008394.1).它们定位于染色体19q13.2,EID3含1个外显子.通过RT-PCR分析发现,EID3基因在43例大肠癌传代细胞株中,39例阳性,阳性率为90.7%.在正常组织中,除睾丸组织外不表达或有极低水平转录.[结论]EID3 mRNA表达检测用于诊断大肠癌,可能具有高特异性和高敏感性的特点.EID3蛋白被首次发现在大肠癌病人中能够诱导机体的抗体免疫应答,为一个新的大肠癌相关性抗原分子.其功能可能与抑制细胞的恶性增殖相关,并可进一步研究其用于治疗和诊断大肠癌的可行性.     

Parameters selection in gene selection using Gaussian kernel support vector machines by genetic algorithm

INTRODUCTION Recent techniques based on oligonucleotide or cDNA microarrays allow the expression level of thousands of genes to be monitored in parallel (Golub et al., 1999). A critically important factor for cancer diagnosis and treatment is the reliable prediction of tumor progression. A remarkable advance for mo- lecular biology and for cancer research is cDNA mi- croarray technology. cDNA microarray datasets havea high dimensionality corresponding to the large number of genes monit…     

An Inexpensive Gel Electrophoresis-Based Polymerase Chain Reaction Method for Quantifying mRNA Levels

In order to engage their students in a core methodology of the new genomics era, an ever-increasing number of faculty at primarily undergraduate institutions are gaining access to microarray technology. Their students are conducting successful microarray experiments designed to address a variety of interesting questions. A next step in these teaching and research laboratory projects is often validation of the microarray data for individual selected genes. In the research community, this usually involves the use of real-time polymerase chain reaction (PCR), a technology that requires instrumentation and reagents that are prohibitively expensive for most undergraduate institutions. The results of a survey of faculty teaching undergraduates in classroom and research settings indicate a clear need for an alternative approach. We sought to develop an inexpensive and student-friendly gel electrophoresis-based PCR method for quantifying messenger RNA (mRNA) levels using undergraduate researchers as models for students in teaching and research laboratories. We compared the results for three selected genes measured by microarray analysis, real-time PCR, and the gel electrophoresis-based method. The data support the use of the gel electrophoresis-based method as an inexpensive, convenient, yet reliable alternative for quantifying mRNA levels in undergraduate laboratories.     

A study of the relationship between expression level of TRF1 protein and telomerase activity in human acute leukemia

INTRODUCTION Telomeres are distinctive DNA-protein struc-tures that cap the ends of linear chromosomes.It is very important to keep the chromosomes stabilization.Telomerase activity is closely linked to attainment of cellular immortality,a step in carcinogenesis,while lack of such activity contributes to cellular senes-cence.Telomerase is activated in more than85%ofmalignant tumors(Hiayma et al.,1997).Human te-lomeric repeat binding factor1(TRF1)is a telomere associated with proteins a…