The utility of epithelial-cell micronuclei in the assessment of intermittent exposures

Epithelial-cell micronuclei (MN) are potentially useful markers of occupational exposure to genotoxicants. With intermittent exposures, cells sampled either before or after a specific time interval, reflecting the time it takes for damaged cells to become available at the epithelial surface, are unlikely to be exposure-related. It may then be important to conduct an exposure-window analysis, with the goal of identifying the relevant exposures.We re-analysed individual exposure data from a previous study (Suruda et al. 1993) of MN formation in 22 male mortuary science students exposed to formaldehyde during a 90-day embalming class. We conducted an exposurewindow analysis and compared the results with those obtained with 90-day cumulative exposure. The window widths varied between 7 and 25 days, in 1 day increments, assuming a constant 7-day cell-cycle. We assessed the fit (likelihood-ratio test) of a linear regression model, regressing the change in buccal MN prevalence on formaldehyde exposure, using both asymptotic and non-asymptotic methods. Exposures defined from 7-15 to 7-18 days before specimen collection provided a slightly better fit than the 90-day cumulative exposure, with a doubling of the regression coefficient for the exposure effect (for the 7-16-days window LR = 5.32, p = 0.032, coefficient = 0.088 MN per 1000 cells per ppm-hr; 95% CI = 0.014, 0.16; for the 90-day cumulative exposure LR = 4.44, p = 0.048, coefficient = 0.045 MN per 1000 cells per ppm-hr, 95% CI = 0.0038, 0.086). Although hampered by the small number of subjects, these results reinforce the potential importance of exposure timing.     

Windows操作系统下二代测序数据处理平台的建立及高通量信息分析标准流程在个人计算机上的实现

当前二代测序数据的处理广泛使用基于标准版本的Linux操作系统分析方法。这一系统专业性强,成本较高,操作界面不够友好,严重限制了大多数科研人员对数据的自主分析。本文创建了一个基于微软Windows操作系统的全功能二代测序数据的生物信息学分析系统,利用该系统经优选实现当前多种高通量测序数据的主流标准化分析流程。通过RNA-Seq的代表性案例,演算实测数据与传统Linux系统驱动的数据分析结果相比较,结果显示,本系统的组件和流程在常用的数据分析过程中,可以基本取代目前主流的Linux服务器或云计算平台,在运行效率相近的情况下,其操作极为简便且成本大大降低。本系统与所配附的编译软件及流程脚本,不仅为测序数据的生物信息学分析实操演练提供全面的解决方案,而且可以直接应用于专业的测序数据分析中。     

Windows环境下生物信号处理系统的软件设计

介绍Ｗｉｎｄｏｗｓ环境下生物信号数据采集与分析系统的软件设计方法。     

Compartmental modeling of whole-body vitamin A kinetics in unsupplemented and vitamin A-retinoic acid-supplemented neonatal rats

Little is known about the contribution of different tissues to whole-body vitamin A (VA) kinetics in neonates. Here, we have used model-based compartmental analysis of tissue tracer kinetic data from unsupplemented (control) and VA-retinoic acid (VARA)-supplemented neonatal rats to determine VA kinetics in specific tissues under control and supplemented conditions. First, compartmental models for retinol kinetics were developed for individual tissues, and then an integrated compartmental model incorporating all tissues was developed for both groups. The models predicted that 52% of chylomicron (CM) retinyl ester was cleared by liver in control pups versus 22% in VARA-treated pups, whereas about 51% of VA was predicted to be extrahepatic in 4- to 6-day-old unsupplemented neonatal rats. VARA increased CM retinyl ester uptake by lung, carcass, and intestine; decreased the release into plasma of retinol that had been cleared by liver and lung as CM retinyl esters; stimulated the uptake of retinol from plasma holo-retinol binding protein into carcass; and decreased the retinol turnover out of the liver. Overall, neonatal VA trafficking differed from that previously described for adult animals, with a larger contribution of extrahepatic tissues to CM clearance, especially after VA supplementation, and a significant amount of VA distributed in extrahepatic tissues.     

基于Cygwin实现生物信息学软件从Unix/Linux向Windows移植

Cygwin可在Windows环境下提供对Unix/Linux环境的模拟与支持,具有较为完善的Unix/Linux工具包和编程环境。利用Cygwin对常用的生物信息学数据分析软件如Sim4、FASTA、Phred/Phrap/RepeatMasker、EMBOSS、HMMER和ClustalW等进行重新编译,发现通过该方式能够获得可在Windows环境下运行的可执行代码,为利用Windows环境优势的同时进行跨平台生物信息学数据分析平台的开发提供重要参考价值。     

The utility of epithelial-cell micronuclei in the assessment of intermittent exposures

Epithelial-cell micronuclei (MN) are potentially useful markers of occupational exposure to genotoxicants. With intermittent exposures, cells sampled either before or after a specific time interval, reflecting the time it takes for damaged cells to become available at the epithelial surface, are unlikely to be exposure-related. It may then be important to conduct an exposure-window analysis, with the goal of identifying the relevant exposures.We re-analysed individual exposure data from a previous study (Suruda et al. 1993) of MN formation in 22 male mortuary science students exposed to formaldehyde during a 90-day embalming class. We conducted an exposurewindow analysis and compared the results with those obtained with 90-day cumulative exposure. The window widths varied between 7 and 25 days, in 1 day increments, assuming a constant 7-day cell-cycle. We assessed the fit (likelihood-ratio test) of a linear regression model, regressing the change in buccal MN prevalence on formaldehyde exposure, using both asymptotic and non-asymptotic methods. Exposures defined from 7-15 to 7-18 days before specimen collection provided a slightly better fit than the 90-day cumulative exposure, with a doubling of the regression coefficient for the exposure effect (for the 7-16-days window LR = 5.32, p = 0.032, coefficient = 0.088 MN per 1000 cells per ppm-hr; 95% CI = 0.014, 0.16; for the 90-day cumulative exposure LR = 4.44, p = 0.048, coefficient = 0.045 MN per 1000 cells per ppm-hr, 95% CI = 0.0038, 0.086). Although hampered by the small number of subjects, these results reinforce the potential importance of exposure timing.     

Model-based compartmental analysis indicates a reduced mobilization of hepatic vitamin A during inflammation in rats

Vitamin A (VA) kinetics was studied in rats with marginal VA stores before, during, and after inflammation. Rats received orally [11,12-(3)H(N)]retinol ([(3)H]VA; day 0), and inflammation was induced on day 21 with lipopolysacchride (LPS) for 3 days (n = 5) or recombinant human interleukin-6 (rhIL-6) for 7 days (n = 5). Both the fraction of [(3)H]VA and retinol concentrations in plasma were reduced significantly by LPS or rhIL-6. Compartmental analysis using the Windows version of Simulation, Analysis, and Modeling software was applied to group mean data, and non-steady-state models were developed. After absorption, VA kinetics was described by a three-compartment model that included plasma, kidney/interstitium, and liver/carcass. Four mechanisms decreasing plasma retinol were investigated: increased urinary excretion, increased irreversible loss, increased movement into interstitium, and decreased hepatic mobilization. Modeling demonstrated that a 79% reduction in hepatic mobilization of retinol (from 4.3 to 0.9 nmol/h) by 15 h after LPS best accounted for the observed changes in plasma VA kinetics (sum of squares = 9.05 x 10(-07)). rhIL-6 caused an earlier reduction (75% by 5.6 h). These models predicted a return to control values by 10 days after inflammation. If prolonged, inflammation-induced hyporetinolemia can render hepatic retinol unavailable to extrahepatic tissues, possibly leading to their impaired function, as observed in VA-deficient children with measles infection.     

一种利用计算机程序计算目的蛋白表达量及表达水平的方法

介绍一种利用Windows操作系统工具及扫描仪,测量和计算发酵工艺研究及摇瓶实验中目的蛋白的表达量的方法。该方法可以扩展到精确计算在琼脂、纤维膜等材料上的溶菌圈的大小、抑菌圈的大小,免疫扩散及其绝对量的确定等。     

视觉皮层复杂细胞时空编码特性

针对输入在视皮层的编码表达,在地空滤波窗口基础上构建了一个复杂细胞时空编码模型,对几种特殊的输入函数进行了编码仿真实验,结果说明了视皮层复杂细胞时空整合编码序列的精细时间结构进行视觉输入的神经表象。     

MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets

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