Bayesian correlated clustering to integrate multiple datasets.

MOTIVATION: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct-but often complementary-information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets. RESULTS: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI's performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques-as well as to non-integrative approaches-demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.

我国东南部地区妇幼人群静脉血多氯联苯水平及危险性研究

目的研究废旧变压器拆解点周围妇女儿童多氯联苯(PCBs)暴露水平及危险性评价。方法以F地区为研究现场,选择该地区中心小学50名8~10岁学龄儿童和其母亲为研究对象,采集妇女儿童空腹外周静脉血,用Agilent 5973N GC-MSD超痕量分析方法检测其PCBs(13个异构体)含量及血液、尿液临床生化检验,并作调查问卷及健康体检,最后作危险度评价。结果妇女和儿童外周静脉血中多氯联苯几何均值分别达175.9 ng/g、191.6 ng/g类脂;健康体检,儿童龋齿率82%。结论该地区妇女儿童血液中的PCBs含

电子废物污染地区水生生物体内多氯联苯的异构体分布特征和毒性

电子废物已被证实是众多污染物的释放源,其引起的环境问题正日益受到人们的关注。利用同位素稀释GC/MS法测定了电子废物污染区的田螺、泥鳅和鲫鱼三种水生生物体内的PCBs含量和异构体组成特征。研究结果表明,田螺、泥鳅和鲫鱼体内PCBs平均浓度分别高达1303.53、3845.00和5645.34 ng/g脂重;毒性当量(TEQs)分别为1.35、8.44和29.18 pg WHO-TEQ/g湿重。其中,泥鳅和鲫鱼体内PCBs的TEQs都高于2006年欧盟规定的鱼类可食用部分最大TEQs允许值。此外,PCB 1

Evidence for X(5) critical point symmetry in 128Ce

Lifetimes of excited states in 128Ce were measured using the recoil distance Doppler-shift (RDDS) and the Doppler-shift attenuation (DSAM) methods. The experiments were performed at the Wright Nuclear Structure Laboratory of Yale University. Excited states of 128Ce were populated in the 100Mo(32Si,4n) reaction at 120 MeV and the nuclear γ decay was measured with an array of eight Clover detectors positioned at forward and backward angles. The deduced yrast transition strengths together with the energies of the levels within the ground-state (gs) band of 128Ce are in agreement with the predicted values for the X(5) critical point symmetry. Thus, we suggest 128Ce as a benchmark X(5) nucleus in the mass A ≈ 130 region. © World Scientific Publishing Company.

次生环境多氯联苯污染水平监测及富集趋势研究

目的研究废旧变压器拆解埸多氯联苯(PCBs)对环境的污染情况。方法以F镇为暴露区Ⅰ;以无该产业、气候条件、地理特征等情况相似间邻的P镇为暴露区Ⅱ;并选择相距500公里外的DXG镇为对照区。随机分层抽取河水(溪水)、稻田土、晚稻谷、鸡(鸭)蛋、淡水鱼等样品,采用超痕量分析方法检测其PCBs含量。结果暴露区Ⅰ各样品中的PCBs含量均超过暴露区Ⅱ(除晚稻谷外)和对照区,三者差异在统计学上有显著的意义。其中,暴露区Ⅰ河鲫鱼的PCBs高达9.1ug/g,是河水的8000多倍,鸡蛋和鸭蛋的PCBs平均含量也高达1.0

南方某地产妇和婴儿体内多氯联苯蓄积水平的调查

目的了解我国南方某多氯联苯(PCBs)高暴露地区的产妇及其婴儿体内PCBs的蓄积水平。方法采集在当地某医院中符合条件的50对母婴对的母乳和脐带血,用GC-MS法进行PCBs含量的测定。结果母乳中13种PCBs总浓度的最大值为237 ng/g类脂,几何均数为138 ng/g类脂。脐带血中13种PCBs总浓度的最大值为102 ng/g类脂,几何均数为56.9 ng/g类脂。结论该地区妇女和婴儿体内普遍检测出较高水平的PCBs

南方某地妇女儿童血液中多氯联苯蓄积水平调查

目的了解我国南方某多氯联苯(PCBs)高暴露地区的妇女、儿童体内PCBs的蓄积水平。方法采集当地某小学中符合条件的50对母子的血液,用GC-MS法进行PCBs含量的测定。结果儿童血液中所测的13种PCBs的浓度最大值为505 ng/g类脂,几何均数为192 ng/g类脂;母亲血液中所测的13种PCBs的总浓度的最大值为461 ng/g类脂,几何均数为176 ng/g类脂;儿童和母亲血液中PCBs含量的相关系数为0.74。结论该地区妇女和儿童血液中检测出较高水平的PCBs,儿童和母亲血液中PCBs含量呈现较

雨水和表面活性剂的淋溶对河道底泥中多氯联苯迁移的影响

利用雨水和表面活性剂(LAS、AE9和NPE10)淋溶多氯联苯(PCBs)污染的河道底泥柱,初步探讨了它们对表层底泥中PCBs洗脱量的影响,同时也研究了从表层洗脱出的PCBs随着淋洗液在下层底泥中的纵向迁移。淋洗液包括雨水和浓度均为1500mg.L-1的LAS、AE9、NPE10溶液以及浓度都是1500mg.L-1的AE9+NPE10和LAS+NPE10混和溶液。实验发现:雨水和同浓度的表面活性剂溶液对表层底泥中PCBs洗脱量大小依次为:雨水

杯[4]芳烃顶空固相微萃取-气相色谱法快速分析环境样品中的多氯联苯

本文以多氯联苯(PCBs)模拟水样为实验样品,优化了杯[4]芳烃探头顶空固相微萃取(HS SPME)的分析条件,并将杯[4]芳烃探头和商用PDMS探头对PCBs的萃取效果进行了比较。利用杯[4]芳烃 HS SPME法与USEPA608法同时测定了模拟水样和典型污染地区环境样品中的多氯联苯。研究结果表明:杯[4]芳烃SPME探头对样品中高氯代PCBs的萃取效果优于商用PDMS探头;杯[4]芳烃 HS SPME和USEP A608法对同一样品的检测结果一致;该法对水样中PCBs的检出限达1～6ng/L,比US

Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm.

We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that accelerates the clustering of time series data using the Bayesian Hierarchical Clustering (BHC) statistical method. BHC is a general method for clustering any discretely sampled time series data. In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. We show that the randomised algorithm leads to substantial gains in speed with minimal loss in clustering quality. The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. We have also made available a set of R scripts which can be used to reproduce the analyses carried out in this paper. These are available from the following URL. https://sites.google.com/site/randomisedbhc/.

Identifying cancer subtypes in glioblastoma by combining genomic, transcriptomic and epigenomic data

We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likely number of disease subtypes, given the data. We apply the method to 277 glioblastoma samples from The Cancer Genome Atlas, for which there are gene expression, copy number variation, methylation and microRNA data. We identify 8 distinct consensus subtypes and study their prognostic value for death, new tumour events, progression and recurrence. The consensus subtypes are prognostic of tumour recurrence (log-rank p-value of $3.6 \times 10^{-4}$ after correction for multiple hypothesis tests). This is driven principally by the methylation data (log-rank p-value of $2.0 \times 10^{-3}$) but the effect is strengthened by the other 3 data types, demonstrating the value of integrating multiple data types. Of particular note is a subtype of 47 patients characterised by very low levels of methylation. This subtype has very low rates of tumour recurrence and no new events in 10 years of follow up. We also identify a small gene expression subtype of 6 patients that shows particularly poor survival outcomes. Additionally, we note a consensus subtype that showly a highly distinctive data signature and suggest that it is therefore a biologically distinct subtype of glioblastoma. The code is available from https://sites.google.com/site/multipledatafusion/

Low-cost PCB-integrated 10-Gb/s optical transceiver built with a novel integration method

A novel integration method for the production of cost-effective optoelectronic printed circuit boards (OE PCBs) is presented. The proposed integration method allows fabrication of OE PCBs with manufacturing processes common to the electronics industry while enabling direct attachment of electronic components onto the board with solder reflow processes as well as board assembly with automated pick-and-place tools. The OE PCB design is based on the use of polymer multimode waveguides, end-fired optical coupling schemes, and simple electro-optic connectors, eliminating the need for additional optical components in the optical layer, such as micro-mirrors and micro-lenses. A proof-of-concept low-cost optical transceiver produced with the proposed integration method is presented. This transceiver is fabricated on a low-cost FR4 substrate, comprises a polymer Y-splitter together with the electronic circuitry of the transmitter and receiver modules and achieves error-free 10-Gb/s bidirectional data transmission. Theoretical studies on the optical coupling efficiencies and alignment tolerances achieved with the employed end-fired coupling schemes are presented while experimental results on the optical transmission characteristics, frequency response, and data transmission performance of the integrated optical links are reported. The demonstrated optoelectronic unit can be used as a front-end optical network unit in short-reach datacommunication links. © 2011-2012 IEEE.

PCB-integrated optical waveguide sensors: An ammonia gas sensor

This paper presents a novel platform for the formation of cost-effective PCB-integrated optical waveguide sensors. The sensor design relies on the use of multimode polymer waveguides that can be formed directly on standard PCBs and commercially-available chemical dyes, enabling the integration of all essential sensor components (electronic, photonic, chemical) on low-cost substrates. Moreover, it enables the detection of multiple analytes from a single device by employing waveguide arrays functionalised with different chemical dyes. The devices can be manufactured with conventional methods of the PCB industry, such as solder-reflow processes and pick-and-place assembly techniques. As a proof of principle, a PCB-integrated ammonia gas sensor is fabricated on a FR4 substrate. The sensor operation relies on the change of the optical transmission characteristics of chemically functionalised optical waveguides in the presence of ammonia molecules. The fabrication and assembly of the sensor unit, as well as fundamental simulation and characterisation studies, are presented. The device achieves a sensitivity of approximately 30 ppm and a linear response up to 600 ppm at room temperature. Finally, the potential to detect multiple analytes from a single device is demonstrated using principal-component analysis. © 1983-2012 IEEE.

环境中二噁■类化合物:多氯代二苯并二噁■/呋喃和多氯联苯的分离纯化及定性定量

利用同位素稀释法、气相色谱质谱联用-多离子检测等现代分析手段,建立了一套有效的多氯代二苯并二(口恶)(口英)/呋喃(PCDD/F)、多氯联苯(PCBs)的分离纯化及准确的定性定量方法。同时,根据PCDD/F的色谱保留关系,编制了一套计算机辅助峰识别软件,能同时对四氯代至八氯代的PCDD/F所有异构体进行色谱峰自动识别,保证了分析数据的可靠性和精确性。

东湖水体中多氯联苯的研究

于1994年6月，采用高分子多孔聚合树脂对武汉东湖水进行富集采样，样品经净化后利用毛细管柱色谱进行多氯联苯（PCBs）总量及同类物（congeners）的分离测定。结果表明，东湖水样中PCBs总含量为2．7ng／L，检出的20多个PCBs同类物其含量分别在0．002－1．12ng／L范围内。其同类物中低氯取代的PCBs相对含量明显高于工业用商品PCBs中的相应含量。