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YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

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Genomics, Proteomics & Bioinformatics 2015年第1期13卷 25-35页

作者： Christopher M.Colangelo Mark Shifman Kei-Hoi Cheung Kathryn L.Stone Nicholas J.Carriero Erol E.Gulcicek TuKiet T.Lam terence wu Robert D.Bjornson Can Bruce Angus C.Nairn Jesse Rinehart Perry L.Miller Kenneth R.Williams W.M.Keck Foundation Biotechnology Resource Laboratory School of Medicine Yale University Department of Molecular Biophysics & Biochemistry Yale University Yale Center for Medical Informatics School of Medicine Yale University Department of Anesthesiology School of Medicine Yale University Department of Emergency Medicine School of Medicine Yale University VA Connecticut Healthcare System W.M. Keck Foundation Biotechnology Resource Laboratory School of Medicine Yale University Department of Computer Science Yale University Yale Center for Genome Analysis West Campus Yale University Yale West Campus Analytical Core West Campus Yale University Yale Bioinformatics Resource School of Medicine Yale University Department of Psychiatry School of Medicine Yale University Department of Cellular & Molecular Physiology School of Medicine Yale University Systems Biology Institute Yale University

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry（LC–MS/MS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring（MRM）/selective reaction monitoring（SRM） assay development. We have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.

关键词： Proteomics Database Bioinformatics Mass spectrometry Repository Spectral library

Metal-organic framework coated titanium dioxide nanorod array p-n heterojunction photoanode for solar water-splitting

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Nano Research 2019年第3期12卷 643-650页

作者： Hui Yang Joeseph Bright Sujan Kasani Peng Zheng terence Musho Banglin Chen Ling Huang Nianqiang wu Department of Mechanical and Aerospace Engineering West Virginia University Morgantown WV 26506-6106 USA C. Eugene Bennett Department of Chemistry West Virginia University Morgantown WV 26506-6045 USA Department of Pharmaceutical Science West Virginia University Morgantown WV 26506-9530 USA Lane Department of Computer Science and Electrical Engineering West Virginia University Morgantown WV 26506 USA Department of Chemistry University of Texas at San Antonio One UTSA Circle San Antonio TX 78249-1604 USA Institute of Advanced Materials (IAM) Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 China

This paper presents a p-n heterojunction photoanode based on a p-type porphyrin metal-organic framework (MOF) thin film and an n-type rutile titanium dioxide nanorod array for photoelectrochemical water splitting. The TiO2@MOF core-shell n anorod array is formed by coati ng an 8 nm thick MOF layer on a vertically aligned TiO2 nanorod array scaffold via a layer-by-layer self-assembly method. This vertically aligned core-shell nanorod array enables a long optical path length but a short path length for extraction of photogenerated minority charge carriers (holes) from TiO2 to the electrolyte. A p-n junction is formed between TiO2 and MOF, which improves the extraction of photogenerated electr ons and holes out of the TiO2 nano rods. In additi on, the MOF coati ng sign ificantly improves the efficie ncy of charge in jecti on at the photoanode/electrolyte interface. Introduction of Co(lll) into the MOF layer further enhances the charge extraction in the photoanode and improves the charge injection efficiency. As a result, the photoelectrochemical cell with the TiO2@Co-MOF nanorod array photoanode exhibits a photocurrent density of 2.93 mA/cm^2 at 1.23 V (vs. RHE), which is ~ 2.7 times the photocurrent achieved with bare T1O2 nanorod array under irradiation of an unfiltered 300 W Xe lamp with an output power density of 100 mW/cm^2.

关键词： metal-organic framework water-splitting p-n junction photoanode titanium dioxide

Body weight and range usage affect net energy utilisation in commercial free-range laying hens when evaluated in net energy chambers

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Animal Nutrition 2020年第2期6卷 192-197页

作者： Manisha Kolakshyapati Shu-Biao wu terence Z.Sibanda Santiago Ramirez-Cuevas Isabelle Ruhnke The School of Environmental and Rural Science Faculty of ScienceAgricultureBusiness and LawUniversity of New EnglandArmidale2351NSWAustralia FCR Consulting Group Brisbane4000QLDAustralia

Within a given free-range flock,some hens prefer to spend the majority of their time in the shed(stayers),while others frequently access the range(rangers).Laying performance has been associated not only with the development of these sub-populations but also with different body weights(BW).The purpose of this study was to determine if range usage,BW or a combination of both is associated with energy metabolism and as such co ntribute to improved hen ***-eight Lohmann Brown hens at 74 wk of age were selected from a commercial free-range farm based on their BW and range usage over a 56-week *** a 2 × 2 factorial arrangement,hens were either classified as heavy(mean ± SEM;2.01±0.02 kg,n=24) or light(1.68±0,01 kg,n=24),and also classified as rangers(accessed the range for 84.1 % of available days,242±3.75 d;n=24) or stayers(accessed the range for 7.17% of available days;23,4±6.08 d,n=24).Stayers had significantly higher metabolizable energy(ME) intake per metabolic BW per d(0.852 vs.0.798 MJ/kg BW0.75 perd;P=0.025),higher heat production(0.637 vs.0.607 MJ/kg BW0.75 perd;P=0.005),higher heat increment(0.267 vs.0.237 MJ/kg BW0.75 per d;P=0.005) and retained more nitrogen(1.59 vs.1.46 g/hen perd;P=0.023) compared to the *** hens had significantly higher metabolic energy intake per metabolic BW(0.854 vs.0.796 MJ/kg BW0.75 per d;P=0.018),net energy(NE) intake(0.595 vs.0.551 MJ/kg BW0.75 per d;P=0.032),and retained energy(0.225 vs.0.181 MJ/kg BW0.75 per d;P=0.032),as well as lower heat production(0.936 vs.1.003 MJ/hen per d;P=0.002) compared to heavier *** interaction was observed across levels of analysis *** light stayers and light *** light rangers had significantly higher NE intake compared to the light stayers(9.77 vs.9.27 MJ/kg BW0.75 per d;P=0.024).In conclusion,light hens were more energy efficient compared to heavy ***,light rangers had a more efficient feed utilisation compared to the light stayers.

关键词： Egg production Health Husbandry Metabolizable energy Poultry nutrition Welfare

Microbial communities biostimulated by ethanol during uranium （VI） bioremediation in contaminated sediment as shown by stable isotope probing

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Frontiers of Environmental Science & Engineering 2015年第3期9卷 453-464页

作者： Mary Beth LEIGH Wei-Min wu Erick CARDENAS Ondrej UHLIK Sue CARROLL Terry GENTRY terence L. MARSH Jizhong ZHOU Philip JARDINE Craig S. CRIDDLE James M. TIEDJE Center for Microbial Ecology Michigan State University East Lansing MI 48824 USA Institute of Arctic Biology University of Alaska Fairbanks Fairbanks AK 99775 USA Department of Civil and Environmental Engineering Center for Sustainable Development & Global Competitiveness Codiga Resource Recovery Center Stanford University Stanford CA 94305-4020 USA Department of Biochemistry and Microbiology Institute of Chemical Technology Prague Technicka 3 166 28 Prague Czech Republic Environmental Sciences Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA Department of Botany and Microbiology University of Oklahoma Norman OK 73019 USA Department of Crop and Soil Sciences Texas A&M University College Station TX 77843 USA

Stable isotope probing （SIP） was used to identify microbes stimulated by ethanol addition in microcosms containing two sediments collected from the bioremediation test zone at the US Department of Energy Oak Ridge site, TN, USA. One sample was highly bioreduced with ethanol while another was less reduced. Microcosms with the respective sediments were amended with ^13C labeled ethanol and incubated for 7 days for SIP. Ethanol was rapidly converted to acetate within 24h accompanied with the reduction of nitrate and sulfate. The accumulation of acetate persisted beyond the 7 d period. Aqueous U did not decline in the microcosm with the reduced sediment due to desorption of U but continuously declined in the less reduced sample. Microbial growth and concomitant 13C-DNA production was detected when ethanol was exhausted and abundant acetate had accumulated in both microcosms. This coincided with U（VI） reduction in the less reduced sample. I3C originating from ethanol was ultimately utilized for growth, either directly or indirectly, by the dominant microbial community members within 7 days of incubation. The microbial community was comprised predominantly of known denitrifiers, sulfate-reducing bacteria and iron （Ⅲ） reducing bacteria including Desulfovibrio, Sphingomonas, Ferribacterium, Rhodanobacter, Geothrix, Thiobacillus and others, including the known U（VI）-redueing bacteria Acidovorax, Anaeromyxobacter, Desulfovibrio, Geobac- ter and Desulfosporosinus. The findings suggest that ethanol biostimulates the U（VI）-reducing microbial com- munity by first serving as an electron donor for nitrate, sulfate, iron （IH） and U（VI） reduction, and acetate which then functions as electron donor for U（VI） reduction and carbon source for microbial growth.

关键词： Stable isotope probing (S/P) ethanol acetate uranium reduction sediment bioremediation

昆虫发育速率模型:文献综述及生物物理模型的应用(节译)

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河南农业 1996年第2期 31-32,34页

作者： terence L Wagner Hsin wu 李军常萍河南省农学会河南省种子站

预测预报昆虫季节性消长的重要性导致了描述昆虫发育速率受温度影响的数学模型的建立。然而许多被广泛使用的模型并不能为预测预报提供可靠的数据。通过对文献的回顾,作者认为,Sharpe & DeMichele的生物物理模型最为适合。这一模型在昆... 详细信息

预测预报昆虫季节性消长的重要性导致了描述昆虫发育速率受温度影响的数学模型的建立。然而许多被广泛使用的模型并不能为预测预报提供可靠的数据。通过对文献的回顾,作者认为,Sharpe & DeMichele的生物物理模型最为适合。这一模型在昆虫适生温度范围内均能很好地描述昆虫的发育速率,而且经过并不复杂的修改就可用来描述上述温度范围内部分温度区间内的发育速率。在这篇文章中,作者回顾了描述昆虫发育速率的文献,重点介绍了Sharpe & DeMichele模型并提供了该模型的使用指导。从统计分析库中(SAS)编制出一计算机程序,用来确定该模型适于某一特定数据时所需参数的数目,并选择用于非线性回归的各参数的初始值以及利用Marguardt技术计算各参数的最小二乘法估计值。

关键词：生物物理模型文献综述速率模型昆虫发育发育速率预测预报非线性回归季节性消长计算机程序最小二乘法

上海市部分男男同性恋者社会学特征及艾滋病知识调查

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上海预防医学 2010年第2期22卷 83-85页

作者：侯建星 wu Lily terence Sio 徐荷孙悦昕林继凯顾一夫上海市宝山区红十字会上海201900 美国布朗大学医学院

大量研究表明,男男性行为者(men who have sex with men,MSM)是造成艾滋病传播和蔓延的高危人群之一。资料显示,我国现有的70万(55－85万)的艾滋病毒(HIV)感染者中,MSM约为7.7万人,占总评估人数的11.0%。MSM有其经常活动的场所,如酒吧... 详细信息

大量研究表明,男男性行为者(men who have sex with men,MSM)是造成艾滋病传播和蔓延的高危人群之一。资料显示,我国现有的70万(55－85万)的艾滋病毒(HIV)感染者中,MSM约为7.7万人,占总评估人数的11.0%。MSM有其经常活动的场所,如酒吧、公园、浴池等。为了解上海地区这一群体的社会学状况以及他们对HIV防治知识的了解情况,[第一段]

关键词：社会学特征艾滋病传播男同性恋者知识调查上海市男男性行为者高危人群艾滋病毒

地下水铀污染的原位微生物还原与固定：在美国能源部田纳西橡树岭放射物污染现场的试验

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环境科学学报 2011年第3期31卷 449-459页

作者：吴唯民 Jack Carley David Watson 顾宝华 Scott Brooks Shelly D.Kelly Kenneth Kemner Joy D.van Nostrand 吴力游许玫英周集中罗剑 Erick Cardenas 黄家琪 Matthew W.Fields terence L.Marsh James M.Tiedje Stefan J.Green Joel E.Kostka Peter K.Kitanidis Philip M.Jardme CraigS.Criddle 美国斯坦福大学土木与环境工程系 StanfordCA94305USA 美国橡树岭国家实验室环境科学部 OakRidgeTN37831USA 美国阿岗国家实验室生物科学部 ArgonneIL60439USA 美国俄克拉荷马大学植物-与微生物学系 NormanOK73019USA 广东省微生物研究所广州510070 美国乔冶亚理工学院土木与环境工程系 AtlantaGA30332USA 美国密歇根州立大学微生物生态中心 EastLansingMI48823USA 美国蒙大拿州立大学生物膜工程中心 BozemanMT59717USA 美国佛罗里达州立大学地球海洋大气科学系 TallahasseeFL32306USA 美国田纳西大学生物系统工程与土壤科学系 KnoxvilleTN37996USA

总结了美国斯坦福大学和橡树岭国家实验室等在美国能源部田纳西州橡树岭综合试验基地进行的铀污染原位微生物修复阶段性试验结果.本试验利用微生物以乙醇为电子供体还原地下水和沉积物中的六价铀为不溶解的四价铀,使之原位固定化.随后... 详细信息

总结了美国斯坦福大学和橡树岭国家实验室等在美国能源部田纳西州橡树岭综合试验基地进行的铀污染原位微生物修复阶段性试验结果.本试验利用微生物以乙醇为电子供体还原地下水和沉积物中的六价铀为不溶解的四价铀,使之原位固定化.随后通过加入溶解氧和硝酸盐来试验微生物还原后的地下水层中还原固定态铀的稳定性.通过预处理和长期间隔注入乙醇溶液,地下水中铀浓度从40～60mg·L-1降至0.03mg·L-1以下,达到了美国环保署饮用水的标准.还原的四价铀主要以U(Ⅳ)-Fe复合物的形态存在.结果表明,固定化后的四价铀只有在厌氧条件下才是稳定的,溶解氧和硝酸盐侵入地下水层后会使固定化的四价铀重新氧化为溶解态的六价铀.在试验过程中,采用多种分子生物学方法检测了微生物种群的变化和与铀氧化还原反应有关的功能微生物.本研究表明,在维持试验系统无氧和无硝酸盐的条件下,通过添加乙醇为电子供体可有效地促进地下水中土著功能微生物的活性,从而实现铀的原位还原固定与稳定.

关键词：铀污染微生物还原原位生物修复地下水沉积物

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评Parsons的亚原子语义学

河北大学学报（哲学社会科学版） 2008年第4期33卷 133-137页

作者：吴平靳惠玲北京语言大学外国语学院北京100083 石家庄学院河北石家庄050035

本文首先分析亚原子语义学思想的理论特色,并接下来介绍这一理论框架内事件结构的具体描写方式。最后,本文讨论并试图说明亚原子语义学是新戴维森分析法发展进程中的一个重要里程碑。

关键词：亚原子语义学事件结构新戴维森分析法