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

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

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Recovery of some valuable elements from lamprophyre dykes in the Abu Rusheid area, Southeastern Desert, egypt

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Chinese Journal Of Geochemistry 2012年第1期31卷 64-73页

作者： Zaki D.I. Shawky N. el-Sheikh e.M. Ahmed F.Y. Ibrahim M.e. Nuclear Materials Authority El MaadiP.O.Box 530 CairoEgypt Chemistry Dept. Faculty of Science for GirlAl-Azhar UniversityEgypt

In the Abu Rusheid area, Southeastern Desert of egypt, polymineralized (HRees, U, Zn and Pb) lam-prophyre dykes are recently recorded. The lamprophyre dykes cut cataclastic rocks along share zones in NNW-SSe trends. The secondary U-minerals are essentially represented by uranophane, kasolite, torbernite and autunite. ex-perimental work was carried out on the lamprophyre dykes for the recovery of uranium and other valuable elements (e.g. Zn, Pb and Al) from 50 kg of technological sample. The optimum conditions were: 100 g/L sulfuric acid con-centration, 1:5 S/L (solid/liquid) and soaking for 15 days at room temperature. The leaching efficiencies for the re-covery of uranium and other elements like Al, Zn and Pb were 40, 33.6, 98.8 and 78, respectively.

关键词：有价元素煌斑岩岩脉沙漠埃及价值最佳工艺条件实验工作

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全人源食管癌噬菌体单链抗体库的筛选及特异性鉴定

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中国肿瘤临床 2008年第12期35卷 714-717页

作者：段红庞华尹晓玲彭志平李少林重庆医科大学病理生理教研室重庆市400016

目的:我们应用噬菌体抗体库技术构建了食管癌相关的人源单链抗体文库,本文目的在于对该抗体库进行鉴定,筛选食管癌抗体,同时对抗体的活性进行检测。方法:PCR鉴定TG1中食管癌单链抗体scFv的插入率;1.5%琼脂糖凝胶电泳鉴定SfiI和NotI双酶... 详细信息

目的:我们应用噬菌体抗体库技术构建了食管癌相关的人源单链抗体文库,本文目的在于对该抗体库进行鉴定,筛选食管癌抗体,同时对抗体的活性进行检测。方法:PCR鉴定TG1中食管癌单链抗体scFv的插入率;1.5%琼脂糖凝胶电泳鉴定SfiI和NotI双酶切质粒的结果;先以人正常食管上皮细胞吸附后再以食管癌细胞eca109为抗原对所建抗体库进行4轮的亲和筛选;将阳性重组噬菌体克隆感染ecoli HB2151进行可溶性抗体表达及经亲和柱层析纯化;用SDS-PAGe测定该抗体的相对分子量;用Western blot鉴定该抗体;用eLISA法、免疫组化法鉴定该抗体与人食管癌细胞的结合的特异性。结果:scFv基因插入率为91.7%;酶切后检测到目的基因片段。在亲和筛选过程中,食管癌噬菌体单链抗体得到富集,收获率逐轮得到提高,第4轮为第1轮的141倍;SDS-PAGe与Western blot结果显示抗体的相对分子量为左右和30kd条带染色;在ecoli HB2151中实现了单链抗体的可溶性表达。免疫组织化学结果提示可溶性抗体仅染食管癌组织,而肝癌组织和胃癌组织不染色。免疫细胞化学结果表明此可溶性抗体可使eca109细胞染色。eLISA测定结果显示可溶性抗体具有较高的免疫活性,能与eca109细胞结合,而不与胃癌BGC-823和NHeeC结合。结论:利用噬菌体抗体库技术的阴性、阳性筛选得到了食管癌噬菌体单链抗体,且筛选后的抗体片段与人食管癌细胞有特异性的结合活性。

关键词：噬菌体抗体库单链抗体食管癌

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优化电子期刊展示与标识的PIe-J规程解析

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图书情报工作 2018年第6期62卷 37-44页

作者：向佳丽林秀丽厦门大学图书馆厦门361005 香港大学图书馆香港

[目的／意义]通过对PIe-J的系统解析，使PIe4在中国获得更多的关注与了解，以期电子期刊供应链上的各方合作优化电子期刊元数据，解决电子期刊难以搜寻这个长期困扰各方的问题。[方法／过程]通过归纳、实例分析等方法对PIe-J的制定背景... 详细信息

[目的／意义]通过对PIe-J的系统解析，使PIe4在中国获得更多的关注与了解，以期电子期刊供应链上的各方合作优化电子期刊元数据，解决电子期刊难以搜寻这个长期困扰各方的问题。[方法／过程]通过归纳、实例分析等方法对PIe-J的制定背景、意义、主要内容、应用情况及其对中国电子期刊展示与标识的启示进行分析。[结果／结论]PIe4通过简明的语言和形象的例子对电子期刊元数据的标识进行详细指引，可提高开放链接质量，提高使用者对期刊文章的查找效率和准确率，进一步完善与发展电子期刊。在我国目前尚未出台电子期刊标识标准的情况下，中国电子期刊出版商或供应商如能参照PIe4优化电子期刊元数据，对于提高自身产品的竞争力，促进国内及海外市场的开拓将大有裨益。

关键词：电子期刊元数据展示期刊标识美国国家信息标准协会

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Numerical prediction experiment on Typhoon Maggie (9903)

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Acta Oceanologica Sinica 2001年第2期20卷 171-182页

作者： Fong Soi Kun, Wu Chisheng, Hao I Pan, lam Kin Hang Ku Chi Meng, Wang Anyu, Lin Wenshi (1. Macao Meteorological and Geophysical Bureau, Macao, China 2. Department of Atmospheric Sciences, Zhongshan University, Guangzhou 510275, China) Macao Meteorological/Geophysical Bur Department of Atmospheric Sciences Zhongshan University Macao Macao

The movement of Typhoon Maggie (9903) in June 1999 is one of the rare cases ever seen in the history. At 00U on June 6 Maggie was located at about 70 km to the southwest of Taiwan. When it arrived at the coastal region of Shanwei City (22.8N, 116.5e), it turned suddenly to move southwestward along the southern China coastal line. De June 7 Maggie finally turned to move northward, making landfall to the north of Shangchuan Island. The experimental numerical prediction system on typhoon movement that was designed based on MM5 is proved quite successful for the 48h prediction of Maggie's movement and rainfall. The mean prediction error of typhoon track is 81 km for 0-24 h and 74 km for 24-48 h. The location of typhoon center in the initial field of the model is approximately 100 km away from the actual observations. In order to modify the location of typhoon center, a bogus typhoon was intro- duced into the model and the prediction of typhoon track was improved in 0-24 h time interval. But the prediction error was enlarged in 24-36 h. We also performed a sensitivity experiment of changing the land of southern China into the ocean. It is found that the orientation of South China coastal line and the topography have no obvious effect on the movement of Typhoon Maggie.

关键词： Typhoon movement numerical prediction South China coastal line

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经肝动脉^90Y放射性栓塞治疗的新进展

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中华核医学与分子影像杂志 2018年第8期38卷 573-581页

作者：李莉(译) 冯对平(译) 李思进(审校) Arthur J.A.T. Braat Maarten L.J. Smits Manon N.G.J.A. Braat Andor F. van den Hoven Jip F. Prince Hugo W.A.M. de Jong Maurice A.A.J. van den Bosch Marnix G.e.H. lam 山西医科大学第一医院核医学科太原030001 山西医科大学第一医院介入科太原030001

放射性栓塞治疗（Re）是经过10余年探索而建立起来的一种治疗模式，发展迅速。该文对Re领域新进展进行综述，就Re患者选择、疗效判断以及将来的临床应用进行探讨。

关键词：放射性栓塞剂量学肝脏恶性肿瘤肝血管系统 ^90Y

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Dogs lacking Apolipoprotein e show advanced atherosclerosis leading to apparent clinical complications

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Science China(Life Sciences) 2022年第7期65卷 1342-1356页

作者： Hui Zhao Jianping Zhao Di Wu Zhaolin Sun Yang Hua Min Zheng Yumei Liu Qi Yang Xiahe Huang Yuan Li Yueshan Piao Yingchun Wang Sin Man lam Huijuan Xu Guanghou Shui Yongjun Wang Haifeng Yao Liangxue Lai Zhuo Du Jidong Mi enqi Liu Xunming Ji Yong Q.Zhang Key Laboratory of Molecular Developmental Biology and CAS Center for Excellence in Brain Science and Intelligence TechnologyInstitute ofGenetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Guangzhou Institutes of Biomedicine and Health Chinese Academy of SciencesGuangzhou 510530China Beijing Sinogene Biotechnology Co.Ltd Beijing 102200China Xuanwu Hospital Capital Medical UniversityBeijing 100053China TianTan Hospital Capital Medical UniversityBeijing 100070China Beijing Petsguard Animal Hospital Beijing 100192China Laboratory Animal Center Xi’an Jiaotong University Health Science CenterXi’an 710049China

Atherosclerotic cardiovascular disease resulting from dysregulated lipid metabolism is the leading cause of morbidity and mortality *** e(Apoe)plays a critical role in cholesterol *** in lipid-metabolizing proteins including Apoe in multiple model organisms such as mice and rats exhibiting elevated levels of cholesterol have been widely used for dissecting the pathology of atherosclerosis,but few of these animal models exhibit advanced atherosclerotic plaques leading to ischemia-induced clinical symptoms,limiting their use for translational *** we report hypercholesterolemia and severe atherosclerosis characterized by stenosis and occlusion of arteries,together with clinical manifestations of stroke and gangrene,in Apoe knockout dogs generated by CRISPR/Cas9 and cloned by somatic cell nuclear transfer ***,the hypercholesterolemia and atherosclerotic complications in F0 mutants are recapitulated in their *** the Apoe-associated atherosclerosis and clinical manifestations in mutant dogs are more similar to that in human patients compared with those in other animal models,these mutant dogs will be invaluable in developing and evaluating new therapies,including endovascular procedures,against atherosclerosis and related disorders.

关键词： Apoe atherosclerosis hypercholesterolemia gangrene stroke

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Recent Progress in Heterogeneous Ⅲ-Ⅴ-on-Silicon Photonic Integration

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Light(Advanced Manufacturing) 2021年第1期2卷 51-75页

作者： Di Liang John e.Bowers Hewlett Packard Labs Hewlett Packard Enterprise6280 American Center DriveSan JoseCA 94088USA Department of electrical and Computer engineering University of CaliforniaSanta BarbaraCA 93106USA

Silicon(Si)photonics is a disruptive technology on the fast track to revolutionise integrated *** indispensable branch thereof,heterogeneous Si integration,has also evolved from a science project 15 years ago to a growing business and compelling research field *** focus on the scope of Ⅲ-Ⅴ compound semiconductors heterogeneously integrated on Si *** commercial success of massively produced integrated optical transceivers based on first-generation innovation is ***,we review a number of technological breakthroughs at the component and platform *** addition to the numerous new device performance records,our emphasis is on the rationale behind and the design principles underlying specific examples of materials and device ***,we offer perspectives on development trends catering to the increasing demand in many existing and emerging applications.

关键词： Silicon breakthrough Integration

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先天性膈疝预后和资源利用的风险校正研究

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世界核心医学期刊文摘（儿科学分册） 2006年第A10期2卷 47-48页

作者： lam J.C. Claydon J. Mitton C.R. Skarsgard e.D. 王经纬 Division of Pediatric Surgery Department of Surgery University of British Columbia Vancouver BC V6H 3V4 Canada

Purpose: Perinatal care of infants with congenital diaphragmatic hernia (CDH) is nonstandardized and costly. We examined a risk- adjusted cohort of patients with CDH and hypothesized that (1) among CDH survivors, the cost of the birth admission would be proportional to illness severity, and (2) this cost would be significantly higher compared with a matched non- CDH cohort. Methods: A retrospective review of costs and outcomes for all patients with CDH admitted to British Columbia Children’ s Hospital between 1999 and 2003 was performed. Risk grouping of patients with CDH using a validated admission severity score (Score for Neonatal Acute Physiology- version II [SNAP- II])was conducted, enabling comparison among infants surviving to discharge. Hospital costs were also compared with a contemporaneous, non- CDH cohort matched for birth weight and SNAP- II. Results: Thirty- two infants with CDH were included, of who 5 required extracorporeal membrane oxygenation. Twenty- three (72% ) infants survived to discharge, with an average length of stay of 46 days. Average cost per survivor to discharge was ＄ 54,102 (vs ＄ 13,722 for the non- CDH cohort; P er SNAP- II stratification of survivors into low- , moderate- , and high- risk groups, a significant cost difference was noted between the moderate- and low- risk and high- and low- risk groups, respectively. Conclusions: Infants born with CDH require costly care and can be expected to consume disproportionate resources. Admission SNAP- II score correlates with total cost to discharge. Risk stratification and cost comparison of larger CDH populations may allow identification of cost- efficient treatment strategies.

关键词：先天性膈疝资源利用患儿疾病严重程度评分存活者疾病严重程度体外膜式氧合围生期儿童医院

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具有聚集诱导发光效应的聚炔材料的合成及光学性能研究

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化学学报 2016年第11期74卷 877-884页

作者：韩婷詹嘉慧林荣业唐本忠香港科技大学化学系国家人体组织功能重建工程技术研究中心香港分中心香港科技大学深圳研究院深圳518057

合成了三种含有四苯基乙烯结构的双炔烃．这些双炔烃单体通过在CuCl催化下在邻二氯苯中进行的均聚反应可以高产率地生成线型聚炔．所得聚合物均可很好地溶解于常见有机溶剂中，并具有很高的热稳定性．这类聚炔材料在溶液态时几乎不发光... 详细信息

合成了三种含有四苯基乙烯结构的双炔烃．这些双炔烃单体通过在CuCl催化下在邻二氯苯中进行的均聚反应可以高产率地生成线型聚炔．所得聚合物均可很好地溶解于常见有机溶剂中，并具有很高的热稳定性．这类聚炔材料在溶液态时几乎不发光，但在聚集态或者固态下可高度发光，表现出典型的聚集诱导发光性质．同时，这些聚合物具有高透光性，可以允许整个可见光区的光透过．其薄膜在4001700nm宽波长范围内表现出高折射率（n=1．7787-1．6543）和低色差（D＇=0．0003）．紫外光照射可诱使聚合物薄膜发生交联过程，从而调控其折射率数值，并可生成高分辨率的荧光图案．

关键词：线型聚炔聚集诱导发光四苯基乙烯折射率

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