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Basophile:Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

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Genomics, Proteomics & Bioinformatics 2013年第2期11卷 86-95页

作者： Dong Wang Surendra Dasari Matthew C.Chambers Jerry D.Holman kan Chen Daniel C.Liebler Daniel J.Orton Samuel O.Purvine Matthew E.Monroe chang Y.Chung kristie L.Rose david L.Tabb Department of Biomedical Informatics Vanderbilt University Medical Center Division of Biomedical Statistics and Informatics Mayo Clinic Department of Biochemistry Vanderbilt University Medical Center Biological Sciences Division and Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Department of Pharmacology Vanderbilt University Medical Center Vanderbilt-Ingram Cancer Center Vanderbilt University School of Medicine

In shotgun proteomics, database search algorithms rely on fragmentation models to pre- dict fragment ions that should be observed for a given peptide sequence. The most widely used strat- egy （Naive model） is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmen- tation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher- energy collision induced dissociation （HCD） of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% （on average） over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.

关键词： Fragmentation Basicity Fragment size Ordinal regression

On the decomposition of forces

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Theoretical & Applied Mechanics Letters 2014年第4期4卷 70-74页

作者： Dong Eui chang Department of Applied Mathematics University of WaterlooWaterloo ON N2L 3G1Canada

We show that any continuously differentiable force is decomposed into the sum of a Rayleigh force and a gyroscopic force. We also extend this result to piecewise continuously differentiable forces. Our result improves the result on the decomposition of forces in a book by david Merkin and further extends it to piecewise continuously differentiable forces.

关键词： force decomposition gyroscopic force Rayleigh force

质谱分析联合网络药理学和动物实验探讨健脑固本方治疗脑小血管病性认知障碍的作用机制

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环球中医药 2024年第9期17卷 1768-1776页

作者：曾伟坤韩振蕴胡玉立王育纯田丹枫常泽北京中医药大学东方医院 100078 北京中医药大学东方医院体检科 100078 北京中医药大学深圳医院(龙岗)脑病科中国医药科学出版社中国中医科学院西苑医院脑病科

目的运用质谱分析、网络药理学和动物实验探讨健脑固本方治疗脑小血管病性认知障碍(cerebral small vessel disease,CSVCI)的作用机制。方法通过质谱分析得出主要活性成分,TCMSP检索其相应作用靶点;通过GeneCards、OMIM数据库检索CSVCI... 详细信息

目的运用质谱分析、网络药理学和动物实验探讨健脑固本方治疗脑小血管病性认知障碍(cerebral small vessel disease,CSVCI)的作用机制。方法通过质谱分析得出主要活性成分,TCMSP检索其相应作用靶点;通过GeneCards、OMIM数据库检索CSVCI疾病靶点;通过String数据库和Cytoscape软件构建药物疾病作用靶点网络可视化;利用david数据库对交集靶点进行GO功能和kEGG信号通路富集分析。结果健脑固本方的有效活性成分有山奈酚、薯蓣皂苷,作用于丝裂原活化蛋白激酶8、蛋白激酶B1等核心靶点,可能通过磷脂酰肌醇3-激酶/蛋白激酶B等信号通路涉及炎症反应。蛋白免疫印迹法检测结果表明健脑固本方抑制Notch-1、RBP-Jκ以及Hes-1的表达。结论本研究初步表明健脑固本方能够通过多靶点、多通路、多途径治疗CSVCI,具体作用机制可能是抑制Notch-1信号通路,进而抑制炎症反应。

关键词：质谱分析网络药理学健脑固本方脑小血管病性认知障碍 Notch-1信号通路炎症反应

De novo Hepatocellular Carcinoma after Liver Transplantation

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Journal of Clinical and Translational Hepatology 2015年第4期3卷 284-287页

作者： Sammy Saab kali Zhou Edward k chang Ronald W Busuttil Department of Medicine David Geffen School of Medicine at UCLALos AngelesCAUSA Department of Surgery David Geffen School of Medicine at UCLALos AngelesCAUSA Department of Medicine David Geffen School of Medicine at UCLALos AngelesCAUSA Department of Surgery David Geffen School of Medicine at UCLALos AngelesCAUSA

Liver transplantation is the definitive therapy for patients with advanced liver disease and its *** who are transplanted with a diagnosis of hepatocellular carcinoma(HCC)are at risk of recurrent cancer,and these patients are monitored on a regular basis for *** contrast,de novo HCC following liver transplantation is a very rare complication,and recipients without HCC at the time of transplantation are not *** describe the clinical features of de novo HCC over a decade after achieving a sustained viral response with treatment of hepatitis C and two decades after liver *** case highlights the necessity of screening for HCC in the post-transplant patient with advanced liver disease even after viral clearance.

关键词： De novo hepatocellular carcinoma Liver transplantation

维普期刊数据库评论

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维普期刊数据库

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高密度磁记录技术研究综述

计算机研究与发展 2018年第9期55卷 2016-2028页

作者：王国华杜宏章吴凤刚刘石勇华南理工大学软件学院广州510006 美国明尼苏达大学计算机科学与工程系明尼苏达州明尼阿波利斯55455 中国海洋大学信息科学与工程学院山东青岛266100

大数据时代对大容量磁盘的需求日益增长,而在对现有的磁盘不进行较大改动的前提下,叠瓦式磁记录技术SMR是提高磁盘存储容量的最佳选择.近年来,兴起了一种新的磁记录技术——交错式磁记录技术IMR,它可以获得比SMR更高的存储密度和随机写... 详细信息

大数据时代对大容量磁盘的需求日益增长,而在对现有的磁盘不进行较大改动的前提下,叠瓦式磁记录技术SMR是提高磁盘存储容量的最佳选择.近年来,兴起了一种新的磁记录技术——交错式磁记录技术IMR,它可以获得比SMR更高的存储密度和随机写性能.首先介绍了SMR磁盘的内部叠瓦式结构以及由此带来的数据写放大问题,并对缓解数据写放大问题的数据管理方式、性能特性评测以及基于SMR的上层应用系统方面的研究进展进行了概述;然后对新兴的IMR磁盘内部结构及其数据写放大问题进行了介绍,并对其将来的研究方向做了一定的分析和展望;最后对SMR磁盘和IMR磁盘在存储密度、数据写性能等方面进行了比较分析.当前有很多基于SMR磁盘的上层应用系统,这表明SMR磁盘可以高效地替代传统磁盘来构建大型的存储系统,而IMR磁盘的优势也将使其未来的发展前景可期.

关键词：高密度磁记录技术叠瓦式磁记录交错式磁记录存储密度写放大

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NF-E2对红系造血相关基因表达的影响

山东医药 2006年第28期46卷 21-22页

作者：谭业辉王畅王冠军 Ben-david Yaacov 吉林大学第一医院吉林长春130021 加拿大多伦多大学

目的探讨红系特异性转录因子NF-E 2对红系造血相关基因表达的影响。方法应用基因芯片方法检测转染p45NF-E 2基因后红白血病细胞株HB 22.2中基因表达的变化;通过改变培养条件诱导红白血病细胞株HB 60-5向成熟细胞分化,检测诱导分化过程中... 详细信息

目的探讨红系特异性转录因子NF-E 2对红系造血相关基因表达的影响。方法应用基因芯片方法检测转染p45NF-E 2基因后红白血病细胞株HB 22.2中基因表达的变化;通过改变培养条件诱导红白血病细胞株HB 60-5向成熟细胞分化,检测诱导分化过程中NF-E 2等红系造血相关基因表达变化。结果p45NF-E 2缺陷细胞HB 22.2转染外源p45NF-E 2后,血红蛋白基因及G ata-1、EDRF基因表达上调,F li基因表达下调;HB 60-5向成熟细胞分化过程中,随着p45NF-E 2的表达上调,同样出现G ata-1和EDRF表达增强,F li表达减弱。结论NF-E 2能对多种红系相关基因表达调控。从而促进红系分化。

关键词：转录因子 NF-E2 红系分化造血调控基因表达

Wikstroelide M potently inhibits HIV replication by targeting reverse transcriptase and integrase nuclear translocation

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Chinese Journal of Natural Medicines 2014年第3期12卷 186-193页

作者： ZHANG Xuan HUANG Sheng-Zhuo GU Wan-Gang YANG Liu-Meng CHEN Huan ZHENG chang-Bo ZHAO You-Xing WAN david Chi-Cheong ZHENG Yong-Tang key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences&Yunnan Province KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common DiseasesKunming Institute of ZoologyChinese Academy of Sciences School of Pharmaceutical Science&Yunnan key Laboratory of Pharmacology for Natural Products Kunming Medical University Institute of Tropical Bioscience and Biotechnology Chinese Academy of Tropical Agricultural Sciences School of Biomedical Sciences KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common DiseasesFaculty of MedicineThe Chinese University of Hong Kong School of Pharmacy China Pharmaceutical University

AIM： To evaluate the anti-HIV activity and mechanism of action of wikstroelide M, a daphnane diterpene from Daphne acutiloba Rehder （Thymelaeaceae）. METHOD： The anti-HIV activities of wikstroelide M against different HIV strains were evaluated by cytopathic effect assay and p24 quantification assay with ELISA. The inhibitory effect of wikstroelide M on HIV reverse transcription was analyzed by real-time PCR and ELISA. The effect of wikstroelide M on HIV-1 integrase nuclear translocation was observed with a cell-based imaging assay. The effect of wikstroelide M on LEDGF/p75-IN interaction was assayed by molecular docking. RESULTS： Wikstroelide M potently inhibited different HIV-1 strains, including HIV-lmn, HIV-1AI7, and HIV-19495, induced a cytopathic effect, with ECs0 values ranging from 3.81 to 15.65 ***-I. Wikstroelide M also had high inhibitory activities against HIV-2noD and HIV-2cBL_20-induced cytopathic effects with ECs0 values of 18.88 and 31.90 *** 1. The inhibitory activities of wikstroelide M on the three HIV-1 strains were further confirmed by p24 quantification assay, with ECs0 values ranging from 15.16 to 35.57 ***-1. Wikstroelide M also potently inhibited HIV-lnm induced cytolysis in MT-4 cells, with an ECs0 value of 9.60 *** ~. The mechanistic assay showed that wikstroelide M targeted HIV-I reverse transcriptase and nuclear translocation of integrase through disrupting the interaction between integrase and LEDGF/p75. CONCLUSION： Wikslroelide M may be a potent HIV-1 and HIV-2 inhibitor, the mechanisms of action may include inhibition of reverse trascriptase activity and inhibition of integrase nuclear Iranslocation through dismpting the interaction between integrase and LEDGF/p75.

关键词： Wikstroelide M Daphnane diterpene Daphne acutiloba Rehder HIV Reverse trascriptase integrase Nucleartranslocation Lens epithelium-derived growth factor (LEDGF/p75) Molecular docking

Hepatic decompensation/serious adverse events in post-liver transplantation recipients on sofosbuvir for recurrent hepatitis C virus

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World Journal of Gastroenterology 2016年第9期22卷 2844-2854页

作者： Neal Patel kian Bichoupan Lawrence ku Rachana Yalamanchili Alyson Harty Donald Gardenier Michel Ng david Motamed Viktoriya khaitova Nancy Bach Charissa chang Priya Grewal Meena Bansal Ritu Agarwal Lawrence Liu Gene Im Jennifer Leong Leona kim-Schluger Joseph Odin Jawad Ahmad Scott Friedman Douglas Dieterich Thomas Schiano Ponni Perumalswami Andrea Branch Division of Liver Diseases Icahn School of Medicine at Mount Sinai Recanati Miller Transplant Institute Icahn School of Medicine at Mount Sinai

AIM: To determine the safety profile of new hepatitis C virus (HCV) treatments in liver transplant (LT) recipients with recurrent HCV ***: Forty-two patients were identified with recurrent HCV infection that underwent LT at least 12 mo prior to initiating treatment with a Sofosbuvir-based regimen during December 2013-June 2014. Cases were patients who experienced hepatic decompensation and/or serious adverse events (SAE) during or within one month of completing treatment. Controls had no evidence of hepatic decompensation and/or SAE. HIV-infected patients were excluded. Cumulative incidence of decompensation/SAE was calculated using the kaplan Meier method. Exact logistic regression analysis was used to identify factors associated with the composite ***: Median age of the 42 patients was 60 years [Interquartile Range (IQR): 56-65 years], 33% (14/42) were female, 21% (9/42) were Hispanic, and 9% (4/42) were Black. The median time from transplant to treatment initiation was 5.4 years (IQR: 2.1-8.8 years). Thirteen patients experienced one or more episodes of hepatic decompensation and/or SAE. Anemia requiring transfusion, the most common event, occurred in 62% (8/13) patients, while 54% (7/13) decompensated. The cumulative incidence of hepatic decompensation/SAE was 31% (95%CI: 16%-41%). Risk factors for decompensation/SAE included lower pre-treatment hemoglobin (OR = 0.61 per g/dL, 95%CI: 0.40-0.88, P 2, 95%CI: 0.90-0.99, P = 0.01), and higher baseline serum total bilirubin (OR = 2.43 per mg/dL, 95%CI: 1.17-8.65, P < 0.01). The sustained virological response rate for the cohort of 42 patients was 45%, while it was 31% for ***: Sofosbuvir/ribavirin will continue to be used in the post-transplant population, including those with HCV genotypes 2 and 3. Management of anemia remains an important clinical challenge.

关键词： Hepatitis C virus Sofosbuvir Ribavirin Anemia Hepatic decompensation Serious adverse event Liver transplant