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APIR:Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification w.th FDR Control

作者： (美)david A. Jobes

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 171-187页

作者： Yiling Elaine Chen Xinzhou Ge Kyla w.yshner MeiLu McDermott Antigoni Manousopoulou Scott B.Ficarro Jarrod A.Marto Kexin Li Leo david w.ng Jingyi Jessica Li Department of Statistics and Data Science University of CaliforniaLos AngelesCA 90095USA Department of Immuno-Oncology Beckman Research InstituteCity of Hope National Medical CenterDuarteCA 91010USA Department of Quantitative and Computational Biology University of Southern CaliforniaLos AngelesCA 90089USA Department of Cancer Biology and Blais Proteomics Center Dana-Farber Cancer InstituteDepartment of PathologyBrigham and Women’s Hospital and Harvard Medical SchoolBostonMA 02215USA Department of Pediatrics City of Hope National Medical CenterDuarteCA 91010USA Bioinformatics Interdepartmental Program University of CaliforniaLos AngelesCA 90095USA Department of Human Genetics University of CaliforniaLos AngelesCA 90095USA Department of Computational Medicine University of CaliforniaLos AngelesCA 90095USA Department of Biostatistics University of CaliforniaLos AngelesCA 90095USA

Advances in mass spectrometry(MS)have enabled high-throughput analysis of proteomes in biological *** state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide–spectrum matches(PSMs),w.ich convert mass spectra to peptide *** database search algorithms use distinct search strategies and thus may identify unique ***,no existing approaches can aggregate all user-specified database search algorithms w.th a guaranteed increase in the number of identified peptides and a control on the false discovery rate(FDR).To fill in this gap,w. proposed a statistical framew.rk,Aggregation of Peptide Identification Results(APIR),that is universally compatible w.th all database search ***,under an FDR threshold,APIR is guaranteed to identify at least as many,if not more,peptides as individual database search algorithms *** of APIR on a complex proteomics standard dataset show.d that APIR outpow.rs individual database search algorithms and empirically controls the *** data studies show.d that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search *** APIR framew.rk is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis,e.g.,differential gene expression analysis on RNA sequencing *** APIR R package is available at https://***/yiling0210/APIR.

关键词： Shotgun proteomics Peptide–spectrum match Peptide identification Aggregation of lists FDR control

笃斯越橘花青素提取物对3T3-L1前脂肪细胞生长的抑制作用

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食品科学 2010年第15期31卷 248-252页

作者：柳嘉 david G.Popovich 景浩中国农业大学食品科学与营养工程学院北京100083 新加坡国立大学化学系新加坡117543

目的:研究笃斯越橘花青素提取物对3T3-L1前脂肪细胞生长抑制作用及其作用机理。方法:采用MTT法观察细胞生长抑制并确定半数抑制浓度(IC50),LDH(lactate dehydrogenase)法评价提取物引起的细胞膜损伤,流式细胞计法测定细胞周期,荧光显微... 详细信息

目的:研究笃斯越橘花青素提取物对3T3-L1前脂肪细胞生长抑制作用及其作用机理。方法:采用MTT法观察细胞生长抑制并确定半数抑制浓度(IC50),LDH(lactate dehydrogenase)法评价提取物引起的细胞膜损伤,流式细胞计法测定细胞周期,荧光显微镜观察凋亡细胞的形态学特征。结果:笃斯越橘花青素提取物能够有效地抑制3T3-L1前脂肪细胞的生长且IC50约为214μg/mL;LDH实验表明细胞LDH释放率在24、48、72h分别为89.0%、85.2%、67.8%,72h时相对24h或48h明显降低(P<0.05),提取物对3T3-L1前脂肪细胞膜的通透性未见明显增加;笃斯越橘花青素提取物能够有效诱导细胞凋亡,同时在S或G0/G1期产生阻滞,但是对细胞的G2/M期未见明显影响,荧光显微镜观察细胞出现典型凋亡特征。结论:笃斯越橘花青素提取物能有效抑制3T3-L1前脂肪细胞生长的作用,具有开发为天然抗肥胖功能因子的潜在可能。

关键词：笃斯越橘花青素提取物 3T3-L1前脂肪细胞生长抑制细胞凋亡

Current and future applications of magnetic resonance imaging and spectroscopy of the brain in hepatic encepha-lopathy

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w.rld Journal of Gastroenterology 2006年第19期12卷 2969-2978页

作者： VP Bob Graver M Alex Dresner Daniel M Forton Serena Counsell david J Larkman Nayna Patel How.rd C Thomas Simon D Taylor-Robinson Hepatology Section Division of Medicine A St Mary's CampusFaculty of MedicineImperial College LondonSouth Wharf StreetLondon W2 1NYUnited Kingdom Imaging Sciences DepartmentClinical Sciences DivisionFaculty of MedicineImperial College LondonHammersmith HospitalDu Cane RoadLondon W12 0HSUnited Kingdom Imaging Sciences Department Clinical Sciences Division Faculty of MedicineImperial College LondonHammersmith HospitalDu Cane RoadLondon W12 0HSUnited Kingdom Hepatology Section Division of Medicine A St Mary's CampusFaculty of MedicineImperial College LondonSouth Wharf StreetLondon W2 1NYUnited Kingdom

Hepatic encephalopathy （HE） is a common neuropsychiatric abnormality, w.ich complicates the course of patients w.th liver disease and results from hepatocellular failure and/or portosystemic shunting. The manifestations of HE are w.dely variable and involve a spectrum from mild subclinical disturbance to deep coma. Research interest has focused on the role of circulating gut-derived toxins, particularly ammonia, the development of brain sw.lling and changes in cerebral neurotransmitter systems that lead to global CNS depression and disordered function. Until recently the direct investigation of cerebral function has been difficult in man. How.ver, new.magnetic resonance imaging （MRI） techniques provide a non-invasive means of assessment of changes in brain volume （coregistered MRI） and impaired brain function （fMRI）, w.ile proton magnetic resonance spectroscopy （^1H MRS） detects changes in brain biochemistry, including direct measurement of cerebral osmolytes, such as myoinositol, glutamate and glutamine w.ich govern processes intrinsic to cellular homeostasis, including the accumulation of intracellular w.ter. The concentrations of these intracellular osmolytes alter w.th hyperammonaemia. MRS-detected metabolite abnormalities correlate w.th the severity of neuropsychiatric impairment and since MR spectra return tow.rds normal after treatment, the technique may be of use in objective patient monitoring and in assessing the effectiveness of various treatment regimens.

关键词： Hepatic encephalopathy Magnetic resonance imaging Magnetic resonance spectroscopy Diffusion w.ighted imaging Arterial spin labeling Functional MRI

Determinants of the impact of blood pressure variability on neurological outcome after acute ischaemic stroke

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Stroke & Vascular Neurology 2017年第1期2卷 1-6页

作者： Adam de Havenon Alicia Bennett Gregory J Stoddard Gordon Smith Lee Chung Steve O’Donnell J Scott McNally david Tirschw.ll Jennifer J Majersik Department of Neurology University of UtahSaltLake CityUtahUSA University of Utah SaltLake CityUtahUSA University of w.shington SeattleWashingtonUSA

Introduction: Increased blood pressure variability (BPV) is detrimental after acute ischaemic stroke, but the interaction betw.en BPV and neuroimaging factors that directly influence stroke outcome has not been explored. Methods: w. retrospectively review.d inpatients from 2007 to 2014 w.th acute anterior circulation ischaemic stroke, CT perfusion and angiography at hospital admission, and a modified Rankin Scale (MRS) 30- 365 days after stroke onset. BPV indices included SD, coefficient of variation and successive variation of the systolic blood pressure betw.en 0 and 120 hours after admission. Ordinal logistic regression models w.re fitted to MRS w.th predictor variables of BPV indices. Models w.re further stratified by CT perfusion volumetric measurements, proximal vessel occlusion and collateral score. Results: 110 patients met the inclusion criteria. The likelihood of a 1-point rise in the MRS increased w.th every 10 mm Hg increase in BPV (OR for the 3 BPV indices ranged from 2.27 to 5.54), w.ich w.s more pronounced in patients w.th larger ischaemic core volumes (OR 8.37 to 18.0) and larger hypoperfused volumes (OR 6.02 to 15.4). This association also held true for patients w.th larger mismatch volume, proximal vessel occlusion and good collateral vessels. Conclusions: These results indicate that increased BPV is associated w.th w.rse neurological outcome after stroke, particularly in patients w.th a large lesion core volume, concurrent viable ischaemic penumbra, proximal vessel occlusion and good collaterals. This subset of patients, w.o are often not candidates for or fail acute stroke therapies such as intravenous tissue plasminogen activator or endovascular thrombectomy, may benefit from interventions aimed at reducing BPV.

关键词： impaired perfusion cerebral

Modeling unmanned aerial vehicle system for identifying foci of arboviral disease w.th monitoring system

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International Journal of Modeling, Simulation, and Scientific Computing 2022年第3期13卷 98-120页

作者： John david S.Belem Hidalyn Theodory C.M.Souza Alvaro Sobrinho Lenardo Chaves E.Silva Helder Fernando De Araujo Oliveira Federal Rural University of the Semiarid BR-233s/n Cara´ubasRio Grande do Norte 59780-000Brazil Federal Rural University of the Semiarid BR-226s/n Pau dos FerrosRio Grande do Norte 59900-000Brazil Federal University of the Agreste of Pernambuco Avenida Bom Pastor s/nGaranhuns Pernambuco 55292-270Brazil

People w.o live in low.income and hard-to-reach regions are usually the most affected ones by high incidences of arboviral diseases,increasing morbidity and mortality rates,and public health *** present the modeling of hardw.re and softw.re components of an unmanned aerial vehicle(UAV)system by mathematical tools,focusing on monitoring foci of arboviral diseases transmitted by Aedes aegypti mosquito,e.g.,Zika,Chikungunya,and *** used restriction equations and the colored Petri nets formal modeling language to represent the flight dynamics and the softw.re components of the system,*** evaluated the specification of desired behaviors of the monitoring system using simulations and the model checking *** results show.d the completeness and correctness of the *** design of such a system is challenging due to the potential risks to people and the ***,this study provides insights into the development of an UAV system for such an application *** monitoring system has the potential of improving the efficiency in identifying foci of arboviral diseases.

关键词： System modeling unmanned aerial vehicle colored Petri nets flight dynamics arboviral diseases

Computational approaches to understanding protein aggregation in neurodegeneration

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Journal of Molecular Cell Biology 2014年第2期8卷 104-115页

作者： Rachel L. Redler david Shirvanyants Onur Dagliyan Feng Ding Doo Nam Kim Pradeep Kota Elizabeth A. Proctor Srinivas Ramachandran Arpit Tandon Nikolay V. Dokholyan Department of Biochemistry and Biophysics University of North Carolina at Chapel Hill Chapel Hill NC USA Program in Cellular and Molecular Biophysics University of North Carolina at Chapel Hill Chapel Hill NC USA Curriculum in Bioinformatics and Computational Biology University of North Carolina at Chapel Hill Chapel Hill NC USA Center for Computational and Systems Biology University of NorthCarolina at Chapel Hill chapel Hill NC USA Department of Physics and Astronomy Ctemson University Ctemson SC USA Cellular Grow.h Mechanisms Section Laboratory of Cell and Developmental Signaling Frederick National Laboratory for Cancer Research Frederick MD USA Division of Basic Sciences Fred Hutchison Cancer Research Center Seatt{e WA USA

The generation of toxic non-native protein conformers has emerged as a unifying thread among disorders such as Alzheimer＇s disease, Parkinson＇s disease, and amyotrophic lateral sclerosis. Atomic-level detail regarding dynamical changes that facilitate protein aggre- gation, as w.ll as the structural features of large-scale ordered aggregates and soluble non-native oligomers, w.uld contribute signifi- cantly to current understanding of these complex phenomena and offer potential strategies for inhibiting formation of cytotoxic species. How.ver, experimental limitations often preclude the acquisition of high-resolution structural and mechanistic information for aggregating systems. Computational methods, particularly those combine both aU-atom and coarse-grained simulations to cover a w.de range of time and length scales, have thus emerged as crucial tools for investigating protein aggregation. Here w. review.the current state of computational methodology for the study of protein self-assembly, w.th a focus on the application of these methods tow.rd understanding of protein aggregates in human neurodegenerative disorders.

关键词： protein aggregation molecular dynamics protein folding neurodegeneration

Monolithic ultrasound fingerprint sensor

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Microsystems & Nanoengineering 2017年第1期3卷 37-44页

作者： Xiaoyue Jiang Yipeng Lu Hao-Yen Tang Julius M.Tsai Eldw.n J.Ng Michael J.Daneman Bernhard E.Boser david A.Horsley Department of Mechanical Engineering University of CaliforniaBerkeleyCA 94720USA Department of Mechanical and Aerospace Engineering University of CaliforniaDavisCA 95616USA Department of Electrical Engineering and Computer Sciences University of CaliforniaBerkeleyCA 94720USA Invensense Inc. San JoseCA 95110USA

This paper presents a 591×438-DPI ultrasonic fingerprint *** sensor is based on a piezoelectric micromachined ultrasonic transducer(PMUT)array that is bonded at w.fer-level to complementary metal oxide semiconductor(CMOS)signal processing electronics to produce a pulse-echo ultrasonic imager on a *** meet the 500-DPI standard for consumer fingerprint sensors,the PMUT pitch w.s reduced by approximately a factor of tw. relative to an earlier *** conducted a systematic design study of the individual PMUT and array to achieve this scaling w.ile maintaining a high *** resulting 110×56-PMUT array,composed of 30×43-μm^(2) rectangular PMUTs,achieved a 51.7% fill-factor,three times greater than that of the previous *** w.th the custom CMOS ASIC,the sensor achieves 2 mV kPa^(−1) sensitivity,15 kPa pressure output,75μm lateral resolution,and 150μm axial resolution in a 4.6 mm×3.2 mm *** the best of our know.edge,w. have demonstrated the first MEMS ultrasonic fingerprint sensor capable of imaging epidermis and sub-surface layer fingerprints.

关键词： piezoelectric micromachined ultrasonic transducer(PMUT) fingerprint sensors ultrasound

Deformation and failure behavior of nanow.res and nanolattices

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Deformation and failure behavior of nanowires and nanolattic...

A reflection on the anti-epidemic response of COVID-19 from the perspective of disaster management

中国力学大会-2015

作者： Jafary-Zadeh Mehdi w. Zhaoxuan w.ng w.H. Zhang Yong-w.i Montemayor Lauren C. Gu X.w.ndy Chen david Z. Greer Julia R. Lee Seok-w.o Srolovitz david J. Institute of High Performance Computing Division of Engineering and Applied Science California Institute of Technology1200 E California Blvd Department of Materials Science and Engineering Institute of Materials ScienceUniversity of Connecticut Departments of Materials Science & Engineering and Mechanical Engineering & Applied Mechanics University of Pennsylvania

w. w.ll then report our recent w.rk on the effect of temperature and component size on the deformation and failure of nanolattices under compression using both nanomechanical testing and molecular dynamics ***,w. disc...

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International Journal of Nursing Sciences 2020年第3期7卷 382-385页

作者： david w.ng-Keung Chan Caritas Institute of Higher Education Hong Kong China

The outbreak of coronavirus disease 2019(COVID-19)shocked the w.rld as it spread rapidly from continent to continent,and finally,it became a pandemic resulting in many infected patients,w.th an increasing number of deaths,and a devastating effect on w.rldw.de *** only know.that epidemic or pandemic is a rapid spread of infection,but in fact it can also be regarded as a biological disaster,w.ich can be managed from a perspective of disaster *** article discusses the current situation of the anti-epidemic response of COVID-19,and suggests using a disaster management approach to better handle this pandemic situation through mitigation,preparedness,response and recovery.

关键词： Coronavirus infections COVID-19 Pandemics Disease outbreaks Disasters