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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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Different xylogenesis responses to atmospheric water demand contribute to species coexistence in a mixed pine–oak forest

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Journal of Forestry Research 2023年第1期34卷 51-62页

作者： marín Pompa-García J.Julio Camarero michele colangelo Facultad de Ciencias Forestales y Ambientales de la Universidad Juárez del Estado de Durango Río Papaloapan y Blvd.Durango S/N Col.Valle del SurDurangoMéxico Instituto Pirenaico de Ecología(IPE-CSIC) Avda.Montanna 1005ZaragozaSpain School of Agricultural ForestFood and Environmental SciencesUniv.BasilicataPotenzaItaly

Seasonal patterns of wood formation(xylogenesis)remain understudied in mixed pine-oak forests despite their contribution to tree coexistence through temporal niche *** was assessed in three pine species(Pinus cembroides,Pinus leiophylla,Pinus engelmannii)and one oak(Quercus grisea)coexisting in a semi-arid mexican *** main xylogenesis phases(production of cambium cells,radial enlargement,cell-wall thickening and maturation)were related to climate data considering 5-15-day temporal *** pines,cambium activity maximized from mid-march to April as temperature and evaporation increased,whereas cell radial enlargement peaked from April to may and was constrained by high evaporation and low ***-wall thickening peaked from June to July and in August-September as maximum temperature and vapour pressure deficit(VPD)*** of earlywood and latewood tracheids occurred in may-June and June-July,enhanced by high minimum temperatures and VPD in *** and *** oak,cambial onset started in march,constrained by high minimum temperatures,and vessel radial enlargement and radial increment maximized in April as temperatures and evaporation increased,whereas early wood vessels matured from may to June as VPD ***,15-day wet conditions enhanced cell radial enlargement in *** and ***,whereas early-summer high 15-day temperature and VPD drove cell-wall thickening in *** night conditions and high evaporation rates during spring and summer enhanced *** earlier growth peak in oak and a higher responsiveness to spring-summer water demand in pines contributed to their coexistence.

关键词： Bimodal growth Drought Vapour pressure deficit Wood formation Xylem phenology

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Exploring the Nicotinic Acetylcholine Receptor-associated Proteome with iTRAQ and Transgenic mice

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Genomics, Proteomics & Bioinformatics 2013年第4期11卷 207-218页

作者： Tristan D. mcClure-Begley Kathy L. Stone michael J. marks Sharon R. Grady christopher m. colangelo Jon m. Lindstrom marina R. Picciotto Department of Psychiatry Yale University School of MedicineNew Haven CT 06508 USA Institute for Behavioral Genetics University of ColoradoBoulder CO 80303 USA W.m. Keck Biotechnology Resource Laboratory Yale University School MedicineNew Haven CT 06509 USA Department of Psychology and Neuroscience University of ColoradoBoulder CO 80309 USA Department of molecular Biophysics & Biochemistry Yale UniversityNew Haven CT 06520 USA Department of Neuroscience Medical School of the University of PennsylvaniaPhiladelphia PA 19104 USA

Neuronal nicotinic acetylcholine receptors （nAChRs） containing Gt4 and 132 subunits are the principal receptors in the mammalian central nervous system that bind nicotine with high affin- ity. These nAChRs are involved in nicotine dependence, mood disorders, neurodegeneration and neuroprotection. However, our understanding of the interactions between a4β2-containing （a4β2） nAChRs and other proteins remains limited. In this study, we identified proteins that inter- act with ct4β2 nAChRs in a gene-dose dependent pattern by immunopurifying β2 nAChRs from mice that differ in ct4 and β2 subunit expression and performing proteomic analysis using isobaric tags for relative and absolute quantitation （iTRAQ）. Reduced expression of either the a4 or the β2 subunit results in a correlated decline in the expression of a number of putative interacting proteins. We identified 208 proteins co-imrnunoprecipitated with these nAChRs. Furthermore, stratified lin- ear regression analysis indicated that levels of 17 proteins was correlated significantly with expres- sion of at4β2 nAChRs, including proteins involved in cytoskeletal rearrangement and calcium signaling. These findings represent the first application of quantitative proteomics to produce a β2 nAChR interactome and describe a novel technique used to discover potential targets for pharma- cological manipulation of a4β2 nAChRs and their downstream signaling mechanisms.

关键词： Nicotinic receptor Affinity purification Quantitative proteomics Transgenic mouse

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Assessing risks from mining-induced ground movements near gas wells

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International Journal of mining Science and Technology 2020年第1期30卷 11-16页

作者： christopher mark Gregory m.Rumbaugh mine Safety and Health Administration PittsburghPAUSA

The proliferation of unconventional gas well development in the Northern Appalachian coalfields has raised a number of mine safety *** wells,which extract gas from deep shale formations,are characterized by gas volumes and pressures that are significantly higher than those observed at many conventional *** gas is composed largely of methane as well as other *** of planned and actively producing wells penetrate protective coal pillars or barriers within active mine boundaries,including chain pillars located between longwall *** released from a well damaged by mining-induced ground movements could pose a risk to miners by flowing into the mine *** mining-induced ground movements that may cause well damage include conventional subsidence,non-conventional subsidence(*** plane slip),pillar failure,and floor *** paper describes the known risk factors for each of the four failure *** includes a framework that can guide the risk assessment process when mining takes place near gas or oil wells.

关键词： Gas well Subsidence Coal protection pillar Risk matrix Longwall mining

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Influence of residual stresses on failure pressure of cylindrical pressure vessels

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Chinese Journal of Aeronautics 2013年第6期26卷 1415-1421页

作者： m.Jeyakumar T.christopher Department of mechanical Engineering Sardar Raja College of EngineeringAlangulamTirunelveli 627 808India Department of mechanical Engineering Government College of EngineeringTirunelveli 627 007India

The utilization of pressure vessels in aerospace applications is *** this work,fnite element analysis（FEA）has been carried out using ANSYS software package with 2D axisymmetric model to access the failure pressure of cylindrical pressure vessel made of ASTm A36 carbon steel having weld-induced residual *** fnd out the effect of residual stresses on failure pressure,frst an elasto-plastic analysis is performed to fnd out the failure pressure of pressure vessel not having residual *** a thermo-mechanical fnite element analysis is performed to assess the residual stresses developed in the pressure vessel during *** one more elasto-plastic analysis is performed to assess the effect of residual stresses on failure pressure of the pressure vessel having residual *** analysis indicates reduction in the failure pressure due to unfavorable residual stresses.

关键词： Aerospace engineering ASTm A36 Finite element analysis Pressure vessels Welding residual stress

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Jet flows from bubbles during subcooled pool boiling on micro wires

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Science China(Technological Sciences) 2005年第4期48卷 385-402页

作者： D. m. christopher Laboratory of Phase Change and Interfacial Transport Phenomena Department of Thermal Engineering Tsinghua University Beijing 100084 China

An experimental investigation was conducted on subcooled nucleate boiling on ultra-small wires having diameters of 25―100 μm. High-speed photography and laser PIV (Particle Image Velocimetry) technology were used to visually observe the bubble dynamics. For highly subcooled boiling at moderate heat fluxes, the bubbles generally remained attached to the micro heating wires and bubble-top jet flows were clearly observed. Smaller bubbles usually had stronger bubble-top jet flows, while larger bubbles seemed to produce multi-jet flows. The structures of the bubble-top jet flows, as well as multi-jet flows, were proposed from the experimental observation. A model was developed to describe jet flow phenomena from bubbles on micro wires. Numerical simulations for bubbles having diameter of 0.03 and 0.06 mm showed that both the bubble-top and multi-jet flows were induced by a strong marangoni effect due to high temperature gradients near the wire. The predicted velocity magnitudes and flow structures agreed very well with experimental measurements. The bubble size relative to the wire is an important factor affecting the jet flow structure. For a 0.03 mm bubble on a 0.1 mm wire, only a bubble-top jet flow forms, while a complex multi-jet flow pattern forms around the bubble with a weak bubble-top jet and two side jet flows for a 0.06 mm bubble.

关键词： subcooled boiling, bubble, multi-jet, jet flow, PIV, marangoni, CFD.

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Updates on treatment of irritable bowel syndrome

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World Journal of Gastroenterology 2008年第17期14卷 2639-2649页

作者： christopher W Hammerle Christina m Surawicz Department of medicine University of Colorado Health Sciences Center Harborview medical Center University of Washington

Irritable bowel syndrome （IBS） is a highly prevalent gastrointestinal disorder characterized by abdominal pain and discomfort in association with altered bowel habits. It is estimated tD affect 10%-15% of the Western population, and has a large impact on quality of life and （in）direct healthcare costs. IBS is a multifactorial disorder involving dysregulation within the brain-gut axis, and it is frequently associated with gastrointestinal motor and sensory dysfunction, enteric and central nervous system irregularities, neuroimmune dysregulation, and postinfectious inflammation. As with other functional medical disorders, the treatment for IBS can be challenging. Conventional therapy for those with moderate to severe symptoms is largely unsatisfactory, and the development of new and effective drugs is made difficult by the complex pathogenesis, variety of symptoms, and lack of objective clinical findings that are the hallmark of this disorder. Fortunately, research advances over the past several decades have provided insight into potential mechanisms responsible for the pathogenesis of IBS, and have led to the development of several promising pharmaceutical agents. In recent years there has been much publicity over several of these new IBS medications （alosetron and tegaserod） because of their reported association with ischemic colitis and cardiovascular disease. While these agents remain available for use under restricted prescribing programs, this highlights the need for continued development of safe and effective medication for IBS. This article provides a physiologicallybased overview of recently developed and frequently employed pharmaceutical agents used to treat IBS, and discusses some non-pharmaceutical options that may be beneficial in this disorder.

关键词： Irritable bowel syndrome Treatment Pharmacotherapy Challenges Opportunities

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CO2 degassing and melting of metasomatized mantle lithosphere during rifting-Numerical study

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Geoscience Frontiers 2019年第4期10卷 1409-1420页

作者： Weronika Gorczyk christopher m. Gonzalez University of Western Australia Centre for Exploration TargetingSchool of Earth SciencesARC Centre of Excellence for Core to Crust Fluid SystemsPerthWestern AustraliaAustralia School of Earth Atmosphere and EnvironmentMonash University ClaytonMelbourneVICAustralia

:Reactivation of metasomatized mantle lithosphere may occur during continental extension,which is an important component of plate *** lower most part of the metasomatized domains in the subcontinental mantle lithosphere can be locally enriched in ***,partial melting of these metasomatized domains may play a crucial role in the global carbon ***,little is known about this process and up until now few numerical constraints are *** we address this knowledge gap and use a 2-D high resolution petrological-thermomechanical model to assess lithospheric ***2 degassing and *** test 4 lithospheric thicknesses:90,110,130 and 200 km with a 10 km thick metasomatized layer at the base using CO2 of 2 wt.%in the bulk *** carbonate enriched layer is stable below^3 GPa(>110 km)for a temperature of 1300℃;therefore,we only observe degassing patterns for lithospheric models that are 130 km and 200 km *** metasomatized layer for the 130 km thick lithosphere mostly comprises carbonatite melting,whereas in the 200 km thick scenario propagation of melt development from kimberlites to carbonatites occurs as the metasomatic mantle is exhumed during *** numerical models fit well into natural rifting zones of the European Cenozoic Rift System for young(shallow)and of the North Atlantic Rift for old(thick)lithosphere.

关键词： Rifting mantle CO2 degassing Carbonate melting

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Teriparatide anabolic therapy as potential treatment of type Ⅱ dens non-union fractures

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World Journal of Orthopedics 2017年第1期8卷 82-86页

作者： Enrico Pola Virginia Pambianco Debora colangelo Virginia m Formica Giovanni Autore Luigi A Nasto Spinal Unit Department of Orthopaedics and Traumatology"A.Gemelli" University HospitalCatholic University of Rome Centre for Spine Studies and Surgery Queen’sMedical CentreNottingham University Hospitals NHS Trust

Odontoid fractures account for 5% to 15% of all cervical spine injuries and 1% to 2% of all spine fractures. Type Ⅱ fractures are the most common fracture pattern in elderly patients. Treatment(rigid and non-rigid immobilization, anterior screw fixation of the odontoid and posterior C1-C2 fusion) remains controversial and represents a unique challenge for the treating surgeon. The aims of treatment in the elderly is to quickly restore pre-injury function while decreasing morbidity and mortality associated with inactivity, immobilization with rigid collar and prolonged hospitalization. Conservative treatment of type Ⅱ odontoid fractures is associated with relatively high rates of non-union and in a few cases delayed instability. Options for treatment of symptomatic non-unions include surgical fixation or prolonged rigid immobilization. In this report we present the case of a 73-year-old woman with post-traumatic odontoid nonunion successfully treated with Teriparatide systemic anabolic therapy. Complete fusion and resolution of the symptoms was achieved 12 wk after the onset of the treatment. Several animal and clinical studies have confirmed the potential role of Teriparatide in enhancing fracture healing. Our case suggests that Teriparatide may have a role in improving fusion rates of C2 fractures in elderly patients.

关键词： Type Ⅱ odontoid fractures Non-union Anabolic therapy Teriparatide Fracture healing

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Heat Transfer in the microlayer Under a Bubble During Nucleate Boiling

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Tsinghua Science and Technology 2010年第4期15卷 404-413页

作者： David m.christopher 张璐 Key Laboratory for Thermal Science and Power Engineering of ministry of Education Department of Thermal Engineering Tsinghua University

many studies have shown that a very thin liquid microlayer forms under vapor bubbles during nucleate boiling. The heat transfer from the surface to the bubble is then significantly affected by this mi- crolayer and the curved region leading into the microlayer. Various models have been developed to predict the microlayer shape and the heat transfer along the curved interfacial region, but they tend to have incon- sistent boundary conditions or unrealistic results. This paper presents a theoretical model to predict the mi- crolayer thickness and the heat transfer rates for a variety of conditions. The results show how the wall su- perheat, the Hamaker constant, the bubble radius, and the accommodation coefficient at the interface affect the evaporation heat transfer rates and the microlayer shape for a large range of conditions for water and FC 72. The microlayer results are then shown to compare well with predictions made by solving the Na- vier-Stokes equations in the microlayer.

关键词： nucleate boiling bubble growth heat transfer microlayer

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