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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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Fracturing,caving propagation and influence of mining on groundwater above longwall panels–a review of predictive models

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International Journal of Mining Science and Technology 2020年第1期30卷 49-54页

作者： bruce Hebblewhite School of Minerals and Energy Resources Engineering University of New South WalesSydney 2052Australia

Historically there have been a number of different hypotheses and empirical models developed in an attempt to describe the nature of fracturing above longwall panels in underground coal *** motivation for suchmodels varies,ranging fromunderstanding the impact ofmining on surface subsidence,to back-analysis of caving behaviour in the immediate roof behind the longwall *** of the most critical motivating factors that is taking on increased importance in many coalfields,is the need for better understanding,and hence prediction of the impact of mining on overlying strata,particularly strata units acting as aquifers for different groundwater *** paper reviews some of the major prediction models in the context of observed behaviour of strata displacement and fracturing above longwall panels in the southern coalfields of New South Wales,south of *** paper discusses the parameter often referred to as"height of fracturing"in terms of the critical parameters that influence it,and the relevance and appropriateness of this terminology in the context of overlying sub-surface subsidence and groundwater *** paper proposes an alternative terminology for this parameter that better reflects what it is and how it is *** paper also addresses the potential role of major bedding shear planes mobilised by mining and their potential influence on overlying subsidence and groundwater interference.

关键词： Longwall mining Subsidence Groundwater Caving Underground coal mining

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Study of Electron Beam Surfi-sculpt during Composite Materials Joining

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稀有金属材料与工程 2011年第S4期40卷 292-296页

作者： bruce Dance The Welding Institute(TWI) Cambridge CB1 6ALUK

Electron beam surfi-sculpt is a new metal surface processing technology,which is widely used in the areas of materials surface treatment,composite materials manufacturing,and so *** this paper,comeld technology,which was an application technology of electron beam surfi-sculpt during composite materials area,was *** tensile experiments results and failure forms of Ti6Al4V/Carbon fibre single step joints were compared with different joining methods,such as slick embedding,adhesive bonding,riveting and *** was found that comeld joint had more advantage of tensile property than other joining *** the same time,tensile process of comeld joint was analyzed with numerical simulation,and key factors of protrusions influenced tensile property were obtained,which was of importance to structure design and joint property improvement.

关键词： electron beam surfi-sculpt comeld joining methods tensile experiments numerical simulation

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A review of the geomechanics aspects of a double fatality coal burst at Austar Colliery in NSW,Australia in April 2014

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International Journal of Mining Science and Technology 2017年第1期27卷 3-7页

作者： Hebblewhite bruce Calvin Jim School of Mining Engineering UNSWSydney 2052Australia

A coal burst occurred on 15 April, 2014 at the Austar Coal Mine, located west of Newcastle, NSW,Australia. The burst resulted in fatal injuries to two men working as part of the mining crew at the development face. At the time, a continuous miner was being used to mine a longwall development gate road through heavily structured coal, at a depth of approximately 550 m. A number of pre-cursor bumps had occurred on previous shifts, emanating from the coal ribs of the roadway, in proximity to the coal *** paper reviews the geological, geotechnical and mining conditions and circumstances leading up to the coal burst event; and presents and discusses the available evidence and possible interpretations relating to the geomechanical behaviour mechanisms that may have been critical factors in this incident. The paper also discusses some key technical and operational considerations of ground support systems and mining practices and strategies needed for operating in such conditions in the future.

关键词： Underground coal mining Roadway development Strata controlCoal burst Coal geology Mine safety

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Biology Past and Biology Future:Where have we been and where are we going?

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Neural Regeneration Research 2013年第25期8卷 2309-2316页

作者： bruce Alberts Department of Biochemistry and Biophysics the University of California San Francisco

bruce Alberts, a prominent biochemist with a strong commitment to the improvement of science and mathematics education, serves as Editor-in-Chief of Science and as one of President Obama＇s first three Science Envoys. Alberts is also Professor Emeritus in the Department of Biochemistry and Biophysics at the University of California, San Francisco, to which he returned after serving two six-year terms as the president of the National Academy of Sciences （NAS）.

关键词： Biology Past and Biology Future

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Two different mathematical schemes for solving chemical dissolution-front instability problems in fluid-saturated rocks

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Science China(Technological Sciences) 2022年第1期65卷 147-156页

作者： ZHAO ChongBin HOBBS bruce ORD Alison Computational Geosciences Research Centre Central South UniversityChangsha 410083China Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring Ministry of EducationCentral South UniversityChangsha 410083China School of Earth and Environment The University of Western AustraliaCrawleyWA 6009Australia

Chemical dissolution-front instability(CDFI)problems usually involve multiple temporal and spatial scales,as well as multiple processes.A key issue associated with solving a CDFI problem in a fluid-saturated rock is to mathematically establish a theoretical criterion,which can be used to judge the instability of a chemical dissolution-front(CDF)propagating in the fluidsaturated *** theoretical paper deals with how two different mathematical schemes can be used to precisely establish such a theoretical criterion in a purely mathematical manner,rather than in a numerical simulation *** main distinguishment between these two different mathematical schemes is that in the first mathematical scheme,a curved surface coordinate system is used,while in the second mathematical scheme,a planar surface coordinate system is *** particular,all the key mathematical deduction steps associated with using these two different mathematical schemes are described and discussed in great *** main theoretical outcomes of this study have demonstrated that(1)two different mathematical schemes under consideration can produce exactly the same theoretical criterion;(2)the main advantage of using the first mathematical scheme is that the interface conditions at the curved interface between the downstream and upstream regions can be easily described mathematically;(3)the main advantage of using the second mathematical scheme is that the first-order perturbation equations of the CDFI problem can be easily described in a purely mathematical manner.

关键词： chemical dissolution theoretical analysis mathematical scheme front instability fluid-saturated rocks

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Transient-state instability analysis of dissolution-timescale reactive infiltration in fluid-saturated porous rocks: Purely mathematical approach

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Science China(Technological Sciences) 2020年第2期63卷 319-328页

This paper deals with how the purely mathematical approach can be used to solve transient-state instability problems of dissolution-timescale reactive infiltration(DTRI) in fluid-saturated porous rocks. Three key steps involved in such an approach are:(1) to mathematically derive an analytical solution(known as the base solution or conventional solution) for a quasi-steady state problem of the dissolution timescale, which is viewed as a frozen state of the original transient-state instability problem;(2)to mathematically deduce a group of first-order perturbation partial-differential equations(PDEs) for the quasi-steady state problem;(3) to mathematically derive an analytical solution(known as the perturbation solution or unconventional solution) for this group of first-order perturbation PDEs. Because of difficulty in mathematically solving a transient-state instability problem of DTRI in general cases, only a special case, in which some nonlinear coupling between governing PDEs of the problem can be decoupled, is considered to illustrate these three key steps in this study. The related theoretical results demonstrated that the transient chemical dissolution front can become unstable in the DTRI system of large Zh numbers when the long wavelength perturbations are applied to the system. This new finding may lay the theoretical foundation for developing innovative technique to exploit shale gas resources in the deep Earth.

关键词： mathematical study dissolution timescale reactive infiltration instability chemical dissolution perturbation solution porous rocks

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Near-field performance of chemical dissolution-front instability around a circular acid-injection-well in fluid-saturated porous media

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Science China(Technological Sciences) 2023年第7期66卷 2025-2035页

作者： ZHAO ChongBin HOBBS bruce ORD Alison Computational Geosciences Research Centre Central South UniversityChangsha 410083China Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring Ministry of EducationCentral South UniversityChangsha 410083China School of Earth and Environment University of Western AustraliaCrawleyWA 6009Australia

This paper investigates the near-field performance of chemical dissolution-front instability(CDFI) around a circular acidinjection-well in fluid-saturated porous media(FSPM) through using purely mathematical *** the mathematical governing equations of the CDFI problem involving radially divergent flow are briefly described,both analytical base solutions and perturbation solutions for the considered problem are mathematically *** analytical solutions lead to the theoretical expression of the perturbation induced dimensionless growth-rate and the following two new *** first new finding is that the critical Peclet number of a chemical dissolution system(CDS) associated with radially divergent flow in FSPM is not only a function of the permeability ratio between the undissolved and dissolved regions as well as the dimensionless wavenumber,but also a function of the circular chemical dissolution-front location relative to the circular acid-injection-well in *** second new finding is that as the direct result of considering a nonzero radius of the circular acid-injection-well,there exits a critical closeness number,which may be used to assess where the circular chemical dissolution-front starts becoming unstable in the CDS associated with radially divergent *** on these two new findings,a theoretical criterion of two parts has been *** first part of the established theoretical criterion answers the scientific question when a circular chemical dissolution-front can become unstable,while the second part of the established theoretical criterion answers the scientific question where a circular chemical dissolution-front can become *** applying the established theoretical criterion,a long-term existing mystery why the wormhole pattern of fractal nature and the compact pattern of fingering nature are formed at different locations away from the circular acid-injection-well circumference in fluid-saturated carbo

关键词： near-field performance circular injection well radially divergent flow analytical solutions dissolution-front instability porous media

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Coal mine roof rating(CMRR),rock mass rating(RMR)and strata control:Carborough Downs Mine,Bowen Basin,Australia

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International Journal of Mining Science and Technology 2020年第2期30卷 225-234页

作者： Martin Brook bruce Hebblewhite Rudrajit Mitra School of Environment University of AucklandAuckland 1010New Zealand School of Mining Engineering University of New South WalesNSW 2052Australia School of Mining Engineering University of the WitwatersrandJohannesburg 2050South Africa

The rock mass rating(RMR)has been used across the geotechnical industry for half a *** contrast,the coal mine roof rating(CMRR)was specifically introduced to underground coal mines two decades ago to link geological characterization with geotechnical risk *** premise of CMRR is that strength properties of mine roof rock are influenced by defects typical of coal measures *** CMRR has been used in longwall pillar design,roof support methods,and evaluation of extended cuts,but is rarely ***,the RMR and CMRR are applied to a longwall coal *** rock mass classifications were undertaken at 67 locations across the *** classifications showed marked spatial variability in terms of roof *** and reverse faulting occur across the mine,and while no clear relationships exist between rock mass character and faulting,a central graben zone showed heterogeneous rock mass properties,and divergence between CMRR and ***,the CMRR data fell within the broad envelope of results reported for extended cuts at Australian and *** *** corollary is that the CMRR is useful,and should not be used in isolation,but rather as a component of a strata control programme.

关键词： Rock mass classification Roof strength Coal mine CMRR RMR Bowen Basin

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A new perspective on quiet Sun magnetism

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Science China(Physics,Mechanics & Astronomy) 2009年第11期52卷 1660-1664页

作者： LITES bruce William High Altitude Observatory National Center for Atmospheric ResearchP.O. Box 3000 Boulder CO 80307 USA

The Hinode mission has provided us with a new, quantitative view of the magnetism of the quiet Sun. It has revealed that the quiet internetwork areas are blanketed by horizontal fields that appear at first sight to have more flux than the vertical fields resolved on the same 0.3 size scale. These measurements point to the possibility that the horizontal fields might be the primary source of the "hidden turbulent flux" of the quiet Sun anticipated from Hanle effect depolarization. In this paper, evidence is presented suggesting that the "seething" horizontal fields observed by Harvey in 2007 and the horizontal fields revealed by Hinode are the same phenomenon. Because the seething fields appear to be of uniform fluctuation over the whole disk, the phenomenon is most likely not associated with the dynamo source of solar activity. Thus, the small-scale "hidden turbulent flux" lends support to the notion of a local solar dynamo acting on granular sizes and time scales.

关键词： Sun magnetism fields granulation

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