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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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Your personal choices in transportation and food are important for lowering carbon emissions

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Frontiers of Environmental Science & Engineering 2024年第6期18卷 27-32页

作者： bruce Logan Fang Zhang Wulin Yang Le Shi Institute of Energy and the Environment The Pennsylvania State UniversityUniversity ParkPA 16802USA School of Environment Tsinghua UniversityBeijing 100084China College of Environmental Sciences and Engineering Peking UniversityBeijing 100871China College of Environmental and Resource Sciences Zhejiang UniversityHangzhou 310058China

There is a global need to reduce greenhouse gas emissions to limit the extent of climate change.A better understanding of how our own activities and lifestyle influence our energy use and carbon emissions can help us enable changes in activities that can lead to reductions in carbon *** we discuss an approach based on examining carbon emissions from the perspective of the unit C,where 1 C is the CO_(2)from food a person would on average eat every *** approach shows that total CO_(2)emissions in China,normalized by the population,is 22.5 C while carbon emissions for a person in the US is 43.9 C.A better appreciation of our own energy use can be obtained by calculating carbon emissions from our own activities in units of C,for example for driving a car gasoline or electric vehicle a certain number of kilometers,using electricity for our homes,and eating different *** this information,we can see how our carbon emissions compare to national averages in different countries and make decisions that could lower our personal CO_(2)emissions.

关键词： Carbon dioxide Climate change Daily energy Greenhouse gas

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Spinal intradural electrodes: opportunities, challenges and translation to the clinic

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Neural Regeneration Research 2024年第3期19卷 503-504页

作者： bruce Harland Chien Yew Kow Darren Svirskis School of Pharmacy University of AucklandAucklandNew Zealand Department of Neurosurgery Auckland City HospitalAucklandNew Zealand

Damage to the spinal cord disrupts the electrically active nerve cells which normally transmit afferent and efferent signals,resulting in loss of motor,sensory,and autonomic *** treatments for spinal cord injury utilizing implanted spinal electrodes can be broadly classified into three different *** first of these approaches is“spinal stimulation”where electrodes,usually positioned above the level of injury,provide electrical stimulation to target and disrupt pain signals before they reach the *** second approach uses“activity-dependent neuro-technologies”,in which electrodes positioned below the level of injury initiate a complex spatiotemporal pattern of stimulation at the lumbar spinal cord to generate a walking gait in the limbs(Minev et al.,2015;Wagner et al.,2018).

关键词： stimulation electrodes utilizing

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Transforming nanoscale VO_(2)(B) into a scalable sodium-ion electrode

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Nano Research 2024年第10期17卷 8809-8818页

作者： Yunkai Luo Swetha Chandrasekaran Bintao Hu Randy Chen Marcus Worsley bruce Dunn Department of Materials Science and Engineering University of CaliforniaLos AngelesCA 90095USA Lawrence Livermore National Laboratory CA 94550USA

The intermittent nature of renewable energies requires highly reliable grid-level energy storage approaches.A critical consideration in developing this technology is the areal capacity which determines battery performance and influences the cost of battery *** related importance is finding new ways of developing scalable *** recent years,threedimensional(3D)printing of conductive scaffolds has emerged as an alternative to overcome the scalability limitations of commercial tape cast *** research carried out in the current study demonstrates a successful scalability pathway for nanoscale VO_(2)(B),a desirable cathode for sodium-ion batteries which has a nano-flower morphology with a crystallite sizecan be scaled up to achieve thick electrodes without compromising their electrochemical properties.

关键词： nano VO_(2)(B) sodium-ion battery scalable electrodes three-dimensional(3D)printed scaffold additive manufacturing

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Are James Webb Space Telescope Observations Consistent with Warm Dark Matter?

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International Journal of Astronomy and Astrophysics 2024年第1期14卷 45-60页

作者： bruce Hoeneisen Universidad San Francisco de Quito Quito Ecuador

We compare observed with predicted distributions of galaxy stellar masses M* and galaxy rest-frame ultra-violet luminosities per unit bandwidth LUV, in the redshift range z=2 to 13. The comparison is presented as a function of the comoving warm dark matter free-streaming cut-off wavenumber kfs. For this comparison the theory is a minimal extension of the Press-Schechter formalism with only two parameters: the star formation efficiency, and a proportionality factor between the star formation rate per galaxy and LUV. These two parameters are fixed to their values obtained prior to the James Webb Space Telescope (JWST) data. The purpose of this comparison is to identify if, and where, detailed astrophysical evolution is needed to account for the new JWST observations.

关键词： James Webb Space Telescope JWST Warm Dark Matter

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Measurements of the Dark Matter Mass, Temperature and Spin

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International Journal of Astronomy and Astrophysics 2024年第3期14卷 184-202页

作者： bruce Hoeneisen Universidad San Francisco de Quito Quito Ecuador

We summarize several measurements of the dark matter temperature-to-mass ratio, or equivalently, of the comoving root-mean-square thermal velocity of warm dark matter particles vhrms(1). The most reliable determination of this parameter comes from well measured rotation curves of dwarf galaxies by the LITTLE THINGS collaboration: vhrms(1)=406±69 m/s. Complementary and consistent measurements are obtained from rotation curves of spiral galaxies measured by the SPARC collaboration, density runs of giant elliptical galaxies, galaxy ultra-violet luminosity distributions, galaxy stellar mass distributions, first galaxies, and reionization. Having measured vhrms(1), we then embark on a journey to the past that leads to a consistent set of measured dark matter properties, including mass, temperature and spin.

关键词： Warm Dark Matter Dwarf Galaxies Spiral Galaxies Elliptical Galaxies Galaxy Distributions First Galaxies Reionization

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Complex ammonium oxidation demands visualized resolution

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Science Bulletin 2024年第16期69卷 2478-2482页

作者： Zhihao Chen Yonghong Wu Jan Dolfing Shunyao Zhuang Baozhan Wang Dan Li Shan Huang bruce E.Rittmann State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China Zigui Three Gorges Reservoir Ecosystem Observation and Research Station of Ministry of Water Resources of the People’s Republic of ChinaYichang 443605China University of Chinese Academy of Sciences Beijing 100049China d College of Nanjing University of Chinese Academy of SciencesNanjing 211135China Faculty of Energy and Environment Northumbria UniversityNewcastle-upon-Tyne NE18QHUK Department of Microbiology College of Life SciencesNanjing Agricultural UniversityKey Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjing 210095China College of Urban Construction Nanjing Tech UniversityNanjing 211816China Department of Civil and Environmental Engineering Princeton UniversityPrinceton NJ 08540USA Biodesign Swette Center for Environmental Biotechnology Arizona State UniversityTempe AZ 85287-5701USA

The nitrogen cycle plays a vital role in sustaining productive and healthy ecosystems,with the microbial nitrogen cycle being a focal point in agriculture and eco-environmental *** these microbially mediated processes is ammonium(NH_(4)^(+))oxidation,the gatekeeper of the nitrogen *** understanding of ammonium oxidation is continuously evolving,thanks to recent research breakthroughs like comammox,Feammox,and dirammox[1-6].The increasing complexity of ammonium oxidation necessitates more precise and well-focused research tools beyond those commonly used today.

关键词： ammonium breakthrough precise

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A Comment on the Hubble Expansion Parameter Tension

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International Journal of Astronomy and Astrophysics 2024年第1期14卷 61-64页

作者： bruce Hoeneisen Universidad San Francisco de Quito Quito Ecuador

We point out that the recent baryon acoustic oscillation measurement by the Dark Energy Survey collaboration relieves the Hubble expansion parameter tension.

关键词： Hubble Parameter H0 Tension

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Rationale and design of Tenecteplase Reperfusion Therapy in Acute Ischaemic Cerebrovascular Events III (TRACE III): a randomised, phase III, open- label, controlled trial

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Stroke & Vascular Neurology 2024年第1期9卷 82-89页

作者： Yunyun Xiong bruce C V Campbell Marc Fisher Lee H Schwamm Mark Parsons Hao Li Yuesong Pan Xia Meng Xingquan Zhao Yongjun Wang Neurology Beijing Tiantan HospitalBeijingChina China National Clinical Research Center for Neurological Diseases BeijingChina Department of Medicine and Neurology The University of MelbourneMelbourneVictoriaAustralia Neurology Beth Israel Deaconess Medical CenterBostonMassachusettsUSA Department of Neurology and Comprehensive Stroke Center Massachusetts General HospitalBostonMassachusettsUSA Department of Neurology University of New South Wales South Western Sydney Clinical SchoolLiverpoolNew South WalesAustralia

Background and purpose Recombinant human TNK tissue-type plasminogen activator(rhTNK-tPA)was not inferior to alteplase for ischaemic stroke within *** study aimed to investigate the efficacy and safety of rhTNK-tPA in patients who had an ischaemic stroke due to large vessel occlusion(LVO)of anterior circulation beyond *** and design Tenecteplase Reperfusion Therapy in Acute Ischaemic Cerebrovascular Events-III(TRACE III)is a multicentre,prospective,randomised,open-label,blind endpoint,controlled clinical *** who had an ischaemic stroke due to anterior circulation LVO(internal carotid artery,middle cerebral artery M1 and M2 segments)within 4.5–24hours from last known well(including wake-up stroke and no witness stroke)and with salvageable tissue(ischaemic core volume6s at 24 hours and NIHSS score change from baseline at *** outcomes are symptomatic intracerebral haemorrhage within 36 hours and mortality at 90 *** TRACE III will provide evidence for the efficacy and safety of rhTNK-tPA in patients who had an ischaemic strokes due to anterior circulation LVO beyond *** registration number NCT05141305.

关键词： Therapy random Rational

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Assessment of groundwater quantity, quality, and associated health risk of the Tano river basin, Ghana

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Acta Geochimica 2024年第2期43卷 325-353页

作者： Adwoba Kua-Manza Edjah bruce Banoeng-Yakubo Anthony Ewusi Enoch Sakyi-Yeboah David Saka Clara Turetta Giulio Cozzi David Atta-Peters Larry Pax Chegbeleh Water Resources Research Centre Ghana Atomic Energy CommissionAccraGhana Earth Science Department University of GhanaLegonAccraGhana Geological Engineering Department University of Mines and TechnologyTarkwaGhana Department of Statistics University of GhanaAccraLegonGhana Institute of Polar Sciences National Research Council of ItalyVeniceItaly

In the Tano River Basin,groundwater serves as a crucial resource;however,its quantity and quality with regard to trace elements and microbiological loadings remain poorly understood due to the lack of groundwater logs and limited water *** study presents a comprehensive analysis of the Tano River Basin,focusing on three key ***,it investigated the aquifer hydraulic parameters and the results showed signiﬁcant spatial variations in borehole depths,yields,transmissivity,hydraulic conductivity,and speciﬁc *** boreholes were concentrated in the northeastern and southeastern zones,while geological formations,particu-larly the Apollonian Formation,exhibit a strong inﬂuence on borehole *** study identiﬁed areas with high transmissivity and hydraulic conductivity in the southern and eastern regions,suggesting good groundwater avail-ability and suitability for sustainable water ***-ondly,the research investigated the groundwater quality and observed that the majority of borehole samples fall within WHO(Guidelines for Drinking-water Quality,Environmental Health Criteria,Geneva,2011,***://***)***,some samples have pH levels below the standards,although the groundwater generally qualiﬁes as *** study further explores hydrochemical facies and health risk assessment,highlighting the dominance of Ca–HCO3 water *** element analysis reveals minimal health risks from most elements,with chromium(Cr)as the primary contributor to chronic health ***,this study has provided a key insights into the Tano River Basin’s hydrogeology and associated health *** outcome of this research has contributed to the broader understanding of hydrogeologi-cal dynamics and the importance of managing groundwater resources sustainably in complex geological environments.

关键词： Groundwater Unsupervised machine learning technique Hydrochemistry Aquifer hydraulic parameter Health risk

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