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Integrated Single-cell multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation

Genomics, Proteomics & Bioinformatics 2024年第1期22卷 67-88页

作者： manickam Ashokkumar Wenwen mei Jackson J.Peterson Yuriko Harigaya David m.murdoch David m.margolis Caleb Kornfein Alex Oesterling Zhicheng Guo Cynthia D.Rudin Yuchao Jiang Edward P.Browne Department of medicine University of North Carolina at Chapel HillChapel HillNC 27599USA HIV Cure Center University of North Carolina at Chapel HillChapel HillNC 27599USA Department of Biostatistics University of North Carolina at Chapel HillChapel HillNC 27599USA Department of microbiology and Immunology University of North Carolina at Chapel HillChapel HillNC 27599USA Department of Genetics University of North Carolina at Chapel HillChapel HillNC 27599USA Department of medicine Duke UniversityDurhamNC 27708USA Department of Computer Science Duke UniversityDurhamNC 27708USA Department of Statistics Texas A&M UniversityCollege StationTX 77843USA Department of Biology Texas A&M UniversityCollege StationTX 77843USA Department of Biomedical Engineering Texas A&M UniversityCollege StationTX 77843USA

Despite the success of antiretroviral therapy,human immunodeficiency virus(HIV)cannot be cured because of a reservoir of latently infected cells that evades *** understand the mechanisms of HIV latency,we employed an integrated single-cell RNA sequencing(scRNA-seq)and single-cell assay for transposase-accessible chromatin with sequencing(scATAC-seq)approach to simultaneously profile the transcriptomic and epigenomic characteristics of~125,000 latently infected primary CD4^(+)T cells after reactivation using three different latency reversing *** expressed genes and differentially accessible motifs were used to examine transcriptional pathways and transcription factor(TF)activities across the cell *** identified cellular transcripts and TFs whose expression/activity was correlated with viral reactivation and demonstrated that a machine learning model trained on these data was 75%-79%accurate at predicting viral ***,we validated the role of two candidate HIV-regulating factors,FOXP1 and GATA3,in viral *** data demonstrate the power of integrated multimodal single-cell analysis to uncover novel relationships between host cell factors and HIV latency.

关键词： HIV latency reversal Primary CD4þT cell Single-cell multiomics HIV-regulating factor machine learning

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Protecting Water Quality and Public Health Using a Smart Grid

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Computational Water, Energy, and Environmental Engineering 2013年第2期2卷 73-80页

作者： Ken Thompson Raja Kadiyala Intelligent Water Solutions CH2M HILL Englewood Colorado USA Intelligent Water Solutions CH2M HILL Oakland California USA

After the attacks on September 11, 2001 and the follow-up risk assessments by utilities across the United States, securing the water distribution system against malevolent attack became a strategic goal for the U.S. Environmental Protection Agency. Following 3 years of development work on a Contamination Warning System (CWS) at the Greater Cincinnati Water Works, four major cities across the United States were selected to enhance the CWS development conducted by the USEPA. One of the major efforts undertaken was to develop a process to seamlessly process “Big Data” sets in real time from different sources (online water quality monitoring, consumer complaints, enhanced security, public health surveillance, and sampling and analysis) and graphically display actionable information for operators to evaluate and respond to appropriately. The most significant finding that arose from the development and implementation of the “dashboard” were the dual benefits observed by all four utilities: the ability to enhance their operations and improve the regulatory compliance of their water distribution systems. challenge: While most of the utilities had systems in place for SCADA, Work Order management, Laboratory management, 311 Call Center management, Hydraulic models, Public Health monitoring, and GIS, these systems were not integrated, resulting in duplicate data entry, which made it difficult to trace back to a “single source of truth.” Each one of these data sources can produce a wealth of raw data. For most utilities, very little of this data is being translated into actionable information as utilities cannot overwhelm their staffs with manually processing the mountains of data generated. Instead, utilities prefer to provide their staffs with actionable information that is easily understood and provides the basis for rapid decision-making. Smart grid systems were developed so utilities can essentially find the actionable needle in the haystack of data. Utilities can then fo

关键词： Smart Grid On-line Water Quality monitoring OWQm Event Detection System EDS TEVA-SPOT

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Bioreduction of nitrate in groundwater using a pilot-scale hydrogen-based membrane biofilm reactor

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Frontiers of Environmental Science & Engineering 2010年第3期4卷 280-285页

作者： Youneng TANG michal ZIV-EL chen ZHOU Jung Hun SHIN chang Hoon AHN Kerry mEYER Daniel CANDELARIA David FRIESE Ryan OVERSTREET Rick SCOTT Bruce ERITTmANN Center for Environmental Biotechnology Biodesign Institute at Arizona State UniversityTempeAZ 85287USA ch2m hill EnglewoodCO 80112USA Applied Process Technology Inc.Pleasant HillCA 94523USA City of Glendale GlendaleAZ 85303USA

A long-term pilot-scale H_(2)-based membrane biofilm reactor(mBfR)was tested for removal of nitrate from actual groundwater.A key feature of this secondgeneration pilot mBfR is that it employed lower cost polyester hollow fibers and still achieved high loading *** steady-state maximum nitrate surface loading at which the effluent nitrate and nitrite concentrations were below the maximum Contaminant Level(mCL)was at least 5.9 g·N·(m^(2)·d)^(–1),which corresponds to a maximum volumetric loading of at least 7.7 kg·N·(m^(3)·d)^(–1).The steady-state maximum nitrate surface area loading was higher than the highest nitrate surface loading reported in the firstgeneration mBfRs using composite fibers(2.6 g·N·(m^(2)·d)^(–1)).This work also evaluated the H_(2)-utilization efficiency in *** measured H_(2)supply rate was only slightly higher than the stoichiometric H_(2)-utilization ***,H_(2)utilization was controlled by diffusion and was close to 100%efficiency,as long as biofilm accumulated on the polyester-fiber surface and the fibers had no leaks.

关键词： denitrification groundwater treatment hydrogen membrane biofilm reactor(mBfR) polyester fiber

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Critical flow-storm approach to total maximum daily load (TmDL) development:an analytical conceptual model

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Frontiers of Environmental Science & Engineering 2008年第3期2卷 267-273页

作者： Harry X.ZHANG Shaw L.YU ch2m hill 15010 Conference Center DriveChantillyVA 20151–3801USA Department of Civil and Environmental Engineering Thornton HallUniversity of VirginiaCharlottesvilleVA 22904–4742USA

One of the key challenges in the total maximum daily load(TmDL)development process is how to define the critical condition for a receiving *** main concern in using a continuous simulation approach is the absence of any guarantee that the most critical condition will be captured during the selected representative hydrologic period,given the scarcity of long-term continuous *** objectives of this paper are to clearly address the critical condition in the TmDL development process and to compare continuous and event-based approaches in defining critical condition during TmDL development for a waterbody impacted by both point and nonpoint source pollution.A practical,event-based critical flow-storm(CFS)approach was developed to explicitly addresses the critical condition as a combination of a low stream flow and a storm event of a selected magnitude,both having certain frequencies of *** paper illustrated the CFS concept and provided its theoretical basis using a derived analytical conceptual *** CFS approach clearly defined a critical condition,obtained reasonable results and could be considered as an alternative method in TmDL development.

关键词： critical condition critical flow-storm(CFS)approach total maximum daily load(TmDL) conceptual model derived analytical model nonpoint source pollution

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Orbal氧化沟同时硝化/反硝化及生物除磷的机理研究

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中国给水排水 1999年第3期15卷 1-7页

作者：门晓欣 ch2 m hill USA 美国 The Alaimo Group

对６个采用分段、闭环沟道的Ｏｒｂａｌ氧化沟工艺运行数据进行了分析评定，以确定在该工艺中同时发生生物脱氮除磷的程度。较低的总氮出水浓度表明，同时硝化／反硝化在Ｏｒｂａｌ工艺中很易发生。由于泥龄较长并保持外沟道低溶解氧，... 详细信息

对６个采用分段、闭环沟道的Ｏｒｂａｌ氧化沟工艺运行数据进行了分析评定，以确定在该工艺中同时发生生物脱氮除磷的程度。较低的总氮出水浓度表明，同时硝化／反硝化在Ｏｒｂａｌ工艺中很易发生。由于泥龄较长并保持外沟道低溶解氧，有利于硝化菌的生长并提高脱氮效率；由于每个沟道处于相对均匀混合的状态，因此沟道内没有明显的好氧或缺氧段之分，表明产生反硝化的必要的缺氧环境可能发生在菌胶团内部。采用国际水协（ＩＡＷＱ）活性污泥１号模型（ＡＳＭⅠ）对出水总磷数据分析及观测到的相对于ＢＯＤ负荷的磷的去除表明，生物除磷可能发生。本研究的基本假设认为，同时生物除营养化产生于三个基本原理：①生物反应池的混合形态可以形成生物除营养所必需的缺氧及／或厌氧段，即大环境；②在菌胶团内部形成的缺氧及／或厌氧段，即微环境；③系统中存在新的、专用微生物。上述机理在任何生物除营养化系统中都会有不同程度的发生。本研究的目的是鉴别影响这三个机理在同时生物除营养化系统中所起相对作用的因素。

关键词：生物除磷硝化/反硝化氧化沟废水处理

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The Potential for Genotype-by-Environment Interactions to maintain Genetic Variation in a model Legume–Rhizobia mutualism

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Plant Communications 2020年第6期1卷 100-111页

作者： Priya Vaidya John R.Stinchcombe Department of Ecology and Evolutionary Biology University of TorontoTorontoON M5S3B2Canada Koffler Scientific Reserve at Joker’s hill University of TorontoTorontoON M5S3B2Canada

The maintenance of genetic variation in mutualism-related traits is key for understanding mutualism evolution,yet the mechanisms maintaining variation remain *** asked whether genotype-byenvironment(G3E)interaction is a potential mechanism maintaining variation in the model legume–rhizobia system,medicago truncatula–Ensifer *** planted 50 legume genotypes in a greenhouse under ambient light and shade to reflect reduced carbon availability for *** found an expected reduction under shaded conditions for plant performance traits,such as leaf number,aboveground and belowground biomass,and a mutualism-related trait,nodule *** also found G3E for nodule number,with83%of this interaction due to shifts in genotype fitness rank order across light environments,coupled with strong positive directional selection on nodule number regardless of light *** results suggest that G3E can maintain genetic variation in a mutualism-related trait that is under consistent positive directional selection across light environments.

关键词： mutualism evolution genetic variation genotype-by-environment interaction medicago truncatula light availability partner quality

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Woody plant taxonomic,functional,and phylogenetic diversity decrease along elevational gradients in Andean tropical montane forests:Environmental filtering and arrival of temperate taxa

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Plant Diversity 2024年第4期46卷 491-501页

作者： Guillermo Bañares-de-Dios manuel J.macía Gabriel Arellano Íñigo Granzow-de la Cerda Julia Vega-álvarez Itziar Arnelas Carlos I.Espinosa Norma Salinas Luis Cayuela Departamento de Biología y Geología Física y Química InorgánicaUniversidad Rey Juan CarlosCalle Tulipán s/nMóstolesMadridES-28933Spain Departamento de Biología Área de BotánicaUniversidad Autónoma de MadridCalle Darwin 2MadridES-28049Spain Centro de Investigación en Biodiversidad y Cambio Global(CIBC-UAm) Universidad Autónoma de MadridCalle Darwin 2MadridES-28049Spain Ecology and Evolutionary Biology University of MichiganAnn ArborMI 48109USA Oikobit LLC ***AlbuquerqueNM87120USA Real Jardín Botánico–CSIC Plaza Murillo 2MadridES-28014Spain Departamento de Biología Animal EcologíaParasitologíaEdafología y Química AgrícolaUniversidad de SalamancaCalle Donantes de Sangre s/nSalamancaES-37007Spain Departamento de Biodiversidad Ecología y EvoluciónUniversidad Complutense de MadridCalle JoséAntonio Nováis 12Ciudad UniversitariaES-28040Spain Departamento de Ciencias Biológicas y Agropecuarias Universidad Técnica Particular de LojaA.P.11-01-608 LojaEcuador Sección Química Pontificia Universidad Católica del PerúA.P.Lima 32LimaPeru ECI School of Geography and EnvironmentUniversity of OxfordOX13QYOxfordshireUnited Kingdom Instituto de Investigación en Cambio Global(IICG-URJC) Universidad Rey Juan CarlosCalle Tulipán s/nMóstolesMadridES-28933Spain

mountains are paramount for exploring biodiversity patterns due to the mosaic of topographies and climates encompassed over short *** research has traditionally focused on taxonomic diversity when investigating changes along elevational gradients,but other facets should be *** first time,we simultaneously assessed elevational trends in taxonomic,functional,and phylogenetic diversity of woody plants in Andean tropical montane forests and explored their underlying ecological and evolutionary *** investigation covered four transects(traversing ca.2200 m a.s.l.) encompassing 114 plots of 0.1 ha across a broad latitudinal range(ca.10°).Using hill numbers to quantify abundance-based diversity among 37,869 individuals we observed a consistent decrease in taxonomic,functional,and phylogenetic diversity as elevation increased,although the decrease was less pronounced for higher hill *** exception was a slight increase in phylogenetic diversity when dominant species were *** decrease in taxonomic and functional diversity might be attributed to an environmental filtering process towards highlands,where the increasingly harsher conditions exclude species and functional ***,the differences in steepness decrease between hill orders suggest that rare species disproportionately contribute to functional *** phylogenetic diversity the shifting elevational trend between hill orders indicates a greater than previously considered influence in central Andean highlands of tropical lowlands originated species with strong niche conservatism relative to distantly related temperate *** could be explained by a decreasing presence and abundance of temperate,extratropical taxa towards the central Andes relative to northern or southern Andes,where they are more prevalent.

关键词： Altitudinal gradients Andes Environmentalﬁltering Out of the Tropical Lowlands Functional rarity Tropical Niche Conservatism

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论新加坡的环境现场评价制度(英文)

论新加坡的环境现场评价制度(英文)

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中国法学会环境资源法学研究会2007年年会与学术研讨会——2007年全国环境资源法学研讨会

作者： HONG SZE YUNN ch2m hill Singapore Pte Ltd 150 Beach Road Gateway West Level 34 Singapore 189720

新加坡国家环境局(NEA)管理着新加坡的土地污染控制及受污染土地的治理工作。为公众的健康及安全着想,国家环境署曾引进并采用了一些国外标准指导已受到污染的土地以敏感用途为开发目的的安全使用情况。2002年,国家环境局融合这些标准... 详细信息

新加坡国家环境局(NEA)管理着新加坡的土地污染控制及受污染土地的治理工作。为公众的健康及安全着想,国家环境署曾引进并采用了一些国外标准指导已受到污染的土地以敏感用途为开发目的的安全使用情况。2002年,国家环境局融合这些标准制定出污染控制实施标准(COPPC),并特别规定针对曾用于污染性行业的土地将其再次开发用于敏感用途的情况,必须开展环境现场评价来评价其受污染的程度。新加坡土地管理局与裕廊集团是土地污染及治理法规的主要利害相关方。一系列的本土环境现场评价导则被制定出来。这些导则包括评价及管理受污染场地的基于风险管理的方法框架。本文将会详细阐述这些评价标准,评价方法以及评价目的。

关键词：污染环境现场评价土地法规

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2024 Adult Compendium of Physical Activities:A third update of the energy costs of human activities

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Journal of Sport and Health Science 2024年第1期13卷 6-12页

作者： Stephen D.Herrmann Erik A.Willis Barbara E.Ainsworth Tiago V.Barreira mary Hastert chelsea L.Kracht John m.Schuna Jr. Zhenghui Cai minghui Quan Catrine Tudor-Locke melicia C.Whitt-Glover David R. Jacobs Jr. Kansas Center for metabolism and Obesity Research University of Kansas Medical CenterKansas CityKS 66160USA Division of Physical Activity and Weight management Department of Internal MedicineUniversity of Kansas Medical CenterKansas CityKS 66160USA Center for Health Promotion and Disease Prevention University of North Carolina at Chapel HillChapel HillNC 27599USA College of Health Solutions Arizona State UniversityPhoenixAZ 85003USA School of Exercise and Health Shanghai University of SportShanghai 200438China Exercise Science Department Syracuse UniversitySyracuseNY 13244USA Clinical Sciences Division Pennington Biomedical Research CenterBaton RougeLA 70808USA School of Exercise and Sport Science Oregon State UniversityCorvallisOR 97331USA College of Health and Human Services University of North Carolina at CharlotteCharlotteNC 28223USA Gramercy Research Group KnightdaleNC 27545USA Division of Epidemiology and Community Health School of Public HealthUniversity of MinnesotaMinneapolisMN 55454USA

Background:The Compendium of Physical Activities was published in 1993 to improve the comparability of energy expenditure values assigned to self-reported physical activity(PA)across *** original version was updated in 2000,and again in 2011,and has been widely used to support PA research,practice,and public health ***:This 2024 update was tailored for adults 19-59 years of age by removing data from those≥60 *** a systematic review and supplementary searches,we identified new activities and their associated measured metabolic equivalent(mET)values(using indirect calorimetry)published since *** replaced estimated mETs with measured values when ***:We screened 32,173 abstracts and 1507 full-text papers and extracted 2356 PA energy expenditure values from 701 *** added303 new PAs and adjusted 176 existing mET values and descriptions to reflect the addition of new data and removal of mETs for older *** added a major Heading(Video Games).The 2024 Adult Compendium includes 1114 PAs(912 with measured and 202 with estimated values)across 22 major ***:This comprehensive update and refinement led to the creation of The 2024 Adult Compendium,which has utility across research,public health,education,and healthcare domains,as well as in the development of consumer health *** new website with the complete lists of PAs and supporting resources is available at https://***.

关键词： Adults Energy expenditure Exercise mET Physical Activities

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Older Adult Compendium of Physical Activities:Energy costs of human activities in adults aged 60 and older

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Journal of Sport and Health Science 2024年第1期13卷 13-17,F0003页

作者： Erik A.Willis Stephen D.Herrmann mary Hastert chelsea L.Kracht Tiago V.Barreira John m.Schuna Jr. Zhenghua Cai minghui Quan Scott A.Conger Wendy J.Brown Barbara E.Ainsworth Center for Health Promotion and Disease Prevention University of North Carolina at Chapel HillChapel HillNC 27599USA Kansas Center for metabolism and Obesity Research The University of Kansas Medical CenterKansas CityKS 66160USA Division of Physical Activity and Weight management Department of Internal MedicineUniversity of Kansas Medical CenterKansas CityKS 66160USA Clinical Science Division Pennington Biomedical Research CenterBaton RougeLA 70808USA Exercise Science Department Syracuse UniversitySyracuseNY 13244USA School of Exercise&Sport Science Oregon State UniversityCorvallisOR 97331USA School of Exercise and Health Shanghai University of SportShanghai 200438China Department of Kinesiology Boise State UniversityBoiseID 83725USA School of Human movement and Nutrition Sciences The University of QueenslandSt.LuciaQLD 4072Australia Faculty of Health Sciences and medicine Bond UniversityGold CoastQLD 4229Australia College of Health Solutions Arizona State UniversityPhoenixAZ 85003USA

Purpose:To describe the development of a Compendium for estimating the energy costs of activities in adults>60 years(OA Compendium).methods:Physical activities(PAs)and their metabolic equivalent of task(mET)values were obtained from a systematic search of studies published in 4 sport and exercise databases(Pubmed,Embase,SPORTDiscus(EBSCOhost),and Scopus)and a review of articles included in the 2011 Adult Compendium that measured PA in older *** values were computed as the oxygen cost(VO_(2),mL/kg/min)during PA divided by 2.7 m L/kg/min(mET_(60+))to account for the lower resting metabolic rate in older ***:We identified 68 articles and extracted energy expenditure data on 427 *** these,we derived 99 unique Specific Activity codes with corresponding mET_(60+)values for older *** developed a website to present the OA Compendium mET_(60+)values:https://***:The OA Compendium uses data collected from adults>60 years for more accurate estimation of the energy cost of PAs in older *** is an accessible resource that will allow researchers,educators,and practitioners to find mET_(60+)values for older adults for use in PA research and practice.

关键词： Energy expenditure Exercise mET Older adults

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