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SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses

Genomics, Proteomics & Bioinformatics 2022年第5期20卷 912-927页

作者： Alexandra j.Lee Dallas L.Mould j.ke Crawford Dongbo Hu Rani K.Powers Georgia Doing j.mes C.Costello Deborah A.Hogan Casey S.greene Genomics and Computational Biology Graduate Program University of PennsylvaniaPhiladelphiaPA 19104USA Department of Microbiology and Immunology Geisel School of Medicine at DartmouthHanoverNH 03755USA Department of Systems Pharmacology and Translational Therapeutics University of PennsylvaniaPhiladelphiaPA 19104USA Wyss Institute for Biologically Inspired Engineering Harvard UniversityBostonMA 02115USA Department of Pharmacology University of Colorado School of MedicineDenverCO 80045USA Center for Health AI University of Colorado School of MedicineDenverCO 80045USA Department of Biochemistry and Molecular Genetics University of Colorado School of MedicineDenverCO 80045USA

Genome-wide transcriptome profiling identifies genes that are prone to differential expression(DE)across contexts,as well as genes with changes specific to the experimental *** genes that are specifically changed in a context of interest from common differentially expressed genes(DEGs)allows more efficient prediction of which genes are specific to a given biological process under ***,common DEGs or pathways can only be identified through the laborious manual curation of experiments,an inordinately time-consuming *** we pioneer an approach,Specific cOntext Pattern Highlighting In Expression data(SOPHIE),for distinguishing between common and specific transcriptional patterns using a generative neural network to create a background set of experiments from which a null distribution of gene and pathway changes can be *** apply SOPHIE to diverse datasets including those from human,human cancer,and bacterial pathogen Pseudomonas *** identifies common DEGs in concordance with previously described,manually and systematically determined common *** molecular validation indicates that SOPHIE detects highly specific but low-magnitude biologically relevant transcriptional ***’s measure of specificity can complement log2 fold change values generated from traditional DE *** example,by filtering the set of DEGs,one can identify genes that are specifically relevant to the experimental condition of ***,these results can inform future research *** scripts used in these analyses are available at https://***/greenelab/*** can access https://***/greenelab/sophie to run SOPHIE on their own data.

关键词： Neural network Transcriptomics Software Differential expression analysis Machine learning

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One Hundred Years of Influenza Since the 1918 Pandemic—Is China Prepared Today?

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China CDC weekly 2019年第4期1卷 56-61页

作者： Ran Zhang Xiaoping Dong Dayan Wang Luzhao Feng Lei Zhou Ruiqi Ren Carolyn greene Ying Song Alexander j.Millman Eduardo Azziz-Baumgartner Zij.an Feng Influenza Division United States Centers for Disease Control and Prevention Chinese Center for Disease Control and Prevention BeijingChina Chinese National Influenza Center National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina

Almost 100 years after the 1918 influenza pandemic,China experienced its largest,most widespread epidemic of human infections with avian influenza A(H7N9),the influenza virus with the greatest pandemic potential of all influenza viruses assessed to date by the United States Centers for Disease Control and Prevention’s Influenza Risk Assessment *** historical review describes how China was affected by the 1918,1958,1968,and 2009 influenza pandemics,records milestones in China’s capacity to detect and respond to influenza threats,and identifies remaining challenges for pandemic *** review suggests that past influenza pandemics have improved China’s national capabilities such that China has become a global leader in influenza detection and *** enhancing China’s pandemic preparedness to address remaining challenges requires government commitment and increased investment in China’s public health and healthcare systems.

关键词： H7N9 demic remaining

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Development of a Portable Electronic Sensor for Detection of the Kudzu Bug, <i>Megacopta cribraria</i>(Fabricius) (Hemiptera: Plataspidae)

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Advances in Entomology 2017年第3期5卷 75-86页

作者： Brittany D. Lampson David C. Degenhardt j.remy K. greene Ahmad Khalilian Young j. Han Department of Agricultural Sciences Clemson University Clemson SC USA Ridge View High School Columbia SC USA Department of Plant and Environmental Sciences Clemson University Clemson SC USA

The kudzu bug, Megacopta cribraria (Fabricius), recently became an invasive insect pest of soybean, Glycine max (L.) Merr. in the southeastern USA capable of reducing crop yield by as much as 60% if left untreated. To reduce these losses and minimize control costs, new methods for detecting kudzu bugs must be investigated in order to optimize control measures. One such method would be to detect volatiles released by kudzu bugs. An electronic portable device was developed to draw volatile organic compounds (VOCs) produced by kudzu bugs over carbon black-polymer composite sensors and measure the change in resistance for each sensor. Sensors made using polymers poly (bisphenol A carbonate) (p = 0.041), poly (styrene-co-allyl alcohol) (p = 0.017) and poly (vinylpyrrolidone) (p = 0.040) showed significant differences in resistance change for M. cribraria VOCs over the control. A logistic regression was 94.4% accurate based on the resistance changes from sensors made from polymers poly (4-vinylphenol), poly (styrene-co-allyl alcohol), and poly (vinylpyrrolidone) as features. These results indicate the capability of the device to detect kudzu bugs by detecting volatiles released by the insects.

关键词： Carbon Black-Polymer Composites Integrated Pest Management (IPM) Megacopta cribraria Sensors Volatiles

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Emerging mechanisms for exercise effects on muscle wasting and anabolic resistance

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Sports Medicine and Health Science 2020年第4期2卷 175-176页

作者： j.William Deaver Nicholas P.greene Cachexia Research Laboratory Exercise Science Research CenterDepartment of HealthHuman Performance and RecreationUniversity of ArkansasFayettevilleARUSA Muscle Biology Laboratory Department of Health and KinesiologyTexas A&M UniversityCollege StationTXUSA

Introduction At the 2018 Annual Meeting of the American College of Sports Medicine,presentations were given by *** ***,j.mes ***,and j.mes ***,at a symposium titled“Emerging Mechanisms for Exercise Effects on Muscle Wasting and Anabolic Resistance”.Inspired by the presentations at this symposium,the following reviews have been crafted to examine the current understanding of muscle diseases characterized by muscle wasting and anabolic resistance,particularly their identification,development,progression,and mitigation.

关键词： resistance mechanisms muscle

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吐哈盆地煤成烃研究

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石油学报 2002年第4期23卷 13-17页

作者：程克明熊英曾晓明 j.M.Moldowan j.greene.Todd 中国石油勘探开发研究院北京100083 吐哈油田研究院新疆哈密839009 斯坦福大学地球科学系

根据原油生物标记化合物有关参数的聚类分析 ,将吐哈盆地原油分成源于侏罗纪煤系沼泽相 (包括煤为源岩 )的第一类原油 ,源于中、下侏罗统过渡相富藻碳质泥岩和富藻煤的第二类原油和源于上二叠统塔尔郎组湖相泥岩的第三类原油。根据原油... 详细信息

根据原油生物标记化合物有关参数的聚类分析 ,将吐哈盆地原油分成源于侏罗纪煤系沼泽相 (包括煤为源岩 )的第一类原油 ,源于中、下侏罗统过渡相富藻碳质泥岩和富藻煤的第二类原油和源于上二叠统塔尔郎组湖相泥岩的第三类原油。根据原油中生物标记物的年代学特征 ,提出利用二萜烷指数将侏罗系的原油 (二萜烷指数 >0 8)与上二叠统的原油 (二萜烷指数 <0 5 )加以区别的方法。根据不同沉积相带原油和相应源岩饱和烃组分中17 降扁枝烷和 5a 雄甾烷以及芳烃中的三芳甾系列化合物进行了精细的油源对比 ,确定了本区三类原油的 17 降扁枝烷、5a 雄甾烷和三芳甾系列化合物的分布特征及沉积相序关系 ,进一步从油源对比的角度证明了本区存在源于中、下侏罗统的具有商业价值的煤成油。

关键词：吐哈盆地煤成烃聚类分析二萜烷烷指数三芳甾烷断代生物标记物

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符合收缩压干预试验标准的美国成人强化收缩压治疗的人群健康获益估计

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中华高血压杂志(中英文) 2024年第8期 800-800页

作者： Derington CG Bress PA Berchie RO Herrick j. Shen j. Ying j.greene T Taj.u GS Sakhuj. S Ruiz-Negrón N Zhang YY Howard G Levitan EB Muntner P Safford MM Whelton PK Weintraub WS Moran AE Bellows BK 袁源练桂丽

收缩压干预试验(systolic blood pressure inter-vention trial,SPRINT)表明,与标准目标收缩压(<140 mm Hg)相比,强化收缩压目标(<120 mm Hg)可降低心血管疾病(cardiovascular disease,CVD)风险。对最有可能获益的符合SPRINT标准的成年患者进行强化降压效果的评估可用于指导临床实践。方法:研究者评估SPRINT参与者及在脑卒中的地理和种族差异原因(reasons for geographic and racial differ-ences in stroke,REGARDS)研究及美国国家健康和营养调查(national health and nutrition examination surveys,NHANES)中符合SPRINT标准的参与者。

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联想、记忆和学习

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环球科学 2010年第9期 72-77页

作者：安东尼·j.格林（Anthony j.greene）周林文（翻译）

很多人希望自己的记忆力像摄像机一样。那该有多方便啊：如果忘记车钥匙放哪儿了，只要从上次拿着钥匙的时候开始“播放”．就能找到它们；我们再也不会错过约会或者忘记还款，会记住每个人的生日，还会在每场考试中拿高分。

关键词：记忆力联想学习摄像机钥匙忘记高分考试

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TILLING and Ecotilling the Plant Kingdom

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分子植物育种 2007年第2期5卷 238-239页

作者： B. Till j. Cooper C. Codomo A. Holm M. Darlow E. greene L. Comai S. Henikoff Fred Hutchinson Cancer Research Center 1100 Fairview Ave N Seattle WA 98109-1024 USA Section of Plant Biology and Genome Center UC Davis Davis California 95616 USA

The modern crop scientist has a large amount of available nucleotide sequence information to identify genes of potential agronomic importance. Using reverse genetic approaches, specifi c genes can be disrupted, and hy-

关键词：基因突变植物耕种

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卡斯特地区的公路设计

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广西地质 1999年第2期12卷 75-77页

作者： j.seph A. Fischer j. Fischer R.W.greene 美国新泽西州地球科学部

１场地考察第一步是利用现有岩土工程资料，如州和政府的资料、航空照片、卫星图像和设计单位的数据库。这些对考察卡斯特地区有用的资料包括：（１）详细地图（这些地图不全发表），一些州的调查实际上包含有碳酸盐岩石详细地图，从中... 详细信息

１场地考察第一步是利用现有岩土工程资料，如州和政府的资料、航空照片、卫星图像和设计单位的数据库。这些对考察卡斯特地区有用的资料包括：（１）详细地图（这些地图不全发表），一些州的调查实际上包含有碳酸盐岩石详细地图，从中可了解到已知的或可疑落水洞地区。（...

关键词：卡斯特地区公路设计场地考察

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Electroosmotic Water Vapor Transport across Novel, Smart, Functionalized Conducting Polymer Microporous Membranes in Active Mode at Very High Rates, with Concomitant Chemical Warfare (CW) Agent Blocking

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Advances in Materials Physics and Chemistry 2013年第4期3卷 217-237页

作者： Prasanna Chandrasekhar Petar Pirgov Brian j. Zay David Lawrence Sean Morefield Tilghman L. Rittenhouse Salvatore G. Clementi Quoc Truong Russell R. greene Ashwin-Ushas Corporation Marlboro NJ USA Chemical and Biological Technologies Directorate US Defense Threat Reduction Agency (DTRA) Fort Belvoir VA USA Hazardous Materials Research Center (HMRC) Battelle Columbus Laboratories Battelle Memorial Institute Columbus OH USA US Army Engineer Research and Development Center Construction Engineering Research Laboratory (ERDC-CERL) Champaign IL USA Warrior Science Technology and Applied Research Directorate US Army Natick Soldier Research Development and Engineering (RD&E) Center Natick MA USA

Electroosmotic water vapor transport (WVT) across very thin, flexible, functionalized conducting polymer (CP) microporous (μP) membranes at a very high rate is reported. Both passive and active (6 VDC applied) WVT are reported, the latter for the first time ever. WVT occurs with concomitant, effective blocking of chemical warfare (CW) agents, again demonstrated for the first time ever. Initial active liquid||membrane||liquid interface studies demonstrated WVT rates of >1.7 × 10-5g .mm-2s-1, >3 × the highest prior reported values of 5 × ***-2s-1. Subsequent vapor||membrane|| vapor interface studies using industry-standard methods (including ASTM E96B Upright Cup (“WVT”), ASTM F2298 (“Dynamic Moisture Permeation Cell”) and ASTM F1868 (“Sweating Guard Hotplate”) were done at independent, external labs for independent corroboration. These yielded, e.g., WVT values of2564.4 g.m2.d-1 (passive) and3706.7 g.m2d-1 (active), to be compared with the highest (passive) value ever reported previously,984.8 g.m2.d-1 for a μP-Nylon membrane. More than 15 different membrane configurations, porosities and types were studied, including membranes with CP + organophosphate hydrolase (OPH), an enzyme reactive to CW agents. Efficient blocking of the actual CW agents GB, HD, VX is also reported, using the TOP-8-2-501standard. Membranes also passed all Industry-standard durability tests, e.g. ASTM D2261 (Tearing), ASTM D5034 (Breaking), ASTM D3886 (Abrasion), ASTM F392 (Gelbo Flex). Incorporation into smart soldiers’ garments was demonstrated;power consumption was -2. Mechanisms of enhanced WVT and CW agent blocking in the membranes are discussed.

关键词： Electroosmotic Transport Smart Microporous Membrane Conducting Polymer Functionalized

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