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An analysis of quantitative PCR reliability through replicates using the C_(t)method

Journal of Biomedical Science and Engineering 2010年第5期3卷 459-469页

作者： Chris C.Stowers Frederick R.Haselton erik m.boczko Bioprocess R&D Division Dow AgroSciences LLC Indianapolis IndianaUSA Department of Biomedical Engineering Vanderbilt University Nashville NashvilleUSA Department of Biomedical Informatics Vanderbilt University medical Center Nashville NashvilleUSA

There is considerable interest in quantitatively measuring nucleic acids from single cells to small populations. The most commonly employed laboratory method is the real-time polymerase chain reaction (PCR) analyzed with the crossing point or crossing threshold (Ct) method. Utilizing a multiwell plate reader we have performed hundreds of replicate reactions each at a set of initial conditions whose initial number of copies span a concentration range of ten orders of magnitude. The resultant Ct value distributions are analyzed with standard and novel statistical techniques to assess the variability/reliability of the PCR process. Our analysis supports the following conclusions. Given sufficient replicates, the mean and/or median Ct values are statistically distinguishable and can be rank ordered across ten orders of magnitude in initial template concentration. As expected, the variances in the Ct distributions grow as the number of initial copies declines to 1. We demonstrate that these variances are large enough to confound quantitative classi?cation of the initial condition at low template concentrations. The data indicate that a misclassi?cation transition is centered around 3000 initial copies of template DNA and that the transition region correlates with independent data on the thermal wear of the TAQ polymerase enzyme. We provide data that indicate that an alternative endpoint detection strategy based on the theory of well mixing and plate ?lling statistics is accurate below the mis- classi?cation transition where the real time method becomes unreliable.

关键词： misclassification Transition Single molecule Counting Rank Ordering Running Title PCR Replicates and Reliability

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Importance of periphytic biofilms for carbon cycling in paddy fields:A review

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Pedosphere 2024年第1期34卷 36-43页

作者： Lei ZHOU Yonghong WU Junzhuo LIU Pengfei SUN Ying XU Jan DOLFING Robert GmSPENCER erik JEPPESEN 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 College of Nanjing University of Chinese Academy of SciencesNanjing 211135China Faculty of Energy and Environment Northumbria UniversityNewcastle upon Tyne NE18QHUK Department of Earth Ocean and Atmospheric ScienceFlorida State UniversityTallahassee FL 32306USA Department of Ecoscience&Centre for Water Technology(WATEC) Aarhus UniversityAarhus DK-8000Denmark Sino-Danish Centre for Education and Research Beijing 100049China Limnology Laboratory Department of Biological Sciences and Centre for Ecosystem Research and Implementation(EKOSAM)Middle East Technical UniversityAnkara 06800Turkiye Institute of marine Sciences Middle East Technical UniversityMersin 33731Turkiye

Paddy fields play an important role in global carbon(C) cycling and are an important source of methane(CH_(4)) emissions. Insights into the processes influencing the dynamics of soil organic C(SOC) in paddy fields are essential for maintaining global soil C stocks and mitigating climate change. Periphytic biofilms composed of microalgae, bacteria, and other microorganisms are ubiquitous in paddy fields, where they directly mediate the transfer of elements at the soil-water interface. However, their contributions to C turnover and exchange have been largely neglected. Periphytic biofilms affect and participate in soil C dynamics by altering both abiotic(e.g., pH and redox potential) and biotic conditions(e.g., microbial community composition and metabolism). This review summarizes the contributions of periphytic biofilms to soil C cycling processes, including carbon dioxide fixation, SOC mineralization, and CH_(4) emissions. Future research should be focused on: i) the mechanisms underlying periphytic biofilm-induced C fixation and turnover and ii) quantifying the contributions of periphytic biofilms to soil C uptake, stabilization, and sequestration in paddy fields.

关键词： carbon fixation carbon mineralization carbon sequestration methane emission microbial aggregates soil organic carbon

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Structure-based design and optimization lead to the identification of novel dihydrothiopyrano[3,2-d]pyrimidine derivatives as potent HIV-1 inhibitors against drug-resistant variants

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Acta Pharmaceutica Sinica B 2024年第3期14卷 1257-1282页

作者： Zhao Wang Heng Zhang Zhen Gao Zihao Sang erik De Clercq Christophe Pannecouque Dongwei Kang Peng Zhan Xinyong Liu Department of medicinal Chemistry Key Laboratory of Chemical Biology(Ministry of Education)School of Pharmaceutical SciencesCheeloo College of MedicineShandong UniversityJinan 250012China Rega Institute for medical Research Laboratory of Virology and ChemotherapyK.U.LeuvenLeuven B-3000Belgium China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province Jinan 250012China Suzhou Research Institute Shandong UniversitySuzhou 215123China

With our continuous endeavors in seeking potent anti-HIV-1 agents,we reported here the discovery,biological characterization,and druggability evaluation of a class of nonnucleoside reverse transcriptase *** fully explore the chemical space of the NNRTI-binding pocket,novel series of dihydrothiopyrano[3,2-d]pyrimidines were developed by employing the structure-based design *** of the derivatives were endowed with prominent antiviral activities against HIV-1 wild-type and resistant strains at nanomolar *** them,compound 23h featuring the aminopiperidine moiety was identified as the most potent inhibitor,with EC50values ranging from 3.43 to 21.4 nmol/***,for the challenging double-mutants F227L+V106A and K103N+Y181C,23h exhibited 2.3-to 14.5-fold more potent activity than the first-line drugs efavirenz and ***,the resistance profiles of 23h achieved remarkable improvement compared to efavirenz and *** binding target of 23h was further confirmed to be HIV-1 reverse *** modeling studies were also performed to elucidate the biological evaluation results and give guidance for the optimization ***,no apparent inhibition of the major CYP450 enzymes and hERG channel was observed for *** importantly,23h was characterized by good pharmacokinetic properties and excellent safety in ***,23h holds great promise as a potential candidate for its effective antiviral efficacy and favorable drug-like profiles.

关键词： HIV-1 Reverse transcriptase Dihydrothiopyrano[3,2-d]pyrimidine Antiviral agent

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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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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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Why ecosystem characteristics predicted from remotely sensed data are unbiased and biased at the same time-and how this affects applications

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Forest Ecosystems 2024年第1期11卷 24-31页

作者： Goran Ståhl Terje Gobakken Svetlana Saarela Henrik J.Persson magnus Ekstrom Sean P.Healey Zhiqiang Yang Johan Holmgren Eva Lindberg Kenneth Nystrom Emanuele Papucci Patrik Ulvdal Hans OleØrka erik Næsset Zhengyang Hou Håkan Olsson Ronald E.mcRoberts Department of Forest Resource management Swedish University of Agricultural Sciences90183UmeåSweden Faculty of Environmental Sciences and Natural Resource management Norwegian University of Life SciencesÅsNorway USDA Forest Service Rocky Mountain Research StationOgdenUTUSA The Key Laboratory for Silviculture and Conservation of ministry of Education Beijing Forestry UniversityBeijing100083China Department of Forest Resources University of MinnesotaSt.PaulMNUSA

Remotely sensed data are frequently used for predicting and mapping ecosystem characteristics,and spatially explicit wall-to-wall information is sometimes proposed as the best possible source of information for ***,wall-to-wall information typically relies on model-based prediction,and several features of model-based prediction should be understood before extensively relying on this type of *** such feature is that model-based predictors can be considered both unbiased and biased at the same time,which has important implications in several areas of *** this discussion paper,we first describe the conventional model-unbiasedness paradigm that underpins most prediction techniques using remotely sensed(or other)auxiliary *** this point of view,model-based predictors are typically ***,we show that for specific domains,identified based on their true values,the same model-based predictors can be considered biased,and sometimes severely *** suggest distinguishing between conventional model-bias,defined in the statistical literature as the difference between the expected value of a predictor and the expected value of the quantity being predicted,and design-bias of model-based estimators,defined as the difference between the expected value of a model-based estimator and the true value of the quantity being *** show that model-based estimators(or predictors)are typically design-biased,and that there is a trend in the design-bias from overestimating small true values to underestimating large true ***,we give examples of applications where this is important to acknowledge and to potentially make adjustments to correct for the design-bias *** argue that relying entirely on conventional model-unbiasedness may lead to mistakes in several areas of application that use predictions from remotely sensed data.

关键词： Bias model-based inference Design-based inference

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Colloidal quantum dot for infrared-absorbing solar cells:State-oftheart and prospects

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Nano Research Energy 2024年第1期3卷 172-219页

作者： Siyu Zheng Xinyi mei Jingxuan Chen erik mJJohansson Xiaoliang Zhang School of materials Science and Engineering Beihang UniversityBeijing 100191China Department of Chemistry-Ångström Physical ChemistryUppsala UniversityUppsala 75120Sweden

Colloidal quantum dot(CQD)shows great potential for application in infrared solar cells due to the simple synthesis techniques,tunable infrared absorption spectrum,and high stability and *** to significant efforts made on the surface chemistry of CQDs,device structure optimization,and device physics of CQD solar cells(CQDSCs),remarkable breakthroughs are achieved to boost the infrared photovoltaic performance and stability of *** particular,the CQDSC with a high power conversion efficiency of~14%and good stability is reported,which is very promising for infrared-absorbing solar *** this review,we highlight the unique optoelectronic properties of CQDs for the development of infrared-absorbing solar ***,the latest advances in finely controlling surface properties of CQDs are comprehensively summarized and ***,the device operation of CQDSCs is discussed in-depth to highlight the impact of the device structure optimization of CQDSCs on their photovoltaic performance,and the emerging novel types of CQDSCs,such as semitransparent,flexible,and lightweight CQDSCs,are also *** device stability of CQDSCs is also highlighted from the viewpoint of practical ***,the conclusions and possible challenges and opportunities are presented to promote the development steps of the CQDSCs with higher infrared photovoltaic performance and robust stability.

关键词： colloidal quantum dot solar cell photovoltaic performance infrared absorbing solar energy

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Increased CO2 Levels during the First Half of Incubation at High Altitude modifies Embryonic Development of Fertile Leghorn Breeder Eggs

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Food and Nutrition Sciences 2024年第7期15卷 524-547页

作者： marco A. Juárez-Estrada erik I. López-Ruiz Sonia López-Cordova Guillermo Tellez-Isaias Omar F. Prado-Rebolledo Departamento de medicina y Zootecnia de Aves Facultad de Medicina Veterinaria y Zootecnia Universidad Nacional Autnoma de Mxico Ciudad de Mxico Mxico Department of Poultry Science Division of Agriculture University of Arkansas Fayetteville USA Facultad de medicina Veterinaria y Zootecnia Universidad de Colima Tecomn Mxico

The exchange of oxygen (O2) and carbon dioxide (CO2) within an incubator has a significant impact on embryonic development (ED) and hatching processes. This study examines the influence of non-ventilation (NV) conditions during the first ten days of incubation at high altitudes on Leghorn hens hatching eggs. Five hundred four hatching eggs were equally divided into three treatment groups and placed in twelve incubators (R = 4). The first group was subjected to standard ventilated conditions (V) during the setting phase. The ventilation inlet holes of the remaining incubators in the NV treatments were closed with either micropore (m) or polypropylene (P) tape, referred to as NVm and NVP groups, respectively. These two different airtight settings were intended to allow for a gradual rise in CO2 naturally generated by the embryos. Results indicate that carbon dioxide concentration gradually increased during the first half of incubation, reaching 1.42% in the NVm group and 1.20% in the NVP group, while the V condition group remained at 0.15%. From 10 days of incubation onwards, normal V conditions were restored in all incubators. The highest hatchability of fertile eggs (HFE) was shown by the NVP group (55.7%), followed by the V (52.6%) and NVm (38.6%) groups. The NVP group showed a greater yolk-free body mass (YFBm) from 10 days of incubation until the hatch basket transfer. NV conditions during the first 10 days of incubation at high altitude produced higher YFBm with gradually decreasing yolk sac mass. In comparison to the NVm and V conditions, the particular NVP condition showed a beneficial impact on the quality of hatched chicks. Sustaining NVP condition (1.2% of CO2) throughout the first half of incubation at high altitude generated the optimal environment in the incubator ensuring the best hatchability results. This study highlights how important it is for hatchery managers to recognize the influence of low O2 and high levels of CO2 on the development trajectori

关键词： Non-Ventilation Hypercapnia Hypoxia Egg mass Loss Hatchability Embryonic mortality Hatchling Chick Quality

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A sequential estimation problem with control and discretionary stopping

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Probability, Uncertainty and Quantitative Risk 2022年第3期7卷 151-168页

作者： erik Ekström Ioannis Karatzas Department of mathematics Uppsala UniversityBox 25675105 UppsalaSweden Departments of mathematics and Statistics Columbia University2990 BroadwayNew YorkNY 10027USA

We show that“full-bang”control is optimal in a problem which combines features of(i)sequential least-squares estimation with Bayesian updating,for a random quantity observed in a bath of white noise;(ii)bounded control of the rate at which observations are received,with a superquadratic cost per unit time;and(iii)“fast”discretionary *** develop also the optimal filtering and stopping rules in this context.

关键词： Sequential analysis Filtering Optimal stopping Stochastic control Bold play

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Controlling membrane Phase Separation of Polymersomes for Programmed Drug Release

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Chinese Journal of Polymer Science 2022年第9期40卷 1006-1015页

作者： Shuai Chen erik Jan Cornel Jian-Zhong Du Department of Orthopedics Shanghai Tenth People’s HospitalSchool of MedicineTongji UniversityShanghai 200072China Department of Polymeric materials School of Materials Science and EngineeringTongji UniversityShanghai 201804China

Programmed release of small molecular drugs from polymersomes is of great importance in drug delivery.A significant challenge is to adjust the membrane permeability in a well-controlled ***,we propose a strategy for controlling membrane phase separation by photo-cross-linking of the membrane-forming blocks with different molecular *** synthesized three amphiphilic block copolymers with different membrane-forming blocks,which are poly(ethylene oxide)_(43)-b-poly((ε-caprolactone)_(45)-stat-((α-(cinnamoyloxymethyl)-1,2,3-triazol)caprolactone)_(25))(PEO_(43)-b-P(CL_(45)-stat-CTCL_(25))),PEO_(43)-b-P(CL_(108)-stat-CTCL_(16)),and PEO_(43)-b-PCTCL_(4)-b-PCL_(79).These polymers were self-assembled into polymersomes using either a solvent-switch or powder rehydration method,and the obtained polymersomes were characterized by dynamic light scattering and transmission electron *** the phase separation patterns within the polymersome membranes were investigated by mesoscopic dynamics(mesoDyn)*** further confirm the change of the membrane permeability that resulted from the phase separation within the membrane,doxorubicin,as a small molecular drug,was loaded and released from the *** to the incompatibility between membrane-forming moieties(PCTCL and PCL),phase separation occurs and the release rate can be tuned by controlling the membrane phase pattern or by ***,besides the compacting effect by formation of chemical bonds in the membrane,the cross-linking process can act as a driving force to facilitate the rearrangement and re-orientation of the phase pattern,which also influences the drug release behavior by modulating the cross-membrane distribution of the amorphous PCTCL *** this way,the strategy of focusing on the membrane phase separation for the preparation of the polymersomes with finely tunable drug release rate can be envisioned and designed accordingly,which is of great signifi

关键词： Polymersome Drug delivery Phase separation Programmed drug release

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