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Interaction specific binding hotspots in Endonuclease colicin-immunity protein complex from md simulations

Science China Chemistry 2013年第8期56卷 1143-1151页

作者： YAO XueXia JI ChangGe XIE DaiQian ZHANG john Z.H. School of Chemistry and Chemical Engineering Nanjing University College of Engineering Nanjing Agricultural University State Key Laboratory of Precision Spectroscopy Department of PhysicsEast China Normal University Department of Chemistry New York University

The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the *** the current work,md simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot *** changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding *** decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to *** binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant *** comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental *** hydrogen bond analysis showed that conformations sampled from md simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein *** current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.

关键词： protein-protein interaction binding hotspot mutation Endonuclease Colicin immunity protein md simulation

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Predictive biomarkers in precision medicine and drug development against lung cancer

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Chinese Journal of Cancer 2015年第7期34卷 295-309页

作者： Bingliang Fang Reza J Mehran john V Heymach Stephen G Swisher Department of Thoracic and Cardiovascular Surgery The University of Texas MD Anderson Cancer Center Department of Thoracic and Head/Neck Medical Oncology The University of Texas MD Anderson Cancer Center

The molecular characterization of various cancers has shown that cancers with the same origins,histopathologic diagnoses,and clinical stages can be highly heterogeneous in their genetic and epigenetic alterations that cause tumorigenesis.A number of cancer driver genes with functional abnormalities that trigger malignant transformation and that are required for the survival of cancer cells have been *** agents targeting some of these cancer drivers have been successfully developed,resulting in substantial improvements in clinical symptom amelioration and outcomes in a subset of cancer ***,because such therapeutic drugs often benefit only a limited number of patients,the successes of clinical development and applications rely on the ability to identify those patients who are sensitive to the targeted ***,biomarkers that can predict treatment responses are critical for the success of precision therapy for cancer patients and of anticancer drug *** review discusses the molecular heterogeneity of lung cancer pathogenesis;predictive biomarkers for precision medicine in lung cancer therapy with drugs targeting epidermal growth factor receptor(EGFR),anaplastic lymphoma kinase(ALK),c-ros oncogene 1 receptor tyrosine kinase[ROSl),and immune checkpoints;biomarkers associated with resistance to these therapeutics;and approaches to identify predictive biomarkers in anticancer drug *** identification of predictive biomarkers during anticancer drug development is expected to greatly facilitate such development because it will increase the chance of success or reduce the attrition ***,such identification will accelerate the drug approval process by providing effective patient stratification strategies in clinical trials to reduce the sample size required to demonstrate clinical benefits.

关键词：生物标志物药物开发预测肺癌医学受体酪氨酸激酶表皮生长因子受体治疗药物

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Predicting pavement condition index based on the utilization of machine learning techniques:A case study

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道路工程学报(英文) 2023年第3期3卷 266-278页

作者： Abdualmtalab Abdualaziz Ali Abdalrhman Milad Amgad Hussein Nur Izzi md Yusoff Usama Heneash Department of Civil Engineering Faculty of Engineering and Applied ScienceMemorial UniversitySt.John'sNL A1B1T5Canada Department of Civil Engineering Faculty of EngineeringAzzaytuna UniversityTarhunaLibya Department of Civil and Environmental Engineering College of EngineeringUniversity of NizwaNizwaOman Department of Civil Engineering Universiti Kebangsaan MalaysiaBangi 43600Malaysia Department of Civil Engineering Faculty of EngineeringKafrelsheikh UniversityKafr El-SheikhEgypt

Pavement management systems(PMS)are used by transportation government agencies to promote sustainable development and to keep road pavement conditions above the minimum performance levels at a reasonable *** accomplish this objective,the pavement condition is monitored to predict deterioration and determine the need for maintenance or rehabilitation at the appropriate *** pavement condition index(PCI)is a commonly usedmetric to evaluate the pavement's *** research aims to create and evaluate prediction models for PCI values using multiple linear regression(MLR),artificial neural networks(ANN),and fuzzy logic inference(FIS)models for flexible pavement *** authors collected field data spans for 2018 and *** pavement distress factors were considered inputs for predicting PCI values,such as rutting,fatigue cracking,block cracking,longitudinal cracking,transverse cracking,patching,potholes,and *** study evaluates the performance of the three techniques based on the coefficient of determination,root mean squared error(RMSE),and mean absolute error(MAE).The results show that the R2 values of the ANN models increased by 51.32%,2.02%,36.55%,and 3.02%compared toMLR and FIS(2018 and 2021).The error in the PCI values predicted by the ANNmodel was significantly lower than the errors in the prediction by the FIS and MLR models.

关键词： Pavement condition index Pavement distresses Machine learning Artificial neural network Multiple linear regression

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LC-HRMS Based Non-Targeted Metabolomic Profiling of Wheat (<I>Triticum aestivum</I>L.) under Post-Anthesis Drought Stress

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American Journal of Plant Sciences 2017年第12期8卷 3024-3061页

作者： Mohammad Atikur Rahman Masum Akond md Ali Babar Chris Beecher john Erickson Kayla Thomason Felice A De Jong Richard Esten Mason Agronomy Department IFAS University of Florida Gainesville FL USA Southeast Center for Integrated Metabolomics (SECIM) University of Florida Gainesville FL USA IROA Technologies LLC Ann Arbor MI USA Crop Soil and Environmental Sciences University of Arkansas Fayetteville AR USA

Drought stress at the reproductive stage causes severe damage to productivity of wheat. However, little is known about the metabolites associated with drought tolerance. The objectives of this study were to elucidate changes in metabolite levels in wheat under drought, and to identify potential metabolites associated with drought stress through untargeted metabolomic profiling using a liquid chromatography-high resolution mass spectrometry (LC-HRMS)-based technique called Isotopic Ratio Outlier Analysis. Metabolomic analysis was performed on flag leaves of drought-stressed and control (well-watered) plants after 18 days of post-anthesis drought stress at three-hour intervals over a 24-hour period. Out of 723 peaks detected in leaves, 221 were identified as known metabolites. Sixty known metabolites were identified as important metabolites by 3 different methods, PLS-DA, RF and SAM. The most pronounced accumulation due to drought stress was demonstrated by tryptophan, proline, pipecolate and linamarin, whereas the most pronounced decrease was demonstrated by serine, trehalose, N-acetyl-glutamic acid, DIBOA-glucoside etc. Three different patterns of metabolite accumulation were observed over 24-hour period. The increased accumulated metabolites remained higher during all 8 time points in drought stressed leaves. On the contrary, metabolites that showed decreased level remained significantly lower during all or the most time points. However, the levels of some decreased metabolites were lower during the day, but higher during night in drought stressed leaves. Both univariate and multivariate analyses predicted that N-acetyl-glutamic acid, proline, pipecolate, linamarin, tryptophan, and DIBOA-glucoside could be potential metabolite biomarkers, and their levels could serve as indicators of drought tolerance in wheat.

关键词： Drought Post-Anthesis Wheat Metabolites LC-MS

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为远期获益密切监测开腹行腹主动脉手术患者的心肌肌钙蛋白具有成本效益：一种决策分析模型

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麻醉与镇痛 2009年第2期5卷 6-17页

作者： Srinivas Mantha, md Joseph Foss, md john E. Ellis, md Michael F. Roizen md 桂波(译) 李静(译) Department of Anesthesiology Nizam's Institute of Medical Sciences Hyderabad Andhra Pradesh India Department of Anesthesiology The Cleveland Clinic Foundation Cleveland Ohio and Department of Anesthesiology and Critical Care The University of Chicago Chicago Illinois 不详

背景控制血管手术后心脏不良事件的策略在不断改进。早期发现和处理心肌缺血是提高手术后生存率的关键因素。心肌肌钙蛋白Ⅰ（cTnⅠ）的筛查是监测手术后心肌缺血性损伤的有效方法，并具有长期的预后价值。方法我们设计了一个马尔柯夫... 详细信息

背景控制血管手术后心脏不良事件的策略在不断改进。早期发现和处理心肌缺血是提高手术后生存率的关键因素。心肌肌钙蛋白Ⅰ（cTnⅠ）的筛查是监测手术后心肌缺血性损伤的有效方法，并具有长期的预后价值。方法我们设计了一个马尔柯夫决策分析模型来评估手术后第0、1、2、3天常规监测cTnⅠ的成本效益，其目的还在于将手术后cTnⅠ〉1．5ng/ml的患者移入重症监护病房观察5天，严格控制目标心率（60～65次／分），并进行严密监测和冠状动脉监护。根据已发表的文献所输入的主要变量如下：心肌梗死的概率0．049；监测cTnⅠ的成本为357美元；干预的成本和效率分别为13145美元和0．55。以寿命为时间轴，目标人群是平均年龄为65岁的行择期开腹腹主动脉手术的患者。此研究分析的费用来自第3方。结果相对于没有监测cTnⅠ的对照组，每个生命质量调整年用于监测cTnⅠ增加的成本效益为12641美元。单因素方差分析显示心肌梗死的可能性和干预的效能会影响成本效益。采用二次合并蒙特卡罗模拟分析行多因素敏感性分析显示，在每个生命质量调整年用低于50000美元的费用监测cTnⅠ，其获益率可达到90．75％。结论对于择期行开腹腹主动脉手术的住院患者，加强cTnⅠ监测并早期积极地使用β-受体阻滞剂会带来成本效益。

关键词：心肌肌钙蛋白Ⅰ 腹主动脉手术常规监测成本效益决策分析开腹模型心肌缺血性损伤

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Tracking domestic ducks:A novel approach for documenting poultry market chains in the context of avian influenza transmission

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Journal of Integrative Agriculture 2016年第7期15卷 1584-1594页

作者： Chang-Yong Choi john Y Takekawa XIONG Yue LIU Ying Martin Wikelski George Heine Diann J Prosser Scott H Newman john Edwards Fusheng Guo Xiangming Xiao Department of Microbiology and Plant Biology Center for Spatial AnalysisUniversity of OklahomaNormanOK 73019USA Western Ecological Research Center U.S.Geological SurveyVallejoCA 94592USA National Audubon Society San FranciscoCA 94104USA Key Laboratory of Poyang Lake Wetland and Watershed Research Jiangxi Normal UniversityNanchang 330022P.R.China Department of Migration and Immuno-Ecology Max Planck Institute for OrnithologyRadolfzell D-78315Germany Department of Biology University of KonstanzKonstanz D-78457Germany Patuxent Wildlife Research Center U.S.Geological SurveyBeltsvilleMD 20705USA Emergency Center for Transboundary Animal Diseases(ECTAD)Vietnam Office Food and Agriculture Organization of the United NationsHanoi 10000Vietnam Emergency Center for Transboundary Animal Diseases(ECTAD)China Office Food and Agriculture Organization of the United NationsBeijing 100600P.R.China Murdoch University MurdochWA 6150Australia Institute of Biodiversity Sciences Fudan UniversityShanghai 200433P.R.China

Agro-ecological conditions associated with the spread and persistence of highly pathogenic avian inlfuenza （HPAI） are not well understood, but the trade of live poultry is suspected to be a major pathway. Although market chains of live bird trade have been studied through indirect means including interviews and questionnaires, direct methods have not been used to identify movements of individual poultry. To bridge the knowledge gap on quantitative movement and transportation of poultry, we introduced a novel approach for applying telemetry to document domestic duck movements from source farms at Poyang Lake, China. We deployed recently developed transmitters that record Global Positioning System （GPS） locations and send them through the Groupe Spécial Mobile （GSM） cellular telephone system. For the ifrst time, we were able to track individually marked ducks from 3 to 396 km from their origin to other farms, distribution facilities, or live bird markets. Our proof of concept test showed that the use of GPS-GSM transmitters may provide di-rect, quantitative information to document the movement of poultry and reveal their market chains. Our ifndings provide an initial indication of the complexity of source-market network connectivity and highlight the great potential for future telemetry studies in poultry network analyses.

关键词： avian inlfuenza domestic duck market chain network poultry telemetry

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A global,high-resolution(30-m)inland water body dataset for 2000:first results of a topographic-spectral classification algorithm

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International Journal of Digital Earth 2016年第2期9卷 113-133页

作者： Min Feng Joseph O.Sexton Saurabh Channan john R.Townshend Global Land Cover Facility Department of Geographical SciencesUniversity of MarylandCollege ParkMDUSA

The science and management of terrestrial ecosystems require accurate,high-resolution mapping of surface *** produced a global,30-m-resolution inland surface water dataset with an automated algorithm using Landsat-based surface reflectance estimates,multispectral water and vegetation indices,terrain metrics,and prior coarse-resolution water *** dataset identified 3,650,723 km2 of inland water globally–nearly three quarters of which was located in North America(40.65%)and Asia(32.77%),followed by Europe(9.64%),Africa(8.47%),South America(6.91%),and Oceania(1.57%).Boreal forests contained the largest portion of terrestrial surface water(25.03%of the global total),followed by the nominal‘inland water’biome(16.36%),tundra(15.67%),and temperate broadleaf and mixed forests(13.91%).Agreement with respect to the Moderate-resolution Imaging Spectroradiometer water mask and Landsat-based national land-cover datasets was very high,with commission errors<4%and omission errors<14%relative to *** of these were accounted for in the seasonality of water cover,snow and ice,and clouds–effects which were compounded by differences in image acquisition date relative to reference *** Global Land Cover Facility(GLCF)inland surface water dataset is available for open access at the GLCF website(http://***).

关键词： inland water Landsat global high resolution MODIS

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Antimicrobial activity of kojic acid from endophytic fungus Colletotrichum gloeosporioides isolated from Sonneratia apetala,a mangrove plant of the Sundarbans

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Asian Pacific Journal of Tropical Medicine 2018年第5期11卷 350-354页

作者： Tauhidur Rahman Nurunnabi Shaymaa Al-Majmaie Ismini Nakouti Lutfun Nahar S.M.Mahbubur Rahman md.Hossain Sohrab md.Morsaline Billah Fyaz M.D.Ismail George P.Sharples Satyajit D.Sarker Medicinal Chemistry and Natural Products Research Group School of Pharmacy and Biomolecular SciencesLiverpool John Moores University Biotechnology and Genetic Engineering Discipline Khulna University Pharmaceutical Sciences Research Division BCSIR Laboratories

Objective: To isolate and evaluate the antimicrobial activity of the active principle(s) from the ethyl acetate(EtOAc) extract of endophytic fungus Colietotrichum gloeosporioides(***) isolated from Sonneratia apetala. Methods: Water agar technique was used to isolate the fungus, and both microscopic and molecular techniques were used for identification of the strain. Potato dextrose broth was used to grow the fungus in large-scale. Reversed-phase preparative HPLC analysis was performed to isolate the major active compound, kojic acid. The EtOAc extract and kojic acid were screened for their antimicrobial activity against two Grampositive and two Gram-negative bacteria as well as a fungal strain using the resazurin 96-well microtitre plate antimicrobial assay. Results: The fungus C. gloeosporioides was isolated from the leaves of Sonneratia apetala. Initial identification of the fugal isolate was carried out using spore characteristics observed under the microscope. Subsequently, the ITS1-5.8 S-ITS2 sequencing was employed for species-level identification of the fungus C. gloeosporioides. Five litres of liquid culture of the fungus produced approximately 610 mg of a mixture of secondary *** acid(1) was isolated as the main secondary metabolite present in the fungal extract, and the structure was confirmed by 1 D, 2 D NMR and mass spectrometry. The EtOAc extract and compound 1 exhibited considerable antimicrobial activity against all tested *** the minimum inhibitory concentration(MIC) values from the EtOAc extract ranged between 2.4×10^(-4)mg/mL and 2.5 mg/mL, those of kojic acid(1) were between 0.125 mg/mL and1 mg/mL. The EtOAc extract and kojic acid(1) were most active against Pseudomonas aeruginosa(MIC = 2.4×10^(-4). mg/mL) and Micrococcus luteus(MIC = 0.125 mg/mL), respectively. Conclusions:The results revealed that the endophytic fungus C. gloeosporioides could be a good source of commercially important kojic acid, w

关键词： Endophytic fungus Mangrove plants Sonneratia apetala Kojic acid Colletrtrichum gloeosporioides Antimicrobial activity

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Geomechanical properties will constrain CO_(2)injection into the lower Ordovician Rose Run sandstone deep saline reservoir,Appalachian Basin,Kentucky,USA

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Journal of Rock Mechanics and Geotechnical Engineering 2021年第5期13卷 947-960页

作者： john Richard Bowersox Stephen F.Greb Junfeng Zhu David C.Harris Kentucky Geological Survey University of KentuckyLexingtonKY40506-0107USA

The Kentucky Geological Survey(KGS)1 Hanson Aggregates stratigraphic research well,Carter County,Kentucky,USA,was drilled to a total depth of 1474 m as a field-scale test of potential CO2 storage reservoir properties in the Central Appalachian *** properties of the Rose Run sandstone(upper Ordovician Knox group)were tested for its suitability as a storage reservoir.A 9.8-m thick section of the Rose Run was penetrated at 1000 m drilled depth and a whole-diameter core and rotary sidewall cores were *** porosity and permeability measured in core plugs were 9.1%and 44.6 md,*** vertical stress gradient calculated in the wellbore was 26 MPa/*** fractures in dolomites underlying and overlying the Rose Run follow the contemporary N53E Appalachian Basin stress *** Rose Run elastic geomechanical properties were calibrated to values measured in core plugs to evaluate its fracturing risk as a CO2 storage *** Young’s modulus and Poisson’s ratio values of the Rose Run were 45 GPa and 0.23,respectively,whereas Young’s modulus and Poisson’s ratio values were 77.1 GPa and 0.28,respectively,in the overlying Beekmantown dolomite,suggesting the Rose Run may fracture if overpressured during CO2 injection but be confined by the *** compressive strength measured in core plugs found the Rose Run and Beekmantown fractured at mean axial stresses of 156.5 MPa and 282.2 MPa,respectively,confirming the Beekmantown as suitable for confining CO2 injected into the Rose Run.A step-rate test was conducted in a mechanically-isolated 18.6-m interval bracketing the Rose *** Rose Run reservoir pressure was 9.3 MPa,and fracture gradient under injection was 13.6 MPa/km,suggesting step-rate testing before CO2 injection,and subsequent pressure monitoring to ensure *** the region around the KGS 1 Hanson Aggregates well is underpressured and adjacent to faulted Precambrian basement,further research is neede

关键词： Appalachian Basin Rose Run sandstone Geomechanics Carbon sequestration Step-rate testing

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Effects of vertical position on trematode parasitism in larval anurans

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Current Zoology 2019年第6期65卷 657-664页

作者： Jacob R.JONES Camille L.STEENROD john A.MARINO Jr. Biology Department Bradley UniversityPeoriaILUSA Department of Geography University of MarylandCollege ParkMDUSA

Spatial distributions of animals can affect interactions with their natural enemies,such as parasites,and thus have important implications for host-parasite *** spatial variation in infection risk has been explored in many systems at the landscape scale,less attention has been paid to spatial structure at smaller ***,we explore a hypothesized relationship between a common spatial variable,vertical position,and risk of parasite infection in a model aquatic system,larval frogs(Rana)and trematode(Digenea)*** position is relevant to this system given evidence that the densities of snail first intermediate hosts,tadpole second intermediate hosts,and trematode infective stages can vary with *** test the effects of depth on infection risk of larval frogs by trematodes,we performed two enclosure experiments,one in the laboratory and one in the field,in which larval frogs in cages just below the water surface or near the bottom of the water column were exposed to *** with near-surface cages,mean infection load(number of cysts)in tadpoles in near-bottom cages was 83%higher after 48-h exposures in the laboratory and 730%higher after 10-day exposures in the *** findings thus indicate that infection risk depends on depth,which may have adaptive significance,as tadpoles have previously been shown to change vertical position in response to parasite *** results motivate future work examining vertical variation in infection risk and may have broader implications for host-parasite dynamics and evolution of host and parasite behavior.

关键词： avoidance behavior cercariae Echinostomatidae host-parasite interactions Rana spatial structure

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