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SubEpipredict:A tutorial-based primer and toolbox for fitting and forecasting growth trajectories using the ensemble n-sub-epidemic modeling framework

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Infectious Disease Modelling 2024年第2期9卷 411-436页

作者： Gerardo Chowell Sushma Dahal Amanda Bleichrodt Amna Tariq james M.Hyman Ruiyan Luo Department of population Health Sciences School of Public HealthGeorgia State UniversityAtlantaGAUSA Department of International Epidemiology and population Studies Fogarty International CenterNational Institutes of HealthBethesdaMDUSA Department of pediatrics School of MedicineStanford UniversityPalo AltoCAUSA Department of Mathematics Center for Computational ScienceTulane UniversityNew OrleansLAUSA

An ensemble n-sub-epidemic modeling framework that integrates sub-epidemics to capture complex temporal dynamics has demonstrated powerful forecasting capability in previous *** modeling framework can characterize complex epidemic patterns,including plateaus,epidemic resurgences,and epidemic waves characterized by multiple peaks of different *** this tutorial paper,we introduce and illustrate SubEpipredict,a user-friendly MATLAB toolbox for fitting and forecasting time series data using an ensemble n-sub-epidemic modeling *** toolbox can be used for model fitting,forecasting,and evaluation of model performance of the calibration and forecasting periods using metrics such as the weighted interval score(WIS).We also provide a detailed description of these methods including the concept of the n-sub-epidemic model,constructing ensemble forecasts from the top-ranking models,*** the illustration of the toolbox,we utilize publicly available daily COVID-19 death data at the national level for the United *** MATLAB toolbox introduced in this paper can be very useful for a wider group of audiences,including policymakers,and can be easily utilized by those without extensive coding and modeling backgrounds.

关键词： n-Sub-epidemic model Forecasting MATLAB Sub-epidemics phenomenological models performance metrics Model evaluation

Remote sensing of quality traits in cereal and arable production systems:A review

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The Crop Journal 2024年第1期12卷 45-57页

作者： Zhenhai Li Chengzhi Fan Yu Zhao Xiuliang Jin Raffaele Casa Wenjiang Huang Xiaoyu Song Gerald Blasch Guijun Yang james Taylor Zhenhong Li College of Geodesy and Geomatics Shandong University of Science and TechnologyQingdao 266590ShandongChina Key Laboratory of Quantitative Remote Sensing in Ministry of Agriculture and Rural Affairs Information Technology Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China Institute of Crop Sciences Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and EcologyMinistry of Agriculture and Rural AffairsBeijing 100081China DAFNE Universitàdella TusciaVia San Camillo de Lellis01100 ViterboItaly Key Laboratory of Digital Earth Science Aerospace Information Research InstituteChinese Academy of SciencesBeijing 100094China International Maize and Wheat Improvement Center(CIMMYT) PO Box 5689Addis AbabaEthiopia ITAp Univ.MontpellierINRAEInstitut AgroMontpellier 34000France College of Geological Engineering and Geomatics Chang’an UniversityXi’an 710054ShaanxiChina

Cereal is an essential source of calories and protein for the global *** predicting cereal quality before harvest is highly desirable in order to optimise management for farmers,grading harvest and categorised storage for enterprises,future trading prices,and policy *** use of remote sensing data with extensive spatial coverage demonstrates some potential in predicting crop quality *** studies have also proposed models and methods for predicting such traits based on multiplatform remote sensing *** this paper,the key quality traits that are of interest to producers and consumers are *** literature related to grain quality prediction was analyzed in detail,and a review was conducted on remote sensing platforms,commonly used methods,potential gaps,and future trends in crop quality *** review recommends new research directions that go beyond the traditional methods and discusses grain quality retrieval and the associated challenges from the perspective of remote sensing data.

关键词： Remote sensing Quality traits Grain protein Cereal

Epigenetic silencing of BEND4,a novel DNA damage repair gene,is a synthetic lethal marker for ATM inhibitor in pancreatic cancer

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Frontiers of Medicine 2024年第4期18卷 721-734页

作者： Yuanxin Yao Honghui Lv Meiying Zhang Yuan Li james G.Herman Malcolm V.Brock Aiai Gao Qian Wang Francois Fuks Lirong Zhang Mingzhou Guo Department of Gastroenterology and Hepatology the First Medical CenterChinese PLA General HospitalBeijing100853China Department of pharmacology School of Basic Medical SciencesZhengzhou UniversityZhengzhou450001China Henan Institute of Advanced Technology Zhengzhou UniversityZhengzhou450001China UpMC Hillman Cancer Center University of Pittsburgh Medical CenterPittsburghPA15213USA Department of surgery School of MedicineJohns Hopkins School of MedicineBaltimoreMD21287USA Laboratory of Cancer Epigenetics Faculty of MedicineULB-Cancer Research Center(U-CRC)Universite Libre de Bruxelles(ULB)Brussels1070Belgium National Key Laboratory of Kidney Diseases the First Medical CenterChinese PLA General HospitalBeijing100853China

Synthetic lethality is a novel model for cancer *** understand the function and mechanism of BEN domain-containing protein 4(BEND4)in pancreatic cancer,eight cell lines and a total of 492 cases of pancreatic neoplasia samples were included in this ***-specific polymerase chain reaction,CRISpR/Cas9,immunoprecipitation assay,comet assay,and xenograft mouse model were ***4 is a new member of the BEN domain *** expression of BEND4 is regulated by promoter region *** is methylated in 58.1%(176/303)of pancreatic ductal adenocarcinoma(pDAC),33.3%(14/42)of intraductal papillary mucinous neoplasm,31.0%(13/42)of pancreatic neuroendocrine tumor,14.3%(3/21)of mucinous cystic neoplasm,4.3%(2/47)of solid pseudopapillary neoplasm,and 2.7%(1/37)of serous cystic ***4 methylation is significantly associated with late-onset pDAC(>50 years,pppendent poor prognostic marker(pplays tumor-suppressive roles in vitro and in ***,BEND4 involves non-homologous end joining signaling by interacting with Ku80 and promotes DNA damage *** of BEND4 increased the sensitivity of pDAC cells to ATM ***,the present study revealed an uncharacterized tumor suppressor BEND4 and indicated that methylation of BEND4 may serve as a potential synthetic lethal marker for ATM inhibitor in pDAC treatment.

关键词： BEND4 DNA methylation synthetic lethality NHEJ pathway

Methionine sources and genotype affect embryonic intestinal development,antioxidants,tight junctions,and growth-related gene expression in chickens

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Animal Nutrition 2024年第1期16卷 218-230页

作者： james K.Lugata Sawadi F.Ndunguru Gebrehaweria K.Reda Xénia E.Ozsváth Eszter Angyal Levente Czeglédi Gabriella Gulyás Renáta Knop János Oláh Zoltán Mészár Rita Varga Brigitta Csernus Csaba Szabó Department of Animal Nutrition and physiology Faculty of Agriculture and Food Sciences and Environmental ManagementUniversity of DebrecenDebrecenHungary Department of Animal Husbandry Faculty of Agriculture and Food Sciences and Environmental ManagementUniversity of DebrecenDebrecenHungary Faculty of Agriculture and Food Sciences and Environmental Management Doctoral School of Animal ScienceUniversity of DebrecenDebrecenHungary Institutes for Agricultural Research and Educational Farm University of DebrecenDebrecenHungary Department of Anatomy Histology and EmbryologyFaculty of MedicineUniversity of DebrecenDebrecenHungary Department of Evolutionary Zoology and Human Biology Faculty of Science and TechnologyUniversity of DebrecenDebrecenHungary

Methionine(Met)is an essential and first limiting amino acid in the poultry diet that plays a significant role in chicken embryonic development and *** present study examined the effect of in ovo injection of DL-Met and L-Met sources and genotypes on chicken embryonic-intestinal development and *** eggs of the two genotypes,TETRA-SL layer hybrid(TSL)—commercial layer hybrid and Hungarian partridge colored hen breed(HpC)—a native genotype,were randomly distributed into four treatments for each *** treatment groups include the following:1)control non-injected eggs(NoIn);2)saline-injected(SaIn);3)DL-Met injected(DLM);and 4)L-Met injected(LM).The in ovo injection was carried out on 17.5 d of embryonic development;after hatching,eight chicks per group were sacrificed,and the jejunum was extracted for *** results showed that both DLM and LM groups had enhanced intestinal development as evidenced by increased villus width,villus height,and villus area(ppared to the *** DLM group had significantly reduced crypt depth,glutathione(GSH)content,glutathione S-transferase 3 alpha(GST3),occludin(OCLN)gene expression and increased villus height to crypt depth ratio in the TSL genotype than the LM group(ppC genotype has overexpressed insulin-like growth factor 1(IGF1)gene,tricellulin(md2),occludin(OCLN),superoxide dismutase 1(SOD1),and GST3 genes than the TSL genotype(ppment,and function,with genotypes responding differently under normal *** also influenced the expression of intestinal antioxidants,tight junction,and growth-related genes.

关键词： DL-Methionine L-Methionine In ovo injection Intestinal development poultry

The HIF-1α/pLOD2 axis integrates extracellular matrix organization and cell metabolism leading to aberrant musculoskeletal repair

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Bone Research 2024年第2期12卷 289-301页

作者： Heeseog Kang Amy L.Strong Yuxiao Sun Lei Guo Conan Juan Alec C.Bancroft Ji Hae Choi Chase A.pagani Aysel A.Fernandes Michael Woodard Juhoon Lee Sowmya Ramesh Aaron W.james David Hudson Kevin N.Dalby Lin Xu Robert J.Tower Benjamin Levi Center for Organogenesis Regeneration and TraumaDepartment of SurgeryUniversity of Texas SouthwesternDallasTX 75390USA Section of plastic Surgery Department of SurgeryUniversity of MichiganAnn ArborMI 48109USA Quantitative Biomedical Research Center Peter O’Donnell Jr.School of Public HealthUniversity of Texas SouthwesternDallasTX 75390USA Department of Orthopedics and Sports Medicine University of WashingtonSeattleWA 98195USA Division of Chemical Biology and Medicinal Chemistry College of PharmacyUniversity of Texas at AustinAustinTX 78712USA Department of pathology Johns Hopkins UniversityBaltimoreMD 21218USA

While hypoxic signaling has been shown to play a role in many cellular processes,its role in metabolism-linked extracellular matrix(ECM)organization and downstream processes of cell fate after musculoskeletal injury remains to be ***(HO)is a debilitating condition where abnormal bone formation occurs within extra-skeletal *** andhypoxia-inducible factor 1α(HIF-1α)activation have been shown to promote ***,the underlying molecular mechanisms bywhich the HIF-1αpathway in mesenchymal progenitor cells(MpCs)contributes to pathologic bone formation remain to ***,we used a proven mouse injury-induced HO model to investigate the role of HIF-1αon aberrant cell ***-cell RNA sequencing(scRNA-seq)and spatial transcriptomics analyses of the HO site,we found that collagen ECM organizationis the most highly up-regulated biological process in *** mesenchymal cell-specific deletion of Hif1α(Hoxa11-CreER^(T2);Hif1a^(fl/fl))significantly mitigated HO in ***-seq analysis of these Hoxa11-CreER^(T2);Hif1a^(fl/fl)mice identified the pLOD2/LOXpathway for collagen cross-linking as downstream of the HIF-1αregulation of ***,our scRNA-seq data and mechanisticstudies further uncovered that glucose metabolism in MpCs is most highly impacted by HIF-1α*** a translational aspect,a pan-LOX inhibitor significantly decreased HO.A newly screened compound revealed that the inhibition of pLOD2 activity in MpCssignificantly decreased osteogenic differentiation and glycolytic *** suggests that the HIF-1α/pLOD2/LOX axis linked tometabolism regulates HO-forming MpC *** results suggest that the HIF-1α/pLOD2/LOX pathway represents a promisingstrategy to mitigate HO formation.

关键词： metabolism skeletal aberrant

Radiopaque nano and polymeric materials for atherosclerosis imaging, embolization and other catheterization procedures

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Acta pharmaceutica Sinica B 2018年第3期8卷 360-370页

作者： Li Tian Linfeng Lu james Feng Marites p.Melancon Department of Interventional Radiology The University of Texas MD Anderson Cancer Center Duke University Graduate School of Biomedical Sciences University of Texas Health Science Center at Houston

A review of radiopaque nano and polymeric materials for atherosclerosis imaging and catheterization procedures is presented in this paper. Cardiovascular diseases(CVDs) are the leading cause of death in the US with atherosclerosis as a significant contributor for mortality and morbidity. In this review paper, we discussed the physics of radiopacity and X-ray/CT, clinically used contrast agents,and the recent progress in the development of radiopaque imaging agents and devices for the diagnosis and treatment of CVDs. We focused on radiopaque imaging agents for atherosclerosis, radiopaque embolic agents and drug eluting beads, and other radiopaque medical devices related to catheterization procedures to treat CVDs. Common strategies of introducing radiopacity in the polymers, together with examples of their applications in imaging and medical devices, are also presented.

关键词： Radiopaque contrast nanoparticles and materials X-ray CT Vascular diseases Atherosclerosis plaque Stenosis Embolization Inferior vena cava filters

Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance

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Journal of Genetics and Genomics 2020年第2期47卷 93-103页

作者： Adam F·Johnson Jie Hou Hua Yang Xiaowen Shi Chen Chen md Soliman Islam Tieming Ji Jianlin Cheng james A·Birchler Institurte of Research and Development Duy Tan UniversityDa Nang50000Viet Nam Department of Electrical Engineering and Computer Science University of MissouriColumbiaMO65211USA Division of Biological Sciences University of MissouriColumbiaMO65211USA Department of Statistics University of MissouriColumbiaMO65211USA

Aneuploidy has profound effects on an organism,typically more so than polyploidy,and the basis of this contrast is not fully understood.A dosage series of the maize long arm of chromosome 1(1L)was used to compa re relative global gene expression in diffe rent types and degrees of aneuploidy to gain insights into how the magnitude of genomic imbalance as well as hypoploidy affects global gene *** previously available methods require a selective examination of specific genes,RNA sequencing provides a whole-genome view of gene expression in *** studies of global aneuploidy effects have concentrated on individual types of aneuploids because multiple dose aneuploidies of the same genomic region are difficult to produce in most model genetic *** genetic toolkit of maize allows the examination of multiple ploidies and 1-4 doses of chromosome ***,a detailed examination of expression changes both on the varied chromosome arms and elsewhere in the genome is possible,in both hypoploids and hyperploids,compared with euploid *** studies observed the inverse trans effect,in which genes not varied in DNA dosage were expressed in a negative relationship to the varied chromosomal *** response was also the major type of changes found globally in this *** genes varied in dosage showed proportional expression changes,though some were seen to be partly or fully dosage *** was also found that the effects of aneuploidy were progressive,with more severe aneuploids producing effects of greater magnitude.

关键词： Aneuploidy polyploidy Inverse effect Gene regulation Dosage compensation Gene balance hypothesis

COVID-19: An overview and a clinical update

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World Journal of Clinical Cases 2021年第1期9卷 8-23页

作者： Arunkumar Krishnan james p Hamilton Saleh A Alqahtani Tinsay A Woreta Division of Gastroenterology and Hepatology Johns Hopkins School of MedicineBaltimoreMD 21287United States Liver Transplant Center King Faisal Specialist Hospital&Research CenterRiyadh 12713Saudi Arabia

The outbreak of coronavirus disease-2019(COVID-19,previously known as 2019 nCoV)caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection in Wuhan City,China,has spread rapidly around the *** patients from the first cluster had an epidemiological connection to the Wuhan's Huanan Seafood Wholesale *** evidence has shown that SARSCoV-2 can be easily transmitted from person to person through close contact and respiratory droplets,posing a substantial challenge to public *** present,the research on SARS-CoV-2 is still in the primary ***,dexamethasone and remdesivir are appeared to be promising medical ***,there is no definite specific treatment,and the mainstay of treatment is still focused on supportive ***,over 150 vaccines are under *** is necessary to understand the nature of the virus and its clinical characteristics in order to find effectively manage the *** knowledge about this virus is rapidly evolving,and clinicians must update themselves *** present review comprehensively summarizes the epidemiology,pathogenesis,clinical characteristics,and management of COVID-19 based on the current evidence.

关键词： Coronaviruses COVID-19 SARS-CoV-2 Epidemiology Symptoms Laboratory Imaging Treatment Vaccines prevention

Multiscale analysis of composite material reinforced by randomly-dispersed particles

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International Journal of Smart and Nano Materials 2012年第1期3卷 2-13页

作者： Jiaoyan Li james D.Lee Ken p.Chong The George Washington University WashingtonDC 20052USA National Institute of Standards and Technology GaithersburgMD 20899USA

A multiscale analysis method is presented in which detailed information on the microscopic level is incorporated into macroscopic models capable of simulating damage evolution and ultimate *** composite considered is reinforced by randomly-dispersed particles,which reflects the statistical characteristics of real materials,such as cement-based ***,a three-dimensional material body is decomposed into many unit *** unit cell is reinforced by a cylindrical particle,the orientation of which is characterized by three Euler angles generated by the random number *** on a detailed finite element analysis,the material properties of the representative volume element are *** verification,the properties of the cylindrical particles are set equal to those of the matrix and the computed‘composite’properties reduce exactly to those of the‘isotropic’material,as *** coordinate transformation,the effective material properties of each unit cell are *** assembly of stiffness matrices of all unit cells leads to the stiffness matrix of the whole *** the simple tension loading condition,the initial damaged unit cell can be identified according to the vonMises yield *** stiffness of the damaged unit cell will then be reduced to zero and it will cause stress redistribution and trigger further *** was found that the reinforcement is effective to mitigate and arrest the damage propagation,and therefore prolongs the material’s *** results suggest that the hierarchical coupling approaches used here may be useful for material design and failure protection in composites.

关键词： multiscale analysis random response finite element method representative volume element Euler angle damage propagation