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scLM:Automatic Detection of Consensus Gene Clusters Across Multiple Single-cell Datasets

Genomics, Proteomics & Bioinformatics 2021年第2期19卷 330-341页

作者： Qianqian Song Jing Su Lance D.miller Wei Zhang Center for Cancer Genomics and Precision Oncology Wake Forest Baptist Comprehensive Cancer CenterWake Forest Baptist Medical CenterWinston SalemNC 27157USA Department of Cancer Biology Wake Forest School of MedicineWinston SalemNC 27157USA Department of Biostatistics Indiana University School of MedicineIndianapolisIN 46202USA

In gene expression profiling studies,including single-cell RNA sequencing(scRNA-seq)analyses,the identification and characterization of co-expressed genes provides critical information on cell identity and *** co-expression clustering in scRNA-seq data presents certain *** show that commonly used methods for single-cell data are not capable of identifying co-expressed genes accurately,and produce results that substantially limit biological expectations of co-expressed ***,we present single-cell Latent-variable Model(scLM),a gene coclustering algorithm tailored to single-cell data that performs well at detecting gene clusters with significant biologic ***,scLM can simultaneously cluster multiple single-cell datasets,i.e.,consensus clustering,enabling users to leverage single-cell data from multiple sources for novel comparative *** takes raw count data as input and preserves biological variation without being influenced by batch effects from multiple *** from both simulation data and experimental data demonstrate that scLM outperforms the existing methods with considerably improved *** illustrate the biological insights of scLM,we apply it to our in-house and public experimental scRNA-seq *** identifies novel functional gene modules and refines cell states,which facilitates mechanism discovery and understanding of complex biosystems such as cancers.A user-friendly R package with all the key features of the scLM method is available at https://***/QSong-github/scLM.

关键词： Single-cell RNA sequencing Consensus clustering Latent space Markov Chain Monte Carlo Maximum likelihood approach

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Nucleation of recrystallization in magnesium alloy grains of varied orientation and the impacts on texture evolution

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Journal of Magnesium and Alloys 2022年第11期10卷 3041-3053页

作者： Victoria M.miller Jian-Feng Nie Tresa M.Pollock Department of Materials Science and Engineering University of FloridaGainesvilleFL 32611USA Department of Materials Science and Engineering Monash UniversityVictoria 3800Australia Materials Department University of California Santa BarbaraSanta BarbaraCA 93106-5050USA

Selection of appropriate thermomechanical processing parameters is crucial for control of the crystallographic texture and grain size distribution in wrought magnesium alloys, which in turn dictate their mechanical properties. In this work, the recrystallization behavior of binary Mg-Zn alloys are examined after warm rolling as a function of alloy content and heat treatment temperature. The Avrami exponent increased with increasing heat treatment temperature up to the Mg Zn solvus, while the strength of the recrystallization texture *** the Avrami exponent nor the qualitative trends in texture evolution were sensitive to the Zn alloying content in the examined *** and transmission electron microscopy observations revealed that the changes in texture and recrystallization kinetics could be attributed to differences in the nucleation behavior of basal and off-basal orientations.

关键词： Magnesium alloys Recrystallization Dislocation substructure Texture

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Mathematical models of SIR disease spread with combined non-sexual and sexual transmission routes

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Infectious Disease Modelling 2017年第1期2卷 35-55页

作者： Joel C.miller Monash University School of Mathematical SciencesMelbourne 3800Australia Institute for Disease Modeling BellevueWAUSA

The emergence of Zika and Ebola demonstrates the importance of understanding the role of sexual transmission in the spread of diseases with a primarily non-sexual transmission *** this paper,we develop low-dimensional models for how an SIR disease will spread if it transmits through a sexual contact network and some other transmission mechanism,such as direct contact or *** show that the models derived accurately predict the dynamics of simulations in the large population limit,and investigateℛ0 and final size relations.

关键词： network Mathematical spread

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Seismic Reflection Characteristics of Naturally-Induced Subsidence Affecting Transportation

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Journal of China University of Geosciences 2009年第3期20卷 496-512页

作者： Richard D miller Jianghai Xia Don W Steeples Kansas Geological Survey The University of Kansas Lawrence KS 66047 USA Department of Geology The University of Kansas Lawrence KS 66047 USA

High-resolution seismic reflections have been used effectively to investigate sinkholes formed from the dissolution of a bedded salt unit found throughout most of Central Kansas. Surface subsidence can have devastating effects on transportation structures. Roads, rails, bridges, and pipelines can even be dramatically affected by minor ground instability. Areas susceptible to surface subsidence can put public safety at risk. Subsurface expressions significantly larger than surface depressions are consistently observed on seismic images recorded over sinkholes in Kansas. Until subsidence reaches the ground surface, failure appears to be controlled by compressional forces evidenced by faults with reverse orientation. Once a surface depression forms or dissolution of the salt slows or stops, subsidence structures are consistent with a tensional stress environment with prevalent normal faults. Detecting areas of rapid subsidence potential, prior to surface failure, is the ultimate goal of any geotechnical survey where the ground surface is susceptible to settling. Seismic reflection images have helped correlate active subsidence to dormant paleofeatures, project horizontal growth of active sinkholes based on subsurface structures, and appraise the risk of catastrophic failure.

关键词： shallow seismic reflection imaging subsidence sinkhole.

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Visualisation techniques to support public interpretation of future climate change and land-use choices:a case study from N-E Scotland

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International Journal of Digital Earth 2016年第6期9卷 586-605页

作者： Chen Wang David miller Iain Brown Yang Jiang Marie Castellazzi Information and Computational Sciences The James Hutton InstituteAberdeenUK School of Computing Science and Digital Media Robert Gordon UniversityAberdeenUK

Mitigating and adapting to climate change includes a requirement to evaluate the role of future land uses in delivering robust integrated responses that are sensitive to local landscape *** practice,this emphasises the need for community engagement,planning and inclusive *** engagement may be potentially facilitated by the use of spatially explicit quantitative scenarios of landuse change in combination with interactive *** requires a coherent framework to integrate spatial data modelling,analytical capabilities and visualisation tools in a format that will also engage diverse public *** challenges were explored with a case study of virtual landscapes from N-E Scotland that was used to test preferences for scenarios of future land *** employed texture-based rendering rather than full photo-realistic rendering to facilitate interactivity and this provided additional scope for audiences to explore multiple future scenarios compared to the present *** voting in a virtual landscape theatre suggested preferences for visual diversity,good stewardship and perceived naturalness that should be considered in developing planned responses to *** investigation of preferences was conducted using interactive 3D features located within the *** findings are reviewed against objectives for inclusive engagement in the Digital Earth agenda and used to make further recommendations on the use of scenarios and visualisation *** particular,technical advances in user engagement need to be developed in conjunction with emerging good practice that addresses ethical,behavioural and inclusion issues so that the content is presented in as transparent and unbiased format as possible.

关键词： Landscape visualisation geographic information systems land-use scenarios public participation knowledge exchange

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Synthesis of Hierarchical SnO2 Nanowire–TiO2 Nanorod Brushes Anchored to Commercially Available FTO-coated Glass Substrates

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Nano-Micro Letters 2017年第3期9卷 93-100页

作者： Derek R.miller Sheikh A.Akbar Pat A.Morris Department of Materials Science and Engineering The Ohio State UniversityColumbusOH 43212USA

Growth of single-crystal Sn O_2 nanowires using a fluorine-doped Sn O_2(FTO) thin film as both the source and substrate is demonstrated for the first time at relatively low temperature(580 °C) which preserves the integrity of the underlying glass support and improves scalability to devices. Furthermore, a microwave hydrothermal process is shown to grow Ti O_2 nanorods on these nanowires to create a hierarchical nanoheterostructure that will lead to efficient photogenerated charge carrier separation and rapid transport of electrons to the substrate. This process simplifies nanowire growth by using commercially available and widely used FTO substrates without the need for an additional upstream Sn source and can be used as a high surface area host structure to many other hierarchical structures.

关键词： SnO2 Nanowire Fluorine-doped SnO2(FTO) Vapor–liquid–solid(VLS) TiO2 Nanorod brush

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Maternal and fetal T cells in term pregnancy and preterm labor

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Cellular & Molecular Immunology 2020年第7期17卷 693-704页

作者： Derek miller Meyer Gershater Rebecca Slutsky Roberto Romero Nardhy Gomez-Lopez Perinatology Research Branch Division of Obstetrics and Maternal–Fetal MedicineDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S.Department of Health and Human ServicesDetroitMIUSA Department of Obstetrics and Gynecology Wayne State University School of MedicineDetroitMIUSA Department of Obstetrics and Gynecology University of MichiganAnn ArborMIUSA Department of Epidemiology and Biostatistics Michigan State UniversityEast LansingMIUSA Center for Molecular Medicine and Genetics Wayne State UniversityDetroitMIUSA Detroit Medical Center DetroitMIUSA Department of Obstetrics and Gynecology Florida International UniversityMiamiFLUSA Department of Biochemistry Microbiology and ImmunologyWayne State University School of MedicineDetroitMIUSA

Pregnancy is a state of immunological balance during which the mother and the developing fetus must tolerate each other while maintaining sufficient immunocompetence to ward off potential *** site of closest contact between the mother and fetus is the decidua,which represents the maternal–fetal *** of the immune cell subsets present at the maternal–fetal interface have been well described;however,the importance of the maternal T cells in this compartment during late gestation and its complications,such as preterm labor and birth,has only recently been ***,pioneer and recent studies have indicated that fetal T cells are activated in different subsets of preterm labor and may elicit distinct inflammatory responses in the amniotic cavity,leading to preterm *** this review,we describe the established and proposed roles for maternal T cells at the maternal–fetal interface in normal term parturition,as well as the demonstrated contributions of such cells to the pathological process of preterm labor and *** also summarize the current knowledge of and proposed roles for fetal T cells in the pathophysiology of the preterm labor *** is our hope that this review provides a solid conceptual framework highlighting the importance of maternal and fetal T cells in late gestation and catalyzes new research questions that can further scientific understanding of these cells and their role in preterm labor and birth,the leading cause of neonatal mortality and morbidity worldwide.

关键词： maternal-fetal interface decidua amniotic fluid adaptive immunity parturition

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Extrinsic visual feedback and additional cognitive/physical demands affect single-limb balance control in individuals with ankle instability

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World Journal of Orthopedics 2016年第12期7卷 801-807页

作者： You-jou Hung Jacob miller Department of Physical Therapy Angelo State University

AIM To investigate the impact of extrinsic visual feedback and additional cognitive/physical demands on single-limb balance in individuals with ankle *** Sixteen subjects with ankle instability participated in the study. Ankle instability was identified using the Cumberland Ankle Instability Tool(CAIT). The subject's unstable ankle was examined using the Athletic Single Leg Stability Test of the Biodex Balance System with 4 different protocols:(1) default setting with extrinsic visual feedback from the monitor;(2) no extrinsic visual feedback;(3) no extrinsic visual feedback with cognitive demands; and(4) no extrinsic visual feedback with physical demands. For the protocol with added cognitive demands,subjects were asked to continue subtracting 7 from a given number while performing the same test without extrinsic visual feedback. For the protocol with added physical demands,subjects were asked to pass and catch a basketball to and from the examiner while performing the same modified test. RESULTS The subject's single-limb postural control varied significantly among different testing protocols(F = 103; P = 0.000). Subjects' postural control was the worst with added physical demands and the best with the default condition with extrinsic visual feedback. Pairwisecomparison shows subjects performed significantly worse in all modified protocols(P < 0.01 in all comparisons) compared to the default protocol. Results from all 4 protocols are significantly different from each other(P < 0.01) except for the comparison between the "no extrinsic visual feedback" and "no extrinsic visual feedback with cognitive demands" protocols. Comparing conditions without extrinsic visual feedback,adding a cognitive demand did not significantly compromise single-limb balance control but adding a physical demand did. Scores from the default protocol are significantly correlated with the results from all 3 modified protocols: No extrinsic visual feedback(r = 0.782; P = 0.000);

关键词： Ankle Balance Instability Motor control Rehabilitation

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Is direct acting antiviral therapy for hepatitis c viral infectionassociated with increased risk of hepatocellular carcinoma before or after liver transplantation?

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Hepatobiliary Surgery and Nutrition 2019年第5期8卷 563-565页

作者： Ashokkumar Jain Danielle miller Zakiyah Kadry Department of Surgery Division of TransplantThe Pennsylvania State UniversityCollege of MedicineHersheyPA 17033USA

Direct acting antiviral(DAA)therapy revolutionized thecurative therapy for>90%of hepatitis C virus(HCV)infected ***,in late 2016,concerns wereraised by several European centers that DAA therapy maybe increasing the in... 详细信息

关键词： hepatocellular hepatitis curative

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Review of issues concerning the use of reproductive inhibitors,with particular emphasis on resolving human-wildlife conflicts in North America

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Integrative Zoology 2010年第1期5卷 15-30页

作者： Kathleen A.FAGERSTONE Lowell A.miller Gary KILLIAN Christi A.YODER Department of Agriculture/Animal and Plant Health Inspection Service/Wildlife Services National Wildlife Research CenterFort Collins Almquist Research Center Pennsylvania State UniversityUniversity ParkUSA

This manuscript provides an overview of past wildlife contraception efforts and discusses the current state of *** fertility control agents,an avian reproductive inhibitor containing the active ingredient nicarbazin and an immunocontraceptive vaccine,have received regulatory approval with the Environmental Protection Agency and are commercially available in the *** G Contraceptive Bait for Canada Geese and Ovo Control for pigeons are delivered as oral *** injectable immunocontraceptive vaccine(GonaCon Immunocontraceptive Vaccine)was registered with the Environmental Protection Agency for use in female white-tailed deer in September *** injectable product(GonaCon Immunocontraceptive Vaccine)is registered for use in female white-tailed *** products are labeled for use in urban/suburban areas where these species are *** other compounds are currently being tested for use in wildlife in the USA,Europe,Australia and New Zealand that could have promise in the *** development and use of reproductive inhibitors for resolving human-wildlife conflicts will depend on a number of factors,including meeting the requirements of regulatory agencies for use in the environment and on the biological and economical feasibility of their *** will also be dependent on health and safety issues and on public acceptance of the techniques.

关键词： contraceptives fertility control registration reproductive inhibitors wildlife

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