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Aneuploidy:An opportunity within single-cell rNA sequencing analysis

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BIOCELL 2021年第5期45卷 1167-1170页

作者： joe r.DELANEY Department of Biochemistry and Molecular Biology Medical University of South CarolinaCharleston29425USA

Single-cell sequencing data has transformed the understanding of biological *** many flavors of single-cell sequencing have been developed,single-cell rNA sequencing(scrNA-seq)is currently the most prolific form in published *** analysis of differential biology within the population of cells studied relies on inferences and grouping of cells due to the spotty nature of data within individual cell scrNA-seq gene *** biologically relevant variable is readily inferred from scrNA-seq gene count tables regardless of individual gene representation within single cells:*** hundreds of genes are present on chromosome arms,high-quality inferences of aneuploidy can be made from scrNA-seq *** viewpoint summarizes how utilization of these bioinformatic pipelines can benefit scrNA-seq studies,particularly in oncology wherein aneuploidy is both rampant and a hallmark of the studied *** and use of these analytical pipelines will improve each field’s ability to understand the studied *** are encouraged to attempt these aneuploid analyses when reporting scrNA-seq data,much like copy-number variants are commonly reported in bulk genome sequencing data.

关键词： scrNA-seq Copy-number alterations Aneuploidy Cancer

Characterization of the surface and interfacial properties of the lamina splendens

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Frontiers of Mechanical Engineering 2017年第2期12卷 234-252页

作者： joe t. rEXWINKLE Heather K. HUNt Ferris M. PFEIFFEr Mechanical Engineering University of Missouri Columbia MO 65211USA Bioengineering University of Missouri Columbia MO 65211 USA Orthopaedic Surgery University of Missouri Columbia MO 65211USA

Joint disease affects approximately 52.5 mil- lion patients in the United States alone, costing 80.8 billion USD in direct healthcare costs. the development of treatment programs for joint disease and trauma requires accurate assessment of articular cartilage degradation. the articular cartilage is the interfacial tissue between articu- lating surfaces, such as bones, and acts as low-friction interfaces. Damage to the lamina splendens, which is the articular cartilage＇s topmost layer, is an early indicator of joint degradation caused by injury or disease. By gaining comprehensive knowledge on the lamina splendens, particularly its structure and interfacial properties, researchers could enhance the accuracy of human and animal biomechanical models, as well as develop appro- priate biomimetic materials for replacing damaged articu- lar cartilage, thereby leading to rational treatment programs for joint disease and injury. Previous studies that utilize light, electron, and force microscopy techniques have found that the lamina splendens is composed of collagen fibers oriented parallel to the cartilage surface and encased in a proteoglycan matrix. Such orientation maximizes wear resistance and proteoglycan retention while promoting the passage of nutrients and synovial fluid. Although the structure of the lamina splendens has been explored in the literature, the low-friction interface of this tissue remains only partially characterized. Various functional models are currently available for the interface, such as pure boundary lubrication, thin films exuded under pressure, and sheets of trapped proteins. recent studies suggest that each of these lubrication models has certain advantages over one another. Further research is needed to fully model the interface of this tissue. In this review, we summarize the methods for characterizing the lamina splendens and the results of each method. this paper aims to serve as a resource for existing studies to date and a roadmap of t

关键词： cartilage lamina splendens characterization,biomechanics orthopaedic review

Bolstering integrity in environmental data science and machine learning requires understanding socioecological inequity

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Frontiers of Environmental Science & Engineering 2024年第5期18卷 171-179页

作者： joe F.Bozeman III School of Civil and Environmental Engineering Georgia Institute of TechnologyAtlantaGA30332USA School of Public Policy Georgia Institute of TechnologyAtlantaGA30332USA

Socioecological inequity in environmental data science—such as inequities deriving from data-driven approaches and machine learning(ML)—are current issues subject to debate and *** is growing consensus around embedding equity throughout all research and design domains—from inception to administration,while also addressing procedural,distributive,and recognitional ***,practically doing so may seem onerous or daunting to *** current perspective helps to alleviate these types of concerns by providing substantiation for the connection between environmental data science and socioecological inequity,using the Systemic Equity Framework,and provides the foundation for a paradigmatic shift toward normalizing the use of equity-centered approaches in environmental data science and ML *** the integrity of environmental data science and ML is just beginning from an equity-centered tool development and rigorous application *** this end,this perspective also provides relevant future directions and challenges by overviewing some meaningful tools and strategies—such as applying the Wells-Du Bois Protocol,employing fairness metrics,and systematically addressing irreproducibility;emerging needs and proposals—such as addressing data-proxy bias and supporting convergence research;and establishes a ten-step path ***,the work that environmental scientists and engineers do ultimately affect the well-being of us all.

关键词： Equity Bias Machine Learning Data Science Justice Systemic Equity

Beta Gyres in Global Analysis Fields

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Advances in Atmospheric Sciences 2009年第5期26卷 984-994页

作者： Sun-Hee KIM H. joe KWON r. L. ELSBErrY Department of Atmospheric Sciences/typhoon research Center Kongju National University Department of Meteorology Naval Postgraduate School

A three-component decomposition is applied to global analysis data to show the existence of a beta gyre, which causes tropical Cyclone （tC） to drift from a large-scale environmental steering current. Analyses from the Global Data Assimilation and Prediction System （GDAPS） of the Korea Meteorological Adminis- tration （KMA）, the Global Forecast System （GFS） of NCEP, and the Navy Operational Global Atmospheric Prediction System （NOGAPS） are used in this study. the structure of the beta gyre obtained in our analyses is in good agreement with the theoretical structure, with a cyclonic circulation to the southwest of the tC center, an anticyclonic circulation to the northeast, and a ventilation flow directed northwestward near the center. the circulation of the beta gyre is strongest at the 850-hPa level where the cyclonically swirling primary circulation is strongest, and decreases with height, in a pyramid shape similar to the primary circulation. the individual structure of the beta gyre is case- and model-dependent. At a certain analysis time, one model may clearly reveal a well-defined beta gyre, but the other models may not. Within one model, the beta gyre may be well defined at some analysis times, but not at other times. the structure of the beta gyre in the analysis field is determined by the nature of the vortex initialization scheme and the model behavior during the 6-h forecast in the operational data assimilation cycle.

关键词： tropical cyclone beta gyre GDAPS GFS NOGAPS tCM-90 final analyses

Enabling Inverter-based resource Stability Control in Power Systems with High renewable Penetration

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CSEE Journal of Power and Energy Systems 2023年第3期9卷 1248-1250页

作者： joe H.Chow rensselaer Polytechnic Institute TroyNY 12180-3590USA

this rapid communication provides the author’s viewpoints on the need to develop grid stability functions for inverter-based resources,in particular,controls to enhance system *** discussion will be focused on transi... 详细信息

关键词： Frequency regulation inverter control time scales transient stability

DEGrEE 3 ALGEBrAIC MINIMAL SUrFACES IN tHE 3-SPHErE

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Acta Mathematica Scientia 2012年第6期32卷 2065-2084页

作者： joe S.Wang 4 ricado Ln St.LauisM063124USA

We give a local analytic characterization that a minimal surface in the 3-sphere S3 C r4 defined by an irreducible cubic polynomial is one of the Lawson＇s minimal tori. this provides an alternative proof of the result by Perdomo （Characterization of order 3 algebraic immersed minimal surfaces of S3, Geom. Dedicata 129 （2007）, 23 34）.

关键词： algebraic minimal surface 3-sphere cubic polynomial

An Epigenetic Perspective on Developmental regulation of Seed Genes

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Molecular Plant 2009年第4期2卷 610-627页

作者： Heng Zhang joe Ogas Department of Biochemistry Purdue University West Lafayette IN 47907-2063 USA

the developmental program of seeds is promoted by master regulators that are expressed in a seed-specific manner. Ectopic expression studies reveal that expression of these master regulators and other transcriptional regulators is sufficient to promote seed-associated traits, including generation of somatic embryos. recent work highlights the importance of chromatin-associated factors in restricting expression of seed-specific genes, in particular PcG proteins and AtP-dependent remodelers. this review summarizes what is known regarding factors that promote zygotic and/or somatic embryogenesis and the chromatin machinery that represses their expression. Characterization of the regulation of seedspecific genes reveals that plant chromatin-based repression systems exhibit broad conservation with and surprising differences from animal repression systems.

关键词： Epigenetics chromatin Polycomb group proteins LEAFY COtYLEDON developmental identity Arabidopsis seed development.

Physician's Guide to the treatment and Follow-Up of Metabolic Diseases 2006

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term-Dependent Confidence Normalisation for Out-of-Vocabulary Spoken term Detection

2006年

作者： Nenad Blau Georg F. Hoffmann J.V. Leonard joe t. r. clarke

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Journal of Computer Science & technology 2012年第2期27卷 358-375页

作者： Javier tejedo Simon King joe Frankel Centre for Speech technology research University of Edinburgh10 Crichton Street Human Computer technology Laboratory (HCtLab) School of Computer Engineering and Telecommunication University Autonomous of MadridAvenue Francisco Tomás y Valiente 1128049MadridSpain

An important component of a spoken term detection （StD） system involves estimating confidence measures of hypothesised detections.A potential problem of the widely used lattice-based confidence estimation,however,is that the confidence scores are treated uniformly for all search terms,regardless of how much they may differ in terms of phonetic or linguistic *** problem is particularly evident for out-of-vocabulary （OOV） terms which tend to exhibit high intra-term *** address the impact of term diversity on confidence measures,we propose in this work a term-dependent normalisation technique which compensates for term diversity in confidence *** first derive an evaluation-metric-oriented normalisation that optimises the evaluation metric by compensating for the diverse occurrence rates among terms,and then propose a linear bias compensation and a discriminative compensation to deal with the bias problem that is inherent in lattice-based confidence measurement and from which the term Specific threshold （tSt） approach *** tested the proposed technique on speech data from the multi-party meeting domain with two state-ofthe-art StD systems based on phonemes and words *** experimental results demonstrate that the confidence normalisation approach leads to a significant performance improvement in StD,particularly for OOV terms with phonemebased systems.

关键词： confidence estimation discriminative model spoken term detection speech recognition