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Profiling Chromatin Accessibility at Single-cell Resolution

Genomics, Proteomics & Bioinformatics 2021年第2期19卷 172-190页

作者： sarthak sinha Ansuman T.Satpathy Weiqiang Zhou Hongkai Ji Jo A.Stratton Arzina Jaffer Nizar Bahlis Sorana Morrissy Jeff A.Biernaskie Department of Comparative Biology&Experimental Medicine Faculty of Veterinary MedicineUniversity of CalgaryCalgaryAB T2N 4N1Canada Department of Pathology Stanford University School of MedicineStanfordCA 94305USA Department of Biostatistics Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMD 21205USA Alberta Children’s Hospital Research Institute University of CalgaryCalgaryAB T2N 4N1Canada Hotchkiss Brain Institute University of CalgaryCalgaryAB T2N 4N1Canada Arnie Charbonneau Cancer Institute University of CalgaryCalgaryAB T2N 4Z6Canada Department of Biochemistry and Molecular Biology Cumming School of MedicineUniversity of CalgaryCalgaryAB T2N 4N1Canada

How distinct transcriptional programs are enacted to generate cellular heterogeneity and plasticity,and enable complex fate decisions are important open *** key regulator is the cell’s epigenome state that drives distinct transcriptional programs by regulating chromatin ***-wide chromatin accessibility measurements can impart insights into regulatory sequences(in)accessible to DNA-binding proteins at a single-cell *** review outlines molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation using single-cell assay for transposase-accessible chromatin using sequencing(scATAC-seq)in a scalable *** also covers joint profiling of chromatin with transcriptome/proteome measurements,computational strategies to integrate multi-omic measurements,and predictive bioinformatic tools to infer chromatin accessibility from single-cell transcriptomic *** refinements that increase power for cell discovery through robust chromatin coverage and integrate measurements from multiple modalities will further expand our understanding of gene regulation during homeostasis and disease.

关键词： Single-cell ATAC-seq Gene regulation Epigenetics Single-cell multi-omics Cis-regulatory elements

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Time-resolved spectral analysis of prompt emission from long gamma-ray bursts with GeV emission

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Research in Astronomy and Astrophysics 2014年第1期14卷 35-46页

作者： Arikkala Raghurama Rao Rupal Basak Jishnu Bhattacharya sarthak Chandra Nikunj Maheshwari Manojendu Choudhury Ranjeev Misra Tata Institute of Fundamental Research Indian Institute of Technology Centre for Excellence in Basic Sciences Inter-University Centre for Astronomy and Astrophysics

We performed detailed time-resolved spectroscopy of bright tong gamma- ray bursts （GRBs） which show significant GeV emissions （GRB 080916C, GRB 090902B and GRB 090926A）. In addition to the standard Band model, we also use a model consisting of a black body and a power law to fit the spectra. We find that for the latter model there are indications of an additional soft component in the spectra. While previous studies have shown that such models are required for GRB 090902B, here we find that a composite spectral model consisting of two blackbodies and a power law adequately fits the data of all the three bright GRBs. We investigate the evolution of the spectral parameters and find several interesting features that appear in all three GRBs, like （a） temperatures of the blackbodies are strongly correlated with each other, （b） fluxes in the black body components are strongly correlated with each other, （c） the temperatures of the black body trace the profile of the individual pulses of the GRBs, and （d） the characteristics of power law components like the spectral index and the delayed onset bear a close similarity to the emission characteristics in the GeV regions. We discuss the implications of these results and the possibility of identifying the radiation mechanisms during the prompt emission of GRBs.

关键词： gamma rays: bursts - gamma rays: observations - methods: data analysis

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An Automatic Threshold Selection Using ALO for Healthcare Duplicate Record Detection with Reciprocal Neuro-Fuzzy Inference System

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Computers, Materials & Continua 2023年第3期74卷 5821-5836页

作者： Ala Saleh Alluhaidan Pushparaj Anitha Subbappa Ved Prakash Mishra P.V.Chandrika Anurika Vaish sarthak Sengupta Department of Information Systems College of Computer and Information SciencesPrincess Nourah bint Abdulrahman UniversityRiyadhKSA.P.O.Box:8442811671 Department of Electronics and Communication Engineering National Institute of Technical Teacher Training and ResearchChandigarh160019India Department of Periodontology JSS Dental College&HospitalJSS Academy of Higher Education and ResearchMysuru570015India Department of Computer Science and Engineering Amity UniversityDubai345019United Arab Emirates Department of Management/Economics Prin LN Welingkar Institute of Management Development and ResearchMumbai400019India Department of Management Studies Indian Institute of Information TechnologyAllahabad211012India

ESystems based on EHRs(Electronic health records)have been in use for many years and their amplified realizations have been felt *** still have been pioneering collections of massive volumes of health *** detections involve discovering records referring to the same practical components,indicating tasks,which are generally dependent on several input parameters that experts *** linkage specifies the issue of finding identical records across various data *** similarity existing between two records is characterized based on domain-based similarity functions over different ***-duplication of one dataset or the linkage of multiple data sets has become a highly significant operation in the data processing stages of different data mining *** objective is to match all the records associated with the same *** measures have been in use for representing the quality and complexity about data linkage algorithms,and many other novel metrics have been *** outline of the problem existing in themeasurement of data linkage and de-duplication quality and complexity is *** article focuses on the reprocessing of health data that is horizontally divided among data custodians,with the purpose of custodians giving similar features to sets of *** first step in this technique is about an automatic selection of training examples with superior quality from the compared record pairs and the second step involves training the reciprocal neuro-fuzzy inference system(RANFIS)*** the Optimal Threshold classifier,it is presumed that there is information about the original match status for all compared record pairs(i.e.,Ant Lion Optimization),and therefore an optimal threshold can be computed based on the respective ***,Clinical Decision(CD),and Cork Open Research Archive(CORA)data repository help analyze the proposed method with evaluated benchmarks with current techniques.

关键词： Duplicate detection healthcare record linkage dataset pre-processing reciprocal neuro-fuzzy inference system and ant lion optimization fuzzy system

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Massive Hemolysis Causing Renal Failure in Acute Hepatitis E Infection

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Journal of Clinical and Translational Hepatology 2016年第4期4卷 345-347页

作者： Pragya Karki sarthak Malik Bipadabhanjan Mallick Vishal Sharma Surinder S Rana Department of Internal Medicine PGIMER Chandigarh India Department of Gastroenterology PGIMER Chandigarh India

Acute viral hepatitis is usually a self-limiting ***,it can lead to complications that can be life-threatening,such as acute liver *** 6 phosphate dehydrogenase (G6PD) deficiency in the setting of acute viral hepatitis can lead to a massive hemolysis,manifesting as acute kidney injury and markedly raised bilirubin levels;although cases are ***,we report such a *** patient had a viral hepatitis E infection and presented with kidney injury requiring *** showed very high mixed hyperbilirubinemia due to massive intravascular *** patient experienced a long,protracted course of illness,requiring renal replacement therapy with other supportive management,which led to improvement over a period of four *** case highlights the importance of recognizing associated hemolysis in a patient with viral hepatitis who presents with very high bilirubin levels or associated kidney *** patients will require aggressive supportive care with prompt fluid and electrolyte management.

关键词： Hepatitis E virus Hemolysis Anemia Hemoglobinuria G6PD deficiency

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R-spondin-2 is a Wnt agonist that regulates osteoblast activity and bone mass

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Bone Research 2018年第3期6卷 289-302页

作者： M.Noelle Knight Kannan Karuppaiah Michele Lowe sarthak Mohanty Robert L.Zondervan Sheila Bell Jaimo Ahn Kurt D.Hankenson Department of Orthopaedic Surgery Perelman School of Medicine University of Pennsylvania Department of Orthopaedic Surgery University of Michigan Medical School Division of Pulmonary Biology Cincinnati Children's Hospital Medical Center

The R-spondin family of proteins are Wnt agonists, and the complete embryonic disruption of Rspo2 results in skeletal developmental defects that recapitulate the phenotype observed with Lrp5/6 deficiency. Previous work has shown that R-spondin-2(Rspo2, RSPO2) is both highly expressed in Wnt-stimulated pre-osteoblasts and its overexpression induces osteoblast differentiation in the same cells, supporting its putative role as a positive autocrine regulator of osteoblastogenesis. However, the role of Rspo2 in regulating osteoblastogenesis and bone formation in postnatal bone has not been explored. Here we show that limb-bud progenitor cells from Rspo2 knockout mice undergo reduced mineralization during osteoblastogenesis in vitro and have a corresponding alteration in their osteogenic gene expression profile. We also generated the first Rspo2 conditional knockout(Rspo2 floxed) mouse and disrupted Rspo2 expression in osteoblast-lineage cells by crossing to the Osteocalcin-Cre mouse line(OcnCre + Rspo2 ^(f/f)). Ocn-Cre + Rspo2 f/fmale and female mice at 1, 3, and 6 months were examined. Ocn-Cre + Rspo2 f/fmice are decreased in overall body size compared to their control littermates and have decreased bone mass. Histomorphometric analysis of1-month-old mice revealed a similar number of osteoblasts and mineralizing surface per bone surface with a simultaneous decrease in mineral apposition and bone formation rates. Consistent with this observation, serum osteocalcin in 3-month-old Ocn-Cre +Rspo2 f/fwas reduced, and bone marrow-mesenchymal stem cells from Ocn-Cre + Rspo2 f/fmice undergo less mineralization in ***, gene expression analysis and immunohistochemistry of mature bone shows reduced beta-catenin signaling in Ocn-Cre +Rspo2 f/f. Overall, RSPO2 reduces osteoblastogenesis and mineralization, leading to reduced bone mass.

关键词： The R-spondin family Wnt-stimulated pre-osteoblasts

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Industry 4.0 Application in Manufacturing for Real-Time Monitoring and Control

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Journal of Dynamics, Monitoring and Diagnostics 2022年第3期1卷 176-187页

作者： Debasish Mishra Ashok Priyadarshi sarthak M Das Sristi Shree Abhinav Gupta Surjya K Pal Debashish Chakravarty Advanced Technology Development Centre Indian Institute of Technology KharagpurKharagpurWest Bengal 721302India Mathematics and Computing Birla Institute of Technology MesraRanchiJharkhand 835215India Information Technology Birla Institute of Technology MesraRanchiJharkhand 835215India Computer Science and Engineering Birla Institute of Technology MesraRanchiJharkhand 835215India Electronics and Communication Engineering Birla Institute of Technology MesraRanchiJharkhand 835215India Department of Mechanical Engineering Indian Institute of Technology KharagpurKharagpurWest Bengal 721302India Department of Mining Engineering Indian Institute of Technology KharagpurKharagpurWest Bengal 721302India

Modern manufacturing aims to reduce downtime and track process anomalies to make profitable business *** ideology is strengthened by Industry 4.0,which aims to continuously monitor high-value manufacturing *** article builds upon the Industry 4.0 concept to improve the efficiency of manufacturing *** major contribution is a framework for continuous monitoring and feedback-based control in the friction stir welding(FSW)*** consists of a CNC manufacturing machine,sensors,edge,cloud systems,and deep neural networks,all working cohesively in real *** edge device,located near the FSW machine,consists of a neural network that receives sensory information and predicts weld quality in real *** addresses time-critical manufacturing *** receives the sensory data if weld quality is poor,and a second neural network predicts the new set of welding parameters that are sent as feedback to the welding *** experiments are conducted for training the neural *** framework successfully tracks process quality and improves the welding by controlling it in real *** system enables faster monitoring and control achieved in less than 1 *** framework is validated through several experiments.

关键词： cloud edge deep neural networks friction stir welding Industry 4.0 internet of things machine learning manufacturing process control process monitoring signal processing

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Overreaction and Availability Bias: Analysis of Real Estate Sector’s Stock Prices and Investors’ Reaction during Demonetisation in India

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Journal of Modern Accounting and Auditing 2019年第5期15卷 232-240页

作者： Kavita Singh sarthak Sengupta Anurika Vaish Indian Institute of Information Technology Allahabad India

The stock market is full of events that affect the sensitivity reaction of investors at a large scale. Individual investor sentiment is just like his/her personal feeling depending upon their nature, risk appetite, and market scenario. This research study investigates the investors’ reaction in the stock market for the real estate segment during the massive market crisis in developing countries. Demonetisation of 2016 in India has been taken with the purpose of implementing a pilot study to analyse the overreaction and availability bias. The primary focus was on analysing how the investors react on the information of demonetisation and their pattern of investment in the stock market with a special emphasis on real estate sector where the effect of the event had dramatically changed the stock prices. Therefore, a pre- and post- analysis had been conducted to gauge the prices, sensitivity, and reaction of investors in the stock market. The reaction of the citizens after these events was found to be drastically affected. Five real estate companies had been focused upon in this study to examine the impact of investors’ overreaction owing to the demonetisation and their investment pattern for stocks during pre- and post- demonetisation period at that timeframe. The analysis was done on a shorter period of time so that the impact of overreaction and availability bias can be critically analysed. The paper thus exhibits how investor sentiments and reaction for stock preference had changed over time through statistical study.

关键词： investor sentiment stock market demonetisation overreaction availability bias

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