Publish in OALib Journal

ISSN: 2333-9721

APC: Only $99


Any time

2019 ( 2 )

2017 ( 2 )

2016 ( 3 )

2015 ( 41 )

Custom range...

Search Results: 1 - 10 of 561 matches for " Soumya Raychaudhuri "
All listed articles are free for downloading (OA Articles)
Page 1 /561
Display every page Item
A general framework for meta-analyzing dependent studies with overlapping subjects in association mapping
Buhm Han,Jae Hoon Sul,Eleazar Eskin,Paul I. W. de Bakker,Soumya Raychaudhuri
Quantitative Biology , 2013,
Abstract: Meta-analysis of genome-wide association studies is increasingly popular and many meta-analytic methods have been recently proposed. A majority of meta-analytic methods combine information from multiple studies by assuming that studies are independent since individuals collected in one study are unlikely to be collected again by another study. However, it has become increasingly common to utilize the same control individuals among multiple studies to reduce genotyping or sequencing cost. This causes those studies that share the same individuals to be dependent, and spurious associations may arise if overlapping subjects are not taken into account in a meta-analysis. In this paper, we propose a general framework for meta-analyzing dependent studies with overlapping subjects. Given dependent studies, our approach "decouples" the studies into independent studies such that meta-analysis methods assuming independent studies can be applied. This enables many meta-analysis methods, such as the random effects model, to account for overlapping subjects. Another advantage is that one can continue to use preferred software in the analysis pipeline which may not support overlapping subjects. Using simulations and the Wellcome Trust Case Control Consortium data, we show that our decoupling approach allows both the fixed and the random effects models to account for overlapping subjects while retaining desirable false positive rate and power.
Kinetic Monte Carlo Study of the Type 1/Type 2 Choice in Apoptosis Elucidates Selective Killing of Cancer Cells under Death Ligand Induction  [PDF]
Subhadip Raychaudhuri
Open Journal of Apoptosis (OJApo) , 2015, DOI: 10.4236/ojapo.2015.41003
Abstract: Death ligand mediated apoptotic activation is a mode of cell death that is widely used in cellular and physiological situations. Interest in studying death ligand induced apoptosis has increased due to the promising role of recombinant soluble forms of death ligands (mainly recombinant TRAIL) in anti-cancer therapy. A clear elucidation of how death ligands activate the type 1 and type 2 apoptotic pathways in healthy and cancer cells may help develop better chemotherapeutic strategies. In this work, we use kinetic Monte Carlo simulations to address the problem of type 1/ type 2 choice in death ligand mediated apoptosis of cancer cells. Our study provides insights into the activation of membrane proximal death module that results from complex interplay between death and decoy receptors. Relative abundance of death and decoy receptors was shown to be a key parameter for activation of the initiator caspases in the membrane module. Increased concentration of death ligands frequently increased the type 1 activation fraction in cancer cells, and, in certain cases changed the signaling phenotype from type 2 to type 1. Results of this study also indicate that inherent differences between cancer and healthy cells, such as in the membrane module, may allow robust activation of cancer cell apoptosis by death ligand induction. At the same time, large cell-to-cell variability through the type 2 pathway was shown to provide protection for healthy cells. Such elucidation of selective activation of apoptosis in cancer cells addresses a key question in cancer biology and cancer therapy.
Accurately Assessing the Risk of Schizophrenia Conferred by Rare Copy-Number Variation Affecting Genes with Brain Function
Soumya Raychaudhuri,Joshua M. Korn,Steven A. McCarroll,The International Schizophrenia Consortium,David Altshuler,Pamela Sklar,Shaun Purcell ,Mark J. Daly
PLOS Genetics , 2010, DOI: 10.1371/journal.pgen.1001097
Abstract: Investigators have linked rare copy number variation (CNVs) to neuropsychiatric diseases, such as schizophrenia. One hypothesis is that CNV events cause disease by affecting genes with specific brain functions. Under these circumstances, we expect that CNV events in cases should impact brain-function genes more frequently than those events in controls. Previous publications have applied “pathway” analyses to genes within neuropsychiatric case CNVs to show enrichment for brain-functions. While such analyses have been suggestive, they often have not rigorously compared the rates of CNVs impacting genes with brain function in cases to controls, and therefore do not address important confounders such as the large size of brain genes and overall differences in rates and sizes of CNVs. To demonstrate the potential impact of confounders, we genotyped rare CNV events in 2,415 unaffected controls with Affymetrix 6.0; we then applied standard pathway analyses using four sets of brain-function genes and observed an apparently highly significant enrichment for each set. The enrichment is simply driven by the large size of brain-function genes. Instead, we propose a case-control statistical test, cnv-enrichment-test, to compare the rate of CNVs impacting specific gene sets in cases versus controls. With simulations, we demonstrate that cnv-enrichment-test is robust to case-control differences in CNV size, CNV rate, and systematic differences in gene size. Finally, we apply cnv-enrichment-test to rare CNV events published by the International Schizophrenia Consortium (ISC). This approach reveals nominal evidence of case-association in neuronal-activity and the learning gene sets, but not the other two examined gene sets. The neuronal-activity genes have been associated in a separate set of schizophrenia cases and controls; however, testing in independent samples is necessary to definitively confirm this association. Our method is implemented in the PLINK software package.
Simulation Study of Active Noise Control in Wind Turbines Using FxLMS Adaptation Algorithm  [PDF]
Soumya Roy, Pratik Naik
Journal of Power and Energy Engineering (JPEE) , 2017, DOI: 10.4236/jpee.2017.58006
Abstract: Utility scale wind turbines produce a significant amount of noise which has been identified as one of the most critical challenges to the widespread use of wind energy. Aerodynamic noise caused primarily by the interaction of the boundary layer and (or) the upstream atmospheric turbulence with the trailing edge of the blade has been identified as the most dominant source of noise in wind turbines. The authors here propose an active noise control system based on the FxLMS algorithm which can achieve suppression of noise from a modern wind turbine. Two types of noise sources have been simulated: monopole and dipole. The results of the active noise control algorithm are validated with simulations in MATLAB. The agreement between the results shows the far impact of active noise control techniques will have in future wind turbines.
Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens
Xiaoming Jia, Buhm Han, Suna Onengut-Gumuscu, Wei-Min Chen, Patrick J. Concannon, Stephen S. Rich, Soumya Raychaudhuri, Paul I.W. de Bakker
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0064683
Abstract: DNA sequence variation within human leukocyte antigen (HLA) genes mediate susceptibility to a wide range of human diseases. The complex genetic structure of the major histocompatibility complex (MHC) makes it difficult, however, to collect genotyping data in large cohorts. Long-range linkage disequilibrium between HLA loci and SNP markers across the major histocompatibility complex (MHC) region offers an alternative approach through imputation to interrogate HLA variation in existing GWAS data sets. Here we describe a computational strategy, SNP2HLA, to impute classical alleles and amino acid polymorphisms at class I (HLA-A, -B, -C) and class II (-DPA1, -DPB1, -DQA1, -DQB1, and -DRB1) loci. To characterize performance of SNP2HLA, we constructed two European ancestry reference panels, one based on data collected in HapMap-CEPH pedigrees (90 individuals) and another based on data collected by the Type 1 Diabetes Genetics Consortium (T1DGC, 5,225 individuals). We imputed HLA alleles in an independent data set from the British 1958 Birth Cohort (N = 918) with gold standard four-digit HLA types and SNPs genotyped using the Affymetrix GeneChip 500 K and Illumina Immunochip microarrays. We demonstrate that the sample size of the reference panel, rather than SNP density of the genotyping platform, is critical to achieve high imputation accuracy. Using the larger T1DGC reference panel, the average accuracy at four-digit resolution is 94.7% using the low-density Affymetrix GeneChip 500 K, and 96.7% using the high-density Illumina Immunochip. For amino acid polymorphisms within HLA genes, we achieve 98.6% and 99.3% accuracy using the Affymetrix GeneChip 500 K and Illumina Immunochip, respectively. Finally, we demonstrate how imputation and association testing at amino acid resolution can facilitate fine-mapping of primary MHC association signals, giving a specific example from type 1 diabetes.
Cellotape Birefringent Filter: Some New Demonstrations  [PDF]
Ayantika Khanra, Barun Raychaudhuri
Optics and Photonics Journal (OPJ) , 2016, DOI: 10.4236/opj.2016.67016
Abstract: An easy method is put forward to estimate the optical bandwidth and the wavelength of maximum transmission of Lyot optical filter by measuring the change in phase retardation of birefringent plates as function of thickness. The objective is to demonstrate the experiment with common undergraduate laboratory equipment and thereby provide with an educational aid. The filter is fabricated with cellotape using its birefringence property. The accuracy of measurement is cross-checked with precision spectroradiometric measurements. Some simplification is suggested in the theoretical derivation of the transmitted intensity and a possibility of realizing tunable filter by changing the angle of incidence is indicated.
Biologics : Target - specific treatment of systemic and cutaneous autoimmune diseases
Raychaudhuri Siba,Raychaudhuri Smriti
Indian Journal of Dermatology , 2009,
Abstract: Biologics are becoming important in the treatment of systemic and cutaneous autoimmune diseases. They are designed to target specific components of immune system. As the new drugs are capable of targeting proteins in a more specific fashion, yet have lower risks of systemic side-effects, they have considerable advantages over the older immunomodulators. The development of TNF-alpha blockers in the treatment of psoriasis, psoriatic arthritis, rheumatoid arthritis, Crohn′s disease and ankylosing spondylitis have been major breakthroughs. Likewise, B-cell depletion has proved to be equally revolutionary for the treatment of lupus, pemphigus, certain vasculitides etc. But all said and done, the development of these molecules and their clinical usage are still at evolving stages. Consensus needs be formed to further categorize the clinical profiles of the patients in whom biologics are to be used in the future, given that the long-term safety profiles of these agents are very much unknown at present.
SCID mouse model of psoriasis: A unique tool for drug development of autoreactive T-cell and TH-17 cell-mediated autoimmune diseases
Raychaudhuri Smriti,Raychaudhuri Siba
Indian Journal of Dermatology , 2010,
Abstract: In both skin and synovial tissues of psoriatic arthritis (PsA) patients, there are prominent lymphocytic infiltrates localized to the dermal papillae in the skin and the sublining layer stroma in the joint. T-cells, with a predominance of CD4+ lymphocytes, are the most significant lymphocytes in the tissues; in contrast, this ratio is reversed in the epidermis, synovial fluid compartment, and at the enthesis, where CD8+ T-cells are more common. This differential tropism of CD8+ T-cell suggests that the CD8+ T-cells may be driving the immune response in the joint and skin. This is supported by an association with MHC class I. The cytokine network in the psoriatic skin and synovium is dominated by monocyte and T-cell-derived cytokines: IL-1β, IL-2, IL-10, IFN-γ, and TNF-α. In PsA synovium, higher levels of IFN-γ, IL-2, and IL-10 have been detected than in psoriatic skin. An analysis of T-cell receptor beta-chain variable (TCRβV) gene repertoires revealed common expansions in both skin and synovial inflammatory sites, suggesting an important role for cognate T-cell responses in the pathogenesis of PsA and that the inciting antigen may be identical or homologous between the afflicted skin and synovium. Traditionally, T-cells have been classified as T helper 1 (Th1) or Th2 cells by production of defining cytokines, IFN- γ and IL-4, respectively. Recently, a new type of T-cell, Th17, has been linked to autoimmune inflammation. T-helper 17 (Th17) cells are a unique effector CD4+ T-cell subset characterized by the production of interleukin (IL)-17. Murine diseases that were previously considered to be pure Th1-mediated responses have been shown to contain mixed populations of Th1 and Th17 cells. Also, in humans, a critical immunoregulatory role of Th-17 cells in infectious and autoimmune diseases has been identified. It has been postulated that IL-17 may be important in psoriasis. Our initial observations demonstrate that IL-17 and its receptor system are important for PsA also. In in vivo and in vitro studies we have demonstrated that IL-17/IL-17R are enriched in skin, synovial tissue, and synovial fluid of psoriatic arthritis patients and Th17 cells are functionally significant in the pathogenesis of psoriasis and psoriatic arthritis. Here we will share our experience of the SCID mouse model of psoriasis in respect to its use in investigating psoriatic diseases and development of immune-based drugs for psoriasis, psoriatic arthritis, and other autoimmune diseases.
Modeling Crash Risk at Rail-Highway Grade Crossings by Track Class  [PDF]
Soumya Sharma, Srinivas S. Pulugurtha
Journal of Transportation Technologies (JTTs) , 2019, DOI: 10.4236/jtts.2019.93016
Abstract: The Federal Railroad Administration (FRA)’s Web Based Accident Prediction System (WBAPS) is used by federal, state and local agencies to get a preliminary idea on safety at a rail-highway grade crossing. It is an interactive and user-friendly tool used to make funding decisions. WBAPS is almost three decades old and involves a three-step approach making it difficult to interpret the contribution of the variables included in the model. It also does not directly account for regional/local developments and technological advancements pertaining to signals and signs implemented at rail-highway grade crossings. Further, characteristics of a rail-highway grade crossing vary by track class which is not explicitly considered by WBAPS. This research, therefore, examines and develops a method and models to estimate crashes at rail-highway grade crossings by track class using regional/local level data. The method and models developed for each track class as well as considering all track classes together are based on data for the state of North Carolina. Linear, as well as count models based on Poisson and Negative Binomial (NB) distributions, was tested for applicability. Negative binomial models were found to be the best fit for the data used in this research. Models for each track class have better goodness of fit statistics compared to the model considering data for all track classes together. This is primarily because traffic, design, and operational characteristics at rail-highway grade crossings are different for each track class. The findings from statistical models in this research are supported by model validation.
A Moving Object Segmentation Method for Low Illumination Night Videos
Soumya. T
Lecture Notes in Engineering and Computer Science , 2008,
Page 1 /561
Display every page Item

Copyright © 2008-2017 Open Access Library. All rights reserved.