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Search Results: 1 - 10 of 155402 matches for " Pulivarthi H. Rao "
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CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling
Joyce Xiuweu-Xu Gu,Michael Yang Wei,Pulivarthi H. Rao,Ching C. Lau
Gene Regulation and Systems Biology , 2007,
Abstract: With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specifi c BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.
Chromosomal aberrations in patients with head and neck squamous cell carcinoma do not vary based on severity of tobacco/alcohol exposure
Bhuvanesh Singh, Volkert B Wreesmann, David Pfister, Ashok Poluri, Ashok R Shaha, Dennis Kraus, Jatin P Shah, Pulivarthi H Rao
BMC Genetics , 2002, DOI: 10.1186/1471-2156-3-22
Abstract: Although the median number of abnormalities (9), gains (6) and losses (2) per case and the overall pattern of abnormalities did not vary significantly by the extent of tobacco/alcohol exposure, individual abnormalities segregating these patients were identified. Gain of 1p (p = 0.03) and 3q amplification (p = 0.05) was significantly more common in patients with a history of tobacco/alcohol exposure.This data suggests that the overall accumulated chromosomal aberrations in head and neck squamous cell carcinoma are not significantly influenced by the severity of tobacco/alcohol exposure with limited exceptions.A causal association between squamous cell carcinoma arising in the head and neck region (HNSCC) and exposure to tobacco and alcohol is well established [1-3]. However, 10–15% HNSCC occur in patients without any antecedent history of tobacco or alcohol exposure [4,5]. Several studies have suggested that these patients have a divergent clinical course compared to patients with tobacco associated HNSCC, which may be a reflection of differences in the genetic composition [4-6]. Empiric evidence suggesting that non-smokers may respond differently to carcinogenic insults is offered in a report by Schantz et al., showing the highest levels of chromosomal sensitivity in lymphocytes after exposure to the clastogen bleomycin in HNSCC patients who were non-smokers [7]. Relatively few studies have directly investigated the impact of tobacco/alcohol exposure on the genetic composition of HNSCC. Amplification and expression of cyclin D1, p53 mutation and deletions of 3p, 5q, and 9p21 are suggested to be influenced by the degree of tobacco exposure [4,6,8]. The largest effort on this topic has been reported by Koch and colleagues, who found significantly higher rates of p53 mutation and loss of heterozygosity at 3p, 4q, and 11q as part of allelotyping analysis of 10 individual loci [4]. No studies have utilized true genome-wide evaluative measures to analyze the impact of car
A systems biology approach reveals common metastatic pathways in osteosarcoma
Ricardo J Flores, Yiting Li, Alexander Yu, Jianhe Shen, Pulivarthi H Rao, Serrine S Lau, Marina Vannucci, Ching C Lau, Tsz-Kwong Man
BMC Systems Biology , 2012, DOI: 10.1186/1752-0509-6-50
Abstract: mRNA expression microarray and N-linked glycoproteomic analyses were performed on two commonly used isogenic pairs of human metastatic OS cell lines, namely HOS/143B and SaOS-2/LM7. Pathway analysis of the differentially regulated genes and glycoproteins separately revealed pathways associated to metastasis including cell cycle regulation, immune response, and epithelial-to-mesenchymal-transition. However, no common significant pathway was found at both genomic and proteomic levels between the two metastatic models, suggesting a very different biological nature of the cell lines. To address this issue, we used a topological significance analysis based on a “shortest-path” algorithm to identify topological nodes, which uncovered additional biological information with respect to the genomic and glycoproteomic profiles but remained hidden from the direct analyses. Pathway analysis of the significant topological nodes revealed a striking concordance between the models and identified significant common pathways, including “Cytoskeleton remodeling/TGF/WNT”, “Cytoskeleton remodeling/Cytoskeleton remodeling”, and “Cell adhesion/Chemokines and adhesion”. Of these, the “Cytoskeleton remodeling/TGF/WNT” was the top ranked common pathway from the topological analysis of the genomic and proteomic profiles in the two metastatic models. The up-regulation of proteins in the “Cytoskeleton remodeling/TGF/WNT” pathway in the SaOS-2/LM7 and HOS/143B models was further validated using an orthogonal Reverse Phase Protein Array platform.In this study, we used a systems biology approach by integrating genomic and proteomic data to identify key and common metastatic mechanisms in OS. The use of the topological analysis revealed hidden biological pathways that are known to play critical roles in metastasis. Wnt signaling has been previously implicated in OS and other tumors, and inhibitors of Wnt signaling pathways are available for clinical testing. Further characterization of this common p
Chromosomal amplifications, 3q gain and deletions of 2q33-q37 are the frequent genetic changes in cervical carcinoma
Pulivarthi H Rao, Hugo Arias-Pulido, Xin-Yan Lu, Charles P Harris, Hernan Vargas, Fang F Zhang, Gopeshwar Narayan, Achim Schneider, Mary Terry, Vundavalli VVS Murty
BMC Cancer , 2004, DOI: 10.1186/1471-2407-4-5
Abstract: We used a genome-wide screening method – comparative genomic hybridization (CGH) to identify DNA copy number changes in 77 patients with cervical cancer. We applied categorical and survival analyses to analyze whether chromosomal changes were related to clinico-pathologic characteristics and patients survival.The CGH analysis revealed a loss of 2q33-q37 (57.1%), gain of 3q (54.5%) and chromosomal amplifications (20.77%) as frequent genetic changes. A total of 15 amplified chromosomal sites were detected in 16 cases that include 1p31, 2q32, 7q22, 8q21.2-q24, 9p22, 10q21, 10q24, 11q13, 11q21, 12q15, 14q12, 17p11.2, 17q22, 18p11.2, and 19q13.1. Recurrent amplified sites were noted at 11q13, 11q21, and 19q13.1. The genomic alterations were further evaluated for prognostic significance in CC patients, and we did not find any correlation with a number of clinical or histological parameters. The tumors harboring HPV18 exhibited higher genomic instability compared to tumors with HPV 16.This study demonstrated that 2q33-q37 deletions, 3q gains and chromosomal amplifications as characteristic changes in invasive CC. These genetic alterations will aid in the identification of novel tumor suppressor gene(s) at 2q33-q37 and oncogenes at amplified chromosomal sites. Molecular characterization of these chromosomal changes utilizing the current genomic technologies will provide new insights into the biology and clinical behavior of CC.Cervical Cancer (CC) is the second most common malignancy among women in both incidence and mortality [1]. The HPV infection has been implicated as the most important etiologic factor in the development of CC [2]. Although 95% of the patients with precancerous lesions harbor HPV, only a small fraction of the cases eventually progress to invasive cancer [3]. Therefore, HPV infection alone was considered insufficient for the malignant conversion suggesting role of other genetic changes in the development of CC. Further identification of such genetic alt
Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma
Tsz-Kwong Man, Xin-Yan Lu, Kim Jaeweon, Laszlo Perlaky, Charles P Harris, Shishir Shah, Marc Ladanyi, Richard Gorlick, Ching C Lau, Pulivarthi H Rao
BMC Cancer , 2004, DOI: 10.1186/1471-2407-4-45
Abstract: We used a genome-wide screening method – array based comparative genomic hybridization (array-CGH) to identify DNA copy number changes in 48 patients with osteosarcoma. We applied fluorescence in situ hybridization (FISH) to validate some of amplified clones in this study.Clones showing gains (79%) were more frequent than losses (66%). High-level amplifications and homozygous deletions constitute 28.6% and 3.8% of tumor genome respectively. High-level amplifications were present in 238 clones, of which about 37% of them showed recurrent amplification. Most frequently amplified clones were mapped to 1p36.32 (PRDM16), 6p21.1 (CDC5L, HSPCB, NFKBIE), 8q24, 12q14.3 (IFNG), 16p13 (MGRN1), and 17p11.2 (PMP22 MYCD, SOX1,ELAC27). We validated some of the amplified clones by FISH from 6p12-p21, 8q23-q24, and 17p11.2 amplicons. Homozygous deletions were noted for 32 clones and only 7 clones showed in more than one case. These 7 clones were mapped to 1q25.1 (4 cases), 3p14.1 (4 cases), 13q12.2 (2 cases), 4p15.1 (2 cases), 6q12 (2 cases), 6q12 (2 cases) and 6q16.3 (2 cases).This study clearly demonstrates the utility of array CGH in defining high-resolution DNA copy number changes and refining amplifications. The resolution of array CGH technology combined with human genome database suggested the possible target genes present in the gained or lost clones.Osteosarcoma (OS) is a primary malignant tumor of bone arising from primitive bone-forming mesenchymal cells and it accounts for approximately 60% of malignant bone tumors in the first two decades of life [1]. These tumors typically arise in the metaphyseal regions of long bones, with the distal femur, proximal tibia and proximal humerus. A significant number of osteosarcomas are of conventional type which can be subdivided into three major categories based on their predominant differentiation of tumor cells: osteoblastic, chondroblastic, and fibroblastic. Currently, only the histological response (degree of necrosis) to therapy
Medulloblastoma outcome is adversely associated with overexpression of EEF1D, RPL30, and RPS20 on the long arm of chromosome 8
Massimiliano De Bortoli, Robert C Castellino, Xin-Yan Lu, Jeffrey Deyo, Lisa Sturla, Adekunle M Adesina, Laszlo Perlaky, Scott L Pomeroy, Ching C Lau, Tsz-Kwong Man, Pulivarthi H Rao, John YH Kim
BMC Cancer , 2006, DOI: 10.1186/1471-2407-6-223
Abstract: We analyzed 71 primary medulloblastomas for chromosomal copy number aberrations (CNAs) using comparative genomic hybridization (CGH). Among 64 tumors that we previously analyzed by gene expression microarrays, 27 were included in our CGH series. We analyzed clinical outcome with respect to CNAs and microarray results. We filtered microarray data using specific CNAs to detect differentially expressed candidate genes associated with survival.The most frequent lesions detected in our series involved chromosome 17; loss of 16q, 10q, or 8p; and gain of 7q or 2p. Recurrent amplifications at 2p23-p24, 2q14, 7q34, and 12p13 were also observed. Gain of 8q is associated with worse overall survival (p = 0.0141), which is not entirely attributable to MYC amplification or overexpression. By applying CGH results to gene expression analysis of medulloblastoma, we identified three 8q-mapped genes that are associated with overall survival in the larger group of 64 patients (p < 0.05): eukaryotic translation elongation factor 1D (EEF1D), ribosomal protein L30 (RPL30), and ribosomal protein S20 (RPS20).The complementary use of CGH and expression profiles can facilitate the identification of clinically significant candidate genes involved in medulloblastoma growth. We demonstrate that gain of 8q and expression levels of three 8q-mapped candidate genes (EEF1D, RPL30, RPS20) are associated with adverse outcome in medulloblastoma.Medulloblastoma is the most common malignant brain tumor of childhood. Treatment with surgery, radiation, and chemotherapy successfully cures many patients, but survivors can suffer significant long-term toxicities affecting their neurocognitive and growth potential. Despite clinical advances, up to 30% of children with medulloblastoma experience tumor progression or recurrence, for which no curative therapy exists [1]. The lack of more effective, less toxic therapies and the inability to stratify patients biologically result from imperfect understanding of the m
Genomic profiling of plasmablastic lymphoma using array comparative genomic hybridization (aCGH): revealing significant overlapping genomic lesions with diffuse large B-cell lymphoma
Chung-Che Chang, Xiaobo Zhou, Jesalyn J Taylor, Wan-Ting Huang, Xianwen Ren, Federico Monzon, Yongdong Feng, Pulivarthi H Rao, Xin-Yan Lu, Facchetti Fabio, Susan Hilsenbeck, Chad J Creighton, Elaine S Jaffe, Ching-Ching Lau
Journal of Hematology & Oncology , 2009, DOI: 10.1186/1756-8722-2-47
Abstract: Examination of genomic data in PL revealed that the most frequent segmental gain (> 40%) include: 1p36.11-1p36.33, 1p34.1-1p36.13, 1q21.1-1q23.1, 7q11.2-7q11.23, 11q12-11q13.2 and 22q12.2-22q13.3. This correlated with segmental gains occurring in high frequency in DLBCL (AIDS-related and non AIDS-related) cases. There were some segmental gains and some segmental loss that occurred in PL but not in the other types of lymphoma suggesting that these foci may contain genes responsible for the differentiation of this lymphoma. Additionally, some segmental gains and some segmental loss occurred only in PL and AIDS associated DLBCL suggesting that these foci may be associated with HIV infection. Furthermore, some segmental gains and some segmental loss occurred only in PL and PCM suggesting that these lesions may be related to plasmacytic differentiation.To the best of our knowledge, the current study represents the first genomic exploration of PL. The genomic aberration pattern of PL appears to be more similar to that of DLBCL (AIDS-related or non AIDS-related) than to PCM. Our findings suggest that PL may remain best classified as a subtype of DLBCL at least at the genome level.Plasmablastic lymphoma (PL), one of the most frequent oral malignancies in human immunodeficiency virus (HIV) infected patients, was first characterized by Delecluse et al [1]. They proposed that this constituted a new subtype of diffuse large B cell lymphoma (DLBCL); it was suggested as a distinct entity based on its blastic morphology, its clinical behavior involving predominantly extramedullary sites (particularly oral cavity), and its limited antigenic phenotype data suggesting differentiation toward plasmacytic differentiation (CD20-, CD79a+ and VS38c+). The incidence of PL has increased following the introduction of highly active antiretroviral therapy (HAART) [2,3]. By WHO Classification, PL is categorized as a subtype of DLBCL associated with HIV and Epstein-Barr virus [1,4,5].Recent morph
Invariant Recognition of Rectangular Biscuits with Fuzzy Moment Descriptors, Flawed Pieces Detection
Pulivarthi Srinivasa Rao, Sheli Sinha Chaudhuri,& Romesh Laishram
International Journal of Image Processing , 2010,
Abstract: In this paper a new approach for invariant recognition of broken rectangularbiscuits is proposed using fuzzy membership-distance products, called fuzzymoment descriptors. The existing methods for recognition of flawed rectangularbiscuits are mostly based on Hough transform. However these methods areprone to error due to noise and/or variation in illumination. Fuzzy momentdescriptors are less sensitive to noise thus making it an effective approach andinvariant to the above stray external disturbances. Further, the normalization andsorting of the moment vectors make it a size and rotation invariant recognitionprocess .In earlier studies fuzzy moment descriptors has successfully beenapplied in image matching problem. In this paper the algorithm is applied inrecognition of flawed and non-flawed rectangular biscuits. In general theproposed algorithm has potential applications in industrial quality control.
Studies of Climate Change with Statistical-Dynamical Models: A Review  [PDF]
Sergio H. Franchito, Vadlamudi B. Rao
American Journal of Climate Change (AJCC) , 2015, DOI: 10.4236/ajcc.2015.41006
Abstract: The cause-effect relationship is not always possible to trace in GCMs because of the simultaneous inclusion of several highly complex physical processes. Furthermore, the inter-GCM differences are large and there is no simple way to reconcile them. So, simple climate models, like statistical-dynamical models (SDMs), appear to be useful in this context. This kind of models is essentially mechanistic, being directed towards understanding the dependence of a particular mechanism on the other parameters of the problem. In this paper, the utility of SDMs for studies of climate change is discussed in some detail. We show that these models are an indispensable part of hierarchy of climate models.
Corticosteroid - Induced Avascular Necrosis of Head of Femur in a Patient with Pemphigus Vulgaris
Hanumanthappa H,Rao Raghavendra
Indian Journal of Dermatology, Venereology and Leprology , 2000,
Abstract: Corticosteroid - induced avascular necrosis of head of femur is reported in an elderly woman patient with pemphigus.
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