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Uncertainty in Geometric Computations 1

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Classification with binary gene expressions

丛书名： The Springer International Series in Engineering and Computer Science

2002年

作者： Joab Winkler mahesan Niranjan

ISBN: (数字)9781461508137

ISBN: (纸本)9780792373094;9781461352525

This book contains the proceedings of the workshop Uncertainty in Geomet ric Computations that was held in Sheffield, England, July 5-6, 2001. A total of 59 delegates from 5 countries in Europe, North America and Asia attended the workshop. The workshop provided a forum for the discussion of com putational methods for quantifying, representing and assessing the effects of uncertainty in geometric computations. It was organised around lectures by invited speakers, and presentations in poster form from participants. Computer simulations and modelling are used frequently in science and engi neering, in applications ranging from the understanding of natural and artificial phenomena, to the design, test and manufacturing stages of production. This widespread use necessarily implies that detailed knowledge of the limitations of computer simulations is required. In particular, the usefulness of a computer simulation is directly dependent on the user's knowledge of the uncertainty in the simulation. Although an understanding of the phenomena being modelled is an important requirement of a good computer simulation, the model will be plagued by deficiencies if the errors and uncertainties in it are not consid ered when the results are analysed. The applications of computer modelling are large and diverse, but the workshop focussed on the management of un certainty in three areas : Geometric modelling, computer vision, and computer graphics.

关键词： Applications of Mathematics Geometry Programming Techniques Numerical Analysis Computer Imaging, Vision, Pattern Recognition and Graphics Computer-Aided Engineering (CAD, CAE) and Design

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Journal of Biomedical Science and Engineering 2009年第6期2卷 390-399页

作者： Salih Tuna mahesan Niranjan 不详

Microarray gene expression measurements are reported, used and archived usually to high numerical precision. However, properties of mRNA molecules, such as their low stability and availability in small copy numbers, and the fact that measurements correspond to a population of cells, rather than a single cell, makes high precision meaningless. Recent work shows that reducing measurement precision leads to very little loss of information, right down to binary levels. In this paper we show how properties of binary spaces can be useful in making inferences from microarray data. In particular, we use the Tanimoto similarity metric for binary vectors, which has been used effectively in the Chemoinformatics literature for retrieving chemical compounds with certain functional properties. This measure, when incorporated in a kernel framework, helps recover any information lost by quantization. By implementing a spectral clustering framework, we further show that a second reason for high performance from the Tanimoto metric can be traced back to a hitherto unnoticed systematic variability in array data: Probe level uncertainties are systematically lower for arrays with large numbers of expressed genes. While we offer no molecular level explanation for this systematic variability, that it could be exploited in a suitable similarity metric is a useful observation in itself. We further show preliminary results that working with binary data considerably reduces variability in the results across choice of algorithms in the preprocessing stages of microarray analysis.

关键词： Microarray Gene Expression Binary Gene Expressions High Numerical Precision mRNA Mole-cules

Sentinel lymph node biopsy in renal malignancy: The past, present and future

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World Journal of Nephrology 2016年第2期5卷 182-188页

作者： Tharani mahesan Alberto Coscione Ben Ayres Nick Watkin Department of Urology St George’s Hospital

Sentinel lymph node biopsy （SLNB） is now an establishedtechnique in penile and pelvic cancers, resulting in alower mortality and morbidity when compared withthe traditional lymph node dissection. In renal cancer however, despite some early successes for the SLNB technique, paucity of data remains a problem, thus lymph node dissection and extended lymph node dissection remain the management of choice in clinically node positive patients, with surveillance of lymph nodes in those who are clinically node negative. SLNB is a rapidly evolving technique and the introduction of new techniques such as near infra-red fuorescence optical imaging agents and positron emission tomography/computed tomography scans, may improve sensitivity. Evidence in support of this has already been recorded in bladder and prostate *** the lack of large multi-centre studies and issues around false negativity currently prevent its widespread use, with evolving techniques improving accuracy and the support of large-scale studies, SLNB does have the potential to become an integral part of staging in renal malignancy.

关键词： Sentinel lymph node biopsy Dynamic sentinel node Renal malignancy Lymphoscintigraphy Near infra-red fuorescence Penile cancer Lymphatic drainage

Nutritional Correlates of Women with a History of Gestational Diabetes and Insulin Resistance in the National Health and Nutrition Examination Survey (NHANES) 2000-2010

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Journal of Diabetes Mellitus 2016年第1期6卷 69-76页

作者： Dotun Ogunyemi Amy Whitten Arnold M. mahesan Anthea B. M. Paul Judy Boura Beaumont Health System Royal Oak USA William Beaumont School of Medicine Oakland University Rochester USA Department of OBGYN St. John Hospital Medical Center Detroit USA

Objective: To evaluate the associations of gestational diabetes (GDM) history with dietary intake, nutritional status, insulin resistance, demographic, and anthropometrical data. Materials & Methods: This cross-sectional study used data from the National Health and Nutrition Examination Survey for the years 2000-2010. Data analysis was based on 290 women who reported a history of GDM compared to 4239 women who denied a GDM history. Insulin resistance [HOMA_IR = (fasting insulin in mU/mL × fasting glucose in mmol/L)/405] was calculated. Pearson correlation, Wilcoxon rank sum tests, Student’s t-tests, and chi-square analysis were used while linear regression assessed independent associations. Results: The median time-lapse from the diagnosis of GDM was 15 years. Women with a GDM history had significantly higher body mass index (BMI), other anthropometric measurements, diastolic blood pressures and insulin resistance. They were also more likely to be Hispanic, have delivered macrosomic infants, and delivered via cesarean. Previous GDM history compared to non-GDM subjects had significantly higher dietary intakes of energy calories, protein, total fat, saturated fatty acids, mono-saturated fatty acids, and cholesterol. Within the entire cohort, increasing insulin resistance was also associated with lower income, less college education, Hispanic or African American ethnicity, obesity, higher systolic and diastolic blood pressures, and with higher dietary cholesterol but lower intake of dietary fiber and micronutrients. Regression analyses showed that GDM history, Hispanic ethnicity, BMI, dietary intake of cholesterol and decreasing income were independently predictive of insulin resistance. Conclusion: The data confirm that even many years after a pregnancy associated with GDM, women with a history of GDM still report significantly higher dietary intakes of energy calories, protein, and fat with no corresponding increase in consumption of dietary fiber or minerals and vit

关键词： Macrosomia Gestational Diabetes Insulin Resistance Nutrition

Insulin Resistance in Pregnancy Is Correlated with Decreased Insulin Receptor Gene Expression in Omental Adipose: Insulin Sensitivity and Adipose Tissue Gene Expression in Normal Pregnancy

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Journal of Diabetes Mellitus 2016年第1期6卷 100-111页

作者： Arnold M. mahesan Dotun Ogunyemi Eric Kim Anthea B. M. Paul Y.-D. Ida Chen Jones Institute for Reproductive Medicine Eastern Virginia Medical School Norfolk VA USA Department of Obstetrics and Gynecology Oakland University William Beaumont School of Medicine Royal Oak MI USA LA Biomedical Research Center Harbor-UCLA Medical Center Torrance CA USA

Aims: To determine correlations of insulin sensitivity to gene expression in omental and subcutaneous adipose tissue of non-obese, non-diabetic pregnant women. Methods: Microarray gene profiling was performed on subcutaneous and omental adipose tissue from 14 patients and obtained while fasting during non-laboring Cesarean section, using Illumina HumanHT-12 V4 Expression BeadChips. Findings were validated by real-time PCR. Matusda-Insulin sensitivity index (IS) and homeostasis model assessment of insulin resistance (HOMA-IR) were calculated from glucose and insulin levels obtained from a frequently sampled oral glucose tolerance test, and correlated with gene expression. Results: Of genes differentially expressed in omental vs. subcutaneous adipose, in omentum 12 genes were expressed toward insulin resistance, whereas only 5 genes were expressed toward insulin sensitivity. In particular, expression of the insulin receptor gene (INSR), which initiates the insulin signaling cascade, is strongly positively correlated with IS and negatively with HOMA-IR in omental tissue (r = 0.84). Conclusion: Differential gene expression in omentum relative to subcutaneous adipose showed a pro-insulin resistance profile in omentum. A clinical importance of omental adipose is observed here, as downregulation of insulin receptor in omentum is correlated with increased systemic insulin resistance.

关键词： DEG Insulin Resistance Insulin Sensitivity Insulin Signaling Pathway Adipose Tissue in Pregnancy Carbohydrate Metabolism Diabetic Pathways

Differentially expressed genes in adipocytokine signaling pathway of adipose tissue in pregnancy

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Journal of Diabetes Mellitus 2013年第2期3卷 86-95页

作者： Dotun Ogunyemi Jun Xu Arnold M. mahesan Steve Rad Eric Kim Jacqueline Yano Carolyn Alexander Jerome I. Rotter Y.-D. Ida Chen Department of Endocrinology Cedars-Sinai Medical Center Los Angeles USA Department of Medical Education David Geffen School of Medicine at UCLA Los Angeles USA Department of Medical Genetics Cedars-Sinai Medical Center Los Angeles USA Department of Obstetrics and Gynecology Cedars-Sinai Medical Center Los Angeles USA

Objective: To profile the differential gene expression of the KEGG Adipocytokine Signaling pathway in omental compared to subcutaneous tissue in normal pregnancy. Study Design: Subjects included 14 nonobese, normal glucose tolerant, healthy pregnant women. Matched omental and subcutaneous tissue were obtained at elective cesarean delivery. Gene expression was evaluated using microarray and validated by RT-PCR. Differential gene expression was defined as ≥1.5 fold increase at p < 0.05. Results: Six genes were significantly downregulated with two upregulated genes in omental tissue. Downregulation of Adiponectin and Insulin Receptor substrate, key genes mediating insulin sensitivity, were observed with borderline upregulation of GLUT-1. There were downregulations of CD36 and acyl-CoA Synthetase Long-chain Family Member 1which are genes involved in fatty acid uptake and activation. There was a novel expression of Carnitine palmitoyltransferase 1C. Conclusion: Differential gene expression of Adipocytokine Signaling Pathway in omental relative to subcutaneous adipose tissue in normal pregnancy suggests a pattern of insulin resistance, hyperlipidemia, and inflammation.

关键词： Adipose Tissue Pregnancy Adipocytokine Pathway Insulin Resistance

Classification with binary gene expressions

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