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TRANSCRIPTION PROFILING OF ART NA(I)VE KAPOSI SARCOMA LESIONS IN PATIENTS FROM LILONGWE, MALAWI

TRANSCRIPTION PROFILING OF ART NA(I)VE KAPOSI SARCOMA LESION...

17th International Workshop on Kaposi’s Sarcoma Associated Herpesvirus (KSHV))and Related Agents(第十七届卡波西肉瘤孢疹病毒(KSHV)及相关病毒国际年会)

作者： Mina Hosseinipour Kristen Sweet Jie Xiong Dan Namarika Albert Mwafongo Michael Nyirenda Loreen Chiwoko Deborah Kamwendo Irving Hoffman Jeanette Lee Sam Phiri Blossom Damania Dirk Dittmer Department of Microbiology and Immunology Curriculum in Genetics UNC Chapel Hill USA Department of Medicine UNC Chapel Hill USA University of Arkansas Center for Infectious Diseases UNC Chapel Hill USA University of Arkansas Center for Infectious Diseases UNC Chapel Hill USA Program in Global Oncology Lineberger Comprehensive Cancer Center and Center for AIDS Research (CfAR) Kamuzu Central Hospital UNC Project Lilongwe Malawi Lighthouse Trust Center for Infectious Diseases UNC Chapel Hill USA AIDS malignancy consortium (AMC) Center for Infectious Diseases UNC Chapel Hill USA Department of Medicine UNC Chapel Hill USA University of Arkansas AIDS malignancy consortium (AMC) UNC Project Lilongwe Malawi Department of Microbiology and Immunology Curriculum in Genetics UNC Chapel Hill USA Department of Statistics and Operations Research UNC Chapel Hill USA

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Clustering of protein structures using hydrophobic free energy and solvent accessibility of proteins

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Physical Review E 2006年第3期73卷 031920-031920页

作者： Z. G. Yu V. V. Anh K. S. Lau L. Q. Zhou Program in Statistics and Operations Research Queensland University of Technology GPO Box 2434 Brisbane Queensland 4001 Australia School of Mathematics and Computing Science Xiangtan University Hunan 411105 China Department of Mathematics Chinese University of Hong Kong Shatin Hong Kong China

The hydrophobic free energy and solvent accessibility of amino acids are used to study the relationship between the primary structure and structural classification of large proteins. A measure representation and a Z curve representation of protein sequences are proposed. Fractal analysis of the measure and Z curve representations of proteins and multifractal analysis of their hydrophobic free energy and solvent accessibility sequences indicate that the protein sequences possess correlations and multifractal scaling. The parameters from the fractal and multifractal analyses on these sequences are used to construct some parameter spaces. Each protein is represented by a point in these spaces. A method is proposed to distinguish and cluster proteins from the α, β, α+β, and α∕β structural classes in these parameter spaces. Fisher’s linear discriminant algorithm is used to give a quantitative assessment of our clustering on the selected proteins. Numerical results indicate that the discriminant accuracies are satisfactory. In particular, they reach 94.12% and 88.89% in separating β proteins from {α,α+β,α∕β} proteins in a three-dimensional space.

关键词： Proteins

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Accuracy of commercial geocoding: Assessment and implications

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Epidemiologic Perspectives and Innovations 2006年第1期3卷 1-12页

作者： Whitsel, Eric A. Quibrera, P. Miguel Smith, Richard L. Catellier, Diane J. Liao, Duanping Henley, Amanda C. Heiss, Gerardo Departments of Epidemiology and Medicine University of North Carolina Cardiovascular Disease Program Chapel Hill NC 27514 137 East Franklin Street United States Department of Epidemiology University of North Carolina Cardiovascular Disease Program Chapel Hill NC 27514 137 East Franklin Street United States Department of Statistics and Operations Research University of North Carolina 201 Smith Building 128 Chapel Hill NC 27599 United States Department of Biostatistics University of North Carolina Collaborative Studies Coordinating Center Chapel Hill NC 27514 137 East Franklin Street United States Department of Health Evaluation Sciences Pennsylvania State University College of Medicine Hershey PA 17033 600 Centerview Drive United States University of North Carolina Reference Department Geographic Information Services Chapel Hill NC 27599 United States

Background: Published studies of geocoding accuracy often focus on a single geographic area, address source or vendor, do not adjust accuracy measures for address characteristics, and do not examine effects of inaccuracy on exposure measures. We addressed these issues in a Women's Health Initiative ancillary study, the Environmental Epidemiology of Arrhythmogenesis in WHI. Results: Addresses in 49 U.S. states (n = 3,615) with established coordinates were geocoded by four vendors (A-D). There were important differences among vendors in address match rate (98%;82%;81%;30%), concordance between established and vendor-assigned census tracts (85%;88%;87%;98%) and distance between established and vendor-assigned coordinates (mean ρ [meters]: 1809;748;704;228). Mean ρ was lowest among street-matched, complete, zip-coded, unedited and urban addresses, and addresses with North American Datum of 1983 or World Geodetic System of 1984 coordinates. In mixed models restricted to vendors with minimally acceptable match rates (A-C) and adjusted for address characteristics, within-address correlation, and among-vendor heteroscedasticity of ρ, differences in mean ρ were small for street-type matches (280;268;275), i.e. likely to bias results relying on them about equally for most applications. In contrast, differences between centroid-type matches were substantial in some vendor contrasts, but not others (5497;4303;4210) p _interaction < 10^-4, i.e. more likely to bias results differently in many applications. The adjusted odds of an address match was higher for vendor A versus C (odds ratio = 66, 95% confidence interval: 47, 93), but not B versus C (OR = 1.1, 95% CI: 0.9, 1.3). That of census tract concordance was no higher for vendor A versus C (OR = 1.0, 95% CI: 0.9, 1.2) or B versus C (OR = 1.1, 95% CI: 0.9, 1.3). Misclassification of a related exposure measure - distance to the nearest highway - increased with mean ρ and in the absence of confounding, non-dif

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Fractal and dynamical language methods to construct phylogenetic tree based on protein sequences from complete genomes

Fractal and dynamical language methods to construct phylogen...

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First International Conference on Natural Computation, ICNC 2005

作者： Yu, Zu-Guo Anh, Vo Zhou, Li-Quan Program in Statistics and Operations Research Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia School of Mathematics and Computing Science Xiangtan University Hunan 411105 China

The complete genomes of living organisms have provided much information on their phylogenetic relationships. In the past few years, we proposed three alternative methods to model the noise background in the composition vector of protein sequences from a complete genome. The first method is based on the frequencies of the 20 kinds of amino acids appearing in the genome and the multiplicative model. The second method is based on the iterated function system model in fractal geometry. The last method is based on the relationship between a word and its two sub-words in the theory of symbolic dynamics. Here we introduce these methods. The complete genomes of prokaryotes and eukaryotes are selected to test these algorithms. Our distance-based phylogenetic tree of prokaryotes and eukaryotes agrees with the biologists' "tree of life" based on the 16S-like rRNA genes in a majority of basic branches and most lower taxa. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Genetic engineering

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Multifractal and correlation analyses of protein sequences from complete genomes

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Physical Review E 2003年第2期68卷 021913-021913页

作者： Zu-Guo Yu Vo Anh Ka-Sing Lau Program in Statistics and Operations Research Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia Department of Mathematics Xiangtan University Hunan 411105 China Department of Mathematics Chinese University of Hong Kong Shatin Hong Kong China

A measure representation of protein sequences similar to the measure representation of DNA sequences proposed in our previous paper [Yu et al., Phys. Rev. E 64, 031903 (2001)] and another induced measure are introduced. Multifractal analysis is then performed on these two kinds of measures of a large number of protein sequences derived from corresponding complete genomes. From the values of the Dq (generalized dimensions) spectra and related Cq (analogous specific heat) curves, it is concluded that these protein sequences are not completely random sequences. For substrings with length K=5, the Dq spectra of all organisms studied are multifractal-like and sufficiently smooth for the Cq curves to be meaningful. The Cq curves of all bacteria resemble a classical phase transition at a critical point. But the “analogous” phase transitions of higher organisms studied exhibit the shape of double-peaked specific heat function. But for the classification problem, the multifractal property is not sufficient. When the measure representations of protein sequences from complete genomes are considered as time series, a method based on correlation analysis after removing some memory from the time series is proposed to construct a phylogenetic tree. This construction is shown to be reasonably satisfactory.

关键词： Proteins

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Monitoring the navy's strategic reserve of ozone-depleting substances

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NAVAL ENGINEERS JOURNAL 2002年第4期114卷 95-104页

作者： Smith, DE Breslin, DA Toms, GS Norton, P DENNIS E. SMITH PH.D. is currently a statistical consultant for GEO-CENTERS INC. He received a B.A. in Mathematics (magna cum laude)from Wabash College and an M.S. in mathematics an M.S. in statistics and a Ph.D. in statistics from the University of Wisconsin. From November 1973 until February 1999 he was president and principal statistician at Desmatics Inc. where he participated in a number of studies involving the application of statistical methods to various technical problems in the Navy's environmental-protection and auxiliary-machinery programs. Dr. Smith was instrumental in developing the statistical procedures underlying the Navy's ODS reserve monitoring plan. DAVID A. BRESLIN P.E. is the director of technical operations for the Naval Surface Warfare Center and chairs the ASNE/SNAME Joint Committee on Environmental Engineering. He received a master of science in aerospace engineering from Virginia Tech a master of engineering administration in industrial and systems engineering from Virginia Tech and a bachelor of engineering in mechanical engineering from Stevens Institute of Technology. From 1993 to 1997 he was the program manager of the Naval Sea Systems Command's CFC and Halon Elimination Program and played a critical role in establishing the Navy's strategic reserve of ozone-depleting substances. Because of his many efforts he received a Stratospheric Ozone Protection Award in 1995 from the U.S. Environmental Protection Agency in recognition of “exceptional contributions to global environmental protection”. GREGORY S. TOMS P.E. is the CFC &Halon Elimination Program Manager for the Naval Sea Systems Command (NAVSEA). He received a master of science degree in mechanical engineering from the University of Maryland and a B.S. degree in mechanical engineering from West Virginia University. From 1984 to 1997 he was employed at the Naval Surface Warfare Center Carderock Division Annapolis Detachment (formerly David Taylor Research Center)where he worked on the development of advanced cent

The domestic production of the most powerful ozone-depleting substances (ODSs) has permanently ceased and the abundant supplies of a number of refrigerants, fire-fighting agents, and solvents, once taken for granted, are now a thing of the past. The Navy has adopted a successful strategy for addressing the threat posed by the unavailability of ODSs. That strategy includes relying on a strategic reserve of ODSs. Considering that the strategic reserve will play a critical role in sustained Fleet operations into the middle of the century, it is important to record the history of the reserve and to document lessons learned in order to educate future generations that may face similar challenges. This is the third of three papers that cover all aspects of the Navy's strategic reserve of ODSs. Breslin (1999) documented the history of the Navy's effort to size, establish, and monitor a reserve designed to support Fleet operations until the middle of the century. Breslin, Smith, and Toms (2000) addressed in detail the process used to estimate the required size of the reserve, including the survey method, statistical analyses, and sizing algorithms. This paper discusses the Navy's plan for monitoring the Navy's strategic reserves of ODSs and describes the methods used in the monitoring process. In particular it discusses the underlying assumptions and statistical techniques associated with the Navy's prediction of the expected drawdown of the reserves. A comparison of actual data, collected since the strategic reserves began operations in 1995, with the predicted reserve drawdown, is included in the paper.

关键词： Marine engineering

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A statistical method for estimating the life expectancy of certain shipboard equipment

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NAVAL ENGINEERS JOURNAL 2002年第1期114卷 27-32页

作者： Smith, DE Breslin, DA Toms, GS DENNIS E. SMITH PH.D. is a statistical consultant for Geo-Centers Inc. He received a B.A. in mathe-matics (magna cum laude) from Wabash College and an M.S. in mathematics an M.S. in statistics and a Ph.D. in statistics from the University of Wisconsin. From November 1973 until February 1999 he was President and Principal Statistician at Desmatics Inc. where he participated in a number of studies involving the application of statistical methods to various technical problems in the Navy's environmental-protection and auxiliary-machinery programs. Dr. Smith was instrumental in developing the statistical procedures underlying the Navy's ODS reserve monitoring plan. DAVID A. BRESLIN P.E. is the Director of Technical Operations for the Naval Surface Warfare Center and is the chairperson of ASNE's Committee on Environmental Engineering. He received a master of science degree in aerospace engineering from Virginia Tech a master of engineering administration in indus-trial & systems engineering from Virginia Tech and a bachelor of engineering in mechanical engineering from Stevens Institute of Technology. From 1993 to 1997 he was the program manager of the Naval Sea Systems Command's CFC & Halon Elimination Program and played a critical role in establishing the Navy's strategic reserve of ozone-depleting substances. Because of his many efforts he received a Stratospheric Ozone Protection Award in 1995 from the U.S. Environmental Protection Agency in recogni-tion of “exceptional contributions to global environmental protection”. GREGORY S. TOMS P.E. is the CFC & Halon Elimination Program Manager for the Naval Sea Systems Command (NAVSEA). He received a master of science degree in mechanical engineering from the University of Maryland and a B.S. degree in mechanical engineering from West Virginia University. From 1984 to 1997 he was employed at the Naval Surface Warfare Center Carderock Division Annapolis Detachment (formerly David Taylor Research Center) where he worked on the development of advanced cent

This paper reviews an inexpensive statistical-sampling methodology that can be used to determine the attrition rates of certain types of shipboard equipment. The methodology relies on surveys that are conducted in conjunction with regularly scheduled ship visits over a period of time and a statistical analysis of the survey results. The statistical technique allows for reasonably accurate estimates to be made of attrition rates. The specific example cited in this paper is related to galley-type refrigeration equipment, such as salad chillers, beverage dispensers, et cetera. In the case of galley-type refrigeration equipment, the Navy needs to know whether the Fleet's inventory of equipment relying on Class I Ozone-Depleting Substances (ODSs) will be replaced through natural attrition by the end of fiscal year (FY) 2005, at which time supplies of ODS-based refrigerants will no longer be available for use by ship galleys. This paper outlines the process used to gather data, the analysis of the data, and concludes that the Navy's inventory of galley equipment using Class I ODSs will be replaced through natural attrition by the end of FY05. The methodology reviewed by this paper has wider applications. For various types of shipboard equipment, the methodology can also be used to estimate with reasonable accuracy life expectancies, configurations, conditions, and other items of interest.

关键词： Ship equipment

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Almost-sure exponential behavior of a stochastic anderson model with continuous space parameter

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Stochastics 1998年第3-4期62卷 251-273页

作者： Ren.A. Carmona[a] Frederi G. Viens[b] [a] Statistics and Operations Research Program Princeton University Princeton [b] Department of Mathematics University of North Texas Denton

We study the almost-sure large time exponential growth of the solution to a linear stochastic parabolic equation with continuous space parameter, and a Gaussian-correlated potential that is white noise in time and homogeneous in space. We use the evolution form of that equation,for which existence and uniqueness are known. We establish a Feynman-Kac formula for the solution. By using a method of discretization of time and space, we prove that for small diffusion parameter κ, there is a deterministic constant c such that almost surely

关键词： Stochastic partial differential equation Lyapunov exponent spatial discretization Gaussian estimates stochastic Feynman-Kac formulastochastic evolution equation AMS Subject Classification Primary: 60H15 Secondary: 60G17

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Diffusive hydrodynamic limits for systems of interacting diffusions with finite range random interaction

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COMMUNICATIONS IN MATHEMATICAL PHYSICS 1997年第3期188卷 565-584页

作者： Carmona, RA Xu, L Statistics & Operations Research Program CEOR Princeton University Princeton NJ 08544 USA US

We consider a system of interacting diffusive particles with finite range random interaction. The variables can be interpreted as charges at sites indexed by a periodic multidimensional lattice. The equilibrium states of the system are canonical Gibbs measures with finite range random interaction. Under the diffusive scaling of lattice spacing and time, we derive a deterministic nonlinear diffusion equation for the time evolution of the macroscopic charge density. This limit is almost sure with respect to the random environment.

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AFFINE-SCALING TRAJECTORIES ASSOCIATED WITH A SEMIINFINITE LINEAR program

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MATHEMATICS OF operations research 1995年第1期20卷 163-174页

作者： VANDERBEI, RJ Program in Statistics and Operations Research Princeton University Princeton New Jersey 08544

Semi-infinite linear programs often arise as the limit of a sequence of approximating linear programs. Hence, studying the behavior of extensions of linear programming algorithms to semi-infinite problems can yield valuable insight into the behavior of the underlying linear programming algorithm when the number of constraints or the number of variables is very large. In this paper, we study the behavior of the affine-scaling algorithm on a particular semi-infinite linear programming problem. We show that the continuous trajectories converge to the optimal solution but that, for any strictly positive step, there are starting points for which the discrete algorithm converges to nonoptimal boundary points.

关键词： SEMIINFINITE programMING AFFINE-SCALING ALGORITHMS INTERIOR POINT METHODS LINEAR programMING THEORY LINEAR programMING ALGORITHMS

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