Physical Sciences and Mathematics Commons^™

Collaborative Targeted Maximum Likelihood Estimation, Mark J. Van Der Laan, Susan Gruber

U.C. Berkeley Division of Biostatistics Working Paper Series

Collaborative double robust targeted maximum likelihood estimators represent a fundamental further advance over standard targeted maximum likelihood estimators of causal inference and variable importance parameters. The targeted maximum likelihood approach involves fluctuating an initial density estimate, (Q), in order to make a bias/variance tradeoff targeted towards a specific parameter in a semi-parametric model. The fluctuation involves estimation of a nuisance parameter portion of the likelihood, g. TMLE and other double robust estimators have been shown to be consistent and asymptotically normally distributed (CAN) under regularity conditions, when either one of these two factors of the likelihood of the data is …

The Hd 40307 Planetary System: Super-Earths Or Mini-Neptunes?, Rory Barnes, Brian Jackson, Sean N. Raymond, Andrew A. West, Richard Greenberg

Brian Jackson

Three planets with minimum masses less than 10 M⊕ orbit the star HD 40307, suggesting these planets may be rocky. However, with only radial velocity data, it is impossible to determine if these planets are rocky or gaseous. Here we exploit various dynamical features of the system in order to assess the physical properties of the planets. Observations allow for circular orbits, but a numerical integration shows that the eccentricities must be at least 10–4. Also, planets b and c are so close to the star that tidal effects are significant. If planet b has tidal parameters similar to the …

The Impact Of Midbrain Cauterize Size On Auditory And Visual Responses' Distribution, Yan Zhang

Mathematics Theses

This thesis presents several statistical analysis on a cooperative project with Dr. Pallas and Yuting Mao from Biology Department of Georgia State University. This research concludes the impact of cauterize size of animals’ midbrain on auditory and visual response in brains. Besides some already commonly used statistical analysis method, such as MANOVA and Frequency Test, a unique combination of Permutation Test, Kolmogorov-Smirnov Test and Wilcoxon Rank Sum Test is applied to our non-parametric data. Some simulation results show the Permutation Test we used has very good powers, and fits the need for this study. The result confirms part of the …

Race, Place, And Identity: Examining Place Identity In The Racialized Landscape Of Buckhead, Atlanta, Robert Edward Cochran

Geosciences Theses

This thesis examines the role of racialized practices in the discourses and processes that alter place identity. Drawing on ethnography from the East Village of Buckhead, a once vibrant nightlife district in Atlanta, I examine how discourses of danger, colorblindness, and the race card have been employed to “whitewash” the discussions about the redevelopment of the Village. In effect, the business and civic elite of Atlanta (and Buckhead) deployed racialized conceptualizations of group identity. In particular, they utilized “public safety” discourses to influence the Atlanta city government to support the redevelopment effort. This led to the elimination of the establishments …

Analysis Of Stream Runoff Trends In The Blue Ridge And Piedmont Of Southeastern United States, Usha Kharel

Geosciences Theses

The purpose of the study was to examine the temporal trends of three monthly variables: stream runoff, rainfall and air temperature and to find out if any correlation exists between rainfall and stream runoff in the Blue Ridge and Piedmont provinces of the southeast United States. Trend significance was determined using the non-parametric Mann-Kendall test on a monthly and annual basis. GIS analysis was used to find and integrate the urban and non-urban stream gauging, rainfall and temperature stations in the study area. The Mann-Kendall test showed a statistically insignificant temporal trend for all three variables. The correlation of 0.4 …

Role Of Bcl-2 Family Members To Promote Glucocorticoid –Induced Apoptosis By Mek Inhibitors In Leukemic Cells, Anila Rambal

Theses and Dissertations

Glucocorticoids (GC) are common components of many chemotherapeutic regimens for lymphoid malignancies. GC-induced apoptosis involves an intrinsic BCL-2 family-regulated pathway. It has been shown that BIM (BCL-2 interacting mediator of cell death), a BH3-only pro-apoptotic protein, is up-regulated by dexamethasone (Dex) treatment in acute lymphoblastic leukemia (ALL) cells. Furthermore, BIM is inactivated by extracellular signal-regulated kinase (ERK)-mediated phosphorylation. We therefore hypothesized co-treatment with Dex and MEK/ERK inhibitors would promote apoptosis in ALL cells through BIM up-regulation and activation. We show here that a MEK inhibitor, PD184352 synergistically enhances Dex lethality in CCRF-CEM (T-ALL) cells. Co-treatment with Dex and PD184352 results …

Veritas Observations Of The Bl Lac Object 1es 1218+304, P. T. Reynolds, Et. Al.

Physical Sciences Publications

The VERITAS collaboration reports the detection of very-high-energy gamma-ray emission from the high-frequency-peaked BL Lac object 1ES 1218+304 located at a redshift of z = 0.182. A gamma-ray signal was detected with a statistical significance of 10.4 standard deviations (10.4σ) for the observations taken during the first three months of 2007, confirming the discovery of this object made by the MAGIC collaboration. The photon spectrum between ~160 GeV and ~1.8 TeV is well described by a power law with an index of Γ = 3.08 ± 0.34stat ± 0.2sys. The integral flux is Φ(E>200GeV) = (12.2 ± 2.6) × …

The Rotational Spectrum Of The Fed Radical In Its X4Δ State, Measured By Far-Infrared Laser Magnetic Resonance, Michael Jackson, Lyndon R. Zink, Jonathan P. Towle, Neil Riley, John M. Brown

All Faculty Scholarship for the College of the Sciences

Transitions between the spin-rotational levels of the FeD radical in the v = 0level of the X ⁴Δ ground state have been detected by the technique of laser magnetic resonance at far-infrared wavelengths. Pure-rotational transitions have been observed for the three lowest spin components. Lambda-type doubling is resolved on all the observed transitions; nuclear hyperfine structure is not observed. The energy levels of FeD are strongly affected by the breakdown of the Born–Oppenheimer approximation and cannot be modeled accurately by an effective Hamiltonian. The data are therefore fitted to an empirical formula to yield term values and g-factors for …

Quaternions, Octonions, And The Quantization Of Games, Aden Omar Ahmed

Dissertations and Theses

We present an effect on classical games that is obtained by replacing the notion of probability distribution with the notions of quantum superposition and measurement. Our particular focus will be on two and three player games where each player has precisely two pure strategic choices. Games in normal form are represented as "payoff" functions.

Game quantization requires the extension of these functions to much larger domains. The main result of this work is the co-ordinatization of these extended functions by either the quaternions or octonions in order to obtain computationally friendly versions of these functions. This computational capability is then …

Adding Escience Assets To The Data Web, Herbert H. Van De Sompel, Carl Lagoze, Michael L. Nelson, Simeon Warner, Robert Sanderson, Pete Johnston

Computer Science Faculty Publications

Aggregations of Web resources are increasingly important in scholarship as it adopts new methods that are data-centric, collaborative, and networked-based. The same notion of aggregations of resources is common to the mashed-up, socially networked information environment of Web 2.0. We present a mechanism to identify and describe aggregations of Web resources that has resulted from the Open Archives Initiative - Object Reuse and Exchange (OAI-ORE) project. The OAI-ORE specifications are based on the principles of the Architecture of the World Wide Web, the Semantic Web, and the Linked Data effort. Therefore, their incorporation into the cyberinfrastructure that supports eScholarship will …

Proc Report In Style, Wendy Boberg

Conference on Applied Statistics in Agriculture

I would like to demonstrate how you can create colorful PDF files using ODS (Output Delivery System) with different predefined style templates for the layout and color scheme of both tables and graphs. There are a few different ways you can customize your reports in the Report Procedure. Traffic lighting is a very popular technique and can be achieved by changing the font and/or the background colors. I prefer to customize my reports by adding background color to highlight a row, column, and/or cell in a table.

I will share my favorite styles and show you how to look at …

Using Time Series To Study Effect Of Air Temperature On Body Temperature Of Cows In Puerto Rico, Y. Zeng, A. M. Parkhurst, J. Pantoja

Conference on Applied Statistics in Agriculture

Body temperature is an important measure for monitoring the health status of cows. The objective of this study is to (1) determine if a cow’s body temperature is related to ambient temperature, relative humidity, and/or temperature humidity index (THI); (2) look for signs of heat stress. The data are collected at five minute intervals during the summer months (December through February) in Puerto Rico. Regression analysis and a succession of time series analyses are conducted in time domains. Nonparametric spectral estimation and cross-spectra analysis are also performed in the frequency domain. A search for indications of heat stress is performed …

Comparing Experimental Designs For A Bi-Logistical Model Used To Estimate Heat Stress When Moving Feedlot Cattle, X. Li, A. M. Parkhurst, T. L. Mader

Conference on Applied Statistics in Agriculture

Processing and handling cattle requires expenditure of energy causing an elevation of body temperature, depending on the ambient conditions. Therefore, caution should be exercised in moving cattle, especially during summer. More knowledge of the dynamics of body temperature, (Tb), could lead to specific recommendations on how far and under what conditions cattle can be moved before becoming thermally challenged. Data comes from feedlot trials conducted over four days. A bi-logistic mixed model of Tb is used to describe the effects of moving and handling on Tb. This model provides estimates for several important biological parameters describing the thermal challenge and …

Using Time Series To Study Dynamics Of Sweat Rates Of Holstein Cows Exposed To Initial And Prolonged Solar Heat Stress, B. Liang, A. M. Parkhurst, K. G. Gebremedhin, C. N. Lee, R. J. Collier, P. E. Hillman

Conference on Applied Statistics in Agriculture

Sweating is a very important way for cows to cope with heat stress. We are interested in the ability of Holstein cows to sustain high sweat or evaporation rates when exposed to solar radiation. There were two solar heat stress treatments: onset and prolonged. The onset data provided an opportunity to examine the impact of sudden exposure to a solar thermal load. The prolonged data allowed us to examine the impact of exposure to solar heat stress for an expended period (5 hr). Two questions of interest were: Do cows sweat at a constant or cyclic rate? Is there a …

Sequential Bayesian Classification: Dna Barcodes, Michael P. Anderson, Suzanne Dubnicka

Conference on Applied Statistics in Agriculture

DNA barcodes are short strands of nucleotide bases taken from the cytochrome c oxidase subunit 1 (COI) of the mitochondrial DNA (mtDNA). A single barcode may have the form C C G G C A T A G T A G G C A C T G and typically ranges in length from 255 to around 700 nucleotide bases. Unlike nuclear DNA (nDNA), mtDNA remains largely unchanged as it is passed from mother to o spring. It has been proposed that these barcodes may be used as a method of di erentiating between biological species (Hebert, Ratnasingham, and deWaard 2003). …

A Stem Profile Model Calibrated By Nonlinear Mixed-Effects Modeling, Yuqing Yang, Shongming Huang, Shawn X. Meng

Conference on Applied Statistics in Agriculture

A stem profile model was developed for black spruce (Picea mariana (Mill.) B.S.P.) trees in Alberta, Canada using a nonlinear mixed model approach. The model included two random parameters to capture between-subject variation and a general covariance structure to model within-subject residual autocorrelation. After evaluating various covariance structures, the 4-banded toeplitz and the spatial power structures were chosen for further evaluation. The 4-banded toeplitz structure provided a better fit. The model was further evaluated using an independent data set to examine its validation accuracy. Model validation results showed that the model was able to accurately predict stem diameters at the …

Mapping Qtl With Covariates, Cherie A. Ochsenfeld, Kristofer Jennings, R. W. Doerge

Conference on Applied Statistics in Agriculture

Quantitative trait loci (QTL) analysis is an effective tool for locating regions of the genome associated with a trait. Quantitative trait data are complex, and when statistically testing for the location of a QTL, the distribution of the test statistic is typically unknown. Historically, asymptotic thresholds have been difficult to derive for QTL analysis. Permutation testing has successfully provided significance thresholds for QTL analysis, but the need for exchangeability among the observations limits these empirically derived thresholds to simple linear models and does not permit the inclusion of important covariates in the model. We address the limitation of permutation theory …

Statistical Methods For Affymetrix Tiling Array Data, Gayla Olbricht, Nagesh Sardesai, Stanton B. Gelvin, Bruce A. Craig, R. W. Doerge

Conference on Applied Statistics in Agriculture

Tiling arrays are a microarray technology currently being used for a variety of genomic and epigenomic applications, such as the mapping of transcription, DNA methylation, and histone modifications. Tiling arrays provide high-density coverage of a genome, or a genomic region, through the systematic and sequential placement of probes without regard to genome annotation. In this paper we compare the Affymetrix tiling array to the Affymetrix GeneChip® 3’ expression array and propose methods that address statistical and bioinformatic issues that accompany gene expression data that are generated from Affymetrix tiling arrays. Real data from the model organism Arabidopsis thaliana motivate this …

Application Of The Dya Method To Compare Wheat Cultivar Yields, Arlin Feyerherm, Allan Fritz

Conference on Applied Statistics in Agriculture

At the 1998 conference, we proposed use of the DYA (differential yielding ability) method to compare the yielding ability of wheat cultivars. In this paper we review the method: its models and assumptions, and then show computation of sample statistics. An example will exhibit the output from performance trial yields when the method is applied in one of the nine ecogeographic areas of fall-planted wheat in the Midwest. Results of comparable outputs over years forecasted which cultivars would become popular with growers in Kansas

Comparative Study Of Time Series And Multiple Regression For Modeling Dependence Of Cattle Body Temperature On Environmental Variables During Heat Stress, M. Pathak, A. M. Parkhurst, R. A. Arias, T. L. Mader

Conference on Applied Statistics in Agriculture

During the summer, a challenging thermal environment is known to cause a significant reduction in food intake, growth, milk production, reproduction and even death in cattle. In this study, we attempt to characterize the relationship of cattle body temperature with several environmental variables, such as air temperature, soil surface temperature, relative humidity, solar radiation, wind speed, incoming and outgoing short and long wave radiation. For these variables, the measurements taken over time are correlated. This places severe restrictions on the applicability of many conventional statistical methods that depend on the assumption of independent and identically distributed errors. In addition to …

Statistical Issues In Next-Generation Sequencing, Paul L. Auer, R. W. Doerge

Conference on Applied Statistics in Agriculture

High throughput deep-sequencing or next-generation sequencing has emerged as an exciting new tool in a great number of applications (e.g., variant discovery, profiling of histone modifications, identifying transcription factor binding sites, resequencing, and transcriptome characterization). Even though this technology has generated unprecedented amounts of data in the scientific community few studies have looked carefully at its inherent variability. Recent studies of mRNA expression levels found little appreciable technical variation in Illumina’s Solexa sequencing platform (a next-generation sequencing device). Although these results are encouraging, they are limited to a specific platform and application, and have been made without any attention to …

Hierarchical Bayesian Methods To Model Heterogeneity In Cow- And Herd-Level Relationships Between Milk Production And Reproduction In Dairy Cows, Nora M. Bello, Juan P. Steibel, Robert J. Tempelman

Conference on Applied Statistics in Agriculture

Two of the most important broad classifications of phenotypes for successful dairy production are milk yield and fertility. The nature of the relationship between milk production and reproductive performance of dairy cows is uncertain due to conflicting results reported in many studies. A common deficiency in many such studies is an underappreciation of the dual dimension of the production-reproduction relationship, as defined by herd (random or u) level and cow (residual or e) level sources of (co)variation. Our overall hypothesis is that the e- and u- level relationships between milk production and reproduction in dairy cows are heterogeneous and depend …

Relative Potency Estimation In Direct Bioassay With Measurement Errors*, Weixing Song

Conference on Applied Statistics in Agriculture

The dosage levels measured in direct bioassays are often contaminated with measurement errors, which are usually neglected in the statistical inference. This paper proposes several estimation procedures for the relative potencies in direct bioassays taking the measurement errors into account. Asymptotic theories are developed for constructing the confidence intervals. Numerical simulations are also included to compare different estimation procedures.

Bayesian Nonparametric Bioassay Estimation, Bahman Shafii, William J. Price

Conference on Applied Statistics in Agriculture

Estimation of unknown pesticide levels in experimental samples is an important aspect of many agricultural and environmental studies. Such measurements are often made utilizing a “standard” dose response curve. This methodology compares the biological response of a target organism at known dosages to the response of the same organism exposed to an unknown sample. These “bioassays” are typically more efficient in time and resources than direct chemical assessment of the unknown sample. The form and choice of the standard curve, however, is subjective and can influence the estimation of the unknown dose. Problems may also arise when incomplete or preliminary …

Associating Snps With Binary Traits, Alexander E. Lipka, George P. Mccabe, R. W. Doerge

Conference on Applied Statistics in Agriculture

Association mapping uses statistical analyses to test for relationships between genomic markers called single nucleotide polymorphisms (SNPs) and traits. This research focuses on the use of logistic regression to assess the additive, dominance, and epistatic effects when investigating associations between SNPs and binary traits, such as disease status. A very specific phenomenon that results in infinite maximum likelihood estimates (MLEs) of logistic regression parameters, called quasi-separation of points (QSP), is investigated. We provide a solution that relies on the use of Firth’s MLE to estimate logistic regression parameters. Simulated and real data are utilized to investigate the use of Firth’s …

Editor's Preface And Table Of Contents, Gary L. Gadbury

Conference on Applied Statistics in Agriculture

These proceedings contain papers presented in the twenty-first annual Kansas State University Conference on Applied Statistics in Agriculture, held in Manhattan, Kansas, April 19 - April 21, 2009.

Phylogeography Of The Rufous-Naped Wren (Campylorhynchus Rufinucha): Speciation And Hybridization In Mesoamerica, Hernan Vazquez-Miranda, Adolfo G. Navarro-Siguenza, Kevin E. Omland

School of Natural Resources: Faculty Publications

The Rufous-naped Wren (Campylorhynchus rufinucha) is a sedentary, morphologically variable species distributed in the dry forests of Mesoamerica. It ranges from Colima, Mexico, south to Costa Rica along the Pacific slope, with a disjunct population in central Veracruz. Populations of two forms on the Pacific slope intergrade in Chiapas, Mexico, apparently as a result of secondary contact. We sequenced a mitochondrial DNA (mtDNA) gene to explore phylogeographic patterns and hybridization. We found three divergent lineages, two geographically spanning the Isthmus of Tehuantepec and a disjunct Veracruz population. Analyses of molecular variation and statistics are consistent with genetically distinct …

Dynamic Universal Accumulators For Ddh Groups And Their Application To Attribute-Based Anonymous Credential Systems, Man Ho Au, Patrick P. Tsang, Willy Susilo, Yi Mu

Computer Science Technical Reports

We present the first dynamic universal accumulator that allows (1) the accumulation of elements in a DDH-hard group G and (2) one who knows x such that y=g^x has --- or has not --- been accumulated, where g generates G, to efficiently prove her knowledge of such x in zero knowledge, and hence without revealing, e.g., x or y. We introduce the Attribute-Based Anonymous Credential System (ABACS), which allows the verifier to authenticate anonymous users according to any access control policy expressible as a formula of possibly negated boolean user attributes. We construct the system from our accumulator.

The Furman Lake Restoration Plan, Wade Worthen

Furman Lake Restoration Book Gallery

A presentation with text and images providing information on the history of the Furman Lake, it's environmental health decline throughout the years, and the lake's restoration. The presentation details the Furman Lake's problems, causes of these problems, and solutions. It describes Furman's progress in the restoration project, as well as it's goals for the future.

3d Medical Collaboration Technology To Enhance Emergency Healthcare, Greg Welch, Diane H. Sonnenwald, Henry Fuchs, Bruce Cairns, Ketan Mayer-Patel, Hanna M. Söderholm, Ruigang Yang, Andrei State, Herman Towles, Adrian Ilie, Manoj Ampalam, Srinivas Krishnan, Vincent Noel, Michael Noland, James E. Manning

Computer Science Faculty Publications

Two-dimensional (2D) videoconferencing has been explored widely in the past 15–20 years to support collaboration in healthcare. Two issues that arise in most evaluations of 2D videoconferencing in telemedicine are the difficulty obtaining optimal camera views and poor depth perception. To address these problems, we are exploring the use of a small array of cameras to reconstruct dynamic three-dimensional (3D) views of a remote environment and of events taking place within. The 3D views could be sent across wired or wireless networks to remote healthcare professionals equipped with fixed displays or with mobile devices such as personal digital assistants (PDAs). …