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Articles 1 - 30 of 58
Full-Text Articles in Life Sciences
Introducing Functional Data Analysis To Neuroimaging, And Vice Versa, Philip T. Reiss
Introducing Functional Data Analysis To Neuroimaging, And Vice Versa, Philip T. Reiss
Philip T. Reiss
No abstract provided.
Habitat Use And Abundance Patterns Of Sandhill Cranes In The Central Platte River Valley, Nebraska, 2003–2010, Todd Joseph Buckley
Habitat Use And Abundance Patterns Of Sandhill Cranes In The Central Platte River Valley, Nebraska, 2003–2010, Todd Joseph Buckley
School of Natural Resources: Dissertations, Theses, and Student Research
The Central Platte River Valley (CPRV) in Nebraska is an important spring stopover area for the midcontinent population of sandhill cranes. Alterations to crop rotation and loss habitat in the CPRV pose a risk to the population. Personnel drove designated routes in the CPRV from 2003–2010 to record the presence of cranes in agricultural fields and estimate abundance. I developed and evaluated models to predict habitat use and flock sizes. Alfalfa was predicted to receive the highest use followed by corn, soybeans, winter wheat, grassland, and shrubland. Use of all habitats and flock size increased as field area increased. Flock …
Assessing The Impact Of Non-Differential Genotyping Errors On Rare Variant Tests Of Association, Scott Powers, Shyam Gopalakrishnan, Nathan L. Tintle
Assessing The Impact Of Non-Differential Genotyping Errors On Rare Variant Tests Of Association, Scott Powers, Shyam Gopalakrishnan, Nathan L. Tintle
Faculty Work Comprehensive List
Background/Aims: We aim to quantify the effect of non-differential genotyping errors on the power of rare variant tests and identify those situations when genotyping errors are most harmful. Methods: We simulated genotype and phenotype data for a range of sample sizes, minor allele frequencies, disease relative risks and numbers of rare variants. Genotype errors were then simulated using five different error models covering a wide range of error rates. Results: Even at very low error rates, misclassifying a common homozygote as a heterozygote translates into a substantial loss of power, a result that is exacerbated even further as the minor …
Estimation Of A Non-Parametric Variable Importance Measure Of A Continuous Exposure, Chambaz Antoine, Pierre Neuvial, Mark J. Van Der Laan
Estimation Of A Non-Parametric Variable Importance Measure Of A Continuous Exposure, Chambaz Antoine, Pierre Neuvial, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
We define a new measure of variable importance of an exposure on a continuous outcome, accounting for potential confounders. The exposure features a reference level x0 with positive mass and a continuum of other levels. For the purpose of estimating it, we fully develop the semi-parametric estimation methodology called targeted minimum loss estimation methodology (TMLE) [van der Laan & Rubin, 2006; van der Laan & Rose, 2011]. We cover the whole spectrum of its theoretical study (convergence of the iterative procedure which is at the core of the TMLE methodology; consistency and asymptotic normality of the estimator), practical implementation, simulation …
The Effects Of 24 Weeks Of Resistance Training With Simultaneous Elastic And Free Weight Loading On Muscular Performance Of Novice Lifters, Todd C. Shoepe, David A. Ramirez, Robert J. Rovetti, David R. Kohler, Hawley C. Almstedt
The Effects Of 24 Weeks Of Resistance Training With Simultaneous Elastic And Free Weight Loading On Muscular Performance Of Novice Lifters, Todd C. Shoepe, David A. Ramirez, Robert J. Rovetti, David R. Kohler, Hawley C. Almstedt
Hawley Almstedt
The purpose of this investigation was to assess the effectiveness of variable resistance as provided through elastic plus free weight techniques in college aged males and females. Twenty novice lifters were randomly assigned to a traditional free weight only (6 males and 5 females) or elastic band plus free weight group (5 males and 5 females) and 9 more normally active controls (5 males and 4 females), were recruited to maintain normal activity for the duration of the study. No differences existed between control, free weight and elastic band at baseline for age, body height, body mass, body mass index, …
The Effects Of 24 Weeks Of Resistance Training With Simultaneous Elastic And Free Weight Loading On Muscular Performance Of Novice Lifters, Todd C. Shoepe, David A. Ramirez, Robert J. Rovetti, David R. Kohler, Hawley C. Almstedt
The Effects Of 24 Weeks Of Resistance Training With Simultaneous Elastic And Free Weight Loading On Muscular Performance Of Novice Lifters, Todd C. Shoepe, David A. Ramirez, Robert J. Rovetti, David R. Kohler, Hawley C. Almstedt
Robert J. Rovetti
The purpose of this investigation was to assess the effectiveness of variable resistance as provided through elastic plus free weight techniques in college aged males and females. Twenty novice lifters were randomly assigned to a traditional free weight only (6 males and 5 females) or elastic band plus free weight group (5 males and 5 females) and 9 more normally active controls (5 males and 4 females), were recruited to maintain normal activity for the duration of the study. No differences existed between control, free weight and elastic band at baseline for age, body height, body mass, body mass index, …
The Effects Of 24 Weeks Of Resistance Training With Simultaneous Elastic And Free Weight Loading On Muscular Performance Of Novice Lifters, Todd C. Shoepe, David A. Ramirez, Robert J. Rovetti, David R. Kohler, Hawley C. Almstedt
The Effects Of 24 Weeks Of Resistance Training With Simultaneous Elastic And Free Weight Loading On Muscular Performance Of Novice Lifters, Todd C. Shoepe, David A. Ramirez, Robert J. Rovetti, David R. Kohler, Hawley C. Almstedt
Todd Shoepe
The purpose of this investigation was to assess the effectiveness of variable resistance as provided through elastic plus free weight techniques in college aged males and females. Twenty novice lifters were randomly assigned to a traditional free weight only (6 males and 5 females) or elastic band plus free weight group (5 males and 5 females) and 9 more normally active controls (5 males and 4 females), were recruited to maintain normal activity for the duration of the study. No differences existed between control, free weight and elastic band at baseline for age, body height, body mass, body mass index, …
Multiple Testing Of Local Maxima For Detection Of Peaks In Chip-Seq Data, Armin Schwartzman, Andrew Jaffe, Yulia Gavrilov, Clifford A. Meyer
Multiple Testing Of Local Maxima For Detection Of Peaks In Chip-Seq Data, Armin Schwartzman, Andrew Jaffe, Yulia Gavrilov, Clifford A. Meyer
Harvard University Biostatistics Working Paper Series
No abstract provided.
A Geospatial Based Decision Framework For Extending Marssim Regulatory Principles Into The Subsurface, Robert Nathan Stewart
A Geospatial Based Decision Framework For Extending Marssim Regulatory Principles Into The Subsurface, Robert Nathan Stewart
Doctoral Dissertations
The Multi-Agency Radiological Site Survey Investigation Manual (MARSSIM) is a regulatory guidance document regarding compliance evaluation of radiologically contaminated soils and buildings (USNRC, 2000). Compliance is determined by comparing radiological measurements to established limits using a combination of hypothesis testing and scanning measurements. Scanning allows investigators to identify localized pockets of contamination missed during sampling and allows investigators to assess radiological exposure at different spatial scales. Scale is important in radiological dose assessment as regulatory limits can vary with the size of the contaminated area and sites are often evaluated at more than one scale (USNRC, 2000). Unfortunately, scanning is …
Gene By Bmi Interactions Influencing C-Reactive Protein Levels In European-Americans, Sarah Tudor
Gene By Bmi Interactions Influencing C-Reactive Protein Levels In European-Americans, Sarah Tudor
Dissertations & Theses (Open Access)
C-Reactive Protein (CRP) is a biomarker indicating tissue damage, inflammation, and infection. High-sensitivity CRP (hsCRP) is an emerging biomarker often used to estimate an individual’s risk for future coronary heart disease (CHD). hsCRP levels falling below 1.00 mg/l indicate a low risk for developing CHD, levels ranging between 1.00 mg/l and 3.00 mg/l indicate an elevated risk, and levels exceeding 3.00 mg/l indicate high risk. Multiple Genome-Wide Association Studies (GWAS) have identified a number of genetic polymorphisms which influence CRP levels. SNPs implicated in such studies have been found in or near genes of interest including: CRP, APOE, APOC, IL-6, …
Heterogeneity, Control, Social Infrastructure, And Possibilities Of Participation: Their Interplay In Modern Understandings Of Heredity And In Interpretation Of Science, Peter J. Taylor
Working Papers on Science in a Changing World
This working paper is a prospectus for research, writing, and engagement. It consists of vignettes, sketches of lines of inquiry, and proposals for engagement, all of which concern modern understandings of heredity and development over the life course as well as the social interpretation of science. The various items address a range of areas of science and of its interpretation: heritability studies, the social uses of genetic information, gene-by-environment interaction, personalized medicine, IQ paradoxes, racial group membership, biobanks, and life events and difficulties research. Fresh perspectives in these areas are opened up by examining the ways that research and application …
The Use Of Imputed Values In The Meta-Analysis Of Genome-Wide Association Studies., Shuo Jiao, Li Hsu, Carolyn Hutter, Ulrike Peters
The Use Of Imputed Values In The Meta-Analysis Of Genome-Wide Association Studies., Shuo Jiao, Li Hsu, Carolyn Hutter, Ulrike Peters
Shuo Jiao
In genome-wide association studies (GWAS), it is a common practice to impute the genotypes of untyped single nucleotide polymorphism (SNP) by exploiting the linkage disequilibrium structure among SNPs. The use of imputed genotypes improves genome coverage and makes it possible to perform meta-analysis combining results from studies genotyped on different platforms. A popular way of using imputed data is the "expectation-substitution" method, which treats the imputed dosage as if it were the true genotype. In current practice, the estimates given by the expectation-substitution method are usually combined using inverse variance weighting (IVM) scheme in meta-analysis. However, the IVM is not …
A Unified Approach To Non-Negative Matrix Factorization And Probabilistic Latent Semantic Indexing, Karthik Devarajan, Guoli Wang, Nader Ebrahimi
A Unified Approach To Non-Negative Matrix Factorization And Probabilistic Latent Semantic Indexing, Karthik Devarajan, Guoli Wang, Nader Ebrahimi
COBRA Preprint Series
Non-negative matrix factorization (NMF) by the multiplicative updates algorithm is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into two matrices, W and H, each with nonnegative entries, V ~ WH. NMF has been shown to have a unique parts-based, sparse representation of the data. The nonnegativity constraints in NMF allow only additive combinations of the data which enables it to learn parts that have distinct physical representations in reality. In the last few years, NMF has been successfully applied in a variety of areas such as natural language processing, information retrieval, image processing, speech recognition …
A Study On Facility Planning Using Discrete Event Simulation: Case Study Of A Grain Delivery Terminal., Sarah M. Asio
A Study On Facility Planning Using Discrete Event Simulation: Case Study Of A Grain Delivery Terminal., Sarah M. Asio
Department of Industrial and Management Systems Engineering: Dissertations, Theses, and Student Research
The application of traditional approaches to the design of efficient facilities can be tedious and time consuming when uncertainty and a number of constraints exist. Queuing models and mathematical programming techniques are not able to capture the complex interaction between resources, the environment and space constraints for dynamic stochastic processes. In the following study discrete event simulation is applied to the facility planning process for a grain delivery terminal. The discrete event simulation approach has been applied to studies such as capacity planning and facility layout for a gasoline station and evaluating the resource requirements for a manufacturing facility. To …
A Bayesian Model Averaging Approach For Observational Gene Expression Studies, Xi Kathy Zhou, Fei Liu, Andrew J. Dannenberg
A Bayesian Model Averaging Approach For Observational Gene Expression Studies, Xi Kathy Zhou, Fei Liu, Andrew J. Dannenberg
COBRA Preprint Series
Identifying differentially expressed (DE) genes associated with a sample characteristic is the primary objective of many microarray studies. As more and more studies are carried out with observational rather than well controlled experimental samples, it becomes important to evaluate and properly control the impact of sample heterogeneity on DE gene finding. Typical methods for identifying DE genes require ranking all the genes according to a pre-selected statistic based on a single model for two or more group comparisons, with or without adjustment for other covariates. Such single model approaches unavoidably result in model misspecification, which can lead to increased error …
Component Extraction Of Complex Biomedical Signal And Performance Analysis Based On Different Algorithm, Hemant Pasusangai Kasturiwale
Component Extraction Of Complex Biomedical Signal And Performance Analysis Based On Different Algorithm, Hemant Pasusangai Kasturiwale
Johns Hopkins University, Dept. of Biostatistics Working Papers
Biomedical signals can arise from one or many sources including heart ,brains and endocrine systems. Multiple sources poses challenge to researchers which may have contaminated with artifacts and noise. The Biomedical time series signal are like electroencephalogram(EEG),electrocardiogram(ECG),etc The morphology of the cardiac signal is very important in most of diagnostics based on the ECG. The diagnosis of patient is based on visual observation of recorded ECG,EEG,etc, may not be accurate. To achieve better understanding , PCA (Principal Component Analysis) and ICA algorithms helps in analyzing ECG signals . The immense scope in the field of biomedical-signal processing Independent Component Analysis( …
Estimating Area And Lag Associated With Thermal Hysteresis In Cattle, F. Yang, A. M. Parkhurst
Estimating Area And Lag Associated With Thermal Hysteresis In Cattle, F. Yang, A. M. Parkhurst
Conference on Applied Statistics in Agriculture
Thermal hysteresis in cattle becomes visible when the phase diagram of body temperature (Tb) vs ambient temperature (Ta) exhibits a loop. The hysteresis loop shows a rotated elliptical pattern which depends on the lag between Tb and Ta. The area of the loop can be used to quantify the amount of heat stress during thermal challenge. Three methods to estimate the area and lag of the elliptical hysteresis loop are: linear least squares method, ellipse-specific nonlinear least squares method, and Lapshin’s analytical method. Linear least squares method uses residual least squares to estimate the coefficients of the ellipse for which …
Comparison Of Linear Mixed Models For Multiple Environment Plant Breeding Trials, Carl A. Walker, Fabiano Pita, Kimberly Garland Campbell
Comparison Of Linear Mixed Models For Multiple Environment Plant Breeding Trials, Carl A. Walker, Fabiano Pita, Kimberly Garland Campbell
Conference on Applied Statistics in Agriculture
Evaluations of multiple environment trials (MET) often reveal substantial genotype by environment interactions, and the effects of genotypes within environments are often estimated using cell means, i.e. the simple mean of the observations of each genotype in each environment. However, these estimates are inaccurate, especially for unreplicated or partially replicated trials, so alternative methods of analysis are necessary. One possible approach utilizes information, often from pedigree data, about relationships among the tested genotypes through the use of a genetic relationship matrix (GRM). Predictive accuracy may also be improved by the use of factor analytic (FA) structures for environmental covariances. In …
A Hierarchical Bayesian Approach For Detecting Differential Gene Expression In Unreplicated Rna-Sequencing Data, Sanvesh Srivastava, R. W. Doerge
A Hierarchical Bayesian Approach For Detecting Differential Gene Expression In Unreplicated Rna-Sequencing Data, Sanvesh Srivastava, R. W. Doerge
Conference on Applied Statistics in Agriculture
Next-generation sequencing technologies have emerged as a promising technology in a variety of fields, including genomics, epigenomics, and transcriptomics. These technologies play an important role in understanding cell organization and functionality. Unlike data from earlier technologies (e.g., microarrays), data from next-generation sequencing technologies are highly replicable with little technical variation. One application of next-generation sequencing technologies is RNA-Sequencing (RNA-Seq). It is used for detecting differential gene expression between different biological conditions. While statistical methods for detecting differential expression in RNA-Seq data exist, one serious limitation to these methods is the absence of biological replication. At present, the high cost of …
Bootstrap Estimation And Comparison Of An Index Of Phylogenetic Correlation, William J. Price, Bahman Shafii, Carole B. Rapo, Sanford D. Eigenbrode, John Gaskin
Bootstrap Estimation And Comparison Of An Index Of Phylogenetic Correlation, William J. Price, Bahman Shafii, Carole B. Rapo, Sanford D. Eigenbrode, John Gaskin
Conference on Applied Statistics in Agriculture
A common objective of bioinformatic analyses is to assess the similarity of species, given a biological trait or characteristic. Phylogenetic correlation is one means to achieve this objective. Such measures provide a means to evaluate evolutionary models and history as well as having potential application to ecological relationships including host preference selection. Typically, these measurements are based on the deviation of an observed phylogeny from a Brownian evolutionary model. Statistical inference for this difference is assessed through likelihood ratio tests. These tests, in turn, rely on the assumption of a Normal likelihood within the phylogenetic trait. In addition, statistical comparison …
Modeling The Root-Knot Nematode/Nutsedge Pest Complex: Perspectives From Weed Science, Nematology And Statistics, Leigh Murray, Stephen H. Thomas, Jill Schroeder, Scott Kreider, Zhining Ou, J. M. Trojan, C. Fiore
Modeling The Root-Knot Nematode/Nutsedge Pest Complex: Perspectives From Weed Science, Nematology And Statistics, Leigh Murray, Stephen H. Thomas, Jill Schroeder, Scott Kreider, Zhining Ou, J. M. Trojan, C. Fiore
Conference on Applied Statistics in Agriculture
Previous research by the authors has established that southern root-knot nematode (SRKN, Meloidogyne incognita (Kofoid & White) Chitwood) and yellow and purple nutsedge (YNS, Cyperus esculentus L. and PNS, C. rotundus L.) form a pest-complex that adversely affects a wide variety of crops in the southern and western U.S. These pests appear to have co-evolved a mutually-beneficial relationship that promotes the survival of both nematodes and weeds to the detriment of crops. Traditional management has usually targeted one pest at a time, but managing this pest complex requires that all members of the complex be managed simultaneously. A series of …
Multi-Parental Mating Design Analysis: Model Evaluation And Application In Spring Wheat, M. Kadariya, K. D. Glover, J. Wu, J. L. Gonzalez
Multi-Parental Mating Design Analysis: Model Evaluation And Application In Spring Wheat, M. Kadariya, K. D. Glover, J. Wu, J. L. Gonzalez
Conference on Applied Statistics in Agriculture
Conventional quantitative genetics studies have mainly focused on bi-parental mating systems. However, genetic potential of selected individuals within a segregating population may be limited due to only two parents being used for each cross. Multiple-parental mating systems have been proposed that involve three or four diverse parents. This provides a higher potential of combining desirable genes. Due to complexity of the data structure of multi-parental mating systems, analysis of variance (ANOVA) methods are not applicable in analysis. The objective of this study is to validate and apply a mixed linear model approach, minimum norm quadratic unbiased estimation (MINQUE), to analyze …
Estimating The Subject By Treatment Interaction In Non-Replicated Crossover Diet Studies, Matthew Kramer, Shirley C. Chen, Sarah K. Gebauer, David J. Baer
Estimating The Subject By Treatment Interaction In Non-Replicated Crossover Diet Studies, Matthew Kramer, Shirley C. Chen, Sarah K. Gebauer, David J. Baer
Conference on Applied Statistics in Agriculture
Researchers in human nutrition commonly refer to the ‘consistent’ diet effect (i.e. the main effect of diet) and an ‘inconsistent’ diet effect (i.e. a subject by diet interaction). However, due to the non-replicated designs of most studies, one can only estimate the first part using ANOVA; the latter (interaction) is confounded with the residual noise. In many diet studies, it appears that subjects do respond differently to the same diet, so the subject by diet interaction may be large. In a search of over 40,000 published human nutrition studies, most using a crossover design, we found that in none was …
Probability Models To Study The Spatial Pattern, Abundance And Diversity Of Tree Species, D. M. Gowda
Probability Models To Study The Spatial Pattern, Abundance And Diversity Of Tree Species, D. M. Gowda
Conference on Applied Statistics in Agriculture
Ecological communities are composed of complex vegetation that differs from community to community and also within the community. The variability of tree species in the community in relation to their environments can be studied by using different statistical tools. The present study was conducted to describe and also to quantify the spatial pattern, abundance and diversity of tree species in the Western Ghats of Karnataka. The spatial pattern of tree species was studied by using Poisson and Negative binomial distributions. Results indicate that most of the selected tree species followed Negative binomial distribution having clumped pattern. The Species abundance distribution …
Spatio-Temporal Covariance Modeling With Some Arma Temporal Margins, Samuel Seth Demel, Juan Du
Spatio-Temporal Covariance Modeling With Some Arma Temporal Margins, Samuel Seth Demel, Juan Du
Conference on Applied Statistics in Agriculture
A valid covariance structure is needed to model spatio-temporal data in various disciplines, such as environmental science, climatology and agriculture. In this work we propose a collection of spatio-temporal functions whose discrete temporal margins are some autoregressive and moving average (ARMA) models, obtain a necessary and sufficient condition for them to be covariance functions. An asymmetric version of this model is also provided to account for space-time irreversibility property in practice. Finally, a spatio-temporal model with AR(2) discrete margin is fitted to wind data from Ireland for estimation and prediction, which are compared with some general existing parametric models in …
Logistic Regression Analysis To Determine Factors Contributing To Summer Feedlot Deaths, J. Clausen, A. M. Parkhurst, T. L. Mader
Logistic Regression Analysis To Determine Factors Contributing To Summer Feedlot Deaths, J. Clausen, A. M. Parkhurst, T. L. Mader
Conference on Applied Statistics in Agriculture
Summer heat has already been identified as a major factor for cattle deaths in the feedlot. This study attempts to assess what other factors contribute to and/or influence cattle deaths. Identifying multiple factors that contribute to summer feedlot deaths could aid feedlot managers in implementation of mitigation strategies and minimize the loss of nearly finished cattle. Daily pen, cattle, and nutritional characteristics were recorded and included in this generalized linear mixed model analysis. Cattle data were obtained from cattle pens at a single location from July 1, 2010 to July 31, 2010. Hourly weather data were acquired from this feed …
Confidence Intervals For Variance Components Using Non-Normal Distributions, Brent D. Burch
Confidence Intervals For Variance Components Using Non-Normal Distributions, Brent D. Burch
Conference on Applied Statistics in Agriculture
Simulation studies are conducted to evaluate the performance of confidence intervals for variance components under non-normal distribution assumptions. Confidence intervals based on the pivotal quantity (PQ) method and the large-sample properties of the restricted maximum likelihood (REML) estimator are considered. Of particular interest is the actual coverage value of nominal 95% confidence intervals for a ratio of variance components. In the context of unbalanced one-way random effects models, simulation results and an empirical example involving arsenic concentrations in oyster tissue suggest that the REML-based confidence interval is preferred.
Ordinary Least Squares Regression Of Ordered Categorical Data: Inferential Implications For Practice, Beth Larrabee, H. Morgan Scott, Nora M. Bello
Ordinary Least Squares Regression Of Ordered Categorical Data: Inferential Implications For Practice, Beth Larrabee, H. Morgan Scott, Nora M. Bello
Conference on Applied Statistics in Agriculture
Ordered categorical responses (OCRs) are frequently encountered in many disciplines. Examples of interest in agriculture include quality assessments, such as for soil or food products, and evaluation of lesion severity, such as teat ends status in dairy cattle. OCRs are characterized by multiple categories recorded on a ranked scale that, while apprising relative order, is not informative of absolute magnitude of or proportionality between the categories. A number of statistically sound models for OCRs are available in the statistical literature, such as logistic regression and probit models, but these are commonly underutilized in practice. Instead, the ordinary least squares linear …
Issues In Testing Dna Methylation Using Next-Generation Sequencing, Douglas Baumann, R. W. Doerge
Issues In Testing Dna Methylation Using Next-Generation Sequencing, Douglas Baumann, R. W. Doerge
Conference on Applied Statistics in Agriculture
DNA methylation is an epigenetic modification known to affect gene expression, cellular differentiation, as well as phenotypes. Recent advancements in next-generation sequencing technologies have provided unparalleled insight into the location and function of DNA methylation in a variety of organisms. These data require vastly different statistical procedures than data from previous genomic-based technologies. We outline the biological and chemical processes involved in several approaches for gaining DNA methylation data. The implications of the differences between the approaches are discussed relative to the statistical methodology, and the use of genome annotation is explored for the purpose of improving the statistical power …
Editor's Preface And Table Of Contents, Weixin Yao
Editor's Preface And Table Of Contents, Weixin Yao
Conference on Applied Statistics in Agriculture
These proceedings contain papers presented in the twenty-third annual Kansas State University Conference on Applied Statistics in Agriculture, held in Manhattan, Kansas, May 01 - May 03, 2011.