Life Sciences Commons^™

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

Community Classification And Distribution Patterns Of Freshwater Mussels Of Strawberry River, Arkansas, Sujata Poudel, David E. Tenenbaum Ph.D, John L. Harris, Alan D. Christian Ph.D

Interdisciplinary Perspectives: a Graduate Student Research Showcase

The purpose of this study is to determine if there are distinct communities of freshwater mussels in the Strawberry River, Arkansas, and if environmental variables influenced these communities. The Strawberry River watershed is located in the Ozark Mountains in northcentral Arkansas. Based on previous studies of interior highland mussels, we expected distinct low, mid, and high order stream mussel communities. Mussels were surveyed from headwaters to mouth and resulted in 38 species from 57 sites. Environmental variables of land cover, geology, soiltype, and drainage area were calculated at local and subwatershed scale using GIS. Mussel presence/absence and environmental variables were …

The Importance Of Metrics And Communication In Cafeteria School Policy, Andre Sanchez, Atreya Chakraborty

Interdisciplinary Perspectives: a Graduate Student Research Showcase

Obesity has become an epidemic amongst American youth in the 21st century, and is spreading not only into other developed nations such as the UK and Australia, but is also beginning to effect developing nations such as India (Bhardwaj, 2008). It is estimated that nationwide, childhood obesity affects around 17% of American children (Center For Disease Control, 2011). Obesity has been linked to many health disorders, including but not limited to, heart disease and diabetes. Subsequently, this rise in childhood obesity is having a severe impact on the healthcare services sector in America, with some studies suggesting childhood obesity in …

Comparing Inter-Examiner Reliability Levels When Diagnosing Male & Female Innominate Dysfunctions Using A Hemi-Pelvise Compression Lateralization Test And Pelvic Landmark Levels., Nicole E. Myers, Michael L. Kuchera Do, Faao, Veronica Ferencz Mba, Jeffrey A. Nelson, Frank Casella Ms

Research Day

BACKGROUND: When diagnosing innominate somatic dysfunctions it may be relevant to recognize that structural, functional, and hormonal differences exist between male and female pelvises. The female pelvis is less massive, ilia are less sloped, and female hormones influence ligamentous tension. Despite these differences, few studies have analyzed gender effects on inter-examiner reliability when using palpatory diagnosis to diagnose innominate dysfunctions. In this study, we hypothesized that interexaminer reliability would be higher in male subjects than in female subjects due cyclic variability of hormonal influence of ligamentous tension in the female pelvis. The kappa (κ) statistic was selected to evaluate …

The Use Of Objective Data To Improve Interexaminer Reliability, Veronica Ferencz Mba, Frank Casella Ms, Jeffrey A. Nelson, Nicole E. Myers, Michael L. Kuchera Do, Faao

Research Day

BACKGROUND: In Osteopathic Manipulative Medicine (OMM) and Manual/Musculoskeletal Medicine (MMM), palpatory diagnosis is performed on a regular basis to diagnose somatic dysfunction (SD). This examination requires careful and precise touch coupled with subjective interpretation by individual examiners who may have been trained to evaluate SD through different methods. Interexaminer reliability studies aim to minimize variance by providing quantifiable scientific data to evaluate specific test protocols which can then be taught to practitioners. In a previous PCOM study, two examiners independently diagnosed innominate bone dysfunction lateralized using the ASIS compression test on a large group of subjects. A pressure monitoring system …

Effect Of Prior Anterior Superior Iliac Spine Compression Testing On Second Assessor Findings: Implications For Inter-Examiner Reliability Testing, Frank Casella Ms, Michael L. Kuchera Do, Faao, Jeffrey A. Nelson, Veronica Ferencz Mba, Nicole E. Myers

Research Day

BACKGROUND: Osteopathic physicians use palpation to diagnose sacroiliac joint somatic dysfunction (SD) -- including the Anterior Superior Iliac Spine (ASIS) Compression Test for dysfunctional side lateralization. (Literature suggests right-sided lateralization in 80% of asymptomatic individuals). Accurate, reliable tests are crucial however to diagnose SD and kappa (κ) analysis is a gold-standard to determine the degree of interexaminer reliability for tests. Few studies have examined the effect the palpatory examination has on subsequent diagnostic findings and therefore on κ-values.

Inter-Examiner Reliability Of An Anterior Superior Iliac Spine Compression Test Used To Lateralize Pelvic Somatic Dysfunction To The Right Side Or Not, Frank Casella Ms, Michael L. Kuchera Do, Faao, Nicole E. Myers, Jeffrey A. Nelson, Veronica Ferencz Mba

Research Day

BACKGROUND: Osteopathic physicians use a number of palpatory structural examinations to diagnose pelvic somatic dysfunction (SD). They may elect to use the Anterior Superior Iliac Spine (ASIS) Compression Test to lateralize the dysfunctional side. Accurate, reliable tests are crucial to neuromusculoskeletal diagnosis and this study employs the kappa (κ) analysis protocol recommended for assessing interexaminer reliability of manual medicine tests (published by the Fédération Internationale de Médecine Manuelle [FIMM]). κ-values ≥0.40 (moderate agreement) are considered to be acceptable for use in the clinical setting.

Analysis Of Morris Water Maze Data With Bayesian Statistical Methods, Maxym V. Myroshnychenko, Anton Westveld, Jefferson Kinney

Festival of Communities: UG Symposium (Posters)

Neuroscientists commonly use a Morris Water Maze to assess learning in rodents. In his kind of a maze, the subjects learn to swim toward a platform hidden in opaque water as they orient themselves according to the cues on the walls. This protocol presents a challenge to statistical analysis, because an artificial cut-off must be set for those experimental subjects that do not reach the platform so as they do not drown from exhaustion. This fact leads to the data being right censored. In our experimental data, which compares learning in rodents that have chemically induced symptoms of schizophrenia to …

Exploring The Potential Of Agave As A Biofuel Crop On Arid Land, Rhea Conlu, Diana Ha, Jeffery Shen

Festival of Communities: UG Symposium (Posters)

Worldwide awareness of global warming and depleting fossil fuel sources has made research into alternative resources, such as plant fuels imperative. Since groundwater irrigation is unsustainable, especially in desert climates, plants that are drought resistant or can utilize otherwise unusable water are more viable sources of future biofuel production. Agave nevadensis, a species belonging to the family Agavaceae are succulent plants native to Las Vegas. This experiment aims to expose A. nevadensis to both wastewater and drought conditions and observe its response. The results can help define Agave as a water-resourceful biofuel both tolerant of drought and capable of utilizing …

Sustainable Alternative To Non-Biological Nitrogen Fixation To Nitrate For Fertilizers, Patrick Freeze, Glenn Miller

Festival of Communities: UG Symposium (Posters)

Currently, the industrial method of nitrogen fixation for use in fertilizers (Haber- Bosch process [N2 (g) + 3 H2 (g) <--> 2 NH3 (g)]) is our main source of non-biological conversion of atmospheric nitrogen to ammonia. The proposed research experiment utilizes the catalytic mechanism of titanium dioxide which, in the presence of heat or sunlight, undergoes fixation of atmospheric nitrogen. This method of nitrate production could serve as a sustainable source of nitrogen for fertilizers. Variables in the experiment included the manipulation of thermal pressure, heat, and base addition to counteract hydrochloric acid production, a selflimiting byproduct.

The Effects Of Climate Change On Basic Animal Cell Functions, Michelle Fulbright, Andrew Andres

Festival of Communities: UG Symposium (Posters)

Increasing global temperatures during the 21st century may have detrimental effects on basic cell functions within ectothermal animals. This project aims to systematically examine the effects of climate change on secretory cargo localization through the analysis of Rab Proteins found in the model organism Drosophila melanogaster. Rab Proteins play an essential role in vesicular transport within the cell and can be genetically manipulated to monitor the biological consequences of global warming.

Accumulation Of Polonium-210 In Different Species Of Fish In Lake Mead, Suraj Ghevarghese John, Shungmugam Nallaperumal, Vernon Hodge

Festival of Communities: UG Symposium (Posters)

Discovered by Pierre Curie and Marie Skłodowska-Curie in 1898, polonium is a chemical element with an atomic number of 84. This rare naturally occurring radioactive element is chemically similar to bismuth and tellurium, and forms in uranium ores. Polonium-210 is an naturally occurring radioactive element with a half-life of 138.376 days(1). This element is found in trace amounts in most organisms. Our research is focused on the accumulation of polonium-210 in fish that occupy in Lake Mead.

The sample species is chosen based on varying lake stratification (layers of the lake). This gives us a good idea of the difference …

Oral Presentation: Plant Genes And Drought Tolerance, Norris Lam

Festival of Communities: UG Symposium (Posters)

Research has shown that a gene from C3 xerophyte Larrea tridentata (creosote bush), LtWRKY21, is involved in pathways governing creosote bush’s high tolerance to environmental stress. By understanding the way in which creosote bush adapts to drought, crop plants can be engineered to be more drought tolerant during times of imminent global climate change. To study the underlying mechanisms of creosote bush drought response, the LtWRKY21 gene was mobilized into the model organism Arabidopsis thaliana. Chlorophyll degradation, cellular electrolyte leakage, and water content in leaves will serve as indicators of drought tolerance in LtWRKY21-transgenic A. thaliana after treatment in chemically …

The Release Of Calcium In Bacillus Anthracis Pathogenicity Methods, Natiera Magnuson, Manomita Patra Bhowmik, Maria Elena Reynaga, Ernesto Abel-Santos

Festival of Communities: UG Symposium (Posters)

Anthrax infection starts with germination of Bacillus anthracis spores in macrophages. Some bacteria, including B. anthracis, can sporulate in response to environmental stress, such as starvation. During germination, large concentrations of calcium ions are released from the B. anthracis spore. Calcium ions are hydrophilic secondary messengers, and may therefore interfere with detection of the spore by confusing the cell signaling pathways. We investigated calcium release on infected macrophage viability by replacing the calcium stored in B. anthracis spores for other cations via demineralization/remineralization. It was discovered that calcium ions typically out-performed other cations in germination of B. anthracis.

Characterization Of Ips Pini Ipsdienol Dehydrogenase (Idol Dh), Heidi Pak, Claus Tittiger, William Welch

Festival of Communities: UG Symposium (Posters)

Ipsdienol is an important pheromone component for pine engraver beetle, Ips pini. Ipsdienol is a ten carbon monoterpenoid secondary alcohol and ipsdienone is the corresponding ketone. We are characterizing the activity of recombinant IDOL DH produced in Sf9 (insect) cells. The enzyme has a high stereospecificity: (-) ipsdienol was found to be a substrate while (+)-ipsdienol was neither a substrate nor inhibitor. Closely related monoterpenoids, such as nerol, geraniol, and citral, were neither substrates nor inhibitors. Smaller compounds, such as 2-propanol, also failed to act as an inhibitor or substrate. This indicates the binding site of this enzyme is highly …

Does Thermal Stress Cause Females Of The Plant Bryum Argenteum To Manipulate The Sex Ratios Of Their Offspring?, Elisha Rhodes, Lloyd Stark

Festival of Communities: UG Symposium (Posters)

About half of all moss taxa exhibit female-biased sex ratios, and bryophyte male rarity remains largely unexplained. One possible explanation is differential stress tolerance of spores due to maternal sporophyte manipulation during stress. To test this hypothesis, sporophytes of the species Bryum argenteum were subjected to thermal stress and observed for growth abnormalities and sporophyte abortions. Data display a correlation between increased temperature and increased sporophyte abortions as well as increased time to complete meiosis, possibly indicating decreased fitness. Continued global warming may create more stressful environments for sporophytes resulting in the elimination of males from local populations.

Effect Of Temperature And Oxygen Levels On Lactate Production In Palaemonetes Pugio, Robin Schofield, Teresa Mika, Carl Reiber

Festival of Communities: UG Symposium (Posters)

Oxygen delivery rates must keep pace with the increased metabolic rate observed in poikilothermic animals exposed to increased temperature if aerobic metabolism is to be maintained. Physical failure of the oxygen delivery system to meet these demands may be a mechanism of cardiac failure in crustaceans at temperature extremes. As part of the determination of the effect of temperature on the cardio-respiratory system, we are measuring whole animal lactate levels in grass shrimp acclimated to 20°C over temperature ranges in normoxic and hyperoxic conditions. Lactate levels are measured as an indicator of a switch from aerobic to anaerobic metabolism. Animals …