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Comparison Of Transcript Profiles In Wild-Type And O2 Maize Endosperm In Different Genetic Backgrounds, Hongwu Jia, Dan Nettleton, Joan M. Peterson, Gricelda Vasquez-Carrillo, Jean-Luc Jannink, M. Paul Scott 2017 Monsanto

Comparison Of Transcript Profiles In Wild-Type And O2 Maize Endosperm In Different Genetic Backgrounds, Hongwu Jia, Dan Nettleton, Joan M. Peterson, Gricelda Vasquez-Carrillo, Jean-Luc Jannink, M. Paul Scott

M. Paul Scott

Mutations in the Opaque2 (O2) gene of maize (Zea mays L.) improve the nutritional value of maize by reducing the level of zeins in the kernel. The phenotype of o2 grain is controlled by many modifier genes and is therefore strongly dependent on genetic background. We propose two hypotheses to explain differences in phenotypic severity in different genetic backgrounds: (i) Specific genes are differentially (o2 vs. wild-type) expressed only in certain genotypes, and (ii) A set of genes are differentially expressed in all backgrounds, but the degree of differential expression differs in different backgrounds. To determine the extent to which ...


Application Of Silicon Ameliorated Salinity Stress And Improved Wheat Yield, M. A. Ibrahim, A. M. Merwad, E. A. Elnaka, C. L. Burras, L. Follett 2017 Iowa State University

Application Of Silicon Ameliorated Salinity Stress And Improved Wheat Yield, M. A. Ibrahim, A. M. Merwad, E. A. Elnaka, C. L. Burras, L. Follett

C. Lee Burras

Management of soil salinity is an important research field around the globe, especially when associated with the limited water resources. This work aimed to improve the growth and yield of wheat (Triticum aestivum L. CV. Sakha-93) grown under salinity stress. A completely randomized design pot experiment with three replications was conducted in a loamy soil with various levels of salinity under local weather conditions. The treatments included five levels of salinity (2.74, 5.96, 8.85, 10.74, and 13.38 dSm-1) prepared by adding NaCl to the selected soil and five treatments of Si (0, 2.1, 4 ...


Marketing The Mountain State: A Large N Study Of User Engagement On Twitter, Kirk Richardson 2017 Illinois State University

Marketing The Mountain State: A Large N Study Of User Engagement On Twitter, Kirk Richardson

Capstone Projects – Politics and Government

Much of the evolving research on the use of social media in destination marketing emphasizes how information diffusion influences the reputational image of place. The present study uses Twitter data to focus on the relative differences in user engagement across discrete account types. Specifically, this is done to examine how the official destination marketing organization of Montana—the Montana Office of Tourism (MTOT)—performs relative to other account types. Several regression analyses conducted on Twitter data associated with an ongoing MTOT place branding campaign reveal that tweets sent from ‘official’ accounts are more likely to be retweeted, and are estimated ...


Constructing A Confidence Interval For The Fraction Who Benefit From Treatment, Using Randomized Trial Data, Emily J. Huang, Ethan X. Fang, Daniel F. Hanley, Michael Rosenblum 2017 Johns Hopkins University School of Public Health, Department of Biostatistics

Constructing A Confidence Interval For The Fraction Who Benefit From Treatment, Using Randomized Trial Data, Emily J. Huang, Ethan X. Fang, Daniel F. Hanley, Michael Rosenblum

Johns Hopkins University, Dept. of Biostatistics Working Papers

The fraction who benefit from treatment is defined as the proportion of patients whose potential outcome under treatment is better than that under control. Statistical inference for this parameter is challenging since it is only partially identifiable, even in our context of a randomized trial. We propose and evaluate a new method for constructing a confidence interval for the fraction who benefit, when the outcome is ordinal-valued (with binary outcomes as a special case). This confidence interval procedure is proved to be pointwise consistent. Our method does not require any assumptions about the joint distribution of the potential outcomes, although ...


Tree-Based Regression For Interval-Valued Data, Chih-Ching Yeh 2017 Utah State University

Tree-Based Regression For Interval-Valued Data, Chih-Ching Yeh

All Graduate Plan B and other Reports

Regression methods for interval-valued data have been increasingly studied in recent years. As most of the existing works focus on linear models, it is important to note that many problems in practice are nonlinear in nature and therefore development of nonlinear regression tools for intervalvalued data is crucial. In this project, we propose a tree-based regression method for interval-valued data, which is well applicable to both linear and nonlinear problems. Unlike linear regression models that usually require additional constraints to ensure positivity of the predicted interval length, the proposed method estimates the regression function in a nonparametric way, so the ...


Qqs Orphan Gene Regulates Carbon And Nitrogen Partitioning Across Species Via Nf-Yc Interactions, Ling Li, Wenguang Zheng, Yanbing Zhu, Huaxun Ye, Buyun Tang, Zebulun W. Arendsee, Dallas Jones, Ruoran Li, Diego Ortiz, Xuefeng Zhao, Chuanlong Du, Dan Nettleton, M. Paul Scott, Maria G. Salas-Fernandez, Yanhai Yin, Eve S. Wurtele 2017 Iowa State University

Qqs Orphan Gene Regulates Carbon And Nitrogen Partitioning Across Species Via Nf-Yc Interactions, Ling Li, Wenguang Zheng, Yanbing Zhu, Huaxun Ye, Buyun Tang, Zebulun W. Arendsee, Dallas Jones, Ruoran Li, Diego Ortiz, Xuefeng Zhao, Chuanlong Du, Dan Nettleton, M. Paul Scott, Maria G. Salas-Fernandez, Yanhai Yin, Eve S. Wurtele

M. Paul Scott

The allocation of carbon and nitrogen resources to the synthesis of plant proteins, carbohydrates, and lipids is complex and under the control of many genes; much remains to be understood about this process. QQS (Qua-Quine Starch; At3g30720), an orphan gene unique to Arabidopsis thaliana, regulates metabolic processes affecting carbon and nitrogen partitioning among proteins and carbohydrates, modulating leaf and seed composition in Arabidopsis and soybean. Here the universality of QQS function in modulating carbon and nitrogen allocation is exemplified by a series of transgenic experiments. We show that ectopic expression of QQS increases soybean protein independent of the genetic background ...


Arca Controls Metabolism, Chemotaxis, And Motility Contributing To The Pathogenicity Of Avian Pathogenic Escherichia Coli, Fengwei Jiang, Chunxia An, Yinli Bao, Xuefeng Zhao, Robert L. Jernigan, Andrew Lithio, Dan Nettleton, Ling Li, Eve S. Wurtele, Lisa K. Nolan, Chengping Lu, Ganwu Li 2017 Nanjing Agricultural University

Arca Controls Metabolism, Chemotaxis, And Motility Contributing To The Pathogenicity Of Avian Pathogenic Escherichia Coli, Fengwei Jiang, Chunxia An, Yinli Bao, Xuefeng Zhao, Robert L. Jernigan, Andrew Lithio, Dan Nettleton, Ling Li, Eve S. Wurtele, Lisa K. Nolan, Chengping Lu, Ganwu Li

Lisa K. Nolan

Avian pathogenic Escherichia coli (APEC) strains cause one of the three most significant infectious diseases in the poultry industry and are also potential food-borne pathogens threating human health. In this study, we showed that ArcA (aerobic respiratory control), a global regulator important for E. coli's adaptation from anaerobic to aerobic conditions and control of that bacterium's enzymatic defenses against reactive oxygen species (ROS), is involved in the virulence of APEC. Deletion of arcA significantly attenuates the virulence of APEC in the duck model. Transcriptome sequencing (RNA-Seq) analyses comparing the APEC wild type and the arcA mutant indicate that ...


Moesin1 And Ve-Cadherin Are Required In Endothelial Cells During In Vivo Tubulogenesis, Ying Wang, Mark S. Kaiser, Jon D. Larson, Aidas Nasevicius, Karl J. Clark, Shannon A. Wadman, Sharon E. Roberg-Perez, Stephen C. Ekker, Perry B. Hackett, Maura McGrail, Jeffrey J. Essner 2017 Iowa State University

Moesin1 And Ve-Cadherin Are Required In Endothelial Cells During In Vivo Tubulogenesis, Ying Wang, Mark S. Kaiser, Jon D. Larson, Aidas Nasevicius, Karl J. Clark, Shannon A. Wadman, Sharon E. Roberg-Perez, Stephen C. Ekker, Perry B. Hackett, Maura Mcgrail, Jeffrey J. Essner

Jeffrey J. Essner

Endothelial tubulogenesis is a crucial step in the formation of functional blood vessels during angiogenesis and vasculogenesis. Here, we use in vivo imaging of living zebrafish embryos expressing fluorescent fusion proteins of β-Actin, α-Catenin, and the ERM family member Moesin1 (Moesin a), to define a novel cord hollowing process that occurs during the initial stages of tubulogenesis in intersegmental vessels (ISVs) in the embryo. We show that the primary lumen elongates along cell junctions between at least two endothelial cells during embryonic angiogenesis. Moesin1-EGFP is enriched around structures that resemble intracellular vacuoles, which fuse with the luminal membrane during expansion ...


Phenotypic Plasticity Of Native Vs. Invasive Purple Loosestrife: A Two-State Multivariate Approach, Young Jin Chun, Michael L. Collyer, Kirk A. Moloney, Jason D. Nason 2017 Iowa State University

Phenotypic Plasticity Of Native Vs. Invasive Purple Loosestrife: A Two-State Multivariate Approach, Young Jin Chun, Michael L. Collyer, Kirk A. Moloney, Jason D. Nason

Jason D Nason

The differences in phenotypic plasticity between invasive (North American) and native (German) provenances of the invasive plant Lythrum salicaria (purple loosestrife) were examined using a multivariate reaction norm approach testing two important attributes of reaction norms described by multivariate vectors of phenotypic change: the magnitude and direction of mean trait differences between environments. Data were collected for six life history traits from native and invasive plants using a split-plot design with experimentally manipulated water and nutrient levels. We found significant differences between native and invasive plants in multivariate phenotypic plasticity for comparisons between low and high water treatments within low ...


Propensity Score Analysis With Matching Weights, Liang Li 2017 Cleveland Clinic

Propensity Score Analysis With Matching Weights, Liang Li

Liang Li

The propensity score analysis is one of the most widely used methods for studying the causal treatment effect in observational studies. This paper studies treatment effect estimation with the method of matching weights. This method resembles propensity score matching but offers a number of new features including efficient estimation, rigorous variance calculation, simple asymptotics, statistical tests of balance, clearly identified target population with optimal sampling property, and no need for choosing matching algorithm and caliper size. In addition, we propose the mirror histogram as a useful tool for graphically displaying balance. The method also shares some features of the inverse ...


Mechanistic Mathematical Models: An Underused Platform For Hpv Research, Marc Ryser, Patti Gravitt, Evan R. Myers 2017 George Washington University

Mechanistic Mathematical Models: An Underused Platform For Hpv Research, Marc Ryser, Patti Gravitt, Evan R. Myers

Global Health Faculty Publications

Health economic modeling has become an invaluable methodology for the design and evaluation of clinical and public health interventions against the human papillomavirus (HPV) and associated diseases. At the same time, relatively little attention has been paid to a different yet complementary class of models, namely that of mechanistic mathematical models. The primary focus of mechanistic mathematical models is to better understand the intricate biologic mechanisms and dynamics of disease. Inspired by a long and successful history of mechanistic modeling in other biomedical fields, we highlight several areas of HPV research where mechanistic models have the potential to advance the ...


Swine Respiratory Disease Minimally Affects Responses Of Nursery Pigs To Gas Euthanasia, Larry J. Sadler, Locke A. Karriker, Anna K. Butters-Johnson, Kent J. Schwartz, Tina M. Widowski, Chong Wang, Suzanne T. Millman 2017 Iowa State University

Swine Respiratory Disease Minimally Affects Responses Of Nursery Pigs To Gas Euthanasia, Larry J. Sadler, Locke A. Karriker, Anna K. Butters-Johnson, Kent J. Schwartz, Tina M. Widowski, Chong Wang, Suzanne T. Millman

Anna K. Butters-Johnson

Objectives: To assess effects of swine respiratory disease (SRD) on nursery pig responses during gas euthanasia and to compare responses to carbon dioxide (CO2) and argon (Ar) gas euthanasia in terms of efficacy and welfare.

Materials and methods: Fifty-four pigs identified for euthanasia were classified as having SRD or euthanized for other reasons (OT). These pigs were distributed among three treatments: prefill CO2 (P-CO2), gradual fill CO2(G-CO2), and prefill Ar (P-Ar). Behavioral and physiological indicators of efficacy and welfare were assessed directly and from video. Modified atmosphere CO2 and O2concentrations (%) were collected throughout the process.

Results: Respiratory disease status ...


Swine Respiratory Disease Minimally Affects Responses Of Nursery Pigs To Gas Euthanasia, Larry J. Sadler, Locke A. Karriker, Anna K. Butters-Johnson, Kent J. Schwartz, Tina M. Widowski, Chong Wang, Suzanne T. Millman 2017 Iowa State University

Swine Respiratory Disease Minimally Affects Responses Of Nursery Pigs To Gas Euthanasia, Larry J. Sadler, Locke A. Karriker, Anna K. Butters-Johnson, Kent J. Schwartz, Tina M. Widowski, Chong Wang, Suzanne T. Millman

Anna K. Butters-Johnson

Objectives: To assess effects of swine respiratory disease (SRD) on nursery pig responses during gas euthanasia and to compare responses to carbon dioxide (CO2) and argon (Ar) gas euthanasia in terms of efficacy and welfare.

Materials and methods: Fifty-four pigs identified for euthanasia were classified as having SRD or euthanized for other reasons (OT). These pigs were distributed among three treatments: prefill CO2 (P-CO2), gradual fill CO2(G-CO2), and prefill Ar (P-Ar). Behavioral and physiological indicators of efficacy and welfare were assessed directly and from video. Modified atmosphere CO2 and O2concentrations (%) were collected throughout the process.

Results: Respiratory disease status ...


Genes And Small Rna Transcripts Exhibit Dosage-Dependent Expression Pattern In Maize Copy-Number Alterations, Tao Zuo, Jianbo Zhang, Andrew Lithio, Sudhansu Dash, David F. Weber, Roger Wise, Dan Nettleton, Thomas Peterson 2017 Iowa State University

Genes And Small Rna Transcripts Exhibit Dosage-Dependent Expression Pattern In Maize Copy-Number Alterations, Tao Zuo, Jianbo Zhang, Andrew Lithio, Sudhansu Dash, David F. Weber, Roger Wise, Dan Nettleton, Thomas Peterson

Thomas Peterson

Copy-number alterations are widespread in animal and plant genomes, but their immediate impact on gene expression is still unclear. In animals, copy-number alterations usually exhibit dosage effects, except for sex chromosomes which tend to be dosage compensated. In plants, genes within small duplications (<100 kb) often exhibit dosage-dependent expression, whereas large duplications (>50 Mb) are more often dosage compensated. However, little or nothing is known about expression in moderately-sized (1–50 Mb) segmental duplications, and about the response of small RNAs to dosage change. Here, we compared maize (Zea mays) plants with two, three, and four doses of a 14.6-Mb segment of chromosome 1 that contains ∼300 genes ...


Gilmore Girls And Instagram: A Statistical Look At The Popularity Of The Television Show Through The Lens Of An Instagram Page, Brittany Simmons 2017 Chapman University

Gilmore Girls And Instagram: A Statistical Look At The Popularity Of The Television Show Through The Lens Of An Instagram Page, Brittany Simmons

Student Research Day Abstracts and Posters

After going on the Warner Brothers Tour in December of 2015, I created a Gilmore Girls Instagram account. This account, which started off as a way for me to create edits of the show and post my photos from the tour turned into something bigger than I ever could have imagined. In just over a year I have over 55,000 followers. I post content including revival news, merchandise, and edits of the show that have been featured in Entertainment Weekly, Bustle, E! News, People Magazine, Yahoo News, & GilmoreNews.

I created a dataset of qualitative and quantitative outcomes from my ...


Comparision Of Survival Curves Between Cox Proportional Hazards, Random Forests, And Conditional Inference Forests In Survival Analysis, Brandon Weathers, Richard Cutler Dr. 2017 Utah State University

Comparision Of Survival Curves Between Cox Proportional Hazards, Random Forests, And Conditional Inference Forests In Survival Analysis, Brandon Weathers, Richard Cutler Dr.

All Graduate Plan B and other Reports

Survival analysis methods are a mainstay of the biomedical fields but are finding increasing use in other disciplines including finance and engineering. A widely used tool in survival analysis is the Cox proportional hazards regression model. For this model, all the predicted survivor curves have the same basic shape, which may not be a good approximation to reality. In contrast the Random Survival Forests does not make the proportional hazards assumption and has the flexibility to model survivor curves that are of quite different shapes for different groups of subjects. We applied both techniques to a number of publicly available ...


Washington State Public Teachers' Ambient Positional Instability From A Statistical Approach Of Retrospective Study & Prospective Study, Bowen Cai, Robert Boruch 2017 University of Pennsylvania

Washington State Public Teachers' Ambient Positional Instability From A Statistical Approach Of Retrospective Study & Prospective Study, Bowen Cai, Robert Boruch

GSE Publications

The purpose of this research is to study the movements of teachers’ churn rate in the state of Washington over the past 14 years. The research of teachers’ churn rate is an integrative study, with retrospective part and prospective part. Retrospective study includes the analysis of descriptive statistics (level I), statistical inference (level II) and causal inference (level III) (Berk, R.A. (2016) Statistical Learning from a Regression Perspective. Philadelphia, PA: Springer). Prospective study is mainly about forecasting and statistical inference that generated from the predictions. In this research, we are using longitudinal data analysis. The good point of longitudinal ...


Denoising Tandem Mass Spectrometry Data, Felix Offei 2017 East Tennessee State Universtiy

Denoising Tandem Mass Spectrometry Data, Felix Offei

Electronic Theses and Dissertations

Protein identification using tandem mass spectrometry (MS/MS) has proven to be an effective way to identify proteins in a biological sample. An observed spectrum is constructed from the data produced by the tandem mass spectrometer. A protein can be identified if the observed spectrum aligns with the theoretical spectrum. However, data generated by the tandem mass spectrometer are affected by errors thus making protein identification challenging in the field of proteomics. Some of these errors include wrong calibration of the instrument, instrument distortion and noise. In this thesis, we present a pre-processing method, which focuses on the removal of ...


On Post-Selection Confidence Intervals In Linear Regression, Xinwei Zhang 2017 Washington University in St. Louis

On Post-Selection Confidence Intervals In Linear Regression, Xinwei Zhang

Arts & Sciences Electronic Theses and Dissertations

The general goal of this thesis is to investigate and examine some issues about post-selection inference which arises from the setting where statistical inference is carried out after a datadriven model selection step. In this setting, the classical inference theory which requires a fixed priori model becomes invalid since the selected model is a result of random event. Hence, a common practice in applied research which ignores the model selection and builds up confidence interval will result in misleading or even false conclusion. In this thesis, specifically, we first discusses some examples to show how the classical inference theory loses ...


Screening Coriander Gene Pool For Special Uses, Pedro A. López, M. P. Widrlechner, P. W. Simon, S. Rai, T. B. Bailey, C. A. Gardner 2017 Colegio de Postgraduados, Puebla

Screening Coriander Gene Pool For Special Uses, Pedro A. López, M. P. Widrlechner, P. W. Simon, S. Rai, T. B. Bailey, C. A. Gardner

Mark P. Widrlechner

Coriander (Coriandrum sativum L.) is an aromatic member of the Apiaceae with a wide diversity of uses (Diederichsen 1996). Its rapid life cycle allows it to fit into different growing seasons, making it possible to grow the crop under a wide range of conditions. Three subspecies and 10 botanical varieties of coriander have been proposed at the infraspecific level (Diederichsen and Hammer 2003) based on phenotypic characteristics; however, molecular evidence does not support classifications based on phenotypic and/or biochemical characteristics (López 2006).

The objectives of our study were to assess the phenotypic and biochemical characteristics of coriander germplasm collections ...


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