Physical Sciences and Mathematics Commons^™

Exploring The Information In P-Values For The Analysis And Planning Of Multiple-Test Experiments, David Ruppert, Dan Nettleton, J.T. Gene Hwang

Dan Nettleton

A new methodology is proposed for estimating the proportion of true null hypotheses in a large collection of tests. Each test concerns a single parameter δ whose value is specified by the null hypothesis. We combines a parametric model for the conditional CDF of the p-value given δ with a nonparametric spline model for the density g(δ) of δ under the alternative hypothesis. The proportion of true null hypotheses and the coefficients in the spline model are estimated by penalized least-squares subject to constraints that guarantee that the spline is a density. The estimator is computed efficiently using quadratic programming. …

Empirical Bayes Analysis Of Rna-Seq Data For Detection Of Gene Expression Heterosis, Jarad Niemi, Eric Mittman, Will Landau, Dan Nettleton

Dan Nettleton

An important type of heterosis, known as hybrid vigor, refers to the enhancements in the phenotype of hybrid progeny relative to their inbred parents. Although hybrid vigor is extensively utilized in agriculture, its molecular basis is still largely unknown. In an effort to understand phenotypic heterosis at the molecular level, researchers are measuring transcript abundance levels of thousands of genes in parental inbred lines and their hybrid offspring using RNA sequencing (RNA-seq) technology. The resulting data allow researchers to search for evidence of gene expression heterosis as one potential molecular mechanism underlying heterosis of agriculturally important traits. The null hypotheses …

Flor Revisited (Again): Eqtl And Mutational Analysis Of Nb-Lrr Mediated Immunity To Powdery Mildew In Barley, Roger P. Wise, Priyanka Surana, Gregory S. Fuerst, Ruo Xu, Divya Mistry, Julie A. Dickerson, Dan Nettleton Dr.

Dan Nettleton

Genes encoding early signaling events in pathogen defense often are identified only by their phenotype. Such genes involved in barley-powdery mildew interactions include Mla, specifying race-specific resistance; Rar1 (Required for Mla12-specified resistance1), and Rom1 (Restoration of Mla-specified resistance1). The HSP90-SGT1-RAR1 complex appears to function as chaperone in MLA-specified resistance, however, much remains to be discovered regarding the precise signaling underlying plant immunity. Genetic analyses of fast-neutron mutants derived from CI 16151 (Mla6) uncovered a novel locus, designated Rar3 (Required for Mla6-specified resistance3). Rar3 segregates independent of Mla6 and Rar1, and rar3 mutants are susceptible to Blumeria graminis f. sp. hordei …

Identification Of Differentially Expressed Gene Categories In Microarray Studies Using Nonparametric Multivariate Analysis, Dan Nettleton, Justin Recknor, James M. Reecy

Dan Nettleton

The field of microarray data analysis is shifting emphasis from methods for identifying differentially expressed genes to methods for identifying differentially expressed gene categories. The latter approaches utilize a priori information about genes to group genes into categories and enhance the interpretation of experiments aimed at identifying expression differences across treatments. While almost all of the existing approaches for identifying differentially expressed gene categories are practically useful, they suffer from a variety of drawbacks. Perhaps most notably, many popular tools are based exclusively on gene-specific statistics that cannot detect many types of multivariate expression change. We have developed a nonparametric …

A Hidden Markov Model Approach To Testing Multiple Hypotheses On A Gene Ontology Graph, Kun Liang, Dan Nettleton

Dan Nettleton

Gene category testing problems involve testing hundreds of null hypotheses that correspond to nodes in a directed acyclic graph. The logical relationships among the nodes in the graph imply that only some configurations of true and false null hypotheses are possible and that a test for a given node should depend on data from neighboring nodes. We developed a method based on a hidden Markov model that takes the whole graph into account and provides coherent decisions in this structured multiple hypothesis testing problem. The method is illustrated by testing Gene Ontology terms for evidence of differential expression.

Developmental Transcript Profiling Of Cyst Nematode Feeding Cells In Soybean Roots, Nagabhushana Ithal, Justin Recknor, Dan Nettleton, Tom Maier, Thomas J. Baum, Melissa G. Mitchum

Dan Nettleton

Cyst nematodes of the genus Heterodera are obligate, sedentary endoparasites that have developed highly evolved relationships with specific host plant species. Successful parasitism involves significant physiological and morphological changes to plant root cells for the formation of specialized feeding cells called syncytia. To better understand the molecular mechanisms that lead to the development of nematode feeding cells, transcript profiling was conducted on developing syncytia induced by the soybean cyst nematode Heterodera glycines in soybean roots by coupling laser capture microdissection with high-density oligonucleotide microarray analysis. This approach has identified pathways that may play intrinsic roles in syncytium induction, formation, and …

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

Dan Nettleton

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 …

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

Dan Nettleton

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 ArcA regulates …

A Diallel Analysis Of A Maize Donor Population Response To In Vivo Maternal Haploid Induction I: Inducibility, Gerald N. De La Fuente, Ursula K. Frei, Benjamin Trampe, Daniel Nettleton, Wei Zhang, Thomas Lubberstedt

Dan Nettleton

The maize in vivo maternal doubled haploid (DH) system is an important tool used by maize breeders and geneticists around the world. The ability to rapidly produce DH lines of maize for breeding allows breeders to quickly respond to new selection criteria based on the ever changing biotic and abiotic stresses that maize is subjected to across its growing area. There are two important steps in the generation of DH lines using the in vivo maternal DH system: 1) the production and identification of haploid progeny, and 2) the doubling of genomes to create fertile, diploid inbred lines that can …

Differentially Expressed Genes In Blood From Young Pigs Between Two Swine Lines Divergently Selected For Feed Efficiency: Potential Biomarkers For Improving Feed Efficiency, Haibo Liu, Yet T. Nguyen, Daniel S. Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle

Dan Nettleton

The goal of this study was to find potential gene expression biomarkers in blood of piglets that can be used to predict pigs’ future feed efficiency. Using RNA-seq technology, we found 453 genes were differentially expressed (false discovery rate (FDR) ≤ 0.05) in the blood of two Yorkshire lines of pigs divergently selected for feed efficiency (FE) based on residual feed intake (RFI). Genes involved in several biosynthetic processes were overrepresented among genes more highly expressed in the low RFI line compared to the high RFI line. Weighted gene co-expression network analysis (WGCNA) also revealed genes involved in some of …

A Clade-Specific Arabidopsis Gene Connects Primary Metabolism And Senescence, Dallas C. Jones, Wenguang Zheng, Sheng Huang, Chuanlong Du, Xuefeng Zhao, Ragothaman M. Yennamalli, Taner Z. Sen, Dan Nettleton, Eve S. Wurtele, Ling Li

Dan Nettleton

Nearly immobile, plants have evolved new components to be able to respond to changing environments. One example is Qua Quine Starch (QQS, AT3G30720), an Arabidopsis thaliana-specific orphan gene that integrates primary metabolism with adaptation to environment changes. SAQR (Senescence-Associated and QQS-Related, AT1G64360), is unique to a clade within the family Brassicaceae; as such, the gene may have arisen about 20 million years ago. SAQR is up-regulated in QQS RNAi mutant and in the apx1 mutant under light-induced oxidative stress. SAQR plays a role in carbon allocation: overexpression lines of SAQR have significantly decreased starch content; …

3 Cara Mudah Menghilangkan Daging Tumbuh Di Kemaluan Tanpa Kedokter, Kutil Kelamin Ampuh

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5 Cara Mudah Pengobatan Daging Tumbuh Di Vagina Paling Aman, Kutil Kelamin Ampuh

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5 Cara Mudah Penanganan Daging Tumbuh Di Vagina Paling Ampuh, Kutil Kelamin Ampuh

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5 Cara Mudah Merontokan Daging Tumbuh Di Vagina Paling Manjur, Kutil Kelamin Ampuh

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5 Cara Mudah Mengatasi Daging Tumbuh Di Vagina Tanpa Oprasi, Kutil Kelamin Ampuh

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5 Tips Mudah Merontokan Benjolan Kasar Di Kelamin Paling Manjur, Kutil Kelamin Ampuh

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5 Tips Mudah Menyembuhkan Benjolan Kasar Di Kelamin Terbukti Manjur, Kutil Kelamin Ampuh

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7 Tips Mudah Pengobatan Daging Tumbuh Di Vagina Paling Aman, Kutil Kelamin Ampuh

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7 Tips Mudah Penanganan Daging Tumbuh Di Vagina Paling Ampuh, Kutil Kelamin Ampuh

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Consider When Deciding On Custom Home Windows, Nerti Gedra

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Laser Induced Desorption Time Of Flight Mass Spectrometer Analysis Of Adsorbed Contaminants On Vacuum Ultraviolet Lithography Optic Materials, Susan D. Allen, Yamini Surpaneni

Susan D. Allen

Adsorbed surface contaminants on optical elements absorb light energy in an optical lithography system and, if left unclean, will result in reduced wafer yield. In order to nondestructively analyze the surface adsorbate of different CaF2 samples, a laser induced desorption-Time of Flight Mass Spectrometer (LID-TOFMS) technique was developed. The main object of this technique is to investigate the surface composition of adsorbed contaminants as a function of position on the sample. An Er:YAG laser at 2.94 μm was used as the light source to induce desorption. Electron impact ionization was used to obtain ionization of desorbed molecules. The detection of …

Nightmares, Jeremiah Farrell, Karen Farrell

Jeremiah Farrell

Jeremiah's puzzle "Nightmare", which was exchanged at the 2013 Washington, DC International Puzzle Party. 100 puzzle designers create 100 copies of their puzzle and pass it out at the party and exchange them. This puzzle was a special puzzle gift that was given to IPP32 exchangers by its designer, Jerry Farrell, in memory of longtime IPP member, Tom Rodgers, Jr.

How I Improved My Keto Slim 7 In One Day, Keto Healthys

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3 Cara Mudah Mengatasi Daging Tumbuh Di Kemaluan Tanpa Oprasi, Kutil Kelamin Ampuh

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Euler Entertainments, Jeremiah Farrell, Karen Farrell

Jeremiah Farrell

No abstract provided.

The White Rabbit 12-Puzzle, Chris Morgan, Jeremiah Farrell

Jeremiah Farrell

Martin Gardner's fondness for the characters and themes of Lewis Carroll's "Alice" is well-known and to honor Gardner we offer two word puzzles to be played on the 12-node diagram of the WHITE RABBIT.

Kate Jones – A Tribute, Karen Farrell, Jeremiah Farrell

Jeremiah Farrell

Kate is also an accomplished recreational mathematician and poet. To try to match in a small way her creative ability, we offer three puzzle-games in her honor: O'BEIRNE's TRI-HEX, PAPPUS and "KATe JONES". These three are specific examples of (9,3) symmetric configurations. More generally an (n,r) configuration is a collection of n "points"and n "lines" subject to the following requirements:

Rl: Any two points belong to at most one line.

R2: Each line has r points, and each point belongs to r lines.

Martin Gardner Puzzle-Games, Stephen Bloom, Lacey Echols, Jeremiah Farrell, Shannon Lieb

Jeremiah Farrell

No abstract provided.