Statistical Methods for Assessing Individual Oocyte Viability Through Gene Expression Profiles

Abstract Statistical Methods for Assessing Individual Oocyte Viability Through Gene Expression Profiles By Michael O. Bishop Utah State University, 2017 Major Professor: Dr. John R. Stevens Department: Mathematics and Statistics Oocytes are the precursor cells to the female gamete, or egg. While reproduction may vary from species to species, within humans and most domesticated animals, the oocyte maturation process is fairly similar. As an oocyte matures, there are various processes that take place, all of which have an effect on the viability of the individual oocyte. Barring outside damage that may come to the oocyte, one of the primary reasons for non-viability is that of abnormal gene expression. Within this project, we focus on two oocyte maturation techniques: in vivo (IVV) derived oocytes (our gold-standard) and in vitro matured (IVM) oocytes. A great disparity exists between the viability rates of the two origination techniques, and this disparity has led to low yields and inefficiency in the fields of cloning, fertility treatments, as well as personalized medicine. Within our project we use existing swine oocyte gene expression profile data as a proxy measure of viability, based on the similarity to IVV oocytes. Four statistical techniques for assessing the individual oocyte viability are proposed and compared, including: a weighted root mean squared deviation (wRMSD) approach, a distance kernel p-value approach, a distance tolerance interval approach, and a classification tree method. The relative performance of these four measures is discussed

Statistical Methods for Assessing Individual Oocyte Viability Through Gene Expression Profiles

In vivo derived oocytes are held as the gold standard for viability, other known origination methods are sub-par by comparison. Due to the low-viability of oocytes originating from these alternate methods, research was conducted to determine and quantify the validity of these alternate origination methods. However, the larger question of viability is on the individual oocyte level. We propose and compare methods of measurement based on gene expression profiles (GEPs) in order to assess oocyte viability, independent of oocyte origin. The first is based on a previously published wRMSD quantification of GEP differences. We also consider three novel methods: a distance comparison method, a tolerance interval method, and a classification-tree decision method; each utilizes a variable selection technique that focuses on the most differentially expressed genes. In our project, we obtain GEPs of individual swine oocytes and a general GEP distribution for in vivo oocytes. This distribution was the comparison standard for all oocytes, to gain a classification of viability. Each method is a valid method for driving viability decisions of the individual oocytes

Correlation effects in MgO and CaO: Cohesive energies and lattice constants

A recently proposed computational scheme based on local increments has been applied to the calculation of correlation contributions to the cohesive energy of the CaO crystal. Using ab-initio quantum chemical methods for evaluating individual increments, we obtain 80% of the difference between the experimental and Hartree-Fock cohesive energies. Lattice constants corrected for correlation effects deviate by less than 1% from experimental values, in the case of MgO and CaO.Comment: LaTeX, 4 figure

Future vision for the quality assurance of oncology clinical trials

The National Cancer Institute clinical cooperative groups have been instrumental over the past 50 years in developing clinical trials and evidence-based process improvements for clinical oncology patient care. The cooperative groups are undergoing a transformation process as we further integrate molecular biology into personalized patient care and move to incorporate international partners in clinical trials. To support this vision, data acquisition and data management informatics tools must become both nimble and robust to support transformational research at an enterprise level. Information, including imaging, pathology, molecular biology, radiation oncology, surgery, systemic therapy, and patient outcome data needs to be integrated into the clinical trial charter using adaptive clinical trial mechanisms for design of the trial. This information needs to be made available to investigators using digital processes for real-time data analysis. Future clinical trials will need to be designed and completed in a timely manner facilitated by nimble informatics processes for data management. This paper discusses both past experience and future vision for clinical trials as we move to develop data management and quality assurance processes to meet the needs of the modern trial

PRIMO: an interactive homology modeling pipeline

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling

Deficiencies in Vadose Zone Understanding at the INEEL

Subsurface contamination in the vadose zone, that portion of the subsurface pathway between land surface and an underlying aquifer, poses environmental problems at the Idaho National Engineering and Environmental Laboratory (INEEL) in eastern Idaho and across the U.S. Department of Energy complex. Assessing potential adverse impacts from these contaminated sites requires an understanding of the mechanisms controlling contaminant transport. Currently, vadose zone experts at the INEEL cannot with confidence predict the movement of water and contaminants in the complex, heterogeneous, fractured subsurface at the INEEL, especially within the vadose zone. In the draft version (Revision 1) of the Vadose Zone Deficiencies document, deficiencies in scientific understanding of flow and transport processes in the vadose zone at the INEEL were identified and grouped into 13 categories and recommendations were provided to address each of the deficiencies. The draft document provided the basis for an INEEL Vadose Zone Workshop that was conducted October 20 and 21, 1999, in Idaho Falls, Idaho. The workshop was conducted to group and rank the previously identified deficiencies and for the subsequent development of science plans to address the deficiencies that limit reliable predictions of water and contaminant movement in the subsurface. The workshop participants, comprising INEEL and scientists and project managers and non-INEEL scientists knowledgeable about the vadose zone, developed science- and technology-based recommendations derived through a series of technical sessions at the workshop. In this document, the final version of the Vadose Zone Deficiencies document, the draft document has been incorporated, largely intact, as well as the results from the workshop. The workshop participants grouped the deficiencies in vadose zone understanding at the INEEL into seven categories. These seven categories will be the focus areas of five science plans that are being developed to address the deficiencies. This document lays the foundation for the INEEL Site-wide vadose zone roadmap

Collage Vol. II

JUDY COCHRAN: Editorial, 4-5 ROBERTA CHAPMEN: Photo, 6 ANITRA CHUGHTAI (Translations): Haikus, 7 CHARLES O\u27KEEFE: Photo, 8 MARK VANDERLINDE-ABERNATHY, ALYSSA LANDRY (Translator): Memories of a Spider (Les souvenirs d\u27une araignee), 9 MARK VANDERLINE-ABERNATHY, AMY NORSKOG (Translator): Tomato Fields (Champ de tomates), 10 SARAH BISHOP, HEFEDH ZANINA (Translator): Dear John (Cher John), 11 RYAN BUTZ (Translator): Basho\u27s Haiku, Issa\u27s Haiku, 12-13 JENNIFER HUMBERT, FADOUA EL BOUAMRAOUI (Translator): Pressed Lips (Levres Serrees), 15 ADELE REEVES (Translator): Contemporary song by Mr. Children, 16-17 BRODY PAGEL, GRACE DUGAR (Translator): The Lizard King (Le Roi Lezard), 18 JIMMY PIPKIN (Translator): In Love with You, 19 MOLLY ROSCOE: Saturday Night at Rusty\u27s (Samedi Soir a Rusty\u27s), 20 CHARLES O\u27KEEFE: Photo, 21 MATT MESSMER (Translator): Waseda University School Song, 22-23 TIMOTHY COOPER: Wenn du grosh bist… (When you\u27re Tall…), 24 DAVID HARMAN: Der Dunkle Stern (The Dark Star), 25 ANN TOWNSEND, JUDY COCHRAN (Translator): From a Window (D\u27une Fenetre), 26-27 SARA CAHILL: El sauce lloron (The Weeping Willow), 28-32 CHARLES O\u27KEEFE: Photo, 30 JENNIFER HUMBERT, MATT BISHOP: Past, Present (passe, present), 33 CAROL GENEYA KAPLAN, FADOUA EL BOUAMRAOUI (Translator): Une Autre Femme (Another Woman), 34-35 CHARLES O\u27KEEFE: Photo, 36 ANN TOWNSEND, JUDY COCHRAN (Translator): The Mowers (Les Faucheurs), 37 PRISCILLA PATON: Photo, 38 GONZALO TUESTA: La Grande Dame De Paris (The Great Lady of Paris), 39 SARAH PILLERDORF (Translator): Japanese Cartoons by Tezuka Osamu, 41-45 DANIELLE GERKEN: Schuhe der Heimat (Boots of Home), 47 CURTIS PLOWGIAN: Le peste de la langue francaise, 48-52 PRISCILLA PATON: Photo, 50 ZANE HOUSEHOLDER: Vive la Republique! (Film), 54 JENNIFER ZIMMER: EL tenis y las frustraciones (Tennis and Frustrations), La tumba de Ben (Ben\u27s Grave), 56-57 AUTUMN LOTZE: Times Square in the rain, 58-59 CHARLES O\u27KEEFE: Photo, 60 STEPHEN M. JULKA: Colors of the Earth, 61 THOMAS BRESSOUD: Java, 62 ERIC NELSON: World, 63 SARAH CLAPP (Translator): At a long day\u27s end (Natsume Soseki), A friend has come and is now leaving, Eating persimmons (Masaoka Shiki), 64 CHARLES O\u27KEEFE: Photo, 65 JOHN BURZYNSKI, MEGAN FETTER (Translator): Home is where the heart is, 66 RICHARD BANAHAN: Photo, 67 KIM FREEMAN: Baltimore, 68 JACOB RIDRIGUEZ-NOBLE: Home (Heimat), 69 SUZANNE KENNEDY: Oft verberge ich mich (Oft I hide myself), 70 RICHARD BANAHAN: Photo, 7

From St. Petersburg to Krushchev\u27s Boot

Program for the first annual RISD Cabaret held in Memorial Hall. Design and layout by Justin Kerr.https://digitalcommons.risd.edu/liberalarts_cabaret_programs/1000/thumbnail.jp

Nongenetic Determinants of Risk for Early-Onset Colorectal Cancer

Background: Incidence of early-onset (younger than 50 years of age) colorectal cancer (CRC) is increasing in many countries. Thus, elucidating the role of traditional CRC risk factors in early-onset CRC is a high priority. We sought to determine whether risk factors associated with late-onset CRC were also linked to early-onset CRC and whether association patterns differed by anatomic subsite. Methods: Using data pooled from 13 population-based studies, we studied 3767 CRC cases and 4049 controls aged younger than 50 years and 23 437 CRC cases and 35 311 controls aged 50 years and older. Using multivariable and multinomial logistic regression, we estimated odds ratios (ORs) and 95% confidence intervals (CIs) to assess the association between risk factors and early-onset CRC and by anatomic subsite. Results: Early-onset CRC was associated with not regularly using nonsteroidal anti-inflammatory drugs (OR = 1.43, 95% CI = 1.21 to 1.68), greater red meat intake (OR = 1.10, 95% CI = 1.04 to 1.16), lower educational attainment (OR = 1.10, 95% CI = 1.04 to 1.16), alcohol abstinence (OR = 1.23, 95% CI = 1.08 to 1.39), and heavier alcohol use (OR = 1.25, 95% CI = 1.04 to 1.50). No factors exhibited a greater excess in early-onset compared with late-onset CRC. Evaluating risks by anatomic subsite, we found that lower total fiber intake was linked more strongly to rectal (OR = 1.30, 95% CI = 1.14 to 1.48) than colon cancer (OR = 1.14, 95% CI = 1.02 to 1.27; P = .04). Conclusion: In this large study, we identified several nongenetic risk factors associated with early-onset CRC, providing a basis for targeted identification of those most at risk, which is imperative in mitigating the rising burden of this disease

The genetic architecture of the MHC class II region in British Texel sheep

Understanding the structure of the major histocompatibility complex, especially the number and frequency of alleles, loci and haplotypes, is crucial for efficient investigation of the way in which the MHC influences susceptibility to disease. Nematode infection is one of the most important diseases suffered by sheep, and the class II region has been repeatedly associated with differences in susceptibility and resistance to infection. Texel sheep are widely used in many different countries and are relatively resistant to infection. This study determined the number and frequency of MHC class II genes in a small flock of Texel sheep. There were 18 alleles at DRB1, 9 alleles at DQA1, 13 alleles at DQB1, 8 alleles at DQA2 and 16 alleles at DQB2. Several haplotypes had no detectable gene products at DQA1, DQB1 or DQB2, and these were defined as null alleles. Despite the large numbers of alleles, there were only 21 distinct haplotypes in the population. The relatively small number of observed haplotypes will simplify finding disease associations because common haplotypes provide more statistical power but complicate the discrimination of causative mutations from linked marker loci