Digital Commons Network^™

Genetic Variation In Lean Body Mass, Changes Of Appetite And Weight Loss In Response To Diet Interventions: The Pounds Lost Trial, Xiang Li, Tao Zhou, Hao Ma, Yoriko Heianza, Catherine M. Champagne, Donald A. Williamson, George A. Bray, Frank M. Sacks, Lu Qi

Population and Public Health Science Faculty Publications

Aim: To investigate whether the genetic risk score (GRS) for lean body mass (LBM) modified the effects of weight-loss diets on changes in appetite and adiposity among overweight and obese individuals. Participants and Methods: In the 2-year Preventing Overweight Using Novel Dietary Strategies (POUNDS Lost) trial, we included 692 adults who were randomly assigned to one of four diets varying in macronutrient intake. A GRS was calculated using five single nucleotide polymorphisms associated with LBM. Results: The LBM-GRS was not associated with the baseline LBM measured by dual-energy x-ray absorptiometry in a subgroup (50%) of the study population. We found …

2020 Who Guidelines On Physical Activity And Sedentary Behaviour For Children And Adolescents Aged 5–17 Years: Summary Of The Evidence, Jean Philippe Chaput, Juana Willumsen, Fiona Bull, Roger Chou, Ulf Ekelund, Joseph Firth, Russell Jago, Francisco B. Ortega, Peter T. Katzmarzyk

Population and Public Health Science Faculty Publications

Background: The World Health Organization (WHO) released in 2020 updated global guidelines on physical activity and sedentary behaviour for children, adolescents, adults, older adults and sub-populations such as pregnant and postpartum women and those living with chronic conditions or disabilities. Objective: To summarize the evidence on the associations between physical activity, sedentary behaviour, and health-related outcomes used to inform the 2020 WHO guidelines on physical activity and sedentary behaviour for children and adolescents aged 5–17 years. Methods: The update of the WHO guideline recommendations for children and adolescents utilized and systematically updated the evidence syntheses on physical activity and sedentary …

A Multivariate Multilevel Analysis Of Youth Motor Competence. The Peruvian Health And Optimist Growth Study, Carla Sofia Pinho Dos Santos, Alcibíades Bustamante, Donald Hedeker, Olga Vasconcelos, Rui Garganta, Go Tani, Peter T. Katzmarzyk, José Maia

Population and Public Health Science Faculty Publications

We use a multivariate multilevel model to study the links between physical fitness (PF) and gross motor coordination (GMC) and investigate the influence of predictors affecting their levels across age. We sampled 7918 Peruvians, aged 6-15 years, from sea-level, Amazon region and high-altitude. Composite markers of GMC and PF were derived (GMCz and PFz, respectively). BMI, biological maturation, and stunting were assessed. School characteristics were obtained via an objective audit. School contexts explained 35% of the associations between PFz and GMCz, whereas children's characteristics explained 65% of the total variation. On average, with increasing age, there was a greater increase …

New Global Guidelines On Sedentary Behaviour And Health For Adults: Broadening The Behavioural Targets, Paddy C. Dempsey, Stuart J.H. Biddle, Matthew P. Buman, Sebastien Chastin, Ulf Ekelund, Christine M. Friedenreich, Peter T. Katzmarzyk, Michael F. Leitzmann, Emmanuel Stamatakis, Hidde P. Van Der Ploeg, Juana Willumsen, Fiona Bull

Population and Public Health Science Faculty Publications

Background: In 2018, the World Health Organisation (WHO) commenced a program of work to update the 2010 Global Recommendations on Physical Activity for Health, for the first-time providing population-based guidelines on sedentary behaviour. This paper briefly summarizes and highlights the scientific evidence behind the new sedentary behaviour guidelines for all adults and discusses its strengths and limitations, including evidence gaps/research needs and potential implications for public health practice. Methods: An overview of the scope and methods used to update the evidence is provided, along with quality assessment and grading methods for the eligible new systematic reviews. The literature search update …

Advancing The Global Physical Activity Agenda: Recommendations For Future Research By The 2020 Who Physical Activity And Sedentary Behavior Guidelines Development Group, Loretta Dipietro, Salih Saad Al-Ansari, Stuart J.H. Biddle, Katja Borodulin, Fiona C. Bull, Matthew P. Buman, Greet Cardon, Catherine Carty, Jean Philippe Chaput, Sebastien Chastin, Roger Chou, Paddy C. Dempsey, Ulf Ekelund, Joseph Firth, Christine M. Friedenreich, Leandro Garcia, Muthoni Gichu, Russell Jago, Peter T. Katzmarzyk, Estelle Lambert, Michael Leitzmann, Karen Milton, Francisco B. Ortega, Chathuranga Ranasinghe, Emmanuel Stamatakis, Anne Tiedemann, Richard P. Troiano, Hidde P. Van Der Ploeg, Juana F. Willumsen

Population and Public Health Science Faculty Publications

Background: In July, 2019, the World Health Organization (WHO) commenced work to update the 2010 Global Recommendations on Physical Activity for Health and established a Guideline Development Group (GDG) comprising expert public health scientists and practitioners to inform the drafting of the 2020 Guidelines on Physical Activity and Sedentary Behavior. The overall task of the GDG was to review the scientific evidence and provide expert advice to the WHO on the amount of physical activity and sedentary behavior associated with optimal health in children and adolescents, adults, older adults (> 64 years), and also specifically in pregnant and postpartum women …

Zinc Finger Transcription Factor Zbtb16 Coordinates The Response To Energy Deficit In The Mouse Hypothalamus, Helia Cheng, Schuyler J. Pablico, Jisu Lee, Ji Suk Chang, Sangho Yu

Division of Basic Science Faculty Publications

The central nervous system controls feeding behavior and energy expenditure in response to various internal and external stimuli to maintain energy balance. Here we report that the newly identified transcription factor zinc finger and BTB domain containing 16 (Zbtb16) is induced by energy deficit in the paraventricular (PVH) and arcuate (ARC) nuclei of the hypothalamus via glucocorticoid (GC) signaling. In the PVH, Zbtb16 is expressed in the anterior half of the PVH and co-expressed with many neuronal markers such as corticotropin-releasing hormone (Crh), thyrotropin-releasing hormone (Trh), oxytocin (Oxt), arginine vasopressin (Avp), and nitric oxide synthase 1 (Nos1). Knockdown (KD) of …

Effect Of Overeating Dietary Protein At Different Levels On Circulating Lipids And Liver Lipid: The Proof Study, George A. Bray, Leanne M. Redman, Jennifer Rood, Elizabeth De Jonge, Steven R. Smith

Clinical Research Faculty Publications

Background: During overeating, a low protein diet slowed the rate of weight gain and increased the energy cost of the added weight, suggesting that low protein diets reduced energy efficiency. The Protein Overfeeding (PROOF) study explored the metabolic changes to low and high protein diets, and this sub-study examined the changes in body composition and blood lipids when eating high and low protein diets during overeating. Methods: Twenty-three healthy volunteers (M = 14; F = 9) participated in an 8-week, parallel arm study where they were overfed by ~40% with diets containing 5% (LPD = low protein diet), 15% (NPD …

Chronic Intermittent Hypoxia Triggers A Senescence-Like Phenotype In Human White Preadipocytes, Katarzyna Polonis, Christiane Becari, C. Anwar A. Chahal, Yuebo Zhang, Alina M. Allen, Todd A. Kellogg, Virend K. Somers, Prachi Singh

Clinical Research Faculty Publications

Obstructive sleep apnea (OSA) is a common sleep disorder associated with obesity. Emerging evidence suggest that OSA increases the risk of cardiovascular morbidity and mortality partly via accelerating the process of cellular aging. Thus, we sought to examine the effects of intermittent hypoxia (IH), a hallmark of OSA, on senescence in human white preadipocytes. We demonstrate that chronic IH is associated with an increased generation of mitochondrial reactive oxygen species along with increased prevalence of cells with nuclear localization of γH2AX & p16. A higher prevalence of cells positive for senescence-associated β-galactosidase activity was also evident with chronic IH exposure. …

Genetic Correlations And Genome-Wide Associations Of Cortical Structure In General Population Samples Of 22,824 Adults, Edith Hofer, Gennady V. Roshchupkin, Hieab H.H. Adams, Maria J. Knol, Honghuang Lin, Shuo Li, Habil Zare, Shahzad Ahmad, Nicola J. Armstrong, Claudia L. Satizabal, Manon Bernard, Joshua C. Bis, Nathan A. Gillespie, Michelle Luciano, Aniket Mishra, Markus Scholz, Alexander Teumer, Rui Xia, Xueqiu Jian, Thomas H. Mosley, Yasaman Saba, Lukas Pirpamer, Stephan Seiler, James T. Becker, Owen Carmichael, Jerome I. Rotter, Bruce M. Psaty, Oscar L. Lopez, Najaf Amin, Sven J. Van Der Lee, Qiong Yang, Jayandra J. Himali, Pauline Maillard, Alexa S. Beiser

Clinical Research Faculty Publications

Cortical thickness, surface area and volumes vary with age and cognitive function, and in neurological and psychiatric diseases. Here we report heritability, genetic correlations and genome-wide associations of these cortical measures across the whole cortex, and in 34 anatomically predefined regions. Our discovery sample comprises 22,824 individuals from 20 cohorts within the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the UK Biobank. We identify genetic heterogeneity between cortical measures and brain regions, and 160 genome-wide significant associations pointing to wnt/β-catenin, TGF-β and sonic hedgehog pathways. There is enrichment for genes involved in anthropometric traits, hindbrain …

A Telescope Gwas Analysis Strategy, Based On Snps-Genes-Pathways Ensamble And On Multivariate Algorithms, To Characterize Late Onset Alzheimer’S Disease, Margherita Squillario, Giulia Abate, Federico Tomasi, Veronica Tozzo, Annalisa Barla, Daniela Uberti, Michael W. Weiner, Paul Aisen, Ronald Petersen, Jack R. Clifford, William Jagust, John Q. Trojanowki, Arthur W. Toga, Laurel Beckett, Robert C. Green, Andrew J. Saykin, John Morris, Leslie M. Shaw, Zaven Khachaturian, Greg Sorensen, Maria Carrillo, Lew Kuller, Marc Raichle, Steven Paul, Peter Davies, Howard Fillit, Franz Hefti, Davie Holtzman, M. Marcel Mesulam, William Potter, Peter Snyder, Tom Montine, Ronald G. Thomas, Michael Donohue

Clinical Research Faculty Publications

Genome–wide association studies (GWAS) have revealed a plethora of putative susceptibility genes for Alzheimer’s disease (AD), with the sole exception of APOE gene unequivocally validated in independent study. Considering that the etiology of complex diseases like AD could depend on functional multiple genes interaction network, here we proposed an alternative GWAS analysis strategy based on (i) multivariate methods and on a (ii) telescope approach, in order to guarantee the identification of correlated variables, and reveal their connections at three biological connected levels. Specifically as multivariate methods, we employed two machine learning algorithms and a genetic association test and we considered …

Long-Term Change In Physiological Markers And Cognitive Performance In Type 2 Diabetes: The Look Ahead Study, Owen T. Carmichael, Rebecca H. Neiberg, Gareth R. Dutton, Kathleen M. Hayden, Edward Horton, F. Xavier Pi-Sunyer, Karen C. Johnson, Stephen R. Rapp, Adam P. Spira, Mark A. Espeland

Clinical Research Faculty Publications

Context: The effects of physiological improvements on cognitive function among persons with type 2 diabetes mellitus (T2DM) are not fully understood. Objective: To determine whether improvements in physiological markers (body weight, blood sugar control, and physical activity) during intensive lifestyle intervention (ILI) are associated with enhancements in cognitive function in older adults with T2DM. Design: Multisite randomized controlled trial. Setting: Academic research centers. Patients or Other Participants: Participants were aged 45-76 years, with T2DM. Intervention: The Action for Health in Diabetes (Look AHEAD) study, a randomized, controlled clinical trial of ILI. Main Outcome Measure: Two to 3 cognitive assessments were …

Spread Of Pathological Tau Proteins Through Communicating Neurons In Human Alzheimer's Disease, Jacob W. Vogel, Yasser Iturria-Medina, Olof T. Strandberg, Ruben Smith, Elizabeth Levitis, Alan C. Evans, Oskar Hansson, Michael Weiner, Paul Aisen, Ronald Petersen, Clifford R. Jack, William Jagust, John Q. Trojanowki, Arthur W. Toga, Laurel Beckett, Robert C. Green, Andrew J. Saykin, John Morris, Leslie M. Shaw, Enchi Liu, Tom Montine, Ronald G. Thomas, Michael Donohue, Michael Donohue, Sarah Walter, Devon Gessert, Tamie Sather, Gus Jiminez, Danielle Harvey, Matthew Bernstein, Nick Fox, Paul Thompson, Norbert Schuff, Charles Decarli

Clinical Research Faculty Publications

Tau is a hallmark pathology of Alzheimer’s disease, and animal models have suggested that tau spreads from cell to cell through neuronal connections, facilitated by β-amyloid (Aβ). We test this hypothesis in humans using an epidemic spreading model (ESM) to simulate tau spread, and compare these simulations to observed patterns measured using tau-PET in 312 individuals along Alzheimer’s disease continuum. Up to 70% of the variance in the overall spatial pattern of tau can be explained by our model. Surprisingly, the ESM predicts the spatial patterns of tau irrespective of whether brain Aβ is present, but regions with greater Aβ …

Fam222a Encodes A Protein Which Accumulates In Plaques In Alzheimer’S Disease, Tingxiang Yan, Jingjing Liang, Ju Gao, Luwen Wang, Hisashi Fujioka, Michael W. Weiner, Norbert Schuff, Howard J. Rosen, Bruce L. Miller, David Perry, Paul Aisen, Paul Aisen, Arthur W. Toga, Gustavo Jimenez, Michael Donohue, Devon Gessert, Kelly Harless, Jennifer Salazar, Yuliana Cabrera, Sarah Walter, Lindsey Hergesheimer, Karen Crawford, Scott Neu, Lon S. Schneider, Sonia Pawluczyk, Mauricio Becerra, Liberty Teodoro, Bryan M. Spann, Ronald Petersen, Clifford R. Jack, Matthew Bernstein, Bret Borowski, Jeff Gunter, Matt Senjem

Clinical Research Faculty Publications

Alzheimer’s disease (AD) is characterized by amyloid plaques and progressive cerebral atrophy. Here, we report FAM222A as a putative brain atrophy susceptibility gene. Our cross-phenotype association analysis of imaging genetics indicates a potential link between FAM222A and AD-related regional brain atrophy. The protein encoded by FAM222A is predominantly expressed in the CNS and is increased in brains of patients with AD and in an AD mouse model. It accumulates within amyloid deposits, physically interacts with amyloid-β (Aβ) via its N-terminal Aβ binding domain, and facilitates Aβ aggregation. Intracerebroventricular infusion or forced expression of this protein exacerbates neuroinflammation and cognitive dysfunction …

Influence Of Energy Removal Rate On The Quality Of Minced Meat From Undersized Crawfish During Frozen Storage, Franklin Bonilla, Vondel Reyes, Alexander Chouljenko, Bennett Dzandu, Subramaniam Sathivel

Faculty Publications

Abstract: Undersized crawfish have little economic value and are often discarded. Producing crawfish minced meat (CMM) from undersized crawfish and using an appropriate freezing technique may enable an economically viable market. The objective of this research was to evaluate the effect of the energy removal rate using two techniques, cryogenic freezing (CF) and air blast freezing (BF), on CMM’s quality during frozen storage. CMM was separated into two batches; one batch was cryogenically frozen with liquid nitrogen and the other batch was frozen with an air blast freezer. CMM batches were frozen and stored at − 18 °C. They were …

Relation Of Oral Ulcers To Quality Of Life: A Cross-Sectional Study, Enji Ahmed, Ayat Gaml Abdelnasser, Mai Zakaria, Soheir Gafar

Dentistry

Oral ulcers affect many dental patients; impairing their lives physically, psychologically, and socially. Due to the absence of information about oral ulcers in our population, the authors undertook a pilot study to obtain a more complete picture of prevalence of oral ulcers, its probable risk factors and its burden on the quality of life. Materials and methods The authors performed a cross‑sectional study with 605 adult dental patients. All patients filled a questionnaire inquiring about the risk factors. An oral examination was performed to each participant to determine presence or absence of oral ulcers; and the type of the oral …

Pharmacy Newsletter : December 2020, Pharmacy Department

Department of Pharmacy Archives

Content:

• COVID-19 Pandemic & the Vaccines trial | Global progress
• ToxTok | Hand Sanitizer, How poisonous they are
• Drugs Safety & Management in Lactation
• Amiodarone Induced Thyrotoxicosis (AIT) | A Case
• Myths & Reality | Flu Vaccine

Instrument Bias Correction With Machine Learning Algorithms: Application To Field-Portable Mass Spectrometry, Brice Loose, R. T. Short, S. Toler

Graduate School of Oceanography Faculty Publications

In situ sensors for environmental chemistry promise more thorough observations, which are necessary for high confidence predictions in earth systems science. However, these can be a challenge to interpret because the sensors are strongly influenced by temperature, humidity, pressure, or other secondary environmental conditions that are not of direct interest. We present a comparison of two statistical learning methods—a generalized additive model and a long short-term memory neural network model for bias correction of in situ sensor data. We discuss their performance and tradeoffs when the two bias correction methods are applied to data from submersible and shipboard mass spectrometers. …

Pathology Findings And Correlation With Body Condition Index In Stranded Killer Whales (Orcinus Orca) In The Northeastern Pacific And Hawaii From 2004 To 2013, Stephen A. Raverty, Judy St. Leger, Dawn P. Noren, Kathy Burek Huntington, David S. Rotstein, Francis M.D. Gulland,, Deborah A. Duffield, Multiple Additional Authors

Biology Faculty Publications and Presentations

Understanding health and mortality in killer whales (Orcinus orca) is crucial for management and conservation actions. We reviewed pathology reports from 53 animals that stranded in the eastern Pacific Ocean and Hawaii between 2004 and 2013 and used data from 35 animals that stranded from 2001 to 2017 to assess association with morphometrics, blubber thickness, body condition and cause of death. Of the 53 cases, cause of death was determined for 22 (42%) and nine additional animals demonstrated findings of significant importance for population health. Causes of calf mortalities included infectious disease, nutritional, and congenital malformations. Mortalities in sub-adults were …

A Snapshot Semester: Students’ Reflections Of Performance And Mental State Throughout A Graduate Course, Bradley D. Borges

Graduate Theses and Dissertations

Graduate students are anecdotally reputed to be among the most stressed groups of young adults. Common sources of stress for graduate students have included coursework, assistantships, finances, career preparation, and family (Wyatt & Oswalt, 2013; Mazzola, Walker, Shockley & Spector, 2011; Oswalt & Riddock, 2007). Guided reflection can be used by educators to assist students in both learning (Boud, Keogh & Walker, 2013; Kolb, 1984) and managing stress (Shoulders, Whitehead, & Morrison, 2018). By understanding how students’ progress through a semester in terms of both their learning and their management of stress, instructors and academic advisors can better anticipate times …

Understanding Radiation Resistance In Head And Neck Tumor Xenografts Using Diffuse Reflectance And Raman Spectroscopy, Sina Dadgar

Graduate Theses and Dissertations

Each year, 800,000 new patients are diagnosed with head and neck squamous cell carcinoma (HNSCC), a majority of whom are treated with a combination of daily fractions of radiation and weekly chemotherapy sessions for up to seven weeks. Current methods to evaluate treatment response of individual patients are limited to anatomical measurements of tumor burden using CT scan or MRI 4-8 weeks after completion of treatment. However, earlier knowledge of radiation-response prior to or at early days after commencement of therapy can aid oncologist with escalating and de-escalating treatment plans for exceptionally non-responding and responding patients. Such a knowledge can …

Comparative Evaluation Of Statistical Dependence Measures, Eman Abdel Rahman Ibrahim

Graduate Theses and Dissertations

Measuring and testing dependence between random variables is of great importance in many scientific fields. In the case of linearly correlated variables, Pearson’s correlation coefficient is a commonly used measure of the correlation strength. In the case of nonlinear correlation, several innovative measures have been proposed, such as distance-based correlation, rank-based correlations, and information theory-based correlation. This thesis focuses on the statistical comparison of several important correlations, including Spearman’s correlation, mutual information, maximal information coefficient, biweight midcorrelation, distance correlation, and copula correlation, under various simulation settings such as correlative patterns and the level of random noise. Furthermore, we apply those …

Assessment Of Dopaminergic And Serotonergic Receptor Antagonists In Male Rats Trained To Discriminate 4-Methylmethcathinone (Mephedrone), Rachel L. Burroughs

Masters Theses

Preclinical drug discrimination studies of the synthetic cathinone, 4-methylmethcathinone (mephedrone) have demonstrated its effects are comparable to those of other popular psychostimulant drugs. Few studies have directly examined the contribution of specific neurotransmitter receptors to mephedrone’s discriminative stimulus effects. The present study investigated the role of dopamine and serotonin receptors in these effects. Eight adult male Sprague-Dawley rats were trained to discriminate 3.0 mg/kg mephedrone from saline. After dose-response curves were determined with mephedrone (0.375-3.0 mg/kg), a series of stimulus antagonism tests were conducted with dopamine antagonists (Sch 23390, haloperidol) and serotonin antagonists (WAY 100,635, MDL 100,907, pirenperone) administered as …

Alaska, Traci N. Bunkers

Texas A&M Journal of Property Law

The First Regular Session of the thirty-first Alaska Legislature began on January 15, 2019, and ended on May 15, 2019. A First Special Session was held from May 16, 2019, through June 13, 2019, with a Second Special Session following from July 8, 2019, through August 6, 2019. The 2019 legislative session resulted in virtually no oil and gas legislation being passed, as the Alaska Legislature focused primarily on legislation regarding the State budget and the funding of the Permanent Fund Dividend. Despite the uncharacteristic lack of oil and gas legislation, the Legislature addressed the prevalent issue of oil and …

Goal Zero: Eliminating Mislabeled Specimens In The Emergency Department, Michele Samsa, Tracie Henderson

General Submissions: Presentations (Oral and Poster)

This emergency department (ED) noticed an increase in misidentified laboratory specimens noted to be the highest in our hospital region. Misidentified specimens can result in misdiagnosis, medication errors and repeat laboratory (Lab) specimen collection with a direct impact on patient comfort, nurse workload and increased cost can result. This project was developed as a quality improvement project aimed at reducing misidentified laboratory specimens and promote patient safety.

A Bibliometric Analysis Of The Aga Khan University Research Contribution In Early Child Development, Peter Gatiti, Anil Khamis

Libraries

The research contribution of the Aga Khan University to the Sustainable Development Goals (SDGs) has been explored through a bibliometric analysis. The analysis shows exponential growth of research across the SDGs undertaken by AKU-affiliated researchers. The analysis identified areas of interdisciplinary research, with a significant focus on societal development of interest to AKU, as per its mandate, and reflective of the work of the Aga Khan Development Network (AKDN) of which AKU is an integral part. Building on the bibliometric analysis, this paper focuses on early childhood development and early childhood education with reference to the SDGs. A specific query …

Final 5-Year Findings From The Phase 3 Helios Study Of Ibrutinib Plus Bendamustine And Rituximab In Patients With Relapsed/Refractory Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma, Graeme A M Fraser, Nancy L. Bartlett, Et Al

Open Access Publications

No abstract provided.

Improving Health Care Accessibility Among Geriatric Patients In Rural Communities, Capriana Calvachi

Honors Projects

The following literature review and analysis compiles information regarding ways to improve rural geriatric healthcare accessibility through the use of interprofessional care and outreach. I also wish to bring to light the various deficiencies often seen in this realm of care, and the reasons behind the inadequate rural physician retention rates. Using this background information, I compiled various collaborative approaches which seek to ease the strain faced by the healthcare system and its elderly patients.

Improving healthcare accessibility through the use of interprofessional care and outreach is an essential facet in geriatric medicine. By exploring the deficiencies of geriactric healthcare …

Review: Influence Of Meteorological Conditions And Algal Community Composition On Hypolimnetic Hypoxia, Ian P. Stone

Honors Projects

Hypoxia has been a central focus of research regarding water quality impairments throughout the world in the past century. The fresh and coastal marine waters affected by hypoxia are of great importance due to the ecosystem services and species habitat they provide, and because of the regional economic activity spurned by these waters in return. As such, a great deal of research effort has been devoted to elucidating the causes and ecological effects of hypoxia with the hopes of remediating the issue. The bulk of this effort has been directed at the role of anthropogenic allochthonous nutrient loading and algal …

Genomics Education Partnership F Element Annotation Report, Amanda Moy

Honors Projects

The Genomics Education Partnership (GEP), headquartered at the University of Alabama, is a collection of over 100 universities that provide training and resources in order to provide students experiential learning in bioinformatics and genomics. The GEP hosts numerous research projects, including the F element project. The F element project has the main focus of annotating the F element genes of the fruit fly species D. ananassae, D. bipectinata, D. kikkawai, and D. takahashii. The Muller F element is the smallest chromosome in Drosophila species. However, the four species listed above have a notably larger F element than other …

Gene Set Testing By Distance Correlation, Sho-Hsien Su

Graduate Theses and Dissertations

Pathways are the functional building blocks of complex diseases such as cancers. Pathway-level studies may provide insights on some important biological processes. Gene set test is an important tool to study the differential expression of a gene set between two groups, e.g., cancer vs normal. The differential expression of a gene set could be due to the difference in mean, variability, or both. However, most existing gene set tests only target the mean difference but overlook other types of differential expression. In this thesis, we propose to use the recently developed distance correlation for gene set testing. To assess the …