Assessing differential expression when the distribution of effect sizes is asymmetric and evaluating concordance of differential expression across multiple gene expression experiments

The emergence and development of gene expression technologies has resulted in an ever-increasing number of high-dimensional data sets available for analysis. The availability of these data sets has prompted much research into the development of methods for statistically analyzing gene expression experiments. Many of these methods focus on identifying genes that are differentially expressed (DE), i.e., exhibit changes in mean expression levels between treatments, in a single experiment. This dissertation presents novel methods for detecting differential expression in one experiment and proposes methods for analyzing gene expression data from two independent experiments. Many methods have been proposed for estimating the number of genes that are equivalently expressed (EE), and thus the number of DE genes, in a single gene expression experiment, but many researchers are interested in comparing the results of two independent experiments. Estimating the number of genes that are DE in two independent experiments is generally performed in two steps. First, data from each experiment are analyzed separately, and a list of genes identified as DE is obtained for each experiment. Each list is generally produced by a method that attempts to control false discovery rate (FDR) at some desired level &alpha. Then, the number of genes common to both lists is used as an estimate of the number of genes DE in both experiments. A major flaw of this method is that the resulting estimates can vary greatly depending on the value of &alpha. Chapter 2 proposes a new method that estimates the number of genes that are DE in both of two independent experiments, which includes analyzing the p-values from each experiment simultaneously, and results in a single estimate that does not depend on &alpha. Through simulation studies, we show the advantages of our approach. In Chapter 3, we extend the idea of Chapter 2 by proposing a new method for identifying genes that are DE in both of two independent experiments while controlling FDR and compare this method to two existing methods. These three methods are compared through simulation studies that show the proposed method controls FDR better as well as provides similar or better power when compared to the existing methods. Chapter 4 proposes a new method for calculating q-values when the distribution of effect sizes in a gene expression experiment is asymmetric. This method first estimates the number of genes that are EE in an experiment based on the distribution of all p-values. Then, the p-values are split into two subsets based on the signs of their corresponding test statistics, and q-values are then calculated separately for each subset. Simulation study results show that the proposed method, when compared to the traditional q-value method, generally provides a better ranking for genes as well as a higher number of truly DE genes identified as DE, while still adequately controlling FDR

Island disaster para-diplomacy in the commonwealth

This chapter covers one particular aspect of the foreign relations of non-sovereign island jurisdictions (SNIJs), namely relations arising from disaster-related activities. Islands are among the territories most seriously affected by calamities, including the spectre of rising seas that may come with climate change. Yet non-sovereign islands are not so well equipped to speak and act effectively for themselves in the face of such threats. This may be true even within the governing structures in which these islands find themselves, but it is even more serious given the weaknesses that may exist in their capacity to speak to and act in the international community on disaster-related activities.peer-reviewe

A Preliminary Comparison of Firefighter Candidates\u27 Biddle Physical Ability Test Performance and Success Based on Training Class Participation

International Journal of Exercise Science 15(4): 1627-1640, 2022. The Biddle Physical Ability Test (BPAT) was developed to identify candidates who possess the physical ability to become structural firefighters. The test must be completed in ≤ 9:34 min:s before a candidate is admitted to an academy. Some community colleges offer semester-long training classes for candidates. This study analyzed whether candidates who completed a training class could perform the BPAT more effectively. Retrospective analysis of 30 males and 2 females who attempted the BPAT was conducted. BPAT tasks were: dry and charged hose drag; halyard raise, roof walk, and attic crawl; roof ventilation and victim removal; ladder removal and carry; stair climb with hose bundle; crawling search and tower exit; stair climb with air bottles; hose hoist; and return to ground floor with air bottles. Independent samples t-tests or Mann-Whitney U tests (p \u3c 0.05) and effect sizes calculated BPAT time differences between candidates who completed a training class or not. Twenty-nine candidates passed the BPAT; 6 completed a training class. The 3 candidates (2 males, 1 female) who failed did not complete a class. There were no significant between-group differences in BPAT times (p = 0.054-0.829). There were moderate effects for faster roof ventilation and victim removal, ladder removal and carry, and hose hoist times for candidates who attended a class (d = 0.74-0.95). While training classes may not be necessary for all candidates, physically demanding BPAT tasks were finished faster by candidates who completed a class. For candidates who find the BPAT physicality difficult, participation in a task-specific fitness and skills class may prove beneficial

Sample designs for measuring the health of small racial/ethnic subgroups

Most national health surveys do not permit precise measurement of the health of racial/ethnic subgroups that comprise <1 per cent of the U.S. population. We identify three potentially promising sample design strategies for increasing the accuracy of national health estimates for a small target subgroup when used to supplement a small probability sample of that group and apply these strategies to American Indians/Alaska Natives (AI/AN) and Chinese using National Health Interview Survey data. These sample design strategies include (1) complete sampling of targets within households, (2) oversampling selected macrogeographic units, and (3) oversampling from an incomplete list frame. Stage (1) is promising for Chinese and AI/AN; (2) works for both groups, but it would be more cost-effective for AI/AN because of their greater residential concentration; (3) is somewhat effective for groups like Chinese with viable surname lists, but not for AI/AN. Both (2) and (3) efficiently improve measurement precision when the supplement is the same size as the existing core sample, with diminishing additional returns as the supplement grows relative to the core sample, especially for (3). To avoid large design effects, the oversampled geographic areas or lists must have good coverage of the target population. To reduce costs, oversampled geographic tracts and lists must consist primarily of targets. These techniques can be used simultaneously to substantially increase effective sample sizes (ESSs). For example, (1) and (2) in combination can be used to multiply the nominal sample size of AI/AN or Chinese by 8 and the ESS by 4. Copyright © 2008 John Wiley & Sons, Ltd.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/60911/1/3244_ftp.pd

The Effects of Traditional versus Ability-Based Physical Training on the Health and Fitness of Custody Assistant Recruits

International Journal of Exercise Science 15(3): 1641-1660, 2022. This study investigated traditional training (TT) versus ability-based training (ABT) in custody assistant recruits. Retrospective analysis was conducted on two recruit classes who completed an 8-week academy. The TT group (18 males, 13 females) followed a physical training model where recruits completed the same exercises with the same intensity; the ABT group (17 males, 12 females) had exercises tailored towards their ability. Pre- and post-academy, recruits were assessed in: body mass; body fat percentage (BF%); resting heart rate (RHR); blood pressure (BP); waist circumference (WC); waist-to-hip ratio (WHR); grip strength; push-ups; sit-ups; YMCA step test recovery HR; 201-m run; and 2.4-km run. Independent samples t-tests evaluated between-class pre-test differences, with significance set at p ≤ 0.05. Paired samples t-tests (p ≤ 0.05) detected within-group training changes. Change scores were calculated for each variable; independent samples t-tests (p ≤ 0.05) compared change scores between groups. The TT group had lower BF%, BP, and WC; and were superior in sit-ups and the 2.4-km run before training. After academy, the TT recruits improved WHR, grip strength, recovery HR, 201-m run, and 2.4-km run, but increased diastolic BP. The ABT recruits decreased BF%, RHR, and WC, and improved push-ups, sit-ups, recovery HR, 201-m run, and the 2.4-km run. ABT recruits had greater positive changes in BF%, RHR, diastolic BP, and sit-ups. TT and ABT recruits generally experienced favorable fitness changes; the degree of positive change tended to be greater for ABT recruits for select tests. Coupled with the diastolic BP increase for TT recruits, this may provide evidence for ABT

Review: The Newsletter of the Literary Managers and Dramaturgs of the Americas, volume 13, issue 1

Contents include: Reading Review (Again), Radical from the Root, Arthur Ballet Recipient of the 2002 LMDA Loessing Award, Notes from the Lunatic Fringe, Regional Reports Info: News and Previews From All Over, Review is Inaugurating a New Section in the Next Issue: Projects-In-Process, and LMDA Prize in Drammatury 2002 The Elliott Hayes Award. Issue editors: D.J. Hopkins, Shelley Orr, Liz Engelman, Madeline Oldham, Jacob Zimmerhttps://soundideas.pugetsound.edu/lmdareview/1026/thumbnail.jp

Strong Concordance Between Transcriptomic Patterns of Spleen and Peripheral Blood Leukocytes in Response to Avian Pathogenic Escherichia coli Infection

Avian pathogenic Escherichia coli (APEC) causes morbidity in chickens and exhibits zoonotic potential. Understanding host transcriptional responses to infection aids the understanding of protective mechanisms and serves to inform future colibacillosis control strategies. Transcriptomes of spleen and peripheral blood leukocytes (PBLs) of the same individual birds in response to APEC infection were compared to identify common response patterns and connecting pathways. More than 100 genes in three contrasts examining pathology and infection status were significantly differentially expressed in both tissues and similarly regulated. Tissue-specific differences in catalytic activity, however, appear between birds with mild and severe pathology responses. Early expression differences, between birds with severe pathology and uninfected controls, in the mitogen-activated protein kinase pathway in PBLs precede spleen responses in the p53 and cytokine-cytokine receptor pathways. Tissue bianalysis is useful in identifying genes and pathways important to the response to APEC, whose role might otherwise be underestimated in importance