ENUMERATION OF MIXED LINEAR MODELS AND A SAS MACRO FOR COMPUTATION OF CONFIDENCE INTERVALS FOR VARIANCE COMPONENTS

It is well known that there is a one-to-one correspondence between fixed effects ANOVA models involving both crossed and nested factors, and combinatorial objects called posets . The enumeration of nonisomorphic posets is an interesting and nontrivial combinatorial problem for which answers are available for posets of order 14 or less, i.e. for fixed effects ANOVA models with 14 or fewer factors. Such an enumeration problem does not appear to have been considered for mixed effects models. In this paper we study this problem and obtain a list of nonisomorphic mixed effects models involving five or fewer factors. For instance, it is shown that there are 576 nonisomorphic mixed effects ANOVA models involving five factors. Confidence intervals for variance components in any of these models, with superior coverage properties than those afforded by the application of the Satterthwaite method, may be computed using the methods discussed in the book Confidence Intervals for Variance Components by Burdick and Graybill [2]. To facilitate these calculations, we have written a SAS macro that will compute these confidence intervals for any mixed effects saturated ANOVA model involving five or fewer factors. User input to the SAS MACRO is the actual data set along with a matrix indicating whether each factor is fixed or random and the nesting/ crossing configuration among the factors. The operation of the MACRO is illustrated using an example involving real data. Such a MACRO is expected to be extremely useful to practitioners in view of the fact that SAS or any other commonly available statistical software package does not have built in commands for obtaining confidence intervals for variance components discussed in [2]. A copy of this MACRO is available at www.stat.colostate.edurhess/MixedModels.htm

Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays

BACKGROUND: Currently, most tests of differential gene expression using Affymetrix expression array data are performed using expression summary values representing each probe set on a microarray. Recently testing methods have been proposed which incorporate probe level information. We propose a new approach that uses Fisher's method of combining evidence from multiple sources of information. Specifically, we combine p-values from probe level tests of significance. RESULTS: The combined p method and other competing methods were compared using three spike-in datasets (where probe sets corresponding differentially spiked transcripts are known) and array data from a biological study validated with qRT-PCR. Based on power and false discovery rates computed for the spike-in datasets, we demonstrate that the combined p method compares favorably with other methods. We find that probe level testing methods select many of the same genes as differentially expressed. We illustrate the use of the combined p method for diagnostic purposes using examples. CONCLUSION: Combined p is a promising alternative to existing methods of testing for differential gene expression. In addition, the combined p method is particularly well suited as a diagnostic tool for exploratory analysis of microarray data

Filtering for increased power for microarray data analysis

<p>Abstract</p> <p>Background</p> <p>Due to the large number of hypothesis tests performed during the process of routine analysis of microarray data, a multiple testing adjustment is certainly warranted. However, when the number of tests is very large and the proportion of differentially expressed genes is relatively low, the use of a multiple testing adjustment can result in very low power to detect those genes which are truly differentially expressed. Filtering allows for a reduction in the number of tests and a corresponding increase in power. Common filtering methods include filtering by variance, average signal or MAS detection call (for Affymetrix arrays). We study the effects of filtering in combination with the Benjamini-Hochberg method for false discovery rate control and q-value for false discovery rate estimation.</p> <p>Results</p> <p>Three case studies are used to compare three different filtering methods in combination with the two false discovery rate methods and three different preprocessing methods. For the case studies considered, filtering by detection call and variance (on the original scale) consistently led to an increase in the number of differentially expressed genes identified. On the other hand, filtering by variance on the log₂scale had a detrimental effect when paired with MAS5 or PLIER preprocessing methods, even when the testing was done on the log₂scale. A simulation study was done to further examine the effect of filtering by variance. We find that filtering by variance leads to higher power, often with a decrease in false discovery rate, when paired with either of the false discovery rate methods considered. This holds regardless of the proportion of genes which are differentially expressed or whether we assume dependence or independence among genes.</p> <p>Conclusion</p> <p>The case studies show that both detection call and variance filtering are viable methods of filtering which can increase the number of differentially expressed genes identified. The simulation study demonstrates that when paired with a false discovery rate method, filtering by variance can increase power while still controlling the false discovery rate. Filtering out 50% of probe sets seems reasonable as long as the majority of genes are not expected to be differentially expressed.</p

Development of the Occupational Performance Inventory of Sexuality and Intimacy (OPISI): Phase One

Background: The occupational therapy profession needs a framework to guide understanding of the occupational nature of sexuality and intimacy, assessment, intervention design, and measurement of outcomes. This study aimed to define the occupational nature of sexuality and intimacy and develop a theoretical and occupation-based screen, in-depth self-assessment, and performance measure. Method: The Occupational Performance Inventory of Sexuality and Intimacy (OPISI) was developed following DeVellis’s (2017) guidelines for scale development that involved mapping the construct, generating an item pool, determining the format for measurement, and reviewing the initial item pool. Results: The Occupational Therapy Sexual Assessment Framework (OTSAF) was developed to define the occupational nature of sexuality and intimacy, depict how the theoretical constructs intertwine with the domain of occupational therapy, and guide scale development. The OPISI includes a self-screen, in-depth self-assessment, and an individualized measure to establish baseline performance and detect self-perceived change in ability, satisfaction, understanding, and confidence in skills and ability to improve occupational performance associated with sexuality and intimacy over time. Conclusion: The OTSAF defines the occupational nature of sexuality and intimacy and informs the occupational therapy scope of practice. The OPISI includes theoretical and occupation-based tools to adequately screen, assess, and measure performance related to the complex occupational nature of sexuality and intimacy. Formal validation is needed prior to releasing the OPISI for clinical use

Roads to the Great Eucatastrophie: The Christian Mythology of C.S. Lewis and J.R.R. Tolkien

The purpose of this thesis is to analyze how C.S. Lewis and J.R.R. Tolkien created mythology that is fundamentally Christian but in vastly different ways. This task will be accomplished by examining the childhood and early adult life of both Lewis and Tolkien, as well as the effect their close friendship had on their writing, and by performing a detailed literary analysis of some of their mythological works. After an introduction, the second and third chapters will scrutinize the elements of their childhood and adolescence that shaped their later mythology. The next chapter will look at the importance of their Christian faith in their writing process, with special attention to Tolkien’s writing philosophy as explained in “On Fairy-Stories.” The fifth chapter analyzes the effect that Lewis and Tolkien’s friendship had on their writing, in conjunction with the effect of their literary club, the Inklings. The next two chapters will provide a literary analysis of Lewis’s and Tolkien’s writing, with a special concentration on how they transformed their fairy-stories into Christian myths. The thesis will finish with a summary of the conclusions found through the examination of Lewis and Tolkien’s lives and the literary analysis of their mythology

Predoctoral Interns\u27 Nondisclosure in Supervision

In interviews with 14 counseling center predoctoral interns regarding a significant nondisclosure in supervision, eight interns reported good supervisory relationships and six indicated that they experienced problematic supervisory relationships. Nondisclosures for the interns in good supervisory relationships related to personal reactions to clients, whereas nondisclosures for interns in problematic supervisory relationships related to global dissatisfaction with the supervisory relationship. In both groups, interns mentioned concerns about evaluation and negative feelings as typical reasons for nondisclosure. Additional reasons for nondisclosure for interns in problematic supervision were power dynamics, inhibiting demographic or cultural variables, and the supervisor\u27s theoretical orientation. Both groups described negative effects of nondisclosure on themselves and their relationships with clients. Interns in problematic supervision also reported that nondisclosures had negative effects on the supervisory relationship

Astrocyte-specific regulation of hMeCP2 expression in \u3ci\u3eDrosophila\u3c/i\u3e

Alterations in the expression of Methyl-CpG-binding protein 2 (MeCP2) either by mutations or gene duplication leads to a wide spectrum of neurodevelopmental disorders including Rett Syndrome and MeCP2 duplication disorder. Common features of Rett Syndrome (RTT), MeCP2 duplication disorder, and neuropsychiatric disorders indicate that even moderate changes in MeCP2 protein levels result in functional and structural cell abnormalities. In this study, we investigated two areas of MeCP2 pathophysiology using Drosophila as a model system: the effects of MeCP2 glial gain-of-function activity on circuits controlling sleep behavior, and the cell-type specific regulation of MeCP2 expression. In this study, we first examined the effects of elevated MeCP2 levels on microcircuits by expressing human MeCP2 (hMeCP2) in astrocytes and distinct subsets of amine neurons including dopamine and octopamine (OA) neurons. Depending on the celltype, hMeCP2 expression reduced sleep levels, altered daytime/ nighttime sleep patterns, and generated sleep maintenance deficits. Second, we identified a 498 base pair region of the MeCP2e2 isoform that is targeted for regulation in distinct subsets of astrocytes. Levels of the full-length hMeCP2e2 and mutant RTT R106W protein decreased in astrocytes in a temporally and spatially regulated manner. In contrast, expression of the deletion D166 hMeCP2 protein was not altered in the entire astrocyte population. qPCR experiments revealed a reduction in full-length hMeCP2e2 transcript levels suggesting transgenic hMeCP2 expression is regulated at the transcriptional level. Given the phenotypic complexities that are caused by alterations in MeCP2 levels, our results provide insight into distinct cellular mechanisms that control MeCP2 expression and link microcircuit abnormalities with defined behavioral deficits

Non-Coding RNA Sequencing of Equine Endometrium During Maternal Recognition of Pregnancy.

Maternal recognition of pregnancy (MRP) in the mare is not well defined. In a non-pregnant mare, prostaglandin F2α (PGF) is released on day 14 post-ovulation (PO) to cause luteal regression, resulting in loss of progesterone production. Equine MRP occurs prior to day 14 to halt PGF production. Studies have failed to identify a gene candidate for MRP, so attention has turned to small, non-coding RNAs. The objective of this study was to evaluate small RNA (&lt;200 nucleotides) content in endometrium during MRP. Mares were used in a cross-over design with each having a pregnant and non-mated cycle. Each mare was randomly assigned to collection day 11 or 13 PO (n = 3/day) and endometrial biopsies were obtained. Total RNA was isolated and sequencing libraries were prepared using a small RNA library preparation kit and sequenced on a HiSeq 2000. EquCab3 was used as the reference genome and DESeq2 was used for statistical analysis. On day 11, 419 ncRNAs, representing miRNA, snRNA, snoRNA, scaRNA, and vaultRNA, were different between pregnancy statuses, but none on day 13. Equine endometrial ncRNAs with unknown structure and function were also identified. This study is the first to describe ncRNA transcriptome in equine endometrium. Identifying targets of these ncRNAs could lead to determining MRP

Informing a social practice theory framework with social-psychological factors for analyzing routinized energy consumption: A multivariate analysis of three practices

A key factor contributing to the non-realization of energy efficiency potentials is the routinized way in which many energy consumption behaviors (ECBs) are performed. To analyze routinized ECBs, we draw on social practice theory and psychological concepts and suggest a framework that considers individual, social, and material factors. Based on our proposed framework and employing multivariate regression analysis, we gain new insights into associated factors of routinized ECBs-particularly for washing and drying clothes and showering. Analyzing data from a survey conducted among Swiss households in 2016 (n = 5015), we find that individual values, practice-specific wants, and materials explain variations in routinized ECB performance. Furthermore, socio-demographic predictors shed light on cultural and status differences associated with routinized ECBs. This paper contributes to understanding associated factors of routinized ECBs by bridging practice theory and psychology-based factors

Changing Routinized Household Energy Consumption Using the Example of Washing, Cooking, and Standby: A Randomized Controlled Field Experiment of Home Energy Advice

Despite advances in understanding routines, there is little knowledge about which aspects of routinized behavior people adjust during interventions. In this study, we applied an adjusted social practice theory framework to disentangle routinized energy consumption, focusing on energy services related to washing, standby, and cooking. We investigate the potential of home energy advice to change elements of routinized behaviors, namely meanings, knowledge, and technologies. Using a randomized controlled field trial on a probabilistic sample of households, we found short-term treatment effects related to increased usage of lids during cooking and improved knowledge of IT-related energy consumption, as well as negative effects regarding multi-sockets and washing frequency. Our findings suggest that meanings (e.g., preferences underlying routinized behaviors) are less subject to change, and that sociodemographic variables are associated with routinized behaviors in complex ways. Our disentangling of energy demand into elements of routines enables us to show how home energy advice may change behaviors and knowledge. This study highlights the benefits of a multifaceted perspective for understanding household energy consumption and can be used to inform intervention and policy design