Mining SOM expression portraits: Feature selection and integrating concepts of molecular function

Background: 
Self organizing maps (SOM) enable the straightforward portraying of high-dimensional data of large sample collections in terms of sample-specific images. The analysis of their texture provides so-called spot-clusters of co-expressed genes which require subsequent significance filtering and functional interpretation. We address feature selection in terms of the gene ranking problem and the interpretation of the obtained spot-related lists using concepts of molecular function.

Results: 
Different expression scores based either on simple fold change-measures or on regularized Students t-statistics are applied to spot-related gene lists and compared with special emphasis on the error characteristics of microarray expression data. The spot-clusters are analyzed using different methods of gene set enrichment analysis with the focus on overexpression and/or overrepresentation of predefined sets of genes. Metagene-related overrepresentation of selected gene sets was mapped into the SOM images to assign gene function to different regions. Alternatively we estimated set-related overexpression profiles over all samples studied using a gene set enrichment score. It was also applied to the spot-clusters to generate lists of enriched gene sets. We used the tissue body index data set, a collection of expression data of human tissues, as an illustrative example. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. In addition, we display special sets of housekeeping and of consistently weak and highly expressed genes using SOM data filtering. 

Conclusions:
The presented methods allow the comprehensive downstream analysis of SOM-transformed expression data in terms of cluster-related gene lists and enriched gene sets for functional interpretation. SOM clustering implies the ability to define either new gene sets using selected SOM spots or to verify and/or to amend existing ones

The Asian American College Experience at a Diverse Institution: Campus Climate as a Predictor of Sense of Belonging

The purpose of this study was to examine the experiences and perceptions of Asian American students at a large, diverse, public institution in order to assess the current campus climate and how this climate may relate to these students’ sense of belonging on campus. The conceptual framework used Hurtado, Milem, Clayton-Pederson and Allen’s (1998) dimensions for understanding the campus climate, focusing primarily on the behavioral and psychological aspects of campus climate. Specifically, the study sought to answer the question: Do the perceptions of the campus climate affect Asian American college students’ sense of belonging on a campus with a diverse student body? This study incorporated a mixed method approach consisting of a series of surveys and interviews. Quantitative data were collected through three different surveys: The Campus Connectedness Scale (Lee & Davis, 2000; α = .92), the Cultural Congruity Scale (Gloria & Robinson-Kurpius, 1996; α =.88) and the University Environment Scale (Gloria & Robinson-Kurpius, 1996; α =.85). To examine the relationship between perceptions of campus climate and overall sense of belonging, Pearson’s correlations, analyses of variances, and simple linear regressions were utilized.This study also used student interviews as a qualitative method to supplement the quantitative data. Findings indicated that Asian American students’ perceptions of the campus climate were strongly related to their sense of belonging via their cultural congruity on campus. Specifically the full regression models identified that campus climate significantly predicted cultural congruity (F = 42.38, p .05). The qualitative findings from the interviews indicated that these students viewed their campus as extremely unique, free of any race-related issues. They also emphasized the importance of student organizations in creating positive feelings of belonging on campus. Reasons for these perceptions revolved around a color-blind ideology as well as a “big-city” exclusion rationale; these students believed their campus, as part of a large urban city, was absent of racial discrimination and stereotypes. Higher education administrators must have the responsibility to ensure a welcoming and supportive environment for all students, including Asian Americans. As the review of literature will demonstrate, too often the Asian American college experience is overlooked or minimalized in academic research. University officials may use the information gained from this study to implement programs and services that support a more successful and rewarding college experience for Asian American students.Educational Leadership and Cultural Studies, Department o

(Un)Grading as Institutional Ecology: How (Alternative) Assessment Choices Shape Writing Classrooms

A longitudinal case study of grades and grading in the 1920s and 30s and the turn towards ungrading (2020-2022) in the First-Year Composition (FYC) program at the University of Tennessee, Knoxville (UTK), this project argues that institutional architecture structures classroom writing assessment and that the outcomes of ungrading (an umbrella term for a range of alternative assessment practices, including labor-based grading) vary based on teachers’ values/beliefs about writing. While rhetoric and composition scholarship on writing assessment typically frames ungrading as an individual, classroom-level choice that improves learning and increases equity, this project approaches ungrading from an institutional perspective, focusing on how programmatic and university contexts shape the function of conventional and alternative writing assessment and teachers’ experiences with ungrading. Drawing on archival data from the University Special Collections, the project opens by arguing that grades/grading prioritize institutional needs/reputation over student learning, mandating the use of standardized American English. Analyzing gradebooks kept by English professor John C. Hodges (1926-1938) shows that grades assigned in first-year writing courses fall along a bell curve, artificially depressing students’ grades and constructing students as in need of remediation. Grades do not track learning but rank students by the then-emerging standard of formal academic English. The project then jumps ahead a century to the contemporary First-Year Composition program (2020-2022), exploring the emergence of ungrading, or non-authoritative forms of writing assessment that center students’ labor and experiences in the course. Drawing on qualitative data from interviews/focus groups with graduate instructors and non-tenure track faculty, the project shows that programmatic architecture is key in depressing or expanding the use of ungrading. A resistant or hostile programmatic architecture may cause instructors to limit their use of ungrading, but writing programs can provide a more hospitable institutional context by ensuring faculty have the permission and resources to use alternative assessment. When instructors do use ungrading, they experience its outcomes as variable, dependent on their own values/beliefs about writing. This variability also means that the longer faculty use ungrading, the more likely they are to see meaningful results from its use

A workbook for the study of astronomy and eleven correlated myths for grades five through seven.

Thesis (M.S.)--Boston University PLEASE NOTE: pages 28-32, 35-37. 40-42, 46-49, 52-54, 57-62, 67-69, 73-75, 78-80, 83-85, 89-91, and 94 are all missing from our only physical copy of this thesis. We apologize for the inconvenience

Expression cartography of human tissues using self organizing maps

Background: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.
Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion, exocrine, epithelium, sexual reproduction, muscle, immune system and nervous tissues). SOM mapping reduces the dimension of expression data from ten thousands of genes to a few thousands of metagenes where each metagene acts as representative of a minicluster of co-regulated single genes. Tissue-specific and common properties shared between groups of tissues emerge as a handful of localized spots in the tissue maps collecting groups of co-regulated and co-expressed metagenes. The functional context of the spots was discovered using overrepresentation analysis with respect to pre-defined gene sets of known functional impact. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. Analysis techniques normally used at the gene-level such as two-way hierarchical clustering provide a better signal-to-noise ratio and a better representativeness of the method if applied to the metagenes. Metagene-based clustering analyses aggregate the tissues into essentially three clusters containing nervous, immune system and the remaining tissues. 
Conclusions: The global view on the behavior of a few well-defined modules of correlated and differentially expressed genes is more intuitive and more informative than the separate discovery of the expression levels of hundreds or thousands of individual genes. The metagene approach is less sensitive to a priori selection of genes. It can detect a coordinated expression pattern whose components would not pass single-gene significance thresholds and it is able to extract context-dependent patterns of gene expression in complex data sets.
&#xa

Emotional Support Animals, Service Animals, and Pets on Campus

For decades, universities have been accommodating physically disabled students who require guide dogs and other types of service animals. Within the past several years, however, mentally disabled students have increasingly petitioned colleges with no-pet policies to permit them to bring their animals on campus because they need a companion or emotional support animal to make college life easier and to reduce their stress, loneliness, depression, and/or anxiety. Institutions that unlawfully reject such requests are finding themselves in court and charged with disability discrimination. Schools are understandably confused about their obligation, if any, to waive their no-pet rules under these circumstances. This article discusses pets on campus and provides administrators guidance with respect to this increasingly contentious issue and to keep their organizations “out of the legal dog house.

La notion du temps à l'école enfantine

Pour résumer en quelques mots ce travail de recherche, je retiendrai la complexité du thème. En effet, la notion du temps est un thème qui nous pousse tous à la réflexion : Comment le définir, et surtout comment l’enseigner ? Voici l’enjeu de ce travail de recherche ; mon but est de comprendre et de m’approprier un peu plus la notion du temps tout en cherchant à comprendre comment nous pouvons l’enseigner à des enfants âgés de 4 à 6 ans, donc dans le cadre de l’école enfantine. Ce travail est basé sur les capacités et les compétences requises des enfants âgés de 4 à 6 ans, dans la perspective de leur aider à progresser dans la compréhension et l’appropriation de la notion du temps. Dans ce travail, je vous explique également la démarche que j’ai mise en place et je vous fais part des différentes informations que j’ai récoltées. Ces informations proviennent de sources variées, une première partie des lectures d’ouvrages que j’ai effectuées, la seconde partie découle des entretiens exploratoires auprès d’enseignantes et de l’expérimentation mise en place dans une classe d’école enfantine. Finalement, dans le bilan des informations récoltées, nous trouvons la réponse à ma question de recherche

A study of the factors causing the breakdown of health of executives

The purpose of this study was to determine (1) the opinions of executives and medical directors as to the contributing factors inn the breakdown of health of top-level executives, and (2) those areas in which there was a significant difference between the opinions of the executives and the medical directors. The study was limited to two hundred and eight executives who attended the Industrail Relations Conference of the National Association of Manufacturers in 1956 and one hundred thirty-three industrial medical directors whose names were suggested by Doctor Edward C. Holmblad, Managing Director of the Industrial Medical Association

In Search of Humble Leaders

The significance of moderation and balance across various domains has been sanctioned for millennia and deviations from midpoints of virtues, traits, qualities, and other attributes have been described as dysfunctional suggesting a nonmonotonic, U-shaped curve. Modern scholarship and lay interpretations of the virtue of humility have neglected this perspective and appear to tacitly assume that humility is an unmitigated good that leaders should develop and that more is better. Here we show, however, that what we refer to as authentic humility, is positioned at an intermediate point between negative and positive views of the self and that deviations from this center adversely impact well-being and offer a nonlinear, inverted U-shaped curve. Such an interpretation reconciles views of humility as a weakness or strength and demonstrates its positive impact on self, followers, and organizational well-being. We conclude by suggesting that humility has costs for leaders and therefore not an unmitigated good.&nbsp