Class discovery via feature selection in unsupervised settings

Identifying genes linked to the appearance of certain types of cancers and their phenotypes is a well-known and challenging problem in bioinformatics. Discovering marker genes which, upon genetic mutation, drive the proliferation of different types and subtypes of cancer is critical for the development of advanced tests and therapies that will specifically identify, target, and treat certain cancers. Therefore, it is crucial to find methods that are successful in recovering "cancer-critical genes" from the (usually much larger) set of all genes in the human genome. We approach this problem in the statistical context as a feature (or variable) selection problem for clustering, in the case where the number of important features is typically small (or rare) and the signal of each important feature is typically minimal (or weak). Genetic datasets typically consist of hundreds of samples (n) each with tens of thousands gene-level measurements (p), resulting in the well-known statistical "large p small n" problem. The class or cluster identification is based on the clinical information associated with the type or subtype of the cancer (either known or unknown) for each individual. We discuss and develop novel feature ranking methods, which complement and build upon current methods in the field. These ranking methods are used to select features which contain the most significant information for clustering. Retaining only a small set of useful features based on this ranking aids in both a reduction in data dimensionality, as well as the identification of a set of genes that are crucial in understanding cancer subtypes. In this paper, we present an outline of cutting-edge feature selection methods, and provide a detailed explanation of our own contributions to the field. We explain both the practical properties and theoretical advantages of the new tools that we have developed. Additionally, we explore a well-developed case study applying these new feature selection methods to different levels of genetic data to explore their practical implementation within the field of bioinformatics

NATURAL HISTORY OF A POPULATION OF WOOD TURTLES (GLYPTEMYS INSCULPTA) IN WEST VIRGINIA

The Wood Turtle (Glyptemys insculpta) is listed as vulnerable in West Virginia and only occurs in the Eastern Panhandle. The study population is unique in West Virginia because it occurs at a much higher mean elevation than other Wood Turtle populations in the state. The primary objective of this study was to determine if, and to what extent, altitude affected this population’s ecology. Turtles were located with opportunistic surveys and captured by hand. I located 31 turtles: 18 males, and 13 females. Turtles were captured a total of 68 times. Ratio of males to females did not differ significantly from 1:1. Morphometric measurements were taken slightly differently than in other studies thus occluding results, but it appears this population may be slightly larger than other WV Wood Turtles. Growth after a conservative estimate of maturity was 1.00 ± 0.56 mm per year, but may occur at an older age. Total adult population was estimated to be 53 ± 14, and the density of turtles in occupied areas was 2.27 adult turtles per hectare. No juveniles were captured, which bodes poorly for the viability of the population. The population is reproducing, owing to the discovery of nests and a hatchling, but may not be recruiting hatchlings into older cohorts. I found some evidence to support the notion that this population has natural history traits more typical of higher latitudes including larger body sizes, maturity at larger body sizes, and lower turtle density, but a lack of recruitment would mean an aging population that would mimic more northerly populations as individuals age. Additional research is needed on this population to determine if it is currently recruiting young turtles or is a ghost population and at risk of extirpation

Agenda Setting on the Supreme Court of the United States in 1960, 1977, and 1992

This dissertation adds to Supreme Court of the United States agenda-setting research by exploring the following overarching research question: How does the Supreme Court of the United States decide which cases it will review? In addition, this study addresses three gaps in the agenda-setting research by considering types of petitions for writ of certiorari that are often ignored by other studies, analyzing the Court’s case-selection process as a two-step process, and studying the Court’s agenda-setting trends over time. To explore these gaps in the research, an original dataset was created by collecting data on a random sample of petitions for writ of certiorari to the Court during its 1960, 1977, and 1992 terms. Selection models were then used to analyze the data and a low-cost, low-value and high-cost, high-value cue theory framework was applied to the results of the models to determine the factors that influence the likelihood a petition for writ of certiorari is discussed by and selected for review during the Court’s case-selection process. The results of this study show that different factors significantly influence the Court’s case-selection process across the terms studied and have varying impact during one or both stages of the case-selection process (which include the selection of petitions for the Court’s discuss list and the selection of petitions from the discuss list for review). This study has implications for future scholarly work on the Supreme Court’s agenda-setting process as it highlights the importance of considering all types of certiorari petitions, the two-step nature of the case-selection process, and changing agenda-setting patterns over time. The findings in this dissertation may also assist potential litigants who hope to have their cases considered by the Supreme Court

The Effects of Interactive Word Walls on English Language Learners’ Academic Vocabulary Acquisition

The purpose of this study was to determine if the implementation of interactive word walls influenced student academic vocabulary acquisition and the academic achievement of students in a tenth-grade biology unit with a focus on English Language Learners (ELL). This study took place in a midsized suburban high school in a midwestern state with 64 tenth-grade biology students. A mixed methods research approach was employed that included analysis of pre- and post-tests, weekly formative assessments (quick writes), observation tallies of student word wall usage, student feedback, and a reflective teacher journal. The data showed that the interactive word wall was effective in helping students gain a stronger understanding of content-specific vocabulary. Both ELL and non-ELL students’ academic vocabulary increased, however ELL students and traditionally low performing students benefited from the use of the word wall the most. It is recommended that implementation of interactive word walls be used in high school science settings

Predicting Support for Oil Industry Regulatory Policy Alternatives During the North Dakota Oil Boom

Given the lax regulatory response of the North Dakota state government during the most recent oil boom in the Bakken Shale, a better understanding of how to frame alternative regulation policies for the general public is needed. A survey of North Dakota residents in 2015 indicates that attitudes towards the oil industry, regulation, property rights, and messaging are associated with policy receptivity. Thus, in framing policy messages, focus should be on confirming what the public already knows about oil industry conduct and its opposition to regulation. Individuals who are more favorable to regulation and have an unfavorable attitude towards the oil industry are more likely to be favorable to pro-regulatory policy alternatives. The results of these findings help us to better understand how the public views the regulation of natural resources and can be used by groups seeking to develop messaging to promote policy receptivity

Corrigendum: Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea.

[This corrects the article on p. 404 in vol. 4, PMID: 24399999.]

Characterizing Participation and Perceived Engagement Benefits in an Integrated Digital Behavioral Health Recovery Community for Women: A Cross-Sectional Survey

Background: Research suggests that digital recovery support services (D-RSSs) may help support individual recovery and augment the availability of in-person supports. Previous studies highlight the use of D-RSSs in supporting individuals in recovery from substance use but have yet to examine the use of D-RSSs in supporting a combination of behavioral health disorders, including substance use, mental health, and trauma. Similarly, few studies on D-RSSs have evaluated gender-specific supports or integrated communities, which may be helpful to women and individuals recovering from behavioral health disorders. Objective: The goal of this study was to evaluate the SHE RECOVERS (SR) recovery community, with the following 3 aims: (1) to characterize the women who engage in SR (including demographics and recovery-related characteristics), (2) describe the ways and frequency in which participants engage with SR, and (3) examine the perception of benefit derived from engagement with SR. Methods: This study used a cross-sectional survey to examine the characteristics of SR participants. Analysis of variance and chi-square tests, as well as univariate logistic regressions, were used to explore each aim. Results: Participants (N=729, mean age 46.83 years; 685/729, 94% Caucasian) reported being in recovery from a variety of conditions, although the most frequent nonexclusive disorder was substance use (86.40%, n=630). Participants had an average length in recovery (LIR) of 6.14 years (SD 7.87), with most having between 1 and 5 years (n=300). The most frequently reported recovery pathway was abstinence-based 12-step mutual aid (38.40%). Participants reported positive perceptions of benefit from SR participation, which did not vary by LIR or recovery pathway. Participants also had high rates of agreement, with SR having a positive impact on their lives, although this too did vary by recovery length and recovery pathway. Participants with 1 to 5 years of recovery used SR to connect with other women in recovery at higher rates, whereas those with less than 1 year used SR to ask for resources at higher rates, and those with 5 or more years used SR to provide support at higher rates. Lifetime engagement with specific supports of SR was also associated with LIR and recovery pathway. Conclusions: Gender-specific and integrated D-RSSs are feasible and beneficial from the perspective of participants. D-RSSs also appear to provide support to a range of recovery typologies and pathways in an effective manner and may be a vital tool for expanding recovery supports for those lacking in access and availability because of geography, social determinants, or other barriers

Georgia Southern’s Checkout Equipment: laptops, cameras, boardgames, and more. How we manage the checkout equipment program

Presentation given at the Georgia Libraries Conference, Macon, GA. Georgia Southern makes available a variety of equipment for student check out including a fleet of approximately 200 laptops, high-end digital cameras, tripods and lighting kits, video recording equipment, high-end microphones, and more. Equipment checkout is popular with students with equipment cycling in and out. Equipment also presents unique cataloging challenges. MARC was designed for books, and providing a good search for pulling statistics for non-traditional items can be a challenge. Items also may be returned needing repairs and Georgia Southern performs in-house repairs on laptops and other electronics. Participants will learn about ways to manage multipart checkout items, such as camera and laptops, a board game with many pieces, or a DSLR camera with lens and an SD card. Participants will learn about ways to better use the ILS, a system designed for books but allowing seamless checkout to students, to manage equipment. Participants will learn about ways Georgia Southern collects statistics on how materials are used and workflows and processes that allow for better statistics. Participants will learn about total costs of operating an equipment program, including commons repairs, average costs of parts to sustain each type of equipment, and employee time needed to perform in-house repairs

Unmanned Aerial Vehicle Ground Control Point Deployment

According to Federal Aviation Regulation (FAR) Part 77, all airports have imaginary approach surfaces which must remain clear of obstructions in order to ensure safe air travel. Threats of penetration to these imaginary surfaces include new construction, telephone poles and lines, and trees. While most potential threats analyzed remain relatively constant in size, objects such as trees which grow require annual analysis for change detection. A variety of methods are available for surveying these surfaces for potential obstructions, one being an aerial mapping from photogrammetric data. Aerial mapping for surveying purposes is a process which ties overlapping photographs together using computer software which detects similar points between the images. These images requires ground control points, also known as GCPs, to create a scale which allows for accurate measurement data. When ground control points with known GPS locations are placed throughout the mapping area all the points within the model can then be tied to their respective GPS coordinates in the longitudinal, latitudinal, and altitude directions. The placement of these markers is one of the most time-consuming but necessary tasks when creating an aerial map. The main objective of this project was for the team to design and produce a method of streamlining the ground control point deployment process. This report introduces a device which, when implemented, can reduce the number of resources and labor needed for this process. A mechanical release system was designed and built to be carried by a drone. Remote control between two XBee RF modules was implemented to activate the rotating notch release system, following user commands. A 90 degree rotation by the servo of the flange would align the flange with the keyslot in the GCP, allowing it to fall. The final design was successfully operated by one pilot and three GCP’s were deployed at various locations. An important factor in designing this system was developing lightweight, high contrast GCPs that would not impact the flight of the drone. The weight and balance of the final product were suitable for the small 3DR Solo drone used in the project. This accomplishment proves this system could be applied to drones with greater payloads and longer flight times for preparing large surveying areas in minimal time