Using signal processing, evolutionary computation, and machine learning to identify transposable elements in genomes

About half of the human genome consists of transposable elements (TE's), sequences that have many copies of themselves distributed throughout the genome. All genomes, from bacterial to human, contain TE's. TE's affect genome function by either creating proteins directly or affecting genome regulation. They serve as molecular fossils, giving clues to the evolutionary history of the organism. TE's are often challenging to identify because they are fragmentary or heavily mutated. In this thesis, novel features for the detection and study of TE's are developed. These features are of two types. The first type are statistical features based on the Fourier transform used to assess reading frame use. These features measure how different the reading frame use is from that of a random sequence, which reading frames the sequence is using, and the proportion of use of the active reading frames. The second type of feature, called side effect machine (SEM) features, are generated by finite state machines augmented with counters that track the number of times the state is visited. These counters then become features of the sequence. The number of possible SEM features is super-exponential in the number of states. New methods for selecting useful feature subsets that incorporate a genetic algorithm and a novel clustering method are introduced. The features produced reveal structural characteristics of the sequences of potential interest to biologists. A detailed analysis of the genetic algorithm, its fitness functions, and its fitness landscapes is performed. The features are used, together with features used in existing exon finding algorithms, to build classifiers that distinguish TE's from other genomic sequences in humans, fruit flies, and ciliates. The classifiers achieve high accuracy (> 85%) on a variety of TE classification problems. The classifiers are used to scan large genomes for TE's. In addition, the features are used to describe the TE's in the newly sequenced ciliate, Tetrahymena thermophile to provide information for biologists useful to them in forming hypotheses to test experimentally concerning the role of these TE's and the mechanisms that govern them

Effects of verbal suggestion and music on mood : [a thesis] ...

This study examined the effects of verbal suggestion and music listening on mood changes of college students. The 135 volunteers were randomly assigned to one of three conditions (Condition 1/somber depiction with music, Condition 2/pleasant depiction with music, or Condition 3/music only). The Profile of Mood States was administered before and after each condition. Significant differences (p\u3c.05) were found between pre and posttest scores within the groups; however, no significant differences were found among the groups for these same measures. A music questionnaire was administered following the posttest which examined the subjects\u27 preference for the music played, the frequency of experiencing images while listening to music, and their opinion concerning whether the depiction complemented the music. Implications of the results are discussed, and suggestions for future research are given

Parental Perceptions of Oral Health and School-Based Dental Sealant Programs

Introduction: Community Health Needs Assessment (University of Vermont Medical Center, 2013) Identified oral health in pediatric population as a primary concern Barriers to dental care cited: access, affordability, education School-Based Sealant Program (SBSP) Dental sealants are an evidence-based method of cavity prevention CDC strongly recommends delivery via SBSPs Few Vermont schools have such a program Vermont Medicaid State Plan amendment allows dental hygienists to bill without on-site dentist (2015)4 Unique opportunity to pilot an SBSP Pilot program implemented by the University of Vermont Medical Center Community Health Improvement Goal: sustainable model able to be replicated in Vermont schools Pilot School Selection – Milton Elementary-Middle School (MEMS) Demographics representative of Vermont schools (46% free & reduced lunch program); school administration supportive of an SBSP; no existing dental education (“Tooth Tutor”) program per Vermont Office of Oral Healthhttps://scholarworks.uvm.edu/comphp_gallery/1232/thumbnail.jp

Woman-centred care and integrated electronic medical records within Australian maternity settings: Point prevalence audit and observational study

Objective: Transition to paperless records brings new challenges to midwifery practice across the continuum of woman-centred care. There is limited and conflicting evidence on the relative benefits of electronic medical records in maternity settings. This article aims to inform the use of integrative electronic medical records within the maternity services’ environment with attention to the midwife-woman relationship. Design: This descriptive two-part study includes 1) an audit of electronic records in the early period following implementation (2-time points); and 2) an observational study to observe midwives’ practice relating to electronic record use. Setting: Two regional tertiary public hospitals Participants: Midwives providing care for childbearing women across antenatal, intrapartum and postnatal areas. Findings: 400 integrated electronic medical records were audited for completeness. Most fields had high levels of complete data in the correct location. However, between time 1 (T1) and time 2 (T2), persistent missing data (foetal heart rate documented 30 minutely T1 36%; T2 42%), and incomplete or incorrectly located data (pathology results T1:63%; T2 54%; perineal repair T1 60%; T2 46%) were identified. Observationally, midwives were actively engaged with the integrative electronic medical record between 23% to 68% (median 46%; IQR 16) of the time. Conclusion: Midwives spent a significant amount of time completing documentation during clinical episodes of care. Largely, this documentation was found to be accurate, yet exceptions to data completeness, precision and location remained, indicating some concerns with software usability. Implications for practice: Time-intensive monitoring and documentation may hinder woman-centred midwifery care

Spatial Distribution of Bednet Coverage under Routine Distribution through the Public Health Sector in a Rural District in Kenya

Insecticide-treated nets (ITNs) are one of the most important and cost-effective tools for malaria control. Maximizing individual and community benefit from ITNs requires high population-based coverage. Several mechanisms are used to distribute ITNs, including health facility-based targeted distribution to high-risk groups; community-based mass distribution; social marketing with or without private sector subsidies; and integrating ITN delivery with other public health interventions. The objective of this analysis is to describe bednet coverage in a district in western Kenya where the primary mechanism for distribution is to pregnant women and infants who attend antenatal and immunization clinics. We use data from a population-based census to examine the extent of, and factors correlated with, ownership of bednets. We use both multivariable logistic regression and spatial techniques to explore the relationship between household bednet ownership and sociodemographic and geographic variables. We show that only 21% of households own any bednets, far lower than the national average, and that ownership is not significantly higher amongst pregnant women attending antenatal clinic. We also show that coverage is spatially heterogeneous with less than 2% of the population residing in zones with adequate coverage to experience indirect effects of ITN protection

A Theoryâ based Didactic Offering Physicians a Method for Learning and Teaching Others About Human Trafficking

Emergency clinicians are on the frontlines of identifying and caring for trafficked persons. However, most emergency providers have never received training on trafficking, and studies report a significant knowledge gap involving this important topic. Workshops often employ a â trainâ theâ trainerâ model to address cliniciansâ knowledge gaps involving various topics (including trafficking). By offering participants knowledge and skills needed to both understand relevant content and teach this content to future learners, this model aims at promoting widespread dissemination of essential information. However, current trainâ theâ trainer workshops typically involve full or multiday sessions and employ multimodal instructional techniques, making them time and resource intensive for both participants and facilitators.To address these challenges, we created a 50â minute trainâ theâ trainer workshop to teach emergency clinicians the knowledge and skills needed to recognize and care for trafficked patients while providing instructional techniques to teach learners this content in the clinical environment. Learning theory and principles informed the choice of instructional methods and were employed when designing the paperâ based learning guides that functioned as this intervention’s primary instructional resource. Guides contained detailed scripts used to perform roleâ playing exercises. These â scripted guidesâ were designed for participants to learn important content while simultaneously practicing techniques to teach this content to one another. They provided the scaffolding necessary to independently direct learning during the workshop (with minimal facilitator intervention), while also being carefully formatted and organized to create an accessible tool for future use during clinical teaching.The session was implemented at the 2018 Society for Academic Emergency Medicine Annual Meeting in Indianapolis, Indiana. Based on participantsâ selfâ assessment using a retrospective preâ post test, the workshop was successful in creating a trainâ theâ trainer model that is brief, requiring minimal facilitator resources and offers instruction on both content knowledge and instructional methods to disseminate this knowledge to future learners.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147170/1/aet210206_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147170/2/aet210206.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147170/3/aet210206-sup-0001-DataS1.pd

CemOrange2 fusions facilitate multifluorophore subcellular imaging in C. elegans

Due to its ease of genetic manipulation and transparency, Caenorhabditis elegans (C. elegans) has become a preferred model system to study gene function by microscopy. The use of Aequorea victoria green fluorescent protein (GFP) fused to proteins or targeting sequences of interest, further expanded upon the utility of C. elegans by labeling subcellular structures, which enables following their disposition during development or in the presence of genetic mutations. Fluorescent proteins with excitation and emission spectra different from that of GFP accelerated the use of multifluorophore imaging in real time. We have expanded the repertoire of fluorescent proteins for use in C. elegans by developing a codon-optimized version of Orange2 (CemOrange2). Proteins or targeting motifs fused to CemOrange2 were distinguishable from the more common fluorophores used in the nematode; such as GFP, YFP, and mKate2. We generated a panel of CemOrange2 fusion constructs, and confirmed they were targeted to their correct subcellular addresses by colocalization with independent markers. To demonstrate the potential usefulness of this new panel of fluorescent protein markers, we showed that CemOrange2 fusion proteins could be used to: 1) monitor biological pathways, 2) multiplex with other fluorescent proteins to determine colocalization and 3) gain phenotypic knowledge of a human ABCA3 orthologue, ABT-4, trafficking variant in the C. elegans model organism

IC‐P2‐074: Differentiating amnestic MCI converting to probable AD from stable amnestic MCI using FDG‐PET and an AD‐related hypometabolism overlap index

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152594/1/alzjjalz200805067.pd