Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation

Ribosome profiling (ribo-seq) is a recently developed technique that provides genomewide information on protein synthesis (GWIPS) in vivo. The high resolution of ribo-seq is one of the exciting properties of this technique. In Chapter 2, I present a computational method that utilises the sub-codon precision and triplet periodicity of ribosome profiling data to detect transitions in the translated reading frame. Application of this method to ribosome profiling data generated for human HeLa cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame. Since the initial publication of the ribosome profiling technique in 2009, there has been a proliferation of studies that have used the technique to explore various questions with respect to translation. A review of the many uses and adaptations of the technique is provided in Chapter 1. Indeed, owing to the increasing popularity of the technique and the growing number of published ribosome profiling datasets, we have developed GWIPS-viz (http://gwips.ucc.ie), a ribo-seq dedicated genome browser. Details on the development of the browser and its usage are provided in Chapter 3. One of the surprising findings of ribosome profiling of initiating ribosomes carried out in 3 independent studies, was the widespread use of non-AUG codons as translation initiation start sites in mammals. Although initiation at non-AUG codons in mammals has been documented for some time, the extent of non-AUG initiation reported by these ribo-seq studies was unexpected. In Chapter 4, I present an approach for estimating the strength of initiating codons based on the leaky scanning model of translation initiation. Application of this approach to ribo-seq data illustrates that initiation at non-AUG codons is inefficient compared to initiation at AUG codons. In addition, our approach provides a probability of initiation score for each start site that allows its strength of initiation to be evaluated.

Kant, le philosophe parodié: “mauvais usage” de la Critique de la raison pure dans le Saint Genet de Sartre

Aachen

Do diabetic veterans use the Internet? Self-reported usage, skills, and interest in using My HealtheVet Web portal.

OBJECTIVE: The Veterans Health Administration has developed My HealtheVet (MHV), a Web-based portal that links veterans to their care in the veteran affairs (VA) system. The objective of this study was to measure diabetic veterans' access to and use of the Internet, and their interest in using MHV to help manage their diabetes. MATERIALS AND METHODS: Cross-sectional mailed survey of 201 patients with type 2 diabetes and hemoglobin A(1c) > 8.0% receiving primary care at any of five primary care clinic sites affiliated with a VA tertiary care facility. Main measures included Internet usage, access, and attitudes; computer skills; interest in using the Internet; awareness of and attitudes toward MHV; demographics; and socioeconomic status. RESULTS: A majority of respondents reported having access to the Internet at home. Nearly half of all respondents had searched online for information about diabetes, including some who did not have home Internet access. More than a third obtained "some" or "a lot" of their health-related information online. Forty-one percent reported being "very interested" in using MHV to help track their home blood glucose readings, a third of whom did not have home Internet access. Factors associated with being "very interested" were as follows: having access to the Internet at home (p < 0.001), "a lot/some" trust in the Internet as a source of health information (p = 0.002), lower age (p = 0.03), and some college (p = 0.04). Neither race (p = 0.44) nor income (p = 0.25) was significantly associated with interest in MHV. CONCLUSIONS: This study found that a diverse sample of older VA patients with sub-optimally controlled diabetes had a level of familiarity with and access to the Internet comparable to an age-matched national sample. In addition, there was a high degree of interest in using the Internet to help manage their diabetes.

The Toronto Word Pool: Norms for imagery, concreteness, orthographic variables, and grammatical usage for 1,080 words

Imagery and concreteness norms and percentage noun usage were obtained on the 1,080 verbal items from the Toronto Word Pool. Imagery was defined as the rated ease with which a word aroused a mental image, and concreteness was defined in relation to level of abstraction. The degree to which a word was functionally a noun was estimated in a sentence generation task. The mean and standard deviation of the imagery and concreteness ratings for each item are reported together with letter and printed frequency counts for the words and indications of sex differences in the ratings. Additional data in the norms include a grammatical function code derived from dictionary definitions, a percent noun judgment, indexes of statistical approximation to English, and an orthographic neighbor ratio. Validity estimates for the imagery and concreteness ratings are derived from comparisons with scale values drawn from the Paivio, Yuille, and Madigan (1968) noun pool and the Toglia and Battig (1978) norms. © 1982 Psychonomic Society, Inc.

Air pollution, Fuel Usage and Health Outcomes in Madre de Dios, Peru: a Comparative Cross Sectional Study

Air pollution is a common problem. Particulate matter generated from air pollution has been tied to adverse health outcomes associated with cardiovascular disease. Biomass fuels are a specific contributor to increased particulate matter and arise as a result of indoor heating, cook stoves and indoor food preparation. This is a two part cross sectional study looking at communities in the Madre de Dios region. Survey data was collected from 9 communities along the Madre de Dios River. Individual level household PM2.5 was also collected as a means to generate average PM data stratified by fuel use. Data collection was affected by a number of outside factors, which resulted in a loss of data. Results from the cross-sectional study indicate that hypertension is not a significant source of morbidity. Obesity is prevalent and significantly associated with kitchen venting method indicating a potential relationship.

A descriptive study of the usage of spinal manipulative therapy techniques within a randomised clinical trial in acute low back pain

The majority of randomized clinical trials (RCTs) of spinal manipulative therapy have not adequately de?ned the terms ‘mobilization’ and ‘manipulation’, nor distinguished between these terms in reporting the trial interventions. The purpose of this study was to describe the spinal manipulative therapy techniques utilized within a RCT of manipulative therapy (MT; n=80), interferential therapy (IFT; n=80), and a combination of both (CT; n=80) for people with acute low back pain (LBP). Spinal manipulative therapy was de?ned as any ‘mobilization’ (low velocity manual force without a thrust) or ‘manipulation’ (high velocity
thrust) techniques of the spine described by Maitland and Cyriax.
The 16 physiotherapists, all members of the Society of Orthopaedic Medicine, utilized three spinal manipulative therapy patterns in the RCT: Maitland Mobilization (40.4%, n=59), Maitland Mobilization/Cyriax Manipulation (40.4%, n=59) and Cyriax Manipulation (19.1%, n=28). There was a signi?cant difference between the MT and CT groups in their usage of spinal manipulative therapy techniques (w2=9.178; df=2;P=0.01); subjects randomized to the CT group received three times more Cyriax Manipulation (29.2%, n=21/72) than those randomized to the MT group (9.5%, n=7/74; df=1; P=0.003).
The use of mobilization techniques within the trial was comparable with their usage by the general population of physiotherapists in Britain and Ireland for LBP management. However, the usage of manipulation techniques was considerably higher than reported in physiotherapy surveys and may re?ect the postgraduate training of trial therapists.

Analysis of receptor (CD46, CD150) usage by measles virus

This is a collaborative paper between Juergen Schneider-Schaulies's group and ours. It shows the differential use of the two measles receptors in various strains.

Computer usage and the validity of self-assessed computer competence among first-year business students

Abstract This study evaluates the reliability of self-assessment as a measure of computer competence. This evaluation is carried out in response to recent research which has employed self-reported ratings as the sole indicator of students’ computer competence. To evaluate the reliability of self-assessed computer competence, the scores achieved by students in self-assessed computer competence tests are compared with scores achieved in objective tests. The results reveal a statistically significantly over-estimation of computer competence among the students surveyed. Furthermore, reported pre-university computer experience in terms of home and school use and formal IT education does not affect this result. The findings call into question the validity of using self-assessment as a measure of computer competence. More generally, the study also provides an up-to-date picture of self-reported computer usage and IT experience among pre-university students from New Zealand and South-east Asia and contrasts these findings with those from previous research.

Social Networks Usage Profile: Descriptive study with students in the University of Murcia

Telematic tools are very important for our lives in the present era and moreover this idea is made more evident if we analyse young people behaviours. However, it seems that the possibilities that these tools allow subjects from a professional point of view, beyond the purely playful aspects, are still not fully exploited both by subjects, neither by educational institutions where they learn. Our work studies the uses of social media in the context of university students. In order to this we have designed a research based on quantitative methodology with a survey. We have applied a questionnaire to students in the University of Murcia. The questionnaire was answered by 487 students in the first half of 2014. The survey results confirm our hypothesis that social networks are part of the basic and habitual tools of communication between the youth of our university and eminently used for leisure purposes, and that the tools used for more academic activities are those allowing greater control of privacy.

Strasheela: Design and usage of a music composition environment based on the Oz programming model

Strasheela provides a means for the composer to create a symbolic score by formally describing it in a rule-based way. The environment defines a rich music representation for complex polyphonic scores. Strasheela enables the user to define expressive compositional rules and then to apply them to the score. Compositional rules can restrict many aspects of the music - including the rhythmic structure, the melodic structure and the harmonic structure - by constraining the parameters (e.g. duration or pitch) of musical events according to some numerical or logical relation. Strasheela combines this expressivity with efficient search strategies.

Systematic Usage of Embedded Modelling Languages in Automated Model Transformation Chains

Annotation of programs using embedded Domain-Specific Languages (embedded DSLs), such as the program annotation facility for the Java programming language, is a well-known practice in computer science. In this paper we argue for and propose a specialized approach for the usage of embedded Domain-Specific Modelling Languages (embedded DSMLs) in Model-Driven Engineering (MDE) processes that in particular supports automated many-step model transformation chains. It can happen that information defined at some point, using an embedded DSML, is not required in the next immediate transformation step, but in a later one. We propose a new approach of model annotation enabling flexible many-step transformation chains. The approach utilizes a combination of embedded DSMLs, trace models and a megamodel. We demonstrate our approach based on an example MDE process and an industrial case study.