Identification of Conserved Splicing Motifs in Mutually Exclusive Exons of 15 Insect Species

Background: During alternative splicing, the inclusion of an exon in the final mRNA molecule is determined by nuclear proteins that bind cis-regulatory sequences in a target pre-mRNA molecule. A recent study suggested that the regulatory codes of individual RNA-binding proteins may be nearly immutable between very diverse species such as mammals and insects. The model system Drosophila melanogaster therefore presents an excellent opportunity for the study of alternative splicing due to the availability of quality EST annotations in FlyBase. Methods: In this paper, we describe an in silico analysis pipeline to extract putative exonic splicing regulatory sequences from a multiple alignment of 15 species of insects. Our method, ESTs-to-ESRs (E2E), uses graph analysis of EST splicing graphs to identify mutually exclusive (ME) exons and combines phylogenetic measures, a sliding window approach along the multiple alignment and the Welch’s t statistic to extract conserved ESR motifs. Results: The most frequent 100% conserved word of length 5 bp in different insect exons was “ATGGA”. We identified 799 statistically significant “spike” hexamers, 218 motifs with either a left or right FDR corrected spike magnitude p-value < 0.05 and 83 with both left and right uncorrected p < 0.01. 11 genes were identified with highly significant motifs in one ME exon but not in the other, suggesting regulation of ME exon splicing through these highly conserved hexamers. The majority of these genes have been shown to have regulated spatiotemporal expression. 10 elements were found to match three mammalian splicing regulator databases. A putative ESR motif, GATGCAG, was identified in the ME-13b but not in the ME-13a of Drosophila N-Cadherin, a gene that has been shown to have a distinct spatiotemporal expression pattern of spliced isoforms in a recent study. Conclusions: Analysis of phylogenetic relationships and variability of sequence conservation as implemented in the E2E spikes method may lead to improved identification of ESRs. We found that approximately half of the putative ESRs in common between insects and mammals have a high statistical support (p < 0.01). Several Drosophila genes with spatiotemporal expression patterns were identified to contain putative ESRs located in one exon of the ME exon pairs but not in the other.

A survey of music educator's understanding and use of advanced audio technology in their instructional methods and strategies

This study examines the correlation between how certified music educators understand audio technology and how they incorporate it in their instructional methods. Participants were classroom music teachers selected from fifty middle schools in Miami- Dade Public Schools. The study adopted a non-experimental research design in which a survey was the primary tool of investigation. The findings reveal that a majority of middle school music teachers in Miami-Dade are not familiar with advanced audiorecording software or any other digital device dedicated to the recording and processing of audio signals. Moreover, they report a lack of opportunities to develop this knowledge. Younger music teachers, however, are more open to developing up-to-date instructional methodologies. Most of the participants agreed that music instruction should be a platform for preparing students for a future in the entertainment industry. A basic knowledge of music business should be delivered to students enrolled in middle-school music courses.

Laboratory focussed learning of core electronic engineering concepts in the first year of an honours degree programme

In common with most universities teaching electronic engineering in the UK, Aston University has seen a shift in the profile of its incoming students in recent years. The educational background of students has moved away from traditional Alevel maths and science and if anything this variation is set to increase with the introduction of engineering diplomas. Another major change to the circumstances of undergraduate students relates to the introduction of tuition fees in 1998 which has resulted in an increased likelihood of them working during term time. This may have resulted in students tending to concentrate on elements of the course that directly provide marks contributing to the degree classification. In the light of these factors a root and branch rethink of the electronic engineering degree programme structures at Aston was required. The factors taken into account during the course revision were:. Changes to the qualifications of incoming students. Changes to the background and experience of incoming students. Increase in overseas students, some with very limited practical experience. Student focus on work directly leading to marks. Modular compartmentalisation of knowledge. The need for provision of continuous feedback on performance We discuss these issues with specific reference to a 40 credit first year electronic engineering course and detail the new course structure and evaluate the effectiveness of the changes. The new approach appears to have been successful both educationally and with regards to student satisfaction. The first cohort of students from the new course will graduate in 2010 and results from student surveys relating particularly to project and design work will be presented at the conference. © 2009 K Sugden, D J Webb and R P Reeves.

Finance past, finance future: a brief exploration of the evolution of financial practices

As we work our way through the latest financial crisis, politicians seem both powerless to act convincingly and unable to craft from the welter of diverse and antagonistic narratives a coherent and convincing vision of the future. In this article, we argue that a temporal lens brings clarity to such confusion, and that thinking in terms of time and reflecting on privileged temporal structures helps to highlight underlying assumptions and distinguish different narratives from one another. We begin by articulating our understanding of temporality, and we proceed to apply this to the evolution of financial practice during different historical epochs as recently delineated by Gordon (2012). We argue that the principles of finance were effectively in place by the eighteenth century and that consequent developments are best conceptualized as phases in which one particular aspect is intensified. We find that in different historical periods, the temporal intensification associated with specific models of finance shifts, over history, from the past to the present to the future. We argue that a quite idiosyncratic understanding of the future has been intensified in the present phase, what we refer to as proximal future, and we explain how this has come to be. We then consider the ethical consequences of privileging an intensification of proximal future before mapping an alternative model centred on intensifying distal future, highlighting early signs of its potential emergence in the shadows of our present.

Child care proceedings in non-specialist courts: the experience in Ireland

It is widely accepted that court proceedings concerning child protection are a particularly sensitive type of court proceedings that warrant a different approach to other types of proceedings. Consequently, the use of specialized family or children’s judges or courts is commonplace across Europe and in common law jurisdictions. By contrast, in Ireland, proceedings under the Child Care Act 1991 are heard in the general courts system by judges who mostly do not specialize in child or family law. In principle, the Act itself and the associated case law accept that the vulnerability of the parties and the sensitivity of the issues involved are such that they need to be singled out for a different approach to other court proceedings. However, it is questionable whether this aspiration has been realized in a system where child care proceedings are mostly heard in a general District Court, using the same judges and the same physical facilities used for proceedings such as minor crime and traffic offences. This article draws on the first major qualitative analysis of professional perspectives on child care proceedings in the Irish District Court. It examines evidence from judges, lawyers, social workers, and guardians ad litem and asks whether non-specialist courts are an appropriate venue for proceedings on an issue as complex and sensitive as child protection, or whether the establishment of specialist family courts with dedicated staff and facilities provides a better solution.

An Exploration of the challenges associated with software logging in large systems

Over the past few years, logging has evolved from from simple printf statements to more complex and widely used logging libraries. Today logging information is used to support various development activities such as fixing bugs, analyzing the results of load tests, monitoring performance and transferring knowledge. Recent research has examined how to improve logging practices by informing developers what to log and where to log. Furthermore, the strong dependence on logging has led to the development of logging libraries that have reduced the intricacies of logging, which has resulted in an abundance of log information. Two recent challenges have emerged as modern software systems start to treat logging as a core aspect of their software. In particular, 1) infrastructural challenges have emerged due to the plethora of logging libraries available today and 2) processing challenges have emerged due to the large number of log processing tools that ingest logs and produce useful information from them. In this thesis, we explore these two challenges. We first explore the infrastructural challenges that arise due to the plethora of logging libraries available today. As systems evolve, their logging infrastructure has to evolve (commonly this is done by migrating to new logging libraries). We explore logging library migrations within Apache Software Foundation (ASF) projects. We i find that close to 14% of the pro jects within the ASF migrate their logging libraries at least once. For processing challenges, we explore the different factors which can affect the likelihood of a logging statement changing in the future in four open source systems namely ActiveMQ, Camel, Cloudstack and Liferay. Such changes are likely to negatively impact the log processing tools that must be updated to accommodate such changes. We find that 20%-45% of the logging statements within the four systems are changed at least once. We construct random forest classifiers and Cox models to determine the likelihood of both just-introduced and long-lived logging statements changing in the future. We find that file ownership, developer experience, log density and SLOC are important factors in determining the stability of logging statements.

Understanding arsenic mobility and speciation in lake sediments impacted by ore roasting near Giant mine, NWT

The roasting of gold-bearing arsenopyrite at Giant mine (Northwest Territories) between 1949 and 1999 released approximately 20,000 tonnes of toxic arsenic-bearing aerosols in the local aerial environment. Detailed examination of lake sediments, sediment porewaters, surface waters and lake hydrology sampled from three lakes of differing limnological characteristics was conducted in summer and winter conditions. Samples were analyzed for solid and dissolved elemental concentrations, speciation and mineralogy. The three lakes are located less than 5km from the mine roaster, and downwind, based on predominant wind direction. The objective of the study was to assess the controls on the mobility and fate of arsenic in these roaster-impacted subarctic lacustrine environments. Results show that the occurrence of arsenic trioxide in lake sediments coincides with the regional onset of industrial activities. The bulk of arsenic in sediments is contained in the form of secondary sulphide precipitates, with iron oxides hosting a minimal amount of arsenic near the surface-water interface. The presence of geogenic arsenic is likely contained as dilute impurities in common rock-forming minerals, and is not believed to be a significant source of arsenic to sediments, porewaters or lake waters. Furthermore, the well correlated depth-profiles of arsenic, antimony and gold in sediments may help reveal roaster impact. The soluble arsenic trioxide particles contained in sediments act as the primary source of arsenic into porewaters. Dissolved arsenic in reducing porewaters both precipitate as secondary sulphides in situ, and diffuse upwards into the overlying lake waters. Arsenic diffusion out of porewaters, combined with watercourse-driven residence time, are estimated to be the predominant mechanisms controlling arsenic concentrations in overlying lake waters. The sequestration of arsenic from porewaters as sulphide precipitates, in the study lakes, is not an effective process in keeping lake-water arsenic concentrations below guidelines for the protection of the freshwater environment and drinking water. Seasonal impacts on lake geochemistry derive from ice covering lake waters, cutting them off from of atmospheric oxygen, along with the exclusion of solutes from the ice. Such effects are limited in deep lakes but are can be an important factor controlling arsenic precipitation and mobility in ponds.

City dweller aspirations for cities of the future: How do environmental and personal wellbeing feature?

This paper explores city dweller aspirations for cities of the future in the context of global commitments to radically reduce carbon emissions by 2050; cities contribute the vast majority of these emissions and a growing bulk of theworld's population lives in cities. The particular challenge of creating a carbon reduced future in democratic countries is that the measures proposed must be acceptable to the electorate. Such acceptability is fostered if carbon reduced ways of living are also felt to bewellbeing maximising. Thus the objective of the paper is to explore what kinds of cities people aspire to live in, to ascertain whether these aspirations align with or undermine carbon reduced ways of living, as well as personal wellbeing. Using a novel free associative technique, city aspirations are found to cluster around seven themes, encompassing physical and social aspects. Physically, people aspire to a city with a range of services and facilities, green and blue spaces, efficient transport, beauty and good design. Socially, people aspire to a sense of community and a safe environment. An exploration of these themes reveals that only a minority of the participants' aspirations for cities relate to lowering carbon or environmental wellbeing. Far more consensual is emphasis on, and a particular vision of, aspirations that will bring personal wellbeing. Furthermore, city dweller aspirations align with evidence concerning factors that maximise personal wellbeing but, far less, with those that produce lowcarbonways of living. In order to shape a lower carbon future that city dwellers accept the potential convergence between environmental and personal wellbeing will need to be capitalised on: primarily aversion to pollution and enjoyment of communal green space.

Colonialism, political unconscious and cognitive mapping in the space of the film "Captain Phillips"

The purpose of this article has been made through a Marxist analysis of the US film "Captain Phillips" (PaulGreengrass, 2013), based on a true story. I have found how the evolution of capitalism in the West continuesto consolidate the belief reified in a historical and geographical superiority of the political and socioeconomicwestern models regarding Africa and Asia lowers models. At the same time, through categories like dialecticalmaterialism, criticism of diffusionist theory and application of cognitive mapping to large geopoliticalspaces located in most poor areas of the world, I have realized a remark about currently being articulatingthe political unconscious of working class in rich countries and the poor in poor countries, establishing arelationship between the ideological representation that takes an individual from his historical reality (ona scale that moves from local to global), and how he has developed a mental ability to escape of the responsibilityto make a critical review of what's happening around him in all areas. Finally, through physicalspace captured in the film, I have realized a materialist critique of globalized business process that takesplace through the carriage of goods, outlining spatial and cognitively limits of the mentality of our time, bothamong "winners"as among the "losers", based on the spatial movement of capital.

Model for integrates community tourism in Ecuador, case study Pastaza

The tourism industry globally has grown steadily in recent decades, showing a progressive interest oriented toward rural areas due to characteristics of tranquility, nature, biodiversity, traditions and culture. Therefore, such aspects should be preserved and can be leveraged through adequate strategic orientation. Within the framework of global tourism trends community tourism is among the options that arise in the tourism market, and is one that is more likely to grow in the future. In the case of Ecuador, community tourism has become more dynamic over the years since many of the natural reserves in the country are in the hands of indigenous communities. Sustainable tourism in this sense is concerned with the maintenance of ethnic, cultural and biological diversity of the country, and current projects and regulatory laws support its development. Therefore, the aim of this paper is to present a strategy for the integrated management of community tourism following the principles of cooperation and collaboration between stakeholders, this study focuses on the Amazon region of Ecuador, specifically the province of Pastaza, in respect to how community tourism contributes to local development

Genetics and Prognostication in Splenic Marginal Zone Lymphoma: Revelations from Deep Sequencing

Purpose: Mounting evidence supports the clinical significance of gene mutations and immunogenetic features in common mature B-cell malignancies.

Experimental Design: We undertook a detailed characterization of the genetic background of splenic marginal zone lymphoma (SMZL), using targeted resequencing and explored potential clinical implications in a multinational cohort of 175 patients with SMZL.

Results: We identified recurrent mutations in TP53 (16%), KLF2 (12%), NOTCH2 (10%), TNFAIP3 (7%), MLL2 (11%), MYD88 (7%), and ARID1A (6%), all genes known to be targeted by somatic mutation in SMZL. KLF2 mutations were early, clonal events, enriched in patients with del(7q) and IGHV1-2*04 B-cell receptor immunoglobulins, and were associated with a short median time to first treatment (0.12 vs. 1.11 years; P = 0.01). In multivariate analysis, mutations in NOTCH2 [HR, 2.12; 95% confidence interval (CI), 1.02–4.4; P = 0.044] and 100% germline IGHV gene identity (HR, 2.19; 95% CI, 1.05–4.55; P = 0.036) were independent markers of short time to first treatment, whereas TP53 mutations were an independent marker of short overall survival (HR, 2.36; 95 % CI, 1.08–5.2; P = 0.03).

Conclusions: We identify key associations between gene mutations and clinical outcome, demonstrating for the first time that NOTCH2 and TP53 gene mutations are independent markers of reduced treatment-free and overall survival, respectively.

Investigations on the structural, optical and magnetic properties of nanostructured cerium oxide in pure and doped forms and its polymer nanocomposites

In recent years, nanoscience and nanotechnology has emerged as one of the most important and exciting frontier areas of research interest in almost all fields of science and technology. This technology provides the path of many breakthrough changes in the near future in many areas of advanced technological applications. Nanotechnology is an interdisciplinary area of research and development. The advent of nanotechnology in the modern times and the beginning of its systematic study can be thought of to have begun with a lecture by the famous physicist Richard Feynman. In 1960 he presented a visionary and prophetic lecture at the meeting of the American Physical Society entitled “there is plenty of room at the bottom” where he speculated on the possibility and potential of nanosized materials. Synthesis of nanomaterials and nanostructures are the essential aspects of nanotechnology. Studies on new physical properties and applications of nanomaterials are possible only when materials are made available with desired size, morphology, crystal structure and chemical composition. Cerium oxide (ceria) is one of the important functional materials with high mechanical strength, thermal stability, excellent optical properties, appreciable oxygen ion conductivity and oxygen storage capacity. Ceria finds a variety of applications in mechanical polishing of microelectronic devices, as catalysts for three-way automatic exhaust systems and as additives in ceramics and phosphors. The doped ceria usually has enhanced catalytic and electrical properties, which depend on a series of factors such as the particle size, the structural characteristics, morphology etc. Ceria based solid solutions have been widely identified as promising electrolytes for intermediate temperature solid oxide fuel cells (SOFC). The success of many promising device technologies depends on the suitable powder synthesis techniques. The challenge for introducing new nanopowder synthesis techniques is to preserve high material quality while attaining the desired composition. The method adopted should give reproducible powder properties, high yield and must be time and energy effective. The use of a variety of new materials in many technological applications has been realized through the use of thin films of these materials. Thus the development of any new material will have good application potential if it can be deposited in thin film form with the same properties. The advantageous properties of thin films include the possibility of tailoring the properties according to film thickness, small mass of the materials involved and high surface to volume ratio. The synthesis of polymer nanocomposites is an integral aspect of polymer nanotechnology. By inserting the nanometric inorganic compounds, the properties of polymers can be improved and this has a lot of applications depending upon the inorganic filler material present in the polymer.

Health in Ireland: Key Trends 2015

Health in Ireland Key Trends gives us insights into trends in demographics, population health, hospital and primary care and health service employment and expenditure. The presentation of trend data over the last decade in the 2015 report highlights the many significant achievements that Ireland has made in terms of key outcomes relating to the health and wellbeing of the population. However, it also highlights the challenges that persist in terms of the accessibility of timely healthcare and in the context of financial constraints. In the last decade alone, there has been an increase of two and a half years in life expectancy. These gains are driven largely by reductions in mortality rates from principal causes of deaths such as those from heart disease and cancer. Another striking feature is the growth in the number of people aged over 65. Each year this cohort increases by 20,000 people. This trend is set to continue into the future and will have implications for future planning and health service delivery. Ireland will see the largest proportional increases in the population aged 85 years and older. Ageing of the population in conjunction with lifestyle-related health threats continue to present major challenges now and into the future in sustaining and further improving health and health services in Ireland. Although difficult to quantify, the contribution of modern health services to these improvements in health outcomes and in life expectancy have been significant. Ireland’s fertility rates are still among the highest in Europe but the birth rate has fallen to its lowest rate for the last decade.  However, Ireland currently has the highest proportion of children and young people in our population among EU countries.  

Digital collaborations and entrepreneurship – the role of shareconomy and crowdsourcing in the era of smart city

The thesis begins with the classical cooperation and transfers it to the digital world. This work gives a detailed overview of the young fields of research smart city, shareconomy and crowdsourcing and links these fields with entrepreneurship. The core research aim is the finding of connections between the research fields smart city, shareconomy and crowdsourcing and entrepreneurial activities and the specific fields of application, success factors and conditions for entrepreneurs. The thesis consists of seven peer-reviewed publications. Based on primary and secondary data, the existence of entrepreneurial opportunities in the fields of smart city, shareconomy and crowdsourcing could be confirmed. The first part (publications 1-3) of the thesis are literature reviews to secure the fundamental base for further research. This part consists of newly created definitions and an extreme sharpening of the research fields for the near future. In the second part of the thesis (publications 4-7), empirical field work (in-depth interviews with entrepreneurs) and quantitative analyses (fuzzy set/qualitative comparative analysis and binary logistic regression analysis) contribute to the field of research with additional new insights. Summarizing, the insights are multi-layered: theoretical (e.g. new definitions, sharpening of the research field), methodical (e.g. first time application of the fuzzy set/qualitative comparative analysis in the field of crowdfunding) and qualitative (first time application of in-depth interviews with entrepreneurs in the fields of smart city and shareconomy). The global research question could be answered: the link between entrepreneurship and smart city, shareconomy and crowdfunding could be confirmed, concrete fields of application could be identified and further developments could be touched upon. This work strongly contributes to the young fields of research through much-needed basic work, new qualitative approaches, innovative methods and new insights and offers opportunities for discussion, criticism and support for further research.