Multi-layered model of individual HIV infection progression and mechanisms of phenotypical expression

Cite as: Perrin, Dimitri (2008) Multi-layered model of individual HIV infection progression and mechanisms of phenotypical expression. PhD thesis, Dublin City University.

High-performance computing for data analytics

One of the main challenges in data analytics is that discovering structures and patterns in complex datasets is a computer-intensive task. Recent advances in high-performance computing provide part of the solution. Multicore systems are now more affordable and more accessible. In this paper, we investigate how this can be used to develop more advanced methods for data analytics. We focus on two specific areas: model-driven analysis and data mining using optimisation techniques.

Bloomsday: Copyright estates and cultural festivals

Copyright estates have been unduly empowered by the extension of the term of copyright protection in Europe, the United States, Australia and elsewhere. The Estate of the Irish novelist, James Joyce, has been particularly aggressive in policing his revived copyrights. The "keepers of the flame" have relied upon threats of legal action to discourage the production of derivative works based upon the canonical texts of the novelist. The Estate has also jealously guarded the reputation of the author by vetoing the use of his work in various scholarly productions. Most radically of all, the grandson Stephen Joyce threatened to take legal action to prevent the staging of "Rejoyce Dublin 2004", a festival celebrating the centenary of Bloomsday. In response, the Irish Parliament rushed through emergency legislation, entitled the Copyright and Related Rights (Amendment) Act 2004 (Ireland) to safeguard the celebrations. The legislation clarified that a person could place literary and artistic works on public exhibition, without breaching the copyright vested in such cultural texts. Arguably, though, the ad hoc legislation passed by the Irish Parliament is inadequate. The Estate of James Joyce remains free to exercise its suite of economic and moral rights to control the use and adaptation of works of the Irish novelist. It is contended that copyright law needs to be revised to promote the interests of libraries and other cultural institutions. Most notably, the defence of fair dealing should be expanded to allow for the transformative use of copyright works, particularly in respect of adaptations and derived works. There should be greater scope for compulsory licensing and crown acquisition of revived copyrights.

Teaching engineering tribology: Elements of assessment design for different learning styles

This study involves teaching engineering students concepts in lubrication engineering that are heavily dependent on mathematics. Excellent learning outcomes have been observed when assessment tasks are devised for a diversity of learning styles. Providing different pathways to knowledge reduces the probability that a single barrier halts progress towards the ultimate learning objective. The interdisciplinary nature of tribology can be used advantageously to tie together multiple elements of engineering to solve real physical problems—an approach that seems to benefit a majority of engineering students. To put this into practice, various assessment items were devised on the study of hydrodynamics, culminating in a project to provide a summative evaluation of the students’ learning achievement. A survey was also conducted to assess other aspects of students’ learning experiences under the headings: ‘perception of learning’ and ‘overall satisfaction’. High degrees of achievement and satisfaction were observed. An attempt has been made to identify the elements contributing to success so that they may be applied to other challenging concepts in engineering education.

Uncovering misconceptions through text analysis

Assessing students’ conceptual understanding of technical content is important for instructors as well as students to learn content and apply knowledge in various contexts. Concept inventories that identify possible misconceptions through validated multiple-choice questions are helpful in identifying a misconception that may exist, but do not provide a meaningful assessment of why they exist or the nature of the students’ understanding. We conducted a case study with undergraduate students in an electrical engineering course by testing a validated multiple-choice response concept inventory that we augmented with a component for students to provide written explanations for their multiple-choice selection. Results revealed that correctly chosen multiple-choice selections did not always match correct conceptual understanding for question testing a specific concept. The addition of a text-response to multiple-choice concept inventory questions provided an enhanced and meaningful assessment of students’ conceptual understanding and highlighted variables associated with current concept inventories or multiple choice questions.

Traces from elsewhere: Nomadism, artistic identity and contemporary dance in Ireland

This keynote presentation explores the connections between nomadism and artistic identity formation by interrogating the creativity that migration elicits and the narratives that surround it. It is further situated in the complex role that emigration has in Irish culture questioning whether contemporary dance in particular is emblematic of this socio-cultural phenomenon. These questions are anchored through descriptions of a creative project currently underway that draws together artists from Ireland and Australia to explore how we manage absence and presence in a globalized yet increasingly virtual world.

HER2 positive gastric and gastroesophageal adenocarcinoma; An Irish tertiary center experience

Background: Trastuzumab has been approved for patients with human epidermal growth factor receptor 2 (HER2) over expression and gene amplification metastatic gastric cancer. Here we present the prevalence of HER2 positive gastric cancer in an Irish population, the use of Trastuzumab in first line and beyond progression. Methods: The study was conducted in St James's Hospital, Dublin. A retrospective analysis of the date of patients with HER2 positive gastric cancer over a period of 3 years was carried out. Her2 positive was defined as immunohistochemistry (IHC) score of +3, of IHC score of +2 and increased gene copy number by fluorescence in situ hybridization (FISH). Overall survival was calculated from the day of initiation of treatment with Trastuzumab until death. Results: During the study period 140 patients with gastric and gastro-esophageal junction adenocarcinoma were treated. Out of those, 30 (21.4%) had HER2 positive disease. Among HER2 positive disease patients 18 (12.8%) were treated with first line Trastuzumab containing regimen with a median overall survival of 13 months. Nine (50%) developed progressive disease while on Trastuzumab and of those, 4 (22.2%) patients continued on Trastuzumab beyond progression, two (11.1%) of whom achieved stable disease and a prolonged survival. Conclusion: HER2 positivity rate in an Irish population with advanced gastric and gastro-esophageal junction adenocarcinoma is 21.4%. Treatment with Trastuzumab in the first line in combination with chemotherapy is a reasonable approach. Continuation of Trastuzumab beyond progression is a feasible strategy that requires further exploration.

Relationships in food chains: an empirical examination of trust, commitment and communication

This report derives from the EU funded research project “Key Factors Influencing Economic Relationships and Communication in European Food Chains” (FOODCOMM). The research consortium consisted of the following organisations: University of Bonn (UNI BONN), Department of Agricultural and Food Marketing Research (overall project co-ordination); Institute of Agricultural Development in Central and Eastern Europe (IAMO), Department for Agricultural Markets, Marketing and World Agricultural Trade, Halle (Saale), Germany; University of Helsinki, Ruralia Institute Seinäjoki Unit, Finland; Scottish Agricultural College (SAC), Food Marketing Research Team - Land Economy Research Group, Edinburgh and Aberdeen; Ashtown Food Research Centre (AFRC), Teagasc, Food Marketing Unit, Dublin; Institute of Agricultural & Food Economics (IAFE), Department of Market Analysis and Food Processing, Warsaw and Government of Aragon, Center for Agro-Food Research and Technology (CITA), Zaragoza, Spain. The aim of the FOODCOMM project was to examine the role (prevalence, necessity and significance) of economic relationships in selected European food chains and to identify the economic, social and cultural factors which influence co-ordination within these chains. The research project considered meat and cereal commodities in six different European countries (Finland, Germany, Ireland, Poland, Spain, UK/Scotland) and was commissioned against a background of changing European food markets. The research project as a whole consisted of seven different work packages. This report presents the results of qualitative research conducted for work package 5 (WP5) in the pig meat and rye bread chains in Finland. Ruralia Institute would like to give special thanks for all the individuals and companies that kindly gave up their time to take part in the study. Their input has been invaluable to the project. The contribution of research assistant Sanna-Helena Rantala was significant in the data gathering. FOODCOMM project was coordinated by the University of Bonn, Department of Agricultural and Food Market Research. Special thanks especially to Professor Monika Hartmann for acting as the project leader of FOODCOMM.

A New Full-diversity Criterion and Low-complexity STBCs with Partial Interference Cancellation Decoding

Recently, Guo and Xia gave sufficient conditions for an STBC to achieve full diversity when a PIC (Partial Interference Cancellation) or a PIC-SIC (PIC with Successive Interference Cancellation) decoder is used at the receiver. In this paper, we give alternative conditions for an STBC to achieve full diversity with PIC and PIC-SIC decoders, which are equivalent to Guo and Xia's conditions, but are much easier to check. Using these conditions, we construct a new class of full diversity PIC-SIC decodable codes, which contain the Toeplitz codes and a family of codes recently proposed by Zhang, Xu et. al. as proper subclasses. With the help of the new criteria, we also show that a class of PIC-SIC decodable codes recently proposed by Zhang, Shi et. al. can be decoded with much lower complexity than what is reported, without compromising on full diversity.

Improving query focused summarization using look-ahead strategy

Query focused summarization is the task of producing a compressed text of original set of documents based on a query. Documents can be viewed as graph with sentences as nodes and edges can be added based on sentence similarity. Graph based ranking algorithms which use 'Biased random surfer model' like topic-sensitive LexRank have been successfully applied to query focused summarization. In these algorithms, random walk will be biased towards the sentences which contain query relevant words. Specifically, it is assumed that random surfer knows the query relevance score of the sentence to where he jumps. However, neighbourhood information of the sentence to where he jumps is completely ignored. In this paper, we propose look-ahead version of topic-sensitive LexRank. We assume that random surfer not only knows the query relevance of the sentence to where he jumps but he can also look N-step ahead from that sentence to find query relevance scores of future set of sentences. Using this look ahead information, we figure out the sentences which are indirectly related to the query by looking at number of hops to reach a sentence which has query relevant words. Then we make the random walk biased towards even to the indirect query relevant sentences along with the sentences which have query relevant words. Experimental results show 20.2% increase in ROUGE-2 score compared to topic-sensitive LexRank on DUC 2007 data set. Further, our system outperforms best systems in DUC 2006 and results are comparable to state of the art systems.