Value-cognizant Speculative Concurrency Control

A problem with Speculative Concurrency Control algorithms and other common concurrency control schemes using forward validation is that committing a transaction as soon as it finishes validating, may result in a value loss to the system. Haritsa showed that by making a lower priority transaction wait after it is validated, the number of transactions meeting their deadlines is increased, which may result in a higher value-added to the system. SCC-based protocols can benefit from the introduction of such delays by giving optimistic shadows with high value-added to the system more time to execute and commit instead of being aborted in favor of other validating transactions, whose value-added to the system is lower. In this paper we present and evaluate an extension to SCC algorithms that allows for commit deferments.

Pinwheel Scheduling for Fault-tolerant Broadcast Disks in Real-time Database Systems

The design of programs for broadcast disks which incorporate real-time and fault-tolerance requirements is considered. A generalized model for real-time fault-tolerant broadcast disks is defined. It is shown that designing programs for broadcast disks specified in this model is closely related to the scheduling of pinwheel task systems. Some new results in pinwheel scheduling theory are derived, which facilitate the efficient generation of real-time fault-tolerant broadcast disk programs.

ImageRover: A Content-Based Image Browser for the World Wide Web

ImageRover is a search by image content navigation tool for the world wide web. To gather images expediently, the image collection subsystem utilizes a distributed fleet of WWW robots running on different computers. The image robots gather information about the images they find, computing the appropriate image decompositions and indices, and store this extracted information in vector form for searches based on image content. At search time, users can iteratively guide the search through the selection of relevant examples. Search performance is made efficient through the use of an approximate, optimized k-d tree algorithm. The system employs a novel relevance feedback algorithm that selects the distance metrics appropriate for a particular query.

Real-Time Mutable Broadcast Disks

There is an increased interest in using broadcast disks to support mobile access to real-time databases. However, previous work has only considered the design of real-time immutable broadcast disks, the contents of which do not change over time. This paper considers the design of programs for real-time mutable broadcast disks - broadcast disks whose contents are occasionally updated. Recent scheduling-theoretic results relating to pinwheel scheduling and pfair scheduling are used to design algorithms for the efficient generation of real-time mutable broadcast disk programs.

Generalized Methods for Discovering Frequent Poly-Regions in DNA

The problem of discovering frequent poly-regions (i.e. regions of high occurrence of a set of items or patterns of a given alphabet) in a sequence is studied, and three efficient approaches are proposed to solve it. The first one is entropy-based and applies a recursive segmentation technique that produces a set of candidate segments which may potentially lead to a poly-region. The key idea of the second approach is the use of a set of sliding windows over the sequence. Each sliding window covers a sequence segment and keeps a set of statistics that mainly include the number of occurrences of each item or pattern in that segment. Combining these statistics efficiently yields the complete set of poly-regions in the given sequence. The third approach applies a technique based on the majority vote, achieving linear running time with a minimal number of false negatives. After identifying the poly-regions, the sequence is converted to a sequence of labeled intervals (each one corresponding to a poly-region). An efficient algorithm for mining frequent arrangements of intervals is applied to the converted sequence to discover frequently occurring arrangements of poly-regions in different parts of DNA, including coding regions. The proposed algorithms are tested on various DNA sequences producing results of significant biological meaning.

Query-Sensitive Embeddings

A common problem in many types of databases is retrieving the most similar matches to a query object. Finding those matches in a large database can be too slow to be practical, especially in domains where objects are compared using computationally expensive similarity (or distance) measures. This paper proposes a novel method for approximate nearest neighbor retrieval in such spaces. Our method is embedding-based, meaning that it constructs a function that maps objects into a real vector space. The mapping preserves a large amount of the proximity structure of the original space, and it can be used to rapidly obtain a short list of likely matches to the query. The main novelty of our method is that it constructs, together with the embedding, a query-sensitive distance measure that should be used when measuring distances in the vector space. The term "query-sensitive" means that the distance measure changes depending on the current query object. We report experiments with an image database of handwritten digits, and a time-series database. In both cases, the proposed method outperforms existing state-of-the-art embedding methods, meaning that it provides significantly better trade-offs between efficiency and retrieval accuracy.

Online and Offline Character Recognition Using Alignment to Prototypes

Nearest neighbor classifiers are simple to implement, yet they can model complex non-parametric distributions, and provide state-of-the-art recognition accuracy in OCR databases. At the same time, they may be too slow for practical character recognition, especially when they rely on similarity measures that require computationally expensive pairwise alignments between characters. This paper proposes an efficient method for computing an approximate similarity score between two characters based on their exact alignment to a small number of prototypes. The proposed method is applied to both online and offline character recognition, where similarity is based on widely used and computationally expensive alignment methods, i.e., Dynamic Time Warping and the Hungarian method respectively. In both cases significant recognition speedup is obtained at the expense of only a minor increase in recognition error.

ARTMAP: Supervised Real-Time Learning and Classification of Nonstationary Data by a Self-Organizing Neural Network

This article introduces a new neural network architecture, called ARTMAP, that autonomously learns to classify arbitrarily many, arbitrarily ordered vectors into recognition categories based on predictive success. This supervised learning system is built up from a pair of Adaptive Resonance Theory modules (ARTa and ARTb) that are capable of self-organizing stable recognition categories in response to arbitrary sequences of input patterns. During training trials, the ARTa module receives a stream {a^(p)} of input patterns, and ARTb receives a stream {b^(p)} of input patterns, where b^(p) is the correct prediction given a^(p). These ART modules are linked by an associative learning network and an internal controller that ensures autonomous system operation in real time. During test trials, the remaining patterns a^(p) are presented without b^(p), and their predictions at ARTb are compared with b^(p). Tested on a benchmark machine learning database in both on-line and off-line simulations, the ARTMAP system learns orders of magnitude more quickly, efficiently, and accurately than alternative algorithms, and achieves 100% accuracy after training on less than half the input patterns in the database. It achieves these properties by using an internal controller that conjointly maximizes predictive generalization and minimizes predictive error by linking predictive success to category size on a trial-by-trial basis, using only local operations. This computation increases the vigilance parameter ρa of ARTa by the minimal amount needed to correct a predictive error at ARTb· Parameter ρa calibrates the minimum confidence that ARTa must have in a category, or hypothesis, activated by an input a^(p) in order for ARTa to accept that category, rather than search for a better one through an automatically controlled process of hypothesis testing. Parameter ρa is compared with the degree of match between a^(p) and the top-down learned expectation, or prototype, that is read-out subsequent to activation of an ARTa category. Search occurs if the degree of match is less than ρa. ARTMAP is hereby a type of self-organizing expert system that calibrates the selectivity of its hypotheses based upon predictive success. As a result, rare but important events can be quickly and sharply distinguished even if they are similar to frequent events with different consequences. Between input trials ρa relaxes to a baseline vigilance pa When ρa is large, the system runs in a conservative mode, wherein predictions are made only if the system is confident of the outcome. Very few false-alarm errors then occur at any stage of learning, yet the system reaches asymptote with no loss of speed. Because ARTMAP learning is self stabilizing, it can continue learning one or more databases, without degrading its corpus of memories, until its full memory capacity is utilized.

Micronutrient intakes and the role of nutritional supplements in the diets of Irish adults and pre-school children

To investigate micronutrient intakes and the role of nutritional supplements in the diets of Irish adults aged 18-64 years and pre-school children aged 1-4 years. Analysis is based on data from the National Adult Nutrition Survey (NANS) (n=1274) and the National Pre-School Nutrition Survey (NPNS) (n=500). Food and beverage intakes and nutritional supplement use were recorded using 4-day food records. Nutrients were estimated using WISP© which is based on McCance and Widdowson’s The Composition of Foods, 6thEd and the Irish Food Composition Database. “Meats”, “milk/yoghurt”, “breads”, “fruit/fruit juices” and “breakfast cereals” made important contributions to the intakes of a number of micronutrients. Micronutrient intakes were generally adequate, with the exception of iron (in adult females and 1 year olds) and vitamin D (in all population groups). For iron, zinc, copper and vitamin B6, up to 2% of adults had intakes that exceeded the upper limit (UL). Small proportions of children had intakes of zinc (11%), copper (2%), retinol (4%) and folic acid (5%) exceeding the UL. Nutritional supplements (predominantly multivitamin and/or mineral preparations) were consumed by 28% of adults and 20% of pre-school children. Among users, supplements were effective in reducing the % with inadequate intakes for vitamins A and D (both population groups) and iron (adult females only). Supplement users had a lower prevalence of inadequate intakes for vitamin A and iron compared to non-users. In adults only, users had a lower prevalence of inadequate intakes for magnesium, calcium and zinc, and displayed better compliance with dietary recommendations and lifestyle characteristics compared with non-users. There is poor compliance among women of childbearing age for the recommendation to take a supplement containing 400µg/day of folic acid. These findings are important for the development of nutrition policies and future recommendations for adults and pre-school children in Ireland and the EU.

Practice Links [Issue 45, December 2011]

Practice Links is a free e-publication for practitioners working in Irish social services, voluntary and nongovernmental sectors. Practice Links was created to enable practitioners to keep up-to-date with new publications, electronic resources and conference opportunities. Issue 45 unveils a new, regular section in the publication entitled Practice Signposts. This section aims to promote quality research- informed databases.

Practice Links [Issue 46, February 2012]

Practice Links is a free e-publication for practitioners working in Irish social services, voluntary and nongovernmental sectors. Practice Links was created to enable practitioners to keep up-to-date with new publications, electronic resources and conference opportunities. Issue 46 features information regarding databases to support practice as well as the latest research being conducted in the fields of youth empowerment programs and relevant podcasts.

The Viking age glass beads of Ireland and their North Atlantic context

Hitherto, the majority of studies which have included the discussion of Viking glass beads have mainly focused on the assemblages from individual sites, with limited use of known parallels. Exceptions to this include recent publications regarding the Icelandic material and Callmer’s 1977 catalogue of the finds from mainland Scandinavia, now over thirty years old. Analysis of these finds from Ireland was, for the most part, non-existent. The aim of this research is to address this lack of analysis within Ireland, while incorporating the wider context of the beads within the Viking North Atlantic. The research thus examines the use of glass beads of diagnostically Scandinavian manufacture and import found in Ireland, particularly in relation to their context and distribution. The history of research from Ireland as well as from across the Viking world is considered and explored throughout the thesis, with critique of methods and discussions used. Focussed analysis of both published and unpublished material detailing artefacts from Scandinavia (especially Vestfold), Britain, Iceland, the Faroe Islands and L’Anse aux Meadows is presented within the thesis in order to provide the greater picture for the core section of the thesis, the glass beads found in Ireland. Three appendices are included within Volume 2, databases of the glass beads under discussion from Ireland, the Vestfold region graves in Norway and the topsoil finds from the Kaupang trading place, also located within Vestfold. These appendices therefore represent the first-hand analysis of glass beads by the author. In total, this research represents the most up-to-date analysis of Viking glass beads from Ireland and presents a new look at the patterns of use, trade and interpersonal contact that affected the everyday lives of individuals living within Viking Age Ireland.

Functional genomics of motile commensal intestinal bacteria

Flagella confer upon bacteria the ability to move and are therefore organelles of significant bacteriological importance. The innate immune system has evolved to recognise flagellin, (the major protein component of the bacterial flagellar filament). Flagellate microbes can potentially stimulate the immune systems of mammals, and thus have significant immunomodulatory potential. The flagellum-biogenesis genotype and phenotype of Lactobacillus ruminis, an autochthonous intestinal commensal, was studied. The flagellum-biogenesis genotypes of motile enteric Eubacterium and Roseburia species were also investigated. Flagellin proteins were recovered from these commensal species, their amino-termini were sequenced and the proteins were found to be pro-inflammatory, as assessed by measurement of interleukin-8 (IL-8) secretion from human intestinal epithelial cell lines. For L. ruminis, this IL-8 secretion required signalling through Toll Like Receptor 5. A model for the regulation of flagellum-biogenesis in L. ruminis was inferred from transcriptomics data and bioinformatics analyses. Motility gene expression in this species may be under the control of a novel regulator, LRC_15730. Potential promoters for genes encoding flagellin proteins in the Eubacterium and Roseburia genomes analysed were inferred in silico. Relative abundances of the target Eubacterium and Roseburia species in the intestinal microbiota of 25 elderly individuals were determined. These species were found to be variably abundant in these individuals. Motility genes from these species were variably detected in the shotgun metagenome databases generated by the ELDERMET project. This suggested that a greater depth of sequencing, or improved evenness of sequencing, would be required to capture the full diversity of microbial functions for specific target or low abundance species in microbial communities by metagenomics. In summary, this thesis used a functional genomics approach to describe flagellum-mediated motility in selected Gram-positive commensal bacteria. The regulation of flagellum biosynthesis in these species, and the consequences of flagella expression from a host-interaction perspective were also considered.

The utility of survey and administrative data to generate information for research and outcomes-based oral health services development

The aim of this research, which focused on the Irish adult population, was to generate information for policymakers by applying statistical analyses and current technologies to oral health administrative and survey databases. Objectives included identifying socio-demographic influences on oral health and utilisation of dental services, comparing epidemiologically-estimated dental treatment need with treatment provided, and investigating the potential of a dental administrative database to provide information on utilisation of services and the volume and types of treatment provided over time. Information was extracted from the claims databases for the Dental Treatment Benefit Scheme (DTBS) for employed adults and the Dental Treatment Services Scheme (DTSS) for less-well-off adults, the National Surveys of Adult Oral Health, and the 2007 Survey of Lifestyle Attitudes and Nutrition in Ireland. Factors associated with utilisation and retention of natural teeth were analysed using count data models and logistic regression. The chi-square test and the student’s t-test were used to compare epidemiologically-estimated need in a representative sample of adults with treatment provided. Differences were found in dental care utilisation and tooth retention by Socio-Economic Status. An analysis of the five-year utilisation behaviour of a 2003 cohort of DTBS dental attendees revealed that age and being female were positively associated with visiting annually and number of treatments. Number of adults using the DTBS increased, and mean number of treatments per patient decreased, between 1997 and 2008. As a percentage of overall treatments, restorations, dentures, and extractions decreased, while prophylaxis increased. Differences were found between epidemiologically-estimated treatment need and treatment provided for those using the DTBS and DTSS. This research confirms the utility of survey and administrative data to generate knowledge for policymakers. Public administrative databases have not been designed for research purposes, but they have the potential to provide a wealth of knowledge on treatments provided and utilisation patterns.

Identification of RNA editing in the human exome and development of DARNED DatabaseSF

RNA editing is a biological phenomena that alters nascent RNA transcripts by insertion, deletion and/or substitution of one or a few nucleotides. It is ubiquitous in all kingdoms of life and in viruses. The predominant editing event in organisms with a developed central nervous system is Adenosine to Inosine deamination. Inosine is recognized as Guanosine by the translational machinery and reverse-transcriptase. In primates, RNA editing occurs frequently in transcripts from repetitive regions of the genome. In humans, more than 500,000 editing instances have been identified, by applying computational pipelines on available ESTs and high-throughput sequencing data, and by using chemical methods. However, the functions of only a small number of cases have been studied thoroughly. RNA editing instances have been found to have roles in peptide variants synthesis by non-synonymous codon substitutions, transcript variants by alterations in splicing sites and gene silencing by miRNAs sequence modifications. We established the Database of RNA EDiting (DARNED) to accommo-date the reference genomic coordinates of substitution editing in human, mouse and fly transcripts from published literatures, with additional information on edited genomic coordinates collected from various databases e.g. UCSC, NCBI. DARNED contains mostly Adenosine to Inosine editing and allows searches based on genomic region, gene ID, and user provided sequence. The Database is accessible at http://darned.ucc.ie RNA editing instances in coding region are likely to result in recoding in protein synthesis. This encouraged me to focus my research on the occurrences of RNA editing specific CDS and non-Alu exonic regions. By applying various filters on discrepancies between available ESTs and their corresponding reference genomic sequences, putative RNA editing candidates were identified. High-throughput sequencing was used to validate these candidates. All predicted coordinates appeared to be either SNPs or unedited.