Computing explanations for interactive constraint-based systems

Constraint programming has emerged as a successful paradigm for modelling combinatorial problems arising from practical situations. In many of those situations, we are not provided with an immutable set of constraints. Instead, a user will modify his requirements, in an interactive fashion, until he is satisfied with a solution. Examples of such applications include, amongst others, model-based diagnosis, expert systems, product configurators. The system he interacts with must be able to assist him by showing the consequences of his requirements. Explanations are the ideal tool for providing this assistance. However, existing notions of explanations fail to provide sufficient information. We define new forms of explanations that aim to be more informative. Even if explanation generation is a very hard task, in the applications we consider, we must manage to provide a satisfactory level of interactivity and, therefore, we cannot afford long computational times. We introduce the concept of representative sets of relaxations, a compact set of relaxations that shows the user at least one way to satisfy each of his requirements and at least one way to relax them, and present an algorithm that efficiently computes such sets. We introduce the concept of most soluble relaxations, maximising the number of products they allow. We present algorithms to compute such relaxations in times compatible with interactivity, achieving this by indifferently making use of different types of compiled representations. We propose to generalise the concept of prime implicates to constraint problems with the concept of domain consequences, and suggest to generate them as a compilation strategy. This sets a new approach in compilation, and allows to address explanation-related queries in an efficient way. We define ordered automata to compactly represent large sets of domain consequences, in an orthogonal way from existing compilation techniques that represent large sets of solutions.

Molecular genetic analysis of DNA alterations in Irish colorectal cancer

Colorectal cancer is the most common cause of death due to malignancy in nonsmokers in the western world. In 1995 there were 1,757 cases of colon cancer in Ireland. Most colon cancer is sporadic, however ten percent of cases occur where there is a previous family history of the disease. In an attempt to understand the tumorigenic pathway in Irish colon cancer patients, a number of genes associated with colorectal cancer development were analysed in Irish sporadic and HNPCC colon cancer patients. The hereditary forms of colon cancer include Familial adenomatous polyposis coli (FAP) and Hereditary Non-Polyposis Colon Cancer (HNPCC). Genetic analysis of the gene responsible for FAP, (the APC gene) has been previously performed on Irish families, however the genetic analysis of HNPCC families is limited. In an attempt to determine the mutation spectrum in Irish HNPCC pedigrees, the hMSH2 and hMLHl mismatch repair genes were screened in 18 Irish HNPCC families. Using SSCP analysis followed by DNA sequencing, five mutations were identified, four novel and a previously reported mutation. In families where a mutation was detected, younger asyptomatic members were screened for the presence of the predisposing mutation (where possible). Detection of mutations is particularly important for the identification of at risk individuals as the early diagnosis of cancer can vastly improve the prognosis. The sensitive and efficient detection of multiple different mutations and polymorphisms in DNA is of prime importance for genetic diagnosis and the identification of disease genes. A novel mutation detection technique has recently been developed in our laboratory. In order to assess the efficacy and application of the methodology in the analysis of cancer associated genes, a protocol for the analysis of the K-ras gene was developed and optimised. Matched normal and tumour DNA from twenty sporadic colon cancer patients was analysed for K-ras mutations using the Glycosylase Mediated Polymorphism Detection technique. Five mutations of the K-ras gene were detected using this technology. Sequencing analysis verified the presence of the mutations and SSCP analysis of the same samples did not identify any additional mutations. The GMPD technology proved to be highly sensitive, accurate and efficient in the identification of K-ras gene mutations. In order to investigate the role of the replication error phenomenon in Irish colon cancer, 3 polyA tract repeat loci were analysed. The repeat loci included a 10 bp intragenic repeat of the TGF-β-RII gene. TGF-β-RII is involved in the TGF-β epithelial cell growth pathway and mutation of the gene is thought to play a role in cell proliferation and tumorigenesis. Due to the presence of a repeat sequence within the gene, TGFB-RII defects are associated with tumours that display the replication error phenomenon. Analysis of the TGF-β-RII 10 bp repeat failed to identify mutations in any colon cancer patients. Analysis of the Bat26 and Bat 40 polyA repeat sequences in the sporadic and HNPCC families revealed that instability is associated with HNPCC tumours harbouring mismatch repair defects and with 20 % of sporadic colon cancer tumours. No correlation between K-ras gene mutations and the RER+ phenotype was detected in sporadic colon cancer tumours.

Deer forests, game shooting and landed estates in the South West of Ireland, 1840 - 1970

This thesis is concentrated on the historical aspects of the elitist field sports of deer stalking and game shooting, as practiced by four Irish landed ascendancy families in the south west of Ireland. Four great estates were selected for study. Two of these were, by Irish standards, very large: the Kenmare estate of over 136,000 acres in the ownership of the Roman Catholic Earls of Kenmare, and the Herbert estate of over 44,000 acres in the ownership of the Protestant Herbert family. The other two were, in relative terms, small: the Grehan estate of c.7,500 acres in the ownership of the Roman Catholic Grehan family, and the Godfrey estate of c.5,000 acres, in the ownership of the Protestant Barons Godfrey. This mixture of contrasting estate size, owner's religions, nobleman, minor aristocrat and untitled gentry should, it is argued, yield a diversity of the field sports and lifestyles of their owners, and go some way to assess the contributions, good or bad, they have bequeathed to modern Ireland. Equally, it should help in assessing what importance, if any, applied to hunting. In this context, hunting is here used in its broadest meaning, and includes deer stalking and game shooting, as well as hunting with dogs and hounds on foot and horseback. Where a specific type of hunting is involved, it is so described; for example, fox hunting, stag hunting, hare hunting. Similarly, the term game is sometimes used in sporting literature to encompass all species of quarry killed, and can include deer, ground game (hares and rabbits), waterfowl, and various species of game birds. Where it refers to specific species, these are so described; for example grouse, pheasants, woodcork, wild duck, etc. Since two of these estates - the Kenmare and Herbert - each created a deer forest, unique in mid-19th century Ireland, they form the core study estates; the two smaller estates serve as comparative studies. And, equally unique, as these two larger estates held the only remnant population of native Irish red deer, the survival of that herd itself forms a concomitant core area of analysis. The numerary descriptions applied to these animals in popular literature are critically reassessed against prime source historical evidence, as are the so-called deer forest 'clearances'. The core period, 1840 to 1970, is selected as the seminal period, spanning 130 years, from the creation of the deer forests to when a fundamental change in policy and administration was introduced by the state. Comparison is made with similar estates elsewhere, in Britain and especially in Scotland. Their influence on the Irish methods and style of hunting is historically examined.

The brand-orientated play-community: toxic play in the marketplace

This ethnographic study makes a number of original contributions to the consumer identity projects and the marketplace cultures dimensions of consumer culture theory research. This study introduces the notion of the brand-orientated play-community, a novel consumption community form, which displays, as locus, a desire to play. This contributes to our understanding of the fluid relationship between subcultures of consumption, consumer tribes, and brand community. It was found that the brand-orientated play-community’s prime celebration, conceptualised as the ‘branded carnival’, displays characteristics of the archetypal carnival. The community access carnivalistic life and a world-upside-down ethos via the use and misuse of marketplace resources. The branded carnival is further supported by the community’s enactment of ‘toxic play’, which entails abnormal alcohol consumption, black market illegal resources, edgework activities, hegemonic masculinity and upsetting the public. This play-community is discussed in terms of a hyper-masculine playpen, as the play enacted has a direct relationship with the enactment of strong masculine roles. It was found that male play-ground members enact the extremes of contrasting masculine roles as a means to subvert the calculated and sedate ‘man-of-action-hero’ synthesis. Carnivals are unisex, and hence, women have begun entering the play-ground. Female members have successfully renegotiated their role within the community, from playthings to players – they have achieved player equality, which within the liminoid zone is more powerful than gender equality. However, while toxic play is essential to the maintenance of collective identity within the culture so too is the more serious form of play: the toxic sport of professional beer pong. The author conceptualises beer pong as a ‘toxic sport’, as it displays the contradictory play foundations of agon and corrupt ilinx: this is understood as a milestone step in the emergence of the postmodern sport era, in which spontaneity and the carnivalesque will dominate.

Isolation, characterization, and functional assessment of novel smooth muscle like stem progenitors

Vascular smooth muscle cells (VSMC) are one of the key players in the pathogenesis of cardiovascular diseases. The origin of neointimal VSMC has thus become a prime focus of research. VSMC originate from multiple progenitors cell types. In embryo the well-defined sources of VSMC include; neural crest cells, proepicardial cells and EPC. In adults, though progenitor cells from bone marrow (BM), circulation and tissues giving rise to SMC have been identified, no progress has been made in terms of isolating highly proliferative clonal population of adult stem cells with potential to differentiate into SMC. Smooth muscle like stem progenitor cells (SMSPC) were isolated from cardiopulmonary bypass filters of adult patients undergoing CABG. Rat SMSPC have previously been isolated by our group from the bone marrow of Fischer rats and also from the peripheral blood of monocrotaline induced pulmonary hypertension (MCT-PHTN) animal model. Characterization of novel SMSPC exhibited stem cell characteristics and machinery for differentiation into SMC. The expression of Isl-1 on SMSPC provided unique molecular identity to these circulating stem progenitor cells. The functional potential of SMSPC was determined by monitoring adoptive transfer of GFP+ SMSPC in rodent models of vascular injury; carotid injury and MCT-PHTN. The participation of SMSPC in vascular pathology was confirmed by quantifying the peripheral blood, and engrafted levels of SMSPC using RT-PCR. In terms of translating into clinical practice, SMSPC could be a good tool for detecting the atherosclerotic plaque burden. The current study demonstrates the existence of novel adult stem progenitor cells in circulation, with the potential role in vascular pathology.

Molecular and cellular aspects of the SREBP pathway

The SREBP (sterol response element binding proteins) transcription factors are central to regulating de novo biosynthesis of cholesterol and fatty acids. The SREBPs are regulated by retention or escape from the ER to the Golgi where they are proteolytically cleaved into active forms. The SREBP cleavage activating protein (SCAP) and the INSIG proteins are essential in this regulatory process. The aim of this thesis is to further characterise the molecular and cellular aspects surrounding regulation of SREBP processing. SREBP and SCAP are known to interact via their carboxy-terminal regulatory domains (CTDs) but this interaction is poorly characterised. Significant steps were achieved in this thesis towards specific mapping of the interaction site. These included cloning and over expression and partial purification of tagged SREBP1 and SREBP2 CTDs and probing of a SCAP peptide array with the CTDs. Results from the SREBP2 probing were difficult to interpret due to insolubility issues with the protein, however, probing with SREBP1 revealed five potential binding sites which were detected reproducibly. Further research is necessary to overcome SREBP2 insolubility issues and to confirm the identified SREBP1 interaction site(s) on SCAP. INSIG1 has a central role in regulating SREBP processing and in regulating stability of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), a rate limiting enzyme in cholesterol biosynthesis. There are two protein isoforms of human INSIG1 produced through the use of two in-frame alternative start sites. Bioinformatic analysis indicated that the presence of two in-frame start sites within the 5-prime region of INSIG1 mRNA is highly conserved and that production of two isoforms of INSIG1is likely a conserved event. Functional differences between these two isoforms were explored. No difference in either the regulation of SREBP processing or HMGCR degradation between the INSIG1 isoforms was observed and the functional significance of the two isoforms is as yet unclear. The final part of this thesis focused on enhancing the cytotoxicity of statins by targeted inhibition of SREBP processing by oxysterols. Statins have significant potential as anti-cancer agents as they inhibit the activity of HMGCR leading to a deficiency in mevalonate which is essential for cell survival. The levels of HMGCR fluctuate widely due to cholesterol feedback of SREBP processing. The relationship between sterol feedback and statin mediated cell death was investigated in depth in HeLa cells. Down regulation of SREBP processing by sterols significantly enhanced the efficacy of statin mediated cell death. Investigation of sterol feedback in additional cancer cell lines showed that sterol feedback was absent in cell lines A- 498, DU-145, MCF-7 and MeWo but was present in cell lines HT-29, HepG2 and KYSE-70. In the latter inhibition of SREBP processing using oxysterols significantly enhanced statin cytotoxicity. The results indicate that this approach is valid to enhance statin cytotoxicity in cancer cells, but may be limited by deregulation of SREBP processing and off target effects of statins, which were observed for some of the cancer cell lines screened.

Exploring alternatives for milk quality improvement and more efficient dairy production in a smallholder farming context – case study: Mantaro Valley (Peru)

Consumer demand is revolutionizing the way products are being produced, distributed and marketed. In relation to the dairy sector in developing countries, aspects of milk quality are receiving more attention from both society and the government. However, milk quality management needs to be better addressed in dairy production systems to guarantee the access of stakeholders, mainly small-holders, into dairy markets. The present study is focused on an analysis of the interaction of the upstream part of the dairy supply chain (farmers and dairies) in the Mantaro Valley (Peruvian central Andes), in order to understand possible constraints both stakeholders face implementing milk quality controls and practices; and evaluate “ex-ante” how different strategies suggested to improve milk quality could affect farmers and processors’ profits. The analysis is based on three complementary field studies conducted between 2012 and 2013. Our work has shown that the presence of a dual supply chain combining both formal and informal markets has a direct impact on dairy production at the technical and organizational levels, affecting small formal dairy processors’ possibilities to implement contracts, including agreements on milk quality standards. The analysis of milk quality management from farms to dairy plants highlighted the poor hygiene in the study area, even when average values of milk composition were usually high. Some husbandry practices evaluated at farm level demonstrated cost effectiveness and a big impact on hygienic quality; however, regular application of these practices was limited, since small-scale farmers do not receive a bonus for producing hygienic milk. On the basis of these two results, we co-designed with formal small-scale dairy processors a simulation tool to show prospective scenarios, in which they could select their best product portfolio but also design milk payment systems to reward farmers’ with high milk quality performances. This type of approach allowed dairy processors to realize the importance of including milk quality management in their collection and manufacturing processes, especially in a context of high competition for milk supply. We concluded that the improvement of milk quality in a smallholder farming context requires a more coordinated effort among stakeholders. Successful implementation of strategies will depend on the willingness of small-scale dairy processors to reward farmers producing high milk quality; but also on the support from the State to provide incentives to the stakeholders in the formal sector.

Investigations into the cellular and molecular changes in the amygdala in models of temporal lobe epilepsy and maternal immune activation

The amygdala is a limbic structure that is involved in many of our emotions and processing of these emotions such as fear, anger and pleasure. Conditions such as anxiety, autism, and also epilepsy, have been linked to abnormal functioning of the amygdala, owing to improper neurodevelopment or damage. This thesis investigated the cellular and molecular changes in the amygdala in models of temporal lobe epilepsy (TLE) and maternal immune activation (MIA). The kainic acid (KA) model of temporal lobe epilepsy (TLE) was used to induce Ammon’s-horn sclerosis (AHS) and to investigate behavioural and cytoarchitectural changes that occur in the amygdala related to Neuropeptide Y1 receptor expression. Results showed that KA-injected animals showed increased anxiety-like behaviours and displayed histopathological hallmarks of AHS including CA1 ablation, granule cell dispersion, volume reduction and astrogliosis. Amygdalar volume and neuronal loss was observed in the ipsilateral nuclei which was accompanied by astrogliosis. In addition, a decrease in Y1 receptor expressing cells in the ipsilateral CA1 and CA3 sectors of the hippocampus, ipsi- and contralateral granule cell layer of the dentate gyrus and ipsilateral central nucleus of the amygdala was found, consistent with a reduction in Y1 receptor protein levels. The results suggest that plastic changes in hippocampal and/or amygdalar Y1 receptor expression may negatively impact anxiety levels. Gamma-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the brain and tight regulation and appropriate control of GABA is vital for neurochemical homeostasis. GABA transporter-1 (GAT-1) is abundantly expressed by neurones and astrocytes and plays a key role in GABA reuptake and regulation. Imbalance in GABA homeostasis has been implicated in epilepsy with GAT-1 being an attractive pharmacological target. Electron microscopy was used to examine the distribution, expression and morphology of GAT-1 expressing structures in the amygdala of the TLE model. Results suggest that GAT-1 was preferentially expressed on putative axon terminals over astrocytic processes in this TLE model. Myelin integrity was examined and results suggested that in the TLE model myelinated fibres were damaged in comparison to controls. Synaptic morphology was studied and results suggested that asymmetric (excitatory) synapses occurred more frequently than symmetric (inhibitory) synapses in the TLE model in comparison to controls. This study illustrated that the amygdala undergoes ultrastructural alterations in this TLE model. Maternal immune activation (MIA) is a risk factor for neurodevelopmental disorders such as autism, schizophrenia and also epilepsy. MIA was induced at a critical window of amygdalar development at E12 using bacterial mimetic lipopolysaccharide (LPS). Results showed that MIA activates cytokine, toll-like receptor and chemokine expression in the fetal brain that is prolonged in the postnatal amygdala. Inflammation elicited by MIA may prime the fetal brain for alterations seen in the glial environment and this in turn have deleterious effects on neuronal populations as seen in the amygdala at P14. These findings may suggest that MIA induced during amygdalar development may predispose offspring to amygdalar related disorders such as heightened anxiety, fear impairment and also neurodevelopmental disorders.

Insertion of metal oxides into block copolymer nanopatterns as robust etch masks for nanolithography

Directed self-assembly (DSA) of block copolymers (BCPs) is a prime candidate to further extend dimensional scaling of silicon integrated circuit features for the nanoelectronic industry. Top-down optical techniques employed for photoresist patterning are predicted to reach an endpoint due to diffraction limits. Additionally, the prohibitive costs for “fabs” and high volume manufacturing tools are issues that have led the search for alternative complementary patterning processes. This thesis reports the fabrication of semiconductor features from nanoscale on-chip etch masks using “high χ” BCP materials. Fabrication of silicon and germanium nanofins via metal-oxide enhanced BCP on-chip etch masks that might be of importance for future Fin-field effect transistor (FinFETs) application are detailed.