The rapid assignment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group-specific fingerprints

Danny S. Tuckwell, Matthew J. Nicholson, Christopher S. McSweeney, Michael K. Theodorou and Jayne L. Brookman (2005). The rapid assignment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group-specific fingerprints. Microbiology, 151 (5) pp.1557-1567 Sponsorship: BBSRC / Stapledon Memorial Trust RAE2008

Czynniki glebowe w infekcji trawy mannicy odstającej (Puccinellia distans) endofitycznym grzybem Epichloё typhina: określenie ich roli z zastosowaniem analiz przestrzennych

Wydział Biologii

Automated Placement of Cameras in a Floorplan to Satisfy Task-Specific Constraints

In many multi-camera vision systems the effect of camera locations on the task-specific quality of service is ignored. Researchers in Computational Geometry have proposed elegant solutions for some sensor location problem classes. Unfortunately, these solutions utilize unrealistic assumptions about the cameras' capabilities that make these algorithms unsuitable for many real-world computer vision applications: unlimited field of view, infinite depth of field, and/or infinite servo precision and speed. In this paper, the general camera placement problem is first defined with assumptions that are more consistent with the capabilities of real-world cameras. The region to be observed by cameras may be volumetric, static or dynamic, and may include holes that are caused, for instance, by columns or furniture in a room that can occlude potential camera views. A subclass of this general problem can be formulated in terms of planar regions that are typical of building floorplans. Given a floorplan to be observed, the problem is then to efficiently compute a camera layout such that certain task-specific constraints are met. A solution to this problem is obtained via binary optimization over a discrete problem space. In preliminary experiments the performance of the resulting system is demonstrated with different real floorplans.

Automated Camera Layout to Satisfy Task-Specific and Floorplan-Specific Coverage Requirements

In many multi-camera vision systems the effect of camera locations on the task-specific quality of service is ignored. Researchers in Computational Geometry have proposed elegant solutions for some sensor location problem classes. Unfortunately, these solutions utilize unrealistic assumptions about the cameras' capabilities that make these algorithms unsuitable for many real-world computer vision applications: unlimited field of view, infinite depth of field, and/or infinite servo precision and speed. In this paper, the general camera placement problem is first defined with assumptions that are more consistent with the capabilities of real-world cameras. The region to be observed by cameras may be volumetric, static or dynamic, and may include holes that are caused, for instance, by columns or furniture in a room that can occlude potential camera views. A subclass of this general problem can be formulated in terms of planar regions that are typical of building floorplans. Given a floorplan to be observed, the problem is then to efficiently compute a camera layout such that certain task-specific constraints are met. A solution to this problem is obtained via binary optimization over a discrete problem space. In experiments the performance of the resulting system is demonstrated with different real floorplans.

An Efficient User-Level Shared Memory Mechanism for Application-Specific Extensions

This paper focuses on an efficient user-level method for the deployment of application-specific extensions, using commodity operating systems and hardware. A sandboxing technique is described that supports multiple extensions within a shared virtual address space. Applications can register sandboxed code with the system, so that it may be executed in the context of any process. Such code may be used to implement generic routines and handlers for a class of applications, or system service extensions that complement the functionality of the core kernel. Using our approach, application-specific extensions can be written like conventional user-level code, utilizing libraries and system calls, with the advantage that they may be executed without the traditional costs of scheduling and context-switching between process-level protection domains. No special hardware support such as segmentation or tagged translation look-aside buffers (TLBs) is required. Instead, our ``user-level sandboxing'' mechanism requires only paged-based virtual memory support, given that sandboxed extensions are either written by a trusted source or are guaranteed to be memory-safe (e.g., using type-safe languages). Using a fast method of upcalls, we show how our mechanism provides significant performance improvements over traditional methods of invoking user-level services. As an application of our approach, we have implemented a user-level network subsystem that avoids data copying via the kernel and, in many cases, yields far greater network throughput than kernel-level approaches.

Dopaminergic and Non-Dopaminergic Value Systems in Conditioning and Outcome-Specific Revaluation

Animals are motivated to choose environmental options that can best satisfy current needs. To explain such choices, this paper introduces the MOTIVATOR (Matching Objects To Internal Values Triggers Option Revaluations) neural model. MOTIVATOR describes cognitiveemotional interactions between higher-order sensory cortices and an evaluative neuraxis composed of the hypothalamus, amygdala, and orbitofrontal cortex. Given a conditioned stimulus (CS), the model amygdala and lateral hypothalamus interact to calculate the expected current value of the subjective outcome that the CS predicts, constrained by the current state of deprivation or satiation. The amygdala relays the expected value information to orbitofrontal cells that receive inputs from anterior inferotemporal cells, and medial orbitofrontal cells that receive inputs from rhinal cortex. The activations of these orbitofrontal cells code the subjective values of objects. These values guide behavioral choices. The model basal ganglia detect errors in CS-specific predictions of the value and timing of rewards. Excitatory inputs from the pedunculopontine nucleus interact with timed inhibitory inputs from model striosomes in the ventral striatum to regulate dopamine burst and dip responses from cells in the substantia nigra pars compacta and ventral tegmental area. Learning in cortical and striatal regions is strongly modulated by dopamine. The model is used to address tasks that examine food-specific satiety, Pavlovian conditioning, reinforcer devaluation, and simultaneous visual discrimination. Model simulations successfully reproduce discharge dynamics of known cell types, including signals that predict saccadic reaction times and CS-dependent changes in systolic blood pressure.

Task-Irrelevant Perceptual Learning Specific to the Contrast Polarity of Motion Stimuli

Studies of perceptual learning have focused on aspects of learning that are related to early stages of sensory processing. However, conclusions that perceptual learning results in low-level sensory plasticity are of great controversy, largely because such learning can often be attributed to plasticity in later stages of sensory processing or in the decision processes. To address this controversy, we developed a novel random dot motion (RDM) stimulus to target motion cells selective to contrast polarity, by ensuring the motion direction information arises only from signal dot onsets and not their offsets, and used these stimuli in conjunction with the paradigm of task-irrelevant perceptual learning (TIPL). In TIPL, learning is achieved in response to a stimulus by subliminally pairing that stimulus with the targets of an unrelated training task. In this manner, we are able to probe learning for an aspect of motion processing thought to be a function of directional V1 simple cells with a learning procedure that dissociates the learned stimulus from the decision processes relevant to the training task. Our results show learning for the exposed contrast polarity and that this learning does not transfer to the unexposed contrast polarity. These results suggest that TIPL for motion stimuli may occur at the stage of directional V1 simple cells.

Pressure induced anisotropy of electrical conductivity in polycrystalline molybdenum disulfide

Anisotropic specimens of MoS2 are obtained by pressing the microcrystalline powder into special die. This inelastic compression results in a rearrangement of the disulfide micro platelets observed by Atomic Force Microscopy and reflected in the macroscopic anisotropy in electrical conductivity in these samples. The conductivity measured parallel and perpendicular to the direction of applied pressure exhibits an anisotropy factor of ∼10 at 1 GPa. This behaviour of the conductivity as a function of applied pressure is explained as the result of the simultaneous influence of a rearrangement of the micro platelets in the solid and the change of the inter-grain distances.

Hazard and early warning analysis based on domain specific modeling technologies

An aim of proactive risk management strategies is the timely identification of safety related risks. One way to achieve this is by deploying early warning systems. Early warning systems aim to provide useful information on the presence of potential threats to the system, the level of vulnerability of a system, or both of these, in a timely manner. This information can then be used to take proactive safety measures. The United Nation’s has recommended that any early warning system need to have four essential elements, which are the risk knowledge element, a monitoring and warning service, dissemination and communication and a response capability. This research deals with the risk knowledge element of an early warning system. The risk knowledge element of an early warning system contains models of possible accident scenarios. These accident scenarios are created by using hazard analysis techniques, which are categorised as traditional and contemporary. The assumption in traditional hazard analysis techniques is that accidents are occurred due to a sequence of events, whereas, the assumption of contemporary hazard analysis techniques is that safety is an emergent property of complex systems. The problem is that there is no availability of a software editor which can be used by analysts to create models of accident scenarios based on contemporary hazard analysis techniques and generate computer code that represent the models at the same time. This research aims to enhance the process of generating computer code based on graphical models that associate early warning signs and causal factors to a hazard, based on contemporary hazard analyses techniques. For this purpose, the thesis investigates the use of Domain Specific Modeling (DSM) technologies. The contributions of this thesis is the design and development of a set of three graphical Domain Specific Modeling languages (DSML)s, that when combined together, provide all of the necessary constructs that will enable safety experts and practitioners to conduct hazard and early warning analysis based on a contemporary hazard analysis approach. The languages represent those elements and relations necessary to define accident scenarios and their associated early warning signs. The three DSMLs were incorporated in to a prototype software editor that enables safety scientists and practitioners to create and edit hazard and early warning analysis models in a usable manner and as a result to generate executable code automatically. This research proves that the DSM technologies can be used to develop a set of three DSMLs which can allow user to conduct hazard and early warning analysis in more usable manner. Furthermore, the three DSMLs and their dedicated editor, which are presented in this thesis, may provide a significant enhancement to the process of creating the risk knowledge element of computer based early warning systems.

A post-structuralist analysis of Irish youth crime prevention policy with specific emphasis on the Garda youth diversion projects

Garda Youth Diversion Projects (GYDPs) have since their beginnings in the early 1990s gained an increasingly important role and now constitute a central feature of Irish youth justice provision. Managed by the Irish Youth Justice Service and implemented by the Gardai and a variety of youth work organisations as well as independent community organisations, GYDPs are located at the crossroads of welfarist and corporatist approaches to youth justice, combining diversionary and preventative aspects in their work. To date, these projects have been subjected to very little systematic analysis and they have thus largely escaped critical scrutiny. To address this gap, this thesis locates the analysis of GYDP policy and practice within a post-structuralist theoretical framework and deploys discourse analysis primarily based on the work of Michel Foucault. It makes visible the official youth crime prevention and GYDP policy discourses and identifies how official discourses relating to youth crime prevention, young people and their offending behaviour, are drawn upon, negotiated, rejected or re-contextualised by project workers and JLOs. It also lays bare how project workers and JLOs draw upon a variety of other discourses, resulting in multi-layered, complex and sometimes contradictory constructions of young people, their offending behaviour and corresponding interventions. At a time when the projects are undergoing significant changes in terms of their repositioning to operate as the support infrastructure underpinning the statutory Garda Youth Diversion Programme, the thesis traces the discursive shifts and the implications for practice that are occurring as the projects move away from a youth work orientation towards a youth justice orientation. A key contribution of this thesis is the insight it provides into how young people and their families are being constituted in individualising and sometimes pathologising ways in GYDP discourses and practices. It reveals the part played by the GYDP intervention in favouring individual and narrow familial causes of offending behaviour while broader societal contexts are sidelined. By explicating the very assumptions upon which contemporary youth crime prevention policy, as well as GYDP policy and practice are based, this thesis offers a counterpoint to the prevailing evidence-based agenda of much research in the field of Irish youth justice theory and youth studies more generally. Rather, it encourages the reader to take a step back and examine some of the most fundamental and unquestioned assumptions about the construction of young people, their offending behaviour and ways of addressing this, in contemporary Irish youth crime prevention policy and practice.

Cereal products for specific dietary requirements. Evaluation and improvement of technological and nutritional properties of gluten free raw materials and end products

Coeliac disease is one of the most common food intolerances worldwide and at present the gluten free diet remains the only suitable treatment. A market overview conducted as part of this thesis on nutritional and sensory quality of commercially available gluten free breads and pasta showed that improvements are necessary. Many products show strong off-flavors, poor mouthfeel and reduced shelf-life. Since the life-long avoidance of the cereal protein gluten means a major change to the diet, it is important to also consider the nutritional value of products intending to replace staple foods such as bread or pasta. This thesis addresses this issue by characterising available gluten free cereal and pseudocereal flours to facilitate a better raw material choice. It was observed that especially quinoa, buckwheat and teff are high in essential nutrients, such as protein, minerals and folate. In addition the potential of functional ingredients such as inulin, β-glucan, HPMC and xanthan to improve loaf quality were evaluated. Results show that these ingredients can increase loaf volume and reduce crumb hardness as well as rate of staling but that the effect diverges strongly depending on the bread formulation used. Furthermore, fresh egg pasta formulations based on teff and oat flour were developed. The resulting products were characterised regarding sensory and textural properties as well as in vitro digestibility. Scanning electron and confocal laser scanning microscopy was used throughout the thesis to visualise structural changes occurring during baking and pasta making

The expression and regulation of pregnancy-specific glycoproteins in the mouse

Pregnancy-Specific Glycoproteins (PSG) are the most abundant fetally expressed proteins in the maternal bloodstream at term. This multigene family are immunoglobulin superfamily members and are predominantly expressed in the syncytiotrophoblast of human placenta and in giant cells and spongiotrophoblast of rodent placenta. PSGs are encoded by seventeen genes in the mouse and ten genes in the human. Little is known about the function of this gene family, although they have been implicated in immune modulation and angiogenesis through the induction of cytokines such as IL-10 and TGFβ1 in monocytes, and more recently, have been shown to inhibit the platelet-fibrinogen interaction. I provide new information concerning the evolution of the murine Psg genomic locus structure and organisation, through the discovery of a recent gene inversion event of Psg22 within the major murine Psg cluster. In addition to this, I have performed an examination of the expression patterns of individual Psg genes in placental and non-placental tissues. This study centres on Psg22, which is the most abundant murine Psg transcript detected in the first half of pregnancy. A novel alternative splice variant transcript of Psg22 lacking the protein N1-domain was discovered, and similar to the full length isoform induces TGFβ1 in macrophage and monocytic cell lines. The identification of a bidirectional antisense long non-coding RNA transcript directly adjacent to Psg22 and its associated active local chromatin conformation, suggests an interesting epigenetic gene-specific regulatory mechanism that may be responsible for the high level of Psg22 expression relative to the other Psg family members upon trophoblast giant cell differentiation

Pregnancy-specific glycoprotein function, conservation and receptor investigation

Pregnancy-specific glycoproteins (PSGs) are highly glycosylated secreted proteins encoded by multi-gene families in some placental mammals. They are carcinoembryonic antigen (CEA) family and immunoglobulin (Ig) superfamily members. PSGs are immunomodulatory, and have been demonstrated to possess antiplatelet and pro-angiogenic properties. Low serum levels of these proteins have been correlated with adverse pregnancy outcomes. Objectives: Main research goals of this thesis were: 1). To attempt to replicate previously reported cytokine responses to PSG-treatment of immune cells and subsequently to investigate functionally important amino acids within PSG1. 2). To determine whether candidate receptor, integrin αvβ3, was a binding partner for PSG1 and to investigate whether PSG1 possessed functionality in a leukocyte-endothelial interaction assay. 3). To determine whether proteins generated from recently identified putative PSG genes in the horse shared functional properties with PSGs from other species. Outcomes: 1). Sequential domain deletion of PSG1 as well as mutation of conserved residues within the PSG1 Ndomain did not affect PSG1-induced TGF-β1. The investigated response was subsequently found to be the result of latent TGF-β1 contaminating the recombinant protein. Protein further purified by SEC to remove this showed no induction of TGF-β1. The most N-terminal glycosylation site was demonstrated to have an important role in PSG N domain secretion. PSG1 attenuated LPS-induced IL-6 and TNF-α. Investigations into signalling underpinning this proved inconclusive. 2). Integrin αvβ3 was identified as a novel PSG1 receptor mediating an as yet unknown function. Preliminary investigations into a role for PSGs as inhibitors of leukocyte endothelial interactions showed no effect by PSG1. 3). Horse PSG protein, CEACAM49, was shown to be similarly contaminated by latent TGF-β1 particle and once removed did not demonstrate TGF-β1 release. Interestingly horse PSG did show anti-platelet properties through inhibition of the plateletfibrinogen interaction as previously published for mouse and human PSGs.

A cultural study on communication and technology with specific reference to media in China

This dissertation examines the role of communications technology in social change. It examines secondary data on contemporary China arguing that many interpretations of events in China are unsuitable at best and at worst conceptually damages our understanding of social change in China. This is especially the case in media studies under the ‘democratic framework’. It proposes that there is an alternative framework in studying the media and social change. This alternative conceptual framework is termed a zone of interpretative development offering a means by which to discuss events that take place in a mediated environment. Taking a theoretical foundation using the philosophy of Mikhail Bakhtin this dissertation develops a platform with which to understand communication technology from an anthropological perspective. Three media events from contemporary China are examined. The first examines the Democracy Wall event and the implications of using a public sphere framework. The second case examines the phenomenon of the Grass Mud Horse, a symbol that has gained popular purchase as a humorous expression of political dissatisfaction and develops the problems seen in the first case but with some solutions. Using a modification of Lev Vygotskiĭ’s zone of proximal development this symbol is understood as an expression of the collective recognition of a shared experience. In the second example from the popular TV talent show contests in China further expressions of collective experience are introduced. With the evidence from these media events in contemporary China this dissertation proposes that we can understand certain modes of communication as occurring in a zone of interpretative development. This proposed anthropological feature of social change via communication and technology can fruitfully describe meaning-formation in society via the expression and recognition of shared experiences.

Identification of ribosomal proteins specific to higher eukaryotic organisms

This report describes the identification of a novel protein named PS1D (Genbank accession number ), which is composed of an S1-like RNA-binding domain, a (cysteine)x3-(histidine) CCCH-zinc finger, and a very basic carboxyl domain. PS1D is expressed as two isoforms, probably resulting from the alternative splicing of mRNA. The long PS1D isoform differs from the short one by the presence of 48 additional amino acids at its amino-terminal extremity. Analysis of PS1D subcellular distribution by cell fractionation reveals that this protein belongs to the core of the eukaryotic 60S ribosomal subunit. Interestingly, PS1D protein is a highly conserved protein among mammalians as murine, human, and simian PS1D homologues share more than 95% identity. In contrast, no homologous protein is found in lower eukaryotes such as yeast and Caenorhabditis elegans. These observations indicate that PS1D is the first eukaryotic ribosomal protein that is specific to higher eukaryotes.