Hyperset Approach to Semi-structured Databases and the Experimental Implementation of the Query Language Delta

This thesis presents practical suggestions towards the implementation of the hyperset approach to semi-structured databases and the associated query language Delta. This work can be characterised as part of a top-down approach to semi-structured databases, from theory to practice. The main original part of this work consisted in implementation of the hyperset Delta query language to semi-structured databases, including worked example queries. In fact, the goal was to demonstrate the practical details of this approach and language. The required development of an extended, practical version of the language based on the existing theoretical version, and the corresponding operational semantics. Here we present detailed description of the most essential steps of the implementation. Another crucial problem for this approach was to demonstrate how to deal in reality with the concept of the equality relation between (hyper)sets, which is computationally realised by the bisimulation relation. In fact, this expensive procedure, especially in the case of distributed semi-structured data, required some additional theoretical considerations and practical suggestions for efficient implementation. To this end the 'local/global' strategy for computing the bisimulation relation over distributed semi-structured data was developed and its efficiency was experimentally confirmed.Comment: Technical Report (PhD thesis), University of Liverpool, Englan

Pipeline Inspection with Autonomous Swarm Robotics

Underground water pipelines require frequent inspection to prevent decay and avoid costly repairs. The use of robots to inspect pipelines is well documented but the uniquely hostile environment of subterranean water networks means pipes require continual inspection. The idea of autonomous inspection robots that can provide continuous coverage has shown promise, but existing methods do not proactively aim to overcome a variety of diverse challenges. Specifically, extreme variability in the pipe conditions and the dense surrounding earth limit the communication capabilities of the robots, while dynamic water flows and power issues have a detrimental effect on their movement. This thesis presents the implementation of a range of path planning algorithms of varying levels of autonomy as governing swarm behaviours, each with a focus on overcoming some of the specific challenges inherent in underground water networks, with the goal of improving the efficiency with which the swarm can inspect a network. The Greedy Walk uses stochastic processes to plan a locally optimal path, the novel Ad Hoc algorithm aims to provide cyclic coverage, with robots moving as a fluid net throughout the network, and the k-Chinese Postman Problem solution explicitly plans optimal paths round subsections of a network. The thesis examines the performance of these behaviours against existing methods and anticipates obstacles in their real world implementation. The thesis then presents tailored versions of the path planning behaviours that include the introduction of more advanced methods focused on circumventing these issues. Specifically, the algorithms are developed to incorporate Gaussian Process Regression models to analyse strong water flows and use the data to plan intelligently, mitigating the detrimental effects of the flow. The flow analysis also provides a platform from which a novel Simultaneous Localisation and Mapping algorithm is presented, alongside a Multi-Objective Genetic Algorithm with the focus of increasing inspection frequency and conserving robot charge. The thesis shows evidence that an approach to pipeline inspection with autonomous swarm robotics based in path planning algorithms can help overcome the likely physical limitations of real world implementation

Hyperset approach to semi-structured databases and the experimental implementation of the query language Delta

This thesis presents practical suggestions towards the implementation of the hyperset approach to semi-structured databases and the associated query language Delta. This work can be characterised as part of a top-down approach to semi-structured databases, from theory to practice. The main original part of this work consisted in implementation of the hyperset Delta query language to semi-structured databases, including worked example queries. In fact, the goal was to demonstrate the practical details of this approach and language. The required development of an extended, practical version of the language based on the existing theoretical version, and the corresponding operational semantics. Here we present detailed description of the most essential steps of the implementation. Another crucial problem for this approach was to demonstrate how to deal in reality with the concept of the equality relation between (hyper)sets, which is computationally realised by the bisimulation relation. In fact, this expensive procedure, especially in the case of distributed semi-structured data, required some additional theoretical considerations and practical suggestions for efficient implementation. To this end the 'local/global' strategy for computing the bisimulation relation over distributed semi-structured data was developed and its efficiency was experimentally confirmed. Finally, the XML-WDB format for representing any distributed WDB as system of set equations was developed so that arbitrary XML elements can participate and, hence, queried by the -language. The query system with the syntax of the language and several example queries from this thesis is available online at http://www.csc.liv.ac.uk/˜molyneux/t

Gauging the impact of glacioeustasy on a mid-latitude early Silurian basin margin, mid Wales, UK

The early Silurian (Llandovery) Gondwanan South Polar ice sheet experienced episodes of ice retreat and re-advance. Marine base level curves constructed for the interval are widely assumed to provide a record of the associated glacioeustasy. In revealing a series of progradational sequences (progrades) bounded by flooding surfaces, recent work on the Type Llandovery succession in mid Wales (UK) has provided an opportunity to test this hypothesis. The grouping of these progrades into three composite sequences underpins the construction of both low order (small amplitude, high frequency) and high order (large amplitude, low frequency) base level movement curves. Revised biostratigraphical datasets for the type succession permit the accurate dating of base level events. The composite sequences record progradational acmes in the acinaces, lower convolutus and upper sedgwickii-halli graptolite biozones. A series of transgressions that postdate the Hirnantian glacial maximum culminated in an upper persculptus Biozone high-stand. Maximum flooding events also occurred during the revolutus and lower sedgwickii biozones, and the base of the early Telychian guerichi Biozone also marked the onset of a pronounced deepening. A review of 62 published datasets, including global and other regional base level curves, records of glacial activity, isotope data, patterns of facies and faunal flux and putative climate models, permits an evaluation of the origins of these local base level events. The concept of a Eustasy Index is introduced and shows that the impacts of global sea level movements can only be demonstrated within narrow ‘eustatic windows’ coincident with times of ice sheet collapse. At other times, the geometry of Llandovery area progrades reflects their accumulation across a faulted basin margin where, during periods of slow ice sheet advance, epeirogenic processes outstripped sea level movements as the dominant forcing factors. Increased levels of Telychian subsidence at first enhanced and then overwhelmed the influence of glacioeustasy as part of the region's response to the north European Scandian deformation

The systemic pathology of cerebral malaria in African children

Pediatric cerebral malaria carries a high mortality rate in sub-Saharan Africa. We present our systematic analysis of the descriptive and quantitative histopathology of all organs sampled from a series of 103 autopsies performed between 1996 and 2010 in Blantyre, Malawi on pediatric cerebral malaria patients and control patients (without coma, or without malaria infection) who were clinically well characterized prior to death. We found brain swelling in all cerebral malaria patients and the majority of controls. The histopathology in patients with sequestration of parasites in the brain demonstrated two patterns: (a) the “classic” appearance (i.e., ring hemorrhages, dense sequestration, and extra-erythrocytic pigment) which was associated with evidence of systemic activation of coagulation and (b) the “sequestration only” appearance associated with shorter duration of illness and higher total burden of parasites in all organs including the spleen. Sequestration of parasites was most intense in the gastrointestinal tract in all parasitemic patients (those with cerebral malarial and those without)

Introducing open book examinations in clinical education: A case study

During the recent COVID-19 pandemic, in common with educators across the Higher Education sector, the School of Dentistry at the University of Liverpool reimagined the learning and assessment strategy by moving from proctored closed-book assessment to largely unmonitored open-book examinations (OBE). This article discusses understandings from an educator perspective following our implementation of OBE. The educator perspective discussed here indicates that OBE have the potential to be an authentic and acceptable form of assessment, but that some reframing of attitudes towards assessment from all stakeholders and their approaches to assessment is necessary when developing these innovative types of assessment

A histological method for quantifying Plasmodium falciparum in the brain in fatal paediatric cerebral malaria

Background: The sequestration of Plasmodium falciparum-infected erythrocytes in brain microvasculature through cytoadherence to endothelium, is the hallmark of the definitive diagnosis of cerebral malaria and plays a critical role in malaria pathogenesis. The complex pathophysiology, which leads each patient to the final outcome of cerebral malaria, is multifaceted and thus, metrics to delineate specific patterns within cerebral malaria are needed to further parse patients. Methods: A method was developed for quantification utilizing counts of capillary contents (early-stage parasites, late-stage parasites and fibrin) from histological preparations of brain tissue after death, and compared it to the standard approach, in which the percentage of parasitized vessels in cross-section is determined. Results: Within the initial cohort of 50 patients, two different observers agreed closely on the percentage of vessels parasitized, pigmented parasites and pigment globules (ICC = 0.795-0.970). Correlations between observers for correct diagnostic classification were high (Kendall’s tau-b = 0.8779, Kappa = 0.8413). When these methods were applied prospectively to a second set of 50 autopsy samples, they revealed a heterogeneous distribution of sequestered parasites in the brain with pigmented parasites and pigment globules present in the cerebellum > cortex > brainstem. There was no difference in the distribution of early stages of parasites or in the percentage of vessels parasitized across the same sites. The second cohort of cases was also used to test a previously published classification and regression tree (CART) analysis; the quantitative data alone were able to accurately classify and distinguish cerebral malaria from non-cerebral malaria. Classification errors occurred within a subclassification of cerebral malaria (CM1 vs CM2). A repeat CART analysis for the second cohort generated slightly different classification rules with more accurate subclassification, although misclassification still occurred. Conclusions: The traditional measure of parasite sequestration in falciparum malaria, the percentage of vessels parasitized, is the most reliable and consistent for the general diagnosis of cerebral malaria. Methods that involve quantitative measures of different life cycle stages are useful for distinguishing patterns within the cerebral malaria population; these subclassifications may be important for studies of disease pathogenesis and ancillary treatment

Tissue distribution of migration inhibitory factor and inducible nitric oxide synthase in falciparum malaria and sepsis in African children

BACKGROUND: The inflammatory nature of falciparum malaria has been acknowledged since increased circulating levels of tumour necrosis factor (TNF) were first measured, but precisely where the mediators downstream from this prototype inflammatory mediator are generated has not been investigated. Here we report on the cellular distribution, by immunohistochemistry, of migration inhibitory factor (MIF) and inducible nitric oxide synthase (iNOS) in this disease, and in sepsis. METHODS: We stained for MIF and iNOS in tissues collected during 44 paediatric autopsies in Blantyre, Malawi. These comprised 42 acutely ill comatose patients, 32 of whom were diagnosed clinically as cerebral malaria and the other 10 as non-malarial diseases. Another 2 were non-malarial, non-comatose deaths. Other control tissues were from Australian adults. RESULTS: Of the 32 clinically diagnosed cerebral malaria cases, 11 had negligible histological change in the brain, and no or scanty intravascular sequestration of parasitised erythrocytes, another 7 had no histological changes in the brain, but sequestered parasitised erythrocytes were present (usually dense), and the remaining 14 brains showed micro-haemorrhages and intravascular mononuclear cell accumulations, plus sequestered parasitised erythrocytes. The vascular walls of the latter group stained most strongly for iNOS. Vascular wall iNOS staining was usually of low intensity in the second group (7 brains) and was virtually absent from the cerebral vascular walls of 8 of the 10 comatose patients without malaria, and also from control brains. The chest wall was chosen as a typical non-cerebral site encompassing a range of tissues of interest. Here pronounced iNOS staining in vascular wall and skeletal muscle was present in some 50% of the children in all groups, including septic meningitis, irrespective of the degree of staining in cerebral vascular walls. Parasites or malarial pigment were rare to absent in all chest wall sections. While MIF was common in chest wall vessels, usually in association with iNOS, it was absent in brain vessels. CONCLUSIONS: These results agree with the view that clinically diagnosed cerebral malaria in African children is a collection of overlapping syndromes acting through different organ systems, with several mechanisms, not necessarily associated with cerebral vascular inflammation and damage, combining to cause death

Platelet Accumulation in Brain Microvessels in Fatal Pediatric Cerebral Malaria

The pathogenesis of fatal cerebral malaria (CM) is not well understood, in part because data from patients in whom a clinical diagnosis was established prior to death are rare. In a murine CM model, platelets accumulate in brain microvasculature, and antiplatelet therapy can improve outcome. We determined whether platelets are also found in cerebral vessels in human CM, and we performed immunohistopathology for platelet-specific glycoprotein, GPIIb-IIIa, on tissue from multiple brain sites in Malawian children whose fatal illness was severe malarial anemia, CM, or nonmalarial encephalopathy. Platelets were observed in 3 locations within microvessels: between malaria pigment and leukocytes, associated with malaria pigment, or alone. The mean surface area of platelet staining and the proportion of vessels showing platelet accumulation were significantly higher in patients with CM than in those without it. Platelet accumulation occurs in the microvasculature of patients with CM and may play a role in the pathogenesis of the diseas