Miracle-dz/UniFAR-FTUs huggingface dataset:
Terrestrial pollutant runoff to the Great Barrier Reef: effects, causes, sources and management

This thesis presents a cross-section of research on the development and application for management of water quality research on the Great Barrier Reef (GBR) and its catchment area undertaken by myself and colleagues between 1980 and 2016. Over this period, I have published ~90 peer-reviewed papers on this topic of which I was first author on 14 (Appendix 1) and ~300 other reports, conference papers and book chapters (Appendix 2). The small selection of papers presented as chapters in this thesis represent benchmarks in the progress of this research. In this introductory chapter I present a background to this research including the historical and political contexts, and the development of research and management of water quality issues and controversies in the GBR region. The science to management analysis ends at the formation of the Reef Water Quality Protection Plan (Reef Plan 2003) in 2003. However, I review the science up to 2016 by discussing the debates towards the resolution of scientific questions for management. In this chapter I highlight all contributions on which I was an author in boldface. In the final chapter I present an analysis of the success of management of the GBR since 2003, the current state of knowledge of the issue drawn from the 2013 Scientific Consensus Statement (Brodie et al. 2013a), including new knowledge gained in the period 2013 – 2016, a summary of the management plans being applied in 2016 and beyond, my own assessment of the management steps needed to improve water quality in the GBR lagoon such that GBR water quality guidelines are largely met, and the likelihood, in my estimation, of further substantive progress in managing the issue.
Nondegeneracy Conditions for Active Memristive Circuits

This brief presents a characterization of nondegenerate circuits with active memristors, i.e., memristors with a negative memductance at certain operating ranges. The analysis proceeds by characterizing index-one configurations in several differential-algebraic models of active memristive circuits. We apply tree-based techniques to the analysis of nodal analysis models and then extend this approach to branch-oriented systems. Some examples illustrate the scope of our results.
Closed-Form Path-Loss Predictor for Gaussianly Distributed Nodes

The emulation of wireless nodes spatial position is a practice used by deployment engineers and network planners to analyze the characteristics of a network. In particular, nodes geolocation will directly impact factors such as connectivity, signals fidelity, and service quality. In literature, in addition to typical homogenous scattering, normal distribution is frequently used to model mobiles concentration in a cellular system. Moreover, Gaussian dropping is often considered as an effective placement method for airborne sensor deployment. Despite the practicality of this model, getting the network channel loss distribution still relies on exhaustive Monte Carlo simulation. In this paper, we argue the need for this inefficient approach and hence derived a generic and exact closed-form expression for the path-loss distribution density between a base-station and a network of nodes. Simulation was used to reaffirm the validity of the theoretical analysis using values from the new IEEE 802.20 standard.
The prevalence and types of coronary artery anomalies in Northern Ireland.

Coronary artery anomalies are uncommon, with a reported prevalence ranging from 0.2% to 1.6%. It is important that those who undertake coronary angiographic procedures are aware of the spectrum of these anomalies. Interventional percutaneous coronary revascularisation procedures are widely used in the management of patients with symptomatic coronary atherosclerosis. The presence of a coronary artery anomaly may make these procedures technically challenging. We have reviewed the Cardiac catheterisation database at the Royal Victoria Hospital, Belfast, and report the prevalence and types of these anomalies. ImagesFig 1Fig 2Fig 3Fig 4
Semi-supervised distance metric learning for collaborative image retrieval and clustering

Learning a good distance metric plays a vital role in many multimedia retrieval and data mining tasks. For example, a typical content-based image retrieval (CBIR) system often relies on an effective distance metric to measure similarity between any two images. Conventional CBIR systems simply adopting Euclidean distance metric often fail to return satisfactory results mainly due to the well-known semantic gap challenge. In this article, we present a novel framework of Semi-Supervised Distance Metric Learning for learning effective distance metrics by exploring the historical relevance feedback log data of a CBIR system and utilizing unlabeled data when log data are limited and noisy. We formally formulate the learning problem into a convex optimization task and then present a new technique, named as “Laplacian Regularized Metric Learning” (LRML). Two efficient algorithms are then proposed to solve the LRML task. Further, we apply the proposed technique to two applications. One direct application is for Collaborative Image Retrieval (CIR), which aims to explore the CBIR log data for improving the retrieval performance of CBIR systems. The other application is for Collaborative Image Clustering (CIC), which aims to explore the CBIR log data for enhancing the clustering performance of image pattern clustering tasks. We conduct extensive evaluation to compare the proposed LRML method with a number of competing methods, including 2 standard metrics, 3 unsupervised metrics, and 4 supervised metrics with side information. Encouraging results validate the effectiveness of the proposed technique.
Prune the Convolutional Neural Networks with Sparse Shrink

Nowadays, it is still difficult to adapt Convolutional Neural Network (CNN) based models for deployment on embedded devices. The heavy computation and large memory footprint of CNN models become the main burden in real application. In this paper, we propose a "Sparse Shrink" algorithm to prune an existing CNN model. By analyzing the importance of each channel via sparse reconstruction, the algorithm is able to prune redundant feature maps accordingly. The resulting pruned model thus directly saves computational resource. We have evaluated our algorithm on CIFAR-100. As shown in our experiments, we can reduce 56.77% parameters and 73.84% multiplication in total with only minor decrease in accuracy. These results have demonstrated the effectiveness of our "Sparse Shrink" algorithm.
Towards Data Spaces for circular economy and green business value networks

: Circular economy (CE) has been identified by several studies as the necessary reformation of the industry to decrease the environmental impact of production in the fight against climate change. Some studies have identified the lack of technological solutions to support the move towards a circular economy where among others the digital networking and data exchange is one of the most pressing and general problems which must be solved cross-industry and cross-country. This paper therefore identifies the most important requirements for a digital infrastructure to support CE and proposes a solution that combines all these factors by using Data Space concepts and technologies as the backbone for collaboratively collecting data in form of Digital Product Passports (DPP).
Critical appraisal of the efficacy, safety, and patient acceptability of hydroxyprogesterone caproate injection to reduce the risk of preterm birth

Prevention of preterm delivery is a major desiderate in contemporary obstetrics and a societal necessity. The means to achieve this goal remain elusive. Progesterone has been used in an attempt to prevent preterm delivery since the 1970s, but the evidence initially accumulated was fraught by mixed results and was based on mostly underpowered studies with variable eligibility criteria, including history of spontaneous abortion as an indication for treatment. More recent randomized controlled clinical trials restimulated the interest in progesterone supplementation, suggesting that progesterone may favorably influence the rate of preterm delivery. Preterm delivery is a complex disorder and consequently it is unlikely that one generalized prevention strategy will be effective in all patients. Further, an additional impediment in accepting progesterone as the “magic bullet” in the prevention of preterm delivery is that its mechanism of action is not fully understood and the optimal formulations, route of administration, and dose have yet to be established. We have concerned ourselves in this review with the most recent status of 17 alpha-hydroxyprogesterone caproate (17OH-PC) supplementation for prevention of preterm delivery. Our intention is to emphasize the efficacy, safety, and patient acceptability of this intervention, based on a comprehensive and unbiased review of the available literature. Currently there are insufficient data to suggest that 17OH-PC is superior or inferior to natural progesterone. Based on available evidence, we suggest a differential approach giving preferential consideration to either 17OH-PC or other progestins based on obstetric history and cervical surveillance. Progestin therapy for risk factors other than a history of preterm birth and/or a short cervix in the current pregnancy is not currently supported by the published evidence. The experience to date with 17OH-PC indicates that there are population subgroups that may be harmed by administration of 17OH-PC. Therefore, extending the use of 17OH-PC to unstudied populations or for indications that are not evidence-based is inadvisable outside of a research protocol.
Effects of b-Blockers and Tricyclic Antidepressants on the Activity of Human Organic Anion Transporting Polypeptide 1 A 2 ( OATP 1 A 2 ) s

The organic anion transporting polypeptide 1A2 (OATP1A2), a membrane drug transporter expressed on important organs (such as the brain, kidney, and intestine) may be a key element in the disposition of drugs. Previous studies demonstrated that it could transport a broad spectrum of substrates, including endogenous molecules and clinically relevant drugs, such as several b-blockers and 3-hydroxy-3-methylglutaryl–CoA reductase inhibitors. The primary objective of this study was to investigate OATP1A2 transport activity using rosuvastatin as a probe substrate and evaluate competitive inhibition of its transport by b-blockers. Rosuvastatin transport was saturable, with a Km of 60.2 mM. With the exception of carvedilol (IC50 of 3.2 mM), all of the other b-blockers that were evaluated had a small or insignificant effect on OATP1A2-mediated uptake of rosuvastatin. Carvedilol differs from the other b-blockers by the tricyclic moiety in its chemical structure. As a secondary objective, the transport of a series of tricyclic compounds by OATP1A2 and their potential for rosuvastatin transport inhibition were evaluated. Tricyclic compounds were not OATP1A2 substrates. On the other hand, tricyclic compounds with a short aliphatic amine chain inhibited OATP1A2-mediated rosuvastatin transport. Our data suggest that these drugs may modulate the transport of OATP1A2 substrates and may affect drug actions.
Novel concepts in sleep regulation

Knowledge regarding the cellular mechanisms of sleep regulation is accumulating rapidly. In addition to neurones, also non‐neuronal brain cells (astrocytes and microglia) are emerging as potential players. New techniques, particularly optogenetics and designed receptors activated by artificial ligands (DREADD), have provided also sleep research with important additional tools to study the effect of either silencing or activating specific neuronal groups/neuronal networks by opening or shutting ion channels on cells. The advantages of these strategies are the possibility to genetically target specific cell populations and the possibility to either activate or inhibit them with inducing light signal into the brain. Studies probing circuits of NREM and REM sleep regulation, as well as their role in memory consolidation, have been conducted recently. In addition, fundamentally new thoughts and potential mechanisms have been introduced to the field. The role of non‐neuronal tissues in the regulation of many brain functions has become evident. These non‐neuronal cells, particularly astrocytes, integrate large number of neurones, and it has been suggested that one of their functions is to integrate the (neural) activity in larger brain areas—a feature that is one of the prominent features of also the state of sleep.
A role for eisosomes in maintenance of plasma membrane phosphoinositide levels

The eisosome protein Pil1 interacts with the PI(4,5)P2 phosphatase Inp51, thereby recruiting it to the plasma membrane. Pil1 is essential for membrane localization of Inp51 but not for the homologous PI(4,5)P2 phosphatases Inp52 and Inp53. Consistent with this, Pil1 plays a crucial role in maintaining normal PI(4,5)P2 levels at the plasma membrane.
Risk of connective tissue disease and related disorders among women with breast implants: a nation-wide retrospective cohort study in Sweden

Abstract Objective: To examine the relation between connective tissue disease and related conditions and breast implants. Design: Retrospective cohort study of all women in the Swedish national inpatient registry who underwent breast augmentation surgery with artificial implants during 1964-93, compared with women who underwent breast reduction surgery during the same period. Setting: Sweden. Subjects: 7442 women with implants for cosmetic reasons or for reconstruction after breast cancer surgery and 3353 women with breast reduction surgery. Main outcome measures: Subsequent hospitalisation for definite connective tissue diseases (rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis, dermatomyositis, and Sjögren's syndrome) or related disorders. Results: 29 women with implants were hospitalised for definite connective tissue disease compared with 25.5 expected based on general population rates (standardised hospitalisation ratio 1.1 (95% confidence interval 0.8 to 1.6)). There were no diagnoses of systemic sclerosis, and no significant excess in risk for polymyalgia rheumatica, fibromyalgia, and several related disorders. Among women who underwent breast reduction surgery, 14 were hospitalised for definite connective tissue disease compared with 10.5 expected (standardised hospitalisation ratio 1.3 (0.7 to 2.2)). Compared with the breast reduction group, women with breast implants showed a slight reduction for all definite connective tissue disease (relative risk 0.8 (95% confidence interval 0.5 to 1.4)). Conclusions: This large nationwide cohort study shows no evidence of association between breast implants and connective tissue disease. Key messages Anecdotal reports have suggested that silicone breast implants may cause immunological disorders In a nationwide study of over 7000 Swedish women with breast implants and a control group of over 3000 women who had undergone breast reduction surgery, we found no excess risk for connective tissue disease Of the women with implants, 29 were hospitalised for connective tissue disease compared with the 25.5 expected from national hospital discharge rates, while, of those who underwent breast reduction, 14 were hospitalised compared with the 10.5 expected Direct comparison of the two groups of women showed that those with implants had a slightly lower risk of connective tissue disease There is little likelihood of an association between breast implants and connective tissue disease
Developing a Validated Tool to Identify Asbestos-Containing Materials in Domestic Settings in the Western Australian Community

Asbestos is widely known to cause a number of health issues when individuals inhale significant amounts of asbestos fibres. Asbestos exposure is an important issue in the community due to asbestos having been used in a large number of household and building products before it was banned in Australia. These products can still be found in Western Australian homes and they present a health hazard when they are damaged or disturbed. However, we do not know how much asbestos-containing material is still found in the Western Australian housing stock, what condition these materials are in, and how many people are currently being exposed to asbestos in the home.
Response of Cambial and Shoot Growth in Trees Treated with Paclobutrazol

Three experiments were conducted to investigate the effect of paclobutrazol on shoot and cambial growth of nine tree species located in Indiana and Louisiana, U.S. In Experiment I, white oak (Quercus alba L.) and red oak (Q. rubra L.) in Indiana were treated in April 1995 with paclobutrazol using the soil drench method. In Experiment II, paclobutrazol was applied in April 1996, using the soil injection method, to eight species growing in Indiana: white oak, red oak, sweetgum (Liquidambar styraciflua L.), black walnut (Juglans nigra L.), European black alder (Alnus glutinosa L.), yellow poplar (Liriodendron tulipifera L.), white ash (Fraxinus americana L.), and white pine (Pinus strobus L.). In Experiment III, two species, sweetgum and cherrybark oak (Q. falcata var. pagodaefolia L.) in Louisiana, were treated with paclobutrazol by the soil drench method in March 1997. At the end of the 1998 growing season, annual shoot growth and annual xylem ring increment were measured for each of the two to four growing seasons after treatment in the three experiments. The effects of paclobutrazol on cambial growth and annual shoot growth at various positions along the trunk and in the canopy varied with species and treatment duration. Paclobutrazol reduced cambial growth in white oak, red oak, cherrybark oak, sweetgum, European black alder, and white pine with the amount varying among species, vertical location in the tree, and year after treatment.
Early visual processing deficits in schizophrenia: impaired P1 generation revealed by high-density electrical mapping

Integrity of early visual sensory processing in schizophrenia was assessed using the well characterized P1 and N1 components of the visual evoked potential (VEP) as our dependent measures. VEPs were recorded in response to successively less fragmented line drawings of common objects. P1 amplitudes were significantly reduced across all stimulus conditions for patients versus controls. Further, this decrement was relatively greater at parieto-occipital than occipito-temporal electrode sites. No differences in N1 amplitude were found. The finding of P1 deficits in patients, particularly over dorsal scalp, supports the view that schizophrenia is associated with impairment of early dorsal visual stream processing. On the other hand, the finding of normal N1 amplitudes in patients suggests that early stages of ventral stream processing may be relatively more intact. These results imply that the cognitive impairment seen in schizophrenia is not just due to deficits in higher order aspects of cognition but also encompasses significant deficits in early sensory processing.
Smallpox transmission and control: Spatial dynamics in Great Britain

Contingency planning for the possible deliberate reintroduction of smallpox has become a priority for many national public health organizations in recent years. We used an individual-based spatial model of smallpox transmission in Great Britain and census-derived journey-to-work data to accurately describe the spatiotemporal dynamics of an outbreak of smallpox in the community. A Markov chain Monte-Carlo algorithm was developed to generate sociospatial contact networks that were consistent with demographic and commuting data. We tested the sensitivity of model predictions to key epidemiological parameters before choosing three representative scenarios from within the range explored. We examined the spatiotemporal dynamics for these illustrative scenarios and assessed the efficacy of symptomatic case isolation, contact tracing with vaccination, and reactive regional mass vaccination as policy options for control. We conclude that case isolation and contact tracing with vaccination would be sufficient to halt ongoing transmission rapidly, unless policy effectiveness was compromised by resource or other constraints. A slight reduction in the expected size and duration of an outbreak could be achieved with regional mass vaccination, but these benefits are small and do not justify the high numbers of vaccine doses required and their associated negative side effects.
Low-Rank Methods in Event Detection

We present low-rank methods for event detection. We assume that normal observation come from a low-rank subspace, prior to being corrupted by a uniformly distributed noise. Correspondingly, we aim at recovering a representation of the subspace, and perform event detection by running point-to-subspace distance query in $\ell^\infty$, for each incoming observation. In particular, we use a variant of matrix completion under interval uncertainty on a suitable flattening $M \in R^{m \times n}$ of the input data to obtain a low-rank model $M \approx L \times R$, $L \in R^{m \times r}$, $R \in R^{r \times n}$, $r \ll m$. On-line, we compute the distance of each incoming $x \in R^n$ to the space spanned by $R$. For the distance computation, we present a constant-time algorithm with a one-sided error bounded by a function of the number of coordinates employed.
Novel treatment strategies in triple-negative breast cancer: specific role of poly(adenosine diphosphate-ribose) polymerase inhibition

Inhibitors of the poly(adenosine triphosphate-ribose) polymerase (PARP)-1 enzyme induce synthetic lethality in cancers with ineffective DNA (DNA) repair or homologous repair deficiency, and have shown promising clinical activity in cancers deficient in DNA repair due to germ-line mutation in BRCA1 and BRCA2. The majority of breast cancers arising in carriers of BRCA1 germ-line mutations, as well as half of those in BRCA2 carriers, are classified as triple-negative breast cancer (TNBC). TNBC is a biologically heterogeneous group of breast cancers characterized by the lack of immunohistochemical expression of the ER, PR, or HER2 proteins, and for which the current standard of care in systemic therapy is cytotoxic chemotherapy. Many “sporadic” cases of TNBC appear to have indicators of DNA repair dysfunction similar to those in BRCA-mutation carriers, suggesting the possible utility of PARP inhibitors in a subset of TNBC. Significant genetic heterogeneity has been observed within the TNBC cohort, creating challenges for interpretation of prior clinical trial data, and for the design of future clinical trials. Several PARP inhibitors are currently in clinical development in BRCA-mutated breast cancer. The use of PARP inhibitors in TNBC without BRCA mutation will require biomarkers that identify cancers with homologous repair deficiency in order to select patients likely to respond. Beyond mutations in the BRCA genes, dysfunction in other genes that interact with the homologous repair pathway may offer opportunities to induce synthetic lethality when combined with PARP inhibition.