Now showing 1 - 10 of 498
  • Publication
    What are the mechanisms that enable the reciprocal involvement of seldom heard groups in health and social care research? A rapid realist review protocol
    Background: The University College Dublin (UCD) PPI Ignite Connect Network will fundamentally embed public and patient involvement (PPI) in health-related research, education and training, professional practice and administration in UCD’s institutional structures and procedures. A significant focus of the programme of work is on actively engaging and developing long-term reciprocal relationships with seldom heard groups, via our ten inaugural partners. Methods: This rapid realist review will explore what are the mechanisms that are important in actively engaging seldom heard groups in health and social care research. The review process will follow five iterative steps: (1) clarify scope, (2) search for evidence, (3) appraise primary studies and extract data, (4) synthesise evidence and draw conclusions, and (5) disseminate findings. The reviewers will consult with expert and reference panels to focus the review, provide local contextual insights and develop a programme theory consisting of context–mechanism–outcome configurations. The expert panel will oversee the review process and agree, via consensus, the final programme theory. Review findings will follow the adopted RAMESES guideline and will be disseminated via a report, presentations and peer-reviewed publication. Discussion: The review will update and consolidate evidence on the mechanisms that enable the reciprocal engagement and participation of ‘seldom heard’ groups in health and social care research. Via the expert and reference process, we will draw from a sizeable body of published and unpublished research and grey literature. The local contextual insights provided will aid the development of our programme theories. This new evidence will inform the design and development of the UCD PPI Ignite program focused on ensuring sustained reciprocal partnerships.
  • Publication
    Diffusion and Fluid-Interaction in Itrongay Pegmatite (Madagascar): The Results of in situ Ar-Ar Dating of Gem-Quality Alkali Feldspar and U-Pb Dating of Apatite Inclusions within it
    Constraining how the temperature of rocks changes with time is an important aspect of many geological studies. Geoscientists commonly address this problem by interpreting step-heating Ar-Ar data obtained from feldspars [e.g. 1 and therein] and increasingly more often by interpreting U-Pb data obtained from apatite [e.g. 2 and therein]. Reconstruction of thermal histories using these approaches is underpinned by the assumption that the redistribution of radiogenic Ar in feldspars and Pb in apatite over geological timescales is controlled by volume diffusion. However, is this assumption always valid? Here we revisit the mechanisms of Ar redistribution in famous gem-quality alkali feldpsar from Itrongay pegmatite by combining in situ Ar-Ar dating with cathodoluminescence imaging. Previous in situ Ar-Ar studies of Itrongay feldspar suggested that it has partially lost radiogenic Ar by diffusion [3, 4], supporting the underlying assumption of feldspar ArAr thermochronology. However, our results indicate that this feldspar records a protracted history of interaction with fluids between ~475 Ma (dates in the core) and ~180 Ma (dates at the rim), casting doubt on previous interpretations. Alongside, we have obtained in situ U-Pb dates of three apparently protogenetic apatite inclusions within the studied feldspar crystal. These yield older dates than feldpsar (~490- 535 Ma), and in contrast to feldspar seem to have been partially reset by diffusion, possibly prior to their entrapment. [1] Harrison and Lovera (2013) GSL Spec. Pub., 378, 91- 106; [2] Paul et al. (2018) GCA, 288, 275-300 [3] Flude et al. (2014) Geol. Soc. London Spec. Pub., 378, 265–275; [4] Arnaud and Kelley (1997) GCA, 61, 3227–3255.
  • Publication
    Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS G13D
    Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.
  • Publication
    Geomechanical modelling of sinkhole development using Distinct Elements: Model verification for a single void space and application to the Dead Sea area
    Mechanical and/or chemical removal of material from the subsurface may generate large subsurface cavities, the destabilisation of which can lead to ground collapse and the formation of sinkholes. Numerical simulation of the interaction of cavity growth, host material deformation and overburden collapse is desirable to better understand the sinkhole hazard but is a challenging task due to the involved high strains and material discontinuities. Here, we present 2-D distinct element method numerical simulations of cavity growth and sinkhole development. Firstly, we simulate cavity formation by quasi-static, stepwise removal of material in a single growing zone of an arbitrary geometry and depth. We benchmark this approach against analytical and boundary element method models of a deep void space in a linear elastic material. Secondly, we explore the effects of properties of different uniform materials on cavity stability and sinkhole development. We perform simulated biaxial tests to calibrate macroscopic geotechnical parameters of three model materials representative of those in which sinkholes develop at the Dead Sea shoreline: mud, alluvium and salt. We show that weak materials do not support large cavities, leading to gradual sagging or suffusion-style subsidence. Strong materials support quasi-stable to stable cavities, the overburdens of which may fail suddenly in a caprock or bedrock collapse style. Thirdly, we examine the consequences of layered arrangements of weak and strong materials. We find that these are more susceptible to sinkhole collapse than uniform materials not only due to a lower integrated strength of the overburden but also due to an inhibition of stabilising stress arching. Finally, we compare our model sinkhole geometries to observations at the Ghor Al-Haditha sinkhole site in Jordan. Sinkhole depth∕diameter ratios of 0.15 in mud, 0.37 in alluvium and 0.33 in salt are reproduced successfully in the calibrated model materials. The model results suggest that the observed distribution of sinkhole depth∕diameter values in each material type may partly reflect sinkhole growth trends.
  • Publication
    Open minded and open access: introducing NeoBiota, a new peer-reviewed journal of biological invasions
    The Editorial presents the focus, scope, policies, and the inaugural issue of NeoBiota, a new open access peer-reviewed journal of biological invasions. The new journal NeoBiota is a continuation of the former NEOBIOTA publication series. The journal will deal with all aspects of invasion biology and impose no restrictions on manuscript size neither on use of color. NeoBiota implies an XML-based editorial workflow and several cutting-edge innovations in publishing and dissemination, such as semantic markup of and enhancements to published texts, data publication, and extensive cross-linking within the journal and to external sources.
  • Publication
    UCD Access Symposium Proceedings 2018: Marking 30 Years of Services for Students with Disabilities in UCD
    This publication contains a series of papers presented at the third Access Symposium held in University College Dublin (UCD) to mark and celebrate thirty years of services for students with disabilities. On a lovely summer day in May, passionate, inspirational and engaging speakers simultaneously whetted our appetites, challenged our view of the world, and propelled us to do more. These speakers gave us both staff and student perspectives on the inclusion of students with disabilities and left us in no doubt as to their commitment, passion and zeal for their subjects.
  • Publication
    Segmentation and Scene Content in Moving Images
    The problem of scene content in moving images was brought by Aralia. The goal in this study group was to consider two problems. The first was image segmentation and the second is the context of the scene. These problems were explored in different areas, namely the Bayesian approach to image segmentation, shadow detection, shape recognition and background separation.
  • Publication
    Background Knowledge Injection for Interpretable Sequence Classification
    Sequence classification is the supervised learning task of building models that predict class labels of unseen sequences of symbols. Although accuracy is paramount, in certain scenarios interpretability is a must. Unfortunately, such trade-off is often hard to achieve since we lack human-independent interpretability metrics. We introduce a novel sequence learning algorithm, that combines (i) linear classifiers - which are known to strike a good balance between predictive power and interpretability, and (ii) background knowledge embeddings. We extend the classic subsequence feature space with groups of symbols which are generated by background knowledge injected via word or graph embeddings, and use this new feature space to learn a linear classifier. We also present a new measure to evaluate the interpretability of a set of symbolic features based on the symbol embeddings. Experiments on human activity recognition from wearables and amino acid sequence classification show that our classification approach preserves predictive power, while delivering more interpretable models.
  • Publication
    TEG Final Report on Climate Benchmarks and Benchmarks’ ESG Disclosure
    (European Commission, 2018-06-13) ; ; ;
    The agreement reached by the European co-legislators on the regulation amending Regulation (EU) 2016/2011, as part of the Commission's Action Plan on Financing Sustainable Growth, resulted in two essential measures regarding investment benchmarks. The first is the creation of two types of climate benchmarks, i.e. the 'EU Climate Transition Benchmark (EU CTB) and EU Paris-aligned Benchmark (EU PAB)’. The second measure is the definition of Environmental, Social and Governance (ESG) disclosure requirements that shall be applicable to all investment benchmarks. The main objectives of the new climate benchmarks are to (i) allow a significant level of comparability of climate benchmarks methodologies while leaving benchmarks’ administrators with an important level of flexibility in designing their methodologies; (ii) provide investors with an appropriate tool that is aligned with their investment strategy; (iii) increase transparency on investors’ impact, specifically with regard to climate change and the energy transition; and (iv) disincentivize greenwashing.
  • Publication
    Factors that influence family and parental preferences and decision making for unscheduled paediatric healthcare: a systematic review protocol
    There is a plethora of factors that dictate where parents and families choose to seek unscheduled healthcare for their child; and the complexity of these decisions can present a challenge for policy makers and healthcare planners as these behaviours can have a significant impact on resources in the health system. The systematic review will seek to identify the factors that influence parents' and families' preferences and decision making when seeking unscheduled paediatric healthcare.  Five databases will be searched for published studies (CINAHL, PubMed, SCOPUS, PsycInfo, EconLit) and grey literature will also be searched. Inclusion and exclusion criteria will be applied and articles assessed for quality. A narrative approach will be used to synthesise the evidence that emerges from the review. By collating the factors that influence decision-making and attendance at these services, the review can inform future health policies and strategies seeking to expand primary care to support the provision of accessible and responsive care. The systematic review will also inform the design of a discrete choice experiment (DCE) which will seek to determine parental and family preferences for unscheduled paediatric healthcare. Policies such as Sláintecare that seek to expand primary care and reduce hospital admissions from emergency departments need to be cognisant of the nuanced and complex factors that govern patients' behaviour.