A low-dimensional cross-attention model for link prediction with applications to drug repurposing

Link prediction, a key technique for knowledge graph completion, has advanced with transformer-based encoders utilizing high-dimensional embeddings and self-attention mechanisms. However, these approaches often result in models with excessive parameters, poor scalability, and substantial computational demands, limiting their practical applicability. To address these limitations, this paper introduces a low-dimensional link prediction model that leverages cross-attention for improved efficiency and scalability. Our approach employs low-dimensional embeddings to capture essential, non-redundant information about entities and relations, significantly reducing computational and memory requirements. Unlike self-attention, which models interactions within a single set of embeddings, cross-attention in our model captures complex interactions between entities and relations in a compact, low-dimensional space. Additionally, a streamlined decoding method simplifies computations, reducing processing time without compromising accuracy. Experimental results show that our model outperforms most state-of-the-art link prediction models on two public datasets, WN18RR and FB15k-237. Compared to these top-performing methods, our model contains only 18.1 % and 25.4 % of the parameters of these comparable models, while incurring a performance loss of merely 2.4 % and 3.1 %, respectively. Furthermore, it achieves an average 72 % reduction in embedding dimensions compared to five leading models. A case study on drug repurposing further illustrates the model's potential for real-world applications in knowledge graph completion.<br/

Electricity to rural No. 1 - the beginning of Ireland’s quiet revolution

From 1945 and into the 1950s in Ireland's economic history has been described as post-war recovery and gloom and doom respectively, leading to the 1960s golden age. However, despite this gloomy outlook, with some delays attributed to the Emergency, a ‘quiet revolution’ kicked off in late 1946. That revolution was the Rural Electrification Scheme (RES) of the Electricity Supply Board of Ireland, a scheme designed to bring electric power to every village in Ireland. While some academic research has addressed the RES, detail on specific locations and effects is lacking, which is surprising given the effects the scheme had on life and economy in rural Ireland. Drawing on archival evidence, existing history texts, media and some oral histories, this paper explores the story of the first village to receive power under the RES, namely the village of Oldtown in County Dublin. This story is largely untold, and in particular, why this village was the first is explored. The benefits of electric power to rural homes and farms are also detailed. In the case of farming, early shoots of today's thriving tillage and horticultural activity typical of North County Dublin are apparent.<br/

Hotspot regions of reactive oxygen species production and their environmental impacts in periodically flooded soil environments: a review

The Intertidal Soil (ITS) zone is a unique and critical component of Earth's ecosystems, characterized by a high diversity of biological species and frequent exchanges of matter and energy. Reactive Oxygen Species (ROS), naturally occurring reactive molecules, play vital roles in chemical cycling. They are also crucial in environmental management and remediation, pollutant degradation, and ecosystem health. Recent research has revealed that substantial ROS production can occur in dark conditions, driven primarily by redox cycles. This finding is particularly significant for the ITS zone, where redox cycles are prevalent. This review first analyzes the shifting research interests in ROS over the past decade and the emerging trends in ITS zone studies, providing a reference for future research. Additionally, it identified key hotspots for ROS generation within the ITS zone and analyzed the mechanisms of ROS production from both biological and abiotic perspectives, aiming to deepen the understanding of material transformation in ITS settings. Furthermore, this review comprehensively summarizes the potential impacts of ROS on biological activity, mineral transformation, organic pollutant degradation, heavy metal (and metalloid) mobility, and microplastic degradation in the ITS zone. This synthesis enhances researchers' understanding of the roles ROS play in these processes. Lastly, current methodologies for detecting and quenching ROS were compiled, along with associated measurement precautions, offering reliable references for subsequent studies on ROS in the ITS zone. In summary, this review extensively covers the sources and sinks of ROS in the ITS zone and outlines current research directions with significant potential. The insights provided hold valuable implications for studying ITS zone biology, ecology, geology, and climate change.<br/

Low-coverage whole genome sequencing of low-grade dysplasia strongly predicts advanced neoplasia risk in ulcerative colitis

Background: The risk of developing advanced neoplasia (AN; colorectal cancer and/or high-grade dysplasia) in ulcerative colitis (UC) patients with a low-grade dysplasia (LGD) lesion is variable and difficult to predict. This is a major challenge for effective clinical management. Objective: We aimed to provide accurate AN risk stratification in UC patients with LGD. We hypothesised that the pattern and burden of somatic genomic copy number alterations (CNAs) in LGD lesions could predict future AN risk. Design: We performed a retrospective multicentre validated case–control study using n=270 LGD samples from n=122 patients with UC. Patients were designated progressors (n=40) if they had a diagnosis of AN in the ~5 years following LGD diagnosis or non-progressors (n=82) if they remained AN-free during follow-up. DNA was extracted from the baseline LGD lesion, low-coverage whole genome sequencing performed and data processed to detect CNAs. Survival analysis was used to evaluate CNAs as predictors of future AN risk. Results: CNA burden was significantly higher in progressors than non-progressors (p=2×10−6 in discovery cohort) and was a very significant predictor of AN risk in univariate analysis (OR=36; p=9×10−7), outperforming existing clinical risk factors such as lesion size, shape and focality. Optimal risk prediction was achieved with a multivariate model combining CNA burden with the known clinical risk factor of incomplete LGD resection. Within-LGD lesion genetic heterogeneity did not confound risk prediction. Conclusion: Measurement of CNAs in LGD is an accurate predictor of AN risk in inflammatory bowel disease and is likely to support clinical management

Cyanopyridinium-based ionic liquids and their mixtures for ethylene and ethane separation

The solubility of ethane and ethylene was determined in a series of cyanopyridinium ionic liquids known to form charge-transfer complexes with polyaromatic hydrocarbons to determine their potential to form specific interactions with the unsaturated gas. The solubilities of ethylene and ethane in 1-butyl-4-cyanopyridinium bis(trifluoromethane)sulfonimide ([C44CNPy][NTf2]) and 1-butyl-3-cyanopyridinium bis(trifluoromethane)sulfonimide ([C43CNPy][NTf2]) were measured using an isochoric saturation method. The mole fraction solubility of ethane in the ionic liquids ranged from 6.0 × 10–3 to 7.2 × 10–3 and from 7.5 × 10–3 to 9.9 × 10–3 for ethylene in [C43CNPy][NTf2] and [C44CNPy][NTf2] at 0.1 MPa and 313 K, respectively. The small preferential solubility of ethylene over ethane in the ionic liquids results in ideal ethylene separation selectivities between 1.2 and 1.4, which is in the same range as typical physisorbent ionic liquids of the same type and molecular weight, indicating that there is no significant preferential interaction between the ionic liquids and ethylene. The calculated thermodynamic properties of solvation reveal that the solvation of both gases is entropically driven. To promote cyanopyridinium–ethylene interactions and decrease the possibility of steric constrictions to the interactions, 1-butyl-4-methylimidazolium bis(trifluoromethane)sulfonimide ([C4C1Im][NTf2]) was added as diluent to [C44CNPy][NTf2]. This IL mixture was found to behave almost ideally based on isothermal titration nanocalorimetry results. The solubility of ethylene or ethane in the mixture was found to be the weighted average of the corresponding solubilities in the two pure ionic liquids, still indicating that no specific ethylene–ionic liquid interactions were formed. Molecular dynamics (MD) simulations of the systems were performed and revealed that the slightly higher ethylene solubility in [C44CNPy][NTf2] is due to a slightly stronger association with this cation compared to the 3-isomer.<br/

Delirium E-Resource

Co-designed digital e-resource about delirium designed in partnership with University of Limerick and Queen's University Belfast

Educational challenges and support for children with congenital heart disease

BackgroundChildren with congenital heart disease (CHD) often face educational challenges due to medical, social, and school-related factors. Early intervention and support for teachers and students are crucial to improving educational outcomes. This study aimed to identify the challenges experienced by teachers, parents, and children with CHD in school settings and explore strategies to enhance their educational experience.MethodA systematic scoping review examined the educational difficulties faced by children with CHD. This was followed by a qualitative study involving three groups: (i) parents of school-aged children with CHD, (ii) teachers with experience teaching these children, and (iii) children and adolescents (ages 11–17) with varying CHD severity. Semi-structured interviews explored participants’ lived experiences and key challenges.ResultsThe scoping review identified challenges in cognitive, psychomotor, behavioural, and emotional domains, as well as issues with school attendance. Teachers often lacked training on CHD-specific needs, impacting their ability to provide adequate support.Qualitative findings revealed concerns from teachers regarding limited CHD-specific knowledge and the risks of having a child with CHD in their class. Parents expressed worries about their children’s academic performance, social interactions, emotional well-being, and physical health. Strong teacher-parent-child communication was seen as essential in reducing anxiety and fostering a supportive school environment.Children’s experiences varied by CHD severity. Children with Hypoplastic Left Heart Syndrome reported most challenges, including fatigue and executive function difficulties. While some children with Transposition of the Great Arteries experienced concentration difficulties, most reported minimal challenges directly related to their condition. Finally, children with Ventricular Septal Defect reported few educational difficulties.ConclusionTeachers require patient-specific information and resources to support children with CHD, especially those with complex conditions. These findings will inform the development of an online training resource to assist teachers and parents in improving educational experiences for children with CHD.<br/

Barriers and facilitators in providing palliative and end of life care in prison settings: A qualitative study of professional stakeholders’ views and experiences in six Western countries

BackgroundIncreasing numbers of people require PEOLC within prison settings, mainly because of ageing populations and increasingly punitive sentencing policies. There is limited research in this area, but evidence suggests that prisons possess limited resources to provide adequate care for ageing and frail people at the end of life.AimThe study aimed to explore how palliative and end of life care (PEOLC) is provided in prisons in different countries, and identify factors that facilitate or impede its provision.MethodsA cross-sectional qualitative study using semi-structured interviews was utilised to interview prison and health care staff involved in the organisation and/or delivery of PEOLC to incarcerated adults in six countries. Sampling was purposive and adopted a snowball technique. Data were analysed using framework analysis.FindingsThe study provides evidence that numerous barriers exist that can impede the organisation and delivery of PEOLC to people in prison, including barriers at individual, staff, organisation, and regulatory level. Facilitators co-existed alongside the barriers. Similar barriers and facilitators were identified in each country.ConclusionsDespite some good practice, multiple challenges remain in providing the same quality of PEOLC that is available outside prison, and thus those dying in prison continue to be disadvantaged

Flying the nest. An explorative study of experiences in transitioning from campus to clinical years

Introduction: The transition to the clinical environment is widely acknowledged as challenging [1]. In moving from the familiar lectures and tutorials to the ward-based application of knowledge students can feel emotionally, socially and practically unprepared [1]. Stress is known to impact student learning and understanding [2]. Furthermore, given early clinical experiences can influence the future careers of resident doctors, it is essential to foster positive experiences, starting with the transition [3]. Educators dedicate time at the end of 2nd year and start of 3rd year to prepare the students for longitudinal clinical attachments. However, the format, topics and themes are decided by the University. This study aims to assess the readiness of students entering clinical attachment and how we can improve preparedness and support during this crucial process.Methods: A retrospective explorative study with 3rd year medical students at Queen’s University Belfast (QUB). Following focus groups and interviews, themes were identified and refined using thematic analysis. Data interpretation, validation, triangulation and reporting were carried out.Results: All current 3rd year students at QUB were invited to participate, with 12 volunteering for focus groups and interviews. The students felt generally unprepared for the transition. Several themes emerged highlighting a lack in clarity of expectations, lack of support, time management issues, rushed and inadequate preparation, fear at practicing skills on patients having only used mannequins and the feeling of exclusion and isolation on the ward. Conclusion: This study highlights a mixture of positive and negative experiences about transitioning to clinical attachments. Despite the effort of medical education there is a clear disconnect between what educators feel is essential as preparation and what students feel is important and required. The themes identified are reshaping the introduction to the first clinical year in QUB