• Backcasting to identify food waste prevention and mitigation opportunities for infant feeding in maternity services

      Ryan-Fogarty, Yvonne; Becker, Genevieve; Moles, Richard; O'Regan, Bernadette (2017-01)
    • Bacteria and tumours: causative agents or opportunistic inhabitants?

      Cummins, Joanne; Tangney, Mark (2013-03-28)
      Abstract Associations between different bacteria and various tumours have been reported in patients for decades. Studies involving characterisation of bacteria within tumour tissues have traditionally been in the context of tumourigenesis as a result of bacterial presence within healthy tissues, and in general, dogma holds that such bacteria are causative agents of malignancy (directly or indirectly). While evidence suggests that this may be the case for certain tumour types and bacterial species, it is plausible that in many cases, clinical observations of bacteria within tumours arise from spontaneous infection of established tumours. Indeed, growth of bacteria specifically within tumours following deliberate systemic administration has been demonstrated for numerous bacterial species at preclinical and clinical levels. We present the available data on links between bacteria and tumours, and propose that besides the few instances in which pathogens are playing a pathogenic role in cancer, in many instances, the prevalent relationship between solid tumours and bacteria is opportunistic rather than causative, and discuss opportunities for exploiting tumour-specific bacterial growth for cancer treatment.
    • Bad laws or bad attitudes? Assessing the impact of societal attitudes upon the conviction rate for rape in Ireland

      Leahy, Susan; University of Limerick (UL) (Irish Journal of Applied Social Studies, 2014-05)
    • BarraCUDA - a fast short read sequence aligner using graphics processing units

      Klus, Petr; Lam, Simon; Lyberg, Dag; Cheung, Ming Sin; Pullan, Graham; McFarlane, Ian; Yeo, Giles S H; Lam, Brian Y H (2012-01-13)
      Abstract Background With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http://seqbarracuda.sf.net
    • The barriers and facilitators to the implementation of National Clinical Programmes in Ireland: using the MRC framework for process evaluations.

      Darker, Catherine D; Nicolson, Gail H; Carroll, Aine; Barry, Joe M; 1 - 2. Department of Public Health & Primary Care, Institute of Population Health, School of Medicine, Trinity College Dublin. 3. Clinical Strategy and Programmes Division, Health Service Executive, Dr Steevens' Hospital. 4.School of Medicine, University College Dublin (BMC Health Services Research, 2018-09-24)
      A major healthcare reform agenda in Ireland is underway which underpins the establishment of a series of National Clinical Programmes (NCPs), which aim to take an evidence based approach to improve quality, access and value. The current study aimed to determine the enablers and barriers to implementation of the NCPs. A qualitative methodology advocated by the Medical Research Council (MRC) framework on conducting process evaluations of complex interventions guided this research. Purposive sampling techniques were used to recruit participants from seven NCPs across both acute and chronic healthcare domains, comprised of orthopaedics, rheumatology, elective surgery, emergency medicine, paediatrics, diabetes and chronic obstructive pulmonary disease. A total of 33 participants were interviewed using a semi-structured interview guide. Participants included current and previous Clinical Leads, Programme Managers, Health Service Executive management, hospital Chief Executive Officers, representatives of General Practice, and a Nursing and a Patient representative. Thematic analyses was conducted. A range of factors of different combinations and co-occurrence were highlighted across a total of six themes, including (i) positive leadership, governance and clinical networks of the NCPs, (ii) the political and social context in which the NCPs operate, (iii) constraints on resources, (iv) a passive attitudinal resistance to change borne from poor consultation and communication, (v) lack of data and information technology, (vi) forces outside of the NCPs such as the general practitioner contract thwarting change of the model of care. The MRC framework proved a useful tool to conduct this process evaluation. Results from this research provide real world experiences and insight from the people charged with implementing large-scale health system improvement initiatives. The findings highlight the need for measured responses that acknowledge both direct and non-direct challenges and opportunities for successful change. Combined, it is recommended that these elements be considered in the planning and implementation of large-scale initiatives across healthcare delivery systems, both in Ireland and internationally.
    • Barriers to progressing through a methadone maintenance treatment programme: perspectives of the clients in the Mid-West of Ireland's drug and alcohol services.

      Moran, Lisa; Keenan, Eamon; Elmusharaf, Khalifa (BMC Health Services Research, 2018-11-29)
      The 'perfect' journey through an Irish Methadone Maintenance Treatment Programme (MMTP) would have a client engage appropriately with all relevant services available to them, inclusive of psychiatry, counselling, out-reach support, nursing and psychology. Concurrently, a client would ideally adhere to their prescribed methadone-dosing regimen, until a client is stabilised allowing them to function optimally. At this point, a client should transfer to the GP community setting. Unfortunately, this fails to occur. To date, very few studies have specifically investigated the reasons why a cohort of clients remain 'trapped' in the high risk, specialist clinical setting. Qualitative detailed semi-structured interviews were undertaken with 17 clients of one of Ireland's Health Service Executive (HSE) Drug and Alcohol Services, entitled 'HSE Mid-West Limerick Drug and Alcohol Service'. Each client had a severe Opioid Use Disorder (OUD) and clients had spent on average 7.5 years engaging with the MMTP. Participants' life journey prior to an OUD included Adverse Childhood Experiences (ACEs) and early exposure to illicit drug use. Shared life events resulting in their initiating and sustaining an OUD involved continuous hardship into adulthood, mental illness and concurrent benzodiazepine use disorder, often resulting in harrowing accounts of participants' loneliness and lack of life purpose. Their living environments, an erroneous understanding of their illness and poor communication with allied health professionals further perpetuated their OUD. Positive factors influencing periods of abstinence were familial incentives and a belief in the efficacy of methadone. Clients own suggestions for improving their journeys included employing a multi-sectorial approach to managing OUD and educating themselves and others on opioid agonist treatments. If clients were not progressing appropriately, they themselves suggested enforcing a 'time-limit' on clients to engage with the programme or indeed for their treatment to be postponed. To optimise the functioning of the MMTP, three tasks need to be fulfilled: 1) Reduce the incidences of ACEs, 2) Diagnose and treat clients with a dual diagnosis 3) Educate clients, their families, the public and allied health care professionals on all aspects of OUD. A cross- departmental, inter-governmental approach is needed to address opioid misuse as a societal issue as a whole.
    • Barriers, activities and participation: Incorporating ICF into service planning datasets.

      O'Donovan, MA; Doyle, A; Gallagher, P; Disability Databases Unit, Health Research Board, Dublin, Ireland. (2009-05-21)
      Purpose. Guided by the World Health Organization's International Classification of Functioning, Disability and Health (ICF), a measure of activity and participation (MAP) was developed and incorporated into the National Physical and Sensory Disability Database in Ireland. The aims of this article are to investigate and explore the relationship between the barriers, participation restriction and functioning levels experienced by people with disabilities. Method. Seven thousand five hundred and sixty-two personal interviews with people meeting specific eligibility criteria for registering onto the database were conducted across four health service executive regions in Ireland. Results. Overall, differences in barriers, participation restriction and activity limitations experienced by people with different types of disabilities were found to be significant. Furthermore, low functioning and experience of barriers were indicators of participation restriction. Conclusions. This article has shown that elements of the ICF have been successfully operationalised in a service planning tool through the development of the MAP. This provides a more holistic view of disability and will enable the impact of service interventions to be measured over time.
    • The Bealtaine Festival: a celebration of older people in the arts

      Ni Leime, Aine; O'Shea, Eamon; National University of Ireland, Galway (Age & Opportunity, 2008)
    • Before and after study of bar workers' perceptions of the impact of smoke-free workplace legislation in the Republic of Ireland.

      Pursell, Lisa; Allwright, Shane; O'Donovan, Diarmuid; Paul, Gillian; Kelly, Alan; Mullally, Bernie J; D'Eath, Maureen; Department of Health Promotion, National University of Ireland, Galway, Republic of Ireland. lisa.pursell@nuigalway.ie (2007)
      BACKGROUND: Objectives: To compare support for, and perceptions of, the impacts of smoke-free workplace legislation among bar workers in the Republic of Ireland (ROI) pre- and post-implementation, and to identify predictors of support for the legislation. METHODS: Setting: Public houses (pubs) in three areas of the ROI. Design: Comparisons pre- and post-implementation of smoke-free workplace legislation. Participants: From a largely non-random selection, 288 bar workers volunteered for the baseline survey; 220 were followed up one year later (76.4%). Outcome measures: Level of support for the legislation, attitude statements concerning potential impacts of the law and modelled predictors of support for the legislation. RESULTS: Pre-implementation 59.5% of participants supported the legislation, increasing to 76.8% post-implementation. Support increased among smokers by 27.3 percentage points from 39.4% to 66.7% (p < 0.001) and among non-smokers by 12.4% percentage points from 68.8% to 81.2% (p = 0.003).Pre-legislation three-quarters of participants agreed that the legislation would make bars more comfortable and was needed to protect workers' health. Post-legislation these proportions increased to over 90% (p < 0.001). However, negative perceptions also increased, particularly for perceptions that the legislation has a negative impact on business (from 50.9% to 62.7%, p = 0.008) and that fewer people would visit pubs (41.8% to 62.7%, p < 0.001). After adjusting for relevant covariates, including responses to the attitude statements, support for the ban increased two to three-fold post-implementation. Regardless of their views on the economic impact, most participants agreed, both pre- and post-implementation, that the legislation was needed to protect bar workers' health. CONCLUSION: Smoke-free legislation had the support of three-quarters of a large sample of bar workers in the ROI. However, this group holds complex sets of both positive and negative perspectives on the legislation. Of particular importance is that negative economic perceptions did not diminish the widely held perception that the ban is needed to protect workers' health.
    • Behaviour change techniques targeting both diet and physical activity in type 2 diabetes: A systematic review and meta-analysis

      Cradock, Kevin A; ÓLaighin, Gearóid; Finucane, Francis M; Gainforth, Heather L; Quinlan, Leo R; Ginis, Kathleen A M (2017-02-08)
      Abstract Background Changing diet and physical activity behaviour is one of the cornerstones of type 2 diabetes treatment, but changing behaviour is challenging. The objective of this study was to identify behaviour change techniques (BCTs) and intervention features of dietary and physical activity interventions for patients with type 2 diabetes that are associated with changes in HbA1c and body weight. Methods We performed a systematic review of papers published between 1975–2015 describing randomised controlled trials (RCTs) that focused exclusively on both diet and physical activity. The constituent BCTs, intervention features and methodological rigour of these interventions were evaluated. Changes in HbA1c and body weight were meta-analysed and examined in relation to use of BCTs. Results Thirteen RCTs were identified. Meta-analyses revealed reductions in HbA1c at 3, 6, 12 and 24 months of -1.11 % (12 mmol/mol), -0.67 % (7 mmol/mol), -0.28 % (3 mmol/mol) and -0.26 % (2 mmol/mol) with an overall reduction of -0.53 % (6 mmol/mol [95 % CI -0.74 to -0.32, P < 0.00001]) in intervention groups compared to control groups. Meta-analyses also showed a reduction in body weight of -2.7 kg, -3.64 kg, -3.77 kg and -3.18 kg at 3, 6, 12 and 24 months, overall reduction was -3.73 kg (95 % CI -6.09 to -1.37 kg, P = 0.002). Four of 46 BCTs identified were associated with >0.3 % reduction in HbA1c: ‘instruction on how to perform a behaviour’, ‘behavioural practice/rehearsal’, ‘demonstration of the behaviour’ and ‘action planning’, as were intervention features ‘supervised physical activity’, ‘group sessions’, ‘contact with an exercise physiologist’, ‘contact with an exercise physiologist and a dietitian’, ‘baseline HbA1c >8 %’ and interventions of greater frequency and intensity. Conclusions Diet and physical activity interventions achieved clinically significant reductions in HbA1c at three and six months, but not at 12 and 24 months. Specific BCTs and intervention features identified may inform more effective structured lifestyle intervention treatment strategies for type 2 diabetes.
    • Behavioural change in relation to alcohol exposure in early pregnancy and impact on perinatal outcomes - a prospective cohort study

      Murphy, Deirdre J; Mullally, Aoife; Cleary, Brian J; Fahey, Tom; Barry, Joe (2013-01-16)
      Abstract Background There has been limited research addressing whether behavioural change in relation to alcohol exposure in pregnancy results in better perinatal outcomes. Methods A cohort study of 6725 women who booked for antenatal care and delivered in a large urban teaching hospital in 2010–2011. A detailed history of alcohol consumption pre-pregnancy and during early pregnancy was recorded at the first antenatal visit with follow-up of the mother and infant until discharge following birth. Adverse perinatal outcomes were compared for ‘non-drinkers’, ‘ex-drinkers’ and ‘current drinkers’. Results Of the 6017 (90%) women who reported alcohol consumption prior to pregnancy 3325 (55%) engaged in binge drinking and 266 (4.4%) consumed more than 14 units on average per week. At the time of booking 5649 (94%) women were ex-drinkers and of the 368 women who continued to drink 338 (92%) had a low intake (0–5 units per week), 30 (8%) an excess intake (6-20+ units per week) and 93 (25%) reported at least one episode of binge drinking. Factors associated with continuing to drink in early pregnancy included older maternal age (30–39 years), (OR 1.6; 95% CI 1.3 to 1.8), Irish nationality (OR 3.1; 95% CI 2.2 to 4.3) and smoking (OR 2.6; 95% CI 1.9 to 3.5). Ex-drinkers had similar perinatal outcomes to non-drinkers. Compared to non-drinkers current drinking was associated with an increased risk of intrauterine growth restriction (IUGR) (13% versus 19%, crude OR 1.6; 95% CI 1.1 to 2.2, adjusted OR 1.2; 95% CI 0.8 to 1.8). The greatest risk of IUGR was among women who continued to both drink and smoke, (9% versus 32%, crude OR 4.8; 95% CI 3.3 to 7.0, adjusted OR 4.5; 95% CI 3.1 to 6.7). Conclusions Public Health campaigns need to emphasise the potential health gains of abstaining from both alcohol and smoking in pregnancy.
    • Beliefs, perceptions and behaviours of GPs towards generic medicines

      Dunne, S. S.; Shannon, B.; Cullen, W.; Dunne, C. P. (Family Practice, 2014-06)
    • Benefits of post-operative oral protein supplementation in gastrointestinal surgery patients: A systematic review of clinical trials

      Crickmer, Mike; Dunne, Colum P; O’Regan, Andrew; Coffey, J Calvin; Dunne, Suzanne S (2016)
    • Benign cystic mesothelioma of the appendix presenting in a woman: a case report

      O' Connor, Donal B; Beddy, David; Aremu, Muyiwa A (2010-12-03)
      Abstract Introduction Benign cystic mesothelioma or peritoneal inclusion cysts are rare benign abdominal tumors usually occurring in females of reproductive age. These cysts present as abdominopelvic pain or masses but are often found on imaging or incidentally at surgery. They are commonly associated with pelvic inflammatory disease, endometriosis, or ovarian cysts. We report what is, to the best of our knowledge, the first case of a benign cystic mesothelioma complicating a presentation of acute appendicitis. Case Presentation A 19-year-old Irish Caucasian woman presented with abdominal pain. Imaging suggested appendicitis with abscess formation. She was treated with antibiotics and scheduled for interval appendicectomy. At laparoscopy, an unusual cystic mass was found arising from the appendix. Histology revealed benign cystic mesothelioma. Conclusion We report what is, to the best of our knowledge, the first case of a benign cystic mesothelioma arising from the appendix and complicating a presentation of acute appendicitis. This is a benign pathology, but recurrences are not uncommon. Benign cystic mesothelioma should be included in the differential when investigating pelvic masses or abscesses associated with either appendicitis or pelvic inflammatory disease in women.
    • Benzodiazepine prescribing in children under 15 years of age receiving free medical care on the General Medical Services scheme in Ireland.

      O'Sullivan, K; Reulbach, U; Boland, F; Motterlini, N; Kelly, D; Bennett, K; Fahey, T (BMJ Open, 2015-06)
      While BZD prescribing trends have decreased in recent years, this study shows that a significant proportion of the GMS children population are being prescribed BZD in the long term. This study highlights the need for guidelines for BZD prescribing in children in terms of clinical indication and responsibility, coprescribing, dosage and duration of treatment.
    • Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome.

      Morine, Melissa J; McMonagle, Jolene; Toomey, Sinead; Reynolds, Clare M; Moloney, Aidan P; Gormley, Isobel C; Gaora, Peadar Ó; Roche, Helen M (2010-10-07)
      Abstract Background Currently, a number of bioinformatics methods are available to generate appropriate lists of genes from a microarray experiment. While these lists represent an accurate primary analysis of the data, fewer options exist to contextualise those lists. The development and validation of such methods is crucial to the wider application of microarray technology in the clinical setting. Two key challenges in clinical bioinformatics involve appropriate statistical modelling of dynamic transcriptomic changes, and extraction of clinically relevant meaning from very large datasets. Results Here, we apply an approach to gene set enrichment analysis that allows for detection of bi-directional enrichment within a gene set. Furthermore, we apply canonical correlation analysis and Fisher's exact test, using plasma marker data with known clinical relevance to aid identification of the most important gene and pathway changes in our transcriptomic dataset. After a 28-day dietary intervention with high-CLA beef, a range of plasma markers indicated a marked improvement in the metabolic health of genetically obese mice. Tissue transcriptomic profiles indicated that the effects were most dramatic in liver (1270 genes significantly changed; p < 0.05), followed by muscle (601 genes) and adipose (16 genes). Results from modified GSEA showed that the high-CLA beef diet affected diverse biological processes across the three tissues, and that the majority of pathway changes reached significance only with the bi-directional test. Combining the liver tissue microarray results with plasma marker data revealed 110 CLA-sensitive genes showing strong canonical correlation with one or more plasma markers of metabolic health, and 9 significantly overrepresented pathways among this set; each of these pathways was also significantly changed by the high-CLA diet. Closer inspection of two of these pathways - selenoamino acid metabolism and steroid biosynthesis - illustrated clear diet-sensitive changes in constituent genes, as well as strong correlations between gene expression and plasma markers of metabolic syndrome independent of the dietary effect. Conclusion Bi-directional gene set enrichment analysis more accurately reflects dynamic regulatory behaviour in biochemical pathways, and as such highlighted biologically relevant changes that were not detected using a traditional approach. In such cases where transcriptomic response to treatment is exceptionally large, canonical correlation analysis in conjunction with Fisher's exact test highlights the subset of pathways showing strongest correlation with the clinical markers of interest. In this case, we have identified selenoamino acid metabolism and steroid biosynthesis as key pathways mediating the observed relationship between metabolic health and high-CLA beef. These results indicate that this type of analysis has the potential to generate novel transcriptome-based biomarkers of disease.
    • Bicaudal is a conserved substrate for Drosophila and mammalian caspases and is essential for cell survival.

      Creagh, Emma M; Brumatti, Gabriela; Sheridan, Clare; Duriez, Patrick J; Taylor, Rebecca C; Cullen, Sean P; Adrain, Colin; Martin, Seamus J; Molecular Cell Biology Laboratory, Department of Genetics, Smurfit Institute, Trinity College, Dublin, Ireland [corrected] (2009)
      Members of the caspase family of cysteine proteases coordinate cell death through restricted proteolysis of diverse protein substrates and play a conserved role in apoptosis from nematodes to man. However, while numerous substrates for the mammalian cell death-associated caspases have now been described, few caspase substrates have been identified in other organisms. Here, we have utilized a proteomics-based approach to identify proteins that are cleaved by caspases during apoptosis in Drosophila D-Mel2 cells, a subline of the Schneider S2 cell line. This approach identified multiple novel substrates for the fly caspases and revealed that bicaudal/betaNAC is a conserved substrate for Drosophila and mammalian caspases. RNAi-mediated silencing of bicaudal expression in Drosophila D-Mel2 cells resulted in a block to proliferation, followed by spontaneous apoptosis. Similarly, silencing of expression of the mammalian bicaudal homologue, betaNAC, in HeLa, HEK293T, MCF-7 and MRC5 cells also resulted in spontaneous apoptosis. These data suggest that bicaudal/betaNAC is essential for cell survival and is a conserved target of caspases from flies to man.