• 'I'm a happy little Vegemite, doctor!'.

      O'Malley, Declan; decomalley@yahoo.co.uk (2009-11)
      At the onset of a mild Victorian winter, four enthusiastic, fresh faced Irish general practice registrars made their way to Australia on an academic and cultural exchange. As registrars in the final throws of our fourth year general practice training in Donegal, we swapped the rugged, windswept northwest coast of Ireland for Gippsland in Victoria.
    • The iceberg of suicide and self-harm in Irish adolescents: a population-based study

      McMahon, Elaine M.; Keeley, Helen; Cannon, Mary; Arensman, Ella; Perry, Ivan J.; Clarke, Mary; Chambers, Derek; Corcoran, Paul (Social Psychiatry and Psychiatric Epidemiology, 2014-06)
    • ICORG 10-14: NEOadjuvant trial in Adenocarcinoma of the oEsophagus and oesophagoGastric junction International Study (Neo-AEGIS)

      Reynolds, JV; Preston, SR; O’Neill, B; Baeksgaard, L; Griffin, SM; Mariette, C; Cuffe, S; Cunningham, M; Crosby, T; Parker, I; et al. (2017-06-03)
      Abstract Background Neoadjuvant therapy is increasingly the standard of care in the management of locally advanced adenocarcinoma of the oesophagus and junction (AEG). In randomised controlled trials (RCTs), the MAGIC regimen of pre- and postoperative chemotherapy, and the CROSS regimen of preoperative chemotherapy combined with radiation, were superior to surgery only in RCTs that included AEG but were not powered on this cohort. No completed RCT has directly compared neoadjuvant or perioperative chemotherapy and neoadjuvant chemoradiation. The Neo-AEGIS trial, uniquely powered on AEG, and including comprehensive modern staging, compares both these regimens. Methods This open label, multicentre, phase III RCT randomises patients (cT2-3, N0-3, M0) in a 1:1 fashion to receive CROSS protocol (Carboplatin and Paclitaxel with concurrent radiotherapy, 41.4Gy/23Fr, over 5 weeks). The power calculation is a 10% difference in favour of CROSS, powered at 80%, two-sided alpha level of 0.05, requiring 540 patients to be evaluable, 594 to be recruited if a 10% dropout is included (297 in each group). The primary endpoint is overall survival, with a minimum 3-year follow up. Secondary endpoints include: disease free survival, recurrence rates, clinical and pathological response rates, toxicities of induction regimens, post-operative pathology and tumour regression grade, operative in-hospital complications, and health-related quality of life. The trial also affords opportunities for establishing a bio-resource of pre-treatment and resected tumour, and translational research. Discussion This RCT directly compares two established treatment regimens, and addresses whether radiation therapy positively impacts on overall survival compared with a standard perioperative chemotherapy regimen Sponsor: Irish Clinical Research Group (ICORG). Trial registration NCT01726452 . Protocol 10-14. Date of registration 06/11/2012.
    • Identification and characterisation of eight novel SERPINA1 Null mutations

      Ferrarotti, Ilaria; Carroll, Tomás P; Ottaviani, Stefania; Fra, Anna M; O’Brien, Geraldine; Molloy, Kevin; Corda, Luciano; Medicina, Daniela; Curran, David R; McElvaney, Noel G; et al. (2014-11-26)
      Abstract Background Alpha-1 antitrypsin (AAT) is the most abundant circulating antiprotease and is a member of the serine protease inhibitor (SERPIN) superfamily. The gene encoding AAT is the highly polymorphic SERPINA1 gene, found at 14q32.1. Mutations in the SERPINA1 gene can lead to AAT deficiency (AATD) which is associated with a substantially increased risk of lung and liver disease. The most common pathogenic AAT variant is Z (Glu342Lys) which causes AAT to misfold and polymerise within hepatocytes and other AAT-producing cells. A group of rare mutations causing AATD, termed Null or Q0, are characterised by a complete absence of AAT in the plasma. While ultra rare, these mutations confer a particularly high risk of emphysema. Methods We performed the determination of AAT serum levels by a rate immune nephelometric method or by immune turbidimetry. The phenotype was determined by isoelectric focusing analysis on agarose gel with specific immunological detection. DNA was isolated from whole peripheral blood or dried blood spot (DBS) samples using a commercial extraction kit. The new mutations were identified by sequencing all coding exons (II-V) of the SERPINA1 gene. Results We have found eight previously unidentified SERPINA1 Null mutations, named: Q0cork, Q0perugia, Q0brescia, Q0torino, Q0cosenza, Q0pordenone, Q0lampedusa, and Q0dublin . Analysis of clinical characteristics revealed evidence of the recurrence of lung symptoms (dyspnoea, cough) and lung diseases (emphysema, asthma, chronic bronchitis) in M/Null subjects, over 45 years-old, irrespective of smoking. Conclusions We have added eight more mutations to the list of SERPINA1 Null alleles. This study underlines that the laboratory diagnosis of AATD is not just a matter of degree, because the precise determination of the deficiency and Null alleles carried by an AATD individual may help to evaluate the risk for the lung disease.
    • Identification and verification of ultrafine particle affinity zones in urban neighbourhoods: sample design and data pre-processing.

      Harris, Paul; Lindley, Sarah; Gallagher, Martin; Agius, Raymond; National Centre for Geocomputation, National University of Ireland, Maynooth, UK. Paul.Harris@nuim.ie (2009)
      A methodology is presented and validated through which long-term fixed site air quality measurements are used to characterise and remove temporal signals in sample-based measurements which have good spatial coverage but poor temporal resolution. The work has been carried out specifically to provide a spatial dataset of atmospheric ultrafine particle (UFP < 100 nm) data for ongoing epidemiologic cohort analysis but the method is readily transferable to wider epidemiologic investigations and research into the health effects of other pollutant species.
    • Identification of a Myometrial Molecular Profile for Dystocic Labor

      Brennan, Donal J; McGee, Sharon F; Rexhepaj, Elton; O'Connor, Darran P; Robson, Michael; O'Herlihy, Colm (2011-10-16)
      Abstract Background The most common indication for cesarean section (CS) in nulliparous women is dystocia secondary to ineffective myometrial contractility. The aim of this study was to identify a molecular profile in myometrium associated with dystocic labor. Methods Myometrial biopsies were obtained from the upper incisional margins of nulliparous women undergoing lower segment CS for dystocia (n = 4) and control women undergoing CS in the second stage who had demonstrated efficient uterine action during the first stage of labor (n = 4). All patients were in spontaneous (non-induced) labor and had received intrapartum oxytocin to accelerate labor. RNA was extracted from biopsies and hybridized to Affymetrix HuGene U133A Plus 2 microarrays. Internal validation was performed using quantitative SYBR Green Real-Time PCR. Results Seventy genes were differentially expressed between the two groups. 58 genes were down-regulated in the dystocia group. Gene ontology analysis revealed 12 of the 58 down-regulated genes were involved in the immune response. These included (ERAP2, (8.67 fold change (FC)) HLA-DQB1 (7.88 FC) CD28 (2.60 FC), LILRA3 (2.87 FC) and TGFBR3 (2.1 FC)) Hierarchical clustering demonstrated a difference in global gene expression patterns between the samples from dystocic and non-dystocic labours. RT-PCR validation was performed on 4 genes ERAP2, CD28, LILRA3 and TGFBR3 Conclusion These findings suggest an underlying molecular basis for dystocia in nulliparous women in spontaneous labor. Differentially expressed genes suggest an important role for the immune response in dystocic labor and may provide important indicators for new diagnostic assays and potential intrapartum therapeutic targets.
    • Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models

      Lacerda, Miguel; Moore, Penny L; Ngandu, Nobubelo K; Seaman, Michael; Gray, Elin S; Murrell, Ben; Krishnamoorthy, Mohan; Nonyane, Molati; Madiga, Maphuti; Wibmer, Constantinos K; et al. (2013-12-02)
      Abstract Background Identification of the epitopes targeted by antibodies that can neutralize diverse HIV-1 strains can provide important clues for the design of a preventative vaccine. Methods We have developed a computational approach that can identify key amino acids within the HIV-1 envelope glycoprotein that influence sensitivity to broadly cross-neutralizing antibodies. Given a sequence alignment and neutralization titers for a panel of viruses, the method works by fitting a phylogenetic model that allows the amino acid frequencies at each site to depend on neutralization sensitivities. Sites at which viral evolution influences neutralization sensitivity were identified using Bayes factors (BFs) to compare the fit of this model to that of a null model in which sequences evolved independently of antibody sensitivity. Conformational epitopes were identified with a Metropolis algorithm that searched for a cluster of sites with large Bayes factors on the tertiary structure of the viral envelope. Results We applied our method to ID50 neutralization data generated from seven HIV-1 subtype C serum samples with neutralization breadth that had been tested against a multi-clade panel of 225 pseudoviruses for which envelope sequences were also available. For each sample, between two and four sites were identified that were strongly associated with neutralization sensitivity (2ln(BF) > 6), a subset of which were experimentally confirmed using site-directed mutagenesis. Conclusions Our results provide strong support for the use of evolutionary models applied to cross-sectional viral neutralization data to identify the epitopes of serum antibodies that confer neutralization breadth.
    • Identification of endogenous control genes for normalisation of real-time quantitative PCR data in colorectal cancer.

      Kheirelseid, Elrasheid A H; Chang, Kah Hoong; Newell, John; Kerin, Michael J; Miller, Nicola; Department of Surgery, National University of Ireland, Galway, Ireland. (2010)
      BACKGROUND: Gene expression analysis has many applications in cancer diagnosis, prognosis and therapeutic care. Relative quantification is the most widely adopted approach whereby quantification of gene expression is normalised relative to an endogenously expressed control (EC) gene. Central to the reliable determination of gene expression is the choice of control gene. The purpose of this study was to evaluate a panel of candidate EC genes from which to identify the most stably expressed gene(s) to normalise RQ-PCR data derived from primary colorectal cancer tissue. RESULTS: The expression of thirteen candidate EC genes: B2M, HPRT, GAPDH, ACTB, PPIA, HCRT, SLC25A23, DTX3, APOC4, RTDR1, KRTAP12-3, CHRNB4 and MRPL19 were analysed in a cohort of 64 colorectal tumours and tumour associated normal specimens. CXCL12, FABP1, MUC2 and PDCD4 genes were chosen as target genes against which a comparison of the effect of each EC gene on gene expression could be determined. Data analysis using descriptive statistics, geNorm, NormFinder and qBasePlus indicated significant difference in variances between candidate EC genes. We determined that two genes were required for optimal normalisation and identified B2M and PPIA as the most stably expressed and reliable EC genes. CONCLUSION: This study identified that the combination of two EC genes (B2M and PPIA) more accurately normalised RQ-PCR data in colorectal tissue. Although these control genes might not be optimal for use in other cancer studies, the approach described herein could serve as a template for the identification of valid ECs in other cancer types.
    • Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences.

      Ivanov, Ivaylo P; Firth, Andrew E; Michel, Audrey M; Atkins, John F; Baranov, Pavel V; BioSciences Institute, University College Cork, Cork, Ireland. iivanov@genetics.utah.edu (2011-05)
      In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5' cap. However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG, UUG, GUG, ACG, AUA and AUU. While non-AUG initiation has been experimentally verified for a handful of human genes, the full extent to which this phenomenon is utilized--both for increased coding capacity and potentially also for novel regulatory mechanisms--remains unclear. To address this issue, and hence to improve the quality of existing coding sequence annotations, we developed a methodology based on phylogenetic analysis of predicted 5' untranslated regions from orthologous genes. We use evolutionary signatures of protein-coding sequences as an indicator of translation initiation upstream of annotated coding sequences. Our search identified novel conserved potential non-AUG-initiated N-terminal extensions in 42 human genes including VANGL2, FGFR1, KCNN4, TRPV6, HDGF, CITED2, EIF4G3 and NTF3, and also affirmed the conservation of known non-AUG-initiated extensions in 17 other genes. In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data.
    • Identification of genes involved in the mutualistic colonization of the nematode Heterorhabditis bacteriophora by the bacterium Photorhabdus luminescens.

      Easom, Catherine A; Joyce, Susan A; Clarke, David J; Department of Microbiology, University College Cork, Ireland. david.clarke@ucc.ie. (2010)
      ABSTRACT: BACKGROUND: Photorhabdus are Gram negative entomopathogenic bacteria that also have a mutualistic association with nematodes from the family Heterorhabditis. An essential part of this symbiosis is the ability of the bacterium to colonize the gut of the freeliving form of the nematode called the infective juvenile (IJ). Although the colonization process (also called transmission) has been described phenomonologically very little is known about the underlying molecular mechanisms. Therefore, in this study, we were interested in identifying genes in Photorhabdus that are important for IJ colonization. RESULTS: In this work we genetically tagged P. luminescens TT01 with gfp and constructed a library containing over 3200 mutants using the suicide vector, pUT-Km2. Using a combination of in vitro symbiosis assays and fluorescent microscopy we screened this library for mutants that were affected in their ability to colonize the IJ i.e. with decreased transmission frequencies. In total 8 mutants were identified with transmission frequencies of
    • Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds

      McKeown, Peter C; Laouielle-Duprat, Sylvia; Prins, Pjotr; Wolff, Philip; Schmid, Marc W; Donoghue, Mark T.A.; Fort, Antoine; Duszynska, Dorota; Comte, Aurelie; Lao, Nga THI; et al. (2011-08-12)
      Abstract Background Epigenetic regulation of gene dosage by genomic imprinting of some autosomal genes facilitates normal reproductive development in both mammals and flowering plants. While many imprinted genes have been identified and intensively studied in mammals, smaller numbers have been characterized in flowering plants, mostly in Arabidopsis thaliana. Identification of additional imprinted loci in flowering plants by genome-wide screening for parent-of-origin specific uniparental expression in seed tissues will facilitate our understanding of the origins and functions of imprinted genes in flowering plants. Results cDNA-AFLP can detect allele-specific expression that is parent-of-origin dependent for expressed genes in which restriction site polymorphisms exist in the transcripts derived from each allele. Using a genome-wide cDNA-AFLP screen surveying allele-specific expression of 4500 transcript-derived fragments, we report the identification of 52 maternally expressed genes (MEGs) displaying parent-of-origin dependent expression patterns in Arabidopsis siliques containing F1 hybrid seeds (3, 4 and 5 days after pollination). We identified these MEGs by developing a bioinformatics tool (GenFrag) which can directly determine the identities of transcript-derived fragments from (i) their size and (ii) which selective nucleotides were added to the primers used to generate them. Hence, GenFrag facilitates increased throughput for genome-wide cDNA-AFLP fragment analyses. The 52 MEGs we identified were further filtered for high expression levels in the endosperm relative to the seed coat to identify the candidate genes most likely representing novel imprinted genes expressed in the endosperm of Arabidopsis thaliana. Expression in seed tissues of the three top-ranked candidate genes, ATCDC48, PDE120 and MS5-like, was confirmed by Laser-Capture Microdissection and qRT-PCR analysis. Maternal-specific expression of these genes in Arabidopsis thaliana F1 seeds was confirmed via allele-specific transcript analysis across a range of different accessions. Differentially methylated regions were identified adjacent to ATCDC48 and PDE120, which may represent candidate imprinting control regions. Finally, we demonstrate that expression levels of these three genes in vegetative tissues are MET1-dependent, while their uniparental maternal expression in the seed is not dependent on MET1. Conclusions Using a cDNA-AFLP transcriptome profiling approach, we have identified three genes, ATCDC48, PDE120 and MS5-like which represent novel maternally expressed imprinted genes in the Arabidopsis thaliana seed. The extent of overlap between our cDNA-AFLP screen for maternally expressed imprinted genes, and other screens for imprinted and endosperm-expressed genes is discussed.
    • Identification of mechanosensitive genes during skeletal development: alteration of genes associated with cytoskeletal rearrangement and cell signalling pathways

      Rolfe, Rebecca A; Nowlan, Niamh C; Kenny, Elaine M; Cormican, Paul; Morris, Derek W; Prendergast, Patrick J; Kelly, Daniel; Murphy, Paula (2014-01-20)
      Abstract Background Mechanical stimulation is necessary for regulating correct formation of the skeleton. Here we test the hypothesis that mechanical stimulation of the embryonic skeletal system impacts expression levels of genes implicated in developmentally important signalling pathways in a genome wide approach. We use a mutant mouse model with altered mechanical stimulation due to the absence of limb skeletal muscle (Splotch-delayed) where muscle-less embryos show specific defects in skeletal elements including delayed ossification, changes in the size and shape of cartilage rudiments and joint fusion. We used Microarray and RNA sequencing analysis tools to identify differentially expressed genes between muscle-less and control embryonic (TS23) humerus tissue. Results We found that 680 independent genes were down-regulated and 452 genes up-regulated in humeri from muscle-less Spd embryos compared to littermate controls (at least 2-fold; corrected p-value ≤0.05). We analysed the resulting differentially expressed gene sets using Gene Ontology annotations to identify significant enrichment of genes associated with particular biological processes, showing that removal of mechanical stimuli from muscle contractions affected genes associated with development and differentiation, cytoskeletal architecture and cell signalling. Among cell signalling pathways, the most strongly disturbed was Wnt signalling, with 34 genes including 19 pathway target genes affected. Spatial gene expression analysis showed that both a Wnt ligand encoding gene (Wnt4) and a pathway antagonist (Sfrp2) are up-regulated specifically in the developing joint line, while the expression of a Wnt target gene, Cd44, is no longer detectable in muscle-less embryos. The identification of 84 genes associated with the cytoskeleton that are down-regulated in the absence of muscle indicates a number of candidate genes that are both mechanoresponsive and potentially involved in mechanotransduction, converting a mechanical stimulus into a transcriptional response. Conclusions This work identifies key developmental regulatory genes impacted by altered mechanical stimulation, sheds light on the molecular mechanisms that interpret mechanical stimulation during skeletal development and provides valuable resources for further investigation of the mechanistic basis of mechanoregulation. In particular it highlights the Wnt signalling pathway as a potential point of integration of mechanical and molecular signalling and cytoskeletal components as mediators of the response.
    • Identification of proteins found to be significantly altered when comparing the serum proteome from Multiple Myeloma patients with varying degrees of bone disease

      Dowling, Paul; Hayes, Catriona; Ting, Kay R; Hameed, Abdul; Meiller, Justine; Mitsiades, Constantine; Anderson, Kenneth C; Clynes, Martin; Clarke, Colin; Richardson, Paul; et al. (2014-10-17)
      Abstract Background Bone destruction is a feature of multiple myeloma, characterised by osteolytic bone destruction due to increased osteoclast activity and suppressed or absent osteoblast activity. Almost all multiple myeloma patients develop osteolytic bone lesions associated with severe and debilitating bone pain, pathologic fractures, hypercalcemia, and spinal cord compression, as well as increased mortality. Biomarkers of bone remodelling are used to identify disease characteristics that can help select the optimal management of patients. However, more accurate biomarkers are needed to effectively mirror the dynamics of bone disease activity. Results A label-free mass spectrometry-based strategy was employed for discovery phase analysis of fractionated patient serum samples associated with no or high bone disease. A number of proteins were identified which were statistically significantly correlated with bone disease, including enzymes, extracellular matrix glycoproteins, and components of the complement system. Conclusions Enzyme-linked immunosorbent assay of complement C4 and serum paraoxonase/arylesterase 1 indicated that these proteins were associated with high bone disease in a larger independent cohort of patient samples. These biomolecules may therefore be clinically useful in assessing the extent of bone disease.
    • Identifying and prioritising midwifery care process metrics and indicators: a Delphi survey and stakeholder consensus process.

      Devane, Declan; Barrett, Nora; Gallen, Anne; O'Reilly, Mary Frances; Nadin, Margaret; Conway, Gillian; Biesty, Linda; Smith, Valerie (2019-06-10)
    • Identifying malnourished patients Nurses in Beaumont Hospital driving change

      Corcoran, Mary (Nursing in General Practice, 2015-07)
    • Identifying strategies to maximise recruitment and retention of practices and patients in a multicentre randomised controlled trial of an intervention to optimise secondary prevention for coronary heart disease in primary care.

      Leathem, Claire S; Cupples, Margaret E; Byrne, Mary C; O'Malley, Mary; Houlihan, Ailish; Murphy, Andrew W; Smith, Susan M; Department of General Practice, National University of Ireland, Galway, Ireland. c.leathem@qub.ac.uk (2009)
      BACKGROUND: Recruitment and retention of patients and healthcare providers in randomised controlled trials (RCTs) is important in order to determine the effectiveness of interventions. However, failure to achieve recruitment targets is common and reasons why a particular recruitment strategy works for one study and not another remain unclear. We sought to describe a strategy used in a multicentre RCT in primary care, to report researchers' and participants' experiences of its implementation and to inform future strategies to maximise recruitment and retention. METHODS: In total 48 general practices and 903 patients were recruited from three different areas of Ireland to a RCT of an intervention designed to optimise secondary prevention of coronary heart disease. The recruitment process involved telephoning practices, posting information, visiting practices, identifying potential participants, posting invitations and obtaining consent. Retention involved patients attending reviews and responding to questionnaires and practices facilitating data collection. RESULTS: We achieved high retention rates for practices (100%) and for patients (85%) over an 18-month intervention period. Pilot work, knowledge of the setting, awareness of change in staff and organisation amongst participant sites, rapid responses to queries and acknowledgement of practitioners' contributions were identified as being important. Minor variations in protocol and research support helped to meet varied, complex and changing individual needs of practitioners and patients and encouraged retention in the trial. A collaborative relationship between researcher and practice staff which required time to develop was perceived as vital for both recruitment and retention. CONCLUSION: Recruiting and retaining the numbers of practices and patients estimated as required to provide findings with adequate power contributes to increased confidence in the validity and generalisability of RCT results. A continuous dynamic process of monitoring progress within trials and tailoring strategies to particular circumstances, whilst not compromising trial protocols, should allow maximal recruitment and retention. TRIAL REGISTRATION: ISRCTN24081411.
    • Identifying the Optimum Role and Function of an Epidermolysis Bullosa (EB) Outreach Nurse

      Donohoe, Ann; Kearney, Sandra; McAuliffe, Eilish; School of Nursing, Midwifery and Health Systems at University College Dublin. (School of Nursing, Midwifery and Health Systems at University College Dublin., 2018-07)
    • Idiopathic toe walking: a gait laboratory review

      O’Sullivan, R; O'Brien, T (Irish Medical Journal, 2015-07)
    • "If you can't treat HPV, why test for it?" Women's attitudes to the changing face of cervical cancer prevention: a focus group study

      McRae, Judith; Martin, Cara; O’Leary, John; Sharp, Linda; Irish Cervical Screening Research Consortium (CERVIVA) (2014-05-06)
      Abstract Background The relationship between infection with high-risk strains of human papillomavirus (HPV) and cervical cancer is transforming prevention through HPV vaccination and HPV oncogenic testing. In Ireland, a national cervical cancer screening programme and HPV vaccination were recently launched; HPV testing is currently being integrated into the screening programme. Women’s views on the transformation of cervical cancer prevention have been relatively little investigated. Methods Using qualitative focus groups, we determined women’s knowledge, attitudes towards, and acceptability of cervical cancer screening, HPV oncogenic testing and vaccination of HPV. Fifty nine women, recruited through primary care in Ireland, participated in ten focus groups. A dynamic topic guide was developed from literature reviewed. Women were provided with standardised information about HPV infection, HPV testing. Discussion transcripts were analysed thematically. Results The primary themes that emerged regarding HPV infection were: knowledge, emotional response and societal influences; especially those of healthcare practitioners. Knowledge, logistics, and psychological impact were the primary themes relating to HPV testing. Women’s attitudes towards HPV testing changed during discussion as issues were explored, thus demonstrating the complexity of this issue; lack of existing treatment for HPV infection influenced women’s attitudes, attachment to existing cervical cancer screening also was a significant factor. Conclusions Women currently have a strong attachment to cytology and any changes towards HPV primary testing will need to be managed carefully. To ensure that future cervical cancer prevention strategies will be acceptable to women, sufficient thought will have to be given to information provision and education. We identified the importance to women of healthcare practitioners’ opinions regarding HPV. Appropriate and timely information on HPV will be crucial in order to minimise possible psychological effects women may have.