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Roche Helen M - One of the best experts on this subject based on the ideXlab platform.

  • Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome.
    2012
    Co-Authors: Morine Melissa J, Gormley Isobel C, Moloney Aidan P, Reynolds Clare M, Toomey Sinead, Mcmonagle Jolene, Gaora O Peadar, Roche Helen M
    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\u27s 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\u27s 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.Department of Agriculture and Food, Ireland - Food Institutional Research Measure (Project no. 5254); IRCSET postgraduate scholarship scheme (MJM); Science Foundation Ireland Principal Investigator Programme (HMR) Programme

  • Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome.
    2010
    Co-Authors: Morine Melissa J, Gormley Isobel C, Moloney Aidan P, Reynolds Clare M, Toomey Sinead, Mcmonagle Jolene, Gaora O Peadar, Roche Helen M
    Abstract:

    peer-reviewedBackground 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.Department of Agriculture and Food, Ireland - Food Institutional Research Measure (Project no. 5254); IRCSET postgraduate scholarship scheme (MJM); Science Foundation Ireland Principal Investigator Programme (HMR) Programme

Rai, Dilip K. - One of the best experts on this subject based on the ideXlab platform.

  • Impact of pulsed electric field pre-treatment on nutritional and polyphenolic contents and bioactivities of light and dark brewer's spent grains
    2019
    Co-Authors: Kumari Bibha, Tiwari, Brijesh K, Walsh Des, Griffin Tomás, Islam Nahidul, Lyng, James G., Brunton Nigel, Rai, Dilip K.
    Abstract:

    peer-reviewedPulsed electric field (PEF) pre-treatment, at 2.8 kV/cm with 3000 pulses of 20 μs pulse-width, was applied on brewer's spent grains (BSG) followed by aqueous extraction at 55 °C, 220 rpm for 16 h. PEF pre-treatment showed significantly increased yields (p 50 mg/mL) with lowest MIC value of 1.56 mg/mL against Staphylococcus aureus. All the BSG extracts induced the release of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and chemokines (IL-8, MCP-1 and MIP-1α) confirming immunomodulatory activity.The authors acknowledge financial support from the ‘NovTechIng’ Project funded under the Food Institutional Research Measure (Project No. FIRM/11/F/050) by the Irish Department of Agriculture, Food and Marine. The immunomodulatory study was performed using funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 634086 (NEPHSTROM). TPG is funded by a Hardiman Research Scholarship from the College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway.The authors acknowledge financial support from the ‘NovTechIng’ Project funded under the Food Institutional Research Measure (Project No. FIRM/11/F/050) by the Irish Department of Agriculture, Food and Marine. The immunomodulatory study was performed using funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 634086 (NEPHSTROM). TPG is funded by a Hardiman Research Scholarship from the College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway

  • Impact of pulsed electric field pre-treatment on nutritional and polyphenolic contents and bioactivities of light and dark brewer\u27s spent grains
    2019
    Co-Authors: Kumari Bibha, Walsh Des, Griffin Tomás, Islam Nahidul, Lyng, James G., Brunton Nigel, Tiwari Brijesh, Rai, Dilip K.
    Abstract:

    Pulsed electric field (PEF) pre-treatment, at 2.8 kV/cm with 3000 pulses of 20 μs pulse-width, was applied on brewer\u27s spent grains (BSG) followed by aqueous extraction at 55 °C, 220 rpm for 16 h. PEF pre-treatment showed significantly increased yields (p 50 mg/mL) with lowest MIC value of 1.56 mg/mL against Staphylococcus aureus. All the BSG extracts induced the release of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and chemokines (IL-8, MCP-1 and MIP-1α) confirming immunomodulatory activity.The authors acknowledge financial support from the ‘NovTechIng’ Project funded under the Food Institutional Research Measure (Project No. FIRM/11/F/050) by the Irish Department of Agriculture, Food and Marine. The immunomodulatory study was performed using funding from the European Union\u27s Horizon 2020 research and innovation programme under grant agreement No 634086 (NEPHSTROM). TPG is funded by a Hardiman Research Scholarship from the College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway

Morine Melissa J - One of the best experts on this subject based on the ideXlab platform.

  • Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome.
    2012
    Co-Authors: Morine Melissa J, Gormley Isobel C, Moloney Aidan P, Reynolds Clare M, Toomey Sinead, Mcmonagle Jolene, Gaora O Peadar, Roche Helen M
    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\u27s 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\u27s 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.Department of Agriculture and Food, Ireland - Food Institutional Research Measure (Project no. 5254); IRCSET postgraduate scholarship scheme (MJM); Science Foundation Ireland Principal Investigator Programme (HMR) Programme

  • Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome.
    2010
    Co-Authors: Morine Melissa J, Gormley Isobel C, Moloney Aidan P, Reynolds Clare M, Toomey Sinead, Mcmonagle Jolene, Gaora O Peadar, Roche Helen M
    Abstract:

    peer-reviewedBackground 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.Department of Agriculture and Food, Ireland - Food Institutional Research Measure (Project no. 5254); IRCSET postgraduate scholarship scheme (MJM); Science Foundation Ireland Principal Investigator Programme (HMR) Programme

Stuart Tennant - One of the best experts on this subject based on the ideXlab platform.

  • construction site management team working a serendipitous event
    2011
    Co-Authors: Stuart Tennant, David Langford, Michael Murray
    Abstract:

    Despite the pervasive appeal of team working in the construction industry, the empirical relationship between team effectiveness and task performance continues to be generally overlooked. Recognized team performance appraisal remains one of the last frontiers of performance management. This paper sets out to challenge the conventional discourse of team working and test the hypothesis that construction site management team working and Project performance is unrelated. The explanatory case-study research method utilizes a variety of data-gathering techniques. An attitude statement questionnaire evaluates team efficacy. A customized suite of key performance indicators sympathetic to Project performance is used to Measure Project success. Statistical examination of the data demonstrates a marked correlation between the two variables. Although the results authenticate the universally acclaimed wisdom; teams and performance are inextricably linked, secondary analysis expose widespread contradictions between the rhetoric of team working and the action of practice. Obstacles to team working include management indifference towards substantive team building, organizational barriers to communication, and the absence of team rewards. A paradigm of individualism predominates, abetted by organizational structures and cultural subsystems that uphold individual answerability at the expense of collective responsibility.

Kumari Bibha - One of the best experts on this subject based on the ideXlab platform.

  • Impact of pulsed electric field pre-treatment on nutritional and polyphenolic contents and bioactivities of light and dark brewer's spent grains
    2019
    Co-Authors: Kumari Bibha, Tiwari, Brijesh K, Walsh Des, Griffin Tomás, Islam Nahidul, Lyng, James G., Brunton Nigel, Rai, Dilip K.
    Abstract:

    peer-reviewedPulsed electric field (PEF) pre-treatment, at 2.8 kV/cm with 3000 pulses of 20 μs pulse-width, was applied on brewer's spent grains (BSG) followed by aqueous extraction at 55 °C, 220 rpm for 16 h. PEF pre-treatment showed significantly increased yields (p 50 mg/mL) with lowest MIC value of 1.56 mg/mL against Staphylococcus aureus. All the BSG extracts induced the release of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and chemokines (IL-8, MCP-1 and MIP-1α) confirming immunomodulatory activity.The authors acknowledge financial support from the ‘NovTechIng’ Project funded under the Food Institutional Research Measure (Project No. FIRM/11/F/050) by the Irish Department of Agriculture, Food and Marine. The immunomodulatory study was performed using funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 634086 (NEPHSTROM). TPG is funded by a Hardiman Research Scholarship from the College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway.The authors acknowledge financial support from the ‘NovTechIng’ Project funded under the Food Institutional Research Measure (Project No. FIRM/11/F/050) by the Irish Department of Agriculture, Food and Marine. The immunomodulatory study was performed using funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 634086 (NEPHSTROM). TPG is funded by a Hardiman Research Scholarship from the College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway

  • Impact of pulsed electric field pre-treatment on nutritional and polyphenolic contents and bioactivities of light and dark brewer\u27s spent grains
    2019
    Co-Authors: Kumari Bibha, Walsh Des, Griffin Tomás, Islam Nahidul, Lyng, James G., Brunton Nigel, Tiwari Brijesh, Rai, Dilip K.
    Abstract:

    Pulsed electric field (PEF) pre-treatment, at 2.8 kV/cm with 3000 pulses of 20 μs pulse-width, was applied on brewer\u27s spent grains (BSG) followed by aqueous extraction at 55 °C, 220 rpm for 16 h. PEF pre-treatment showed significantly increased yields (p 50 mg/mL) with lowest MIC value of 1.56 mg/mL against Staphylococcus aureus. All the BSG extracts induced the release of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and chemokines (IL-8, MCP-1 and MIP-1α) confirming immunomodulatory activity.The authors acknowledge financial support from the ‘NovTechIng’ Project funded under the Food Institutional Research Measure (Project No. FIRM/11/F/050) by the Irish Department of Agriculture, Food and Marine. The immunomodulatory study was performed using funding from the European Union\u27s Horizon 2020 research and innovation programme under grant agreement No 634086 (NEPHSTROM). TPG is funded by a Hardiman Research Scholarship from the College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway