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Search Results: 1 - 10 of 3347 matches for " Santiyagu Francis "
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Expression profiling identifies genes involved in emphysema severity
Santiyagu Francis, Jill E Larsen, Sandra J Pavey, Rayleen V Bowman, Nicholas K Hayward, Kwun M Fong, Ian A Yang
Respiratory Research , 2009, DOI: 10.1186/1465-9921-10-81
Abstract: Gene expression profiling was performed on total RNA extracted from non-tumor lung tissue from 30 smokers with emphysema. Class comparison analysis based on gas transfer measurement was performed to identify differentially expressed genes. Genes were then selected for technical validation by quantitative reverse transcriptase-PCR (qRT-PCR) if also represented on microarray platforms used in previously published emphysema studies. Genes technically validated advanced to tests of biological replication by qRT-PCR using an independent test set of 62 lung samples.Class comparison identified 98 differentially expressed genes (p < 0.01). Fifty-one of those genes had been previously evaluated in differentiation between normal and severe emphysema lung. qRT-PCR confirmed the direction of change in expression in 29 of the 51 genes and 11 of those validated, remaining significant at p < 0.05. Biological replication in an independent cohort confirmed the altered expression of eight genes, with seven genes differentially expressed by greater than 1.3 fold, identifying these as candidate determinants of emphysema severity.Gene expression profiling of lung from emphysema patients identified seven candidate genes associated with emphysema severity including COL6A3, SERPINF1, ZNHIT6, NEDD4, CDKN2A, NRN1 and GSTM3.Chronic obstructive pulmonary disease (COPD) is a major health burden worldwide [1]. Smoking is the primary cause of COPD, with up to 50% of smokers developing the disease [2]. It is frequently under-diagnosed and under-treated [3] since its early stages are often asymptomatic. COPD patients are classified into mild, moderate and severe based on the degree of airflow limitation, which is a result of damage in the large airways (bronchitis), small airways (bronchiolitis) and or alveoli (emphysema). Emphysema affects 40% of heavy smokers [4] and causes loss of elastic recoil, leading to abnormal gas exchange and breathlessness. Despite smoking cessation, some individuals con
Genes and Gene Ontologies Common to Airflow Obstruction and Emphysema in the Lungs of Patients with COPD
Santiyagu M. Savarimuthu Francis,Jill E. Larsen,Sandra J. Pavey,Edwina E. Duhig,Belinda E. Clarke,Rayleen V. Bowman,Nick K. Hayward,Kwun M. Fong,Ian A. Yang
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0017442
Abstract: Chronic obstructive pulmonary disease (COPD) is a major public health problem with increasing prevalence worldwide. The primary aim of this study was to identify genes and gene ontologies associated with COPD severity. Gene expression profiling was performed on total RNA extracted from lung tissue of 18 former smokers with COPD. Class comparison analysis on mild (n = 9, FEV1 80–110% predicted) and moderate (n = 9, FEV1 50–60% predicted) COPD patients identified 46 differentially expressed genes (p<0.01), of which 14 genes were technically confirmed by quantitative real-time-PCR. Biological replication in an independent test set of 58 lung samples confirmed the altered expression of ten genes with increasing COPD severity, with eight of these genes (NNMT, THBS1, HLA-DPB1, IGHD, ETS2, ELF1, PTGDS and CYRBD1) being differentially expressed by greater than 1.8 fold between mild and moderate COPD, identifying these as candidate determinants of COPD severity. These genes belonged to ontologies potentially implicated in COPD including angiogenesis, cell migration, proliferation and apoptosis. Our secondary aim was to identify gene ontologies common to airway obstruction, indicated by impaired FEV1 and KCO. Using gene ontology enrichment analysis we have identified relevant biological and molecular processes including regulation of cell-matrix adhesion, leukocyte activation, cell and substrate adhesion, cell adhesion, angiogenesis, cell activation that are enriched among genes involved in airflow obstruction. Exploring the functional significance of these genes and their gene ontologies will provide clues to molecular changes involved in severity of COPD, which could be developed as targets for therapy or biomarkers for early diagnosis.
Array-Comparative Genomic Hybridization Reveals Loss of SOCS6 Is Associated with Poor Prognosis in Primary Lung Squamous Cell Carcinoma
Krishna B. Sriram, Jill E. Larsen, Santiyagu M. Savarimuthu Francis, Casey M. Wright, Belinda E. Clarke, Edwina E. Duhig, Kevin M. Brown, Nicholas K. Hayward, Ian A. Yang, Rayleen V. Bowman, Kwun M. Fong
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0030398
Abstract: Background Primary tumor recurrence commonly occurs after surgical resection of lung squamous cell carcinoma (SCC). Little is known about the genes driving SCC recurrence. Methods We used array comparative genomic hybridization (aCGH) to identify genes affected by copy number alterations that may be involved in SCC recurrence. Training and test sets of resected primary lung SCC were assembled. aCGH was used to determine genomic copy number in a training set of 62 primary lung SCCs (28 with recurrence and 34 with no evidence of recurrence) and the altered copy number of candidate genes was confirmed by quantitative PCR (qPCR). An independent test set of 72 primary lung SCCs (20 with recurrence and 52 with no evidence of recurrence) was used for biological validation. mRNA expression of candidate genes was studied using qRT-PCR. Candidate gene promoter methylation was evaluated using methylation microarrays and Sequenom EpiTYPER analysis. Results 18q22.3 loss was identified by aCGH as being significantly associated with recurrence (p = 0.038). Seven genes within 18q22.3 had aCGH copy number loss associated with recurrence but only SOCS6 copy number was both technically replicated by qPCR and biologically validated in the test set. SOCS6 copy number loss correlated with reduced mRNA expression in the study samples and in the samples with copy number loss, there was a trend for increased methylation, albeit non-significant. Overall survival was significantly poorer in patients with SOCS6 loss compared to patients without SOCS6 loss in both the training (30 vs. 43 months, p = 0.023) and test set (27 vs. 43 months, p = 0.010). Conclusion Reduced copy number and mRNA expression of SOCS6 are associated with disease recurrence in primary lung SCC and may be useful prognostic biomarkers.
MS4A1 Dysregulation in Asbestos-Related Lung Squamous Cell Carcinoma Is Due to CD20 Stromal Lymphocyte Expression
Casey M. Wright, Santiyagu M. Savarimuthu Francis, Maxine E. Tan, Maria U. Martins, Clay Winterford, Morgan R. Davidson, Edwina E. Duhig, Belinda E. Clarke, Nicholas K. Hayward, Ian A. Yang, Rayleen V. Bowman, Kwun M. Fong
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0034943
Abstract: Asbestos-related lung cancer accounts for 4–12% of lung cancers worldwide. We have previously identified ADAM28 as a putative oncogene involved in asbestos-related lung adenocarcinoma (ARLC-AC). We hypothesised that similarly gene expression profiling of asbestos-related lung squamous cell carcinomas (ARLC-SCC) may identify candidate oncogenes for ARLC-SCC. We undertook a microarray gene expression study in 56 subjects; 26 ARLC-SCC (defined as lung asbestos body (AB) counts >20AB/gram wet weight (gww) and 30 non-asbestos related lung squamous cell carcinoma (NARLC-SCC; no detectable lung asbestos bodies; 0AB/gww). Microarray and bioinformatics analysis identified six candidate genes differentially expressed between ARLC-SCC and NARLC-SCC based on statistical significance (p<0.001) and fold change (FC) of >2-fold. Two genes MS4A1 and CARD18, were technically replicated by qRT-PCR and showed consistent directional changes. As we also found MS4A1 to be overexpressed in ARLC-ACs, we selected this gene for biological validation in independent test sets (one internal, and one external dataset (2 primary tumor sets)). MS4A1 RNA expression dysregulation was validated in the external dataset but not in our internal dataset, likely due to the small sample size in the test set as immunohistochemical (IHC) staining for MS4A1 (CD20) showed that protein expression localized predominantly to stromal lymphocytes rather than tumor cells in ARLC-SCC. We conclude that differential expression of MS4A1 in this comparative gene expression study of ARLC-SCC versus NARLC-SCC is a stromal signal of uncertain significance, and an example of the rationale for tumor cell enrichment in preparation for gene expression studies where the aim is to identify markers of particular tumor phenotypes. Finally, our study failed to identify any strong gene candidates whose expression serves as a marker of asbestos etiology. Future research is required to determine the role of stromal lymphocyte MS4A1 dysregulation in pulmonary SCCs caused by asbestos.
Influence of Deposition Time on the Microstructure and Transport Properties of CdO Thin Films Prepared by Chemical Bath Deposition  [PDF]
P. Perumal, A. Gowri Manohari, Santiyagu Valanarasu, Adaikalam Kathalingam, Jin-Koo Rhee, Narayanan Soundaram, Rathinam Chandramohan
Journal of Surface Engineered Materials and Advanced Technology (JSEMAT) , 2012, DOI: 10.4236/jsemat.2012.22013
Abstract: Transparent thin films of CdO has been deposited on to glass substrates employing chemical bath deposition. The prepared films are reproducible, adherent to the substrate, pinhole free and uniform. Amongst the different process parameters, the deposition time plays a significant role in obtaining device quality transparent CdO thin films. X-ray powder diffraction (XRD) studies indicated that the thin films are polycrystalline in nature with cubic phase with a cell constant of a = 4.638 ?. The surface morphology of the prepared CdO thin films was examined by scanning electron microscopy. The films deposited at 24 hrs exhibited highest optical transmittivity (>80%) and the direct band gap energy was found to vary from 2.50 to 2.91 eV with a rise deposition time from 6 to 30 hrs. The electrical resitivity variations of these films were measured in the temperature range between 30?C and 150?C by four-probe technique.
Effect of Asian Dust Storms on the Ambient SO2 Concentration over North-East India: A Case Study  [PDF]
Timmy Francis
Journal of Environmental Protection (JEP) , 2011, DOI: 10.4236/jep.2011.26090
Abstract: Ambient SO2 concentration at a high rain fall site, Shillong (25.67oN, 91.91oE, 1064 m ASL), located in North-East India, was measured during March 2009 and January 2010 with the aim to understand the effect of long range transport of pollutants from North-East Asia on the ambient SO2 levels at this relatively clean site. The concentrations recorded during the former sampling period were very high (Max: 262.3 ppb)—which decayed down gradually towards the end the sampling period—whereas those during the latter sampling period were well within the acceptable limits (Max: 29.7 ppb). This elevated SO2 concentrations during March 2009 is proposed to have association with a major cold air outbreak and an associated cyclone preceding one of the dust storm events reported in China, and a resultant sudden change in wind trajectory leading to the long range transport of pollutants to the sampling site. The argument is formulated on the basis of the back trajectory analysis performed using HYSPLIT for the month of March 2009—the plots clearly showed a drastic change in wind trajectories between 8th and 15th of March 2009 wherein the winds traveled over some of the highly polluted regions such as the Perm region of Russia—and on the results from model runs performed using the global 3-D model of tropospheric chemistry, GEOS-Chem (v8-03-01)—it clearly showed the tropospheric SO2 over Perm region in Russia peaking during Nov, Dec, Jan, Feb and Mar every year, possibly due to central heating. The observation of long range transport of SO2 from the highly industrialized areas of Perm in Russia to North-East India during dust storm events has important implications to the present understanding on its relative contribution to the Asian pollutant outflow to the Pacific during spring as the GEOS-Chem model runs also showed regions in and around Russia with relatively high concentrations of atmospheric NOx, Peroxyacetyl Nitrate, Lumped Peroxypropionyl Nitrate, HNO3, HNO4,C3H8, C2H6, SO4, NH4, Inorganic Sulphur Nitrates and Lumped Alkyl Nitrate.
Temporal Trends in Ambient SO2 at a High Altitude Site in Semi-Arid Western India: Observations versus Chemical Transport Modeling  [PDF]
Timmy Francis
Journal of Environmental Protection (JEP) , 2012, DOI: 10.4236/jep.2012.37079
Abstract: Ambient sulphur dioxide (SO2) measurements have been performed at a high altitude site in the semi arid region of western India, Gurushikhar, Mt. Abu (24.6°N, 72.7°E, 1680 m ASL), during different sampling periods span over Sep-Dec 2009 and Feb-Mar 2010. A global three dimensional chemical transport Model, GEOS-Chem, (v8-03-01) is employed to generate the SO2 profile for the entire region for the different sampling months which in turn is used to explain the major features in the measured SO2 spectra via correlating with HYSPLIT generated wind back trajectories. The mean SO2 concentrations recorded at the sampling site varied for the different sampling periods (4.3 ppbv in Sep-Oct 2009, 3.4 ppbv in Nov 2009, 3.5 ppbv in Dec 2009, 7.7 ppbv in Feb 2010 and 9.2 ppbv in Mar 2010) which were found to be strongly influenced by long range transport from a source region surrounding 30°N, 75°E—the one projected with the highest SO2 concentration in the GEOS-Chem generated profiles for the region—lying only a few co-ordinates away. A diurnal cycle of SO2 concentration exists throughout the sampling periods, with the greatest day-night changes observed during Feb and Mar 2010, barely detectable during Sep-Oct 2009, and intermediate values for Nov and Dec 2009 which are systematically studied using the time series PBL height and OH radical values from the GEOS-Chem model. During the sampling period in Nov 2009, a plume transport to the sampling site also was detected when a major fire erupted at an oil depot in Jaipur (26.92°N, 75.82°E), located few co-ordinates away. Separate runs of the model, performed to study the long range transport effects, show a drop in the SO2 levels over the sampling region in the absence of transport, throughout the year with Jan to Apr seen to be influenced the lowest by long range transport while Jul and Dec influenced the highest.
Personal Identity and “Life-Here-After Poetics”: A Critique of Maduabuchi Dukor’s Metaphysics  [PDF]
Francis Offor
Open Journal of Philosophy (OJPP) , 2013, DOI: 10.4236/ojpp.2013.31A024
Abstract:

This essay examines Maduabuchi Dukor’s perspective on the African conception of man, personal identity and“life-here-after”. This is with a view to showing that although, Dukor’s views represent what obtain among some ethnic nationalities in Africa, this nevertheless does not provide a basis for generalising across the whole of Africa, as there are countless number of ethnic groups in Africa to which Dukor’s general claims may not be applicable. Given the varieties of metaphysical conceptions of man and destiny in Africa which we are yet to fully explore, and given also the inherent contradictions in some of these conceptions, which calls into questioning, the veracity of claims made therein, it will amount to a major logical error to make sweeping generalisations that would be representative of the whole of Africa. Such generalisations would remain a non-holistic, but partial representation of the African conception of man and human destiny.

For a Holistic View of Biotechnology in West and Central Africa: What Can Integrated Development Approaches Contribute?  [PDF]
Francis Rosillon
Journal of Environmental Protection (JEP) , 2013, DOI: 10.4236/jep.2013.49112
Abstract:

Africa, ever on the lookout for development levers that will allow its economy to take off, is turning more and more towards technology. This is one of the possible modern avenues to success, especially the use of the biotechnologies that are so touted by Western countries. However, the hope placed in these new technologies must not hide the long-proven fact that technology alone is not enough to solve development problems. Biotechnologies do not escape this rule. Biotechnologies can be the best and the worst things for the people of Africa. Beyond their technical contributions, we must be wary of their boomerang effects and collateral damage. A country’s development is actually more complex than simply implementing technology, and in the current global environmental context a holistic vision is necessary to ensure sustainable development. In the area of water, this integrated vision emerged on the international scene during the Dublin Conference in 1992, which consecrated the principles of Integrated Water Resources Management (IWRM). More recently, the Eco-Health concept strives to combine human health and ecosystem health while incorporating a socioeconomic dimension into the health and environmental spheres. The concern to mesh human activities better with environmental protection was materialized previously, in the 1970s already, through impact studies. After presenting this set of tools in the service of a holistic approach to the environment and development, we shall see that these approaches can inspire the players when it comes to the ways they implement biotechnologies. At the end of the day, a holistic approach to biotechnologies in Africa will be facilitated by enhanced information and communication and reliance on peasant farmers’ expertise. It will have to be rooted in broader participation of the players concerned. This integration will also concern environmental and land-owning aspects, without forgetting socio-cultural acceptance of the projects and the links with health. Ultimately, it will also mean putting the human at the heart of development by taking all the richness and particularities of African society into account.

Udo Etuk on the “God of Africa”: A Response  [PDF]
Francis Etim
Open Journal of Philosophy (OJPP) , 2018, DOI: 10.4236/ojpp.2018.85041
Abstract: Some scholars like Rabbi Ini Mbebeng, Rabbi Ettah Essien and Prof Udo Etuk have argued against Ibibio nay Africans having the idea of Supreme Being identical with that of the West given their polytheistic conception of God with attendant pan-theistic proclivities. On the other hand, scholars like Idowu regard such position as anachronistic and retrogressive since African has what he calls, “diffused monotheistic” idea of God which in description and analysis is similar to that of Western typology. This article as a contribution to that debate examines Abasi as a name of the God among the Ibibio from philo-ontos-linguistic perspectives and comes to the conclusion that not only is it true that the Ibibio nay Africans in general have a superlative idea of God but that the African idea of God is more humanistic and existentially relevant than that of the West thus solving the attendant difficulties of explaining the relationship between God and the world and the issue of the problem of evil which resulted in such idea as Dues abscunditus in Western conception of God.
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