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Search Results: 1 - 10 of 240955 matches for " James R. Davie "
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An integrated analysis of genes and pathways exhibiting metabolic differences between estrogen receptor positive breast cancer cells
Soma Mandal, James R Davie
BMC Cancer , 2007, DOI: 10.1186/1471-2407-7-181
Abstract: Public repositories of SAGE and MA gene expression data generated from E2 deprived ER(+)ve breast cancer cell lines, MCF-7 and ZR75-1 were compared with normal breast tissue. We analyzed gene ontology (GO), enrichment, clustering, chromosome localization, and pathway profiles and performed multiple comparisons with cell lines and tumors with different ER status.In all GO terms, biological process (BP), molecular function (MF), and cellular component (CC), MCF-7 had higher gene utilization than ZR75-1. Various analyses showed a down-regulated immune function, an up-regulated protein (ZR75-1) and glucose metabolism (MCF-7). A greater percentage of 77 common genes localized to the q arm of all chromosomes, but in ZR75-1 chromosomes 11, 16, and 19 harbored more overexpressed genes. Despite differences in gene utilization (electron transport, proteasome, glycolysis/gluconeogenesis) and expression (ribosome) in both cells, there was an overall similarity of ZR75-1 with ER(-)ve cell lines and ER(+)ve/ER(-)ve breast tumors.This study demonstrates integral metabolic differences may exist within the same cell subtype (luminal A) in representative ER(+)ve cell line models. Selectivity of gene and pathway usage for strategies such as energy requirement minimization, sugar utilization by ZR75-1 contrasted with MCF-7 cells, expressing genes whose protein products require ATP utilization. Such characteristics may impart aggressiveness to ZR75-1 and may be prognostic determinants of ER(+)ve breast tumors.Breast cancer among other diseases, is a major cause of mortality in women, worldwide. Phenotypic changes during breast cancer progression reflect aberrant gene expression and pathways supporting deregulated growth. Thus, it is crucial to understand the events of initiation, transformation and metastasis using global gene expression approaches. Public database repositories of global gene expression data generated from high-throughput gene expression techniques such as SAGE and micr
Roles of histone deacetylases in epigenetic regulation: emerging paradigms from studies with inhibitors
Geneviève P Delcuve, Dilshad H Khan, James R Davie
Clinical Epigenetics , 2012, DOI: 10.1186/1868-7083-4-5
Abstract: Acetylation of the lysine ε-amino group, first discovered on histones, is a dynamic posttranslational modification (PTM) regulated by the opposing activities of lysine acetyltransferases (KATs) and histone deacetylases (HDACs). Histone acetylation is a modulator of chromatin structure involved in DNA replication, DNA repair, heterochromatin silencing and gene transcription [1,2]. Hyperacetylation usually marks transcriptionally active genes, as it contributes to the decondensed chromatin state and maintains the unfolded structure of the transcribed nucleosome [2-6]. Moreover, specific acetylated sites on core histones are read by bromodomain modules found in proteins, and sometimes in KATs, which are components of chromatin-remodeling complexes involved in transcriptional activation [7]. Conversely, HDACs are found in corepressor complexes and, by removing acetyl groups from histones, induce the formation of a compacted, transcriptionally repressed chromatin structure. As discussed below, however, this model reflects quite an oversimplification of the role of HDACs in transcription regulation.Many nonhistone proteins (transcription factors, regulators of DNA repair, recombination and replication, chaperones, viral proteins and others) are also subject to acetylation [8-10]. Investigators in a recent study used high-resolution mass spectrometry to identify 3,600 acetylation sites in 1,750 human proteins and showed that lysine acetylation is implicated in the regulation of nearly all nuclear functions and many cytoplasmic processes [11]. Furthermore, acetylation is regulated by and/or regulates other PTMs. Through either recruitment or occlusion of binding proteins, PTMs may lead to or prevent a secondary PTM on histones and nonhistone proteins [12,13]. In particular, histone H3 phosphorylation on serine 10 or 28, rapid and transient PTMs in response to the stimulation of signaling pathways such as the mitogen-activated protein kinase (MAPK) pathways, are associated w
Yin Yang Gene Expression Ratio Signature for Lung Cancer Prognosis
Wayne Xu, Shantanu Banerji, James R. Davie, Fekadu Kassie, Douglas Yee, Robert Kratzke
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0068742
Abstract: Many studies have established gene expression-based prognostic signatures for lung cancer. All of these signatures were built from training data sets by learning the correlation of gene expression with the patients' survival time. They require all new sample data to be normalized to the training data, ultimately resulting in common problems of low reproducibility and impracticality. To overcome these problems, we propose a new signature model which does not involve data training. We hypothesize that the imbalance of two opposing effects in lung cancer cells, represented by Yin and Yang genes, determines a patient’s prognosis. We selected the Yin and Yang genes by comparing expression data from normal lung and lung cancer tissue samples using both unsupervised clustering and pathways analyses. We calculated the Yin and Yang gene expression mean ratio (YMR) as patient risk scores. Thirty-one Yin and thirty-two Yang genes were identified and selected for the signature development. In normal lung tissues, the YMR is less than 1.0; in lung cancer cases, the YMR is greater than 1.0. The YMR was tested for lung cancer prognosis prediction in four independent data sets and it significantly stratified patients into high- and low-risk survival groups (p = 0.02, HR = 2.72; p = 0.01, HR = 2.70; p = 0.007, HR = 2.73; p = 0.005, HR = 2.63). It also showed prediction of the chemotherapy outcomes for stage II & III. In multivariate analysis, the YMR risk factor was more successful at predicting clinical outcomes than other commonly used clinical factors, with the exception of tumor stage. The YMR can be measured in an individual patient in the clinic independent of gene expression platform. This study provided a novel insight into the biology of lung cancer and shed light on the clinical applicability.
Mitogen- and Stress-Activated Kinase 1 (MSK1) Regulates Cigarette Smoke-Induced Histone Modifications on NF-κB-dependent Genes
Isaac K. Sundar, Sangwoon Chung, Jae-woong Hwang, John D. Lapek, Michael Bulger, Alan E. Friedman, Hongwei Yao, James R. Davie, Irfan Rahman
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031378
Abstract: Cigarette smoke (CS) causes sustained lung inflammation, which is an important event in the pathogenesis of chronic obstructive pulmonary disease (COPD). We have previously reported that IKKα (I kappaB kinase alpha) plays a key role in CS-induced pro-inflammatory gene transcription by chromatin modifications; however, the underlying role of downstream signaling kinase is not known. Mitogen- and stress-activated kinase 1 (MSK1) serves as a specific downstream NF-κB RelA/p65 kinase, mediating transcriptional activation of NF-κB-dependent pro-inflammatory genes. The role of MSK1 in nuclear signaling and chromatin modifications is not known, particularly in response to environmental stimuli. We hypothesized that MSK1 regulates chromatin modifications of pro-inflammatory gene promoters in response to CS. Here, we report that CS extract activates MSK1 in human lung epithelial (H292 and BEAS-2B) cell lines, human primary small airway epithelial cells (SAEC), and in mouse lung, resulting in phosphorylation of nuclear MSK1 (Thr581), phospho-acetylation of RelA/p65 at Ser276 and Lys310 respectively. This event was associated with phospho-acetylation of histone H3 (Ser10/Lys9) and acetylation of histone H4 (Lys12). MSK1 N- and C-terminal kinase-dead mutants, MSK1 siRNA-mediated knock-down in transiently transfected H292 cells, and MSK1 stable knock-down mouse embryonic fibroblasts significantly reduced CS extract-induced MSK1, NF-κB RelA/p65 activation, and posttranslational modifications of histones. CS extract/CS promotes the direct interaction of MSK1 with RelA/p65 and p300 in epithelial cells and in mouse lung. Furthermore, CS-mediated recruitment of MSK1 and its substrates to the promoters of NF-κB-dependent pro-inflammatory genes leads to transcriptional activation, as determined by chromatin immunoprecipitation. Thus, MSK1 is an important downstream kinase involved in CS-induced NF-κB activation and chromatin modifications, which have implications in pathogenesis of COPD.
Impacts of Small-Scale Water Management Interventions on Crop Yield, Water Use and Productivity in Two Agro-Ecologies of Malawi  [PDF]
Davie M. Kadyampakeni, Samson Kazombo-Phiri, Bancy Mati, Isaac R. Fandika
Agricultural Sciences (AS) , 2014, DOI: 10.4236/as.2014.55046

A study was conducted in Malawi to compare the performance of improved agricultural water ma- nagement interventions with traditional water management practices to assess the impact of the interventions on crop yield and water use productivity. The study used questionnaires and focused group discussions to collect data from farmers and key informants. The results showed significant gains in crop yield, farmer income, and water use productivity using the regulated surface irrigation compared with unregulated surface irrigation. Treadle pump irrigation increased crop production by 5% - 54% compared with water can irrigation. Treadle pumps also increased gross and net incomes by >12% suggesting that farmers using the treadle pump were able to realize higher incomes across all crop enterprises compared with farmers using water cans. However, there is a dire need to improve the efficiency of the surface irrigation systems for rice production because the water applied was about 2 to 3 times the gross irrigation requirement (~10,780 m3·ha-1) which could result in environmental degradation through increased salinity and water logging.

Optimal protocols and the Jarzynski equality
Stuart J. Davie,Owen G. Jepps,Lamberto Rondoni,James C. Reid,Debra J. Searles
Physics , 2013, DOI: 10.1088/0031-8949/89/04/048002
Abstract: The Jarzynski Equality is a well-known and widely used identity, relating the free energy difference between two states of a system to the work done over some arbitrary, nonequilibrium transformation between the two states. Despite being valid for both stochastic and deterministic systems, we show that the optimal transformation protocol for the deterministic case seems to differ from that predicated from an analysis of the stochastic dynamics. In addition, it is shown that for certain situations, more dissipative processes can sometimes lead to better numerical results for the free energy differences.
Dobbelstrategie vir toevalsrye
George Davie
Suid-Afrikaanse Tydskrif vir Natuurwetenskap en Tegnologie , 2010, DOI: 10.4102/satnt.v29i1.3
Abstract: Dit is ’n algemene opvatting dat dit nie moontlik is om suksesvol te dobbel teen ’n toevalsry (of aleatoriese ry) van nulle en ene nie. Ons gebruik idees van Kolmogorov-kompleksiteit om hierdie opvatting te bevraagteken. Ons wys dat alhoewel daar geen algoritme is waarmee ons ’n onbeperkte hoeveelheid geld kan wen teen ’n algoritmiese toevalsry nie6, is daar wel vir elke so ’n ry ’n dobbel strategie waarmee ons enige gewenste bedrag kan wen deur met ’n voorafbepaalbare bedrag ’n eenvoudige verdubbelingstrategie uit te voer. Ons kan ook dieselfde strategie gebruik om ’n onbeperkte hoeveelheid geld te wen, in die geval moet ons herhaaldelik geld rentevry kan leen. Please refer to PDF for english Abstract
Au prisme de l’altérité, les orthodoxes de Beyrouth au début du xix esiècle The Orthodox Community in Beirut at the Beginning of the 19th Century as seen through the Prism of Otherness.
May Davie
Revue des Mondes Musulmans et de la Méditerranée , 2012, DOI: 10.4000/remmm.2805
Abstract: La construction sociale des orthodoxes de Beyrouth, au début du xixe siècle, s’effectue autant dans le cadre de la communauté qu’à travers un réseau de relations et d’obligations économiques et sociales extérieures. Cet article, par une approche d’histoire urbaine, contredit les thèses du cloisonnement confessionnel. The social constructs of the Orthodox of Beirut, at the beginning of the 19th century, took place as much in the framework of the community as through external networks of social and economic relations. Using urban history approaches, this article contradicts the theories of religious segregation.
L’expertise médicale et légale dans l’émergence de la criminologie en Grande-Bretagne (1870-1918)
Neil Davie
Criminocorpus, Revue Hypermédia , 2005, DOI: 10.4000/criminocorpus.133
Abstract: L’étude scientifique systématique du criminel en Grande-Bretagne a co ncidé avec la mise en place d’un corps médical dans les prisons pour for ats du pays. Les premiers postes furent pourvus dans les années 1840. Il faut attendre le vote d’une loi, en 1850, sur les prisons pour for ats (Act for the Better Government of Convict Prisons) et la nomination d’une direction centrale professionnelle pour que l’on puisse parler d’un véritable service médical en milieu carcéral, composé de praticiens ...
The Role of Medico-legal Expertise in the Emergence of Criminology in Britain (1870-1918)
Neil Davie
Criminocorpus, Revue Hypermédia , 2010, DOI: 10.4000/criminocorpus.316
Abstract: The beginning of the systematic scientific study of the Criminal in Britain coincided with the emergence of a corps of professional medical officers in the country’s convict prisons. Although the first appointments were made in the 1840s, it was not until the passage of the Act for the Better Government of Convict Prisons in 1850 and the creation of a central Directorate of Convict Prisons that a fully-fledged prison medical service came into existence. However, the mere presence of medical p...
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