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Search Results: 1 - 10 of 330100 matches for " Mohammed S. Orloff "
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Integrative Genomic Analysis Reveals Extended Germline Homozygosity with Lung Cancer Risk in the PLCO Cohort
Mohammed S. Orloff, Li Zhang, Gurkan Bebek, Charis Eng
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031975
Abstract: Susceptibility to common cancers is multigenic resulting from low-to-high penetrance predisposition-factors and environmental exposure. Genomic studies suggest germline homozygosity as a novel low-penetrance factor contributing to common cancers. We hypothesized that long homozygous regions (tracts-of-homozygosity [TOH]) harbor tobacco-dependent and independent lung-cancer predisposition (or protection) genes. We performed in silico genome-wide SNP-array-based analysis of lung-cancer patients of European-ancestry from the PLCO screening-trial cohort to identify TOH regions amongst 788 cancer-cases and 830 ancestry-matched controls. Association analyses was then performed between presence of lung cancer and common(c)TOHs (operationally defined as 10 or more subjects sharing ≥100 identical homozygous calls), aTOHs (allelically-matched groups within a cTOH), demographics and tobacco-exposure. Finally, integration of significant c/aTOH with transcriptome was performed to functionally-map lung-cancer risk-genes. After controlling for demographics and smoking, we identified 7 cTOHs and 5 aTOHs associated with lung cancer (adjusted p<0.01). Three cTOHs were over-represented in cases over controls (OR = 1.75–2.06, p = 0.007–0.001), whereas 4 were under-represented (OR = 0.28–0.69, p = 0.006–0.001). Interaction between smoking status and cTOH3/aTOH2 (2p16.3–2p16.1) was observed (adjusted p<0.03). The remaining significant aTOHs have ORs 0.23–0.50 (p = 0.004–0.006) and 2.95–3.97 (p = 0.008–0.001). After integrating significant cTOH/aTOHs with publicly-available lung-cancer transcriptome datasets followed by filtering based on lung cancer and its relevant pathways revealed 9 putative predisposing genes (p<0.0001). In conclusion, differentially-distributed cTOH/aTOH genomic variants between cases and controls harbor sets of plausible differentially-expressed genes accounting for the complexity of lung-cancer predisposition.
cgaTOH: Extended Approach for Identifying Tracts of Homozygosity
Li Zhang, Mohammed S. Orloff, Sean Reber, Shengchao Li, Ye Zhao, Charis Eng
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0057772
Abstract: Identification of disease variants via homozygosity mapping and investigation of the effects of genome-wide homozygosity regions on traits of biomedical importance have been widely applied recently. Nonetheless, the existing methods and algorithms to identify long tracts of homozygosity (TOH) are not able to provide efficient and rigorous regions for further downstream association investigation. We expanded current methods to identify TOHs by defining “surrogate-TOH”, a region covering a cluster of TOHs with specific characteristics. Our defined surrogate-TOH includes cTOH, viz a common TOH region where at least ten TOHs present; gTOH, whereby a group of highly overlapping TOHs share proximal boundaries; and aTOH, which are allelically-matched TOHs. Searching for gTOH and aTOH was based on a repeated binary spectral clustering algorithm, where a hierarchy of clusters is created and represented by a TOH cluster tree. Based on the proposed method of identifying different species of surrogate-TOH, our cgaTOH software was developed. The software provides an intuitive and interactive visualization tool for better investigation of the high-throughput output with special interactive navigation rings, which will find its applicability in both conventional association studies and more sophisticated downstream analyses. NCBI genome map viewer is incorporated into the system. Moreover, we discuss the choice of implementing appropriate empirical ranges of critical parameters by applying to disease models. This method identifies various patterned clusters of SNPs demonstrating extended homozygosity, thus one can observe different aspects of the multi-faceted characteristics of TOHs.
Microenvironmental genomic alterations reveal signaling networks for head and neck squamous cell carcinoma
Gurkan Bebek, Mohammed Orloff, Charis Eng
Journal of Clinical Bioinformatics , 2011, DOI: 10.1186/2043-9113-1-21
Abstract: Under the assumption that genes in proximity to identified LOH/AI regions are correlated with the tumorigenic phenotype, we mined publicly available biological information to identify pathway segments (signaling proteins connected to each other in a network) and identify the role of tumor microenvironment in HNSCC. Across both neoplastic epithelial cells and the surrounding stromal cells, genetic alterations in HNSCC were successfully identified, and 75 markers were observed to have significantly different LOH/AI frequencies in these compartments (p < 0.026). We applied a network identification approach to the genes in proximity to these 75 markers in cancer epithelium and stroma in order to identify biological networks that can describe functional associations amongst these marker-associated genes.We verified the involvement of T-cell receptor signaling pathways in HNSCC as well as associated oncogenes such as LCK and PLCB1, and tumor suppressors such as STAT5A, PTPN6, PARK2. We identified expression levels of genes within significant LOH/AI regions specific to stroma networks that correlate with better outcome in radiation therapy. By integrating various levels of high-throughput data, we were able to precisely focus on specific proteins and genes that are germane to HNSCC.HNSCC is the sixth most common cancer and remains a major cause of cancer morbidity and mortality worldwide [1]. More than 85% of head and neck squamous cell carcinomas (HNSCC) are related to tobacco use, while others may have a relationship to viral etiologies such as human papillomavirus (HPV) infection/colonization. Nevertheless, advanced stage HNSCC remains an aggressive cancer with low survival rates. Molecular studies suggest that HNSCC results from cumulative epigenetic and genetic alterations [2-4]. Various genomic regions and/or genes have been correlated with survival in HNSCC or classified as early detection/aggressiveness markers [2]. Albeit incomplete, such baseline knowledge of HNS
Structural Behavior of Tall Building Raft Foundations in Earthquake Zones  [PDF]
Mohammed S. Al- Ansari
Open Journal of Earthquake Research (OJER) , 2017, DOI: 10.4236/ojer.2017.64011
The paper studies the behavior of reinforced concrete raft foundations for multi-story buildings. It also develops a reliability assessment tool for multi- story building raft foundations subjected to earthquake loading. Several multi-story buildings with various configurations, heights, and soil profiles, were subjected to several ACI code combinations of gravity and earthquake loads from different seismic zones. The reliability of the raft foundations of these buildings was assessed using the reliability index approach based on their resistance to the applied loads. Also, the responses of the multi-story buildings under these loading combinations were studied and analyzed in order to draw recommendations and guidelines for the preliminary design of structurally efficient and reliable raft foundations in earthquake zones.
Could a Gamma Line Betray the Mass of Light Dark Matter?
Orloff, Jean
High Energy Physics - Phenomenology , 2007,
Abstract: We compute the pair annihilation cross section of light dark matter scalar particles into two photons, and discuss the detectability of the monochromatic line associated with these annihilations.
The U.V. Price for Symmetry Non-Restoration
Jean Orloff
Physics , 1996, DOI: 10.1016/S0370-2693(97)00552-2
Abstract: We study the non restoration of symmetries with a local order parameter in field theory at finite temperature. After giving an interpretation of the phenomenon, we show that hierarchy problems are a necessary condition for its realization in renormalizable theories. We then use a large N treatment, and find that high temperature symmetry can stay broken in this limit (in opposition with a previous result), and further that the running of couplings reinforces the effect in the simplest model with two scalars.
Numerical Study of Fractional Differential Equations of Lane-Emden Type by Method of Collocation  [PDF]
Mohammed S. Mechee, Norazak Senu
Applied Mathematics (AM) , 2012, DOI: 10.4236/am.2012.38126
Abstract: Lane-Emden differential equations of order fractional has been studied.Numerical solution of this type is considered by collocation method. Some of examples are illustrated. The comparison between numerical and analytic methods has been introduced.
Reliability Index of Tall Buildings in Earthquake Zones  [PDF]
Mohammed S. Al-Ansari
Open Journal of Earthquake Research (OJER) , 2013, DOI: 10.4236/ojer.2013.23005

The paper develops a reliability index approach to assess the reliability of tall buildings subjected to earthquake loading. The reliability index β model measures the level of reliability of tall buildings in earthquake zones based on their response to earthquake loading and according to their design code. The reliability index model is flexible and can be used for: 1) all types of concrete and steel buildings and 2) all local and international codes of design. Each design code has its unique reliability index β as a magnitude and the interaction chart corresponding to it. The interaction chart is a very useful tool in determining the building drift for the desired level of reliability during the preliminary design of the building members. The assessments obtained using the reliability index approach of simulated, tested, and actual buildings in earthquake zones were acceptable as indicators of the buildings reliability.

Down Scaling Interest in Interest Rate  [PDF]
Mohammed H. S. Al Ashry
Theoretical Economics Letters (TEL) , 2015, DOI: 10.4236/tel.2015.51012
Abstract: During periods of high interest rates, businesses utilize their own capital, merge with other businesses, or diversify, and borrow when it is absolutely necessary. People also avoid hardship through refinancing during economic slowdowns because interest rates are low enough to recover some of their income and lower debt interest. High interest rates are more inviting to investments although hard to sustain in the long run. The future looks grim and interest rates have been down for a while, and will probably stay down for some time to come. This paper investigates ways to lower the earnings percentage in interest rates. A new set of the uniform series of the future worth of money involving linear gradients will be mathematically reformulated to investigate the possibility of lowering the interest rate for long term loans and mortgages. A new equation will be formulated and put into a tabulated practical example.
Large Scale Desalination: A Comparative Cost Affective Economic Analyses of Nuclear, Gas and Solar Powered Plants  [PDF]
Mohammed H. S. Al Ashry
Theoretical Economics Letters (TEL) , 2015, DOI: 10.4236/tel.2015.51015
Abstract: The main objective, here, is to explore the economic viability of the solar powered desalination method through a cost and benefit comparative and contrast study. Using the initial construction expenditure, the annual maintenance cost and energy consumed or produced, a variance ratio test of the random walk hypothesis will be implemented to determine their relative financial efficiency. This paper will also utilize the first order autoregressive multivariate estimation model to analyze the methods and identify the most productive process with most financial promise for future investment. The total deviations of the estimated variables from the actual are accounted for by the variations of the variances of the estimates from the actual. The higher the percentage of the unexplained deviation, the higher the risk involved. The portfolio variance will be utilized to measure the investment risk in three desalination industries.
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