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Search Results: 1 - 10 of 3899 matches for " Nameeta Shah "
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Comprehensive Analysis of MGMT Promoter Methylation: Correlation with MGMT Expression and Clinical Response in GBM
Nameeta Shah,Biaoyang Lin,Zita Sibenaller,Timothy Ryken,Hwahyung Lee,Jae-Geun Yoon,Steven Rostad,Greg Foltz
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0016146
Abstract: O6-methylguanine DNA-methyltransferase (MGMT) promoter methylation has been identified as a potential prognostic marker for glioblastoma patients. The relationship between the exact site of promoter methylation and its effect on gene silencing, and the patient's subsequent response to therapy, is still being defined. The aim of this study was to comprehensively characterize cytosine-guanine (CpG) dinucleotide methylation across the entire MGMT promoter and to correlate individual CpG site methylation patterns to mRNA expression, protein expression, and progression-free survival. To best identify the specific MGMT promoter region most predictive of gene silencing and response to therapy, we determined the methylation status of all 97 CpG sites in the MGMT promoter in tumor samples from 70 GBM patients using quantitative bisulfite sequencing. We next identified the CpG site specific and regional methylation patterns most predictive of gene silencing and improved progression-free survival. Using this data, we propose a new classification scheme utilizing methylation data from across the entire promoter and show that an analysis based on this approach, which we call 3R classification, is predictive of progression-free survival (HR = 5.23, 95% CI [2.089–13.097], p<0.0001). To adapt this approach to the clinical setting, we used a methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) test based on the 3R classification and show that this test is both feasible in the clinical setting and predictive of progression free survival (HR = 3.076, 95% CI [1.301–7.27], p = 0.007). We discuss the potential advantages of a test based on this promoter-wide analysis and compare it to the commonly used methylation-specific PCR test. Further prospective validation of these two methods in a large independent patient cohort will be needed to confirm the added value of promoter wide analysis of MGMT methylation in the clinical setting.
SNP-VISTA: An interactive SNP visualization tool
Nameeta Shah, Michael V Teplitsky, Simon Minovitsky, Len A Pennacchio, Philip Hugenholtz, Bernd Hamann, Inna L Dubchak
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-292
Abstract: We have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein evolutionary conservation visualization; and 5) display of automatically calculated recombination points that are user-editable.The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNP data by the user.Polymorphisms are nucleotide differences in genomic DNA sequences that naturally occur within a population. A single nucleotide substitution is called a single nucleotide polymorphism (SNP) and these variants occur at a frequency of approximately one every 1,000 bases in humans [2]. SNPs are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryote species. The recent completion of a single version of the human genome [3,4] has now provided the substrates for direct comparison of individuals in both health and disease. Ideally, to better understand the genetic contributions to severe diseases, one would obtain the entire human genome sequence for all disease-carrying individuals for comparison to unaffected control groups. While these complete datasets are not readily obtainable today, a strategy that is currently approachable i
Effect of Aerated Drinks on Force Decay Properties of Elastomeric Chains: An In Vitro Study
Reena R Kumar,Mayank Gahlot,Nameeta Kaur,Anil Miglani
Orthodontic Journal of Nepal , 2011, DOI: 10.3126/ojn.v1i1.9361
Abstract: DOI: http://dx.doi.org/10.3126/ojn.v1i1.9361 Orthodontic Journal of Nepal Vol.1(1) 2011: 20-23
Residual Effect of Biochar on Soil Properties and Yield of Maize (Zea mays L.) under Different Cropping Systems  [PDF]
Sara, Z. Shah, T. Shah
Open Journal of Soil Science (OJSS) , 2018, DOI: 10.4236/ojss.2018.81002
Abstract: A field experiment was conducted to examine the residual influence of biochar applied previously to an established experiment at the Agriculture University Research Farm, Peshawar on soil properties and yield of maize crop during summer 2016. The experiment was established in RCB design with split plot arrangements having cropping systems (CS) in main plots and biochar (BC) in sub-plots. Cropping systems were: 1) wheat-mung bean; 2) wheat-maize; 3) chickpea-maize; and 4) chickpea-mung bean. During the past three seasons, each cropping system received biochar at 0, 40, 60 and 80 t·ha-1 along with recommended dose of NPK in each season. For this study, maize was planted after chickpea and wheat in summer 2016. The results showed that grain yield, cobs weight and total N uptake of maize was significantly greater for chickpea-maize than for wheat-maize cropping system. Soil organic C was also significantly higher in soil under chickpea-maize than under wheat-maize cropping system. However, other yield components such as stover yield, harvest index and N concentration in grain and stover of maize and soil properties such as pH, EC and mineral N were non-significantly affected by cropping systems. With respect to residual effect of biochar grain yield of maize and bulk density of soil were maximum for treatment receiving biochar at 40 t·ha-1 whereas cobs weight soil pH and mineral N were highest receiving biochar at 60 t·ha-1. Moreover, N concentration in stover, N uptake and soil organic C were maximum for treatment receiving biochar at 80 t
Ytterbium Doped Gadolinium Oxide (Gd2O3:Yb3+) Phosphor: Topology, Morphology, and Luminescence Behaviour
Raunak Kumar Tamrakar,Durga Prasad Bisen,Chandra Shekher Robinson,Ishwar Prasad Sahu,Nameeta Brahme
Indian Journal of Materials Science , 2014, DOI: 10.1155/2014/396147
Abstract: Gd2O3:Yb3+ phosphor has been synthesized by the solid state reaction method with boric acid used as a flux. The resulting Gd2O3:Yb3+ phosphor was characterized by X-ray diffraction (XRD) technique, Fourier transmission infrared spectroscopy (FTIR), scanning electron microscope (SEM) and transmission electron microscope (TEM), and photoluminescence and thermoluminescence. The results of the XRD show that obtained Gd2O3:Yb3+ phosphor has a cubic structure. The average crystallite sizes could be calculated as 42.9?nm, confirmed by the TEM results. The study suggested that Yb3+ doped phosphors are potential luminescence material for IR laser diode pumping. 1. Introduction Luminescent materials in various forms such as colloidal, bulk, nano, crystals, and nanocrystals are of interest not only for basic research, but also for interesting application [1–3]. Rare earth activated phosphors have attracted great interest because of their marked improvements in lumen output, color rendering index, and energy efficiency, and greater radiation stability Lanthanum oxide (La2O3) is recognized as an excellent host material for rare earth (RE) with luminescence applications with a relatively low cost. These phosphors have been recognized to hold tremendous potential in the field of photonic applications. The doping concentration is controlled over a broad range without the host structure influence. The luminescent properties of RE in La2O3 nanocrystalline powders using different synthesis methods have been recently reported [4, 5]. Gd2O3 is an Ln2O3-type oxide. The Ln2O3 (Ln = Gd, Y, Sc, Lu, Dy, etc.) oxides have been extensively studied because of their optoelectronic and display applications. Gadolinium oxide (Gd2O3) has been studied widely as the host matrix for downconversion [6–8] processes because of its interesting physical properties, such as high melting point (2320°C), chemical durability, thermal stability, and low phonon energy (~600?cm?1). Gd2O3 hosts have smaller phonon energies compared to hosts such as YAG or YAP; smaller phonon energies lead to a reduction in nonradiative losses and hence lead to increases in the luminescence efficiency [9, 10]. The Yb3+ ion has several advantages compared with other rare earth ions due to its very simple energy level scheme, constituting of only two 2F5/2 and 2F7/2 levels. There is no excited state absorption, no cross-relaxation process, and no more upconversion internal mechanism able to reduce the effective laser cross section and, in addition, the intense and broad Yb3+ absorption lines are well suited for IR laser
Numerical Simulation of Two-Dimensional Dendritic Growth Using Phase-Field Model  [PDF]
Abdullah Shah, Ali Haider, Said Karim Shah
World Journal of Mechanics (WJM) , 2014, DOI: 10.4236/wjm.2014.45015

In this article, we study the phase-field model of solidification for numerical simulation of dendritic crystal growth that occurs during the casting of metals and alloys. Phase-field model of solidification describes the physics of dendritic growth in any material during the process of under cooling. The numerical procedure in this work is based on finite difference scheme for space and the 4th-order Runge-Kutta method for time discretization. The effect of each physical parameter on the shape and growth of dendritic crystal is studied and visualized in detail.

Urban Green Spaces and an Integrative Approach to Sustainable Environment  [PDF]
Shah Md. Atiqul Haq
Journal of Environmental Protection (JEP) , 2011, DOI: 10.4236/jep.2011.25069
Abstract: This paper explains the benefits and challenges of urban green spaces based on the critical discussion of study results from different studies in different cities. The important roles played by green spaces are social, economic, cultural and environmental aspects of sustainable development. Urban green spaces can be a comprehensive tool for long term protection of environmental sustainability through improving the quality of life and air quality, increasing property value due to their amenity and aesthetic characteristics, and reducing the energy costs of cooling buildings. Urban green spaces also can provide ecosystem services in which the recreation and relaxation facilities are especially available to urban dwellers and tourists too. To confirm the multiple roles played by green spaces, certain level of qualitative improvements and distribution of green spaces within the urban area should be considered and incorporated effectively into the environmental sustainability agenda. To do this, an integrated approach regarding the planning, monitoring, designing and maintaining of urban green spaces is required for improving the environmental sustainability in cities in different countries.
Vibration Analysis of an Infinite Poroelastic Circular Cylindrical Shell Immersed in Fluid  [PDF]
Syed Ahmed Shah
Open Journal of Acoustics (OJA) , 2012, DOI: 10.4236/oja.2012.22010
Abstract: The purpose of this paper is to study the effect of presence of fluid within and around a poroelastic circular cylindrical shell of infinite extent on axially symmetric vibrations. The frequency equation each for a pervious and an impervious surface is obtained employing Biot’s theory. Radial vibrations and axially symmetric shear vibrations are uncoupled when the wavenumber is vanished. The propagation of axially symmetric shear vibrations is independent of presence of fluid within and around the poroelastic cylindrical shell while the radial vibrations are affected by the presence of fluid. The frequencies of radial vibrations and axially symmetric shear vibrations are the cut-off frequencies for the coupled motion of axially symmetric vibrations. The non-dimensional phase velocity as a function of ratio of thickness to wavelength is computed and presented graphically for two different types of poroelastic materials for thin poroelastic shell, thick poroelastic shell and poroelastic solid cylinder.
A Survey of High Performance Concrete Developments in Civil Engineering Field  [PDF]
Vatsal Patel, Niraj Shah
Open Journal of Civil Engineering (OJCE) , 2013, DOI: 10.4236/ojce.2013.32007

High Performance concrete (HPC) has received increased attention in the development of infrastructure Viz., Buildings, Industrial Structures, Hydraulic Structures, Bridges and Highways etc. leading to utilization of large quantity of concrete. This paper presents a comprehensive coverage of High Performance concrete developments in civil engineering field. It highlights the High Performance concrete features and requirements over conventional concrete. Furthermore, recent trends with regard to High Performance Concrete development in this area are explored. This paper also includes effect of Mineral and Chemical Admixtures used to improve performance of concrete.

Stochastic Logistic Model for Fish Growth  [PDF]
Md. Asaduzzaman Shah
Open Journal of Statistics (OJS) , 2014, DOI: 10.4236/ojs.2014.41002

Two extensions of stochastic logistic model for fish growth have been examined. The basic features of a logistic growth rate are deeply influenced by the carrying capacity of the system and the changes are periodical with time. Introduction of a new parameter \"\", enlarges the scope of investing the growth\"\"of different fish species. For rapid growth lying between 1 and 2 and for slowly growing\"\".

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