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Search Results: 1 - 10 of 3216 matches for " Animesh Ray "
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A signature of power law network dynamics
Ashish Bhan,Animesh Ray
Computer Science , 2014,
Abstract: Can one hear the 'sound' of a growing network? We address the problem of recognizing the topology of evolving biological or social networks. Starting from percolation theory, we analytically prove a linear inverse relationship between two simple graph parameters--the logarithm of the average cluster size and logarithm of the ratio of the edges of the graph to the theoretically maximum number of edges for that graph--that holds for all growing power law graphs. The result establishes a novel property of evolving power-law networks in the asymptotic limit of network size. Numerical simulations as well as fitting to real-world citation co-authorship networks demonstrate that the result holds for networks of finite sizes, and provides a convenient measure of the extent to which an evolving family of networks belongs to the same power-law class.
Development of Indium Tin Oxide by Pulsed RF Sputtering Method for Solar Cell Application
Somnath Middya,Animesh Layek,Partha Pratim Ray
Journal of Applied Sciences , 2012,
Abstract: The present study has deposited Indium Tin Oxide (ITO) thin films by pulsed RF sputtering technique at low temperature for the application in solar cell. In stead of using RF magnetron sputtering we have used pulsed RF sputtering to deposit ITO thin film. We have been able to deposit about 90 nm thin ITO films with both low resistivity and high transmittance at low substrate temperature (100°C). The effect of Oxygen (O2) admixture to sputtering gas (Argon) and different pulse modes on the electrical and optical properties of ITO thin films was investigated. We have used different pulse modes to see their effect on material properties. It is found that the increase in O2 admixture percentage to Ar decreases the growth rate. At certain oxygen percentage film shows low resistivity and high transparency. A minimum value of resistivity (2x10-5 Ω cm) and an average transmittance of ~80% in UV-VIS range have been found at 1% of O2 admixture. During deposition we also monitored plasma by Optical Emission Spectroscopy (OES). By using OES we have studied the emission lines arising due to Indium at 451 nm and Argon neutral at 811.5 nm. Variation of integral peak intensities were studied for different deposition conditions and correlated with material properties.
Possibility to Use Low Temperature Pulsed RF Sputtered Indium Tin Oxide for the Fabrication of Organic Solar Cell
Somnath Middya,Animesh Layek,Partha Pratim Ray
Conference Papers in Science , 2013, DOI: 10.1155/2013/542726
Abstract: In this work we have used pulsed RF sputtering method to deposit indium tin oxide (ITO) for the fabrication of P3HT:PCBM based bulk heterojunction polymer solar cell. We have deposited ITO at low substrate temperature (100°C) and for different pulse modes. Oxygen was used as an admixture to the sputtering gas argon, and the percentage was varied from 0 to 6%. During deposition, plasma was studied by optical emission spectroscopy (OES) method. For our present range of deposition conditions lowest resistivity of ITO is around 2 × 10?4?Ω-cm, and it is deposited in High-Low mode with 1% of oxygen added to argon. The effect of oxygen admixture on electrical and optical properties of ITO thin films has been studied for different pulse modes. ITO films have been optimised by measuring their resistivity, transparency, and X-ray diffraction. Finally we have applied the ITO film for the fabrication of P3HT:PCBM based solar cell. 1. Introduction Many parameters of ITO thin film such as electrical conductivity, optical transparency, and depth of film to minimize sheet resistance must be considered in solar cell fabrication. The electrical and optical properties of this wide bandgap oxide semiconductor can be controlled by adjusting the deposition conditions. Various techniques, such as electron beam evaporation [1], ion beam assisted deposition [2], pulsed laser ablation [3], ion implantation [4], and DC/RF magnetron sputtering [5], are used for the growth of ITO thin films. Pulsed RF sputtering technique is a promising technique which can modify and improve the properties of sputtered films via control of energy of ions impinging on substrates. But pulsed RF sputtering is still not well tested for the deposition of thin ITO film at low temperature. In this work we have developed ITO by pulsed RF sputtering technique and applied that film for the fabrication of P3HT:PCBM based solar cell. We have also compared the cell performance with the cell deposited on commercially available ITO. 2. Experimental Thin film of ITO was deposited using a pulsed RF (13.56?MHz) sputtering system (ANELVA). An indium tin alloy (95:5) of 99.99% purity was used as target. Initially, the chamber was evacuated to 1 × 10?6 Torr (base pressure), and the required sputtering pressure inside the chamber was achieved by introducing argon gas through mass flow controller. Once the pressure was achieved, the deposition was carried out in argon and oxygen atmosphere. Oxygen was used as admixture to the sputtering gas, and the percentage was varied from 0 to 6%. The target was presputtered in argon
Advantages of multiple algorithm support in treatment planning system for external beam dose calculations
Journal of Cancer Research and Therapeutics , 2005,
Abstract: The complexity of interactions and the nature of the approximations made in the formulation of the algorithm require that the user be familiar with the limitations of various models. As computer power keeps growing, calculation algorithms are tending more towards physically based models. The nature and quantity of the data required varies according to the model which may be either measurement based models or physical based models. Multiple dose calculation algorithm support found in XiO Treatment Planning System can be used to advantage when choice is to be made between speed and accuracy. Thus XiO allows end users generate plans accurately and quickly to optimize the delivery of radiation therapy.
Transposon Excision from an Atypical Site: A Mechanism of Evolution of Novel Transposable Elements
Marybeth Langer, Lynn F. Sniderhan, Ueli Grossniklaus, Animesh Ray
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0000965
Abstract: The role of transposable elements in sculpting the genome is well appreciated but remains poorly understood. Some organisms, such as humans, do not have active transposons; however, transposable elements were presumably active in their ancestral genomes. Of specific interest is whether the DNA surrounding the sites of transposon excision become recombinogenic, thus bringing about homologous recombination. Previous studies in maize and Drosophila have provided conflicting evidence on whether transposon excision is correlated with homologous recombination. Here we take advantage of an atypical Dissociation (Ds) element, a maize transposon that can be mobilized by the Ac transposase gene in Arabidopsis thaliana, to address questions on the mechanism of Ds excision. This atypical Ds element contains an adjacent 598 base pairs (bp) inverted repeat; the element was allowed to excise by the introduction of an unlinked Ac transposase source through mating. Footprints at the excision site suggest a micro-homology mediated non-homologous end joining reminiscent of V(D)J recombination involving the formation of intra-helix 3′ to 5′ trans-esterification as an intermediate, a mechanism consistent with previous observations in maize, Antirrhinum and in certain insects. The proposed mechanism suggests that the broken chromosome at the excision site should not allow recombinational interaction with the homologous chromosome, and that the linked inverted repeat should also be mobilizable. To test the first prediction, we measured recombination of flanking chromosomal arms selected for the excision of Ds. In congruence with the model, Ds excision did not influence crossover recombination. Furthermore, evidence for correlated movement of the adjacent inverted repeat sequence is presented; its origin and movement suggest a novel mechanism for the evolution of repeated elements. Taken together these results suggest that the movement of transposable elements themselves may not directly influence linkage. Possibility remains, however, for novel repeated DNA sequences produced as a consequence of transposon movement to influence crossover in subsequent generations.
Mining protein networks for synthetic genetic interactions
Sri R Paladugu, Shan Zhao, Animesh Ray, Alpan Raval
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-426
Abstract: We design a support vector machine system that uses graph-theoretic properties of two proteins in a protein interaction network as input features for prediction of synthetic sick/lethal interactions. The system is trained on interacting and non-interacting gene pairs culled from large scale genetic screens as well as literature-curated data. We find that the method is capable of predicting synthetic genetic interactions with sensitivity and specificity both exceeding 85%. We further find that the prediction performance is reasonably robust with respect to errors in the protein interaction network and with respect to changes in the features of test datasets. Using the prediction system, we carried out novel predictions of synthetic sick/lethal gene pairs at a genome-wide scale. These pairs appear to have functional properties that are similar to those that characterize the known synthetic lethal gene pairs.Our analysis shows that protein interaction networks can be used to predict synthetic lethal interactions with accuracies on par with or exceeding that of other computational methods that use a variety of input features, including functional annotations. This indicates that protein interaction networks could plausibly be rich sources of information about epistatic effects among genes.Successful prediction of gene function from disparate data sources is an important challenge in the post-genomic era. Methods to do so can illuminate new mechanisms for the emergence and organization of function at the genome level, and lead to the understanding of disease mechanisms or prediction of drug targets. Functional organization of genes is often dramatically revealed by their positions in biomolecular networks and the topological constraints that these positions entail. Much work has been done on using graph properties of protein interaction networks (PINs) to elucidate gene and protein function, particularly in the baker's yeast Saccharomyces cerevisiae for which high qualit
A p53 Oscillator Model of DNA Break Repair Control
Vijay Chickarmane,Ali Nadim,Animesh Ray,Herbert M. Sauro
Quantitative Biology , 2005,
Abstract: The transcription factor p53 is an important regulator of cell fate. Mutations in p53 gene are associated with many cancers. In response to signals such as DNA damage, p53 controls the transcription of a series of genes that cause cell cycle arrest during which DNA damage is repaired, or triggers programmed cell death that eliminates possibly cancerous cells wherein DNA damage might have remained unrepaired. Previous experiments showed oscillations in p53 level in response to DNA damage, but the mechanism of oscillation remained unclear. Here we examine a model where the concentrations of p53 isoforms are regulated by Mdm22, Arf, Siah, and beta-catenin. The extent of DNA damage is signalled through the switch-like activity of a DNA damage sensor, the DNA-dependent protein kinase Atm. This switch is responsible for initiating and terminating oscillations in p53 concentration. The strength of the DNA damage signal modulates the number of oscillatory waves of p53 and Mdm22 but not the frequency or amplitude of oscillations{a result that recapitulates experimental findings. A critical fnding was that the phosphorylated form of Nbs11, a member of the DNA break repair complex Mre11-Rad50-Nbs11 (MRN), must augment the activity of Atm kinase. While there is in vitro support for this assumption, this activity appears essential for p53 dynamics. The model provides several predictions concerning, among others, degradation of the phosphorylated form of p53, the rate of DNA repair as a function of DNA damage, the sensitivity of p53 oscillation to transcription rates of SIAH, beta-CATENIN and ARF, and the hysteretic behavior of active Atm kinase levels with respect to the DNA damage signal
Identifying Hubs in Protein Interaction Networks
Ravishankar R. Vallabhajosyula, Deboki Chakravarti, Samina Lutfeali, Animesh Ray, Alpan Raval
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0005344
Abstract: Background In spite of the scale-free degree distribution that characterizes most protein interaction networks (PINs), it is common to define an ad hoc degree scale that defines “hub” proteins having special topological and functional significance. This raises the concern that some conclusions on the functional significance of proteins based on network properties may not be robust. Methodology In this paper we present three objective methods to define hub proteins in PINs: one is a purely topological method and two others are based on gene expression and function. By applying these methods to four distinct PINs, we examine the extent of agreement among these methods and implications of these results on network construction. Conclusions We find that the methods agree well for networks that contain a balance between error-free and unbiased interactions, indicating that the hub concept is meaningful for such networks.
PathSys: integrating molecular interaction graphs for systems biology
Michael Baitaluk, Xufei Qian, Shubhada Godbole, Alpan Raval, Animesh Ray, Amarnath Gupta
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-55
Abstract: Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae) and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping.Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks webcite.Complex networks of molecular and genetic interactions are increasingly being studied for insights into biological mechanisms [1-3]. Such studies include deciphering genome-wide protein-protein interactions [4]], large-scale analysis and prediction of gene regulatory networks [5], construction of metabolic pathways [6], and development of synthetic genetic interaction networks [7,8]. Here we collectively call these different networks Molecular Interaction Graphs (MIGs). The availability of MIGs has paved the way for the emergence of a new paradigm of biology in which networks of interactions are being analyzed for understanding of biological phenomena [3,9-12]. Truly integrated analyses across multiple databases of different functionalities are still rare yet promising [13]. Suc
BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies
Sergey Kozhenkov, Mayya Sedova, Yulia Dubinina, Amarnath Gupta, Animesh Ray, Julia Ponomarenko, Michael Baitaluk
BMC Systems Biology , 2011, DOI: 10.1186/1752-0509-5-7
Abstract: To study host-pathogen interaction on the systems biology level, an extension to the previously described BiologicalNetworks system is proposed. The developed methods and data integration and querying tools allow simplifying and streamlining the process of integration of diverse experimental data types, including molecular interactions and phylogenetic classifications, genomic sequences and protein structure information, gene expression and virulence data for pathogen-related studies. The data can be integrated from the databases and user's files for both public and private use.The developed system can be used for the systems-level analysis of host-pathogen interactions, including host molecular pathways that are induced/repressed during the infections, co-expressed genes, and conserved transcription factor binding sites. Previously unknown to be associated with the influenza infection genes were identified and suggested for further investigation as potential drug targets. Developed methods and data are available through the Java application (from BiologicalNetworks program at http://www.biologicalnetworks.org webcite) and web interface (at http://flu.sdsc.edu webcite).Public health initiatives increasingly recognize the importance of the cross-scale data integration, such as mounting a data-driven risk assessment of potential pandemic outbreak in specific geographical locations or discovering novel therapeutic approaches [1-6]. For example, to facilitate the study of the Influenza infection outbreaks [7,8], it is desirable to apply the systems biology approach that requires integration of heterogeneous data from various domains of knowledge: flight paths of migrating birds, animals and humans; virological aspects, such as the efficiency with which the virus can be transmitted from the infected subject; cellular phenomena, such as interaction of viral proteins with surface receptors in the inner and outer respiratory tracts of hosts; phylogenetic properties of viral
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