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  • 1
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    Radio variability from corotating interaction regions threading Wolf–Rayet winds (2020)
    Oxford University Press
    Details
    Publication Date: 2020-07-10
    Description: The structured winds of single massive stars can be classified into two broad groups: stochastic structure and organized structure. While the former is typically identified with clumping, the latter is typically associated with rotational modulations, particularly the paradigm of corotating interaction regions (CIRs). While CIRs have been explored extensively in the ultraviolet band, and moderately in the X-ray and optical, here we evaluate radio variability from CIR structures assuming free–free opacity in a dense wind. Our goal is to conduct a broad parameter study to assess the observational feasibility, and to this end, we adopt a phenomenological model for a CIR that threads an otherwise spherical wind. We find that under reasonable assumptions, it is possible to obtain radio variability at the 10 per cent level. The detailed structure of the folded light curve depends not only on the curvature of the CIR, the density contrast of the CIR relative to the wind, and viewing inclination, but also on wavelength. Comparing light curves at different wavelengths, we find that the amplitude can change, that there can be phase shifts in the waveform, and the entire waveform itself can change. These characterstics could be exploited to detect the presence of CIRs in dense, hot winds.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 2
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    Synthetic biosensors for precise gene control and real-time monitoring of metabolites (2015)
    Oxford University Press
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    Publication Date: 2015-08-29
    Description: Characterization and standardization of inducible transcriptional regulators has transformed how scientists approach biology by allowing precise and tunable control of gene expression. Despite their utility, only a handful of well-characterized regulators exist, limiting the complexity of engineered biological systems. We apply a characterization pipeline to four genetically encoded sensors that respond to acrylate, glucarate, erythromycin and naringenin. We evaluate how the concentration of the inducing chemical relates to protein expression, how the extent of induction affects protein expression kinetics, and how the activation behavior of single cells relates to ensemble measurements. We show that activation of each sensor is orthogonal to the other sensors, and to other common inducible systems. We demonstrate independent control of three fluorescent proteins in a single cell, chemically defining eight unique transcriptional states. To demonstrate biosensor utility in metabolic engineering, we apply the glucarate biosensor to monitor product formation in a heterologous glucarate biosynthesis pathway and identify superior enzyme variants. Doubling the number of well-characterized inducible systems makes more complex synthetic biological circuits accessible. Characterizing sensors that transduce the intracellular concentration of valuable metabolites into fluorescent readouts enables high-throughput screening of biological catalysts and alleviates the primary bottleneck of the metabolic engineering design-build-test cycle.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-28
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 4
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    Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks (2015)
    Oxford University Press
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    Publication Date: 2015-10-08
    Description: Motivation: Synthetic lethal sets are sets of reactions/genes where only the simultaneous removal of all reactions/genes in the set abolishes growth of an organism. Previous approaches to identify synthetic lethal genes in genome-scale metabolic networks have built on the framework of flux balance analysis (FBA), extending it either to exhaustively analyze all possible combinations of genes or formulate the problem as a bi-level mixed integer linear programming (MILP) problem. We here propose an algorithm, Fast-SL, which surmounts the computational complexity of previous approaches by iteratively reducing the search space for synthetic lethals, resulting in a substantial reduction in running time, even for higher order synthetic lethals. Results: We performed synthetic reaction and gene lethality analysis, using Fast-SL, for genome-scale metabolic networks of Escherichia coli , Salmonella enterica Typhimurium and Mycobacterium tuberculosis. Fast-SL also rigorously identifies synthetic lethal gene deletions, uncovering synthetic lethal triplets that were not reported previously. We confirm that the triple lethal gene sets obtained for the three organisms have a precise match with the results obtained through exhaustive enumeration of lethals performed on a computer cluster. We also parallelized our algorithm, enabling the identification of synthetic lethal gene quadruplets for all three organisms in under 6 h. Overall, Fast-SL enables an efficient enumeration of higher order synthetic lethals in metabolic networks, which may help uncover previously unknown genetic interactions and combinatorial drug targets. Availability and implementation: The MATLAB implementation of the algorithm, compatible with COBRA toolbox v2.0, is available at https://github.com/RamanLab/FastSL Contact: kraman@iitm.ac.in Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    Critical assessment of genome-scale metabolic networks: the need for a unified standard (2015)
    Oxford University Press
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    Publication Date: 2015-11-20
    Description: Genome-scale metabolic networks have been reconstructed for several organisms. These metabolic networks provide detailed information about the metabolism inside the cells, coupled with the genomic, proteomic and thermodynamic information. These networks are widely simulated using ‘constraint-based’ modelling techniques and find applications ranging from strain improvement for metabolic engineering to prediction of drug targets in pathogenic organisms. Components of these metabolic networks are represented in multiple file formats and also using different markup languages, with varying levels of annotations; this leads to inconsistencies and increases the complexities in comparing and analysing reconstructions on multiple platforms. In this work, we critically examine nearly 100 published genome-scale metabolic networks and their corresponding constraint-based models and discuss various issues with respect to model quality. One of the major concerns is the lack of annotations using standard identifiers that can uniquely describe several components such as metabolites, genes, proteins and reactions. We also find that many models do not have complete information regarding constraints on reactions fluxes and objective functions for carrying out simulations. Overall, our analysis highlights the need for a widely acceptable standard for representing constraint-based models. A rigorous standard can help in streamlining the process of reconstruction and improve the quality of reconstructed metabolic models.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 6
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    Image and Video Encryption based on Dual Space-Filling Curves (2012)
    Oxford University Press
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    Publication Date: 2012-05-31
    Description: In this paper, a new encryption scheme with three different modes of operations is proposed based on dual space-filling curves (SFSs) and a fractional wavelet transform (FrWT). This scheme is initially proposed for images and then extended to videos. The core idea behind the proposed schemes is to decompose an image/video first by the FrWT followed by the shuffling of each sub-band coefficients by means of a dual SFC. At last, an inverse FrWT is performed to get the encrypted image/video. A reliable decryption process is also proposed to construct the original image from the encrypted image. The experimental results, security and comparative analysis demonstrate the efficiency and robustness of the proposed scheme. Further, this paper also proposes an efficient implementation of an FrWT based on chaotic maps.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 7
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    UDP-N-acetyl-{alpha}-D-galactosamine:polypeptide N-acetylgalactosaminyltransferases: Completion of the family tree (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-26
    Description: The formation of mucin-type O -glycans is initiated by an evolutionarily conserved family of enzymes, the UDP- N -acetyl-α- d -galactosamine:polypeptide N -acetylgalactosaminyltransferases (GalNAc-Ts). The human genome encodes 20 transferases; 17 of which have been characterized functionally. The complexity of the GalNAc-T family reflects the differential patterns of expression among the individual enzyme isoforms and the unique substrate specificities which are required to form the dense arrays of glycans that are essential for mucin function. We report the expression patterns and enzymatic activity of the remaining three members of the family and the further characterization of a recently reported isoform, GalNAc-T17. One isoform, GalNAcT-16 that is most homologous to GalNAc-T14, is widely expressed (abundantly in the heart) and has robust polypeptide transferase activity. The second isoform GalNAc-T18, most similar to GalNAc-T8, -T9 and -T19, completes a discrete subfamily of GalNAc-Ts. It is widely expressed and has low, albeit detectable, activity. The final isoform, GalNAc-T20, is most homologous to GalNAc-T11 but lacks a lectin domain and has no detectable transferase activity with the panel of substrates tested. We have also identified and characterized enzymatically active splice variants of GalNAc-T13 that differ in the sequence of their lectin domain. The variants differ in their affinities for glycopeptide substrates. Our findings provide a comprehensive view of the complexities of mucin-type O -glycan formation and provide insight into the underlying mechanisms employed to heavily decorate mucins and mucin-like domains with carbohydrate.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    UDP-N-acetyl-{alpha}-D-galactosamine: polypeptide N-acetylgalactosaminyltransferases: completion of the family tree (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-26
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 9
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    SALT observation of X-ray pulse reprocessing in 4U 1626-67 (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-17
    Description: We investigate optical reprocessing of X-rays in the low-mass X-ray binary (LMXB) pulsar 4U 1626–67 in its current spin-up phase using observations with Southern African Large Telescope (SALT), near-simultaneous observations with Swift -X-ray Telescope and non-simultaneous RXTE -Proportional Counter Array (PCA) observations and present the results of timing analysis. Using SALT observations carried out on 2014 March 5 and 6, we detect some interesting reprocessing signatures. We detect a weak optical quasiperiodic oscillation (QPO) in the power density spectrum on March 5 at 48 mHz with a fractional rms of 3.3 per cent in spite of the fact that source shows no corresponding X-ray QPO in the spin-up phase. In the light curve obtained on March 5, we detect a coherent pulsation at the spin period of ~7.677 s. A previously known, slightly down-shifted side-band is also detected at 129.92 mHz. The frequency spacing between main pulse and this side-band is different from earlier observations, though the statistical significance of the difference is limited. The light curve of March 6 displays short time-scale variability in the form of flares on time-scales of a few minutes. Folded pulse profiles resulting from data of this night show an interesting trend of pulse peak drifting. This drift could be due to (i) rapid changes in the reprocessing agent, like orbital motion of an accretion disc warp around the neutron star, or (ii) intrinsic pulse phase changes in X-rays. We also examine some X-ray light curves obtained with RXTE -PCA during 2008–2010 for pulse shape changes in short time-scales during X-ray flares.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    The Year of Glycosciences (2013)
    Oxford University Press
    Details
    Publication Date: 2013-01-10
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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