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  • 1
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    Seismic attenuation structure across the Karakoram fault in western Tibet (2020)
    Oxford University Press
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    Publication Date: 2020-08-18
    Description: SUMMARY 2-D attenuation maps are produced for the crust of western Tibet using local earthquakes which are recorded by an array of 31 broad-band stations operated from 2007 July to 2011 May. Relative contribution of scattering ($Q_{sc}^{-1}$) and intrinsic ($Q_{i}^{-1}$) attenuation have been calculated using Multiple Lapse Time Window Analysis under the assumption of uniform distribution of multiple isotropic scattering and intrinsic absorption in a medium for five different frequency bands centred at 1.5, 3, 6, 12 and 18 Hz, respectively. All the events are selected on the basis of high signal-to-noise ratio having hypocentral distance within 200 km from the respective stations. The obtained Q−1 values show a strong frequency dependent nature which can be correlated to the degree of tectonic complexity and the heterogeneities present in the medium. The intrinsic absorption is found to be the dominant mechanism at all the frequency ranges for all stations except few (WT03, WT07 and WT13) at 18 Hz, which may be correlated with the presence of partial melt, geothermal fluids, hydrothermal springs, mantle-derived fluids and radioactivity in the crust of western Tibet. We have divided the entire area into two regions across the Karakoram fault (KKF) to explore the variations of crustal attenuation properties. The first part covers the northeastern of KKF referred as Region 1 while the second part covers the southwestern of KKF referred as Region 2. The spatial variations of $Q_{i}^{-1}$ across the region exhibit significant differences between Regions 1 and 2 at all the investigated frequencies. Interestingly, Region 1 exhibits higher $Q_{i}^{-1}$ than Region 2 at lower frequencies, whereas $Q_{i}^{-1}$ shows opposite trends at higher frequencies (〉 6 Hz) as it shows higher values in Region 2 than Region 1. We find that the obtained values of Q−1 are also in good agreement with the other segments of Himalaya and Tibet as well as different tectonic regions in the world.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 2
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    SIFT-Based Visual Tracking using Optical Flow and Belief Propagation Algorithm (2020)
    Oxford University Press
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    Publication Date: 2020-01-02
    Description: Perceptible visual tracking acts as an important module for distinct perception tasks of autonomous robots. Better features help in easier decision-making process. The evaluation of tracking objects, dynamic positions and their visual information in results are quite difficult tasks. Until now, most real-time visual tracking algorithms suffer from poor robustness and low occurrence as they deal with complex real-world data. In this paper, we have proposed more robust and faster visual tracking framework using scale invariant feature transform (SIFT) and the optical flow in belief propagation (BF) algorithm for efficient processing in real scenarios. Here, a new feature-based optical flow along with BF algorithm is utilized to compute the affine matrix of a regional center on SIFT key points in frames. Experimental results depict that the proposed approach is more efficient and more robust in comparison with the state-of-the-art tracking algorithms with more complex scenarios.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 3
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    Structural disruption of exonic stem–loops immediately upstream of the intron regulates mammalian splicing (2020)
    Oxford University Press
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    Publication Date: 2020-05-13
    Description: Recognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly single-stranded exonic segment downstream. Splicing assays with select pre-mRNA substrates demonstrate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, the substitution or hybridization of which impedes splicing. Additionally, the exonic segments flanking the retained introns appeared to be more enriched in a previously identified set of hexameric exonic splicing enhancer (ESE) sequences compared to their spliced counterparts, suggesting that base-pairing in the exonic segments upstream of retained introns could be a means for occlusion of ESEs. The upstream exonic loops of the test substrate promoted recruitment of splicing factors and consequent pre-mRNA structural remodeling, leading up to assembly of the early spliceosome. These results suggest that disruption of exonic stem–loop structures immediately upstream (but not downstream) of the introns regulate alternative splicing events, likely through modulating accessibility of splicing factors.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Studies on the gene regulation involved in the lytic–lysogenic switch in Staphylococcus aureus temperate bacteriophage Phi11 (2020)
    Oxford University Press
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    Publication Date: 2020-07-23
    Description: Antirepressor proteins of bacteriophages are chiefly involved in interfering with the function of the repressor protein and forcing the bacteriophage to adopt the lytic cycle. The genome of Staphylococcus aureus phage, Phi11 has already been sequenced; from the genome sequence, we amplified gp07 gene and analysed its involvement in the developmental pathway of Phi11. Our results indicate that Gp07 functions as a novel antirepressor and regulates the developmental pathway of Phi11 by enhancing the binding of the Cro repressor protein to its cognate operator. We also report our finding that the CI repressor protein of Phi11 binds to the putative operator of Gp07 and regulates its expression. We further report that S.aureus transcriptional repressor LexA and coprotease RecA play a crucial role in the lytic–lysogenic switching in Phi11. We also identified that the N-terminal domain (Bro-N) of Gp07 is actually responsible for enhancing the binding of Cro repressor to its cognate operator. Our results suggest that Phi11 prophage induction is different from other bacteriophages. This study furnishes a first-hand report regarding the regulation involved in the developmental pathway of Phi11.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of Japanese Biochemical Society.
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  • 5
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    Fink, a new generation of broker for the LSST community (2020)
    Oxford University Press
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    Publication Date: 2020-11-19
    Description: Fink is a broker designed to enable science with large time-domain alert streams such as the one from the upcoming Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). It exhibits traditional astronomy broker features such as automatised ingestion, annotation, selection and redistribution of promising alerts for transient science. It is also designed to go beyond traditional broker features by providing real-time transient classification which is continuously improved by using state-of-the-art Deep Learning and Adaptive Learning techniques. These evolving added values will enable more accurate scientific output from LSST photometric data for diverse science cases while also leading to a higher incidence of new discoveries which shall accompany the evolution of the survey. In this paper we introduce Fink, its science motivation, architecture and current status including first science verification cases using the Zwicky Transient Facility alert stream.
    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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  • 6
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    COVID19 Drug Repository: text-mining the literature in search of putative COVID19 therapeutics (2020)
    Oxford University Press
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    Publication Date: 2020-11-09
    Description: The recent outbreak of COVID-19 has generated an enormous amount of Big Data. To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar. According to LitCovid (11 August 2020), ∼40,300 COVID19-related articles are currently listed in PubMed. It has been shown in clinical settings that the analysis of past research results and the mining of available data can provide novel opportunities for the successful application of currently approved therapeutics and their combinations for the treatment of conditions caused by a novel SARS-CoV-2 infection. As such, effective responses to the pandemic require the development of efficient applications, methods and algorithms for data navigation, text-mining, clustering, classification, analysis, and reasoning. Thus, our COVID19 Drug Repository represents a modular platform for drug data navigation and analysis, with an emphasis on COVID-19-related information currently being reported. The COVID19 Drug Repository enables users to focus on different levels of complexity, starting from general information about (FDA-) approved drugs, PubMed references, clinical trials, recipes as well as the descriptions of molecular mechanisms of drugs’ action. Our COVID19 drug repository provide a most updated world-wide collection of drugs that has been repurposed for COVID19 treatments around the world.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Multiwavelength analysis of low surface brightness galaxies to study possible dark matter signature (2020)
    Oxford University Press
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    Publication Date: 2020-12-17
    Description: Low Surface Brightness (LSB) galaxies have very diffuse, low surface density stellar disks which appear faint in optical images. They are very rich in neutral hydrogen (HI) gas, which extends well beyond the stellar disks. Their extended HI rotation curves and stellar disks indicate that they have very massive dark matter (DM) halos compared to normal bright galaxies. Hence, LSB galaxies may represent valuable laboratories for the indirect detection of DM. In this paper, we search for WIMP annihilation signatures in four LSB galaxies and present an analysis of nearly nine years of data from the Fermi Large Area Telescope (LAT). Above 500 MeV, no excess emission was detected from the LSB galaxies. We obtain constraints on the DM cross-section for different annihilation channels, for both individual and stacked targets. In addition to this, we use radio data from the Very Large Array (VLA) radio telescope in order to derive DM constraints, following a multiwavelength approach. The constraints obtained from the four considered LSB galaxies are nearly 3 orders of magnitude weaker than the predicted limits for the thermal relic abundances and the combined limits achieved from Fermi-LAT observations of dwarf spheroidal galaxies. Finally, we discuss the possibility of detecting emission from LSB galaxies using the upcoming ground-based γ-ray and radio observatories, namely the Cherenkov Telescope Array (CTA) and the Square Kilometre Array (SKA).
    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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  • 8
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    Resolving diverse protein–DNA footprints from exonuclease-based ChIP experiments (2021)
    Oxford University Press
    Details
    Publication Date: 2021-07-01
    Description: Motivation High-throughput chromatin immunoprecipitation (ChIP) sequencing-based assays capture genomic regions associated with the profiled transcription factor (TF). ChIP-exo is a modified protocol, which uses lambda exonuclease to digest DNA close to the TF-DNA complex, in order to improve on the positional resolution of the TF-DNA contact. Because the digestion occurs in the 5′–3′ orientation, the protocol produces directional footprints close to the complex, on both sides of the double stranded DNA. Like all ChIP-based methods, ChIP-exo reports a mixture of different regions associated with the TF: those bound directly to the TF as well as via intermediaries. However, the distribution of footprints are likely to be indicative of the complex forming at the DNA. Results We present ExoDiversity, which uses a model-based framework to learn a joint distribution over footprints and motifs, thus resolving the mixture of ChIP-exo footprints into diverse binding modes. It uses no prior motif or TF information and automatically learns the number of different modes from the data. We show its application on a wide range of TFs and organisms/cell-types. Because its goal is to explain the complete set of reported regions, it is able to identify co-factor TF motifs that appear in a small fraction of the dataset. Further, ExoDiversity discovers small nucleotide variations within and outside canonical motifs, which co-occur with variations in footprints, suggesting that the TF-DNA structural configuration at those regions is likely to be different. Finally, we show that detected modes have specific DNA shape features and conservation signals, giving insights into the structure and function of the putative TF-DNA complexes. Availability and implementation The code for ExoDiversity is available on https://github.com/NarlikarLab/exoDIVERSITY. 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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  • 9
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    Interactions between invasive plants and heavy metal stresses: a review (2021)
    Oxford University Press
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    Publication Date: 2021-08-27
    Description: Global changes have altered the distribution pattern of the plant communities, including invasive species. Anthropogenic contamination may reduce native plant resistance to the invasive species. Thus, the focus of the current review is on the contaminant biogeochemical behavior among native plants, invasive species and the soil within the plant-soil ecosystem to improve our understanding of the interactions between invasive plants and environmental stressors. Our studies together with synthesis of the literature showed that a) the impacts of invasive species on environmental stress were heterogeneous, b) the size of the impact was variable, and c) the influence types were multidirectional even within the same impact type. However, invasive plants showed self-protective mechanisms when exposed to heavy metals (HMs) and provided either positive or negative influence on the bioavailability and toxicity of HMs. On the other hand, HMs may favor plant invasion due to the widespread higher tolerance of invasive plants to HMS together with the “escape behavior” of native plants when exposed to toxic HM pollution. However, there has been no consensus on whether elemental compositions of invasive plants are different from the natives in the polluted regions. A quantitative research comparing plant, litter and soil contaminant contents between native plants and the invaders in a global context is an indispensable research focus in the future.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Year 1 of the ZTF high-cadence Galactic plane survey: strategy, goals, and early results on new single-mode hot subdwarf B-star pulsators (2021)
    Oxford University Press
    Details
    Publication Date: 2021-05-12
    Description: We present the goals, strategy, and first results of the high-cadence Galactic plane survey using the Zwicky Transient Facility (ZTF). The goal of the survey is to unveil the Galactic population of short-period variable stars, including short-period binaries, and stellar pulsators with periods less than a few hours. Between 2018 June and 2019 January, we observed 64 ZTF fields resulting in 2990 deg2 of high stellar density in the ZTF-r band along the Galactic plane. Each field was observed continuously for 1.5 to 6 h with a cadence of 40 sec. Most fields have between 200 and 400 observations obtained over 2–3  continuous nights. As part of this survey, we extract a total of ≈230 million individual objects with at least 80 epochs obtained during the high-cadence Galactic plane survey reaching an average depth of ZTF–r ≈ 20.5 mag. For four selected fields with 2–10 million individual objects per field, we calculate different variability statistics and find that ≈1–2  per cent of the objects are astrophysically variable over the observed period. We present a progress report on recent discoveries, including a new class of compact pulsators, the first members of a new class of Roche lobe filling hot subdwarf binaries as well as new ultracompact double white dwarfs and flaring stars. Finally, we present a sample of 12 new single-mode hot subdwarf B-star pulsators with pulsation amplitudes between ZTF–r = 20–76 mmag and pulsation periods between P = 5.8–16 min with a strong cluster of systems with periods ≈6 min. All of the data have now been released in either ZTF Data Release 3 or Data Release 4.
    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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