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  • Oxford University Press  (22)
  • Wiley  (11)
  • International Union of Crystallography (IUC)  (7)
  • Cambridge University Press
  • 1
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    On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-07
    Description: Type II topoisomerases (Top2s) alter DNA topology via the formation of an enzyme–DNA adduct termed cleavage complex, which harbors a transient double-strand break in one DNA to allow the passage of another. Agents targeting human Top2s are clinically active anticancer drugs whose trapping of Top2-mediated DNA breakage effectively induces genome fragmentation and cell death. To understand the structural basis of this drug action, we previously determined the structure of human Top2 β-isoform forming a cleavage complex with the drug etoposide and DNA, and described the insertion of drug into DNA cleavage site and drug-induced decoupling of catalytic groups. By developing a post-crystallization drug replacement procedure that simplifies structural characterization of drug-stabilized cleavage complexes, we have extended the analysis toward other structurally distinct drugs, m -AMSA and mitoxantrone. Besides the expected drug intercalation, a switch in ribose puckering in the 3'-nucleotide of the cleavage site was robustly observed in the new structures, representing a new mechanism for trapping the Top2 cleavage complex. Analysis of drug-binding modes and the conformational landscapes of the drug-binding pockets provide rationalization of the drugs’ structural-activity relationships and explain why Top2 mutants exhibit differential effects toward each drug. Drug design guidelines were proposed to facilitate the development of isoform-specific Top2-targeting anticancer agents.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-23
    Description: With the rapid accumulation of our knowledge on diseases, disease-related genes and drug targets, network-based analysis plays an increasingly important role in systems biology, systems pharmacology and translational science. The new release of VisANT aims to provide new functions to facilitate the convenient network analysis of diseases, therapies, genes and drugs. With improved understanding of the mechanisms of complex diseases and drug actions through network analysis, novel drug methods (e.g., drug repositioning, multi-target drug and combination therapy) can be designed. More specifically, the new update includes (i) integrated search and navigation of disease and drug hierarchies; (ii) integrated disease–gene, therapy–drug and drug–target association to aid the network construction and filtering; (iii) annotation of genes/drugs using disease/therapy information; (iv) prediction of associated diseases/therapies for a given set of genes/drugs using enrichment analysis; (v) network transformation to support construction of versatile network of drugs, genes, diseases and therapies; (vi) enhanced user interface using docking windows to allow easy customization of node and edge properties with build-in legend node to distinguish different node type. VisANT is freely available at: http://visant.bu.edu .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    A model for 3:2 HFQPO pairs in black hole binaries based on cosmic battery (2016)
    Oxford University Press
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    Publication Date: 2016-02-28
    Description: A model for 3:2 high-frequency quasi-periodic oscillations (HFQPOs) with 3:2 pairs observed in four black hole X-ray binaries (BHXBs) is proposed by invoking the epicyclic resonances with the magnetic connection (MC) between a spinning black hole (BH) with a relativistic accretion disc. It turns out that the MC can be worked out due to Poynting–Robertson cosmic battery, and the 3:2 HFQPO pairs associated with the steep power-law states can be fitted in this model. Furthermore, the severe damping problem in the epicyclic resonance model can be overcome by transferring energy from the BH to the inner disc via the MC process for emitting X-rays with sufficient amplitude and coherence to produce the HFQPOs. In addition, we discuss the important role of the magnetic field in state transition of BHXBs.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Solution structure and tandem DNA recognition of the C-terminal effector domain of PmrA from Klebsiella pneumoniae (2014)
    Oxford University Press
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    Publication Date: 2014-04-03
    Description: Klebsiella pneumoniae PmrA is a polymyxin-resistance-associated response regulator. The C-terminal effector/DNA-binding domain of PmrA (PmrA C ) recognizes tandem imperfect repeat sequences on the promoters of genes to induce antimicrobial peptide resistance after phosphorylation and dimerization of its N-terminal receiver domain (PmrA N ). However, structural information concerning how phosphorylation of the response regulator enhances DNA recognition remains elusive. To gain insights, we determined the nuclear magnetic resonance solution structure of PmrA C and characterized the interactions between PmrA C or BeF 3 – -activated full-length PmrA (PmrA F ) and two DNA sequences from the pbgP promoter of K. pneumoniae . We showed that PmrA C binds to the PmrA box, which was verified to contain two half-sites, 5'-CTTAAT-3' and 5'-CCTAAG-3', in a head-to-tail fashion with much stronger affinity to the first than the second site without cooperativity. The structural basis for the PmrA C –DNA complex was investigated using HADDOCK docking and confirmed by paramagnetic relaxation enhancement. Unlike PmrA C , PmrA F recognizes the two sites simultaneously and specifically. In the PmrA F –DNA complex, PmrA N may maintain an activated homodimeric conformation analogous to that in the free form and the interactions between two PmrA C molecules aid in bending and binding of the DNA duplex for transcription activation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    A bio-inspired computing model for ovarian carcinoma classification and oncogene detection (2015)
    Oxford University Press
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    Publication Date: 2015-04-03
    Description: Motivation: Ovarian cancer is the fifth leading cause of cancer deaths in women in the western world for 2013. In ovarian cancer, benign tumors turn malignant, but the point of transition is difficult to predict and diagnose. The 5-year survival rate of all types of ovarian cancer is 44%, but this can be improved to 92% if the cancer is found and treated before it spreads beyond the ovary. However, only 15% of all ovarian cancers are found at this early stage. Therefore, the ability to automatically identify and diagnose ovarian cancer precisely and efficiently as the tissue changes from benign to invasive is important for clinical treatment and for increasing the cure rate. This study proposes a new ovarian carcinoma classification model using two algorithms: a novel discretization of food sources for an artificial bee colony (DfABC), and a support vector machine (SVM). For the first time in the literature, oncogene detection using this method is also investigated. Results: A novel bio-inspired computing model and hybrid algorithms combining DfABC and SVM was applied to ovarian carcinoma and oncogene classification. This study used the human ovarian cDNA expression database to collect 41 patient samples and 9600 genes in each pathological stage. Feature selection methods were used to detect and extract 15 notable oncogenes. We then used the DfABC-SVM model to examine these 15 oncogenes, dividing them into eight different classifications according to their gene expressions of various pathological stages. The average accuracyof the eight classification experiments was 94.76%. This research also found some oncogenes that had not been discovered or indicated in previous scientific studies. The main contribution of this research is the proof that these newly discovered oncogenes are highly related to ovarian or other cancers. Availability and implementation: http://mht.mis.nchu.edu.tw/moodle/course/view.php?id=7 Contact: mychen@nutc.edu.tw
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 6
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    Haploinsufficiency of RCBTB1 is associated with Coats disease and familial exudative vitreoretinopathy (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-24
    Description: Familial exudative vitreoretinopathy (FEVR) belongs to a group of genetically and clinically heterogeneous disorders in retinal vascular development. To date, in approximately 50% of patients with FEVR, pathogenic mutations have been detected in FZD4 , LRP5 , TSPAN12 , NDP and ZNF408 . In this study, we identified two heterozygous frameshift mutations in RCBTB1 from three Taiwanese cases through exome sequencing. In patient-derived lymphoblastoid cell lines (LCLs), the protein level of RCBTB1 is approximately half that of unaffected control LCLs, which is indicative of a haploinsufficiency mechanism. By employing transient transfection and reporter assays for the transcriptional activity of β-catenin, we demonstrated that RCBTB1 participates in the Norrin/FZD4 signaling pathway and that knockdown of RCBTB1 by shRNA significantly reduced nuclear accumulation of β-catenin under Norrin and Wnt3a treatments. Furthermore, transgenic fli1 :EGFP zebrafish with rcbtb1 knockdown exhibited anomalies in intersegmental and intraocular vessels. These results strongly support that reduced RCBTB1 expression may lead to defects in angiogenesis through the Norrin-dependent Wnt pathway, and that RCBTB1 is a putative genetic cause of vitreoretinopathies.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 7
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    Long-term X-ray emission from Swift J1644+57 (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-06
    Description: The X-ray emission from Swift J1644+57 is not steadily decreasing; instead, it shows multiple pulses with declining amplitudes. We model the pulses as reverse shocks from collisions between the late ejected shells and the externally shocked material, which is decelerated while sweeping the ambient medium. The peak of each pulse is taken as the maximum emission of each reverse shock. With a proper set of parameters, the envelope of peaks in the light curve as well as the spectrum can be modelled well.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Introduction to CAUSES: Description of weather and climate models and their near-surface temperature errors in 5-day hindcasts near the Southern Great Plains (2018)
    Wiley
    Details
    Publication Date: 2018-02-17
    Description: We introduce the Clouds Above the United States and Errors at the Surface (CAUSES) project with its aim of better understanding the physical processes leading to warm screen-temperature biases over the American Midwest in many numerical models. In this first of four companion papers, 11 different models, from 9 institutes, perform a series of 5-day hindcasts, each initialised from reanalyses. After describing the common experimental protocol and detailing each model configuration, a gridded temperature data set is derived from observations and used to show that all the models have a warm bias over parts of the Midwest. Additionally, a strong diurnal cycle in the screen-temperature bias is found in most models. In some models the bias is largest around midday, while in others it is largest during the night. At the Department of Energy Atmospheric Radiation Measurement Southern Great Plains (SGP) site, the model biases are shown to extend several kilometers into the atmosphere. Finally, to provide context for the companion papers, in which observations from the SGP site are used to evaluate the different processes contributing to errors there, it is shown that there are numerous locations across the Midwest where the diurnal cycle of the error is highly correlated with the diurnal cycle of the error at SGP. This suggests that conclusions drawn from detailed evaluation of models using instruments located at SGP will be representative of errors that are prevalent over a larger spatial scale.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
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    CAUSES: Attribution of Surface Radiation Biases in NWP and Climate Models near the U.S. Southern Great Plains (2018)
    Wiley
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    Publication Date: 2018-03-06
    Description: Many numerical weather prediction and climate models exhibit too warm lower tropospheres near the mid-latitude continents. The warm bias has been shown to coincide with important surface radiation biases that likely play a critical role in the inception or the growth of the warm bias. This paper presents an attribution study on the net radiation biases in 9 model simulations, performed in the framework of the CAUSES project (Clouds Above the United States and Errors at the Surface). Contributions from deficiencies in the surface properties, clouds, water vapor and aerosols are quantified, using an array of radiation measurement stations near the ARM SGP site. Furthermore, an in-depth analysis is shown to attribute the radiation errors to specific cloud regimes. The net surface shortwave radiation is overestimated in all models throughout most of the simulation period. Cloud errors are shown to contribute most to this overestimation, although non-negligible contributions from the surface albedo exist in most models. Missing deep cloud events and/or simulating deep clouds with too weak cloud-radiative effects dominate in the cloud-related radiation errors. Some models have compensating errors between excessive occurrence of deep cloud, but largely underestimating their radiative effect, while other models miss deep cloud events altogether. Surprisingly, even the latter models tend to produce too much and too frequent afternoon surface precipitation. This suggests that rather than issues with the triggering of deep convection, cloud-radiative deficiencies are related to too weak convective cloud detrainment and too large precipitation efficiencies.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
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    CAUSES: On the role of surface energy budget errors to the warm surface air temperature error over the Central U.S. (2018)
    Wiley
    Details
    Publication Date: 2018-02-28
    Description: Many weather forecast and climate models simulate warm surface air temperature (T 2m ) biases over mid-latitude continents during the summertime, especially over the Great Plains. We present here one of a series of papers from a multi-model intercomparison project (CAUSES: Cloud Above the United States and Errors at the Surface), which aims to evaluate the role of cloud, radiation, and precipitation biases in contributing to the T 2m bias using a short-term hindcast approach during the spring and summer of 2011. Observations are mainly from the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) sites. The present study examines the contributions of surface energy budget errors. All participating models simulate too much net shortwave and longwave fluxes at the surface but with no consistent mean bias sign in turbulent fluxes over the Central U.S. and SGP. Nevertheless, biases in the net shortwave and downward longwave fluxes, as well as surface evaporative fraction (EF) are contributors to T 2m bias. Radiation biases are largely affected by cloud simulations, while EF bias is largely affected by soil moisture modulated by seasonal accumulated precipitation and evaporation. An approximate equation based upon the surface energy budget is derived to further quantify the magnitudes of radiation and EF contributions to T 2m bias. Our analysis ascribes that a large EF underestimate is the dominant source of error in all models with a large positive temperature bias, whereas an EF overestimate compensates for an excess of absorbed shortwave radiation in nearly all the models with the smallest temperature bias.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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