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  • 1
    Language: English
    In: Journal of chemical theory and computation, 2017-09-12, Vol.13 (9), p.4553-4566
    Description: The rapid spreading of antimicrobial resistance in Gram-negative bacteria has become a major threat for humans as well as animals. As one of the main factors involved, the permeability of the outer membrane has attracted a great deal of attention recently. However, the knowledge regarding the translocation mechanisms for most available antibiotics is so far rather limited. Here, a theoretical study concerning the diffusion route of ciprofloxacin across the outer membrane porin OmpC from E. coli is presented. To this end, we establish a protocol to characterize meaningful permeation pathways by combining metadynamics with the zero-temperature string method. It was found that the lowest-energy pathway requires a reorientation of ciprofloxacin in the extracellular side of the porin before reaching the constriction region with its carboxyl group ahead. Several affinity sites have been identified, and their metastability has been evaluated using unbiased simulations. Such a detailed understanding is potentially very helpful in guiding the development of next generation antibiotics.
    Subject(s): Index Medicus
    ISSN: 1549-9618
    E-ISSN: 1549-9626
    Source: Hellenic Academic Libraries Link
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 2
    Language: English
    In: Biophysical journal, 2016-02-16, Vol.110 (3), p.328a-328a
    Subject(s): Algorithms
    ISSN: 0006-3495
    E-ISSN: 1542-0086
    Source: ScienceDirect Journals
    Source: PubMed Central
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  • 3
    Language: English
    In: Geophysics, 2019-11, Vol.84 (6), p.R977-R988
    Description: Full-waveform inversion is a powerful data-fitting technique that is used for velocity-model building in seismic exploration. The inversion approach exploits the sensitivity of long-offset, wide-aperture, low-frequency data to the P-wave velocity properties in the subsurface. In the geologically complex land context in which different lithologies interleave and create large elastic property contrasts, acoustic waveform inversion is challenged due to the elastic nature of the data. The large elastic property contrasts create mode conversions. At low-to-intermediate frequencies, due to tuning/interference effects, the changes in the amplitudes of the different events affect amplitude and phase of the waveforms. We found that elastic waveform inversion of the long-offset, wide-aperture, low-frequency data leads to better retrieval of the compressional velocity model than the acoustic inversion and it is more stable. To obtain a good resolution in the shallow part of the model in an efficient manner, we have developed a two-stage inversion workflow that combines offset and frequency continuation. We have evaluated the relevance of this workflow with a challenging data set from South Oman.
    Subject(s): onshore ; Arabian Peninsula ; inverse problem ; applied (geophysical surveys & methods) ; energy sources ; data processing ; Geophysics ; surveys ; elastic waves ; P-waves ; velocity ; Oman ; seismic methods ; Economic geology ; Asia ; imagery ; body waves ; data acquisition ; geophysical methods ; petroleum ; petroleum exploration ; waveforms ; geophysical surveys ; seismic waves
    ISSN: 0016-8033
    E-ISSN: 1942-2156
    Source: SEG Digital Library
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  • 4
    Language: English
    In: Journal of medical virology, 2021-04, Vol.93 (4), p.2301-2306
    Description: Assessment of commercial severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) immunoassays for their capacity to provide reliable information on sera neutralizing activity is an emerging need. We evaluated the performance of two commercially available lateral flow immunochromatographic assays (LFIC; Wondfo SARS‐CoV‐2 Antibody test and the INNOVITA 2019‐nCoV Ab test) in comparison with a SARS‐CoV‐2 neutralization pseudotyped assay for coronavirus disease 2019 (COVID‐19) diagnosis in hospitalized patients and investigate whether the intensity of the test band in LFIC associates with neutralizing antibody (NtAb) titers. Ninety sera were included from 51 patients with moderate to severe COVID‐19. A green fluorescent protein (GFP) reporter‐based pseudotyped neutralization assay (vesicular stomatitis virus coated with SARS‐CoV‐2 spike protein) was used. Test line intensity was scored using a 4‐level scale (0 to 3+). The overall sensitivity of LFIC assays was 91.1% for the Wondfo SARS‐CoV‐2 Antibody test, 72.2% for the INNOVITA 2019‐nCoV IgG, 85.6% for the INNOVITA 2019‐nCoV IgM, and 92.2% for the NtAb assay. Sensitivity increased for all assays in sera collected beyond day 14 after symptoms onset (93.9%, 79.6%, 93.9%, and 93.9%, respectively). Reactivities equal to or more intense than the positive control line (≥2+) in the Wondfo assay had a negative predictive value of 100% and a positive predictive value of 96.4% for high NtAb50 titers (≥1/160). Our findings support the use of LFIC assays evaluated herein, particularly the Wondfo test, for COVID‐19 diagnosis. We also find evidence that these rapid immunoassays can be used to predict high SARS‐CoV‐2‐S NtAb50 titers.
    Subject(s): neutralizing antibodies ; COVID‐19 ; lateral flow immunochromatographic assays ; SARS‐CoV‐2 ; COVID-19 - immunology ; COVID-19 - virology ; Green Fluorescent Proteins ; Immunoglobulin G - blood ; Humans ; Antibodies, Viral - blood ; COVID-19 - diagnosis ; Antibodies, Neutralizing - immunology ; Immunoglobulin M - blood ; COVID-19 - blood ; Immunoassay - methods ; Antibodies, Viral - immunology ; SARS-CoV-2 - immunology ; Spike Glycoprotein, Coronavirus - immunology ; Antibodies, Neutralizing - blood ; COVID-19 Testing - methods ; Index Medicus
    ISSN: 0146-6615
    E-ISSN: 1096-9071
    Source: Alma/SFX Local Collection
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 5
    Language: English
    In: The New England journal of medicine, 2016-01-07, Vol.374 (1), p.43-53
    Description: Antilymphocyte globulin (ATG) added to the conditioning regimen before allogeneic hematopoietic stem-cell transplantation resulted in a lower rate of chronic graft-versus-host disease at 2 years than the rate without ATG (32% vs. 68%), with no apparent increased risk of relapse. Chronic graft-versus-host disease (GVHD) is a major complication of allogeneic stem-cell transplantation that results in later illness and death and a reduction in quality of life. 1 , 2 Risk factors for chronic GVHD are the use of peripheral blood as a source of stem cells, a history of acute GVHD, and the use of donated stem cells with high numbers of T cells. 3 – 7 In a meta-analysis, the Stem Cell Trialists’ Collaborative Group reported an incidence of extensive chronic GVHD of 47% after peripheral-blood stem-cell transplantation from an HLA-identical sibling. 4 In 2012, more than 70% of the stem-cell transplantations performed in . . .
    Subject(s): Graft vs Host Disease - epidemiology ; Prospective Studies ; Humans ; Immunosuppressive Agents - therapeutic use ; Middle Aged ; Proportional Hazards Models ; Child, Preschool ; Male ; Survival Rate ; Transplantation, Homologous ; Incidence ; Young Adult ; Disease-Free Survival ; Graft vs Host Disease - mortality ; Adolescent ; Antilymphocyte Serum - therapeutic use ; Adult ; Female ; Graft vs Host Disease - prevention & control ; T-Lymphocytes - immunology ; Child ; Chronic Disease ; Prevention ; Treatment outcome ; Graft versus host reaction ; Immunoglobulins ; Dosage and administration ; Analysis ; Graft-versus-host reaction ; Transplants & implants ; Leukemia ; Stem cell transplantation ; Lymphocytes T ; Preventive medicine ; Hemopoiesis ; Globulins ; Risk assessment ; Peripheral blood ; Stem cells ; Bone marrow ; Histocompatibility antigen HLA ; Index Medicus ; Abridged Index Medicus
    ISSN: 0028-4793
    E-ISSN: 1533-4406
    Source: Single Journals
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 6
    Language: English
    In: Geophysical journal international, 2014-09-01, Vol.198 (3), p.1359-1372
    Description: In the context of near surface seismic imaging (a few hundreds of metres), we propose an alternative approach for inversion of surface waves in 2-D media with laterally varying velocities. It is based on Full Waveform Inversion (FWI) but using an alternative objective function formulated in the frequency–wavenumber f − k domain. The classical FWI objective function suffers from severe local minima problems in the presence of surface waves. It thus requires a very accurate initial model. The proposed objective function is similar to the one used in classical surface wave analysis. In this approach, the data are first split using sliding windows in the time–space t − x domain. For each window, the amplitude of the f − k spectrum is computed. The objective function measures the least-squares misfit between the amplitude of observed and modelled 2-D Fourier transformed data sets. We call this formulation the windowed-amplitude waveform inversion (w-AWI). The w-AWI objective function reduces some local minima problems as shown here through numerical examples. The global minimum basin is wider in the w-AWI approach than in FWI. Synthetic examples show that w-AWI may achieve convergence if the lowest data frequency content is twice higher than the one needed by FWI. For elastic inversion, w-AWI can be used to reconstruct a velocity model explaining surface waves. This surface wave inversion procedure can be used to retrieve near-surface model parameters in lateral-varying media
    Subject(s): Earth Sciences ; Sciences of the Universe ; Geophysics
    ISSN: 0956-540X
    E-ISSN: 1365-246X
    Source: Alma/SFX Local Collection
    Source: Oxford Journals 2016 Current and Archive A-Z Collection
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  • 7
    Language: English
    In: Journal of chemical theory and computation, 2018-12-11, Vol.14 (12), p.6701-6713
    Description: A Brownian dynamics (BD) approach including explicit atoms called BRODEA is presented to model ion permeation and molecule translocation across a nanopore confinement. This approach generalizes our previous hybrid molecular dynamics–Brownian dynamics framework (J. Chem. Theory Comput. 2016, 12, 2401) by incorporating a widespread and enhanced set of simulation schemes based on several boundary conditions and electrostatic models, as well as a temperature accelerated method for sampling free energy surfaces and determining substrate translocation pathways. As a test case, BRODEA was applied to study the ion diffusion as well as to ciprofloxacin and enrofloxacin transport through the outer membrane porin OmpC from E. coli. The equivalence between the different simulation schemes was demonstrated and their computational efficiency evaluated. The BRODEA results are able to reproduce the main features of the ion currents and free energy surfaces determined by all-atom molecular dynamics simulations and validated by experiments. Furthermore, the BRODEA results are able to determine the ciprofloxacin and enrofloxacin permeation pathways showing a remarkable agreement with the results obtained from a computational protocol that combines metadynamics and a zero-temperature string method (J. Chem. Theory Comput. 2017, 13, 4553; J. Phys. Chem. B 2018, 122, 1417). To our knowledge, this is the first time such antibiotic permeation pathways have been characterized by a technique based on Brownian dynamics.
    Subject(s): Thermodynamics ; Porins - metabolism ; Porins - chemistry ; Protein Conformation ; Permeability ; Nanopores ; Molecular Dynamics Simulation ; Index Medicus
    ISSN: 1549-9618
    E-ISSN: 1549-9626
    Source: Hellenic Academic Libraries Link
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 8
    Language: English
    In: Geophysical journal international, 2015-06-01, Vol.201 (3), p.1324-1334
    ISSN: 0956-540X
    E-ISSN: 1365-246X
    Source: Alma/SFX Local Collection
    Source: Oxford Journals 2016 Current and Archive A-Z Collection
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  • 9
    Language: English
    In: American journal of transplantation, 2019-09, Vol.19 (9), p.2479-2494
    Description: Controversy surrounds the potential association between cytomegalovirus (CMV) infection and increased risk of mortality after allogeneic hematopoietic stem cell transplantation (Allo‐HSCT). A systematic literature search was conducted using the PubMed, EMBASE, and Web of Science databases, assessing the association between CMV infection, as documented by the pp65 antigenemia assay or by polymerase chain reaction (PCR) using blood specimens, and overall mortality (OM) and nonrelapse mortality (NRM) in the allo‐HSCT setting. Pooled effects were estimated using the generic inverse variance random effects model. Heterogeneity was evaluated by Cochrane's Q test and I2 statistics. The source of heterogeneity was investigated by meta‐regression and subgroup analyses. Twenty‐six of 1367 studies fulfilled eligibility criteria. CMV infection identified by PCR monitoring was significantly associated with an increased risk of OM and NRM (hazard ratio 1.47, 95% confidence interval [1.20‐1.81], P ≤ .001; hazard ratio 1.68, 95% confidence interval [1.14‐2.49], P = .05, respectively). In this setting, the use of preemptive antiviral therapy (PET) resulted in a twofold increased risk of OM and NRM. The estimated effect sizes were associated with allo‐HSCT modalities. Although our analyses point to an association between CMV infection and an increased risk of OM and NRM in allo‐HSCT recipients, the high heterogeneity across studies prevented drawing of robust conclusions on this matter. The authors find a moderate association between CMV viremia and the risk of overall and nonrelapse mortality in allogeneic hematopoietic stem cell transplant recipients, which appears to be modulated by the transplant modality and the use of pre‐emptive antiviral therapy.
    Subject(s): bone marrow/hematopoietic stem cell transplantation ; meta‐analysis ; infection and infectious agents – viral: cytomegalovirus (CMV) ; infectious disease ; clinical research/practice ; Antiviral agents ; Stem cell research ; Communicable diseases ; Mortality ; Stem cells ; Cytomegalovirus infections ; Transplantation ; Health aspects ; Risk factors ; Hematopoietic stem cells ; Index Medicus
    ISSN: 1600-6135
    E-ISSN: 1600-6143
    Source: Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 10
    Language: English
    In: Scientific reports, 2015-05-06, Vol.5 (1), p.9769-9769
    Description: REarranged during Transfection (RET) is a transmembrane receptor tyrosine kinase required for normal development and maintenance of neurons of the central and peripheral nervous systems. Deregulation of RET and hyperactivity of the RET kinase is intimately connected to several types of human cancers, most notably thyroid cancers, making it an attractive therapeutic target for small-molecule kinase inhibitors. Novel approaches, allowing external control of the activity of RET, would be key additions to the signal transduction toolbox. In this work, photoswitchable RET kinase inhibitors based on azo-functionalized pyrazolopyrimidines were developed, enabling photonic control of RET activity. The most promising compound displays excellent switching properties and stability with good inhibitory effect towards RET in cell-free as well as live-cell assays and a significant difference in inhibitory activity between its two photoisomeric forms. As the first reported photoswitchable small-molecule kinase inhibitor, we consider the herein presented effector to be a significant step forward in the development of tools for kinase signal transduction studies with spatiotemporal control over inhibitor concentration in situ.
    Subject(s): Protein Kinase Inhibitors - chemistry ; Protein Kinase Inhibitors - analysis ; Photochemistry - methods ; Light ; Drug Design ; Protein Binding ; Receptor Protein-Tyrosine Kinases - antagonists & inhibitors ; Delayed-Action Preparations - chemical synthesis ; Protein Kinase Inhibitors - radiation effects ; Binding Sites ; Tyrosine ; Signal transduction ; Transfection ; Ret protein ; Protease inhibitors ; Hyperactivity ; Cyclin-dependent kinases ; Protein-tyrosine kinase receptors ; Protein-tyrosine kinase ; Pyrazolopyrimidines ; Thyroid ; Index Medicus ; Kemi ; Chemical Sciences
    ISSN: 2045-2322
    E-ISSN: 2045-2322
    Source: Nature Open Access
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: SWEPUB Freely available online
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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