gebhart/patrepeval huggingface dataset:
Antiviral Properties of Deazaadenine Nucleoside Derivatives (2006)

Viral infections have menaced human beings since time immemorial, and even today new viral strains that cause lethal diseases are being discovered with alarming frequency. One major example is HIV, the etiological agent of AIDS, which spread up in the last two decades. Very recently, other virus based diseases such as avian flu have spread fear around the world, and hemorrhagic fevers from central Africa serious threaten human health because of their very deadly effects. New antiviral agents are still greatly needed to counter these menaces. Many scientists are involved in this field of research, and many of the recently discovered effective antiviral compounds are nucleoside analogues. Among those derivatives, deazapurine nucleoside analogues have demonstrated potent inhibitory effect of viral replication. This review reports on recently generated data from preparing and testing deazapurine nucleoside derivatives as inhibitors in virus replication systems. Although most of the reported data have been produced in antiHIV, antiHCMV, and antiHSV biological testing, very recently other new important fields of application have been discovered, all in topical subjects of strong interest. In fact, deazapurine nucleosides have been found to be active as chemotherapeutics for some veterinary systemic viral infections, for which no antiviral drugs are licensed yet. Furthermore, they demonstrated efficacy in the inhibition of Hepatitis C virus replication. Finally, these compounds showed high potency as virucides against Ebola Virus, curing Ebola infected mice with a single dose administration.
PZ calibration by applying the equation of motion to critically refracted waves (2002)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2002PZ calibration by applying the equation of motion to critically refracted wavesAuthors: Aslaug H. S. MelboJohan O. A. RobertssonDirk‐Jan van ManenAslaug H. S. MelboWesternGeco, Oslo, Norway, Johan O. A. RobertssonWesternGeco, Oslo, Norway, and Dirk‐Jan van ManenWesternGeco, Oslo, Norwayhttps://doi.org/10.1190/1.1816819 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1816819FiguresReferencesRelatedDetailsCited byApplied 3D salt body reconstruction using shape optimization with level setsTaylor Dahlke, Biondo Biondi, and Robert Clapp11 September 2020 | GEOPHYSICS, Vol. 85, No. 5Applied 3D salt body reconstruction using shape optimization with level setsTaylor Dahlke10 August 2019Up-down separation and debubble using a multicomponent non-stationary prediction-error filterKaiwen Wang, Joseph Jennings, and Jon Claerbout1 August 2019PZ calibration in shallow waters: The Britannia OBS exampleYi Wang and Sergio Grion15 December 2008OBC sensor response and calibrated reflectivityMilo M. Backus, Paul E. Murray, Robert J. Graebner, and Bob A. Hardage14 September 2007Surface multiple attenuation by up‐down wavefield deconvolution: an OBC case studyJoffrey Brunellière, Philippe Caprioli, Sergio Grion, Dave Tilling, Lasse Amundsen, and Hans Aronsen3 January 2005 SEG Technical Program Expanded Abstracts 2002ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2002 Pages: 2478 publication data© 2002 Copyright © 2002 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 03 Jan 2005 CITATION INFORMATION Aslaug H. S. Melbo, Johan O. A. Robertsson, and Dirk‐Jan van Manen, (2002), "PZ calibration by applying the equation of motion to critically refracted waves," SEG Technical Program Expanded Abstracts : 1030-1033. https://doi.org/10.1190/1.1816819 Plain-Language Summary PDF DownloadLoading ...
Resonant clocking using distributed parasitic capacitance (2004)

A resonant clock distribution scheme that dissipates less power than conventional, buffer-driven clock distribution is described. All clock buffers are removed and the clock energy is resonated between integrated inductors and the parasitic capacitance of the local clock network, which form the energy storage elements of an LC VCO. Designed and fabricated in IBM's 0.13 /spl mu/m partially-depleted SOI, measurements show that the resonant clock dissipates 63% less power than a conventional, buffer-driven clock driving the same clock network.
Remote System for Characterizing, Monitoring and Inspecting the Inside of Contaminated Nuclear Stacks - 11567 (2011)

The Stack Characterization System (SCS) is a collaborative project with the Robotics and Energetic Systems Group (RESG) at Oak Ridge National Laboratory (ORNL) and the Applied Research Center (ARC) at Florida International University (FIU). The SCS is a robotic system that will be deployed into off-gas stacks located around the central campus at ORNL. The system will consists of surveying equipment capable of taking surface contamination samples, radiation readings, core samples and transmit live video to its operators. Trade studies were conducted on varying concrete materials to determine the best way of retrieving loose contamination from the surface. The studies were performed at the ARC facility by FIU students, where traditional cloth wipes were compared to adhesive material. The adhesive material was tested on the RESG’s smear sampler to record how much loose surface material could be retrieved. The FIU students completed a summer internship during which conceptual designs were created for a deployable radiation detector and core drill capable of retrieving multiple core samples.
Risk Analysis Based On Design Version Control Data (2019)

Early identification of areas that are at-risk in a design under development can help design and verification teams take early preventive and corrective measures. We propose a novel system that predicts which files are at risk of being buggy. Our simple, machine learning-based, regression system receives data from various sources, including the version control and defect tracking tools. After automatically labeling historic data and training sets, the system predicts the risk level of each file. Experimental results show that the proposed system has fairly high positive precision and recall and that its predictions are better than trivial predictions, such as files that recently changed or had bugs.
Fluorescent Ligand Enables Target Engagement Studies for the Intracellular Allosteric Binding Site of the Chemokine Receptor CXCR2 (2023)

Fluorescently labeled ligands are versatile molecular tools to study G protein-coupled receptors (GPCRs) and can be used for a range of different applications, including bioluminescence resonance energy transfer (BRET) assays and fluorescence microscopy. Herein, we report the structure-based development of a fluorescent ligand targeting the intracellular allosteric binding site (IABS) of the CXC chemokine receptor 2 (CXCR2), a class A GPCR that has been pursued as a drug target in oncology and inflammation. Starting from the co-crystallized intracellular CXCR2 antagonist 00767013 (1), a tetramethylrhodamine (TAMRA)-labeled CXCR2 ligand was designed, synthesized, and tested for its suitability as fluorescent reporter to probe binding to the IABS of CXCR2. By means of these studies, we developed Mz438 (9) as a high affinity fluorescent CXCR2 ligand, enabling cell-free as well as cellular NanoBRET-based binding studies in a non-isotopic and high-throughput manner. Further, we show that 9 can be used as a tool to visualize intracellular target engagement for CXCR2 via fluorescence microscopy. Thus, our small molecule-based fluorescent CXCR2 ligand 9 represents a promising tool for future studies of CXCR2 pharmacology.
Multiplexed Enzyme Activity-Based Probe Display via Hybridization (2020)

Emulsions offer the means to miniaturize and parallelize high-throughput screening but require a robust method to localize activity-based fluorescent probes in each droplet. Multiplexing probes in droplets is impractical, though highly desirable for identifying library members that possess very specific activity. Here, we present multiplexed probe immobilization on library beads for emulsion screening. During library bead preparation, we quantitated ∼10<sup>6</sup> primers per bead by fluorescence in situ hybridization, however emulsion PCR yielded only ∼10<sup>3</sup> gene copies per bead. We leveraged the unextended bead-bound primers to hybridize complementary probe-oligonucleotide heteroconjugates to the library beads. The probe-hybridized bead libraries were then used to program emulsion in vitro transcription/translation reactions and analyzed by FACS to perform multiplexed activity-based screening of trypsin and chymotrypsin mutant libraries for novel proteolytic specificity. The approach's modularity should permit a high degree of probe multiplexing and appears extensible to other enzyme classes and library types.
Front Matter: Volume 6897 (2008)

A unique, consistent, permanent citation identifier (CID) number is
Perfomance evaluation of maximum likelihood sequence estimation receivers in lightwave systems with optical amplifiers (2005)

Maximum likelihood sequence estimation (MLSE) has been proposed in earlier literature to combat the e®ects of nonlinear dispersion in intensity modulation/direct detection (IM/DD) optical channels. In this paper, we develop a theory of the bit error rate (BER) of MLSE-based IM/DD receivers operating in the presence of nonlinear dispersion and amplified spontaneous emission (ASE) noise. We focus on long haul or metro links spanning several hundred kilometers of single model fibers with optical amplifiers. Numerical results show a close agreement between the predictions of the theory and computer simulations.
Potent, Selective Inhibitors of Fibroblast Growth Factor Receptor Define Fibroblast Growth Factor Dependence in Preclinical Cancer Models (2011)

We describe here the identification and characterization of 2 novel inhibitors of the fibroblast growth factor receptor (FGFR) family of receptor tyrosine kinases. The compounds exhibit selective inhibition of FGFR over the closely related VEGFR2 receptor in cell lines and in vivo. The pharmacologic profile of these inhibitors was defined using a panel of human tumor cell lines characterized for specific mutations, amplifications, or translocations known to activate one of the four FGFR receptor isoforms. This pharmacology defines a profile for inhibitors that are likely to be of use in clinical settings in disease types where FGFR is shown to play an important role.
Two-dimensional correlation between blood glucose and optical scattering for noninvasive blood glucose sensing with optical coherence tomography (2016)

We propose an algorithm of using two-dimensional correlation analysis between blood glucose and optical scattering coefficient of skin tissues for the noninvasive blood glucose measurement with optical coherence tomography (OCT).
Therapeutic Cancer Vaccines: Clinical Trials and Applications (2008)

This chapter contains sections titled: Introduction Innate and Adaptive Immunity in Relation to Cancer Immunotherapy Design Issues for Clinical Cancer Vaccine Trials Clinical Development of Cancer Vaccines Proof of Principle Trials Efficacy Trials Clinical Endpoints in Efficacy Trials Challenges in Vaccine Development Defining the Target Tumor-Associated Antigens Production and Storage Issues Clinical Trials Conclusions Acknowledgment References
ACTH/beta-endorphins and ACTH/cortisol ratios as early biological markers in HIV infection. (1991)

Three groups of male homosexuals: AIDS (n = 19), HIV seropositive (n = 15), and seronegative partners of seropositive subjects (n = 15), were compared to a heterosexual seronegative control group (n = 13). Twice daily evaluations (8 A.M. and 5 P.M.) of plasma levels of beta-endorphin, ACTH, and cortisol were done by radioimmunoassay. Seropositive subjects and their seronegative partners showed similar levels of neurohormones: 1. An elevation in the ACTH/beta-endorphin ratio in the plasma, (C = 0.69 +/- 0.84, AIDS = 0.44 +/- 0.32, S+ = 0.42 +/- 0.28, and S- = 0.42 +/- 0.5); 2. A loss of normal relationship of the coupling ACTH/total cortisol, (C = 0.00035 +/- 0.00028, AIDS = 0.00042 +/- 0.0034, S+ = 0.00074 +/- 0.00068, and S- = 0.00072 +/- 0.0008. Neuroendocrinological disorders have been observed in HIV-infected subjects and in their seronegative partners. These could be related to their sexual behavior, as well as to the HIV infection. If this last hypothesis is confirmed, the ACTH/beta-endorphin and ACTH/cortisol ratios may be seen as possible early signs of HIV infection.
A new antibiotic with potent activity targets MscL (2015)

The growing problem of antibiotic-resistant bacteria is a major threat to human health. Paradoxically, new antibiotic discovery is declining, with most of the recently approved antibiotics corresponding to new uses for old antibiotics or structurally similar derivatives of known antibiotics. We used an in silico approach to design a new class of nontoxic antimicrobials for the bacteria-specific mechanosensitive ion channel of large conductance, MscL. One antimicrobial of this class, compound 10, is effective against methicillin-resistant Staphylococcus aureus with no cytotoxicity in human cell lines at the therapeutic concentrations. As predicted from in silico modeling, we show that the mechanism of action of compound 10 is at least partly dependent on interactions with MscL. Moreover we show that compound 10 cured a methicillin-resistant S. aureus infection in the model nematode Caenorhabditis elegans. Our work shows that compound 10, and other drugs that target MscL, are potentially important therapeutics against antibiotic-resistant bacterial infections.
Observation of $\mathrm{B^{0}_{s}}$ mesons and measurement of the $\mathrm{B^{0}_{s}}/\mathrm{B^{+}}$ yield ratio in PbPb collisions at ${\sqrt {\smash [b]{s_{_{\mathrm {NN}}}}}} = $ 5.02 TeV (2021)

The $\mathrm{B^{0}_{s}}$ and $\mathrm{B^{+}}$ production yields are measured in PbPb collisions at a center-of-mass energy per nucleon pair of 5.02 TeV. The data sample, collected with the CMS detector at the LHC, corresponds to an integrated luminosity of 1.7 nb$^{-1}$. The mesons are reconstructed in the exclusive decay channels ${\mathrm{B^{0}_{s}} \to \mathrm{J}/\psi\,\phi}$ and ${\mathrm{B^{+}} \to \mathrm{J}/\psi\,\mathrm{K^{+}}}$. The $\mathrm{B^{0}_{s}}$ meson is observed with a statistical significance in excess of five standard deviations for the first time in nucleus-nucleus collisions. The measurements are performed as functions of the transverse momentum of the B mesons and of the PbPb collision centrality. The ratio of production yields of $\mathrm{B^{0}_{s}}$ and $\mathrm{B^{+}}$ is measured and compared to theoretical models that include quark recombination effects.
Rapid Induction of Apoptosis in CD8+ HIV-1 Envelope-Specific Murine CTLs by Short Exposure to Antigenic Peptide (2002)

During primary viral infection, in vivo exposure to high doses of virus causes a loss of Ag-specific CD8(+) T cells. This phenomenon, termed clonal exhaustion, and other mechanisms by which CTLs are deleted are poorly understood. Here we show evidence for a novel form of cell death in which recently stimulated CD8(+) HIV-1 envelope gp160-specific murine CTLs become apoptotic in vitro after brief exposure to free antigenic peptide (P18-I10). Peak apoptosis occurred within 3 h of treatment with peptide, and the level of apoptosis was dependent on both the time after initial stimulation with target cells and the number of targets. Using T cell-specific H-2D(d)/P18-I10 tetramers, we observed that the apoptosis was induced by such complexes. Induction of apoptosis was blocked by cyclosporin A, a caspase 3 inhibitor, and a mitogen-activated protein kinase inhibitor, but not by Abs to either Fas ligand or to TNF-alpha. Thus, these observations suggest the existence of a Fas- or TNF-alpha-independent pathway initiated by TCR signaling that is involved in the rapid induction of CTL apoptosis. Such a pathway may prove important in the mechanism by which virus-specific CTLs are deleted in the presence of high viral burdens.
Thin Phytoplankton Layers: Characteristics, Mechanisms, and Consequences (2011)

For over four decades, aggregations of phytoplankton known as thin layers have been observed to harbor large amounts of photosynthetic cells within narrow horizontal bands. Field observations have revealed complex linkages among thin phytoplankton layers, the physical environment, cell behavior, and higher trophic levels. Several mechanisms have been proposed to explain layer formation and persistence, in the face of the homogenizing effect of turbulent dispersion. The challenge ahead is to connect mechanistic hypotheses with field observations to gain better insight on the phenomena that shape layer dynamics. Only through a mechanistic understanding of the relevant biological and physical processes can we begin to predict the effect of thin layers on the ecology of phytoplankton and higher organisms.
Coherent Interlayer Tunneling and Negative Differential Resistance with High Current Density in Double Bilayer Graphene–WSe2 Heterostructures (2017)

We demonstrate gate-tunable resonant tunneling and negative differential resistance between two rotationally aligned bilayer graphene sheets separated by bilayer WSe<sub>2</sub>. We observe large interlayer current densities of 2 and 2.5 μA/μm<sup>2</sup> and peak-to-valley ratios approaching 4 and 6 at room temperature and 1.5 K, respectively, values that are comparable to epitaxially grown resonant tunneling heterostructures. An excellent agreement between theoretical calculations using a Lorentzian spectral function for the two-dimensional (2D) quasiparticle states, and the experimental data indicates that the interlayer current stems primarily from energy and in-plane momentum conserving 2D-2D tunneling, with minimal contributions from inelastic or non-momentum-conserving tunneling. We demonstrate narrow tunneling resonances with intrinsic half-widths of 4 and 6 meV at 1.5 and 300 K, respectively.
Development and characterization of the first dsRNA-resistant insect population from western corn rootworm, Diabrotica virgifera virgifera LeConte (2018)

The use of dsRNA to control insect pests via the RNA interference (RNAi) pathway is being explored by researchers globally. However, with every new class of insect control compounds, the evolution of insect resistance needs to be considered, and understanding resistance mechanisms is essential in designing durable technologies and effective resistance management strategies. To gain insight into insect resistance to dsRNA, a field screen with subsequent laboratory selection was used to establish a population of DvSnf7 dsRNA-resistant western corn rootworm, Diabrotica virgifera virgifera, a major maize insect pest. WCR resistant to ingested DvSnf7 dsRNA had impaired luminal uptake and resistance was not DvSnf7 dsRNA-specific, as indicated by cross resistance to all other dsRNAs tested. No resistance to the Bacillus thuringiensis Cry3Bb1 protein was observed. DvSnf7 dsRNA resistance was inherited recessively, located on a single locus, and autosomal. Together these findings will provide insights for dsRNA deployment for insect pest control.
Alleviation of neuronal energy deficiency by mTOR inhibition as a treatment for mitochondria-related neurodegeneration (2016)

mTOR inhibition is beneficial in neurodegenerative disease models and its effects are often attributable to the modulation of autophagy and anti-apoptosis. Here, we report a neglected but important bioenergetic effect of mTOR inhibition in neurons. mTOR inhibition by rapamycin significantly preserves neuronal ATP levels, particularly when oxidative phosphorylation is impaired, such as in neurons treated with mitochondrial inhibitors, or in neurons derived from maternally inherited Leigh syndrome (MILS) patient iPS cells with ATP synthase deficiency. Rapamycin treatment significantly improves the resistance of MILS neurons to glutamate toxicity. Surprisingly, in mitochondrially defective neurons, but not neuroprogenitor cells, ribosomal S6 and S6 kinase phosphorylation increased over time, despite activation of AMPK, which is often linked to mTOR inhibition. A rapamycin-induced decrease in protein synthesis, a major energy-consuming process, may account for its ATP-saving effect. We propose that a mild reduction in protein synthesis may have the potential to treat mitochondria-related neurodegeneration.
Modeling of Side Chain Degradation in PEMFC Membranes (2012)

Abstract not Available.
Stacked 2D Photonic Crystal Reflectance Filters Fabricated by Nanoreplica Molding for Improving Optical Density and Angular Tolerance (2010)

Nanoreplica molding enables stacking of multiple 2D photonic crystals on a large area plastic substrate to improve optical density and angular tolerance of the resulting narrowband optical limiting filter, used for laser eye/sensor protection.
Twinning of High-Tc Ba2YCu3O7-x Oxides (1987)

Orthorhombic crystallites of the high-Tc superconductor Ba 2 YCu 3 O 7- x oxide prepared by the standard sintering technique are heavily laminated by twinning on (110) lattice planes. Upon heating these crystals under a vacuum in an electron microscope, the orthorhombic structure transformed irreversibly to a tetragonal one. Between these two forms, a transitional orthorhombic form was observed. This irreversible transformation seems to be caused by a lack of oxygen in the evacuated microscope.
Distinct functions of integrin alpha and beta subunit cytoplasmic domains in cell spreading and formation of focal adhesions (1993)

Integrin-mediated cell adhesion often results in cell spreading and the formation of focal adhesions. We exploited the capacity of recombinant human alpha IIb beta 3 integrin to endow heterologous cells with the ability to adhere and spread on fibrinogen to study the role of integrin cytoplasmic domains in initiation of cell spreading and focal adhesions. The same constructs were also used to analyze the role of the cytoplasmic domains in maintenance of the fidelity of the integrin repertoire at focal adhesions. Truncation mutants of the cytoplasmic domain of alpha IIb did not interfere with the ability of alpha IIb beta 3 to initiate cell spreading and form focal adhesions. Nevertheless, deletion of the alpha IIb cytoplasmic domain allowed indiscriminate recruitment of alpha IIb beta 3 to focal adhesions formed by other integrins. Truncation of the beta 3 subunit cytoplasmic domain abolished cell spreading mediated by alpha IIb beta 3 and also abrogated recruitment of alpha IIb beta 3 to focal adhesions. This truncation also dramatically impaired the ability of alpha IIb beta 3 to mediate the contraction of fibrin gels. In contrast, the beta 3 subunit cytoplasmic truncation did not reduce the fibrinogen binding affinity of alpha IIb beta 3. Thus, the integrin beta 3 subunit cytoplasmic domain is necessary and sufficient for initiation of cell spreading and focal adhesion formation. Further, the beta 3 cytoplasmic domain is required for the transmission of intracellular contractile forces to fibrin gels. The alpha subunit cytoplasmic domain maintains the fidelity of recruitment of the integrins to focal adhesions and thus regulates their repertoire of integrins.