gebhart/patrepeval huggingface dataset:
1H NMR Studies of Sarafotoxin SRTb, a Nonselective Endothelin Receptor Agonist, and IRL 1620, an ETB Receptor-Specific Agonist (1995)

1H NMR studies on the nonselective endothelin receptor agonist sarafotoxin SRTb have identified a helix between residues Asp 8 and His 16, and a beta-turn involving residues Cys 3 to Met 6; however, the biologically important C-terminal five residues were found to be conformationally variable. The average RMSD, measured for the final 43 refined structures to the average structure over residues 1-16, was 0.78 +/- 0.18 A for the backbone atoms and 1.39 +/- 0.22 A for all atoms. The torsion angles Cys 3 psi/Lys 4 theta, Thr 7 psi/Asp 8 theta and Gln 17 theta were identified as sites of conformational variability. Differences were found between the structures in the bicyclic loop region for SRTb and those published for ET1, another nonselective receptor agonist, which may explain the observed differences in potency of these peptides. The conformation of an ETB receptor-specific agonist, IRL 1620, which lacks the N-terminal seven residues and the two intrachain disulfides, was found by NMR and circular dichroism spectroscopy to be predominantly random coil, despite the fact that its affinity for the ETB receptor almost equals that of ET1. However, close analysis of the NMR results indicated the presence of turn-like structures, or a nascent helix, in the part of the sequence corresponding to the helical region in the parent peptides. These results suggest that the helical conformation may be required for ligand binding to the ETB receptor as well as to the ETA receptor.
Brief Report: Subclinical Carotid Artery Atherosclerosis Is Associated With Increased Expression of Peripheral Blood IL-32 Isoforms Among Women Living With HIV (2021)

IL-32 isoforms should be studied further as potential CVD biomarkers. This is of particular interest in WLWH by virtue of altered IL-32 levels in this population.
The Human RAD5 Homologs, HLTF and SHPRH, Have Separate Functions in DNA Damage Tolerance Dependent on the DNA Lesion Type (2020)

Helicase-like transcription factor (HLTF) and SNF2, histone-linker, PHD and RING finger domain-containing helicase (SHPRH), the two human homologs of yeast Rad5, are believed to have a vital role in DNA damage tolerance (DDT). Here we show that HLTF, SHPRH and HLTF/SHPRH knockout cell lines show different sensitivities towards UV-irradiation, methyl methanesulfonate (MMS), cisplatin and mitomycin C (MMC), which are drugs that induce different types of DNA lesions. In general, the HLTF/SHPRH double knockout cell line was less sensitive than the single knockouts in response to all drugs, and interestingly, especially to MMS and cisplatin. Using the SupF assay, we detected an increase in the mutation frequency in HLTF knockout cells both after UV- and MMS-induced DNA lesions, while we detected a decrease in mutation frequency over UV lesions in the HLTF/SHPRH double knockout cells. No change in the mutation frequency was detected in the HLTF/SHPRH double knockout cell line after MMS treatment, even though these cells were more resistant to MMS and grew faster than the other cell lines after treatment with DNA damaging agents. This phenotype could possibly be explained by a reduced activation of checkpoint kinase 2 (CHK2) and MCM2 (a component of the pre-replication complex) after MMS treatment in cells lacking SHPRH. Our data reveal both distinct and common roles of the human RAD5 homologs dependent on the nature of DNA lesions, and identified SHPRH as a regulator of CHK2, a central player in DNA damage response.
Dicyclopentadienyldimethylthorium/silica surface chemistry. High-resolution carbon-13 CPMAS NMR evidence for alkylation of surface silicon sites (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDicyclopentadienyldimethylthorium/silica surface chemistry. High-resolution carbon-13 CPMAS NMR evidence for alkylation of surface silicon sitesPaul J. Toscano and Tobin J. MarksCite this: Langmuir 1986, 2, 6, 820–823Publication Date (Print):November 1, 1986Publication History Published online1 May 2002Published inissue 1 November 1986https://pubs.acs.org/doi/10.1021/la00072a029https://doi.org/10.1021/la00072a029research-articleACS PublicationsRequest reuse permissionsArticle Views126Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Molecular, Epigenetic, and Phenotypic Repolarization of T Lymphocytes From Chronic Lymphocytic Leukemia Patients Using 5-Aza-2′-Deoxycytidine (2010)

Abstract Abstract 4651 The improper polarization of helper and cytotoxic T lymphocytes is a trademark immunosuppressive strategy employed by chronic lymphocytic leukemia (CLL). Mounting data implicates chromatin regulation, namely promoter methylation, in the plasticity of naïve human T cells. Very recent in-vitro evidence indicates that this plasticity may be phenotypically replicated by using methylation inhibitors which are approved for clinical use in certain types of cancer, however the longevity and therapeutic potential of repolarized cells remains to be elucidated. These results beg the question: can the ineffective polarization of T lymphocytes in the context of CLL be effectively modulated using methylation inhibitors in a sustainable therapeutic fashion? To answer this question our laboratory has focused on repolarizing helper and cytotoxic T lymphocytes using 5-aza-2′-deoxycytidine (5A2) tracking changes in well characterized molecular and epigenetic signaling pathways involved in effective polarization. Moreover, we sought to investigate the consequences of methylation inhibitor treatment on lymphocyte survival, activation intensity, and naïve cell polarization. Our studies relied upon intracellular staining, methylation specific PCR, western blot, and phosflow anlaysis. The data indicates that 5A2 treatment can repolarize Th2 cells to effectively secrete interferon gamma, signal via T-bet, and achieve demethylation of critical Th1 specific promoters. We also show that this repolarization can be maintained. Moreover, we demonstrate that 5A2 can force Th1 polarization of naïve T cells despite a strong IL-4 stimuli and a lack of IL-12. Finally, we have identified a cytotoxic threshold for 5A2 treatment which is above the concentration necessary to achieve effective and sustained molecular and epigenetic repolarization. All in all our data seeks to define a modality in which improper or ineffective T cell polarization can be altered ex post facto and continued immunotherapeutic intervention may benefit from the naïve polarization of anti-cancer responses. Disclosures: No relevant conflicts of interest to declare.
In situ microscopy of rapidly heated nano-Al and nano-Al/WO3 thermites (2010)

The initiation and reaction mechanism of nano-Al and nano-Al thermites in rapid heating environments is investigated in this work. A semiconductor-based grid/stage was used, capable of in situ heating of a sample from room temperature to 1473 K, and at a rate of 106 K/s, inside an electron microscope. Nano-Al was rapidly heated in a transmission electron microscope, and before and after images indicate that the aluminum migrates through the shell, consistent with a diffusion-based mechanism. A nano-Al/WO3 composite was then heated in a scanning electron microscope. The results indicate that a reactive sintering mechanism is occurring for the nano-Al/WO3 thermite, as the products are found to be in surface contact and significantly deformed after the heating pulse.
GUIDELINES FOR PLACEMENT OF LONGITUDINAL BARRIERS ON SLOPES (1984)

This research was undertaken to investigate the impact performance of longitudinal barriers when placed on sloping terrain. Tasks performed included (a) a determination of typical conditions for which longitudinal barriers are placed on sloping terrain, (b) an evaluation of the impact behavior of widely used barrier systems when placed on sloping terrain, and (c) the development of guidelines for selection and placement of barriers on sloping terrain. Crash tests and the HVOSM computer program were used to evaluate impact behavior and to develop guidelines. Factors considered in the guidelines include roadway and shoulder cross slope, cut and fill slope, barrier offset, and barrier type. It was found that W-beam and Thrie-beam barriers are more sensitive to the effects of sloping terrain than are cable barriers.
Phosphorylation state of the native high‐molecular‐weight neurofilament subunit protein from cervical spinal cord in sporadic amyotrophic lateral sclerosis (2001)

The intraneuronal aggregation of phosphorylated high-molecular-weight neurofilament protein (NFH) in spinal cord motor neurons is considered to be a key pathological marker of amyotrophic lateral sclerosis (ALS). In order to determine whether this observation is due to the aberrant or hyper-phosphorylation of NFH, we have purified and characterized NFH from the cervical spinal cords of ALS patients and controls. We observed no differences between ALS and normal controls in the physicochemical properties of NFH in Triton X-100 insoluble protein fractions, with respect to migration patterns on 2D-iso electrofocusing (IEF) gels, the rate of Escherichia coli alkaline phosphatase mediated dephosphorylation, or the rate of calpain-mediated proteolysis. The rate of calpain-mediated proteolysis was unaffected by either exhaustive NFH dephosphorylation or by the addition of calmodulin to the reaction. Phosphopeptides and the phosphorylated motifs characterized by liquid chromatography tandem mass spectroscopy (LC/MS/MS) analysis demonstrated that all the phosphorylated residues found in ALS NFH were also found to be phosphorylated in normal human NFH samples. Hence, we have observed no difference in the physicochemical properties of normal and ALS NFH extracted from cervical spinal cords, suggesting that the perikaryal aggregation of highly phosphorylated NF in ALS neurons reflects the aberrant somatotopic localization of normally phosphorylated NFH.
Multiplex and division techniques of non-spread and spread spectrum signals (2004)

This paper proposes a technique where non-spread and spread spectrum (SS) signals are combined in the same frequency band. It shows that the multiplex technique proposed is an effective method for making good use of a limited frequency band. Furthermore a system using this multiplex technique can transmit data of different speeds and quality at the same time. The multiplex signal presented here is where non-spread quadrature phase shift keying (QPSK) and direct sequence spread spectrum DS-SS signals are combined, with reference symbols being inserted without multiplexing for easy estimation of the channel condition. A technique is then proposed to divide the multiplex signal in the receiver. Using this technique, bit error rate (BER) performances of non-spread QPSK and DS-SS are calculated under additive white Gaussian noise (AWGN) and Rayleigh fading channels. According to the results of the BER performance for non-spread QPSK and DS-SS, it is clear that the multiplex signal can be divided and data can be retrieved in the receiver.
A 108-Gbps, 162-mW Cherry-Hooper Transimpedance Amplifier (2020)

This paper reports an energy-efficient optical receiver based on a Cherry-Hooper emitter follower topology. Electrical measurements on a standard FR-4 PCB assembly indicate an error-free (BER <; 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-11</sup> ) operation up to 96 Gbps with open eye diagrams observed up to 108 Gbps. The TIA is implemented in a compact 1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> padframe in 130-nm SiGe HBT technology (fT = 300 GHz) and consumes 162 mW of DC power for a best-case energy efficiency of 1.5 pJ/bit.
Lewis Base Activation of Grignard Reagents with N‐Heterocyclic Carbenes. Cu‐Free Catalytic Enantioselective Additions to γ‐Chloro‐α,β‐Unsaturated Esters. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Nanostructure-Assisted Phonon Scattering in Lead-Free Thermoelectric Materials: A TEM Investigation of the SnTe System (2014)

An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
The Effect of Tip Leakage Vortex for Operating Range Enhancement of Centrifugal Compressor (2012)

Recently, the application of turbochargers is increasing because they are effective in improving fuel consumption of engines. One of the most important turbocharger characteristics is compressor operating range, since it has been used in various driving patterns with the advent of variable geometry turbochargers. Owing to the complicated phenomena such as rotating stall occurring at low flow rate condition, flow analysis is very difficult and details of flow structure have not been fully understood for a long time since the early 1970’s. In this study, two compressors with different operating range width were investigated with experimental and computational flow analysis. In the compressor with narrow operating range, the amplitude of blade passing pressure fluctuation decreases rapidly and rotating stall occurs near surging. On the other hand, in the compressor with wide operating range, the blockage by the tip leakage vortex breakdown play a role in stabilizing the flow filed and keeping up a high performance even at low flow rates.
Phosphotyrosine 1173 Mediates Binding of the Protein-tyrosine Phosphatase SHP-1 to the Epidermal Growth Factor Receptor and Attenuation of Receptor Signaling (1998)

The protein-tyrosine phosphatase SHP-1 binds to and dephosphorylates the epidermal growth factor receptor (EGFR), and both SH2 domains of SHP-1 are important for this interaction (Tenev, T., Keilhack, H., Tomic, S., Stoyanov, B., Stein-Gerlach, M., Lammers, R., Krivtsov, A. V., Ullrich, A., and Böhmer, F. D. (1997) J. Biol. Chem. 272, 5966-5973). We mapped the EGFR phosphotyrosine 1173 as the major binding site for SHP-1 by a combination of phosphopeptide activation, phosphopeptide competition, and receptor YF mutant analysis. Mutational conversion of the EGFR sequence 1171-1176 AEYLRV into the high affinity SHP-1 binding sequence LEYLYL of the erythropoietin receptor (EpoR) led to a highly elevated SHP-1 binding to the mutant EGFR (EGFR1171-1176EpoR) and in turn to an enhanced dephosphorylation of the receptor. SHP-1 expression interfered with EGF-dependent mitogen-activated protein kinase stimulation, and this effect was more pronounced in case of EGFR1171-1176EpoR. Reduced SHP-1 binding to the EGFR Y1173F mutant resulted in a reduced receptor dephosphorylation by coexpressed SHP-1 and less interference with EGF-dependent mitogen-activated protein kinase stimulation. The effects of receptor mutations on SHP-1 binding were, however, stronger than those on receptor dephosphorylation by SHP-1. Therefore, receptor dephosphorylation may be the result of the combined activity of receptor-bound SHP-1 and SHP-1 bound to an auxiliary docking protein.
A Single-Processor Approach to Speech Processing Pipeline of Bilateral\n Cochlear Implants (2014)

This dissertation covers a single-processor approach to the speech processing\npipeline of bilateral Cochlear Implants (CIs). The use of only a single\nprocessor to provide binaural stimulation signals overcomes the synchronization\nproblem, which is an existing challenging problem in the deployment of\nbilateral CI devices. The developed single-processor speech processing pipeline\nprovides CI users with a sense of directionality. Its non-synchronization\nfeature as well as low computational and memory requirements make it a suitable\nsolution for actual deployment. A speech enhancement framework is developed\nthat incorporates different non-Euclidean speech distortion criteria and\ndifferent noise environments. This framework not only allows the design of\nenvironment-optimized parameters but also enables a user-specific solution\nwhere the anthropometric measurements of an individual user are incorporated\ninto the training process to obtain individualized bilateral parameters. The\ndeveloped techniques are primarily meant for bilateral CIs, however, they are\ngeneral purpose in the sense that they are also applicable to binaural hearing\naids, bimodal devices having hearing aid in one ear and cochlear implant in the\nother ear as well as dual-channel speech enhancement applications. Extensive\nexperiments have shown the effectiveness of the developed solution in six\ncommonly encountered noise environments compared to a similar one-channel\npipeline when using two separate processors or when using independent\nsequential processing.\n
Scaling to 1024 software processes and hardware cores of the distributed simulation of a spiking neural network including up to 20G synapses (2015)

This short report describes the scaling, up to 1024 software processes and hardware cores, of a distributed simulator of plastic spiking neural networks. A previous report demonstrated good scalability of the simulator up to 128 processes. Herein we extend the speed-up measurements and strong and weak scaling analysis of the simulator to the range between 1 and 1024 software processes and hardware cores. We simulated two-dimensional grids of cortical columns including up to ~20G synapses connecting ~11M neurons. The neural network was distributed over a set of MPI processes and the simulations were run on a server platform composed of up to 64 dual-socket nodes, each socket equipped with Intel Haswell E5-2630 v3 processors (8 cores @ 2.4 GHz clock). All nodes are interconned through an InfiniBand network. The DPSNN simulator has been developed by INFN in the framework of EURETILE and CORTICONIC European FET Project and will be used by the WaveScalEW tem in the framework of the Human Brain Project (HBP), SubProject 2 - Cognitive and Systems Neuroscience. This report lays the groundwork for a more thorough comparison with the neural simulation tool NEST.
Radioimmunotherapy of Experimental Human Metastatic Melanoma with Melanin-Binding Antibodies and in Combination with Dacarbazine (2009)

These results provide encouragement for the development of RIT for melanoma with melanin-binding mAbs and suggest that combining chemotherapy and RIT may be a promising approach for the treatment of metastatic melanoma.
Protection of cucumber against Pythium root rot by fluorescent pseudomonads: predominant role of induced resistance over siderophores and antibiosis (1999)

Four Pseudomonas strains were evaluated for their intrinsic properties conferring their ability to protect long English cucumber against Pythium aphanidermatum in hydroponic culture. Two of the strains, BTP1 and its siderophore‐negative mutant M3, increased plant yield as compared with the non‐inoculated control plants. Strain BTP7 was intermediate in its biocontrol activity while strain ATCC 17400 failed to reduce disease development. The role of pyoverdines could not be confirmed since treatment with either BTP1 or its siderophore‐negative mutant M3 provided similar suppression of Pythium disease. In addition, no siderophores were detected in the nutrient solution. BTP1 did not inhibit pathogen growth in vitro on several media, suggesting that antibiosis was not a mechanism of suppression. Quantification of root bacterial populations did not indicate differences among the strains. On the other hand, roots treated with either BTP1 or its sid − mutant M3 contained more antifungal phenolics than roots from any other treatments including controls. These results suggest that antifungal compounds induced by inoculation of cucumber roots with the fluorescent Pseudomonas strains BTP1 and M3 participate actively in the protection of cucumber plants against P. aphanidermatum
Online Orbital Explorer and BingOrbital Game for Inquiry-Based Activities (2022)

We report a new online suite of tools that enables inquiry-based active-learning activities to develop students' representational competence about atomic orbitals. Orbital Explorer is Web site hub for the visualization and interactive investigation of atomic orbital properties. Orbital Explorer contains two integrated tools, namely, Atomic Orbital Explorer, which enables one to visualize and interrogate individual atomic orbitals, and Orbital RDF Comparison, which enables one to make a more detailed quantitative comparison of orbital energies and properties of orbital radial distribution functions (RDFs). In addition, we present an original chemistry educational gamification design, BingOrbital, constructed in a format resembling Bingo (American version). The game aims to reinforce the recognition of atomic orbitals based on the RDF and 3D isosurface and has been applied as an engaging retrieval practice tool. A companion set of example activities that use the Orbital Explorer and BingOrbital game have been presented in another article.
Application of B cell immortalization for the isolation of antibodies and B cell clones from vaccine and infection settings (2022)

The isolation and characterization of neutralizing antibodies from infection and vaccine settings informs future vaccine design, and methodologies that streamline the isolation of antibodies and the generation of B cell clones are of great interest. Retroviral transduction to express Bcl-6 and Bcl-xL and transform primary B cells has been shown to promote long-term B cell survival and antibody secretion <i>in vitro</i>, and can be used to isolate antibodies from memory B cells. However, application of this methodology to B cell subsets from different tissues and B cells from chronically infected individuals has not been well characterized. Here, we characterize Bcl-6/Bcl-xL B cell immortalization across multiple tissue types and B cell subsets in healthy and HIV-1 infected individuals, as well as individuals recovering from malaria. In healthy individuals, naïve and memory B cell subsets from PBMCs and tonsil tissue transformed with similar efficiencies, and displayed similar characteristics with respect to their longevity and immunoglobulin secretion. In HIV-1-viremic individuals or in individuals with recent malaria infections, the exhausted CD27<sup>-</sup>CD21<sup>-</sup> memory B cells transformed with lower efficiency, but the transformed B cells expanded and secreted IgG with similar efficiency. Importantly, we show that this methodology can be used to isolate broadly neutralizing antibodies from HIV-infected individuals. Overall, we demonstrate that Bcl-6/Bcl-xL B cell immortalization can be used to isolate antibodies and generate B cell clones from different B cell populations, albeit with varying efficiencies.