gebhart/patrepeval huggingface dataset:
Control of Human Immunodeficiency Virus Type 1 Is Associated with HLA-B*13 and Targeting of Multiple Gag-Specific CD8+T-Cell Epitopes (2007)

To better understand relationships between CD8+ T-cell specificity and the immune control of human immunodeficiency virus type 1 (HIV-1), we analyzed the role of HLA-B*13, an allele associated with low viremia, in a cohort of 578 C clade-infected individuals in Durban, South Africa. Six novel B*13-restricted cytotoxic T lymphocyte epitopes were defined from analyses of 37 B*13-positive subjects, including three Gag epitopes. These B*13-restricted epitopes contribute to a broad Gag-specific CD8+ response that is associated with the control of viremia. These data are consistent with data from studies of other HLA-class I alleles associated with HIV control that have shown that the targeting of multiple Gag epitopes is associated with relative suppression of viremia.
Tandem mass spectrometry identifies many mouse brain O -GlcNAcylated proteins including EGF domain-specific O -GlcNAc transferase targets (2012)

O -linked N -acetylglucosamine ( O -GlcNAc) is a reversible posttranslational modification of Ser and Thr residues on cytosolic and nuclear proteins of higher eukaryotes catalyzed by O -GlcNAc transferase (OGT). O -GlcNAc has recently been found on Notch1 extracellular domain catalyzed by EGF domain-specific OGT. Aberrant O -GlcNAc modification of brain proteins has been linked to Alzheimer's disease (AD). However, understanding specific functions of O -GlcNAcylation in AD has been impeded by the difficulty in characterization of O -GlcNAc sites on proteins. In this study, we modified a chemical/enzymatic photochemical cleavage approach for enriching O -GlcNAcylated peptides in samples containing ∼100 μg of tryptic peptides from mouse cerebrocortical brain tissue. A total of 274 O -GlcNAcylated proteins were identified. Of these, 168 were not previously known to be modified by O -GlcNAc. Overall, 458 O -GlcNAc sites in 195 proteins were identified. Many of the modified residues are either known phosphorylation sites or located proximal to known phosphorylation sites. These findings support the proposed regulatory cross-talk between O -GlcNAcylation and phosphorylation. This study produced the most comprehensive O -GlcNAc proteome of mammalian brain tissue with both protein identification and O -GlcNAc site assignment. Interestingly, we observed O -β-GlcNAc on EGF-like repeats in the extracellular domains of five membrane proteins, expanding the evidence for extracellular O -GlcNAcylation by the EGF domain-specific OGT. We also report a GlcNAc-β-1,3-Fuc-α-1- O -Thr modification on the EGF-like repeat of the versican core protein, a proposed substrate of Fringe β-1,3- N -acetylglucosaminyltransferases.
A Fibrin Adhesive Seal for the Repair of Osteochondral Fracture Fragments (1984)

A biologic tissue adhesive, a two-component fibrin sealant, for the immobilization of experimentally produced osteochondral fractures of the radial head and femoral condyle was investigated in dogs. The two components of the fibrin sealant were a sealer protein solution (fibrinogen) and a thrombin solution. A fibrinolytic inhibitor (C-esterase inhibitor) was added to prevent degradation of the fibrin by proteolytic enzymes. The operation was performed in 16 joints in four dogs. Control fractures on the right side were fixed with 5-cm Kirschner wires. No external immobilization was utilized. The dogs were killed at intervals of two, four, and eight weeks. There were no complications. All fractures healed uneventfully by eight weeks. Osseous repair seemed to be stimulated by the sealant and to occur faster than in the fractures fixed with pins.
N,N'-Carbonyldiimidazole, a New Peptide Forming Reagent1 (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTN,N'-Carbonyldiimidazole, a New Peptide Forming Reagent1Rolf Paul and George W. AndersonCite this: J. Am. Chem. Soc. 1960, 82, 17, 4596–4600Publication Date (Print):September 1, 1960Publication History Published online1 May 2002Published inissue 1 September 1960https://pubs.acs.org/doi/10.1021/ja01502a038https://doi.org/10.1021/ja01502a038research-articleACS PublicationsRequest reuse permissionsArticle Views5529Altmetric-Citations269LEARN 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
ACAM2000 clonal Vero cell culture vaccinia virus (New York City Board of Health strain) – a second-generation smallpox vaccine for biological defense (2004)

The threat of smallpox as a biological weapon has spurred efforts to create stockpiles of vaccine for emergency preparedness. In lieu of preparing vaccine in animal skin (the original method), we cloned vaccinia virus (New York City Board of Health strain, Dryvax by plaque purification and amplified the clone in cell culture. The overarching goal was to produce a modern vaccine that was equivalent to the currently licensed Dryvax in its preclinical and clinical properties, and could thus reliably protect humans against smallpox. A variety of clones were evaluated, and many were unacceptably virulent in animal models. One clonal virus (ACAM1000) was selected and produced at clinical grade in MRC-5 human diploid cells. ACAM1000 was comparable to Dryvax in immunogenicity and protective activity but was less neurovirulent for mice and nonhuman primates. To meet requirements for large quantities of vaccine after the events of September 11th 2001, the ACAM1000 master virus seed was used to prepare vaccine (designated ACAM2000) at large scale in Vero cells under serum-free conditions. The genomes of ACAM1000 and ACAM2000 had identical nucleotide sequences, and the vaccines had comparable biological phenotypes. ACAM1000 and ACAM2000 were evaluated in three Phase 1 clinical trials. The vaccines produced major cutaneous reactions and evoked neutralizing antibody and cell-mediated immune responses in the vast majority of subjects and had a reactogenicity profile similar to that of Dryvax.
Unconscious and conscious priming by forms and their parts (2005)

Abstract Using metacontrast masking techniques, in two experiments we compare unconscious and conscious response priming by targets consisting of either whole forms or else their parts. In Experiment 1 we investigate the contribution of whole forms and their figural primitives, viz., edges and corners, to the unconscious priming effect. As expected, choice RTs were fast when the invisible target and visible mask shape pairings were congruent and slower when they were incongruent. This trend, while strongest for whole-targets, also held for the target primes composed only of corners but did not hold for target primes composed only of sides. Experiment 2 showed, replicating the results of Experiment 1, that while invisible corner targets produced weaker priming effects than invisible whole targets, paradoxically visible corner target produced stronger priming effects than visible whole targets. Taken together the results of the two experiments indicate (a) that unconscious target representations and, thus, unconscious priming effects are strongest when the target is a complete rather than a partial configuration, (b) that conjunctions of line or edge orientations forming corners produce stronger unconscious target representations and priming effects than do unconscious target representations formed from nonconjoined edge or line primitives, (c) that metacontrast masking of form occurs at or beyond levels of visual processing at which feature integration of visual form primitives occurs, and (d) that, when consciously perceived, partial forms can act as stronger primes than whole forms.
Shared annotation for cooperative learning (1995)

Article Free Access Share on Shared annotation for cooperative learning Authors: James R. Davis View Profile , Daniel P. Huttenlocher View Profile Authors Info & Claims CSCL '95: The first international conference on Computer support for collaborative learningOctober 1995 Pages 84–88https://doi.org/10.3115/222020.222073Online:01 October 1995Publication History 20citation288DownloadsMetricsTotal Citations20Total Downloads288Last 12 Months6Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Interactions between SV40 T antigen and DNA polymerase alpha. (1990)

Simian virus 40 large T antigen is the only viral protein required for SV40 DNA synthesis in vivo and in vitro. This complex protein recruits the cellular DNA replication apparatus to the SV40 origin and provides a good model for the initiation of cellular DNA replication. The interaction between SV40 large T antigen (TAg) and DNA polymerase alpha has been shown previously to be inhibited by murine p53, the nuclear protein product of a cellular anti-oncogene. The murine p53 protein will inhibit SV40 replication both in vivo and in vitro. Using monoclonal antibodies to TAg, p53, and polymerase alpha, we developed immunoassays to measure the complexes formed between TAg and polymerase alpha and between TAg and p53. The assays allowed us to detect the TAg-polymerase alpha and TAg-p53 complexes in lytically infected and transformed cells. The amount of TAg complexed to p53 was far lower in infected cells than in transformed cells. We used a large range of monoclonal antibodies to different sites on T antigen and found that antibodies that inhibited the formation of the TAg-polymerase alpha complex also inhibited the formation of the TAg-p53 complex. Finally, we found that the tsA58 and 5080 point mutations in TAg, previously shown to inhibit the binding of TAg to p53, also inhibit its binding to polymerase alpha. Together these results emphasize the specificity and functional importance of the TAg-polymerase alpha complex. The disruption of this interaction by the cellular anti-oncogene p53 provides an interesting model for the normal action of p53 and the effects of its removal on the regulation of cellular DNA synthesis.
Tile-based bottom-up compilation of custom mesh-of-functional-units FPGA overlays (2014)

Mesh-of-functional-units (mesh-of-FUs) overlays can deliver high-performance because they expose the massively parallel FPGA fabric and have the ability to be customized for different applications. However, a key challenge is how to quickly compile a number of custom mesh-of-FUs overlays to FPGA fabric such that they achieve high f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MAX</sub> and scale to large mesh sizes. We propose a tile-based bottom-up CAD flow that utilizes the hierarchical physical design techniques of partitioning and floorplanning. Our flow partitions the overlay circuit into tiles, groups of adjacent overlay cells, and then compiles the tiles to a rectangular coarse-grain floorplan. Independent compilation of tiles is made possible by inserting complementary elastic buffers on inter-tile paths to ensure that these paths are not a bottleneck for f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MAX</sub> . As a result, an overlay can be formed by only “stitching” a set of pre-compiled tiles.We show that compared to the flat flow, our bottom-up flow results in higher f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MAX</sub> that degrades little with increasing overlay size. Further, our flow can generate a library of pre-compiled tiles that can be reused - it can stitch a set of library tiles into a new overlay in only 35 minutes. It also allows a divide-and-conquer overlay compilation flow by compiling its tiles in parallel on multiple machines.
Proteoglycans (2000)

Introductory remarks and overview structure and biosynthesis of chondroitin sulfate and hyaluronan heparin sulfate - molecular structure and interactions with growth factors and morphogens hyaluronan catabolism of proteoglycans glypicans serglycin proteoglycans - the family of proteoglycans stored in the secretory granules of varied effector cells of the immune response the small leucine-rich proteoglycans corneal proteoglycans heparan sulfate proteoglycans in basement membranes - perlecan, agrin, and collagen XVIII versican aggrecan chrondroitin sulfate proteoglycans in the nervous system.
A Data-Driven Statistical Approach to Analyzing Process Variation in 65nm SOI Technology (2007)

This paper presents a simple yet effective method to analyze process variations using statistics on manufacturing in-line data without assuming any explicit underlying model for process variations. Our method is based on a variant of principal component analysis and is able to reveal systematic variation patterns existing on a die-to-die and wafer-to-wafer level individually. The separation of die variation from wafer variation can enhance the understanding of a nature of the process uncertainty. Our case study based on the proposed decomposition method shows that the dominating die-to-die variation and wafer-to-wafer variation represent 31% and 25% of the total variance of a large set of in-line parameters in 65nm SOI CMOS technology
The Pharmacology of CP‐154,526, a Non‐Peptide Antagonist of the CRH1 Receptor: A Review (2003)

Since CRH has been shown to mediate stress-induced physiological and behavioral changes, it has been hypothesized that CRH receptor antagonists may have therapeutic potential in disorders that involve excessive CRH activity. CP-154,526 and its close analog antalarmin are potent, brain-penetrable, selective nonpeptide CRH1 receptor antagonists that were discovered in an effort to develop compounds with efficacy in CNS disorders precipitated by stress. Since its discovery many investigators have used CP-154,526 as a tool to study the pharmacology of CRH and its receptors and to evaluate its therapeutic potential in a variety of CNS and peripheral disorders. Systemically-administered CP-154,526 has been demonstrated to antagonize CRH- and stress-induced neuroendocrine, neurochemical, electrophysiological, and behavioral effects. These findings support the hypothesis that CRH1 receptor antagonists may have therapeutic utility in a number of neuropsychiatric disorders. CP-154,526, as well as other CRH1 receptor antagonists that have since been discovered, have also shown activity in several preclinical models of anxiety, depression, and substance abuse, while having little effect on locomotor activity and motor function. Although these effects are on occasion inconsistent among different laboratories, clinical evaluation of CRH1 antagonists appears justified on the basis of these and clinical data implicating the involvement of CRH in several CNS disorders. The effects of CRH1 antagonists on cognition, neurodegeneration, inflammation, and the gastrointestinal system have not been as extensively characterized and additional studies will be necessary to evaluate their therapeutic potential in these areas.
Relationships between structure and kinetics of cyclization of 2-aminoaryl amides: potential prodrugs of cyclization-activated aromatic mustards (1994)

2-Nitroaryl amides of general structure I are proposed as bioreducible prodrugs, capable of releasing cytotoxic aminoaniline mustards V on bioactivation by spontaneous cyclization of the resulting 2-aminoarylamides II via a tetrahedral intermediate, III. This concept allows separate optimization of the substituent effects influencing nitro-group reduction and mustard reactivity. A series of model 2-aminoaryl amides has been synthesized, and their rates of cyclization have been studied; these varied by a factor of more than 50,000-fold (kobs from 0.00040 to 21 min-1) at pH 2.4. For three compounds studied in detail, the rates were linearly dependent of pH, indicating that no change in the mechanism of the rate-determining step occurs over the pH range studied. The nucleophilicity of the amino group had a modest influence on the kinetics of cyclization, with electron-withdrawing groups slowing the rate. The geometry of the compound was also important, with structure-activity relationships indicating that the rate of cyclization is greatly enhanced by the preorganization of the molecule. In contrast, 4-substitution on the leaving aniline by a variety of groups had little effect on the cyclization reaction. These results are consistent with the rate-determining step being formation of the tetrahedral intermediate. These model studies suggest that the phenyldimethylacetamide system could be developed as a prodrug system for the bioreductively-triggered release of amines. Further substantial rate enhancements appear possible by alterations in the geometry of the system, whereas substitution of electron-withdrawing groups (required to raise the nitro-group reduction potential into the appropriate range) has only relatively modest retardation effects on rates of cyclization. More rigid systems may also be useful; a nitronaphthaleneacetamide analogue cyclized spontaneously during nitro-group reduction, suggesting a very short half-life for the reduced intermediate (amine or hydroxylamine).
beta-Amyloid-(1-42) is a major component of cerebrovascular amyloid deposits: implications for the pathology of Alzheimer disease. (1993)

Reinvestigation of the chemical structure of beta-amyloid peptide (A beta) deposits in the vascular tissue of Alzheimer disease brains revealed that the 42-residue form A beta-(1-42), rather than the more soluble A beta-(1-40) form, is the predominant peptide. Following removal of the surrounding tissue with SDS and collagenase, A beta was solubilized in formic acid and purified by Superose 12 chromatography. Peptides generated by enzymatic and chemical digestion of the A beta were purified by HPLC and characterized by amino acid analysis, sequence analysis, and mass spectrometry. In the leptomeningeal vessels, the average ratio of A beta-(1-42)/A beta-(1-40) was 58:42, whereas in the parenchymal vessels this ratio was 75:25. Interestingly, vascular A beta contains considerably less isomerized and racemized aspartyl residues than does neuritic plaque A beta, suggesting that the vascular amyloid is "younger." The discrete nature of the bands and spherical deposits of A beta associated with arterioles and capillaries, respectively, suggests that this amyloid arises from the vascular tissue itself. Increasing A beta deposition appears to lead to the distortion and occlusion of capillaries, which may contribute significantly to the pathology of Alzheimer disease.
Expression,purification and characterization of human heparanase N-terminal subunit protein (2005)

Objectives:To express and purify the N-terminal subunit of haparanase which plays an important role in metastasis. Methods: The full encoding gene was isolated from the human placenta cDNA library and the N-terminal subunit gene was cloned into the pGEX-2TK vector for expressing the N-terminal subunit protein. After the fermentation, a series of purifications and renaturing,the target protein got weighted (6.9 g) and the purity was about 90%. Results: GST pull down assay presented that the expressed fusion protein could combine with the C-terminal subunit protein of heparanase. The target fusion protein could be cleaved into GST protein and the heparanase N-terminal subunit protein. Conclusion: The N-terminal subunit protein of heparanase obtained can be used for studying the immuno-sublocation and function of the N-terminal subunit.
Regulation of Diurnal Variation of Cholesterol 7α-hydroxylase(CYP7A1) Activity in Healthy Subjects (2010)

Cholesterol 7alpha-hydroxylase (CYP7A1), the key regulatory enzyme of bile acid synthesis, displays a pronounced diurnal variation. To better understand the regulation of CYP7A1 activity, three day-long examinations were carried out in 12 healthy men. The concentrations of 7alpha-hydroxycholest-4-en-3-one (C4), a surrogate marker of CYP7A1 activity, bile acids (BA), insulin, glucose, nonesterified fatty acids, triglycerides, and cholesterol were measured in serum in 90-min intervals from 7 AM till 10 PM. To lower and to increase BA concentration during the study, the subjects received cholestyramine and chenodeoxycholic acid (CDCA), respectively, in two examinations. No drug was used in the control examination. There was a pronounced diurnal variation of C4 concentration with a peak around 1 PM in most of the subjects. The area under the curve (AUC) of C4 concentration was five times higher and three times lower when subjects were treated with cholestyramine and CDCA, respectively. No relationship was found between AUC of C4 and AUC of BA concentration, but AUC of C4 correlated positively with that of insulin. Moreover, short-term treatment with cholestyramine resulted in about 10 % suppression of glycemia throughout the day. Our results suggest that insulin is involved in the regulation of diurnal variation of CYP7A1 activity in humans.
Enhanced current density J c and extended irreversibility in single-crystal Bi2Sr2Ca1Cu2O8 via linear defects from heavy ion irradiation (1992)

Large enhancements in the critical current density Jc were produced in single crystals of the high-temperature superconductor Bi2Sr2Ca1Cu2O8 by irradiation with high energy Sn ions. In addition, the irreversibility line was moved to considerably higher magnetic fields. In contrast with analogous studies on Y1Ba2Cu3O7, there was little, if any, selective pinning when the magnetizing field was applied parallel to the linear, ion-damage-produced tracks.