gebhart/patrepeval huggingface dataset:
Platelet Agonist F11 Receptor Is a Member of the Immunoglobulin Superfamily and Identical with Junctional Adhesion Molecule (JAM): Regulation of Expression in Human Endothelial Cells and Macrophages (2000)

The stimulatory mAb F11 binds two platelet membrane proteins of 32 and 35 kDa and causes activation of platelets when cross-linked with the FcgammaRII receptor. We used bioinformatics to identify expressed sequence tags from libraries of cytokine-stimulated human endothelial cell (EC) cDNAs. The protein sequence deduced from full-length F11 cDNA was identical to partial sequences of peptides derived from affinity-purified platelet F11 antigen. F11 mRNA is expressed in human EC, macrophages, and a variety of non-hematopoietic vascular tissues. Expression of F11 mRNA is modulated by cytokines in EC and is up-regulated by oxidized low-density lipoprotein in human macrophages. The F11 receptor contains two immunoglobulin-like domains in its 236-amino-acid-long extracellular region, and has identity to the recently described junctional adhesion molecule. The data indicate that the F11 antigen is a novel receptor or cell adhesion molecule belonging to the immunoglobulin superfamily.
Chemical Property Calculation through JavaScript and Applications in QSAR (1999)

The inorganic property (I) and organic property (O) values of general organic groups are re-proposed here. Both I and O values of drug and biological molecules or groups can be calculated based on their common group values. The calculation can be performed easily on-line through JavaScript. Similar calculation can be done for the drug and biological molecular group electronegativity (X) according to the author's published paper. The calculation of lipophilicity (π or logP) parameter of (macro)molecules (like proteins) can also be performed on-line through JavaScript. Two equations expressed with I and O are provided here to define the hydrophobicity of each amino acid. The correlations of inorganic property and organic property values with other parameters are also discussed. These calculated parameters combined with other parameters can be used for QSAR studies in some drug molecules.
Limited Proteolysis and a Reactive Cysteine Residue Define Accessible Regions in the Native Conformation of the Adenovirus Hexon Protein (1980)

The sulfhydryl group of one cysteine residue in the adenovirus hexon protein is accessible to alkylation in the absence of denaturating agents. This residue was [14C]carboxymethylated and characterized in peptides after proteolytic treatments. It was identified in two different types of digest and corresponded to the cysteine residue most accessible to oxidation. It is located close to residue 670 in the tentative amino acid sequence of the entire polypeptide. Trypsin has a highly limited action on the native hexon protein. Only three peptide bonds are fully susceptible to cleavage. These were found to occur in the N-terminal third of the protein, and were characterized as cleavages close to positions 150, 180 and 320 in the tentative structure of the polypeptide. Trypsin therefore liberates four fragments in major yield, with approximate Mr of 3000, 15000, 17000 and 78000. The smallest fragment corresponds to a highly acidic region. A limited, but less restricted susceptibility of hexon to chymotryptic cleavage was also found, and four major sites were characterized. The cysteine labelling and the proteolytic treatments define accessible regions in the native conformation of hexon. Together with previously assigned residue distributions, they suggest the subdivision of the entire polypeptide chain into three approximately equal parts, with accessible sites in the border regions, as well as in the middle of at least the N-terminal third. One model compatible with all data is presented.
Touring Traumascapes: Touristifcation of an Okinawan Battlefield Memorial (2010)

Keywords: commentary, tourism, commodification, war, peace movement, Okinawa, historical memory, trauma tourism, Himeyuri Cenotaph, Japan, Eastern Asia
Anaphylaxis mediated through a humanized high affinity IgE receptor. (1996)

Mast cells and basophils, which are activated by IgE and allergens through the high affinity IgE receptor (Fc epsilon RI), play a prominent role in anaphylaxis in the mouse. Mice deficient in this receptor become resistant to passive anaphylaxis. As a first step in developing an in vivo model that more closely mimics the IgE-mediated responses in man, we used a combination of transgenic and embryonic stem cell technology to generate a mouse line in which the murine Fc epsilon RI alpha-chain has been replaced with its human homologue. We demonstrate here that these mice express a tetrameric high affinity IgE receptor, in which the human alpha-chain associates with the murine beta- and gamma-chains, and that upon triggering with relevant Ag, this receptor mediates the initiation of the expected intracellular events. In addition, we show that the human alpha-chain restores an anaphylactic response to the nonresponsive alpha-deficient parental mouse line. This "humanized" mouse represents a potentially important model system, not only for studying the role of IgE in human immune responses, but also for testing potential therapeutic reagents that can interfere with responses mediated through the human Fc epsilon RI receptor.
Adenoviral-Mediated, High-Level, Cell-Specific Transgene Expression: A SYN1-WPRE Cassette Mediates Increased Transgene Expression with No Loss of Neuron Specificity (2002)

Viral vectors are excellent tools for studying gene function in the brain, although a limitation has been the ability to effectively target transgene expression to specific neuronal populations. This generally cannot be overcome by the use of neuron-specific promoters, as most are too large to be used with current viral vectors and expression from these promoters is often relatively weak. We therefore developed a composite expression cassette, comprising 495 bp of the weak human SYN1 (synapsin-1) promoter and 800 bp of the woodchuck hepatitis virus posttranscriptional regulatory element (WPRE). Studies in hippocampal cultures, organotypic cultures, and in vivo showed that the 3' addition of the WPRE to the SYN1 element greatly increased enhanced green fluorescent protein expression levels with no loss of neuronal specificity. In vivo studies also showed that transgene expression was enhanced with no loss of neuronal specificity in dentate-gyrus neurons for at least 6 weeks following transfection. Therefore, unlike most powerful promoter systems, which mediate expression in neurons and glia, this SYN1-WPRE cassette can target powerful long-term transgene expression to central nervous system neurons when delivered at relatively low titers of adenovirus. Its use should therefore facilitate both gene therapy studies and investigations of neuronal gene function.
Meta-Analysis of Probiotics for the Prevention of Antibiotic Associated Diarrhea and the Treatment of Clostridium difficile Disease (2006)

A variety of different types of probiotics show promise as effective therapies for these two diseases. Using meta-analyses, three types of probiotics (Saccharomyces boulardii, Lactobacillus rhamnosus GG, and probiotic mixtures) significantly reduced the development of antibiotic-associated diarrhea. Only S. boulardii was effective for CDD.
Vertically coupled glass microring resonator channel dropping filters (1999)

Air-clad glass microring resonators vertically coupled to buried channel waveguides are experimentally investigated. Ring radii of 10 μm, and channel drop bandwidths of 5 nm are reported. Vertical coupling eliminates the need for the etching of fine features, and relaxes the alignment of the resonator with respect to the input and output bus waveguides.
Vaccinia Virus Entry into Cells Is Dependent on a Virion Surface Protein Encoded by the A28L Gene (2004)

The A28L gene of vaccinia virus is conserved in all poxviruses and encodes a protein that is anchored to the surface of infectious intracellular mature virions (IMV) and consequently lies beneath the additional envelope of extracellular virions. A conditional lethal recombinant vaccinia virus, vA28-HAi, with an inducible A28L gene, undergoes a single round of replication in the absence of inducer, producing IMV, as well as extracellular virions with actin tails, but fails to infect neighboring cells. We show here that purified A28-deficient IMV appeared to be indistinguishable from wild-type IMV and were competent to synthesize RNA in vitro. Nevertheless, A28-deficient virions did not induce cytopathic effects, express early genes, or initiate a productive infection. Although A28-deficient IMV bound to the surface of cells, their cores did not penetrate into the cytoplasm. An associated defect in membrane fusion was demonstrated by the failure of low pH to trigger syncytium formation when cells were infected with vA28-HAi in the absence of inducer (fusion from within) or when cells were incubated with a high multiplicity of A28-deficient virions (fusion from without). The correlation between the entry block and the inability of A28-deficient virions to mediate fusion provided compelling evidence for a relationship between these events. Because repression of A28 inhibited cell-to-cell spread, which is mediated by extracellular virions, all forms of vaccinia virus regardless of their outer coat must use a common A28-dependent mechanism of cell penetration. Furthermore, since A28 is conserved, all poxviruses are likely to penetrate cells in a similar way.
ABSORPTION OF INTACT PEPTIDES: STUDIES ON TRANSPORT OF PROTEIN DIGESTS AND DIPEPTIDES ACROSS RAT SMALL INTESTINE IN VITRO (1982)

Passage of intact peptides across isolated rat small intestine has been studied during luminal perfusion with partial digests of proteins or with dipeptides. Significant passage of intact peptide does occur, the amount depending upon the luminal concentration. It probably reflects the 'digestibility' of the protein or protein digest. Previous studies are discussed and, although intact peptide transport is probably not of major nutritional importance, it is suggested that the pathophysiological significance of this process and of peptidaemia merits further attention.
Acylcarnitines: Analysis in Plasma and Whole Blood Using Tandem Mass Spectrometry (2010)

The acylcarnitine profile is a diagnostic test for inherited disorders of fatty acid and branched-chain amino acid catabolism. Patients with this type of metabolic disorder accumulate disease-specific acylcarnitines that correlate with the acyl coenzyme A compounds in the affected mitochondrial metabolic pathways. For example, propionylcarnitine accumulates in patients with both propionic and methylmalonic acidemias. The test identifies and quantifies the species of acylcarnitines in the whole blood or blood plasma of patients at risk for or suspected of having such a disorder. The acylcarnitines are analyzed using electrospray ionization-tandem mass spectrometry. The instrument is used in the precursor ion scan mode to record the molecular species giving rise to fragment ions at m/z 99, derived specifically from the methylated acylcarnitines within the specimen. Quantification is based on the principle of stable isotope dilution, whereby concentrations are derived from the response ratio of each acylcarnitine species to that of a deuterium-labeled acylcarnitine standard. Interpretation of the acylcarnitine profile requires recognition of abnormal concentrations of specific analytes or patterns of analytes and knowledge of their metabolic origin.
Large rate accelerations in the stille reaction with tri-2-furylphosphine and triphenylarsine as palladium ligands: mechanistic and synthetic implications (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLarge rate accelerations in the stille reaction with tri-2-furylphosphine and triphenylarsine as palladium ligands: mechanistic and synthetic implicationsVittorio Farina and Bala KrishnanCite this: J. Am. Chem. Soc. 1991, 113, 25, 9585–9595Publication Date (Print):December 1, 1991Publication History Published online1 May 2002Published inissue 1 December 1991https://pubs.acs.org/doi/10.1021/ja00025a025https://doi.org/10.1021/ja00025a025research-articleACS PublicationsRequest reuse permissionsArticle Views7993Altmetric-Citations957LEARN 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
Structure–activity analysis of aging and reactivation of human butyrylcholinesterase inhibited by analogues of tabun (2009)

hBChE [human BChE (butyrylcholinesterase)] naturally scavenges OPs (organophosphates). This bioscavenger is currently in Clinical Phase I for pretreatment of OP intoxication. Phosphylated ChEs (cholinesterases) can undergo a spontaneous time-dependent process called 'aging' during which the conjugate is dealkylated, leading to creation of an enzyme that cannot be reactivated. hBChE inhibited by phosphoramidates such as tabun displays a peculiar resistance to oxime-mediated reactivation. We investigated the basis of oxime resistance of phosphoramidyl-BChE conjugates by determining the kinetics of inhibition, reactivation (obidoxime {1,1'-(oxybis-methylene) bis[4-(hydroxyimino) methyl] pyridinium dichloride}, TMB-4 [1,3-trimethylene-bis(4-hydroxyiminomethylpyridinium) dibromide], HLö 7 {1-[[[4-(aminocarbonyl) pyridinio]methoxy]methyl]-2,4-bis-[(hydroxyimino)methyl] pyridinium dimethanesulfonate)}, HI-6 {1-[[[4-(aminocarbonyl) pyridinio] methoxy] methyl]-2-[(hydroxyimino)methyl]pyridinium dichloride monohydrate} and aging, and the crystal structures of hBChE inhibited by different N-monoalkyl and N,N-dialkyl tabun analogues. The refined structures of aged hBChE conjugates show that aging proceeds through O-dealkylation of the P(R) enantiomer of N,N-diethyl and N-propyl analogues, with subsequent formation of a salt bridge preventing reactivation, similarly to a previous observation made on tabun-ChE conjugates. Interestingly, the N-methyl analogue projects its amino group towards the choline-binding pocket, so that aging proceeds through deamination. This orientation results from a preference of hBChE's acyl-binding pocket for larger than 2-atoms linear substituents. The correlation between the inhibitory potency and the N-monoalkyl chain length is related to increasingly optimized interactions with the acyl-binding pocket as shown by the X-ray structures. These kinetics and X-ray data lead to a structure-activity relationship that highlights steric and electronic effects of the amino substituent of phosphoramidate. This study provides the structural basis to design new oximes capable of reactivating phosphoramidyl-hBChE conjugates after intoxication, notably when hBChE is used as pretreatment, or to design BChE-based catalytic bioscavengers.
Identification of the Major Brown Shrimp <i>(Penaeus aztecus)</i> Allergen as the Muscle Protein Tropomyosin (1994)

Shrimp, a major seafood allergen, was investigated as a model food allergen. Extracts from both shrimp (Penaeus aztecus) meat and cooking fluid contain a substantial and similar amount of allergenic activity. A 36-kD allergen, demonstrated in both extracts by SDS-PAGE/Western blot analysis, reacted with 28/34 (82%) sera from shrimp-sensitive, skin test and RAST-positive, individuals. This allergen, named Pen a I, was isolated by SDS-PAGE; its amino acid composition was rich in aspartic and glutamic acids. A 21-residue peptide, obtained from endoproteinase Lys-C digested Pen a I by high-performance liquid chromatography, demonstrated significant homology (60-87%) with the muscle protein tropomyosin from various species and origins. The greatest homology (87%) was noted with tropomyosin of the fruit fly (Drosophila melanogaster) reflecting the phylogenic relationship between these two arthropods. These studies demonstrate that tropomyosin is the major shrimp allergen. Although the amino acid sequence of this shrimp muscle protein shares considerable homology with tropomyosins of other species including man, significant differences remain in allergenic activity.
Chemokine receptors as fusion cofactors for human immunodeficiency virus type 1 (HIV-1) (1997)

CD4 is the primary cellular receptor for human immunodeficiency virus type 1 (HIV-1), but is not sufficient for entry of HIV-1 into cells. After a decade-long search, the cellular coreceptors that HIV-1 requires in conjunction with CD4 have been identified as members of the chemokine receptor family of seven-transmembrane G-protein coupled receptors. The discovery of distinct chemokine receptors that support entry of T-cell tropic (CXCR-4) and macrophage tropic HIV-1 strains (CCR-5) explains the differences in cell tropism between viral strains, the inability of HIV-1 to infect most nonprimate cells, and the resistance of a small percentage of the population to HIV-1 infection. Further understanding of the role of chemokine receptors in viral entry may also help explain the evolution of more pathogenic forms of the virus, viral transmission, and HIV-induced pathogenesis. These recent discoveries will aid the development of strategies for combating HIV-1 transmission and spread, the understanding of HIV-1 fusion mechanisms, and the possible development of small animal models for HIV-1 drug and vaccine testing.
Characterisation of alginates from mucoid strains of Pseudomonas aeruginosa (1996)

Conference Article| August 01 1996 Characterisation of alginates from mucoid strains of Pseudomonas aeruginosa Peter J. Tatnell; Peter J. Tatnell 1School of Molecular and Medical Biosciences, University of Wales College of Cardiff, Cardiff, CF1 3US Search for other works by this author on: This Site PubMed Google Scholar Nicholas J. Russell; Nicholas J. Russell 2Department of Biological Sciences, Wye College, Ashford, TN25 5AH Search for other works by this author on: This Site PubMed Google Scholar John R. W. Govan; John R. W. Govan 3Department of Medical Microbiology, University of Edinburgh Medical School, Edinburgh EH8 9AG Search for other works by this author on: This Site PubMed Google Scholar Peter Gacesa Peter Gacesa 4Department of Applied Biology, University of Central Lancashire, Preston, PR1 2HE Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1996) 24 (3): 404S. https://doi.org/10.1042/bst024404s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation Peter J. Tatnell, Nicholas J. Russell, John R. W. Govan, Peter Gacesa; Characterisation of alginates from mucoid strains of Pseudomonas aeruginosa. Biochem Soc Trans 1 August 1996; 24 (3): 404S. doi: https://doi.org/10.1042/bst024404s Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1996 Biochemical Society1996 Article PDF first page preview Close Modal You do not currently have access to this content.
Transient Hydrogen Bonds Identified on the Surface of the NMR Solution Structure of Hirudin (1994)

Recombinant desulfatohirudin retains largely the thrombin-inhibitory activity of natural hirudin from Hirudo medicinalis and causes at most minimal immune response in humans. With regard to potential pharmaceutical applications it is of interest to further investigate the structural basis of hirudin functions. In this paper transient hydrogen bonds between backbone amide protons and side-chain carboxylates on the protein surface of desulfatohirudin (variant 1) have been identified using two-dimensional 1H NMR experiments and site-directed mutagenesis. The analysis of pH titration curves measured with NMR enabled the determination of the pK values of all 13 carboxylates, and downfield shifts larger than 0.2 ppm arising from weak bonding interactions with carboxylates were observed for the amide protons of Gly 25, Ser 32, Glu 35, and Cys 39. For these backbone amide protons virtually identical titration parameters were observed in intact desulfatohirudin and the mutant, truncated hirudin(1-51), demonstrating that the hydrogen bond acceptors are located in the N-terminal polypeptide segment 1-51. The hydrogen bonds Gly 25 NH-Glu 43 delta COO-, Ser 32 NH-Glu 35 delta COO-, Glu 35 NH-Asp 33 gamma COO-, Glu 35 NH-Glu 35 delta COO-, and Cys 39 NH-Glu 17 delta COO- were identified by considering spatial proximity in the NMR solution structure of hirudin(1-51), and comparing the pK values for the amide protons and the carboxylates in desulfatohirudin and the mutants hirudin(E43Q), hirudin(E35Q), hirudin(D33N) and hirudin(E17A).(ABSTRACT TRUNCATED AT 250 WORDS)
Advanced Glycation End Products-driven Angiogenesis in Vitro (1997)

This study was undertaken to determine whether and how advanced glycation end products (AGE), senescent macroproteins accumulated in various tissues under hyperglycemic states, cause angiogenesis, the principal vascular derangement in diabetic microangiopathy. We first prepared AGE-bovine serum albumin (BSA) and anti-AGE antiserum using AGE-RNase A. Then AGE-BSA was administered to human skin microvascular endothelial cells in culture, and their growth was examined. The AGE-BSA, but not nonglycated BSA, was found to induce a statistically significant increase in the number of viable endothelial cells as well as their synthesis of DNA. The increase in DNA synthesis by AGE-BSA was abolished by anti-AGE antibodies. AGE-BSA also stimulated the tube formation of endothelial cells on Matrigel. We obtained the following evidence that it is vascular endothelial growth factor (VEGF) that mainly mediates the angiogenic activities of AGE. (1) Quantitative reverse transcription-polymerase chain reaction analysis of poly(A)+ RNA from microvascular endothelial cells revealed that AGE-BSA up-regulated the levels of mRNAs for the secretory forms of VEGF in time- and dose-dependent manners, while endothelial cell expression of the genes encoding the two VEGF receptors, kinase insert domain-containing receptor and fms-like tyrosine kinase 1, remained unchanged by the AGE treatment. Immunoprecipitation analysis revealed that AGE-BSA did increase de novo synthesis of VEGF. (2) Monoclonal antibody against human VEGF completely neutralized both the AGE-induced DNA synthesis and tube formation of the endothelial cells. The results suggest that AGE can elicit angiogenesis through the induction of autocrine vascular VEGF, thereby playing an active part in the development and progression of diabetic microangiopathies.