gebhart/patrepeval huggingface dataset:
Platelet Factor 4: Production, Structure, and Physiologic and Immunologic Action (1991)

Platelet factor 4 (PF4) is a protein found in megakaryocytes and platelet α-granules (1, 2). Immunocytochemical studies show that it is present as well in mast cell granules (3) and on the endothelium of human umbilical veins, but not arteries (4). Early work on PF4 has been reviewed elsewhere (5–7). Human platelets contain about 18 ± 4 μg of PF4/109 (8).Thrombospondin, platelet-derived growth factor, and compounds derived from platelet basic protein such as β-thromboglobulin (β-TG) are found in platelet α-granules in addition to PF4. All are secreted when platelets are appropriately stimulated; for example, since thrombin is a strong stimulus, these compounds are present in much higher concentrations in serum than in plasma (e.g., 5334 vs 1.8 ng/ml for PF4 [9]). They are also secreted after contact of platelets with collagen in damaged blood vessels, for example.Production and StructurePF4 is synthesized by megakaryocytes (10), an ability that correlates with cytoplasmic maturity (2, 11). The PF4 is first packaged into vesicles and from there it is transferred to α-granules (2). Megakaryocytes express mRNA transcripts for PF4, but not for fibrinogen or albumin, which are taken up by megakaryocytes from plasma (12). Even blood platelets, which contain little mRNA, contain mRNA for PF4, whereas none is evident in human lymphocytes, cultured fibroblasts, and four types of malignant cells (13).Human PF4 is a 7.8-kDa protein that contains 70 amino acids, with two disulfide bonds, no tryptophan or methionine, two histidines, and a single tyrosine (Fig. 1). The position of its two disulfide bridges has been inferred by homology with the related compound β-TG (14). Its isoelectric point is 7.6 (15) and its extinction coefficient (1%, 280 μm) is reported to be 2.9 (3) or 5.4 (9).
Replication and packaging of Norwalk virus RNA in cultured mammalian cells (2005)

Human noroviruses, the most common cause of nonbacterial gastroenteritis, are characterized by high infectivity rate, low infectious dose, and unusually high stability outside the host. However, human norovirus research is hindered by the lack of a cell culture system and a small animal model of infection. Norwalk virus (NV) is the prototype strain of human noroviruses. We report here replication of NV viral RNA and its packaging into virus particles in mammalian cells by intracellular expression of native forms of NV viral RNA devoid of extraneous nucleotide sequences derived from the expression vector by the use of replication-deficient vaccinia virus MVA encoding the bacteriophage T7 RNA polymerase (MVA/T7). Expressed genomic RNA was found to replicate; NV subgenomic RNA was transcribed from genomic RNA by use of NV nonstructural proteins expressed from genomic RNA and was subsequently translated into NV capsid protein VP1. Viral genomic RNA was packaged into virus particles generated in mammalian cells. The cesium chloride (CsCl) density gradient profile of virus particles containing genomic RNA was similar to that of NV purified from stool. These observations indicate that the NV cDNA constructed here is a biologically infectious clone, and that mammalian cells have the ability to replicate NV genomic RNA. This work establishes a mammalian cell-based system for analysis of human norovirus replication and, thus, makes it feasible to investigate antiviral agents in mammalian cells.
Crystal structure of aStaphylococcus aureusprotein A domain complexed with the Fab fragment of a human IgM antibody: Structural basis for recognition of B-cell receptors and superantigen activity (2000)

Staphylococcus aureus produces a virulence factor, protein A (SpA), that contains five homologous Ig-binding domains. The interactions of SpA with the Fab region of membrane-anchored Igs can stimulate a large fraction of B cells, contributing to lymphocyte clonal selection. To understand the molecular basis for this activity, we have solved the crystal structure of the complex between domain D of SpA and the Fab fragment of a human IgM antibody to 2.7-A resolution. In the complex, helices II and III of domain D interact with the variable region of the Fab heavy chain (V(H)) through framework residues, without the involvement of the hypervariable regions implicated in antigen recognition. The contact residues are highly conserved in human V(H)3 antibodies but not in other families. The contact residues from domain D also are conserved among all SpA Ig-binding domains, suggesting that each could bind in a similar manner. Features of this interaction parallel those reported for staphylococcal enterotoxins that are superantigens for many T cells. The structural homology between Ig V(H) regions and the T-cell receptor V(beta) regions facilitates their comparison, and both types of interactions involve lymphocyte receptor surface remote from the antigen binding site. However, T-cell superantigens reportedly interact through hydrogen bonds with T-cell receptor V(beta) backbone atoms in a primary sequence-independent manner, whereas SpA relies on a sequence-restricted conformational binding with residue side chains, suggesting that this common bacterial pathogen has adopted distinct molecular recognition strategies for affecting large sets of B and T lymphocytes.
Cellular expression of liver and neural cell adhesion molecules after transfection with their cDNAs results in specific cell-cell binding. (1987)

Mouse L cells, which do not express the known primary cell adhesion molecules (CAMs), were permanently transfected with vectors containing the simian virus 40 early promoter and cDNA sequences encoding chicken liver CAM (L-CAM) or each of the three major polypeptide forms of chicken neural CAM (N-CAM). Transfected cells in culture expressing the Ca2+-dependent L-CAM showed uniform surface expression of the molecule. Unlike untransfected L cells, these cells aggregated readily; the aggregation was inhibited by Fab' fragments of antibodies to L-CAM but not by fragments of anti-N-CAM. These cells spread more efficiently in culture than did their untransfected counterparts, forming small colonies of flattened cells that gradually assumed morphologies resembling closely packed L cells. Transfected L cells expressing either the small or large intercellular domain polypeptide (sd or ld) chains of N-CAM aggregated specifically with each other or bound membrane vesicles from chick brain. Both types of binding were specifically inhibited by Fab' fragments of anti-N-CAM antibodies. These cells, in contrast to those transfected with vectors for L-CAM, showed rounded morphologies and spread inefficiently in culture. L cells transfected with vectors specifying the small surface domain polypeptide (ssd) chain of N-CAM showed no phenotypic changes and no evidence for linkage of ssd chains to the cell membrane by phosphatidylinositol intermediates. Instead, these cells synthesized the molecule and released it into the medium. These findings complete the demonstration that different CAMs have specific roles in ligating the cells that synthesize them, and they provide further evidence that L-CAM and N-CAM bind by homophilic mechanisms. The different phenotypic changes observed for each specific CAM are consistent with the hypothesis that CAM synthesis or differing associations of CAM carboxyl-terminal domains with the cell surface and cortex may lead directly or indirectly to specific alterations in the cells bound together by that CAM.
Pathway Signature and Cellular Differentiation in Clear Cell Renal Cell Carcinoma (2010)

ccRCC is characterized by a lack of epithelial differentiation, mesenchymal/adipogenic transdifferentiation, and pluripotent mesenchymal stem cell-like differentiation capacity in vitro. We suggest that down-regulation of developmental transcription factors may mediate the aberrant differentiation in ccRCC. We propose a model in which normal renal epithelial cells undergo dedifferentiation, EMT, and adipogenic transdifferentiation, resulting in ccRCC. Because ccRCC cells grown in adipogenic media regain the characteristic ccRCC phenotype, we have identified a new in vitro ccRCC cell model more resembling ccRCC tumor morphology.
Structure-function relationships in serpins: current concepts and controversies. (1998)

Almost two decades ago, a new superfamily of proteins was proposed, based on the similarity between the primary structure of ovalbumin, α1-antitrypsin (also known as α1-proteinase inhibitor) and antithrombin III (1). Even though the acronym “serpins” (serine proteinase inhibitors) was given to these proteins (2), it became soon apparent that a variety of non-inhibitory serpins [e.g. ovalbumin (3), maspin (4), pigment epithelium-derived factor (5)] as well as serpins that inhibit cysteine proteinases [e.g. interleukin-1 β converting enzyme inhibitor (6), cathepsin L inhibitor (7)] belong to this superfamily. Serpins represent about 10% of the total protein in plasma. From these serpins, α1-proteinase inhibitor represents 70%. A number of serpins play a critical role in the regulation of important physiological processes such as blood coagulation (e.g. antithrombin III), fibrinolysis (e.g. plasminogen activator inhibitor 1, PAI-1), complement activation (e.g. C1-inhibitor), and inflammation (e.g. α1-antichymotrypsin) (8) (Table 1). The serpins comprise more than 40 proteins identified from viruses, plants, insects and animals but not from prokaryotes (9). All serpins consist of about 400 residues with molecular masses in the range of 38 to 70 kDa (dependent on the degree of glycosylation) and an overall amino acid homology of approximately 35% (10). Huber and Carrell (10) reported that the conserved residues are localized either internal or in niches on the surface. All serpins have the same highly ordered tertiary structure consisting of 3 β-pleated sheets A, B and C, α-helices A through I and a reactive site loop containing residues P16 to P10’ (10, 11) (Fig. 1). The reactive site, designated P1P1’ and comprising the bait peptide bond, is located within this loop structure situated 30-40 amino acids from the carboxy-terminal end. Using the nomenclature of Schechter and Berger (13), the residues N-terminal to the scissile bond are designated the P-residues (P16 up to P1) whereas the residues to the C-terminal end are designated the P’-residues (P1’ up to P10’) (Table 2). Even though almost all serpins contain Cys residues, only few of them (α2-antiplasmin, C1-inhibitor and antithrombin III) harbor disulfide bridges (10). For α2-antiplasmin it was recently shown that abolishing the disulfide bridge does not influence the thermodynamic stability, the inhibitory activity and the clearance by the receptors (14). Even though reduction of one of the three antithrombin III disulfide bonds does not affect the rate of thrombin inhibition as such, it does abolish the heparin-induced acceleration of the thrombin-antithrombin III interaction (15). These findings suggest that under certain conditions disulfide bridges may play a role in the functional properties of a serpin.
Generation and characterization of anti-sulfoglucuronosyl paragloboside monoclonal antibody NGR50 and its immunoreactivity with peripheral nerve (1996)

Sulfoglucuronosyl paragloboside (SGPG) is a member of the sulfated glucuronic acid-containing glycolipid (SGGL) family found primarily in peripheral nerves. These glycolipids contain the HNK-1 carbohydrate epitope and are recognized by monoclonal IgM from patients with chronic demyelinating neuropathy and paraproteinemia. Recent studies indicate that SGGLs may serve as ligands for selectins, amphoterin, and laminin, suggesting that these glycolipids may play an important role in cellular adhesion. To elucidate the biological function of these glycolipids, we produced a murine monoclonal antibody (mAb) and studied its antigenic specificity. Using an enzyme-linked immunosorbent assay (ELISA), we found that the mAb designated as NGR50 belonged to the IgG2a subclass, and that the minimal titer (2 SD above the mean optical density value of control) of this mAb was 1:640, with 20 ng of purified SGPG as the antigen. Thin-layer chromatography (TLC) immunoblotting revealed that this mAb reacted specifically with SGPG and sulfoglucuronosyl lactosaminyl paragloboside (SGLPG), which is a structural analogue of the former, but not with other glycolipids. Desulfated derivates of SGPG and SGLPG did not react with mAb NGR50. Western blot analysis showed crossreactivity with human myelin-associated glycoprotein (MAG), but not with rat MAG or rat glycoprotein P0. Unlike anti-HNK-1 monoclonal antibody, however, NGR50 reacted only weakly with several proteins in the 20-30-kD regions, including human P0, suggesting that mAb50 has a different fine specificity as an anti-HNK-1 antibody. Immunocytochemical study of rat sciatic nerve using mAb NGR50 revealed positive staining at the outer surface of the myelin sheath and Schwann cells, as well as in the intervening connective tissues. Faint staining was also visible at the axolemmal-myelin interface; however, compact myelin was not stained.
Common Oncogenic Mutations Are Infrequent in Oral Squamous Cell Carcinoma of Asian Origin (2013)

Hotspot oncogenic mutations which are frequently present in common solid tumors are exceedingly rare in OSCC. Despite differences in risk habit exposure, the mutation frequency of PIK3CA and HRAS in Asian OSCC were similar to that reported in OSCC among Caucasians, whereas TP53 mutations rates were significantly lower. The lack of actionable hotspot mutations argue strongly for the need to comprehensively characterize gene mutations associated with OSCC for the development of new diagnostic and therapeutic tools.
A chloroplast homologue of the signal recognition particle subunit SRP54 is involved in the posttranslational integration of a protein into thylakoid membranes. (1995)

The mechanisms involved in the integration of proteins into the thylakoid membrane are largely unknown. However, many of the steps of this process for the light-harvesting chlorophyll a/b protein (LHCP) have been described and reconstituted in vitro. LHCP is synthesized as a precursor in the cytosol and posttranslationally imported into chloroplasts. Upon translocation across the envelope membranes, the N-terminal transit peptide is cleaved, and the apoprotein is assembled into a soluble "transit complex" and then integrated into the thylakoid membrane via three transmembrane helices. Here we show that 54CP, a chloroplast homologue of the 54-kDa subunit of the mammalian signal recognition particle (SRP54), is essential for transit complex formation, is present in the complex, and is required for LHCP integration into the thylakoid membrane. Our data indicate that 54CP functions posttranslationally as a molecular chaperone and potentially pilots LHCP to the thylakoids. These results demonstrate that one of several pathways for protein routing to the thylakoids is homologous to the SRP pathway and point to a common evolutionary origin for the protein transport systems of the endoplasmic reticulum and the thylakoid membrane.
Repositioning of a Domain in a Modular Polyketide Synthase to Promote Specific Chain Cleavage (1995)

Macrocyclic polyketides exhibit an impressive range of medically useful activities, and there is great interest in manipulating the genes that govern their synthesis. The 6-deoxyerythronolide B synthase (DEBS) of Saccharopolyspora erythraea, which synthesizes the aglycone core of the antibiotic erythromycin A, has been modified by repositioning of a chain-terminating cyclase domain to the carboxyl-terminus of DEBS1, the multienzyme that catalyzes the first two rounds of polyketide chain extension. The resulting mutant markedly accelerates formation of the predicted triketide lactone, compared to a control in which the repositioned domain is inactive. Repositioning of the cyclase should be generally useful for redirecting polyketide synthesis to obtain polyketides of specified chain lengths.
Logical Partitions on Many-Core Platforms (2015)

Cloud platforms that use logical partitions to allocate dedicated resources to VMs can benefit from small and therefore secure hypervisors. Many-core platforms, with their abundant resources, are an attractive basis to create and deploy logical partitions on a large scale. However, many-core platforms are designed for efficient cross-core data sharing rather than isolation, which is a key requirement for logical partitions. Typically, logical partitions leverage hardware virtualization extensions that require complex CPU core enhancements. These extensions are not optimal for many-core platforms, where it is preferable to keep the cores as simple as possible.
Prosthetic Joint Infection Diagnosed Postoperatively by Intraoperative Culture (2005)

The purpose of this study was to assess the outcome of prosthetic joint infection initially diagnosed by multiple positive intraoperative cultures after revision arthroplasty and treated by strategies that include less than 6 weeks of intravenous antimicrobial therapy. Between January 1995 and December 1999, 16 of 509 (3%) episodes of prosthetic joint infection in 16 patients initially were diagnosed by positive intraoperative cultures after revision arthroplasty. Patients were followed up for a median of 1057 days (range, 731-1969 days). The median age of the patients was 65 years, and 65% of patients had revision total hip arthroplasty. Coagulase-negative staphylococci and Propionibacterium spp were the main pathogens identified. Intravenous antimicrobial therapy was used in 81% of patients and chronic oral suppression was used in 56% of patients. Three patients received no antimicrobial therapy. The median duration of intravenous antimicrobial therapy was 28 days (range, 2-42 days). The 5-year survival free of treatment failure for the 16 episodes was 89%. These results suggest a favorable outcome of prosthetic joint infections because of low virulence pathogens initially diagnosed as positive intraoperative cultures after revision arthroplasty with a variety of medical treatment strategies, including strategies that contain less than 6 weeks intravenous antimicrobial therapy.
Tetanus and botulinum neurotoxins: mechanism of action and therapeutic uses (1999)

The clostridial neurotoxins responsible for tetanus and botulism are proteins consisting of three domains endowed with different functions: neurospecific binding, membrane translocation and proteolysis for specific components of the neuroexocytosis apparatus. Tetanus neurotoxin (TeNT) binds to the presynaptic membrane of the neuromuscular junction, is internalized and transported retroaxonally to the spinal cord. The spastic paralysis induced by the toxin is due to the blockade of neurotransmitter release from spinal inhibitory interneurons. In contrast, the seven serotypes of botulinum neurotoxins (BoNTs) act at the periphery by inducing a flaccid paralysis due to the inhibition of acetylcholine release at the neuromuscular junction. TeNT and BoNT serotypes B, D, F and G cleave specifically at single but different peptide bonds, of the vesicle associated membrane protein (VAMP) synaptobrevin, a membrane protein of small synaptic vesicles (SSVs). BoNT types A, C and E cleave SNAP-25 at different sites located within the carboxyl-terminus, while BoNT type C additionally cleaves syntaxin. The remarkable specificity of BoNTs is exploited in the treatment of human diseases characterized by a hyperfunction of cholinergic terminals.
G2019S leucine-rich repeat kinase 2 causes uncoupling protein-mediated mitochondrial depolarization (2012)

The G2019S leucine rich repeat kinase 2 (LRRK2) mutation is the most common genetic cause of Parkinson's disease (PD), clinically and pathologically indistinguishable from idiopathic PD. Mitochondrial abnormalities are a common feature in PD pathogenesis and we have investigated the impact of G2019S mutant LRRK2 expression on mitochondrial bioenergetics. LRRK2 protein expression was detected in fibroblasts and lymphoblasts at levels higher than those observed in the mouse brain. The presence of G2019S LRRK2 mutation did not influence LRRK2 expression in fibroblasts. However, the expression of the G2019S LRRK2 mutation in both fibroblast and neuroblastoma cells was associated with mitochondrial uncoupling. This was characterized by decreased mitochondrial membrane potential and increased oxygen utilization under basal and oligomycin-inhibited conditions. This resulted in a decrease in cellular ATP levels consistent with compromised cellular function. This uncoupling of mitochondrial oxidative phosphorylation was associated with a cell-specific increase in uncoupling protein (UCP) 2 and 4 expression. Restoration of mitochondrial membrane potential by the UCP inhibitor genipin confirmed the role of UCPs in this mechanism. The G2019S LRRK2-induced mitochondrial uncoupling and UCP4 mRNA up-regulation were LRRK2 kinase-dependent, whereas endogenous LRRK2 levels were required for constitutive UCP expression. We propose that normal mitochondrial function was deregulated by the expression of G2019S LRRK2 in a kinase-dependent mechanism that is a modification of the normal LRRK2 function, and this leads to the vulnerability of selected neuronal populations in PD.
Mass spectrometric identification of a naturally processed melanoma peptide recognized by CD8+ cytotoxic T lymphocytes. (1995)

We and others have previously reported that melanoma-specific, cytotoxic T lymphocytes (CTL) define a minimum of six class I-presented peptide epitopes common to most HLA-A2+ melanomas. Here we show that three of these peptide epitopes are coordinately recognized by a CTL clone obtained by limiting dilution from the peripheral blood of an HLA-A2+ melanoma patient. Tandem mass spectrometry was used to characterize and sequence one of these three naturally processed melanoma peptides. One of the potential forms of the deduced peptide sequence (XXTVXXGVX, X = I or L) matches positions 32-40 of the recently identified melanoma gene MART-1/Melan-A. This peptide (p939; ILTVILGVL) binds to HLA-A2 with an intermediate-to-low affinity and is capable of sensitizing the HLA-A2+ T2 cell line to lysis by CTL lines and clones derived from five different melanoma patients. A relative high frequency of anti-p939-specific effector cells appear to be present in situ in HLA-A2+ melanoma patients, since p939 is also recognized by freshly isolated tumor infiltrating lymphocytes. p939 represents a good candidate for the development of peptide-based immunotherapies for the treatment of patients with melanoma.