gebhart/patrepeval huggingface dataset:
Identification of a Titin-Derived HLA-A1–Presented Peptide as a Cross-Reactive Target for Engineered MAGE A3–Directed T Cells (2013)

MAGE A3, which belongs to the family of cancer-testis antigens, is an attractive target for adoptive therapy given its reactivation in various tumors and limited expression in normal tissues. We developed an affinity-enhanced T cell receptor (TCR) directed to a human leukocyte antigen (HLA)-A*01-restricted MAGE A3 antigen (EVDPIGHLY) for use in adoptive therapy. Extensive preclinical investigations revealed no off-target antigen recognition concerns; nonetheless, administration to patients of T cells expressing the affinity-enhanced MAGE A3 TCR resulted in a serious adverse event (SAE) and fatal toxicity against cardiac tissue. We present a description of the preclinical in vitro functional analysis of the MAGE A3 TCR, which failed to reveal any evidence of off-target activity, and a full analysis of the post-SAE in vitro investigations, which reveal cross-recognition of an off-target peptide. Using an amino acid scanning approach, a peptide from the muscle protein Titin (ESDPIVAQY) was identified as an alternative target for the MAGE A3 TCR and the most likely cause of in vivo toxicity. These results demonstrate that affinity-enhanced TCRs have considerable effector functions in vivo and highlight the potential safety concerns for TCR-engineered T cells. Strategies such as peptide scanning and the use of more complex cell cultures are recommended in preclinical studies to mitigate the risk of off-target toxicity in future clinical investigations.
Sustained Activation of ERK1/2 MAPK in Oligodendrocytes and Schwann Cells Enhances Myelin Growth and Stimulates Oligodendrocyte Progenitor Expansion (2013)

Myelin is a biologically active membrane receiving and processing signals from axons. Although much is known about its structure and molecular composition, the intracellular signal transduction pathways, active during specific phases of myelinogenesis for regulating myelin formation, remain poorly understood. Recent genetic loss-of-function studies have suggested a key role of extracelluar signal-regulated kinases-1 and -2 (ERK1/2), downstream mediators of mitogen-activated protein kinases (MAPKs), in promoting CNS and PNS myelination. In contrast, other studies, largely in vitro, have suggested that activation of ERK1/2 pathway can be detrimental for glial cell function and myelination. Given these conflicting reports, we investigated the effects of cell-autonomous activation of ERK1/2 in glial cells during developmental myelination in the intact CNS and PNS. Two lines of transgenic mice with sustained activation of ERK1/2 in oligodendrocyte progenitors (OPCs), oligodendrocytes, and Schwann cells were generated. Consistent with our loss-of-function studies, gain of ERK1/2 function in oligodendrocyte-lineage cells significantly increased myelin thickness, independent of oligodendrocyte differentiation or initiation of myelination. Additionally, increased activation of ERK1/2 in OPCs during early development resulted in transient hyperproliferation and overproduction of OPCs but generation of normal numbers of myelinating oligodendrocytes. Thus, these in vivo studies suggest a beneficial biphasic requirement of ERK1/2 during developmental myelination in the CNS, deployed first during early stages of the oligodendrocyte lineage for promoting OPC expansion and then redeployed later in myelinating oligodendrocytes for promoting myelin growth. Furthermore, Schwann cells with activated ERK1/2 hypermyelinate PNS axons, suggesting that ERK1/2 signaling is a conserved mechanism that promotes both CNS and PNS developmental myelination.
Daptomycin Pharmacokinetics and Safety following Administration of Escalating Doses Once Daily to Healthy Subjects (2003)

The purpose of this paper is to establish the pharmacokinetics and safety of escalating, once-daily doses of daptomycin, a novel lipopeptide antibiotic active against gram-positive pathogens, including those resistant to methicillin and vancomycin. This phase 1, multiple-dose, double-blind study involved 24 healthy subjects in three dose cohorts (4, 6, and 8 mg/kg of body weight) who were randomized to receive daptomycin or the control at a 3:1 ratio and administered the study medication by a 30-min intravenous infusion every 24 h for 7 to 14 days. Daptomycin pharmacokinetics was assessed by blood and urine sampling. Safety and tolerability were evaluated by monitoring adverse events (AEs) and laboratory parameters. Daptomycin pharmacokinetics was linear through 6 mg/kg, with a slight ( approximately 20%) nonlinearity in the area under the curve and trough concentration at the highest dose studied (8 mg/kg). The pharmacokinetic parameters measured on the median day of the study period, (day 7) were half-life ( approximately 9 h), volume of distribution ( approximately 0.1 liters/kg), systemic clearance ( approximately 8.2 ml/h/kg), and percentage of the drug excreted intact in urine from 0 to 24 h ( approximately 54%). Daptomycin protein binding (mean amount bound, 91.7%) was independent of the drug concentration. No gender effect was observed. All subjects who received daptomycin completed the study. The frequencies and distributions of treatment-emergent AEs were similar for the subjects who received daptomycin and the control subjects. There were no serious AEs and no pattern of dose-related events. The pharmacokinetics of once-daily administration of daptomycin was linear through 6 mg/kg. For all three doses, plasma daptomycin concentrations were consistent and predictable throughout the dosing interval. Daptomycin was well tolerated when it was administered once daily at a dose as high as 8 mg/kg for 14 days.
Enhancing Wet Cellulose Adhesion with Proteins (2005)

Twenty proteins were compared as potential paper wet strengthening additives by measuring the peel force required to delaminate wet, regenerated cellulose films laminated with a thin (3 mg/m2) protein layer. Wet adhesion results ranged over nearly an order of magnitude, reflecting the importance of protein composition. The proteins with the highest contents of lysine and arginine gave the strongest adhesion with secondary contributions from hydroxyl and phenolic amino acid residues. Wet adhesion was performed with TEMPO oxidized cellulose and with laminates that were cured at high temperatures (120 °C), suggesting that protein grafting to the cellulose and protein cross-linking was important for good wet strength. Although none of the protein laminates was as strong as polyvinylamine or a commercial PAE resin used in the paper industry, this paper suggests that increasing the primary amine (amino group) content as well as optimizing heat-induced bond formation may someday lead to a protein-based paper wet strength resin.
Autism Spectrum Disorders in Relation to Distribution of Hazardous Air Pollutants in the San Francisco Bay Area (2006)

Our results suggest a potential association between autism and estimated metal concentrations, and possibly solvents, in ambient air around the birth residence, requiring confirmation and more refined exposure assessment in future studies.
Glycated Lysine Residues: A Marker for Non-Enzymatic Protein Glycation in Age-Related Diseases (2011)

Nonenzymatic glycosylation or glycation of macromolecules, especially proteins leading to their oxidation, play an important role in diseases. Glycation of proteins primarily results in the formation of an early stage and stable Amadori-lysine product which undergo further irreversible chemical reactions to form advanced glycation endproducts (AGEs). This review focuses these products in lysine rich proteins such as collagen and human serum albumin for their role in aging and age-related diseases. Antigenic characteristics of glycated lysine residues in proteins together with the presence of serum autoantibodies to the glycated lysine products and lysine-rich proteins in diabetes and arthritis patients indicates that these modified lysine residues may be a novel biomarker for protein glycation in aging and age-related diseases.
Multiplexed, particle‐based detection of DNA using flow cytometry with 3DNA dendrimers for signal amplification (2004)

Multiplexed detection of DNA hybridization on a single molecule level per bead was achieved with conventional flow cytometry instrumentation. This assay is useful for detecting target DNAs at low concentrations.
Nonorganic Physical Signs in Low-Back Pain (1980)

Nonorganic physical signs in low-back pain are described and standardized in 350 North American and British patients. These nonorganic signs are distinguishable from the standard clinical signs of physical pathology and correlate with other psychological data. By helping to separate the physical from the nonorganic they clarify the assessment of purely physical pathologic conditions. It is suggested also that the nonorganic signs can be used as a simple clinical screen to help identify patients who require more detailed psychological assessment.
Juvenile Papilloma of the Larynx (1971)

A two-year-old Negro-South American girl presented with juvenile laryngeal papilloma which necessitated an emergency tracheostomy. During the next 1½ years of hospitalization, she required general anesthesia for surgical excision of recurrent growths on an average of once every 3.7 weeks. Inasmuch as the process continued unabated, autogenous vaccine prepared from her tumor was administered by 15 weekly injections. There was an apparent dramatic beneficial response with vocalization around the tracheostomy tube occurring for the first time within two months of the start of vaccine therapy. Tumor growth regressed completely, the tracheostomy tube was removed within six months of the utilization of vaccine treatment and the patient was discharged after two years of hospitalization.
Attentional deficits in concussion (2005)

These results suggest that the orienting and executive components of attention are most susceptible to the effects of concussion.
Synthesis and Applications of Polysiloxane Macromers (1985)

The surface of polymers have been known to be of importance in many applications of polymers. Polyorganosiloxanes are industrially produced in large quantity for various purposes depending molecular weight and copolymer composition. The inherent hydrophobic nature of siloxanes coupled with their ability to accumulate on the surface of polymer blends has allowed the polyorganosiloxanes to be used widely to impart hydrophobicity to the surfaces of other materials, particularly in the case of polymers which by themselves are devoid of such properties.(1-3.) Among the many physicochemical methods employed for the surface modification of polymers, the use of graft copolymers for the purpose is being recognized to be promising.(4-8) This is because the graft copolymers containing surface active segments can be tailor-made for a specific need. However, the availability of well characterized graft copolymers is essential not only for understanding of their action, but also for maximum efficiency. Polyorganosiloxanes are also noteworthy
Murine L1210 and P388 Leukemias (1997)

L1210 and P388 leukemias were developed in 1948 (1) and 1955 (2), respectively. Each leukemia played an important role in both screening and detailed evaluations of candidate anticancer agents. Forty years later, these in vivo models are still used to evaluate anticancer activity, although at a greatly reduced level. This chapter reviews their past and present roles in the evaluation of anticancer drugs. Data for the sensitivity of these two leukemias and the drug-resistant P388 sublines to clinically useful drugs are reported.
Suppression of tumor necrosis factor-alpha, interleukin-1 beta, interleukin-6 and granulocyte-monocyte colony stimulating factor secretion from human monocytes by an extract of Poria cocos. (1992)

Fu-Ling, the sclederma of Poria cocos (Schw.) Wolf, has long been used as a sedative and diuretic. However, data in this report suggest that Fu-Ling is a potential suppressor of cytokine secretion from human peripheral blood monocytes under in vitro condition. Monocyte culture medium containing 10% of Fu-Ling extract significantly inhibited secretion of TNF-alpha, IL-beta, IL-6 and GM-CSF from the monocyte monolayer. However, as Fu-Ling extract content was gradually reduced, cytokine secretion was augmented in comparison with the cytokine secretion in drug-free controls. This augmentative effect resulted from the trace amount (1.24 ng/ml in 0.62% of Fu-Ling extract) of lipopolysaccharide (LPS) which contaminated the Fu-Ling extract during the preparation process, since TNF-alpha, IL-1 beta and IL-6 secretion induced by 0.62% Fu-Ling extract could be significantly inhibited by polymyxin B, an LPS inhibitor. Furthermore, the amounts of TNF-alpha IL-1 beta and IL-6 induced by 1 ng/ml of LPS without the presence of drug were more than that induced by 0.62% of Fu-Ling extract. Thus, cytokine secretion induced by LPS contamination (1.24 ng/ml) in the Fu-Ling extract was partially suppressed by 0.62% of the Fu-Ling extract itself. GM-CSF secretion in the medium containing 0.62% of Fu-Ling extract was not induced by LPS since: a) GM-CSF induced by 0.62% Fu-Ling extract could not be inhibited by polymyxin B; b) LPS at 1 ng/ml showed no activity indicating induction of GM-CSF secretion.
Chondrogenesis of Adipose-Derived Adult Stem Cells in a Poly-Lactide-Co-Glycolide Scaffold (2009)

Adult adipose-derived stem cells (ASCs) are considered to be an alternative cell source for cell-based cartilage repair because of their multiple differentiation potentials. This article addresses the chondrogenic differentiation of ASCs seeded into poly-lactide-co-glycolide (PLGA) scaffolds after implantation in a subcutaneous pocket of nude mice. Human ASCs were seeded into PLGA (polylactic acid:polyglycolic acid = 90:10) scaffolds and cultured in transforming growth factor beta 1 (TGF-beta1)-containing medium for 3 weeks in vitro. Then specimens were implanted into a subcutaneous pocket of severe combined immunodeficiency mice and harvested after 8 weeks. Chondrospecific messenger RNA (mRNA) expression was analyzed using reverse transcriptase polymerase chain reaction. Corresponding extracellular matrix (ECM) synthesis was demonstrated using immunohistochemical staining. Chondrospecific marker molecules such as collagen type II and type X, cartilage oligomeric matrix protein, and aggrecan subsequently increased during the 3 weeks period in vitro. After a further 8 weeks, in vivo samples pretreated with TGF-beta1 continued expressing collagen type II and aggrecan mRNA, and collagen type II was found within the ECM using immunohistochemistry. Chondrospecific mRNA was not detected in control samples. ASC-seeded PLGA scaffolds express a stable chondrogenic phenotype in a heterotopic model of cartilage transplantation and represent a suitable tool for tissue engineering of cartilage.
On the Shapley value of Minimum cost spanning tree problems (2005)

We associate to each minimum cost spanning tree problem a characteristic function v+ where v+ (S) denotes the cost of connecting agents in S to the source assuming that agents of N n S are already connected. We define the rule as the Shapley value of the game v+: We prove that coincides with a rule present in the literature under different names. We also present a new characterization of this rule using a property of equal contributions.
Immune Responses to Hepatitis C Virus Structural and Nonstructural Proteins Induced by Plasmid DNA Immunizations (2000)

DNA-based immunizations have been used to elicit cellular immunity to hepatitis C virus (HCV) proteins in mice. Mice were immunized by intramuscular or intradermal injections of plasmid DNA derived from a near-full-length HCV genotype 1b genomic clone (pRC/B2) or individual genomic clones. These immunizations induced cytotoxic T lymphocytes (CTLs), as revealed in standard chromium-release assays that used syngeneic peptide-pulsed or transfected target cells. These assays identified four CTL epitopes within the capsid, E1, and E2 regions of the polyprotein sequence of HCV genotype 1a that were cross-reactive with HCV genotype 1b. Additionally, CTLs derived from mice immunized with either NS3 or NS5 specifically lysed target cells sensitized to either the genotype 1a or 1b gene products. Nucleic acid immunizations also generated humoral immunity to HCV proteins, as detected by anti-HCV reactivity to NS3 and capsid in ELISAs and immunoblot assays.
Telomerase RNAs of different ciliates have a common secondary structure and a permuted template. (1994)

Telomerase is composed of protein and RNA. The RNA serves as a template for telomere DNA synthesis and may also be important for enzyme structure or catalysis. We have used the presence of conserved sequence elements in the promoter and template regions to amplify by PCR the telomerase RNA genes from six different hypotrichous ciliates: Oxytricha nova, Oxytricha trifallax, Stylonychia mytilis, Stylonychia lemnae, Euplotes aediculatus, and Euplotes eurystomus. RNaseH cleavage of the O. nova RNA in extracts by use of a complementary oligonucleotide leads to loss of telomerase activity, supporting the identification. Primary sequence and biochemical experiments suggest that the templates of Oxytricha and Stylonychia are circularly permuted relative to that of E. aediculatus. On the basis of the pause sites, the former two add G4T4 during a single primer elongation cycle, whereas E. aediculatus adds G3T4G. The only primary sequence element outside the template that is conserved between these phylogenetically distant telomerase RNAs is the sequence 5'-(C)UGUCA-3', which precedes the template regions by exactly two bases. We propose a common secondary structure model that is based on nucleotide covariations, a model which resembles that proposed previously for tetrahymenine telomerase RNAs.
Conserved and unique amino acid residues in the domains of the growth hormones (1989)

Growth hormone (GH), prolactin (PRL), and placental lactogen (PL) constitute a protein family whose genes are considered to have evolved from a common ancestral gene. GHs isolated from various vertebrate species are known to possess highly conserved structural and functional features. In the present study we have cloned and sequenced flounder growth hormone (fGH) cDNA to predict the primary structure of the hormone. The preprotein of fGH is composed of 190 amino acids, and mature fGH is found to be extraordinarily small, having 171 or 173 amino acid residues. The estimated molecular masses of mature fGH are 19.4 to 19.7 kDa. This minimal size of fGH enabled an extended analysis of the essential domains and of amino acid residues required in hormone-specific activities. fGH conserves and shares 37 residues with 20 other vertebrate GHs. These common residues are seen to cluster in five distinct domains (GD1 to GD5). In human PL (hPL), which has low growth-promoting activity, 35 of these 37 residues are conserved, while the other 2 residues in the GD1 domain (Arg-16 and Leu-20) are replaced by Gln and Ala, respectively. In a less active variant of human GH, hGH-V, only 1 residue (His-21) of the 37 residues is replaced by Tyr. Besides these 3 residues, 6 other residues unique to the GHs and some PLs, that is, Ala-24 (GD1), Ser-54 (GD2), Ser-78 (GD3), Leu-106, Leu-116, and Asp-122 (GD4), appear to be important for specific binding of the GHs. The GD5 domain, at the carboxyl-terminal ends of the GHs is considered to be involved mainly in the formation and stabilization of GH molecules.
Interferon‐γ in vivo. Induction and loss of class IIMHC antigens and immature myelomonocytic cells in rat organs (1988)

The effects of recombinant rat interferon-gamma on class II major histocompatibility complex antigen expression in vivo were studied by immunohistology in LEW rats after continuous intravenous infusion for three days. Interferon-gamma administration led to a systemic induction of class II molecules in previously negative parenchymal and stromal cells. The induction patterns observed were highly reproducible, but not closely dose dependent within a 25-fold dose difference tested. However, the effect of interferon infusion differed profoundly in individual cell types, and appeared to be related to the differentiation stage of each cell population. Thus, epithelial cells like duct epithelia, urothelium or basal ear skin keratinocytes as well as endothelia in big vessels were strongly and easily induced for class II antigen expression. Parenchymal cells like cardiomyocytes and hepatocytes showed intermediate reactivity, while capillary endothelia, neurons in the brain, straight proximal kidney tubules or endocrine pancreatic islet cells did not express class II antigens. The induced expression was rapidly lost from most cells within one or two days after interferon withdrawal; the only exception occurred in keratinocytes. Long-term alterations were, however, still found 14 days after infusion. Interstitial class II-positive dendritic-shaped cells were increased in the organs and hepatic Kupffer cells carried class II antigens. On conventional histology all organs appeared perfectly normal at this date. After three days of interferon, cells of an immature myelomonocytic phenotype occluded medium-sized and small veins in all organs and occurred in granuloma-like lesions in the liver. Although these cells quickly disappeared after interferon withdrawal they might have been at least partially responsible for single deaths on day three. Our study provides a basis for testing the immunological in vivo function of parenchymal class II antigen expression and its differentiation-specific regulation.
Morphine-induced conformational changes in human monocytes, granulocytes, and endothelial cells and in invertebrate immunocytes and microglia are mediated by nitric oxide (1996)

We evaluated the contribution of nitric oxide (NO) to morphine-induced rounding of spontaneously activated (mobile) ameboid human monocytes, granulocytes, or arterial endothelial cells and invertebrate immunocytes and microglia. Morphine induced significant rounding and inactivation of ameboid cells within 20 min except for arterial endothelial cells, which became rounded 24 h after morphine exposure. The effects of morphine on cell conformation were blocked in the presence of N-nitro-L-arginine, a nitric oxide synthase inhibitor. Treatment of cells with the NO donor, sodium nitroprusside, induced cell rounding similar to that observed following morphine exposure, suggesting that NO release may mediate morphine-induced changes in cell conformation. The contribution of NO release to morphine-induced cell rounding was determined by direct evaluation of NO concentration in real-time using a NO-specific amperometric probe. Significant increases in NO concentration were observed 2 min after morphine stimulation, whereas morphine-induced NO release was markedly impaired by pretreatment with N-nitro-L-arginine or the opiate alkaloid antagonist, naloxone. In contrast, opioid peptides failed to induce NO release, consistent with our previous observations that demonstrated the failure of opioid peptides to promote cell rounding. Taken together, these data suggest that morphine-induced NO release may be mediated by activation of the opiate alkaloid-selective, opioid peptide-insensitive micro3 receptor, and that functional coupling of morphine to NO production has been conserved during evolution and may modulate cellular activation.