gebhart/patrepeval huggingface dataset:
Chromosomal protein HMG-17. Complete human cDNA sequence and evidence for a multigene family. (1986)

Antibodies elicited against chromosomal protein HMG-17, purified from calf, were used to screen a human lambda gt11 cDNA expression library and isolate the full length cDNA coding for this protein. Sequence analysis reveals that the nucleotide distribution along this cDNA is highly asymmetric. The amino acid sequence, deduced from the reading frame, reveals that the human HMG-17 is, respectively, 96 and 92% homologous with the calf and chicken protein. The amino acid substitution are conservative suggesting evolutionary constraints on the conformation of the protein. The human genome contains 35-50 HMG-17 gene copies which, as revealed by Southern analysis, are distributed at several loci. Northern analysis of total RNA isolated from 3 human cell lines, indicates that each cell contains a single-size mRNA coding for this protein. Nucleotide sequences which cross-hybridize, under stringent conditions, with the human HMG-17 cDNA are present in the genome of rodents and absent from the genomes of sea urchin, Drosophila, and yeast. The availability of a probe for the HMG-17 gene may help elucidate the cellular role of this protein which may confer specific conformations to transcribable regions in the genome.
Platelet, Not Endothelial, P-Selectin Is Required for Neointimal Formation After Vascular Injury (2005)

Platelet P-selectin expression, but not endothelial P-selectin, plays a crucial role in the development of neointimal formation after arterial injury, and therapeutic strategies targeting leukocyte-platelet interactions could be effective in inhibiting restenosis.
Catalytic Electrophilic Halogenation of Silyl‐Protected and Terminal Alkynes: Trapping Gold(I) Acetylides vs. a Brønsted Acid‐Promoted Reaction (2012)

Abstract In the presence of a cationic gold(I) catalyst and N ‐halosuccinimide, both trimethylsilyl‐protected and terminal alkynes are converted into alkynyl halides. Further experiments showed that silyl‐protected alkynes undergo electrophilic iodination and bromination under Brønsted acid catalysis, whilst terminal alkynes require a cationic gold catalyst. The former reactions probably proceed via activation of the electrophile, whilst the latter reactions proceed via a gold(I) acetylide intermediate. Gold‐catalysed halogenation was further combined with gold‐catalysed hydration and subsequent annulation to provide convenient routes to iodomethyl ketones and five‐membered aromatic heterocycles.
A One-Pot, High-Yield Synthesis of a Paramagnetic Nickel Square from Divergent Precursors by Anion Template Assembly (1999)

A paramagnetic Ni-containing molecular square has been synthesized in high yield from divergent precursors. An X-ray structure (shown in the picture) reveals the presence of an encapsulated tetrafluoroborate anion, which appears to be a requisite condition for the formation of the cyclic oligomer.
The Application of Solid Phase Microextraction in the Analysis of Organophosphorus Pesticides in a Food Plant (1998)

A SPME method for the determination of organophosphorus pesticide residues in a local food plant, Chrysanthemum coronarium, was established. Pesticide residues were extracted by SPME fiber (with 100 μm poly(dimethylsiloxane) coating) from a biphasic water/plant tissues mixture and determined by GC-FPD. An equilibrium model was derived for the system and revealed that pesticide recoveries were related to the water:plant tissues ratio, f, and the partition coefficient, KWV, for the distribution of pesticides between the aqueous phase and the plant tissues. The model was verified by four organophosphorus pesticides, namely phorate, diazinon, methyl parathion, and ethion. The best fitted KWV values (P < 0.05) for the pesticides were found to be 4.73 ± 0.32 × 10-2 (phorate); 1.11 ± 0.10 × 10-1 (diazinon); 9.18 ± 0.95 × 10-2 (methyl parathion); and 8.21 ± 1.28 × 10-3 (ethion). Remarkable correlation between the KWV of the organophosphorus pesticides and their octanol/water partition coefficients, KOW, was also established.
A Randomized Controlled Trial to Evaluate S-Caine Patch™ for Reducing Pain Associated with Vascular Access in Children (2005)

This study demonstrated that a 20-min application of the S-Caine Patch is effective in lessening pain associated with venipuncture procedures. Adverse events after S-Caine Patch application were mild and transient.
Mechanism of Inhibition of Protein-tyrosine Phosphatases by Vanadate and Pervanadate (1997)

Vanadate and pervanadate (the complexes of vanadate with hydrogen peroxide) are two commonly used general protein-tyrosine phosphatase (PTP) inhibitors. These compounds also have insulin-mimetic properties, an observation that has generated a great deal of interest and study. Since a careful kinetic study of the two inhibitors has been lacking, we sought to analyze their mechanisms of inhibition. Our results show that vanadate is a competitive inhibitor for the protein-tyrosine phosphatase PTP1B, with a Ki of 0.38+/-0.02 microM. EDTA, which is known to chelate vanadate, causes an immediate and complete reversal of the inhibition due to vanadate when added to an enzyme assay. Pervanadate, by contrast, inhibits by irreversibly oxidizing the catalytic cysteine of PTP1B, as determined by mass spectrometry. Reducing agents such as dithiothreitol that are used in PTP assays to keep the catalytic cysteine reduced and active were found to convert pervanadate rapidly to vanadate. Under certain conditions, slow time-dependent inactivation by vanadate was observed; since catalase blocked this inactivation, it was ascribed to in situ generation of hydrogen peroxide and subsequent formation of pervanadate. Implications for the use of these compounds as inhibitors and rationalization for some of their in vivo effects are considered.
Fabrication of a Nonvolatile Lookup-Table Circuit Chip Using Magneto/Semiconductor-Hybrid Structure for an Immediate-Power-Up Field Programmable Gate Array (2009)

Series connection of metal-oxide semiconductor transistors and spin-injection-writable magneto-resistive junction devices based on logic-in-memory architecture realizes both programmable logic operation and nonvolatile storage function. A lookup table (LUT) circuit in field-programmable gate array fabricated by a 0.14µm magneto/semiconductor-hybrid process achieves area reduction by 2/3 compared to a conventional static random-access-memory-based one, and realizes complete standby power reduction.
FSSA: a novel method for identifying functional signatures from structural alignments (2005)

We propose a method for accurate functional annotation, based on identification of functional signatures from structural alignments (FSSA) using the Structural Classification of Proteins (SCOP) database. The FSSA method is superior at function discrimination and classification compared with several methods that directly inherit functional annotation information from homology inference, such as Smith-Waterman, PSI-BLAST, hidden Markov models and structure comparison methods, for a large number of structural fold families. Our results indicate that the contributions of amino acid residue types and positions to structure and function are largely separable for proteins in multi-functional fold families.
The role of biologically active peptides in tissue repair using umbilical cord mesenchymal stem cells (2012)

The role of bioactive compounds in wound repair is critical. The preliminary work described herein includes the study of the effects of second degree burns in a Rex rabbit model and the action of human umbilical cord cells on the regulation and secretion of bioactive compounds. When applied on blood scaffolds as heterograft matrices, fibroblasts proliferate from these primary cultures and release biologically active peptides under tight control. Our work in progress indicates that mesenchymal stem cell (MSC)-mediated therapy provides better quality and more efficient burn reepithelialization of injured tissues by controlling the release of these peptides. Improvement of wound aesthetics is achieved in less time than without MSC-mediated therapy. Well-organized epidermal regeneration and overall better quality of reepithelialization, with no rejection, can be demonstrated consistently with periodic biopsies. Our studies indicate that MSCs have the capacity to produce, regulate, and deliver biologically active peptides that result in superior regeneration, compared with conventional treatments.
Monoclonal Antibodies to Cytochromes P450 (2003)

Monoclonal antibodies (MAbs) are produced by the “hybridoma” technology developed by Kohler and Milstem in 1975 (1), which is a major and defining achievement of modern biology (2). The hybridoma methodology producmg MAbs was derived from the clonal selection theory of Burnet and colleagues (3), which stated that each B-lymphocyte antibody-forming cell and its progeny is committed to the production of a single, unique type of antibody molecule. This chemically defined MAb molecule specifically recognizes a single antigenic determinant or “epltope” on the protein antigen, which, in our studies, is a specific individual cytochrome P450 (P450). This specificity of the MAb continues for the lifetime of the hybridoma cell, which can be frozen or grown in culture indefinitely, and with its progeny, is a immortal source of an epitope-specific MAb. The MAbs are chemically defined, pure, epitope specific, and reproducible for limitless generations of cells.
Human Homologue of the Drosophila Discs Large Tumor Suppressor Binds to p56 Tyrosine Kinase and Shaker Type Kv1.3 Potassium Channel in T Lymphocytes (1997)

Human homologue of the Drosophila discs large tumor suppressor protein (hDlg) belongs to a newly discovered family of proteins termed MAGUKs that appear to have structural as well as signaling functions. Consistent with the multi-domain organization of MAGUKs, hDlg consists of three copies of the PDZ (PSD-95/Discs large/zO-1) domain, an SH3 motif, and a guanylate kinase-like domain. In addition, the hDlg contains an amino-terminal proline-rich domain that is absent in other MAGUKs. To explore the role of hDlg in cell signaling pathways, we used human T lymphocytes as a model system to investigate interaction of hDlg with known tyrosine kinases. In human T lymphocyte cell lines, binding properties of hDlg were studied by immunoprecipitation, immunoblotting, and immune complex kinase assays. Our results show that protein tyrosine kinase activity is associated with the immunoprecipitates of hDlg. Immunoblotting experiments revealed that the immunoprecipitates of hDlg contain p56lck, a member of the Src family of tyrosine kinases. The specificity of the interaction is demonstrated by the lack of p59fyn tyrosine kinase and phosphotidylinositol 3-kinase in the hDlg immunoprecipitates. Direct interaction between hDlg and p56lck is demonstrated using glutathione S-transferase fusion proteins of hDlg and recombinant p56lck expressed in the baculovirus-infected Sf9 cells. The p56lck binding site was localized within the amino-terminal segment of hDlg containing proline-rich domain. In addition, we show in vivo association of hDlg with Kv1.3 channel, which was expressed in T lymphocytes as an epitope-tagged protein using a vaccinia virus expression system. Taken together, these results provide the first evidence of a direct interaction between hDlg and p56lck tyrosine kinase and suggest a novel function of hDlg in coupling tyrosine kinase and voltage-gated potassium channel in T lymphocytes.
On the Use of Stable Organic Nitroxyl Radicals for the Oxidation of Primary and Secondary Alcohols (1996)

This article reviews the oxidation of primary and secondary alcohols using nitroxyl radicals from the first publication in which this reaction was described in 1965. A variety of stoichiometric and catalytic methods is discussed, with reactions in organic solvents, under biphasic conditions as well as in water. Mechanistic studies and general experimental procedures are included. The high regioselectivity for the oxidation of primary alcohols that can be achieved in the presence of secondary alcohols is emphasised.
Congestive Heart Failure (1998)

Congestive heart failure (CHF) patients who exercise regularly can increase exercise tolerance, decrease dyspnea and fatigue, reduce the risk of arrhythmias, and improve quality of life. Initial stress testing is important for assessing a patient's physiologic response to exercise and for establishing a target heart rate for an individualized exercise program. Patients may need to begin aerobic exercise with interval training and progress slowly. Strength exercise is also useful. Exercise used along with the customarily prescribed CHF medications improves symptoms more than either modality alone.
Macroporous hydrogel membranes for a hybrid artificial pancreas. I. Synthesis and chamber fabrication (1983)

We report development of special macroporous semipermeable membranes and diffusion chambers made of polymerized 2-hydroxyethyl methacrylate (pHEMA), synthesized specifically to enclose living insulin-producing pancreatic islet cells for the treatment of diabetes. This material was selected to minimize the fibrotic encapsulation which has limited hybrid artificial pancreas efforts with other membranes, including Millipore and Nuclepore filters. The pore density and pore size distribution were dependent on the ratio of water to HEMA monomer and also on the crosslinker (EGDMA) concentration. A macroporous membrane resulted only when the ratio of water/HEMA monomer was greater than 50%. 125I-insulin permeability was studied in vitro. A technique is also described to fuse the membranes to form diffusion chambers used for implantation into diabetic rats.
Gardiquimod: A Toll-Like Receptor-7 Agonist That Inhibits HIV Type 1 Infection of Human Macrophages and Activated T Cells (2013)

Immune response modifiers are being studied as therapeutic agents for viral infections and cancer. These molecules include agonists for the Toll-like receptors (TLR), a family of innate immune receptors. TLR7 and 8, located in cellular endosomes, bind single-stranded RNA characteristic of viral genomes, and trigger intracellular signaling pathways that induce inflammatory cytokines and antiviral innate immune factors. We studied the anti-HIV-1 effects of gardiquimod, a specific TLR7 agonist when used at concentrations below 10 μM, in macrophages and activated peripheral blood mononuclear cells (PBMCs). Gardiquimod, added prior to or within 2 days after infection with X4, R5, or dual-tropic (R5/X4) strains of HIV-1, significantly reduced infection in these cells. Cocultures of activated PBMCs added to gardiquimod-treated and HIV-1-exposed macrophages demonstrated minimal HIV-1 replication for up to 10 days, suggesting that gardiquimod inhibited activated PBMCs viral amplification from HIV-1-exposed macrophages. Gardiquimod treatment of both activated PBMCs and macrophages induced interferon-alpha (IFN-α) transcription within hours of addition, and sustained IFN-α protein secretion for several days. Treatment of cells with a peptide inhibitor to the MyD88 adaptor protein blocked the induction of IFN-α by gardiquimod, and partially reversed the anti-HIV effects in activated PBMCs. Blocking the IFN-α receptor with a neutralizing antibody also reduced the anti-HIV effect of gardiquimod. Gardiquimod inhibited HIV-1 reverse transcriptase, an early step in the life cycle of HIV-1. These findings suggest that gardiquimod, functioning as both an immune system modifier and a reverse transcriptase inhibitor, could be developed as a novel therapeutic agent to block systemic and mucosal transmission of HIV-1.
Maturation of Human Embryonic Stem Cell–Derived Pancreatic Progenitors Into Functional Islets Capable of Treating Pre-existing Diabetes in Mice (2012)

Diabetes is a chronic debilitating disease that results from insufficient production of insulin from pancreatic β-cells. Islet cell replacement can effectively treat diabetes but is currently severely limited by the reliance upon cadaveric donor tissue. We have developed a protocol to efficiently differentiate commercially available human embryonic stem cells (hESCs) in vitro into a highly enriched PDX1+ pancreatic progenitor cell population that further develops in vivo to mature pancreatic endocrine cells. Immature pancreatic precursor cells were transplanted into immunodeficient mice with streptozotocin-induced diabetes, and glycemia was initially controlled with exogenous insulin. As graft-derived insulin levels increased over time, diabetic mice were weaned from exogenous insulin and human C-peptide secretion was eventually regulated by meal and glucose challenges. Similar differentiation of pancreatic precursor cells was observed after transplant in immunodeficient rats. Throughout the in vivo maturation period hESC-derived endocrine cells exhibited gene and protein expression profiles that were remarkably similar to the developing human fetal pancreas. Our findings support the feasibility of using differentiated hESCs as an alternative to cadaveric islets for treating patients with diabetes.
Estimation of the Stoichiometric Air-Fuel Ratio in Liquefied Petroleum Gas-Injected Engines (2002)

&lt;div class="htmlview paragraph"&gt;Air-fuel ratio control in gasoline engines has so far relied upon the fact that the stoichiometric air-fuel ratio of gasoline is an identified constant, largely thanks to its consistent chemical composition. In the case of Liquefied Petroleum Gas (LPG), chemical composition is subject to high variability due to geological and economic factors, amongst others. The implication of this variability is unpredictable stoichiometric air-fuel ratio of the fuel supply within any given vehicle, and ultimately degraded control of air-fuel ratio. This paper addresses the problem of stoichiometric air-fuel ratio estimation by evaluating the measurement and modeling of the relative permittivity of fuel, and also the method of iterative computation. For the estimation method proposed in this paper, simulation results are presented to demonstrate its effectiveness.&lt;/div&gt;
Knowledge acquisition, consistency checking andconcurrency control for Gene Ontology (GO) (2003)

Gene Ontology in Protégé-2000 and the associated code are located at http://smi.stanford.edu/projects/helix/gokbms/. Protégé-2000 is available from http://protege.stanford.edu.
OBSERVATIONS CONCERNING THE ACTION OF 5‐HYDROXYTRYPTAMINE ON THE PERISTALTIC REFLEX (1958)

In isolated guinea-pig intestine 5-hydroxytryptamine increased the longitudinal muscle contractions in response to acetylcholine while the ganglionic action of nicotine was first facilitated and then blocked. Phenyldiguanide, veratrine, veratridine and protoveratrine, like 5-hydroxytryptamine, depressed the response to nicotine, leaving that to acetylcholine unaffected.The sensory stimulants, like 5-hydroxytryptamine, facilitated the peristaltic reflex when applied to the mucosa, and abolished it when applied to the serosa. Preceding the block, the initial effect of low concentrations of 5-hydroxytryptamine applied to the serosa was a short stimulation of peristalsis.Concentrations of 5-hydroxytryptamine which had an approximately equal stimulant action (mucosal 1 to 4 x 10(-6), serosal 2 to 8 x 10(-8)) were tested when various parts of the reflex arc were blocked. During block by procaine introduced into the lumen, mucosal application of 5-hydroxytryptamine re-established peristalsis, but serosal application of 5-hydroxytryptamine had no effect. During block by hexamethonium or atropine present in the bath, 5-hydroxytryptamine restored peristalsis more effectively by serosal application than by mucosal application. During block by serosal application of 5-hydroxytryptamine, morphine, phenoxybenzamine or dihydroergotamine, mucosal application of 5-hydroxytryptamine restored the peristaltic reflex while serosal application had no effect. During block by 2-bromo-lysergic acid diethylamide or lysergic acid diethylamide acting from the serosal surface, 5-hydroxytryptamine had no effect whether acting on the mucosal or on the serosal surface.It is concluded that 5-hydroxytryptamine facilitates the peristaltic reflex at two sites: when introduced into the lumen it stimulates mucosal sensory receptors; when acting from the serosal surface it sensitizes the muscle to the transmitter acetylcholine. There is also a transient stimulant action on the ganglia which is soon followed by inhibition; this indicates that 5-hydroxytryptamine applied to the serosa abolishes peristalsis by ganglion block.
Inactivation of small Rho GTPases by the multifunctional RTX toxin from Vibrio cholerae (2007)

Many bacterial toxins target small Rho GTPases in order to manipulate the actin cytoskeleton. The depolymerization of the actin cytoskeleton by the Vibrio cholerae RTX toxin was previously identified to be due to the unique mechanism of covalent actin cross-linking. However, identification and subsequent deletion of the actin cross-linking domain within the RTX toxin revealed that this toxin has an additional cell rounding activity. In this study, we identified that the multifunctional RTX toxin also disrupts the actin cytoskeleton by causing the inactivation of small Rho GTPases, Rho, Rac and Cdc42. Inactivation of Rho by RTX was reversible in the presence of cycloheximide and by treatment of cells with CNF1 to constitutively activate Rho. These data suggest that RTX targets Rho GTPase regulation rather than affecting Rho GTPase directly. A novel 548-amino-acid region of RTX was identified to be responsible for the toxin-induced inactivation of the Rho GTPases. This domain did not carry GAP or phosphatase activities. Overall, these data show that the RTX toxin reversibly inactivates Rho GTPases by a mechanism distinct from other Rho-modifying bacterial toxins.
Human T-cell clonal anergy is induced by antigen presentation in the absence of B7 costimulation. (1993)

The maximal T-cell response to its antigen requires presentation of the antigen by a major histocompatibility complex class II molecule as well as the delivery of one or more costimulatory signals provided by the antigen-presenting cell (APC). Although a number of candidate molecules have been identified that are capable of delivering a costimulatory signal, increasing evidence suggests that one such critical pathway involves the interaction of the T-cell surface antigen CD28 with its ligand B7, expressed on APCs. In view of the number of potential costimulatory molecules that might be expressed on the cell surface of APCs, artificial APCs were constructed by stable transfection of NIH 3T3 cells with HLA-DR7, B7, or both. Here, we show that in a human antigen-specific model system, when tetanus toxoid peptide antigen is presented by cells cotransfected with HLA-DR7 and B7, optimal T-cell proliferation and interleukin 2 production result. In contrast, antigen presentation, in the absence of B7 costimulation, results in T-cell clonal anergy. These results demonstrate that it is possible to induce antigen-specific clonal tolerance in human T cells that have been previously sensitized to antigen. The artificial antigen-presenting system provides a useful model for the investigation of the biochemical events involved in the generation of tolerance and for the study of signals necessary to overcome tolerance.