gebhart/patrepeval huggingface dataset:
Expression, Characterization, and Mutagenesis of theYersinia pestis Murine Toxin, a Phospholipase D Superfamily Member (1999)

A phospholipase D (PLD) superfamily was recently identified that contains proteins of highly diverse functions with the conserved motif HXKX4DX6G(G/S). The superfamily includes a bacterial nuclease, human and plant PLD enzymes, cardiolipin synthases, phosphatidylserine synthases, and the murine toxin from Yersinia pestis (Ymt). Ymt is particularly effective as a prototype for family members containing two conserved motifs, because it is smaller than many other two-domain superfamily enzymes, and it can be overexpressed. Large quantities of pure recombinant Ymt allowed the formation of diffraction-quality crystals for x-ray structure determination. Dimeric Ymt was shown to have PLD-like activity as demonstrated by the hydrolysis of phosphatidylcholine. Ymt also used bis(para-nitrophenol) phosphate as a substrate. Using these substrates, the amino acids essential for Ymt function were determined. Specifically, substitution of histidine or lysine in the conserved motifs reduced the turnover rate of bis(para-nitrophenol) phosphate by a factor of 10(4) and phospholipid turnover to an undetectable level. The role of the conserved residues in catalysis was further defined by the isolation of a radiolabeled phosphoenzyme intermediate, which identified a conserved histidine residue as the nucleophile in the catalytic reaction. Based on these data, a unifying two-step catalytic mechanism is proposed for this diverse family of enzymes.
A Specific STAT3-Binding Peptide Exerts Antiproliferative Effects and Antitumor Activity by Inhibiting STAT3 Phosphorylation and Signaling (2014)

STAT3 promotes the survival, proliferation, metastasis, immune escape, and drug resistance of cancer cells, making its targeting an appealing prospect. However, although multiple inhibitors of STAT3 and its regulatory or effector pathway elements have been developed, bioactive agents have been somewhat elusive. In this report, we report the identification of a specific STAT3-binding peptide (APTSTAT3) through phage display of a novel "aptide" library. APTSTAT3 bound STAT3 with high specificity and affinity (∼231 nmol/L). Addition of a cell-penetrating motif to the peptide to yield APTSTAT3-9R enabled uptake by murine B16F1 melanoma cells. Treatment of various types of cancer cells with APTSTAT3-9R blocked STAT3 phosphorylation and reduced expression of STAT targets, including cyclin D1, Bcl-xL, and survivin. As a result, APTSTAT3-9R suppressed the viability and proliferation of cancer cells. Furthermore, intratumoral injection of APTSTAT3-9R exerted potent antitumor activity in both xenograft and allograft tumor models. Our results offer a preclinical proof-of-concept for APTSTAT3 as a tractable agent for translation to target the broad array of cancers harboring constitutively activated STAT3.
Cutting Edge: Murine Dendritic Cells Require IL-15Rα to Prime NK Cells (2004)

NK cells protect hosts against viral pathogens and transformed cells, and dendritic cells (DCs) play important roles in activating NK cells. We now find that murine IL-15Ralpha-deficient DCs fail to support NK cell cytolytic activity and elaboration of IFN-gamma, despite the fact that these DCs express normal levels of costimulatory molecules and IL-12. By contrast, IL-15Ralpha expression on NK cells is entirely dispensable for their activation by DCs. In addition, blockade with anti-IL-15Ralpha and anti-IL-2Rbeta but not anti-IL-2Ralpha-specific Abs prevents NK cell activation by wild-type DCs. Finally, presentation of IL-15 by purified IL-15Ralpha/Fc in trans synergizes with IL-12 to support NK cell priming. These findings suggest that murine DCs require IL-15Ralpha to present IL-15 in trans to NK cells during NK cell priming.
Mitochondrial Localization of Superoxide Dismutase is Required for Decreasing Radiation-Induced Cellular Damage (2003)

We investigated the importance of mitochondrial localization of the SOD2 (MnSOD) transgene product for protection of 32D cl 3 hematopoietic cells from radiation-induced killing. Four plasmids containing (1) the native human copper/zinc superoxide dismutase (Cu/ZnSOD, SOD1) transgene, (2) the native SOD2 transgene, (3), the SOD2 transgene minus the mitochondrial localization leader sequence (MnSOD-ML), and (4) the SOD2 mitochondrial leader sequence attached to the active portion of the SOD1 transgene (ML-Cu/ZnSOD) were transfected into 32D cl 3 cells and subclonal lines selected by kanamycin resistance. Clonogenic in vitro radiation survival curves derived for each cell clone showed that Cu/ZnSOD- and MnSOD-ML-expressing clones had no increase in cellular radiation resistance (D0=0.89 +/- 0.01 and 1.08 +/- 0.02 Gy, respectively) compared to parent line 32D cl 3 (D0=1.15 +/- 0.11 Gy). In contrast, cell clones expressing either SOD2 or ML-Cu/ZnSOD were significantly radioresistant (D0=2.1 +/- 0.1 and 1.97 +/- 0.17 Gy, respectively). Mice injected intraesophageally with SOD2-plasmid/liposome (MnSOD-PL) complex demonstrated significantly less esophagitis after 35 Gy compared to control irradiated mice or mice injected intraesophageally with Cu/ZnSOD-PL or MnSOD-ML-PL. Mice injected with intraesophageal ML-Cu/ZnSOD-PL showed significant radioprotection in one experiment. The data demonstrate the importance of mitochondrial localization of SOD in the in vitro and in vivo protection of cells from radiation-induced cellular damage.
Effect of chemical deglycosylation of ricin A chain on the in vivo fate and cytotoxic activity of an immunotoxin composed of ricin A chain and anti-Thy 1.1 antibody. (1987)

The carbohydrate present on ricin A chain causes ricin A chain immunotoxins to be cleared rapidly in animals by the reticuloendothelial system. In an effort to overcome this problem we destroyed the carbohydrate on ricin A chain by treating it with a mixture of sodium metaperiodate and sodium cyanoborohydride and then linked the "deglycosylated" A chain to monoclonal anti-Thy 1.1 antibody. The deglycosylation procedure did not affect the ability of the A chain component of the immunotoxin to inhibit protein synthesis in a cell-free system or the capacity of the immunotoxin to inhibit protein synthesis in Thy-1.1 positive lymphoma cells in vitro. Immunotoxins prepared with deglycosylated A chain were cleared from the bloodstream of mice more slowly than native ricin A chain immunotoxins. The difference in the blood clearance rates of the two immunotoxins could be accounted for by a decreased entrapment of the deglycosylated ricin A chain immunotoxin by the liver. Both immunotoxins broke down in vivo with the appearance of free antibody in the bloodstream. The site of cleavage of the immunotoxin was possibly the liver because immunotoxins taken up by it rapidly became unreactive with antiricin but retained reactivity with anti-mouse immunoglobulin G suggesting that dissociation of the A chain from the antibody had occurred. The immunotoxins taken up by the liver were metabolized further and the acid insoluble radioactive metabolites gradually accumulated in the stomach, thyroid, and salivary gland. The deglycosylated ricin A chain immunotoxin should be a more effective antitumor agent in vivo because it is cleared from the blood more slowly and so has greater opportunity to localize within the tumor target.
Strong Binding in the DNA Minor Groove by an Aromatic Diamidine with a Shape That Does Not Match the Curvature of the Groove (2002)

A combination of biophysical techniques has been used to characterize the interaction of an antitrypanosomal agent, CGP 40215A, with DNA. The results from a broad array of methods (DNase I footprinting, surface plasmon resonance, X-ray crystallography, and molecular dynamics) indicate that this compound binds to the minor groove of AT DNA sequences. Despite its unusual linear shape that is not complementary to that of the DNA groove, a high binding affinity was observed in comparison with other similar but more curved diamidine compounds. The amidine groups at both ends of the ligand and the -NH groups on the linker are involved in extensive and dynamic H-bonds to the DNA bases. Complementary and consistent results were obtained from both the X-ray and molecular dynamics studies; both of these methods reveal direct and water-mediated H-bonds between the ligand and the DNA.
Threading dislocations in GaAs grown with free sidewalls on Si mesas (1994)

We have studied the mechanisms that determine the density and structure of threading dislocations (TDs) in GaAs on Si by growing GaAs films on continuous Si substrates and on 10–34-μm-wide Si mesas that provided free-sidewall growth. The effects of a soft ZnSe interlayer and of postgrowth annealing to 850 °C were also investigated. TD densities were accurately determined using large area plan-view transmission electron microscopy. Burgers vector analysis of the TDs showed that threading segments associated with both sessile 90° misfit dislocations and glissile 60° misfit dislocations were present after growth. A difference in dislocation structure between the annealed and unannealed samples was observed. It was also found that the dislocations were unaffected by proximity to free sidewalls and by the ZnSe interlayer. The results indicate that dislocation interactions during the early stages of growth determine the structure and density of TDs in as-grown films. It was also concluded that plastic relaxation of thermal mismatch strain during cooldown from the growth temperature does not strongly affect the TD density in the films. This is in contradiction to previous studies.
Biometric identification via eye movement scanpaths in reading (2011)

This paper presents an objective evaluation of various eye movement-based biometric features and their ability to accurately and precisely distinguish unique individuals. Eye movements are uniquely counterfeit resistant due to the complex neurological interactions and the extraocular muscle properties involved in their generation. Considered biometric candidates cover a number of basic eye movements and their aggregated scanpath characteristics, including: fixation count, average fixation duration, average saccade amplitudes, average saccade velocities, average saccade peak velocities, the velocity waveform, scanpath length, scanpath area, regions of interest, scanpath inflections, the amplitude-duration relationship, the main sequence relationship, and the pairwise distance between fixations. As well, an information fusion method for combining these metrics into a single identification algorithm is presented. With limited testing this method was able to identify subjects with an equal error rate of 27%. These results indicate that scanpath-based biometric identification holds promise as a behavioral biometric technique.
Fermi-Level-Pinning Defects in Highlyn-Doped Silicon (1997)

Based on first-principles calculations and analysis of x-ray absorption measurements, an unconventional mechanism is proposed for the saturation of carriers in highly $n$-doped Si. The mechanism is Fermi-level pinning from a new class of defect centers containing two separated but interacting dopant atoms with no associated Si vacancies. The number of such centers increases sharply at high doping levels. A simple model provides very good agreement with the maximum carrier concentrations observed in Si.
The amino acid composition of mammalian collagen and gelatin (1955)

hyde, but the most serious errors arise when small quantities of amino sugar are estimated in the presence
Effects of Lycopene and Sho-saiko-to on Hepatocarcinogenesis in a Rat Model of Spontaneous Liver Cancer (2001)

The Long-Evans Cinnamon (LEC) rat is a well-characterized model of spontaneous hepatocarcinogenesis. It has been shown that dietary administration of lycopene or the herbal medicine Sho-saiko-to (TJ-9) has anticarcinogenic activity, although the mechanism by which these products protect against carcinogenesis is not well known. We investigated the outcome of administration of lycopene and TJ-9 on the occurrence of hepatic neoplasia in LEC rats. A diet containing 0.005% lycopene (originally the product of tomato oleoresin containing 13% lycopene) and 1% TJ-9 (crude extracts of 7 herbs: bupleurum root, pinellia tuber, scutellaria root, jujube fruit, ginseng root, glycyrrhiza root, and ginger rhizome) was administered from 6 weeks of age until the rats were sacrificed at 76 weeks of age, at which time most of the nontreated animals were known to have hepatocellular carcinoma (HCC). Development of HCC in treated groups was analyzed histologically by comparison with untreated controls. Glutathione S-transferase placental form (GST-P) was analyzed by an immunohistochemical method. Concentration of copper, iron, and zinc, which appear to play a role in hepatocarcinogenesis in LEC rats, was analyzed. The percent areas of HCC in the liver specimens of control, lycopene, and TJ-9 groups were 17.9 +/- 17.1%, 27.2 +/- 20.8%, and 27.6 +/- 18.4%, respectively. These intergroup differences were not significant. The percent area, number of areas, and mean size of area staining positively for GST-P revealed no significant differences between the groups. The number of GST-P-positive areas within the HCC lesions was greater in the TJ-9 group than in the control or lycopene group (p = 0.024 and p = 0.012, respectively). The study also demonstrated a lower concentration of iron in livers of the lycopene group than the control group (p = 0.019). There were no differences in serum alpha-fetoprotein levels or the cumulative survival rates between the groups. In conclusion, long-term administration of lycopene or TJ-9 did not reduce the risk of hepatocarcinogenesis in LEC rats.
Inverse agonists and neutral antagonists at µ opioid receptor (MOR): possible role of basal receptor signaling in narcotic dependence (2001)

The mu opioid receptor, MOR, displays spontaneous agonist-independent (basal) G protein coupling in vitro. To determine whether basal MOR signaling contributes to narcotic dependence, antagonists were tested for intrinsic effects on basal MOR signaling in vitro and in vivo, before and after morphine pretreatment. Intrinsic effects of MOR ligands were tested by measuring GTPgammaS binding to cell membranes and cAMP levels in intact cells. beta-CNA, C-CAM, BNTX, and nalmefene were identified as inverse agonists (suppressing basal MOR signaling). Naloxone and naltrexone were neutral antagonists (not affecting basal signaling) in untreated cells, whereas inverse agonistic effects became apparent only after morphine pretreatment. In contrast, 6alpha- and 6beta-naltrexol and -naloxol, and 6beta-naltrexamine were neutral antagonists regardless of morphine pretreatment. In an acute and chronic mouse model of morphine-induced dependence, 6beta-naltrexol caused significantly reduced withdrawal jumping compared to naloxone and naltrexone, at doses effective in blocking morphine antinociception. This supports the hypothesis that naloxone-induced withdrawal symptoms result at least in part from suppression of basal signaling activity of MOR in morphine-dependent animals. Neutral antagonists have promise in treatment of narcotic addiction.
Circulating CSF-1 Promotes Monocyte and Macrophage Phenotypes that Enhance Lupus Nephritis (2009)

Macrophages mediate kidney disease and are prominent in a mouse model (MRL-Fas(lpr)) of lupus nephritis. Colony stimulating factor-1 (CSF-1) is the primary growth factor for macrophages, and CSF-1 deficiency protects MRL-Fas(lpr) mice from kidney disease and systemic illness. Whether this renoprotection derives from a reduction of macrophages and whether systemic CSF-1, as opposed to intrarenal CSF-1, promotes macrophage-dependent lupus nephritis remain unclear. Here, we found that increasing systemic CSF-1 hastened the onset of lupus nephritis in MRL-Fas(lpr) mice. Using mutant MRL-Fas(lpr) strains that express high, moderate, or no systemic CSF-1, we detected a much higher tempo of kidney disease in mice with the highest level of CSF-1. Furthermore, we uncovered a multistep CSF-1-dependent systemic mechanism central to lupus nephritis. CSF-1 heightened monocyte proliferation in the bone marrow (SSC(low)CD11b(+)), and these monocytes subsequently seeded the circulation. Systemic CSF-1 skewed the frequency of monocytes toward "inflammatory" (SSC(low)CD11b(+)Ly6C(high)) and activated populations that homed to sites of inflammation, resulting in a more rapid accumulation of intrarenal macrophages (CD11b(+)CSF-1R(+) or CD68(+)) that induced apoptosis of tubular epithelial cells, damaging the kidney. In humans, we found increased levels of CSF-1 in the serum, urine, and kidneys of patients with lupus compared with healthy controls. Furthermore, serum and urine CSF-1 levels correlated with lupus activity, and intrarenal CSF-1 expression correlated with the histopathology activity index of lupus nephritis. Taken together, circulating CSF-1 is a potential therapeutic target for lupus nephritis.
Growth and genetic stability of the ts-1 mutant of respiratory syncytial virus at restrictive temperatures (1976)

An in vitro study was performed to define in greater detail those factors which favored the growth of the ts-1 mutant of respiratory syncytial virus under restrictive conditions and the emergence of genetically altered virus with decreased temperature sensitivity. Replication of ts-1 occurred at each of the restrictive temperatures of 37, 38, and 39 C, even through plaque formation was not observed. The level of virus growth under restrictive conditions was inversely related to the incubation temperature and directly related to the multiplicity of infection. These relationships appeared to reflect the effect of restrictive temperature in reducing the quantity of virus produced and released from an infected cell. Under restrictive conditions the production of genetically altered virus which exhibited reduced temperature sensitivity was directly related to the multiplicity of infection and inversely related to temperature. Production of genetically altered virus was not observed under permissive conditions.
Human purine nucleoside phosphorylase cDNA sequence and genomic clone characterization (1984)

The isolation of a cDNA clone containing the complete coding region for human purine nucleoside phosphorylase (PNP) has been described previously. In this report we present the nucleotide sequence of this cDNA clone and compare the derived amino acid sequence, encoding a protein of 32 kilodaltons, with the published amino acid composition. Using a fragment of the cDNA clone as a probe, human PNP genomic clones from a bacteriophage lambda library have been isolated and the structural organization of the wild type PNP gene determined.
Development of highly selective and sensitive probes for hydrogen peroxideElectronic supplementary information (ESI) available: general methods. See http://www.rsc.org/suppdata/cc/b3/b309393j/ (2003)

Probes that react specifically with hydrogen peroxide to release chromophoric or fluorescent reporter groups were designed and synthesized.
Mechanisms of Fast Ripples in the Hippocampus (2004)

Hippocampal fast ripples (FRs) have been associated with seizure onset in both human and experimental epilepsy. To characterize the mechanisms underlying FR oscillations (200-600 Hz), we studied activity of single neurons and neuronal networks in rat hippocampal slices in vitro. The correlation between the action potentials of bursting pyramidal cells and local field potential oscillations suggests that synchronous onset of action potential bursts and similar intrinsic firing patterns among local neurons are both necessary conditions for FR oscillations. Increasing the fidelity of individual pyramidal cell spike train timing by blocking accommodation dramatically increased FR amplitude, whereas blockade of potassium conductances decreased the fidelity of action potential timing in individual pyramidal cell action potential bursts and decreased FR amplitude. Blockade of ionotropic glutamate receptors desynchronized onset of action potential bursts in individual pyramidal cells and abolished fast ripples. Thus, synchronous burst onset mediated by recurrent excitatory synaptic transmission and similar intrinsic spike timing mechanisms in neighboring pyramidal cells are necessary conditions for FR oscillations within the hippocampal network.
Construction of protein analogs by site-specific condensation of unprotected fragments (1992)

The extreme sensitivity to periodate of 1-amino, 2-hydroxy compounds permits the selective conversion of N-terminal serine and threonine to an aldehydic group. We have used this reaction to construct analogues of human granulocyte colony stimulating factor (G-CSF) by allowing such oxidized peptides to react with others that have had a hydrazide derivative attached to the C-terminus by reversed proteolysis. Two recombinant analogues of G-CSF were used as starting materials. Both had only a single lysine residue (at position 62 and 75, respectively) followed immediately by a serine. Digestion of each analogue by the lysine-specific protease from Achromobacter lyticus gave two fragments, one of which could be N-terminally oxidized and the other converted to the C-terminal hydrazide derivative by reversed proteolysis using the same enzyme. After preliminary studies with model peptides, we first reacted the corresponding peptide pairs together and then, in order to eliminate the 64-74 disulfide loop, fragment 1-62 from the first analogue with fragment 76-174 from the second. Reactions are efficient (up to 80% product based on the oxidized fragment) and take place under very mild conditions. The hydrazone bond can easily be stabilized by reduction with NaBH3CN. This method represents a new, reasonably general route for the construction of large protein chimeras of precisely controlled structure.
Electron transfer in ruthenium-modified cytochromes c. .sigma.-tunneling pathways through aromatic residues (1993)

The rates of intramolecular electron-transfer (ET) reactions from the ferroheme to bis(2,2'-bipyridine)(imidazole)-ruthenium(II1) complexes bound to genetically engineered histidines (58 and 66) on the surface of yeast iso-1-cytochrome c (cyt c) have been measured by using a laser flashquench technique. The crystal structure of&#13;\nthe wild-type protein indicates that the ET pathways involve aromatic side chains: Ru(His58)cyt c includes&#13;\na bridging tryptophan at position 59, and Ru(His66)cyt c has a tyrosine at 67. A variant in which the bridging&#13;\nTyr67 in the His66 mutant had been replaced with a phenylalanine also was examined. The Fe^2+ → Ru^(3+)ET&#13;\nrate constants (25 °C, pH 7.0) are as follows: 5.2(5) × l0^4 (ΔE° = 0.69(5)), Ru(His58)cyt c; 1.0(1) × 10^6&#13;\n(ΔE° = 0.72(5)), Ru(His66)cyt c; and 3.1(3) × l0^6 s^-1 (ΔE° = 0.77(5) eV), Ru(His66Phe67)cyt c. The experimentally derived electronic coupling constants [H_AB(His66)= 0.014; H_AB(HiS66)= 0.060 cm-1 are in closer agreement with the lengths of a-tunneling pathways than with the direct donor-acceptor distances, and there is no indication that the u orbitals of intervening groups enhance any of these couplings. Maximum ET rates in the modified cytochromes drop by 2 orders of magnitude for every 6.3-A increase in the a-tunneling length. Analysis of the results also suggests that an internal water molecule in Ru(His66Phe67)cyt c plays a role in linking the Ru(His66) group to the heme.
New methods for adaptation of quadrature modulators and demodulators in amplifier linearization circuits (1997)

Imperfections in analog quadrature modulators (QMs) and demodulators-gain and phase imbalance and DC offset-have a devastating effect on amplifier linearization circuits. Correction circuits have a simple structure, but their parameters must be adjusted adaptively. This paper introduces two new methods for such an adaptation. The first is based on a training sequence consisting of a tone at one or more amplitudes, and the second needs no training sequence at all. They are faster and more robust than previously published methods.