gebhart/patrepeval huggingface dataset:
Effect of differences in antibody and complement requirements on phagocytic uptake and intracellular killing of "c" protein-positive and -negative strains of type II group B streptococci (1987)

The influence of antibody and complement on the polymorphonuclear leukocytic uptake and killing of type II group B streptococci (GBS) was examined with 11 adult sera and three type II strains possessing the trypsin-resistant and trypsin-sensitive components (II/TR+TS) of the "c" (formerly Ibc) protein or two type II strains lacking both components (II/no c) of the c protein. All tested sera mediated a greater than 1 log10 reduction in colony-forming units (CFUR) of a type II/no c strain, even in the absence of measurable type-specific antibody (less than 1.08 micrograms/ml), but only 5 of 11 mediated a greater than 1 log10 CFUR of any type II/TR/TS strain, even in the presence of moderate levels of type-specific antibody. The classical pathway of complement activation appeared to be more important than the alternative pathway, and even absorbed or immunoglobulin G (IgG)-depleted serum (IgG, 10 mg/dl) mediated a greater than 1 log10 CFUR without magnesium ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (magnesium EGTA) chelation. Chelation with magnesium EGTA reduced the CFUR in 4 of 11 test sera and greatly reduced the CFUR in absorbed or IgG-depleted sera for type II/no c strains. Despite variation in the phagocytic killing of two representative strains of type II GBS, both strains were well phagocytized, as measured by radiolabeled bacterial uptake or electron microscopy. This study suggested that poorly killed type II/TR+TS GBS were easily phagocytized but apparently resisted intracellular killing.
Bovine brain and pituitary fibroblast growth factors: comparison of their abilities to support the proliferation of human and bovine vascular endothelial cells. (1983)

The mitogenic effects of brain and pituitary fibroblast growth factors (FGF) on vascular endothelial cells derived from either human umbilical vein or bovine aortic arch have been compared. Both brain and pituitary FGF are mitogenic for low density human umbilical endothelial (HUE) cell cultures maintained on either fibronectin- or laminin-coated dishes or on biomatrices produced by cultured cells such as bovine corneal endothelial cells or the teratocarcinoma cell line PF-HR-9. Pituitary FGF triggered the proliferation of HUE cells at concentrations as low as 0.25 ng/ml, with a half-maximal response at 0.55 ng/ml and optimal effect at 2.5 to 5 ng/ml. It was 50,000-fold more potent than commercial preparations of endothelial cell growth factor and 40 times more potent than commercial preparations of pituitary FGF. Similar results were observed when the effect of pituitary FGF was tested on low density cultures of adult bovine aortic endothelial cells. When the activity of brain and pituitary FGF on low density HUE cell cultures was compared, both mitogens were active. To confirm the presence in brain extract of both acidic and neutral, as well as of basic mitogen, for HUE cells, brain tissues were extracted at acidic (4.5), neutral (7.2), and basic (8.5) pH. The three types of extracts were equally potent in supporting the proliferation of either HUE or adult bovine aortic endothelial cells. When the various extracts were absorbed at pH 6.0 on a carboxymethyl Sephadex C-50 column, the neutral and basic extracts had an activity after adsorption similar to that of unadsorbed extracts. In contrast, extracts prepared at pH 4.5 lost 90-95% of their activity which was recovered in the adsorbed fraction containing FGF.
Synthesis of deuterium labelled penicillamine and its use for the assignment of the 1H NMR spectra of two cyclic enkephalin analogs (1987)

Abstract The synthesis of D,L ‐[4,4′‐ 2 H 6 ]penicillamine ( D,L ‐[ 2 H 6 ]Pen) and its incorporation into the cyclic, disulfide‐containing peptides, [ D ‐Pen 2 , D ‐[ 2 H 6 ]Pen 5 ]enkephalin (DPDPE) and [ D ‐Pen 2 , L ‐[ 2 H 6 ]Pen 5 ]enkephalin (DPLPE), both highly δ opioid receptor‐selective analogs, are described. The deuterium‐labelled peptides allowed the assignment of the four Pen methyl group resonances in each of the corresponding unlabelled peptides to specific Pen residues.
Effect of amino acids on the expression of antiviral activity of different types of human interferon. I. Effect of single amino acids. (1985)

It has been observed that certain amino acids may influence the antiviral activity of different types of human interferon (IFN). The effect may be enhancing or inhibitory. A qualitative survey is provided on all three types of human IFN using 23 different amino acids. A more detailed study was carried out with 10 amino acids which proved to be active towards HuIFN-alpha. Their influences on the synergistic antiviral effects of HuIFN-alpha and HuIFN-gamma were also investigated. The dose-dependence curves of their effects on HuIFN-alpha were established.
Ethylene glycol-mediated synthesis of metal oxide nanowires (2004)

A simple and convenient method has been demonstrated for large-scale synthesis of metal oxide (including TiO2, SnO2, In2O3, and PbO) nanowires with diameters around 50 nm and lengths up to 30 µm. In a typical procedure, tetraalkoxyltitanium, Ti(OR)4 (with R = –C2H5, –iso-C3H7, or –n-C4H9), was added to ethylene glycol and heated to 170 °C for 2 h under vigorous stirring. The alkoxide was transformed into a chain-like, glycolate complex that subsequently crystallized into uniform nanowires. Similarly, nanowires made of tin glycolate were synthesized by refluxing SnC2O4·2H2O in ethylene glycol at 195 °C for 2 h, and nanowires consisting of indium and lead glycolates were prepared by adding In(OOCC7H15)(OiPr)2 and Pb(CH3COO)2 to ethylene glycol, followed by heating at 170 °C for 2 h. The nanowires could be readily collected as precipitates after the reaction solutions had been cooled down to room temperature. By calcining at elevated temperatures, each glycolate precursor could be transformed into the corresponding metal oxide without changing the wire-like morphology. Electron microscopic and XRD powder diffraction studies were used to characterize the morphology, crystallinity, and structure of these nanowires before and after calcination at various temperatures. A plausible mechanism was also proposed to account for the one-dimensional growth of such nanostructures in a highly isotropic medium. This mechanism was supported by XRD, FT-IR, solid state 13C-NMR, and TGA measurements. As a demonstration of potential applications, the polycrystalline nanowires made of SnO2 were used as functional components to fabricate sensors that could detect combustible gases (CO and H2) with greatly enhanced sensitivity under ambient conditions.
Living Skin Equivalents for the Diabetic Foot Ulcer (2007)

Foot ulceration remains the leading diabetic complication requiring hospitalization (1). Treatment of the diabetic foot ulcer is often a complex process that involves a multidisciplinary approach. Despite best efforts, failure to heal a diabetic foot ulcer can lead to amputation (2). As the incidence of diabetes in the general population is expected to rise, the prevalence of ulcerations and amputations will follow. The resulting cost to society can be measured in direct costs attributed to treatment, as well as indirect costs in lost productivity. The total cost of diabetic foot ulcerations in the United States has been estimated to approach $4 billion annually, as extrapolated from the costs of ulcer care and amputations (3). However the costs are measured, diabetic foot ulcerations represent a major public health challenge of growing proportions.
COMBINING SCHATTEN'S SOLAR ACTIVITY PREDICTION MODEL WITH A CHAOTIC PREDICTION MODEL (1991)

554-FDD-91/125SEAS (550)/IM-91/047 (52 404)FUTURE MISSIONS STUDIESCOMBINING SCHATTEN'S SOLAR ACTIVITY PREDICTION MODELWITH A CHAOTIC PREDICTION MODELPrepared forGODDARD SPACE FLIGHT CENTERByS. AshrafiCOMPUTER SCIENCES CORPORATIONUnderContract NAS 5-31500Task Assignments 51 404 and 52 404November 1991
NF-κB Activation Is a Critical Regulator of Human Granulocyte Apoptosis in Vitro (1999)

During beneficial inflammation, potentially tissue-damaging granulocytes undergo apoptosis before being cleared by phagocytes in a non-phlogistic manner. Here we show that the rate of constitutive apoptosis in human neutrophils and eosinophils is greatly accelerated in both a rapid and concentration-dependent manner by the fungal metabolite gliotoxin, but not by its inactive analog methylthiogliotoxin. This induction of apoptosis was abolished by the caspase inhibitor zVAD-fmk, correlated with the inhibition of nuclear factor-kappa B (NF-kappaB), and was mimicked by a cell permeable inhibitory peptide of NF-kappaB, SN-50; other NF-kappaB inhibitors, curcumin and pyrrolidine dithiocarbamate; and the proteasome inhibitor, MG-132. Gliotoxin also augmented dramatically the early (2-6 h) pro-apoptotic effects of tumor necrosis factor-alpha (TNF-alpha) in neutrophils and unmasked the ability of TNF-alpha to induce eosinophil apoptosis. In neutrophils, TNF-alpha caused a gliotoxin-inhibitable activation of an inducible form of NF-kappaB, a response that may underlie the ability of TNF-alpha to delay apoptosis at later times (12-24 h) and limit its early killing effect. Furthermore, cycloheximide displayed a similar capacity to enhance TNF-alpha induced neutrophil apoptosis even at time points when cycloheximide alone had no pro-apoptotic effect, suggesting that NF-kappaB may regulate the production of protein(s) which protect neutrophils from the cytotoxic effects of TNF-alpha. These data shed light on the biochemical and molecular mechanisms regulating human granulocyte apoptosis and, in particular, indicate that the transcription factor NF-kappaB plays a crucial role in regulating the physiological cell death pathway in granulocytes.
Isoflurane Protects Human Kidney Proximal Tubule Cells against Necrosis via Sphingosine Kinase and Sphingosine-1-Phosphate Generation (2010)

Collectively, our study demonstrates that S1P released via isoflurane-mediated SK1 stimulation produces direct anti-necrotic effects probably via S1P(1) receptor-mediated cytoprotective signaling (ERK/Akt phosphorylation and HSP70 induction) in HK-2 cells. Our findings may help to unravel the cellular signaling pathways of volatile anesthetic-mediated renal protection and lead to new therapeutic applications of volatile anesthetics during the perioperative period.
Fiber-Optic Evanescent Wave Biosensor for the Detection of Oligonucleotides (1996)

An automated optical biosensor system based on fluorescence excitation and detection in the evanescent field of a quartz fiber was used to detect 16-mer oligonucleotides in DNA hybridization assays. A biotinylated capture probe was immobilized on the fiber surface via avidin or streptavidin. The hybridization with fluorescein-labeled complementary strands was monitored in real time by fluorescence detection. The double strands formed by hybridization could be dissociated by chemical or thermal regeneration, allowing one to perform hundreds of assay cycles with the same fiber. The signal loss during longtime measurements, i.e., consecutive hybridization assays, can be described by a single-exponential function. Over more than 200 cycles, the net signal decreased by 50% with a signal variation of 2.4% after correction for this signal loss. By binding the capture probe with the 5'-end to the optical fiber surface, and by using a 50% (w/w) aqueous urea solution for chemical regeneration, the duration of an assay cycle could be reduced to 3 min. By applying longer assay cycles, the detection limit for the hybridization with a complementary fluorescein-labeled oligonucleotide was 2.0 x 10(-13) M (24 fmol). To detect an unlabeled complementary 16-mer oligonucleotide, competitive hybridization assays were performed, resulting in a detection limit of 1.1 x 10(-9) M (132 pmol). Poly-(acrylic acid) 5100 sodium salt and Tween 20 were used in the hybridization buffer to prevent nonspecific binding caused by ionic or hydrophobic interaction. The amount of nonspecific binding of noncomplementary oligonucleotides was in the range of 1-2%, compared with the specific binding in the different hybridization assays.
Asymmetry in RNA pseudoknots: observation and theory (2005)

RNA can fold into a topological structure called a pseudoknot, composed of non-nested double-stranded stems connected by single-stranded loops. Our examination of the PseudoBase database of pseudoknotted RNA structures reveals asymmetries in the stem and loop lengths and provocative composition differences between the loops. By taking into account differences between major and minor grooves of the RNA double helix, we explain much of the asymmetry with a simple polymer physics model and statistical mechanical theory, with only one adjustable parameter.
The 170-kDa glucose-regulated stress protein is an endoplasmic reticulum protein that binds immunoglobulin. (1993)

Anoxia, glucose starvation, calcium ionophore A23187, EDTA, glucosamine, and several other conditions that adversely affect the function of the endoplasmic reticulum (ER) induce the synthesis of the glucose-regulated class of stress proteins (GRPs). The primary GRPs induced by these stresses migrate at 78 and 94 kDa (GRP78 and GRP94). In addition, another protein of approximately 150-170 kDa (GRP170) has been previously observed and is coordinately induced with GRP78 and GRP94. To characterize this novel stress protein, we have prepared an antisera against purified GRP170. Immunofluorescence, Endoglycosidase H sensitivity, and protease resistance of this protein in microsomes indicates that GRP170 is an ER lumenal glycoprotein retained in a pre-Golgi compartment. Immunoprecipitation of GRP170 with our antibody coprecipitates the GRP78 (also referred to as the B cell immunoglobulin-binding protein) and GRP94 members of this stress protein family in Chinese hamster ovary cells under stress conditions. ATP depletion, by immunoprecipitation in the presence of apyrase, does not affect the interaction between GRP78 and GRP170 but results in the coprecipitation of an unidentified 60-kDa protein. In addition, GRP170 is found to be coprecipitated with immunoglobulin (Ig) in four different B cell hybridomas expressing surface IgM, cytoplasmic Ig light chain only, cytoplasmic Ig heavy chain only, or an antigen specific secreted IgG. In addition, in IgM surface expressing WEHI-231 B cells, anti-IgM coprecipitates GRP78, GRP94, as well as GRP170; antibodies against GRP170 and GRP94 reciprocally coprecipitate GRP94/GRP170 as well as GRP78. Results suggest that this 170-kDa GRP is a retained ER lumenal glycoprotein that is constitutively present and that may play a role in immunoglobulin folding and assembly in conjunction or consecutively with GRP78 and GRP94.
Gemcitabine sensitization by checkpoint kinase 1 inhibition correlates with inhibition of a Rad51 DNA damage response in pancreatic cancer cells (2009)

The protein kinase checkpoint kinase 1 (Chk1) has been implicated as a key regulator of cell cycle progression and DNA repair, and inhibitors of Chk1 (e.g., UCN-01 and EXEL-9844) potentiate the cytotoxic actions of chemotherapeutic drugs in tumor cells. We have examined the ability of PD-321852, a small-molecule Chk1 inhibitor, to potentiate gemcitabine-induced clonogenic death in a panel of pancreatic cancer cell lines and evaluated the relationship between endpoints associated with Chk1 inhibition and chemosensitization. Gemcitabine chemosensitization by minimally toxic concentrations of PD-321852 ranged from minimal (<3-fold change in survival) in Panc1 cells to >30-fold in MiaPaCa2 cells. PD-321852 inhibited Chk1 in all cell lines as evidenced by stabilization of Cdc25A; in combination with gemcitabine, a synergistic loss of Chk1 protein was observed in the more sensitized cell lines. Gemcitabine chemosensitization, however, did not correlate with abrogation of the S-M or G2-M checkpoint; PD-321852 did not induce premature mitotic entry in gemcitabine-treated BxPC3 or M-Panc96 cells, which were sensitized to gemcitabine 6.2- and 4.6-fold, respectively. In the more sensitized cells lines, PD-321852 not only inhibited gemcitabine-induced Rad51 focus formation and the recovery from gemcitabine-induced replication stress, as evidenced by persistence of gamma-H2AX, but also depleted these cells of Rad51 protein. Our data suggest the inhibition of this Chk1-mediated Rad51 response to gemcitabine-induced replication stress is an important factor in determining gemcitabine chemosensitization by Chk1 inhibition in pancreatic cancer cells.
Tungsten-Doped TiO2 vs Pure TiO2 Photocatalysts:  Effects on Photobleaching Kinetics and Mechanism (2008)

Sol gel prepared tungsten (VI) doped TiO2 powders were evaluated as photocatalysts for crystal violet (CV) bleaching under UV irradiation, in the presence of oxygen. The incorporation of the hexavalent cation affects both surface and bulk properties. The optimum activity observed results from the competition between higher surface areas and lower specific activities per adsorption site. At pH 4.0, doped particles share a common photodegradation mechanism, where the relative contribution of the aromatic structure rupture over the loss of terminal methyl groups (N-demethylation) is more relevant than in the case of non-doped titania. This behavior can be minimized shifting the pH into basic condition.
Telomerase Catalytic Subunit Homologs from Fission Yeast and Human (1997)

Catalytic protein subunits of telomerase from the ciliate Euplotes aediculatus and the yeast Saccharomyces cerevisiae contain reverse transcriptase motifs. Here the homologous genes from the fission yeast Schizosaccharomyces pombe and human are identified. Disruption of the S. pombe gene resulted in telomere shortening and senescence, and expression of mRNA from the human gene correlated with telomerase activity in cell lines. Sequence comparisons placed the telomerase proteins in the reverse transcriptase family but revealed hallmarks that distinguish them from retroviral and retrotransposon relatives. Thus, the proposed telomerase catalytic subunits are phylogenetically conserved and represent a deep branch in the evolution of reverse transcriptases.
Halogenation of 2-Hydroxynicotinic Acid (1989)

Abstract A convenient method to prepare 5-halo-2-hydroxy-nicotinic acid is described.
An RNAi therapeutic targeting Tmprss6 decreases iron overload in Hfe−/− mice and ameliorates anemia and iron overload in murine β-thalassemia intermedia (2012)

Mutations in HFE lead to hereditary hemochromatosis (HH) because of inappropriately high iron uptake from the diet resulting from decreased hepatic expression of the iron-regulatory hormone hepcidin. -thalassemia is a congenital anemia caused by partial or complete loss of -globin synthesis causing ineffective erythropoiesis, anemia, decreased hepcidin production, and secondary iron overload. Tmprss6 is postulated to regulate hepcidin production by cleaving Hemojuvelin (Hjv), a key modulator of hepcidin expression, from the hepatocyte surface. On this basis, we hypothesized that treatment of mouse models of HH (Hfe(-/-)) and -thalassemia intermedia (Hbb(th3/+)) with Tmprss6 siRNA formulated in lipid nanoparticles (LNPs) that are preferentially taken up by the liver would increase hepcidin expression and lessen the iron loading in both models. In the present study, we demonstrate that LNP-Tmprss6 siRNA treatment of Hfe(-/-) and Hbb(th3/+) mice induces hepcidin and diminishes tissue and serum iron levels. Furthermore, LNP-Tmprss6 siRNA treatment of Hbb(th3/+) mice substantially improved the anemia by altering RBC survival and ineffective erythropoiesis. Our results indicate that pharmacologic manipulation of Tmprss6 with RNAi therapeutics isa practical approach to treating iron overload diseases associated with diminished hepcidin expression and may have efficacy in modifying disease-associated morbidities of -thalassemia intermedia.
Ribozyme mediated degradation of β-amyloid peptide precursor mRNA in COS-7 cells (1994)

Two sets of eucaryotic expression vectors encoding trans-acting hammerhead ribozymes and trans-acting hairpin ribozymes were constructed. In one set of vectors ribozyme RNA transcription was placed under the control of a mouse mammary tumor virus long terminal repeat (MMTV-LTR). In the other set ribozyme expression was controlled by a metallothionein IIA (Mt-IIA) promoter. Each ribozyme was directed to the first target sequence in the Alzheimer amyloid peptide precursor mRNA (beta APP mRNA), 5' decreases GUC decreases 3'. Ribozyme RNA transcribed from these vectors, which should cleave all six alternatively spliced forms of beta APP mRNA as well as beta APP pre-mRNA, was shown to cleave a beta APP RNA substrate analog in vitro. Stably transfected COS-7 cell lines bearing both vector types were prepared. Steady-state levels of beta APP mRNA were reduced 25-30% in cells containing either active or mutant hammerhead ribozyme vectors driven by the MMTV-LTR promoter grown in the presence of glucocorticoids. In cell lines bearing Mt-IIA driven ribozymes steady-state levels of beta APP mRNA were reduced 67-80% in both hammerhead and hairpin ribozyme containing cell lines following promoter induction by glucocorticoids. These levels correlate with the appearance of low levels of induced ribozyme RNA. In contrast, steady-state alpha-actin mRNA and G3PDH mRNA levels in these cells remained constant. Western blotting of cell extracts revealed that all forms of beta APP were correspondingly reduced. Neither the RNA nor protein decreases observed in ribozyme transfected cell lines were observed in stably transfected control cells bearing the vector alone. These results suggest that ribozyme-mediated degradation of beta APP mRNA in COS-7 cells does not depend on ribozyme cleavage.
Effect of Inhaled Formoterol and Budesonide on Exacerbations of Asthma (1997)

In patients who have persistent symptoms of asthma despite treatment with inhaled glucocorticoids, the addition of formoterol to budesonide therapy or the use of a higher dose of budesonide may be beneficial. The addition of formoterol to budesonide therapy improves symptoms and lung function without lessening the control of asthma.
Ketone Formation via Mild Nickel-Catalyzed Reductive Coupling of Alkyl Halides with Aryl Acid Chlorides (2012)

The present work highlights unprecedented Ni-catalyzed reductive coupling of unactivated alkyl iodides with aryl acid chlorides to efficiently generate alkyl aryl ketones under mild conditions.
Triple Combination of siRNAs Targeting TGFβ1, TGFβR2, and CTGF Enhances Reduction of Collagen I and Smooth Muscle Actin in Corneal Fibroblasts (2013)

Simultaneous targeting of TGFβ1, TGFβR2, and CTGF genes by effective triple siRNA combination produced high knockdown of target and downstream scarring genes without cell toxicity, which may have clinical applications in reducing corneal fibrosis and scarring in other tissues.
Harmonic coordinates for character articulation (2007)

In this paper we consider the problem of creating and controlling volume deformations used to articulate characters for use in high-end applications such as computer generated feature films. We introduce a method we call harmonic coordinates that significantly improves upon existing volume deformation techniques. Our deformations are controlled using a topologically flexible structure, called a cage, that consists of a closed three dimensional mesh. The cage can optionally be augmented with additional interior vertices, edges, and faces to more precisely control the interior behavior of the deformation. We show that harmonic coordinates are generalized barycentric coordinates that can be extended to any dimension. Moreover, they are the first system of generalized barycentric coordinates that are non-negative even in strongly concave situations, and their magnitude falls off with distance as measured within the cage.