gebhart/patrepeval huggingface dataset:
Novel Fluorescence-Based Screen To Identify Small Synthetic Internal Ribosome Entry Site Elements (2001)

We report here a novel fluorescent protein-based screen to identify small, synthetic internal ribosome entry site (IRES) elements in vivo. A library of bicistronic plasmids encoding the enhanced blue and green fluorescent proteins (EBFP and EGFP) separated by randomized 50-nucleotide-long sequences was amplified in bacteria and delivered into mammalian cells via protoplast fusion. Cells that received functional IRES elements were isolated using the EBFP and EGFP reporters and fluorescence-activated cell sorting, and several small IRES elements were identified. Two of these elements were subsequently shown to possess IRES activity comparable to that of a variant of the encephalomyocarditis virus IRES element in a context-independent manner both in vitro and in vivo, and these elements functioned in multiple cell types. Although no sequence or structural homology was apparent between the synthetic IRES elements and known viral and cellular IRES elements, the two synthetic IRES elements specifically blocked poliovirus (PV) IRES-mediated translation in vitro. Competitive protein-binding experiments suggested that these IRES elements compete with PV IRES-mediated translation by utilizing some of the same factors as the PV IRES to direct translation. The utility of this fluorescent protein-based screen in identifying IRES elements with improved activity as well as in probing the mechanism of IRES-mediated translation is discussed.
Isoproterenol antagonizes prolongation of refractory period by the class III antiarrhythmic agent E-4031 in guinea pig myocytes. Mechanism of action. (1991)

The mechanism by which isoproterenol (ISO) prevents the prolongation of action potential duration (APD) and refractory period (RP) by the class III antiarrhythmic agent E-4031 was studied. E-4031 (1 microM) increased RP by 50% with no effect on contractile force in papillary muscles isolated from guinea pig heart. ISO (1 microM) increased force of contraction more than fivefold and decreased RP by 25%. The prolongation of RP by E-4031 was prevented by pretreatment of muscles with ISO. The prolongation of APD in isolated guinea pig ventricular myocytes by 5 microM E-4031 also was antagonized by prior exposure of the cells to 1 microM ISO. Instantaneous currents and delayed rectifier K+ currents, IK, were measured in isolated myocytes using the suction microelectrode voltage-clamp technique. Currents were measured in response to 225-msec depolarizing pulses from a holding potential of -40 mV. Previous studies have demonstrated that IK in these cells results from activation of two distinct outward K+ currents, IKs and IKr (specifically blocked by E-4031). ISO doubled the magnitude of IKs without significant effect on IKr. The instantaneous current, putatively identified as a Cl- current, also was doubled by ISO but was unaffected by E-4031. The augmented conductance of IKs and instantaneous current by ISO results in a decrease in RP. The small effect of E-4031 on APD and RP in the presence of ISO results from the smaller contribution of IKr relative to the augmented repolarizing currents.
Mechanisms and therapy of myocardial reperfusion injury. (1990)

Recent advances in thrombolytic therapy and balloon angioplasty have resulted in reperfusion therapy as a logical maneuver in the treatment of evolving myocardial infarction. The introduction of electrolytes, oxygen, and cellular elements, especially neutrophils, however, into the previously ischemic bed may initiate cellular and biochemical changes that limit the amount of potentially salvageable myocardium (reperfusion injury). Experimental studies have demonstrated that microvascular damage may play an important role in the pathogenesis of this phenomenon. Reperfusion enhances the infiltration of activated neutrophils into the ischemic bed, and neutrophil plugging of capillary lumens in association with extensive disruption of endothelial cells results in a progressive decrease in blood flow (the "no-reflow" phenomenon). Activated neutrophils may potentiate the inflammatory response, produce cellular damage, and reduce capillary blood flow by producing chemoattractants, proteolytic enzymes and reactive oxygen species, and arachidonate products, respectively. Therapeutic strategies that modify the interaction between neutrophils and endothelium have shown promising results in experimental preparations for reperfusion. The administration of both perfluorochemical (Fluosol, Alpha Therapeutic Corp., Los Angeles, California) and adenosine after reperfusion has resulted in enhanced myocardial salvage after 90 minutes of ischemia in the canine model. Histological studies have shown reduced neutrophil infiltration and relative preservation of endothelial cells without neutrophil plugging with both agents. Both adenosine and perfluorochemical have been shown to reduce neutrophil adherence and cytotoxicity to endothelial cell cultures. These findings suggest that suppression of neutrophil activation, especially chemotaxis, might be an ideal step to reduce this component from the inflammatory response in the ischemic myocardium after reperfusion. Clinical trials seem warranted to determine the role of reperfusion injury in limiting myocardial salvage in patients undergoing reperfusion within the first few hours of a thrombotic event.
Identification of a conserved protein involved in anaerobic unsaturated fatty acid synthesis in Neiserria gonorrhoeae: implications for facultative and obligate anaerobes that lack FabA (2011)

Transcriptome analysis of the facultative anaerobe, Neisseria gonorrhoeae, revealed that many genes of unknown function were induced under anaerobic conditions. Mutation of one such gene, NGO1024, encoding a protein belonging to the 2-nitropropane dioxygenase-like superfamily of proteins, was found to result in an inability of gonococci to grow anaerobically. Anaerobic growth of an NG1024 mutant was restored upon supplementation with unsaturated fatty acids (UFA), but not with the saturated fatty acid palmitate. Gonococcal fatty acid profiles confirmed that NGO1024 was involved in UFA synthesis anaerobically, but not aerobically, demonstrating that gonococci contain two distinct pathways for the production of UFAs, with a yet unidentified aerobic mechanism, and an anaerobic mechanism involving NGO1024. Expression of genes involved in classical anaerobic UFA synthesis, fabA, fabM and fabB, was toxic in gonococci and unable to complement a NGO1024 mutation, suggesting that the chemistry involved in gonococcal anaerobic UFA synthesis is distinct from that of the classical pathway. NGO1024 homologues, which we suggest naming UfaA, form a distinct lineage within the 2-nitropropane dioxygenase-like superfamily, and are found in many facultative and obligate anaerobes that produce UFAs but lack fabA, suggesting that UfaA is part of a widespread pathway involved in UFA synthesis.
Multimarker assay for early diagnosis of ovarian cancer (2006)

653 Clinical outcome of ovarian cancer patients may be improved by early detection. We hypothesized that a panel comprised of multiple ovarian cancer-associated biomarkers may yield a better diagnostic tool than each individual marker. We utilized the same novel multiplexing LapMAP™ technology that allowed us to evaluate the large panel of biomarkers that have previously shown correlation with epithelial cancers. Concentrations of 46 biomarkers, cancer antigens, CA 125, CEA, CA 15-3, AFP, CA19-9, CA 72-4; growth/angiogenic factors, VEGF, bFGF, EGF, IGFBPI, HGF ErbB2, EGFR; apoptosis-related molecules, Fas, FasL, CK19; metastasis-related molecules, MMP-2, MMP-3, MMP-7, tPAI, sICAM, V-CAM, sE-selectin; Cytokines, IL-6, IL-8, G-CSF, IP-10, MCP-1, MIP-1a, MIP-1b MIF, IL-2R, Eotaxin; hormones, bHCG, FSH, LH, GH, TSH, ACH, and prolactin; kallikreins 8 and 11, HE4, soluble mesothelin-related marker (SMR), mesothelin, and myeloperoxidase (MPO), were measured in sera of 109 patients with stages I-II ovarian cancer, 200 healthy women, and 111 patients with benign pelvic tumors. IL-6, CA 125, CK 19, IGFBPI, MIF, HE4, IL-2R, and MIP-1b, CA19-9, CA 125, CK19, CA 72-4, TSH, GH, ACTH, and prolactin were significantly higher in cancer, while Eotaxin, ErbB2, EGFR, MMP-2, MMP-3, sICAM, V-CAM, mesothelin, sE-selectin, and FSH were significantly lower in cancer as compared to healthy controls. Additionally, serum levels of CA19-9, CA 125, Cyfra 21-1, CA 72-4, prolactin, and tPAI were significantly higher and TNF-α levels were significantly lower in ovarian cancer group compared to benign group. Three different statistical methods were used to create diagnostic models: logistic regression, mixture discriminant analysis and 2D correlation. 2D correlation demonstrated the best performance offering a sensitivity of 100% at a specificity of 98.6% in a postmenopausal group. The multimarker panel offering the highest diagnostic power was comprised of 8 biomarkers: CA 125, CA 19-9, EGFR, G-CSF, Eotaxin, IL-2R, cVCAM, and MIF. In comparison with published evidence, the presented assay offers so far the best diagnostic power for early detection of ovarian cancer. The discrimination between ovarian cancer and benign pelvic disease was performed using the 2D correlation algorithm and, when utilized the multimarker panel resulted in 98.2% sensitivity at 98.7% specificity. To the best of our knowledge, thus far, this assay provides the highest diagnostic power for early detection of ovarian cancer compared to other published assays.
Analysis of the expression of N-glycolylneuraminic acid-containing gangliosides in cells and tissues using two human monoclonal antibodies. (1988)

The specificities of two human monoclonal antibodies (2-39M and 32-27M), produced by hybridomas derived from the lymphocytes of melanoma patients (Yamaguchi, H., Furukawa, K., Fortunato, S. R., Livingston, P. O., Lloyd, K. O., Oettgen, H. F., and Old, L. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 2416-2420) have been elucidated. Using a large panel of glycolipids, it has been shown that the two monoclonal antibodies (mAbs) identified a number of N-glycolylneuraminic acid (NeuGc)-containing gangliosides. mAb 2-39M reacted with (NeuGc)GM3, (NeuGc)sialylparagloboside, and (NeuGc)sialylhexaglycosylceramide; no reactivity was observed with gangliosides containing only N-acetylneuraminic acid (NeuAc) or with disialogangliosides. These reactive species have the NeuGc alpha 2----3Gal- sequence in common. mAb 32-27M reacted strongly with (NeuGc)2 GD3 and (NeuGc)2disialylparagloboside, and moderately with (NeuAc-NeuGc-)GD3 and (NeuAc-NeuGc-)disialylparagloboside. The reactive species have sialic acid alpha 2----8NeuGc alpha 2----3Gal- sequences in common. These two antibodies were used to demonstrate the species-related presence of different NeuGc-containing gangliosides in various animal erythrocytes by thin layer chromatography immunostaining. No reactivity of either mAb was observed with gangliosides isolated from fresh human colon cancer, melanoma specimens, or some normal tissues, including brain. On the other hand, it was shown that mAb 32-27M reacted with gangliosides isolated from human melanoma and astrocytoma cells grown in fetal bovine serum but not from those grown in synthetic medium. Within the sensitivities of the methods used, these data, and related chemical analyses, do not support the presence of NeuGc-containing gangliosides in human tumors.
Broad-Spectrum Antivirals against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses (2012)

Phylogenetic analysis has demonstrated that some positive-sense RNA viruses can be classified into the picornavirus-like supercluster, which includes picornaviruses, caliciviruses, and coronaviruses. These viruses possess 3C or 3C-like proteases (3Cpro or 3CLpro, respectively), which contain a typical chymotrypsin-like fold and a catalytic triad (or dyad) with a Cys residue as a nucleophile. The conserved key sites of 3Cpro or 3CLpro may serve as attractive targets for the design of broad-spectrum antivirals for multiple viruses in the supercluster. We previously reported the structure-based design and synthesis of potent protease inhibitors of Norwalk virus (NV), a member of the Caliciviridae family. We report herein the broad-spectrum antiviral activities of three compounds possessing a common dipeptidyl residue with different warheads, i.e., an aldehyde (GC373), a bisulfite adduct (GC376), and an α-ketoamide (GC375), against viruses that belong to the supercluster. All compounds were highly effective against the majority of tested viruses, with half-maximal inhibitory concentrations in the high nanomolar or low micromolar range in enzyme- and/or cell-based assays and with high therapeutic indices. We also report the high-resolution X-ray cocrystal structures of NV 3CLpro-, poliovirus 3Cpro-, and transmissible gastroenteritis virus 3CLpro- GC376 inhibitor complexes, which show the compound covalently bound to a nucleophilic Cys residue in the catalytic site of the corresponding protease. We conclude that these compounds have the potential to be developed as antiviral therapeutics aimed at a single virus or multiple viruses in the picornavirus-like supercluster by targeting 3Cpro or 3CLpro.
An improved helper-dependent adenoviral vector allows persistent gene expression after intramuscular delivery and overcomes preexisting immunity to adenovirus (2001)

Helper-dependent adenoviral vectors deleted of all viral coding sequences have shown an excellent gene expression profile in a variety of animal models, as well as a reduced toxicity after systemic delivery. What is still unclear is whether long-term expression and therapeutic dosages of these vectors can be obtained also in the presence of a preexisting immunity to adenovirus, a condition found in a high proportion of the adult human population. In this study we performed intramuscular delivery of helper-dependent vectors carrying mouse erythropoietin as a marker transgene. We found that low doses of helper-dependent adenoviral vectors can direct long-lasting gene expression in the muscles of fully immunocompetent mice. The best performance-i.e., 100% of treated animals showing sustained expression after 4 months-was achieved with the latest generation helper-dependent backbones, which replicate and package at high efficiency during vector propagation. Moreover, efficient and prolonged transgene expression after intramuscular injection was observed with limited vector load also in animals previously immunized against the same adenovirus serotype. These data suggest that human gene therapy by intramuscular delivery of helper-dependent adenoviral vectors is feasible.
Effect on Gel Formation Time of Adding Topical Ophthalmic Medications to ReSure Sealant, an In Situ Hydrogel (2016)

Certain medications, specifically bromfenac, may not substantially alter time to gel formation of ReSure Sealant when added to the hydrogel. In fact, bromfenac added to moxifloxacin, ofloxacin, or gatifloxacin reduced gel formation time to acceptable levels. All other medications and combinations of medications added to ReSure Sealant produced unacceptably long gel times to be used routinely. Clinical studies may be considered based on these results to assess the safety and efficacy of this strategy.
Prediction of short term mortality in systemic lupus erythematosus with time dependent measures of disease activity. (2000)

This time dependent Cox regression analysis identified the extent to which SLE disease activity, revealed by SLEDAI, is prognostic for short term mortality. Further, important individual components were identified and their prognostic value for death was estimated.
Molecular Recognition in Polymers Prepared by Imprinting with Templates (1986)

This is a review on attempts to produce specific binding sites in synthetic polymers analogous to those of biological receptors or natural enzymes. For this goal an imprinting procedure was used with the aid of templates in crosslinked polymers. Suitable polymerizable binding groups were bound to a template molecule. This was copolymerized into highly crosslinked polymers. After the removal of the templates the remaining cavities possessed a shape and an arrangement of their functional groups corresponding that of the template. Applications of these polymers for optical resolution of racemates, for selective metal ion binding, and for stereoselective reactions are reviewed. The optimization of the polymer structure is described and the origin of the memory effect discussed. Similar imprints can be obtained on surfaces of silica.
Identification of a proteolipid oligomer as a constituent part of CF0, the proton channel of the chloroplast ATP synthase (1989)

We studied the action of the photophosphorylation inhibitor, N,N ′‐dicyclohexylcarbodiimide (DCCD) on the channel portion (CF 0 ) of the chloroplast ATP synthase (CF 0 CF 1 ). We found that the target for binding of [ 14 C]DCCD was an oligomer of the small proteolipid‐subunit (subunit III) of CF 0 . We treated thylakoids with low concentrations of DCCD, sufficient to inhibit photophosphorylation. The 14 C‐labelled inhibitor was found on polyacrylamide gels in a position corresponding to an apparent molecular mass of 50 kDa. This band comprised a homooligomer of proteolipid subunits of CF 0 . At higher concentrations of DCCD, it fell apart into proteolipid monomers. This dissociation was prevented by the presence of venturicidin, another CF 0 inhibitor acting on the proteolipid subunit, during the incubation with DCCD. The existence of such an oligomeric substructure in CF 0 is discussed in the light of diverging structural models for the proton channel of F 0 F 1 ‐type ATPases.
Identification of Small Molecules from Human Embryonic Stem Cells Using Metabolomics (2007)

Metabolomics enables the discovery of small molecules that may serve as candidate biomarkers of pharmacological efficacy or toxicity. Biochemical pathways of human development are likely active in human embryonic stem (hES) cells and derivatives, since they recapitulate organogenesis in vitro. We hypothesized that small molecules could be measured from undifferentiated hES cells and hES cell-derived neural precursors (hNPs) using metabolomics and that these compounds are altered in response to known disruptors of human development. Metabolite profiling was performed in hES cells and hNPs after exposure to valproate, an inducer of neurodevelopmental disorders. Kynurenine, an intermediate in tryptophan metabolism, and other small molecules in glutamate metabolism were significantly upregulated in response to valproate. Thus, for the first time, we have been able to measure and identify small molecules secreted from hES cells and cells derived from hES cells. The hES cell metabolome may thus serve as a source of candidate biomarkers to predict or measure pharmacological efficacy or toxic response.
Redox Control and High Conductivity of Nickel Bis(dithiolene) Complex π-Nanosheet: A Potential Organic Two-Dimensional Topological Insulator (2014)

A bulk material comprising stacked nanosheets of nickel bis(dithiolene) complexes is investigated. The average oxidation number is -3/4 for each complex unit in the as-prepared sample; oxidation or reduction respectively can change this to 0 or -1. Refined electrical conductivity measurement, involving a single microflake sample being subjected to the van der Pauw method under scanning electron microscopy control, reveals a conductivity of 1.6 × 10(2) S cm(-1), which is remarkably high for a coordination polymeric material. Conductivity is also noted to modulate with the change of oxidation state. Theoretical calculation and photoelectron emission spectroscopy reveal the stacked nanosheets to have a metallic nature. This work provides a foothold for the development of the first organic-based two-dimensional topological insulator, which will require the precise control of the oxidation state in the single-layer nickel bisdithiolene complex nanosheet (cf. Liu, F. et al. Nano Lett. 2013, 13, 2842).
Immunotherapy of lymphoma and leukemia with T-cell engaging BiTE antibody blinatumomab (2009)

Hematologic malignancies are predominantly treated with chemotherapy or a combination of chemotherapy with monoclonal antibodies. Current treatment regimens often are not satisfactory due to severe side effects and a substantial proportion of relapsed patients. This has prompted the development of better tolerated and more efficacious immunotherapeutic strategies for the treatment of lymphoma and leukemia. With blinatumomab (MT103) a first antibody, which can potentially engage all cytotoxic T cells of a patient for tumor cell lysis, is now available for clinical evaluation. Blinatumomab is a single-chain bispecific antibody construct with specificity for CD19 and CD3 belonging to the class of bispecific T cell engager. Here, we review the current progress in development of blinatumomab for treatment of patients with CD19-expressing hematological malignancies.
Identification of the 6-Sulfate Binding Site Unique to α-Subunit-Containing Isozymes of Human β-Hexosaminidase (2001)

In humans, beta-hexosaminidase A (alphabeta) is required to hydrolyze GM2 ganglioside. A deficiency of either the alpha- or beta-subunit leads to a severe neurological disease, Tay-Sachs or Sandhoff disease, respectively. In mammals beta-hexosaminidase B (betabeta) and S (alphaalpha) are other major and minor isozymes. The primary structures of the alpha- and beta-subunits are 60% identical, but only the alpha-containing isozymes can efficiently hydrolyze beta-linked GlcNAc-6-SO(4) from natural or artificial substrates. Hexosaminidase has been grouped with glycosidases in family 20. A molecular model of the active site of the human hexosaminidase has been generated from the crystal structure of a family 20 bacterial chitobiase. We now use the chitobiase structure to identify residues close to the carbon-6 oxygen of NAG-A, the nonreducing beta-GlcNAc residue of its bound substrate. The chitobiase side chains in the best interactive positions align with alpha-Asn(423)Arg(424) and beta-Asp(453)Leu(454). The change in charge from positive in alpha to negative in beta is consistent with the lower K(m) of hexosaminidase S, and the much higher K(m) and lower pH optimum of hexosaminidase B, toward sulfated versus unsulfated substrates. In vitro mutagenesis, CHO cell expression, and kinetic analyses of an alphaArg(424)Lys hexosaminidase S detected little change in V(max) but a 2-fold increase in K(m) for the sulfated substrate. Its K(m) for the nonsulfated substrate was unaffected. When alphaAsn(423) was converted to Asp, again only the K(m) for the sulfated substrate was changed, increasing by 6-fold. Neutralization of the charge on alphaArg(424) by substituting Gln produced a hexosaminidase S with a K(m) decrease of 3-fold and a V(max) increased by 6-fold for the unsulfated substrate, parameters nearly identical to those of hexosaminidase B at pH 4.2. As well, for the sulfated substrate at pH 4.2 its K(m) was increased 9-fold and its V(max) decreased 1.5-fold, values very similar to those of hexosaminidase B obtained at pH 3.0, where its betaAsp(453) becomes protonated.