gebhart/patrepeval huggingface dataset:
Fatty Liver Disease (2004)

Fibrosis is the most significant pathological con- sequence associated with non-alcoholic steatohepatitis (NASH). Activation of hepatic stellate cells (HSC) into extracellular matrix (ECM) producing myofibroblasts, the central event in hepatic fibrosis, is recognized in NASH. Hepatic fibrogenesis could represent the healing and tissue repair response to chronic necroinflammat- ory injury associated with NASH. However, there is Fatty Liver Disease: NASH and Related Disorders Edited by Geoffrey C. Farrell, Jacob George, Pauline de la M. Hall, Arthur J. McCullough Copyright © 2005 Blackwell Publishing Ltd
Induction of plasminogen activator by UV light in normal and xeroderma pigmentosum fibroblasts. (1981)

Normal and DNA repair-deficient human fibroblasts have been used to study induction of plasminogen activator (PA) by DNA damage. UV light induced the synthesis of PA in skin fibroblasts of all types of xeroderma pigmentosum (XP) in XP heterozygotes and in human amniotic cells. Enzyme induction was, however, not observed in fibroblasts of normal adults. In classical XP, which are deficient in excision repair, PA synthesis occurred in a narrow range of low-UV fluences. In such strains, the level of enzyme produced was correlated with the extent of repair deficiency. UV fluences required for PA induction in XP variants and XP heterozygotes were at least 10 times those inducing enzyme synthesis in excision-deficient XP. Maximum enzyme induction occurred 48 hr after irradiation, and the highest levels of enzyme produced were 15-20 times those of PA baseline levels. Electrophoretic analysis showed that UV irradiation enhances the synthesis of the Mr 60,000 human urokinase-type PA, which is present in low amounts in untreated cells. Our results suggest that PA induction in human cells is caused by unrepaired DNA damage and represents a eukaryotic SOS-like function. In addition, PA induction may provide a sensitive assay for detection of cellular DNA repair deficiencies and identification of XP heterozygotes.
Charcot-Leyden Crystal Protein (Galectin-10) Is Not a Dual Function Galectin with Lysophospholipase Activity but Binds a Lysophospholipase Inhibitor in a Novel Structural Fashion (2002)

Charcot-Leyden crystal (CLC) protein, initially reported to possess weak lysophospholipase activity, is still considered to be the eosinophil's lysophospholipase, but it shows no sequence similarities to any known lysophospholipases. In contrast, CLC protein has moderate sequence similarity, conserved genomic organization, and near structural identity to members of the galectin superfamily, and it has been designated galectin-10. To definitively determine whether or not CLC protein is a lysophospholipase, we reassessed its enzymatic activity in peripheral blood eosinophils and an eosinophil myelocyte cell line (AML14.3D10). Antibody affinity chromatography was used to fully deplete CLC protein from eosinophil lysates. The CLC-depleted lysates retained their full lysophospholipase activity, and this activity could be blocked by sulfhydryl group-reactive inhibitors, N-ethylmaleimide and p-chloromercuribenzenesulfonate, previously reported to inhibit the eosinophil enzyme. In contrast, the affinity-purified CLC protein lacked significant lysophospholipase activity. X-ray crystallographic structures of CLC protein in complex with the inhibitors showed that p-chloromercuribenzenesulfonate bound CLC protein via disulfide bonds with Cys(29) and with Cys(57) near the carbohydrate recognition domain (CRD), whereas N-ethylmaleimide bound to the galectin-10 CRD via ring stacking interactions with Trp(72), in a manner highly analogous to mannose binding to this CRD. Antibodies to rat pancreatic lysophospholipase identified a protein in eosinophil and AML14.3D10 cell lysates, comparable in size with human pancreatic lysophospholipase, which co-purifies in small quantities with CLC protein. Ligand blotting of human and murine eosinophil lysates with CLC protein as probe showed that it binds proteins also recognized by antibodies to pancreatic lysophospholipase. Our results definitively show that CLC protein is not one of the eosinophil's lysophospholipases but that it does interact with eosinophil lysophospholipases and known inhibitors of this lipolytic activity.
A Scoring Scheme for Discriminating between Drugs and Nondrugs (1998)

A scoring scheme for the rapid and automatic classification of molecules into drugs and nondrugs was developed. The method is a valuable new tool that can aid in the selection and prioritization of compounds from large compound collections for purchase or biological testing and that can replace a considerable amount of laborious manual work by a more unbiased approach. It is based on the extraction of knowledge from large databases of drugs and nondrugs. The method was set up by using atom type descriptors for encoding the molecular structures and by training a feedforward neural network for classifying the molecules. It was parametrized and validated by using large databases of drugs and nondrugs (169 331 molecules from the Available Chemicals Directory, ACD, and 38 416 molecules from the World Drug Index, WDI). The method revealed features in the molecular descriptors that either qualify or disqualify a molecule for being a drug and classified 83% of the ACD and 77% of the WDI adequately.
Polarization maintaining large mode area photonic crystal fiber (2004)

We report on a polarization maintaining large mode area photonic crystal fiber. Unlike, previous work on polarization maintaining photonic crystal fibers, birefringence is introduced using stress applying parts. This has allowed us to realize fibers, which are both single mode at any wavelength and have a practically constant birefringence for any wavelength. The fibers presented in this work have mode field diameters from about 4 to 6.5 micron, and exhibit a typical birefringence of 1.510(-4).
Scalable Synthesis of Multivalent Macromonomers for ROMP (2018)

The polymerization of functional monomers provides direct access to functional polymers without need for postpolymerization modification; however, monomer synthesis can become a bottleneck of this approach. New methods that enable rapid installation of functionality into monomers for living polymerization are valuable. Here, we report the three-step convergent synthesis (two-step longest linear sequence) of a divalent <i>exo</i>-norbornene imide capable of efficient coupling with various nucleophiles and azides to produce diversely functionalized branched macromonomers optimized for ring-opening metathesis polymerization (ROMP). In addition, we describe an efficient iterative procedure for the synthesis of tri-and tetra-valent branched macromonomers. We demonstrate the use of these branched macromonomers for the synthesis of Janus bottlebrush block copolymers as well as for the generation of bottlebrush polymers with up to three conjugated small molecules per repeat unit. This work significantly expands the scalability and diversity of nanostructured macromolecules accessible via ROMP.
Multiphase Well Test Analysis: Pressure and Pressure-Squared Methods (1989)

ABSTRACT There are two practical approaches to analyze multiphase well tests. These are the pressure and the pressure squared methods. This paper investigates the limits of these methods as they apply to different reservoir and testing conditions. The pressure squared approach is applicable to systems in which a gas phase is present (i.e. gas-oil and gas-oil-water systems), while the pressure approach is superior for application in oil-water systems. Unlike the pressure squared approach, the pressure approach is found to be rate sensitive and only applies at low flowing rates. The higher the flow rate, the greater the underestimation of the individual and total system mobilities. For some cases, the pressure semilog plot does not exhibit any straight line; while for other cases it shows two straight lines which may be misinterpreted as an indication of a composite system. This sensitivity to rate is due to the assumptions involved in deriving the pressure diffusivity equation and the improper linearization of the inner boundary condition. On the other hand, the pressure squared approach is insensitive to rate because of the proper linearization of the inner boundary condition and the better treatment of the nonlinear terms when deriving the diffusivity equation in terms of p2. This paper also discusses the rate normalization of multiphase well tests with varying flow rates, i.e. buildup tests dominated by afterflow, and drawdown tests dominated by unloading effects. The rate normalization, currently used in the industry, is based on the pressure approach which requires that the total rate in RB/D be monitored throughout the test. This is not easily done in practice. Furthermore, this normalization results in underestimated values of total system mobility and yields no individual phase permeability. This paper proposes a new rate normalization method based on the pressure squared approach. The proposed normalization requires only surface oil rates to be monitored. Moreover, it results in reasonable estimates of individual phase permeabilities and thereby an accurate value of total system mobility. A simulated example which demonstrates the applicability of this proposed normalization is presented.
Effect of conjugation methodology on the immunogenicity and protective efficacy of meningococcal group C polysaccharideâP64k protein conjugates (2003)

Neisseria meningitidis serogroup C polysaccharide (CCPS) was conjugated to the carrier protein P64k using two different conjugation procedures, condensation mediated by carbodiimide with adipic acid dihydrazide as spacer and the reductive amination method. BALB/c mice were immunized with the resultant polysaccharide-protein conjugates and the immune response was evaluated. All conjugates assayed generated at least 10-fold higher antibody titers than the free polysaccharide. The reductive amination method rendered the best conjugate (CCPS-P64kR) that was able to elicit antibody titers statistically higher than the titer elicited by the plain CCPS (P<0.001). The sera of the group immunized with CCPS-P64kR showed a three-fold higher bactericidal response than the sera of the group immunized with the plain CCPS and they were able to protect against challenge with meningococci in the infant rat protection model. In addition, three different conjugates were obtained from polysaccharides with molecular relative sizes of 2000-4000 Da, 4000-10,000 Da or 10,000-50,000 Da, but no differences were detected in the immune response obtained against the three conjugates. Our experiments demonstrate that it is possible to generate a protective, T-cell-dependent response against CCPS using the P64k protein as carrier.
Selection of Smart Aptamers by Methods of Kinetic Capillary Electrophoresis (2006)

We coin the term "smart aptamers" -- aptamers with predefined binding parameters (k(on), k(off), Kd) of aptamer-target interaction. Aptamers, in general, are oligonucleotides, which are capable of binding target molecules with high affinity and selectivity. They are considered as potential therapeutic targets and also thought to rival antibodies in immunoassay-like analyses. Aptamers are selected from combinatorial libraries of oligonucleotides by affinity methods. Until now, technological limitations have precluded the development of smart aptamers. Here, we report on two kinetic capillary electrophoresis techniques applicable to the selection of smart aptamers. Equilibrium capillary electrophoresis of equilibrium mixtures was used to develop aptamers with predefined equilibrium dissociation constants (Kd), while nonequilibrium capillary electrophoresis of equilibrium mixtures facilitated selection of aptamers with different dissociation rate constants (k(off)). Selections were made for MutS protein, for which aptamers have never been previously developed. Both theoretical and practical aspects of smart aptamer development are presented, and the advantages of this new type of affinity probes are described.
Targeting of Endopeptidase 24.16 to Different Subcellular Compartments by Alternative Promoter Usage (1997)

Endopeptidase 24.16 or mitochondrial oligopeptidase, abbreviated here as EP 24.16 (MOP), is a thiol- and metal-dependent oligopeptidase that is found in multiple intracellular compartments in mammalian cells. From an analysis of the corresponding gene, we found that the distribution of the enzyme to appropriate subcellular locations is achieved by the use of alternative sites for the initiation of transcription. The pig EP 24.16 (MOP) gene spans over 100 kilobases and is organized into 16 exons. The core protein sequence is encoded by exons 5-16 which match perfectly with exons 2-13 of the gene for endopeptidase 24.15, another member of the thimet oligopeptidase family. These two sets of 11 exons share the same splice sites, suggesting a common ancestor. Multiple species of mRNA for EP 24.16 (MOP) were detected by the 5'-rapid amplification of cDNA ends and they were shown to have been generated from a single gene by alternative choices of sites for the initiation of transcription and splicing. Two types of transcript were prepared, corresponding to transcription from distal and proximal sites. Their expression in vitro in COS-1 cells indicated that they encoded two isoforms (long and short) which differed only at their amino termini: the long form contained a cleavable mitochondrial targeting sequence and was directed to mitochondria; the short form, lacking such a signal sequence, remained in the cytosol. The complex structure of the EP 24.16 (MOP) gene thus allows, by alternative promoter usage, a fine transcriptional regulation of coordinate expression, in the different subcellular compartments, of the two isoforms arising from a single gene.
Natural killer cells kill human melanoma cells with characteristics of cancer stem cells (2009)

Experimental and clinical data suggest that tumours harbour a cell population retaining stem cell characteristics that can drive tumorigenesis. CD133 is considered an important cancer stem cells (CSC)-associated marker. In a large variety of human malignancies, including melanoma, CD133(+) cells have been reported to comprise CSC. In this study, we show that melanoma cell lines are highly heterogeneous for the expression of several stem cell-associated markers including CD133, c-kit/CD117 and p75 neurotrophin receptor/CD271. Since no information is available on the ability of NK cells to recognize and lyse melanoma stem cells, we assessed whether melanoma cell lines, characterized by stem cell-like features, were susceptible to lysis by IL-2-activated NK cells. We show that activated NK cells efficiently kill malignant melanoma cell lines that were enriched in putative CSC by the use of different selection methods (i.e. CD133 expression, radioresistance or the ability to form melanospheres in stem cell-supportive medium). NK cell-mediated recognition and lysis of melanoma cells involved different combinations of activating NK receptors. Since CSC have been reported to be both drug resistant and radioresistant, our present data suggest that NK-based adoptive immunotherapy could represent a novel therapeutic approach to possibly eradicate metastatic melanoma.
Relationship between the neurotoxicity of the hypoxic cell radiosensitizer SR 2508 and the pharmacokinetic profile. (1987)

Complete pharmacological data from 71 patients treated on the phase I trial of SR 2508 were analyzed to see if the dose-limiting toxicity of peripheral neuropathy is related to the individual patient's pharmacokinetic profile. In a retrospective analysis, the risk of toxicity was best predicted by using the bivariate model of total drug exposure and the time over which the treatment course was given. Drug exposure [area under the curve (AUC)] for a single treatment was calculated by the integral over time of the serum concentration of SR 2508. Since the AUC was constant during the course of a patient's treatment, the total drug exposure (total-AUC) was estimated by the product of the AUC times the number of drug administrations. While the clinical efficacy of hypoxic cell sensitizers remains to be proven, SR 2508 is better tolerated than its predecessors, misonidazole and desmethylmisonidazole, as three times the amount of SR 2508 can be given. If this model is confirmed in the current phase II and III trials, the probability of developing neuropathy would be predictable for an individual patient from measurements made at the time of the first drug dose, allowing for the adjustment of drug schedule to avoid all but minor toxicity.
Four recombinant isoforms of Cor a I, the major allergen of hazel pollen, show different IgE‐binding properties (1993)

Previous studies showed that pollens from trees of the order Fagales (e.g. birch, alder, hazel and hornbeam) all contain one major allergen. These proteins are cross-reactive between these tree species, and approximately 95% of tree-pollen-allergic patients display IgE binding to these allergens. Using the reported N-terminal amino acid sequence of the hazel pollen allergen Cor a I, it was possible to amplify Cor-a-I cDNA by use of the polymerase chain reaction. Four clones with cDNA inserts were isolated. All four clones contained an open reading frame of 477 nucleotides (159 amino acids) but differed in length of their 3'-non-coding regions. Within the overlapping regions, the nucleotide sequence of the 3'-non-coding regions of the four clones were nearly identical. The open reading frames coded for different isoforms of the major hazel pollen allergen, Cor a I. The clones were designated Cor a I/5, 6, 11 and 16, respectively. Comparison of the deduced amino acid sequences of these Cor a I isoforms revealed identities of 96-99%. The sequence identities between the Cor a I isoforms and Bet v I, the major birch pollen allergen, were 71-73% (80.5-83% similarity). Comparing amino acid sequences of Cor a I isoforms with the published sequences of Aln g I, the major allergen from alder, and Car b I and isoforms, the major allergen from hornbeam, 75.5-76.7% identity (83.6-85% similarity) and 83.6-89.9% sequence identity (89.3-95% similarity), respectively, was found. The four Cor a I cDNAs were subcloned into plasmid pKK223-3 and expressed in Escherichia coli as non-fusion proteins; their capacity to bind serum IgE from tree-pollen-allergic patients was investigated. The four cloned isoforms showed an apparent molecular mass of 17 kDa in SDS/PAGE, identical to the natural, pollen-derived Cor a I. IgE antibodies from tree-pollen-allergic patients reacted with all four recombinant isoforms. However, we noted marked differences in the IgE-binding patterns of the distinct isoforms. Furthermore, Cor a I/11 was the only isoform recognized by the anti-(Bet v I) mAb, BIP 1. Our results demonstrate that Cor a I isoforms display different antigenic and allergenic properties, very likely due to few but significant changes in their amino acid sequences. These findings have implications for the development of reagents for diagnosis and immunotherapy of type I allergies.
Liposomal delivery of methylphosphonate antisense oligodeoxynucleotides in chronic myelogenous leukemia [see comments] (1994)

Chronic myelogenous leukemia (CML) is a hematologic malignancy characterized by the presence of the Philadelphia (Ph) chromosome. Bcr- abl, the fusion gene associated with the Ph chromosome, expresses a p210bcr-abl protein that promotes a selective expansion of mature myeloid progenitor cells. Methylphosphonate (MP) oligodeoxynucleotides complementary to specific regions of the bcr-abl mRNA were incorporated in liposomes. We studied the effects of liposomal MP (L-MP) on the growth inhibition of CML-like cell lines. L-MP targeted to the breakpoint junctions of the bcr-abl mRNA inhibited the growth of CML cells. Fifty percent inhibition was achieved at approximately 1 mumol/L of L-MP oligonucleotide concentrations. The inhibitory effect was selective because growth inhibition was observed only with CML but not with control cell lines. Moreover, CML cell growth inhibition was dependent on the sequence of the MP oligodeoxynucleotides incorporated in the liposomes. The growth inhibition of CML cells by L-MP resulted from selective inhibition of the expression of the p210bcr-abl protein.
CH3NH3PbI3 Perovskite/Fullerene Planar‐Heterojunction Hybrid Solar Cells (2013)

All-solid-state donor/acceptor planar-heterojunction (PHJ) hybrid solar cells are constructed and their excellent performance measured. The deposition of a thin C60 fullerene or fullerene-derivative (acceptor) layer in vacuum on a CH3 NH3 PbI3 perovskite (donor) layer creates a hybrid PHJ that displays the photovoltaic effect. Such heterojunctions are shown to be suitable for the development of newly structured, hybrid, efficient solar cells.
Novel resveratrol derivatives induce apoptosis and cause cell cycle arrest in prostate cancer cell lines. (2007)

Introducing additional hydroxy- and methoxymoieties to the stilbene ring of RV is capable of enhancing its cytotoxic and pro-apoptotic effects in hormone-responsive and non-responsive prostate cancer cells.
All-fiber, octave-spanning supercontinuum (2003)

We present an all-fiber supercontinuum source based on a passively mode-locked erbium fiber laser and a small-effective-area, germanium-doped silica fiber. The parallels between this system and the continuum generated in microstructured fibers with 800-nm pulses are discussed, and the role of dispersion is investigated experimentally. We construct a hybrid fiber by fusion splicing lengths of different-dispersion fiber together, generating more than an octave of bandwidth.
The End of the Networks (2007)

At one time, traditional television networks controlled 95% of American viewing.The power and strength of the networks as shapers of American thought and agendas was unparalleled.2 They influenced the discussion of America and the morals of the country through their prime time programming.They shaped the news that was important through editorial decisions made by a few people located within blocks of each other in New York City.3 The concentration of power was readily apparent and it was publicly noted.The power of the networks over political thinking and Presidential policymaking was directly criticized by Vice President Spiro Agnew.
Improving the performance of the four-state continuous-variable quantum key distribution by using optical amplifiers (2012)

We propose a method to improve the secret key rates of four-state continuous-variable quantum key distribution by using an optical preamplifier. The modified protocol allows the distribution of higher secret key rates over long distances. Included in this paper is a detailed investigation of the effects of inserting an optical parametric amplifier into the output of the quantum channel in the four-state protocol, which will be instructive and meaningful about the usage of amplifiers in order to achieve the optimal performance of the protocol in a specific scenario.
Cellular Level Biocompatibility and Biosafety of ZnO Nanowires (2008)

We report the first cellular level study on the biocompatibility and biosafety of ZnO nanowires (NWs). Hela cell line showed a complete biocompatibility to ZnO nanostructures from low to high NW concentrations beyond a couple of production periods. The L929 cell line showed a good reproduction behavior at lower NW concentration, but when the concentration was close to 100 μg/ml, the viability dropped to ∼50%. Our study shows the biocompetability and biosafety of ZnO NWs when they are applied in biological applications at normal concentration range.