gebhart/patrepeval huggingface dataset:
Endogenous Proteins Controlling Amyloid β-Peptide Polymerization (1999)

We report that certain plasma proteins, at physiological concentrations, are potent inhibitors of amyloid beta-peptide (Abeta) polymerization. These proteins are also present in cerebrospinal fluid, but at low concentrations having little or no effect on Abeta. Thirteen proteins representing more than 90% of the protein content in plasma and cerebrospinal fluid were studied. Quantitatively, albumin was the most important protein, representing 60% of the total amyloid inhibitory activity, followed by alpha1-antitrypsin and immunoglobulins A and G. Albumin suppressed amyloid formation by binding to the oligomeric or polymeric Abeta, blocking a further addition of peptide. This effect was also observed when the incorporation of labeled Abeta into genuine beta-amyloid in tissue section was studied. The Abeta and the anti-diabetic drug tolbutamide apparently bind to the same site on albumin. Tolbutamide displaces Abeta from albumin, increasing its free concentration and enhancing amyloid formation. The present results suggest that several endogenous proteins are negative regulators of amyloid formation. Plasma contains at least 300 times more amyloid inhibitory activity than cerebrospinal fluid. These findings may provide one explanation as to why beta-amyloid deposits are not found in peripheral tissues but are only found in the central nervous system. Moreover, the data suggest that some drugs that display an affinity for albumin may enhance beta-amyloid formation and promote the development of Alzheimer's disease.
Determination of 3,4-Dihydroxyphenylacetic Acid and 5-Hydroxyindoleacetic Acid in Human Plasma by a Simple and Rapid High-performance Liquid Chromatography Assay* (1996)

In order to study the pharmacodynamic effects of drugs on dopamine and serotonin metabolism, a reversed-phase HPLC assay coupled with electrochemical detection (ECD) for measuring plasma concentrations of 3,4-dihydroxyphenylacetic acid (DOPAC) and 5-hydroxyindoleacetic acid (5-HIAA) was developed. The system was operated isocratically using a mobile phase of aqueous 0.03 M KH2PO4 buffer containing 0.15 mM EDTA in methanol (8.75:1.25), with a final pH of 4.0. The flow rate was set at 1.5 mL/min, and potentials at +450 mV. Using a signal to noise ratio of > 3, the minimum detection limit assessed by direct on-column injection of a standard solution for DOPAC and 5-HIAA was < 1 pg. The assays were linear from basal concentrations (1-10 ng/mL) to 100 ng/mL. The intra- and interassay variations were < 10% and < 20%, respectively.
A facile electrochemical approach for the synthesis of macrocyclic alkanones (2002)

The synthesis of macrocyclic alkanones, viz. cyclotet-radecanone 4a, cyclohexadecanone 4b, cyclooctadecanone 4c, cyclopentadecanone 4d and cycloheptadecanone 4e have been carried out by using Kolbe symmetrical/unsymmetrical dimerization followed by cyclization in Na-xylene and subsequent reduction with Zn-HCl in 70-80% yield. The products of anodic cross coupling have been separated by column chromatography over silica gel (60-120 mesh) by eluting with benzene-methanol (95: 5). An effort has been made to optimize the electrochemical step by investigating the effect of different parameters, viz. degree of partial neutralization, current density and electrode material. The products have been characterised by elemental analyses and IR and 'H NMR spectral data.
Expression of GATA-1 mRNA in human myeloid leukemic cells. (1994)

Expression of the transcription factor GATA-1, which regulates several erythroid specific genes and possibly also some megakaryocytic genes, has been previously detected in normal erythroblasts, megakaryocytes, and basophils, and in some myeloid cell lines. It has been suggested that GATA-1 may be first expressed in a common progenitor and then further activated during erythroid-megakaryocytic and basophilic differentiation and repressed during myeloid maturation. We investigated GATA-1 mRNA expression in highly purified leukemic blasts representing different lineages and stages of myeloid differentiation and in a recently established leukemic cell line, GF-D8, which exhibits morphological, cytochemical and immunophenotypic characteristics of early myeloid progenitor cells. We found GATA-1 expression in five of five myeloid and in one megakaryocytic blast crisis of CML, in four of six cases of myelomonocytic leukemias (M4 according to FAB classification), in one case of erythroleukemia (M6), whereas lymphoid blast crisis of CML and all other FAB groups were completely negative. In addition, a low level of GATA-1 mRNA was also expressed by the GF-D8 cell line. These data further support the hypothesis that GATA-1 expression may occur not only in erythroid and megakaryocytic progenitors, but also in early myeloid progenitors, and then be further regulated during lineage-specific maturation.
Acyl-chain specificity of human milk bile-salt-activated lipase (1991)

In order to probe the active-site structure of human milk bile-salt-activated lipase (BAL), the kinetics of the BAL-catalysed reaction were studied using monoesters as substrates. Among the fatty acyl chains, ranging from C8 to C16 of monoacylglycerols in a single equimolar assay mixture, there was a consistent trend of increased reactivity with decreased fatty-acyl-chain length for both the basal and taurocholate-stimulated activities of BAL. In addition, the detection of hydrolysis of long-chain monoacylglycerols in the absence of bile salt indicates that it is possible for the long-chain fatty acid monoester to form an enzyme-substrate complex with the basal form of BAL. I further examined the reaction kinetics of BAL with water-soluble short-chain esters of p-nitrophenol. The results indicated that there is a consistent trend towards a decreased Michaelis-Menten constant with increased acyl-chain length. Therefore it was concluded that the decreased reactivity with increased acyl-chain length of acylglycerols is probably not a consequence of the lowered affinity of the substrate for the enzyme. The fact that butyrate ester has the optimum acyl chain to be a substrate of BAL can be attributed to its acyl-chain length being long enough for interaction with the active centre of BAL and short enough to provide adequate positioning of the ester bond for transition state complex formation. The calculated free energy of BAL catalysis based on the derived kinetic parameters provides additional insight into the effect on the enzyme-substrate interaction of increasing the number of methylene groups in the acyl chain of substrates.
Increased Mortality in Patients With Congenital Adrenal Hyperplasia Due to 21-Hydroxylase Deficiency (2014)

CAH is a potentially lethal condition and was associated with excess mortality due to adrenal crisis. The SW phenotype also seemed to have worse outcome in children and adults due to adrenal crisis and not only before the introduction of neonatal screening.
Interfaces for Crowdsourcing Platforms (2013)

This chapter on interfaces for crowdsourcing platforms and applications is divided into three sections. The first section gives a brief outline of the current web technology and terminology. It introduces network architectures, communication protocols, markup languages, programming paradigms, and technology for media playback. The second section presents three commercial crowdsourcing platforms (CrowdFlower, Amazon Mechanical Turk (MTurk), and Clickworker) as typical examples of such platforms. This section also covers WikiSpeech, a system for speech recording, annotation and online perception experiments that offer many features typical of crowdsourcing platforms. Finally, the third section describes in detail how tasks are implemented using the interfaces of crowdsourcing platforms. Three main options are available: implementing tasks manually using a graphical user interface, using command-line tools that generate tasks from configuration files, or writing application programs that interact directly with the crowdsourcing platform programming interfaces.
Targeting Human T Cells by Retroviral Vectors Displaying Antibody Domains Selected from a Phage Display Library (2000)

To generate T cell-specific retroviral vectors an scFv phage display library derived from immunized mice was selected for binding to the human T cell line Molt-4/8. The scFv cDNAs recovered from the selected phages were transiently expressed as an N-terminal fusion of the spleen necrosis virus (SNV) transmembrane protein (TM) subunit of the viral envelope protein (Env) in the cell line DSH-cxl, which packages the beta-galactosidase gene into SNV particles. Screening of supernatants from about 150 transfections resulted in the identification of 5 scFvs that mediated efficient transduction of Molt-4/8 cells. Using stable packaging cell lines vector preparations with titers greater than 10(4) EFU/ml on human T cells were obtained. The scFv 7A5 in particular was able to mediate selective transduction of human T cells with high efficiency. Titers of up to 106 EFU/ml were reached on Molt-4/8, Jurkat, and A301 cells, while titers on HeLa cells, TE671 cells, 293T cells, and HT1080 cells were below 102 EFU/ml. Transduction of stimulated primary human peripheral blood cells, which consisted mainly of T cells, was about fivefold more efficient than transduction of B cells. Western blot analysis of supernatant from the 7A5 packaging cells demonstrated incorporation of 7A5-TM into vector particles and indicated proteolytic processing of the coexpressed unmodified TM during particle formation. Binding of bacterially expressed 7A5-scFv to a panel of cell lines correlated well with the transduction results. These data provide the first proof of concept that a general approach can be taken to obtain scFvs able to mediate selective gene transfer into target cells.
Microtubule-associated protein tau (tau) is a major antigenic component of paired helical filaments in Alzheimer disease. (1986)

The detailed protein composition of the paired helical filaments (PHF) that accumulate in human neurons in aging and Alzheimer disease is unknown. However, the identity of certain components has been surmised by using immunocytochemical techniques. Whereas PHF share epitopes with neurofilament proteins and microtubule-associated protein (MAP) 2, we report evidence that the MAP tau (tau) appears to be their major antigenic component. Immunization of rabbits with NaDodSO4-extracted, partially purified PHF (free of normal cytoskeletal elements, including tau) consistently produces antibodies to tau but not, for example, to neurofilaments. Such PHF antibodies label all of the heterogeneous fetal and mature forms of tau from rat and human brain. Absorption of PHF antisera with heat-stable MAPs (rich in tau) results in almost complete loss of staining of neurofibrillary tangles (NFT) in human brain sections. An affinity-purified antibody to tau specifically labels NFT and the neurites of senile plaques in human brain sections as well as NaDodSO4-extracted NFT. tau-Immunoreactive NFT frequently extend into the apical dendrites of pyramidal neurons, suggesting an aberrant intracellular locus for this axonal protein. tau and PHF antibodies label tau proteins identically on electrophoretic transfer blots and stain the gel-excluded protein representing NaDodSO4-insoluble PHF in homogenates of human brain. The progressive accumulation of altered tau protein in neurons in Alzheimer disease may result in instability of microtubules, consequent loss of effective transport of molecules and organelles, and, ultimately, neuronal death.
Localized Synthesis of Metal Nanoparticles Using Nanoscale Corona Discharge in Aqueous Solutions (2009)

Highly localized and controlled metal nanoparticle synthesis using nanoscale corona discharge in aqueous solutions is illustrated. As a case study, gold nanoparticles are successfully deposited at the very tip of carbon nanopipettes to act as surface-enhanced Raman spectroscopy (SERS) probes. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Catalytic Asymmetric Synthesis of (R)-(-)-Calycotomine, (S)-(-)-Salsolidine and (S)-(-)-Carnegine (2006)

A simple and efficient procedure for a synthesis of isoquinoline alkaloids is described. The key step of the synthesis was a hydrocyanation of 6,7-dimethoxy-3,4-dihydroisoqunoline giving the corresponding 1-cyano-1,2,3,4-tetrahydroisoquinoline. The asymmetric Strecker reaction was accomplished in high yield and high enantiomeric excess using Jacobsen's thiourea-containing ­catalyst. The 1-cyanoisoquinoline thus obtained was transformed to natural products, (R)-(-)-calycotomine, (S)-(-)-salsolidine and (S)-(-)-carnegine.
Genetic alphabet expansion transcription generating functional RNA molecules containing a five-letter alphabet including modified unnatural and natural base nucleotides by thermostable T7 RNA polymerase variants (2017)

Thermostable T7 RNA polymerase variants were explored for genetic alphabet expansion transcription involving the unnatural Ds-Pa pair. One variant exhibited high incorporation efficiencies of functionally modified Pa substrates and enabled the simultaneous incorporation of 2'-fluoro-nucleoside triphosphates of pyrimidines into transcripts, allowing the generation of novel, highly functional RNA molecules.
Identification and characterization of two bile acid coenzyme A transferases from Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium (2011)

The human bile acid pool composition is composed of both primary bile acids (cholic acid and chenodeoxycholic acid) and secondary bile acids (deoxycholic acid and lithocholic acid). Secondary bile acids are formed by the 7α-dehydroxylation of primary bile acids carried out by intestinal anaerobic bacteria. We have previously described a multistep biochemical pathway in Clostridium scindens that is responsible for bile acid 7α-dehydroxylation. We have identified a large (12 kb) bile acid inducible (bai) operon in this bacterium that encodes eight genes involved in bile acid 7α-dehydroxylation. However, the function of the baiF gene product in this operon has not been elucidated. In the current study, we cloned and expressed the baiF gene in E. coli and discovered it has bile acid CoA transferase activity. In addition, we discovered a second bai operon encoding three genes. The baiK gene in this operon was expressed in E. coli and found to encode a second bile acid CoA transferase. Both bile acid CoA transferases were determined to be members of the type III family by amino acid sequence comparisons. Both bile acid CoA transferases had broad substrate specificity, except the baiK gene product, which failed to use lithocholyl-CoA as a CoA donor. Primary bile acids are ligated to CoA via an ATP-dependent mechanism during the initial steps of 7α-dehydroxylation. The bile acid CoA transferases conserve the thioester bond energy, saving the cell ATP molecules during bile acid 7α-dehydroxylation. ATP-dependent CoA ligation is likely quickly supplanted by ATP-independent CoA transfer.
Generic real-time uniform K-space sampling method for high-speed swept-Source optical coherence tomography (2010)

We developed a universal, real-time uniform K-space sampling (Rt-UKSS) method for high-speed swept-source optical coherence tomography (SS-OCT). An external clock uniform in K-space was generated. The clock was synchronized with the zero-crossing time of an interferometric calibration signal and used as triggers for a high-speed data acquisition system in a point-by-point fashion, hence enabling uniform data sampling in K-space. Different from the numerical calibration algorithm commonly used in an SS-OCT system, the method reported here does not require over-sampling, thus greatly reducing the demand for digitization, data processing and storage speed. The Rt-UKSS method is adaptive and applicable to a generic SS-OCT system of a wide range of A-scan rates without special adjustment. We successfully implemented the Rt-UKSS method in an SS-OCT system based on a Fourier-domain mode-locked laser (FDML) of a 40-kHz scanning rate. Real-time imaging of biological tissues using such a system was demonstrated with a measured axial resolution of 9.3 mum and detection sensitivity greater than 120dB.
A compare between myocardial topical negative pressure levels of -25 mmHg and -50 mmHg in a porcine model (2008)

Topical negative pressure of -25 mmHg and -50 mmHg both induced a significant increase in microvascular blood flow in normal and in ischemic myocardium. The increase in microvascular blood flow was larger when using -25 mmHg on normal myocardium, and was larger when using -50 mmHg on ischemic myocardium; however these differences were not statistically significant.
The Growth Factor Progranulin Binds to TNF Receptors and Is Therapeutic Against Inflammatory Arthritis in Mice (2011)

The growth factor progranulin (PGRN) has been implicated in embryonic development, tissue repair, tumorigenesis, and inflammation, but its receptors remain unidentified. We report that PGRN bound directly to tumor necrosis factor receptors (TNFRs) and disturbed the TNFα-TNFR interaction. PGRN-deficient mice were susceptible to collagen-induced arthritis, and administration of PGRN reversed inflammatory arthritis. Atsttrin, an engineered protein composed of three PGRN fragments, exhibited selective TNFR binding. PGRN and Atsttrin prevented inflammation in multiple arthritis mouse models and inhibited TNFα-activated intracellular signaling. Collectively, these findings demonstrate that PGRN is a ligand of TNFR, an antagonist of TNFα signaling, and plays a critical role in the pathogenesis of inflammatory arthritis in mice. They also suggest new potential therapeutic interventions for various TNFα-mediated pathologies and conditions, including rheumatoid arthritis.
Asthmatic bronchial epithelial cells have a deficient innate immune response to infection with rhinovirus (2005)

Rhinoviruses are the major trigger of acute asthma exacerbations and asthmatic subjects are more susceptible to these infections. To investigate the underlying mechanisms of this increased susceptibility, we examined virus replication and innate responses to rhinovirus (RV)-16 infection of primary bronchial epithelial cells from asthmatic and healthy control subjects. Viral RNA expression and late virus release into supernatant was increased 50- and 7-fold, respectively in asthmatic cells compared with healthy controls. Virus infection induced late cell lysis in asthmatic cells but not in normal cells. Examination of the early cellular response to infection revealed impairment of virus induced caspase 3/7 activity and of apoptotic responses in the asthmatic cultures. Inhibition of apoptosis in normal cultures resulted in enhanced viral yield, comparable to that seen in infected asthmatic cultures. Examination of early innate immune responses revealed profound impairment of virus-induced interferon-beta mRNA expression in asthmatic cultures and they produced >2.5 times less interferon-beta protein. In infected asthmatic cells, exogenous interferon-beta induced apoptosis and reduced virus replication, demonstrating a causal link between deficient interferon-beta, impaired apoptosis and increased virus replication. These data suggest a novel use for type I interferons in the treatment or prevention of virus-induced asthma exacerbations.
Assessment of re‐aggregated human pancreatic islets for secondary drug screening (2014)

Human re-aggregated clusters of islet cells, of a constant size were more responsive to all compounds tested than native human islets. Importantly, the assay variability was less in the re-aggregated cluster preparations, which suggests that such re-aggregated cells could be useful for drug development.
Negative regulation of c-kit-mediated cell proliferation by Fc gamma RIIB. (1999)

Fc gamma RIIB are single-chain low-affinity receptors for IgG that bear an immunoreceptor tyrosine-based inhibition motif in their intracytoplasmic domain and that negatively regulate immunoreceptor tyrosine-based activation motif-dependent cell activation. They are widely expressed by cells of hematopoietic origin. We investigated here whether Fc gamma RIIB could also negatively regulate protein tyrosine kinase receptor (RTK)-dependent cell proliferation. As an experimental model, we used growth factor-dependent mast cells that constitutively express Fc gamma RIIB and c-kit, an RTK prototype. We found that anti-c-kit Abs mimicked the effect of stem cell factor and induced thymidine incorporation in Fc gamma RIIB-/-, but not in wild-type (wt) mast cells unless Fc gamma RIIB were blocked or anti-c-kit F(ab')2 were used. When coaggregated with c-kit by intact Abs in wt mast cells, Fc gamma RIIB inhibited thymidine incorporation, as well as cell proliferation, and inhibition was correlated with an arrest of cells in G1 during the cell cycle. The coaggregation of c-kit with Fc gamma RIIB did not affect ligand-induced c-kit phosphorylation and induced the tyrosyl-phosphorylation of Fc gamma RIIB, which selectively recruited the Src homology 2 domain-bearing inositol 5-phosphatase SHIP. Our results indicate that IgG Abs to growth factors or growth factor receptors may control RTK-dependent proliferation of a variety of cells that express Fc gamma RIIB.
Sexual agglutination in Saccharomyces cerevisiae (1981)

Treatment of either mating type of Saccharomyces cerevisiae with the appropriate sex pheromone increased cell-cell binding in a modified cocentrifugation assay. Constitutive agglutination of haploids was qualitatively similar to pheromone-induced agglutination. Regardless of exposure to pheromone, agglutinable combinations of cells exhibited maximal binding across similar ranges of ionic strength, pH, and temperature. Binding of all combinations was inhibited by 8 M urea, 1 M pyridine, or 0.05% sodium dodecyl sulfate. From alpha-cells we solubilized and partially purified an inhibitor of a-cell agglutinability. This inhibitor reversibly masked all a-cell adhesion sites and inactivated pheromone-treated and control cells with similar kinetics. The inhibitor behaved as a homogeneous species in heat inactivation experiments. Based on these results, we proposed a model for pheromone effects on agglutination in S. cerevisiae.