gebhart/patrepeval huggingface dataset:
A Global Regulatory Role of Gluconeogenic Genes in Escherichia coli Revealed by Transcriptome Network Analysis (2005)

In bacterial adaptation to the dynamic environment, metabolic genes are typically thought to be the executors, whereas global transcription regulators are regarded as the decision makers. Although the feedback from metabolic consequence is believed to be important, much less is understood. This work demonstrates that the gluconeogenic genes in Escherichia coli, ppsA, sfcA, and maeB, provide a feedback loop to the global regulator, cAMP receptor protein (CRP), in carbon source transition. Disruption of one of the gluconeogenic pathways has no phenotype in balanced growth, but causes a significant delay in the diauxic transition from glucose to acetate. To investigate the underlying mechanism, we measured the transcriptome profiles during the transition using DNA microarray, and network component analysis was employed to obtain the transcription factor activities. Results showed that one of the global regulators, CRP, was insufficiently activated during the transition in the ppsA deletion mutant. Indeed, addition of cAMP partially rescued the delay in transition. These results suggest that the gluconeogenic flux to phosphoenolpyruvate is important for full activation of adenylate cyclase through the phosphorylated enzyme IIA(glu) of the phosphotransferase system. Reduction of this flux causes insufficient activation of CRP and a global metabolic deficiency, which exemplifies a significant feedback interaction from metabolism to the a global regulatory system.
PLECKSTRIN HOMOLOGY DOMAINS: A Common Fold with Diverse Functions (1998)

Pleckstrin homology (PH) motifs are approximately 100 amino-acid residues long and have been identified in nearly 100 different eukaryotic proteins, many of which participate in cell signaling and cytoskeletal regulation. Despite minimal sequence homology, the three-dimensional structures are remarkably conserved. This review gives an overview of the PH domain architecture and examines the best-studied examples in an attempt to understand their function.
αvβ3Integrin Mediates the Cell-adhesive Capacity and Biological Activity of Basic Fibroblast Growth Factor (FGF-2) in Cultured Endothelial Cells (1997)

Fibroblast growth factor-2 (FGF-2) immobilized on non-tissue culture plastic promotes adhesion and spreading of bovine and human endothelial cells that are inhibited by anti-FGF-2 antibody. Heat-inactivated FGF-2 retains its cell-adhesive activity despite its incapacity to bind to tyrosine-kinase FGF receptors or to cell-surface heparan sulfate proteoglycans. Recombinant glutathione-S-transferase-FGF-2 chimeras and synthetic FGF-2 fragments identify two cell-adhesive domains in FGF-2 corresponding to amino acid sequences 38-61 and 82-101. Both regions are distinct from the FGF-receptor-binding domain of FGF-2 and contain a DGR sequence that is the inverse of the RGD cell-recognition sequence. Calcium deprivation, RGD-containing eptapeptides, soluble vitronectin (VN), but not fibronectin (FN), inhibit cell adhesion to FGF-2. Conversely, soluble FGF-2 prevents cell adhesion to VN but not FN, thus implicating VN receptor in the cell-adhesive activity of FGF-2. Accordingly, monoclonal and polyclonal anti-alphavbeta3 antibodies prevent cell adhesion to FGF-2. Also, purified human alphavbeta3 binds to immobilized FGF-2 in a cation-dependent manner, and this interaction is competed by soluble VN but not by soluble FN. Finally, anti-alphavbeta3 monoclonal and polyclonal antibodies specifically inhibit mitogenesis and urokinase-type plasminogen activator (uPA) up-regulation induced by free FGF-2 in endothelial cells adherent to tissue culture plastic. These data demonstrate that FGF-2 interacts with alphavbeta3 integrin and that this interaction mediates the capacity of the angiogenic growth factor to induce cell adhesion, mitogenesis, and uPA up-regulation in endothelial cells.
Identification of The Tocopherol‐Cyclase in the Blue‐Green Algae Anabaena variabilis KÜTZING (Cyanobacteria) (1993)

Abstract Incubation of Spheroplats of Anabaena variabilis ( Cyanobacteria ) with 22 the 2,6‐ O ‐dimetyl‐ß‐cycoldextrin complex of 2,3‐dimethyl‐5‐phytylhydroquinone ( 11 ), revealed the presence of a hitherto unknown enzyme which catalyzes the cyclization of th substrate 11 to give enantiomerically pure γ‐tocopherol ( 3 ) in ⩾ 93% yield.
Direct analysis of C 60 and related compounds with electrospray mass spectrometry (1995)

Abstract Without performing any charge transfer chemical reaction, C 60 and its derivatives could be analyzed directly by electrospray mass spectrometry. Oxidation or reduction at the metal/solution interface of the probe tip was probably responsible for the formation of these radical cations and anions. This technique appeared to be superior to desorption chemical ionization and fast‐atom bombardment ionization in the analysis of C 60 derivatives because the mass spectra were characterized by molecular ions with little or no fragmentation.
Expression of thioredoxin is enhanced in atherosclerotic plaques and during neointima formation in rat arteries. (1998)

Thioredoxin (TRX) is an intracellular enzyme that has a variety of activities as a hydrogen donor for various intracellular molecules. In the present study, we investigated the role of TRX in atherosclerotic lesions. In human atherosclerotic specimens, TRX and TRX mRNA were enhanced in endothelial cells and macrophages in the atherosclerotic plaques. In balloon-injured rat arteries, TRX expression increased from 2 to 6 weeks after injury; TRX was induced in the neointimal regenerating endothelial cells. In hybridization experiments, TRX mRNA was also induced from 2 to 6 weeks in the endothelium. In this model, inducible nitric oxide synthase immunoreactivity in the neointimal smooth muscle cells and endothelial cells increased from 2 to 6 weeks after surgical procedures were performed. During this period, the immunoreactivity of nitrotyrosine, which is a marker of nitric oxide (NO) production, also increased. We focused on the association between TRX and NO. In vitro studies using a murine endothelial cell line showed TRX and TRX mRNA induction by NO and peroxynitrite donors. Enhanced expression of TRX was detected mainly within the cytoplasm in immunocytochemical studies. In addition, TRX-transfected cells showed resistance to peroxynitrite-induced cytotoxicity. These findings indicate that TRX and the cellular redox state modified by TRX play a crucial role in arterial neointima formation in atherosclerosis.
Site-Directed Mutagenesis of Ubiquitin. Differential Roles for Arginine in the Interaction with Ubiquitin-Activating Enzyme (1994)

The strict evolutionary conservation of ubiquitin suggests an essential role for each residue in the folding, stability, or function of the protein but precludes identification of such contributions through interspecies comparison of ubiquitin sequences. However, site-directed mutagenesis potentially allows assignment of specific function(s) for each residue. The four arginines present on ubiquitin at positions 42, 54, 72, and 74 were independently mutated to leucine and their effects on the interaction of the resulting polypeptides with ubiquitin-activating enzyme (E1) were characterized. All of the mutants except UbR54L exhibited altered kinetics for E1-catalyzed ATP:PPi exchange compared to wild-type ubiquitin. In addition, the UbR72L mutant altered the mechanism of E1 from strictly order addition of substrates to random addition with respect to ATP and ubiquitin. Values for the intrinsic Kd of ubiquitin binding were determined by coupling the net forward reaction of E1 to the E232K-catalyzed conjugation of histone H2B. Only R54 and R72 residues participate in the initial binding of free ubiquitin, resulting in a 6- or 58-fold increase in Kd for UbR54L or UbR72L, respectively, compared to wild type. More significant effects of the UbR42L and UbR72L mutants were observed for binding of their respective ubiquitin adenylate intermediates within the E1 active site. Wild-type ubiquitin adenylate binds to E1 with an estimated Kd < or = 8 x 10(-12) M while intermediates formed with UbR42L or UbR72L each bind with ca. 10(3)-fold lower affinity, representing a destabilization of > or = 7 kcal/mol.(ABSTRACT TRUNCATED AT 250 WORDS)
Some statistical methods useful in circulation research. (1980)

Some statistical techniques for analyzing the kinds of studies typically reported in Circulation Research are described. Particular emphasis is given to the comparison of means from more than two populations, the joint effect of several experimentally controlled variables, and the analysis of studies with repeated measurements on the same experimental units.
Delineation of myocardial oxygen utilization with carbon-11-labeled acetate. (1987)

Although positron-emission tomography (PET) with labeled fatty acid delineates infarct size and permits qualitative assessment of fatty acid utilization, quantification of oxidative metabolism is limited by complex alterations in the pattern of utilization of fatty acid during ischemia and reperfusion. Because metabolism of acetate by myocardium is less complex than that of glucose or palmitate, we characterized kinetics of utilization of radiolabeled acetate in 37 isolated rabbit hearts perfused with modified Krebs-Henseleit buffer and performed a pilot tomographic study in man. Results of initial experiments with carbon-14-labeled acetate (14C-acetate) indicated that the steady-state extraction fraction of acetate averaged 61.5 +/- 4.0% in control hearts (n = 4), 93.6 +/- 0.9% in hearts rendered ischemic (n = 4), and 54.8 +/- 4.0% in hearts reperfused after 60 min of ischemia (n = 3). Oxidation of 14C-acetate, assessed from the rate of efflux of 14CO2 in the venous effluent, correlated closely with the rate of oxygen consumption under diverse metabolic conditions (r = .97, p less than .001). In addition, no significant differences were observed between rates of efflux of total 14C in all chemical species (reflecting total clearance of tracer from myocardium) and efflux of 14CO2. Clearance of 11C-acetate, measured externally with gamma probes in normal and ischemic myocardium, correlated closely with clearance of 14C-acetate measured directly in the effluent (r = .99, p less than .001) and with overall myocardial oxygen consumption (r = .95, p less than .001). Accumulation and clearance of 11C-acetate from human myocardium with PET demonstrated kinetics comparable to those seen with radiolabeled acetate in vitro. Thus externally detectable clearance of 11C-acetate provides a quantitative index of myocardial oxidative metabolism despite variation in the patterns of intermediary metabolism that confounds interpretation of results with conventionally used tracers such as glucose and fatty acid.
Medicinal Chemistry. (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMedicinal Chemistry.Alfred BurgerCite this: J. Med. Chem. 1963, 6, 6, 829Publication Date (Print):November 1, 1963Publication History Published online1 May 2002Published inissue 1 November 1963https://pubs.acs.org/doi/10.1021/jm00342a066https://doi.org/10.1021/jm00342a066research-articleACS PublicationsRequest reuse permissionsArticle Views140Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Therapy of hepatitis C: Cost-effectiveness analysis (1997)

The natural history of untreated chronic hepatitis C is controversial, and direct knowledge of the long-term clinical and economic outcomes of current alpha interferon treatment regimens remains limited. Decision analytic models using available information on outcome probabilities and associated health care costs in the United States have been developed but are available only in abstract form. They suggest that chronic hepatitis C is a life-shortening disease and that alpha interferon treatment, for 6 or 12 months, despite its up-front costs and failure to induce a prolonged therapeutic response in most patients, increases life expectancy (which nevertheless is still reduced). It does so with a marginal cost-effectiveness well within the acceptable range of medical interventions in the United States. Even empiric therapy, without regard to viral level, genotype, and baseline histology, is within an acceptable cost-effectiveness range. Improving the response rate is likely to make treatment even more cost-effective and possibly cost-saving. Discounting at 3% would also lower the marginal cost-effectiveness; treatment of younger patients would likely lead to cost-savings. Future needs include the development of better databases and cost data for estimating outcomes.
Using photographs to enhance videos of a static scene (2007)

We present a framework for automatically enhancing videos of a static scene using a few photographs of the same scene. For example, our system can transfer photographic qualities such as high resolution, high dynamic range and better lighting from the photographs to the video. Additionally, the user can quickly modify the video by editing only a few still images of the scene. Finally, our system allows a user to remove unwanted objects and camera shake from the video. These capabilities are enabled by two technical contributions presented in this paper. First, we make several improvements to a state-of-the-art multiview stereo algorithm in order to compute view-dependent depths using video, photographs, and structure-from-motion data. Second, we present a novel image-based rendering algorithm that can re-render the input video using the appearance of the photographs while preserving certain temporal dynamics such as specularities and dynamic scene lighting.
Duration of amantadine benefit on dyskinesia of severe Parkinson's disease. (2004)

300 mg amantadine reduces dyskinesia in Parkinson's disease by approximately 45% but the benefit lasted less than eight months.
Pseudoprolines: Targeting acis Conformation in a Mimetic of the gp120 V3 Loop of HIV-1 (2000)

The specific recognition of cis peptide bonds is possible with antibodies that are directed against cyclic and linear peptide antigens derived from the V3 loop of the HIV-1 protein gp120, into which a thiazolidine derivative (pseudoproline) has been introduced (see schematic representation). This extension of the pseudoproline concept may help to decipher the unique role of proline residues in biologically relevant systems.
Wavenet Based Low Rate Speech Coding (2018)

Traditional parametric coding of speech facilitates low rate but provides poor reconstruction quality because of the inadequacy of the model used. We describe how a WaveNet generative speech model can be used to generate high quality speech from the bit stream of a standard parametric coder operating at 2.4 kb/s. We compare this parametric coder with a waveform coder based on the same generative model and show that approximating the signal waveform incurs a large rate penalty. Our experiments confirm the high performance of the WaveNet based coder and show that the speech produced by the system is able to additionally perform implicit bandwidth extension and does not significantly impair recognition of the original speaker for the human listener, even when that speaker has not been used during the training of the generative model.
Nitazoxanide: pharmacokinetics and metabolism in man (2000)

Elimination of radiocarbon occurred both in the urine (31.5% of the dose on average) and in the feces (66.2% on average). T and T-glucuronide contributed 15% of total urine radioactivity. N was found to deacetylate extremely rapidly to T in plasma (half-life of about 6 minutes at 37 degrees C) as well as in presence of liver microsomes. T was the only species obtained by incubation with human microsomes while rat microsomes yielded hydroxylated T in addition. The main species identified in human plasma, urine and bile was T-glucuronide, the identification of which was confirmed by comparison with an authentic sample. No species other than T was detected in feces, indicating intensive intestinal deconjugation, while radioactivity and absorbance detectors showed largely unresolved clusters.
Reliable long‐lasting depression interacts with variable short‐term facilitation to determine corticostriatal paired‐pulse plasticity in young rats (2007)

Synaptic plasticity at corticostraital synapses is proposed to fine tune movment and improve motor skills. We found paired-pulse plasticity at corticostriatal synapses reflected variably expressed short-term facilitation blended with a consistent background of longer-lasting depression. Presynaptic modulation via neuotransmitter receptor activation was ruled out as a mechanism for long-lasting paired-pulse depression by examining the effect of selective receptor antagonists. EPSC amplitude and paired-pulse plasticity, however, was influenced by block of D2 dopamine receptors. Block of glutamate transport with l-transdicarboxylic acid (PDC) reduced EPSCs, possibly through a mechanism of AMPA receptor desensitization. Removal of AMPA receptor desensitization with cyclothiazide reduced the paired-pulse depression at long-duration interstimulus intervals (ISIs), indicating that AMPA receptor desensitization participates in corticostriatal paired-pulse plasticity. The low-affinity glutamate receptor antagonist cis-2,3-piperidine dicarboxylic acid (PDA) increased paired-pulse depression, suggesting that a presynaptic component also exists for long-lasting paired-pulse depression. Low Ca(2+)-high Mg(2+) or BAPTA-AM dramatically reduced the amplitude of corticostriatal EPSCs and both manipulations increased the expression of facilitation and, to a lesser extent, they reduced long-lasting paired-pulse depression. EGTA-AM produced a smaller reduction in EPSC amplitude and it did not alter paired-pulse facilitation, but in contrast to low Ca(2+) and BAPTA-AM, EGTA-AM increased long-lasting paired-pulse depression. These experiments suggest that facilitation and depression are sensitive to vesicle depletion, which is dependent upon changes in peak Ca(2+) (i.e. low Ca(2+)-high Mg(2+) or BAPTA-AM). In addition, the action of EGTA-AM suggests that basal Ca(2+) regulates the recovery from long-lasting paired-pulse depression, possibly thourgh a Ca(2+)-sensitive process of vesicle delivery.
Human follicle-stimulating hormone produced by recombinant DNA technology: a review for clinicians (1995)

Human follicle-stimulating hormone (FSH) is now produced in vitro by recombinant DNA technology. FSH being a complex heterodimeric protein, a eukaryotic cell line has been selected for expression work (Chinese hamster ovary cells). The pharmaceutical preparation of recombinant human FSH (r-FSH) differs from that of human menopausal gonadotrophin (HMG) and the first generation of urinary human FSH (u-FSH) in terms of (i) source of bulk materials, (ii) purity and specific activity, (iii) batch to batch consistency, and (iv) complete absence of luteinizing hormone (LH) activity. Pharmacokinetic characterization of r-FSH has shown an absolute bioavailability of approximately 75% after both s.c. and i.m. administration and an apparent terminal half-life of 37 +/- 25 h. These characteristics are very similar to those of u-FSH. Clinical efficacy and safety are currently demonstrated through several randomized, well controlled studies, comparing r-FSH administered s.c. with u-FSH administered i.m. for stimulating follicular development prior to assisted reproduction treatment and in World Health Organization (WHO) group II anovulation. To date, approximately 1000 patients have been treated with r-FSH. Moreover, r-FSH has recently been used successfully in association with recombinant human LH for inducing ovulation and pregnancy in WHO group I anovulatory patients. At this stage of r-FSH preparation assessment, it is likely that r-FSH will replace all urinary-derived FSH preparations for stimulating ovarian follicular development. For clinicians, current experience with r-FSH indicates that it should be used with the regimes and doses applied to u-FSH.
IL-6 stimulates osteoclast-like multinucleated cell formation in long term human marrow cultures by inducing IL-1 release. (1990)

IL-6 enhances the differentiation of pluripotent hematopoietic stem cells but predominantly affects the differentiation of hematopoietic cells in the granulocyte-macrophage lineage. We have previously shown that multinucleated cells (MNC) with many features of the osteoclast phenotype form in long term human marrow cultures. Addition of rhIL-6 (10 to 100 pg/ml) to these cultures significantly increased MNC formation, with greater than 80% of the MNC expressing an Ag that cross-reacts with the mAb 23c6. This antibody preferentially binds to osteoclasts. rhIL-6 did not enhance MNC formation in marrow cultures treated with 1,25 dihydroxyvitamin D3, a potent stimulator of MNC formation, but significantly increased the percentage of MNC that cross-reacted with the 23c6 mAb. Addition of antihuman IL-1 to cultures treated with rhIL-6 totally inhibited the increase in MNC formation stimulated by rhIL-6. In contrast, anti-IL-1 did not affect MNC formation stimulated by 1,25 dihydroxyvitamin D3. Further, conditioned media from marrow cultures exposed to rhIL-6 contained elevated levels of IL-1 beta (500 pg/ml compared to 23 pg/ml in control cultures 15 h after IL-6 addition). These results suggest that the capacity of rhIL-6 to stimulate formation of MNC which cross-react with 23c6 is mediated by induction of release of IL-1 beta.
Rapid, noninvasive concentration measurements of aqueous biological analytes by near-infrared Raman spectroscopy (1996)

Accurate concentration measurements of glucose, lactic acid, and creatinine in saline solution have beena chieved with near-IR Raman spectroscopy and a partial least-squares analysis. The Raman spectra were acquired remotely through optical fibers. A root-mean-squared prediction error of 1.2 mM for glucose concentration was achieved in 100 s. Concentrations of other analytes were predicted with similar accuracy.