gebhart/patrepeval huggingface dataset:
Purification and Refolding of Recombinant Human proMMP-7 (pro-Matrilysin) Expressed inEscherichia coli and Its Characterization (1996)

Human matrix metalloproteinase-7 (MMP-7 = matrilysin) was overproduced in Escherichia coli as a recombinant zymogen (31 kDa), the C-terminus of which bears artificial hexa-histidines. Most of the enzyme was isolated from the insoluble fraction of the cell lysate and purified by a single step using Ni-NTA resin after solubilization of the precipitates with 8 M urea solution. The resin-bound recombinant protein was refolded into a form that is activatable by p-amino-phenylmercuric acetate in an autocatalytic manner. The activated enzyme cleaved a synthetic peptide substrate at the reported site for MMP-7. Digestion of carboxymethylated transferrin (a natural substrate of MMP-7) by the recombinant proteinase generated fragments with the same peptide map as in the case of native purified MMP-7. The autocatalytic activation and enzyme reaction were entirely dependent on the presence of calcium and zinc ions. The enzyme activity to cleave carboxymethylated transferrin was inhibited by tissue inhibitors of metalloproteinases-1 and -2, MMP-specific inhibitors. The activity of the recombinant MMP-7 was also inhibited by a synthetic peptide derived from a part of the cysteine switch that maintains the zymogen in an inactive state. Thus, we report here a simple means of preparing a large quantity of recombinant proMMP-7 that can be used to study the activation mechanism and to screen synthetic inhibitors.
An Image Archive With The ACR/NEMA Message Formats (1988)

An image archive has been designed to manage and store radiologic images received from within the main Hospital and a from a suburban orthopedic clinic. Images are stored on both magnetic as well as optical media. Prior comparison examinations are combined with the current examination to generate a &apos;viewing folder&apos; that is sent to the display station for primary diagnosis. An &apos;archive-manager&apos; controls the database managment, periodic optical disk backup and &apos;viewing-folder&apos; generation. Images are converted into the ACR/NEMA message format before being written to the optical disk. The software design of the &apos;archive-manager&apos; and its associated modules is presented. Enhancements to the system are discussed.
On the Mechanism of NO Release from Sydnonimines (1989)

The vasodilator and antiaggregatory properties of sydnonimines like SIN-1 are thought to be due to their marked stimulatory action on soluble guanylate cyclase. Enzyme activation and consecutive cyclic GMP accumulation is mediated by the liberation of nitric oxide (NO) from the open-ring A forms of sydnonimines. The purpose of the present study was to investigate the mechanism of NO release from sydnonimines in direct comparison to their stimulatory effect at the target enzyme, soluble guanylate cyclase. All sydnonimines tested were found to spontaneously liberate NO, the rate of which closely correlated with the extent of enzyme activation. NO release occurred nonlinearly with time and became maximal at high sydnonimine concentration. The in vitro stability of the A forms neither correlated with the measured rate of NO release nor with enzyme activation, indicating that a direct stimulation of guanylate cyclase by the A forms is rather unlikely. Besides NO, all sydnonimines generated NO2- and NO3- at a nearly equimolar rate. The addition of cysteine induced a marked shift from NO3- to NO2- with a small reduction in NO release, which is paralleled by a weak rightward shift of the EC50 at the guanylate cyclase. All tested sydnonimines were found to consume molecular oxygen at rates that closely corresponded to the measured rates of NO formation. By a molar comparison, the amounts of consumed oxygen are clearly higher, as would be expected for the oxidative conversion of NO to NO2- and NO3-. Oxygen seems to be additionally involved in the induction of NO formation while being converted to superoxide (O2-). In accordance with an autocatalytic process, O2- further enhances sydnonimine decomposition, since in the presence of superoxide dismutase (SOD) the rate of SIN-1C and NO2-/NO3- formation from SIN-1A was reduced, whereas the rate of NO liberation seemingly increased. O2- has, however, no influence on the rate of hydrolysis of SIN-1 to SIN-1A. At the level of guanylate cyclase, the presence of SOD induced a leftward shift of the concentration-response curve to SIN-1, in agreement with an enhancement of efficacy of NO by blocking the NO-scavenging effect of O2-. An additional O2- generation markedly enhanced SIN-1A decomposition to NO2-/NO3- and reduced the apparent rate of NO formation. We conclude from our results that oxygen plays a key role in the decomposition of sydnonimines and thus in the formation of NO as their pharmacodynamically active principle. Oxygen attack most probably occurs by one-electron abstraction from the A form of the respective sydnonimine compound.(ABSTRACT TRUNCATED AT 400 WORDS)
Vacuolar H+-ATPase in human breast cancer cells with distinct metastatic potential: distribution and functional activity (2004)

Tumor cells thrive in a hypoxic microenvironment with an acidic extracellular pH. To survive in this harsh environment, tumor cells must exhibit a dynamic cytosolic pH regulatory system. We hypothesize that vacuolar H(+)-ATPases (V-ATPases) that normally reside in acidic organelles are also located at the cell surface, thus regulating cytosolic pH and exacerbating the migratory ability of metastatic cells. Immunocytochemical data revealed for the first time that V-ATPase is located at the plasma membrane of human breast cancer cells: prominent in the highly metastatic and inconspicuous in the lowly metastatic cells. The V-ATPase activities in isolated plasma membranes were greater in highly than in lowly metastatic cells. The proton fluxes via V-ATPase evaluated by fluorescence spectroscopy in living cells were greater in highly than in lowly metastatic cells. Interestingly, lowly metastatic cells preferentially used the ubiquitous Na(+)/H(+) exchanger and HCO(3)(-)-based H(+)-transporting mechanisms, whereas highly metastatic cells used plasma membrane V-ATPases. The highly metastatic cells were more invasive and migratory than the lowly metastatic cells. V-ATPase inhibitors decreased the invasion and migration in the highly metastatic cells. Altogether, these data indicate that V-ATPases located at the plasma membrane are involved in the acquisition of a more metastatic phenotype.
Derivation of Human Embryonic Stem Cell Lines From Biopsied Blastomeres on Human Feeders With Minimal Exposure to Xenomaterials (2009)

In a continuous effort to improve the generation of therapeutic grade human embryonic stem cell (hESC) lines, we focused on preserving developmental capacity of the embryos, minimizing the exposure to xenomaterials, increasing derivation efficacy, and reducing the complexity of the derivation procedure. In this study, we describe an improved method for efficient derivation of hESC lines from blastomeres of biopsied embryos. Our protocol substituted feeder cells of mouse origin with human foreskin fibroblasts (HFFs), limited serum exposure of cells to formation of the initial outgrowth, and increased derivation efficacy from 12.5% (one hESC line out of 13 biopsies) to 50% (3 out of 6 biopsies) by using early population doubling (PD) HFFs. In addition, it eliminated a need for embryo-blastomere coculture, thus reducing the complexity of the culture and enabling continued development of the biopsied embryo under optimal conditions. All derived lines maintained normal karyotype and expressed totipotent phenotype including the ability to differentiate into trophectoderm and all three germ layers.
Fas ligand mediates activation-induced cell death in human T lymphocytes. (1995)

A significant proportion of previously activated human T cells undergo apoptosis when triggered through the CD3/T cell receptor complex, a process termed activation-induced cell death (AICD). Ligation of Fas on activated T cells by either Fas antibodies or recombinant human Fas-ligand (Fas-L) also results in cytolysis. We demonstrate that these two pathways of apoptosis are causally related. Stimulation of previously activated T cells resulted in the expression of Fas-L mRNA and lysis of Fas-positive target cells. Fas-L antagonists inhibited AICD of T cell clones and staphylococcus enterotoxin B (SEB)-specific T cell lines. The data indicate AICD in previously stimulated T cells is mediated by Fas/Fas-L interactions.
A Fuzzy-Neural Approach with Collaboration Mechanisms for Semiconductor Yield Forecasting (2010)

Yield forecasting is critical to a semiconductor manufacturing factory. To further enhance the effectiveness of semiconductor yield forecasting, a fuzzy-neural approach with collaboration mechanisms is proposed in this study. The proposed methodology is modified from Chen and Lin’s approach by incorporating two collaboration mechanisms: favoring mechanism and disfavoring mechanism. The former helps to achieve the consensus among multiple experts to avoid the missing of actual yield, while the latter shrinks the search region to increase the probability of finding out actual yield. To evaluate the effectiveness of the proposed methodology, it was applied to some real cases. According to experimental results, the proposed methodology improved both precision and accuracy of semiconductor yield forecasting by 58% and 35%, respectively.
Interrogation and control of condensed phase chemical dynamics with linearly chirped pulses: I2 in solid Kr (1996)

The effect of linearly chirped pulses in condensed phase ultrafast pump–probe experiments is investigated by classical simulations for the model system of I2 isolated in a Kr matrix. The central frequency of the probe laser is selected to monitor exclusively the event of first collision and recoil of atoms from the host cage. It is shown that a chirped probe pulse enables characterization of the magnitude and sign of the momentum of the evolving trajectory flux. This can be understood by transforming the frequency–time profile of the probe pulse to coordinate–time space, and noting that the observable signal is a function of the relative group velocities of the traveling wave packet and the traveling window function. The effect of the pump pulse chirp, is a measure of the controllability of the evolving dynamics. In the particular case studied, breaking and remaking of the I2 bond near the dissociation limit of the bare molecule, it is shown that the memory of the system outlasts the collision with the cage. Negatively chirped pulses produce a more tightly focused wave packet during recoil, leading to a stronger population coherence in the subsequent dynamics.
Protein tyrosine phosphatases: their roles in signal transduction. (1996)

Protein tyrosine phosphatases play critical roles in a number of cellular signal transduction pathways. Receptor-like PTPases such as CD45 are essential for antigen-induced proliferative responses of T-cells. Intracellular PTPases have been shown to associate with specific growth factor receptors and this association has a dramatic effect on receptor signaling mechanisms. Other phosphatases (e.g., the product of the CDC25 gene) are essential for cell cycle progression. It appears that the cellular location of the intracellular PTPases plays an important role in defining the substrate specificity. Phosphatases are also present in both pathogenic bacteria and viruses. These PTPases most likely function to disrupt important signal transduction pathways present in the host. More than 30 different phosphatases have been cloned and characterized. A detailed understanding of their catalytic properties suggests that all PTPases use a common mechanism for removing phosphatase from various phosphoproteins. Two PTPase structures recently have been determined. The structural information along with biochemical and kinetic data provides a basis for understanding the catalytic properties of these enzymes.
Degradation of 2-Chlorobenzoate byPseudomonas cepacia2CBS (1989)

A bacterium was isolated from water by enrichment on 2-chlorobenzoate as sole source of carbon and energy. Based on morphological and physiological properties, this microorganism was assigned to the species Pseudomonas cepacia. The organism was designated Pseudomonas cepacia 2CBS. During growth on 2-chlorobenzoate, the chlorine substituent was released quantitatively, and a small amount of 2,3-dihydroxybenzoate accumulated in the culture medium. Mutants of Pseudomonas cepacia 2CBS were induced by treatment with N-methyl-N'-nitro-N-nitrosoguanidine. Some of these mutants produced catechol from 2-chlorobenzoate. Other mutants accumulated the meta-cleavage product of catechol, 2-hydroxy-cis,cis-muconic acid semialdehyde. In crude cell-free extracts of Pseudomonas cepacia 2CBS, an enzyme was detected which catalysed the conversion of 2-chlorobenzoate to catechol. Molecular oxygen, NADH and exogenous Fe2+ were required for activity. Stoichiometric amounts of chloride were released. Experiments with 18O2 revealed that both oxygen atoms in the hydroxyl groups of the product were derived from molecular oxygen. Thus, the enzyme catalysing the conversion of 2-chlorobenzoate was identified as 2-chlorobenzoate 1,2-dioxygenase (1,2-hydroxylating, dehalogenating, decarboxylating). 2-Chlorobenzoate 1,2-dioxygenase from Pseudomonas cepacia 2CBS was shown to be a multicomponent enzyme system. The activities of catechol 2,3-dioxygenase and catechol 1,2-dioxygenase were detected in crude cell-free extracts. The activity of catechol 2,3-dioxygenase was 60 times higher than the activity of catechol 1,2-dioxygenase, indicating that catechol is mainly degraded via meta-cleavage in Pseudomonas cepacia 2CBS. No enzyme was found which converted 2,3-dihydroxybenzoate, suggesting that this compound is a dead-end metabolite of 2-chlorobenzoate catabolism. A pathway for the degradation of 2-chlorobenzoate by Pseudomonas cepacia 2CBS is proposed.
Diabetes Promotes Cardiac Stem Cell Aging and Heart Failure, Which Are Prevented by Deletion of the p66 shc Gene (2006)

Diabetes leads to a decompensated myopathy, but the etiology of the cardiac disease is poorly understood. Oxidative stress is enhanced with diabetes and oxygen toxicity may alter cardiac progenitor cell (CPC) function resulting in defects in CPC growth and myocyte formation, which may favor premature myocardial aging and heart failure. We report that in a model of insulin-dependent diabetes mellitus, the generation of reactive oxygen species (ROS) leads to telomeric shortening, expression of the senescent associated proteins p53 and p16INK4a, and apoptosis of CPCs, impairing the growth reserve of the heart. However, ablation of the p66shc gene prevents these negative adaptations of the CPC compartment, interfering with the acquisition of the heart senescent phenotype and the development of heart failure with diabetes. ROS elicit 3 cellular reactions: low levels activate cell growth, intermediate quantities trigger cell apoptosis, and high amounts initiate cell necrosis. CPC replication predominates in diabetic p66shc-/-, whereas CPC apoptosis and myocyte apoptosis and necrosis prevail in diabetic wild type. Expansion of CPCs and developing myocytes preserves cardiac function in diabetic p66shc-/-, suggesting that intact CPCs can effectively counteract the impact of uncontrolled diabetes on the heart. The recognition that p66shc conditions the destiny of CPCs raises the possibility that diabetic cardiomyopathy is a stem cell disease in which abnormalities in CPCs define the life and death of the heart. Together, these data point to a genetic link between diabetes and ROS, on the one hand, and CPC survival and growth, on the other.
Pharmacogenomics of CYP2D6: Molecular Genetics, Interethnic Differences and Clinical Importance (2011)

CYP2D6 has received intense attention since the beginning of the pharmacogenetic era in the 1970s. This is because of its involvement in the metabolism of more than 25% of the marketed drugs, the large geographical and inter-ethnic differences in the genetic polymorphism and possible drug-induced toxicity. Many interesting reviews have been published on CYP2D6 and this review aims to reinstate the importance of the genetic polymorphism of CYP2D6 in different populations as well as some clinical implications and important drug interactions.
Growth factor‐induced proliferation of human fibroblasts in serum‐free culture depends on cell density and extracellular calcium concentration (1984)

Human neonatal skin fibroblasts plated sparsely in MCDB 105 traversed a complete cell cycle in the absence of serum or serum-derived proteins. Addition of pure PDGF did not significantly increase entrance into S phase as revealed by 3H-thymidine labeling index or clonal growth on palladium islands. In subphysiologic Ca2+ concentrations or in the presence of a calmodulin inhibitor, W7, proliferation in the absence of growth factors ceased and PDGF became mitogenic. In contrast, confluent fibroblast cultures were stimulated by PDGF in physiologic Ca2+ concentrations. This was also the case with sparse adult skin fibroblast cultures while a fetal strain entered S in the absence of PDGF even in low extracellular Ca2+ concentrations. EGF gave similar results as PDGF in all experiments performed. This proposes a similar role for the two growth factors in the cell cycle. However, a difference in the mechanisms of action of PDGF and EGF is indicated by the fact that PDGF and EGF were additive at optimal concentrations when maximal growth response by a single growth factor was restricted by a subphysiologic extracellular Ca2+ concentration.
Generalized guaranteed rate scheduling algorithms: a framework (1997)

In this paper, we define a class of generalized guaranteed rate (GR) scheduling algorithms that includes algorithms which allocate a variable rate to the packets of a flow. We define work-conserving generalized virtual clock, packet-by-packet generalized processor sharing, and self-clocked fair queueing scheduling algorithms that can allocate a variable rate to the packets of a flow. We also define scheduling algorithms suitable for servers where packet fragmentation may occur. We demonstrate that if a class of rate controllers is employed for a flow in conjunction with any scheduling algorithm in GR, then the resulting non-work-conserving algorithm also belongs to GR. This leads to the definition of several non-work-conserving algorithms. We then present a method for deriving the delay guarantee of a network of servers when: (1) different rates are allocated to packets of a flow at different servers along the path and the bottleneck server for each packet may be different, and (2) packet fragmentation and/or reassembly may occur. This delay guarantee enables a network to provide various service guarantees to flows conforming to any specification. We illustrate this by utilizing delay guarantee to derive delay bounds for flows conforming to leaky bucket, exponentially bounded burstiness, and flow specification. Our method for determining these bounds is valid in internetworks and leads to tighter results.
DNA recognition by intercalator-minor-groove binder hybrid molecules (1991)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTDNA recognition by intercalator-minor-groove binder hybrid moleculesChristian Bailly and Jean Pierre HenichartCite this: Bioconjugate Chem. 1991, 2, 6, 379–393Publication Date (Print):November 1, 1991Publication History Published online1 May 2002Published inissue 1 November 1991https://pubs.acs.org/doi/10.1021/bc00012a001https://doi.org/10.1021/bc00012a001research-articleACS PublicationsRequest reuse permissionsArticle Views586Altmetric-Citations64LEARN 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
Molecular Cloning and Sequence of a Complementary DNA Encoding 1-Aminocyclopropane-l-carboxylate Synthase Induced by Tissue Wounding (1990)

1-Aminocyclopropane-l-carboxylate (ACC) synthase [EC 4.4.1.14] is the key enzyme regulating ethylene biosynthesis in higher plants. A complementary DNA encoding wound-induced ACC synthase from mesocarp of winter squash (Cucurbita maxima Duch.) fruits was cloned, and its complete nucleotide sequence determined. The cloned cDNA contained an open reading frame of 1479 base pairs encoding a sequence of 493 amino acids. Identification of the cDNA was accomplished by expression of active enzyme in Escherichia coli harboring the cDNA and by the presence of a partial amino acid sequence identical to that found in the purified enzyme. A putative pyridoxal phosphate binding site of the enzyme is suggested. Northern blot analysis showed that the ACC synthase gene was activated by tissue wounding, and its expression was repressed by ethylene. Genomic Southern analysis indicates the presence of at least another sequence which weakly hybridizes with the cDNA.
Effects of a NR2B selective NMDA glutamate antagonist, CP‐101,606, on dyskinesia and parkinsonism (2008)

Glutamate antagonists decrease dyskinesia and augment the antiparkinsonian effects of levodopa in animal models of Parkinson's disease (PD). In a randomized, double-blind, placebo-controlled clinical trial, we investigated the acute effects of placebo and two doses of a NR2B subunit selective NMDA glutamate antagonist, CP-101,606, on the response to 2-hour levodopa infusions in 12 PD subjects with motor fluctuations and dyskinesia. Both doses of CP-101,606 reduced the maximum severity of levodopa-induced dyskinesia approximately 30% but neither dose improved Parkinsonism. CP-101,606 was associated with a dose-related dissociation and amnesia. These results support the hypothesis that glutamate antagonists may be useful antidyskinetic agents. However, future studies will have to determine if the benefits of dyskinesia suppression can be achieved without adverse cognitive effects.
Zwitterionic Polymerization to Generate High Molecular Weight Cyclic Poly(Carbosiloxane)s (2013)

The zwitterionic ring-opening of 2,2,5,5-tetramethyl-2,5-disila-1-oxacyclopentane (TMOSC) with N-heterocyclic carbenes generates high molecular weight cyclic p(TMOSC). The NHC-mediated polymerization of TMOSC with 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene (IMes, 1) generates the poly(carbosiloxane) p(TMOSC) with molecular weights from 27,000 < Mn < 80,000 Da (1.4 < Mw/Mn < 2.2) within 30 min at room temp. With the more nucleophilic carbene 1,3,4,5-tetramethyl-imidazol-2-ylidene (4), the ring-opening polymerization occurs within minutes at room temperature to generate cyclic p(TMOSC) with molecular weights up to Mn = 940,000 Da (Mw/Mn = 3.2). The resulting p(TMOSC)s are predominantly cyclic as evidenced by dilute solution viscosity studies and MALDI-TOF MS. DFT calculations provide support for both zwitterionic and neutral, cyclic intermediates.