WorldWideScience

Sample records for automated thrombin generation

  1. Calibrated automated thrombin generation measurement in clotting plasma.

    Science.gov (United States)

    Hemker, H Coenraad; Giesen, Peter; Al Dieri, Raed; Regnault, Véronique; de Smedt, Eric; Wagenvoord, Rob; Lecompte, Thomas; Béguin, Suzette

    2003-01-01

    Calibrated automated thrombography displays the concentration of thrombin in clotting plasma with or without platelets (platelet-rich plasma/platelet-poor plasma, PRP/PPP) in up to 48 samples by monitoring the splitting of a fluorogenic substrate and comparing it to a constant known thrombin activity in a parallel, non-clotting sample. Thus, the non-linearity of the reaction rate with thrombin concentration is compensated for, and adding an excess of substrate can be avoided. Standard conditions were established at which acceptable experimental variation accompanies sensitivity to pathological changes. The coefficients of variation of the surface under the curve (endogenous thrombin potential) are: within experiment approximately 3%; intra-individual: AVK, heparin(-likes), direct inhibitors]. In PRP, it is diminished in von Willebrand's disease, but it also shows the effect of platelet inhibitors (e.g. aspirin and abciximab). Addition of activated protein C (APC) or thrombomodulin inhibits thrombin generation and reflects disorders of the APC system (congenital and acquired resistance, deficiencies and lupus antibodies) independent of concomitant inhibition of the procoagulant pathway as for example by anticoagulants.

  2. International Normalized Ratio (INR), coagulation factor activities and calibrated automated thrombin generation - influence of 24 h storage at ambient temperature

    DEFF Research Database (Denmark)

    Christensen, T D; Jensen, C; Larsen, T B;

    2010-01-01

    clotting activity of coagulation factors II, VII, IX, and X as well as CAT generation was recorded after 0 and 24 h respectively. Statistical analyses included Bland-Altman plot, 95% limits of agreement, and a variability test using a mixed effect model. The level of INR remained statistically unchanged......International Normalized Ratio (INR) measurements are used to monitor oral anticoagulation therapy with coumarins. Single coagulation factor activities and calibrated automated thrombin (CAT) generation are considered as more advanced methods for evaluating overall haemostatic capacity. The aims...

  3. The modification of the thrombin generation test for the clinical assessment of dabigatran etexilate efficiency

    OpenAIRE

    Gribkova, Irina V.; Lipets, Elena N; Rekhtina, Irina G.; Alex I. Bernakevich; Ayusheev, Dorzho B.; Ruzanna A. Ovsepyan; Ataullakhanov, Fazoil I.; Elena I Sinauridze

    2016-01-01

    A new oral anticoagulant, dabigatran etexilate (DE, a prodrug of direct thrombin inhibitor (DTI) dabigatran), has been used clinically to prevent thrombosis. The assessment of dabigatran efficiency is necessary in some clinical cases, such as renal insufficiency, risk of bleeding, and drug interactions. However, a specific thrombin generation test (TGT) that is one of the most informative and sensitive to anticoagulant therapy (calibrated automated thrombinography (САТ)) shows a paradoxical i...

  4. Poor prognosis of hypocoagulability assessed by thrombin generation assay in disseminated intravascular coagulation.

    Science.gov (United States)

    Lee, Kyunghoon; Kim, Ji-Eun; Kwon, Jihyun; Kim, Inho; Yoon, Sung-Soo; Park, Seonyang; Han, Kyou-Sup; Kim, Hyun Kyung

    2014-04-01

    Overall assessment of the hemostatic system including procoagulant and anticoagulant changes may help assess the clinical status and prognosis of disseminated intravascular coagulation (DIC). The thrombin generation assay provides useful information about the global hemostatic status. Therefore, we measured several parameters of global hemostatic potential by the thrombin generation assay in patients suspected of having DIC. A total of 114 patients with suspected DIC were included. The thrombin generation assay was performed on the calibrated automated thrombogram using tissue factor with or without the addition of thrombomodulin, showing three parameters: lag time, endogenous thrombin potential (ETP), and peak thrombin. Both 1 and 5 pmol/l tissue factor-stimulated ETP and peak thrombin were well correlated with DIC severity. Interestingly, antithrombin level greatly affected ETP, whereas protein C influenced lag time. Prognostic analysis revealed that the area under the curve of peak thrombin stimulated by 1 pmol/l tissue factor was superior to that of D-dimer. Moreover, multivariate Cox analysis showed that the lag time and time to peak with both 1 and 5 pmol/l tissue factor were independent prognostic markers. ETP and peak thrombin well reflect DIC severity. Hypocoagulability manifesting as prolonged lag time and time to peak is expected to be an independent prognostic marker in DIC.

  5. The modification of the thrombin generation test for the clinical assessment of dabigatran etexilate efficiency.

    Science.gov (United States)

    Gribkova, Irina V; Lipets, Elena N; Rekhtina, Irina G; Bernakevich, Alex I; Ayusheev, Dorzho B; Ovsepyan, Ruzanna A; Ataullakhanov, Fazoil I; Sinauridze, Elena I

    2016-01-01

    A new oral anticoagulant, dabigatran etexilate (DE, a prodrug of direct thrombin inhibitor (DTI) dabigatran), has been used clinically to prevent thrombosis. The assessment of dabigatran efficiency is necessary in some clinical cases, such as renal insufficiency, risk of bleeding, and drug interactions. However, a specific thrombin generation test (TGT) that is one of the most informative and sensitive to anticoagulant therapy (calibrated automated thrombinography (САТ)) shows a paradoxical increase of test parameters, such as endogenous thrombin potential (ETP) and peak thrombin, in patients receiving DE. The paradoxical behaviour of ETP and peak thrombin in these patients in the presence of DTIs is mostly caused by a decrease in the activity of thrombin in the α2-macroglobulin-thrombin complex that is used as a calibrator in CAT. For a correct estimation of the TGT parameters in patient's plasma containing DTIs we proposed to use our previously described alternative calibration method that is based on the measurement of the fluorescence signal of a well-known concentration of the reaction product (7-amino-4-methylcoumarin). In this study, the validity of such approach was demonstrated in an ex vivo study in patients with knee replacement and two special patients with multiple myeloma, who received DE for thrombosis prophylaxis. PMID:27377013

  6. The modification of the thrombin generation test for the clinical assessment of dabigatran etexilate efficiency

    Science.gov (United States)

    Gribkova, Irina V.; Lipets, Elena N.; Rekhtina, Irina G.; Bernakevich, Alex I.; Ayusheev, Dorzho B.; Ovsepyan, Ruzanna A.; Ataullakhanov, Fazoil I.; Sinauridze, Elena I.

    2016-01-01

    A new oral anticoagulant, dabigatran etexilate (DE, a prodrug of direct thrombin inhibitor (DTI) dabigatran), has been used clinically to prevent thrombosis. The assessment of dabigatran efficiency is necessary in some clinical cases, such as renal insufficiency, risk of bleeding, and drug interactions. However, a specific thrombin generation test (TGT) that is one of the most informative and sensitive to anticoagulant therapy (calibrated automated thrombinography (САТ)) shows a paradoxical increase of test parameters, such as endogenous thrombin potential (ETP) and peak thrombin, in patients receiving DE. The paradoxical behaviour of ETP and peak thrombin in these patients in the presence of DTIs is mostly caused by a decrease in the activity of thrombin in the α2-macroglobulin-thrombin complex that is used as a calibrator in CAT. For a correct estimation of the TGT parameters in patient’s plasma containing DTIs we proposed to use our previously described alternative calibration method that is based on the measurement of the fluorescence signal of a well-known concentration of the reaction product (7-amino-4-methylcoumarin). In this study, the validity of such approach was demonstrated in an ex vivo study in patients with knee replacement and two special patients with multiple myeloma, who received DE for thrombosis prophylaxis. PMID:27377013

  7. Anticoagulants and the propagation phase of thrombin generation.

    Directory of Open Access Journals (Sweden)

    Thomas Orfeo

    Full Text Available The view that clot time-based assays do not provide a sufficient assessment of an individual's hemostatic competence, especially in the context of anticoagulant therapy, has provoked a search for new metrics, with significant focus directed at techniques that define the propagation phase of thrombin generation. Here we use our deterministic mathematical model of tissue-factor initiated thrombin generation in combination with reconstructions using purified protein components to characterize how the interplay between anticoagulant mechanisms and variable composition of the coagulation proteome result in differential regulation of the propagation phase of thrombin generation. Thrombin parameters were extracted from computationally derived thrombin generation profiles generated using coagulation proteome factor data from warfarin-treated individuals (N = 54 and matching groups of control individuals (N = 37. A computational clot time prolongation value (cINR was devised that correlated with their actual International Normalized Ratio (INR values, with differences between individual INR and cINR values shown to derive from the insensitivity of the INR to tissue factor pathway inhibitor (TFPI. The analysis suggests that normal range variation in TFPI levels could be an important contributor to the failure of the INR to adequately reflect the anticoagulated state in some individuals. Warfarin-induced changes in thrombin propagation phase parameters were then compared to those induced by unfractionated heparin, fondaparinux, rivaroxaban, and a reversible thrombin inhibitor. Anticoagulants were assessed at concentrations yielding equivalent cINR values, with each anticoagulant evaluated using 32 unique coagulation proteome compositions. The analyses showed that no anticoagulant recapitulated all features of warfarin propagation phase dynamics; differences in propagation phase effects suggest that anticoagulants that selectively target fXa or

  8. Inhibitory effect of apixaban compared with rivaroxaban and dabigatran on thrombin generation assay.

    Science.gov (United States)

    Wong, Pancras C; White, Andrew; Luettgen, Joseph

    2013-02-01

    The effect of the oral direct activated factor X (factor Xa) inhibitor apixaban on tissue factor-induced thrombin generation in human plasma was investigated in vitro using the calibrated automated thrombogram (CAT) method and compared with the oral direct factor Xa inhibitor rivaroxaban and the direct thrombin inhibitor dabigatran. Pooled citrated, anticoagulated, platelet-poor human plasma was spiked with apixaban, rivaroxaban, or dabigatran at concentrations of 0.01 to 10 μM. The inhibitory potencies of the compounds were quantified by 5 CAT parameters: the control thrombin lag time (LT) and time to thrombin peak (TTP) for the doubling of inhibitor concentration (IC2x); and the control endogenous thrombin potential (ETP), thrombin peak, and maximum rate of thrombin generation (Vmax) for the inhibitor concentration, which inhibited 50% (IC50). The inhibitors modified CAT concentration dependently. Their inhibitory potencies, expressed as IC2x LT, IC2x TTP, IC50 ETP, IC50 peak thrombin, and IC50 Vmax, were as follows: 0.10 ± 0.01, 0.19 ± 0.02, 0.65 ± 0.11, 0.089 ± 0.019, and 0.049 ± 0.007 μM for apixaban; 0.049 ± 0.007, 0.070 ± 0.009, 0.43 ± 0.07, 0.048 ± 0.008, and 0.022 ± 0.005 μM for rivaroxaban; and 0.063 ± 0.019, 0.18 ± 0.06, 0.50 ± 0.08, 0.55 ± 0.06, and 0.57 ± 0.27 μM for dabigatran. In summary, apixaban, rivaroxaban, and dabigatran have similar potencies in the prolongation of LT and TTP. The CAT parameters that are related to the rate of thrombin generation during the propagation phase (ie, peak thrombin and Vmax) are more sensitive to activities of apixaban and rivaroxaban than dabigatran. The ETP is the least sensitive parameter for measuring the activities of these inhibitors. Recombinant activated factor VII at 5 and 50 μg/mL reversed the anticoagulant effects of apixaban more at 0.2 μM than at 2 μM. Our study suggests that the CAT method is a sensitive assay to monitor the pharmacodynamic and pharmacokinetic properties of

  9. Increased thrombin generation in women with polycystic ovary syndrome

    DEFF Research Database (Denmark)

    Glintborg, Dorte; Sidelmann, Johannes Jakobsen; Lambaa Altinok, Magda;

    2015-01-01

    Objective. Polycystic ovary syndrome (PCOS) is associated with risk factors for cardiovascular disease (CVD) which may be modified by the use of metformin and oral contraceptives (OC). Thrombin generation (TG) measures are risk markers of CVD and address the composite of multiple factors...... randomized to 12 months treatment with metformin, metformin + OC or OC alone. C-reactive protein (CRP), fibrinogen, total cholesterol, trunk fat mass, body mass index, estradiol, testosterone, sex hormone binding globulin (SHBG) as well as TG measures, i.e. the lag time for formation of thrombin...... significantly. Conclusions. PCOS is associated with increase in TG measures independent of other risk factors of CVD. OC increases TG measures further and may thus add to the increased risk of CVD already present in women with PCOS....

  10. Heparin coating of tantalum coronary stents reduces surface thrombin generation but not factor IXa generation.

    Science.gov (United States)

    Blezer, R; Cahalan, L; Cahalan, P T; Lindhout, T

    1998-07-01

    In the present study we used an in-vitro technique to examine initiation and propagation of blood coagulation at the surface of tantalum coronary stents exposed to flowing platelet-rich and platelet-free plasma. The time course of factor IXa production at the surface of the stent was not influenced by platelets. In spite of a significant factor IXa production, no thrombin activity was detected when the tantalum stent was exposed to platelet-free plasma; only when the stent was exposed to platelet-rich plasma was extensive thrombin production observed. These findings indicate that tantalum triggers blood coagulation, but that (adherent) platelets are essential for thrombin generation. Heparin-coated tantalum stents exposed to flowing platelet-rich plasma showed that factor IXa generation was slightly reduced compared with the bare stent. However, the heparin coating drastically delayed the onset of thrombin generation and largely reduced the steady-state production of thrombin. We found a clear relationship between the antithrombin binding capacity and the antithrombogenic potential of the heparin-coated stents. The mode of action of immobilized heparin is thought to abrogate thrombin generation by inhibiting thrombin-dependent positive feedback reactions at the surface of the coronary stent. PMID:9712292

  11. Low paediatric thrombin generation is caused by an attenuation of prothrombin conversion.

    Science.gov (United States)

    Kremers, Romy M W; Wagenvoord, Rob J; de Laat, H Bas; Monagle, Paul; Hemker, H Coenraad; Ignjatovic, Vera

    2016-06-01

    Thrombin generation (TG) is decreased in children. TG is determined by two underlying processes: the conversion of prothrombin to thrombin and the inactivation of thrombin. Therefore, lower TG capacity in children can either be caused by a reduction of prothrombin conversion, an increase of thrombin inactivation, or both. In 36 children and 8 adults, TG and the factors that determine thrombin inactivation (antithrombin, α2Macroglobulin (α2M) and fibrinogen) were measured. Prothrombin conversion, thrombin inhibitor complex formation, and the overall thrombin decay capacity were determined. In silico modelling was performed to determine the contribution prothrombin conversion and thrombin inactivation to deviant paediatric TG. Both the amount of prothrombin converted and the maximal prothrombin conversion rate are significantly reduced in children as compared to adults. This is partly due to the prothrombin levels being lower and partly to a lower prothrombin conversion rate. The overall thrombin decay capacity is not significantly different in children, but α2Macroglobulin plays a more important role than it does in adults. In silico experiments demonstrate that reduced prothrombin conversion and to a lesser extent elevated α2M levels provide an explanation for low TG in children. Young age has a dual effect on prothrombin conversion. Lower plasma prothrombin levels result in decreased prothrombin conversion but the rate of prothrombin conversion is also decreased, i. e. the development of prothrombinase is lower than in adults.

  12. Factor Xa generation by computational modeling: an additional discriminator to thrombin generation evaluation.

    Directory of Open Access Journals (Sweden)

    Kathleen E Brummel-Ziedins

    Full Text Available Factor (fXa is a critical enzyme in blood coagulation that is responsible for the initiation and propagation of thrombin generation. Previously we have shown that analysis of computationally generated thrombin profiles is a tool to investigate hemostasis in various populations. In this study, we evaluate the potential of computationally derived time courses of fXa generation as another approach for investigating thrombotic risk. Utilizing the case (n = 473 and control (n = 426 population from the Leiden Thrombophilia Study and each individual's plasma protein factor composition for fII, fV, fVII, fVIII, fIX, fX, antithrombin and tissue factor pathway inhibitor, tissue factor-initiated total active fXa generation was assessed using a mathematical model. FXa generation was evaluated by the area under the curve (AUC, the maximum rate (MaxR and level (MaxL and the time to reach these, TMaxR and TMaxL, respectively. FXa generation was analyzed in the entire populations and in defined subgroups (by sex, age, body mass index, oral contraceptive use. The maximum rates and levels of fXa generation occur over a 10- to 12- fold range in both cases and controls. This variation is larger than that observed with thrombin (3-6 fold in the same population. The greatest risk association was obtained using either MaxR or MaxL of fXa generation; with an ∼2.2 fold increased risk for individuals exceeding the 90(th percentile. This risk was similar to that of thrombin generation(MaxR OR 2.6. Grouping defined by oral contraceptive (OC use in the control population showed the biggest differences in fXa generation; a >60% increase in the MaxR upon OC use. FXa generation can distinguish between a subset of individuals characterized by overlapping thrombin generation profiles. Analysis of fXa generation is a phenotypic characteristic which may prove to be a more sensitive discriminator than thrombin generation among all individuals.

  13. Protamine sulfate down-regulates thrombin generation by inhibiting factor V activation.

    LENUS (Irish Health Repository)

    Ni Ainle, Fionnuala

    2009-08-20

    Protamine sulfate is a positively charged polypeptide widely used to reverse heparin-induced anticoagulation. Paradoxically, prospective randomized trials have shown that protamine administration for heparin neutralization is associated with increased bleeding, particularly after cardiothoracic surgery with cardiopulmonary bypass. The molecular mechanism(s) through which protamine mediates this anticoagulant effect has not been defined. In vivo administration of pharmacologic doses of protamine to BALB\\/c mice significantly reduced plasma thrombin generation and prolonged tail-bleeding time (from 120 to 199 seconds). Similarly, in pooled normal human plasma, protamine caused significant dose-dependent prolongations of both prothrombin time and activated partial thromboplastin time. Protamine also markedly attenuated tissue factor-initiated thrombin generation in human plasma, causing a significant decrease in endogenous thrombin potential (41% +\\/- 7%). As expected, low-dose protamine effectively reversed the anticoagulant activity of unfractionated heparin in plasma. However, elevated protamine concentrations were associated with progressive dose-dependent reduction in thrombin generation. To assess the mechanism by which protamine mediates down-regulation of thrombin generation, the effect of protamine on factor V activation was assessed. Protamine was found to significantly reduce the rate of factor V activation by both thrombin and factor Xa. Protamine mediates its anticoagulant activity in plasma by down-regulation of thrombin generation via a novel mechanism, specifically inhibition of factor V activation.

  14. Automated Test Case Generation

    CERN Document Server

    CERN. Geneva

    2015-01-01

    I would like to present the concept of automated test case generation. I work on it as part of my PhD and I think it would be interesting also for other people. It is also the topic of a workshop paper that I am introducing in Paris. (abstract below) Please note that the talk itself would be more general and not about the specifics of my PhD, but about the broad field of Automated Test Case Generation. I would introduce the main approaches (combinatorial testing, symbolic execution, adaptive random testing) and their advantages and problems. (oracle problem, combinatorial explosion, ...) Abstract of the paper: Over the last decade code-based test case generation techniques such as combinatorial testing or dynamic symbolic execution have seen growing research popularity. Most algorithms and tool implementations are based on finding assignments for input parameter values in order to maximise the execution branch coverage. Only few of them consider dependencies from outside the Code Under Test’s scope such...

  15. Automated synthetic scene generation

    Science.gov (United States)

    Givens, Ryan N.

    Physics-based simulations generate synthetic imagery to help organizations anticipate system performance of proposed remote sensing systems. However, manually constructing synthetic scenes which are sophisticated enough to capture the complexity of real-world sites can take days to months depending on the size of the site and desired fidelity of the scene. This research, sponsored by the Air Force Research Laboratory's Sensors Directorate, successfully developed an automated approach to fuse high-resolution RGB imagery, lidar data, and hyperspectral imagery and then extract the necessary scene components. The method greatly reduces the time and money required to generate realistic synthetic scenes and developed new approaches to improve material identification using information from all three of the input datasets.

  16. Systems biology of coagulation initiation: kinetics of thrombin generation in resting and activated human blood.

    Directory of Open Access Journals (Sweden)

    Manash S Chatterjee

    Full Text Available Blood function defines bleeding and clotting risks and dictates approaches for clinical intervention. Independent of adding exogenous tissue factor (TF, human blood treated in vitro with corn trypsin inhibitor (CTI, to block Factor XIIa will generate thrombin after an initiation time (T(i of 1 to 2 hours (depending on donor, while activation of platelets with the GPVI-activator convulxin reduces T(i to ∼20 minutes. Since current kinetic models fail to generate thrombin in the absence of added TF, we implemented a Platelet-Plasma ODE model accounting for: the Hockin-Mann protease reaction network, thrombin-dependent display of platelet phosphatidylserine, VIIa function on activated platelets, XIIa and XIa generation and function, competitive thrombin substrates (fluorogenic detector and fibrinogen, and thrombin consumption during fibrin polymerization. The kinetic model consisting of 76 ordinary differential equations (76 species, 57 reactions, 105 kinetic parameters predicted the clotting of resting and convulxin-activated human blood as well as predicted T(i of human blood under 50 different initial conditions that titrated increasing levels of TF, Xa, Va, XIa, IXa, and VIIa. Experiments with combined anti-XI and anti-XII antibodies prevented thrombin production, demonstrating that a leak of XIIa past saturating amounts of CTI (and not "blood-borne TF" alone was responsible for in vitro initiation without added TF. Clotting was not blocked by antibodies used individually against TF, VII/VIIa, P-selectin, GPIb, protein disulfide isomerase, cathepsin G, nor blocked by the ribosome inhibitor puromycin, the Clk1 kinase inhibitor Tg003, or inhibited VIIa (VIIai. This is the first model to predict the observed behavior of CTI-treated human blood, either resting or stimulated with platelet activators. CTI-treated human blood will clot in vitro due to the combined activity of XIIa and XIa, a process enhanced by platelet activators and which proceeds

  17. Placental vascular pathology and increased thrombin generation as mechanisms of disease in obstetrical syndromes

    Directory of Open Access Journals (Sweden)

    Salvatore Andrea Mastrolia

    2014-11-01

    Full Text Available Obstetrical complications including preeclampsia, fetal growth restriction, preterm labor, preterm prelabor rupture of membranes and fetal demise are all the clinical endpoint of several underlying mechanisms (i.e., infection, inflammation, thrombosis, endocrine disorder, immunologic rejection, genetic, and environmental, therefore, they may be regarded as syndromes. Placental vascular pathology and increased thrombin generation were reported in all of these obstetrical syndromes. Moreover, elevated concentrations of thrombin-anti thrombin III complexes and changes in the coagulation as well as anticoagulation factors can be detected in the maternal circulation prior to the clinical development of the disease in some of these syndromes. In this review, we will assess the changes in the hemostatic system during normal and complicated pregnancy in maternal blood, maternal–fetal interface and amniotic fluid, and describe the contribution of thrombosis and vascular pathology to the development of the great obstetrical syndromes.

  18. Hypercoagulability following major partial liver resection - detected by thrombomodulin-modified thrombin generation testing

    NARCIS (Netherlands)

    Potze, W.; Alkozai, E. M.; Adelmeijer, J.; Porte, R. J.; Lisman, T.

    2015-01-01

    BackgroundConventional coagulation tests are frequently prolonged after liver surgery, suggesting a post-operative hypocoagulability. However, these tests are unreliable for assessment of the haemostatic status in these patients. In contrast, thrombin generation testing measures the true balance bet

  19. Longitudinal assessment of thrombin generation potential in response to alteration of antiplatelet therapy after TIA or ischaemic stroke.

    LENUS (Irish Health Repository)

    Tobin, W O

    2013-02-01

    The impact of changing antiplatelet therapy on thrombin generation potential in patients with ischaemic cerebrovascular disease (CVD) is unclear. We assessed patients within 4 weeks of TIA or ischaemic stroke (baseline), and then 14 days (14d) and >90 days (90d) after altering antiplatelet therapy. Thrombin generation was assessed in platelet poor plasma. Ninety-one patients were recruited. Twenty-four were initially assessed on no antiplatelet therapy, and then after 14d (N = 23) and 90d (N = 8) on aspirin monotherapy; 52 were assessed on aspirin monotherapy, and after 14 and 90 days on aspirin and dipyridamole combination therapy; 21 patients were assessed on aspirin and after 14 days (N = 21) and 90 days (N = 19) on clopidogrel. Peak thrombin generation and endogenous thrombin potential were reduced at 14 and 90 days (p ≤ 0.04) in the overall cohort. We assessed the impact of individual antiplatelet regimens on thrombin generation parameters to investigate the cause of this effect. Lag time and time-to-peak thrombin generation were unchanged at 14 days, but reduced 90 days after commencing aspirin (p ≤ 0.009). Lag time, peak thrombin generation and endogenous thrombin potential were reduced at both 14 and 90 days after adding dipyridamole to aspirin (p ≤ 0.01). Lag time was reduced 14 days after changing from aspirin to clopidogrel (p = 0.045), but this effect was not maintained at 90 days (p = 0.2). This pilot study did not show any consistent effects of commencing aspirin, or of changing from aspirin to clopidogrel on thrombin generation potential during follow-up. The addition of dipyridamole to aspirin led to a persistent reduction in peak and total thrombin generation ex vivo, and illustrates the diverse, potentially beneficial, newly recognised \\'anti-coagulant\\' effects of dipyridamole in ischaemic CVD.

  20. Thrombography reveals thrombin generation potential continues to deteriorate following cardiopulmonary bypass surgery despite adequate hemostasis.

    Science.gov (United States)

    Wong, Raymond K; Sleep, Joseph R; Visner, Allison J; Raasch, David J; Lanza, Louis A; DeValeria, Patrick A; Torloni, Antonio S; Arabia, Francisco A

    2011-03-01

    The intrinsic and extrinsic activation pathways of the hemostatic system converge when prothrombin is converted to thrombin. The ability to generate an adequate thrombin burst is the most central aspect of the coagulation cascade. The thrombin-generating potential in patients following cardiopulmonary bypass (CPB) may be indicative of their hemostatic status. In this report, thrombography, a unique technique for directly measuring the potential of patients' blood samples to generate adequate thrombin bursts, is used to characterize the coagulopathic profile in post-CPB patients. Post-CPB hemostasis is typically achieved with protamine reversal of heparin anticoagulation and occasionally supplemented with blood product component transfusions. In this pilot study, platelet poor plasma samples were derived from 11 primary cardiac surgery patients at five time points: prior to CPB, immediately post-protamine, upon arrival to the intensive care unit (ICU), 3 hours post-ICU admission, and 24 hours after ICU arrival. Thrombography revealed that the Endogenous Thrombin Potential (ETP) was not different between [Baseline] and [PostProtamine] but proceeded to deteriorate in the immediate postoperative period. At the [3HourPostICU] time point, the ETP was significantly lower than the [Baseline] values, 1233 +/- 591 versus 595 +/- 379 nM.min (mean +/- SD; n=9, p coagulation testing results, and blood loss volumes are also presented. Despite adequate hemostasis, thrombography reveals an underlying coagulopathic process that could put some cardiac surgical patients at risk for postoperative bleeding. Thrombography is a novel technique that could be developed into a useful tool for perfusionists and physicians to identify coagulopathies and optimize blood management following CPB. PMID:21449230

  1. Thrombin generation by activated factor VII on platelet activated by different agonists. Extending the cell-based model of hemostasis

    Directory of Open Access Journals (Sweden)

    Herrera Maria

    2006-04-01

    Full Text Available Abstract Background Platelet activation is crucial in normal hemostasis. Using a clotting system free of external tissue factor, we investigated whether activated Factor VII in combination with platelet agonists increased thrombin generation (TG in vitro. Methods and results TG was quantified by time parameters: lag time (LT and time to peak (TTP, and by amount of TG: peak of TG (PTG and area under thrombin formation curve after 35 minutes (AUC→35min in plasma from 29 healthy volunteers using the calibrated automated thrombography (CAT technique. TG parameters were measured at basal conditions and after platelet stimulation by sodium arachidonate (AA, ADP, and collagen (Col. In addition, the effects of recombinant activated FVII (rFVIIa alone or combined with the other platelet agonists on TG parameters were investigated. We found that LT and TTP were significantly decreased (p 35min were significantly increased (p 35min (but not PTG when compared to platelet rich plasma activated with agonists in the absence of rFVIIa. Conclusion Platelets activated by AA, ADP, Col or rFVIIa triggered TG. This effect was increased by combining rFVIIa with other agonists. Our intrinsic coagulation system produced a burst in TG independent of external tissue factor activity an apparent hemostatic effect with little thrombotic capacity. Thus we suggest a modification in the cell-based model of hemostasis.

  2. Thrombin generation by exposure of blood to endotoxin: a simple model to study disseminated intravascular coagulation.

    Science.gov (United States)

    Stief, T W

    2006-04-01

    Pathologic disseminated intravascular coagulation (PDIC) is a serious complication in sepsis. In an in-vitro system consisting of incubation of fresh citrated blood with lipopolysaccharides (LPS) or glucans and subsequent plasma recalcification plasmatic thrombin was quantified. Five hundred microliters of freshly drawn citrated blood of healthy donors were incubated with up to 800 ng/mL LPS (Escherichia coli) or up to 80 microg/mL Zymosan A (ZyA; Candida albicans) for 30 minutes at room temperature (RT). The samples were centrifuged, and 30 microL plasma were recalcified with 1 volume or less of CaCl(2) (25 micromoles Ca(2+)/mL plasma). After 0 to 12 minutes (37 degrees C), 20 microL 2.5 M arginine, pH 8.6, were added. Thirty microliters 0.9 mM HD-CHG-Ala-Arg-pNA in 2.3 M arginine were added, and the absorbance increase at 405 nm was determined. Fifty microliters plasma were also incubated with 5 microL 250 mM CaCl2 for 5, 10, or 15 minutes (37 degrees C). Fifty microliters 2.5 M arginine stops coagulation, and 50 microL 0.77 mM HD-CHG-Ala-Arg-pNA in 2.3 M arginine starts the thrombin detection. The standard was 1 IU/mL thrombin in 7% human albumin instead of plasma. Arginine was also added in the endotoxin exposure time (EET) or in the plasma coagulation reaction time (CRT). Tissue factor (TF)-antigen and soluble CD14 were determined. LPS at blood concentrations greater than 10 ng/mL or ZyA at greater than 1 microg/mL severalfold enhance thrombin generation, when the respective plasmas are recalcified. After 30 minutes EET at RT, the thrombin activity at 12 minutes CRT generated by the addition of 200 ng/mL LPS or 20 microg/mL ZyA is approximately 200 mIU/mL compared to approximately 20 mIU/mL without addition of endotoxin, or compared to about 7 mIU/mL thrombin at 0 minutes CRT. Arginine added to blood or to plasma inhibits thrombin generation; the inhibitory concentration 50% (IC 50) is approximately 15 mM plasma concentration. Endotoxin incubation of blood

  3. Cassini Tour Atlas Automated Generation

    Science.gov (United States)

    Grazier, Kevin R.; Roumeliotis, Chris; Lange, Robert D.

    2011-01-01

    During the Cassini spacecraft s cruise phase and nominal mission, the Cassini Science Planning Team developed and maintained an online database of geometric and timing information called the Cassini Tour Atlas. The Tour Atlas consisted of several hundreds of megabytes of EVENTS mission planning software outputs, tables, plots, and images used by mission scientists for observation planning. Each time the nominal mission trajectory was altered or tweaked, a new Tour Atlas had to be regenerated manually. In the early phases of Cassini s Equinox Mission planning, an a priori estimate suggested that mission tour designers would develop approximately 30 candidate tours within a short period of time. So that Cassini scientists could properly analyze the science opportunities in each candidate tour quickly and thoroughly so that the optimal series of orbits for science return could be selected, a separate Tour Atlas was required for each trajectory. The task of manually generating the number of trajectory analyses in the allotted time would have been impossible, so the entire task was automated using code written in five different programming languages. This software automates the generation of the Cassini Tour Atlas database. It performs with one UNIX command what previously took a day or two of human labor.

  4. Automated Test-Form Generation

    Science.gov (United States)

    van der Linden, Wim J.; Diao, Qi

    2011-01-01

    In automated test assembly (ATA), the methodology of mixed-integer programming is used to select test items from an item bank to meet the specifications for a desired test form and optimize its measurement accuracy. The same methodology can be used to automate the formatting of the set of selected items into the actual test form. Three different…

  5. Potentiation of thrombin generation in hemophilia A plasma by coagulation factor VIII and characterization of antibody-specific inhibition.

    Directory of Open Access Journals (Sweden)

    Bhavya S Doshi

    Full Text Available Development of inhibitory antibodies to coagulation factor VIII (fVIII is the primary obstacle to the treatment of hemophilia A in the developed world. This adverse reaction occurs in 20-30% of persons with severe hemophilia A treated with fVIII-replacement products and is characterized by the development of a humoral and neutralizing immune response to fVIII. Patients with inhibitory anti-fVIII antibodies are treated with bypassing agents including recombinant factor VIIa (rfVIIa. However, some patients display poor hemostatic response to bypass therapy and improved treatment options are needed. Recently, we demonstrated that fVIII inhibitors display widely variable kinetics of inhibition that correlate with their respective target epitopes. Thus, it was hypothesized that for antibodies that display slow rates of inhibition, supplementation of rfVIIa with fVIII would result in improved thrombin generation and be predictive of clinical responses to this novel treatment regimen. In order to test this hypothesis, 10 murine monoclonal antibodies (MAbs with non-overlapping epitopes spanning fVIII, differential inhibition titers, and inhibition kinetics were studied using a thrombin generation assay. Of the 3 MAbs with high inhibitory titers, only the one with fast and complete (classically defined as "type I" kinetics displayed significant inhibition of thrombin generation with no improvement upon supplementation of rfVIIa with fVIII. The other two MAbs that displayed incomplete (classically defined as "type II" inhibition did not suppress the potentiation of thrombin generation by fVIII. All antibodies that did not completely inhibit fVIII activity demonstrated potentiation of thrombin generation by the addition of fVIII as compared to rfVIIa alone. In conclusion, fVIII alone or in combination with rfVIIa corrects the thrombin generation defect produced by the majority of anti-fVIII MAbs better than single agent rfVIIa. Therefore, combined f

  6. Statins but not aspirin reduce thrombotic risk assessed by thrombin generation in diabetic patients without cardiovascular events: the RATIONAL trial.

    Directory of Open Access Journals (Sweden)

    Alejandro Macchia

    Full Text Available BACKGROUND: The systematic use of aspirin and statins in patients with diabetes and no previous cardiovascular events is controversial. We sought to assess the effects of aspirin and statins on the thrombotic risk assessed by thrombin generation (TG among patients with type II diabetes mellitus and no previous cardiovascular events. METHODOLOGY/PRINCIPAL FINDINGS: Prospective, randomized, open, blinded to events evaluation, controlled, 2×2 factorial clinical trial including 30 patients randomly allocated to aspirin 100 mg/d, atorvastatin 40 mg/d, both or none. Outcome measurements included changes in TG levels after treatment (8 to 10 weeks, assessed by a calibrated automated thrombogram. At baseline all groups had similar clinical and biochemical profiles, including TG levels. There was no interaction between aspirin and atorvastatin. Atorvastatin significantly reduced TG measured as peak TG with saline (85.09±55.34 nmol vs 153.26±75.55 nmol for atorvastatin and control groups, respectively; p = 0.018. On the other hand, aspirin had no effect on TG (121.51±81.83 nmol vs 116.85±67.66 nmol, for aspirin and control groups, respectively; p = 0.716. The effects of treatments on measurements of TG using other agonists were consistent. CONCLUSIONS/SIGNIFICANCE: While waiting for data from ongoing large clinical randomized trials to definitively outline the role of aspirin in primary prevention, our study shows that among diabetic patients without previous vascular events, statins but not aspirin reduce thrombotic risk assessed by TG. TRIAL REGISTRATION: ClinicalTrials.gov NCT00793754.

  7. Random Forests Are Able to Identify Differences in Clotting Dynamics from Kinetic Models of Thrombin Generation.

    Science.gov (United States)

    Arumugam, Jayavel; Bukkapatnam, Satish T S; Narayanan, Krishna R; Srinivasa, Arun R

    2016-01-01

    Current methods for distinguishing acute coronary syndromes such as heart attack from stable coronary artery disease, based on the kinetics of thrombin formation, have been limited to evaluating sensitivity of well-established chemical species (e.g., thrombin) using simple quantifiers of their concentration profiles (e.g., maximum level of thrombin concentration, area under the thrombin concentration versus time curve). In order to get an improved classifier, we use a 34-protein factor clotting cascade model and convert the simulation data into a high-dimensional representation (about 19000 features) using a piecewise cubic polynomial fit. Then, we systematically find plausible assays to effectively gauge changes in acute coronary syndrome/coronary artery disease populations by introducing a statistical learning technique called Random Forests. We find that differences associated with acute coronary syndromes emerge in combinations of a handful of features. For instance, concentrations of 3 chemical species, namely, active alpha-thrombin, tissue factor-factor VIIa-factor Xa ternary complex, and intrinsic tenase complex with factor X, at specific time windows, could be used to classify acute coronary syndromes to an accuracy of about 87.2%. Such a combination could be used to efficiently assay the coagulation system. PMID:27171403

  8. Random Forests Are Able to Identify Differences in Clotting Dynamics from Kinetic Models of Thrombin Generation.

    Directory of Open Access Journals (Sweden)

    Jayavel Arumugam

    Full Text Available Current methods for distinguishing acute coronary syndromes such as heart attack from stable coronary artery disease, based on the kinetics of thrombin formation, have been limited to evaluating sensitivity of well-established chemical species (e.g., thrombin using simple quantifiers of their concentration profiles (e.g., maximum level of thrombin concentration, area under the thrombin concentration versus time curve. In order to get an improved classifier, we use a 34-protein factor clotting cascade model and convert the simulation data into a high-dimensional representation (about 19000 features using a piecewise cubic polynomial fit. Then, we systematically find plausible assays to effectively gauge changes in acute coronary syndrome/coronary artery disease populations by introducing a statistical learning technique called Random Forests. We find that differences associated with acute coronary syndromes emerge in combinations of a handful of features. For instance, concentrations of 3 chemical species, namely, active alpha-thrombin, tissue factor-factor VIIa-factor Xa ternary complex, and intrinsic tenase complex with factor X, at specific time windows, could be used to classify acute coronary syndromes to an accuracy of about 87.2%. Such a combination could be used to efficiently assay the coagulation system.

  9. Three months of strictly controlled daily endurance exercise reduces thrombin generation and fibrinolytic risk markers in younger moderately overweight men

    DEFF Research Database (Denmark)

    Gram, Anne Sofie; Bladbjerg, Else-Marie; Skov, Jane;

    2015-01-01

    PURPOSE: Physical activity is associated with a decreased risk of cardiovascular disease, but dose dependency of long-term physical exercise on biomarkers within coagulation and fibrinolysis is unknown. We aimed to investigate effects of two doses of daily endurance exercise on biomarkers...... of 600 kcal/day (HIGH), 300 kcal/day (MOD), or to maintain their habitual lifestyle (CON). Fasting blood samples were collected before and after the intervention and analysed for thrombin generation (endogenous thrombin potential, ETP) and concentrations of tissue-type plasminogen activator (t...... of the haemostatic balance in overweight men. METHODS: Haemostatic variables were investigated in 53 healthy, younger (20-40 years), moderately overweight (BMI 25-30 kg/m(2)) men randomly assigned to 3 months of strictly controlled endurance exercise at two different doses corresponding to an energy expenditure...

  10. Generation and characterization of a highly stable form of activated thrombin-activable fibrinolysis inhibitor

    NARCIS (Netherlands)

    Marx, PF; Havik, [No Value; Marquart, JA; Meijers, JCM; Bouma, Bonno N.

    2004-01-01

    Activated thrombin-activable fibrinolysis inhibitor (TAFIa) is a carboxypeptidase B that can down-regulate fibrinolysis. TAFIa is a labile enzyme that can be inactivated by conformational instability or proteolysis. TAFI is similar to 40% identical to pancreatic carboxypeptidase B (CPB). In contrast

  11. Thrombin Inhibitors from Different Animals

    OpenAIRE

    Tanaka-Azevedo, A. M.; Morais-Zani, K.; Torquato, R. J. S.; A. S. Tanaka

    2010-01-01

    Venous and arterial thromboembolic diseases are still the most frequent causes of death and disability in high-income countries. Clinical anticoagulants are inhibitors of enzymes involved in the coagulation pathway, such as thrombin and factor Xa. Thrombin is a key enzyme of blood coagulation system, activating the platelets, converting the fibrinogen to the fibrin net, and amplifying its self-generation by the activation of factors V, VIII, and XI. Thrombin has long been a target for the dev...

  12. Automated Liquibase Generator And ValidatorALGV

    Directory of Open Access Journals (Sweden)

    Manik Jain

    2015-08-01

    Full Text Available Abstract This paper presents an automation tool namely ALGV Automated Liquibase Generator and Validator for the automated generation and verification of liquibase scripts. Liquibase is one of the most efficient ways of applying and persisting changes to a database schema. Since its invention by Nathan Voxland 1 it has become de facto standard for database change management. The advantages of using liquibase scripts over traditional sql queries ranges from version control to reusing the same scripts over multiple database platforms. Irrespective of its advantages manual creation of liquibase scripts takes a lot of effort and sometimes is error-prone. ALGV helps to reduce the time consuming liquibase script generation manual typing efforts possible error occurrence and manual verification process and time by 75. Automating the liquibase generation process also helps to remove the burden of recollecting specific tags to be used for a particular change. Moreover developers can concentrate on the business logic and business data rather than wasting their precious efforts in writing files.

  13. Automated generation of lattice QCD Feynman rules

    Energy Technology Data Exchange (ETDEWEB)

    Hart, A.; Mueller, E.H. [Edinburgh Univ. (United Kingdom). SUPA School of Physics and Astronomy; von Hippel, G.M. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Horgan, R.R. [Cambridge Univ. (United Kingdom). DAMTP, CMS

    2009-04-15

    The derivation of the Feynman rules for lattice perturbation theory from actions and operators is complicated, especially for highly improved actions such as HISQ. This task is, however, both important and particularly suitable for automation. We describe a suite of software to generate and evaluate Feynman rules for a wide range of lattice field theories with gluons and (relativistic and/or heavy) quarks. Our programs are capable of dealing with actions as complicated as (m)NRQCD and HISQ. Automated differentiation methods are used to calculate also the derivatives of Feynman diagrams. (orig.)

  14. Investigation of the thrombin-generating capacity, evaluated by thrombogram, and clot formation evaluated by thrombelastography of platelets stored in the blood bank for up to 7 days

    DEFF Research Database (Denmark)

    Johansson, Per Ingemar; Svendsen, M.S.; Salado, J.;

    2008-01-01

    .0035). No correlation between ETP and TTG was found (P = 0.65). CONCLUSION: The kinetics of thrombin generation, as evaluated by CAT, correlates with the thrombus generation, as evaluated by thrombelastography and this may in part explain the clinical utility of the TEG in identifying clinically relevant coagulopathies...

  15. Association of thrombin generation potential with platelet PAR-1 regulation and P-selectin expression in patients on dual antiplatelet therapy.

    Science.gov (United States)

    Badr Eslam, Roza; Posch, Florian; Lang, Irene M; Gremmel, Thomas; Eichelberger, Beate; Ay, Cihan; Panzer, Simon

    2014-02-01

    We studied the association of thrombin generation potential with platelet protease activated receptor (PAR)-1 regulation and platelet activation in 52 stable coronary artery disease patients on continuous therapy with aspirin and clopidogrel (n = 42) or prasugrel (n = 10). Compared to controls, peak thrombin generation potential was elevated in only 11 patients (p > 0.05), while F1.2 was elevated in 26 patients (p P-selectin expression were significantly elevated in patients compared to controls (p P-selectin (p = 0.002), suggesting in vivo depletion of platelet alpha granules due to ongoing platelet activation.

  16. Monitoring low molecular weight heparins at therapeutic levels: dose-responses of, and correlations and differences between aPTT, anti-factor Xa and thrombin generation assays.

    Directory of Open Access Journals (Sweden)

    Owain Thomas

    Full Text Available Low molecular weight heparins (LMWH's are used to prevent and treat thrombosis. Tests for monitoring LMWH's include anti-factor Xa (anti-FXa, activated partial thromboplastin time (aPTT and thrombin generation. Anti-FXa is the current gold standard despite LMWH's varying affinities for FXa and thrombin.To examine the effects of two different LMWH's on the results of 4 different aPTT-tests, anti-FXa activity and thrombin generation and to assess the tests' concordance.Enoxaparin and tinzaparin were added ex-vivo in concentrations of 0.0, 0.5, 1.0 and 1.5 anti-FXa international units (IU/mL, to blood from 10 volunteers. aPTT was measured using two whole blood methods (Free oscillation rheometry (FOR and Hemochron Jr (HCJ and an optical plasma method using two different reagents (ActinFSL and PTT-Automat. Anti-FXa activity was quantified using a chromogenic assay. Thrombin generation (Endogenous Thrombin Potential, ETP was measured on a Ceveron Alpha instrument using the TGA RB and more tissue-factor rich TGA RC reagents.Methods' mean aPTT at 1.0 IU/mL LMWH varied between 54s (SD 11 and 69s (SD 14 for enoxaparin and between 101s (SD 21 and 140s (SD 28 for tinzaparin. ActinFSL gave significantly shorter aPTT results. aPTT and anti-FXa generally correlated well. ETP as measured with the TGA RC reagent but not the TGA RB reagent showed an inverse exponential relationship to the concentration of LMWH. The HCJ-aPTT results had the weakest correlation to anti-FXa and thrombin generation (Rs0.62-0.87, whereas the other aPTT methods had similar correlation coefficients (Rs0.80-0.92.aPTT displays a linear dose-response to LMWH. There is variation between aPTT assays. Tinzaparin increases aPTT and decreases thrombin generation more than enoxaparin at any given level of anti-FXa activity, casting doubt on anti-FXa's present gold standard status. Thrombin generation with tissue factor-rich activator is a promising method for monitoring LMWH's.

  17. The Automated Emotional Music Generator With Emotion and Season Features

    OpenAIRE

    Huang, Chih-Fang; Li, Chi-Jung

    2013-01-01

    Nowadays, there are various types of automated music generating systems to automatically compose music clips instantly; however, those randomly-generated music clips still sounded uncomfortable and discordant. This paper attempts to add with emotion and season features to assist automated music generating systems based on algorithm, and then tries to make all generative music clips sound with harmonious and emotional meaning to listeners. The automated music generator used in this topic is no...

  18. Semi-automated ontology generation and evolution

    Science.gov (United States)

    Stirtzinger, Anthony P.; Anken, Craig S.

    2009-05-01

    Extending the notion of data models or object models, ontology can provide rich semantic definition not only to the meta-data but also to the instance data of domain knowledge, making these semantic definitions available in machine readable form. However, the generation of an effective ontology is a difficult task involving considerable labor and skill. This paper discusses an Ontology Generation and Evolution Processor (OGEP) aimed at automating this process, only requesting user input when un-resolvable ambiguous situations occur. OGEP directly attacks the main barrier which prevents automated (or self learning) ontology generation: the ability to understand the meaning of artifacts and the relationships the artifacts have to the domain space. OGEP leverages existing lexical to ontological mappings in the form of WordNet, and Suggested Upper Merged Ontology (SUMO) integrated with a semantic pattern-based structure referred to as the Semantic Grounding Mechanism (SGM) and implemented as a Corpus Reasoner. The OGEP processing is initiated by a Corpus Parser performing a lexical analysis of the corpus, reading in a document (or corpus) and preparing it for processing by annotating words and phrases. After the Corpus Parser is done, the Corpus Reasoner uses the parts of speech output to determine the semantic meaning of a word or phrase. The Corpus Reasoner is the crux of the OGEP system, analyzing, extrapolating, and evolving data from free text into cohesive semantic relationships. The Semantic Grounding Mechanism provides a basis for identifying and mapping semantic relationships. By blending together the WordNet lexicon and SUMO ontological layout, the SGM is given breadth and depth in its ability to extrapolate semantic relationships between domain entities. The combination of all these components results in an innovative approach to user assisted semantic-based ontology generation. This paper will describe the OGEP technology in the context of the architectural

  19. Automated generation of lattice QCD Feynman rules

    Science.gov (United States)

    Hart, A.; von Hippel, G. M.; Horgan, R. R.; Müller, E. H.

    2009-12-01

    The derivation of the Feynman rules for lattice perturbation theory from actions and operators is complicated, especially for highly improved actions such as HISQ. This task is, however, both important and particularly suitable for automation. We describe a suite of software to generate and evaluate Feynman rules for a wide range of lattice field theories with gluons and (relativistic and/or heavy) quarks. Our programs are capable of dealing with actions as complicated as (m)NRQCD and HISQ. Automated differentiation methods are used to calculate also the derivatives of Feynman diagrams. Program summaryProgram title: HiPPY, HPsrc Catalogue identifier: AEDX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv2 (see Additional comments below) No. of lines in distributed program, including test data, etc.: 513 426 No. of bytes in distributed program, including test data, etc.: 4 893 707 Distribution format: tar.gz Programming language: Python, Fortran95 Computer: HiPPy: Single-processor workstations. HPsrc: Single-processor workstations and MPI-enabled multi-processor systems Operating system: HiPPy: Any for which Python v2.5.x is available. HPsrc: Any for which a standards-compliant Fortran95 compiler is available Has the code been vectorised or parallelised?: Yes RAM: Problem specific, typically less than 1 GB for either code Classification: 4.4, 11.5 Nature of problem: Derivation and use of perturbative Feynman rules for complicated lattice QCD actions. Solution method: An automated expansion method implemented in Python (HiPPy) and code to use expansions to generate Feynman rules in Fortran95 (HPsrc). Restrictions: No general restrictions. Specific restrictions are discussed in the text. Additional comments: The HiPPy and HPsrc codes are released under the second version of the GNU General Public Licence (GPL v2). Therefore anyone is

  20. Integrated, Automated Distributed Generation Technologies Demonstration

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, Kevin [Atk Launch Systems Inc., Brigham City, UT (United States)

    2014-09-01

    The purpose of the NETL Project was to develop a diverse combination of distributed renewable generation technologies and controls and demonstrate how the renewable generation could help manage substation peak demand at the ATK Promontory plant site. The Promontory plant site is located in the northwestern Utah desert approximately 25 miles west of Brigham City, Utah. The plant encompasses 20,000 acres and has over 500 buildings. The ATK Promontory plant primarily manufactures solid propellant rocket motors for both commercial and government launch systems. The original project objectives focused on distributed generation; a 100 kW (kilowatt) wind turbine, a 100 kW new technology waste heat generation unit, a 500 kW energy storage system, and an intelligent system-wide automation system to monitor and control the renewable energy devices then release the stored energy during the peak demand time. The original goal was to reduce peak demand from the electrical utility company, Rocky Mountain Power (RMP), by 3.4%. For a period of time we also sought to integrate our energy storage requirements with a flywheel storage system (500 kW) proposed for the Promontory/RMP Substation. Ultimately the flywheel storage system could not meet our project timetable, so the storage requirement was switched to a battery storage system (300 kW.) A secondary objective was to design/install a bi-directional customer/utility gateway application for real-time visibility and communications between RMP, and ATK. This objective was not achieved because of technical issues with RMP, ATK Information Technology Department’s stringent requirements based on being a rocket motor manufacturing facility, and budget constraints. Of the original objectives, the following were achieved: • Installation of a 100 kW wind turbine. • Installation of a 300 kW battery storage system. • Integrated control system installed to offset electrical demand by releasing stored energy from renewable sources

  1. Integrated, Automated Distributed Generation Technologies Demonstration

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, Kevin

    2014-09-30

    The purpose of the NETL Project was to develop a diverse combination of distributed renewable generation technologies and controls and demonstrate how the renewable generation could help manage substation peak demand at the ATK Promontory plant site. The Promontory plant site is located in the northwestern Utah desert approximately 25 miles west of Brigham City, Utah. The plant encompasses 20,000 acres and has over 500 buildings. The ATK Promontory plant primarily manufactures solid propellant rocket motors for both commercial and government launch systems. The original project objectives focused on distributed generation; a 100 kW (kilowatt) wind turbine, a 100 kW new technology waste heat generation unit, a 500 kW energy storage system, and an intelligent system-wide automation system to monitor and control the renewable energy devices then release the stored energy during the peak demand time. The original goal was to reduce peak demand from the electrical utility company, Rocky Mountain Power (RMP), by 3.4%. For a period of time we also sought to integrate our energy storage requirements with a flywheel storage system (500 kW) proposed for the Promontory/RMP Substation. Ultimately the flywheel storage system could not meet our project timetable, so the storage requirement was switched to a battery storage system (300 kW.) A secondary objective was to design/install a bi-directional customer/utility gateway application for real-time visibility and communications between RMP, and ATK. This objective was not achieved because of technical issues with RMP, ATK Information Technology Department’s stringent requirements based on being a rocket motor manufacturing facility, and budget constraints. Of the original objectives, the following were achieved: • Installation of a 100 kW wind turbine. • Installation of a 300 kW battery storage system. • Integrated control system installed to offset electrical demand by releasing stored energy from renewable sources

  2. Differential Contributions of Intrinsic and Extrinsic Pathways to Thrombin Generation in Adult, Maternal and Cord Plasma Samples

    Science.gov (United States)

    Rice, Nicklaus T.; Szlam, Fania; Varner, Jeffrey D.; Bernstein, Peter S.; Szlam, Arthur D.; Tanaka, Kenichi A.

    2016-01-01

    Background Thrombin generation (TG) is a pivotal process in achieving hemostasis. Coagulation profiles during pregnancy and early neonatal period are different from that of normal (non-pregnant) adults. In this ex vivo study, the differences in TG in maternal and cord plasma relative to normal adult plasma were studied. Methods Twenty consented pregnant women and ten consented healthy adults were included in the study. Maternal and cord blood samples were collected at the time of delivery. Platelet-poor plasma was isolated for the measurement of TG. In some samples, anti-FIXa aptamer, RB006, or a TFPI inhibitor, BAX499 were added to elucidate the contribution of intrinsic and extrinsic pathway to TG. Additionally, procoagulant and inhibitor levels were measured in maternal and cord plasma, and these values were used to mathematically simulate TG. Results Peak TG was increased in maternal plasma (393.6±57.9 nM) compared to adult and cord samples (323.2±38.9 nM and 209.9±29.5 nM, respectively). Inhibitory effects of RB006 on TG were less robust in maternal or cord plasma (52% vs. 12% respectively) than in adult plasma (81%). Likewise the effectiveness of BAX499 as represented by the increase in peak TG was much greater in adult (21%) than in maternal (10%) or cord plasma (12%). Further, BAX499 was more effective in reversing RB006 in adult plasma than in maternal or cord plasma. Ex vivo data were reproducible with the results of the mathematical simulation of TG. Conclusion Normal parturient plasma shows a large intrinsic pathway reserve for TG compared to adult and cord plasma, while TG in cord plasma is sustained by extrinsic pathway, and low levels of TFPI and AT. PMID:27196067

  3. Differential Contributions of Intrinsic and Extrinsic Pathways to Thrombin Generation in Adult, Maternal and Cord Plasma Samples.

    Directory of Open Access Journals (Sweden)

    Nicklaus T Rice

    Full Text Available Thrombin generation (TG is a pivotal process in achieving hemostasis. Coagulation profiles during pregnancy and early neonatal period are different from that of normal (non-pregnant adults. In this ex vivo study, the differences in TG in maternal and cord plasma relative to normal adult plasma were studied.Twenty consented pregnant women and ten consented healthy adults were included in the study. Maternal and cord blood samples were collected at the time of delivery. Platelet-poor plasma was isolated for the measurement of TG. In some samples, anti-FIXa aptamer, RB006, or a TFPI inhibitor, BAX499 were added to elucidate the contribution of intrinsic and extrinsic pathway to TG. Additionally, procoagulant and inhibitor levels were measured in maternal and cord plasma, and these values were used to mathematically simulate TG.Peak TG was increased in maternal plasma (393.6±57.9 nM compared to adult and cord samples (323.2±38.9 nM and 209.9±29.5 nM, respectively. Inhibitory effects of RB006 on TG were less robust in maternal or cord plasma (52% vs. 12% respectively than in adult plasma (81%. Likewise the effectiveness of BAX499 as represented by the increase in peak TG was much greater in adult (21% than in maternal (10% or cord plasma (12%. Further, BAX499 was more effective in reversing RB006 in adult plasma than in maternal or cord plasma. Ex vivo data were reproducible with the results of the mathematical simulation of TG.Normal parturient plasma shows a large intrinsic pathway reserve for TG compared to adult and cord plasma, while TG in cord plasma is sustained by extrinsic pathway, and low levels of TFPI and AT.

  4. Lyso-Sulfatide Binds Factor Xa and Inhibits Thrombin Generation by the Prothrombinase Complex.

    Directory of Open Access Journals (Sweden)

    Subramanian Yegneswaran

    Full Text Available Blood coagulation reactions are strongly influenced by phospholipids, but little is known about the influence of sphingolipids on coagulation mechanisms. Lysosulfatide (lyso-SF (sulfogalactosyl sphingosine prolonged factor Xa (fXa 1-stage plasma clotting assays, showing it had robust anticoagulant activity. In studies using purified clotting factors, lyso-SF inhibited >90% of prothrombin (II activation for reaction mixtures containing fXa/factor Va (fVa/II, and also inhibited II activation generation by fXa/ phospholipids and by Gla-domainless-fXa/fVa/phospholipids. When lyso-SF analogs were tested, results showed that N-acetyl-sulfatide was not anticoagulant, implying that the free amine group was essential for the anticoagulant effects of lyso-SF. Lyso-SF did not inhibit fXa enzymatic hydrolysis of small peptide substrates, showing it did not directly inhibit the fXa activity. In surface plasmon resonance studies, lyso-SF bound to immobilized inactivated fXa as well as inactivated Gla-domainless-fXa. Confirming this lyso-SF:fXa interaction, fluorescence studies showed that fluorescently-labeled-fXa in solution bound to lyso-SF. Thus, lyso-SF is an anticoagulant lipid that inhibits fXa when this enzyme is bound to either phospholipids or to fVa. Mechanisms for inhibition of procoagulant activity are likely to involve lyso-SF binding to fXa domain(s that are distinct from the fXa Gla domain. This suggests that certain sphingolipids, including lyso-SF and some of its analogs, may down-regulate fXa activity without inhibiting the enzyme's active site or binding to the fXa Gla domain.

  5. Automation Framework for Flight Dynamics Products Generation

    Science.gov (United States)

    Wiegand, Robert E.; Esposito, Timothy C.; Watson, John S.; Jun, Linda; Shoan, Wendy; Matusow, Carla

    2010-01-01

    XFDS provides an easily adaptable automation platform. To date it has been used to support flight dynamics operations. It coordinates the execution of other applications such as Satellite TookKit, FreeFlyer, MATLAB, and Perl code. It provides a mechanism for passing messages among a collection of XFDS processes, and allows sending and receiving of GMSEC messages. A unified and consistent graphical user interface (GUI) is used for the various tools. Its automation configuration is stored in text files, and can be edited either directly or using the GUI.

  6. Activation of pro-(matrix metalloproteinase-2) (pro-MMP-2) by thrombin is membrane-type-MMP-dependent in human umbilical vein endothelial cells and generates a distinct 63 kDa active species.

    Science.gov (United States)

    Lafleur, M A; Hollenberg, M D; Atkinson, S J; Knäuper, V; Murphy, G; Edwards, D R

    2001-01-01

    Thrombin, a critical enzyme in the coagulation cascade, has also been associated with angiogenesis and activation of the zymogen form of matrix metalloproteinase-2 (MMP-2 or gelatinase-A). We show that thrombin activated pro-MMP-2 in a dose- and time-dependent manner in cultured human umbilical-vein endothelial cells (HUVECs) to generate a catalytically active 63 kDa protein that accumulated as the predominant form in the conditioned medium. This 63 kDa thrombin-activated MMP-2 is distinct from the 62 kDa species found following concanavalin A or PMA stimulated pro-MMP-2 activation. Hirudin and leupeptin blocked thrombin-induced pro-MMP-2 activation, demonstrating that the proteolytic activity of thrombin is essential. However, activation was also dependent upon membrane-type-MMP (MT-MMP) action, since it was blocked by EDTA, o-phenanthroline, hydroxamate metalloproteinase inhibitors, tissue inhibitor of metalloproteinase-2 (TIMP-2) and TIMP-4, but not TIMP-1. Thrombin inefficiently cleaved recombinant 72 kDa pro-MMP-2, but efficiently cleaved the 64 kDa MT-MMP-processed intermediate form in the presence of cells. Thrombin also rapidly (within 1 h) increased cellular MT-MMP activity, and at longer time points (>6 h) it increased expression of MT1-MMP mRNA and protein. Thus signalling via proteinase-activated receptors (PARs) may play a role in thrombin-induced MMP-2 activation, though this does not appear to involve PAR1, PAR2, or PAR4 in HUVECs. These results indicate that in HUVECs the activation of pro-MMP-2 by thrombin involves increased MT-MMP activity and preferential cleavage of the MT-MMP-processed 64 kDa MMP-2 form in the presence of cells. The integration of these proteinase systems in the vascular endothelium may be important during thrombogenesis and tissue remodelling associated with neovascularization. PMID:11415441

  7. Automation scope at Roxboro generating station

    International Nuclear Information System (INIS)

    Many fossil fired power plant have replaced their aging unit control hardware with modern DCS technology. This paper describes a jointly sponsored project by EPRI, Carolina Power and Light Co. (CP and L) and ABB, to implement plant automation functions which would complement DCS technology, and result in improvements in plant operations in terms of heat rate, availability, and operations cost. These will be demonstrated at CP and L's Roxboro Station, a 4 unit coal fired plant with total capacity of nearly 2,477 MW. The scope of this four year project includes installation of a plant-wide information management system, automation of unit testing, implementation of advanced controls, intelligent alarms, operator advisory functions, and a plant-wide simulator, as well as support for plant unit economic dispatch

  8. [Monitoring of Oral Thrombin Inhibitor].

    Science.gov (United States)

    Matsuno, Kazuhiko; Usami, Takayuki; Hatuse, Masanao; Shimizu, Chikara

    2014-10-01

    Dabigatran etexilate is a prodrug that is converted into its active metabolite, dabigatran, by hydrolysis. Dabigatran is a selective thrombin inhibitor that has been approved for the prevention of stroke in patients with non-valvular atrial fibrillation in Japan. Laboratory monitoring is not needed, but an assessment of its anticoagulant effect in certain clinical settings, such as emergency surgery, suspected overdose, or the occurrence of bleeding, is desirable. We overview the special coagulation assays, such as Hemoclot Thrombin Inhibitor (HTI), the thrombin generation assay (TGA), ecarin clotting time (ECT), ecarin chromogenic assay (ECA), prothrombinase-induced clotting time (PiCT), and activated clotting time (ACT). We also examined the relationship between dabigatran levels as determined by HTI, and the activated partial thromboplastin time (APTT) and prothrombin time (PT). APTT and PT demonstrated a positive correlation with the dabigatran levels. APTT, PT, and the combination of APTT and PT may estimate the dabigatran levels in plasma. PMID:27526541

  9. Automated Test Case Generation for an Autopilot Requirement Prototype

    Science.gov (United States)

    Giannakopoulou, Dimitra; Rungta, Neha; Feary, Michael

    2011-01-01

    Designing safety-critical automation with robust human interaction is a difficult task that is susceptible to a number of known Human-Automation Interaction (HAI) vulnerabilities. It is therefore essential to develop automated tools that provide support both in the design and rapid evaluation of such automation. The Automation Design and Evaluation Prototyping Toolset (ADEPT) enables the rapid development of an executable specification for automation behavior and user interaction. ADEPT supports a number of analysis capabilities, thus enabling the detection of HAI vulnerabilities early in the design process, when modifications are less costly. In this paper, we advocate the introduction of a new capability to model-based prototyping tools such as ADEPT. The new capability is based on symbolic execution that allows us to automatically generate quality test suites based on the system design. Symbolic execution is used to generate both user input and test oracles user input drives the testing of the system implementation, and test oracles ensure that the system behaves as designed. We present early results in the context of a component in the Autopilot system modeled in ADEPT, and discuss the challenges of test case generation in the HAI domain.

  10. Automated Software Test Data Generation: Direction of Research

    Directory of Open Access Journals (Sweden)

    Hitesh Tahbildar

    2011-02-01

    Full Text Available In this paper we are giving an overview of automatic test data generation. The basic objective of thispaper is to acquire the basic concepts related to automated test data generation research. The differentimplementation techniques are described with their relative merits and demerits. The future challengesand problems of test data generation are explained. Finally we describe the area where more focus isrequired for making automatic test data generation more effective in industry.

  11. DABIGATRAN ETEXILATE: NEW DIRECT THROMBIN INHIBITORS ANTICOAGULANTS

    Directory of Open Access Journals (Sweden)

    Patel Kinjal B

    2011-04-01

    Full Text Available Thrombin plays a key role in thrombotic events, and therefore thrombin inhibition represents a therapeutic target for numerous thromboembolic diseases. Thrombin is responsible for the conversion of soluble fibrinogen to fibrin; clot stabilization through activation of factor XIII and the formation of cross-linkage among fibrin molecules; and the generation of additional thrombin through activation of factors V, VIII, and XI. Direct thrombin inhibitors are an innovative class of anticoagulants that bind directly to thrombin to inhibit its actions and impede the clotting process. Dabigatran is the first direct thrombin inhibitor, orally available first approval by US Food and Drugs Administration in 2010. Specifically and reversibly inhibits thrombin, so the duration of action is predictable. The anticoagulant effect correlates well with plasma drug concentrations, which implies an effective anticoagulation with low bleeding risk without major problems of interactions with other drugs. The predictable pharmacokinetics and pharmacodynamics characteristics of dabigatran may facilitate dental management of patients who until now have been in treatment with traditional anticoagulants, given that it doesn’t require routine laboratory monitoring in the vast majority of patients treated. They also present a profile of drug interactions very favorable.

  12. Influenza virus H1N1 activates platelets through FcγRIIA signaling and thrombin generation.

    Science.gov (United States)

    Boilard, Eric; Paré, Guillaume; Rousseau, Matthieu; Cloutier, Nathalie; Dubuc, Isabelle; Lévesque, Tania; Borgeat, Pierre; Flamand, Louis

    2014-05-01

    Platelets play crucial functions in hemostasis and the prevention of bleeding. During H1N1 influenza A virus infection, platelets display activation markers. The platelet activation triggers during H1N1 infection remain elusive. We observed that H1N1 induces surface receptor activation, lipid mediator synthesis, and release of microparticles from platelets. These activation processes require the presence of serum/plasma, pointing to the contribution of soluble factor(s). Considering that immune complexes in the H1N1 pandemic were reported to play a pathogenic role, we assessed their contribution in H1N1-induced platelet activation. In influenza-immunized subjects, we observed that the virus scaffolds with immunoglobulin G (IgG) to form immune complexes that promote platelet activation. Mechanistically, this activation occurs through stimulation of low-affinity type 2 receptor for Fc portion of IgG (FcγRIIA), a receptor for immune complexes, independently of thrombin. Using a combination of in vitro and in vivo approaches, we found that the antibodies from H3N2-immunized mice activate transgenic mouse platelets that express FcγRIIA when put in the presence of H1N1, suggesting that cross-reacting influenza antibodies suffice. Alternatively, H1N1 can activate platelets via thrombin formation, independently of complement and FcγRIIA. These observations identify both the adaptive immune response and the innate response against pathogens as 2 intertwined processes that activate platelets during influenza infections.

  13. An automated data generator for NASTRAN

    Science.gov (United States)

    Stanton, E. L.

    1977-01-01

    A modeling system based on construction-in-context of geometry and physical properties data is adapted for NASTRAN finite element data generation. This system was originally developed for generating three-dimensional finite data for composite structures in PATCHES-III using parametric cubic models. These finite line, surface and volume models constructed using simple data directives will be subdivided into NASTRAN finite elements and their supporting data in the new data generator. Any geometry can be constructed as illustrated by a compressor fan blade with camber, twist and changing airfoil section and the shape then subdivided using a uniform or non-uniform mesh. Special emphasis is given to the adaption of construction-in-context to composite material property modeling. A PMAT series of directives is described for any one, two or three-dimensionally reinforced composite that allows the phase properties, as well as composite properties, to be generated.

  14. Thrombin during cardiopulmonary bypass.

    Science.gov (United States)

    Edmunds, L Henry; Colman, Robert W

    2006-12-01

    Cardiopulmonary bypass (CPB) ignites a massive defense reaction that stimulates all blood cells and five plasma protein systems to produce a myriad of vasoactive and cytotoxic substances, cell-signaling molecules, and upregulated cellular receptors. Thrombin is the key enzyme in the thrombotic portion of the defense reaction and is only partially suppressed by heparin. During CPB, thrombin is produced by both extrinsic and intrinsic coagulation pathways and activated platelets. The routine use of a cell saver and the eventual introduction of direct thrombin inhibitors now offer the possibility of completely suppressing thrombin production and fibrinolysis during cardiac surgery with CPB. PMID:17126170

  15. Automated mass spectrum generation for new physics

    CERN Document Server

    Alloul, Adam; De Causmaecker, Karen; Fuks, Benjamin; de Traubenberg, Michel Rausch

    2013-01-01

    We describe an extension of the FeynRules package dedicated to the automatic generation of the mass spectrum associated with any Lagrangian-based quantum field theory. After introducing a simplified way to implement particle mixings, we present a new class of FeynRules functions allowing both for the analytical computation of all the model mass matrices and for the generation of a C++ package, dubbed ASperGe. This program can then be further employed for a numerical evaluation of the rotation matrices necessary to diagonalize the field basis. We illustrate these features in the context of the Two-Higgs-Doublet Model, the Minimal Left-Right Symmetric Standard Model and the Minimal Supersymmetric Standard Model.

  16. Automating Traceability for Generated Software Artifacts

    Science.gov (United States)

    Richardson, Julian; Green, Jeffrey

    2004-01-01

    Program synthesis automatically derives programs from specifications of their behavior. One advantage of program synthesis, as opposed to manual coding, is that there is a direct link between the specification and the derived program. This link is, however, not very fine-grained: it can be best characterized as Program is-derived- from Specification. When the generated program needs to be understood or modified, more $ne-grained linking is useful. In this paper, we present a novel technique for automatically deriving traceability relations between parts of a specification and parts of the synthesized program. The technique is very lightweight and works -- with varying degrees of success - for any process in which one artifact is automatically derived from another. We illustrate the generality of the technique by applying it to two kinds of automatic generation: synthesis of Kalman Filter programs from speci3cations using the Aut- oFilter program synthesis system, and generation of assembly language programs from C source code using the GCC C compilel: We evaluate the effectiveness of the technique in the latter application.

  17. Automated Layout Generation of Analogue and Mixed-Signal ASIC's

    DEFF Research Database (Denmark)

    Bloch, Rene

    The research and development carried out in this Ph.D. study focusses on two key areas of the design flow for analogue and mixed-signal integrated circuit design, the mixed-signal floorplanning and the analogue layout generation.A novel approach to floorplanning is presented which provides true...... flow.A new design flow for automated layout generation of general analogue integrated circuits is presented. The design flow provides an automated design path from a sized circuit schematic to the final layout containing the placed, but unrouted, devices of the circuit. The analogue circuit layout...... is generated using a full-custom layout style and is based on a library of CMOS process independent device generators. The placement for the analogue circuit is derived using the interactive floorplan optimization algorithm described above. This ensures that a high degree of user control is implemented...

  18. Fully integrated, fully automated generation of short tandem repeat profiles

    OpenAIRE

    Tan, Eugene; Rosemary S. Turingan; Hogan, Catherine; Vasantgadkar, Sameer; Palombo, Luke; Schumm, James W.; Richard F Selden

    2013-01-01

    Background The generation of short tandem repeat profiles, also referred to as ‘DNA typing,’ is not currently performed outside the laboratory because the process requires highly skilled technical operators and a controlled laboratory environment and infrastructure with several specialized instruments. The goal of this work was to develop a fully integrated system for the automated generation of short tandem repeat profiles from buccal swab samples, to improve forensic laboratory process flow...

  19. AutoDipole - Automated generation of dipole subtraction terms

    Energy Technology Data Exchange (ETDEWEB)

    Hasegawa, K.; Uwer, P. [Humboldt-Universitaet, Berlin (Germany). Inst. fuer Physik; Moch, S. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany)

    2009-11-15

    We present an automated generation of the subtraction terms for next-to-leading order QCD calculations in the Catani-Seymour dipole formalism. For a given scattering process with n external particles our Mathematica package generates all dipole terms, allowing for bothmassless and massive dipoles. The numerical evaluation of the subtraction terms proceeds with MadGraph, which provides Fortran code for the necessary scattering amplitudes. Checks of the numerical stability are discussed. (orig.)

  20. Automating Visualization Service Generation with the WATT Compiler

    Science.gov (United States)

    Bollig, E. F.; Lyness, M. D.; Erlebacher, G.; Yuen, D. A.

    2007-12-01

    As tasks and workflows become increasingly complex, software developers are devoting increasing attention to automation tools. Among many examples, the Automator tool from Apple collects components of a workflow into a single script, with very little effort on the part of the user. Tasks are most often described as a series of instructions. The granularity of the tasks dictates the tools to use. Compilers translate fine-grained instructions to assembler code, while scripting languages (ruby, perl) are used to describe a series of tasks at a higher level. Compilers can also be viewed as transformational tools: a cross-compiler can translate executable code written on one computer to assembler code understood on another, while transformational tools can translate from one high-level language to another. We are interested in creating visualization web services automatically, starting from stand-alone VTK (Visualization Toolkit) code written in Tcl. To this end, using the OCaml programming language, we have developed a compiler that translates Tcl into C++, including all the stubs, classes and methods to interface with gSOAP, a C++ implementation of the Soap 1.1/1.2 protocols. This compiler, referred to as the Web Automation and Translation Toolkit (WATT), is the first step towards automated creation of specialized visualization web services without input from the user. The WATT compiler seeks to automate all aspects of web service generation, including the transport layer, the division of labor and the details related to interface generation. The WATT compiler is part of ongoing efforts within the NSF funded VLab consortium [1] to facilitate and automate time-consuming tasks for the science related to understanding planetary materials. Through examples of services produced by WATT for the VLab portal, we will illustrate features, limitations and the improvements necessary to achieve the ultimate goal of complete and transparent automation in the generation of web

  1. A scheme on automated test data generation and its evaluation

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    By analyzing some existing test data generation methods, a new automated test data generation approach was presented. The linear predicate functions on a given path was directly used to construct a linear constrain system for input variables. Only when the predicate function is nonlinear, does the linear arithmetic representation need to be computed. If the entire predicate functions on the given path are linear, either the desired test data or the guarantee that the path is infeasible can be gotten from the solution of the constrain system. Otherwise, the iterative refining for the input is required to obtain the desired test data. Theoretical analysis and test results show that the approach is simple and effective, and takes less computation. The scheme can also be used to generate path-based test data for the programs with arrays and loops.

  2. Automated Generation of User Guidance by Combining Computation and Deduction

    CERN Document Server

    Neuper, Walther

    2012-01-01

    Herewith, a fairly old concept is published for the first time and named "Lucas Interpretation". This has been implemented in a prototype, which has been proved useful in educational practice and has gained academic relevance with an emerging generation of educational mathematics assistants (EMA) based on Computer Theorem Proving (CTP). Automated Theorem Proving (ATP), i.e. deduction, is the most reliable technology used to check user input. However ATP is inherently weak in automatically generating solutions for arbitrary problems in applied mathematics. This weakness is crucial for EMAs: when ATP checks user input as incorrect and the learner gets stuck then the system should be able to suggest possible next steps. The key idea of Lucas Interpretation is to compute the steps of a calculation following a program written in a novel CTP-based programming language, i.e. computation provides the next steps. User guidance is generated by combining deduction and computation: the latter is performed by a specific l...

  3. Method and apparatus for automated, modular, biomass power generation

    Science.gov (United States)

    Diebold, James P.; Lilley, Arthur; Browne, Kingsbury III; Walt, Robb Ray; Duncan, Dustin; Walker, Michael; Steele, John; Fields, Michael; Smith, Trevor

    2011-03-22

    Method and apparatus for generating a low tar, renewable fuel gas from biomass and using it in other energy conversion devices, many of which were designed for use with gaseous and liquid fossil fuels. An automated, downdraft gasifier incorporates extensive air injection into the char bed to maintain the conditions that promote the destruction of residual tars. The resulting fuel gas and entrained char and ash are cooled in a special heat exchanger, and then continuously cleaned in a filter prior to usage in standalone as well as networked power systems.

  4. Endogenous thrombin potential in polycystic ovary syndrome

    DEFF Research Database (Denmark)

    Aziz, Mubeena; Sidelmann, Johannes J; Wissing, Marie Louise Muff;

    2015-01-01

    OBJECTIVES: The objective of this study is to investigate plasma endogenous thrombin generation in four different phenotypes of polycystic ovary syndrome (PCOS) defined by Body Mass Index (BMI) and insulin resistance (IR). PCOS is diagnosed according to the Rotterdam criteria. DESIGN: Multicenter...... cross-sectional study. SETTING: Two major University Hospitals in the Capital region of Denmark. PATIENTS: Hundred forty-eight European women with PCOS were consecutively recruited during April 2010-February 2012. Clinical examination, blood sampling, and DEXA scan were performed. MAIN OUTCOME MEASURES......: Endogenous thrombin potential (ETP). RESULTS: PCOS women with phenotype BMI > 25 + IR have increased potential of thrombin generation. ETP is associated with total body fat mass, IR, and CRP. CONCLUSIONS: Obese and insulin resistant women with PCOS have elevated level of ETP corresponding to increased risk...

  5. Fully integrated, fully automated generation of short tandem repeat profiles

    Science.gov (United States)

    2013-01-01

    Background The generation of short tandem repeat profiles, also referred to as ‘DNA typing,’ is not currently performed outside the laboratory because the process requires highly skilled technical operators and a controlled laboratory environment and infrastructure with several specialized instruments. The goal of this work was to develop a fully integrated system for the automated generation of short tandem repeat profiles from buccal swab samples, to improve forensic laboratory process flow as well as to enable short tandem repeat profile generation to be performed in police stations and in field-forward military, intelligence, and homeland security settings. Results An integrated system was developed consisting of an injection-molded microfluidic BioChipSet cassette, a ruggedized instrument, and expert system software. For each of five buccal swabs, the system purifies DNA using guanidinium-based lysis and silica binding, amplifies 15 short tandem repeat loci and the amelogenin locus, electrophoretically separates the resulting amplicons, and generates a profile. No operator processing of the samples is required, and the time from swab insertion to profile generation is 84 minutes. All required reagents are contained within the BioChipSet cassette; these consist of a lyophilized polymerase chain reaction mix and liquids for purification and electrophoretic separation. Profiles obtained from fully automated runs demonstrate that the integrated system generates concordant short tandem repeat profiles. The system exhibits single-base resolution from 100 to greater than 500 bases, with inter-run precision with a standard deviation of ±0.05 - 0.10 bases for most alleles. The reagents are stable for at least 6 months at 22°C, and the instrument has been designed and tested to Military Standard 810F for shock and vibration ruggedization. A nontechnical user can operate the system within or outside the laboratory. Conclusions The integrated system represents the

  6. The phosphorylation status of extracellular-regulated kinase 1/2 in astrocytes and neurons from rat hippocampus determines the thrombin-induced calcium release and ROS generation.

    Science.gov (United States)

    Zündorf, Gregor; Reiser, Georg

    2011-12-01

    Challenge of protease-activated receptors induces cytosolic Ca(2+) concentration ([Ca(2+) ](c)) increase, mitogen-activated protein kinase activation and reactive oxygen species (ROS) formation with a bandwidth of responses in individual cells. We detected in this study in situ the thrombin-induced [Ca(2+) ](c) rise and ROS formation in dissociated hippocampal astrocytes and neurons in a mixed culture. In identified cells, single cell responses were correlated with extracellular-regulated kinase (ERK)1/2 phosphorylation level. On average, in astrocytes, thrombin induced a transient [Ca(2+) ](c) rise with concentration-dependent increase in amplitude and extrusion rate and high ERK1/2 phosphorylation level. Correlation analysis of [Ca(2+) ](c) response characteristics of single astrocytes reveals that astrocytes with nuclear phosphoERK1/2 localization have a smaller Ca(2+) amplitude and extrusion rate compared with cells with a cytosolic phosphoERK1/2 localization. In naive neurons, without thrombin challenge, variable ERK1/2 phosphorylation patterns are observed. ROS were detected by hydroethidine. Only in neurons with increased ERK1/2 phosphorylation level, we see sustained intracellular rise in fluorescence of the dye lasting over several minutes. ROS formation was abolished by pre-incubation with the NADPH oxidase inhibitor apocynin. Additionally, thrombin induced an immediate, transient hydroethidine fluorescence increase. This was interpreted as NADPH oxidase-mediated O(2) (•-) -release into the extracellular milieu, because it was decreased by pre-incubation with apocynin, and could be eluted by superfusion. In conclusion, the phosphorylation status of ERK1/2 determines the thrombin-dependent [Ca(2+) ](c) increase and ROS formation and, thus, influences the capacity of thrombin to regulate neuroprotection or neurodegeneration. PMID:21988180

  7. Automated Generation of User Guidance by Combining Computation and Deduction

    Directory of Open Access Journals (Sweden)

    Walther Neuper

    2012-02-01

    Full Text Available Herewith, a fairly old concept is published for the first time and named "Lucas Interpretation". This has been implemented in a prototype, which has been proved useful in educational practice and has gained academic relevance with an emerging generation of educational mathematics assistants (EMA based on Computer Theorem Proving (CTP. Automated Theorem Proving (ATP, i.e. deduction, is the most reliable technology used to check user input. However ATP is inherently weak in automatically generating solutions for arbitrary problems in applied mathematics. This weakness is crucial for EMAs: when ATP checks user input as incorrect and the learner gets stuck then the system should be able to suggest possible next steps. The key idea of Lucas Interpretation is to compute the steps of a calculation following a program written in a novel CTP-based programming language, i.e. computation provides the next steps. User guidance is generated by combining deduction and computation: the latter is performed by a specific language interpreter, which works like a debugger and hands over control to the learner at breakpoints, i.e. tactics generating the steps of calculation. The interpreter also builds up logical contexts providing ATP with the data required for checking user input, thus combining computation and deduction. The paper describes the concepts underlying Lucas Interpretation so that open questions can adequately be addressed, and prerequisites for further work are provided.

  8. Automated generation of burnup chain for reactor analysis applications

    International Nuclear Information System (INIS)

    This paper presents the development of an automated generation of a new burnup chain for reactor analysis applications. The JENDL FP Decay Data File 2011 and Fission Yields Data File 2011 were used as the data sources. The nuclides in the new chain are determined by restrictions of the half-life and cumulative yield of fission products or from a given list. Then, decay modes, branching ratios and fission yields are recalculated taking into account intermediate reactions. The new burnup chain is output according to the format for the SRAC code system. Verification was performed to evaluate the accuracy of the new burnup chain. The results show that the new burnup chain reproduces well the results of a reference one with 193 fission products used in SRAC. Further development and applications are being planned with the burnup chain code. (author)

  9. Automated generation of highly accurate, efficient and transferable pseudopotentials

    Science.gov (United States)

    Hansel, R. A.; Brock, C. N.; Paikoff, B. C.; Tackett, A. R.; Walker, D. G.

    2015-11-01

    A multi-objective genetic algorithm (MOGA) was used to automate a search for optimized pseudopotential parameters. Pseudopotentials were generated using the atomPAW program and density functional theory (DFT) simulations were conducted using the pwPAW program. The optimized parameters were the cutoff radius and projector energies for the s and p orbitals. The two objectives were low pseudopotential error and low computational work requirements. The error was determined from (1) the root mean square difference between the all-electron and pseudized-electron log derivative, (2) the calculated lattice constant versus reference data of Holzwarth et al., and (3) the calculated bulk modulus versus reference potentials. The computational work was defined as the number of flops required to perform the DFT simulation. Pseudopotential transferability was encouraged by optimizing each element in different lattices: (1) nitrogen in GaN, AlN, and YN, (2) oxygen in NO, ZnO, and SiO4, and (3) fluorine in LiF, NaF, and KF. The optimal solutions were equivalent in error and required significantly less computational work than the reference data. This proof-of-concept study demonstrates that the combination of MOGA and ab-initio simulations is a powerful tool that can generate a set of transferable potentials with a trade-off between accuracy (error) and computational efficiency (work).

  10. Toward Fully Automated Multicriterial Plan Generation: A Prospective Clinical Study

    Energy Technology Data Exchange (ETDEWEB)

    Voet, Peter W.J., E-mail: p.voet@erasmusmc.nl [Department of Radiation Oncology, Erasmus Medical Center–Daniel den Hoed Cancer Center, Groene Hilledijk 301, Rotterdam 3075EA (Netherlands); Dirkx, Maarten L.P.; Breedveld, Sebastiaan; Fransen, Dennie; Levendag, Peter C.; Heijmen, Ben J.M. [Department of Radiation Oncology, Erasmus Medical Center–Daniel den Hoed Cancer Center, Groene Hilledijk 301, Rotterdam 3075EA (Netherlands)

    2013-03-01

    Purpose: To prospectively compare plans generated with iCycle, an in-house-developed algorithm for fully automated multicriterial intensity modulated radiation therapy (IMRT) beam profile and beam orientation optimization, with plans manually generated by dosimetrists using the clinical treatment planning system. Methods and Materials: For 20 randomly selected head-and-neck cancer patients with various tumor locations (of whom 13 received sequential boost treatments), we offered the treating physician the choice between an automatically generated iCycle plan and a manually optimized plan using standard clinical procedures. Although iCycle used a fixed “wish list” with hard constraints and prioritized objectives, the dosimetrists manually selected the beam configuration and fine tuned the constraints and objectives for each IMRT plan. Dosimetrists were not informed in advance whether a competing iCycle plan was made. The 2 plans were simultaneously presented to the physician, who then selected the plan to be used for treatment. For the patient group, differences in planning target volume coverage and sparing of critical tissues were quantified. Results: In 32 of 33 plan comparisons, the physician selected the iCycle plan for treatment. This highly consistent preference for the automatically generated plans was mainly caused by the improved sparing for the large majority of critical structures. With iCycle, the normal tissue complication probabilities for the parotid and submandibular glands were reduced by 2.4% ± 4.9% (maximum, 18.5%, P=.001) and 6.5% ± 8.3% (maximum, 27%, P=.005), respectively. The reduction in the mean oral cavity dose was 2.8 ± 2.8 Gy (maximum, 8.1 Gy, P=.005). For the swallowing muscles, the esophagus and larynx, the mean dose reduction was 3.3 ± 1.1 Gy (maximum, 9.2 Gy, P<.001). For 15 of the 20 patients, target coverage was also improved. Conclusions: In 97% of cases, automatically generated plans were selected for treatment because of

  11. Automated Generation and Assessment of Autonomous Systems Test Cases

    Science.gov (United States)

    Barltrop, Kevin J.; Friberg, Kenneth H.; Horvath, Gregory A.

    2008-01-01

    This slide presentation reviews some of the issues concerning verification and validation testing of autonomous spacecraft routinely culminates in the exploration of anomalous or faulted mission-like scenarios using the work involved during the Dawn mission's tests as examples. Prioritizing which scenarios to develop usually comes down to focusing on the most vulnerable areas and ensuring the best return on investment of test time. Rules-of-thumb strategies often come into play, such as injecting applicable anomalies prior to, during, and after system state changes; or, creating cases that ensure good safety-net algorithm coverage. Although experience and judgment in test selection can lead to high levels of confidence about the majority of a system's autonomy, it's likely that important test cases are overlooked. One method to fill in potential test coverage gaps is to automatically generate and execute test cases using algorithms that ensure desirable properties about the coverage. For example, generate cases for all possible fault monitors, and across all state change boundaries. Of course, the scope of coverage is determined by the test environment capabilities, where a faster-than-real-time, high-fidelity, software-only simulation would allow the broadest coverage. Even real-time systems that can be replicated and run in parallel, and that have reliable set-up and operations features provide an excellent resource for automated testing. Making detailed predictions for the outcome of such tests can be difficult, and when algorithmic means are employed to produce hundreds or even thousands of cases, generating predicts individually is impractical, and generating predicts with tools requires executable models of the design and environment that themselves require a complete test program. Therefore, evaluating the results of large number of mission scenario tests poses special challenges. A good approach to address this problem is to automatically score the results

  12. "Mirror image" antagonists of thrombin-induced platelet activation based on thrombin receptor structure.

    OpenAIRE

    Hung, D. T.; Vu, T K; Wheaton, V I; Charo, I F; Nelken, N A; Esmon, N; Esmon, C T; Coughlin, S R

    1992-01-01

    Platelet activation by thrombin plays a critical role in hemostasis and thrombosis. Based on structure-activity studies of a cloned platelet thrombin receptor, we designed two "mirror image" antagonists of thrombin and thrombin receptor function. First, "uncleavable" peptides mimicking the receptor domain postulated to interact with thrombin were found to be potent thrombin inhibitors. Second, proteolytically inactive mutant thrombins designed to bind but not cleave the thrombin receptor were...

  13. Automated Theorem Proving for Cryptographic Protocols with Automatic Attack Generation

    OpenAIRE

    Jan Juerjens; Thomas A. Kuhn

    2016-01-01

    Automated theorem proving is both automatic and can be quite efficient. When using theorem proving approaches for security protocol analysis, however, the problem is often that absence of a proof of security of a protocol may give little hint as to where the security weakness lies, to enable the protocol designer to improve the protocol. For our approach to verify cryptographic protocols using automated theorem provers for first-order logic (such as e-SETHEO or SPASS), we demonstrate a method...

  14. Implementing the WebSocket Protocol Based on Formal Modelling and Automated Code Generation

    OpenAIRE

    Simonsen, Kent,; Kristensen, Lars,

    2014-01-01

    Model-based software engineering offers several attractive benefits for the implementation of protocols, including automated code generation for different platforms from design-level models. In earlier work, we have proposed a template-based approach using Coloured Petri Net formal models with pragmatic annotations for automated code generation of protocol software. The contribution of this paper is an application of the approach as implemented in the PetriCode tool to obtain protocol softwar...

  15. Ximelagatran: direct thrombin inhibitor

    Directory of Open Access Journals (Sweden)

    Shir-Jing Ho

    2006-03-01

    Full Text Available Shir-Jing Ho1, Tim A Brighton2,31St George Hospital, Sydney, NSW, Australia; 2University of New South Wales, Sydney, Australia; 3SEALS (Randwick, Prince of Wales Hospital, Sydney, AustraliaAbstract: Warfarin sodium is an effective oral anticoagulant drug. However, warfarin has a narrow therapeutic window with significant risks of hemorrhage at therapeutic concentrations. Dosing is difficult and requires frequent monitoring. New oral anticoagulant agents are required to improve current anticoagulant therapy. Furthermore, while warfarin is effective in venous disease, it does not provide more than 60% risk reduction compared with placebo in venous thrombosis prophylaxis and considerably lower risk reduction in terms of arterial thrombosis. Ximelagatran is an oral pro-drug of melagatran, a synthetic small peptidomimetic with direct thrombin inhibitory actions and anticoagulant activity. As an oral agent, ximelagatran has a number of desirable properties including a rapid onset of action, fixed dosing, stable absorption, apparent low potential for medication interactions, and no requirement for monitoring of drug levels or dose adjustment. It has a short plasma elimination half-life of about 4 hours in cases of unexpected hemorrhage or need for reversal. Its main toxicity relates to the development of abnormal liver biochemistry and/or liver dysfunction with “long-term” use of the drug. This usually occurs within the first 6 months of commencing therapy, with a small percentage of patients developing jaundice. The biochemical abnormality usually resolves despite continuation of the drug. The cause of this toxicity remains unknown. Clinical studies to date have shown that ximelagatran is noninferior to warfarin in stroke prevention in patients with nonvalvular atrial fibrillation, noninferior to standard therapy as acute and extended therapy of deep vein thrombosis (DVT, and superior to warfarin for the prevention of venous thromboembolism post

  16. Using machine learning techniques to automate sky survey catalog generation

    Science.gov (United States)

    Fayyad, Usama M.; Roden, J. C.; Doyle, R. J.; Weir, Nicholas; Djorgovski, S. G.

    1993-01-01

    We describe the application of machine classification techniques to the development of an automated tool for the reduction of a large scientific data set. The 2nd Palomar Observatory Sky Survey provides comprehensive photographic coverage of the northern celestial hemisphere. The photographic plates are being digitized into images containing on the order of 10(exp 7) galaxies and 10(exp 8) stars. Since the size of this data set precludes manual analysis and classification of objects, our approach is to develop a software system which integrates independently developed techniques for image processing and data classification. Image processing routines are applied to identify and measure features of sky objects. Selected features are used to determine the classification of each object. GID3* and O-BTree, two inductive learning techniques, are used to automatically learn classification decision trees from examples. We describe the techniques used, the details of our specific application, and the initial encouraging results which indicate that our approach is well-suited to the problem. The benefits of the approach are increased data reduction throughput, consistency of classification, and the automated derivation of classification rules that will form an objective, examinable basis for classifying sky objects. Furthermore, astronomers will be freed from the tedium of an intensely visual task to pursue more challenging analysis and interpretation problems given automatically cataloged data.

  17. Thrombin, a mediator of cerebrovascular inflammation in AD and hypoxia

    Directory of Open Access Journals (Sweden)

    Debjani eTripathy

    2013-05-01

    Full Text Available Considerable evidence implicates hypoxia and vascular inflammation in Alzheimer’s disease (AD. Thrombin, a multifunctional inflammatory mediator, is demonstrable in the brains of AD patients both in the vessel walls and senile plaques. Hypoxia-inducible factor 1α (HIF-1α, a key regulator of the cellular response to hypoxia, is also upregulated in the vasculature of human AD brains. The objective of this study is to investigate inflammatory protein expression in the cerebrovasculature of transgenic AD mice and to explore the role of thrombin as a mediator of cerebrovascular inflammation and oxidative stress in AD and in hypoxia-induced changes in brain endothelial cells. Immunofluorescent analysis of the cerebrovasculature in AD mice demonstrates significant (p<0.01-0.001 increases in thrombin, HIF-1α, interleukin-6 (IL-6, monocyte chemoattractant protein-1 (MCP-1, matrix metalloproteinases (MMPs, and reactive oxygen species (ROS compared to controls. Administration of the thrombin inhibitor dabigatran (100 mg/kg to AD mice for 34 wks significantly decreases expression of inflammatory proteins and ROS. Exposure of cultured brain endothelial cells to hypoxia for 6 h causes an upregulation of thrombin, HIF-1α, MCP-1, IL-6 and MMP2 and ROS. Treatment of endothelial cells with the dabigatran (1 nM reduces ROS generation and inflammatory protein expression (p<0.01-0.001. The data demonstrate that inhibition of thrombin in culture blocks the increase in inflammatory protein expression and ROS generation evoked by hypoxia. Also, administration of dabigatran to transgenic AD mice diminishes expression of inflammatory proteins and ROS in the cerebromicrovasculature. Taken together, these results suggest that inhibiting thrombin generation could have therapeutic value in AD and other disorders where hypoxia, inflammation and oxidative stress are involved.

  18. Automated Test Data Generation Based On Individual Constraints and Boundary Value

    Directory of Open Access Journals (Sweden)

    Hitesh Tahbildar

    2010-09-01

    Full Text Available Testing is an important activity in software development. Unfortunately till today testing is done manually by most of the industry due to high cost and complexity of automation. Automated testing can reduce the cost of software significantly. Automated Software Test Data Generation is an activity that in the course of software testing automatically generates test data for the software under test. Most of the automated test data generation uses constraint solver to generate test data. But it cannot generate test data when the constraints are not solvable. Although method can be found to generate test data even if the constraints are unsolvable, but it is poor in terms of code coverage. In this paper, we propose a test data generation method to improve test coverage and to avoid the unsolvable constraints problem. Our method is based on the individual constraints and same or dependent variable to create the path table which holds the information about the path traversed by various input test data. For generating unique test data for all the linearly independent feasible path we created equivalence class from the path table on the basis of path traversed by the various input test data. The input data is taken based on individual constraints or boundary value. Our results are compared with cyclomatic complexity and number of possible infeasible paths. The comparison shows the effectiveness of our method.

  19. Automated quadrilateral mesh generation for digital image structures

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    With the development of advanced imaging technology, digital images are widely used. This paper proposes an automatic quadrilateral mesh generation algorithm for multi-colour imaged structures. It takes an original arbitrary digital image as an input for automatic quadrilateral mesh generation, this includes removing the noise, extracting and smoothing the boundary geometries between different colours, and automatic all-quad mesh generation with the above boundaries as constraints. An application example is...

  20. Automated Generation of Kempe Linkage and Its Complexity

    Institute of Scientific and Technical Information of China (English)

    高小山; 朱长才

    1999-01-01

    It is a famous result of Kempe that a linkage can be designed to generate any given plane algebraic curve.In this paper,Kempe's result is improved to give a precise algorithm for generating Kempe linkage.We proved that for an algebraic plane curve of degrenn n,Kempe linkage uses at most O(n4) links.Efforts to implement a program which may generate Kempe linkage and simulation of the generation process of the plane curves are presented in the paper.

  1. Automated Generation of Safety Requirements from Railway Interlocking Tables

    DEFF Research Database (Denmark)

    Haxthausen, Anne Elisabeth

    2012-01-01

    This paper describes a tool for extracting formal safety conditions from interlocking tables for railway interlocking systems. The tool has been applied to generate safety conditions for the interlocking system at Stenstrup station in Denmark, and the generated conditions were then checked to hold...... by the SAL model checker tool....

  2. Software Test Case Automated Generation Algorithm with Extended EDPN Model

    Directory of Open Access Journals (Sweden)

    Jinlong Tao

    2013-08-01

    Full Text Available To improve the sufficiency for software testing and the performance of testing algorithms, an improved event-driven Petri network model using combination method is proposed, abbreviated as OEDPN model. Then it is applied to OATS method to extend the implementation of OATS. On the basis of OEDPN model, the marked associate recursive method of state combination on category is presented to solve problems of combined conflict. It is also for test case explosion generated by redundant test cases and hard extension of OATS method. Meanwhile, the generation methods on interactive test cases of extended OATS are also presented by research on generation test cases.

  3. Automated Generation of Tabular Equations of State with Uncertainty Information

    Science.gov (United States)

    Carpenter, John H.; Robinson, Allen C.; Debusschere, Bert J.; Mattsson, Ann E.

    2015-06-01

    As computational science pushes toward higher fidelity prediction, understanding the uncertainty associated with closure models, such as the equation of state (EOS), has become a key focus. Traditional EOS development often involves a fair amount of art, where expert modelers may appear as magicians, providing what is felt to be the closest possible representation of the truth. Automation of the development process gives a means by which one may demystify the art of EOS, while simultaneously obtaining uncertainty information in a manner that is both quantifiable and reproducible. We describe our progress on the implementation of such a system to provide tabular EOS tables with uncertainty information to hydrocodes. Key challenges include encoding the artistic expert opinion into an algorithmic form and preserving the analytic models and uncertainty information in a manner that is both accurate and computationally efficient. Results are demonstrated on a multi-phase aluminum model. *Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  4. UNICOS CPC6: Automated Code Generation for Process Control Applications

    CERN Document Server

    Fernandez Adiego, B; Prieto Barreiro, I

    2011-01-01

    The Continuous Process Control package (CPC) is one of the components of the CERN Unified Industrial Control System framework (UNICOS) [1]. As a part of this framework, UNICOS-CPC provides a well defined library of device types, amethodology and a set of tools to design and implement industrial control applications. The new CPC version uses the software factory UNICOS Application Builder (UAB) [2] to develop CPC applications. The CPC component is composed of several platform oriented plugins PLCs and SCADA) describing the structure and the format of the generated code. It uses a resource package where both, the library of device types and the generated file syntax, are defined. The UAB core is the generic part of this software, it discovers and calls dynamically the different plug-ins and provides the required common services. In this paper the UNICOS CPC6 package is introduced. It is composed of several plug-ins: the Instance generator and the Logic generator for both, Siemens and Schneider PLCs, the SCADA g...

  5. Aptamer Based Microsphere Biosensor for Thrombin Detection

    OpenAIRE

    Xudong Fan; White, Ian M.; Suter, Jonathan D.; Hongying Zhu

    2006-01-01

    We have developed an optical microsphere resonator biosensor using aptamer as receptor for the measurement of the important biomolecule thrombin. The sphere surface is modified with anti-thrombin aptamer, which has excellent binding affinity and selectivity for thrombin. Binding of the thrombin at the sphere surface is monitored by the spectral position of the microsphere's whispering gallery mode resonances. A detection limit on the order of 1 NIH Unit/mL is demonstrated. Control experiments...

  6. Automated Code Generation for Lattice Quantum Chromodynamics and beyond

    CERN Document Server

    Barthou, Denis; Dolbeau, Romain; Grosdidier, Gilbert; Eisenbeis, Christina; Kruse, Michael; Pene, Olivier; Petrov, Konstantin; Tadonki, Claude

    2014-01-01

    We present here our ongoing work on a Domain Specific Language which aims to simplify Monte-Carlo simulations and measurements in the domain of Lattice Quantum Chromodynamics. The tool-chain, called Qiral, is used to produce high-performance OpenMP C code from LaTeX sources. We discuss conceptual issues and details of implementation and optimization. The comparison of the performance of the generated code to the well-established simulation software is also made.

  7. Automated generation of formal safety conditions from railway interlocking tables

    DEFF Research Database (Denmark)

    Haxthausen, Anne Elisabeth

    2014-01-01

    This paper describes a tool for extracting formal safety conditions from interlocking tables for railway interlocking systems. The tool has been applied to generate safety conditions for the interlocking system at Stenstrup station in Denmark, and the SAL model checker tool has been used to check...... that these conditions were satisfied by a model of the relay circuits implementing the interlocking system at Stenstrup station....

  8. Implementing the WebSocket Protocol Based on Formal Modelling and Automated Code Generation

    DEFF Research Database (Denmark)

    Simonsen, Kent Inge; Kristensen, Lars Michael

    2014-01-01

    with pragmatic annotations for automated code generation of protocol software. The contribution of this paper is an application of the approach as implemented in the PetriCode tool to obtain protocol software implementing the IETF WebSocket protocol. This demonstrates the scalability of our approach to real...

  9. Automated generation of program translation and verification tools using annotated grammars

    NARCIS (Netherlands)

    Ordonez Camacho, D.; Mens, K.; Brand, M.G.J. van den; Vinju, J.J.

    2010-01-01

    Automatically generating program translators from source and target language specifications is a non-trivial problem. In this paper we focus on the problem of automating the process of building translators between operations languages, a family of DSLs used to program satellite operations procedures

  10. Automated Testcase Generation for Numerical Support Functions in Embedded Systems

    Science.gov (United States)

    Schumann, Johann; Schnieder, Stefan-Alexander

    2014-01-01

    We present a tool for the automatic generation of test stimuli for small numerical support functions, e.g., code for trigonometric functions, quaternions, filters, or table lookup. Our tool is based on KLEE to produce a set of test stimuli for full path coverage. We use a method of iterative deepening over abstractions to deal with floating-point values. During actual testing the stimuli exercise the code against a reference implementation. We illustrate our approach with results of experiments with low-level trigonometric functions, interpolation routines, and mathematical support functions from an open source UAS autopilot.

  11. Electronic design automation of multi-scroll chaos generators

    CERN Document Server

    Pacheco, Jesus Manuel Muñoz

    2010-01-01

    This book is unique when compared with books on non-linear circuits and systems. The book introduces novel concepts of physics, computer and electrical engineering. The synthesis of Multi-scroll chaotic oscillators is performed through three hierarchical levels of abstractions. A good repertoire of multi-scroll chaos generators is presented by dealing with 1D, 2D ad 3D oscillators which require one, two or three piece-wise linear functions, respectively. Each function is designed using operational amplifiers. Since the approach uses behavioral models, other electronic devices including novel i

  12. An automated framework for hypotheses generation using literature

    Directory of Open Access Journals (Sweden)

    Abedi Vida

    2012-08-01

    Full Text Available Abstract Background In bio-medicine, exploratory studies and hypothesis generation often begin with researching existing literature to identify a set of factors and their association with diseases, phenotypes, or biological processes. Many scientists are overwhelmed by the sheer volume of literature on a disease when they plan to generate a new hypothesis or study a biological phenomenon. The situation is even worse for junior investigators who often find it difficult to formulate new hypotheses or, more importantly, corroborate if their hypothesis is consistent with existing literature. It is a daunting task to be abreast with so much being published and also remember all combinations of direct and indirect associations. Fortunately there is a growing trend of using literature mining and knowledge discovery tools in biomedical research. However, there is still a large gap between the huge amount of effort and resources invested in disease research and the little effort in harvesting the published knowledge. The proposed hypothesis generation framework (HGF finds “crisp semantic associations” among entities of interest - that is a step towards bridging such gaps. Methodology The proposed HGF shares similar end goals like the SWAN but are more holistic in nature and was designed and implemented using scalable and efficient computational models of disease-disease interaction. The integration of mapping ontologies with latent semantic analysis is critical in capturing domain specific direct and indirect “crisp” associations, and making assertions about entities (such as disease X is associated with a set of factors Z. Results Pilot studies were performed using two diseases. A comparative analysis of the computed “associations” and “assertions” with curated expert knowledge was performed to validate the results. It was observed that the HGF is able to capture “crisp” direct and indirect associations, and provide knowledge

  13. ADVANTG An Automated Variance Reduction Parameter Generator, Rev. 1

    Energy Technology Data Exchange (ETDEWEB)

    Mosher, Scott W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Johnson, Seth R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bevill, Aaron M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ibrahim, Ahmad M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Daily, Charles R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Evans, Thomas M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Wagner, John C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Johnson, Jeffrey O. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Grove, Robert E. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-08-01

    The primary objective of ADVANTG is to reduce both the user effort and the computational time required to obtain accurate and precise tally estimates across a broad range of challenging transport applications. ADVANTG has been applied to simulations of real-world radiation shielding, detection, and neutron activation problems. Examples of shielding applications include material damage and dose rate analyses of the Oak Ridge National Laboratory (ORNL) Spallation Neutron Source and High Flux Isotope Reactor (Risner and Blakeman 2013) and the ITER Tokamak (Ibrahim et al. 2011). ADVANTG has been applied to a suite of radiation detection, safeguards, and special nuclear material movement detection test problems (Shaver et al. 2011). ADVANTG has also been used in the prediction of activation rates within light water reactor facilities (Pantelias and Mosher 2013). In these projects, ADVANTG was demonstrated to significantly increase the tally figure of merit (FOM) relative to an analog MCNP simulation. The ADVANTG-generated parameters were also shown to be more effective than manually generated geometry splitting parameters.

  14. New Approaches to the Role of Thrombin in Acute Coronary Syndromes: Quo Vadis Bivalirudin, a Direct Thrombin Inhibitor?

    Directory of Open Access Journals (Sweden)

    María Asunción Esteve-Pastor

    2016-02-01

    Full Text Available The pathophysiology of acute coronary syndrome (ACS involves platelet activation and thrombus formation after the rupture of atherosclerotic plaques. Thrombin is generated at the blood-plaque interface in association with cellular membranes on cells and platelets. Thrombin also amplifies the response to the tissue injury, coagulation and platelet response, so the treatment of ACS is based on the combined use of both antiplatelet (such as aspirin, clopidogrel, prasugrel and ticagrelor and antithrombotic drugs (unfractionated heparin, enoxaparin, fondaparinux and bivalirudin. Bivalirudin competitively inhibits thrombin with high affinity, a predictable response from its linear pharmacokinetics and short action. However, a present remarkable controversy exists between the latest main Guidelines in Clinical Practice and the key trials evaluating the use of bivalirudin in ACS. The aim of this review is to update the development of bivalirudin, including pharmacological properties, obtained information from clinical trials evaluating efficacy and safety of bivalirudin in ACS; as well as the recommendations of clinical Guidelines.

  15. M073: Monte Carlo generated spectra for QA/QC of automated NAA routine

    Energy Technology Data Exchange (ETDEWEB)

    Jackman, K. R. (Kevin R.); Biegalski, S. R.

    2004-01-01

    A quality check for an automated system of analyzing large sets of neutron activated samples has been developed. Activated samples are counted with an HPGe detector, in conjunction with an automated sample changer and spectral analysis tools, controlled by the Canberra GENIE 2K and REXX software. After each sample is acquired and analyzed, a Microsoft Visual Basic program imports the results into a template Microsoft Excel file where the final concentrations, uncertainties, and detection limits are determined. Standard reference materials are included in each set of 40 samples as a standard quality assurance/quality control (QA/QC) test. A select group of sample spectra are also visually reviewed to check the peak fitting routines. A reference spectrum was generated in MCNP 4c2 using an F8, pulse height, tally with a detector model of the actual detector used in counting. The detector model matches the detector resolution, energy calibration, and counting geometry. The generated spectrum also contained a radioisotope matrix that was similar to what was expected in the samples. This spectrum can then be put through the automated system and analyzed along with the other samples. The automated results are then compared to expected results for QA/QC assurance.

  16. Challenges of the management of severe hemophilia A with inhibitors: two case reports emphasizing the potential interest of a high-purity human Factor VIII/von Willebrand factor concentrate and individually tailored prophylaxis guided by thrombin-generation test.

    Science.gov (United States)

    Mathieu, Sophie; Crampe, Carine; Dargaud, Yesim; Lavigne-Lissalde, Géraldine; Escuriola-Ettingshausen, Carmen; Tardy, Brigitte; Meley, Roland; Thouvenin, Sandrine; Stephan, Jean L; Berger, Claire

    2015-12-01

    Severe hemophilia A is an X-linked bleeding disorder. Immune tolerance induction (ITI) is the best strategy of treatment when patients develop inhibitors. The objective is to illustrate the benefit of a high-purity human factor VIII/von Willebrand factor (VWF) concentrate (Octanate) in the management of ITI. We also wanted to raise the potential interest of laboratory assays such as thrombin-generation test (TGT) and epitope mapping. Two patients were treated during ITI, first with a recombinant FVIII and then with plasma-derived factor VIII without success, and, finally, with Octanate. Bypassing agents were used based on the results of TGT. Epitope mapping was performed during ITI therapy. These observations suggest the potential contribution of Octanate in the management of ITI in difficult cases. The use of bypassing agents can be necessary in prophylaxis or to treat bleedings, and may be guided by TGT results. Epitope mapping is used to describe the inhibitor. This article shows a decrease of the inhibitor directed against the C2 domain after initiation of Octanate. A high-purity human factor VIII/von Willebrand factor concentrate (Octanate) may be a valuable therapeutical option for ITI therapy. TGT and epitope mapping could be of help in the management of ITI. PMID:26517064

  17. Challenges of the management of severe hemophilia A with inhibitors: two case reports emphasizing the potential interest of a high-purity human Factor VIII/von Willebrand factor concentrate and individually tailored prophylaxis guided by thrombin-generation test.

    Science.gov (United States)

    Mathieu, Sophie; Crampe, Carine; Dargaud, Yesim; Lavigne-Lissalde, Géraldine; Escuriola-Ettingshausen, Carmen; Tardy, Brigitte; Meley, Roland; Thouvenin, Sandrine; Stephan, Jean L; Berger, Claire

    2015-12-01

    Severe hemophilia A is an X-linked bleeding disorder. Immune tolerance induction (ITI) is the best strategy of treatment when patients develop inhibitors. The objective is to illustrate the benefit of a high-purity human factor VIII/von Willebrand factor (VWF) concentrate (Octanate) in the management of ITI. We also wanted to raise the potential interest of laboratory assays such as thrombin-generation test (TGT) and epitope mapping. Two patients were treated during ITI, first with a recombinant FVIII and then with plasma-derived factor VIII without success, and, finally, with Octanate. Bypassing agents were used based on the results of TGT. Epitope mapping was performed during ITI therapy. These observations suggest the potential contribution of Octanate in the management of ITI in difficult cases. The use of bypassing agents can be necessary in prophylaxis or to treat bleedings, and may be guided by TGT results. Epitope mapping is used to describe the inhibitor. This article shows a decrease of the inhibitor directed against the C2 domain after initiation of Octanate. A high-purity human factor VIII/von Willebrand factor concentrate (Octanate) may be a valuable therapeutical option for ITI therapy. TGT and epitope mapping could be of help in the management of ITI.

  18. Thrombin-linked aptamer assay for detection of platelet derived growth factor BB on magnetic beads in a sandwich format.

    Science.gov (United States)

    Guo, Limin; Zhao, Qiang

    2016-09-01

    Here we describe a thrombin-linked aptamer assay (TLAA) for protein by using thrombin as an enzyme label, harnessing enzyme activity of thrombin and aptamer affinity binding. TLAA converts detection of specific target proteins to the detection of thrombin by using a DNA sequence that consists of two aptamers with the first aptamer binding to the specific target protein and the second aptamer binding to thrombin. Through the affinity binding, the thrombin enzyme is labeled on the protein target, and thrombin catalyzes the hydrolysis of small peptide substrate into product, generating signals for quantification. As a proof of principle, we show a sandwich TLAA for platelet derived growth factor BB (PDGF-BB) by using anti-PDGF-BB antibody coated on magnetic beads and an oligonucleotide containing the aptamer for PDGF-BB and the aptamer for thrombin. The binding of PDGF-BB to both the antibody and the aptamer results in labeling the complex with thrombin. We achieved detection of PDGF-BB at 16 pM. This TLAA contributes a new application of thrombin and its aptamer in bioanalysis, and shows potentials in assay developments. PMID:27343590

  19. Development of a Prototype Automation Simulation Scenario Generator for Air Traffic Management Software Simulations

    Science.gov (United States)

    Khambatta, Cyrus F.

    2007-01-01

    A technique for automated development of scenarios for use in the Multi-Center Traffic Management Advisor (McTMA) software simulations is described. The resulting software is designed and implemented to automate the generation of simulation scenarios with the intent of reducing the time it currently takes using an observational approach. The software program is effective in achieving this goal. The scenarios created for use in the McTMA simulations are based on data taken from data files from the McTMA system, and were manually edited before incorporation into the simulations to ensure accuracy. Despite the software s overall favorable performance, several key software issues are identified. Proposed solutions to these issues are discussed. Future enhancements to the scenario generator software may address the limitations identified in this paper.

  20. Thrombin interaction with fibrin polymerization sites.

    Science.gov (United States)

    Hsieh, K

    1997-05-15

    Thrombin is central to hemostasis, and postclotting fibrinolysis and wound healing. During clotting, thrombin transforms plasma fibrinogen into polymerizing fibrin, which selectively adsorbs the enzyme into the clot. This protects thrombin from heparin-antithrombin inactivation, thus preserving the enzyme for postclotting events. To determine how the fibrin N-terminal polymerization sites of A alpha 17-23 (GPRVVER) and B beta 15-25 (GHRPLDKKREE) and their analogs may interact with thrombin, amidolysis vs. plasma- and fibrinogen-clotting assays were used to differentiate blockade of catalytic site vs. other thrombin domains. Amidolysis studies suggest GPRVVER inhibition of thrombin catalytic site through hydrophobic interaction, and GPRVVER inhibited clotting. Neither GPRP nor VVER nor the B beta 15-25 homologs inhibited amidolysis. Contrary to heparin, acyl-DKKREE promoted plasma-clotting, but inhibited fibrinogen-clotting. In addition, acyl-DKKREE reversed the anticoagulant effect of heparin (0.1 U/ml) in plasma. The results suggest fibrin B beta 15-25 interaction with thrombin, possibly by blocking the heparin-binding site. Together with the reported fibrin A alpha 27-50 binding to thrombin, polymerizing fibrin appears to initially bind to thrombin catalytic site and exosite-1 through A alpha 17-50, and to another thrombin site through B beta 15-25. As these fibrin sites are also involved in polymerization, competition of the polymerization process with thrombin-binding could subsequently dislodge thrombin from fibrin alpha-chain. This may re-expose the catalytic site and exosite-1, thus explaining the thrombogenicity of clot-bound thrombin. The implications of these findings in polymerization mechanism and anticoagulant design are discussed.

  1. Aptaligner: Automated Software for Aligning Pseudorandom DNA X-Aptamers from Next-Generation Sequencing Data

    OpenAIRE

    Lu, Emily; Elizondo-Riojas, Miguel-Angel; Chang, Jeffrey T.; Volk, David E.

    2014-01-01

    Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient. This is particularly true for X-aptamers containing specialty bases (W, X, Y, Z, ...) that are identified by special encoding. Thus, we sought an automated program that uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov modeling techniques to provide improved alignments. Aptaligner provid...

  2. Automated importance generation and biasing techniques for Monte Carlo shielding techniques by the TRIPOLI-3 code

    Energy Technology Data Exchange (ETDEWEB)

    Both, J.P.; Nimal, J.C.; Vergnaud, T. (CEA Centre d' Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France). Service d' Etudes des Reacteurs et de Mathematiques Appliquees)

    1990-01-01

    We discuss an automated biasing procedure for generating the parameters necessary to achieve efficient Monte Carlo biasing shielding calculations. The biasing techniques considered here are exponential transform and collision biasing deriving from the concept of the biased game based on the importance function. We use a simple model of the importance function with exponential attenuation as the distance to the detector increases. This importance function is generated on a three-dimensional mesh including geometry and with graph theory algorithms. This scheme is currently being implemented in the third version of the neutron and gamma ray transport code TRIPOLI-3. (author).

  3. Automated protein motif generation in the structure-based protein function prediction tool ProMOL.

    Science.gov (United States)

    Osipovitch, Mikhail; Lambrecht, Mitchell; Baker, Cameron; Madha, Shariq; Mills, Jeffrey L; Craig, Paul A; Bernstein, Herbert J

    2015-12-01

    ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077. PMID:26573864

  4. Automated Generation of Finite-Element Meshes for Aircraft Conceptual Design

    Science.gov (United States)

    Li, Wu; Robinson, Jay

    2016-01-01

    This paper presents a novel approach for automated generation of fully connected finite-element meshes for all internal structural components and skins of a given wing-body geometry model, controlled by a few conceptual-level structural layout parameters. Internal structural components include spars, ribs, frames, and bulkheads. Structural layout parameters include spar/rib locations in wing chordwise/spanwise direction and frame/bulkhead locations in longitudinal direction. A simple shell thickness optimization problem with two load conditions is used to verify versatility and robustness of the automated meshing process. The automation process is implemented in ModelCenter starting from an OpenVSP geometry and ending with a NASTRAN 200 solution. One subsonic configuration and one supersonic configuration are used for numerical verification. Two different structural layouts are constructed for each configuration and five finite-element meshes of different sizes are generated for each layout. The paper includes various comparisons of solutions of 20 thickness optimization problems, as well as discussions on how the optimal solutions are affected by the stress constraint bound and the initial guess of design variables.

  5. Automated test data generation for branch testing using incremental genetic algorithm

    Indian Academy of Sciences (India)

    T MANIKUMAR; A JOHN SANJEEV KUMAR; R MARUTHAMUTHU

    2016-09-01

    Cost of software testing can be reduced by automated test data generation to find a minimal set of data that has maximum coverage. Search-based software testing (SBST) is one of the techniques recently used for automated testing task. SBST makes use of control flow graph (CFG) and meta-heuristic search algorithms to accomplish the process. This paper focuses on test data generation for branch coverage. A major drawback in using meta-heuristic techniques is that the CFG paths have to be traversed from the starting node to end node for each automated test data. This kind of traversal could be improved by branch ordering, together with elitism. But still the population size and the number of iterations are maintained as the same to keep all the branches alive. In this paper, we present an incremental genetic algorithm (IGA) for branch coverage testing. Initially, a classical genetic algorithm (GA) is used to construct the population with the best parents for each branch node, and the IGA is started with these parents as the initial population. Hence, it is not necessary to maintain a huge population size and large number of iterations to cover all the branches. The performance is analyzed with five benchmark programs studied from the literature. The experimental results indicate that the proposed IGA search technique outperforms the other meta-heuristic search techniques in terms of memory usage and scalability.

  6. Consistency and accuracy of diagnostic cancer codes generated by automated registration: comparison with manual registration

    Directory of Open Access Journals (Sweden)

    Codazzi Tiziana

    2006-09-01

    Full Text Available Abstract Background Automated procedures are increasingly used in cancer registration, and it is important that the data produced are systematically checked for consistency and accuracy. We evaluated an automated procedure for cancer registration adopted by the Lombardy Cancer Registry in 1997, comparing automatically-generated diagnostic codes with those produced manually over one year (1997. Methods The automatically generated cancer cases were produced by Open Registry algorithms. For manual registration, trained staff consulted clinical records, pathology reports and death certificates. The social security code, present and checked in both databases in all cases, was used to match the files in the automatic and manual databases. The cancer cases generated by the two methods were compared by manual revision. Results The automated procedure generated 5027 cases: 2959 (59% were accepted automatically and 2068 (41% were flagged for manual checking. Among the cases accepted automatically, discrepancies in data items (surname, first name, sex and date of birth constituted 8.5% of cases, and discrepancies in the first three digits of the ICD-9 code constituted 1.6%. Among flagged cases, cancers of female genital tract, hematopoietic system, metastatic and ill-defined sites, and oropharynx predominated. The usual reasons were use of specific vs. generic codes, presence of multiple primaries, and use of extranodal vs. nodal codes for lymphomas. The percentage of automatically accepted cases ranged from 83% for breast and thyroid cancers to 13% for metastatic and ill-defined cancer sites. Conclusion Since 59% of cases were accepted automatically and contained relatively few, mostly trivial discrepancies, the automatic procedure is efficient for routine case generation effectively cutting the workload required for routine case checking by this amount. Among cases not accepted automatically, discrepancies were mainly due to variations in coding practice.

  7. An automation of design and modelling tasks in NX Siemens environment with original software - generator module

    Science.gov (United States)

    Zbiciak, M.; Grabowik, C.; Janik, W.

    2015-11-01

    Nowadays the design constructional process is almost exclusively aided with CAD/CAE/CAM systems. It is evaluated that nearly 80% of design activities have a routine nature. These design routine tasks are highly susceptible to automation. Design automation is usually made with API tools which allow building original software responsible for adding different engineering activities. In this paper the original software worked out in order to automate engineering tasks at the stage of a product geometrical shape design is presented. The elaborated software works exclusively in NX Siemens CAD/CAM/CAE environment and was prepared in Microsoft Visual Studio with application of the .NET technology and NX SNAP library. The software functionality allows designing and modelling of spur and helicoidal involute gears. Moreover, it is possible to estimate relative manufacturing costs. With the Generator module it is possible to design and model both standard and non-standard gear wheels. The main advantage of the model generated in such a way is its better representation of an involute curve in comparison to those which are drawn in specialized standard CAD systems tools. It comes from fact that usually in CAD systems an involute curve is drawn by 3 points that respond to points located on the addendum circle, the reference diameter of a gear and the base circle respectively. In the Generator module the involute curve is drawn by 11 involute points which are located on and upper the base and the addendum circles therefore 3D gear wheels models are highly accurate. Application of the Generator module makes the modelling process very rapid so that the gear wheel modelling time is reduced to several seconds. During the conducted research the analysis of differences between standard 3 points and 11 points involutes was made. The results and conclusions drawn upon analysis are shown in details.

  8. Investigation of the selectivity of thrombin-binding aptamers for thrombin titration in murine plasma.

    Science.gov (United States)

    Trapaidze, Ana; Hérault, Jean-Pascal; Herbert, Jean-Marc; Bancaud, Aurélien; Gué, Anne-Marie

    2016-04-15

    Detection of thrombin in plasma raises timely challenges to enable therapeutic management of thrombosis in patients under vital threat. Thrombin binding aptamers represent promising candidates as sensing elements for the development of real-time thrombin biosensors; however implementation of such biosensor requires the clear understanding of thrombin-aptamer interaction properties in real-like environment. In this study, we used Surface Plasmon Resonance technique to answer the questions of specificity and sensitivity of thrombin detection by the thrombin-binding aptamers HD1, NU172 and HD22. We systematically characterized their properties in the presence of thrombin, as well as interfering molecular species such as the thrombin precursor prothrombin, thrombin in complex with some of its natural inhibitors, nonspecific serum proteins, and diluted plasma. Kinetic experiments show the multiple binding modes of HD1 and NU172, which both interact with multiple sites of thrombin with low nanomolar affinities and show little specificity of interaction for prothrombin vs. thrombin. HD22, on the other hand, binds specifically to thrombin exosite II and has no affinity to prothrombin at all. While thrombin in complex with some of its inhibitors could not be recognized by any aptamer, the binding of HD1 and NU172 properties is compromised by thrombin inhibitors alone, as well as with serum albumin. Finally, the complex nature of plasma was overwhelming for HD1, but we define conditions for the thrombin detection at 10nM range in 100-fold diluted plasma by HD22. Consequently HD22 showed key advantage over HD1 and NU172, and appears as the only alternative to design an aptasensor.

  9. Quantitative phosphoproteomics unveils temporal dynamics of thrombin signaling in human endothelial cells.

    Science.gov (United States)

    van den Biggelaar, Maartje; Hernández-Fernaud, Juan Ramon; van den Eshof, Bart L; Neilson, Lisa J; Meijer, Alexander B; Mertens, Koen; Zanivan, Sara

    2014-03-20

    Thrombin is the key serine protease of the coagulation cascade and a potent trigger of protease-activated receptor 1 (PAR1)-mediated platelet aggregation. In recent years, PAR1 has become an appealing target for anticoagulant therapies. However, the inhibitors that have been developed so far increase bleeding risk in patients, likely because they interfere with endogenous PAR1 signaling in the endothelium. Because of its complexity, thrombin-induced signaling in endothelial cells has remained incompletely understood. Here, we have combined stable isotope amino acids in cell culture, affinity-based phosphopeptide enrichment, and high-resolution mass spectrometry and performed a time-resolved analysis of the thrombin-induced signaling in human primary endothelial cells. We identified 2224 thrombin-regulated phosphorylation sites, the majority of which have not been previously related to thrombin. Those sites were localized on proteins that are novel to thrombin signaling, but also on well-known players such as PAR1, Rho-associated kinase 2, phospholipase C, and proteins related to actin cytoskeleton, cell-cell junctions, and Weibel-Palade body release. Our study provides a unique resource of phosphoproteins and phosphorylation sites that may generate novel insights into an intimate understanding of thrombin-mediated PAR signaling and the development of improved PAR1 antagonists that affect platelet but not endothelial cell function. PMID:24501219

  10. STIM1 and Orai1 mediate thrombin-induced Ca(2+) influx in rat cortical astrocytes.

    Science.gov (United States)

    Moreno, Claudia; Sampieri, Alicia; Vivas, Oscar; Peña-Segura, Claudia; Vaca, Luis

    2012-12-01

    In astrocytes, thrombin leads to cytoplasmic Ca(2+) elevations modulating a variety of cytoprotective and cytotoxic responses. Astrocytes respond to thrombin stimulation with a biphasic Ca(2+) increase generated by an interplay between ER-Ca(2+) release and store-operated Ca(2+) entry (SOCE). In many cell types, STIM1 and Orai1 have been demonstrated to be central components of SOCE. STIM1 senses the ER-Ca(2+) depletion and binds Orai1 to activate Ca(2+) influx. Here we used immunocytochemistry, overexpression and siRNA assays to investigate the role of STIM1 and Orai1 in the thrombin-induced Ca(2+) response in primary cultures of rat cortical astrocytes. We found that STIM1 and Orai1 are endogenously expressed in cortical astrocytes and distribute accordingly with other mammalian cells. Importantly, native and overexpressed STIM1 reorganized in puncta under thrombin stimulation and this reorganization was reversible. In addition, the overexpression of STIM1 and Orai1 increased by twofold the Ca(2+) influx evoked by thrombin, while knockdown of endogenous STIM1 and Orai1 significantly decreased this Ca(2+) influx. These results indicate that STIM1 and Orai1 underlie an important fraction of the Ca(2+) response that astrocytes exhibit in the presence of thrombin. Thrombin stimulation in astrocytes leads to ER-Ca(2+) release which causes STIM1 reorganization allowing the activation of Orai1 and the subsequent Ca(2+) influx.

  11. Implementing the WebSocket Protocol Based on Formal Modelling and Automated Code Generation

    DEFF Research Database (Denmark)

    Simonsen, Kent Inge; Kristensen, Lars Michael

    2014-01-01

    protocols. Furthermore, we perform formal verification of the CPN model prior to code generation, and test the implementation for interoperability against the Autobahn WebSocket test-suite resulting in 97% and 99% success rate for the client and server implementation, respectively. The tests show that the...... pragmatic annotations for automated code generation of protocol software. The contribution of this paper is an application of the approach as implemented in the PetriCode tool to obtain protocol software implementing the IETF WebSocket protocol. This demonstrates the scalability of our approach to real...... cause of test failures were mostly due to local and trivial errors in newly written code-generation templates, and not related to the overall logical operation of the protocol as specified by the CPN model....

  12. Vacuum pressure generation via microfabricated converging-diverging nozzles for operation of automated pneumatic logic.

    Science.gov (United States)

    Christoforidis, Theodore; Werner, Erik M; Hui, Elliot E; Eddington, David T

    2016-08-01

    Microfluidic devices with integrated pneumatic logic enable automated fluid handling without requiring external control instruments. These chips offer the additional advantage that they may be powered by vacuum and do not require an electricity source. This work describes a microfluidic converging-diverging (CD) nozzle optimized to generate vacuum at low input pressures, making it suitable for microfluidic applications including powering integrated pneumatic logic. It was found that efficient vacuum pressure was generated for high aspect ratios of the CD nozzle constriction (or throat) width to height and diverging angle of 3.6(o). In specific, for an inlet pressure of 42.2 psia (290.8 kPa) and a volumetric flow rate of approximately 1700 sccm, a vacuum pressure of 8.03 psia (55.3 kPa) was generated. To demonstrate the capabilities of our converging - diverging nozzle device, we connected it to a vacuum powered peristaltic pump driven by integrated pneumatic logic and obtained tunable flow rates from 0 to 130 μL/min. Finally, we demonstrate a proof of concept system for use where electricity and vacuum pressure are not readily available by powering a CD nozzle with a bicycle tire pump and pressure regulator. This system is able to produce a stable vacuum sufficient to drive pneumatic logic, and could be applied to power automated microfluidics in limited resource settings.

  13. Vacuum pressure generation via microfabricated converging-diverging nozzles for operation of automated pneumatic logic.

    Science.gov (United States)

    Christoforidis, Theodore; Werner, Erik M; Hui, Elliot E; Eddington, David T

    2016-08-01

    Microfluidic devices with integrated pneumatic logic enable automated fluid handling without requiring external control instruments. These chips offer the additional advantage that they may be powered by vacuum and do not require an electricity source. This work describes a microfluidic converging-diverging (CD) nozzle optimized to generate vacuum at low input pressures, making it suitable for microfluidic applications including powering integrated pneumatic logic. It was found that efficient vacuum pressure was generated for high aspect ratios of the CD nozzle constriction (or throat) width to height and diverging angle of 3.6(o). In specific, for an inlet pressure of 42.2 psia (290.8 kPa) and a volumetric flow rate of approximately 1700 sccm, a vacuum pressure of 8.03 psia (55.3 kPa) was generated. To demonstrate the capabilities of our converging - diverging nozzle device, we connected it to a vacuum powered peristaltic pump driven by integrated pneumatic logic and obtained tunable flow rates from 0 to 130 μL/min. Finally, we demonstrate a proof of concept system for use where electricity and vacuum pressure are not readily available by powering a CD nozzle with a bicycle tire pump and pressure regulator. This system is able to produce a stable vacuum sufficient to drive pneumatic logic, and could be applied to power automated microfluidics in limited resource settings. PMID:27469475

  14. Generation and performance of automated jarosite mineral detectors for visible/near-infrared spectrometers at Mars

    Science.gov (United States)

    Gilmore, Martha S.; Bornstein, Benjamin; Merrill, Matthew D.; Castaño, Rebecca; Greenwood, James P.

    2008-05-01

    We have developed two automated detectors that can recognize the sulfate mineral jarosite in unknown visible to near-infrared spectra (350-2500 nm). The two detectors are optimized for use within the terrestrial and martian atmospheres. The detectors are built from Support Vector Machines trained using a generative model to create linear mixtures of library mineral spectra. Both detectors performed with an average ˜90% accuracy on laboratory spectra of single minerals and the laboratory and field spectra of rocks collected in a hydrothermal environment. This type of algorithm will contribute to the efficiency of onboard data analysis of landed and orbital visible/near-infrared spectrometers at Mars.

  15. Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data.

    Science.gov (United States)

    Lu, Emily; Elizondo-Riojas, Miguel-Angel; Chang, Jeffrey T; Volk, David E

    2014-06-10

    Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient. This is particularly true for X-aptamers containing specialty bases (W, X, Y, Z, ...) that are identified by special encoding. Thus, we sought an automated program that uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov modeling techniques to provide improved alignments. Aptaligner provides this feature as well as length error and noise level cutoff features, is parallelized to run on multiple central processing units (cores), and sorts sequences from a single chip into projects and subprojects.

  16. An automated method for generating analogic signals that embody the Markov kinetics of model ionic channels.

    Science.gov (United States)

    Luchian, Tudor

    2005-08-30

    In this work we present an automated method for generating electrical signals which reflect the kinetics of ionic channels that have custom-tailored intermediate sub-states and intermediate reaction constants. The concept of our virtual single-channel waveform generator makes use of two software platforms, one for the numerical generation of single channel traces stemming from a pre-defined model and another for the digital-to-analog conversion of such numerical generated single channel traces. This technique of continuous generation and recording of the activity of a model ionic channel provides an efficient protocol to teach neophytes in the field of single-channel electrophysiology about its major phenomenological facets. Random analogic signals generated by using our technique can be successfully employed in a number of applications, such us: assisted learning of the single-molecule kinetic investigation via electrical recordings, impedance spectroscopy, the evaluation of linear frequency response of neurons and the study of stochastic resonance of ion channels. PMID:16054511

  17. Automated Verification of Code Generated from Models: Comparing Specifications with Observations

    Science.gov (United States)

    Gerlich, R.; Sigg, D.; Gerlich, R.

    2008-08-01

    The interest for automatic code generation from models is increasing. A specification is expressed as model and verification and validation is performed in the application domain. Once the model is formally correct and complete, code can be generated automatically. The general belief is that this code should be correct as well. However, this might be not true: Many parameters impact the generation of code and its correctness: it depends on conditions changing from application to application, the properties of the code depend on the environment where it is executed. From the principles of ISVV (Independent Software Verification and Validation) it even must be doubted that the automatically generated code is correct. Therefore an additional activity is required proving the correctness of the whole chain from modelling level down to execution on the target platform. Certification of a code generator is the state-of-the-art approach dealing with such risks,. Scade [1] was the first code generator certified according to DO178B. The certification costs are a significant disadvantage of this certification approach. All codes needs to be analysed manually, and this procedure has to be repeated for recertification after each maintenance step. But certification does not guarantee at all that the generated code does comply with the model. Certification is based on compliance of the code of the code generator with given standards. Such compliance never can guarantee correctness of the whole chain through transformation down to the environment for execution, though the belief is that certification implies well-formed code at a reduced fault rate. The approach presented here goes a direction different from manual certification.. It is guided by the idea of automated proof: each time code is generated from a model the properties of the code when being executed in its environment are compared with the properties specified in the model. This allows to conclude on the correctness of

  18. Extending and automating a Systems-Theoretic hazard analysis for requirements generation and analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, John (Massachusetts Institute of Technology)

    2012-05-01

    Systems Theoretic Process Analysis (STPA) is a powerful new hazard analysis method designed to go beyond traditional safety techniques - such as Fault Tree Analysis (FTA) - that overlook important causes of accidents like flawed requirements, dysfunctional component interactions, and software errors. While proving to be very effective on real systems, no formal structure has been defined for STPA and its application has been ad-hoc with no rigorous procedures or model-based design tools. This report defines a formal mathematical structure underlying STPA and describes a procedure for systematically performing an STPA analysis based on that structure. A method for using the results of the hazard analysis to generate formal safety-critical, model-based system and software requirements is also presented. Techniques to automate both the analysis and the requirements generation are introduced, as well as a method to detect conflicts between the safety and other functional model-based requirements during early development of the system.

  19. Automated Generation of Digital Terrain Model using Point Clouds of Digital Surface Model in Forest Area

    Directory of Open Access Journals (Sweden)

    Yoshikazu Kamiya

    2011-04-01

    Full Text Available At present, most of the digital data acquisition methods generate Digital Surface Model (DSM and not a Digital Elevation Model (DEM. Conversion from DSM to DEM still has some drawbacks, especially the removing of off terrain point clouds and subsequently the generation of DEM within these spaces even though the methods are automated. In this paper it was intended to overcome this issue by attempting to project off terrain point clouds to the terrain in forest areas using Artificial Neural Networks (ANN instead of removing them and then filling gaps by interpolation. Five sites were tested and accuracies assessed. They all give almost the same results. In conclusion, the ANN has ability to obtain the DEM by projecting the DSM point clouds and greater accuracies of DEMs were obtained. If the size of the hollow areas resulting from the removal of DSM point clouds are larger the accuracies are reduced.

  20. Automated Generation of Formal Models from ST Control Programs for Verification Purposes

    CERN Document Server

    Fernandez Adiego, B; Tournier, J-C; Blanco Vinuela, E; Blech, J-O; Gonzalez Suarez, V

    2014-01-01

    In large industrial control systems such as the ones installed at CERN, one of the main issues is the ability to verify the correct behaviour of the Programmable Logic Controller (PLC) programs. While manual and automated testing can achieve good results, some obvious problems remain unsolved such as the difficulty to check safety or liveness properties. This paper proposes a general methodology and a tool to verify PLC programs by automatically generating formal models for different model checkers out of ST code. The proposed methodology defines an automata-based formalism used as intermediate model (IM) to transform PLC programs written in ST language into different formal models for verification purposes. A tool based on Xtext has been implemented that automatically generates models for the NuSMV and UPPAAL model checkers and the BIP framework.

  1. Multimedia abstract generation of intensive care data: the automation of clinical processes through AI methodologies.

    Science.gov (United States)

    Jordan, Desmond; Rose, Sydney E

    2010-04-01

    Medical errors from communication failures are enormous during the perioperative period of cardiac surgical patients. As caregivers change shifts or surgical patients change location within the hospital, key information is lost or misconstrued. After a baseline cognitive study of information need and caregiver workflow, we implemented an advanced clinical decision support tool of intelligent agents, medical logic modules, and text generators called the "Inference Engine" to summarize individual patient's raw medical data elements into procedural milestones, illness severity, and care therapies. The system generates two displays: 1) the continuum of care, multimedia abstract generation of intensive care data (MAGIC)-an expert system that would automatically generate a physician briefing of a cardiac patient's operative course in a multimodal format; and 2) the isolated point in time, "Inference Engine"-a system that provides a real-time, high-level, summarized depiction of a patient's clinical status. In our studies, system accuracy and efficacy was judged against clinician performance in the workplace. To test the automated physician briefing, "MAGIC," the patient's intraoperative course, was reviewed in the intensive care unit before patient arrival. It was then judged against the actual physician briefing and that given in a cohort of patients where the system was not used. To test the real-time representation of the patient's clinical status, system inferences were judged against clinician decisions. Changes in workflow and situational awareness were assessed by questionnaires and process evaluation. MAGIC provides 200% more information, twice the accuracy, and enhances situational awareness. This study demonstrates that the automation of clinical processes through AI methodologies yields positive results. PMID:20012610

  2. [Direct oral thrombin inhibitor, "dabigatran"].

    Science.gov (United States)

    Yasaka, Masahiro

    2013-01-01

    Dabigatran is an oral, direct, and competitive inhibitor of thrombin, which is administered to patients with non-valvular atrial fibrillation for prevention of stroke at a dose of 110 mg twice daily or 150 mg twice daily. Anticoagulation by dabigatran is "hybrid anticoagulation", consisting of action of both dabigatran and physiological coagulation inhibitors because warfarin inhibits production of protein C and protein S but dabigatran does not. Management of dabigatran is easier than that of warfarin because food restriction is unnecessary, drug interaction is small, and absorption time is short and serum concentration corresponds to the anticoagulatory effect in dabigatran treatment. The RE-LY trial confirmed effectiveness and safety of both doses of dabigatran for prevention of stroke and both doses of dabigatran had much lower risks of intracranial bleeding compared with warfarin. Compliance to guidance of dabigatran treatment is essential for avoidance of severe hemorrhagic complications. PMID:23631181

  3. Automating methods to improve precision in Monte-Carlo event generation for particle colliders

    Energy Technology Data Exchange (ETDEWEB)

    Gleisberg, Tanju

    2008-07-01

    The subject of this thesis was the development of tools for the automated calculation of exact matrix elements, which are a key for the systematic improvement of precision and confidence for theoretical predictions. Part I of this thesis concentrates on the calculations of cross sections at tree level. A number of extensions have been implemented in the matrix element generator AMEGIC++, namely new interaction models such as effective loop-induced couplings of the Higgs boson with massless gauge bosons, required for a number of channels for the Higgs boson search at LHC and anomalous gauge couplings, parameterizing a number of models beyond th SM. Further a special treatment to deal with complicated decay chains of heavy particles has been constructed. A significant effort went into the implementation of methods to push the limits on particle multiplicities. Two recursive methods have been implemented, the Cachazo-Svrcek-Witten recursion and the colour dressed Berends-Giele recursion. For the latter the new module COMIX has been added to the SHERPA framework. The Monte-Carlo phase space integration techniques have been completely revised, which led to significantly reduced statistical error estimates when calculating cross sections and a greatly improved unweighting efficiency for the event generation. Special integration methods have been developed to cope with the newly accessible final states. The event generation framework SHERPA directly benefits from those new developments, improving the precision and the efficiency. Part II was addressed to the automation of QCD calculations at next-to-leading order. A code has been developed, that, for the first time fully automates the real correction part of a NLO calculation. To calculate the correction for a m-parton process obeying the Catani-Seymour dipole subtraction method the following components are provided: 1. the corresponding m+1-parton tree level matrix elements, 2. a number dipole subtraction terms to remove

  4. TOBAGO — a semi-automated approach for the generation of 3-D building models

    Science.gov (United States)

    Gruen, Armin

    3-D city models are in increasing demand for a great number of applications. Photogrammetry is a relevant technology that can provide an abundance of geometric, topologic and semantic information concerning these models. The pressure to generate a large amount of data with high degree of accuracy and completeness poses a great challenge to phtogrammetry. The development of automated and semi-automated methods for the generation of those data sets is therefore a key issue in photogrammetric research. We present in this article a strategy and methodology for an efficient generation of even fairly complex building models. Within this concept we request the operator to measure the house roofs from a stereomodel in form of an unstructured point cloud. According to our experience this can be done very quickly. Even a non-experienced operator can measure several hundred roofs or roof units per day. In a second step we fit generic building models fully automatically to these point clouds. The structure information is inherently included in these building models. In such a way geometric, topologic and even semantic data can be handed over to a CAD-system, in our case AutoCad, for further visualization and manipulation. The structuring is achieved in three steps. In a first step a classifier is initiated which recognizes the class of houses a particular roof point cloud belongs to. This recognition step is primarily based on the analysis of the number of ridge points. In the second and third steps the concrete topological relations between roof points are investigated and generic building models are fitted to the point clouds. Based on the technique of constraint-based reasoning two geometrical parsers are solving this problem. We have tested the methodology under a variety of different conditions in several pilot projects. The results will indicate the good performance of our approach. In addition we will demonstrate how the results can be used for visualization (texture

  5. Automated biphasic morphological assessment of hepatitis B-related liver fibrosis using second harmonic generation microscopy

    Science.gov (United States)

    Wang, Tong-Hong; Chen, Tse-Ching; Teng, Xiao; Liang, Kung-Hao; Yeh, Chau-Ting

    2015-08-01

    Liver fibrosis assessment by biopsy and conventional staining scores is based on histopathological criteria. Variations in sample preparation and the use of semi-quantitative histopathological methods commonly result in discrepancies between medical centers. Thus, minor changes in liver fibrosis might be overlooked in multi-center clinical trials, leading to statistically non-significant data. Here, we developed a computer-assisted, fully automated, staining-free method for hepatitis B-related liver fibrosis assessment. In total, 175 liver biopsies were divided into training (n = 105) and verification (n = 70) cohorts. Collagen was observed using second harmonic generation (SHG) microscopy without prior staining, and hepatocyte morphology was recorded using two-photon excitation fluorescence (TPEF) microscopy. The training cohort was utilized to establish a quantification algorithm. Eleven of 19 computer-recognizable SHG/TPEF microscopic morphological features were significantly correlated with the ISHAK fibrosis stages (P 0.82 for liver cirrhosis detection. Since no subjective gradings are needed, interobserver discrepancies could be avoided using this fully automated method.

  6. A Logic Design Automation System for Generating Logic Diagram from Hardware Description

    Institute of Scientific and Technical Information of China (English)

    刘明业; 郭书明; 杨淮; 贾良玉; 洪恩宇

    1989-01-01

    This paper discusses a logic design automation system (LODAS) implemented on APOLLO DOMAIN workstation. LODAS can generate VLSI logic diagram from the hardware description. The system accepts many kinds of input description such as DDL or AHPL language description, functinual array (truth table), covering array , Boolean equations or state transition tables. The system first simulates the functional description to verify the functional description of the system designed, then the translator translates the fnnctional descriptong into register transfer equations, Boolean equatinos and state transition equations antomatically.Logic synthesis software partitions the translation result into a series of blocks, and transforma every small block into a mnlti-level NAND/NOR network according to the fan - in and fan - out restriction.

  7. A Logic Design Automation System for Generating Logic Diagram from Hardware Description

    Institute of Scientific and Technical Information of China (English)

    刘明业; 郭书明; 等

    1989-01-01

    This paper discusses a logic design automation system(LODAS) implemented on APOLLO DOMAIN workstation.LODAS can generate VLSI logic diagram from the hardware description.The system accepts many kinds of input description such as DDL or AHPL language description.Functional array(truth table).covering array,Boolean equations or state transition tables,The system first simulates the functional desecription to verify the functional description of the system designed.then translator translates the functional description into resgister transfer equation.Boolean equations and state transition equations automatically.Logic synthesis software partitions the translation result into a series of blocks,and transforms every small block into a multi-level NAND /NOR network according to the fan-in and fan-out restriction.

  8. Automated Narratives and Journalistic Text Generation: The Lead Organization Structure Translated into Code.

    Directory of Open Access Journals (Sweden)

    Márcio Carneiro dos Santos

    2016-07-01

    Full Text Available It describes the experiment of building a software capable of generating leads and newspaper titles in an automated fashion from information obtained from the Internet. The theoretical possibility Lage already provided by the end of last century is based on relatively rigid and simple structure of this type of story construction, which facilitates the representation or translation of its syntax in terms of instructions that the computer can execute. The paper also discusses the relationship between society, technique and technology, making a brief history of the introduction of digital solutions in newsrooms and their impacts. The development was done with the Python programming language and NLTK- Natural Language Toolkit library - and used the results of the Brazilian Soccer Championship 2013 published on an internet portal as a data source.

  9. Study on an electrochemical biosensor for thrombin recognition based on aptamers and nano particles

    Institute of Scientific and Technical Information of China (English)

    ZHENG Jing; LIN Li; CHENG GuiFang; WANG AnBao; TAN XueLian; HE PinGang; FANG YuZhi

    2007-01-01

    This paper presents a high specific, sensitive electrochemical biosensor for recognition of protein such as thrombin based on aptamers and nano particles. Two different aptamers were chosen to construct a sandwich manner for detecting thrombin. Aptamer Ⅰ was immobilized on nano magnetic particle for capturing thrombin, and aptamer Ⅱ labled with nano gold was used for detection. The electrical current generated from gold after the formation of the complex of magnetic particle, thrombin and nano gold,and then an electrochemical cell designed by ourselves was used for separating, gathering, and electrochemical detecting. Through magnetic separation, high specific and sensitive detection of the target protein, thrombin, was achieved. Linear response was observed over the range 5.6×10-12-1.12×10-9mol/L, with a detection limit of 1.42×10-12 mol/L. The presence of other protein as BSA did not affect the detection, which indicates that high selective recognition of thrombin can be achieved in complex biological samples such as human plasma.

  10. Study on an electrochemical biosensor for thrombin recognition based on aptamers and nano particles

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This paper presents a high specific, sensitive electrochemical biosensor for recognition of protein such as thrombin based on aptamers and nano particles. Two different aptamers were chosen to construct a sandwich manner for detecting thrombin. Aptamer I was immobilized on nano magnetic particle for capturing thrombin, and aptamer II labled with nano gold was used for detection. The electrical current generated from gold after the formation of the complex of magnetic particle, thrombin and nano gold, and then an electrochemical cell designed by ourselves was used for separating, gathering, and electrochemical detecting. Through magnetic separation, high specific and sensitive detection of the target protein, thrombin, was achieved. Linear response was observed over the range 5.6×10-12―1.12×10-9 mol/L, with a detection limit of 1.42×10-12 mol/L. The presence of other protein as BSA did not affect the detection, which indicates that high selective recognition of thrombin can be achieved in complex biological samples such as human plasma.

  11. Horizon: The Portable, Scalable, and Reusable Framework for Developing Automated Data Management and Product Generation Systems

    Science.gov (United States)

    Huang, T.; Alarcon, C.; Quach, N. T.

    2014-12-01

    Capture, curate, and analysis are the typical activities performed at any given Earth Science data center. Modern data management systems must be adaptable to heterogeneous science data formats, scalable to meet the mission's quality of service requirements, and able to manage the life-cycle of any given science data product. Designing a scalable data management doesn't happen overnight. It takes countless hours of refining, refactoring, retesting, and re-architecting. The Horizon data management and workflow framework, developed at the Jet Propulsion Laboratory, is a portable, scalable, and reusable framework for developing high-performance data management and product generation workflow systems to automate data capturing, data curation, and data analysis activities. The NASA's Physical Oceanography Distributed Active Archive Center (PO.DAAC)'s Data Management and Archive System (DMAS) is its core data infrastructure that handles capturing and distribution of hundreds of thousands of satellite observations each day around the clock. DMAS is an application of the Horizon framework. The NASA Global Imagery Browse Services (GIBS) is NASA's Earth Observing System Data and Information System (EOSDIS)'s solution for making high-resolution global imageries available to the science communities. The Imagery Exchange (TIE), an application of the Horizon framework, is a core subsystem for GIBS responsible for data capturing and imagery generation automation to support the EOSDIS' 12 distributed active archive centers and 17 Science Investigator-led Processing Systems (SIPS). This presentation discusses our ongoing effort in refining, refactoring, retesting, and re-architecting the Horizon framework to enable data-intensive science and its applications.

  12. Toward the automated generation of genome-scale metabolic networks in the SEED

    Directory of Open Access Journals (Sweden)

    Gould John

    2007-04-01

    Full Text Available Abstract Background Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. Results We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that are common across organisms, and have created tools for automatically assembling appropriate components for a particular organism based on the metabolic pathways encoded in the organism's genome. This focuses manual efforts on that portion of an organism's metabolism that is not yet represented in the database. We have demonstrated the efficacy of our method by reverse-engineering and automatically regenerating the reaction network from a published genome-scale metabolic model for Staphylococcus aureus. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for S. aureus, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (Escherichia coli, Helicobacter pylori, and Lactococcus lactis. We have implemented our tools and database within the SEED, an open-source software environment for comparative

  13. Automated determinations of selenium in thermal power plant wastewater by sequential hydride generation and chemiluminescence detection.

    Science.gov (United States)

    Ezoe, Kentaro; Ohyama, Seiichi; Hashem, Md Abul; Ohira, Shin-Ichi; Toda, Kei

    2016-02-01

    After the Fukushima disaster, power generation from nuclear power plants in Japan was completely stopped and old coal-based power plants were re-commissioned to compensate for the decrease in power generation capacity. Although coal is a relatively inexpensive fuel for power generation, it contains high levels (mgkg(-1)) of selenium, which could contaminate the wastewater from thermal power plants. In this work, an automated selenium monitoring system was developed based on sequential hydride generation and chemiluminescence detection. This method could be applied to control of wastewater contamination. In this method, selenium is vaporized as H2Se, which reacts with ozone to produce chemiluminescence. However, interference from arsenic is of concern because the ozone-induced chemiluminescence intensity of H2Se is much lower than that of AsH3. This problem was successfully addressed by vaporizing arsenic and selenium individually in a sequential procedure using a syringe pump equipped with an eight-port selection valve and hot and cold reactors. Oxidative decomposition of organoselenium compounds and pre-reduction of the selenium were performed in the hot reactor, and vapor generation of arsenic and selenium were performed separately in the cold reactor. Sample transfers between the reactors were carried out by a pneumatic air operation by switching with three-way solenoid valves. The detection limit for selenium was 0.008 mg L(-1) and calibration curve was linear up to 1.0 mg L(-1), which provided suitable performance for controlling selenium in wastewater to around the allowable limit (0.1 mg L(-1)). This system consumes few chemicals and is stable for more than a month without any maintenance. Wastewater samples from thermal power plants were collected, and data obtained by the proposed method were compared with those from batchwise water treatment followed by hydride generation-atomic fluorescence spectrometry. PMID:26653491

  14. Automated hexahedral mesh generation from biomedical image data: applications in limb prosthetics.

    Science.gov (United States)

    Zachariah, S G; Sanders, J E; Turkiyyah, G M

    1996-06-01

    A general method to generate hexahedral meshes for finite element analysis of residual limbs and similar biomedical geometries is presented. The method utilizes skeleton-based subdivision of cross-sectional domains to produce simple subdomains in which structured meshes are easily generated. Application to a below-knee residual limb and external prosthetic socket is described. The residual limb was modeled as consisting of bones, soft tissue, and skin. The prosthetic socket model comprised a socket wall with an inner liner. The geometries of these structures were defined using axial cross-sectional contour data from X-ray computed tomography, optical scanning, and mechanical surface digitization. A tubular surface representation, using B-splines to define the directrix and generator, is shown to be convenient for definition of the structure geometries. Conversion of cross-sectional data to the compact tubular surface representation is direct, and the analytical representation simplifies geometric querying and numerical optimization within the mesh generation algorithms. The element meshes remain geometrically accurate since boundary nodes are constrained to lie on the tubular surfaces. Several element meshes of increasing mesh density were generated for two residual limbs and prosthetic sockets. Convergence testing demonstrated that approximately 19 elements are required along a circumference of the residual limb surface for a simple linear elastic model. A model with the fibula absent compared with the same geometry with the fibula present showed differences suggesting higher distal stresses in the absence of the fibula. Automated hexahedral mesh generation algorithms for sliced data represent an advancement in prosthetic stress analysis since they allow rapid modeling of any given residual limb and optimization of mesh parameters.

  15. Automated Mosaicking of Multiple 3d Point Clouds Generated from a Depth Camera

    Science.gov (United States)

    Kim, H.; Yoon, W.; Kim, T.

    2016-06-01

    In this paper, we propose a method for automated mosaicking of multiple 3D point clouds generated from a depth camera. A depth camera generates depth data by using ToF (Time of Flight) method and intensity data by using intensity of returned signal. The depth camera used in this paper was a SR4000 from MESA Imaging. This camera generates a depth map and intensity map of 176 x 44 pixels. Generated depth map saves physical depth data with mm of precision. Generated intensity map contains texture data with many noises. We used texture maps for extracting tiepoints and depth maps for assigning z coordinates to tiepoints and point cloud mosaicking. There are four steps in the proposed mosaicking method. In the first step, we acquired multiple 3D point clouds by rotating depth camera and capturing data per rotation. In the second step, we estimated 3D-3D transformation relationships between subsequent point clouds. For this, 2D tiepoints were extracted automatically from the corresponding two intensity maps. They were converted into 3D tiepoints using depth maps. We used a 3D similarity transformation model for estimating the 3D-3D transformation relationships. In the third step, we converted local 3D-3D transformations into a global transformation for all point clouds with respect to a reference one. In the last step, the extent of single depth map mosaic was calculated and depth values per mosaic pixel were determined by a ray tracing method. For experiments, 8 depth maps and intensity maps were used. After the four steps, an output mosaicked depth map of 454x144 was generated. It is expected that the proposed method would be useful for developing an effective 3D indoor mapping method in future.

  16. An electrochemical aptasensor electrocatalyst for detection of thrombin.

    Science.gov (United States)

    Tian, Rong; Chen, Xiaojun; Li, Qingwen; Yao, Cheng

    2016-05-01

    This work reports a novel signal amplification strategy based on three-dimensional ordered macroporous C60-poly(3,4-ethylenedioxythiophene)-1-butyl-3-methylimidazolium hexafluorophosphate (3DOM C60-PEDOT-[BMIm][BF6]) for ultrasensitive detection of thrombin by cascade catalysis of Au-PEDOT@SiO2 microspheres and alcohol dehydrogenase (ADH). Au-PEDOT@SiO2 microspheres were constructed not only as nanocarriers to anchor the large amounts of secondary thrombin aptamers but also as nanocatalysts to catalyze the oxidation of ethanol efficiently. Significantly, the electrochemical signal was greatly enhanced based on cascade catalysis: First, ADH catalyzed the oxidation of ethanol to acetaldehyde with the concomitant generation of NADH in the presence of β-nicotinamide adenine dinucleotide hydrate (NAD(+)). Then, gold nanoparticles (AuNPs) as nanocatalysts could effectively catalyze NADH to produce NAD(+) with the help of PEDOT as redox probe. Under the optimal conditions, the proposed aptasensor exhibits a linear range of 2 × 10(-13) to 2 × 10(-8) M with a low detection limit of 2 × 10(-14) M for thrombin detection and shows high sensitivity and good specificity. PMID:26869084

  17. An automated pipeline for cortical surface generation and registration of the cerebral cortex

    Science.gov (United States)

    Li, Wen; Ibanez, Luis; Gelas, Arnaud; Yeo, B. T. Thomas; Niethammer, Marc; Andreasen, Nancy C.; Magnotta, Vincent A.

    2011-03-01

    The human cerebral cortex is one of the most complicated structures in the body. It has a highly convoluted structure with much of the cortical sheet buried in sulci. Based on cytoarchitectural and functional imaging studies, it is possible to segment the cerebral cortex into several subregions. While it is only possible to differentiate the true anatomical subregions based on cytoarchitecture, the surface morphometry aligns closely with the underlying cytoarchitecture and provides features that allow the surface of the cortex to be parcellated based on the sulcal and gyral patterns that are readily visible on the MR images. We have developed a fully automated pipeline for the generation and registration of cortical surfaces in the spherical domain. The pipeline initiates with the BRAINS AutoWorkup pipeline. Subsequently, topology correction and surface generation is performed to generate a genus zero surface and mapped to a sphere. Several surface features are then calculated to drive the registration between the atlas surface and other datasets. A spherical diffeomorphic demons algorithm is used to co-register an atlas surface onto a subject surface. A lobar based atlas of the cerebral cortex was created from a manual parcellation of the cortex. The atlas surface was then co-registered to five additional subjects using a spherical diffeomorphic demons algorithm. The labels from the atlas surface were warped on the subject surface and compared to the manual raters. The average Dice overlap index was 0.89 across all regions.

  18. SEMANTIC WEB-BASED SOFTWARE ENGINEERING BY AUTOMATED REQUIREMENTS ONTOLOGY GENERATION IN SOA

    Directory of Open Access Journals (Sweden)

    Vahid Rastgoo

    2014-04-01

    Full Text Available This paper presents an approach for automated generation of requirements ontology using UML diagrams in service-oriented architecture (SOA. The goal of this paper is to convenience progress of software engineering processes like software design, software reuse, service discovering and etc. The proposed method is based on a four conceptual layers. The first layer includes requirements achieved by stakeholders, the second one designs service-oriented diagrams from the data in first layer and extracts XMI codes of them. The third layer includes requirement ontology and protocol ontology to describe behavior of services and relationships between them semantically. Finally the forth layer makes standard the concepts exists in ontologies of previous layer. The generated ontology exceeds absolute domain ontology because it considers the behavior of services moreover the hierarchical relationship of them. Experimental results conducted on a set of UML4Soa diagrams in different scopes demonstrate the improvement of the proposed approach from different points of view such as: completeness of requirements ontology, automatic generation and considering SOA.

  19. Automated As-Built Model Generation of Subway Tunnels from Mobile LiDAR Data

    Directory of Open Access Journals (Sweden)

    Mostafa Arastounia

    2016-09-01

    Full Text Available This study proposes fully-automated methods for as-built model generation of subway tunnels employing mobile Light Detection and Ranging (LiDAR data. The employed dataset is acquired by a Velodyne HDL 32E and covers 155 m of a subway tunnel containing six million points. First, the tunnel’s main axis and cross sections are extracted. Next, a preliminary model is created by fitting an ellipse to each extracted cross section. The model is refined by employing residual analysis and Baarda’s data snooping method to eliminate outliers. The final model is then generated by applying least squares adjustment to outlier-free data. The obtained results indicate that the tunnel’s main axis and 1551 cross sections at 0.1 m intervals are successfully extracted. Cross sections have an average semi-major axis of 7.8508 m with a standard deviation of 0.2 mm and semi-minor axis of 7.7509 m with a standard deviation of 0.1 mm. The average normal distance of points from the constructed model (average absolute error is also 0.012 m. The developed algorithm is applicable to tunnels with any horizontal orientation and degree of curvature since it makes no assumptions, nor does it use any a priori knowledge regarding the tunnel’s curvature and horizontal orientation.

  20. Automated As-Built Model Generation of Subway Tunnels from Mobile LiDAR Data

    Science.gov (United States)

    Arastounia, Mostafa

    2016-01-01

    This study proposes fully-automated methods for as-built model generation of subway tunnels employing mobile Light Detection and Ranging (LiDAR) data. The employed dataset is acquired by a Velodyne HDL 32E and covers 155 m of a subway tunnel containing six million points. First, the tunnel’s main axis and cross sections are extracted. Next, a preliminary model is created by fitting an ellipse to each extracted cross section. The model is refined by employing residual analysis and Baarda’s data snooping method to eliminate outliers. The final model is then generated by applying least squares adjustment to outlier-free data. The obtained results indicate that the tunnel’s main axis and 1551 cross sections at 0.1 m intervals are successfully extracted. Cross sections have an average semi-major axis of 7.8508 m with a standard deviation of 0.2 mm and semi-minor axis of 7.7509 m with a standard deviation of 0.1 mm. The average normal distance of points from the constructed model (average absolute error) is also 0.012 m. The developed algorithm is applicable to tunnels with any horizontal orientation and degree of curvature since it makes no assumptions, nor does it use any a priori knowledge regarding the tunnel’s curvature and horizontal orientation. PMID:27649172

  1. Laser materials processing of complex components. From reverse engineering via automated beam path generation to short process development cycles.

    Science.gov (United States)

    Görgl, R.; Brandstätter, E.

    2016-03-01

    The article presents an overview of what is possible nowadays in the field of laser materials processing. The state of the art in the complete process chain is shown, starting with the generation of a specific components CAD data and continuing with the automated motion path generation for the laser head carried by a CNC or robot system. Application examples from laser welding, laser cladding and additive laser manufacturing are given.

  2. A NOVEL METHOD FOR AUTOMATION OF 3D HYDRO BREAK LINE GENERATION FROM LIDAR DATA USING MATLAB

    OpenAIRE

    Toscano, G. J.; U. Gopalam; V. Devarajan

    2013-01-01

    Water body detection is necessary to generate hydro break lines, which are in turn useful in creating deliverables such as TINs, contours, DEMs from LiDAR data. Hydro flattening follows the detection and delineation of water bodies (lakes, rivers, ponds, reservoirs, streams etc.) with hydro break lines. Manual hydro break line generation is time consuming and expensive. Accuracy and processing time depend on the number of vertices marked for delineation of break lines. Automation wit...

  3. Automated Generation of Fault Management Artifacts from a Simple System Model

    Science.gov (United States)

    Kennedy, Andrew K.; Day, John C.

    2013-01-01

    Our understanding of off-nominal behavior - failure modes and fault propagation - in complex systems is often based purely on engineering intuition; specific cases are assessed in an ad hoc fashion as a (fallible) fault management engineer sees fit. This work is an attempt to provide a more rigorous approach to this understanding and assessment by automating the creation of a fault management artifact, the Failure Modes and Effects Analysis (FMEA) through querying a representation of the system in a SysML model. This work builds off the previous development of an off-nominal behavior model for the upcoming Soil Moisture Active-Passive (SMAP) mission at the Jet Propulsion Laboratory. We further developed the previous system model to more fully incorporate the ideas of State Analysis, and it was restructured in an organizational hierarchy that models the system as layers of control systems while also incorporating the concept of "design authority". We present software that was developed to traverse the elements and relationships in this model to automatically construct an FMEA spreadsheet. We further discuss extending this model to automatically generate other typical fault management artifacts, such as Fault Trees, to efficiently portray system behavior, and depend less on the intuition of fault management engineers to ensure complete examination of off-nominal behavior.

  4. Use of automated image registration to generate mean brain SPECT image of Alzheimer's patients

    International Nuclear Information System (INIS)

    The purpose of this study was to compute and compare the group mean HMPAO brain SPECT images of patients with senile dementia of Alzheimer's type (SDAT) and age matched control subjects after transformation of the individual images to a standard size and shape. Ten patients with Alzheimer's disease (age 71.6±5.0 yr) and ten age matched normal subjects (age 71.0±6.1 yr) participated in this study. Tc-99m HMPAO brain SPECT and X-ray CT scans were acquired for each subject. SPECT images were normalized to an average activity of 100 counts/pixel. Individual brain images were transformed to a standard size and shape with the help of Automated Image Registration (AIR). Realigned brain SPECT images of both groups were used to generate mean and standard deviation images by arithmetic operations on voxel based numerical values. Mean images of both groups were compared by applying the unpaired t-test on a voxel by voxel basis to generate three dimensional T-maps. X-ray CT images of individual subjects were evaluated by means of a computer program for brain atrophy. A significant decrease in relative radioisotope (RI) uptake was present in the bilateral superior and inferior parietal lobules (p<0.05), bilateral inferior temporal gyri, and the bilateral superior and middle frontal gyri (p<0.001). The mean brain atrophy indices for patients and normal subjects were 0.853±0.042 and 0.933±0.017 respectively, the difference being statistically significant (p<0.001). The use of a brain image standardization procedure increases the accuracy of voxel based group comparisons. Thus, intersubject averaging enhances the capacity for detection of abnormalities in functional brain images by minimizing the influence of individual variation. (author)

  5. Automated Euler and Navier-Stokes Database Generation for a Glide-Back Booster

    Science.gov (United States)

    Chaderjian, Neal M.; Rogers, Stuart E.; Aftosmis, Mike J.; Pandya, Shishir A.; Ahmad, Jasim U.; Tejnil, Edward

    2004-01-01

    The past two decades have seen a sustained increase in the use of high fidelity Computational Fluid Dynamics (CFD) in basic research, aircraft design, and the analysis of post-design issues. As the fidelity of a CFD method increases, the number of cases that can be readily and affordably computed greatly diminishes. However, computer speeds now exceed 2 GHz, hundreds of processors are currently available and more affordable, and advances in parallel CFD algorithms scale more readily with large numbers of processors. All of these factors make it feasible to compute thousands of high fidelity cases. However, there still remains the overwhelming task of monitoring the solution process. This paper presents an approach to automate the CFD solution process. A new software tool, AeroDB, is used to compute thousands of Euler and Navier-Stokes solutions for a 2nd generation glide-back booster in one week. The solution process exploits a common job-submission grid environment, the NASA Information Power Grid (IPG), using 13 computers located at 4 different geographical sites. Process automation and web-based access to a MySql database greatly reduces the user workload, removing much of the tedium and tendency for user input errors. The AeroDB framework is shown. The user submits/deletes jobs, monitors AeroDB's progress, and retrieves data and plots via a web portal. Once a job is in the database, a job launcher uses an IPG resource broker to decide which computers are best suited to run the job. Job/code requirements, the number of CPUs free on a remote system, and queue lengths are some of the parameters the broker takes into account. The Globus software provides secure services for user authentication, remote shell execution, and secure file transfers over an open network. AeroDB automatically decides when a job is completed. Currently, the Cart3D unstructured flow solver is used for the Euler equations, and the Overflow structured overset flow solver is used for the

  6. Thrombin Hydrolysis of Human Osteopontin Is Dependent on Thrombin Anion-binding Exosites*

    OpenAIRE

    Myles, Timothy; Leung, Lawrence L. K.

    2008-01-01

    The cytokine osteopontin (OPN) can be hydrolyzed by thrombin exposing a cryptic α4β1/α9β1 integrin-binding motif (SVVYGLR), thereby acting as a potent cytokine for cells bearing these activated integrins. We show that purified milk OPN is a substrate for thrombin with a kcat/Km value of 1.14 × 105 m–1 s–1. Thrombin cleavage of OPN was inhibited by unsulfated hirugen (IC50 = 1.2 ± 0.2 μm), unfractionated heparin (IC50 = 56.6 ± 8.4 μg/ml) and low molecular ...

  7. Ru(bpy)32+-doped Silica Nanoparticle Aptasensor for Detection of Thrombin Based on Electrogenerated Chemiluminescence

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-Ying; YUN Wen; ZHOU Jing-Ming; DONG Ping; HE Pin-Gang; FANG Yu-Zhi

    2008-01-01

    A new electrogenerated chemiluminescent (ECL) detection system for protein using the aptamers was developed.Two different aptamers, which recognize different positions of thrombin, were chosen to construct sandwich type sensing system for protein, one was immobilized onto the gold electrode for capturing thrombin onto the electrode and the other was used for detection.To obtain the signal, the aptamer for detection was labeled with tris(2,2'-bipyridyl)ruthenium(Ⅱ)-doped silica nanoparticles ( Ru(bpy)32+-doped SNPs).The increase of the ECL signal generated by Ru(bpy)32+-doped SNPs was observed in dependent manner on the concentration of thrombin added.Bovine serum albumin and bovine hemoglobin had almost negligible responses.The assay allows detection at levels as low as 1.0 fmol·L-1 of the thrombin due to that there are a large number of Ru(bpy)32+ molecules inside SNPs labeled on the aptamer used for detection.The ECL signal was linearly related to the concentration of the thrombin analyte in the range of 2.0 fmol·L-1 to 2.0 pmol·L-1.

  8. Computer vision: automating DEM generation of active lava flows and domes from photos

    Science.gov (United States)

    James, M. R.; Varley, N. R.; Tuffen, H.

    2012-12-01

    Accurate digital elevation models (DEMs) form fundamental data for assessing many volcanic processes. We present a photo-based approach developed within the computer vision community to produce DEMs from a consumer-grade digital camera and freely available software. Two case studies, based on the Volcán de Colima lava dome and the Puyehue Cordón-Caulle obsidian flow, highlight the advantages of the technique in terms of the minimal expertise required, the speed of data acquisition and the automated processing involved. The reconstruction procedure combines structure-from-motion and multi-view stereo algorithms (SfM-MVS) and can generate dense 3D point clouds (millions of points) from multiple photographs of a scene taken from different positions. Processing is carried out by automated software (e.g. http://blog.neonascent.net/archives/bundler-photogrammetry-package/). SfM-MVS reconstructions are initally un-scaled and un-oriented so additional geo-referencing software has been developed. Although this step requires the presence of some control points, the SfM-MVS approach has significantly easier image acquisition and control requirements than traditional photogrammetry, facilitating its use in a broad range of difficult environments. At Colima, the lava dome surface was reconstructed from recent and archive images taken from light aircraft over flights (2007-2011). Scaling and geo-referencing was carried out using features identified in web-sourced ortho-imagery obtained as a basemap layer in ArcMap - no ground-based measurements were required. Average surface measurement densities are typically 10-40 points per m2. Over mean viewing distances of ~500-2500 m (for different surveys), RMS error on the control features is ~1.5 m. The derived DEMs (with 1-m grid resolution) are sufficient to quantify volumetric change, as well as to highlight the structural evolution of the upper surface of the dome following an explosion in June 2011. At Puyehue Cord

  9. Discovery of thrombin activatable fibrinolysis inhibitor (TAFI)

    NARCIS (Netherlands)

    Bertina, R.M.; Tilburg, N.H. van; Haverkate, F.; Bouma, B.N.; Borne, P.A.K. von dem; Meijers, J.C.M.; Campbell, W.; Eaton, D.; Hendriks, D.F.; Willemse, J.L.

    2006-01-01

    CAS: blood clotting factor 11, 9013-55-2; thrombin, 9002-04-4; tissue plasminogen activator, 105913-11-9; protein C, 60202-16-6; Carboxypeptidase U, 3.4.17.20; Protein C; Tissue Plasminogen Activator, 3.4.21.68

  10. A nanoresonant gold-aptamer probe for rapid and sensitive detection of thrombin

    International Nuclear Information System (INIS)

    Resonance light scattering (RLS) is a sensitive technique for monitoring scattered light induced by extended aggregates of chromophores. It has been widely used to study aggregations for its simple manipulation, high sensitivity and great versatility. Gold nanoparticles generate colorful light-scattering signals due to their unique surface plasmon resonances, hence extraordinary light scattering upon aggregation. In this paper we report a rapid and sensitive method based on gold nanoparticles and DNA aptamer to detect protein biomarkers by RLS. Thiol modified thrombin aptamer was covalently assembled to the surface of gold nanoparticles as nanobio probes. As thrombin has two specific binding sites for its aptamer, it can bridge the well dispersed nanoparticles and lead to a network of particle aggregations. The formation of aggregation ia measured by RLS, and the specific detection of thrombin at nM level is achieved. The method has good specificity. (authors)

  11. Thrombin-Mediated Direct Activation of Proteinase-Activated Receptor-2: Another Target for Thrombin Signaling.

    Science.gov (United States)

    Mihara, Koichiro; Ramachandran, Rithwik; Saifeddine, Mahmoud; Hansen, Kristina K; Renaux, Bernard; Polley, Danny; Gibson, Stacy; Vanderboor, Christina; Hollenberg, Morley D

    2016-05-01

    Thrombin is known to signal to cells by cleaving/activating a G-protein-coupled family of proteinase-activated receptors (PARs). The signaling mechanism involves the proteolytic unmasking of an N-terminal receptor sequence that acts as a tethered receptor-activating ligand. To date, the recognized targets of thrombin cleavage and activation for signaling are PAR1 and PAR4, in which thrombin cleaves at a conserved target arginine to reveal a tethered ligand. PAR2, which like PAR1 is also cleaved at an N-terminal arginine to unmask its tethered ligand, is generally regarded as a target for trypsin but not for thrombin signaling. We now show that thrombin, at concentrations that can be achieved at sites of acute injury or in a tumor microenvironment, can directly activate PAR2 vasorelaxation and signaling, stimulating calcium and mitogen-activated protein kinase responses along with triggeringβ-arrestin recruitment. Thus, PAR2 can be added alongside PAR1 and PAR4 to the targets, whereby thrombin can affect tissue function.

  12. Goal-driven Automation of a Deep Space Communications Station: A Case Study in Knowledge Engineering for Plan Generation and Execution

    Science.gov (United States)

    Hill, R. W., Jr.; Chien, S. A.; Fayyad, K. V.; Chien, S.

    1997-01-01

    This paper describes the application of Artificial Intelligence techniques for plan generation, plan execution, and plan monitoring to automate a Deep Space Communication Station. This automation allows a Communication station to respond to a set of tracking goals by appropriately reconfiguring the communications hardware and software to provide the requested communications services.

  13. Heparin enhances the catalytic activity of des-ETW-thrombin.

    Science.gov (United States)

    Goodwin, C A; Deadman, J J; Le Bonniec, B F; Elgendy, S; Kakkar, V V; Scully, M F

    1996-04-01

    The thrombin mutant, des-ETW-thrombin, lacking Glu(146), Thr(147), and Trp(148) within a unique insertion loop located at the extreme end of the primary specificity pocket, has been shown previously to exhibit reduced catalytic activity with respect to macromolecular and synthetic thrombin substrates and reduced or enhanced susceptibility to inhibition. Investigation of the hydrolysis of peptidyl p-nitroanilide substrates by des-ETW-thrombin showed increased activity in the presence of heparin and other sulphated glycosaminoglycans. No effect was observed upon the activity of wild-type thrombin. Heparin was found to decrease the K(m) for cleavage of four thrombin-specific substrates by des-ETW-thrombin by 3-4-fold. Similarly, pentosan polysulphate (PPS) decreased the K(m) with these substrates by 8-10-fold. Heparin also increased the rate of inhibition of des-ETW-thrombin by antithrombin III and D-phenylalanyl-prolyl-arginylchloromethane (PPACK). The inhibition of des-ETW-thrombin by a number of thrombin-specific peptide boronic acids also showed significant reduction in the final K(i) in the presence of heparin, due to reduction in the off-rate. A peptide analogue of a sequence of hirudin which binds thrombin tightly to exosite I (fibrinogen recognition site) potentiated the activity of des-ETW-thrombin against peptide p-nitroanilide substrates in a manner similar to heparin. The K(i) for the inhibition of des-ETW-thrombin by p-aminobenzamidine was decreased by these ligands from 9.7 mM to 7.5 mM, 5.1 mM, and 2.5 mM in the presence of heparin, hirudin peptide and PPS respectively, suggesting the increased catalytic activity is due to enhanced access to the primary specificity pocket. The positive influence of these ligands on des-ETW-thrombin was reversed in the presence of ATP or ADP; the latter has previously been shown to inhibit thrombin activity by blocking initial interaction with fibrinogen at exosite 1. Because the effect of heparin and PPS is similar to

  14. Label-free cascade amplification strategy for sensitive visual detection of thrombin based on target-triggered hybridization chain reaction-mediated in situ generation of DNAzymes and Pt nanochains.

    Science.gov (United States)

    Zhang, Ying; Ren, Wang; Luo, Hong Qun; Li, Nian Bing

    2016-06-15

    A new magnetic bead-based cascade amplification strategy for highly sensitive visual detection of proteins (thrombin as a model analyte) was developed by coupling target-triggered hybridization chain reaction (HCR) with the synergistic catalysis of DNA concatemer-mediated hemin/G-quadruplex DNAzymes and Pt nanozymes. Initially, the biotinylated primer DNA (P-DNA) was complementary with aptamer to form dsDNA which was further linked to streptavidin-coated magnetic bead (MB), thereby fabricating the expected MB-based aptasensor. In the presence of target TB, the aptamer was taken away from the aptasensor, and the free P-DNA immediately triggered HCR to spontaneously form DNA concatemer-directed nanochains with numerous DNAzymes and Pt nanoclusters (PtNCs) to achieve cascades signal amplification. The dual peroxidase mimetics catalyzed the H2O2-mediated oxidation of colorless 3,3',5,5'-tetramethylbenzidine (TMB) into the colored TMB oxides (oxTMB), causing intensified color change of the chromogenic solution for the highly sensitive naked-eye detection of as low as 100.0 pM TB. In this strategy, the employment of magnetic separation and exonuclease III (Exo III)-assisted digestion of residual dsDNA minimized the background noise and avoided the false positive results, greatly improving the detection accuracy and sensitivity with a low limit of detection (LOD=15.0 pM). The proposed visual platform has promise for detecting various types of proteins with careful DNA sequence designs. PMID:26878483

  15. Automated Generation of Phase Diagrams for Binary Systems with Azeotropic Behavior

    DEFF Research Database (Denmark)

    Cismondi, Martin; Michelsen, Michael Locht; Zabaloy, Marcelo S.

    2008-01-01

    In this work, we propose a computational strategy and methods for the automated calculation of complete loci of homogeneous azeotropy of binary mixtures and the related Pxy and Txy diagrams for models of the equation-of-state (EOS) type. The strategy consists of first finding the system's azeotro......In this work, we propose a computational strategy and methods for the automated calculation of complete loci of homogeneous azeotropy of binary mixtures and the related Pxy and Txy diagrams for models of the equation-of-state (EOS) type. The strategy consists of first finding the system...

  16. Crystal structure of two new bifunctional nonsubstrate type thrombin inhibitors complexed with human alpha-thrombin.

    Science.gov (United States)

    Féthière, J.; Tsuda, Y.; Coulombe, R.; Konishi, Y.; Cygler, M.

    1996-01-01

    The crystal structures of two new thrombin inhibitors, P498 and P500, complexed with human alpha-thrombin have been determined at 2.0 A resolution and refined to crystallographic R-factors of 0.170 and 0.169, respectively. These compounds, with picomolar binding constants, belong to a family of potent bifunctional inhibitors that bind thrombin at two remote sites: the active site and the fibrinogen recognition exosite (FRE). The inhibitors incorporate a nonsubstrate type active site binding fragment: Dansyl-Arg-(D)Pipecolic acid (Dns-Arg-(D)Pip), reminiscent of the active-site directed inhibitors MD-805 and MQPA, rendering them resistant to thrombin-induced hydrolysis. The FRE binding fragment of these inhibitors corresponds to the hirudin55-65 sequence. They differ in the chemical nature of the nonpeptidyl linker bridging these two functional activities. In both cases, the active site binding fragment is well defined in the electron density. The DnsH1, ArgH2, and (D)PipH3 groups occupy the S3, S1, and S2 subsites of thrombin, respectively, in a way similar to that observed in the thrombin-MQPA complexes. Binding in the active site of thrombin is characterized by numerous van der Waals contacts and ring-ring system interactions. Unlike in the substrate-like inhibitors, ArgH2 enters the S1 specificity pocket from the P2 position and adopts a bent conformation to make an hydrogen bond to the carboxylate of Asp189. In this noncanonical position, its carbonyl points away from the oxyanion hole, which is now occupied by well-ordered solvent molecules. The linkers fit in the groove extending from the active site to the FRE. The C-terminal fragments of both inhibitors bind in the same way as analogous FRE binding elements in previously described complexes. PMID:8762149

  17. Speciation analysis of arsenic in biological matrices by automated hydride generation-cryotrapping-atomic absorption spectrometry with multiple microflame quartz tube atomizer (multiatomizer).

    Science.gov (United States)

    This paper describes an automated system for the oxidation state specific speciation of inorganic and methylated arsenicals by selective hydride generation - cryotrapping- gas chromatography - atomic absorption spectrometry with the multiatomizer. The corresponding arsines are ge...

  18. Planning linear construction projects: automated method for the generation of earthwork activities

    NARCIS (Netherlands)

    Askew, W.H.; Al-Jibouri, S.H.; Mawdesley, M.J.; Patterson, D.E.

    2002-01-01

    Earthworks planning for road construction projects is a complex operation and the planning rules used are usually intuitive and not well defined. An approach to automate the earthworks planning process is described and the basic techniques that are used are outlined. A computer-based system has been

  19. Large-scale preparation of active caspase-3 in E. coli by designing its thrombin-activatable precursors

    Directory of Open Access Journals (Sweden)

    Park Sung

    2008-12-01

    Full Text Available Abstract Background Caspase-3, a principal apoptotic effector that cleaves the majority of cellular substrates, is an important medicinal target for the treatment of cancers and neurodegenerative diseases. Large amounts of the protein are required for drug discovery research. However, previous efforts to express the full-length caspase-3 gene in E. coli have been unsuccessful. Results Overproducers of thrombin-activatable full-length caspase-3 precursors were prepared by engineering the auto-activation sites of caspase-3 precursor into a sequence susceptible to thrombin hydrolysis. The engineered precursors were highly expressed as soluble proteins in E. coli and easily purified by affinity chromatography, to levels of 10–15 mg from 1 L of E. coli culture, and readily activated by thrombin digestion. Kinetic evaluation disclosed that thrombin digestion enhanced catalytic activity (kcat/KM of the precursor proteins by two orders of magnitude. Conclusion A novel method for a large-scale preparation of active caspase-3 was developed by a strategic engineering to lack auto-activation during expression with amino acid sequences susceptible to thrombin, facilitating high-level expression in E. coli. The precursor protein was easily purified and activated through specific cleavage at the engineered sites by thrombin, generating active caspase-3 in high yields.

  20. The use of thrombin in the radiology department.

    LENUS (Irish Health Repository)

    Ward, E

    2009-03-01

    Thrombin is a naturally occurring coagulation protein that converts soluble fibrinogen into insoluble fibrin and plays a vital role in the coagulation cascade and in turn haemostasis. Thrombin also promotes platelet activation. In the last few years, there has been a rapid increase in the use of thrombin by radiologists in a variety of clinical circumstances. It is best known for its use in the treatment of pseudoaneurysms following angiography. However, there are now a variety of cases in the literature describing the treatment of traumatic, inflammatory and infected aneurysms with thrombin in a variety of locations within the human body. There have even been recent reports describing the use of thrombin in conventional aneurysms as well as ruptured aneurysms. Its use has also been described in the treatment of endoleaks (type II) following aneurysm repair. In nearly all of these cases, treatment with thrombin requires imaging guidance. Recently, thrombin has also been used as a topical treatment post-percutaneous intervention to reduce or stop bleeding. Most radiologists have only a limited knowledge of the pharmacodynamics of thrombin, its wide range of utilisation and its limitations. Apart from a few case reports and case series, there is little in the radiological literature encompassing the wide range of applications that thrombin may have in the radiology department. In this review article, we comprehensively describe the role and pathophysiology of thrombin, describing with examples many of its potential uses. Techniques of usage as well as pitfalls and limitations are also described.

  1. Automated generation of linkage loop equations for planar 1-DOF linkages, demonstrated up to 8-bar

    OpenAIRE

    Parrish, BE; McCarthy, JM; Eppstein, D

    2014-01-01

    Copyright © 2014 by ASME. In this paper we present an algorithm that automatically creates the linkage loop equations for planar 1-DoF linkages of any topology with rotating joints, demonstrated up to 8-bars. The algorithm derives the linkage loop equations from the linkage graph by establishing a cycle basis through a single common edge. Divergent and convergent loops are identified and used to establish the fixed angles of the ternary and higher links. Results demonstrate the automated gene...

  2. Automated Monte Carlo biasing for photon-generated electrons near surfaces.

    Energy Technology Data Exchange (ETDEWEB)

    Franke, Brian Claude; Crawford, Martin James; Kensek, Ronald Patrick

    2009-09-01

    This report describes efforts to automate the biasing of coupled electron-photon Monte Carlo particle transport calculations. The approach was based on weight-windows biasing. Weight-window settings were determined using adjoint-flux Monte Carlo calculations. A variety of algorithms were investigated for adaptivity of the Monte Carlo tallies. Tree data structures were used to investigate spatial partitioning. Functional-expansion tallies were used to investigate higher-order spatial representations.

  3. Topical thrombin preparations and their use in cardiac surgery

    Directory of Open Access Journals (Sweden)

    Brianne L Dunn

    2009-10-01

    Full Text Available Brianne L Dunn1, Walter E Uber1, John S Ikonomidis21Department of Pharmacy Services and 2Division of Cardiothoracic Surgery, Medical University of South Carolina, Charleston, South Carolina, USAAbstract: Coagulopathic bleeding may lead to increased morbidity and mortality after cardiac surgery. Topical bovine thrombin has been used to promote hemostasis after surgical procedures for over 60 years and is used frequently as a topical hemostatic agent in cardiac surgery. Recently, use of bovine thrombin has been reported to be associated with increased risk for anaphylaxis, thrombosis, and immune-mediated coagulopathy thought secondary to the production of antifactor V and antithrombin antibodies. In patients who develop bovine thrombin-induced immune-mediated coagulopathy, clinical manifestations may range from asymptomatic alterations in coagulation tests to severe hemorrhage and death. Patients undergoing cardiac surgical procedures may be at increased risk for development of antibodies to bovine thrombin products and associated complications. This adverse immunologic profile has led to the development of alternative preparations including a human and a recombinant thrombin which have been shown to be equally efficacious to bovine thrombin and have reduced antigenicity. However, the potential benefit associated with reduced antigenicity is not truly known secondary to the lack of long-term experience with these products. Given the potentially higher margin of safety and less stringent storage concerns compared to human thrombin, recombinant thrombin may be the most reasonable approach in cardiac surgery.Keywords: bovine thrombin, human thrombin, recombinant thrombin, immune-mediated coagulopathy, topical hemostatic agents, thrombin 

  4. Mutant B-Raf(V600E) Promotes Melanoma Paracellular Transmigration by Inducing Thrombin-mediated Endothelial Junction Breakdown.

    Science.gov (United States)

    Zhang, Pu; Feng, Shan; Liu, Gentao; Wang, Heyong; Zhu, Huifeng; Ren, Qiao; Bai, Huiyuan; Fu, Changliang; Dong, Cheng

    2016-01-29

    Tumor invasiveness depends on the ability of tumor cells to breach endothelial barriers. In this study, we investigated the mechanism by which the adhesion of melanoma cells to endothelium regulates adherens junction integrity and modulates tumor transendothelial migration (TEM) by initiating thrombin generation. We found that the B-Raf(V600E) mutation in metastatic melanoma cells up-regulated tissue factor (TF) expression on cell membranes and promoted thrombin production. Co-culture of endothelial monolayers with metastatic melanoma cells mediated the opening of inter-endothelial spaces near melanoma cell contact sites in the presence of platelet-free plasma (PFP). By using small interfering RNA (siRNA), we demonstrated that B-Raf(V600E) and TF silencing attenuated the focal disassembly of adherens junction induced by tumor contact. Vascular endothelial-cadherin (VE-cadherin) disassembly was dependent on phosphorylation of p120-catenin on Ser-879 and VE-cadherin on Tyr-658, Tyr-685, and Tyr-731, which can be prevented by treatment with the thrombin inhibitor, hirudin, or by silencing the thrombin receptor, protease-activated receptor-1, in endothelial cells. We also provided strong evidence that tumor-derived thrombin enhanced melanoma TEM by inducing ubiquitination-coupled VE-cadherin internalization, focal adhesion formation, and actin assembly in endothelium. Confocal microscopic analysis of tumor TEM revealed that junctions transiently opened and resealed as tumor cells accomplished TEM. In addition, in the presence of PFP, tumor cells preferentially transmigrated via paracellular routes. PFP supported melanoma transmigration under shear conditions via a B-Raf(V600E)-thrombin-dependent mechanism. We concluded that the activation of thrombin generation by cancer cells in plasma is an important process regulating melanoma extravasation by disrupting endothelial junction integrity. PMID:26504080

  5. Codon-Precise, Synthetic, Antibody Fragment Libraries Built Using Automated Hexamer Codon Additions and Validated through Next Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Laura Frigotto

    2015-05-01

    Full Text Available We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR in antibody fragment libraries and next generation sequencing (NGS analysis of their quality and diversity.

  6. XIMELAGATRAN: A NEW DIRECT THROMBIN INHIBITOR

    Directory of Open Access Journals (Sweden)

    Mehta Hiren R

    2011-04-01

    Full Text Available Venous thromboembolism is a serious illness that affects patient morbidity and mortality and presents a significant management challenge to healthcare providers world-wide. Despite major achievements in the significant reduction of thromboembolic complications, the most common therapies currently used for prevention and treatment of venous thromboembolism – heparins and vitamin K antagonists such as warfarin – have several limitations. Warfarin sodium is an effective oral anticoagulant drug. However, warfarin has a narrow therapeutic window with significant risks of hemorrhage at therapeutic concentrations. Dosing is difficult and requires frequent monitoring. New oral anticoagulant agents are required to improve current anticoagulant therapy. Furthermore, while warfarin is effective in venous disease, it does not provide more than 60% risk reduction compared with placebo in venous thrombosis prophylaxis and considerably lower risk reduction in terms of arterial thrombosis. Unlike warfarin and heparin, these direct thrombin inhibitors are able to inhibit fibrin-bound thrombin and so produce more effective inhibition of coagulation. Importantly, some members of this class of drugs have been developed for oral administration. Ximelagatran is an oral pro-drug of melagatran, a synthetic small peptidomimetic with direct thrombin inhibitory actions and anticoagulant activity. As an oral agent, ximelagatran has a number of desirable properties including a rapid onset of action, fixed dosing, stable absorption, apparent low potential for medication interactions, and no requirement for monitoring of drug levels or dose adjustment. It has a short plasma elimination half-life of about 4 hours in cases of unexpected hemorrhage or need for reversal.

  7. A electrochemiluminescence aptasensor for detection of thrombin incorporating the capture aptamer labeled with gold nanoparticles immobilized onto the thio-silanized ITO electrode

    Energy Technology Data Exchange (ETDEWEB)

    Fang Lanyun [State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin (China); Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, Zhejiang (China); Lue Zhaozi [State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin (China); Wei Hui [State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin (China); Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Wang Erkang [State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin (China)], E-mail: ekwang@ciac.jl.cn

    2008-10-17

    A novel electrochemiluminescence (ECL) aptasensor was proposed for sensitive and cost-effective detection of the target thrombin adopted an aptamer-based sandwich format. To detect thrombin, capture aptamers labeled with gold nanoparticles (AuNPs) were first immobilized onto the thio-silanized ITO electrode surface through strong Au-S bonds. After catching the target thrombin, signal aptamers tagged with ECL labels were attached to the assembled electrode surface. As a result, an AuNPs-capture-aptamer/thrombin/ECL-tagged-signal-aptamer sandwich type was formed. Treating the resulting electrode surface with tri-n-propylamine (TPA) and applying a swept potential to the electrode, ECL response was generated which realized the detection of target protein. Spectroscopy and electrochemical impedance techniques were used to characterize and confirm the fabrication of the ECL aptasensor. AuNPs amplification and smart sensor fabrication art were implemented for the sensitive and cost-effective detection purpose. Signal-to-dose curve excellently followed a sandwich format equation and could be used to quantify the protein, and the detection limit was estimated to be 10 nM. Other forms of thrombin such as {beta}- and {gamma}-thrombins had negligible response, which indicated a high specificity of {alpha}-thrombin detection. The aptasensor opened up new fields of aptamer applications in ECL domain, a highly sensitive technique, and had a promising perspective to be applied in microarray analysis.

  8. A electrochemiluminescence aptasensor for detection of thrombin incorporating the capture aptamer labeled with gold nanoparticles immobilized onto the thio-silanized ITO electrode

    International Nuclear Information System (INIS)

    A novel electrochemiluminescence (ECL) aptasensor was proposed for sensitive and cost-effective detection of the target thrombin adopted an aptamer-based sandwich format. To detect thrombin, capture aptamers labeled with gold nanoparticles (AuNPs) were first immobilized onto the thio-silanized ITO electrode surface through strong Au-S bonds. After catching the target thrombin, signal aptamers tagged with ECL labels were attached to the assembled electrode surface. As a result, an AuNPs-capture-aptamer/thrombin/ECL-tagged-signal-aptamer sandwich type was formed. Treating the resulting electrode surface with tri-n-propylamine (TPA) and applying a swept potential to the electrode, ECL response was generated which realized the detection of target protein. Spectroscopy and electrochemical impedance techniques were used to characterize and confirm the fabrication of the ECL aptasensor. AuNPs amplification and smart sensor fabrication art were implemented for the sensitive and cost-effective detection purpose. Signal-to-dose curve excellently followed a sandwich format equation and could be used to quantify the protein, and the detection limit was estimated to be 10 nM. Other forms of thrombin such as β- and γ-thrombins had negligible response, which indicated a high specificity of α-thrombin detection. The aptasensor opened up new fields of aptamer applications in ECL domain, a highly sensitive technique, and had a promising perspective to be applied in microarray analysis

  9. Hypersensitivity to thrombin of platelets from hypercholesterolemic rats

    International Nuclear Information System (INIS)

    Hypersensitivity of platelets to thrombin has been associated with hypercholesterolemia. The authors have examined the mechanisms involved in this hypersensitivity. Rats were given diets rich in milk fat and containing added cholesterol and taurocholate to produce hypercholesterolemia (HC) (262 +/- 25 mg%) or added sitosterol as a normocholesterolemic control (NC) (89 +/- 6 mg%). Washed platelets were prelabelled with 14C-serotonin. In the presence of acetylsalicyclic acid (ASA) (to inhibit thromboxane A2 (TXA2) formation) and creatine phosphate/creatine phosphokinase (CP/CPK) (to remove released ADP), HC platelets aggregated more (26 +/- 1%) and released more 14C (9.1 +/- 2.0%) than NC platelets (aggregation: 0%, p 14C release: 1.5 +/- 0.5%, p 2 formation is involved in the hypersensitivity of HC platelets to thrombin. Total binding of 125I-thrombin to HC platelets was less than that to NC platelets but HC platelets were smaller and had less protein than NC platelets; the thrombin binding per mg platelet protein was the same for HC and NC platelets, indicating that hypersensitivity to thrombin of HC platelets does not result from increased thrombin binding. Thus, hypersensitivity of HC platelets to thrombin is not due to TXA2 formation, the action of released ADP or increased thrombin binding

  10. The Toxic Effect of Thrombin on Periventricular Tissue

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective To investigate the effect of thrombin on periventricular tissue. Methods Thrombin solution (10U/10μl) was infused into the ventricles of rats. Then, the local cerebral blood flow (rCBF) and blood-brain barrier (BBB) permeability in the area of basal ganglia and thalamus were measured. In separate experiments neurons were cultured in the medium with thrombin, and lactate dehydrogenase was determined. Results The thrombin induced blood-brain barrier disruption and neuron death in the culture, whereas cerebral blood flow did not drop to the injury level. Conclusion Periventricular tissue damage suffering from the thrombin and blood-brain barrier disruption and cell toxicity could elicit pathological mechanisms.

  11. Creating harmonious and legible colour schemes in the automated generation of multimedia presentations

    NARCIS (Netherlands)

    Manniesing, A.S.K.

    2003-01-01

    Due to the growing amount of information on the web, the user specific requirements and different characteristics of output devices, the opportunities for the automatic generation of multimedia presentations grow. The multimedia presentation generator, that resides in a dynamic environment, such as

  12. Instructional Topics in Educational Measurement (ITEMS) Module: Using Automated Processes to Generate Test Items

    Science.gov (United States)

    Gierl, Mark J.; Lai, Hollis

    2013-01-01

    Changes to the design and development of our educational assessments are resulting in the unprecedented demand for a large and continuous supply of content-specific test items. One way to address this growing demand is with automatic item generation (AIG). AIG is the process of using item models to generate test items with the aid of computer…

  13. Generation and Performance of Automated Jarosite Mineral Detectors for Vis/NIR Spectrometers at Mars

    Science.gov (United States)

    Gilmore, M. S.; Bornstein, B.; Merrill, M. D.; Castano, R.; Greenwood, J. P.

    2005-01-01

    Sulfate salt discoveries at the Eagle and Endurance craters in Meridiani Planum by the Mars Exploration Rover Opportunity have proven mineralogically the existence and involvement of water in Mars past. Visible and near infrared spectrometers like the Mars Express OMEGA, the Mars Reconnaissance Orbiter CRISM and the 2009 Mars Science Laboratory Rover cameras are powerful tools for the identification of water-bearing salts and other high priority minerals at Mars. The increasing spectral resolution and rover mission lifetimes represented by these missions currently necessitate data compression in order to ease downlink restrictions. On board data processing techniques can be used to guide the selection, measurement and return of scientifically important data from relevant targets, thus easing bandwidth stress and increasing scientific return. We have developed an automated support vector machine (SVM) detector operating in the visible/near-infrared (VisNIR, 300-2500 nm) spectral range trained to recognize the mineral jarosite (typically KFe3(SO4)2(OH)6), positively identified by the Mossbauer spectrometer at Meridiani Planum. Additional information is included in the original extended abstract.

  14. Movie magic in the clinic: computer-generated characters for automated health counseling.

    Science.gov (United States)

    Bickmore, Timothy

    2008-01-01

    In this presentation, I demonstrate how many of the technologies used in movie special effects and games have been successfully used in health education and behavior change interventions. Computer-animated health counselors simulate human face-to-face dialogue as a computer interface medium, including not only verbal behavior but nonverbal conversational behavior such as hand gesture, body posture shifts, and facial display of emotion. This technology has now been successfully used in a wide range of health interventions for education and counseling of patients and consumers, including applications in physical activity promotion, medication adherence, and hospital discharge. These automated counselors have been deployed on home computers, hospital-based touch screen kiosks, and mobile devices with integrated health behavior sensing capability. Development of these agents is an interdisciplinary endeavor spanning the fields of character modeling and animation, computational linguistics, artificial intelligence, health communication and behavioral medicine. I will give demonstrations of several fielded systems, describe the technologies and methodologies underlying their development, and present results from five randomized controlled trials that have been completed or are in progress. PMID:18999232

  15. Low cost home automation system: a support to the ecological electricity generation in Colombia

    Directory of Open Access Journals (Sweden)

    Elmer Alejandro Parada Prieto

    2016-09-01

    Full Text Available Context/Objective: In Colombia, consumption of residential electricity accounts for about 40% of the national demand; therefore, alternatives to reduce this consumption are needed. The goal of this study was to develop a home automation prototype to control the illumination of a household and to foster the efficient use of energy.Method: The system consists of independent control modules and an information manager module; the control module regulates the luminaires using a microcontroller and a presence sensor, and exchanges data by means of a radio frequency transceiver; the manager module allows the access to the control modules from a Web interface. The prototype was implemented in a household located in the city of San José de Cúcuta, Colombia, during a 60 days period.Results: The operation of the system diminished the total electricity consumption by 3,75 %, with a z-score of -1,93 that was obtained from the statistical analysis.Conclusions: We concluded that the prototype is inexpensive in comparison to similar technologies available in the national and international markets, and it reduces the waste of electrical energy due to the consumption habits of the residents in the case study.

  16. Long-term evaluation of TiO2-based 68Ge/68Ga generators and optimized automation of [68Ga]DOTATOC radiosynthesis.

    Science.gov (United States)

    Lin, Mai; Ranganathan, David; Mori, Tetsuya; Hagooly, Aviv; Rossin, Raffaella; Welch, Michael J; Lapi, Suzanne E

    2012-10-01

    Interest in using (68)Ga is rapidly increasing for clinical PET applications due to its favorable imaging characteristics and increased accessibility. The focus of this study was to provide our long-term evaluations of the two TiO(2)-based (68)Ge/(68)Ga generators and develop an optimized automation strategy to synthesize [(68)Ga]DOTATOC by using HEPES as a buffer system. This data will be useful in standardizing the evaluation of (68)Ge/(68)Ga generators and automation strategies to comply with regulatory issues for clinical use. PMID:22897970

  17. TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data

    Directory of Open Access Journals (Sweden)

    Sarver Aaron L

    2012-06-01

    Full Text Available Abstract Background Next generation sequencing approaches applied to the analyses of transposon insertion junction fragments generated in high throughput forward genetic screens has created the need for clear informatics and statistical approaches to deal with the massive amount of data currently being generated. Previous approaches utilized to 1 map junction fragments within the genome and 2 identify Common Insertion Sites (CISs within the genome are not practical due to the volume of data generated by current sequencing technologies. Previous approaches applied to this problem also required significant manual annotation. Results We describe Transposon Annotation Poisson Distribution Association Network Connectivity Environment (TAPDANCE software, which automates the identification of CISs within transposon junction fragment insertion data. Starting with barcoded sequence data, the software identifies and trims sequences and maps putative genomic sequence to a reference genome using the bowtie short read mapper. Poisson distribution statistics are then applied to assess and rank genomic regions showing significant enrichment for transposon insertion. Novel methods of counting insertions are used to ensure that the results presented have the expected characteristics of informative CISs. A persistent mySQL database is generated and utilized to keep track of sequences, mappings and common insertion sites. Additionally, associations between phenotypes and CISs are also identified using Fisher’s exact test with multiple testing correction. In a case study using previously published data we show that the TAPDANCE software identifies CISs as previously described, prioritizes them based on p-value, allows holistic visualization of the data within genome browser software and identifies relationships present in the structure of the data. Conclusions The TAPDANCE process is fully automated, performs similarly to previous labor intensive approaches

  18. Using Genetic Algorithm for Automated Efficient Software Test Case Generation for Path Testing

    Directory of Open Access Journals (Sweden)

    Premal B. Nirpal

    2011-05-01

    Full Text Available This paper discusses genetic algorithms that can automatically generate test cases to test selected path. This algorithm takes a selected path as a target and executes sequences of operators iteratively for test cases to evolve. The evolved test case can lead the program execution to achieve the target path. An automatic path-oriented test data generation is not only a crucial problem but also a hot issue in the research area of software testing today.

  19. Label-free impedimetric biosensor for thrombin using the thrombin-binding aptamer as receptor

    Science.gov (United States)

    Frense, D.; Kang, S.; Schieke, K.; Reich, P.; Barthel, A.; Pliquett, U.; Nacke, T.; Brian, C.; Beckmann, D.

    2013-04-01

    This study presents the further establishment of impedimetric biosensors with aptamers as receptors. Aptamers are short single-stranded oligonucleotides which bind analytes with a specific region of their 3D structure. Electrical impedance spectroscopy is a sensitive method for analyzing changes on the electrode surface, e.g. caused by receptor-ligand-interactions. Fast and inexpensive prototyping of electrodes on the basis of commercially available compact discs having a 24 carat gold reflective layer was investigated. Electrode structures (CDtrodes [1]) in the range from few millimetres down to 100 microns were realized. The well-studied thrombin-binding aptamer (TBA) was used as receptor for characterizing these micro- and macro-electrodes. The impedance signal showed a linear correlation for concentrations of thrombin between 1.0 nM to 100 nM. This range corresponds well with most of the references and may be useful for the point-of-care testing (POCT).

  20. Hierarchical Testing with Automated Document Generation for Amanzi, ASCEM's Subsurface Flow and Reactive Transport Simulator

    Science.gov (United States)

    Moulton, J. D.; Steefel, C. I.; Yabusaki, S.; Castleton, K.; Scheibe, T. D.; Keating, E. H.; Freedman, V. L.

    2013-12-01

    The Advanced Simulation Capabililty for Environmental Management (ASCEM) program is developing an approach and open-source tool suite for standardized risk and performance assessments at legacy nuclear waste sites. These assessments use a graded and iterative approach, beginning with simplified highly abstracted models, and adding geometric and geologic complexity as understanding is gained. To build confidence in this assessment capability, extensive testing of the underlying tools is needed. Since the tools themselves, such as the subsurface flow and reactive-transport simulator, Amanzi, are under active development, testing must be both hierarchical and highly automated. In this presentation we show how we have met these requirements, by leveraging the python-based open-source documentation system called Sphinx with several other open-source tools. Sphinx builds on the reStructured text tool docutils, with important extensions that include high-quality formatting of equations, and integrated plotting through matplotlib. This allows the documentation, as well as the input files for tests, benchmark and tutorial problems, to be maintained with the source code under a version control system. In addition, it enables developers to build documentation in several different formats (e.g., html and pdf) from a single source. We will highlight these features, and discuss important benefits of this approach for Amanzi. In addition, we'll show that some of ASCEM's other tools, such as the sampling provided by the Uncertainty Quantification toolset, are naturally leveraged to enable more comprehensive testing. Finally, we will highlight the integration of this hiearchical testing and documentation framework with our build system and tools (CMake, CTest, and CDash).

  1. Aptamer-based SERRS sensor for thrombin detection.

    Science.gov (United States)

    Cho, Hansang; Baker, Brian R; Wachsmann-Hogiu, Sebastian; Pagba, Cynthia V; Laurence, Ted A; Lane, Stephen M; Lee, Luke P; Tok, Jeffrey B H

    2008-12-01

    We describe an aptamer-based surface enhanced resonance Raman scattering (SERRS) sensor with high sensitivity, specificity, and stability for the detection of a coagulation protein, human alpha-thrombin. The sensor achieves high sensitivity and a limit of detection of 100 pM by monitoring the SERRS signal change upon the single-step of thrombin binding to immobilized thrombin binding aptamer. The selectivity of the sensor is demonstrated by the specific discrimination of thrombin from other protein analytes. The specific recognition and binding of thrombin by the thrombin binding aptamer is essential to the mechanism of the aptamer-based sensor, as shown through measurements using negative control oligonucleotides. In addition, the sensor can detect 1 nM thrombin in the presence of complex biofluids, such as 10% fetal calf serum, demonstrating that the immobilized, 5'-capped, 3'-capped aptamer is sufficiently robust for clinical diagnostic applications. Furthermore, the proposed sensor may be implemented for multiplexed detection using different aptamer-Raman probe complexes. PMID:19367849

  2. Clinical use of topical thrombin as a surgical hemostat

    Directory of Open Access Journals (Sweden)

    Wesley K Lew

    2008-08-01

    Full Text Available Wesley K Lew1, Fred A Weaver21University of Southern California, Department of Surgery, Los Angeles, CA, USA; 2CardioVascular Thoracic Institute at the University of Southern California, Los Angeles, CA, USAAbstract: When surgical ligation of bleeding fails, or is not possible, surgeons rely on a number of hemostatic aids, including thrombin. This review discusses the history, pharmacology and clinical application of thrombin as a surgical hemostat. The initial thrombin was bovine in origin, but its use has been complicated by the formation of antibodies that cross react with human coagulation factors. This has been associated with life threatening bleeding and in some circumstances anaphylaxis and death. Human thrombin, isolated from pooled plasma of donors, has been developed in an effort to minimize these risks, but its downside is the potential of transmitting blood-borne pathogens and limited availability. Recently a recombinant thrombin has been developed and approved for use by the FDA. It has the advantage of being minimally antigenic and devoid of the risk if viral transmission. Thrombin is often used in conjunction with other hemostatic aids, including absorbable agents (like gelfoam, collagen, and cellulose, and with fibrinogen in fibrin glues. The last part of this review will discuss these agents in detail, and review their clinical applications.Keywords: bovine, recombinant, human, thrombin, antigenicity, antibodies

  3. APTAMER-BASED SERRS SENSOR FOR THROMBIN DETECTION

    Energy Technology Data Exchange (ETDEWEB)

    Cho, H; Baker, B R; Wachsmann-Hogiu, S; Pagba, C V; Laurence, T A; Lane, S M; Lee, L P; Tok, J B

    2008-07-02

    We describe an aptamer-based Surface Enhanced Resonance Raman Scattering (SERRS) sensor with high sensitivity, specificity, and stability for the detection of a coagulation protein, human a-thrombin. The sensor achieves high sensitivity and a limit of detection of 100 pM by monitoring the SERRS signal change upon the single step of thrombin binding to immobilized thrombin binding aptamer. The selectivity of the sensor is demonstrated by the specific discrimination of thrombin from other protein analytes. The specific recognition and binding of thrombin by the thrombin binding aptamer is essential to the mechanism of the aptamer-based sensor, as shown through measurements using negative control oligonucleotides. In addition, the sensor can detect 1 nM thrombin in the presence of complex biofluids, such as 10% fetal calf serum, demonstrating that the immobilized, 5{prime}-capped, 3{prime}-capped aptamer is sufficiently robust for clinical diagnostic applications. Furthermore, the proposed sensor may be implemented for multiplexed detection using different aptamer-Raman probe complexes.

  4. Development of Closed-Loop Simulation Methods for a Next-Generation Terminal Area Automation System

    Science.gov (United States)

    Robinson, John E., III; Isaacson, Douglas R.

    2002-01-01

    A next-generation air traffic decision support tool, known as the Active Final Approach Spacing Tool (aFAST), will generate heading, speed and altitude commands to achieve more precise separation of aircraft in the terminal area. The techniques used to analyze the performance of earlier generation decision support tools are not adequate to analyze the performance of aFAST. This paper summarizes the development of a new and innovative fully closed-loop testing method for aFAST. This method, called trajectory feedback testing, closes each aircraft's control loop inside of the aFAST scheduling algorithm. Validation of trajectory feedback testing by examination of the variation of aircraft time-of-arrival predictions between schedule updates and the variation of aircraft excess separation distances between simulation runs is presented.

  5. Integrated Design Engineering Analysis (IDEA) Environment Automated Generation of Structured CFD Grids using Topology Methods

    Science.gov (United States)

    Kamhawi, Hilmi N.

    2012-01-01

    This report documents the work performed from March 2010 to March 2012. The Integrated Design and Engineering Analysis (IDEA) environment is a collaborative environment based on an object-oriented, multidisciplinary, distributed framework using the Adaptive Modeling Language (AML) as a framework and supporting the configuration design and parametric CFD grid generation. This report will focus on describing the work in the area of parametric CFD grid generation using novel concepts for defining the interaction between the mesh topology and the geometry in such a way as to separate the mesh topology from the geometric topology while maintaining the link between the mesh topology and the actual geometry.

  6. Automated, computer generated reminders and increased detection of gonorrhoea, chlamydia and syphilis in men who have sex with men.

    Directory of Open Access Journals (Sweden)

    Huachun Zou

    Full Text Available BACKGROUND: Guidelines recommend frequent screening of men who have sex with men (MSM for sexually transmissible infections (STIs but few interventions have demonstrated increased testing and detection of bacterial STIs among MSM in controlled studies. METHODS: We used automated text message and email reminders generated by computer assisted self-interview (CASI to remind MSM to retest for syphilis. We compared clinic visits, STI testing and detection rates over 12 month between men receiving reminders (reminder group and men not offered the reminders (concurrent control group. RESULTS: Men who chose 3-monthly reminders had more clinic visits (median 3 vs 1 and higher testing rates for pharyngeal gonorrhoea (67.0% vs 33.6%, rectal gonorrhoea (62.7% vs 31.1%, urethral chlamydia (67.3% vs 39.3%, rectal chlamydia (62.9% vs 31.3%, syphilis (67.0% vs 39.3% and HIV (64.9% vs 36.7% (all p<0.001 than concurrent controls, within 12 months after their first visit. Also, men receiving reminders had a higher combined testing rate for all the aforementioned STIs at a same visit (55.7% vs 25.5%, p<0.001 compared with concurrent controls. This association remained after adjusting for differences in characteristics between the two groups (adjusted odds ratio:1.77, 95% confidence interval:1.51-2.08. Men receiving reminders also had a higher detection rate of: rectal gonorrhoea (3.7% vs 1.2%, p = 0.001, urethral chlamydia (3.1% vs 1.4%, p = 0.027, rectal chlamydia (6.6% vs 2.8%, p<0.001, and early, latent syphilis (1.7% vs 0.4%, p = 0.008 compared with concurrent controls. CONCLUSION: This is the first study to demonstate that a fully automated reminder system using CASI was associated with increased detection of bacterial STIs among MSM.

  7. An automated tetrahedral mesh generator for computer simulation in Odontology based on the Delaunay's algorithm

    OpenAIRE

    Mauro Massayoshi Sakamoto; José Roberto Cardoso; José Marcio Machado

    2008-01-01

    In this work, a software package based on the Delaunay´s algorithm is described. The main feature of this package is the capability in applying discretization in geometric domains of teeth taking into account their complex inner structures and the materials with different hardness. Usually, the mesh generators reported in literature treat molars and other teeth by using simplified geometric models, or even considering the teeth as homogeneous structures.

  8. An automated tetrahedral mesh generator for computer simulation in Odontology based on the Delaunay's algorithm

    Directory of Open Access Journals (Sweden)

    Mauro Massayoshi Sakamoto

    2008-01-01

    Full Text Available In this work, a software package based on the Delaunay´s algorithm is described. The main feature of this package is the capability in applying discretization in geometric domains of teeth taking into account their complex inner structures and the materials with different hardness. Usually, the mesh generators reported in literature treat molars and other teeth by using simplified geometric models, or even considering the teeth as homogeneous structures.

  9. Grayscale lithography-automated mask generation for complex three-dimensional topography

    Science.gov (United States)

    Loomis, James; Ratnayake, Dilan; McKenna, Curtis; Walsh, Kevin M.

    2016-01-01

    Grayscale lithography is a relatively underutilized technique that enables fabrication of three-dimensional (3-D) microstructures in photosensitive polymers (photoresists). By spatially modulating ultraviolet (UV) dosage during the writing process, one can vary the depth at which photoresist is developed. This means complex structures and bioinspired designs can readily be produced that would otherwise be cost prohibitive or too time intensive to fabricate. The main barrier to widespread grayscale implementation, however, stems from the laborious generation of mask files required to create complex surface topography. We present a process and associated software utility for automatically generating grayscale mask files from 3-D models created within industry-standard computer-aided design (CAD) suites. By shifting the microelectromechanical systems (MEMS) design onus to commonly used CAD programs ideal for complex surfacing, engineering professionals already familiar with traditional 3-D CAD software can readily utilize their pre-existing skills to make valuable contributions to the MEMS community. Our conversion process is demonstrated by prototyping several samples on a laser pattern generator-capital equipment already in use in many foundries. Finally, an empirical calibration technique is shown that compensates for nonlinear relationships between UV exposure intensity and photoresist development depth as well as a thermal reflow technique to help smooth microstructure surfaces.

  10. SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory.

    Science.gov (United States)

    Roy, Somak; Durso, Mary Beth; Wald, Abigail; Nikiforov, Yuri E; Nikiforova, Marina N

    2014-01-01

    A wide repertoire of bioinformatics applications exist for next-generation sequencing data analysis; however, certain requirements of the clinical molecular laboratory limit their use: i) comprehensive report generation, ii) compatibility with existing laboratory information systems and computer operating system, iii) knowledgebase development, iv) quality management, and v) data security. SeqReporter is a web-based application developed using ASP.NET framework version 4.0. The client-side was designed using HTML5, CSS3, and Javascript. The server-side processing (VB.NET) relied on interaction with a customized SQL server 2008 R2 database. Overall, 104 cases (1062 variant calls) were analyzed by SeqReporter. Each variant call was classified into one of five report levels: i) known clinical significance, ii) uncertain clinical significance, iii) pending pathologists' review, iv) synonymous and deep intronic, and v) platform and panel-specific sequence errors. SeqReporter correctly annotated and classified 99.9% (859 of 860) of sequence variants, including 68.7% synonymous single-nucleotide variants, 28.3% nonsynonymous single-nucleotide variants, 1.7% insertions, and 1.3% deletions. One variant of potential clinical significance was re-classified after pathologist review. Laboratory information system-compatible clinical reports were generated automatically. SeqReporter also facilitated quality management activities. SeqReporter is an example of a customized and well-designed informatics solution to optimize and automate the downstream analysis of clinical next-generation sequencing data. We propose it as a model that may envisage the development of a comprehensive clinical informatics solution. PMID:24220144

  11. Toward Automated FAÇADE Texture Generation for 3d Photorealistic City Modelling with Smartphones or Tablet Pcs

    Science.gov (United States)

    Wang, S.

    2012-07-01

    An automated model-image fitting algorithm is proposed in this paper for generating façade texture image from pictures taken by smartphones or tablet PCs. The façade texture generation requires tremendous labour work and thus, has been the bottleneck of 3D photo-realistic city modelling. With advanced developments of the micro electro mechanical system (MEMS), camera, global positioning system (GPS), and gyroscope (G-sensors) can all be integrated into a smartphone or a table PC. These sensors bring the possibility of direct-georeferencing for the pictures taken by smartphones or tablet PCs. Since the accuracy of these sensors cannot compared to the surveying instruments, the image position and orientation derived from these sensors are not capable of photogrammetric measurements. This paper adopted the least-squares model-image fitting (LSMIF) algorithm to iteratively improve the image's exterior orientation. The image position from GPS and the image orientation from gyroscope are treated as the initial values. By fitting the projection of the wireframe model to the extracted edge pixels on image, the image exterior orientation elements are solved when the optimal fitting achieved. With the exact exterior orientation elements, the wireframe model of the building can be correctly projected on the image and, therefore, the façade texture image can be extracted from the picture.

  12. Automated Music Video Generation Using Multi-level Feature-based Segmentation

    Science.gov (United States)

    Yoon, Jong-Chul; Lee, In-Kwon; Byun, Siwoo

    The expansion of the home video market has created a requirement for video editing tools to allow ordinary people to assemble videos from short clips. However, professional skills are still necessary to create a music video, which requires a stream to be synchronized with pre-composed music. Because the music and the video are pre-generated in separate environments, even a professional producer usually requires a number of trials to obtain a satisfactory synchronization, which is something that most amateurs are unable to achieve.

  13. Struktur und kinetische Charakterisierung vom Blutegel-Inhibitor Haemadin im Komplex mit humanem alpha;-Thrombin

    OpenAIRE

    Richardson, John Lee

    2007-01-01

    Haemadin, a peptide from the Indian land living leech Haemadipsa sylvestris was expressed, purified and crystallised in complex with human alpha-thrombin, and the structure solved to 3.1 Å. The inhibitor was thoroughly characterised with thrombin and ten thrombin mutants, which revealed which residues were important for binding. Synthetic tsetse thrombin inhibitor originally isolated from the tsetse fly was crystallised in complex with bovine alpha-thrombin and the structure was solved after ...

  14. MicroRNA-146a Decreases High Glucose/Thrombin-Induced Endothelial Inflammation by Inhibiting NAPDH Oxidase 4 Expression

    Directory of Open Access Journals (Sweden)

    Huang-Joe Wang

    2014-01-01

    Full Text Available Diabetes is associated with hyperglycemia and increased thrombin production. However, it is unknown whether a combination of high glucose and thrombin can modulate the expression of NAPDH oxidase (Nox subtypes in human aortic endothelial cells (HAECs. Moreover, we investigated the role of a diabetes-associated microRNA (miR-146a in a diabetic atherothrombosis model. We showed that high glucose (HG exerted a synergistic effect with thrombin to induce a 10.69-fold increase in Nox4 mRNA level in HAECs. Increased Nox4 mRNA expression was associated with increased Nox4 protein expression and ROS production. Inflammatory cytokine kit identified that the treatment increased IL-8 and IL-6 levels. Moreover, HG/thrombin treatment caused an 11.43-fold increase of THP-1 adhesion to HAECs. In silico analysis identified the homology between miR-146a and the 3′-untranslated region of the Nox4 mRNA, and a luciferase reporter assay confirmed that the miR-146a mimic bound to this Nox4 regulatory region. Additionally, miR-146a expression was decreased to 58% of that in the control, indicating impaired feedback restraint of HG/thrombin-induced endothelial inflammation. In contrast, miR-146a mimic transfection attenuated HG/thrombin-induced upregulation of Nox4 expression, ROS generation, and inflammatory phenotypes. In conclusion, miR-146a is involved in the regulation of endothelial inflammation via modulation of Nox4 expression in a diabetic atherothrombosis model.

  15. MicroRNA-146a decreases high glucose/thrombin-induced endothelial inflammation by inhibiting NAPDH oxidase 4 expression.

    Science.gov (United States)

    Wang, Huang-Joe; Huang, Yuan-Li; Shih, Ya-Yun; Wu, Hsing-Yu; Peng, Ching-Tien; Lo, Wan-Yu

    2014-01-01

    Diabetes is associated with hyperglycemia and increased thrombin production. However, it is unknown whether a combination of high glucose and thrombin can modulate the expression of NAPDH oxidase (Nox) subtypes in human aortic endothelial cells (HAECs). Moreover, we investigated the role of a diabetes-associated microRNA (miR-146a) in a diabetic atherothrombosis model. We showed that high glucose (HG) exerted a synergistic effect with thrombin to induce a 10.69-fold increase in Nox4 mRNA level in HAECs. Increased Nox4 mRNA expression was associated with increased Nox4 protein expression and ROS production. Inflammatory cytokine kit identified that the treatment increased IL-8 and IL-6 levels. Moreover, HG/thrombin treatment caused an 11.43-fold increase of THP-1 adhesion to HAECs. In silico analysis identified the homology between miR-146a and the 3'-untranslated region of the Nox4 mRNA, and a luciferase reporter assay confirmed that the miR-146a mimic bound to this Nox4 regulatory region. Additionally, miR-146a expression was decreased to 58% of that in the control, indicating impaired feedback restraint of HG/thrombin-induced endothelial inflammation. In contrast, miR-146a mimic transfection attenuated HG/thrombin-induced upregulation of Nox4 expression, ROS generation, and inflammatory phenotypes. In conclusion, miR-146a is involved in the regulation of endothelial inflammation via modulation of Nox4 expression in a diabetic atherothrombosis model. PMID:25298619

  16. The Characteristics of Thrombin in Osteoarthritic Pathogenesis and Treatment

    Directory of Open Access Journals (Sweden)

    Pei-Yu Chou

    2014-01-01

    Full Text Available Osteoarthritis (OA is a mechanical abnormality associated with degradation of joints. It is characterized by chronic, progressive degeneration of articular cartilage, abnormalities of bone, and synovial change. The most common symptom of OA is local inflammation resulting from exogenous stress or endogenous abnormal cytokines. Additionally, OA is associated with local and/or systemic activation of coagulation and anticoagulation pathways. Thrombin plays an important role in the stimulation of fibrin deposition and the proinflammatory processes in OA. Thrombin mediates hemostatic and inflammatory responses and guides the immune response to tissue damage. Thrombin activates intracellular signaling pathways by interacting with transmembrane domain G protein coupled receptors (GPCRs, known as protease-activated receptors (PARs. In pathogenic mechanisms, PARs have been implicated in the development of acute and chronic inflammatory responses in OA. Therefore, discovery of thrombin signaling pathways would help us to understand the mechanism of OA pathogenesis and lead us to develop therapeutic drugs in the future.

  17. Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin.

    Science.gov (United States)

    Handley, Lindsey D; Treuheit, Nicholas A; Venkatesh, Varun J; Komives, Elizabeth A

    2015-11-01

    Human α-thrombin is a serine protease with dual functions. Thrombin acts as a procoagulant, cleaving fibrinogen to make the fibrin clot, but when bound to thrombomodulin (TM), it acts as an anticoagulant, cleaving protein C. A minimal TM fragment consisting of the fourth, fifth, and most of the sixth EGF-like domain (TM456m) that has been prepared has much improved solubility, thrombin binding capacity, and anticoagulant activity versus those of previous TM456 constructs. In this work, we compare backbone amide exchange of human α-thrombin in three states: apo, D-Phe-Pro-Arg-chloromethylketone (PPACK)-bound, and TM456m-bound. Beyond causing a decreased level of amide exchange at their binding sites, TM and PPACK both cause a decreased level of amide exchange in other regions including the γ-loop and the adjacent N-terminus of the heavy chain. The decreased level of amide exchange in the N-terminus of the heavy chain is consistent with the historic model of activation of serine proteases, which involves insertion of this region into the β-barrel promoting the correct conformation of the catalytic residues. Contrary to crystal structures of thrombin, hydrogen-deuterium exchange mass spectrometry results suggest that the conformation of apo-thrombin does not yet have the N-terminus of the heavy chain properly inserted for optimal catalytic activity, and that binding of TM allosterically promotes the catalytically active conformation. PMID:26468766

  18. Molecular modeling studies, synthesis and biological evaluation of dabigatran analogues as thrombin inhibitors.

    Science.gov (United States)

    Dong, Ming-Hui; Chen, Hai-Feng; Ren, Yu-Jie; Shao, Fang-Ming

    2016-01-15

    In this work, 48 thrombin inhibitors based on the structural scaffold of dabigatran were analyzed using a combination of molecular modeling techniques. We generated three-dimensional quantitative structure-activity relationship (3D-QSAR) models based on three alignments for both comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) to highlight the structural requirements for thrombin protein inhibition. In addition to the 3D-QSAR study, Topomer CoMFA model also was established with a higher leave-one-out cross-validation q(2) and a non-cross-validation r(2), which suggest that the three models have good predictive ability. The results indicated that the steric, hydrophobic and electrostatic fields play key roles in QSAR model. Furthermore, we employed molecular docking and re-docking simulation explored the binding relationship of the ligand and the receptor protein in detail. Molecular docking simulations identified several key interactions that were also indicated through 3D-QSAR analysis. On the basis of the obtained results, two compounds were designed and predicted by three models, the biological evaluation in vitro (IC50) demonstrated that these molecular models were effective for the development of novel potent thrombin inhibitors.

  19. Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules.

    Directory of Open Access Journals (Sweden)

    Gregory R Johnson

    2015-12-01

    Full Text Available Characterizing the spatial distribution of proteins directly from microscopy images is a difficult problem with numerous applications in cell biology (e.g. identifying motor-related proteins and clinical research (e.g. identification of cancer biomarkers. Here we describe the design of a system that provides automated analysis of punctate protein patterns in microscope images, including quantification of their relationships to microtubules. We constructed the system using confocal immunofluorescence microscopy images from the Human Protein Atlas project for 11 punctate proteins in three cultured cell lines. These proteins have previously been characterized as being primarily located in punctate structures, but their images had all been annotated by visual examination as being simply "vesicular". We were able to show that these patterns could be distinguished from each other with high accuracy, and we were able to assign to one of these subclasses hundreds of proteins whose subcellular localization had not previously been well defined. In addition to providing these novel annotations, we built a generative approach to modeling of punctate distributions that captures the essential characteristics of the distinct patterns. Such models are expected to be valuable for representing and summarizing each pattern and for constructing systems biology simulations of cell behaviors.

  20. The Expression of the Thrombin Receptors PAR-3 and PAR-4 is Downregulated in Pancreatic Cancer Cell Lines

    Directory of Open Access Journals (Sweden)

    Claudia Rudroff

    2015-05-01

    Full Text Available Background: Patients with pancreatic cancer frequently suffer from thrombosis as a consequence of excess thrombin generation. In addition to its role in the plasmatic coagulation cascade, thrombin induces numerous cellular effects by activating a unique group of G-protein-coupled receptors on the cell membrane, the proteinase-activated receptors (PARs. At present, PAR-1, PAR-3 and PAR-4 are known to be activated by thrombin. We previously demonstrated a putative role for PAR-1 in pancreatic cancer progression, but little is known about the physiological and pathophysiological roles of PAR-3 and PAR-4. In the present study, we examined the expression patterns of PAR-3 and PAR-4 in pancreatic tissue and pancreatic cancer cells. Methods: Tissue samples from three patients with pancreatic adenocarcinoma and six human pancreatic carcinoma cell lines were examined. Gene expression was analysed by RT-PCR and quantified by HPLC. Protein expression was determined by Western blot analysis. Data analysis was performed using ANOVA in SPSS. Results and Conclusion: In contrast to PAR-1, both PAR-3 and PAR-4 were expressed in healthy pancreases but downregulated in pancreatic cancer. The contrasting expression patterns of PAR-3 and PAR-4 compared with PAR-1 indicate that the mechanism that regulates the cellular effects of thrombin on tumor progression remains to be fully elucidated.

  1. Enhanced thrombin generation in children with sickle cell disease

    NARCIS (Netherlands)

    Peters, M; Plaat, B E; ten Cate, H; Wolters, H J; Weening, R S; Brandjes, D P

    1994-01-01

    Recent studies suggest that increased activity of the coagulation system, measured with sensitive assays for activation markers, may be important in the pathogenesis of vascular occlusion in sickle cell disease (SCD). Since most of these studies were carried out in adult patients and SCD is an inher

  2. A Novel Photoelectrochemical Biosensor for Tyrosinase and Thrombin Detection

    Directory of Open Access Journals (Sweden)

    Jiexia Chen

    2016-01-01

    Full Text Available A novel photoelectrochemical biosensor for step-by-step assay of tyrosinase and thrombin was fabricated based on the specific interactions between the designed peptide and the target enzymes. A peptide chain with a special sequence which contains a positively charged lysine-labeled terminal, tyrosine at the other end and a cleavage site recognized by thrombin between them was designed. The designed peptide can be fixed on surface of the CdTe quantum dots (QDs-modified indium-tin oxide (ITO electrode through electrostatic attraction to construct the photoelectrochemical biosensor. The tyrosinase target can catalyze the oxidization of tyrosine by oxygen into ortho-benzoquinone residues, which results in a decrease in the sensor photocurrent. Subsequently, the cleavage site could be recognized and cut off by another thrombin target, restoring the sensor photocurrent. The decrease or increase of photocurrent in the sensor enables us to assay tyrosinase and thrombin. Thus, the detection of tyrosinase and thrombin can be achieved in the linear range from 2.6 to 32 μg/mL and from 4.5 to 100 μg/mL with detection limits of 1.5 μg/mL and 1.9 μg/mL, respectively. Most importantly, this strategy shall allow us to detect different classes of enzymes simultaneously by designing various enzyme-specific peptide substrates.

  3. Thrombin-Responsive Gated Silica Mesoporous Nanoparticles As Coagulation Regulators.

    Science.gov (United States)

    Bhat, Ravishankar; Ribes, Àngela; Mas, Núria; Aznar, Elena; Sancenón, Félix; Marcos, M Dolores; Murguía, Jose R; Venkataraman, Abbaraju; Martínez-Máñez, Ramón

    2016-02-01

    The possibility of achieving sophisticated actions in complex biological environments using gated nanoparticles is an exciting prospect with much potential. We herein describe new gated mesoporous silica nanoparticles (MSN) loaded with an anticoagulant drug and capped with a peptide containing a thrombin-specific cleavage site. When the coagulation cascade was triggered, active thrombin degraded the capping peptidic sequence and induced the release of anticoagulant drugs to delay the clotting process. The thrombin-dependent response was assessed and a significant increase in coagulation time in plasma from 2.6 min to 5 min was found. This work broadens the application of gated silica nanoparticles and demonstrates their ability to act as controllers in a complex scenario such as hemostasis. PMID:26794474

  4. Human thrombin for the treatment of gastric and ectopic varices

    Institute of Scientific and Technical Information of China (English)

    Norma C McAvoy; John N Plevris; Peter C Hayes

    2012-01-01

    AIM:To evaluate the efficacy of human thrombin in the treatment of bleeding gastric and ectopic varices.METHODS:Retrospective observational study in a Tertiary Referral Centre.Between January 1999-October 2005,we identified 37 patients who were endoscopically treated with human thrombin injection therapy for bleeding gastric and ectopic varices.Patient details including age,gender and aetiology of liver disease/ segmental portal hypertension were documented.The thrombin was obtained from the Scottish National Blood Transfusion Service and prepared to give a solution of 250 IU/mL which was injected via a standard injection needle.All patient case notes were reviewed and the total dose of thrombin given along with the number of endoscopy sessions was recorded.Initial haemostasis rates,rebleeding rates and mortality were catalogued along with the incidence of any immediate complications which could be attributable to the thrombin therapy.The duration of follow up was also listed.The study was conducted according to the United Kingdom research ethics guidelines.RESULTS:Thirty-seven patients were included.33 patients (89%) had thrombin (250 U/mL) for gastric varices,2 (5.4%) for duodenal varices,1 for rectal varices and 1 for gastric and rectal varices.(1) Gastric varices,an average of 15.2 mL of thrombin was used per patient.Re-bleeding occurred in 4 patients (10.8%),managed in 2 by a transjugular intrahepatic portosystemic shunt (TIPSS) (one unsuccessfully who died) and in other 2 by a distal splenorenal shunt; (2) Duodenal varices (or type 2 isolated gastric varices),an average of 12.5 mL was used per patient over 2-3 endoscopy sessions.Re-bleeding occurred in one patient,which was treated by TIPSS; and (3) Rectal varices,an average of 18.3 mL was used per patient over 3 endoscopy sessions.No re-bleeding occurred in this group.CONCLUSION:Human thrombin is a safe,easy to use and effective therapeutic option to control haemorrhage from gastric and ectopic varices.

  5. Single amino acid substitutions dissociate fibrinogen-clotting and thrombomodulin-binding activities of human thrombin.

    OpenAIRE

    Wu, Q Y; Sheehan, J P; Tsiang, M; Lentz, S R; Birktoft, J J; Sadler, J E

    1991-01-01

    Thrombin is a serine protease that acts as a procoagulant by clotting fibrinogen and activating platelets and as an anticoagulant by activating protein C in a thrombomodulin-dependent reaction. Fibrinogen and thrombomodulin bind competitively to an anion-binding exosite on thrombin. We prepared recombinant normal human thrombin and mutant thrombins with single amino acid substitutions in order to localize and distinguish the fibrinogen- and thrombomodulin-binding sites. Normal and mutant thro...

  6. Increased anticoagulant activity of thrombin-binding DNA aptamers by nanoscale organization on DNA nanostructures

    DEFF Research Database (Denmark)

    Rangnekar, Abhijit; Zhang, Alex M.; Shiyuan Li, Susan;

    2012-01-01

    Control over thrombin activity is much desired to regulate blood clotting in surgical and therapeutic situations. Thrombin-binding RNA and DNA aptamers have been used to inhibit thrombin activity and thus the coagulation cascade. Soluble DNA aptamers, as well as two different aptamers tethered by...

  7. Facile fabrication of an aptasensor for thrombin based on graphitic carbon nitride/TiO2 with high visible-light photoelectrochemical activity.

    Science.gov (United States)

    Fan, Dawei; Guo, Cuijuan; Ma, Hongmin; Zhao, Di; Li, Yina; Wu, Dan; Wei, Qin

    2016-01-15

    A novel aptasensor for thrombin with high visible-light activity was facilely fabricated based on graphitic carbon nitride/TiO2 (g-C3N4/TiO2) photoelectrochemical (PEC) composite. Crystallization of TiO2 nanoparticles (NPs) and their strong interaction with g-C3N4 sheet were confirmed by high-resolution transmission electron microscope (HR-TEM), both of which contributed to the high photocurrent intensity under visible-light irradiation. Carboxyl functionalized thrombin aptamers were first successfully bound to the g-C3N4/TiO2 modified electrode as proven by photoelectrochemical test and electrochemical impedance spectroscopy (EIS) analysis. Ascorbic acid was utilized as the electron donor for scavenging photo-generated holes and inhibiting light driven electron-hole pair recombination. The specific recognition between thrombin aptamer and thrombin led to the linear decrease of photocurrent with the increase of logarithm of thrombin concentration in the range of 5.0×10(-13)molL(-1) to 5.0×10(-9)molL(-1) with a detection limit of 1.2×10(-13)molL(-1). This proposed low-cost, convenient and sensitive aptasensor showed promising applications in biosensor and photoelectrochemical analysis.

  8. Benchmarks on automated system and software generation higher flexibility increased productivity and shorter time-to-market by ScaPable software

    Science.gov (United States)

    Gerlich, Rainer

    2002-07-01

    "ScaPable" is an acronym derived from "scalable" and "portable". The attribute "scalable" indicates that specific application software can automatically be built from scratch and verified without writing any statement in a programming language like C, thereby covering a large variety of embedded and/or distributed applications. The term "portable" addresses the capability to automatically port parts of such an application from one physical node to another one - the processor and operating system type may change - only requiring the names of the nodes, their processor type and operating system. This way the infrastructure of an embedded / distributed system can be built just by provision of literals and figures which define the system interaction, communication, topology and performance. Moreover, dedicated application software like needed for on-board command handling, data acquisition and processing, and telemetry handling can be built from generic templates. The generation time range from less than one second up to about twenty minutes on a PC/Linux platform (800 MHz). By this extremely short generation time risks can be identified early because the executable application is immediately available for validation. A rough estimation shows that one hour of automated system and software generation is equivalent to about 5 .. 50 man years. Currently, about 50% of a typical space embedded system can be covered by the available automated approach. However, the more it is applied, the more can be covered by automation. A system is constructed by applying a formal transformation to the few information as delivered by the user. This approach is not limited to the space domain, although the first industrial application was a space project. Quite different domains can take advantage of such principles of system construction. This paper explains the approach, compares it with other approaches, and provides figures on productivity, duration of system generation and reliability.

  9. A Guided Mode Resonance Aptasensor for Thrombin Detection

    Directory of Open Access Journals (Sweden)

    Wen-Yih Chen

    2011-09-01

    Full Text Available Recent developments in aptamers have led to their widespread use in analytical and diagnostic applications, particularly for biosensing. Previous studies have combined aptamers as ligands with various sensors for numerous applications. However, merging the aptamer developments with guided mode resonance (GMR devices has not been attempted. This study reports an aptasensor based home built GMR device. The 29-mer thrombin aptamer was immobilized on the surface of a GMR device as a recognizing ligand for thrombin detection. The sensitivity reported in this first trial study is 0.04 nm/μM for thrombin detection in the concentration range from 0.25 to 1 μM and the limit of detection (LOD is 0.19 μM. Furthermore, the binding affinity constant (Ka measured is in the range of 106 M−1. The investigation has demonstrated that such a GMR aptasensor has the required sensitivity for the real time, label-free, in situ detection of thrombin and provides kinetic information related to the binding.

  10. Translational success stories: development of direct thrombin inhibitors.

    Science.gov (United States)

    Coppens, Michiel; Eikelboom, John W; Gustafsson, David; Weitz, Jeffrey I; Hirsh, Jack

    2012-09-14

    Anticoagulants are the cornerstone of therapy for conditions associated with arterial and venous thrombosis. Direct thrombin inhibitors (DTIs) are anticoagulants that bind to thrombin and block its enzymatic activity. The bivalent parenteral DTIs hirudin and bivalirudin were based on the observation that the salivary extracts of medicinal leeches prevented blood from clotting. Key events that facilitated the subsequent development of small molecule active site inhibitors, such as argatroban, were the observation that fibrinopeptide A had antithrombotic properties and determination of the crystal structure of thrombin. Hirudin and argatroban have found their niche for the treatment of patients with heparin-induced thrombocytopenia, whereas bivalirudin is approved as an alternative to heparin for patients undergoing percutaneous coronary intervention. The development of orally active direct thrombin inhibitors was challenging because of the need to convert water-soluble, poorly absorbable, active site inhibitors into fat-soluble prodrugs that were then transformed back to the active drug after intestinal absorption. Dabigatran etexilate was the first new oral anticoagulant to be approved for long-term anticoagulant treatment in 6 decades. This Review highlights the development of DTIs as a translational success story; an example in which the combination of scientific ingenuity, structure-based design, and rigorous clinical trials has created a new class of anticoagulants that has improved patient care. PMID:22982873

  11. Recent Developments in Thrombin-Activatable Fibrinolysis Inhibitor Research

    NARCIS (Netherlands)

    P.F. Marx; C.J.N. Verkleij; M.V. Seron; J.C.M. Meijers

    2009-01-01

    Thrombin-activatable fibrinolysis inhibitor (TAFI) provides an important molecular link between the coagulation and fibrinolytic systems. In this review, recent major advances in TAFI research, including the elucidation of crystal structures, the development of small inhibitors and the role of TAFI

  12. Thrombin regulates components of the fibrinolytic system in human mesangial cells

    International Nuclear Information System (INIS)

    Besides its procoagulant activity, thrombin has been shown to stimulate cell proliferation and to regulate the fibrinolytic pathway. We report here the effect of purified human alpha thrombin on the synthesis of tissue-type plasminogen activator (t-PA) and plasminogen activator inhibitor 1 (PAI-1) by cultured human mesangial cells. Thrombin (0 to 2.5 U/ml) increased in a time- and dose-dependent manner the production of t-PA and PAI-1 (2- to 3-fold increase of secreted t-PA and PAI-1 release during a 24 hour incubation). This effect was associated with a twofold increase in DNA synthesis measured by 3H-thymidine incorporation. Zymographic analysis and reverse fibrin autography showed that thrombin also increased the level of the 110 Kd t-PA-PAI-1 complex, whereas PAI-1 was present as a free 50 Kd form in the culture medium conditioned by unstimulated and thrombin-stimulated cells. Free t-PA was never observed. Both membrane binding and catalytic activity of thrombin were required since the effects of 1 U/ml thrombin were inhibited by addition 2 U/ml hirudin, which inhibits the membrane binding and catalytic activity of thrombin, and since DFP-inactivated thrombin, which has the ability to bind but which has no enzymatic activity, did not induce t-PA or PAI-1. Gamma thrombin, which does not bind to thrombin receptor, did not increase t-PA and PAI-1 releases. The effects of thrombin were probably mediated by protein kinase C activation since H7, an inhibitor of protein kinases, inhibited significantly thrombin effects on t-PA and PAI-1 production, and since addition of an activator of protein kinase A, 8-bromocyclic AMP (100 microM), induced a significant inhibition of the thrombin effect. The effects of thrombin were also suppressed by 1.25 micrograms/ml alpha amanitin, suggesting a requirement of de novo RNA synthesis

  13. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

    Directory of Open Access Journals (Sweden)

    Villoutreix Bruno O

    2009-11-01

    Full Text Available Abstract Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods.

  14. Homologous desensitization of HEL cell thrombin receptors. Distinguishable roles for proteolysis and phosphorylation.

    Science.gov (United States)

    Brass, L F

    1992-03-25

    Loss of sensitivity to thrombin following an initial response is characteristic of a number of cell types, including platelets. It has recently been proposed that thrombin receptors resemble other G protein-coupled receptors, but that activation involves a novel mechanism in which thrombin cleaves the receptor, exposing a new N terminus that serves as the ligand for the receptor. Based upon this model, we have examined the mechanism of thrombin receptor desensitization by comparing the effects of thrombin with those of a peptide corresponding to the N-terminal sequence of the receptor following proteolysis by thrombin: SFLLRNPNDKYEPF or TRP42/55. Like thrombin, TRP42/55 stimulated pertussis toxin-sensitive inositol 1,4,5-trisphosphate formation, raised cytosolic Ca2+, and inhibited cAMP formation in the megakaryoblastic HEL cell line. Exposure to either thrombin or TRP42/55 desensitized the cells to both, but not to a third agonist, neuropeptide Y. The rate of recovery after desensitization depended upon the order of agonist addition. Resensitization of the cell to thrombin following a brief exposure to thrombin required up to 24 h and could be inhibited with cycloheximide. Resensitization to TRP42/55 after exposure to thrombin, or to thrombin after exposure to TRP42/55, on the other hand, was detectable within 30 min and could be inhibited by serine/threonine phosphatase inhibitors, but not by cycloheximide. Loss of responsiveness to thrombin and TRP42/55 was also observed following addition of the phorbol ester, 12-O-tetradecanoylphorbol-13-acetate (TPA). However, while the protein kinase inhibitor staurosporine completely prevented the desensitization caused by TPA, it had only a limited effect on the desensitization caused by TRP42/55. These results demonstrate that the G protein-mediated effects of thrombin can be reproduced by a receptor-derived peptide and suggest that desensitization occurs by at least two mechanisms. The first, which is seen with thrombin

  15. AG-NGS: a powerful and user-friendly computing application for the semi-automated preparation of next-generation sequencing libraries using open liquid handling platforms.

    Science.gov (United States)

    Callejas, Sergio; Álvarez, Rebeca; Benguria, Alberto; Dopazo, Ana

    2014-01-01

    Next-generation sequencing (NGS) is becoming one of the most widely used technologies in the field of genomics. Library preparation is one of the most critical, hands-on, and time-consuming steps in the NGS workflow. Each library must be prepared in an independent well, increasing the number of hours required for a sequencing run and the risk of human-introduced error. Automation of library preparation is the best option to avoid these problems. With this in mind, we have developed automatic genomics NGS (AG-NGS), a computing application that allows an open liquid handling platform to be transformed into a library preparation station without losing the potential of an open platform. Implementation of AG-NGS does not require programming experience, and the application has also been designed to minimize implementation costs. Automated library preparation with AG-NGS generated high-quality libraries from different samples, demonstrating its efficiency, and all quality control parameters fell within the range of optimal values.

  16. A novel histochemical method for the visualization of thrombin activity in the nervous system.

    Science.gov (United States)

    Bushi, D; Gera, O; Kostenich, G; Shavit-Stein, E; Weiss, R; Chapman, J; Tanne, D

    2016-04-21

    Although thrombin has an important role in both central and peripheral nerve diseases, characterization of the anatomical distribution of its proteolytic activity has been limited by available methods. This study presents the development, challenges, validation and implementation of a novel histochemical method for visualization of thrombin activity in the nervous system. The method is based on the cleavage of the substrate, Boc-Asp(OBzl)-Pro-Arg-4MβNA by thrombin to liberate free 4-methoxy-2-naphthylamine (4MβNA). In the presence of 5-nitrosalicylaldehyde, free 4MβNA is captured, yielding an insoluble yellow fluorescent precipitate which marks the site of thrombin activity. The sensitivity of the method was determined in vitro using known concentrations of thrombin while the specificity was verified using a highly specific thrombin inhibitor. Using this method we determined the spatial distribution of thrombin activity in mouse brain following transient middle cerebral artery occlusion (tMCAo) and in mouse sciatic nerve following crush injury. Fluorescence microscopy revealed well-defined thrombin activity localized to the right ischemic hemisphere in cortical areas and in the striatum compared to negligible thrombin activity contralaterally. The histochemical localization of thrombin activity following tMCAo was in good correlation with the infarct areas per triphenyltetrazolium chloride staining and to thrombin activity measured biochemically in tissue punches (85 ± 35 and 20 ± 3 mU/ml, in the cortical and striatum areas respectively, compared to 7 ± 2 and 13 ± 2 mU/ml, in the corresponding contralateral areas; mean ± SEM; p<0.05). In addition, 24 h following crush injury, focal areas of highly elevated thrombin activity were detected in teased sciatic fibers. This observation was supported by the biochemical assay and western blot technique. The histochemical method developed in this study can serve as an important tool for studying the role of thrombin

  17. Metabolic Plasticity in Resting and Thrombin Activated Platelets

    OpenAIRE

    Ravi, Saranya; Chacko, Balu; Sawada, Hirotaka; Kramer, Philip A.; Johnson, Michelle S.; Benavides, Gloria A.; O’DONNELL, Valerie; Marques, Marisa B.; Darley-Usmar, Victor M.

    2015-01-01

    Platelet thrombus formation includes several integrated processes involving aggregation, secretion of granules, release of arachidonic acid and clot retraction, but it is not clear which metabolic fuels are required to support these events. We hypothesized that there is flexibility in the fuels that can be utilized to serve the energetic and metabolic needs for resting and thrombin-dependent platelet aggregation. Using platelets from healthy human donors, we found that there was a rapid throm...

  18. A signal amplification strategy using the cascade catalysis of gold nanoclusters and glucose dehydrogenase for ultrasensitive detection of thrombin.

    Science.gov (United States)

    Han, Jing; Zhuo, Ying; Chai, Yaqin; Gui, Guofeng; Zhao, Min; Zhu, Qiang; Yuan, Ruo

    2013-12-15

    This work reports a novel signal amplification strategy for ultrasensitive detection of thrombin by cascade catalysis of gold nanoclusters (AuNCs) and glucose dehydrogenase (GDH). Herein, the AuNCs prepared by using polyamidoamine dendrimer as template were constructed not only as nanocarriers for anchoring the large amounts of secondary thrombin aptamers but also as nanocatalysts to catalyze the oxidation of NADH efficiently. Moreover, a large amount of GDH was loaded through the immobilization technology of DNA hybridization and a large amount of toluidine blue (Tb) was intercalated into the DNA grooves via electrostatic interaction. Significantly, the electrochemical signal was greatly enhanced based on cascade catalysis: firstly, GDH catalyzed the oxidation of glucose to gluconolactone with the concomitant generation of NADH in the presence of NAD(+). Then, AuNCs as nanocatalysts could effectively catalyze NADH to produce NAD(+) with the help of Tb as redox probe. Under the optimal conditions, the proposed aptasensor exhibits a linear range of 1.0×10(-14)-5×10(-9) M with a low detection limit of 3.3×10(-15) M for thrombin detection and shows high sensitivity and good specificity. PMID:23850783

  19. Thrombin-cleaved COOH(-) terminal osteopontin peptide binds with cyclophilin C to CD147 in murine breast cancer cells.

    Science.gov (United States)

    Mi, Zhiyong; Oliver, Tim; Guo, Hongtao; Gao, Chengjiang; Kuo, Paul C

    2007-05-01

    Osteopontin is a glycoprotein that has been linked to metastatic function in breast, lung, and prostate cancers. However, the mechanism by which osteopontin acts to induce metastatic properties is largely unknown. One intriguing feature of osteopontin is the presence of a conserved thrombin cleavage site that is COOH-terminal from a well-characterized RGD domain. Although the COOH-terminal fragment may bind to cell surface CD44 receptors, little is known about the COOH-terminal osteopontin fragment. In the current study, we use the murine mammary epithelial tumor cell lines 4T1 and 4T07; these cells are thioguanine-resistant sublines derived from the parental population of 410.4 cells from Balb/cfC3H mice. Using flow cytometry and Forster resonance energy transfer, we show that the COOH-terminal fragment of osteopontin binds with another marker of metastatic function (cyclophilin C or rotamase) to the CD147 cell surface glycoprotein (also known as extracellular matrix metalloproteinase inducer), to activate Akt1/2 and matrix metalloproteinase-2. In in vitro assays, thrombin cleavage of osteopontin to generate short COOH-terminal osteopontin in the presence of cyclophilin C increases migration and invasion of both 4T07 and 4T1 cells. This interaction between osteopontin peptide and cyclophilin C has not been previously described but assigns a heretofore unknown function for the thrombin-cleaved osteopontin COOH-terminal fragment.

  20. Metabolic plasticity in resting and thrombin activated platelets.

    Directory of Open Access Journals (Sweden)

    Saranya Ravi

    Full Text Available Platelet thrombus formation includes several integrated processes involving aggregation, secretion of granules, release of arachidonic acid and clot retraction, but it is not clear which metabolic fuels are required to support these events. We hypothesized that there is flexibility in the fuels that can be utilized to serve the energetic and metabolic needs for resting and thrombin-dependent platelet aggregation. Using platelets from healthy human donors, we found that there was a rapid thrombin-dependent increase in oxidative phosphorylation which required both glutamine and fatty acids but not glucose. Inhibition of fatty acid oxidation or glutamine utilization could be compensated for by increased glycolytic flux. No evidence for significant mitochondrial dysfunction was found, and ATP/ADP ratios were maintained following the addition of thrombin, indicating the presence of functional and active mitochondrial oxidative phosphorylation during the early stages of aggregation. Interestingly, inhibition of fatty acid oxidation and glutaminolysis alone or in combination is not sufficient to prevent platelet aggregation, due to compensation from glycolysis, whereas inhibitors of glycolysis inhibited aggregation approximately 50%. The combined effects of inhibitors of glycolysis and oxidative phosphorylation were synergistic in the inhibition of platelet aggregation. In summary, both glycolysis and oxidative phosphorylation contribute to platelet metabolism in the resting and activated state, with fatty acid oxidation and to a smaller extent glutaminolysis contributing to the increased energy demand.

  1. Stabilization of the E* Form Turns Thrombin into an Anticoagulant

    Energy Technology Data Exchange (ETDEWEB)

    Bah, Alaji; Carrell, Christopher J.; Chen, Zhiwei; Gandhi, Prafull S.; Di Cera, Enrico; (WU-MED)

    2009-07-31

    Previous studies have shown that deletion of nine residues in the autolysis loop of thrombin produces a mutant with an anticoagulant propensity of potential clinical relevance, but the molecular origin of the effect has remained unresolved. The x-ray crystal structure of this mutant solved in the free form at 1.55 {angstrom} resolution reveals an inactive conformation that is practically identical (root mean square deviation of 0.154 {angstrom}) to the recently identified E* form. The side chain of Trp215 collapses into the active site by shifting >10 {angstrom} from its position in the active E form, and the oxyanion hole is disrupted by a flip of the Glu192-Gly193 peptide bond. This finding confirms the existence of the inactive form E* in essentially the same incarnation as first identified in the structure of the thrombin mutant D102N. In addition, it demonstrates that the anticoagulant profile often caused by a mutation of the thrombin scaffold finds its likely molecular origin in the stabilization of the inactive E* form that is selectively shifted to the active E form upon thrombomodulin and protein C binding.

  2. Activation of PAR-1/NADPH Oxidase/ROS Signaling Pathways is Crucial for the Thrombin-Induced sFlt-1 Production in Extravillous Trophoblasts: Possible Involvement in the Pathogenesis of Preeclampsia

    Directory of Open Access Journals (Sweden)

    Qi-tao Huang

    2015-03-01

    Full Text Available Backgrounds/Aims: Preeclampsia was characterized by excessive thrombin generation in placentas and previous researches showed that thrombin could enhance soluble Fms-like tyrosine kinase 1 (sFlt-1 expression in first trimester trophoblasts. However, the detailed mechanism for the sFlt-1 over-production induced by thrombin was largely unknown. The purpose of this study was to explore the possible signaling pathway of thrombin-induced sFlt-1 production in extravillous trophoblasts (EVT. Methods: An EVT cell line (HRT-8/SVneo was treated with various concentrations of thrombin. The mRNA expression and protein secretion of sFlt-1 in EVT were detected with real-time polymerase chain reaction and ELISA, respectively. The levels of intracellular reactive oxygen species (ROS production were determined by DCFH-DA. Results: Exposure of EVT to thrombin induced increased intracellular ROS generation and overexpression of sFlt-1 at both mRNA and protein levels in a dose dependent manner. Short interfering RNA (siRNA directed against PAR-1 or apocynin (an inhibitor of NADPH oxidase could decrease the intracellular ROS generation and subsequently suppressed the production of sFlt-1 at mRNA and protein levels. Conclusions: Our results suggested that thrombin increased sFlt-1 production in EVT via the PAR-1 /NADPH oxidase /ROS signaling pathway. This also highlights the PAR-1 / NADPH oxidase / ROS pathway might be a potential therapeutic target for the prevention of preeclampsia in the future.

  3. Home Automation

    OpenAIRE

    Ahmed, Zeeshan

    2010-01-01

    In this paper I briefly discuss the importance of home automation system. Going in to the details I briefly present a real time designed and implemented software and hardware oriented house automation research project, capable of automating house's electricity and providing a security system to detect the presence of unexpected behavior.

  4. Increased anticoagulant activity of thrombin-binding DNA aptamers by nanoscale organization on DNA nanostructures

    OpenAIRE

    Rangnekar, Abhijit; Zhang, Alex M.; Shiyuan Li, Susan; M. Bompiani, Kristin; Hansen, Majken Nørgaard; Gothelf, Kurt Vesterager; Sullenger, Bruce A; LaBean, Thomas H.

    2012-01-01

    Control over thrombin activity is much desired to regulate blood clotting in surgical and therapeutic situations. Thrombin-binding RNA and DNA aptamers have been used to inhibit thrombin activity and thus the coagulation cascade. Soluble DNA aptamers, as well as two different aptamers tethered by a flexible single-strand linker, have been shown to possess anticoagulant activity. Here, we link multiple aptamers at programmed positions on DNA nanostructures to optimize spacing and orientation o...

  5. Regulation of tissue inflammation by thrombin-activatable carboxypeptidase B (or TAFI)

    OpenAIRE

    Leung, Lawrence L. K.; Myles, Timothy; Nishimura, Toshihiko; Song, Jason J.; Robinson, William H.

    2008-01-01

    Thrombin-activatable procarboxypeptidase B (proCPB or thrombin-activatable fibrinolysis inhibitor or TAFI) is a plasma procarboxypeptidase that is activated by the thrombin-thrombomodulin complex on the vascular endothelial surface. The activated CPB removes the newly exposed carboxyl terminal lysines in the partially digested fibrin clot, diminishes tissue plasminogen activator and plasminogen binding, and protects the clot from premature lysis. We have recently shown that CPB is catalytical...

  6. Arsenic fractionation in agricultural soil using an automated three-step sequential extraction method coupled to hydride generation-atomic fluorescence spectrometry

    International Nuclear Information System (INIS)

    Highlights: • A fully automated flow-based modified-BCR extraction method was developed to evaluate the extractable As of soil. • The MSFIA–HG-AFS system included an UV photo-oxidation step for organic species degradation. • The accuracy and precision of the proposed method were found satisfactory. • The time analysis can be reduced up to eight times by using the proposed flow-based BCR method. • The labile As (F1 + F2) was <50% of total As in soil samples from As-contaminated-mining zones. - Abstract: A fully automated modified three-step BCR flow-through sequential extraction method was developed for the fractionation of the arsenic (As) content from agricultural soil based on a multi-syringe flow injection analysis (MSFIA) system coupled to hydride generation-atomic fluorescence spectrometry (HG-AFS). Critical parameters that affect the performance of the automated system were optimized by exploiting a multivariate approach using a Doehlert design. The validation of the flow-based modified-BCR method was carried out by comparison with the conventional BCR method. Thus, the total As content was determined in the following three fractions: fraction 1 (F1), the acid-soluble or interchangeable fraction; fraction 2 (F2), the reducible fraction; and fraction 3 (F3), the oxidizable fraction. The limits of detection (LOD) were 4.0, 3.4, and 23.6 μg L−1 for F1, F2, and F3, respectively. A wide working concentration range was obtained for the analysis of each fraction, i.e., 0.013–0.800, 0.011–0.900 and 0.079–1.400 mg L−1 for F1, F2, and F3, respectively. The precision of the automated MSFIA–HG-AFS system, expressed as the relative standard deviation (RSD), was evaluated for a 200 μg L−1 As standard solution, and RSD values between 5 and 8% were achieved for the three BCR fractions. The new modified three-step BCR flow-based sequential extraction method was satisfactorily applied for arsenic fractionation in real agricultural soil samples from

  7. Arsenic fractionation in agricultural soil using an automated three-step sequential extraction method coupled to hydride generation-atomic fluorescence spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Rosas-Castor, J.M. [Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Químicas, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, C.P. 66451 Nuevo León (Mexico); Group of Analytical Chemistry, Automation and Environment, University of Balearic Islands, Cra. Valldemossa km 7.5, 07122 Palma de Mallorca (Spain); Portugal, L.; Ferrer, L. [Group of Analytical Chemistry, Automation and Environment, University of Balearic Islands, Cra. Valldemossa km 7.5, 07122 Palma de Mallorca (Spain); Guzmán-Mar, J.L.; Hernández-Ramírez, A. [Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Químicas, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, C.P. 66451 Nuevo León (Mexico); Cerdà, V. [Group of Analytical Chemistry, Automation and Environment, University of Balearic Islands, Cra. Valldemossa km 7.5, 07122 Palma de Mallorca (Spain); Hinojosa-Reyes, L., E-mail: laura.hinojosary@uanl.edu.mx [Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Químicas, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, C.P. 66451 Nuevo León (Mexico)

    2015-05-18

    Highlights: • A fully automated flow-based modified-BCR extraction method was developed to evaluate the extractable As of soil. • The MSFIA–HG-AFS system included an UV photo-oxidation step for organic species degradation. • The accuracy and precision of the proposed method were found satisfactory. • The time analysis can be reduced up to eight times by using the proposed flow-based BCR method. • The labile As (F1 + F2) was <50% of total As in soil samples from As-contaminated-mining zones. - Abstract: A fully automated modified three-step BCR flow-through sequential extraction method was developed for the fractionation of the arsenic (As) content from agricultural soil based on a multi-syringe flow injection analysis (MSFIA) system coupled to hydride generation-atomic fluorescence spectrometry (HG-AFS). Critical parameters that affect the performance of the automated system were optimized by exploiting a multivariate approach using a Doehlert design. The validation of the flow-based modified-BCR method was carried out by comparison with the conventional BCR method. Thus, the total As content was determined in the following three fractions: fraction 1 (F1), the acid-soluble or interchangeable fraction; fraction 2 (F2), the reducible fraction; and fraction 3 (F3), the oxidizable fraction. The limits of detection (LOD) were 4.0, 3.4, and 23.6 μg L{sup −1} for F1, F2, and F3, respectively. A wide working concentration range was obtained for the analysis of each fraction, i.e., 0.013–0.800, 0.011–0.900 and 0.079–1.400 mg L{sup −1} for F1, F2, and F3, respectively. The precision of the automated MSFIA–HG-AFS system, expressed as the relative standard deviation (RSD), was evaluated for a 200 μg L{sup −1} As standard solution, and RSD values between 5 and 8% were achieved for the three BCR fractions. The new modified three-step BCR flow-based sequential extraction method was satisfactorily applied for arsenic fractionation in real agricultural

  8. Binding modes of thrombin binding aptamers investigated by simulations and experiments

    Science.gov (United States)

    Trapaidze, A.; Bancaud, A.; Brut, M.

    2015-01-01

    Thrombin binding aptamers HD1 and HD22 are the most studied aptamers, both for therapeutic and sensing purposes. Yet, there is still no commercialized aptamer-based sensor device for thrombin detection, suggesting that the binding modes of these aptamers remain to be precisely described. Here, we investigate thrombin-aptamer interactions with molecular dynamics simulations, and show that the different solved structures of HD1-thrombin complex are energetically similar and consequently possibly co-existing. Conversely, HD22 folding is much more stable, and its binding energy with thrombin is significantly larger than that of HD1 complexes. These results are confronted to experiments, which consist in monitoring aggregation of aptamer-functionalized gold nanoparticles triggered by thrombin. HD1 alone, but not HD22, can trigger aggregation, meaning that this aptamer has multiple sites of interactions with thrombin. Furthermore, pre-incubation of HD22 with thrombin impedes HD1 aggregation, suggesting that HD1 and HD22 have competing affinities for the same binding site. Altogether, this study shows that the characterization of aptamer-thrombin interactions by structural and kinetic experiments joined to simulations is necessary for the development of biosensors.

  9. Percutaneous Ultrasound-Guided Thrombin Injection in Iatrogenic Arterial Pseudoaneurysms: Effectiveness and Complications

    Energy Technology Data Exchange (ETDEWEB)

    Koh, Young Hwan [Boramae Hospital, Seoul (Korea, Republic of); Kim, Hak Soo; Kim, Hyung Sik; Min, Seung Kee [Gachon Medical School, Incheon (Korea, Republic of)

    2005-09-15

    To evaluate and describe the efficacy and side effects of a percutaneous thrombin injection under ultrasonography guidance for the treatment of iatrogenic pseudo aneurysms Eighteen consecutive iatrogenic pseudo aneurysm cases were treated with a thrombin injection. The thrombin was injected into the pseudo aneurysm cavity using a 22-gauge needle under ultrasonographic guidance. The causes of the pseudo aneurysms are as follows: post coronary angiography (9 cases), percutaneous coronary balloon angioplasty (5 cases), cerebral angiography (1 case), transhepatic chemo embolization (1 case), percutaneous trans femoral arterial stent insertion (1 case) and bone marrow aspiration for a marrow transplant (1 case). Only one case required a secondary thrombin injection due to recurrent flow in the pseudo aneurysm lumen, which was detected at the follow up Doppler ultrasound. Other seventeen cases were successfully treated on the first trial. There were no technical failures or complication related to the procedure. The average amount of thrombin injected was 733 IU. Nine out of 18 treated patients (50%) showed mild reactions to the thrombin including mild fever (4 cases), chilling sensation (3 cases), a chilling sensation with mild dyspnea (1 case), mild chest discomfort (1 case) after the thrombin injection. All these side effects were transient and improved several hours later. All the iatrogenic pseudo aneurysms were treated successfully with an ultrasound-guided percutaneous thrombin injection. There was a high rate of hypersensitivity to the bovine thrombin, which precaution should be taken to prevent more serious side effects

  10. Active Data Archive Product Tracking and Automated SPASE Metadata Generation in Support of the Heliophysics Data Environment

    Science.gov (United States)

    Bargatze, L. F.

    2013-12-01

    The understanding of Solar interaction with the Earth and other bodies in the solar system is a primary goal of Heliophysics as outlined in the NASA Science Mission Directive Science Plan. Heliophysics researchers need access to a vast collection of satellite and ground-based observations coupled with numerical simulation data to study complex processes some of which, as in the case of space weather, pose danger to physical elements of modern society. The infrastructure of the Heliophysics data environment plays a vital role in furthering the understanding of space physics processes by providing researchers with means for data discovery and access. The Heliophysics data environment is highly dynamic with thousands of data products involved. Access to data is facilitated via the Heliophysics Virtual Observatories (VxO) but routine access is possible only if the VxO SPASE metadata repositories contain accurate and up to date information. The Heliophysics Data Consortium has the stated goal of providing routine access to all relevant data products inclusively. Currently, only a small fraction of the data products relevant to Heliophysics studies have been described and registered in a VxO repository. And, for those products that have been described in SPASE, there is a significant time lag from when new data becomes available to when VxO metadata are updated to provide access. It is possible to utilize automated tools to shorten the response time of VxO data product registration via active data archive product tracking. Such a systematic approach is designed to address data access reliability by embracing the highly dynamic nature of the Heliophysics data environment. For example, the CDAWEB data repository located at the NASA Space Science Physics Data facility maintains logs of the data products served to the community. These files include two that pertain to full directory list information, updated daily, and a set of SHA1SUM hash value files, one for each of more

  11. Binding of thrombin-activated platelets to a fibrin scaffold through α(IIbβ₃ evokes phosphatidylserine exposure on their cell surface.

    Directory of Open Access Journals (Sweden)

    Tomasz Brzoska

    Full Text Available Recently, by employing intra-vital confocal microscopy, we demonstrated that platelets expose phosphatidylserine (PS and fibrin accumulate only in the center of the thrombus but not in its periphery. To address the question how exposure of platelet anionic phospholipids is regulated within the thrombus, an in-vitro experiment using diluted platelet-rich plasma was employed, in which the fibrin network was formed in the presence of platelets, and PS exposure on the platelet surface was analyzed using Confocal Laser Scanning Microscopy. Almost all platelets exposed PS after treatment with tissue factor, thrombin or ionomycin. Argatroban abrogated fibrin network formation in all samples, however, platelet PS exposure was inhibited only in tissue factor- and thrombin-treated samples but not in ionomycin-treated samples. FK633, an α(IIbβ₃ antagonist, and cytochalasin B impaired platelet binding to the fibrin scaffold and significantly reduced PS exposure evoked by thrombin. Gly-Pro-Arg-Pro amide abrogated not only fibrin network formation, but also PS exposure on platelets without suppressing platelet binding to fibrin/fibrinogen. These results suggest that outside-in signals in platelets generated by their binding to the rigid fibrin network are essential for PS exposure after thrombin treatment.

  12. Automated family-based naming of small RNAs for next generation sequencing data using a modified MD5-digest algorithm

    OpenAIRE

    Liu, Guodong; Li, Zhihua; Lin, Yuefeng; John, Bino

    2012-01-01

    We developed NameMyGene, a web tool and a stand alone program to easily generate putative family-based names for small RNA sequences so that laboratories can easily organize, analyze, and observe patterns from, the massive amount of data generated by next-generation sequencers. NameMyGene, also applicable to other emerging methods such as RNA-Seq, and Chip-Seq, solely uses the input small RNA sequence and does not require any additional data such as other sequence data sets. The web server an...

  13. Using Automated Processes to Generate Test Items And Their Associated Solutions and Rationales to Support Formative Feedback

    Directory of Open Access Journals (Sweden)

    Mark Gierl

    2015-08-01

    Full Text Available Automatic item generation is the process of using item models to produce assessment tasks using computer technology. An item model is similar to a template that highlights the elements in the task that must be manipulated to produce new items. The purpose of our study is to describe an innovative method for generating large numbers of diverse and heterogeneous items along with their solutions and associated rationales to support formative feedback. We demonstrate the method by generating items in two diverse content areas, mathematics and nonverbal reasoning

  14. DEFINITION OF A SEMANTIC PLATAFORM FOR AUTOMATED CODE GENERATION BASED ON UML CLASS DIAGRAMS AND DSL SEMANTIC ANNOTATIONS

    Directory of Open Access Journals (Sweden)

    ANDRÉS MUÑETÓN

    2012-01-01

    Full Text Available En este trabajo se propone una plataforma semántica de servicios que implementan los pasos de un método para la generación automática de código. El método se basa en información semántica y en MDA (model-driven architecture. La generación de código se logra relacionando semánticamente operaciones en diagramas de clases en UML (unified modeling language con operaciones implementadas. La relación entre operaciones se hace consultando operaciones implementadas que tengan la misma postcondición de la operación bajo implementación. El código resultante es una secuencia de invocaciones a operaciones implementadas que, en conjunto, alcancen la postcondición de la operación bajo implementación. La semántica se especifica mediante un DSL (domain-specific language, también definido en este artículo. Los servicios de la plataforma y el método se prueban mediante un caso de estudio.

  15. Interaction of C1 inhibitor with thrombin on the endothelial surface.

    Science.gov (United States)

    Caccia, Sonia; Castelli, Roberto; Maiocchi, Diana; Bergamaschini, Luigi; Cugno, Massimo

    2011-10-01

    Thrombin, the central bioregulatory enzyme of haemostasis, also has a potent vasopermeability effect on the surface of endothelial cells, and has therefore been considered a major link between the activation of the coagulation pathway and inflammation. C1 inhibitor inhibits thrombin with a low second-order rate constant that can be increased by heparin. The aim of this study was to investigate whether the C1 inhibitor-induced inhibition of thrombin is potentiated on the endothelial surface. The interaction of C1 inhibitor and thrombin was evaluated in an in-vitro system of human umbilical vein endothelial cells (HUVECs) to which purified C1 inhibitor and thrombin have been added. The role of heparins and selectins has been tested by adding heparinase and Mab to selectins. Kinetic analysis under pseudo-first-order conditions showed that the inhibitory effect of C1 inhibitor on thrombin is greater on the surface of endothelial cells. After incubating nanomolar concentrations of thrombin and micromolar concentrations of C1 inhibitor in a purified system, thrombin activity remained significant, but was almost totally suppressed in the presence of HUVECs. The abolition of such suppression by heparinase and Mab to selectins supports the involvement of heparin and selectins in C1 inhibitor-thrombin interaction. Furthermore, the second-order rate constant was 25 ± 3 /s per mol/l in our purified system, but increased to 100 ± 9 /s per mol/l in the presence of HUVECs. Our results indicate that C1 inhibitor can inhibit thrombin activity on vascular endothelium via binding to selectins and potentiation by heparins. This may contribute to the modulation of thrombin activity on vasopermeability and on coagulation especially when the major natural anticoagulant pathways are impaired. PMID:21959589

  16. Rule-based programming and strategies for automated generation of detailed kinetic models for gas phase combustion of polycyclic hydrocarbon molecules; Programmation par regles et strategies pour la generation automatique de mecanismes de combustion d'hydrocarbures polycycliques

    Energy Technology Data Exchange (ETDEWEB)

    Ibanescu, L.

    2004-06-15

    The primary objective of this thesis is to explore the approach of using rule-based systems and strategies, for a complex problem of chemical kinetic: the automated generation of reaction mechanisms. The chemical reactions are naturally expressed as conditional rewriting rules. The control of the chemical reactions chaining is easy to describe using a strategies language, such as the one of the ELAN system, developed in the Protheo team. The thesis presents the basic concepts of the chemical kinetics, the chemical and computational problems related to the conception and validation of a reaction mechanism, and gives a general structure for the generator of reaction mechanisms called GasEI. Our research focuses on the primary mechanism generator. We give solutions for encoding the chemical species, the reactions and their chaining, and we present the prototype developed in ELAN. The representation of the chemical species uses the notion of molecular graphs, encoded by a term structure called GasEI terms. The chemical reactions are expressed by rewriting rules on molecular graphs, encoded by a set of conditional rewriting rules on GasEI terms. The strategies language of the ELAN system is used to express the reactions chaining in the primary mechanism generator. This approach is illustrated by coding ten generic reactions of the oxidizing pyrolysis. Qualitative chemical validations of the prototype show that our approach gives, for acyclic molecules, the same results as the existing mechanism generators, and for polycyclic molecules produces original results.

  17. Application of Discrete Control System in Automation of 200 MW Power Generating Set%分散控制系统在200 MW机组自动化中的应用

    Institute of Scientific and Technical Information of China (English)

    李维群; 陈勇; 赖建明; 王志兵; 孙德利

    2000-01-01

    Justifies the automation of 200 MW power generating set, illustrates the automation scheme for 200 MW power generating set, its technical specisl features, technical problems to be solved, operational efficiency with typical examples, and suggests further actions for future automation.%阐述200 MW机组自动化改造的必要性,通过实例介绍了200 MW机组自动化改造的技术方案、技术特点、解决的技术问题、运行效果以及对今后自动化改造的一些探讨性建议。

  18. iGen 0.1: the automated generation of a parameterisation of entrainment in marine stratocumulus

    Science.gov (United States)

    Tang, D. F.; Dobbie, S.

    2011-09-01

    In a previous paper we described a new technique for automatically generating parameterisations using a program called iGen. iGen generates parameterisations by analysing the source code of a~high resolution model that resolves the physics to be parameterised. In order to demonstrate that this technique scales up to deal with models of realistic complexity we have used iGen to generate a parameterisation of entrainment in marine stratocumulus. We describe how iGen was used to analyse the source code of an eddy resolving model (ERM) and generate a parameterisation of entrainment velocity in marine stratocumulus in terms of the large-scale state of the boundary layer. The parameterisation was tested against results from the DYCOMS-II intercomparison of ERM models and iGen's parameterisation of mean entrainment velocity was found to be 5.27 × 10-3 ± 0.62 × 10-3 m s-1 compared to 5.2 × 10-3 ± 0.8 × 10-3 m s-1 for the DYCOMS-II ensemble of large eddy simulation (LES) models.

  19. Thrombin stimulates VSMC proliferation through an EGFR-dependent pathway: involvement of MMP-2.

    Science.gov (United States)

    Smiljanic, Katarina; Obradovic, Milan; Jovanovic, Aleksandra; Djordjevic, Jelena; Dobutovic, Branislava; Jevremovic, Danimir; Marche, Pierre; Isenovic, Esma R

    2014-11-01

    In this study, the role of epidermal growth factor receptor (EGFR), extracellular signal-regulated kinase (ERK1/2), heparin-binding EGF-like growth factor (HB-EGF), general metalloproteinases, matrix metalloproteinases-2 (MMP-2) in mediating the mitogenic action of thrombin in rat vascular smooth muscle cells (VSMC) was investigated. The incubation of rat VSMC with thrombin (1 U/ml) for 5 min resulted in significant (p EGFR phosphorylation by 8.5 ± 1.3-fold (p EGFR tyrosine kinase irreversible inhibitor, 10 µM PD169540 (PD), and 20 µM anti-HB-EGF antibody significantly reduced thrombin-stimulated EGFR and ERK1/2 phosphorylation by 81, 72 % and by 48 and 61 %, respectively. Furthermore, the same pretreatments with PD or anti-HB-EGF antibody reduced thrombin-induced VSMC proliferation by 44 and 45 %, respectively. In addition, 30-min pretreatments with 10 µM specific MMP-2 inhibitor significantly reduced thrombin-stimulated phosphorylation of both EGFR and ERK1/2 by 25 %. Moreover, the same pretreatment with MMP-2 inhibitor reduced thrombin-induced VSMC proliferation by 45 %. These results show that the thrombin-induced DNA synthesis correlates with the level of ERK1/2 activation rather than EGFR activation. These results further suggest that thrombin acts through EGFR and ERK 1/2 signaling pathways involving MMP-2 to upregulate proliferation of VSMC.

  20. Thrombin-specific inactivation of endothelial cell derived plasminogen activator

    International Nuclear Information System (INIS)

    Although thrombin (T) has diverse functions in the overall hemostatic mechanism, relatively little is known about its direct effect on components of the fibrinolytic enzyme system. The authors have investigated the interaction of T with plasminogen activators (PA) derived from bovine aortic endothelial cells (EC) in culture (2-5th passage, preconfluent monolayers). Varying concentrations of purified bovine or human thrombin were added to EC-conditioned media (CM). CM + T mixtures were assayed at various times for PA activity using purified plasminogen and a sensitive 125I-fibrinogenolytic or caseinolytic assay. T (5 nM), but not plasmin or trypsin at equivalent concentrations, resulted in a time-dependent inhibition of the PA activity in CM. T had no effect on the PA activity of urokinase, streptokinase or preformed plasmin. The ability of T to inactivate the EC-derived PA was abolished by prior treatment of T with active site-directed reagents. SDS-PAGE and zymography with copolymerized fibrinogen and plasminogen revealed further specificity in that only one of the multiple-molecular weight forms of PA present in EC-CM was inactivated by T. The authors conclude that in a highly specific fashion, T inactivates the predominant PA present in EC-CM by limited proteolysis. Thus, another potentially important function of T is suggested which may have particular significance in the temporal regulation of coagulation and fibrinolysis at the blood-endothelium interface

  1. Photoactivation by visible light of CdTe quantum dots for inline generation of reactive oxygen species in an automated multipumping flow system

    Energy Technology Data Exchange (ETDEWEB)

    Ribeiro, David S.M.; Frigerio, Christian; Santos, Joao L.M. [Requimte, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira no. 228, 4050-313 Porto (Portugal); Prior, Joao A.V., E-mail: joaoavp@ff.up.pt [Requimte, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira no. 228, 4050-313 Porto (Portugal)

    2012-07-20

    Highlights: Black-Right-Pointing-Pointer CdTe quantum dots generate free radical species upon exposure to visible radiation. Black-Right-Pointing-Pointer A high power visible LED lamp was used as photoirradiation element. Black-Right-Pointing-Pointer The laboratory-made LED photocatalytic unit was implemented inline in a MPFS. Black-Right-Pointing-Pointer Free radical species oxidize luminol producing a strong chemiluminescence emission. Black-Right-Pointing-Pointer Epinephrine scavenges free radical species quenching chemiluminescence emission. - Abstract: Quantum dots (QD) are semiconductor nanocrystals able to generate free radical species upon exposure to an electromagnetic radiation, usually in the ultraviolet wavelength range. In this work, CdTe QD were used as highly reactive oxygen species (ROS) generators for the control of pharmaceutical formulations containing epinephrine. The developed approach was based on the chemiluminometric monitoring of the quenching effect of epinephrine on the oxidation of luminol by the produced ROS. Due to the relatively low energy band-gap of this chalcogenide a high power visible light emitting diode (LED) lamp was used as photoirradiation element and assembled in a laboratory-made photocatalytic unit. Owing to the very short lifetime of ROS and to ensure both reproducible generation and time-controlled reaction implementation and development, all reactional processes were implemented inline by using an automated multipumping micro-flow system. A linear working range for epinephrine concentration of up to 2.28 Multiplication-Sign 10{sup -6} mol L{sup -1} (r = 0.9953; n = 5) was verified. The determination rate was about 79 determinations per hour and the detection limit was about 8.69 Multiplication-Sign 10{sup -8} mol L{sup -1}. The results obtained in the analysis of epinephrine pharmaceutical formulations by using the proposed methodology were in good agreement with those furnished by the reference procedure, with

  2. The thrombin E192Q-BPTI complex reveals gross structural rearrangements: implications for the interaction with antithrombin and thrombomodulin.

    OpenAIRE

    van de Locht, A; Bode, W.; Huber, R; Le Bonniec, B F; Stone, S R; Esmon, C T; Stubbs, M T

    1997-01-01

    Previous crystal structures of thrombin indicate that the 60-insertion loop is a rigid moiety that partially occludes the active site, suggesting that this structural feature plays a decisive role in restricting thrombin's specificity. This restricted specificity is typified by the experimental observation that thrombin is not inhibited by micromolar concentrations of basic pancreatic trypsin inhibitor (BPTI). Surprisingly, a single atom mutation in thrombin (E192Q) results in a 10(-8) M affi...

  3. Batroxobin binds fibrin with higher affinity and promotes clot expansion to a greater extent than thrombin.

    Science.gov (United States)

    Vu, Trang T; Stafford, Alan R; Leslie, Beverly A; Kim, Paul Y; Fredenburgh, James C; Weitz, Jeffrey I

    2013-06-01

    Batroxobin is a thrombin-like serine protease from the venom of Bothrops atrox moojeni that clots fibrinogen. In contrast to thrombin, which releases fibrinopeptide A and B from the NH2-terminal domains of the Aα- and Bβ-chains of fibrinogen, respectively, batroxobin only releases fibrinopeptide A. Because the mechanism responsible for these differences is unknown, we compared the interactions of batroxobin and thrombin with the predominant γA/γA isoform of fibrin(ogen) and the γA/γ' variant with an extended γ-chain. Thrombin binds to the γ'-chain and forms a higher affinity interaction with γA/γ'-fibrin(ogen) than γA/γA-fibrin(ogen). In contrast, batroxobin binds both fibrin(ogen) isoforms with similar high affinity (Kd values of about 0.5 μM) even though it does not interact with the γ'-chain. The batroxobin-binding sites on fibrin(ogen) only partially overlap with those of thrombin because thrombin attenuates, but does not abrogate, the interaction of γA/γA-fibrinogen with batroxobin. Furthermore, although both thrombin and batroxobin bind to the central E-region of fibrinogen with a Kd value of 2-5 μM, the α(17-51) and Bβ(1-42) regions bind thrombin but not batroxobin. Once bound to fibrin, the capacity of batroxobin to promote fibrin accretion is 18-fold greater than that of thrombin, a finding that may explain the microvascular thrombosis that complicates envenomation by B. atrox moojeni. Therefore, batroxobin binds fibrin(ogen) in a manner distinct from thrombin, which may contribute to its higher affinity interaction, selective fibrinopeptide A release, and prothrombotic properties. PMID:23612970

  4. Library Automation

    OpenAIRE

    Dhakne, B. N.; Giri, V. V; Waghmode, S. S.

    2010-01-01

    New technologies library provides several new materials, media and mode of storing and communicating the information. Library Automation reduces the drudgery of repeated manual efforts in library routine. By use of library automation collection, Storage, Administration, Processing, Preservation and communication etc.

  5. Automated generation of IMRT treatment plans for prostate cancer patients with metal hip prostheses: Comparison of different planning strategies

    Energy Technology Data Exchange (ETDEWEB)

    Voet, Peter W. J.; Dirkx, Maarten L. P.; Breedveld, Sebastiaan; Heijmen, Ben J. M. [Erasmus MC - Daniel den Hoed Cancer Center, Department of Radiation Oncology, Groene Hilledijk 301, 3075EA Rotterdam (Netherlands)

    2013-07-15

    Purpose: To compare IMRT planning strategies for prostate cancer patients with metal hip prostheses.Methods: All plans were generated fully automatically (i.e., no human trial-and-error interactions) using iCycle, the authors' in-house developed algorithm for multicriterial selection of beam angles and optimization of fluence profiles, allowing objective comparison of planning strategies. For 18 prostate cancer patients (eight with bilateral hip prostheses, ten with a right-sided unilateral prosthesis), two planning strategies were evaluated: (i) full exclusion of beams containing beamlets that would deliver dose to the target after passing a prosthesis (IMRT{sub remove}) and (ii) exclusion of those beamlets only (IMRT{sub cut}). Plans with optimized coplanar and noncoplanar beam arrangements were generated. Differences in PTV coverage and sparing of organs at risk (OARs) were quantified. The impact of beam number on plan quality was evaluated.Results: Especially for patients with bilateral hip prostheses, IMRT{sub cut} significantly improved rectum and bladder sparing compared to IMRT{sub remove}. For 9-beam coplanar plans, rectum V{sub 60Gy} reduced by 17.5%{+-} 15.0% (maximum 37.4%, p= 0.036) and rectum D{sub mean} by 9.4%{+-} 7.8% (maximum 19.8%, p= 0.036). Further improvements in OAR sparing were achievable by using noncoplanar beam setups, reducing rectum V{sub 60Gy} by another 4.6%{+-} 4.9% (p= 0.012) for noncoplanar 9-beam IMRT{sub cut} plans. Large reductions in rectum dose delivery were also observed when increasing the number of beam directions in the plans. For bilateral implants, the rectum V{sub 60Gy} was 37.3%{+-} 12.1% for coplanar 7-beam plans and reduced on average by 13.5% (maximum 30.1%, p= 0.012) for 15 directions.Conclusions: iCycle was able to automatically generate high quality plans for prostate cancer patients with prostheses. Excluding only beamlets that passed through the prostheses (IMRT{sub cut} strategy) significantly improved

  6. An efficient approach to bioconversion kinetic model generation based on automated microscale experimentation integrated with model driven experimental design

    DEFF Research Database (Denmark)

    Chen, B. H.; Micheletti, M.; Baganz, F.;

    2009-01-01

    design. It incorporates a model driven approach to the experimental design that minimises the number of experiments to be performed, while still generating accurate values of kinetic parameters. The approach has been illustrated with the transketolase mediated asymmetric synthesis of L...... experimental design.]it comparison with conventional methodology, the modelling approach enabled a nearly 4-fold decrease in the number of experiments while the microwell experimentation enabled a 45-fold decrease in material requirements and a significant increase in experimental throughput. The approach......Reliable models of enzyme kinetics are required for the effective design of bioconversion processes. Kinetic expressions of the enzyme-catalysed reaction rate however, are frequently complex and establishing accurate values of kinetic parameters normally requires a large number of experiments...

  7. Targeted virus detection in next-generation sequencing data using an automated e-probe based approach.

    Science.gov (United States)

    Visser, Marike; Burger, Johan T; Maree, Hans J

    2016-08-01

    The use of next-generation sequencing for plant virus detection is rapidly expanding, necessitating the development of bioinformatic pipelines to support analysis of these large datasets. Pipelines need to be easy implementable to mitigate potential insufficient computational infrastructure and/or skills. In this study user-friendly software was developed for the targeted detection of plant viruses based on e-probes. It can be used for both custom e-probe design, as well as screening preloaded probes against raw NGS data for virus detection. The pipeline was compared to de novo assembly-based virus detection in grapevine and produced comparable results, requiring less time and computational resources. The software, named Truffle, is available for the design and screening of e-probes tailored for user-specific virus species and data, along with preloaded probe-sets for grapevine virus detection. PMID:27209446

  8. Prospective evaluation of hemostatic system activation and thrombin potential in healthy pregnant women with and without factor V Leiden.

    Science.gov (United States)

    Eichinger, S; Weltermann, A; Philipp, K; Hafner, E; Kaider, A; Kittl, E M; Brenner, B; Mannhalter, C; Lechner, K; Kyrle, P A

    1999-10-01

    Normal pregnancy is associated with alterations of the hemostatic system towards a hypercoagulable state and an increased risk of venous thromboembolism. The risk of venous thrombosis is higher in pregnant women with factor V Leiden (FVL) than in those with wildtype factor V. Routine laboratory assays are not useful to detect hypercoagulable conditions. A prospective and systematic evaluation of hemostatic system activation in women with and without FVL during an uncomplicated pregnancy employing more sensitive markers of hypercoagulability, such as prothrombin fragment 1+2 (F1+2), thrombin-antithrombin complex (TAT), D-Dimer, or the endogenous thrombin potential (ETP), an indicator of the plasma's potential to generate thrombin, has not been performed. We prospectively followed 113 pregnant women with (n = 11) and without (n = 102) FVL and measured F1+2. TAT, D-Dimer and the ETP at the 12th, 22nd and 34th gestational week as well as 3 months after delivery (baseline) in each subject. None of the women developed clinical signs of venous thromboembolism during pregnancy or postpartum. Pregnant women with and without FVL exhibited substantial activation of the coagulation and fibrinolytic system as indicated by a gradual increase of F1+2, TAT and D-Dimer throughout uncomplicated pregnancy up to levels similar to those found in acute thromboembolic events (p < 0.0001 by analysis of variance for each parameters). Levels of F1+2 and TAT were comparable between women with and without FVL, but levels of D-Dimer were significantly higher in women with FVL than in those without the mutation (p = 0.0005). The ETP remained unchanged in both women with and without FVL at all timepoints. Our data demonstrate a substantial coagulation and fibrinolytic system activation in healthy women with and without FVL during uncomplicated pregnancy. An elevated F1+2, TAT or D-Dimer level during pregnancy is not necessarily indicative for an acute thromboembolic event. The normal ETP in both

  9. Automated generation of a World Wide Web-based data entry and check program for medical applications.

    Science.gov (United States)

    Kiuchi, T; Kaihara, S

    1997-02-01

    The World Wide Web-based form is a promising method for the construction of an on-line data collection system for clinical and epidemiological research. It is, however, laborious to prepare a common gateway interface (CGI) program for each project, which the World Wide Web server needs to handle the submitted data. In medicine, it is even more laborious because the CGI program must check deficits, type, ranges, and logical errors (bad combination of data) of entered data for quality assurance as well as data length and meta-characters of the entered data to enhance the security of the server. We have extended the specification of the hypertext markup language (HTML) form to accommodate information necessary for such data checking and we have developed software named AUTOFORM for this purpose. The software automatically analyzes the extended HTML form and generates the corresponding ordinary HTML form, 'Makefile', and C source of CGI programs. The resultant CGI program checks the entered data through the HTML form, records them in a computer, and returns them to the end-user. AUTOFORM drastically reduces the burden of development of the World Wide Web-based data entry system and allows the CGI programs to be more securely and reliably prepared than had they been written from scratch.

  10. Automated generation of a World Wide Web-based data entry and check program for medical applications.

    Science.gov (United States)

    Kiuchi, T; Kaihara, S

    1997-02-01

    The World Wide Web-based form is a promising method for the construction of an on-line data collection system for clinical and epidemiological research. It is, however, laborious to prepare a common gateway interface (CGI) program for each project, which the World Wide Web server needs to handle the submitted data. In medicine, it is even more laborious because the CGI program must check deficits, type, ranges, and logical errors (bad combination of data) of entered data for quality assurance as well as data length and meta-characters of the entered data to enhance the security of the server. We have extended the specification of the hypertext markup language (HTML) form to accommodate information necessary for such data checking and we have developed software named AUTOFORM for this purpose. The software automatically analyzes the extended HTML form and generates the corresponding ordinary HTML form, 'Makefile', and C source of CGI programs. The resultant CGI program checks the entered data through the HTML form, records them in a computer, and returns them to the end-user. AUTOFORM drastically reduces the burden of development of the World Wide Web-based data entry system and allows the CGI programs to be more securely and reliably prepared than had they been written from scratch. PMID:9034677

  11. ESBL Detection: Comparison of a Commercially Available Chromogenic Test for Third Generation Cephalosporine Resistance and Automated Susceptibility Testing in Enterobactericeae

    Science.gov (United States)

    El-Jade, Mohamed Ramadan; Parcina, Marijo; Schmithausen, Ricarda Maria; Stein, Christoph; Meilaender, Alina; Hoerauf, Achim; Molitor, Ernst

    2016-01-01

    Rapid detection and reporting of third generation cephalosporine resistance (3GC-R) and of extended spectrum betalactamases in Enterobacteriaceae (ESBL-E) is a diagnostic and therapeutic priority to avoid inefficacy of the initial antibiotic regimen. In this study we evaluated a commercially available chromogenic screen for 3GC-R as a predictive and/or confirmatory test for ESBL and AmpC activity in clinical and veterinary Enterobacteriaceae isolates. The test was highly reliable in the prediction of cefotaxime and cefpodoxime resistance, but there was no correlation with ceftazidime and piperacillin/tazobactam minimal inhibitory concentrations. All human and porcine ESBL-E tested were detected with exception of one genetically positive but phenotypically negative isolate. By contrast, AmpC detection rates lay below 30%. Notably, exclusion of piperacillin/tazobactam resistant, 3GC susceptible K1+ Klebsiella isolates increased the sensitivity and specificity of the test for ESBL detection. Our data further imply that in regions with low prevalence of AmpC and K1 positive E. coli strains chromogenic testing for 3GC-R can substitute for more time consuming ESBL confirmative testing in E. coli isolates tested positive by Phoenix or VITEK2 ESBL screen. We, therefore, suggest a diagnostic algorithm that distinguishes 3GC-R screening from primary culture and species-dependent confirmatory ESBL testing by βLACTATM and discuss the implications of MIC distribution results on the choice of antibiotic regimen. PMID:27494134

  12. Process automation

    International Nuclear Information System (INIS)

    Process automation technology has been pursued in the chemical processing industries and to a very limited extent in nuclear fuel reprocessing. Its effective use has been restricted in the past by the lack of diverse and reliable process instrumentation and the unavailability of sophisticated software designed for process control. The Integrated Equipment Test (IET) facility was developed by the Consolidated Fuel Reprocessing Program (CFRP) in part to demonstrate new concepts for control of advanced nuclear fuel reprocessing plants. A demonstration of fuel reprocessing equipment automation using advanced instrumentation and a modern, microprocessor-based control system is nearing completion in the facility. This facility provides for the synergistic testing of all chemical process features of a prototypical fuel reprocessing plant that can be attained with unirradiated uranium-bearing feed materials. The unique equipment and mission of the IET facility make it an ideal test bed for automation studies. This effort will provide for the demonstration of the plant automation concept and for the development of techniques for similar applications in a full-scale plant. A set of preliminary recommendations for implementing process automation has been compiled. Some of these concepts are not generally recognized or accepted. The automation work now under way in the IET facility should be useful to others in helping avoid costly mistakes because of the underutilization or misapplication of process automation. 6 figs

  13. Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin.

    Science.gov (United States)

    Pozzi, Nicola; Zerbetto, Mirco; Acquasaliente, Laura; Tescari, Simone; Frezzato, Diego; Polimeno, Antonino; Gohara, David W; Di Cera, Enrico; De Filippis, Vincenzo

    2016-07-19

    Thrombin exists as an ensemble of active (E) and inactive (E*) conformations that differ in their accessibility to the active site. Here we show that redistribution of the E*-E equilibrium can be achieved by perturbing the electrostatic properties of the enzyme. Removal of the negative charge of the catalytic Asp102 or Asp189 in the primary specificity site destabilizes the E form and causes a shift in the 215-217 segment that compromises substrate entrance. Solution studies and existing structures of D102N document stabilization of the E* form. A new high-resolution structure of D189A also reveals the mutant in the collapsed E* form. These findings establish a new paradigm for the control of the E*-E equilibrium in the trypsin fold. PMID:27347732

  14. Thrombostatin FM compounds: direct thrombin inhibitors - mechanism of action in vitro and in vivo

    Energy Technology Data Exchange (ETDEWEB)

    Nieman, M T; Burke, F; Warnock, M; Zhou, Y; Sweigart, J; Chen, A; Ricketts, D; Lucchesi, B R; Chen, Z; Cera, E Di; Hilfinger, J; Kim, J S; Mosberg, H I; Schmaier, A H [Case Western; (Michigan); (TSRL); (WU-MED)

    2008-04-29

    Novel pentapeptides called Thrombostatin FM compounds consisting mostly of D-isomers and unusual amino acids were prepared based upon the stable angiotensin converting enzyme breakdown product of bradykinin - RPPGF. These peptides are direct thrombin inhibitors prolonging the thrombin clotting time, activated partial thromboplastin time, and prothrombin time at ≥0.78, 1.6, and 1.6 μm, respectively. They competitively inhibit α-thrombin-induced cleavage of a chromogenic substrate at 4.4--8.2 μm. They do not significantly inhibit plasma kallikrein, factor (F) XIIa, FXIa, FIXa, FVIIa-TF, FXa, plasmin or cathepsin G. One form, FM19 [rOicPaF(p-Me)], blocks α-thrombin-induced calcium flux in fibroblasts with an IC50 of 6.9 ± 1.2 μm. FM19 achieved 100% inhibition of threshold α- or γ-thrombin-induced platelet aggregation at 8.4 ± 4.7 μm and 16 ± 4 μm, respectively. The crystal structure of thrombin in complex with FM19 shows that the N-terminal D-Arg retrobinds into the S1 pocket, its second residue Oic interacts with His-57, Tyr-60a and Trp-60d, and its C-terminal p-methyl Phe engages thrombin's aryl binding site composed of Ile-174, Trp-215, and Leu-99. When administered intraperitoneal, intraduodenal, or orally to mice, FM19 prolongs thrombin clotting times and delays carotid artery thrombosis. FM19, a low affinity reversible direct thrombin inhibitor, might be useful as an add-on agent to address an unmet need in platelet inhibition in acute coronary syndromes in diabetics and others who with all current antiplatelet therapy still have reactive platelets.

  15. Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer

    DEFF Research Database (Denmark)

    Pasternak, Anna; Hernandez, Frank J; Rasmussen, Lars Melholt;

    2011-01-01

    A 15-mer DNA aptamer (named TBA) adopts a G-quadruplex structure that strongly inhibits fibrin-clot formation by binding to thrombin. We have performed thermodynamic analysis, binding affinity and biological activity studies of TBA variants modified by unlocked nucleic acid (UNA) monomers. UNA...... that a UNA monomer is allowed in many positions of the aptamer without significantly changing the thrombin-binding properties. The biological effect of a selection of the modified aptamers was tested by a thrombin time assay and showed that most of the UNA-modified TBAs possess anticoagulant properties...

  16. Fluorescent reporters of thrombin, heparin cofactor II, and heparin binding in a ternary complex

    OpenAIRE

    Verhamme, Ingrid M.

    2011-01-01

    Thrombin inactivation by heparin cofactor II (HCII) is accelerated by ternary complex formation with heparin. The novel active-site-labeled thrombins, [4′F]FPR-T and [6F]FFR-T, and the exosite I probe, Hir-(54–65)( SO3−), characterized thrombin exosite I and II interactions with HCII and heparin in the complex. HCII binding to exosite I of heparin-bound [4′F]FPR-T caused a saturable fluorescence increase, absent with antithrombin. Heparin binding to exosite II and a second weaker site caus...

  17. Crystallization and preliminary X-ray analysis of the complex of human α-thrombin with a modified thrombin-binding aptamer

    International Nuclear Information System (INIS)

    The complex between human α-thrombin and a modified thrombin-binding aptamer has been crystallized. Diffraction data were collected to 2.15 Å resolution, the structure was solved by molecular replacement and refinement of the model is in progress. The thrombin-binding aptamer (TBA) is a consensus DNA 15-mer that binds specifically to human α-thrombin at nanomolar concentrations and inhibits its procoagulant functions. Recently, a modified TBA (mTBA) containing a 5′–5′ inversion-of-polarity site has been shown to be more stable and to possess a higher thrombin affinity than its unmodified counterpart. The structure of the thrombin–TBA complex has previously been determined at low resolution, but did not provide a detailed picture of the aptamer conformation or of the protein–DNA assembly, while that of the complex with mTBA is unknown. Crystallographic analysis of the thrombin–mTBA complex has been attempted. The crystals diffracted to 2.15 Å resolution and belonged to space group I222

  18. Materials Testing and Automation

    Science.gov (United States)

    Cooper, Wayne D.; Zweigoron, Ronald B.

    1980-07-01

    The advent of automation in materials testing has been in large part responsible for recent radical changes in the materials testing field: Tests virtually impossible to perform without a computer have become more straightforward to conduct. In addition, standardized tests may be performed with enhanced efficiency and repeatability. A typical automated system is described in terms of its primary subsystems — an analog station, a digital computer, and a processor interface. The processor interface links the analog functions with the digital computer; it includes data acquisition, command function generation, and test control functions. Features of automated testing are described with emphasis on calculated variable control, control of a variable that is computed by the processor and cannot be read directly from a transducer. Three calculated variable tests are described: a yield surface probe test, a thermomechanical fatigue test, and a constant-stress-intensity range crack-growth test. Future developments are discussed.

  19. Fibrinolytic action of an enzyme preparation covalently bound with modified thrombin

    Energy Technology Data Exchange (ETDEWEB)

    Maksimenko, A.V.; Rusetskii, A.N.; Torchilin, V.P.

    1987-06-01

    It was pointed out previously that modification of thrombin at the tryptophan, tyrosine, arginine and lysine residues impairs its affinity for fibrinogen. Since a long binding site of macromolecular substrate in the thrombin molecule is responsible for binding of the enzyme with the platelet membrane also, it is probably preferable to carry out the modification at other amino acid residues. The purpose of this paper was to confirm experimentally the validity of this approach to the targeted modification of alpha-thrombin in order to obtain a protein polymer matrix with affinity for centers of thrombus formation. Technetium 99m was used as a label in assessing the ability of the modified thrombin to destroy the fibrin clot.

  20. Reduced activity of TAFI (thrombin-activatable fibrinolysis inhibitor) in acute promyelocytic leukaemia

    NARCIS (Netherlands)

    Meijers, JCM; Oudijk, EJD; Mosnier, LO; Nieuwenhuis, HK; Fijnheer, R; Bouma, Bonno N.; Bos, R

    2000-01-01

    Acute promyelocytic leukaemia (APL) is a disease that is distinguished from other leukaemias by the high potential for early haemorrhagic death. Several processes are involved, such as disseminated intravascular coagulation and hyperfibrinolysis. Recently, TAFI (thrombin-activatable fibrinolysis inh

  1. A fluorescent sandwich assay for thrombin using aptamer modified magnetic beads and quantum dots

    International Nuclear Information System (INIS)

    We describe an aptamer-based sandwich assay for thrombin by using a pair of thrombin-binding aptamers, namely one 15-mer aptamer (denoted as Apt15) and one 29-mer aptamer (denoted as Apt29). Either Apt29 or Apt15 can be used as capture aptamers on magnetic beads or reporter aptamers on the quantum dots to form the sandwich complex. Detection of thrombin is achieved by the fluorescent measurement of quantum dots in the sandwich complex. The choice of capture aptamers and reporter aptamers, and the effect of the addition order of the aptamers modified magnetic beads and the aptamers modified quantum dots were investigated. Detection of 0.05 nM thrombin was accomplished. The proteins hemoglobin, lysozyme, and transferrin did not interfere in this assay. (author)

  2. Modeling the microscopic electrical properties of thrombin binding aptamer (TBA) for label-free biosensors

    CERN Document Server

    Alfinito, Eleonora; Cataldo, Rosella; De Nunzio, Giorgio; Giotta, Livia; Guascito, Maria Rachele

    2016-01-01

    Aptamers are chemically produced oligonucleotides, able to bind a variety of targets such as drugs, proteins and pathogens with high sensitivity and selectivity. Therefore, aptamers are largely employed for producing label-free biosensors, with significant applications in diagnostics and drug delivery. In particular, the anti-thrombin aptamers are biomolecules of high interest for clinical use, because of their ability to recognize and bind the thrombin enzyme. Among them, the DNA 15-mer thrombin-binding aptamer (TBA), has been widely explored concerning both its structure, which was resolved with different techniques, and its function, especially about the possibility of using it as the active part of biosensors. This paper proposes a microscopic model of the electrical properties of TBA and the aptamer-thrombin complex, combining information from both structure and function. The novelty consists in describing both the aptamer alone and the complex as an impedance network, thus going deeper inside the issues...

  3. Thrombin Cleavage of Osteopontin Modulates Its Activities in Human Cells In Vitro and Mouse Experimental Autoimmune Encephalomyelitis In Vivo

    Directory of Open Access Journals (Sweden)

    Elena Boggio

    2016-01-01

    Full Text Available Osteopontin is a proinflammatory cytokine and plays a pathogenetic role in multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE, by recruiting autoreactive T cells into the central nervous system. Osteopontin functions are modulated by thrombin cleavage generating N- and C-terminal fragment, whose individual roles are only partly known. Published data are difficult to compare since they have been obtained with heterogeneous approaches. Interestingly, thrombin cleavage of osteopontin unmasks a cryptic domain of interaction with α4β1 integrin that is the main adhesion molecule involved in lymphocyte transmigration to the brain and is the target for natalizumab, the most potent drug preventing relapses. We produced recombinant osteopontin and its N- and C-terminal fragments in an eukaryotic system in order to allow their posttranslational modifications. We investigated, in vitro, their effect on human cells and in vivo in EAE. We found that the osteopontin cleavage plays a key role in the function of this cytokine and that the two fragments exert distinct effects both in vitro and in vivo. These findings suggest that drugs targeting each fragment may be used to fine-tune the pathological effects of osteopontin in several diseases.

  4. Automated Generation of Attack Trees

    DEFF Research Database (Denmark)

    Vigo, Roberto; Nielson, Flemming; Nielson, Hanne Riis

    2014-01-01

    are automatically inferred from a process algebraic specification in a syntax-directed fashion, encompassing a great many application domains and avoiding incurring systematically an exponential explosion. Moreover, we show how the standard propositional denotation of an attack tree can be used to phrase...

  5. Membrane lipid peroxidation in neurodegeneration: Role of thrombin and proteinase-activated receptor-1.

    Science.gov (United States)

    Citron, Bruce A; Ameenuddin, Syed; Uchida, K; Suo, William Z; SantaCruz, Karen; Festoff, Barry W

    2016-07-15

    Thrombin and membrane lipid peroxidation (MLP) have been implicated in various central nervous system (CNS) disorders from CNS trauma to stroke, Alzheimer's (AD) and Parkinson's (PD) diseases. Because thrombin also induces MLP in platelets and its involvement in neurodegenerative diseases we hypothesized that its deleterious effects might, in part, involve formation of MLP in neuronal cells. We previously showed that thrombin induced caspase-3 mediated apoptosis in motor neurons, via a proteinase-activated receptor (PAR1). We have now investigated thrombin's influence on the oxidative state of neurons leading to induction of MLP-protein adducts. Translational relevance of thrombin-induced MLP is supported by increased levels of 4-hydroxynonenal-protein adducts (HNEPA) in AD and PD brains. We now report for the first time that thrombin dose-dependently induces formation of HNEPA in NSC34 mouse motor neuron cells using anti-HNE and anti-acrolein monoclonal antibodies. The most prominent immunoreactive band, in SDS-PAGE, was at ∼54kDa. Membrane fractions displayed higher amounts of the protein-adduct than cytosolic fractions. Thrombin induced MLP was mediated, at least in part, through PAR1 since a PAR1 active peptide, PAR1AP, also elevated HNEPA levels. Of interest, glutamate and Fe2SO4 also increased the ∼54kDa HNEPA band in these cells but to a lesser extent. Taken together our results implicate the involvement of thrombin and MLP in neuronal cell loss observed in various CNS degenerative and traumatic pathologies. PMID:27138068

  6. Gold nanoparticles doped conducting polymer nanorod electrodes: ferrocene catalyzed aptamer-based thrombin immunosensor.

    Science.gov (United States)

    Rahman, Md Aminur; Son, Jung Ik; Won, Mi-Sook; Shim, Yoon-Bo

    2009-08-15

    Au nanoparticles-doped conducting polymer nanorods electrodes (AuNPs/CPNEs) were prepared by coating Au nanorods (AuNRs) with a conducting polymer layer. The AuNRs were prepared through an electroless deposition method using the polycarbonate membrane (pore diameter, 50 nm, pore density, 6 x 10(8) pores/cm(2)) as a template. The AuNPs/CPNEs combining catalytic activity of ferrocene to ascorbic acid were used for the fabrication of an ultrasensitive aptamer sensor for thrombin detection. The AuNPs/3D-CPNEs were characterized employing cyclic voltammetry (CV), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and atomic force microscopy (AFM). Sandwiched immunoassay for alpha-human thrombin with NH(2)-functionalized-thrombin binding aptamer (Apt) immobilized on AuNPs/3D-CPNEs was studied through the electrocatalytic oxidation of ascorbic acid by the ferrocene moiety that was bound with an antithrombin antibody and attached with the Apt/3D-CPNEs probe through target binding. Various experimental parameters affecting thrombin detection were optimized, and the performance of the thrombin aptamer sensor was examined. The Apt/AuNPs/3D-CPNEs based thrombin sensor exhibited a wide dynamic range of 5-2000 ng L(-1) and a low detection limit of 5 ng L(-1) (0.14 pM). The selectivity and the stability of the proposed thrombin aptamer sensor were excellent, and it was tested in a real human serum sample for the detection of spiked concentrations of thrombin. PMID:20337374

  7. Thrombin Binding Aptamer, More than a Simple Aptamer: Chemically Modified Derivatives and Biomedical Applications

    OpenAIRE

    Aviñó, Anna Maria; Eritja Casadellà, Ramón; Fàbrega, Carme; Tintoré, María

    2012-01-01

    The thrombin binding aptamer (TBA) is a well characterized chair-like, antiparallel quadruplex structure that binds specifically to thrombin at nanomolar concentrations and therefore it has interesting anticoagulant properties. In this article we review the research involved in the development of new TBA derivatives with improved anticoagulant properties as well as the use of the TBA as a model compound for the study of quadruplex structures. Specifically, we describe the impact of modified n...

  8. Thrombin stimulates albumin transcytosis in lung microvascular endothelial cells via activation of acid sphingomyelinase.

    Science.gov (United States)

    Kuebler, Wolfgang M; Wittenberg, Claudia; Lee, Warren L; Reppien, Eike; Goldenberg, Neil M; Lindner, Karsten; Gao, Yizhuo; Winoto-Morbach, Supandi; Drab, Marek; Mühlfeld, Christian; Dombrowsky, Heike; Ochs, Matthias; Schütze, Stefan; Uhlig, Stefan

    2016-04-15

    Transcellular albumin transport occurs via caveolae that are abundant in lung microvascular endothelial cells. Stimulation of albumin transcytosis by proinflammatory mediators may contribute to alveolar protein leak in lung injury, yet the regulation of albumin transport and its underlying molecular mechanisms are so far incompletely understood. Here we tested the hypothesis that thrombin may stimulate transcellular albumin transport across lung microvascular endothelial cells in an acid-sphingomyelinase dependent manner. Thrombin increased the transport of fluorescently labeled albumin across confluent human lung microvascular endothelial cell (HMVEC-L) monolayers to an extent that markedly exceeds the rate of passive diffusion. Thrombin activated acid sphingomyelinase (ASM) and increased ceramide production in HMVEC-L, but not in bovine pulmonary artery cells, which showed little albumin transport in response to thrombin. Thrombin increased total caveolin-1 (cav-1) content in both whole cell lysates and lipid rafts from HMVEC-L, and this effect was blocked by inhibition of ASM or de novo protein biosynthesis. Thrombin-induced uptake of albumin into lung microvascular endothelial cells was confirmed in isolated-perfused lungs by real-time fluorescence imaging and electron microscopy of gold-labeled albumin. Inhibition of ASM attenuated thrombin-induced albumin transport both in confluent HMVEC-L and in intact lungs, whereas HMVEC-L treatment with exogenous ASM increased albumin transport and enriched lipid rafts in cav-1. Our findings indicate that thrombin stimulates transcellular albumin transport in an acid sphingomyelinase-dependent manner by inducing de novo synthesis of cav-1 and its recruitment to membrane lipid rafts. PMID:26851257

  9. Thrombin Production and Human Neutrophil Elastase Sequestration by Modified Cellulosic Dressings and Their Electrokinetic Analysis

    Directory of Open Access Journals (Sweden)

    Nicolette Prevost

    2011-12-01

    Full Text Available Wound healing is a complex series of biochemical and cellular events. Optimally, functional material design addresses the overlapping acute and inflammatory stages of wound healing based on molecular, cellular, and bio-compatibility issues. In this paper the issues addressed are uncontrolled hemostasis and inflammation which can interfere with the orderly flow of wound healing. In this regard, we review the serine proteases thrombin and elastase relative to dressing functionality that improves wound healing and examine the effects of charge in cotton/cellulosic dressing design on thrombin production and elastase sequestration (uptake by the wound dressing. Thrombin is central to the initiation and propagation of coagulation, and elastase is released from neutrophils that can function detrimentally in a stalled inflammatory phase characteristic of chronic wounds. Electrokinetic fiber surface properties of the biomaterials of this study were determined to correlate material charge and polarity with function relative to thrombin production and elastase sequestration. Human neutrophil elastase sequestration was assessed with an assay representative of chronic wound concentration with cotton gauze cross-linked with three types of polycarboxylic acids and one phosphorylation finish; thrombin production, which was assessed in a plasma-based assay via a fluorogenic peptide substrate, was determined for cotton, cotton-grafted chitosan, chitosan, rayon/polyester, and two kaolin-treated materials including a commercial hemorrhage control dressing (QuickClot Combat Gauze. A correlation in thrombin production to zeta potential was found. Two polycarboxylic acid cross linked and a phosphorylated cotton dressing gave high elastase sequestration.

  10. Targeting thrombin long-term after an acute coronary syndrome: Opportunities and challenges.

    Science.gov (United States)

    De Caterina, Raffaele; Goto, Shinya

    2016-06-01

    Patients after an acute coronary syndrome (ACS) are at increased risk of recurrent thrombotic events, justifying the search for additional antithrombotic treatments. The pathophysiology of ACS involves arterial thrombus formation, in turn occurring because of a combination of platelet activation and fibrin formation, with thrombin playing a key role in both. Antiplatelet therapy, targeting the thromboxane pathway and the ADP P2Y12 receptor has been widely accepted for secondary prevention after an ACS. Now, data from recent clinical trials in such patients also encourage the pursuit of inhibiting thrombin formation or thrombin-mediated platelet activation in addition to antiplatelet therapy. This "triple pathway inhibition", including inhibition of thrombin activity or thrombin receptor(s), is currently an option in pure ACS, but already a must in the setting of ACS accompanied by atrial fibrillation (AF), where anticoagulants have been shown to be much more effective than antiplatelet agents in preventing stroke. We here discuss the challenges of managing combined thrombin activity or receptor inhibition and antiplatelet therapy in all such patients. Translating this into practice still requires further studies and patient tailoring to fully exploit its potential. PMID:26994821

  11. Expression of thrombin and its associated protein in cerebellum of human and rat after intracerebral hemorrhage

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zhi-yi; QI Ji-ping; ZHU Hong; SONG Yue-jia; WU He; JIA Ying; ZHANG Guang-mei

    2010-01-01

    Background Intracerebral hemorrhage (ICH) can cause brain damage through a number of pathways.The purpose of the study was to explore the effect of thrombin, protease nexin-1 (PN-1) and protease activated receptor-1 (PAR-1) in rat and human cerebellum after ICH.Methods A model of ICH was produced in adult Sprague-Dawley rats by direct injection of autologous blood (50 μl) into caudate nucleus.Patients with injured hemorrhage were also enrolled in this study.Different expressions of thrombin,PAR-1, PN-1 were detected in rat and human cerebellum by immunohistochemistry and in situ hybridization.Results In rat cerebellum, thrombin protein significantly increased at 6 hours and reached the maximum 2 days afterICH.The expression of PAR-1 protein reached the maximum at 24-48 hours, and then began to decrease.The expression of PN-1 protein reached the maximum at 3 hours, decreased somewhat after that and increased a little at 5days after ICH.While in human cerebellum, the changing tendency of thrombin, PAR-1 and PN-1 was almost conform to the rat.Conclusion In cerebellum, thrombin can activate PAR-1 expression after ICH, and PN-1 appears quickly after ICH in order to control the deleterious effect of thrombin.

  12. A cascade signal amplification strategy for surface enhanced Raman spectroscopy detection of thrombin based on DNAzyme assistant DNA recycling and rolling circle amplification.

    Science.gov (United States)

    Gao, Fenglei; Du, Lili; Tang, Daoquan; Lu, Yao; Zhang, Yanzhuo; Zhang, Lixian

    2015-04-15

    A sensitive protocol for surface enhanced Raman spectroscopy (SERS) detection of thrombin is designed with R6G-Ag NPs as a signal tag by combining DNAzyme assistant DNA recycling and rolling circle amplification (RCA). Molecular beacon (MB) as recognition probe immobilizes on the glass slides and performs the amplification procedure. After thrombin-induced structure-switching DNA hairpins of probe 1, the DNAzyme is liberated from the caged structure, which hybridizes with the MB for cleavage of the MB in the presence of cofactor Zn(2+) and initiates the DNA recycling process, leading to the cleavage of a large number of MB and the generation of numerous primers for triggering RCA reaction. The long amplified RCA product which contained hundreds of tandem-repeat sequences, which can bind with oligonucleotide functionalized Ag NPs reporters. The attached signal tags can be easily read out by SERS. Because of the cascade signal amplification, these newly designed protocols provides a sensitive SERS detection of thrombin down to the femolar level (2.3fM) with a linear range of 5 orders of magnitude (from 10(-14) to 10(-9)M) and have high selectivity toward its target protein. The proposed method is expected to be a good clinical tool for the diagnosis of a thrombotic disease.

  13. Thrombin mutant W215A/E217A treatment improves neurological outcome and attenuates central nervous system damage in experimental autoimmune encephalomyelitis.

    Science.gov (United States)

    Verbout, Norah G; Yu, Xiaolin; Healy, Laura D; Phillips, Kevin G; Tucker, Erik I; Gruber, András; McCarty, Owen J T; Offner, Halina

    2015-02-01

    Multiple sclerosis (MS) is a neuroinflammatory disease characterized by demyelination and axonal damage of the central nervous system. The pathogenesis of MS has also been linked to vascular inflammation and local activation of the coagulation system, resulting in perivascular fibrin deposition. Treatment of experimental autoimmune encephalomyelitis (EAE), a model of human MS, with antithrombotic and antiinflammatory activated protein C (APC) reduces disease severity. Since recombinant APC (Drotecogin alfa), originally approved for the treatment of severe sepsis, is not available for human MS studies, we tested the hypothesis that pharmacologic activation of endogenous protein C could likewise improve the outcome of EAE. Mice were immunized with murine myelin oligodendrocyte glycoprotein (MOG) peptides and at the onset of EAE symptoms, were treated every other day with either WE thrombin (25 μg/kg; i.v.), a selective recombinant protein C activator thrombin analog, or saline control. Mice were monitored for changes in disease score until euthanized for ex vivo analysis of inflammation. Administration of WE thrombin significantly ameliorated clinical severity of EAE, reduced inflammatory cell infiltration and demyelination, suppressed the activation of macrophages comprising the CD11b + population and reduced accumulation of fibrin (ogen) in the spinal cord. These data suggest that symptomatic MS may respond to a treatment strategy that involves temporal pharmacological enhancement of endogenous APC generation. PMID:24810631

  14. Thrombin-Binding Aptamer Quadruplex Formation: AFM and Voltammetric Characterization

    Directory of Open Access Journals (Sweden)

    Victor Constantin Diculescu

    2010-01-01

    Full Text Available The adsorption and the redox behaviour of thrombin-binding aptamer (TBA and extended TBA (eTBA were studied using atomic force microscopy and voltammetry at highly oriented pyrolytic graphite and glassy carbon. The different adsorption patterns and degree of surface coverage were correlated with the sequence base composition, presence/absence of K+, and voltammetric behaviour of TBA and eTBA. In the presence of K+, only a few single-stranded sequences present adsorption, while the majority of the molecules forms stable and rigid quadruplexes with no adsorption. Both TBA and eTBA are oxidized and the only anodic peak corresponds to guanine oxidation. Upon addition of K+ ions, TBA and eTBA fold into a quadruplex, causing the decrease of guanine oxidation peak and occurrence of a new peak at a higher potential due to the oxidation of G-quartets. The higher oxidation potential of G-quartets is due to the greater difficulty of electron transfer from the inside of the quadruplex to the electrode surface than electron transfer from the more flexible single strands.

  15. [Sodium ions as the effector of catalytic action of alpha-thrombin].

    Science.gov (United States)

    Kolodzeĭskaia, M V; Volkov, G L

    2007-01-01

    A process of thrombin interaction with synthetic and natural substrates in the presence of Na+ ions has been analyzed in the survey. Molecular bases of this interaction have been presented, interrelation between the structure and function of thrombin has been noted; the nature of the unique site of its active centre which determines high thrombin affinity for the substrates and increase of its catalytic activity defined by the term of "specificity to univalent cations" have been considered in detail. Na+ ions play the role of allosteric effector in realization of two informational states of thrombin which penform, respectively, two fundamental and competing functions in the process of hemostasis. The molecular basis of the process of Na+ binding with thrombin is rather simple and depends only on the single site which importance for the enzyme function is marked by numerous investigations of a number of authors, and it is shown that Na(+)-binding site is distributed in the other zone of thrombin molecule as compared to exosites I and II, which do not take part in Na(+)-binding and allosteric transduction. Considerable attention was given to conformational conversions of a thrombin molecule caused by Na+ ions binding. It was shown that the transition slow fast of the enzyme forms leads to formation of the ion pair Arg-187: Asp-222, optimal orientation of Asp-189 and Ser-195 for binding of substrates and considerable shift of the lateral chain Glu-192 determined by the disturbance of the lattice of water molecules which connects Na(+)-binding site with aminoacid Ser-195 of the active centre of the enzyme. New data have been presented which indicate that the changes in the lattice of water molecules and allosteric nucleus of Na(+)-binding site of the enzyme are the basic link of raising the affinity between the thrombin and substrate and mechanism of the enzyme activation by Na(+)-ions. The survey touches some problems of creation of allosteric inhibitors of thrombin

  16. Automating Finance

    Science.gov (United States)

    Moore, John

    2007-01-01

    In past years, higher education's financial management side has been riddled with manual processes and aging mainframe applications. This article discusses schools which had taken advantage of an array of technologies that automate billing, payment processing, and refund processing in the case of overpayment. The investments are well worth it:…

  17. An electrochemical label-free and sensitive thrombin aptasensor based on graphene oxide modified pencil graphite electrode.

    Science.gov (United States)

    Ahour, F; Ahsani, M K

    2016-12-15

    In this work, we tactfully constructed a novel label-free electrochemical aptasensor for rapid and facile detection of thrombin using graphene oxide (GO) and thrombin binding aptamer (TBA). The strategy relies on the preferential adsorption of single-stranded DNA (ssDNA) to GO over aptamer-target complexes. The TBA-thrombin complex formation was monitored by differential pulse voltammetry (DPV) using the guanine oxidation signal. In the absence of thrombin, the aptamers adsorbed onto the surface of GO leading to a strong background guanine oxidation signal. Conversely, in the presence of thrombin, the conformational transformation of TBA after incubating with the thrombin solution and formation of the aptamer-thrombin complexes which had weak binding ability to GO, leads to the desorption of TBA-thrombin complex from electrode surface and significant oxidation signal decrease. The selectivity of the biosensor was studied using other biological substances. The biosensor's signal was proportional to the thrombin concentration from 0.1 to 10nM with a detection limit of 0.07nM. Particularly, the proposed method could be widely applied to the aptamer-based determination of other target analytes. PMID:27476058

  18. Ultrasound-guided Thrombin Injection: An Alternative Treatment for Femoral Artery Pseudoaneurysm with Better Efficiency and Safety

    Institute of Scientific and Technical Information of China (English)

    Qinghai YAO; Hongliang CONG; Shangqin WU; Shan SUN; Qike DONG; Dongmei CHEN; Peng LI

    2008-01-01

    The aim of this study was to evaluate the efficiency and safety of ultrasound-guided thrombin injection on femoral pseudoaneurysm (FPA) as compared to ultrasound-guided local oppression. Eleven cases of FPA were enrolled and 7 cases received ultrasound-guide thrombin injection (injection group), and the remaining 4 cases were treated with local oppression (oppression group). Efficiency and safety were analyzed by ultrasound and subsequent follow-up. The results showed that 1 case relapsed in oppression group while no relapse occurred in thrombin injection group. Ultrasound-guided thrombin injection is better for treatment of FPA in terms of effectiveness and safety.

  19. Myths in test automation

    Directory of Open Access Journals (Sweden)

    Jazmine Francis

    2015-01-01

    Full Text Available Myths in automation of software testing is an issue of discussion that echoes about the areas of service in validation of software industry. Probably, the first though that appears in knowledgeable reader would be Why this old topic again? What's New to discuss the matter? But, for the first time everyone agrees that undoubtedly automation testing today is not today what it used to be ten or fifteen years ago, because it has evolved in scope and magnitude. What began as a simple linear scripts for web applications today has a complex architecture and a hybrid framework to facilitate the implementation of testing applications developed with various platforms and technologies. Undoubtedly automation has advanced, but so did the myths associated with it. The change in perspective and knowledge of people on automation has altered the terrain. This article reflects the points of views and experience of the author in what has to do with the transformation of the original myths in new versions, and how they are derived; also provides his thoughts on the new generation of myths.

  20. A multifunctional hemin@metal-organic framework and its application to construct an electrochemical aptasensor for thrombin detection

    Science.gov (United States)

    Xie, Shunbi; Ye, Jiawei; Yuan, Yali; Chai, Yaqin; Yuan, Ruo

    2015-10-01

    A new type of multifunctional metal-organic framework (MOF) has been synthesized by encapsulating hemin into the nano-sized Fe-MIL-88 MOFs (hemin@MOFs) and first applied in an electrochemical aptasensor to detect thrombin (TB) with the aid of an enzyme for signal amplification. The gold nanoparticle functionalized hemin@MOFs (Au/hemin@MOFs) have not only simultaneously served as redox mediators and solid electrocatalysts, but have also been utilized as an ideal loading platform to immobilize a large number of biomolecules. In this aptasensor, Au/hemin@MOFs conjugated with glucose oxidase (GOD) and thrombin binding aptamer (TBA II) were used as the secondary aptamer bioconjugates (Au/hemin@MOF-TBA II-GOD bioconjugates), and TB was sandwiched between Au/hemin@MOF-TBA II-GOD bioconjugates and the amino-terminated TBA I which was self-assembled on the gold nanoparticle (AuNP) modified electrode. The GOD could oxidize glucose into gluconic acid accompanied by the generation of H2O2. The generated H2O2 on the electrode surface was further electrocatalyzed by hemin@MOFs to amplify the electrochemical signal of hemin contained in hemin@MOFs. Therefore, the synthesized hemin@MOFs represented a new paradigm for multifunctional materials since it combined three different functions including serving as catalysts, redox mediators and loading platforms within a single material. With such an ingenious design, a wide linear range of 0.0001 nM to 30 nM was acquired with a relatively low detection limit of 0.068 pM for TB detection.A new type of multifunctional metal-organic framework (MOF) has been synthesized by encapsulating hemin into the nano-sized Fe-MIL-88 MOFs (hemin@MOFs) and first applied in an electrochemical aptasensor to detect thrombin (TB) with the aid of an enzyme for signal amplification. The gold nanoparticle functionalized hemin@MOFs (Au/hemin@MOFs) have not only simultaneously served as redox mediators and solid electrocatalysts, but have also been utilized as an

  1. Automation Security

    OpenAIRE

    Mirzoev, Dr. Timur

    2014-01-01

    Web-based Automated Process Control systems are a new type of applications that use the Internet to control industrial processes with the access to the real-time data. Supervisory control and data acquisition (SCADA) networks contain computers and applications that perform key functions in providing essential services and commodities (e.g., electricity, natural gas, gasoline, water, waste treatment, transportation) to all Americans. As such, they are part of the nation s critical infrastructu...

  2. Differential effects on glial activation by a direct versus an indirect thrombin inhibitor.

    Science.gov (United States)

    Marangoni, M Natalia; Braun, David; Situ, Annie; Moyano, Ana L; Kalinin, Sergey; Polak, Paul; Givogri, Maria I; Feinstein, Douglas L

    2016-08-15

    Thrombin is a potent regulator of brain function in health and disease, modulating glial activation and brain inflammation. Thrombin inhibitors, several of which are in clinical use as anti-coagulants, can reduce thrombin-dependent neuroinflammation in pathological conditions. However, their effects in a healthy CNS are largely unknown. In adult healthy mice, we compared the effects of treatment by the direct thrombin inhibitor dabigatran etexilate (DE), to those of warfarin, which acts by preventing vitamin K recycling essential for coagulation. After 4weeks, warfarin increased both astrocyte GFAP and microglia Iba-1 staining throughout the CNS; whereas DE reduced expression of both markers. Warfarin, but not DE, reduced sulfatide levels; and warfarin showed longer lasting changes in cerebellar gene expression. DE also reduced glial activation in a mouse model of Alzheimer's disease, although no changes in amyloid plaque burden were observed. These results suggest that treatment with direct thrombin inhibitors may be preferable to those agents which reduce vitamin K levels and have the potential to increase glial activation. PMID:27397090

  3. Particle analysis for uranium isotopes on swipe samples using new generation Cameca IMS 7f SIMS supported by SEM automated uranium detection

    International Nuclear Information System (INIS)

    Full text: Recent safeguard issues revealed a need for increasing swipe samples analysis capability within the Agency's Network of Analytical Laboratories (NWAL). Our laboratory is qualified for uranium isotopic analysis of particles based on fission track and Thermo-Ionization Mass Spectrometry method (FT-TIMS). In addition, we recently acquired a Secondary Ion Mass Spectrometer (SIMS) in order to broaden particle analysis capabilities in the laboratory. The SIMS technique enables to lower the response time for urgent analysis and to maintain a swipe sample analysis capacity even when our reactor for neutron irradiation is not available. This presentation focuses on the results that have been obtained on swipes particle analysis for uranium isotopes using our new generation Cameca IMS 7f. In this study, all sample processing steps have been examined with the view to improve the reliability of the results and to shorten analytical response time. The IMS 7f instrument mainly differs from other small radius magnetic sector SIMS by ultra high vacuum conditions (-10 mbar in the sample chamber) likely to improve sensitivity as well as to lower hydride ion formation rates. Sensitivity is critical in particle analysis, considering the very small amounts of uranium to be analyzed (∼ a few pg) whereas isobaric interferences due to uranium hydride ions have been shown to cause dramatic artifacts in 236U/238U ratio determination. Particle extraction and sample mounting -- All sample preparation operations have been conducted in a class 10 clean laboratory. A special attention has been paid to the choice of solvents in order to minimize uranium dissolution during liquid-phase particle extraction. Particle suspensions have been deposited and evaporated onto 1 inch diameter carbon disks. Several deposition techniques have been investigated in order to minimize deposition diameters. Sample mountings have been equipped with an internal reference consisting of 2 aluminum foil

  4. A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole

    Science.gov (United States)

    Tsvetkov, Vladimir B.; Varizhuk, Anna M.; Pozmogova, Galina E.; Smirnov, Igor P.; Kolganova, Natalia A.; Timofeev, Edward N.

    2015-11-01

    In this study we describe new modified analogs of the thrombin binding aptamer (TBA) containing 5-nitroindole residues. It has been shown that all modified TBAs form an anti-parallel G-quadruplex structure and retain the ability to inhibit thrombin. The most advanced TBA variant (TBA-N8) has a substantially increased clotting time and two-fold lower IC50 value compared to the unmodified prototype. Molecular modelling studies suggest that the improved anticoagulant properties of TBA-N8 result from changes in the binding mode of the analog. A modified central loop in TBA-N8 is presumed to participate in the binding of the target protein. Studies of FAM labelled TBA and TBA-N8 showed an improved binding affinity of the modified aptamer and provided evidence of a direct interaction between the modified central loop and thrombin. Our findings have implications for the design of new aptamers with improved binding affinities.

  5. PAR1-dependent and independent increases in COX-2 and PGE2 in human colonic myofibroblasts stimulated by thrombin.

    Science.gov (United States)

    Seymour, Michelle L; Zaidi, Nosheen F; Hollenberg, Morley D; MacNaughton, Wallace K

    2003-05-01

    Subepithelial myofibroblast-derived prostaglandin E(2) (PGE(2)) regulates epithelial chloride secretion in the intestine. Thrombin is elevated in inflammatory conditions of the bowel. Therefore, we sought to determine a role for thrombin in regulating PGE(2) synthesis by colonic myofibroblasts. Incubation of cultured CCD-18Co colonic myofibroblasts with thrombin, the proteinase-activated receptor 1 (PAR(1))-activating peptide (Cit-NH(2)), and peptides corresponding to 2 noncatalytic regions of thrombin (TP367 and TP508) for 18 h increased both cyclooxygenase (COX)-2 expression (immunocytochemistry) and PGE(2) synthesis (enzyme immunoassay). Inhibition of thrombin by D-Phe-Pro-Arg-chloromethylketone (PPACK) did not significantly reduce PGE(2) synthesis, which remained elevated compared with control. We also investigated the basic fibroblast growth factor (bFGF) dependence of thrombin-induced PGE(2) elevations. Recombinant human bFGF concentration dependently increased PGE(2) synthesis, and a bFGF neutralizing antibody inhibited PGE(2) synthesis induced by TP367 and TP508 (approximately 40%) and by thrombin (approximately 20%) (but not Cit-NH(2)). Thrombin, therefore, upregulates COX-2-derived PGE(2) synthesis by both catalytic cleavage of PAR(1) and bFGF-dependent noncatalytic activity. This presents a novel mechanism by which intestinal myofibroblasts might regulate epithelial chloride secretion. PMID:12505789

  6. Thrombin stimulation of inflammatory breast cancer cells leads to aggressiveness via the EGFR-PAR1-Pak1 pathway.

    Science.gov (United States)

    Ohshiro, Kazufumi; Bui-Nguyen, Tri M; Divijendra Natha, Reddy S; Schwartz, Arnold M; Levine, Paul; Kumar, Rakesh

    2012-12-27

    Inflammatory breast cancer (IBC) accounts for a small fraction but aggressive form of epithelial breast cancer. Although the role of thrombin in cancer is beginning to be unfolded, its impact on the biology of IBC remains unknown. The purpose of this study was to establish the role of thrombin on the invasiveness of IBC cells. The IBC SUM149 cell line was treated with thrombin in the absence or presence of the epidermal growth factor receptor (EGFR) inhibitor erlotinib and protease-activated receptor 1 (PAR1) inhibitor. The effects of pharmacological inhibitors on the ability of thrombin to stimulate the growth rate and invasiveness were examined. We found that the inhibition of putative cellular targets of thrombin action suppresses both the growth and invasiveness of SUM149 cells in a concentration-dependent manner. In addition, thrombin-mediated increased invasion of SUM149 cells was routed through EGFR phosphorylation, and in turn, stimulation of the p21-activated kinase (Pak1) activity in a EGFR-sensitive manner. Interestingly, thrombin-mediated activation of the Pak1 pathway stimulation was blocked by erlotinib and PAR1 inhibitor. For proof-of-principle studies, we found immunohistochemical evidence of Pak1 activation as well as expression of PAR1 in IBC. Thrombin utilizes EGFR to relay signals promoting SUM149 cell growth and invasion via the Pak1 pathway. The study provides the rationale for future therapeutic approaches in mitigating the invasive nature of IBC by targeting Pak1 and/or EGFR.

  7. Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors.

    Science.gov (United States)

    Fox, T; Haaksma, E E

    2000-07-01

    We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRID. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3D database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.

  8. Biochemical characterization of bovine plasma thrombin-activatable fibrinolysis inhibitor (TAFI)

    DEFF Research Database (Denmark)

    Valnickova, Zuzana; Thaysen-Andersen, Morten; Højrup, Peter;

    2009-01-01

    BACKGROUND: TAFI is a plasma protein assumed to be an important link between coagulation and fibrinolysis. The three-dimensional crystal structures of authentic mature bovine TAFI (TAFIa) in complex with tick carboxypeptidase inhibitor, authentic full lenght bovine plasma thrombin-activatable fib......BACKGROUND: TAFI is a plasma protein assumed to be an important link between coagulation and fibrinolysis. The three-dimensional crystal structures of authentic mature bovine TAFI (TAFIa) in complex with tick carboxypeptidase inhibitor, authentic full lenght bovine plasma thrombin...

  9. Effects on coagulation and fibrinolysis induced by influenza in mice with a reduced capacity to generate activated protein C and a deficiency in plasminogen activator inhibitor type 1.

    Science.gov (United States)

    Keller, Tymen T; van der Sluijs, Koen F; de Kruif, Martijn D; Gerdes, Victor E A; Meijers, Joost C M; Florquin, Sandrine; van der Poll, Tom; van Gorp, Eric C M; Brandjes, Dees P M; Büller, Harry R; Levi, Marcel

    2006-11-24

    Influenza infections increase the risk of diseases associated with a prothrombotic state, such as venous thrombosis and atherothrombotic diseases. However, it is unclear whether influenza leads to a prothrombotic state in vivo. To determine whether influenza activates coagulation, we measured coagulation and fibrinolysis in influenza-infected C57BL/6 mice. We found that influenza increased thrombin generation, fibrin deposition, and fibrinolysis. In addition, we used various anti- and prothrombotic models to study pathways involved in the influenza-induced prothrombotic state. A reduced capacity to generate activated protein C in TM(pro/pro) mice increased thrombin generation and fibrinolysis, whereas treatment with heparin decreased thrombin generation in influenza-infected C57Bl/6 mice. Thrombin generation was not changed in hyperfibrinolytic mice, deficient in plasminogen activator inhibitor type-1 (PAI-1(-/-)); however, increased fibrin degradation was seen. Treatment with tranexamic acid reduced fibrinolysis, but thrombin generation was unchanged. We conclude that influenza infection generates thrombin, increased by reduced levels of protein C and decreased by heparin. The fibrinolytic system appears not to be important for thrombin generation. These findings suggest that influenza leads to a prothrombotic state by coagulation activation. Heparin treatment reduces the influenza induced prothrombotic state. PMID:17068293

  10. In vitro study of the role of thrombin in platelet rich plasma (PRP) preparation: utility for gel formation and impact in growth factors release

    OpenAIRE

    Huber, Stephany Cares; Cunha Júnior, José Luiz Rosenberis; Montalvão, Silmara; da Silva, Letícia Queiroz; Paffaro, Aline Urban; da Silva, Francesca Aparecida Ramos; Rodrigues, Bruno Lima; Lana, José Fabio Santos Duarte; Annichino-Bizzacchi, Joyce Maria

    2016-01-01

    Introduction: The use of PRP has been studied for different fields, with promising results in regenerative medicine. Until now, there is no study in the literature evaluating thrombin levels in serum, used as autologous thrombin preparation. Therefore, in the present study we evaluated the role played by different thrombin concentrations in PRP and the impact in the release of growth factors. Also, different activators for PRP gel formation were evaluated. Methods: Thrombin levels were measur...

  11. Maneuver Automation Software

    Science.gov (United States)

    Uffelman, Hal; Goodson, Troy; Pellegrin, Michael; Stavert, Lynn; Burk, Thomas; Beach, David; Signorelli, Joel; Jones, Jeremy; Hahn, Yungsun; Attiyah, Ahlam; Illsley, Jeannette

    2009-01-01

    The Maneuver Automation Software (MAS) automates the process of generating commands for maneuvers to keep the spacecraft of the Cassini-Huygens mission on a predetermined prime mission trajectory. Before MAS became available, a team of approximately 10 members had to work about two weeks to design, test, and implement each maneuver in a process that involved running many maneuver-related application programs and then serially handing off data products to other parts of the team. MAS enables a three-member team to design, test, and implement a maneuver in about one-half hour after Navigation has process-tracking data. MAS accepts more than 60 parameters and 22 files as input directly from users. MAS consists of Practical Extraction and Reporting Language (PERL) scripts that link, sequence, and execute the maneuver- related application programs: "Pushing a single button" on a graphical user interface causes MAS to run navigation programs that design a maneuver; programs that create sequences of commands to execute the maneuver on the spacecraft; and a program that generates predictions about maneuver performance and generates reports and other files that enable users to quickly review and verify the maneuver design. MAS can also generate presentation materials, initiate electronic command request forms, and archive all data products for future reference.

  12. Automated Budget System

    Data.gov (United States)

    Department of Transportation — The Automated Budget System (ABS) automates management and planning of the Mike Monroney Aeronautical Center (MMAC) budget by providing enhanced capability to plan,...

  13. Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy.

    Science.gov (United States)

    Duan, Li L; Feng, Guo Q; Zhang, Qing G

    2016-01-01

    Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding. PMID:27507430

  14. Regulation of Thrombin-Induced Lung Endothelial Cell Barrier Disruption by Protein Kinase C Delta

    Science.gov (United States)

    Xie, Lishi; Chiang, Eddie T.; Kelly, Gabriel T.; Kanteti, Prasad; Singleton, Patrick A.; Camp, Sara M.; Zhou, Tingting; Dudek, Steven M.; Natarajan, Viswanathan; Wang, Ting; Black, Steven M.; Garcia, Joe G. N.; Jacobson, Jeffrey R.

    2016-01-01

    Protein Kinase C (PKC) plays a significant role in thrombin-induced loss of endothelial cell (EC) barrier integrity; however, the existence of more than 10 isozymes of PKC and tissue–specific isoform expression has limited our understanding of this important second messenger in vascular homeostasis. In this study, we show that PKCδ isoform promotes thrombin-induced loss of human pulmonary artery EC barrier integrity, findings substantiated by PKCδ inhibitory studies (rottlerin), dominant negative PKCδ construct and PKCδ silencing (siRNA). In addition, we identified PKCδ as a signaling mediator upstream of both thrombin-induced MLC phosphorylation and Rho GTPase activation affecting stress fiber formation, cell contraction and loss of EC barrier integrity. Our inhibitor-based studies indicate that thrombin-induced PKCδ activation exerts a positive feedback on Rho GTPase activation and contributes to Rac1 GTPase inhibition. Moreover, PKD (or PKCμ) and CPI-17, two known PKCδ targets, were found to be activated by PKCδ in EC and served as modulators of cytoskeleton rearrangement. These studies clarify the role of PKCδ in EC cytoskeleton regulation, and highlight PKCδ as a therapeutic target in inflammatory lung disorders, characterized by the loss of barrier integrity, such as acute lung injury and sepsis. PMID:27442243

  15. Regulation of Thrombin-Induced Lung Endothelial Cell Barrier Disruption by Protein Kinase C Delta.

    Directory of Open Access Journals (Sweden)

    Lishi Xie

    Full Text Available Protein Kinase C (PKC plays a significant role in thrombin-induced loss of endothelial cell (EC barrier integrity; however, the existence of more than 10 isozymes of PKC and tissue-specific isoform expression has limited our understanding of this important second messenger in vascular homeostasis. In this study, we show that PKCδ isoform promotes thrombin-induced loss of human pulmonary artery EC barrier integrity, findings substantiated by PKCδ inhibitory studies (rottlerin, dominant negative PKCδ construct and PKCδ silencing (siRNA. In addition, we identified PKCδ as a signaling mediator upstream of both thrombin-induced MLC phosphorylation and Rho GTPase activation affecting stress fiber formation, cell contraction and loss of EC barrier integrity. Our inhibitor-based studies indicate that thrombin-induced PKCδ activation exerts a positive feedback on Rho GTPase activation and contributes to Rac1 GTPase inhibition. Moreover, PKD (or PKCμ and CPI-17, two known PKCδ targets, were found to be activated by PKCδ in EC and served as modulators of cytoskeleton rearrangement. These studies clarify the role of PKCδ in EC cytoskeleton regulation, and highlight PKCδ as a therapeutic target in inflammatory lung disorders, characterized by the loss of barrier integrity, such as acute lung injury and sepsis.

  16. The role of thrombin-activatable fibrinolysis inhibitor in diabetic wound healing

    NARCIS (Netherlands)

    C.J.N. Verkleij; J.J.T.H. Roelofs; S.R. Havik; J.C.M. Meijers; P.F. Marx

    2010-01-01

    Introduction: One of the major complications in patients with diabetes mellitus is impaired wound healing. The fibrinolytic system is involved in parts of the wound healing process and deficiency of thrombin-activatable fibrinolysis inhibitor (TAFI) results in delayed wound closure. Moreover, levels

  17. Quantitative phosphoproteomics unveils temporal dynamics of thrombin signaling in human endothelial cells

    NARCIS (Netherlands)

    van den Biggelaar, Maartje; Hernández-Fernaud, Juan Ramon; van den Eshof, Bart L; Neilson, Lisa J; Meijer, Alexander B; Mertens, Koenraad; Zanivan, Sara

    2014-01-01

    Thrombin is the key serine protease of the coagulation cascade and a potent trigger of protease-activated receptor 1 (PAR1)-mediated platelet aggregation. In recent years, PAR1 has become an appealing target for anticoagulant therapies. However, the inhibitors that have been developed so far increas

  18. Targeting the thrombin receptor modulates inflammation and astrogliosis to improve recovery after spinal cord injury.

    Science.gov (United States)

    Radulovic, Maja; Yoon, Hyesook; Wu, Jianmin; Mustafa, Karim; Scarisbrick, Isobel A

    2016-09-01

    The deregulation of serine protease activity is a common feature of neurological injury, but little is known regarding their mechanisms of action or whether they can be targeted to facilitate repair. In this study we demonstrate that the thrombin receptor (Protease Activated Receptor 1, (PAR1)) serves as a critical translator of the spinal cord injury (SCI) proteolytic microenvironment into a cascade of pro-inflammatory events that contribute to astrogliosis and functional decline. PAR1 knockout mice displayed improved locomotor recovery after SCI and reduced signatures of inflammation and astrogliosis, including expression of glial fibrillary acidic protein (GFAP), vimentin, and STAT3 signaling. SCI-associated elevations in pro-inflammatory cytokines such as IL-1β and IL-6 were also reduced in PAR1-/- mice and co-ordinate improvements in tissue sparing and preservation of NeuN-positive ventral horn neurons, and PKCγ corticospinal axons, were observed. PAR1 and its agonist's thrombin and neurosin were expressed by perilesional astrocytes and each agonist increased the production of IL-6 and STAT3 signaling in primary astrocyte cultures in a PAR1-dependent manner. In turn, IL-6-stimulated astrocytes increased expression of PAR1, thrombin, and neurosin, pointing to a model in which PAR1 activation contributes to increased astrogliosis by feedforward- and feedback-signaling dynamics. Collectively, these findings identify the thrombin receptor as a key mediator of inflammation and astrogliosis in the aftermath of SCI that can be targeted to reduce neurodegeneration and improve neurobehavioral recovery. PMID:27145117

  19. Pleiotropic effects of factor Xa and thrombin : what to expect from novel anticoagulants

    NARCIS (Netherlands)

    Spronk, Henri M. H.; de Jong, Anne Margreet; Crijns, Harry J.; Schotten, Ulrich; Van Gelder, Isabelle C.; ten Cate, Hugo

    2014-01-01

    Factor Xa and thrombin are well-known components of the coagulation cascade and have been proven to be viable targets for effective anticoagulation treatment. However, accumulating evidence suggests that these serine proteases are also crucial modulators of other cellular mechanisms through the acti

  20. Effects of fused hirudin on activity of thrombin and function of platelets

    Institute of Scientific and Technical Information of China (English)

    SHEN Li; CHEN Shao-ping; CAI Zai-long; YANG Sheng-sheng; QIN Yong-wen

    2005-01-01

    Objective: To investigate whether fused hirudin peptide has both antithrombin and antiplatelet functions. Methods: The core region of fused hirudin was the C-terminal tail of hirudin(hirudin53-64),which could bind to the anion binding exosite (ABE) of thrombin.Arg-Pro-Pro-Gly-Phe(RPPGF) amino acid sequence,a metabolite of bradykinin,was added to the N-terminus of hirudin53-64.It bound to the active site of thrombin.Additionally,Arg-Gly-Asp(RGD)amino acid sequence,an inibitor of glycoprotein Ⅱb/Ⅲa( GP Ⅱb/Ⅲa) receptor,was linked to C-terminus of hirudin53-64.This 26-animo acid-fused hirudin peptide was artificially synthesized,purified and analysed. Results: Fused hirudin peptide significantly lengthened the activated partial thromboplastin time(APTT),thrombin time(TT)and prothrombin time(PT) and inhibited the amidolytic activity of thrombin.The ADP-induced platelet aggregation was markedly inhibited by fused hirudin peptide. Conclusion: Fused hirudin peptide has activity of antithrombin as well as antiplatelet.Therefore bifunctional anticoagulation peptide has capacity to target various components of haemostatic process and may become more powerful antithrombosis agent.

  1. Thrombin action decreases acetylcholine receptor aggregate number and stability in cultured mouse myotubes.

    Science.gov (United States)

    Davenport, R W; Lanuza, M; Kim, S; Jia, M; Snyder, E; Nelson, P G

    2000-08-30

    Neurons develop and make very stable, long-term synaptic connections with other nerve cells and with muscle. Synaptic stability at the neuromuscular junction changes over development in that a proliferation of synaptic input are made to individual myotubes and synapses from all but one neuron are lost during development. In an established co-culture paradigm in which spinal motoneurons synaptically contact myotubes, thrombin and associated protease inhibitors have been shown to affect the loss of functional synaptic contacts [6]. Evidence has not been provided which clearly demonstrate whether protease/protease inhibitors affect either the pre- or postsynaptic terminal, or both. In an effort to determine whether these reagents directly affect postsynaptic receptors on myotubes, myotubes were cultured in the absence of neurons and the spontaneous presence and stability of aggregates of acetylcholine receptors (AChR) in control and thrombin-containing media were evaluated. In dishes fixed after treatment and in dishes in which individual aggregates were observed live, thrombin action appeared to increase loss of AChR aggregates over time. Hirudin, a specific inhibitor of the thrombin protease, diminished this loss. Neither reagent affected the overall incorporation or degradation of AChR; therefore, it appears these protease/protease inhibitors affect the state of AChR aggregation. PMID:10960680

  2. Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy

    Science.gov (United States)

    Duan, Li L.; Feng, Guo Q.; Zhang, Qing G.

    2016-01-01

    Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding. PMID:27507430

  3. Thrombin inhibition by dabigatran attenuates atherosclerosis in ApoE deficient mice

    OpenAIRE

    Pingel, Simon; Tiyerili, Vedat; Mueller, Jens; Werner, Nikos; Nickenig, Georg; Mueller, Cornelius

    2014-01-01

    Introduction Atherosclerosis is a chronic inflammatory disease characterized by endothelial cell damage, infiltration, proliferation and accumulation of macrophages, lymphocytes and transformed vascular smooth muscle cells within the vascular wall and procoagulation processes involving activation of plasmatic coagulation events and platelets. Numerous studies suggested a close interaction between thrombin action and atherogenesis, but possibly underlying mechanisms are multiple and specific t...

  4. (-)-Epigallocatechin-3-gallate decreases thrombin/paclitaxel-induced endothelial tissue factor expression via the inhibition of c-Jun terminal NH2 kinase phosphorylation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Huang-Joe [Institute of Biotechnology, National Tsing Hua University, No. 101, Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan (China); Division of Cardiology, Department of Medicine, China Medical University Hospital, No. 2, Yuh-Der Road, Taichung 40447, Taiwan (China); Lo, Wan-Yu [Department of Medical Research, China Medical University Hospital, No. 2, Yuh-Der Road, Taichung 40447, Taiwan (China); Graduate Integration of Chinese and Western Medicine, China Medical University, No. 91, Hsueh-Shih Road, Taichung 40402, Taiwan (China); Lu, Te-Ling [School of Pharmacy, China Medical University, No. 91, Hsueh-Shih Road, Taichung 40402, Taiwan (China); Huang, Haimei, E-mail: hmhuang@life.nthu.edu.tw [Institute of Biotechnology, National Tsing Hua University, No. 101, Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan (China)

    2010-01-01

    Patients with paclitaxel-eluting stents are concerned with stent thrombosis caused by premature discontinuation of dual antiplatelet therapy or clopidogrel resistance. This study investigates the effect of (-)-epigallocatechin-3-gallate (EGCG) on the expression of thrombin/paclitaxel-induced endothelial tissue factor (TF) expressions in human aortic endothelial cells (HAECs). EGCG was nontoxic to HAECs at 6 h up to a concentration of 25 {mu}mol/L. At a concentration of 25 {mu}mol/L, EGCG pretreatment potently inhibited both thrombin-stimulated and thrombin/paclitaxel-stimulated endothelial TF protein expression. Thrombin and thrombin/paclitaxel-induced 2.6-fold and 2.9-fold increases in TF activity compared with the control. EGCG pretreatment caused a 29% and 38% decrease in TF activity on thrombin and thrombin/paclitaxel treatment, respectively. Real-time polymerase chain reaction (PCR) showed that thrombin and thrombin/paclitaxel-induced 3.0-fold and 4.6-fold TF mRNA expressions compared with the control. EGCG pretreatment caused an 82% and 72% decrease in TF mRNA expression on thrombin and thrombin/paclitaxel treatment, respectively. The c-Jun terminal NH2 kinase (JNK) inhibitor SP600125 reduced thrombin/paclitaxel-induced TF expression. Furthermore, EGCG significantly inhibited the phosphorylation of JNK to 49% of thrombin/paclitaxel-stimulated HAECs at 60 min. Immunofluorescence assay did not show an inhibitory effect of EGCG on P65 NF-{kappa}B nuclear translocation in the thrombin/paclitaxel-stimulated endothelial cells. In conclusion, EGCG can inhibit TF expression in thrombin/paclitaxel-stimulated endothelial cells via the inhibition of JNK phosphorylation. The unique property of EGCG may be used to develop a new drug-eluting stent by co-coating EGCG and paclitaxel.

  5. The direct thrombin inhibitors (argatroban, bivalirudin and lepirudin) and the indirect Xa-inhibitor (danaparoid) increase fibrin network porosity and thus facilitate fibrinolysis.

    Science.gov (United States)

    He, Shu; Blombäck, Margareta; Bark, Niklas; Johnsson, Hans; Wallén, N Hakan

    2010-05-01

    The present study aimed to assess whether the fibrin network structure is modified by the direct thrombin-inhibitors lepirudin, argatroban or bivalirudin and by the indirect Xa-inhibitor danaparoid. Using an in vitro assay that imitates the physiological process of coagulation from thrombin generation to fibrin formation, we examined a normal plasma pool spiked with one of the inhibitors. At concentrations considered to be the plasma levels observed during therapy, almost no influence was detected for lepirudin despite clear-cut effects on "clotting time". However, argatroban, bivalirudin and danaparoid increased the fibrin gel permeability (Ks) to a similar extent. At concentrations higher than the "therapeutic" levels, the dose-response curve in the Ks assay became very steep for lepirudin while those were shallow for the others. In parallel with the drug-induced increases of Ks, larger network pores in 3D-microscopic images and significant shortenings in "clot lysis time" induced by addition of rtPA were observed. Recombinant factor VIII (rFVIII) added to danaparoid-treated samples profoundly counteracted the increase of Ks but had only a slight or no effect on the other drugs. Thus, in vitro, argatroban, bivalirudin and danaparoid have comparable anticoagulating effects, rendering the fibrin network more permeable and less resistant to fibrinolysis. For lepirudin, the steep dose-response curve supports previous clinical findings, i.e. this thrombin inhibitor has a narrow therapeutic window. Furthermore, our data suggest that the haemostatic agent, rFVIII, might be effective in treatment of bleeding complications induced by danaparoid. PMID:20216982

  6. Genetic and pharmacological modifications of thrombin formation in apolipoprotein e-deficient mice determine atherosclerosis severity and atherothrombosis onset in a neutrophil-dependent manner.

    Directory of Open Access Journals (Sweden)

    Julian I Borissoff

    Full Text Available BACKGROUND: Variations in the blood coagulation activity, determined genetically or by medication, may alter atherosclerotic plaque progression, by influencing pleiotropic effects of coagulation proteases. Published experimental studies have yielded contradictory findings on the role of hypercoagulability in atherogenesis. We therefore sought to address this matter by extensively investigating the in vivo significance of genetic alterations and pharmacologic inhibition of thrombin formation for the onset and progression of atherosclerosis, and plaque phenotype determination. METHODOLOGY/PRINCIPAL FINDINGS: We generated transgenic atherosclerosis-prone mice with diminished coagulant or hypercoagulable phenotype and employed two distinct models of atherosclerosis. Gene-targeted 50% reduction in prothrombin (FII(-/WT:ApoE(-/- was remarkably effective in limiting disease compared to control ApoE(-/- mice, associated with significant qualitative benefits, including diminished leukocyte infiltration, altered collagen and vascular smooth muscle cell content. Genetically-imposed hypercoagulability in TM(Pro/Pro:ApoE(-/- mice resulted in severe atherosclerosis, plaque vulnerability and spontaneous atherothrombosis. Hypercoagulability was associated with a pronounced neutrophilia, neutrophil hyper-reactivity, markedly increased oxidative stress, neutrophil intraplaque infiltration and apoptosis. Administration of either the synthetic specific thrombin inhibitor Dabigatran etexilate, or recombinant activated protein C (APC, counteracted the pro-inflammatory and pro-atherogenic phenotype of pro-thrombotic TM(Pro/Pro:ApoE(-/- mice. CONCLUSIONS/SIGNIFICANCE: We provide new evidence highlighting the importance of neutrophils in the coagulation-inflammation interplay during atherogenesis. Our findings reveal that thrombin-mediated proteolysis is an unexpectedly powerful determinant of atherosclerosis in multiple distinct settings. These studies suggest that

  7. Modulation of 3D Fibrin Matrix Stiffness by Intrinsic Fibrinogen–Thrombin Compositions and by Extrinsic Cellular Activity

    Science.gov (United States)

    Duong, Haison; Wu, Benjamin

    2009-01-01

    Fibrin is a substance formed through catalytic conversion of coagulation constituents: fibrinogen and thrombin. The kinetics of the two constituents determines the structural properties of the fibrin architecture. We have shown previously that changing the fibrinogen and thrombin concentrations in the final three-dimensional (3D) fibrin matrix influenced cell proliferation and differentiation. In this study, we further examined the effect of changing fibrinogen and thrombin concentrations in the absence or presence of fibroblasts on the structural modulus or stiffness of 3D fibrin matrices. We have prepared fibroblast-free and fibroblast-embedded 3D fibrin matrices of different fibrinogen and thrombin formulations, and tested the stiffness of these constructs using standard mechanical testing assays. Results showed that there was a corresponding increase in stiffness with increasing thrombin and fibrinogen concentrations; the increase was more notable with fibrinogen and to a lesser degree with thrombin. The effect of fibroblasts on the stiffness of the fibrin construct was also examined. We have observed a small increase in the stiffness of the fibroblast-incorporated fibrin construct as they proliferated and exhibited spreading morphology. To our knowledge, this is the first comprehensive report detailing the relationship between fibrinogen and thrombin concentrations, cell proliferation, and stiffness in 3D fibrin matrices. The data obtained may lead to optimally design suitable bioscaffolds where we can control both cell proliferation and structural integrity for a variety of tissue engineering applications. PMID:19309239

  8. Automated Clustering of Similar Amendments

    CERN Document Server

    CERN. Geneva

    2016-01-01

    The Italian Senate is clogged by computer-generated amendments. This talk will describe a simple strategy to cluster them in an automated fashion, so that the appropriate Senate procedures can be used to get rid of them in one sweep.

  9. MicroRNA-146a Decreases High Glucose/Thrombin-Induced Endothelial Inflammation by Inhibiting NAPDH Oxidase 4 Expression

    OpenAIRE

    Huang-Joe Wang; Yuan-Li Huang; Ya-Yun Shih; Hsing-Yu Wu; Ching-Tien Peng; Wan-Yu Lo

    2014-01-01

    Diabetes is associated with hyperglycemia and increased thrombin production. However, it is unknown whether a combination of high glucose and thrombin can modulate the expression of NAPDH oxidase (Nox) subtypes in human aortic endothelial cells (HAECs). Moreover, we investigated the role of a diabetes-associated microRNA (miR-146a) in a diabetic atherothrombosis model. We showed that high glucose (HG) exerted a synergistic effect with thrombin to induce a 10.69-fold increase in Nox4 mRNA leve...

  10. Common variants in the human platelet PAR4 thrombin receptor alter platelet function and differ by race

    Science.gov (United States)

    Edelstein, Leonard C.; Simon, Lukas M.; Lindsay, Cory R.; Kong, Xianguo; Teruel-Montoya, Raúl; Tourdot, Benjamin E.; Chen, Edward S.; Ma, Lin; Coughlin, Shaun; Nieman, Marvin; Holinstat, Michael; Shaw, Chad A.

    2014-01-01

    Human platelets express 2 thrombin receptors: protease-activated receptor (PAR)-1 and PAR4. Recently, we reported 3.7-fold increased PAR4-mediated aggregation kinetics in platelets from black subjects compared with white subjects. We now show that platelets from blacks (n = 70) express 14% more PAR4 protein than those from whites (n = 84), but this difference is not associated with platelet PAR4 function. Quantitative trait locus analysis identified 3 common single nucleotide polymorphisms in the PAR4 gene (F2RL3) associated with PAR4-induced platelet aggregation. Among these single nucleotide polymorphisms, rs773902 determines whether residue 120 in transmembrane domain 2 is an alanine (Ala) or threonine (Thr). Compared with the Ala120 variant, Thr120 was more common in black subjects than in white subjects (63% vs 19%), was associated with higher PAR4-induced human platelet aggregation and Ca2+ flux, and generated greater inositol 1,4,5-triphosphate in transfected cells. A second, less frequent F2RL3 variant, Phe296Val, was only observed in blacks and abolished the enhanced PAR4-induced platelet aggregation and 1,4,5-triphosphate generation associated with PAR4-Thr120. PAR4 genotype did not affect vorapaxar inhibition of platelet PAR1 function, but a strong pharmacogenetic effect was observed with the PAR4-specific antagonist YD-3 [1-benzyl-3(ethoxycarbonylphenyl)-indazole]. These findings may have an important pharmacogenetic effect on the development of new PAR antagonists. PMID:25293779

  11. Increased thrombin generation and fibrinogen level after therapeutic plasma transfusion: relation to bleeding.

    NARCIS (Netherlands)

    Schols, S.E.; Meijden, PE van der; Oerle, R. van; Curvers, J.; Heemskerk, J.W.M.; Pampus, EC van

    2008-01-01

    In a clinical setting, fresh frozen plasma (FFP) is transfused to diluted patients with complicated surgery or trauma, as guided by prolonged conventional coagulation times or low fibrinogen levels. However, the limited sensitivity of these coagulation tests may restrict their use in measuring the e

  12. Thrombotic risk assessment in antiphospholipid syndrome: the role of new antibody specificities and thrombin generation assay.

    Science.gov (United States)

    Sciascia, Savino; Baldovino, Simone; Schreiber, Karen; Solfietti, Laura; Radin, Massimo; Cuadrado, Maria J; Menegatti, Elisa; Erkan, Doruk; Roccatello, Dario

    2016-01-01

    Antiphospholipid syndrome (APS) is an autoimmune condition characterized by the presence of antiphospholipid antibodies (aPL) in subjects presenting with thrombosis and/or pregnancy loss. The currently used classification criteria were updated in the international consensus held in Sidney in 2005. Vascular events seem to result of local procoagulative alterations upon triggers influence (the so called "second-hit theory"), while placental thrombosis and complement activation seem to lead to pregnancy morbidity. The laboratory tests suggested by the current classification criteria include lupus anticoagulant, a functional coagulation assay, and anticardiolipin and anti-β2-glycoprotein-I antibodies, generally detected by solid phase enzyme-linked immunosorbent assay. The real challenge for treating physicians is understanding what is the actual weight of aPL in provoking clinical manifestations in each case. As thrombosis has a multi-factorial cause, each patient needs a risk-stratified approach. In this review we discuss the role of thrombotic risk assessment in primary and secondary prevention of venous and arterial thromboembolic disease in patients with APS, focusing on new antibody specificities, available risk scoring models and new coagulation assays. PMID:27429595

  13. Robust Automated Image Co-Registration of Optical Multi-Sensor Time Series Data: Database Generation for Multi-Temporal Landslide Detection

    Directory of Open Access Journals (Sweden)

    Robert Behling

    2014-03-01

    Full Text Available Reliable multi-temporal landslide detection over longer periods of time requires multi-sensor time series data characterized by high internal geometric stability, as well as high relative and absolute accuracy. For this purpose, a new methodology for fully automated co-registration has been developed allowing efficient and robust spatial alignment of standard orthorectified data products originating from a multitude of optical satellite remote sensing data of varying spatial resolution. Correlation-based co-registration uses world-wide available terrain corrected Landsat Level 1T time series data as the spatial reference, ensuring global applicability. The developed approach has been applied to a multi-sensor time series of 592 remote sensing datasets covering an approximately 12,000 km2 area in Southern Kyrgyzstan (Central Asia strongly affected by landslides. The database contains images acquired during the last 26 years by Landsat (ETM, ASTER, SPOT and RapidEye sensors. Analysis of the spatial shifts obtained from co-registration has revealed sensor-specific alignments ranging between 5 m and more than 400 m. Overall accuracy assessment of these alignments has resulted in a high relative image-to-image accuracy of 17 m (RMSE and a high absolute accuracy of 23 m (RMSE for the whole co-registered database, making it suitable for multi-temporal landslide detection at a regional scale in Southern Kyrgyzstan.

  14. Cardiovascular and biochemical studies on the effects of thrombin and dabigatran and the interaction with vasopressor molecules

    Directory of Open Access Journals (Sweden)

    R. Anand

    2014-10-01

    Conclusion: The thrombin inhibitor, dabigatran reduces vascular oxidative stress and inflammation, improves endothelial function, and decreases atherosclerosis in rodents. [Int J Basic Clin Pharmacol 2014; 3(5.000: 874-878

  15. Comparative evaluation of direct thrombin and factor Xa inhibitors with antiplatelet agents under flow and static conditions: an in vitro flow chamber model.

    Directory of Open Access Journals (Sweden)

    Kazuya Hosokawa

    Full Text Available Dabigatran and rivaroxaban are novel oral anticoagulants that specifically inhibit thrombin and factor Xa, respectively. The aim of this study is to elucidate antithrombotic properties of these anticoagulant agents under arterial and venous shear conditions. Whole blood samples treated with dabigatran or rivaroxaban at 250, 500, and 1000 nM, with/without aspirin and AR-C66096, a P2Y12 antagonist, were perfused over a microchip coated with collagen and tissue thromboplastin at shear rates of 240 and 600 s(-1. Fibrin-rich platelet thrombus formation was quantified by monitoring flow pressure changes. Dabigatran at higher concentrations (500 and 1000 nM potently inhibited thrombus formation at both shear rates, whereas 1000 nM of rivaroxaban delayed, but did not completely inhibit, thrombus formation. Dual antiplatelet agents weakly suppressed thrombus formation at both shear rates, but intensified the anticoagulant effects of dabigatran and rivaroxaban. The anticoagulant effects of dabigatran and rivaroxaban were also evaluated under static conditions using thrombin generation (TG assay. In platelet-poor plasma, dabigatran at 250 and 500 nM efficiently prolonged the lag time (LT and moderately reduce peak height (PH of TG, whereas rivaroxaban at 250 nM efficiently prolonged LT and reduced PH of TG. In platelet-rich plasma, however, both anticoagulants efficiently delayed LT and reduced PH of TG. Our results suggest that dabigatran and rivaroxaban may exert distinct antithrombotic effects under flow conditions, particularly in combination with dual antiplatelet therapy.

  16. Mutations in the fourth EGF-like domain affect thrombomodulin-induced changes in the active site of thrombin

    OpenAIRE

    Koeppe, Julia R.; Beach, Muneera A.; Baerga-Ortiz, Abel; Jordan Kerns, S.; Komives, Elizabeth A.

    2008-01-01

    A number of alanine and more conservative mutants of residues in the fourth domain of thrombomodulin (TM) were prepared and assayed for protein C activation and for thrombin binding. Several of the alanine mutations appeared to cause misfolding or structural defects as assessed by poor expression and/or NMR HSQC experiments, while more conservative mutations at the same site appeared to fold correctly and retain activity. Several of the conservative mutants bound more weakly to thrombin despi...

  17. Endoscopic ultrasound guided thrombin injection of angiographically occult pancreatitis associated visceral artery pseudoaneurysms:Case series

    Institute of Scientific and Technical Information of China (English)

    Shivanand; Gamanagatti; Usha; Thingujam; Pramod; Garg; Surajkumar; Nongthombam; Nihar; Ranjan; Dash

    2015-01-01

    Pseudoaneurysm is a known complication of pancreatitis associated with significant mortality and morbidity. Imaging plays an important role in the diagnosis and management. Computed tomography(CT) helps localize the lesion and the severity of the background pancreatitis but digital subtraction angiography with coil embolization is recommended to avoid bleeding and inadvertent surgery. However, in cases where angiographic coil embolization is not feasible due to technical reasons, thrombin injection via CT or ultrasound guidance remains a viable option and often described in literature. In this series, effort has been made to highlight the role of endoscopic ultrasound guided thrombin instillation especially in patients with poorly visualized pseudoaneurysm on ultrasound thereby avoiding surgery and the associated mortality and morbidity.

  18. Implications of Dabigatran, a direct thrombin inhibitor, for oral surgery practice.

    Science.gov (United States)

    Davis, Clayton; Robertson, Chad; Shivakumar, Sudeep; Lee, Min

    2013-01-01

    Direct thrombin inhibitors, specifically orally administered dabigatran etexilate, are emerging as alternatives to warfarin for anticoagulation in the management of atrial fibrillation and venous thromboembolism. The risk associated with bleeding events while taking dabigatran has been documented in multiple randomized controlled trials, but to date, no studies have focused on the risk of bleeding after dental extraction. Extraction of teeth is one of the most common surgical procedures and may cause significant bleeding, so a thorough understanding of the pharmacology of anticoagulant medications is required to prevent complications. With the increasing use of direct thrombin inhibitors, the safe management of patients taking these anticoagulants must be delineated. This review compares dabigatran and warfarin, especially in terms of their effects on dental and oral surgery practice, and examines best management of these patients in light of the existing literature. PMID:23920075

  19. Sensitive electrochemical aptasensor for thrombin detection based on graphene served as platform and graphene oxide as enhancer.

    Science.gov (United States)

    He, Chun; Xu, Zenghong; Sun, Tao; Wang, Li

    2014-01-01

    A sensitive electrochemical aptasensor was developed with conductive graphene served as platform and inert graphene oxide (GO) as enhancer. An electrodeposited nano-Au layer was firstly formed on conductive graphene modified glass carbon electrode surface for further immobilizing of electrochemical redox probe hexacyanoferrates nanoparticles (NiHCFNPs). Subsequently, another nano-Au layer was formed for immobilizing of thrombin aptamer (TBA). In the presence of thrombin, the TBA on the electrode surface could bind with thrombin, which made a barrier for electrons and inhibited the electro-transfer, resulting in the decreased electrochemical signals of NiHCFNPs. Owing to the non-conductivity property of graphene oxide, further decreased electrochemical signals of NiHCFNPs could be obtained via the sandwich reaction with GO-labeled TBA. According to the signal changes before the thrombin recognition and after sandwich reaction, trace detection of thrombin could be achieved. As a result, the proposed approach showed a high sensitivity and a wider linearity to thrombin in the range from 0.005 nM to 50 nM with a detection limit of 1 pM. PMID:24142359

  20. Deletion of the thrombin cleavage domain of osteopontin mediates breast cancer cell adhesion, proteolytic activity, tumorgenicity, and metastasis

    Directory of Open Access Journals (Sweden)

    Postenka Carl O

    2011-01-01

    Full Text Available Abstract Background Osteopontin (OPN is a secreted phosphoprotein often overexpressed at high levels in the blood and primary tumors of breast cancer patients. OPN contains two integrin-binding sites and a thrombin cleavage domain located in close proximity to each other. Methods To study the role of the thrombin cleavage site of OPN, MDA-MB-468 human breast cancer cells were stably transfected with either wildtype OPN (468-OPN, mutant OPN lacking the thrombin cleavage domain (468-ΔTC or an empty vector (468-CON and assessed for in vitro and in vivo functional differences in malignant/metastatic behavior. Results All three cell lines were found to equivalently express thrombin, tissue factor, CD44, αvβ5 integrin and β1 integrin. Relative to 468-OPN and 468-CON cells, 468-ΔTC cells expressing OPN with a deleted thrombin cleavage domain demonstrated decreased cell adhesion (p in vitro. Furthermore, injection of 468-ΔTC cells into the mammary fat pad of nude mice resulted in decreased primary tumor latency time (p Conclusions The results presented here suggest that expression of thrombin-uncleavable OPN imparts an early tumor formation advantage as well as a metastatic advantage for breast cancer cells, possibly due to increased proteolytic activity and decreased adhesion and apoptosis. Clarification of the mechanisms responsible for these observations and the translation of this knowledge into the clinic could ultimately provide new therapeutic opportunities for combating breast cancer.

  1. Spontaneous pseudoaneurysm of the uterine artery during pregnancy treated by direct thrombin injection: A case report

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Jung Hee; Kim, See Hyung; Kim, Young Hwan [Dept. Radiology, Keimyung University School of Medicine, Dongsan Medical Center, Daegu (Korea, Republic of)

    2016-04-15

    Pseudoaneurysm of uterine artery during pregnancy is a very rare disease. It is mostly associated with uterine artery injury, usually occurring after proceeding conditions such as history of gynecologic operation and infection. However, the best treatment modality has not been established yet. Herein, we reported a case of spontaneous formation of uterine artery pseudoaneurysm during pregnancy treated by direct thrombin injection without any complication or recurrence.

  2. A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm

    OpenAIRE

    Ikebukuro, Kazunori; Okumura, Yuji; SUMIKURA, Koichi; Karube, Isao

    2005-01-01

    Thrombin-inhibiting DNA aptamers have already been obtained through the systematic evolution of ligands by exponential enrichment (SELEX). However, SELEX is a method that screens DNA aptamers that bind to their target molecules, and it sometimes fails to screen good inhibitors. Therefore, it is necessary to develop a method of screening DNA aptamers based on their inhibitory effects on the target molecules. We developed a novel method of detecting aptamers using an evolution-mimicking algorit...

  3. A New Potent Inhibitor of Thrombin from the Leech Haemendipsa Yanyuanensis

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Two components of anticoagulant protein were isolated from the leech Haemendipsa yanyuanensis by heparin agarose affinity chromatography and ultracentrifugation. The determination of anticoagulant activity and characterization analysis of the pro tein using the method of chromogenic substrate indicates that the anticoagulant protein is thrombin-specific but not factor Xa-specific. The results lay a foundation for the research of the anticoagulant mechanism and application of anticoagulant protein from H. yanyua nensis.

  4. Endoscopic ultrasound guided thrombin injection of angiographically occult pancreatitis associated visceral artery pseudoaneurysms: Case series

    OpenAIRE

    Gamanagatti, Shivanand; Thingujam, Usha; Garg, Pramod; Nongthombam, Surajkumar; Dash, Nihar Ranjan

    2015-01-01

    Pseudoaneurysm is a known complication of pancreatitis associated with significant mortality and morbidity. Imaging plays an important role in the diagnosis and management. Computed tomography (CT) helps localize the lesion and the severity of the background pancreatitis but digital subtraction angiography with coil embolization is recommended to avoid bleeding and inadvertent surgery. However, in cases where angiographic coil embolization is not feasible due to technical reasons, thrombin in...

  5. Successful endovascular treatment of a hemodialysis graft pseudoaneurysm by covered stent and direct percutaneous thrombin injection.

    LENUS (Irish Health Repository)

    Keeling, Aoife N

    2011-07-25

    Vascular access for hemodialysis remains a challenge for nephrologists, vascular surgeons, and interventional radiologists alike. Arteriovenous fistula and synthetic grafts remain the access of choice for long-term hemodialysis; however, they are subject to complications from infection and repeated needle cannulation. Pseudoaneurysms are an increasingly recognized adverse event. At present, there are many minimally invasive methods to repair these wall defects. We present a graft pseudoaneurysm, which required a combination of endovascular stent graft placement and percutaneous thrombin injection for successful occlusion.

  6. Raman and surface-enhanced Raman scattering (SERS) studies of the thrombin-binding aptamer.

    Science.gov (United States)

    Wu, Tsai-Chin; Vasudev, Milana; Dutta, Mitra; Stroscio, Michael A

    2013-06-01

    Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection.

  7. Allosteric Partial Inhibition of Monomeric Proteases. Sulfated Coumarins Induce Regulation, not just Inhibition, of Thrombin

    OpenAIRE

    Stephen Verespy III; Mehta, Akul Y.; Daniel Afosah; Al-Horani, Rami A.; Desai, Umesh R.

    2016-01-01

    Allosteric partial inhibition of soluble, monomeric proteases can offer major regulatory advantages, but remains a concept on paper to date; although it has been routinely documented for receptors and oligomeric proteins. Thrombin, a key protease of the coagulation cascade, displays significant conformational plasticity, which presents an attractive opportunity to discover small molecule probes that induce sub-maximal allosteric inhibition. We synthesized a focused library of some 36 sulfated...

  8. Direct thrombin inhibitors in acute coronary syndromes: effect in patients undergoing early percutaneous coronary intervention

    OpenAIRE

    Sinnaeve, Peter; Simes, John; Yusuf, Salim; Garg, Jyotsna; Mehta, Shamir; Eikelboom, John; Bittl, John A; Serruys, Patrick; Topol, Eric J.; Granger, Christopher B

    2005-01-01

    AIMS: We evaluated the effect of direct thrombin inhibitors (DTIs) in patients undergoing early percutaneous coronary intervention (PCI), using the DTI Trialists' Collaboration database of 35,970 patients from 11 randomized trials of DTIs vs. heparin. METHODS AND RESULTS: We performed a Cox proportional hazards regression analysis with PCI as a time-dependent covariate to assess the independent impact of DTIs according to the performance of early PCI. PCI was performed in 7049 patients in the...

  9. Manufacturing and automation

    Directory of Open Access Journals (Sweden)

    Ernesto Córdoba Nieto

    2010-04-01

    Full Text Available The article presents concepts and definitions from different sources concerning automation. The work approaches automation by virtue of the author’s experience in manufacturing production; why and how automation prolects are embarked upon is considered. Technological reflection regarding the progressive advances or stages of automation in the production area is stressed. Coriat and Freyssenet’s thoughts about and approaches to the problem of automation and its current state are taken and examined, especially that referring to the problem’s relationship with reconciling the level of automation with the flexibility and productivity demanded by competitive, worldwide manufacturing.

  10. Electrochemiluminescence biosensor based on CdSe quantum dots for the detection of thrombin

    International Nuclear Information System (INIS)

    A novel QDs electrochemiluminescence (ECL) biosensor for the determination of thrombin was described. The CdSe QDs solution was dripped onto the clear surface of the ITO and then immersed in PBS which contained EDC and NHS as a coupling agent to activate the carboxyl-terminated surface of the CdSe QDs. The ITO electrode was immersed in the PBS containing 0.4 μM aptamer, followed by rinsing with PBS and dried with N2 again, then dipped in the BSA solution for 30 min to decrease the non-specific binding. After that, the aptamer modified ITO was soaked in PBS to remove unbound aptamer. Under optimal conditions, the linear range was obtained from 0 to 64 μg mL−1 with a correlation coefficient of 0.9986 (n = 16). The control experiment was also carried out by using BSA, lysozyme and IgG in the absence of thrombin. The results showed that the aptasensor had good specificity, stability and reproducibility to the thrombin. Moreover, the aptasensor could be used for detection of real sample with consistent results in comparison with those obtained by electrochemical method which could provide a promising platform for fabrication of aptamer based biosensors.

  11. Amino acid residues of heparin cofactor II required for stimulation of thrombin inhibition by sulphated polyanions.

    Science.gov (United States)

    Colwell, N S; Grupe, M J; Tollefsen, D M

    1999-04-12

    A variety of sulphated polyanions in addition to heparin and dermatan sulphate stimulate the inhibition of thrombin by heparin cofactor II (HCII). Previous investigations indicated that the binding sites on HCII for heparin and dermatan sulphate overlap but are not identical. In this study we determined the concentrations (IC50) of various polyanions required to stimulate thrombin inhibition by native recombinant HCII in comparison with three recombinant HCII variants having decreased affinity for heparin (Lys-173-->Gln), dermatan sulphate (Arg-189-->His), or both heparin and dermatan sulphate (Lys-185-->Asn). Pentosan polysulphate, sulphated bis-lactobionic acid amide, and sulphated bis-maltobionic acid amide resembled dermatan sulphate, since their IC50 values were increased to a much greater degree (>/=8-fold) by the mutations Arg-189-->His and Lys-185-->Asn than by Lys-173-->Gln (Gln and Lys-185-->Asn (>/=6-fold) than by Arg-189-->His (thrombin by an N-terminal deletion mutant of HCII (Delta1-74). These results suggest that, like dermatan sulphate and heparin, other polyanions stimulate HCII primarily by an allosteric mechanism requiring the N-terminal acidic domain. PMID:10209287

  12. Mutant N143P Reveals How Na[superscript +] Activates Thrombin

    Energy Technology Data Exchange (ETDEWEB)

    Niu, Weiling; Chen, Zhiwei; Bush-Pelc, Leslie A.; Bah, Alaji; Gandhi, Prafull S.; Di Cera, Enrico; (WU-MED)

    2010-01-12

    The molecular mechanism of thrombin activation by Na{sup +} remains elusive. Its kinetic formulation requires extension of the classical Botts-Morales theory for the action of a modifier on an enzyme to correctly account for the contribution of the E*, E, and E:Na{sup +} forms. The extended scheme establishes that analysis of k{sub cat} unequivocally identifies allosteric transduction of Na{sup +} binding into enhanced catalytic activity. The thrombin mutant N143P features no Na{sup +}-dependent enhancement of k{sub cat} yet binds Na{sup +} with an affinity comparable to that of wild type. Crystal structures of the mutant in the presence and absence of Na{sup +} confirm that Pro{sup 143} abrogates the important H-bond between the backbone N atom of residue 143 and the carbonyl O atom of Glu{sup 192}, which in turn controls the orientation of the Glu{sup 192}-Gly{sup 193} peptide bond and the correct architecture of the oxyanion hole. We conclude that Na{sup +} activates thrombin by securing the correct orientation of the Glu{sup 192}-Gly{sup 193} peptide bond, which is likely flipped in the absence of cation. Absolute conservation of the 143-192 H-bond in trypsin-like proteases and the importance of the oxyanion hole in protease function suggest that this mechanism of Na{sup +} activation is present in all Na{sup +}-activated trypsin-like proteases.

  13. Elevated Cytokines, Thrombin and PAI-1 in Severe HCPS Patients Due to Sin Nombre Virus

    Directory of Open Access Journals (Sweden)

    Virginie Bondu

    2015-02-01

    Full Text Available Sin Nombre Hantavirus (SNV, Bunyaviridae Hantavirus is a Category A pathogen that causes Hantavirus Cardiopulmonary Syndrome (HCPS with case fatality ratios generally ranging from 30% to 50%. HCPS is characterized by vascular leakage due to dysregulation of the endothelial barrier function. The loss of vascular integrity results in non-cardiogenic pulmonary edema, shock, multi-organ failure and death. Using Electric Cell-substrate Impedance Sensing (ECIS measurements, we found that plasma samples drawn from University of New Mexico Hospital patients with serologically-confirmed HCPS, induce loss of cell-cell adhesion in confluent epithelial and endothelial cell monolayers grown in ECIS cultureware. We show that the loss of cell-cell adhesion is sensitive to both thrombin and plasmin inhibitors in mild cases, and to thrombin only inhibition in severe cases, suggesting an increasing prothrombotic state with disease severity. A proteomic profile (2D gel electrophoresis and mass spectrometry of HCPS plasma samples in our cohort revealed robust antifibrinolytic activity among terminal case patients. The prothrombotic activity is highlighted by acute ≥30 to >100 fold increases in active plasminogen activator inhibitor (PAI-1 which, preceded death of the subjects within 48 h. Taken together, this suggests that PAI-1 might be a response to the severe pathology as it is expected to reduce plasmin activity and possibly thrombin activity in the terminal patients.

  14. Development of gel-forming lyophilized formulation with recombinant human thrombin.

    Science.gov (United States)

    Murányi, Andrej; Bartoš, Peter; Tichý, Eduard; Lazová, Jana; Pšenková, Jana; Žabka, Marián

    2015-01-01

    The objective of this work was development and evaluation of gel-forming lyophilized formulation with recombinant human thrombin for topical administration. The influence of pH, ionic strength and buffer type on protein stability was evaluated as part of the pre-formulation screening studies. Results indicated an optimal pH from 6.0 to 7.0 and increased stability with increasing content of sodium chloride. The tested buffer types had no significant effect on thrombin stability. For further development, thermosensitive Pluronic® F-127 was employed as a bulking and gelling agent. Physical and mechanical characterization and viscosity measurement confirmed the gel-forming properties of the formulation at the application temperature of 32 °C. Several techniques (addition of well-soluble polyols, different freezing protocols and reconstitution under vacuum) were tested to decrease the reconstitution time. The obtained results revealed that a vacuum in the vial headspace is crucial for acceptable reconstitution. The freeze drying process has no negative impact on recombinant thrombin stability, and this was confirmed by reverse-phase-HPLC, activity assay and optical density measurements.

  15. A Kazal-type inhibitor with thrombin specificity from Rhodnius prolixus.

    Science.gov (United States)

    Friedrich, T; Kröger, B; Bialojan, S; Lemaire, H G; Höffken, H W; Reuschenbach, P; Otte, M; Dodt, J

    1993-08-01

    A thrombin-specific inhibitor with an apparent molecular mass of 11 kDa has been purified from the insect Rhodnius prolixus. Amino-terminal protein sequence analysis allowed the molecular cloning of the corresponding cDNA. The open reading frame codes for a protein of about 103 amino acid residues and displays an internal sequence homology of residues 6-48 with residues 57-101 indicating a two-domain structure. Based on the amino acid sequence the two domains exhibit high homology to protease inhibitors belonging to the Kazal-type family. Model building suggests that the first domain binds to the active site with residue His10 pointing into the specificity pocket. From gel filtration and tight-binding inhibition experiments the inhibitor appears to form 1:1 complexes with thrombin. Periplasma-directed heterologous expression of the rhodniin cDNA in Escherichia coli yields the intact thrombin inhibitor. Natural and recombinant rhodniin both display inhibition constants of about 2 x 10(-13) M.

  16. Posttraumatic lingual artery pseudoaneurysm treated with ultrasound-guided percutaneous thrombin injection.

    Science.gov (United States)

    Masella, Pamela C; Hanson, Megan M; Hall, Brian T; Verghese, John J; Kellicut, Dwight C

    2014-07-01

    Pseudoaneurysms of the lingual artery are extremely rare and are commonly iatrogenic in nature or less frequently a result of blunt or penetrating trauma. Traditionally, these vascular abnormalities have been repaired with open or endovascular techniques. Although ultrasound-guided percutaneous thrombin injection has become a standard treatment for superficial pseudoaneurysms, there are no reports of this being used in the treatment of lingual artery pseudoaneurysms. We report the case of a 26-year-old man who suffered a penetrating head and neck injury after an improvised explosive device blast in Iraq who presented with persistent oropharyngeal swelling. Color-flow Doppler ultrasonography revealed the classic yin/yang sign of a pseudoaneurysm, and a computed tomography scan was obtained that revealed a right lingual artery pseudoaneurysm. With the lack of endovascular capabilities and the excessive risk of open surgery, thrombin was injected directly into the pseudoaneurysm under ultrasound guidance. A computed tomography scan and Doppler ultrasonography revealed complete resolution of the aneurysm. This article presents the first reported case in the English literature of a lingual artery aneurysm after penetrating trauma managed successfully with ultrasound-guided percutaneous thrombin injection. PMID:24365080

  17. Allosteric Partial Inhibition of Monomeric Proteases. Sulfated Coumarins Induce Regulation, not just Inhibition, of Thrombin

    Science.gov (United States)

    Verespy III, Stephen; Mehta, Akul Y.; Afosah, Daniel; Al-Horani, Rami A.; Desai, Umesh R.

    2016-01-01

    Allosteric partial inhibition of soluble, monomeric proteases can offer major regulatory advantages, but remains a concept on paper to date; although it has been routinely documented for receptors and oligomeric proteins. Thrombin, a key protease of the coagulation cascade, displays significant conformational plasticity, which presents an attractive opportunity to discover small molecule probes that induce sub-maximal allosteric inhibition. We synthesized a focused library of some 36 sulfated coumarins to discover two agents that display sub-maximal efficacy (~50%), high potency (150-fold). Michaelis-Menten, competitive inhibition, and site-directed mutagenesis studies identified exosite 2 as the site of binding for the most potent sulfated coumarin. Stern-Volmer quenching of active site-labeled fluorophore suggested that the allosteric regulators induce intermediate structural changes in the active site as compared to those that display ~80–100% efficacy. Antithrombin inactivation of thrombin was impaired in the presence of the sulfated coumarins suggesting that allosteric partial inhibition arises from catalytic dysfunction of the active site. Overall, sulfated coumarins represent first-in-class, sub-maximal inhibitors of thrombin. The probes establish the concept of allosteric partial inhibition of soluble, monomeric proteins. This concept may lead to a new class of anticoagulants that are completely devoid of bleeding. PMID:27053426

  18. Automated Postediting of Documents

    CERN Document Server

    Knight, K; Knight, Kevin; Chander, Ishwar

    1994-01-01

    Large amounts of low- to medium-quality English texts are now being produced by machine translation (MT) systems, optical character readers (OCR), and non-native speakers of English. Most of this text must be postedited by hand before it sees the light of day. Improving text quality is tedious work, but its automation has not received much research attention. Anyone who has postedited a technical report or thesis written by a non-native speaker of English knows the potential of an automated postediting system. For the case of MT-generated text, we argue for the construction of postediting modules that are portable across MT systems, as an alternative to hardcoding improvements inside any one system. As an example, we have built a complete self-contained postediting module for the task of article selection (a, an, the) for English noun phrases. This is a notoriously difficult problem for Japanese-English MT. Our system contains over 200,000 rules derived automatically from online text resources. We report on l...

  19. Configuration Management Automation (CMA)

    Data.gov (United States)

    Department of Transportation — Configuration Management Automation (CMA) will provide an automated, integrated enterprise solution to support CM of FAA NAS and Non-NAS assets and investments. CMA...

  20. Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors.

    Directory of Open Access Journals (Sweden)

    Ana C Figueiredo

    Full Text Available The tremendous social and economic impact of thrombotic disorders, together with the considerable risks associated to the currently available therapies, prompt for the development of more efficient and safer anticoagulants. Novel peptide-based thrombin inhibitors were identified using in silico structure-based design and further validated in vitro. The best candidate compounds contained both L- and D-amino acids, with the general sequence D-Phe(P3-Pro(P2-D-Arg(P1-P1'-CONH₂. The P1' position was scanned with L- and D-isomers of natural or unnatural amino acids, covering the major chemical classes. The most potent non-covalent and proteolysis-resistant inhibitors contain small hydrophobic or polar amino acids (Gly, Ala, Ser, Cys, Thr at the P1' position. The lead tetrapeptide, D-Phe-Pro-D-Arg-D-Thr-CONH₂, competitively inhibits α-thrombin's cleavage of the S2238 chromogenic substrate with a K(i of 0.92 µM. In order to understand the molecular details of their inhibitory action, the three-dimensional structure of three peptides (with P1' L-isoleucine (fPrI, L-cysteine (fPrC or D-threonine (fPrt in complex with human α-thrombin were determined by X-ray crystallography. All the inhibitors bind in a substrate-like orientation to the active site of the enzyme. The contacts established between the D-Arg residue in position P1 and thrombin are similar to those observed for the L-isomer in other substrates and inhibitors. However, fPrC and fPrt disrupt the active site His57-Ser195 hydrogen bond, while the combination of a P1 D-Arg and a bulkier P1' residue in fPrI induce an unfavorable geometry for the nucleophilic attack of the scissile bond by the catalytic serine. The experimental models explain the observed relative potency of the inhibitors, as well as their stability to proteolysis. Moreover, the newly identified direct thrombin inhibitors provide a novel pharmacophore platform for developing antithrombotic agents by exploring the

  1. Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors.

    Science.gov (United States)

    Figueiredo, Ana C; Clement, Cristina C; Zakia, Sheuli; Gingold, Julian; Philipp, Manfred; Pereira, Pedro J B

    2012-01-01

    The tremendous social and economic impact of thrombotic disorders, together with the considerable risks associated to the currently available therapies, prompt for the development of more efficient and safer anticoagulants. Novel peptide-based thrombin inhibitors were identified using in silico structure-based design and further validated in vitro. The best candidate compounds contained both L- and D-amino acids, with the general sequence D-Phe(P3)-Pro(P2)-D-Arg(P1)-P1'-CONH₂. The P1' position was scanned with L- and D-isomers of natural or unnatural amino acids, covering the major chemical classes. The most potent non-covalent and proteolysis-resistant inhibitors contain small hydrophobic or polar amino acids (Gly, Ala, Ser, Cys, Thr) at the P1' position. The lead tetrapeptide, D-Phe-Pro-D-Arg-D-Thr-CONH₂, competitively inhibits α-thrombin's cleavage of the S2238 chromogenic substrate with a K(i) of 0.92 µM. In order to understand the molecular details of their inhibitory action, the three-dimensional structure of three peptides (with P1' L-isoleucine (fPrI), L-cysteine (fPrC) or D-threonine (fPrt)) in complex with human α-thrombin were determined by X-ray crystallography. All the inhibitors bind in a substrate-like orientation to the active site of the enzyme. The contacts established between the D-Arg residue in position P1 and thrombin are similar to those observed for the L-isomer in other substrates and inhibitors. However, fPrC and fPrt disrupt the active site His57-Ser195 hydrogen bond, while the combination of a P1 D-Arg and a bulkier P1' residue in fPrI induce an unfavorable geometry for the nucleophilic attack of the scissile bond by the catalytic serine. The experimental models explain the observed relative potency of the inhibitors, as well as their stability to proteolysis. Moreover, the newly identified direct thrombin inhibitors provide a novel pharmacophore platform for developing antithrombotic agents by exploring the conformational

  2. Detection of BRAF Mutations Using a Fully Automated Platform and Comparison with High Resolution Melting, Real-Time Allele Specific Amplification, Immunohistochemistry and Next Generation Sequencing Assays, for Patients with Metastatic Melanoma.

    Directory of Open Access Journals (Sweden)

    Alexandre Harlé

    Full Text Available Metastatic melanoma is a severe disease with one of the highest mortality rate in skin diseases. Overall survival has significantly improved with immunotherapy and targeted therapies. Kinase inhibitors targeting BRAF V600 showed promising results. BRAF genotyping is mandatory for the prescription of anti-BRAF therapies.Fifty-nine formalin-fixed paraffin-embedded melanoma samples were assessed using High-Resolution-Melting (HRM PCR, Real-time allele-specific amplification (RT-ASA PCR, Next generation sequencing (NGS, immunohistochemistry (IHC and the fully-automated molecular diagnostics platform IdyllaTM. Sensitivity, specificity, positive predictive value and negative predictive value were calculated using NGS as the reference standard to compare the different assays.BRAF mutations were found in 28(47.5%, 29(49.2%, 31(52.5%, 29(49.2% and 27(45.8% samples with HRM, RT-ASA, NGS, IdyllaTM and IHC respectively. Twenty-six (81.2% samples were found bearing a c.1799T>A (p.Val600Glu mutation, three (9.4% with a c.1798_1799delinsAA (p.Val600Lys mutation and one with c.1789_1790delinsTC (p.Leu597Ser mutation. Two samples were found bearing complex mutations.HRM appears the less sensitive assay for the detection of BRAF V600 mutations. The RT-ASA, IdyllaTM and IHC assays are suitable for routine molecular diagnostics aiming at the prescription of anti-BRAF therapies. IdyllaTM assay is fully-automated and requires less than 2 minutes for samples preparation and is the fastest of the tested assays.

  3. Automated Standard Hazard Tool

    Science.gov (United States)

    Stebler, Shane

    2014-01-01

    The current system used to generate standard hazard reports is considered cumbersome and iterative. This study defines a structure for this system's process in a clear, algorithmic way so that standard hazard reports and basic hazard analysis may be completed using a centralized, web-based computer application. To accomplish this task, a test server is used to host a prototype of the tool during development. The prototype is configured to easily integrate into NASA's current server systems with minimal alteration. Additionally, the tool is easily updated and provides NASA with a system that may grow to accommodate future requirements and possibly, different applications. Results of this project's success are outlined in positive, subjective reviews complete by payload providers and NASA Safety and Mission Assurance personnel. Ideally, this prototype will increase interest in the concept of standard hazard automation and lead to the full-scale production of a user-ready application.

  4. Workflow automation architecture standard

    Energy Technology Data Exchange (ETDEWEB)

    Moshofsky, R.P.; Rohen, W.T. [Boeing Computer Services Co., Richland, WA (United States)

    1994-11-14

    This document presents an architectural standard for application of workflow automation technology. The standard includes a functional architecture, process for developing an automated workflow system for a work group, functional and collateral specifications for workflow automation, and results of a proof of concept prototype.

  5. Activated thrombin-activatable fibrinolysis inhibitor (TAFIa) attenuates breast cancer cell metastatic behaviors through inhibition of plasminogen activation and extracellular proteolysis

    OpenAIRE

    Bazzi, Zainab A.; Lanoue, Danielle; El-Youssef, Mouhanned; Romagnuolo, Rocco; Tubman, Janice; Cavallo-Medved, Dora; Porter, Lisa A.; Boffa, Michael B.

    2016-01-01

    Background Thrombin activatable fibrinolysis inhibitor (TAFI) is a plasma zymogen, which can be converted to activated TAFI (TAFIa) through proteolytic cleavage by thrombin, plasmin, and most effectively thrombin in complex with the endothelial cofactor thrombomodulin (TM). TAFIa is a carboxypeptidase that cleaves carboxyl terminal lysine and arginine residues from protein and peptide substrates, including plasminogen-binding sites on cell surface receptors. Carboxyl terminal lysine residues ...

  6. DOLFIN: Automated Finite Element Computing

    CERN Document Server

    Logg, Anders; 10.1145/1731022.1731030

    2011-01-01

    We describe here a library aimed at automating the solution of partial differential equations using the finite element method. By employing novel techniques for automated code generation, the library combines a high level of expressiveness with efficient computation. Finite element variational forms may be expressed in near mathematical notation, from which low-level code is automatically generated, compiled and seamlessly integrated with efficient implementations of computational meshes and high-performance linear algebra. Easy-to-use object-oriented interfaces to the library are provided in the form of a C++ library and a Python module. This paper discusses the mathematical abstractions and methods used in the design of the library and its implementation. A number of examples are presented to demonstrate the use of the library in application code.

  7. Automated Planning and Scheduling for Planetary Rover Distributed Operations

    Science.gov (United States)

    Backes, Paul G.; Rabideau, Gregg; Tso, Kam S.; Chien, Steve

    1999-01-01

    Automated planning and Scheduling, including automated path planning, has been integrated with an Internet-based distributed operations system for planetary rover operations. The resulting prototype system enables faster generation of valid rover command sequences by a distributed planetary rover operations team. The Web Interface for Telescience (WITS) provides Internet-based distributed collaboration, the Automated Scheduling and Planning Environment (ASPEN) provides automated planning and scheduling, and an automated path planner provided path planning. The system was demonstrated on the Rocky 7 research rover at JPL.

  8. A label-free and high sensitive aptamer biosensor based on hyperbranched polyester microspheres for thrombin detection

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Chong [Jiangsu Key Laboratory of Biofunctional Materials, Biomedical Functional Materials Collaborative Innovation Center, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023 (China); Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014 (China); Han, Qiaorong [Jiangsu Key Laboratory of Biofunctional Materials, Biomedical Functional Materials Collaborative Innovation Center, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023 (China); Wang, Daoying; Xu, Weimin [Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014 (China); Wang, Weijuan [Jiangsu Key Laboratory of Biofunctional Materials, Biomedical Functional Materials Collaborative Innovation Center, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023 (China); Zhao, Wenbo, E-mail: zhaowenbo@njnu.edu.cn [Jiangsu Key Laboratory of Biofunctional Materials, Biomedical Functional Materials Collaborative Innovation Center, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023 (China); Zhou, Min, E-mail: zhouminnju@126.com [Department of Vascular Surgery, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008 (China)

    2014-11-19

    Highlights: • A label-free thrombin aptamer biosensor applied in whole blood has been developed. • The aptamer biosensor showed a wide detection range and a low detection limit. • The antibiofouling idea utilized for biosensor is significant for diagnostics. - Abstract: In this paper, we have synthesized hyperbranched polyester microspheres with carboxylic acid functional groups (HBPE-CA) and developed a label-free electrochemical aptamer biosensor using thrombin-binding aptamer (TBA) as receptor for the measurement of thrombin in whole blood. The indium tin oxide (ITO) electrode surface modified with HBPE-CA microspheres was grafted with TBA, which has excellent binding affinity and selectivity for thrombin. Binding of the thrombin at the modified ITO electrode surface greatly restrained access of electrons for a redox probe of [Fe(CN){sub 6}]{sup 3−/4−}. Moreover, the aptamer biosensor could be used for detection of thrombin in whole blood, a wide detection range (10 fM–100 nM) and a detection limit on the order of 0.90 fM were demonstrated. Control experiments were also carried out by using bull serum albumin (BSA) and lysozyme in the absence of thrombin. The good stability and repeatability of this aptamer biosensor were also proved. We expect that this demonstration will lead to the development of highly sensitive label-free sensors based on aptamer with lower cost than current technology. The integration of the technologies, which include anticoagulant, sensor and nanoscience, will bring significant input to high-performance biosensors relevant to diagnostics and therapy of interest for human health.

  9. A label-free and high sensitive aptamer biosensor based on hyperbranched polyester microspheres for thrombin detection

    International Nuclear Information System (INIS)

    Highlights: • A label-free thrombin aptamer biosensor applied in whole blood has been developed. • The aptamer biosensor showed a wide detection range and a low detection limit. • The antibiofouling idea utilized for biosensor is significant for diagnostics. - Abstract: In this paper, we have synthesized hyperbranched polyester microspheres with carboxylic acid functional groups (HBPE-CA) and developed a label-free electrochemical aptamer biosensor using thrombin-binding aptamer (TBA) as receptor for the measurement of thrombin in whole blood. The indium tin oxide (ITO) electrode surface modified with HBPE-CA microspheres was grafted with TBA, which has excellent binding affinity and selectivity for thrombin. Binding of the thrombin at the modified ITO electrode surface greatly restrained access of electrons for a redox probe of [Fe(CN)6]3−/4−. Moreover, the aptamer biosensor could be used for detection of thrombin in whole blood, a wide detection range (10 fM–100 nM) and a detection limit on the order of 0.90 fM were demonstrated. Control experiments were also carried out by using bull serum albumin (BSA) and lysozyme in the absence of thrombin. The good stability and repeatability of this aptamer biosensor were also proved. We expect that this demonstration will lead to the development of highly sensitive label-free sensors based on aptamer with lower cost than current technology. The integration of the technologies, which include anticoagulant, sensor and nanoscience, will bring significant input to high-performance biosensors relevant to diagnostics and therapy of interest for human health

  10. NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data.

    Science.gov (United States)

    Katta, Mohan A V S K; Khan, Aamir W; Doddamani, Dadakhalandar; Thudi, Mahendar; Varshney, Rajeev K

    2015-01-01

    Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina) data.

  11. NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina Data.

    Directory of Open Access Journals (Sweden)

    Mohan A V S K Katta

    Full Text Available Rapid popularity and adaptation of next generation sequencing (NGS approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1 (http://htslib.org, for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2, SNP calling (SAMtools and other utilities (bedtools towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina data.

  12. NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data.

    Science.gov (United States)

    Katta, Mohan A V S K; Khan, Aamir W; Doddamani, Dadakhalandar; Thudi, Mahendar; Varshney, Rajeev K

    2015-01-01

    Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina) data. PMID:26460497

  13. Automated Scheduling Via Artificial Intelligence

    Science.gov (United States)

    Biefeld, Eric W.; Cooper, Lynne P.

    1991-01-01

    Artificial-intelligence software that automates scheduling developed in Operations Mission Planner (OMP) research project. Software used in both generation of new schedules and modification of existing schedules in view of changes in tasks and/or available resources. Approach based on iterative refinement. Although project focused upon scheduling of operations of scientific instruments and other equipment aboard spacecraft, also applicable to such terrestrial problems as scheduling production in factory.

  14. METHODS OF TREATING OR PREVENTING DEMYELINATION USING THROMBIN INHIBITORS AND METHODS OF DETECTING DEMYELINATION USING NEUROFASCIN 155 | NCI Technology Transfer Center | TTC

    Science.gov (United States)

    Researchers at the Eunice Kennedy Shriver National Institute of Child Health and Human Development (“NICHD”), seek CRADA partner or collaboration for development of agents to treat multiple sclerosis or other conditions associated with myelin remodeling by administering an agent that inhibits cleavage of Neurofascin 155 or Caspr1. The agent could be a thrombin inhibitor, an agent that inhibits thrombin expression, an anti-thrombin antibody that specifically inhibits thrombin mediated cleavage of Neurofascin 155, a mutated version or fragment of Neurofascin 155 or Caspr1, or antibodies to Neurofascin 155 or Caspr1.

  15. DETERMINATION OF ELECTROMAGNETIC PARAMETERS AND PHASE RELATIONS IN TURBO-GENERATORS BY THE AUTOMATED CALCULATION OF THE MAGNETIC FIELD IN THE SOFTWARE ENVIRONMENT FEMM

    Directory of Open Access Journals (Sweden)

    V.I. Milykh

    2016-03-01

    Full Text Available The theoretical bases of calculation of electromagnetic quantities and time-phase relationship are presented for the turbo-generators. This is done by numerical calculations of the magnetic field in the software environment package FEMM (Finite Element Method Magnetics. A program which controls calculations and organizes the issuance of the results to a text file is created on the algorithmic language Lua. The program is universal in terms of a turbo-generator models, as well as steady-state modes of their work with a minimum of input data. The exciting current of the rotor and the phase currents of three-phase stator winding in accordance with their initial phase are given for the calculation of the magnetic field. The key function for the analysis of electromagnetic parameters is the calculated angular function of the magnetic flux phase stator winding. The expansion in the harmonic series is carried out and amplitude and initial phase are received for this function. Next, the phase EMF and voltage, phase shifts between all values, active power, electromagnetic torque, the magnetic flux in the gap and other parameters are determined. The presented Lua script is a prototype for a similar calculation software of electric machines of other types.

  16. Shoe-String Automation

    Energy Technology Data Exchange (ETDEWEB)

    Duncan, M.L.

    2001-07-30

    Faced with a downsizing organization, serious budget reductions and retirement of key metrology personnel, maintaining capabilities to provide necessary services to our customers was becoming increasingly difficult. It appeared that the only solution was to automate some of our more personnel-intensive processes; however, it was crucial that the most personnel-intensive candidate process be automated, at the lowest price possible and with the lowest risk of failure. This discussion relates factors in the selection of the Standard Leak Calibration System for automation, the methods of automation used to provide the lowest-cost solution and the benefits realized as a result of the automation.

  17. AXIOME: automated exploration of microbial diversity

    OpenAIRE

    Lynch, Michael DJ; Andre P Masella; Hall, Michael W; Bartram, Andrea K.; Neufeld, Josh D.

    2013-01-01

    Background Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research. Findings AXIOME streamlin...

  18. Effects of argatroban, danaparoid, and fondaparinux on trombin generation in heparin-induced thrombocytopenia.

    Science.gov (United States)

    Tardy-Poncet, Brigitte; Combe, Marion; Piot, Michèle; Chapelle, Céline; Akrour, Majid; Tardy, Bernard

    2013-03-01

    There is no in vitro data on the comparison of the effects of danaparoid, argatroban and fondaparinux on thrombin generation in patients with heparin-induced thrombocytopenia. It was the study objective to compare the in vitro anticoagulant potential of argatroban, danaparoid and fondaparinux using a thrombin generation assay TGA on a mixture of control platelet-rich plasma (PRP) and HIT patient platelet-poor plasma (PPP). The plasma of seven patients with a clear HIT diagnosed at our institution was selected. Mixtures of donor PRP and patient PPP were incubated with unfractionated heparin 0.2 U.mL⁻¹, argatroban at 600 ng.mL⁻¹, argatroban at 400 ng.mL⁻¹, danaparoid at 0.65 IU.mL⁻¹ and fondaparinux at 1 μg.mL⁻¹. Thrombin generation was assessed by calibrated thrombinography. The percentage of inhibition of the endogenous thrombin potential observed with argatroban at 600 ng.mL⁻¹ was statistically significantly higher compared with those observed with fondaparinux (median: 53.6% vs. 3.9%; p=0.031) but not compared with argatroban at 400 ng.mL⁻¹ and danaparoid. The percentage of inhibition of the thrombin peak observed with argatroban at 600 ng.mL⁻¹ was statistically significantly higher compared with those observed with danaparoid (median: 71.2 vs. 56.8; p=0.031) and fondaparinux (mean: 71.2 vs. 30; p=0.031) but not with argatroban at 400 ng.mL⁻¹. In conclusion, the in vitro effect of argatroban and danaparoid on thrombin generation seems to corroborate the results of clinical studies of these drugs in the treatment of HIT in term of efficiency. Fondaparinux showed a very small effect on thrombin generation evaluated by calibrated thrombinography. PMID:23328916

  19. Enhancement of aptamer immobilization using egg shell-derived nano-sized spherical hydroxyapatite for thrombin detection in neuroclinic.

    Science.gov (United States)

    Derkus, Burak; Arslan, Yavuz Emre; Emregul, Kaan C; Emregul, Emel

    2016-09-01

    In the present study, we describe the sonochemical isolation of nano-sized spherical hydroxyapatite (nHA) from egg shell and application towards thrombin aptasensing. In addition to the sonochemical method, two conventional methods present in literature were carried out to perform a comparative study. Various analysis methods including Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), X-Ray Diffraction (XRD), Energy-Dispersive Analysis of X-Rays (EDAX), and Thermal Gravimetric Analysis (TGA) have been applied for the characterization of nHA and its nanocomposite with marine-derived collagen isolated from Rhizostoma pulmo jellyfish. TEM micrographs revealed the sonochemically synthesized nHA nanoparticles to have a unique porous spherical shape with a diameter of approximately 60-80nm when compared to hydroxyapatite nanoparticles synthesized using the other two methods which had a typical needle shaped morphology. EDAX, XRD and FTIR results demonstrated that the obtained patterns belonged to hydroxyapatite. Electrochemical impedance spectroscopy (EIS) is the main analyzing technique of the developed thrombin aptasensor. The proposed aptasensor has a detection limit of 0.25nM thrombin. For clinical application of the developed aptasensor, thrombin levels in blood and cerebrospinal fluid (CSF) samples obtained from patients with Multiple Sclerosis, Myastenia Gravis, Epilepsy, Parkinson, polyneuropathy and healthy donors were analyzed using both the aptasensor and commercial ELISA kit. The results showed that the proposed system is a promising candidate for clinical analysis of thrombin. PMID:27343583

  20. Magnetic relaxation switch and colorimetric detection of thrombin using aptamer-functionalized gold-coated iron oxide nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Liang Guohai; Cai Shaoyu; Zhang Peng [Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433 (China); Peng Youyuan [Department of Chemistry, Quanzhou Normal University, Quanzhou 362000 (China); Chen Hui; Zhang Song [Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433 (China); Kong Jilie, E-mail: jlkong@fudan.edu.cn [Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433 (China)

    2011-03-18

    We describe a sensitive biosensing system combining magnetic relaxation switch diagnosis and colorimetric detection of human {alpha}-thrombin, based on the aptamer-protein interaction induced aggregation of Fe{sub 3}O{sub 4}-Au nanoparticles. To demonstrate the concept, gold-coated iron oxide nanoparticle was synthesized by iterative reduction of HAuCl{sub 4} onto the dextran-coated Fe{sub 3}O{sub 4} nanoparticles. The resulting core-shell structure had a flowerlike shape with pretty narrow size distribution (referred to as 'nanorose'). The two aptamers corresponding to human {alpha}-thrombin were conjugated separately to two distinct nanorose populations. Once a solution containing human {alpha}-thrombin was introduced, the nanoroses switched from a well dispersed state to an aggregated one, leading to a change in the spin-spin relaxation time (T{sub 2}) as well as the UV-Vis absorption spectra of the solution. Thus the qualitative and quantitative detection method for human {alpha}-thrombin was established. The dual-mode detection is clearly advantageous in obtaining a more reliable result; the detection range is widened as well. By using the dual-mode detection method, a detectable T{sub 2} change is observed with 1.0 nM human {alpha}-thrombin, and the detection range is from 1.6 nM to 30.4 nM.

  1. Endoscopic injection sclerotherapy in non-variceal upper gastrointestinal bleeding. A comparative study of polidocanol and thrombin.

    Science.gov (United States)

    Benedetti, G; Sablich, R; Lacchin, T

    1991-01-01

    To date several agents have been used to achieve haemostasis in patients with non-variceal upper gastrointestinal bleeding using endoscopic sclerotherapy techniques. Polidocanol has been widely used but local complications have been reported after treatment. We have compared the efficacy and safety of thrombin and polidocanol in 82 consecutive patients with ongoing or recent bleeding from duodenal, gastric, or anastomotic ulcers. Primary control of haemostasis from spurting vessels was achieved in 90% of cases using polidocanol and in 86.6% using thrombin. Definitive haemostasis was obtained in 80% of patients in both groups. When a non-bleeding vessel was visible, injection of polidocanol or thrombin effectively prevented rebleeding in 90.9% and 85.7% of cases, respectively. When a non-bleeding sentinel clot was present, injection of polidocanol or thrombin provided definitive haemostasis in 100% and 92.8% of cases, respectively. No statistically significant difference was evident between the two agents. In the polidocanol group, one local haemorrhagic complication was noted. No general or local complications were recorded in the thrombin group.

  2. Fibrinogen and thrombin concentrations are critical for fibrin glue adherence in rat high-risk colon anastomoses

    Directory of Open Access Journals (Sweden)

    Eliseo Portilla-de Buen

    2014-04-01

    Full Text Available OBJECTIVE: Fibrin glues have not been consistently successful in preventing the dehiscence of high-risk colonic anastomoses. Fibrinogen and thrombin concentrations in glues determine their ability to function as sealants, healers, and/or adhesives. The objective of the current study was to compare the effects of different concentrations of fibrinogen and thrombin on bursting pressure, leaks, dehiscence, and morphology of high-risk ischemic colonic anastomoses using fibrin glue in rats. METHODS: Colonic anastomoses in adult female Sprague-Dawley rats (weight, 250-350 g treated with fibrin glue containing different concentrations of fibrinogen and thrombin were evaluated at post-operative day 5. The interventions were low-risk (normal or high-risk (ischemic end-to-end colonic anastomoses using polypropylene sutures and topical application of fibrinogen at high (120 mg/mL or low (40 mg/mL concentrations and thrombin at high (1000 IU/mL or low (500 IU/mL concentrations. RESULTS: Ischemia alone, anastomosis alone, or both together reduced the bursting pressure. Glues containing a low fibrinogen concentration improved this parameter in all cases. High thrombin in combination with low fibrinogen also improved adherence exclusively in low-risk anastomoses. No differences were detected with respect to macroscopic parameters, histopathology, or hydroxyproline content at 5 days post-anastomosis. CONCLUSIONS: Fibrin glue with a low fibrinogen content normalizes the bursting pressure of high-risk ischemic left-colon anastomoses in rats at day 5 after surgery.

  3. Effects of thrombin, PAR-1 activating peptide and a PAR-1 antagonist on umbilical artery resistance in vitro

    Directory of Open Access Journals (Sweden)

    Elliott John T

    2005-02-01

    Full Text Available Abstract Background The non-thrombotic effects of thrombin in cardiovascular tissues, as mediated via the protease activated receptors (PARs, and particularly PAR-1, have been the focus of much recent research. The aims of this study were to evaluate the effects of thrombin, a specific PAR-1 activating peptide (PAR1-AP, and a PAR-1 antagonist on human umbilical artery tone in vitro. Methods Human umbilical artery samples were obtained from 17 women at term. Arterial rings were suspended under physiologic conditions for isometric recording. The in vitro effects of thrombin (0.5 units/mL to 3 units/mL, PAR1-AP TFLLR-NH2 [10(-9 to 10(-6 M], and PAR-1 antagonist (N-trans cinnamoyl- p-fluoroPhe-p-guanidinoPhe-Leu-Arg-Orn-NH2 [10(-9 M to 10(-5 M] on umbilical artery tone were measured. Results Both thrombin and TFLLR-NH2 exerted a potent cumulative vasodilatory effect on human umbilical artery resistance (P 0.05. Conclusion These findings highlight a potential role for thrombin and PAR-1 receptors in vascular regulation of feto-placental blood flow in normal pregnancy, and in association with the vascular lesions associated with IUGR and pre-eclampsia.

  4. Rapid Detection of Thrombin and Other Protease Activity Directly in Whole Blood

    Science.gov (United States)

    Yu, Johnson Chung Sing

    Thrombin is a serine protease that plays a key role in the clotting cascade to promote hemostasis following injury to the endothelium. From a clinical diagnostic perspective, in-vivo thrombin activity is linked to various blood clotting disorders, as well as cardiovascular disease (DVT, arteriosclerosis, etc). Thus, the ability to rapidly measure protease activity directly in whole blood will provide important new diagnostics, and clinical researchers with a powerful tool to further elucidate the relationship between circulating protease levels and disease. The ultimate goal is to design novel point of care (POC) diagnostic devices that are capable of monitoring protease activities directly in whole blood and biological sample. A charge-changing substrate specific to the thrombin enzyme was engineered and its functionality was confirmed by a series of experiments. This led to the preliminary design, construction, and testing of two device platforms deemed fully functional for the electrophoretic separation and focusing of charged peptide fragments. The concept of using the existing charge-changing substrate platform for bacterial protease detection was also investigated. Certain strains of E coli are associated with severe symptoms such as abdominal cramps, bloody diarrhea, and vomiting. The OmpT protease is expressed on the outer membrane of E coli and plays a role in the cleavage of antimicrobial peptides, the degradation of recombinant heterologous proteins, and the activation of plasminogen in the host. Thus, a synthetic peptide substrate specific to the OmpT protease was designed and modeled for the purpose of detecting E coli in biological sample.

  5. Thrombin in combination with intensive nursing in treating upper gastrointestinal bleeding in children.

    Science.gov (United States)

    Yang, F; Xiang, M L; Liu, Y M

    2016-01-01

    Pediatric upper gastrointestinal bleeding, a commonly seen pediatric emergency, needs timely symptomatic treatment to avoid a worse outcome. To discuss the clinical effect of thrombin treatment in combination with intensive nursing on pediatric upper gastrointestinal bleeding, this study analyzed 128 children who were treated in the second ward of the Children’s Internal Medical Department in the First Affiliated Hospital of Zhengzhou University between February 2012 and December 2014. The patients were divided into two groups, an experimental group and a control group. Besides thrombin, the experimental group was given intensive nursing, consisting of regular nursing and targeted nursing, while the control group was given regular nursing only. Clinical indexes of the two groups, such as effective rate, nursing satisfaction and side effect rate, were compared. Relevant clinical indexes such as duration of hospital stay, time to stopping of bleeding and Self-Rating Anxiety Scale (SAS) score, as well as overall satisfaction level of the observation group were all better than those of the control group and differences between the two groups had statistical significance (P less than 0.05). Furthermore, difference of overall effective rate between the experimental group (90.63%) and the control group (68.75%) was significant. Difference of incidence of side effects between the two groups was statistically significant. Thus thrombin treatment in combination with intensive nursing proved to have a remarkable clinical effect and high safety level in treating pediatric upper gastrointestinal bleeding and, moreover, it shortens treatment time and enhances the patients’ quality of life. PMID:27358137

  6. Structure-based organic synthesis of unnatural aeruginosin hybrids as potent inhibitors of thrombin.

    Science.gov (United States)

    Hanessian, Stephen; Ersmark, Karolina; Wang, Xiaotian; Del Valle, Juan R; Blomberg, Niklas; Xue, Yafeng; Fjellström, Ola

    2007-06-15

    Based on X-ray crystallographic data of complexes of chlorodysinosin A with the enzyme thrombin, a series of analogs were synthesized varying the nature of the P(1), P(2), and P(3) pharmacophoric sites and the central octahydroindole carboxyamide core. In general, introduction of a hydrophobic substituent on the d-leucine amide residue dramatically improved the inhibition of the enzyme. This is rationalized based on a better fit of the P(3) subunit in the hydrophobic S(3) enzyme site. Single digit nanomolar inhibition expressed as IC(50) was observed for several analogs. PMID:17428662

  7. Two related thrombin-like enzymes present in Bothrops atrox venom

    OpenAIRE

    J.H. Petretski; Kanashiro, M; Silva, C. P.; E.W. Alves; Kipnis, T L

    2000-01-01

    This article describes the presence of two new forms of a thrombin-like enzyme, both with apparent molecular masses of 38 kDa, in Bothrops atrox venom. Both share the ability to cleave fibrinogen into fibrin and to digest casein. Both present identical Km on the substrate BApNA. Their N-terminal amino acid sequences are identical for 26 residues, sharing 80% homology with batroxobin and flavoxobin. Two groups of monoclonal antibodies (mAbs) raised against the purified enzyme forms recognized ...

  8. Automation tools for flexible aircraft maintenance.

    Energy Technology Data Exchange (ETDEWEB)

    Prentice, William J.; Drotning, William D.; Watterberg, Peter A.; Loucks, Clifford S.; Kozlowski, David M.

    2003-11-01

    This report summarizes the accomplishments of the Laboratory Directed Research and Development (LDRD) project 26546 at Sandia, during the period FY01 through FY03. The project team visited four DoD depots that support extensive aircraft maintenance in order to understand critical needs for automation, and to identify maintenance processes for potential automation or integration opportunities. From the visits, the team identified technology needs and application issues, as well as non-technical drivers that influence the application of automation in depot maintenance of aircraft. Software tools for automation facility design analysis were developed, improved, extended, and integrated to encompass greater breadth for eventual application as a generalized design tool. The design tools for automated path planning and path generation have been enhanced to incorporate those complex robot systems with redundant joint configurations, which are likely candidate designs for a complex aircraft maintenance facility. A prototype force-controlled actively compliant end-effector was designed and developed based on a parallel kinematic mechanism design. This device was developed for demonstration of surface finishing, one of many in-contact operations performed during aircraft maintenance. This end-effector tool was positioned along the workpiece by a robot manipulator, programmed for operation by the automated planning tools integrated for this project. Together, the hardware and software tools demonstrate many of the technologies required for flexible automation in a maintenance facility.

  9. pHAST (pH-Driven Aptamer Switch for Thrombin) Catch-and-Release of Target Protein.

    Science.gov (United States)

    McConnell, E M; Bolzon, R; Mezin, P; Frahm, G; Johnston, M; DeRosa, M C

    2016-06-15

    A pH-driven DNA nanomachine based on the human α-thrombin binding aptamer was designed for the specific catch-and-release of human α-thrombin at neutral and acidic pH, respectively. In neutral conditions, the thrombin aptamer component of the nanomachine is exposed and exists in the G-quadruplex conformation required to bind to the target protein. At slightly acidic pH, the polyadenine tail of the nanomachine becomes partially protonated and A+(anti)•G(syn) mispairing results in a conformational change, causing the target protein to be released. Förster resonance energy transfer (FRET) was used to monitor conformational switching over multiple pH cycles. Electrophoretic mobility shift assay (EMSA) and fluorescence anisotropy were used to show pH dependent protein binding and release by the nanomachine. This approach could be applied generally to existing G-rich aptamers to develop novel biosensors, theranostics, and nanoswitches. PMID:27115292

  10. Protein kinase C is differentially regulated by thrombin, insulin, and epidermal growth factor in human mammary tumor cells

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, M.L.; Tellez-Inon, M.T. (Instituto de Ingenieria Genetica y Biologia Molecular, Buenos Aires (Argentina)); Medrano, E.E.; Cafferatta, E.G.A. (Instituto de Investigaciones Bioquimicas Fundacion Campomar, Buenos Aires (Argentina))

    1988-03-01

    The exposure of serum-deprived mammary tumor cells MCF-7 and T-47D to insulin, thrombin, and epidermal growth factor (EGF) resulted in dramatic modifications in the activity and in the translocation capacity of protein kinase C from cytosol to membrane fractions. Insulin induces a 600% activation of the enzyme after 5 h of exposure to the hormone in MCF-7 cells; thrombin either activates (200% in MCF-7) or down-regulates (in T-47D), and EGF exerts only a moderate effect. Thus, the growth factors studied modulate differentially the protein kinase C activity in human mammary tumor cells. The physiological significance of the results obtained are discussed in terms of the growth response elicited by insulin, thrombin, and EGF.

  11. Automated mass action model space generation and analysis methods for two-reactant combinatorially complex equilibriums: An analysis of ATP-induced ribonucleotide reductase R1 hexamerization data

    Directory of Open Access Journals (Sweden)

    Radivoyevitch Tomas

    2009-12-01

    Full Text Available Abstract Background Ribonucleotide reductase is the main control point of dNTP production. It has two subunits, R1, and R2 or p53R2. R1 has 5 possible catalytic site states (empty or filled with 1 of 4 NDPs, 5 possible s-site states (empty or filled with ATP, dATP, dTTP or dGTP, 3 possible a-site states (empty or filled with ATP or dATP, perhaps two possible h-site states (empty or filled with ATP, and all of this is folded into an R1 monomer-dimer-tetramer-hexamer equilibrium where R1 j-mers can be bound by variable numbers of R2 or p53R2 dimers. Trillions of RNR complexes are possible as a result. The problem is to determine which are needed in models to explain available data. This problem is intractable for 10 reactants, but it can be solved for 2 and is here for R1 and ATP. Results Thousands of ATP-induced R1 hexamerization models with up to three (s, a and h ATP binding sites per R1 subunit were automatically generated via hypotheses that complete dissociation constants are infinite and/or that binary dissociation constants are equal. To limit the model space size, it was assumed that s-sites are always filled in oligomers and never filled in monomers, and to interpret model terms it was assumed that a-sites fill before h-sites. The models were fitted to published dynamic light scattering data. As the lowest Akaike Information Criterion (AIC of the 3-parameter models was greater than the lowest of the 2-parameter models, only models with up to 3 parameters were fitted. Models with sums of squared errors less than twice the minimum were then partitioned into two groups: those that contained no occupied h-site terms (508 models and those that contained at least one (1580 models. Normalized AIC densities of these two groups of models differed significantly in favor of models that did not include an h-site term (Kolmogorov-Smirnov p -15; consistent with this, 28 of the top 30 models (ranked by AICs did not include an h-site term and 28

  12. Deletion of the thrombin cleavage domain of osteopontin mediates breast cancer cell adhesion, proteolytic activity, tumorgenicity, and metastasis

    International Nuclear Information System (INIS)

    Osteopontin (OPN) is a secreted phosphoprotein often overexpressed at high levels in the blood and primary tumors of breast cancer patients. OPN contains two integrin-binding sites and a thrombin cleavage domain located in close proximity to each other. To study the role of the thrombin cleavage site of OPN, MDA-MB-468 human breast cancer cells were stably transfected with either wildtype OPN (468-OPN), mutant OPN lacking the thrombin cleavage domain (468-ΔTC) or an empty vector (468-CON) and assessed for in vitro and in vivo functional differences in malignant/metastatic behavior. All three cell lines were found to equivalently express thrombin, tissue factor, CD44, αvβ5 integrin and β1 integrin. Relative to 468-OPN and 468-CON cells, 468-ΔTC cells expressing OPN with a deleted thrombin cleavage domain demonstrated decreased cell adhesion (p < 0.001), decreased mRNA expression of MCAM, maspin and TRAIL (p < 0.01), and increased uPA expression and activity (p < 0.01) in vitro. Furthermore, injection of 468-ΔTC cells into the mammary fat pad of nude mice resulted in decreased primary tumor latency time (p < 0.01) and increased primary tumor growth and lymph node metastatic burden (p < 0.001) compared to 468-OPN and 468-CON cells. The results presented here suggest that expression of thrombin-uncleavable OPN imparts an early tumor formation advantage as well as a metastatic advantage for breast cancer cells, possibly due to increased proteolytic activity and decreased adhesion and apoptosis. Clarification of the mechanisms responsible for these observations and the translation of this knowledge into the clinic could ultimately provide new therapeutic opportunities for combating breast cancer

  13. Automated illustration of patients instructions.

    Science.gov (United States)

    Bui, Duy; Nakamura, Carlos; Bray, Bruce E; Zeng-Treitler, Qing

    2012-01-01

    A picture can be a powerful communication tool. However, creating pictures to illustrate patient instructions can be a costly and time-consuming task. Building on our prior research in this area, we developed a computer application that automatically converts text to pictures using natural language processing and computer graphics techniques. After iterative testing, the automated illustration system was evaluated using 49 previously unseen cardiology discharge instructions. The completeness of the system-generated illustrations was assessed by three raters using a three-level scale. The average inter-rater agreement for text correctly represented in the pictograph was about 66 percent. Since illustration in this context is intended to enhance rather than replace text, these results support the feasibility of conducting automated illustration.

  14. Thermodynamic and biological evaluation of a thrombin binding aptamer modified with several unlocked nucleic acid (UNA) monomers and a 2′-C-piperazino-UNA monomer

    DEFF Research Database (Denmark)

    Jensen, Troels B.; Henriksen, Jonas Rosager; Rasmussen, Bjarne E.;

    2011-01-01

    Thrombin binding aptamer is a DNA 15-mer which forms a G-quadruplex structure and possess promising anticoagulant properties due to specific interactions with thrombin. Herein we present the influence of a single 2′-C-piperazino-UNA residue and UNA residues incorporated in several positions on th...

  15. Aptamer-based fluorescent solid-phase thrombin assay using a silver-coated glass substrate and signal amplification by glucose oxidase

    International Nuclear Information System (INIS)

    We describe an aptamer-based solid-state biosensor for the fluorometric determination of thrombin. The surface of silver-coated glass was modified with the thrombin-binding aptamer 1 (TBA 1) of the sequence 5′-HS-TTT TTT TTT TTT TTT GGT TGG TGT GGT TGG-3′. A second (and biotinylated) thrombin -binding aptamer (TBA 2) with the sequence 5′-biotin-AGT CCG TGG TAG GGC AGG TTG GGG TGA CT-3′ was applied as the signaling aptamer. Following binding of thrombin by TBA 1 on the surface, TBA 2 is added and then binds to the thrombin on the surface of the silver-coated glass to form the thrombin-aptamer complex. The biotin groups on TBA 2 are then coated with streptavidin, and biotin-labeled glucose oxidase (biotin-GOx) is added to bind to streptavidin. The quantity of GOx immobilized in this way is directly related to the quantity of thrombin bound on the surface. Following cleavage of the aptamer with DNase I, glucose is added and oxidized by GOx to yield H2O2. Horseradish peroxidase is added and causes the oxidation of 3-p-hydroxyphenylpropanoic acid to yield a fluorescent product. The intensity of the blue fluorescence is directly related to the thrombin concentration in the 300 pM to 6500 pM range, and the detection limit is as low as 82 pM. The assay has good selectivity and practicability. (author)

  16. Aptamer-based luminescence energy transfer from near-infrared-to-near-infrared upconverting nanoparticles to gold nanorods and its application for the detection of thrombin.

    Science.gov (United States)

    Yuan, Fei; Chen, Hongqi; Xu, Juan; Zhang, Yiyan; Wu, Yong; Wang, Lun

    2014-03-01

    A new luminescence energy transfer (LET) system has been designed for the detection of thrombin in the near-infrared (NIR) region by utilizing NIR-to-NIR upconversion lanthanide nanophosphors (UCNPs) as the donor and gold nanorods (Au NRs) as the acceptor. The use of upconverting NaYF4 :Yb(3+) ,Tm(3+) nanoparticles with sharp NIR emission peaks upon NIR excitation by an inexpensive infrared continuous wave laser diode provided large spectral overlap between the donor and the acceptor. Both the Au NRs and carboxyl-terminated NaYF4 :Yb(3+) ,Tm(3+) UCNPs were first modified with different thrombin aptamers. When thrombin was added, a LET system was then formed because of the specific recognition between the thrombin aptamers and thrombin. The LET system was used to monitor thrombin concentrations in aqueous buffer and human blood samples. The limits of detection for thrombin are as low as 0.118 nM in buffer solution and 0.129 nM in human serum. The method was also successfully applied to thrombin detection in blood samples. PMID:24501010

  17. Inactivation of active thrombin-activable fibrinolysis inhibitor takes place by a process that involves conformational instability rather than proteolytic cleavage

    NARCIS (Netherlands)

    Marx, PF; Hackeng, TM; Dawson, PE; Griffin, JH; Meijers, JCM; Bouma, Bonno N.

    2000-01-01

    Thrombin-activable fibrinolysis inhibitor (TAFI) is present in the circulation as an inactive zymogen. Thrombin converts TAFI to a carboxypeptidase B-like enzyme (TAFIa) by cleaving at Arg(92) in a process accelerated by the cofactor, thrombomodulin. TAFIa attenuates fibrinolysis. TAFIa can be inact

  18. Effect of long-term hormone replacement therapy on tissue factor pathway inhibitor and thrombin activatable fibrinolysis inhibitor in healthy postmenopausal women: a randomized controlled study

    DEFF Research Database (Denmark)

    Bladbjerg, E-M; Madsen, J S; Kristensen, S R;

    2003-01-01

    arterial tissue factor expression and higher thrombin formation, and changes in tissue factor pathway coagulation inhibitor (TFPI) and thrombin activatable fibrinolysis inhibitor (TAFI) may be deleterious. Healthy postmenopausal women (n = 719) were randomized to hormone therapy [n = 357; opposed (n = 290...

  19. Prelabeled glycoprotein Ib/IX receptors are not cleared from exposed surfaces of thrombin-activated platelets.

    OpenAIRE

    White, J. G.; Krumwiede, M. D.; Cocking-Johnson, D.; Escolar, G.

    1996-01-01

    The present investigation has re-examined the hypothesis proposing that glycoprotein (GP)Ib/IX receptors for von Willebrand factor are rapidly cleared from exposed surfaces to internal membrane systems after activation of platelets by thrombin in suspension. Platelets were prelabeled with either a polyclonal antibody to GPIb alpha, antiglycocalicin (A-Gl), or a cocktail of two monoclonal antibodies, AP1 and 6D1, exposed to 0.1 or 0.2 U/ml thrombin for 5 or 10 minutes, fixed and stained with S...

  20. DESIGN AUTOMATION OF PERMUTATIONS GENERATORS Автоматизация проектирования устройств генерации комбинаторных перестановок

    Directory of Open Access Journals (Sweden)

    Zolnikov V. K.

    2012-03-01

    Full Text Available The models, algorithms, methods of design automation of specialized devices of permutations generation within the variable width string are presented in this article. The methodology of design of such devices, which provides high-quality project and maximal automation of design process at system level and register-transfer level (RTL is offered. At the end of the article, the efficiency of the offered solutions is estimated

  1. Phosphoproteomic analysis of platelets activated by pro-thrombotic oxidized phospholipids and thrombin.

    Directory of Open Access Journals (Sweden)

    Alejandro Zimman

    Full Text Available Specific oxidized phospholipids (oxPCCD36 promote platelet hyper-reactivity and thrombosis in hyperlipidemia via the scavenger receptor CD36, however the signaling pathway(s induced in platelets by oxPCCD36 are not well defined. We have employed mass spectrometry-based tyrosine, serine, and threonine phosphoproteomics for the unbiased analysis of platelet signaling pathways induced by oxPCCD36 as well as by the strong physiological agonist thrombin. oxPCCD36 and thrombin induced differential phosphorylation of 115 proteins (162 phosphorylation sites and 181 proteins (334 phosphorylation sites respectively. Most of the phosphoproteome changes induced by either agonist have never been reported in platelets; thus they provide candidates in the study of platelet signaling. Bioinformatic analyses of protein phosphorylation dependent responses were used to categorize preferential motifs for (dephosphorylation, predict pathways and kinase activity, and construct a phosphoproteome network regulating integrin activation. A putative signaling pathway involving Src-family kinases, SYK, and PLCγ2 was identified in platelets activated by oxPCCD36. Subsequent ex vivo studies in human platelets demonstrated that this pathway is downstream of the scavenger receptor CD36 and is critical for platelet activation by oxPCCD36. Our results provide multiple insights into the mechanism of platelet activation and specifically in platelet regulation by oxPCCD36.

  2. A sensitive HIV-1 envelope induced fusion assay identifies fusion enhancement of thrombin

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, De-Chun; Zhong, Guo-Cai; Su, Ju-Xiang [Department of Microbiology, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081 (China); Liu, Yan-Hong [Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, Heilongjiang 150081 (China); Li, Yan; Wang, Jia-Ye [Department of Microbiology, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081 (China); Hattori, Toshio [Department of Emerging Infectious Diseases, Division of Internal Medicine, Graduate School of Medicine, Tohoku University, Sendai 9808574 (Japan); Ling, Hong, E-mail: lingh@ems.hrbmu.edu.cn [Department of Microbiology, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081 (China); Department of Parasitology, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081 (China); Key Lab of Heilongjiang Province for Infection and Immunity, Key Lab of Heilongjiang Province Education Bureau for Etiology, Harbin, Heilongjiang 150081 (China); Zhang, Feng-Min, E-mail: fengminzhang@yahoo.com.cn [Department of Microbiology, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081 (China); Key Lab of Heilongjiang Province for Infection and Immunity, Key Lab of Heilongjiang Province Education Bureau for Etiology, Harbin, Heilongjiang 150081 (China)

    2010-01-22

    To evaluate the interaction between HIV-1 envelope glycoprotein (Env) and target cell receptors, various cell-cell-fusion assays have been developed. In the present study, we established a novel fusion system. In this system, the expression of the sensitive reporter gene, firefly luciferase (FL) gene, in the target cells was used to evaluate cell fusion event. Simultaneously, constitutively expressed Renilla luciferase (RL) gene was used to monitor effector cell number and viability. FL gave a wider dynamic range than other known reporters and the introduction of RL made the assay accurate and reproducible. This system is especially beneficial for investigation of potential entry-influencing agents, for its power of ruling out the false inhibition or enhancement caused by the artificial cell-number variation. As a case study, we applied this fusion system to observe the effect of a serine protease, thrombin, on HIV Env-mediated cell-cell fusion and have found the fusion enhancement activity of thrombin over two R5-tropic HIV strains.

  3. Biochemical characterization of bovine plasma thrombin-activatable fibrinolysis inhibitor (TAFI

    Directory of Open Access Journals (Sweden)

    Kristensen Torsten

    2009-05-01

    Full Text Available Abstract Background TAFI is a plasma protein assumed to be an important link between coagulation and fibrinolysis. The three-dimensional crystal structures of authentic mature bovine TAFI (TAFIa in complex with tick carboxypeptidase inhibitor, authentic full lenght bovine plasma thrombin-activatable fibrinolysis inhibitor (TAFI, and recombinant human TAFI have recently been solved. In light of these recent advances, we have characterized authentic bovine TAFI biochemically and compared it to human TAFI. Results The four N-linked glycosylation sequons within the activation peptide were all occupied in bovine TAFI, similar to human TAFI, while the sequon located within the enzyme moiety of the bovine protein was non-glycosylated. The enzymatic stability and the kinetic constants of TAFIa differed somewhat between the two proteins, as did the isoelectric point of TAFI, but not TAFIa. Equivalent to human TAFI, bovine TAFI was a substrate for transglutaminases and could be proteolytically cleaved by trypsin or thrombin/solulin complex, although small differences in the fragmentation patterns were observed. Furthermore, bovine TAFI exhibited intrinsic activity and TAFIa attenuated tPA-mediated fibrinolysis similar to the human protein. Conclusion The findings presented here suggest that the properties of these two orthologous proteins are similar and that conclusions reached using the bovine TAFI may be extrapolated to the human protein.

  4. Mechanism of the Anticoagulant Activity of Thrombin Mutant W215A/E217A

    Energy Technology Data Exchange (ETDEWEB)

    Gandhi, Prafull S.; Page, Michael J.; Chen, Zhiwei; Bush-Pelc, Leslie; Di Cera, Enrico; (WU-MED)

    2009-09-15

    The thrombin mutant W215A/E217A (WE) is a potent anticoagulant both in vitro and in vivo. Previous x-ray structural studies have shown that WE assumes a partially collapsed conformation that is similar to the inactive E* form, which explains its drastically reduced activity toward substrate. Whether this collapsed conformation is genuine, rather than the result of crystal packing or the mutation introduced in the critical 215-217 {beta}-strand, and whether binding of thrombomodulin to exosite I can allosterically shift the E* form to the active E form to restore activity toward protein C are issues of considerable mechanistic importance to improve the design of an anticoagulant thrombin mutant for therapeutic applications. Here we present four crystal structures of WE in the human and murine forms that confirm the collapsed conformation reported previously under different experimental conditions and crystal packing. We also present structures of human and murine WE bound to exosite I with a fragment of the platelet receptor PAR1, which is unable to shift WE to the E form. These structural findings, along with kinetic and calorimetry data, indicate that WE is strongly stabilized in the E* form and explain why binding of ligands to exosite I has only a modest effect on the E*-E equilibrium for this mutant. The E* {yields} E transition requires the combined binding of thrombomodulin and protein C and restores activity of the mutant WE in the anticoagulant pathway.

  5. A systems approach to hemostasis: 3. Thrombus consolidation regulates intrathrombus solute transport and local thrombin activity.

    Science.gov (United States)

    Stalker, Timothy J; Welsh, John D; Tomaiuolo, Maurizio; Wu, Jie; Colace, Thomas V; Diamond, Scott L; Brass, Lawrence F

    2014-09-11

    Hemostatic thrombi formed after a penetrating injury have a distinctive structure in which a core of highly activated, closely packed platelets is covered by a shell of less-activated, loosely packed platelets. We have shown that differences in intrathrombus molecular transport emerge in parallel with regional differences in platelet packing density and predicted that these differences affect thrombus growth and stability. Here we test that prediction in a mouse vascular injury model. The studies use a novel method for measuring thrombus contraction in vivo and a previously characterized mouse line with a defect in integrin αIIbβ3 outside-in signaling that affects clot retraction ex vivo. The results show that the mutant mice have a defect in thrombus consolidation following vascular injury, resulting in an increase in intrathrombus transport rates and, as predicted by computational modeling, a decrease in thrombin activity and platelet activation in the thrombus core. Collectively, these data (1) demonstrate that in addition to the activation state of individual platelets, the physical properties of the accumulated mass of adherent platelets is critical in determining intrathrombus agonist distribution and platelet activation and (2) define a novel role for integrin signaling in the regulation of intrathrombus transport rates and localization of thrombin activity. PMID:24951426

  6. The role of structural information in the discovery of direct thrombin and factor Xa inhibitors.

    Science.gov (United States)

    Nar, Herbert

    2012-05-01

    The quest for novel medications to treat thromboembolic disorders such as venous thrombosis, pulmonary embolism and stroke received a boost when the 3D structures of two major players in the blood coagulation cascade were determined in 1989 and 1993. Structure-guided design of inhibitors of thrombin (factor IIa, fIIa) and factor Xa (fXa) eventually led to the discovery of potent, selective, efficacious, orally active and safe compounds that proved successful in clinical studies. In 2008, the direct thrombin inhibitor dabigatran etexilate developed by Boehringer Ingelheim became the first novel antithrombotic molecular entity to enter the market in 50 years. Additional compounds targeting factor Xa were subsequently granted marketing authorization or are in late-stage clinical studies. In this review, I use selected case studies to describe the discovery of novel fIIa and fXa inhibitors, with a particular emphasis on the pre-eminent role that structural information played in this process. PMID:22503439

  7. Automated washing of FTA Card punches and PCR setup for reference samples using a LIMS-controlled Sias Xantus automated liquid handler

    DEFF Research Database (Denmark)

    Stangegaard, Michael; Olsen, Addie Nina; Frøslev, Tobias G.;

    2009-01-01

    We have implemented and validated automated methods for washing FTA Card punches containing buccal samples and subsequent PCR setup using a Sias Xantus automated liquid handler. The automated methods were controlled by worklists generated by our LabWare Laboratory Information Management System...

  8. Determination of the Optimized Automation Rate considering Effects of Automation on Human Operators in Nuclear Power Plants

    International Nuclear Information System (INIS)

    Automation refers to the use of a device or a system to perform a function previously performed by a human operator. It is introduced to reduce the human errors and to enhance the performance in various industrial fields, including the nuclear industry. However, these positive effects are not always achieved in complex systems such as nuclear power plants (NPPs). An excessive introduction of automation can generate new roles for human operators and change activities in unexpected ways. As more automation systems are accepted, the ability of human operators to detect automation failures and resume manual control is diminished. This disadvantage of automation is called the Out-of-the- Loop (OOTL) problem. We should consider the positive and negative effects of automation at the same time to determine the appropriate level of the introduction of automation. Thus, in this paper, we suggest an estimation method to consider the positive and negative effects of automation at the same time to determine the appropriate introduction of automation. This concept is limited in that it does not consider the effects of automation on human operators. Thus, a new estimation method for automation rate was suggested to overcome this problem

  9. Automate functional testing

    Directory of Open Access Journals (Sweden)

    Ramesh Kalindri

    2014-06-01

    Full Text Available Currently, software engineers are increasingly turning to the option of automating functional tests, but not always have successful in this endeavor. Reasons range from low planning until over cost in the process. Some principles that can guide teams in automating these tests are described in this article.

  10. Automation in Warehouse Development

    NARCIS (Netherlands)

    Hamberg, R.; Verriet, J.

    2012-01-01

    The warehouses of the future will come in a variety of forms, but with a few common ingredients. Firstly, human operational handling of items in warehouses is increasingly being replaced by automated item handling. Extended warehouse automation counteracts the scarcity of human operators and support

  11. Work and Programmable Automation.

    Science.gov (United States)

    DeVore, Paul W.

    A new industrial era based on electronics and the microprocessor has arrived, an era that is being called intelligent automation. Intelligent automation, in the form of robots, replaces workers, and the new products, using microelectronic devices, require significantly less labor to produce than the goods they replace. The microprocessor thus…

  12. Library Automation Style Guide.

    Science.gov (United States)

    Gaylord Bros., Liverpool, NY.

    This library automation style guide lists specific terms and names often used in the library automation industry. The terms and/or acronyms are listed alphabetically and each is followed by a brief definition. The guide refers to the "Chicago Manual of Style" for general rules, and a notes section is included for the convenience of individual…

  13. Automated Testing with Targeted Event Sequence Generation

    DEFF Research Database (Denmark)

    Jensen, Casper Svenning; Prasad, Mukul R.; Møller, Anders

    2013-01-01

    of the individual event handlers of the application. The second phase builds event sequences backward from the target, using the summaries together with a UI model of the application. Our experiments on a collection of open source Android applications show that this technique can successfully produce event...

  14. Automated feedback generation for introductory programming assignments

    OpenAIRE

    Singh, Rishabh; Gulwani, Sumit; Solar-Lezama, Armando

    2013-01-01

    We present a new method for automatically providing feedback for introductory programming problems. In order to use this method, we need a reference implementation of the assignment, and an error model consisting of potential corrections to errors that students might make. Using this information, the system automatically derives minimal corrections to student's incorrect solutions, providing them with a measure of exactly how incorrect a given solution was, as well as feedback about what they...

  15. Automation in immunohematology.

    Science.gov (United States)

    Bajpai, Meenu; Kaur, Ravneet; Gupta, Ekta

    2012-07-01

    There have been rapid technological advances in blood banking in South Asian region over the past decade with an increasing emphasis on quality and safety of blood products. The conventional test tube technique has given way to newer techniques such as column agglutination technique, solid phase red cell adherence assay, and erythrocyte-magnetized technique. These new technologies are adaptable to automation and major manufacturers in this field have come up with semi and fully automated equipments for immunohematology tests in the blood bank. Automation improves the objectivity and reproducibility of tests. It reduces human errors in patient identification and transcription errors. Documentation and traceability of tests, reagents and processes and archiving of results is another major advantage of automation. Shifting from manual methods to automation is a major undertaking for any transfusion service to provide quality patient care with lesser turnaround time for their ever increasing workload. This article discusses the various issues involved in the process.

  16. Automation in Immunohematology

    Directory of Open Access Journals (Sweden)

    Meenu Bajpai

    2012-01-01

    Full Text Available There have been rapid technological advances in blood banking in South Asian region over the past decade with an increasing emphasis on quality and safety of blood products. The conventional test tube technique has given way to newer techniques such as column agglutination technique, solid phase red cell adherence assay, and erythrocyte-magnetized technique. These new technologies are adaptable to automation and major manufacturers in this field have come up with semi and fully automated equipments for immunohematology tests in the blood bank. Automation improves the objectivity and reproducibility of tests. It reduces human errors in patient identification and transcription errors. Documentation and traceability of tests, reagents and processes and archiving of results is another major advantage of automation. Shifting from manual methods to automation is a major undertaking for any transfusion service to provide quality patient care with lesser turnaround time for their ever increasing workload. This article discusses the various issues involved in the process.

  17. Automation in immunohematology.

    Science.gov (United States)

    Bajpai, Meenu; Kaur, Ravneet; Gupta, Ekta

    2012-07-01

    There have been rapid technological advances in blood banking in South Asian region over the past decade with an increasing emphasis on quality and safety of blood products. The conventional test tube technique has given way to newer techniques such as column agglutination technique, solid phase red cell adherence assay, and erythrocyte-magnetized technique. These new technologies are adaptable to automation and major manufacturers in this field have come up with semi and fully automated equipments for immunohematology tests in the blood bank. Automation improves the objectivity and reproducibility of tests. It reduces human errors in patient identification and transcription errors. Documentation and traceability of tests, reagents and processes and archiving of results is another major advantage of automation. Shifting from manual methods to automation is a major undertaking for any transfusion service to provide quality patient care with lesser turnaround time for their ever increasing workload. This article discusses the various issues involved in the process. PMID:22988378

  18. Automation in Warehouse Development

    CERN Document Server

    Verriet, Jacques

    2012-01-01

    The warehouses of the future will come in a variety of forms, but with a few common ingredients. Firstly, human operational handling of items in warehouses is increasingly being replaced by automated item handling. Extended warehouse automation counteracts the scarcity of human operators and supports the quality of picking processes. Secondly, the development of models to simulate and analyse warehouse designs and their components facilitates the challenging task of developing warehouses that take into account each customer’s individual requirements and logistic processes. Automation in Warehouse Development addresses both types of automation from the innovative perspective of applied science. In particular, it describes the outcomes of the Falcon project, a joint endeavour by a consortium of industrial and academic partners. The results include a model-based approach to automate warehouse control design, analysis models for warehouse design, concepts for robotic item handling and computer vision, and auton...

  19. Advances in inspection automation

    Science.gov (United States)

    Weber, Walter H.; Mair, H. Douglas; Jansen, Dion; Lombardi, Luciano

    2013-01-01

    This new session at QNDE reflects the growing interest in inspection automation. Our paper describes a newly developed platform that makes the complex NDE automation possible without the need for software programmers. Inspection tasks that are tedious, error-prone or impossible for humans to perform can now be automated using a form of drag and drop visual scripting. Our work attempts to rectify the problem that NDE is not keeping pace with the rest of factory automation. Outside of NDE, robots routinely and autonomously machine parts, assemble components, weld structures and report progress to corporate databases. By contrast, components arriving in the NDT department typically require manual part handling, calibrations and analysis. The automation examples in this paper cover the development of robotic thickness gauging and the use of adaptive contour following on the NRU reactor inspection at Chalk River.

  20. Automated model building

    CERN Document Server

    Caferra, Ricardo; Peltier, Nicholas

    2004-01-01

    This is the first book on automated model building, a discipline of automated deduction that is of growing importance Although models and their construction are important per se, automated model building has appeared as a natural enrichment of automated deduction, especially in the attempt to capture the human way of reasoning The book provides an historical overview of the field of automated deduction, and presents the foundations of different existing approaches to model construction, in particular those developed by the authors Finite and infinite model building techniques are presented The main emphasis is on calculi-based methods, and relevant practical results are provided The book is of interest to researchers and graduate students in computer science, computational logic and artificial intelligence It can also be used as a textbook in advanced undergraduate courses

  1. Automated Gas Distribution System

    Science.gov (United States)

    Starke, Allen; Clark, Henry

    2012-10-01

    The cyclotron of Texas A&M University is one of the few and prized cyclotrons in the country. Behind the scenes of the cyclotron is a confusing, and dangerous setup of the ion sources that supplies the cyclotron with particles for acceleration. To use this machine there is a time consuming, and even wasteful step by step process of switching gases, purging, and other important features that must be done manually to keep the system functioning properly, while also trying to maintain the safety of the working environment. Developing a new gas distribution system to the ion source prevents many of the problems generated by the older manually setup process. This developed system can be controlled manually in an easier fashion than before, but like most of the technology and machines in the cyclotron now, is mainly operated based on software programming developed through graphical coding environment Labview. The automated gas distribution system provides multi-ports for a selection of different gases to decrease the amount of gas wasted through switching gases, and a port for the vacuum to decrease the amount of time spent purging the manifold. The Labview software makes the operation of the cyclotron and ion sources easier, and safer for anyone to use.

  2. Methodology for Automatic Generation of Models for Large Urban Spaces Based on GIS Data/Metodología para la generación automática de modelos de grandes espacios urbanos desde información SIG/

    Directory of Open Access Journals (Sweden)

    Sergio Arturo Ordóñez Medina

    2012-12-01

    Full Text Available In the planning and evaluation stages of infrastructure projects, it is necessary to manage huge quantities of information. Cities are very complex systems, which need to be modeled when an intervention is required. Suchmodels allow us to measure the impact of infrastructure changes, simulating hypothetic scenarios and evaluating results. This paper describes a methodology for the automatic generation of urban space models from GIS sources. A Voronoi diagram is used to partition large urban regions and subsequently define zones of interest. Finally, some examples of application models are presented, one used for microsimulation of traffic and another for air pollution simulation.En las etapas de planeación y evaluación de proyectos de infraestructura es necesario manejar grandes cantidades de información. Las ciudades son sistemas complejos que deben ser modeladas para ser intervenidas. Estos modelos permitirón medir el impacto de los cambios de infraestructura, simular escenarios hipotéticos y evaluar resultados. Este artículo describe una metodología para generar automáticamente modelos espaciales urbanos desde fuentes SIG: Un diagrama de Voronoi es usado para dividir grandes regiones urbanas, y a continuación serán definidas las zonas de interés. Finalmente, algunos ejemplos de modelos de aplicación serán presentados, uno usado para microsimulación de tráfico y el otro para simular contaminación atmosférica.

  3. Integrating Test-Form Formatting into Automated Test Assembly

    Science.gov (United States)

    Diao, Qi; van der Linden, Wim J.

    2013-01-01

    Automated test assembly uses the methodology of mixed integer programming to select an optimal set of items from an item bank. Automated test-form generation uses the same methodology to optimally order the items and format the test form. From an optimization point of view, production of fully formatted test forms directly from the item pool using…

  4. INVOLVEMENT OF BACTERICIDAL FACTORS FROM THROMBIN-STIMULATED PLATELETS IN CLEARANCE OF ADHERENT VIRIDANS STREPTOCOCCI IN EXPERIMENTAL INFECTIVE ENDOCARDITIS

    NARCIS (Netherlands)

    VANDERWERFF, J; ZAAT, SAJ; JOLDERSMA, W; HESS, J

    1995-01-01

    Platelets activated with thrombin release bactericidal factors. We studied the role of the susceptibility of viridans streptococci to these bactericidal factors in the development of infective endocarditis (IE). By using the experimental endocarditis rabbit model, the initial adherence and the devel

  5. In vitro effect of hemodilution on activated clotting time and high-dose thrombin time during cardiopulmonary bypass

    NARCIS (Netherlands)

    Huyzen, RJ; vanOeveren, W; Wei, FY; Stellingwerf, P; Boonstra, PW; Gu, YJ

    1996-01-01

    Background. Extreme dilution of clotting factors, as may occur during pediatric or neonatal cardiopulmonary bypass, often leads to inadequate monitoring of anticoagulation with activated dotting time (ACT). In this study we postulate that the high-dose thrombin time (HiTT) is less influenced by extr

  6. Binding characteristics of thrombin-activatable fibrinolysis inhibitor to streptococcal surface collagen-like proteins A and B

    NARCIS (Netherlands)

    Seron, Mercedes Valls; Plug, Tom; Marquart, J. Arnoud; Marx, Pauline F.; Herwald, Heiko; de Groot, Philip G.; Meijers, Joost C. M.

    2011-01-01

    Streptococcus pyogenes is the causative agent in a wide range of diseases in humans. Thrombin-activatable fibrinolysis inhibitor (TAFI) binds to collagen-like proteins ScIA and ScIB at the surface of S. pyogenes. Activation of TAFI at this surface redirects inflammation from a transient to chronic s

  7. Binding characteristics of thrombin-activatable fibrinolysis inhibitor to streptococcal surface collagen-like proteins A and B

    NARCIS (Netherlands)

    M.V. Serón; T. Plug; J.A. Marquart; P.F. Marx; H. Herwald; P.G. de Groot; J.C.M. Meijers

    2011-01-01

    Streptococcus pyogenes is the causative agent in a wide range of diseases in humans. Thrombin-activatable fibrinolysis inhibitor (TAFI) binds to collagen-like proteins SclA and SclB at the surface of S. pyogenes. Activation of TAFI at this surface redirects inflammation from a transient to chronic s

  8. Mechanism of poly(acrylic acid) acceleration of antithrombin inhibition of thrombin: implications for the design of novel heparin mimics.

    Science.gov (United States)

    Monien, Bernhard H; Cheang, Kai I; Desai, Umesh R

    2005-08-11

    The bridging mechanism of antithrombin inhibition of thrombin is a dominant mechanism contributing a massive approximately 2500-fold acceleration in the reaction rate and is also a key reason for the clinical usage of heparin. Our recent study of the antithrombin-activating properties of a carboxylic acid-based polymer, poly(acrylic acid) (PAA), demonstrated a surprisingly high acceleration in thrombin inhibition (Monien, B. H.; Desai, U. R. J. Med. Chem. 2005, 48, 1269). To better understand this interesting phenomenon, we have studied the mechanism of PAA-dependent acceleration in antithrombin inhibition of thrombin. Competitive binding studies with low-affinity heparin and a heparin tetrasaccharide suggest that PAA binds antithrombin in both the pentasaccharide- and the extended heparin-binding sites, and these results are corroborated by molecular modeling. The salt-dependence of the K(D) of the PAA-antithrombin interaction shows the formation of five ionic interactions. In contrast, the contribution of nonionic forces is miniscule, resulting in an interaction that is significantly weaker than that observed for heparins. A bell-shaped profile of the observed rate constant for antithrombin inhibition of thrombin as a function of PAA concentration was observed, suggesting that inhibition proceeds through the "bridging" mechanism. The knowledge gained in this mechanistic study highlights important rules for the rational design of orally available heparin mimics. PMID:16078853

  9. Rapid Upregulation of Orai1 Abundance in the Plasma Membrane of Platelets Following Activation with Thrombin and Collagen Related Peptide

    Directory of Open Access Journals (Sweden)

    Guilai Liu

    2015-11-01

    Full Text Available Background: Blood platelets accomplish primary hemostasis following vascular injury and contribute to the orchestration of occlusive vascular disease. Platelets are activated by an increase of cytosolic Ca2+-activity ([Ca2+]i, which is accomplished by Ca2+-release from intracellular stores and subsequent store operated Ca2+ entry (SOCE through Ca2+ release activated Ca2+ channel moiety Orai1. Powerful activators of platelets include thrombin and collagen related peptide (CRP, which are in part effective by activation of small G- protein Rac1. The present study explored the influence of thrombin and CRP on Orai1 protein abundance and cytosolic Ca2+-activity ([Ca2+]i in platelets drawn from wild type mice. Methods: Orai1 protein surface abundance was quantified utilizing CF™488A conjugated antibodies, and [Ca2+]i was determined with Fluo3-fluorescence. Results: In resting platelets, Orai1 protein abundance and [Ca2+]i were low. Thrombin (0.02 U/ml and CRP (5ug/ml within 2 min increased [Ca2+]i and Orai1 protein abundance at the platelet surface. [Ca2+]i was further increased by Ca2+ ionophore ionomycin (1 µM and by store depletion with the sarcoendoplasmatic Ca2+ ATPase inhibitor thapsigargin (1 µM. However, Orai1 protein abundance at the platelet surface was not significantly affected by ionomycin and only slightly increased by thapsigargin. The effect of thrombin and CRP on Orai1 abundance and [Ca2+]i was significantly blunted by Rac1 inhibitor NSC23766 (50 µM. Conclusion: The increase of [Ca2+]i following stimulation of platelets with thrombin and collagen related peptide is potentiated by ultrarapid Rac1 sensitive translocation of Orai1 into the cell membrane.

  10. Antithrombotic effects of LB30870, a potent, orally active, selective and direct thrombin inhibitor, and pharmacokinetics of its prodrug.

    Science.gov (United States)

    Park, Hee Dong; Lee, Sung-Hack; Kim, Tae Hoon; Lee, Sun Hwa; Cho, Kwan Hyung; Kim, Aeri

    2013-09-01

    Antithrombotic activity and bleeding complication of a new potent, selective, and direct thrombin inhibitor, LB30870, were evaluated in comparison with other anticoagulants. In order to improve oral absorption of LB30870, pharmacokinetics of LB30889, which is a double prodrug with blocking groups in both amidine and carboxyl groups, was studied in rats and dogs. LB30870 was more potent than melagatran or argatroban with thrombin inhibition constants of 0.02, 1.3 and 4.5 nM, respectively. All three direct thrombin inhibitors were selective towards other serine proteases with selectivity ratio greater than 1000, except for trypsin. Thrombin binding kinetics of LB30870 showed rapid association and slow dissociation rate constants, demonstrating its potential as anticoagulant. LB30870 was more effective than melagatran or argatroban in plasma clot-bound thrombin inhibition. In the rat venous stasis model of the caval vein, LB30870 reduced wet clot weights in a dose dependent manner after the intravenous bolus with infusion administration. The ED50 of LB30870, melagatran and enoxaparin were 50 μg/kg+2 μg/kg/min, 35 μg/kg+1.4 μg/kg/min and 200 μg/kg+8.3 μg/kg/min, respectively. No significant bleeding problem was observed with LB30870 at the dose up to two times ED80 in rats. LB30889, a double prodrug of LB30870, showed species difference in pharmacokinetics. Its oral bioavailability in rats or dogs was not better than that of LB30870. In conclusion, LB30870 has the potential to be useful as an effective oral anticoagulant for the prevention and treatment of thromboembolic diseases. PMID:23899618

  11. Design, synthesis and antithrombotic evaluation of novel dabigatran etexilate analogs, a new series of non-peptides thrombin inhibitors.

    Science.gov (United States)

    Chen, Dongxing; Wang, Shaochi; Diao, Xiaojuan; Zhu, Qihua; Shen, Huiliang; Han, Xueqing; Wang, Yiwei; Gong, Guoqing; Xu, Yungen

    2015-12-01

    Thrombin is a serine protease that plays a key role in blood clotting, which makes it a promising target for the treatment of thrombotic diseases. Dabigatran is direct potent thrombin inhibitor. Based on bioisosteric and scaffold hopping principle, two dabigatran mimics (I-1 and II-1) in which the benzamidine moiety of dabigatran was replaced by a tricyclic fused scaffold were designed, synthesized and evaluated for their in vitro activities for inhibiting thrombin. The results reveal that compounds I-1 (IC50=9.20nM) and II-1 (IC50=7.48nM) are potent direct thrombin inhibitors and the activity is in the range of reference drug. On this basis, twenty-two ester and carbamate derivatives of I-1 or II-1 were prepared and evaluated for their anticoagulant activity. Prodrugs I-4a (IC50=0.73μM), I-4b (IC50=0.75μM), II-2a (IC50=1.44μM) and II-2b (IC50=0.91μM) display excellent effects of inhibiting thrombin induced-platelet aggregation. Moreover, compounds I-9 and II-4, which contain a cleavable moiety with anti-platelet activity, show the best anticoagulant efficacy among the tested compounds in the rat venous thrombosis model. The compounds which have better in vitro and in vivo activity were subjected to rat tail bleeding test, and the result demonstrates that compound I-9 is less likely to have bleeding risk than dabigatran etexilate.

  12. Thrombin-activatable fibrinolysis inhibitor activity in healthy and diseased dogs

    DEFF Research Database (Denmark)

    Jessen, Lisbeth Rem; Wiinberg, Bo; Kjelgaard-Hansen, Mads;

    2010-01-01

    Background: In people, increased thrombin-activatable fibrinolysis inhibitor (TAFI) antigen has been associated with increased risk of thrombosis, and decreased TAFI may contribute to bleeding diathesis. TAFI activity in dogs has been described in experimental models, but not in dogs...... with spontaneous disease. Objective: The aim of this study was to compare TAFI activity in healthy dogs with TAFI activity in dogs with spontaneous disease. Methods: Plasma samples from 20 clinically healthy Beagles and from 35 dogs with various diseases were analyzed using a commercial chromogenic assay...... that measured TAFI activity relative to activity in standardized pooled human plasma. Results: Median TAFI activity for the 20 Beagles was 46.1% (range 32.2-70.8%) compared with 62.6% (29.1-250%) for the 35 diseased dogs, and 14/35 (40%) had TAFI activities >the upper limit for controls. The highest individual...

  13. Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin.

    Directory of Open Access Journals (Sweden)

    Julian E Fuchs

    Full Text Available Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm "dynamics govern specificity" might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.

  14. Thrombin inhibition with melagatran does not attenuate renal ischaemia-reperfusion injury in rats

    DEFF Research Database (Denmark)

    Nitescu, Nicoletta; Grimberg, Elisabeth; Ricksten, Sven-Erik;

    2007-01-01

    BACKGROUND: Renal ischaemia-reperfusion (IR) is associated with activation of the coagulation system and inflammation within the kidney. The aim of the present study was to examine the effects of selective thrombin inhibition with melagatran on kidney morphology and function in rats subjected...... of saline vehicle or melagatran [0.5 mumol/kg, subcutaneously (s.c.)] followed by a continuous infusion throughout (0.08 micromol/kg/h, s.c.). Forty-eight hours after IR, renal function was assessed in anaesthetized animals and kidney histology was analysed semi-quantitatively. RESULTS: Rats in group IR......-Saline showed an approximate 85% reduction in glomerular filtration rate, 5-fold increases in fractional urinary excretion rates of sodium, potassium and water, and marked renal histological abnormalities, compared with sham (P histopathological changes in the cortex and outer medulla were...

  15. A study of the conditions and accuracy of the thrombin time assay of plasma fibrinogen

    DEFF Research Database (Denmark)

    Jespersen, J; Sidelmann, Johannes Jakobsen

    1982-01-01

    The conditions, accuracy, precision and possible error of the thrombin time assay of plasma fibrinogen are determined. Comparison with an estimation of clottable protein by absorbance at 280 nm gave a correlation coefficient of 0.96 and the regression line y = 1.00 x + 0.56 (n = 34). Comparison...... with a radial immunodiffusion method yielded the correlation coefficient 0.97 and the regression line y = 1.18 x = 2.47 (n = 26). The presence of heparin in clinically applied concentrations produced a slight shortening of the clotting times. The resulting error in the estimated concentrations of fibrinogen...... was too small to affect the clinical usefulness of the determinations. The influence of fibrin(ogen) degradation products was significant only in excessive amounts in samples containing low levels of fibrinogen....

  16. Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin.

    Science.gov (United States)

    Fuchs, Julian E; Huber, Roland G; Waldner, Birgit J; Kahler, Ursula; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

    2015-01-01

    Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm "dynamics govern specificity" might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design. PMID:26496636

  17. Historical perspective and contemporary management of acute coronary syndromes: from MONA to THROMBINS2.

    Science.gov (United States)

    Kline, Kristopher P; Conti, C Richard; Winchester, David E

    2015-01-01

    Acute coronary syndrome (ACS) remains a major burden on morbidity and mortality in the United States. Medical professionals and students often use the mnemonic 'MONA' (morphine, oxygen, nitroglycerin and aspirin) to recall treatments for ACS; however, this list of therapies is outdated. We provide a historical perspective on 'MONA,' attempt to uncover its origin in the medical literature, and demonstrate the myriad changes that have occurred over the last 50 years of ACS management. We have developed a novel mnemonic, 'THROMBINS2' (thienopyridines, heparin/enoxaparin, renin-angiotensin system blockers, oxygen, morphine, beta blocker, intervention, nitroglycerin, statin/salicylate) to help bedside clinicians recall all the elements of contemporary ACS management. We demonstrate the mortality benefit for each component of contemporary ACS management, correlating the continued improvement with historical data on mortality after myocardial infarction. We encourage providers to utilize this mnemonic to explore options and guide treatments in ACS patients. PMID:26457728

  18. Historical perspective and contemporary management of acute coronary syndromes: from MONA to THROMBINS2.

    Science.gov (United States)

    Kline, Kristopher P; Conti, C Richard; Winchester, David E

    2015-01-01

    Acute coronary syndrome (ACS) remains a major burden on morbidity and mortality in the United States. Medical professionals and students often use the mnemonic 'MONA' (morphine, oxygen, nitroglycerin and aspirin) to recall treatments for ACS; however, this list of therapies is outdated. We provide a historical perspective on 'MONA,' attempt to uncover its origin in the medical literature, and demonstrate the myriad changes that have occurred over the last 50 years of ACS management. We have developed a novel mnemonic, 'THROMBINS2' (thienopyridines, heparin/enoxaparin, renin-angiotensin system blockers, oxygen, morphine, beta blocker, intervention, nitroglycerin, statin/salicylate) to help bedside clinicians recall all the elements of contemporary ACS management. We demonstrate the mortality benefit for each component of contemporary ACS management, correlating the continued improvement with historical data on mortality after myocardial infarction. We encourage providers to utilize this mnemonic to explore options and guide treatments in ACS patients.

  19. Functional characterization of recombinant batroxobin, a snake venom thrombin-like enzyme, expressed from Pichia pastoris.

    Science.gov (United States)

    You, Weon-Kyoo; Choi, Won-Seok; Koh, You-Seok; Shin, Hang-Cheol; Jang, Yangsoo; Chung, Kwang-Hoe

    2004-07-30

    A thrombin-like enzyme of Bothrops atrox moojeni venom, batroxobin, specifically cleaves fibrinogen alpha chain, resulting in the formation of non-crosslinked fibrin clots. The cDNA encoding batroxobin was cloned, expressed in Pichia pastoris and the molecular function of purified recombinant protein was also characterized. The recombinant batroxobin had an apparent molecular weight of 33 kDa by SDS-PAGE analysis and biochemical activities similar to those of native batroxobin. The purified recombinant protein strongly converted fibrinogen into fibrin clot in vitro, and shortened bleeding time and whole blood coagulation time in vivo. However, it did not make any considerable alterations on other blood coagulation factors. Several lines of experimental evidence in this study suggest that the recombinant batroxobin is a potent pro-coagulant agent. PMID:15280019

  20. Effect of Locked-Nucleic Acid on a Biologically Active G-Quadruplex. A Structure-Activity Relationship of the Thrombin Aptamer

    Directory of Open Access Journals (Sweden)

    Michael B. Jarstfer

    2008-03-01

    Full Text Available Here we tested the ability to augment the biological activity of the thrombin aptamer, d(GGTTGGTGTGGTTGG, by using locked nucleic acid (LNA to influence its G-quadruplex structure. Compared to un-substituted control aptamer, LNA-containing aptamers displayed varying degrees of thrombin inhibition. Aptamers with LNA substituted in either positions G5, T7, or G8 showed decreased thrombin inhibition, whereas LNA at position G2 displayed activity comparable to un-substituted control aptamer. Interestingly, the thermal stability of the substituted aptamers does not correlate to activity – the more stable aptamers with LNA in position G5, T7, or G8 showed the least thrombin inhibition, while a less stable aptamer with LNA at G2 was as active as the un-substituted aptamer. These results suggest that LNA substitution at sites G5, T7, and G8 directly perturbs aptamer-thrombin affinity. This further implies that for the thrombin aptamer, activity is not dictated solely by the stability of the G-quadruplex structure, but by specific interactions between the central TGT loop and thrombin and that LNA can be tolerated in a biologically active nucleic acid structure albeit in a position dependent fashion.

  1. GDP beta S enhances the activation of phospholipase C caused by thrombin in human platelets: evidence for involvement of an inhibitory GTP-binding protein

    Energy Technology Data Exchange (ETDEWEB)

    Oberdisse, E.; Lapetina, E.G.

    1987-05-14

    Guanosine 5'-O-thiotriphosphate (GTP gamma S) and thrombin stimulate the activity of phospholipase C in platelets that have been permeabilized with saponin and whose inositol phospholipids have been prelabeled with (/sup 3/H)inositol. Ca/sup 2 +/ has opposite effects on the formation of (/sup 3/H)inositol phosphates induced by thrombin or GTP gamma S. While the action of GTP gamma S on the formation of (/sup 3/H)inositol phosphates is inhibited by Ca/sup 2 +/, action of thrombin is stimulated by Ca/sup 2 +/. Guanosine 5'-O-(2-thiodiphosphate) (GDP beta S), which inhibits the function of GTP-binding proteins, also inhibits the effect of GTP gamma S on phospholipase C stimulation but, surprisingly, increases the effect of thrombin. Ca/sup 2 +/ increases the inhibitory effect of GDP beta S on GTP gamma S activation of phospholipase C, but Ca/sup 2 +/ further enhances the stimulatory effect of GDP beta S on the thrombin activation of phospholipase C. This indicates that two mechanisms are responsible for the activation of phospholipase C in platelets. A GTP-binding protein is responsible for regulation of phospholipase C induced by GTP gamma S, while the effect of thrombin on the stimulation of phospholipase C is independent of GTP-binding proteins. However, the effect of thrombin may be modulated by the action of an inhibitory GTP-binding protein.

  2. Development of aptamer-conjugated magnetic graphene/gold nanoparticle hybrid nanocomposites for specific enrichment and rapid analysis of thrombin by MALDI-TOF MS.

    Science.gov (United States)

    Xiong, Ya; Deng, Chunhui; Zhang, Xiangmin

    2014-11-01

    Simple, rapid and sensitive analysis of thrombin (a tumor biomarker) in complex samples is quite clinical relevant and essential for the development of disease diagnosis and pharmacotherapy. Herein, we developed a novel method based on aptamer-conjugated magnetic graphene/gold nanoparticles nanocomposites (MagG@Au) for specific enrichment and rapid analysis of thrombin in biological samples using MALDI-TOF-MS. At first, gold nanoparticles were compactly deposited on PDDA functionalized magnetic graphene through electrostatic interaction. Afterwards, aptamer was easily conjugated to gold nanoparticles via Au-S bond formation. The as-made aptamer-conjugated nanocomposites took advantage of the magnetism of magnetic graphene, the high affinity and specificity of aptamer, facilitating a high-efficient separation and enrichment of thrombin. More importantly, due to the large surface area of the hybrid substrate, the average coverage density of aptamer achieved 0.34 nmol/mg, which enhanced the thrombin binding capacity and the recovery of thrombin in real samples. In turn, the enriched thrombin attributed to the sensitive output of MALDI-TOF mass spectrometry signal, 0.085 ng μL(-1) (2.36 nM) thrombin could be detected. This proposed method has a relatively wide linear relation ranging from 0.1 ng μL(-1) to 10 ng μL(-1), and satisfactory specificity. The proposed high-throughput method based on MALDI-TOF MS is expected to the application in the disease biomarker detection and clinical diagnosis. PMID:25127596

  3. Ultrasensitive electrochemical aptasensor for the detection of thrombin based on dual signal amplification strategy of Au@GS and DNA-CoPd NPs conjugates.

    Science.gov (United States)

    Wang, Yaoguang; Zhang, Yong; Yan, Tao; Fan, Dawei; Du, Bin; Ma, Hongmin; Wei, Qin

    2016-06-15

    In this work, an ultrasensitive electrochemical aptasensor for the detection of thrombin was developed based on Au nanoparticles decorated graphene sheet (Au@GS) and CoPd binary nanoparticles (CoPd NPs). A sulfydryl-labeled thrombin capture probe (Apt1) and a biotin-labeled thrombin reporter probe (Apt2) were designed to achieve a sandwich-type strategy. Au@GS was used as a sensing platform for the facile immobilization of Apt1 through Au-S bond, forming a sensing interface for thrombin. The specific recognition of thrombin induced the attachment of Apt2-CoPd NPs to the electrode. The labeled CoPd NPs showed good catalytic properties toward the reduction of H2O2, resulting in an amperometric signal. The amperometric response was correlated to the thrombin concentration in sample solutions. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) confirmed the successful fabrication of the aptasensor. A linear response to thrombin in the range of 0.01-2.00 ng mL(-1) with a low detection limit (5 pg mL(-1)) was achieved. The proposed aptasensor showed good selectivity, good reproducibility and acceptable stability. This proposed strategy may find many potential applications in the detection of other biomolecules.

  4. Chef infrastructure automation cookbook

    CERN Document Server

    Marschall, Matthias

    2013-01-01

    Chef Infrastructure Automation Cookbook contains practical recipes on everything you will need to automate your infrastructure using Chef. The book is packed with illustrated code examples to automate your server and cloud infrastructure.The book first shows you the simplest way to achieve a certain task. Then it explains every step in detail, so that you can build your knowledge about how things work. Eventually, the book shows you additional things to consider for each approach. That way, you can learn step-by-step and build profound knowledge on how to go about your configuration management

  5. A plasmin-activatable thrombin inhibitor reduces experimental thrombosis and assists experimental thrombolysis in murine models.

    Science.gov (United States)

    Sheffield, W P; Eltringham-Smith, L J; Gataiance, S; Bhakta, V

    2015-05-01

    The leech protein hirudin is a potent natural thrombin inhibitor. Its potential as an antithrombotic agent is limited by its promotion of bleeding. We attempted to modify this profile by positioning albumin and a plasmin cleavage site on its N-terminus, in recombinant protein HSACHV3 [comprising hirudin variant 3 (HV3) fused to the C-terminus of human serum albumin (HSA) via a plasmin cleavage site (C)], Previously we showed that HSACHV3 inhibited thrombin in a plasmin-dependent manner, and that, unlike HV3, it did not increase bleeding in vivo when administered to mice. Here we tested HSACHV3 for the ability to reduce thrombosis and assist enzymatic thrombolysis in animal models. Intravenous administration of HSACHV3, but not a control protein lacking the plasmin cleavage site (HSAHV3), reduced thrombus weight by 2.1-fold in the ferric chloride-injured mouse vena cava. Similarly, thrombi formed in a rabbit jugular vein stasis model were 1.7-fold lighter in animals treated with HSACHV3 compared to those receiving HSAHV3. Administration of 60 mg/kg body weight HSACHV3 prolonged the time to occlusion in the ferric chloride-injured mouse carotid artery by threefold compared to vehicle controls, while equimolar HSAHV3 had no effect. HSACHV3 had no ability to restore flow to the murine carotid arteries occluded by ferric chloride treatment, but combining HSACHV3 (60 mg/kg) with recombinant mutant tissue plasminogen activator (TNKase) significantly reduced the time to restore patency to the artery compared to TNKase alone. Unlike unfused HV3, HSACHV3 did not increase bleeding in a mouse liver laceration model. Our results show that HSACHV3 acts as an antithrombotic agent that does not promote bleeding and which speeds the time to flow restoration when used as an adjunct to pharmacological thrombolysis in animal models. PMID:25481811

  6. Characterization of Ixophilin, a thrombin inhibitor from the gut of Ixodes scapularis.

    Directory of Open Access Journals (Sweden)

    Sukanya Narasimhan

    Full Text Available Ixodes scapularis, the black-legged tick, vectors several human pathogens including Borrelia burgdorferi, the agent of Lyme disease in North America. Pathogen transmission to the vertebrate host occurs when infected ticks feed on the mammalian host to obtain a blood meal. Efforts to understand how the tick confronts host hemostatic mechanisms and imbibes a fluid blood meal have largely focused on the anticoagulation strategies of tick saliva. The blood meal that enters the tick gut remains in a fluid state for several days during the process of feeding, and the role of the tick gut in maintaining the blood-meal fluid is not understood. We now demonstrate that the tick gut produces a potent inhibitor of thrombin, a key enzyme in the mammalian coagulation cascade. Chromatographic fractionation of engorged tick gut proteins identified one predominant thrombin inhibitory activity associated with an approximately 18 kDa protein, henceforth referred to as Ixophilin. The ixophilin gene was preferentially transcribed in the guts of feeding nymphs. Expression began after 24 hours of feeding, coincident with the flow of host blood into the tick gut. Immunity against Ixophilin delayed tick feeding, and decreased feeding efficiency significantly. Surprisingly, immunity against Ixophilin resulted in increased Borrelia burgdorferi transmission to the host, possibly due to delayed feeding and increased transmission opportunity. These observations illuminate the potential drawbacks of targeting individual tick proteins in a functional suite. They also underscore the need to identify the "anticoagulome" of the tick gut, and to prioritize a critical subset of anticoagulants that could be targeted to efficiently thwart tick feeding, and block pathogen transmission to the vertebrate host.

  7. Management of major bleedings during anticoagulant treatment with the oral direct thrombin inhibitor ximelagatran or warfarin.

    Science.gov (United States)

    Fernlöf, Gunilla; Sjöström, Britta M; Lindell, Klas M; Wall, Ulrika E

    2009-12-01

    Several new oral anticoagulants are currently investigated in phase III programmes, mainly with inhibition of factor Xa or thrombin as their pharmacological target. Advantages are expected with these new drugs compared with vitamin K antagonists, but one potential drawback is the lack of specific antidotes. During the clinical studies with ximelagatran, an oral direct thrombin inhibitor withdrawn due to hepatic side effects, investigators were instructed to manage bleedings with routine measures. We have retrospectively tried to assess whether this was sufficient or whether there was a need for reversal strategies. The study population consisted of patients with major bleedings in three long-term studies (104 ximelagatran, 155 warfarin). All individual patient narratives were reviewed with respect to management of the bleeding. Complementary data were retrieved from the data-based case report forms. Approximately, two of three of the patients in both groups were subject to some kind of treatment. One-third (1/3) in both groups had transfusions documented and/or received specific medication. Vitamin K was given more often to warfarin patients. Two ximelagatran patients received prothrombin complex (four-factor concentrate), but one was a patient with a severe hepatopathy suspected to be drug-induced. Overall, the case descriptions did not reveal any apparent differences in the course of events between groups. We found no indications that the lack of an antidote posed a clinical problem in patients treated with ximelagatran as compared with warfarin. The relatively short half-life of melagatran, the active metabolite of ximelagatran, may have contributed to these results.

  8. Thrombin induced connective tissue growth factor expression in rat vascular smooth muscle cells via the PAR-1/JNK/AP-1 pathway

    Institute of Scientific and Technical Information of China (English)

    Wen-chin KO; Bing-chang CHEN; Ming-jen HSU; Chia-ti TSAI; Chuang-ye HONG; Chien-huang LIN

    2012-01-01

    To investigate the signaling pathways involved in thrombin-induced connective tissue growth factor (CTGF) expression in rat vascular smooth muscle cells (VSMCs).Methods:Experiments were preformed on primary rat aortic smooth muscle cells (RASMCs) and a rat VSMC line (A10).CTGF protein levels were measured using Western blotting.Luciferase reporter genes and dominant negative mutants (DNs) were used to investigate the signaling pathways mediating the induction of CTGF expression by thrombin.Results:Thrombin (0.3-3.0 U/mL) caused a concentration- and time-dependent increase in CTGF expression in both RASMCs and A10 cells.Pretreating A10 cells with the protease-activated receptor 1 (PAR-1) antagonist SCH79797 (0.1 μmol/L) significantly blocked thrombin-induced CTGF expression,while the PAR-4 antagonist tcY-NH2 (30 μmol/L) had no effect.The PAR-1 agonist SFLLRN-NH2 (300 μmol/L) induced CTGF expression,while the PAR-4 agonist GYPGQV-NH2 (300 μmol/L) had no effect.Thrombin (1 U/mL) caused time-dependent phosphorylation of c-Jun N-terminal kinase (JNK).Pretreating with the JNK inhibitor SP600125 (3-30 μmol/L) or transfection with DNs of JNK1/2 significantly attenuated thrombin-induced CTGF expression.Thrombin (0.3-3.0 U/mL) increased activator protein-1 (AP-1)-Iuciferase activity,which was inhibited by the JNK inhibitor SP600125.The AP-1 inhibitor curcumin (1-10 μmol/L) concentration-dependently attenuated thrombin-induced CTGF expression.Conclusion:Thrombin acts on PAR-1 to activate the JNK signaling pathway,which in turn initiates AP-1 activation and ultimately induces CTGF expression in VSMCs.

  9. Thrombin-anti-thrombin levels and patency of arterio-venous fistula in patients undergoing haemodialysis compared to healthy volunteers: a prospective analysis.

    Directory of Open Access Journals (Sweden)

    James A Milburn

    Full Text Available BACKGROUND: Patients on haemodialysis (HD are at an increased risk of sustaining thrombotic events especially to their vascular access which is essential for maintenance of HD. OBJECTIVES: To assess whether 1 markers of coagulation, fibrinolysis or endothelial activation are increased in patients on HD compared to controls and 2 if measurement of any of these factors could help to identify patients at increased risk of arteriovenous (AVF access occlusion. PATIENTS/METHODS: Venous blood samples were taken from 70 patients immediately before a session of HD and from 78 resting healthy volunteers. Thrombin-antithrombin (TAT, D-dimer, von Willebrand factor (vWF, plasminogen activator inhibitor-1 antigen (PAI-1 and soluble p-selectin were measured by ELISA. C-reactive protein (hsCRP was measured by an immunonephelometric kinetic assay. Determination of the patency of the AVF was based upon international standards and was prospectively followed up for a minimum of four years or until the AVF was non-functioning. RESULTS: A total of 70 patients were studied with a median follow-up of 740 days (range 72-1788 days. TAT, D-dimer, vWF, p-selectin and hsCRP were elevated in patients on HD compared with controls. At one year follow-up, primary patency was 66% (46 patients. In multivariate analysis TAT was inversely associated with primary assisted patency (r = -0.250, p = 0.044 and secondary patency (r = -0.267, p= 0.031. CONCLUSIONS: The novel finding of this study is that in patients on haemodialysis, TAT levels were increased and inversely correlated with primary assisted patency and secondary patency. Further evaluation is required into the possible role of TAT as a biomarker of AVF occlusion.

  10. A Simulation Study of Automated Treatment Planning in a Mental Hospital

    OpenAIRE

    Craig, T. J.; Richardson, M. A.; Pass, R.; Simpson, F.; Summers, I.

    1983-01-01

    A simulation study of automated treatment planning in a state mental hospital revealed that automation, per se, was of little direct benefit to clinicians and had virtually no impact on the clinical process. However, supervisory and quality assurance staff found considerable utility in the ability to generate reports previously unavailable. The implications for planning automated clinical systems are discussed.

  11. Thrombin induces Egr-1 expression in fibroblasts involving elevation of the intracellular Ca2+ concentration, phosphorylation of ERK and activation of ternary complex factor

    Directory of Open Access Journals (Sweden)

    Thiel Gerald

    2009-05-01

    Full Text Available Abstract Background The serine protease thrombin catalyzes fibrin clot formation by converting fibrinogen into fibrin. Additionally, thrombin stimulation leads to an activation of stimulus-responsive transcription factors in different cell types, indicating that the gene expression pattern is changed in thrombin-stimulated cells. The objective of this study was to analyze the signaling cascade leading to the expression of the zinc finger transcription factor Egr-1 in thrombin-stimulated lung fibroblasts. Results Stimulation of 39M1-81 fibroblasts with thrombin induced a robust and transient biosynthesis of Egr-1. Reporter gene analysis revealed that the newly synthesized Egr-1 was biologically active. The signaling cascade connecting thrombin stimulation with Egr-1 gene expression required elevated levels of cytosolic Ca2+, the activation of diacylgycerol-dependent protein kinase C isoenzymes, and the activation of extracellular signal-regulated protein kinase (ERK. Stimulation of the cells with thrombin triggered the phosphorylation of the transcription factor Elk-1. Expression of a dominant-negative mutant of Elk-1 completely prevented Egr-1 expression in stimulated 39M1-81 cells, indicating that Elk-1 or related ternary complex factors connect the intracellular signaling cascade elicited by activation of protease-activated receptors with transcription of the Egr-1 gene. Lentiviral-mediated expression of MAP kinase phosphatase-1, a dual-specific phosphatase that dephosphorylates and inactivates ERK in the nucleus, prevented Elk-1 phosphorylation and Egr-1 biosynthesis in thrombin stimulated 39M1-81 cells, confirming the importance of nuclear ERK and Elk-1 for the upregulation of Egr-1 expression in thrombin-stimulated lung fibroblasts. 39M1-81 cells additionally express M1 muscarinic acetylcholine receptors. A comparison between the signaling cascades induced by thrombin or carbachol showed no differences, except that signal transduction via M

  12. I-94 Automation FAQs

    Data.gov (United States)

    Department of Homeland Security — In order to increase efficiency, reduce operating costs and streamline the admissions process, U.S. Customs and Border Protection has automated Form I-94 at air and...

  13. Hydrometeorological Automated Data System

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Office of Hydrologic Development of the National Weather Service operates HADS, the Hydrometeorological Automated Data System. This data set contains the last...

  14. Automated Vehicles Symposium 2015

    CERN Document Server

    Beiker, Sven

    2016-01-01

    This edited book comprises papers about the impacts, benefits and challenges of connected and automated cars. It is the third volume of the LNMOB series dealing with Road Vehicle Automation. The book comprises contributions from researchers, industry practitioners and policy makers, covering perspectives from the U.S., Europe and Japan. It is based on the Automated Vehicles Symposium 2015 which was jointly organized by the Association of Unmanned Vehicle Systems International (AUVSI) and the Transportation Research Board (TRB) in Ann Arbor, Michigan, in July 2015. The topical spectrum includes, but is not limited to, public sector activities, human factors, ethical and business aspects, energy and technological perspectives, vehicle systems and transportation infrastructure. This book is an indispensable source of information for academic researchers, industrial engineers and policy makers interested in the topic of road vehicle automation.

  15. Automated Vehicles Symposium 2014

    CERN Document Server

    Beiker, Sven; Road Vehicle Automation 2

    2015-01-01

    This paper collection is the second volume of the LNMOB series on Road Vehicle Automation. The book contains a comprehensive review of current technical, socio-economic, and legal perspectives written by experts coming from public authorities, companies and universities in the U.S., Europe and Japan. It originates from the Automated Vehicle Symposium 2014, which was jointly organized by the Association for Unmanned Vehicle Systems International (AUVSI) and the Transportation Research Board (TRB) in Burlingame, CA, in July 2014. The contributions discuss the challenges arising from the integration of highly automated and self-driving vehicles into the transportation system, with a focus on human factors and different deployment scenarios. This book is an indispensable source of information for academic researchers, industrial engineers, and policy makers interested in the topic of road vehicle automation.

  16. JTst - An Automated Unit Testing Tool for Java Program

    Directory of Open Access Journals (Sweden)

    Kamal Z.  Zamli

    2008-01-01

    Full Text Available Software testing is an integral part of software development lifecycle. Lack of testing can often lead to disastrous consequences including lost of data, fortunes, and even lives. Despite its importance, current software testing practice lacks automation, and is still primarily based on highly manual processes from the generation of test cases up to the actual execution of the test. Although the emergence of helpful automated testing tools in the market is blooming, their adoptions are lacking as they do not adequately provide the right level abstraction and automation required by test engineers. JTst is a Java based automated unit testing tool that addresses some of the aforementioned issues. The main novel features are the fact that JTst automates the test preparation activities, facilitates the test data generation through recombination, and allows concurrent execution of test data, in order to encourage higher product quality at lower testing costs.

  17. Disassembly automation automated systems with cognitive abilities

    CERN Document Server

    Vongbunyong, Supachai

    2015-01-01

    This book presents a number of aspects to be considered in the development of disassembly automation, including the mechanical system, vision system and intelligent planner. The implementation of cognitive robotics increases the flexibility and degree of autonomy of the disassembly system. Disassembly, as a step in the treatment of end-of-life products, can allow the recovery of embodied value left within disposed products, as well as the appropriate separation of potentially-hazardous components. In the end-of-life treatment industry, disassembly has largely been limited to manual labor, which is expensive in developed countries. Automation is one possible solution for economic feasibility. The target audience primarily comprises researchers and experts in the field, but the book may also be beneficial for graduate students.

  18. Instant Sikuli test automation

    CERN Document Server

    Lau, Ben

    2013-01-01

    Get to grips with a new technology, understand what it is and what it can do for you, and then get to work with the most important features and tasks. A concise guide written in an easy-to follow style using the Starter guide approach.This book is aimed at automation and testing professionals who want to use Sikuli to automate GUI. Some Python programming experience is assumed.

  19. Automated security management

    CERN Document Server

    Al-Shaer, Ehab; Xie, Geoffrey

    2013-01-01

    In this contributed volume, leading international researchers explore configuration modeling and checking, vulnerability and risk assessment, configuration analysis, and diagnostics and discovery. The authors equip readers to understand automated security management systems and techniques that increase overall network assurability and usability. These constantly changing networks defend against cyber attacks by integrating hundreds of security devices such as firewalls, IPSec gateways, IDS/IPS, authentication servers, authorization/RBAC servers, and crypto systems. Automated Security Managemen

  20. Automated Lattice Perturbation Theory

    Energy Technology Data Exchange (ETDEWEB)

    Monahan, Christopher

    2014-11-01

    I review recent developments in automated lattice perturbation theory. Starting with an overview of lattice perturbation theory, I focus on the three automation packages currently "on the market": HiPPy/HPsrc, Pastor and PhySyCAl. I highlight some recent applications of these methods, particularly in B physics. In the final section I briefly discuss the related, but distinct, approach of numerical stochastic perturbation theory.

  1. Architectures and design patterns for functional design of logic control and diagnostics in industrial automation

    OpenAIRE

    Sartini, Matteo

    2010-01-01

    Recently in most of the industrial automation process an ever increasing degree of automation has been observed. This increasing is motivated by the higher requirement of systems with great performance in terms of quality of products/services generated, productivity, efficiency and low costs in the design, realization and maintenance. This trend in the growth of complex automation systems is rapidly spreading over automated manufacturing systems (AMS), where the integration of the mechanic...

  2. Preparation of brightly fluorescent silica nanoparticles modified with lucigenin and chitosan, and their application to an aptamer-based sandwich assay for thrombin

    International Nuclear Information System (INIS)

    We report on the preparation of fluorescent silica nanoparticles (SiNPs) modified with chitosan and lucigenin by using a reverse microemulsion method. The introduction of chitosan to the lucigenin doped SiNPs is shown to improve the fluorescence quantum yield. The modified SiNPs were used as fluorescent markers in an aptamer-based method for selective determination of thrombin. In this protocol, thrombin was sandwiched between streptavidin-coated magnetic beads and the fluorescent SiNPs modified with a thrombin-binding aptamer. The method was successfully applied to the determination of thrombin in human serum and showed a detection limit as low as 0.02 nM. In our perception, the protocol presented here is promising in that such SiNPs may be applied to the sensitive fluorescent detection of other analytes by changing the corresponding aptamer. (author)

  3. Thrombin mediates migration of rat brain astrocytes via PLC, Ca²⁺, CaMKII, PKCα, and AP-1-dependent matrix metalloproteinase-9 expression.

    Science.gov (United States)

    Lin, Chih-Chung; Lee, I-Ta; Wu, Wen-Bin; Liu, Chiung-Ju; Hsieh, Hsi-Lung; Hsiao, Li-Der; Yang, Chien-Chung; Yang, Chuen-Mao

    2013-12-01

    Matrix metalloproteinase-9 (MMP-9) plays a crucial role in pathological processes of brain inflammation, injury, and neurodegeneration. Thrombin has been known as a regulator of MMP-9 expression and cells migration. However, the mechanisms underlying thrombin-induced MMP-9 expression in rat brain astrocytes (RBA-1 cells) remain unclear. Here, we demonstrated that thrombin induced the expression of pro-form MMP-9 and migration of RBA-1 cells, which were inhibited by pretreatment with the inhibitor of Gq-coupled receptor (GPAnt2A), Gi/o-coupled receptor (GPAnt2), PC-PLC (D609), PI-PLC (U73122), Ca(2+)-ATPase (thapsigargin, TG), calmodulin (CaMI), CaMKII (KN62), PKC (Gö6976 or GF109203X), MEK1/2 (PD98059), p38 MAPK (SB202190), JNK1/2 (SP600125), or AP-1 (Tanshinone IIA) or the intracellular calcium chelator (BAPTA/AM) and transfection with siRNA of PKCα, Erk2, JNK1, p38 MAPK, c-Jun, or c-Fos. In addition, thrombin-induced elevation of intracellular Ca(2+) concentration was attenuated by PPACK (a thrombin inhibitor). Thrombin further induced CaMKII phosphorylation and PKCα translocation, which were inhibited by U73122, D609, KN62, TG, or BAPTA/AM. Thrombin also induced PKCα-dependent p42/p44 MAPK and JNK1/2, but not p38 MAPK activation. Finally, we showed that thrombin enhanced c-Fos expression and c-Jun phosphorylation. c-Fos mRNA levels induced by thrombin were reduced by PD98059, SP600125, and Gö6976, but not SB202190. Thrombin stimulated in vivo binding of c-Fos to the MMP-9 promoter, which was reduced by pretreatment with SP600125 or PD98059, but not SB202190. These results concluded that thrombin activated a PLC/Ca(2+)/CaMKII/PKCα/p42/p44 MAPK and JNK1/2 pathway, which in turn triggered AP-1 activation and ultimately induced MMP-9 expression in RBA-1 cells.

  4. An electrochemical aptasensor based on TiO2/MWCNT and a novel synthesized Schiff base nanocomposite for the ultrasensitive detection of thrombin.

    Science.gov (United States)

    Heydari-Bafrooei, Esmaeil; Amini, Maryam; Ardakani, Mehdi Hatefi

    2016-11-15

    A sensitive aptasensor based on a robust nanocomposite of titanium dioxide nanoparticles, multiwalled carbon nanotubes (MWCNT), chitosan and a novel synthesized Schiff base (SB) (TiO2/MWCNT/CHIT/SB) on the surface of a glassy carbon electrode (GCE) was developed for thrombin detection. The resultant nanocomposite can provide a large surface area, excellent electrocatalytic activity, and high stability, which would improve immobilization sites for biological molecules, allow remarkable amplification of the electrochemical signal and contribute to improved sensitivity. Thrombin aptamers were simply immobilized onto the TiO2-MWCNT/CHIT-SB nanocomposite matrix through simple π - π stacking and electrostatic interactions between CHIT/SB and aptamer strands. The electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV) and differential pulse voltammetry (DPV) were used to analyze the surface characterization of unmodified GCE and TiO2-MWCNT/CHIT-SB modified GCE, and also the interaction between aptamer and thrombin. In the presence of thrombin, the aptamer on the adsorbent layer captures the target on the electrode interface, which makes a barrier for electrons and inhibits electron transfer, thereby resulting in decreased DPV and increased impedance signals of the TiO2-MWCNT/CHIT-SB modified GCE. Furthermore, the proposed aptasensor has a very low LOD of 1.0fmolL(-1) thrombin within the detection range of 0.00005-10nmolL(-1). The aptasensor also presents high specificity and reproducibility for thrombin, which is unaffected by the coexistence of other proteins. Clinical application was performed with analysis of the thrombin levels in blood and CSF samples obtained from patients with MS, Parkinson, Epilepsy and Polyneuropathy using both the aptasensor and commercial ELISA kit. The results revealed the proposed system to be a promising candidate for clinical analysis of thrombin. PMID:27295570

  5. Dabigatran, a direct thrombin inhibitor, blocks differentiation of normal fibroblasts to a myofibroblast phenotype and demonstrates anti-fibrotic effects on scleroderma lung fibroblasts

    OpenAIRE

    Bogatkevich, Galina S.; Ludwicka-Bradley, Anna; Silver, Richard M.

    2009-01-01

    Myofibroblasts are the principal mesenchymal cells responsible for tissue remodeling, collagen deposition, and the restrictive nature of lung parenchyma associated with pulmonary fibrosis. We previously reported that thrombin activates protease-activated receptor (PAR)-1 thereby inducing normal lung fibroblasts to differentiate to a myofibroblast phenotype resembling scleroderma lung myofibroblasts. Here we demonstrate that the thrombin inhibitor dabigatran inhibits in a dose-dependant manner...

  6. A colorimetric sandwich-type assay for sensitive thrombin detection based on enzyme-linked aptamer assay.

    Science.gov (United States)

    Park, Jun Hee; Cho, Yea Seul; Kang, Sungmuk; Lee, Eun Jeong; Lee, Gwan-Ho; Hah, Sang Soo

    2014-10-01

    A colorimetric sandwich-type assay based on enzyme-linked aptamer assay has been developed for the fast and sensitive detection of as low as 25 fM of thrombin with high linearity. Aptamer-immobilized glass was used to capture the target analyte, whereas a second aptamer, functionalized with horseradish peroxidase (HRP), was employed for the conventional 3,5,3',5'-tetramethylbenzidine (TMB)-based colorimetric detection. Without the troublesome antibody requirement of the conventional enzyme-linked immunosorbent assay (ELISA), as low as 25 fM of thrombin could be rapidly and reproducibly detected. This assay has superior, or at least equal, recovery and accuracy to that of conventional antibody-based ELISA.

  7. Purification and Characterization of Jararassin-I,A Thrombin-like Enzyme from Bothrops jararaca Snake Venom

    Institute of Scientific and Technical Information of China (English)

    Débora F. VIEIRA; Leandra WATANABE; Carolina D. SANT'ANA; Silvana MARCUSSI; Suely V. SAMPAIO; Andreimar M. SOARES; Raghuvir K. ARNI

    2004-01-01

    A thrombin-like serine protease, jararassin-I, was isolated from the venom of Bothrops jararaca. The protein was obtained in high yield and purity by a single chromatographic step using the affinity resin Benzamidine-Sepharose CL-6B. SDS-PAGE and dynamic light scattering analyses indicated that the molecular mass of the enzyme was about 30 kD. The enzyme possessed fibrinogenolytic and coagulant activities. The jararassin-I degraded the Bβ chain of fibrinogen while the Aα chain and γ chain were unchanged.Proteases inhibitors, PMSF and benzamidine inhibited the coagulant activity. These results showed jararassinI is a serine protease similar to coagulating thrombin-like snake venom proteases, but it specifically cleaves Bβ chain of bovine fibrinogen. Single crystals of enzyme were obtained (0.2 mm×0.2 mm×0.2 mm) and used for X-ray diffraction experiments.

  8. Spectroscopic and Electrochemical Detection of Thrombin/5'-SH or 3'-SH Aptamer Immobilized on (porous) Gold Substrates

    Energy Technology Data Exchange (ETDEWEB)

    Park, Buem Jin; Sa, Young Seung; Kim, Yong Hwan; Kim, Young Hun [Kwangwoon University, Seoul (Korea, Republic of)

    2012-01-15

    Thrombin is a serine protease that catalyzes the conversion of soluble fibrinogen to insoluble fibrin, and thus induces physiological and pathological blood coagulation. Therefore, it is important to detect thrombin in blood serum for purposes of diagnosis. To achieve this goal, it has been suggested that a 15-mer aptamer strongly binds with thrombin to form a G-quartet structure of the aptamer. Generally, 5'-end thiol-functionalized aptamer has been used as an anti-thrombin binder. Herein, we evaluate the possibility of utilizing a 3'-SH aptasensor for thrombin detection using SPR spectroscopy, and compare the enhancement of the electrochemical signal of the thrombin-aptamer bound on a porous gold substrate. Although the two aptamers have similar configurations, in SPR analysis, the 3'-SH aptamer was a effective aptasensor as well as 5'-SH aptamer. Results from electrochemical analysis showed that the porous gold substrate acted as a good substrate for an aptasensor and demonstrated 5-fold enhancement of current change, as compared to gold thin film.

  9. The Selection of DNA Aptamers for Two Different Epitopes of Thrombin Was Not Due to Different Partitioning Methods

    OpenAIRE

    Wilson, Robert; Cossins, Andrew; Nicolau, Dan V.; Missailidis, Sotiris

    2013-01-01

    Nearly all aptamers identified so far for any given target molecule have been specific for the same binding site (epitope). The most notable exception to the 1 aptamer per target molecule rule is the pair of DNA aptamers that bind to different epitopes of thrombin. This communication refutes the suggestion that these aptamers exist because different partitioning methods were used when they were selected. The possibility that selection of these aptamers was biased by conflicting secondary stru...

  10. Shc adaptor proteins are key transducers of mitogenic signaling mediated by the G protein-coupled thrombin receptor

    DEFF Research Database (Denmark)

    Chen, Y; Grall, D; Salcini, A E;

    1996-01-01

    The serine protease thrombin activates G protein signaling systems that lead to Ras activation and, in certain cells, proliferation. Whereas the steps leading to Ras activation by G protein-coupled receptors are not well defined, the mechanisms of Ras activation by receptor tyrosine kinases have...... kinase activation, gene induction and cell growth. From these data, we conclude that Shc represents a crucial point of convergence between signaling pathways activated by receptor tyrosine kinases and G protein-coupled receptors....

  11. Comparison of ultrasound-guided thrombin injection and compression repair in treatment of iatrogenic femoral arterial pseudoaneurysms

    Institute of Scientific and Technical Information of China (English)

    QIN Jun; GAO Yun-hua; ZHUO Zhong-xiong; HUANG Lan; LI Ai-min; SONG Yao-ming; JIN Jun; YU Xue-jun; GENG Zhao-hua; ZHOU Xia-bo; LIN Chun-mei

    2006-01-01

    Objective:To retrospectively compare the efficacy and safety of ultrasound-guided thrombin injection (UGTI) with ultrasound-guided compression repair (UGCR) in patients with postcatheterizational femoral arterial pseudoaneurysms (PSA). Methods: Thirty patients of this iatrogenic PSA [8males, 22 females, average age (66.5± 5.2) years] in our nstitution from 1997 to 2004 were retrospectively analyzed. Among them, 11 patients were treated with UGCR, 2 under continuous ultrasonographic (US) guidance and 9 under the guidance of femoral arterial bruit auscultation and dorsalis pedis artery palpation. Because UGCR was failed in 5 patients, consecutively 24 patients were treated with UGTI. Wine thrombin solution at a concentration of 200 U/ml was injected percutaneously using 22-25 gauge needles under color Doppler US. Demographics, clinical variables, pseudoaneurysm characteristics, and results of the 2 groups were compared by using Fisher's exact test and Student's t test. Results: The initial success rate of UGCR was 36.4% (4/11) nd the overall success rate was 45.5% (5/11). Ten of 11 patients suffered from local pain during the compression, but there was no any complication in UGTI group. The average dose of injected thrombin was (180±82) U for PSA of a single loculus and (315±150) U for multiloculated PSA. The initial success rate of UGTI was 89.5% (17/19) and the verall uccess rate was 100% (24/24). Conclusion:UGTI offers a safe, quick and effective means of definitively treating femoral pseudoaneurysms and seems superior to UGCR. The amount of thrombin applied on our people seems smaller compared with others' work.

  12. Novel magnetic fibrin hydrogel scaffolds containing thrombin and growth factors conjugated iron oxide nanoparticles for tissue engineering

    OpenAIRE

    Ziv-Polat O; Skaat H; Shahar A; Margel S

    2012-01-01

    Ofra Ziv-Polat1, Hadas Skaat1, Abraham Shahar2, Shlomo Margel11Department of Chemistry, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Ramat-Gan 52900, Israel; 2NVR Research Ltd, Nes-Ziona 74031, IsraelAbstract: Novel tissue-engineered magnetic fibrin hydrogel scaffolds were prepared by the interaction of thrombin-conjugated iron oxide magnetic nanoparticles with fibrinogen. In addition, stabilization of basal fibroblast growth factor (bFGF) was achieved by the covalent and phys...

  13. Anti-thrombin therapy during warm ischemia and cold preservation prevents chronic kidney graft fibrosis in a DCD model

    OpenAIRE

    Favreau, F.; Thuillier, R.; Cau, J; S. Milin; Manguy, E; Mauco, G; Zhu, X.; Lerman, LO; Hauet, T.

    2009-01-01

    Ischemia reperfusion injury (IRI) is pivotal for renal fibrosis development via peritubular capillaries injury. Coagulation represents a key mechanism involved in this process. Melagatran® (M), a thrombin inhibitor, was evaluated in an autotransplanted kidney model, using Large White pigs. To mimic deceased after cardiac death donor conditions, kidneys underwent warm ischemia (WI) for 60 min before cold preservation for 24 hours in University of Wisconsin solution. Treatment with M before WI ...

  14. Microfluidic Chip-Based Online Screening Coupled to Mass Spectrometry: Identification of Inhibitors of Thrombin and Factor Xa.

    Science.gov (United States)

    Iyer, Janaki Krishnamoorthy; Otvos, Reka A; Kool, Jeroen; Kini, R Manjunatha

    2016-02-01

    Thrombin and factor Xa (FXa) are critical enzymes of the blood coagulation cascade and are excellent targets of anticoagulant agents. Natural sources present an array of anticoagulants that can be developed as antithrombotic drugs. High-resolution, online screening techniques have been developed for the identification of drug leads from complex mixtures. In this study, we have developed and optimized a microfluidic online screening technique coupled to nano-liquid chromatography (LC) and in parallel with a mass spectrometer for the identification of thrombin and FXa inhibitors in mixtures. Inhibitors eluting from the nano-LC were split postcolumn in a 1:1 ratio; half was fed into a mass spectrometer (where its mass is detected), and the other half was fed into a microfluidic chip (which acts as a microreactor for the online assays). With our platform, thrombin and FXa inhibitors were detected in the assay in parallel with their mass identification. These methods are suitable for the identification of inhibitors from sample amounts as low as sub-microliter volumes. PMID:26323281

  15. 3,4,9,10-Perylenetetracarboxylic dianhydride functionalized graphene sheet as labels for ultrasensitive electrochemiluminescent detection of thrombin.

    Science.gov (United States)

    Gan, Xianxue; Yuan, Ruo; Chai, Yaqin; Yuan, Yali; Cao, Yaling; Liao, Yuhong; Liu, Huijing

    2012-05-13

    A novel tracer, 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) functionalized graphene sheet (GS) composite (GS-TCDA), is employed to label the secondary anti-thrombin aptamer (TBA) to construct an ultrasensitive electrochemiluminescent sandwich-type aptasensor. The GS provided large surface area for loading abundant PTCDA and TBA with good stability and biocompatibility. Because of the excellent electroconductivity of GS and the desirable optical properties of PTCDA, the as-formed Apt II bioconjugate considerably amplified the electrochmiluminescence (ECL) signal of peroxydisulfate (S(2)O(8)(2-)) and worked as the desirable label for Apt II. On the basis of the considerably amplified ECL signal and sandwich format, an extremely wide range from 1 fM to 1 nM with an ultralow detection limit of 0.33 fM for thrombin was obtained. Additionally, the selectivity and stability of the proposed aptasensor were also excellent. Thus, this procedure has great promise for detection of thrombin present at ultra-trace levels during early stage of diseases. PMID:22541015

  16. A sensitive sandwich-type electrochemical aptasensor for thrombin detection based on platinum nanoparticles decorated carbon nanocages as signal labels.

    Science.gov (United States)

    Gao, Fenglei; Du, Lili; Zhang, Yu; Zhou, Fuyi; Tang, Daoquan

    2016-12-15

    In this work, a novel and sensitive sandwich-type electrochemical aptasensor has been developed for thrombin detection based on platinum nanoparticles (Pt NPs) decorated carbon nanocages (CNCs) as signal tags. The morphological and compositional of the Pt NPs/CNCs were examined using transmission electron microscopy, X-ray diffraction, and Raman spectroscopy. The results showed that the Pt NPs with about 3-5nm in diameter were well dispersed on the surface of CNCs. The thiolated aptamer was firstly immobilized on the gold electrode to capture the thrombin molecules, and then aptamer functionalized Pt NPs/CNCs nanocomposites were used to fabricate a sandwich sensing platform. Then, the high-content Pt NPs on carbon nanocages acting as hydrogen peroxide-mimicking enzyme catalyzed the reduction of H2O2, resulting in significant electrochemical signal amplification. Differential pulse voltammetry is employed to detect thrombin with different concentrations. Under optimized conditions, the approach provided a good linear response range from 0.05 pM to 20nM with a low detection limit of 10fM. This Pt NPs/CNCs-based aptasensor shows good precision, acceptable stability and reproducibility, which provided a promising strategy for electrochemical aptamer-based detection of other biomolecules. PMID:27376191

  17. Effect of the oral thrombin inhibitor dabigatran on allergic lung inflammation induced by repeated house dust mite administration in mice.

    Science.gov (United States)

    de Boer, Johannes D; Berkhout, Lea C; de Stoppelaar, Sacha F; Yang, Jack; Ottenhoff, Roelof; Meijers, Joost C M; Roelofs, Joris J T H; van't Veer, Cornelis; van der Poll, Tom

    2015-10-15

    Asthma is a chronic disease of the airways; asthma patients are hampered by recurrent symptoms of dyspnoea and wheezing caused by bronchial obstruction. Most asthma patients suffer from chronic allergic lung inflammation triggered by allergens such as house dust mite (HDM). Coagulation activation in the pulmonary compartment is currently recognized as a feature of allergic lung inflammation, and data suggest that coagulation proteases further drive inflammatory mechanisms. Here, we tested whether treatment with the oral thrombin inhibitor dabigatran attenuates allergic lung inflammation in a recently developed HDM-based murine asthma model. Mice were fed dabigatran (10 mg/g) or placebo chow during a 3-wk HDM airway exposure model. Dabigatran treatment caused systemic thrombin inhibitory activity corresponding with dabigatran levels reported in human trials. Surprisingly, dabigatran did not lead to inhibition of HDM-evoked coagulation activation in the lung as measured by levels of thrombin-antithrombin complexes and D-dimer. Repeated HDM administration caused an influx of eosinophils and neutrophils into the lungs, mucus production in the airways, and a T helper 2 response, as reflected by a rise in bronchoalveolar IL-4 and IL-5 levels and a systemic rise in IgE and HDM-IgG1. Dabigatran modestly improved HDM-induced lung pathology (P dabigatran in spite of adequate plasma levels, these results argue against clinical evaluation of dabigatran in patients with asthma.

  18. A sensitive electrochemical aptasensor based on water soluble CdSe quantum dots (QDs) for thrombin determination

    Energy Technology Data Exchange (ETDEWEB)

    Li Yanfen; Han Min [Jiangsu Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofuctional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097 (China); Bai Hongyan [Jiangsu Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofuctional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097 (China); College of Biological and Chemical Engineering, Jiaxing College, Jiaxing 314001 (China); Wu Yong [Jiangsu Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofuctional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097 (China); Dai Zhihui, E-mail: daizhihuii@njnu.edu.cn [Jiangsu Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofuctional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097 (China); Bao Jianchun, E-mail: baojianchun@njnu.edu.cn [Jiangsu Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofuctional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097 (China)

    2011-08-01

    A novel aptamer biosensor with easy operation and good sensitivity, specificity, stability and reproducibility was developed by immobilizing the aptamer on water soluble CdSe quantum dots (QDs) modified on the top of the glassy carbon electrode (GCE). Methylene blue (MB) was intercalated into the aptamer sequence and used as an electrochemical marker. CdSe QDs improved the electrochemical signal because of their larger surface area and ion centers of CdSe QDs may also had a major role on amplifying the signal. The higher ion concentration caused more combination of aptamer which caused larger signal. The thrombin was detected by differential pulse voltammetry (DPV) quantitatively. Under optimal conditions, the two linear ranges were obtained from 3 to 13 {mu}g mL{sup -1} and from 14 to 31 {mu}g mL{sup -1}, respectively. The detection limit was 0.08 {mu}g mL{sup -1} at 3{sigma}. The constructed biosensor had better responses compared with that in the absence of the CdSe QDs immobilizing. The control experiment was also carried out by using BSA, casein and IgG in the absence of thrombin. The results showed that the aptasensor had good specificity, stability and reproducibility to the thrombin. Moreover, the aptasensor could be used for detection of real sample with consistent results in comparison with those obtained by fluorescence method which could provide a promising platform for fabrication of aptamer based biosensors.

  19. Automating the CMS DAQ

    Energy Technology Data Exchange (ETDEWEB)

    Bauer, G.; et al.

    2014-01-01

    We present the automation mechanisms that have been added to the Data Acquisition and Run Control systems of the Compact Muon Solenoid (CMS) experiment during Run 1 of the LHC, ranging from the automation of routine tasks to automatic error recovery and context-sensitive guidance to the operator. These mechanisms helped CMS to maintain a data taking efficiency above 90% and to even improve it to 95% towards the end of Run 1, despite an increase in the occurrence of single-event upsets in sub-detector electronics at high LHC luminosity.

  20. Automated phantom assay system

    International Nuclear Information System (INIS)

    This paper describes an automated phantom assay system developed for assaying phantoms spiked with minute quantities of radionuclides. The system includes a computer-controlled linear-translation table that positions the phantom at exact distances from a spectrometer. A multichannel analyzer (MCA) interfaces with a computer to collect gamma spectral data. Signals transmitted between the controller and MCA synchronize data collection and phantom positioning. Measured data are then stored on disk for subsequent analysis. The automated system allows continuous unattended operation and ensures reproducible results

  1. Automated gas chromatography

    Science.gov (United States)

    Mowry, Curtis D.; Blair, Dianna S.; Rodacy, Philip J.; Reber, Stephen D.

    1999-01-01

    An apparatus and process for the continuous, near real-time monitoring of low-level concentrations of organic compounds in a liquid, and, more particularly, a water stream. A small liquid volume of flow from a liquid process stream containing organic compounds is diverted by an automated process to a heated vaporization capillary where the liquid volume is vaporized to a gas that flows to an automated gas chromatograph separation column to chromatographically separate the organic compounds. Organic compounds are detected and the information transmitted to a control system for use in process control. Concentrations of organic compounds less than one part per million are detected in less than one minute.

  2. Adequacy and adjustment of electromechanical elements of a X radiation generator for automation of system of additional filtration; Adequacao e ajuste dos elementos eletromecanicos de um gerador de radiacao X para automacao do sistema de filtracao adicional

    Energy Technology Data Exchange (ETDEWEB)

    Alves Junior, Iremar; Santos, Lucas dos; Potiens, Maria da Penha A.; Vivolo, Vitor, E-mail: iremarjr@usp.b, E-mail: lucas.se@usp.b, E-mail: mppalbu@ipen.b, E-mail: vivolo@ipen.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2011-10-26

    This paper dimensioned the filter wheel components and the adequacy of additional filtrations for the implantation of the OTW automated system with complete replacement of previous used filtration by new set of machine-made filters to be used as the qualities already implanted at the Instrument Calibration Laboratory of the IPEN, Sao Paulo, Brazil. In the sequence, it was performed the measurements of kerma i the air in each quality to be used as reference values

  3. Preliminary Framework for Human-Automation Collaboration

    Energy Technology Data Exchange (ETDEWEB)

    Oxstrand, Johanna Helene [Idaho National Lab. (INL), Idaho Falls, ID (United States); Le Blanc, Katya Lee [Idaho National Lab. (INL), Idaho Falls, ID (United States); Spielman, Zachary Alexander [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-09-01

    The Department of Energy’s Advanced Reactor Technologies Program sponsors research, development and deployment activities through its Next Generation Nuclear Plant, Advanced Reactor Concepts, and Advanced Small Modular Reactor (aSMR) Programs to promote safety, technical, economical, and environmental advancements of innovative Generation IV nuclear energy technologies. The Human Automation Collaboration (HAC) Research Project is located under the aSMR Program, which identifies developing advanced instrumentation and controls and human-machine interfaces as one of four key research areas. It is expected that the new nuclear power plant designs will employ technology significantly more advanced than the analog systems in the existing reactor fleet as well as utilizing automation to a greater extent. Moving towards more advanced technology and more automation does not necessary imply more efficient and safer operation of the plant. Instead, a number of concerns about how these technologies will affect human performance and the overall safety of the plant need to be addressed. More specifically, it is important to investigate how the operator and the automation work as a team to ensure effective and safe plant operation, also known as the human-automation collaboration (HAC). The focus of the HAC research is to understand how various characteristics of automation (such as its reliability, processes, and modes) effect an operator’s use and awareness of plant conditions. In other words, the research team investigates how to best design the collaboration between the operators and the automated systems in a manner that has the greatest positive impact on overall plant performance and reliability. This report addresses the Department of Energy milestone M4AT-15IN2302054, Complete Preliminary Framework for Human-Automation Collaboration, by discussing the two phased development of a preliminary HAC framework. The framework developed in the first phase was used as the

  4. Preliminary Framework for Human-Automation Collaboration

    International Nuclear Information System (INIS)

    The Department of Energy's Advanced Reactor Technologies Program sponsors research, development and deployment activities through its Next Generation Nuclear Plant, Advanced Reactor Concepts, and Advanced Small Modular Reactor (aSMR) Programs to promote safety, technical, economical, and environmental advancements of innovative Generation IV nuclear energy technologies. The Human Automation Collaboration (HAC) Research Project is located under the aSMR Program, which identifies developing advanced instrumentation and controls and human-machine interfaces as one of four key research areas. It is expected that the new nuclear power plant designs will employ technology significantly more advanced than the analog systems in the existing reactor fleet as well as utilizing automation to a greater extent. Moving towards more advanced technology and more automation does not necessary imply more efficient and safer operation of the plant. Instead, a number of concerns about how these technologies will affect human performance and the overall safety of the plant need to be addressed. More specifically, it is important to investigate how the operator and the automation work as a team to ensure effective and safe plant operation, also known as the human-automation collaboration (HAC). The focus of the HAC research is to understand how various characteristics of automation (such as its reliability, processes, and modes) effect an operator's use and awareness of plant conditions. In other words, the research team investigates how to best design the collaboration between the operators and the automated systems in a manner that has the greatest positive impact on overall plant performance and reliability. This report addresses the Department of Energy milestone M4AT-15IN2302054, Complete Preliminary Framework for Human-Automation Collaboration, by discussing the two phased development of a preliminary HAC framework. The framework developed in the first phase was used as

  5. Peptide affinity labels for thrombin and other trypsin-like proteases

    Science.gov (United States)

    Shaw, Elliott N.; Kettner, Charles A.

    1982-03-09

    A peptide affinity label of the formula (I): ##STR1## wherein X is a radical capable of acting as a leaving group in a nucleophilic substitution reaction; A is an aromatic amino acid residue; B is H, or a C.sub.1 -C.sub.4 alkyl group, or aryl; Y is selected from the group consisting of hydrogen, aroyl, C.sub.1 -C.sub.6 acyl, and Q--(A)--.sub.n, wherein Q=hydrogen, aroyl, or C.sub.1 -C.sub.6 acyl, n=1-10, A is an amino acid residue selected from the aliphatic, hydroxy-containing, carboxylic acid group, and amide-thereof-containing, aromatic, sulfur-containing and imino-containing amino acids; and wherein J is selected from the group consisting of --CH.sub.2 --, --CH.sub.2 --CH.sub.2 --,--CH.sub.2 --CH.sub.2 --CH.sub.2 --, --CH.dbd.CH-- and --CH(OH)--CH.sub.2. The affinity label is useful for irreversibly inactivating thrombin and trypsin-like enzymes and may be used as a potential anticlotting agent.

  6. Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model

    Science.gov (United States)

    Zeng, Xiaojun; Zhang, Liyun; Xiao, Xiuchan; Jiang, Yuanyuan; Guo, Yanzhi; Yu, Xinyan; Pu, Xuemei; Li, Menglong

    2016-04-01

    Thrombin-binding aptamer (TBA) with the sequence 5‧GGTTGGTGTGGTTGG3‧ could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.

  7. Thrombin Activatable Fibrinolysis Inhibitor in Preeclmapsia and Gestational Hypertension throughout the Gestation

    Institute of Scientific and Technical Information of China (English)

    Yinghong ZHANG; Yu HU; Tao GUO; Wenning WEI; Xiaoping ZHANG

    2008-01-01

    To clarify the role of TAFI in hypertensive disorders in pregnancy, 22 subjects, including 10 with pre-eclampsia (PE) and 12 with gestational hypertension were examined for the levels of TAFI and thrombin-antithrombin (TAT) complex. Thirty normal pregnant women served as controls. ELISA was employed for the detection. The results showed that the TAFI antigen levels in normal pregnancy group, gestational hypertension group and PE group were (85.35±24.69)%, (99.65±18.27)%, (110.12±23.36)%; (97.06±21.40)%, (114.08±27.76)%, (125.49±24.70)%; (106.6±19.21)%, (129.2±25.07)%, (139.1±30.12)%, in the 1st, 2nd and 3rd trimester respectively. No significant differences were found between the normal pregnancy group and gestational hypertension group but significant difference existed between normal pregnancy group and PE group in each tri- mester (P<0.05). TAT complexes were significantly higher in patients with PE than that in controls (P<0.05), but no correlation was found between TAT and TAFI. It is concluded that TAFI may con- tributed to the impairment of fibrinolysis in the patients with PE and may serves as a sensitive indi- cator for PE, but it may not help in the diagnosis of the gestational hypertension.

  8. Two related thrombin-like enzymes present in Bothrops atrox venom

    Directory of Open Access Journals (Sweden)

    J.H. Petretski

    2000-11-01

    Full Text Available This article describes the presence of two new forms of a thrombin-like enzyme, both with apparent molecular masses of 38 kDa, in Bothrops atrox venom. Both share the ability to cleave fibrinogen into fibrin and to digest casein. Both present identical Km on the substrate BApNA. Their N-terminal amino acid sequences are identical for 26 residues, sharing 80% homology with batroxobin and flavoxobin. Two groups of monoclonal antibodies (mAbs raised against the purified enzyme forms recognized different epitopes of the putative corresponding enzymes present in B. atrox crude venom. On Western blotting analysis of B. atrox crude venom, mAbs 5DB2C8, 5AA10 and 5CF11, but not mAbs 6CC5 and 6AD2-G5, revealed two or more protein bands ranging from 25 to 38 kDa. By immunoprecipitation assays, the 6AD2-G5 mAb was able to precipitate protein bands of 36-38 kDa from B. atrox, B. leucurus, B. pradoi, B. moojeni, B. jararaca and B. neuwiedii crude venoms. Fibrinogen-clotting activity was inhibited when the same venom specimens were pre-incubated with mAb 6AD2-G5, except for B. jararaca and B. neuwiedii.

  9. Complex Domains Call for Automation but Automation Requires More Knowledge and Learning

    DEFF Research Database (Denmark)

    Madsen, Erik Skov; Mikkelsen, Lars Lindegaard

    studies investigate operation and automation of oil and gas production in the North Sea. Semi-structured interviews, surveys, and observations are the main methods used. The paper provides a novel conceptual framework around which management may generate discussions about productivity and the need...

  10. Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures.

    Science.gov (United States)

    Rühmann, Eggert H; Rupp, Melinda; Betz, Michael; Heine, Andreas; Klebe, Gerhard

    2016-02-01

    Structural preorganization to fix bioactive conformations at protein binding sites is a popular strategy to enhance binding affinity during late-stage optimization. The rationale for this enhancement relates to entropic advantages assigned to rigidified versus flexible ligands. We analyzed a narrow series of peptidomimetics binding to thrombin. The individual ligands exhibit at P2 a conformationally flexible glycine, more restricted alanine, N-methylglycine, N-methylhomoalanine, and largely rigidified proline moiety. Overall, affinity was found to increase by a factor of 1000, explained partly by an entropic advantage. All ligands adopt the same binding mode with small deviations. The residual mobility of the bound ligands is decreased across the series, and a protein side chain differs in its order/disorder behavior along with changes in the surface-water network pattern established across the newly generated protein-ligand surfaces. The enthalpy/entropy inventory displays a rather complex picture and emphasizes that thermodynamics can only be compared in terms of relative differences within a structurally similar ligand series.

  11. Porous platinum nanotubes labeled with hemin/G-quadruplex based electrochemical aptasensor for sensitive thrombin analysis via the cascade signal amplification.

    Science.gov (United States)

    Sun, Aili; Qi, Qingan; Wang, Xuannian; Bie, Ping

    2014-07-15

    For the first time, a sensitive electrochemical aptasensor for thrombin (TB) was developed by using porous platinum nanotubes (PtNTs) labeled with hemin/G-quadruplex and glucose dehydrogenase (GDH) as labels. Porous PtNTs with large surface area exhibited the peroxidase-like activity. Coupling with GDH and hemin/G-quadruplex as NADH oxidase and HRP-mimicking DNAzyme, the cascade signal amplification was achieved by the following ways: in the presence of glucose and NAD(+) in the working buffer, GDH electrocatalyzed the oxidation of glucose with the production of NADH. Then, hemin/G-quadruplex as NADH oxidase catalyzed the oxidation of NADH to in situ generate H2O2. Based on the corporate electrocatalysis of PtNTs and hemin/G-quadruplex toward H2O2, the electrochemical signal was significantly amplified, allowing the detection limit of TB down to 0.15 pM level. Moreover, the proposed strategy was simple because the intercalated hemin offered the readout signal, avoiding the adding of additional redox mediator as signal donator. Such an electrochemical aptasensor is highly promising for sensitive detection of other proteins in clinical diagnostics. PMID:24534575

  12. Automated solvent concentrator

    Science.gov (United States)

    Griffith, J. S.; Stuart, J. L.

    1976-01-01

    Designed for automated drug identification system (AUDRI), device increases concentration by 100. Sample is first filtered, removing particulate contaminants and reducing water content of sample. Sample is extracted from filtered residue by specific solvent. Concentrator provides input material to analysis subsystem.

  13. Protokoller til Home Automation

    DEFF Research Database (Denmark)

    Kjær, Kristian Ellebæk

    2008-01-01

    computer, der kan skifte mellem foruddefinerede indstillinger. Nogle gange kan computeren fjernstyres over internettet, så man kan se hjemmets status fra en computer eller måske endda fra en mobiltelefon. Mens nævnte anvendelser er klassiske indenfor home automation, er yderligere funktionalitet dukket op...

  14. ELECTROPNEUMATIC AUTOMATION EDUCATIONAL LABORATORY

    OpenAIRE

    Dolgorukov, S. O.; National Aviation University; Roman, B. V.; National Aviation University

    2013-01-01

    The article reflects current situation in education regarding mechatronics learning difficulties. Com-plex of laboratory test benches on electropneumatic automation are considered as a tool in advancing through technical science. Course of laboratory works developed to meet the requirement of efficient and reliable way of practical skills acquisition is regarded the simplest way for students to learn the ba-sics of mechatronics.

  15. Building Automation Systems.

    Science.gov (United States)

    Honeywell, Inc., Minneapolis, Minn.

    A number of different automation systems for use in monitoring and controlling building equipment are described in this brochure. The system functions include--(1) collection of information, (2) processing and display of data at a central panel, and (3) taking corrective action by sounding alarms, making adjustments, or automatically starting and…

  16. Test Construction: Automated

    NARCIS (Netherlands)

    Veldkamp, Bernard P.

    2014-01-01

    Optimal test construction deals with automated assembly of tests for educational and psychological measurement. Items are selected from an item bank to meet a predefined set of test specifications. Several models for optimal test construction are presented, and two algorithms for optimal test assemb

  17. Test Construction: Automated

    NARCIS (Netherlands)

    Veldkamp, Bernard P.

    2016-01-01

    Optimal test construction deals with automated assembly of tests for educational and psychological measurement. Items are selected from an item bank to meet a predefined set of test specifications. Several models for optimal test construction are presented, and two algorithms for optimal test assemb

  18. Automated Web Applications Testing

    Directory of Open Access Journals (Sweden)

    Alexandru Dan CĂPRIŢĂ

    2009-01-01

    Full Text Available Unit tests are a vital part of several software development practicesand processes such as Test-First Programming, Extreme Programming andTest-Driven Development. This article shortly presents the software quality andtesting concepts as well as an introduction to an automated unit testingframework for PHP web based applications.

  19. Automated Student Model Improvement

    Science.gov (United States)

    Koedinger, Kenneth R.; McLaughlin, Elizabeth A.; Stamper, John C.

    2012-01-01

    Student modeling plays a critical role in developing and improving instruction and instructional technologies. We present a technique for automated improvement of student models that leverages the DataShop repository, crowd sourcing, and a version of the Learning Factors Analysis algorithm. We demonstrate this method on eleven educational…

  20. Automation of finite element methods

    CERN Document Server

    Korelc, Jože

    2016-01-01

    New finite elements are needed as well in research as in industry environments for the development of virtual prediction techniques. The design and implementation of novel finite elements for specific purposes is a tedious and time consuming task, especially for nonlinear formulations. The automation of this process can help to speed up this process considerably since the generation of the final computer code can be accelerated by order of several magnitudes. This book provides the reader with the required knowledge needed to employ modern automatic tools like AceGen within solid mechanics in a successful way. It covers the range from the theoretical background, algorithmic treatments to many different applications. The book is written for advanced students in the engineering field and for researchers in educational and industrial environments.

  1. Automating spectral measurements

    Science.gov (United States)

    Goldstein, Fred T.

    2008-09-01

    This paper discusses the architecture of software utilized in spectroscopic measurements. As optical coatings become more sophisticated, there is mounting need to automate data acquisition (DAQ) from spectrophotometers. Such need is exacerbated when 100% inspection is required, ancillary devices are utilized, cost reduction is crucial, or security is vital. While instrument manufacturers normally provide point-and-click DAQ software, an application programming interface (API) may be missing. In such cases automation is impossible or expensive. An API is typically provided in libraries (*.dll, *.ocx) which may be embedded in user-developed applications. Users can thereby implement DAQ automation in several Windows languages. Another possibility, developed by FTG as an alternative to instrument manufacturers' software, is the ActiveX application (*.exe). ActiveX, a component of many Windows applications, provides means for programming and interoperability. This architecture permits a point-and-click program to act as automation client and server. Excel, for example, can control and be controlled by DAQ applications. Most importantly, ActiveX permits ancillary devices such as barcode readers and XY-stages to be easily and economically integrated into scanning procedures. Since an ActiveX application has its own user-interface, it can be independently tested. The ActiveX application then runs (visibly or invisibly) under DAQ software control. Automation capabilities are accessed via a built-in spectro-BASIC language with industry-standard (VBA-compatible) syntax. Supplementing ActiveX, spectro-BASIC also includes auxiliary serial port commands for interfacing programmable logic controllers (PLC). A typical application is automatic filter handling.

  2. A quantum dot-aptamer beacon using a DNA intercalating dye as the FRET reporter: application to label-free thrombin detection.

    Science.gov (United States)

    Chi, Chun-Wei; Lao, Yeh-Hsing; Li, Yi-Shan; Chen, Lin-Chi

    2011-03-15

    A new quantum dot (QD)-aptamer (apt) beacon that acts by folding-induced dissociation of a DNA intercalating dye, BOBO-3(B), is demonstrated with label-free thrombin detection. The beacon, denoted as QD-apt:B, is constructed by (1) coupling of a single-stranded thrombin aptamer to Qdot 565 via EDC/Sulfo-NHS chemistry and (2) staining the duplex regions of the aptamer on QD with excess BOBO-3 before thrombin binding. When mixing a thrombin sample with QD-apt:B, BOBO-3 is competed away from the beacon due to target-induced aptamer folding, which then causes a decrease in QD fluorescence resonance energy transfer (FRET)-mediated BOBO-3 emission and achieves thrombin quantitation. In this work, the effects of Mg(2+), coupling time, and aptamer type on the beacon's performances are investigated and discussed thoroughly with various methods, including transmission electron microscopy (TEM), dynamic light scattering (DLS), and two-color differential gel electrophoresis. Using the best aptamer beacon (HTQ37), we attain highly specific and wide-range detection (from nM to μM) of thrombin in buffer, and the beacon can sense nM-range thrombin in 15% diluted serum. Compared to the reported QD aptamer assays, our method is advantageous from the aspect of using a simple sensory unit design without losing the detection sensitivity. Therefore, we consider the QD-apt:B beacon a potential alternative to immuno-reagents and an effective tool to study nucleic acid folding on QD as well. PMID:21306887

  3. A quantum dot-aptamer beacon using a DNA intercalating dye as the FRET reporter: application to label-free thrombin detection.

    Science.gov (United States)

    Chi, Chun-Wei; Lao, Yeh-Hsing; Li, Yi-Shan; Chen, Lin-Chi

    2011-03-15

    A new quantum dot (QD)-aptamer (apt) beacon that acts by folding-induced dissociation of a DNA intercalating dye, BOBO-3(B), is demonstrated with label-free thrombin detection. The beacon, denoted as QD-apt:B, is constructed by (1) coupling of a single-stranded thrombin aptamer to Qdot 565 via EDC/Sulfo-NHS chemistry and (2) staining the duplex regions of the aptamer on QD with excess BOBO-3 before thrombin binding. When mixing a thrombin sample with QD-apt:B, BOBO-3 is competed away from the beacon due to target-induced aptamer folding, which then causes a decrease in QD fluorescence resonance energy transfer (FRET)-mediated BOBO-3 emission and achieves thrombin quantitation. In this work, the effects of Mg(2+), coupling time, and aptamer type on the beacon's performances are investigated and discussed thoroughly with various methods, including transmission electron microscopy (TEM), dynamic light scattering (DLS), and two-color differential gel electrophoresis. Using the best aptamer beacon (HTQ37), we attain highly specific and wide-range detection (from nM to μM) of thrombin in buffer, and the beacon can sense nM-range thrombin in 15% diluted serum. Compared to the reported QD aptamer assays, our method is advantageous from the aspect of using a simple sensory unit design without losing the detection sensitivity. Therefore, we consider the QD-apt:B beacon a potential alternative to immuno-reagents and an effective tool to study nucleic acid folding on QD as well.

  4. Test of hirudin activity by tracking the binding of hirudin to thrombin in the presence of BS3 cross-linking.

    Science.gov (United States)

    Liu, Yanfang; Yang, Jian; Wang, Jiangmin; Huang, Qingmei; Yang, Xiaohong; Zhang, Jianhua

    2015-10-01

    Hirudin has a great potential in inhibiting thrombin, and its antithrombin activity has direct bearing on its clinical application. Using bovine alpha-thrombin and recombinant hirudin of Poecilobdella javanica purified from Phichia pastoris as materials, this study introduced a novel method to testing antithrombin activity of hirudin visually and dynamically by tracking the binding of hirudin to thrombin. After incubating the mixture of thrombin and hirudin at 37 °C for 5 min, the binding of hirudin to thrombin was cross-linked by bis[sulfosuccinimidyl] suberate for 30 min and visualized by SDS-polyacrylamide gel electrophoresis. With the aid of image analysis on the basis of INRA-Noésis E1D analysis software, antithrombin activity of hirudin was calculated through intensity variations of protein bands of either thrombin-hirudin compound, unbound thrombin, or unbound hirudin. In this regard, activity of the given hirudin was tested to be 5625 ATU/mg based on a single reaction, and 5675.3 ATU/mg based on a series of reactions in a stepwise manner, close to the result of 6000 ATU/mg concluded by titration method. The superiorities of the method include good accuracy (the minimum testable concentration of hirudin is 1.5 μg/ml) and little sample consumption (sample consumption of hirudin is generally 1-11.5 μl using the apparatus of Mini Protean 3 Cell). Easy operation, low input, and equipment requirement also grant it as an effective way. PMID:26332983

  5. Control and automation, and energy system engineering

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tai-hoon [Hannam Univ., Daejeon (Korea, Republic of); Adeli, Hojjat [Ohio State Univ., Columbus, OH (United States); Stoica, Adrian [Jet Propulsion Laboratory, Pasadena, CA (United States); Kang, Byeong-Ho (eds.) [Tasmania Univ., Hobart, TAS (Australia)

    2011-07-01

    This book comprises selected papers of the International Conferences, CA and CES3 2011, held as Part of the Future Generation Information Technology Conference, FGIT 2011, in Conjunction with GDC 2011, Jeju Island, Korea, in December 2011. The papers presented were carefully reviewed and selected from numerous submissions and focused on the various aspects of control and automation, and circuits, control, communication, electricity, electronics, energy, system, signal and simulation. (orig.)

  6. Prothrombotic markers and early spontaneous recanalization in ST-segment elevation myocardial infarction. : Thrombin and plasmin generation in early recanalization

    OpenAIRE

    Huisse, Marie-Geneviève; Lanoy, Emilie; Tcheche, Didier; Feldman, Laurent,; Bezeaud, Annie; Anglès-Cano, Eduardo; Mary-Krause, Murielle; de Prost, Dominique; Guillin, Marie-Claude; Steg, Ph.Gabriel

    2007-01-01

    28 pages International audience We tested the hypothesis that selected prothrombotic biomarkers might be associated with early spontaneous coronary recanalization in patients with ST-segment elevation acute myocardial infarction (STEMI). We prospectively enrolled 123 patients with STEMI including 53 patients with spontaneous coronary recanalization (cases) and 70 patients with persistent occlusion (controls) at the time of emergent coronary angiography and before angioplasty. All had re...

  7. Changes in the pattern of distribution of von Willebrand factor in rat aortic endothelial cells following thrombin generation in vivo.

    Science.gov (United States)

    Senis, Y A; Richardson, M; Tinlin, S; Maurice, D H; Giles, A R

    1996-04-01

    The pattern of distribution of von Willebrand factor (VWF) in relatively large sheets of rat aortic endothelial cells (EC) obtained by the Häutchen technique were analysed by immunocytochemistry and light microscopy. EC were examined pre and post administration of a procoagulant mixture of factor Xa (F.Xa) and phosphotidylcholine/phosphotidylserine (PCPS) vesicles which was demonstrated to result in the selective loss of high molecular weight multimers (HMWM) of plasma VWF in the rat. In placebo animals the pattern was heterogenous both in overall distribution and in individual cells which showed both a diffuse and granular pattern. Groups of intensely stained EC were oriented parallel to the longitudinal axis of the aorta and staining was particularly prominent around the orifices of the intercostal arteries, implicating shear-stress as a possible factor in VWF expression by EC. Changes in the pattern of distribution of staining were observed at various time points post-infusion of F.Xa/PCPS, suggesting the immediate release of VWF from EC stores followed by the recruitment of EC to synthesize and store VWF. These changes are consistent with the decrease in EC Weibel-Palade Body (WPB) content observed by EM in previously reported studies using this model. PMID:8611460

  8. Fibrinogen-thrombin collagen patch reinforcement of high-risk colonic anastomoses in rats

    Science.gov (United States)

    Suárez-Grau, Juan Manuel; Bernardos García, Carlos; Cepeda Franco, Carmen; Mendez García, Cristina; García Ruiz, Salud; Docobo Durantez, Fernando; Morales-Conde, Salvador; Padillo Ruiz, Javier

    2016-01-01

    AIM To evaluate the effectiveness of human fibrinogen-thrombin collagen patch (TachoSil®) in the reinforcement of high-risk colon anastomoses. METHODS A quasi-experimental study was conducted in Wistar rats (n = 56) that all underwent high-risk anastomoses (anastomosis with only two sutures) after colectomies. The rats were divided into two randomized groups: Control group (24 rats) and treatment group (24 rats). In the treatment group, high-risk anastomosis was reinforced with TachoSil® (a piece of TachoSil® was applied over this high-risk anastomosis, covering the gap). Leak incidence, overall survival, intra-abdominal adhesions, and histologic healing of anastomoses were analyzed. Survivors were divided into two subgroups and euthanized at 15 and 30 d after intervention in order to analyze the adhesions and histologic changes. RESULTS Overall survival was 71.4% and 57.14% in the TachoSil® group and control group, respectively (P = 0.29); four rats died from other causes and six rats in the treatment group and 10 in the control group experienced colonic leakage (P > 0.05). The intra-abdominal adhesion score was similar in both groups, with no differences between subgroups. We found non-significant differences in the healing process according to the histologic score used in both groups (P = 0.066). CONCLUSION In our study, the use of TachoSil® was associated with a non-statistically significant reduction in the rate of leakage in high-risk anastomoses. TachoSil® has been shown to be a safe product because it does not affect the histologic healing process or increase intra-abdominal adhesions. PMID:27721926

  9. [Laboratory assessment of haemostatic parameters in patients taking a direct thrombin inhibitor].

    Science.gov (United States)

    Beliavskaia, O O; Vavilova, T V

    2014-01-01

    The problem of prevention and treatment of thromboembolic complications has a significant place in clinical practice for many years. The gold-standard agents in long-term protection from embologenic strokes, secondary prevention of venous thromboses and embolisms still remain vitamin K antagonists (in Russia - warfarin). However, despite high efficacy, administration of warfarin is fraught with dangers and associated with a series of inconveniences. A direct thrombin inhibitor, dabigatran etexilate (hereinafter referred to as dabigatran) was approved in the Russian Federation for prevention of thromboembolic complications in orthopaedic practice (2009), for prevention of ischaemic embologenic stroke in atrial fibrillation (2011) and for treatment of recurrent thrombosis of deep veins and pulmonary artery thromboembolism (2014). A characteristic feature of a therapeutic agent possessing an anticoagulation effect is correlation between intensity of hypocoagulation and haemorrhage. The effect of dabigatran on the laboratory parameters of haemostasis has been studied insufficiently, with no practical guidelines on assessing these alterations for prediction of the risk for haemorrhagic and thromboembolic complications. The present study included a total of 65 patients with non-valvular aetiology atrial fibrillation, taking dabigatran during from 6 to 18 months. All patients underwent laboratory assessment of the coagulation level and measuring blood coagulation activation markers in dynamics 10-14 days, 1, 6, 12 and 18 months after taking the agent. Thromboembolic and haemorrhagic risks were also assessed. It was revealed that administration of dabigatran leads to alterations in the main parameters of coagulogram. Determination of prothrombin (in % according to Quick's method) and activated partial thromboplastin time may be used for qualitative assessment of hypocoagulation. During the follow up period no statistically significant changes in the coagulation activation

  10. Thrombin-dependent Incorporation of von Willebrand Factor into a Fibrin Network.

    Science.gov (United States)

    Miszta, Adam; Pelkmans, Leonie; Lindhout, Theo; Krishnamoorthy, Ganeshram; de Groot, Philip G; Hemker, Coenraad H; Heemskerk, Johan W M; Kelchtermans, Hilde; de Laat, Bas

    2014-12-26

    Attachment of platelets from the circulation onto a growing thrombus is a process involving multiple platelet receptors, endothelial matrix components, and coagulation factors. It has been indicated previously that during a transglutaminase reaction activated factor XIII (FXIIIa) covalently cross-links von Willebrand factor (VWF) to polymerizing fibrin. Bound VWF further recruits and activates platelets via interactions with the platelet receptor complex glycoprotein Ib (GPIb). In the present study we found proof for binding of VWF to a fibrin monomer layer during the process of fibrinogen-to-fibrin conversion in the presence of thrombin, arvin, or a snake venom from Crotalus atrox. Using a domain deletion mutant we demonstrated the involvement of the C domains of VWF in this binding. Substantial binding of VWF to fibrin monomers persisted in the presence of the FXIIIa inhibitor K9-DON, illustrating that cross-linking via factor XIII is not essential for this phenomenon and suggesting the identification of a second mechanism through which VWF multimers incorporate into a fibrin network. Under high shear conditions, platelets were shown to adhere to fibrin only if VWF had been incorporated. In conclusion, our experiments show that the C domains of VWF and the E domain of fibrin monomers are involved in the incorporation of VWF during the polymerization of fibrin and that this incorporation fosters binding and activation of platelets. Fibrin thus is not an inert end product but partakes in further thrombus growth. Our findings help to elucidate the mechanism of thrombus growth and platelet adhesion under conditions of arterial shear rate. PMID:25381443

  11. Antithrombotic properties of SSR182289A, a new, orally active thrombin inhibitor.

    Science.gov (United States)

    Lorrain, J; Millet, L; Lechaire, I; Lochot, S; Ferrari, P; Visconte, C; Sainte-Marie, M; Lunven, C; Berry, C N; Schaeffer, P; Herbert, J-M; O'Connor, S E

    2003-02-01

    N-[3-[[[(1S)-4-(5-Amino-2-pyridinyl)-1-[[4-difluoromethylene)-1-piperidinyl]carbonyl]butyl]amino]sulfonyl][1,1'-biphenyl]-2-yl]acetamide hydrochloride (SSR182289A) is a novel, potent, and selective thrombin inhibitor. We have examined the antithrombotic properties of SSR182289A administered by i.v. and p.o. routes in several different animal thrombosis models in comparison with reference antithrombotic agents. Oral administration of SSR182289A produced dose-related antithrombotic effects in the following models; rat venous thrombosis (ED(50) 0.9 mg/kg p.o.), rat silk thread arterio-venous (AV) shunt (ED(50) 3.8 mg/kg p.o.), rat thromboplastin-induced AV shunt (ED(50) 3.1 mg/kg p.o.), rat carotid artery thrombosis (ED(200) 5.9 mg/kg p.o.), and rabbit venous thrombosis (ED(50) 7.5 mg/kg p.o.). Administered as an i.v. bolus, SSR182289A showed antithrombotic activity in the above models with ED(50)/ED(200) values in the range of 0.2 to 1.9 mg/kg i.v. SSR182289A increased rat tail transection bleeding time at doses > or =10 mg/kg p.o. In the rat thromboplastin-induced AV shunt model, SSR182289A 10 mg/kg p.o. produced marked antithrombotic effects at 30, 60, 120, and 240 min after administration. Hence, SSR182289A demonstrates potent oral antithrombotic properties in animal venous, AV-shunt, and arterial thrombosis models.

  12. Intelligent design system for design automation

    Science.gov (United States)

    Shakeri, Cirrus; Deif, Ismail; Katragadda, Prasanna; Knutson, Stanley

    2000-10-01

    In order to succeed in today's global, competitive market, companies need continuous improvements in their product development processes. These improvements should result in expending fewer resources on the design process while achieving better quality. Automating the design process reduces resources needed and allows designers to spend more time on creative aspects that improve the quality of design. For the last three decades, engineers and designers have been searching for better ways to automate the product development process. For certain classes of design problems, which cover a large portion of real world design situations, the process can be automated using knowledge-based systems. These are design problems in which the knowledge sources are known in advance. Using techniques from Knowledge-Based Engineering, knowledge is codified and inserted into a knowledge-based system. The system activates the design knowledge, automatically generating designs that satisfy the design constraints. To increase the return on investment of building automated design systems, Knowledge management methodologies and techniques are required for capturing, formalizing, storing, and searching design knowledge.

  13. Phage display of the serpin alpha-1 proteinase inhibitor randomized at consecutive residues in the reactive centre loop and biopanned with or without thrombin.

    Directory of Open Access Journals (Sweden)

    Benjamin M Scott

    Full Text Available In spite of the power of phage display technology to identify variant proteins with novel properties in large libraries, it has only been previously applied to one member of the serpin superfamily. Here we describe phage display of human alpha-1 proteinase inhibitor (API in a T7 bacteriophage system. API M358R fused to the C-terminus of T7 capsid protein 10B was directly shown to form denaturation-resistant complexes with thrombin by electrophoresis and immunoblotting following exposure of intact phages to thrombin. We therefore developed a biopanning protocol in which thrombin-reactive phages were selected using biotinylated anti-thrombin antibodies and streptavidin-coated magnetic beads. A library consisting of displayed API randomized at residues 357 and 358 (P2-P1 yielded predominantly Pro-Arg at these positions after five rounds of thrombin selection; in contrast the same degree of mock selection yielded only non-functional variants. A more diverse library of API M358R randomized at residues 352-356 (P7-P3 was also probed, yielding numerous variants fitting a loose consensus of DLTVS as judged by sequencing of the inserts of plaque-purified phages. The thrombin-selected sequences were transferred en masse into bacterial expression plasmids, and lysates from individual colonies were screening for API-thrombin complexing. The most active candidates from this sixth round of screening contained DITMA and AAFVS at P7-P3 and inhibited thrombin 2.1-fold more rapidly than API M358R with no change in reaction stoichiometry. Deep sequencing using the Ion Torrent platform confirmed that over 800 sequences were significantly enriched in the thrombin-panned versus naïve phage display library, including some detected using the combined phage display/bacterial lysate screening approach. Our results show that API joins Plasminogen Activator Inhibitor-1 (PAI-1 as a serpin amenable to phage display and suggest the utility of this approach for the selection

  14. Rapid automated nuclear chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, R.A.

    1979-05-31

    Rapid Automated Nuclear Chemistry (RANC) can be thought of as the Z-separation of Neutron-rich Isotopes by Automated Methods. The range of RANC studies of fission and its products is large. In a sense, the studies can be categorized into various energy ranges from the highest where the fission process and particle emission are considered, to low energies where nuclear dynamics are being explored. This paper presents a table which gives examples of current research using RANC on fission and fission products. The remainder of this text is divided into three parts. The first contains a discussion of the chemical methods available for the fission product elements, the second describes the major techniques, and in the last section, examples of recent results are discussed as illustrations of the use of RANC.

  15. Automated theorem proving.

    Science.gov (United States)

    Plaisted, David A

    2014-03-01

    Automated theorem proving is the use of computers to prove or disprove mathematical or logical statements. Such statements can express properties of hardware or software systems, or facts about the world that are relevant for applications such as natural language processing and planning. A brief introduction to propositional and first-order logic is given, along with some of the main methods of automated theorem proving in these logics. These methods of theorem proving include resolution, Davis and Putnam-style approaches, and others. Methods for handling the equality axioms are also presented. Methods of theorem proving in propositional logic are presented first, and then methods for first-order logic. WIREs Cogn Sci 2014, 5:115-128. doi: 10.1002/wcs.1269 CONFLICT OF INTEREST: The authors has declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website. PMID:26304304

  16. ATLAS Distributed Computing Automation

    CERN Document Server

    Schovancova, J; The ATLAS collaboration; Borrego, C; Campana, S; Di Girolamo, A; Elmsheuser, J; Hejbal, J; Kouba, T; Legger, F; Magradze, E; Medrano Llamas, R; Negri, G; Rinaldi, L; Sciacca, G; Serfon, C; Van Der Ster, D C

    2012-01-01

    The ATLAS Experiment benefits from computing resources distributed worldwide at more than 100 WLCG sites. The ATLAS Grid sites provide over 100k CPU job slots, over 100 PB of storage space on disk or tape. Monitoring of status of such a complex infrastructure is essential. The ATLAS Grid infrastructure is monitored 24/7 by two teams of shifters distributed world-wide, by the ATLAS Distributed Computing experts, and by site administrators. In this paper we summarize automation efforts performed within the ATLAS Distributed Computing team in order to reduce manpower costs and improve the reliability of the system. Different aspects of the automation process are described: from the ATLAS Grid site topology provided by the ATLAS Grid Information System, via automatic site testing by the HammerCloud, to automatic exclusion from production or analysis activities.

  17. Rapid automated nuclear chemistry

    International Nuclear Information System (INIS)

    Rapid Automated Nuclear Chemistry (RANC) can be thought of as the Z-separation of Neutron-rich Isotopes by Automated Methods. The range of RANC studies of fission and its products is large. In a sense, the studies can be categorized into various energy ranges from the highest where the fission process and particle emission are considered, to low energies where nuclear dynamics are being explored. This paper presents a table which gives examples of current research using RANC on fission and fission products. The remainder of this text is divided into three parts. The first contains a discussion of the chemical methods available for the fission product elements, the second describes the major techniques, and in the last section, examples of recent results are discussed as illustrations of the use of RANC

  18. The Automated Medical Office

    OpenAIRE

    Petreman, Mel

    1990-01-01

    With shock and surprise many physicians learned in the 1980s that they must change the way they do business. Competition for patients, increasing government regulation, and the rapidly escalating risk of litigation forces physicians to seek modern remedies in office management. The author describes a medical clinic that strives to be paperless using electronic innovation to solve the problems of medical practice management. A computer software program to automate information management in a c...

  19. Label-free electrochemical aptasensor for sensitive thrombin detection using layer-by-layer self-assembled multilayers with toluidine blue-graphene composites and gold nanoparticles.

    Science.gov (United States)

    Xie, Shunbi; Yuan, Ruo; Chai, Yaqin; Bai, Lijuan; Yuan, Yali; Wang, Yan

    2012-08-30

    In the present study, toluidine blue-graphene (Tb-Gra) nanocomposites were prepared to design a Lable-free electrochemical aptasensor for highly sensitive detection of thrombin based on layer-by-layer (LBL) technology. The nanocomposites with excellent redox electrochemical activities were first immobilized on the gold nanoparticles (nano-Au) modified glassy carbon electrodes (GCE). Then, the LBL structure was performed by electrostatic adsorption between the positively charged Tb-Gra and negatively charged nano-Au, which formed {Tb-Gra/nano-Au}(n) multilayer films for electroactive species enrichment and biomolecule immobilization. Subsequently, the thiolated thrombin binding aptamer (TBA) was assembled on the nano-Au surface through Au-S bond. In the presence of target thrombin (TB), the TBA on the multilayer could catch the thrombin onto the electrode surface, which resulted in a barrier for electro-transfer, leading to the decrease of the electrochemical signal of Tb-Gra nanocomposites. Under the optimal conditions, a wide detection range from 0.001 nM to 80 nM and a low detection limit of 0.33 pM (defined as S/N=3) for thrombin were obtained. In addition, the sensor exhibited excellent selectivity against other proteins. PMID:22939121

  20. Automation in biological crystallization.

    Science.gov (United States)

    Stewart, Patrick Shaw; Mueller-Dieckmann, Jochen

    2014-06-01

    Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.