WorldWideScience

Sample records for automated thrombin generation

  1. Analytical and between-subject variation of thrombin generation measured by calibrated automated thrombography on plasma samples

    DEFF Research Database (Denmark)

    Kristensen, Anne F; Kristensen, Søren R; Falkmer, Ursula

    2018-01-01

    BACKGROUND: The Calibrated Automated Thrombography (CAT) is an in vitro thrombin generation (TG) assay that holds promise as a valuable tool within clinical diagnostics. However, the technique has a considerable analytical variation, and we therefore, investigated the analytical and between...

  2. Reproducibility, stability, and biological variability of thrombin generation using calibrated automated thrombography in healthy dogs.

    Science.gov (United States)

    Cuq, Benoît; Blois, Shauna L; Wood, R Darren; Monteith, Gabrielle; Abrams-Ogg, Anthony C; Bédard, Christian; Wood, Geoffrey A

    2018-03-26

    Thrombin plays a central role in hemostasis and thrombosis. Calibrated automated thrombography (CAT), a thrombin generation assay, may be a useful test for hemostatic disorders in dogs. To describe CAT results in a group of healthy dogs, and assess preanalytical variables and biological variability. Forty healthy dogs were enrolled. Lag time (Lag), time to peak (ttpeak), peak thrombin generation (peak), and endogenous thrombin potential (ETP) were measured. Direct jugular venipuncture and winged-needle catheter-assisted saphenous venipuncture were used to collect samples from each dog, and results were compared between methods. Sample stability at -80°C was assessed over 12 months in a subset of samples. Biological variability of CAT was assessed via nested ANOVA using samples obtained weekly from a subset of 9 dogs for 4 consecutive weeks. Samples for CAT were stable at -80°C over 12 months of storage. Samples collected via winged-needle catheter venipuncture showed poor repeatability compared to direct venipuncture samples; there was also poor agreement between the 2 sampling methods. Intra-individual variability of CAT parameters was below 25%; inter-individual variability ranged from 36.9% to 78.5%. Measurement of thrombin generation using CAT appears to be repeatable in healthy dogs, and samples are stable for at least 12 months when stored at -80°C. Direct venipuncture sampling is recommended for CAT. Low indices of individuality suggest that subject-based reference intervals are more suitable when interpreting CAT results. © 2018 American Society for Veterinary Clinical Pathology.

  3. 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

    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...... were to assess the variability of INR, coagulation factor activities, and CAT, during 24 h of storage of blood samples at ambient temperature. A total of 24 patients on stable coumarin treatment were followed prospectively for 6 weeks. INR was analyzed at 0, 6 and 24 h after blood sampling and 1-stage...

  4. Thrombin Generation in Acute Ischaemic Stroke

    Directory of Open Access Journals (Sweden)

    Ibrahim O. Balogun

    2016-01-01

    Full Text Available Introduction. Stroke remains a global leading cause of death and disability. Traditional description of plasma biology in the aftermath of acute ischaemic stroke favours development of hypercoagulability, resulting from complex interplay between plasma and endothelial factors. However, no single assay measures the overall global coagulation process. We postulate that thrombin generation would assist in identifying coagulation abnormalities after acute stroke. Aim. To investigate the coagulation abnormalities after acute ischaemic stroke using thrombin generation. Methods. We evaluated thrombin generation, measured with calibrated automated thrombography in stroke of different aetiological types (n=170 within 48 hours of symptoms onset (baseline and in the second week (time 2 and in normal healthy volunteers (n=71. Results. Two-point thrombin generation assays showed prolonged lag time and time to peak at baseline (3.3 (2.9, 4.0 versus 3.6 (3.2, 4.7; p=0.005 and (3.3 (2.9, 4.0 versus 3.6 (3.2, 4.7; p=0.002, respectively, and at time 2 (3.5 (2.9, 4.2 versus 4.0 (3.1, 4.9; p=0.004 and (5.9 (5.3, 6.6 versus 6.8 (5.8, 7.7 p=0.05, respectively, in cardioembolic stroke (n=39, when compared to noncardioembolic stroke (n=117. The result was reproduced in multiple comparisons between acute ischaemic stroke subgroups and normal healthy volunteers. Endogenous thrombin potential and peak thrombin did not indicate hypercoagulability after acute ischaemic stroke, and thrombolytic therapy did not affect thrombin generation assays. Conclusion. Our findings suggest that thrombin generation in platelet poor plasma is not useful in defining hypercoagulability in acute ischaemic stroke. This is similar to observed trend in coronary artery disease and contrary to other hypercoagulable states.

  5. Inhibition of Intrinsic Thrombin Generation

    Directory of Open Access Journals (Sweden)

    Thomas W. Stief MD

    2006-01-01

    Full Text Available Background The contact phase of coagulation is of physiologic/pathophysiologic importance, whenever unphysiologic polynegative substances such as cell fragments (microparticles get in contact with blood. There are several clinically used inhibitors of intrinsic thrombin generation. Here the inhibitory concentrations 50% (IC50 of these anticoagulants are measured by the highly specific thrombin generation assay INCA. Methods Unfrozen pooled normal citrated plasma in polystyrole tubes was supplemented at 23°C in duplicate with 0–2 IU/ml low molecular weight heparin (dalteparin, 0–2 IU/ml unfractionated heparin, 0–500 KIU/ml aprotinin, or 0–40 mM arginine. 50 μl plasma or 1 IU/ml thrombin standard were pipetted into a polystyrole microtiter plate with flat bottom. 5 μl SiO 2 /CaCl 2 - reagent (INCA activator were added and after 0–30 min incubation at 37°C 100 μl 2.5 M arginine, pH 8.6, were added; arginine inhibits hemostasis activation and depolymerizes generated fibrin within 20 min at 23°C. The in the physiologic 37°C incubation phase generated thrombin was then chromogenically detected. The intra-assay CV values were < 5%. Results and Discussion The approximate IC50 were 0.01 IU/ml dalteparin, 0.02 IU/ml heparin, 25 KIU/ml aprotinin, and 12 mM arginine. The efficiency of any anticoagulant on intrinsic thrombin generation should be measured for each individual patient. Abbreviations IIa, thrombin; δA, increase in absorbance; APTT, activated partial thromboplastin time; CRT, coagulation reaction time (at 37°C in water-bath; F-wells, polystyrole microtiter plates with flat bottom; IC50, inhibitory concentration 50%; INCA, intrinsic coagulation activity assay; IU, international units; KIU, kallikrein inhibiting unis; LMWH, low molecular weight heparin; mA, milli-absorbance units; PSL, pathromtin SL®; RT, room temperature (23°C; U-wells, polystyrole microtiter plates with round bottom.

  6. THROMBIN GENERATION AND BLEEDING IN HEMOPHILIA A

    Science.gov (United States)

    Brummel-Ziedins, Kathleen E.; Whelihan, Matthew F.; Gissel, Matthew; Mann, Kenneth G.; Rivard, Georges E.

    2012-01-01

    Introduction Hemophilia A displays phenotypic heterogeneity with respect to clinical severity. Aim To determine if tissue factor (TF)-initiated thrombin generation profiles in whole blood in the presence of corn trypsin inhibitor (CTI) are predictive of bleeding risk in hemophilia A. Methods We studied factor(F) VIII deficient individuals (11 mild, 4 moderate and 12 severe) with a well-characterized five-year bleeding history that included hemarthrosis, soft tissue hematoma and annual FVIII concentrate usage. This clinical information was used to generate a bleeding score. The bleeding scores (range 0–32) were separated into three groups (bleeding score groupings: 0, 0 and ≤9.6, >9.6), with the higher bleeding tendency having a higher score. Whole blood collected by phlebotomy and contact pathway suppressed by 100μg/mL CTI was stimulated to react by the addition of 5pM TF. Reactions were quenched at 20min by inhibitors. Thrombin generation, determined by ELISA for thrombin – antithrombin was evaluated in terms of clot time (CT), maximum level (MaxL) and maximum rate (MaxR) and compared to the bleeding score. Results Data are shown as the mean±SD. MaxL was significantly different (phemophilia A. PMID:19563500

  7. Decreased prothrombin conversion and reduced thrombin inactivation explain rebalanced thrombin generation in liver cirrhosis.

    Directory of Open Access Journals (Sweden)

    Romy M W Kremers

    Full Text Available Impaired coagulation factor synthesis in cirrhosis causes a reduction of most pro- and anticoagulant factors. Cirrhosis patients show no clear bleeding or thrombotic phenotype, although they are at risk for both types of hemostatic event. Thrombin generation (TG is a global coagulation test and its outcome depends on underlying pro- and anticoagulant processes (prothrombin conversion and thrombin inactivation. We quantified the prothrombin conversion and thrombin inactivation during TG in 30 healthy subjects and 52 Child-Pugh (CP- A, 15 CP-B and 6 CP-C cirrhosis patients to test the hypothesis that coagulation is rebalanced in liver cirrhosis patients. Both prothrombin conversion and thrombin inactivation are reduced in cirrhosis patients. The effect on pro- and anticoagulant processes partially cancel each other out and as a result TG is comparable at 5 pM tissue factor between healthy subjects and patients. This supports the hypothesis of rebalanced hemostasis, as TG in cirrhosis patients remains within the normal range, despite large changes in prothrombin conversion and thrombin inactivation. Nevertheless, in silico analysis shows that normalization of either prothrombin conversion or thrombin inactivation to physiological levels, by for example the administration of prothrombin complex concentrates would cause an elevation of TG, whereas the normalization of both simultaneously maintains a balanced TG. Therefore, cirrhosis patients might require adapted hemostatic treatment.

  8. Thrombin generation and coagulation factor activities: evaluation and comparison with the international normalized ratio

    DEFF Research Database (Denmark)

    Christensen, Thomas D; Jensen, Claus; Larsen, Torben B

    2009-01-01

    of calibrated automated thrombin generation (CAT) and clotting activity of coagulation factors II, VII, IX and X and to compare these parameters with the INR measured in a central laboratory as well as using portable coagulometers. Twenty-four patients on stable oral anticoagulation therapy with coumarins were...

  9. Thrombin generation assays for global evaluation of the hemostatic system: perspectives and limitations

    Directory of Open Access Journals (Sweden)

    Rita Carolina Figueiredo Duarte

    Full Text Available Abstract The existing techniques to evaluate hemostasis in clinical laboratories are not sensitive enough to detect hypercoagulable and mild hypocoagulable states. Under different experimental conditions, the thrombin generation test may meet these requirements. This technique evaluates the overall balance between procoagulant and anticoagulant forces and has provided new insights in our understanding of the coagulation cascade, as well as of the diagnosis of hypocoagulability and hypercoagulability conditions. Thrombin generated in the thrombin generation test can be quantified as platelet-rich or platelet-poor plasma using the calibrated automated thrombogram method, which monitors the cleavage of a fluorogenic substrate that is simultaneously compared to the known thrombin activity in a non-clotting plasma sample. The calibrated automated thrombogram method is an open system, in which different antibodies, proteins, enzymes and peptides can be introduced to answer specific questions regarding hemostatic processes. The thrombin generation test has great clinical potential, such as in monitoring patients taking anticoagulants and antiplatelet drugs, screening for genetic or acquired thrombotic disorders, and evaluating bleeding risk control in patients with hemophilia using bypass agents or replacement therapy. Different to conventional coagulation tests, the thrombin generation test can be used for an overall evaluation of hemostasis, the results of which can then be used to evaluate specific characteristics of hemostasis, such as prothrombin time, activated partial thromboplastin time, and levels of fibrinogen and other coagulation factors. The introduction of this method will contribute to a better understanding and evaluation of overall hemostatic processes; however, this method still requires standardization and clinical validation.

  10. Thrombin generation in abdominal sepsis is Rho-kinase-dependent.

    Science.gov (United States)

    Wang, Yongzhi; Braun, Oscar Ö; Zhang, Su; Norström, Eva; Thorlacius, Henrik

    2015-05-08

    Sepsis causes severe derangements of the coagulation system. However, the signaling mechanisms regulating sepsis-induced thrombin generation remain elusive. Herein, we hypothesized that Rho-kinase might be an important regulator of thrombin generation in abdominal sepsis. Abdominal sepsis was induced by cecal ligation and puncture (CLP) in C57Bl/6 mice. Thrombin generation, coagulation factors, lung histology and myeloperoxidase (MPO) activity were determined 6 h and 24 h after induction of CLP. Induction of CLP triggered a systemic inflammatory response characterized by neutrophil accumulation and tissue injury in the lung as well as thrombocytopenia and leukocytopenia. Administration of Y-27632, a Rho-kinase inhibitor, attenuated these markers of systemic inflammation in CLP animals. Moreover, peak thrombin formation was decreased by 77% and 81% in plasma from mice 6 h and 24 h after induction of CLP. Total thrombin generation was reduced by 64% and 67% 6 h and 24 h after CLP induction, respectively. Notably, administration of Y-27632 increased peak formation by 99% and total thrombin generation by 66% in plasma from septic animals. In addition, CLP markedly decreased plasma levels of prothrombin, factor V and factor X at 6 h and 24 h. Interestingly, Rho-kinase inhibition significantly enhanced levels of prothrombin, factor V and factor X in plasma from septic mice. In addition, inhibition of Rho-kinase decreased CLP-induced elevations of CXCL2 by 36% and interleukin-6 by 38%. These novel findings suggest that sepsis-induced thrombin generation is regulated by Rho-kinase. Moreover, inhibition of Rho-kinase reverses sepsis-evoked consumption of coagulation factors. Thus, our results show that targeting Rho-kinase signaling might protect against coagulation dysfunction in abdominal sepsis. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. 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

    , in part, depend on its reflection of the dynamics of thrombin generation. MATERIAL AND METHODS: The kinetics of thrombin generation of platelets stored for 2 and 7 days, respectively, was assessed by calibrated automated thrombogram (CAT) and the lag time (min), time to peak (ttPeak; min), peak (nm...

  12. Thrombin Generating Capacity and Phenotypic Association in ABO Blood Groups.

    Science.gov (United States)

    Kremers, Romy M W; Mohamed, Abdulrahman B O; Pelkmans, Leonie; Hindawi, Salwa; Hemker, H Coenraad; de Laat, H Bas; Huskens, Dana; Al Dieri, Raed

    2015-01-01

    Individuals with blood group O have a higher bleeding risk than non-O blood groups. This could be explained by the lower levels of FVIII and von Willebrand Factor (VWF) levels in O individuals. We investigated the relationship between blood groups, thrombin generation (TG), prothrombin activation and thrombin inactivation. Plasma levels of VWF, FVIII, antithrombin, fibrinogen, prothrombin and α2Macroglobulin (α2M) levels were determined. TG was measured in platelet rich (PRP) and platelet poor plasma (PPP) of 217 healthy donors and prothrombin conversion and thrombin inactivation were calculated. VWF and FVIII levels were lower (75% and 78%) and α2M levels were higher (125%) in the O group. TG is 10% lower in the O group in PPP and PRP. Less prothrombin was converted in the O group (86%) and the thrombin decay capacity was lower as well. In the O group, α2M plays a significantly larger role in the inhibition of thrombin (126%). In conclusion, TG is lower in the O group due to lower prothrombin conversion, and a larger contribution of α2M to thrombin inactivation. The former is unrelated to platelet function because it is similar in PRP and PPP, but can be explained by the lower levels of FVIII.

  13. Exploring potential anticoagulant drug formulations using thrombin generation test

    Directory of Open Access Journals (Sweden)

    Elena Zavyalova

    2016-03-01

    The thrombin generation test was used to assess the whole coagulation cascade in normal and factor-deficient human blood plasma. Potential therapeutic windows were estimated for coagulation factors, ranking them as targets for anticoagulant drugs. Thrombin and factor Xa have been revealed as the most promising targets, which fully agrees with the current drug development strategy. Inhibitors of factors Va and VIIa are expected to have narrow therapeutic windows. Inhibitors of factors VIIIa and IXa are expected to have a moderate anticoagulant effect. Factors XI and XII are poor targets for anticoagulant drugs. Compared with plasma that is deficient in factor II, the thrombin inhibitors bivalirudin and aptamer HD1 had increased activity. Both inhibitors were tested in deficient plasma providing a model of potential drug combination. The most promising combinations were anti-thrombin with anti-V/Va and also anti-thrombin with anti-IX/IXa. Each combination had an incremental dose-effect dependence that is promising from the standpoint of the therapeutic window.

  14. 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...

  15. Protein Z efficiently depletes thrombin generation in disseminated intravascular coagulation with poor prognosis.

    Science.gov (United States)

    Lee, Nuri; Kim, Ji-Eun; Gu, Ja-Yoon; Yoo, Hyun Ju; Kim, Inho; Yoon, Sung-Soo; Park, Seonyang; Han, Kyou-Sup; Kim, Hyun Kyung

    2016-01-01

    Disseminated intravascular coagulation (DIC) is characterized by consumption of coagulation factors and anticoagulants. Thrombin generation assay (TGA) gives useful information about global hemostatic status. We developed a new TGA system that anticoagulant addition can deplete thrombin generation in plasma, which may reflect defective anticoagulant system in DIC. TGAs were measured on the calibrated automated thrombogram with and without thrombomodulin or protein Z in 152 patients who were suspected of having DIC, yielding four parameters including lag time, endogenous thrombin potential, peak thrombin and time-to-peak in each experiment. Nonsurvivors showed significantly prolonged lag time and time-to-peak in TGA-protein Z system, which was performed with added protein Z. In multivariate Cox regression analysis, lag time and time-to-peak in TGA system were significant independent prognostic factors. In TGA-protein Z system, lag time and time-to-peak were revealed as independent prognostic factors of DIC. Protein Z addition could potentiate its anticoagulant effect in DIC with poor prognosis, suggesting the presence of defective protein Z system. The prolonged lag time and time-to-peak in both TGA and TGA-protein Z systems are expected to be used as independent prognostic factors of DIC.

  16. Extracellular histones promote thrombin generation through platelet-dependent mechanisms: involvement of platelet TLR2 and TLR4

    Science.gov (United States)

    Semeraro, Fabrizio; Ammollo, Concetta T.; Morrissey, James H.; Dale, George L.; Friese, Paul; Esmon, Naomi L.

    2011-01-01

    The release of histones from dying cells is associated with microvascular thrombosis and, because histones activate platelets, this could represent a possible pathogenic mechanism. In the present study, we assessed the influence of histones on the procoagulant potential of human platelets in platelet-rich plasma (PRP) and in purified systems. Histones dose-dependently enhanced thrombin generation in PRP in the absence of any trigger, as evaluated by calibrated automated thrombinography regardless of whether the contact phase was inhibited. Activation of coagulation required the presence of fully activatable platelets and was not ascribable to platelet tissue factor, whereas targeting polyphosphate with phosphatase reduced thrombin generation even when factor XII (FXII) was blocked or absent. In the presence of histones, purified polyphosphate was able to induce thrombin generation in plasma independently of FXII. In purified systems, histones induced platelet aggregation; P-selectin, phosphatidylserine, and FV/Va expression; and prothrombinase activity. Blocking platelet TLR2 and TLR4 with mAbs reduced the percentage of activated platelets and lowered the amount of thrombin generated in PRP. These data show that histone-activated platelets possess a procoagulant phenotype that drives plasma thrombin generation and suggest that TLR2 and TLR4 mediate the activation process. PMID:21673343

  17. Changes in thrombin generation in children after cardiac surgery and ex-vivo response to blood products and haemostatic agents

    DEFF Research Database (Denmark)

    Andreasen, Jo B; Ravn, Hanne B; Hvas, Anne-Mette

    2016-01-01

    surgery including cardiopulmonary bypass. Thrombin generation was analysed both in platelet-poor plasma and platelet-rich plasma. Analysis of the thrombin generation showed a significantly prolonged lag time (Pplatelet-poorandplatelet-richplasma ... thrombin generation significantly (all P platelet concentrate. The present study showed that thrombin generation was significantly reduced after cardiopulmonary bypass in children, both when analysed in platelet-poor and platelet-rich plasma...... to test the hypothesis that thrombin generation reveals an impaired haemostasis after paediatric cardiac surgery and that ex-vivo addition of platelet concentrate and haemostatic agents improves thrombin generation. The study comprised 29 children with congenital heart disease, who underwent corrective...

  18. Reduced peak, but no diurnal variation, in thrombin generation upon melatonin supplementation in tetraplegia. A randomised, placebo-controlled study.

    Science.gov (United States)

    Iversen, Per Ole; Dahm, Anders; Skretting, Grethe; Mowinckel, Marie-Christine; Stranda, Annicke; Østerud, Bjarne; Sandset, Per Morten; Kostovski, Emil

    2015-11-01

    Tetraplegic patients have increased risk of venous thrombosis despite anti-thrombotic prophylaxis. Moreover, they have blunted plasma variations in melatonin and altered diurnal variation of several haemostatic markers, compared with able-bodied. However, whether healthy individuals and tetraplegic patients, with or without melatonin, display abnormalities in thrombin generation during a 24-hour (h) cycle, is unknown. We therefore used the Calibrated Automated Thrombogram (CAT) assay to examine diurnal variations and the possible role of melatonin in thrombin generation. Six men with long-standing complete tetraplegia were included in a randomised placebo-controlled cross-over study with melatonin supplementation (2 mg, 4 consecutive nights), whereas six healthy, able-bodied men served as controls. Ten plasma samples were collected frequently during a 24-h awake/sleep cycle. No significant diurnal variation of any of the measured CAT indices was detected in the three study groups. Whereas endogenous thrombin potential (ETP) was independent (p > 0.05) of whether the tetraplegic men received melatonin or placebo, melatonin decreased (p = 0.005) peak values in tetraplegia compared with those given placebo. Able-bodied men had lower (p = 0.019) ETP and Lag-Time (p = 0.018) compared with tetraplegics receiving placebo. Neither the Time-to-Peak nor the Start-Tail was affected (p > 0.05) by melatonin in tetraplegia. In conclusion, indices of thrombin generation are not subjected to diurnal variation in healthy able-bodied or tetraplegia, but peak thrombin generation is reduced in tetraplegic men receiving oral melatonin.

  19. 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.

  20. Implication of Free Fatty Acids in Thrombin Generation and Fibrinolysis in Vascular Inflammation in Zucker Rats and Evolution with Aging

    Directory of Open Access Journals (Sweden)

    Jérémy Lagrange

    2017-11-01

    Full Text Available Background: The metabolic syndrome (MetS and aging are associated with modifications in blood coagulation factors, vascular inflammation, and increased risk of thrombosis.Objectives: Our aim was to determine concomitant changes in thrombin generation in the blood compartment and at the surface of vascular smooth muscle cells (VSMCs and its interplay with adipokines, free fatty acids (FFA, and metalloproteinases (MMPs in obese Zucker rats that share features of the human MetS.Methods: Obese and age-matched lean Zucker rats were compared at 25 and 80 weeks of age. Thrombin generation was assessed by calibrated automated thrombography (CAT.Results: Endogenous thrombin potential (ETP was increased in obese rats independent of platelets and age. Clot half-lysis time was delayed with obesity and age. Interleukin (IL-1β and IL-13 were increased with obesity and age respectively. Addition of exogenous fibrinogen, leptin, linoleic, or palmitic acid increased thrombin generation in plasma whereas adiponectin had an opposite effect. ETP was increased at the surface of VSMCs from obese rats and addition of exogenous palmitic acid further enhanced ETP values. Gelatinase activity was increased in aorta at both ages in obese rats and MMP-2 activity was increased in VSMCs from obese rats.Conclusions: Our study demonstrated in MetS an early prothrombotic phenotype of the blood compartment reinforced by procoagulant properties of dedifferentiated and inflammatory VSMCs. Mechanisms involved (1 increased fibrinogen and impaired fibrinolysis and (2 increased saturated fatty acids responsible for additive procoagulant effects. Whether specifically targeting this hypercoagulability using direct thrombin inhibitors would improve outcome in MetS is worth investigating.

  1. Automated lattice data generation

    Directory of Open Access Journals (Sweden)

    Ayyar Venkitesh

    2018-01-01

    Full Text Available The process of generating ensembles of gauge configurations (and measuring various observables over them can be tedious and error-prone when done “by hand”. In practice, most of this procedure can be automated with the use of a workflow manager. We discuss how this automation can be accomplished using Taxi, a minimal Python-based workflow manager built for generating lattice data. We present a case study demonstrating this technology.

  2. Comparison by sex between thrombin generation and fibrin network characteristics in a healthy population.

    Science.gov (United States)

    Marchi, R; Marcos, L; Paradisi, I

    2015-02-20

    The aim of the present work was to compare sex differences in thrombin generation and fibrin network characteristics in a young healthy population, and correlate thrombin generation parameters with fibrin network characteristics. Sixty individuals aged 21 y (18-26), 50% men and 50% women were selected. Thrombin generation was performed with the Technothrombin TGA kit. Plasma fibrin formation kinetic was followed by turbidity at 350 nm, and the fibrin elastic modulus was measured with the Hemodyne. In addition, the prothrombin polymorphism G20210A was assessed. Thrombin generation in men was: lag time (LT): 12.5 ± 3.0 min, peak thrombin: 257 ± 135 nmol/l, and endogenous thrombin potential (ETP): 3459 ± 449 nmol/l·min, while in women the LT was shortened (9.7 ± 2.8 min, pgeneration between women and men were not related to prothrombin concentration, prothrombin polymorphism G20210A or fibrinogen concentration. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. The Phosphatase Inhibitor Calyculin-A Impairs Clot Retraction, Platelet Activation, and Thrombin Generation

    Directory of Open Access Journals (Sweden)

    Renáta Hudák

    2017-01-01

    Full Text Available The aim of this study was to investigate the effect of the serine/threonine protein phosphatase inhibitor, calyculin-A (CLA, on clot formation and on the procoagulant activity of human platelets. Platelet-rich plasma (PRP samples were preincubated with buffer or CLA and subsequently platelets were activated by the protease-activated receptor 1 (PAR-1 activator, thrombin receptor activating peptide (TRAP. Clot retraction was detected by observing clot morphology up to 1 hour, phosphatidylserine- (PS- expression was studied by flow cytometry, and thrombin generation was measured by a fluorimetric assay. For the intracellular Ca2+ assay, platelets were loaded with calcium-indicator dyes and the measurements were carried out using a ratiometric method with real-time confocal microscopy. CLA preincubation inhibited clot retraction, PS-expression, and thrombin formation. TRAP activation elicited Ca2+ response and PS-expression in a subset of platelets. The activated PRP displayed significantly faster and enhanced thrombin generation compared to nonactivated samples. CLA pretreatment abrogated PS-exposure and clot retraction also in TRAP-activated samples. As a consequence of the inhibitory effect on calcium elevation and PS-expression, CLA significantly downregulated thrombin generation in PRP. Our results show that CLA pretreatment may be a useful tool to investigate platelet activation mechanisms that contribute to clot formation and thrombin generation.

  4. Platelet- and erythrocyte-derived microparticles trigger thrombin generation via factor XIIa.

    Science.gov (United States)

    Van Der Meijden, P E J; Van Schilfgaarde, M; Van Oerle, R; Renné, T; ten Cate, H; Spronk, H M H

    2012-07-01

    The procoagulant properties of microparticles (MPs) are due to the of the presence of phosphatidylserine (PS) and tissue factor (TF) on their surface. The latter has been demonstrated especially on MPs derived from monocytes. To investigate the relative contribution of TF and factor (F)XII in initiating coagulation on MPs derived from monocytes, platelets and erythrocytes. Microparticles were isolated from calcium ionophore-stimulated platelets, erythrocytes and monocytic THP-1 cells. MPs were quantified, characterized for cell-specific antigens and analyzed for TF, PS exposure and their thrombin-generating potential. The MP number was not proportional to PS exposure and the majority of the MPs exposed PS. TF activity was undetectable on platelet- and erythrocyte-derived MPs (monocyte-derived MPs exposed TF (32 fM nM(-1) PS). Platelet-, erythrocyte- and monocyte-derived MPs, but not purified phospholipids, initiated thrombin generation in normal plasma in the absence of an external trigger (lag time derived MPs, but interfered with monocyte MP-triggered coagulation. Platelet- and erythrocyte-derived MPs completely failed to induce thrombin generation in FXII-deficient plasma. In contrast, monocyte-derived MPs induced similar thrombin generation in normal vs. FXII-deficient plasma. MPs from platelets and erythrocytes not only propagate coagulation by exposing PS but also initiate thrombin generation independently of TF in a FXII-dependent manner. In contrast, monocyte-derived MPs trigger coagulation predominantly via TF. © 2012 International Society on Thrombosis and Haemostasis.

  5. Influence of single nucleotide polymorphisms on thrombin generation in factor V Leiden heterozygotes.

    Science.gov (United States)

    Segers, O; Simioni, P; Tormene, D; Castoldi, E

    2014-03-03

    Carriership of the factor V (FV) Leiden mutation increases the risk of venous thromboembolism (VTE) ~4-fold, but the individual risk of each FV Leiden carrier depends on several co-inherited risk and protective factors. Under the hypothesis that thrombin generation might serve as an intermediate phenotype to identify genetic modulators of VTE risk, we enrolled 188 FV Leiden heterozygotes (11 with VTE) and determined the following parameters: thrombin generation in the absence and presence of activated protein C (APC); plasma levels of prothrombin, factor X, antithrombin, protein S and tissue factor pathway inhibitor; and the genotypes of 24 SNPs located in the genes encoding these coagulation factors and inhibitors. Multiple regression analysis was subsequently applied to identify the (genetic) determinants of thrombin generation. The endogenous thrombin potential (ETP) showed a striking inter-individual variability among different FV Leiden carriers and, especially when measured in the presence of APC, correlated with VTE risk. Several SNPs in the F2 (rs1799963, rs3136516), F10 (rs693335), SERPINC1 (rs2227589), PROS1 (Heerlen polymorphism) and TFPI (rs5940) genes significantly affected the ETP-APC and/or the ETP+APC in FV Leiden carriers. Most of these SNPs have shown an association with VTE risk in conventional epidemiological studies, suggesting that the genetic dissection of thrombin generation leads to the detection of clinically relevant SNPs. In conclusion, we have identified several SNPs that modulate thrombin generation in FV Leiden heterozygotes. These SNPs may help explain the large variability in VTE risk observed among different FV Leiden carriers.

  6. Platelet-derived microparticles regulates thrombin generation via phophatidylserine in abdominal sepsis.

    Science.gov (United States)

    Wang, Yongzhi; Zhang, Su; Luo, Lingtao; Norström, Eva; Braun, Oscar Ö; Mörgelin, Matthias; Thorlacius, Henrik

    2018-02-01

    Sepsis is associated with dysfunctional coagulation. Recent data suggest that platelets play a role in sepsis by promoting neutrophil accumulation. Herein, we show that cecal ligation and puncture (CLP) triggered systemic inflammation, which is characterized by formation of IL-6 and CXC chemokines as well as neutrophil accumulation in the lung. Platelet depletion decreased neutrophil accumulation, IL-6, and CXC chemokines formation in septic lungs. Depletion of platelets increased peak thrombin formation and total thrombin generation (TG) in plasma from septic animals. CLP elevated circulating levels of platelet-derived microparticles (PMPs). In vitro generated PMPs were a potent inducer of TG. Interestingly, in vitro wild-type recombinant annexin V abolished PMP-induced thrombin formation whereas a mutant annexin V protein, which does not bind to phosphatidylserine (PS), had no effect. Administration of wild-type, but not mutant annexin V, significantly inhibited thrombin formation in septic animals. Moreover, CLP-induced formation of thrombin-antithrombin complexes were reduced in platelet-depleted mice and in animals pretreated with annexin V. PMP-induced TG attenuated in FXII- and FVII-deficient plasma. These findings suggest that sepsis-induced TG is dependent on platelets. Moreover, PMPs formed in sepsis are a potent inducer of TG via PS exposure, and activation of both the intrinsic and extrinsic pathway of coagulation. In conclusion, these observations suggest that PMPs and PS play an important role in dysfunctional coagulation in abdominal sepsis. © 2017 Wiley Periodicals, Inc.

  7. Automated drawing generation system

    International Nuclear Information System (INIS)

    Yoshinaga, Toshiaki; Kawahata, Junichi; Yoshida, Naoto; Ono, Satoru

    1991-01-01

    Since automated CAD drawing generation systems still require human intervention, improvements were focussed on an interactive processing section (data input and correcting operation) which necessitates a vast amount of work. As a result, human intervention was eliminated, the original objective of a computerized system. This is the first step taken towards complete automation. The effects of development and commercialization of the system are as described below. (1) The interactive processing time required for generating drawings was improved. It was determined that introduction of the CAD system has reduced the time required for generating drawings. (2) The difference in skills between workers preparing drawings has been eliminated and the quality of drawings has been made uniform. (3) The extent of knowledge and experience demanded of workers has been reduced. (author)

  8. Extracellular Histones Increase Tissue Factor Activity and Enhance Thrombin Generation by Human Blood Monocytes.

    Science.gov (United States)

    Gould, Travis J; Lysov, Zakhar; Swystun, Laura L; Dwivedi, Dhruva J; Zarychanski, Ryan; Fox-Robichaud, Alison E; Liaw, Patricia C

    2016-12-01

    Sepsis is characterized by systemic activation of inflammatory and coagulation pathways in response to infection. Recently, it was demonstrated that histones released into the circulation by dying/activated cells may contribute to sepsis pathology. Although the ability of extracellular histones to modulate the procoagulant activities of several cell types has been investigated, the influence of histones on the hemostatic functions of circulating monocytes is unknown. To address this, we investigated the ability of histones to modulate the procoagulant potential of THP-1 cells and peripheral blood monocytes, and examined the effects of plasmas obtained from septic patients to induce a procoagulant phenotype on monocytic cells. Tissue factor (TF) activity assays were performed on histone-treated THP-1 cells and blood monocytes. Exposure of monocytic cells to histones resulted in increases in TF activity, TF antigen, and phosphatidylserine exposure. Histones modulate the procoagulant activity via engagement of Toll-like receptors 2 and 4, and this effect was abrogated with inhibitory antibodies. Increased TF activity of histone-treated cells corresponded to enhanced thrombin generation in plasma determined by calibrated automated thrombography. Finally, TF activity was increased on monocytes exposed to plasma from septic patients, an effect that was attenuated in plasma from patients receiving unfractionated heparin (UFH). Our studies suggest that increased levels of extracellular histones found in sepsis contribute to dysregulated coagulation by increasing TF activity of monocytes. These procoagulant effects can be partially ameliorated in sepsis patients receiving UFH, thereby identifying extracellular histones as a potential therapeutic target for sepsis treatment.

  9. Low thrombin generation predicts poor prognosis in ischemic stroke patients after thrombolysis.

    Directory of Open Access Journals (Sweden)

    Renáta Hudák

    Full Text Available Thrombolysis by intravenous recombinant tissue plasminogen activator (rt-PA is an effective therapy in acute ischemic stroke (AIS. Thrombin generation test (TGT is a global hemostasis test providing information about the speed and amount of generated thrombin in plasma. Here we aimed to find out whether results of this test before the initiation of thrombolysis might predict outcomes. Study population included 120 consecutive AIS patients, all within 4.5 hours of their symptom onset, who underwent thrombolysis by rt-PA. Blood samples were collected from all patients upon admission and TGT was performed using platelet poor plasma. Clinical data of patients including the NIHSS were registered at admission, day 1 and 7 after therapy. The ASPECT score was assessed using CT images taken before and 24 hours after thrombolysis. Long-term functional outcome was defined 3 months after the event by the modified Rankin Scale. Endogenous Thrombin Potential (ETP and Peak Thrombin were significantly lower in patients with cardioembolic IS. Symptomatic intracranial hemorrhage (SICH was found in 6 patients and was significantly associated with low ETP and Peak Thrombin levels. A multiple logistic regression model revealed that an ETP result in the lower quartile is an independent predictor of mortality within the first two weeks (OR: 6.03; 95%CI: 1.2-30.16, p<0.05 and three months after the event (OR: 5.28; 95%CI: 1.27-21.86, p<0.05. Low levels of ETP and Peak Thrombin parameters increase the risk of therapy associated SICH. A low ETP result is an independent predictor of short- and long-term mortality following thrombolysis.

  10. Computational Analysis of Intersubject Variability and Thrombin Generation in Dilutional Coagulopathy

    Science.gov (United States)

    2012-11-01

    Mann15,30-32 and S. Dia- mond ,33,34 as well as by our own research group.16 We used the computational model to calculate the five thrombin generation...approach to modeling dilution did not take into account the specific type of liquid that dilutes the blood. While it is known that the type of

  11. Flow cytometric analysis of microparticle phenotype and their role in thrombin generation.

    Science.gov (United States)

    Macey, M G; Enniks, N; Bevan, S

    2011-01-01

    Microparticles may be generated from a number of cell types and are known to play a role in haemostasis by a variety of mechanisms. We investigated the role of platelet, red cell, and leucocyte-derived microparticles in the measurement of thrombin generation. Four parameters of thrombin generation (the endogenous thrombin potential (ETP), lag time, time to peak, peak height) and microparticle content was determined in 35 plasma samples from normal individuals pre and post filtration to remove microparticles. Immunofluorescent flow cytometry was used to identify and enumerate platelet, leucocyte, monocyte and red cell derived microparticles in plasma samples based on the expression of CD42b, CD45, CD15, and Glycophorin A respectively. Expression of phosphatidylserine and tissue factor by microparticles was determined by Annexin V and anti CD142 binding. The pre and post filtration results were compared. There was a significant decrease in ETP and Peak Height, and an increase in the time to peak post filtration (P microparticles was also observed. The change in CD42b+ microparticles correlated highly with the change in Annexin V+ microparticles (r = 0.68). Whilst the change in ETP correlated best with the change in CD15+ microparticles (r = 0.45) and the change in time to peak correlated with the change in Annexin V binding (r = 0.52) (P < 0.01). The presence of micropartcles in plasma significantly affects thrombin generation. Copyright © 2010 International Clinical Cytometry Society.

  12. Variable hypocoagulant effect of fish oil intake in humans: Modulation of fibrinogen level and thrombin generation

    NARCIS (Netherlands)

    Schoonbeek, K.van; Feijge, M.A.H.; Paquay, M.; Rosing, J.; Saris, W.; Kluft, C.; Giesen, P.L.A.; Maat, M.P.M.de; Heemskerk, J.W.M.

    2004-01-01

    Objective-The beneficial effect of dietary fish oil, rich in omega-3 polyunsaturated fatty acids (PUFAs), on cardiovascular disease is multifactorial and may partly rely on their anticoagulant action. We studied how fish oil intake influenced thrombin generation in plasma and which factors were

  13. Ex vivo reversal of effects of rivaroxaban evaluated using thromboelastometry and thrombin generation assay

    Science.gov (United States)

    Schenk, B.; Würtinger, P.; Streif, W.; Sturm, W.; Fries, D.; Bachler, M.

    2016-01-01

    Background In major bleeding events, the new direct oral anticoagulants pose a great challenge for physicians. The aim of the study was to test for ex vivo reversal of the direct oral anticoagulant rivaroxaban with various non-specific reversal agents: prothrombin complex concentrate (PCC), activated prothrombin complex concentrate (aPCC), recombinant activated factor VII (rFVIIa), and fibrinogen concentrate (FI). Methods Blood was obtained from healthy volunteers and from patients treated with rivaroxaban. Blood samples from healthy volunteers were spiked with rivaroxaban to test the correlation between rivaroxaban concentration and coagulation tests. Patient blood samples were spiked with various concentrations of the above-mentioned agents and analysed using thromboelastometry and thrombin generation. Results When added in vitro, rivaroxaban was significantly (P<0.05) correlated with ROTEM® thromboelastometry EXTEM (extrinsic coagulation pathway) clotting time (CT), time to maximal velocity (MaxV−t), and with all measured thrombin generation parameters. In vivo, CT, MaxV−t, lag time, and peak thrombin generation (Cmax) were significantly correlated with rivaroxaban concentrations. Regarding reversal of rivaroxaban, all tested agents significantly (P<0.05) reduced EXTEM CT, but to different extents: rFVIIa by 68%, aPCC by 47%, PCC by 17%, and FI by 9%. Only rFVIIa reversed EXTEM CT to baseline values. Both PCC (+102%) and aPCC (+232%) altered overall thrombin generation (area under the curve) and increased Cmax (+461% for PCC, +87.5% for aPCC). Conclusions Thromboelastometry and thrombin generation assays do not favour the same reversal agents for rivaroxaban anticoagulation. Controlled clinical trials are urgently needed to establish doses and clinical efficacy of potential reversal agents. Clinical trial registration EudracCT trial no. 213-00474-30. PMID:27623677

  14. 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.

  15. Automated Test Case Generation

    CERN Multimedia

    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...

  16. 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.

  17. Effects of recombinant human prothrombin on thrombin generation in plasma from patients with hemophilia A and B.

    Science.gov (United States)

    Hansson, K M; Gustafsson, D; Skärby, T; Frison, L; Berntorp, E

    2015-07-01

    The present study was carried out to investigate the impact of FII levels, and their increase, on the hemostatic potential in plasma from hemophilia A and B patients with and without inhibitors. Recombinant human factor (F) II (rhFII) was added ex vivo to plasma from 68 patients with hemophilia A and B, with or without inhibitors. The hemostatic potential as measured by thrombin generation (calibrated automated thrombogram [CAT]) was focused on the endogenous thrombin potential (ETP) as it has been shown to correlate with the clinical phenotype of bleeding in hemophilia patients and has also been used to guide bypassing therapy in hemophilia patients with inhibitors before elective surgery. The factor eight inhibitor bypassing agent (FEIBA(®) ) was used as a reference to the clinical situation. The study shows that rhFII concentration-dependently increased ETP by a similar magnitude in hemophilia A and B, both with and without inhibitors. Compared with FEIBA, rhFII showed a shallower concentration-response curve. In both types of hemophilia 100 mg L(-1) of rhFII roughly doubled the ETP. A corresponding response was obtained by 0.5 U mL(-1) of FEIBA. These data support the theory that FII is one of the major components responsible for the efficacy of FEIBA. The data also indicate that rhFII may be useful, alone or in combination with other coagulation factors, in some of the conditions for which FEIBA is used today, although more data are needed to substantiate this. © 2015 International Society on Thrombosis and Haemostasis.

  18. Comparing thrombin generation in patients with hemophilia A and patients on vitamin K antagonists.

    Science.gov (United States)

    de Koning, M L Y; Fischer, K; de Laat, B; Huisman, A; Ninivaggi, M; Schutgens, R E G

    2017-05-01

    Essentials It is unknown if hemophilia patients with atrial fibrillation need anticoagulation. Endogenous thrombin potentials (ETP) in hemophilia patients and patients on coumarins were compared. Severe hemophilia patients had comparable ETP to therapeutic international normalized ratio (INR). In non-severe hemophilia, 33% had higher ETP than therapeutic INR and may need anticoagulation. Click to hear Dr Negrier's perspective on global assays for assessing coagulation SUMMARY: Background It is unknown whether patients with hemophilia A with atrial fibrillation require treatment with vitamin K antagonists (VKAs) to the same extent as the normal population. Objective To compare hemostatic potential in hemophilia patients and patients on VKAs using thrombin generation (TG). Methods In this cross-sectional study, TG, initiated with 1pM tissue factor, was measured in 133 patients with severe (FVIII hemophilia A, 97 patients on a VKA with an international normalized ratio (INR) ≥ 1.5 and healthy controls. Endogenous thrombin potential (ETP) (nm*min) was compared according to FVIII level (hemophilia patients and patients on VKAs had lower median ETPs at 304 (196-449) and 176 (100-250), respectively. ETP was quite similar in severe hemophilia patients (185 [116-307]) and patients with a therapeutic INR (156 [90-225]). Compared with patients with therapeutic INR, ETP in patients with FVIII 1-19% and patients with FVIII 20-50% was higher at 296 (203-430) and 397 (219-632), respectively. All patients with therapeutic INR had an ETP hemophilia patients, 70% of patients with FVIII 1-19% and 52% of patients with FVIII 20-50% had an ETP hemophilia patients, TG was comparable to that in patients with a therapeutic INR. In one-third of non-severe hemophilia patients, TG was higher. These results suggest that anticoagulation therapy should be considered in a substantial proportion of non-severe hemophilia patients. © 2017 International Society on Thrombosis and Haemostasis.

  19. Factor Xa inhibition by rivaroxaban in the trough steady state can significantly reduce thrombin generation.

    Science.gov (United States)

    Horinaka, Shigeo; Sugawara, Rie; Yonezawa, Yutaka; Ishimitsu, Toshihiko

    2018-01-01

    The aim of the present study was to demonstrate evidence of reduced thrombin generation at the trough plasma rivaroxaban concentration. A single-centre, prospective, nonrandomized, drug-intervention, self-controlled study was conducted in 51 anticoagulation therapy-naïve patients with nonvalvular atrial fibrillation. Plasma rivaroxaban concentration was measured by liquid chromatography tandem mass spectrometry (LC-MS/MS) and the anti-factor Xa chromogenic assay. Partial thrombin time (PT), protein C activity, and protein S antigen, prothrombin fragment 1 + 2 (F1 + 2), D-dimer, thrombomodulin (TM), thrombin-antithrombin complex (TAT), plasminogen activator inhibitor-1 (PAI-1) and tissue factor pathway inhibitor (TFPI) levels were also measured at the trough steady state after 4 weeks of rivaroxaban treatment and compared with baseline. Plasma concentrations obtained by the LC-MS/MS and anti-Xa assays were correlated (r = 0.841, P steady state was 23.6 ng ml -1 , at which F1 + 2, TAT and D-dimer had decreased from the baseline values (P steady state in the first to third quartile groups (+0.79 pg ml -1 , P = 0.048). By contrast, PAI-1, protein C activity, protein S antigen and TM remained within the normal range at the trough steady state. Residual plasma rivaroxaban at the trough steady state may explain the antithrombin effect of rivaroxaban in patients with nonvalvular atrial fibrillation. © 2017 The Authors. British Journal of Clinical Pharmacology published by John Wiley & Sons Ltd on behalf of British Pharmacological Society.

  20. Differential contributions of monocyte- and platelet-derived microparticles towards thrombin generation and fibrin formation and stability.

    Science.gov (United States)

    Aleman, M M; Gardiner, C; Harrison, P; Wolberg, A S

    2011-11-01

    Microparticles (MPs) are sub-micron vesicles shed by activated or apoptotic cells, including platelets and monocytes. Increased circulating MPs are associated with thrombosis; however, their role in thrombogenesis is poorly understood. To determine how MPs promote thrombin generation and modulate fibrin density and stability. Platelets and monocytes were isolated from healthy donors. Platelets were stimulated with calcium ionophore, thrombin receptor agonist peptide (TRAP) or TRAP/convulxin. Monocytes and human monocytic THP-1 cells were stimulated with lipopolysaccharide (LPS). MPs were isolated, washed by high-speed centrifugation and assessed using the following: transmission electron microscopy (TEM), Nanoparticle Tracking Analysis (NTA), flow cytometry, tissue factor (TF) activity, prothrombinase activity, thrombin generation, and clot formation, density and stability. MPs from monocytes (M-MPs) and platelets (PMPs) had similar shapes and diameters (100-300 nm). M-MPs had TF activity (16.7 ± 2.4 pm TF per 10(6) MP), supported prothrombinase activity and triggered shorter thrombin generation lag times than buffer controls (5.4 ± 0.5 vs. 84.2 ± 4.8 min, respectively). Compared with controls, M-MPs supported faster fibrin formation (0.24 ± 0.24 vs. 76.7 ± 15.1 mOD min(-1) , respectively), 38% higher fibrin network density and higher clot stability (3.8-fold higher turbidity in the presence of tissue plasminogen activator). In contrast, PMPs did not have TF activity and supported 2.8-fold lower prothrombinase activity than M-MPs. PMPs supported contact-dependent thrombin generation, but did not independently increase fibrin network density or stability. Interestingly, PMPs increased rates of thrombin generation and fibrin formation (1.7- and 1.3-fold, respectively) when mixed with THP-1-derived MPs. MPs from platelets and monocytes differentially modulate clot formation, structure and stability, suggesting unique contributions to thrombosis. © 2011

  1. Automated Generation of Attack Trees

    DEFF Research Database (Denmark)

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

    2014-01-01

    -prone and impracticable for large systems. Nonetheless, the automated generation of attack trees has only been explored in connection to computer networks and levering rich models, whose analysis typically leads to an exponential blow-up of the state space. We propose a static analysis approach where attack trees...

  2. In vivo increase in thrombin generation by four-factor prothrombin complex concentrate in apixaban-treated healthy volunteers

    NARCIS (Netherlands)

    Cheung, Y. W.; Barco, S.; Hutten, B. A.; Meijers, J. C. M.; Middeldorp, S.; Coppens, M.

    2015-01-01

    Four-factor prothrombin complex concentrate (PCC) (Cofact; Sanquin Blood Supply) 50 IU kg(-1) increased thrombin generation beyond baseline values in healthy, rivaroxaban-treated subjects. To assess whether infusion with doses of 37.5 IU kg(-1) and 25 IU kg(-1) PCC reverses the anticoagulant effect

  3. Comparing thrombin generation in patients with hemophilia A and patients on vitamin K antagonists

    NARCIS (Netherlands)

    de Koning, M L Y; Fischer, K; de Laat, B; Huisman, A; Ninivaggi, M; Schutgens, R E G

    Essentials: It is unknown if hemophilia patients with atrial fibrillation need anticoagulation. Endogenous thrombin potentials (ETP) in hemophilia patients and patients on coumarins were compared. Severe hemophilia patients had comparable ETP to therapeutic international normalized ratio (INR). In

  4. Effects of thromboprophylactic doses of apixaban and rivaroxaban on coagulation and thrombin generation in association with total hip replacement.

    Science.gov (United States)

    Helin, Tuukka A; Virtanen, Lauri; Manninen, Mikko; Leskinen, Jarkko; Leppilahti, Juhana; Joutsi-Korhonen, Lotta; Lassila, Riitta

    2017-05-01

    Factor Xa inhibitors (FXaI) apixaban and rivaroxaban are used for thromboprophylaxis after major elective orthopaedic surgery. Because few patient sample studies exist, we postoperatively assessed patients undergoing unilateral total hip arthroplasty, including 22 treated with apixaban (2.5 mg BID) and 20 treated with rivaroxaban (10 mg OD). We collected blood samples before and 3 h after drug intake at 4 time points, preoperatively, as well as on day 1, week 1 (day 2-8) and day 28 post-operation. APTT and PT were immediately analysed. Calibrated anti-FXa activity, Russel's Viper Venom Time (RVVT) and thrombin generation (TG; Calibrated Automated Thrombogram ® ) captured the effects of FXaI on coagulation and TG. APTT and PT remained within the reference interval throughout, and did not correlate with FXaI levels (PT R 2  = 0.44, APTT R 2  = 0.07). Mean apixaban concentration at the peak varied by eightfold (19-153 ng/mL), but rivaroxaban only by 1.5-fold (111-183 ng/mL). Rivaroxaban, but not apixaban prolonged RVVT at peak levels. Both FXaIs had a prolonged lag time of TG (p < 0.001). Rivaroxaban decreased ETP peak at all time points and reached a minimum at day 28 (540 nM/min at rivaroxaban 184 ng/mL, p < 0.001), while rivaroxaban trough levels were low and ETP values normal. However, with apixaban, after an initial decrease, ETP did not differ between peak and trough levels until decreasing on day 28 at peak (990 nM/min at apixaban 112 ng/mL, p = 0.005). In conclusion, due to different dosing and pharmacology rivaroxaban and apixaban distinctly inhibited TG under postoperative conditions.

  5. 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 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.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.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.ClinicalTrials.gov NCT00793754.

  6. Does Lipid Profile Affect Thrombin Generation During Ramadan Fasting in Patients With Cardiovascular Risks?

    Science.gov (United States)

    Sassi, Mouna; Chakroun, Taher; Chouchène, Saoussen; Hellara, Ilhem; Boubaker, Hamdi; Grissa, Mohamed Habib; Khochtali, Ines; Hassine, Mohsen; Addad, Faouzi; Elalamy, Ismail; Nouira, Semir

    2017-11-01

    There is evidence that diet and variation in lipid metabolism can influence blood coagulation, but little is known about the effect of Ramadan fasting on plasmatic coagulation pattern. We investigated the effect of Ramadan fasting on thrombin generation (TG) in patients with cardiovascular disease (CVD) risks, and we aimed to assess the effect of lipid profile on TG parameters. The study was conducted in 36 adults having at least 2 CVD risks and in 30 healthy controls. Coagulation pattern was assessed by both classical clotting times and TG test. A complete lipid profile was performed simultaneously. Patients were invited 2 times: 1 week before Ramadan and during the last week of the Ramadan. The TG parameters were not different in patients with CVD risks compared to healthy controls. Fasting had no effect on plasmatic coagulation parameters and on TG profile. Individual analysis of the mean rate index (MRI) of TG revealed 3 groups: group 1 with no modification of MRI, group 2 with a significant increase in MRI (81.64 nM/min vs 136.07 nM/min; P fasting did not influence the global coagulation pattern in patients with CVD risks. Whereas, a significant increase in the propagation phase of TG was associated with a significant increase in cholesterol levels, which was not found with the other TG parameters.

  7. Thrombin generation and fibrin clot formation under hypothermic conditions: an in vitro evaluation of tissue factor initiated whole blood coagulation.

    Science.gov (United States)

    Whelihan, Matthew F; Kiankhooy, Armin; Brummel-Ziedins, Kathleen E

    2014-02-01

    Despite trauma-induced hypothermic coagulopathy being familiar in the clinical setting, empirical experimentation concerning this phenomenon is lacking. In this study, we investigated the effects of hypothermia on thrombin generation, clot formation, and global hemostatic functions in an in vitro environment using a whole blood model and thromboelastography, which can recapitulate hypothermia. Blood was collected from healthy individuals through venipuncture and treated with corn trypsin inhibitor, to block the contact pathway. Coagulation was initiated with 5pM tissue factor at temperatures 37°C, 32°C, and 27°C. Reactions were quenched over time, with soluble and insoluble components analyzed for thrombin generation, fibrinogen consumption, factor (f)XIII activation, and fibrin deposition. Global coagulation potential was evaluated through thromboelastography. Data showed that thrombin generation in samples at 37°C and 32°C had comparable rates, whereas 27°C had a much lower rate (39.2 ± 1.1 and 43 ± 2.4 nM/min vs 28.6 ± 4.4 nM/min, respectively). Fibrinogen consumption and fXIII activation were highest at 37°C, followed by 32°C and 27°C. Fibrin formation as seen through clot weights also followed this trend. Thromboelastography data showed that clot formation was fastest in samples at 37°C and lowest at 27°C. Maximum clot strength was similar for each temperature. Also, percent lysis of clots was highest at 37°C followed by 32°C and then 27°C. Induced hypothermic conditions directly affect the rate of thrombin generation and clot formation, whereas global clot stability remains intact. © 2013.

  8. 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

    BACKGROUND AND OBJECTIVES: Transfusion based on the Thrombelastograph (TEG) results reduces transfusion requirements in cardiac surgery and in liver transplantation. Taking the pivotal role of thrombin generation in the coagulation process into consideration, the clinical utility of the TEG may...

  9. 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.

  10. 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.

  11. 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......-PA), plasminogen activator inhibitor type 1 (PAI-1), and von Willebrand factor (vWF). RESULTS: We observed significant within-group decreases in ETP (MOD 7 %; HIGH 6 %) and in t-PA (MOD 22 %; HIGH 21 %) and PAI-1 (MOD 16 %; HIGH 32 %) in both training groups, and no changes in the CON group. At 3 months, between...

  12. Thrombin generation assay as a possible tool for assessment of reduced activity of clotting factors induced by antiphospholipid antibodies and in-vitro evaluation of treatment options.

    Science.gov (United States)

    Livnat, Tami; Zivelin, Ariella; Tamarin, Ilia; Guetta, Victor; Salomon, Ophira

    2009-12-01

    Bleeding is a rare manifestation of antiphospholipid syndrome, unless associated with reduced clotting factors or severe thrombocytopenia. Accurate assessment of the autoantibodies in plasma is very important since the autoantibodies can lead to bleeding or thrombosis. The objective of the present study was to define the inhibitors causing reduced clotting activity in a patient with antiphospholipids antibodies and to assess the potential of thrombin generation assay to assist in establishment of optimal treatment in case of major bleeding. Levels of clotting factors as well as inhibitors to factors II, V, VII, VIII, IX, X and XI were defined. For detection of inhibitors to prothrombin crossed immunoelectrophoresis was used. IgG was purified by commercial protein A column. Thrombin generation was measured using a fluorometric assay in platelet-poor and platelet-rich plasma. Inhibitors toward the activity of factors V, VII, VIII, IX, X and XI were defined and also an inhibitor to prothrombin antigen. No thrombin generation was induced in the patient's plasma by recalcification even in the presence of recombinant factor VIIa or factor VIII inhibitor bypassing activity. In contrast, addition of platelets from either donor or patient or synthetic phospholipids normalized the thrombin generation. The thrombin generation model showed that the addition of platelets and no recombinant factor VIIa or factor VIII inhibitor bypassing activity would correct thrombin generation in vitro. On this basis, platelet concentrates were administered to a patient with bleeding caused by lupus anticoagulant and low clotting factors activity.

  13. Effects of normoxic and hypoxic exercise regimens on monocyte-mediated thrombin generation in sedentary men.

    Science.gov (United States)

    Wang, Jong-Shyan; Chang, Ya-Lun; Chen, Yi-Ching; Tsai, Hsing-Hua; Fu, Tieh-Cheng

    2015-08-01

    Exercise and hypoxia paradoxically modulate vascular thrombotic risks. The shedding of procoagulant-rich microparticles from monocytes may accelerate the pathogenesis of atherothrombosis. The present study explores the manner in which normoxic and hypoxic exercise regimens affect procoagulant monocyte-derived microparticle (MDMP) formation and monocyte-promoted thrombin generation (TG). Forty sedentary healthy males were randomized to perform either normoxic (NET; 21% O2, n=20) or hypoxic (HET; 15% O2, n=20) exercise training (60% VO(2max)) for 30 min/day, 5 days/week for 5 weeks. At rest and immediately after HET (100 W under 12% O2 for 30 min), the MDMP characteristics and dynamic TG were measured by flow cytometry and thrombinography respectively. The results demonstrated that acute 12% O2 exercise (i) increased the release of coagulant factor V (FV)/FVIII-rich, phosphatidylserine (PS)-exposed and tissue factor (TF)-expressed microparticles from monocytes, (ii) enhanced the peak height and rate of TG in monocyte-rich plasma (MRP) and (iii) elevated concentrations of norepinephrine/epinephrine, myeloperoxidase (MPO) and interleukin-6 (IL-6) in plasma. Following the 5-week intervention, HET exhibited higher enhancements of peak work-rate and cardiopulmonary fitness than NET did. Moreover, both NET and HET decreased the FV/FVIII-rich, PS-exposed and TF-expressed MDMP counts and the peak height and rate of TG in MRP following the HET. However, HET elicited more suppression for the HE (hypoxic exercise)-enhanced procoagulant MDMP formation and dynamic TG in MPR and catecholamine/peroxide/pro-inflammatory cytokine levels in plasma than NET. Hence, we conclude that HET is superior to NET for enhancing aerobic capacity. Furthermore, HET effectively suppresses procoagulant MDMP formation and monocyte-mediated TG under severe hypoxic stress, compared with NET.

  14. Increased Clot Formation in the Absence of Increased Thrombin Generation in Patients with Peripheral Arterial Disease: A Case–Control Study

    Directory of Open Access Journals (Sweden)

    Marie-Claire F. Kleinegris

    2017-04-01

    Full Text Available BackgroundIn peripheral arterial disease (PAD, activation of the hemostatic system may contribute to atherosclerosis progression and atherothrombotic events.ObjectiveThis case–control study assesses the overall coagulation status in PAD patients by evaluating coagulation markers in combination with thrombin generation potential, whole blood (WB clot formation, and fibrinolysis.MethodsIn blood from 40 PAD patients (n = 20 with cardiovascular event within 1 year after initial diagnosis, n = 20 without and 40 apparently healthy controls, thrombin generation was determined in WB and platelet-poor plasma. Whole blood rotational thromboelastometry (ROTEM measurements were triggered with tissue factor with/without tissue plasminogen activator.ResultsWe observed increased levels of erythrocyte sedimentation rate, leukocytes, eosinophil granulocytes, vWF antigen, fibrinogen, and D-dimer in PAD patients (p < 0.05. Markers of thrombin generation potential showed no difference between patients and healthy controls. In PAD patients with event compared to patients without, WB-thrombin generation showed a lower thrombin potential when triggered with 0 and 2.5 pM tissue factor. The ROTEM clotting assay showed significantly faster clot formation and increased clot firmness in PAD patients compared to controls. No significant differences were found for parameters of clot degradation.ConclusionThere are no significant differences between the thrombin generation profiles of PAD patients and healthy controls. Between PAD patients with and without cardiovascular event, the WB thrombin generation appears to differ. Mechanistically, PAD patients show an increased ability to form a stable clot in WB in comparison to healthy controls. This is most likely due to the increased fibrinogen levels related to the inflammation in atherosclerosis, confirming the importance of the inflammation-coagulation axis.

  15. 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…

  16. Large external quality assessment survey on thrombin generation with CAT: further evidence for the usefulness of normalisation with an external reference plasma.

    Science.gov (United States)

    Perrin, Julien; Depasse, François; Lecompte, Thomas

    2015-07-01

    Calibrated Automated Thrombography (CAT) has been widely used to assess in vitro thrombin generation as an informative intermediary phenotype of coagulation. Interlaboratory exercises have documented a worrisome poor reproducibility. There are some data on the normalisation with an appropriate external reference plasma (RP). This multicentre study of the French-speaking CAT Club aimed at providing further evidence for the usefulness of such a normalisation. Lyophilised aliquots of a RP along with 3 plasmas (P1=normal; P2=hypo-; P3=hypercoagulable) were sent to 34 laboratories (corresponding to 38 instruments). CAT was studied using 1 and 5 pM tissue factor and other dedicated reagents. Normalisation with the local RP in use in the laboratory could also be performed. Interlaboratory CVs were calculated for each plasma before and after normalisation. Regarding endogenous thrombin potential, a good discrimination between the 3 plasmas was achieved in all laboratories but there was no overlap after normalisation only. CVs were generally not reduced with the use of local RP but were generally improved with normalisation using the external RP, often becoming lower than 10%. Regarding P2 however, the benefit of normalisation was poor, and there were analytical difficulties as well, some laboratories being unable to get a useable signal. We confirm that normalisation of CAT results with a suitable external RP is useful in "real life" practice as it often permits an acceptable level of interlaboratory variability. In case of frank hypocoagulability, further improvements are required to get reliable, potentially clinically relevant results. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Thrombin Time

    Science.gov (United States)

    ... functional fibrinogen assay is now routinely available in clinical laboratories and has largely replaced the need for thrombin ... including fibrinogen activity assay (now routinely available in clinical laboratories), fibrinogen antigen assay, and liver function tests . Is ...

  18. Monocyte IL-10 produced in response to lipopolysaccharide modulates thrombin generation by inhibiting tissue factor expression and release of active tissue factor-bound microparticles.

    Science.gov (United States)

    Poitevin, Stéphane; Cochery-Nouvellon, Eva; Dupont, Annick; Nguyen, Philippe

    2007-04-01

    Lipopolysaccharide (LPS)-stimulated monocytes are known to have a procoagulant effect. This property is currently explained by the fact that monocytes, in response to LPS, can express tissue factor (TF) and undergo a process of membrane microvesiculation. Interleukin-10 (IL-10) has been shown to downregulate TF expression and inhibit procoagulant activity (PCA). In order to further characterize the inhibitory effect of IL-10 on LPS-induced PCA, we used the integrated system of analysis of kinetics of thrombin generation in normal plasma (thrombinography). For this, we developed an original method of elutriation allowing to obtain a highly purified monocyte preparation, under endotoxin-free conditions. Thrombin generation was measured using a highly sensitive and specific fluorogenic method which we adapted to inhibit the contact factor pathway. Results show that recombinant human IL-10 decreased the kinetics of thrombin generation in a dose-dependent manner. Furthermore, the inhibition of endogenous IL-10 released by monocytes in response to LPS is associated with an increase in the kinetics of thrombin generation. We demonstrated that this effect was a consequence of the up-regulation of TF expression and TF-bound microparticle release. In conclusion, we report that IL-10 can regulate thrombin generation in conditions close to physiology as allowed by thrombinography, and that endogenous IL-10 regulates TF expression and release of active TF-bound microparticles by a negative feed back loop through IL-10 receptor alpha.

  19. Contributions of procoagulants and anticoagulants to the international normalized ratio and thrombin generation assay in patients treated with warfarin: potential role of protein Z as a powerful determinant of coagulation assays.

    Science.gov (United States)

    Choi, Qute; Kim, Ji-Eun; Hyun, Jungwon; Han, Kyou-Sup; Kim, Hyun Kyung

    2013-07-01

    The effects of warfarin are measured with the international normalized ratio (INR). However, the thrombin generation assay (TGA) may offer more information about global coagulation. We analyzed the monitoring performance of the TGA and INR and investigated the impact of procoagulants (fibrinogen, factor (F)II, FVII, FIX, and FX) and anticoagulants (proteins C, S, and Z) on them. The TGA was performed on a calibrated automated thrombogram, producing lag time, endogenous thrombin potential (ETP), and peak thrombin in 239 patients treated with warfarin. Pro- and anticoagulant levels were also measured. The INR was significantly and inversely correlated with ETP. The therapeutic range of ETP comparable to an INR range of 2.0-3.0 was 290.1-494.6. ETP showed comparable performance to the INR as a warfarin-monitoring parameter with respect to clinical complication rate. The median levels of FII, FVII, FIX, and FX and proteins C and Z tended to decrease gradually with increasing anticoagulation intensity according to the INR or ETP. Of note, protein Z levels decreased dramatically with increasing anticoagulation status. INRs were significantly determined by FII, FVII, and protein Z. ETP was significantly dependent on FVII, and proteins C and Z concentration. Protein Z significantly reduced the total amount of thrombin generation and prolonged PT value in vitro. The INR and ETP exhibit similar efficacy for warfarin monitoring according to the clinical complication rate. Protein Z is considered to be a significant determinant of INR and ETP in patients on warfarin therapy. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. 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.

  1. Automated Test Requirement Document Generation

    Science.gov (United States)

    1987-11-01

    DIAGNOSTICS BASED ON THE PRINCIPLES OF ARTIFICIAL INTELIGENCE ", 1984 International Test Conference, 01Oct84, (A3, 3, Cs D3, E2, G2, H2, 13, J6, K) 425...j0O GLOSSARY OF ACRONYMS 0 ABBREVIATION DEFINITION AFSATCOM Air Force Satellite Communication Al Artificial Intelligence ASIC Application Specific...In-Test Equipment (BITE) and AI ( Artificial Intelligence) - Expert Systems - need to be fully applied before a completely automated process can be

  2. "First generation" automated DNA sequencing technology.

    Science.gov (United States)

    Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

    2011-10-01

    Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

  3. Thrombin generation assay and transmission electron microscopy: a useful combination to study tissue factor-bearing microvesicles

    Directory of Open Access Journals (Sweden)

    Damien Gheldof

    2013-03-01

    Full Text Available Introduction. Patients with cancer have a 7- to 10-fold increased risk of developing venous thromboembolism. Circulating microvesicles could be a useful predictive biomarker for venous thromboembolism in cancer. Validated and standardised techniques that could be used to determine the complete microvesicle phenotype are required. These were two-fold: a to characterise tissue factor (TF-bearing microvesicles released by cultured breast cancer cells MDA-MB-231 by flow cytometry (FCM, transmission electron microscopy (TEM and thrombin generation assay (TGA; and b to validate the sensitivity and variability intra/inter-assay of TGA as a useful method to study the procoagulant activity (PCA of microvesicles. Methods. Cultured breast cancer cells MDA-MB-231 were incubated for 45 minutes at 37°C. Samples were then centrifuged or not at 4,500 g for 15 minutes, and cells and MVs or MV-containing supernatants were used for TEM, FCM and TGA. In activity assays, microvesicles (i.e. cell-depleted supernatants were incubated with anti-TF antibodies or with annexin V to assess the contribution of TF and phospholipids to the PCA. Alternatively, supernatants were filtered through 0.1, 0.22, 0.45 or 0.65 µm membranes and subjected to TGA. Results. The majority of the PCA was associated with microvesicles smaller than 0.1 µm, and the mean microvesicle size estimated by TEM after 10,000 g centrifugation was 121±54 nm with a majority of vesicles between 100 and 200 nm. Microvesicles derived from 5,000 MDA-MB-231cells/ml were sufficient to significantly increase the thrombin generation of normal pooled plasma. Conclusions. TEM, FCM and filtration coupled to TGA represent a useful combination to study the PCA of TF-bearing microvesicles, whatever their size. And it will be interesting to implement these techniques in patients.

  4. Differential inhibitory action of apixaban on platelet and fibrin components of forming thrombi: Studies with circulating blood and in a platelet-based model of thrombin generation.

    Directory of Open Access Journals (Sweden)

    Lluis Pujadas-Mestres

    Full Text Available Mechanisms of action of direct oral anticoagulants (DOAC suggest a potential therapeutic use in the prevention of thrombotic complications in arterial territories. However, effects of DOACs on platelet activation and aggregation have not been explored in detail. We have investigated the effects of apixaban on platelet and fibrin components of thrombus formation under static and flow conditions.We assessed the effects of apixaban (10, 40 and 160 ng/mL on: 1 platelet deposition and fibrin formation onto a thrombogenic surface, with blood circulating at arterial shear-rates; 2 viscoelastic properties of forming clots, and 3 thrombin generation in a cell-model of coagulation primed by platelets.In studies with flowing blood, only the highest concentration of apixaban, equivalent to the therapeutic Cmax, was capable to significantly reduce thrombus formation, fibrin association and platelet-aggregate formation. Apixaban significantly prolonged thromboelastometry parameters, but did not affect clot firmness. Interestingly, results in a platelet-based model of thrombin generation under more static conditions, revealed a dose dependent persistent inhibitory action by apixaban, with concentrations 4 to 16 times below the therapeutic Cmax significantly prolonging kinetic parameters and reducing the total amount of thrombin generated.Our studies demonstrate the critical impact of rheological conditions on the antithrombotic effects of apixaban. Studies under flow conditions combined with modified thrombin generation assays could help discriminating concentrations of apixaban that prevent excessive platelet accumulation, from those that deeply impair fibrin formation and may unnecessarily compromise hemostasis.

  5. Automated generation of lattice QCD Feynman rules

    International Nuclear Information System (INIS)

    Hart, A.; Mueller, E.H.; Horgan, R.R.

    2009-04-01

    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. (orig.)

  6. 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.)

  7. Generative Representations for Automated Design of Robots

    Science.gov (United States)

    Homby, Gregory S.; Lipson, Hod; Pollack, Jordan B.

    2007-01-01

    A method of automated design of complex, modular robots involves an evolutionary process in which generative representations of designs are used. The term generative representations as used here signifies, loosely, representations that consist of or include algorithms, computer programs, and the like, wherein encoded designs can reuse elements of their encoding and thereby evolve toward greater complexity. Automated design of robots through synthetic evolutionary processes has already been demonstrated, but it is not clear whether genetically inspired search algorithms can yield designs that are sufficiently complex for practical engineering. The ultimate success of such algorithms as tools for automation of design depends on the scaling properties of representations of designs. A nongenerative representation (one in which each element of the encoded design is used at most once in translating to the design) scales linearly with the number of elements. Search algorithms that use nongenerative representations quickly become intractable (search times vary approximately exponentially with numbers of design elements), and thus are not amenable to scaling to complex designs. Generative representations are compact representations and were devised as means to circumvent the above-mentioned fundamental restriction on scalability. In the present method, a robot is defined by a compact programmatic form (its generative representation) and the evolutionary variation takes place on this form. The evolutionary process is an iterative one, wherein each cycle consists of the following steps: 1. Generative representations are generated in an evolutionary subprocess. 2. Each generative representation is a program that, when compiled, produces an assembly procedure. 3. In a computational simulation, a constructor executes an assembly procedure to generate a robot. 4. A physical-simulation program tests the performance of a simulated constructed robot, evaluating the performance

  8. Automated Induction Thermography of Generator Components

    Science.gov (United States)

    Goldammer, M.; Mooshofer, H.; Rothenfusser, M.; Bass, J.; Vrana, J.

    2010-02-01

    Using Active Thermography defects such as cracks can be detected fast and reliably. Choosing from a wide range of excitation techniques the method can be adapted to a number of tasks in non-destructive evaluation. Induction thermography is ideally suited for testing metallic components for cracks at or close to the surface. In power generation a number of components are subjected to high loads and stresses—therefore defect detection is crucial for a safe operation of the engines. Apart from combustion turbines this also applies to generators: At regular inspection intervals even small cracks have to be detected to avoid crack growth and consequently failure of the component. As an imaging technique thermography allows for a fast 100% testing of the complete surface of all relevant parts. An automated setup increases the cost effectiveness of induction thermography significantly. Time needed to test a single part is reduced, the number of tested parts per shift is increased, and cost for testing is reduced significantly. In addition, automation guarantees a reliable testing procedure which detects all critical defects. We present how non-destructive testing can be automated using as an example an industrial application at the Siemens sector Energy, and a new induction thermography setup for generator components.

  9. Thrombin generation, ProC(®)Global, prothrombin time and activated partial thromboplastin time in thawed plasma stored for seven days and after methylene blue/light pathogen inactivation.

    Science.gov (United States)

    Thiele, Thomas; Hron, Gregor; Kellner, Sarah; Wasner, Christina; Westphal, Antje; Warkentin, Theodore E; Greinacher, Andreas; Selleng, Kathleen

    2016-01-01

    Methylene blue pathogen inactivation and storage of thawed plasma both lead to changes in the activity of several clotting factors. We investigated how this translates into a global loss of thrombin generation potential and alterations in the protein C pathway. Fifty apheresis plasma samples were thawed and each divided into three subunits. One subunit was stored for 7 days at 4 °C, one was stored for 7 days at 22 °C and one was stored at 4 °C after methylene blue/light treatment. Thrombin generation parameters, ProC(®)Global-NR, prothrombin time and activated partial thromboplastin time were assessed on days 0 and 7. The velocity of thrombin generation increased significantly after methylene blue treatment (increased thrombin generation rate; time to peak decreased) and decreased after storage (decreased thrombin generation rate and peak thrombin; increased lag time and time to peak). The endogenous thrombin generation potential remained stable after methylene blue treatment and storage at 4 °C. Methylene blue treatment and 7 days of storage at 4 °C activated the protein C pathway, whereas storage at room temperature and storage after methylene blue treatment decreased the functional capacity of the protein C pathway. Prothrombin time and activated partial thromboplastin time showed only modest alterations. The global clotting capacity of thawed plasma is maintained at 4 °C for 7 days and directly after methylene blue treatment of thawed plasma. Thrombin generation and ProC(®)Global are useful tools for investigating the impact of pathogen inactivation and storage on the clotting capacity of therapeutic plasma preparations.

  10. 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.

  11. Automated speech understanding: the next generation

    Science.gov (United States)

    Picone, J.; Ebel, W. J.; Deshmukh, N.

    1995-04-01

    Modern speech understanding systems merge interdisciplinary technologies from Signal Processing, Pattern Recognition, Natural Language, and Linguistics into a unified statistical framework. These systems, which have applications in a wide range of signal processing problems, represent a revolution in Digital Signal Processing (DSP). Once a field dominated by vector-oriented processors and linear algebra-based mathematics, the current generation of DSP-based systems rely on sophisticated statistical models implemented using a complex software paradigm. Such systems are now capable of understanding continuous speech input for vocabularies of several thousand words in operational environments. The current generation of deployed systems, based on small vocabularies of isolated words, will soon be replaced by a new technology offering natural language access to vast information resources such as the Internet, and provide completely automated voice interfaces for mundane tasks such as travel planning and directory assistance.

  12. 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

  13. 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......: 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...

  14. A Fully Automated Mesh Generation Tool, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase I project proposes to develop a fully automated mesh generation tool which contains two parts: surface mesh generation from the imported Computer...

  15. 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

  16. Inhibition of Cellular Adhesion by Immunological Targeting of Osteopontin Neoepitopes Generated through Matrix Metalloproteinase and Thrombin Cleavage.

    Science.gov (United States)

    Jürets, Alexander; Le Bras, Marie; Staffler, Günther; Stein, Gesine; Leitner, Lukas; Neuhofer, Angelika; Tardelli, Matteo; Turkof, Edvin; Zeyda, Maximilian; Stulnig, Thomas M

    2016-01-01

    Osteopontin (OPN), a secreted protein involved in inflammatory processes and cancer, induces cell adhesion, migration, and activation of inflammatory pathways in various cell types. Cells bind OPN via integrins at a canonical RGD region in the full length form as well as to a contiguous cryptic site that some have shown is unmasked upon thrombin or matrix metalloproteinase cleavage. Thus, the adhesive capacity of osteopontin is enhanced by proteolytic cleavage that may occur in inflammatory conditions such as obesity, atherosclerosis, rheumatoid arthritis, tumor growth and metastasis. Our aim was to inhibit cellular adhesion to recombinant truncated proteins that correspond to the N-terminal cleavage products of thrombin- or matrix metalloproteinase-cleaved OPN in vitro. We specifically targeted the cryptic integrin binding site with monoclonal antibodies and antisera induced by peptide immunization of mice. HEK 293 cells adhered markedly stronger to truncated OPN proteins than to full length OPN. Without affecting cell binding to the full length form, the raised monoclonal antibodies specifically impeded cellular adhesion to the OPN fragments. Moreover, we show that the peptides used for immunization were able to induce antisera, which impeded adhesion either to all OPN forms, including the full-length form, or selectively to the corresponding truncated recombinant proteins. In conclusion, we developed immunological tools to selectively target functional properties of protease-cleaved OPN forms, which could find applications in treatment and prevention of various inflammatory diseases and cancers.

  17. Automated test data generation for branch testing using incremental ...

    Indian Academy of Sciences (India)

    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 ...

  18. Four-factor prothrombin complex concentrate improves thrombin generation and prothrombin time in patients with bleeding complications related to rivaroxaban: a single-center pilot trial.

    Science.gov (United States)

    Schenk, Bettina; Goerke, Stephanie; Beer, Ronny; Helbok, Raimund; Fries, Dietmar; Bachler, Mirjam

    2018-01-01

    Direct oral anticoagulants (DOACs) pose a great challenge for physicians in life-threatening bleeding events. The aim of this study was to test the efficacy of reversing the DOAC rivaroxaban using four-factor PCC (prothrombin complex concentrate), a non-specific reversing agent. Patients with life-threatening bleeding events during rivaroxaban treatment were included and administered 25 U kg -1 of PCC. Blood samples were collected immediately prior to as well as after PCC treatment at predefined time intervals. The primary endpoint was defined as the difference in thrombin generation (TG) parameters ETP (endogenous thrombin potential) and C max (peak thrombin generation) prior to and ten minutes subsequent to PCC treatment. Thirteen patients, of whom the majority suffered from intra-cranial haemorrhage (ICH) or subdural haemorrhage (SDH), were included and administered PCC. The results show that the ETP (TG) significantly ( p  = 0.001) improved by 68% and C max (TG) by 54% (p = 0.001) during PCC treatment. In addition, the Quick value (prothrombin time: Quick PT ) significantly improved by 28% and the activated partial thromboplastin time (aPTT) was decreased by 7% ten minutes after PCC administration. C max was reduced at baseline, but not ETP, aPTT or Quick PT . Lag time until initiation (TG, t lag ), thromboelastometry clotting time (CT EXTEM ) and time to peak (TG, t max ) correlated best with measured rivaroxaban levels and were out of normal ranges at baseline, but did not improve after PCC administration. In 77% of the patients bleeding (ICH/SDH-progression) ceased following PCC administration. During the study three participants passed away due to other complications not related to PCC treatment. The possibility of thrombosis formation was also evaluated seven days after administering PCC and no thromboses were found. This study shows that use of PCC improved ETP, C max, Quick PT and aPTT. However, of these parameters, only C max was reduced at the

  19. Unfavorably Altered Fibrin Clot Properties in Patients with Eosinophilic Granulomatosis with Polyangiitis (Churg-Strauss Syndrome): Association with Thrombin Generation and Eosinophilia

    Science.gov (United States)

    Mastalerz, Lucyna; Celińska-Lӧwenhoff, Magdalena; Krawiec, Piotr; Batko, Bogdan; Tłustochowicz, Witold; Undas, Anetta

    2015-01-01

    Objectives Given reports on the increased prevalence of thromboembolic incidents in patients with eosinophilic granulomatosis with polyangiitis (EGPA; Churg-Strauss syndrome), we investigated whether fibrin clot properties are unfavorably altered in EGPA. Methods Ex vivo plasma fibrin clot characteristics, including clot permeability, turbidimetry and efficiency of fibrinolysis using two assays, were investigated in 34 consecutive patients with remission in EGPA according to the Birmingham Vasculitis Activity Score version 3 (23 female, 11 male), aged 48 (range, 21–80) years. The control group comprised 34 age- and sex- matched volunteers. Results Compared with controls, patients with EGPA were characterized by denser fiber clots (estimated pore size, Ks, 7.30±0.93 vs 10.14±1.07 10−9 cm2), faster fibrin polymerization (lag phase in a turbidimetric curve, 41.8±3.6 vs 47.4±2.9 s), thicker fibrin fibers (maximum absorbance, ΔAbs, 0.87±0.09 vs 0.72±0.07), higher maximum levels of D-dimer released from clots (DDmax 4.10±0.46 vs 3.54±0.35 mg/L), and prolonged clot lysis time (t50%; 9.50±1.45 vs 7.56±0.87 min); all p<0.0001. Scanning electron microscopy images confirmed denser plasma fibrin networks composed of thinner fibers formed in EGPA. Antineutrophil cytoplasmic antibody status and C-reactive protein did not affect clot variables. Multivariate analysis adjusted for fibrinogen showed that Ks was predicted by eosinophil count, peak thrombin generation, factor VIII, and soluble CD40 ligand, whereas eosinophil count, peak thrombin generation and antiplasmin predicted t50%. Conclusion This study is the first to show that EGPA is associated with prothrombotic plasma fibrin clot phenotype, which may contribute to thromboembolic manifestations reported in this disease. PMID:26540111

  20. Unfavorably Altered Fibrin Clot Properties in Patients with Eosinophilic Granulomatosis with Polyangiitis (Churg-Strauss Syndrome: Association with Thrombin Generation and Eosinophilia.

    Directory of Open Access Journals (Sweden)

    Lucyna Mastalerz

    Full Text Available Given reports on the increased prevalence of thromboembolic incidents in patients with eosinophilic granulomatosis with polyangiitis (EGPA; Churg-Strauss syndrome, we investigated whether fibrin clot properties are unfavorably altered in EGPA.Ex vivo plasma fibrin clot characteristics, including clot permeability, turbidimetry and efficiency of fibrinolysis using two assays, were investigated in 34 consecutive patients with remission in EGPA according to the Birmingham Vasculitis Activity Score version 3 (23 female, 11 male, aged 48 (range, 21-80 years. The control group comprised 34 age- and sex- matched volunteers.Compared with controls, patients with EGPA were characterized by denser fiber clots (estimated pore size, Ks, 7.30±0.93 vs 10.14±1.07 10-9 cm2, faster fibrin polymerization (lag phase in a turbidimetric curve, 41.8±3.6 vs 47.4±2.9 s, thicker fibrin fibers (maximum absorbance, ΔAbs, 0.87±0.09 vs 0.72±0.07, higher maximum levels of D-dimer released from clots (DDmax 4.10±0.46 vs 3.54±0.35 mg/L, and prolonged clot lysis time (t50%; 9.50±1.45 vs 7.56±0.87 min; all p<0.0001. Scanning electron microscopy images confirmed denser plasma fibrin networks composed of thinner fibers formed in EGPA. Antineutrophil cytoplasmic antibody status and C-reactive protein did not affect clot variables. Multivariate analysis adjusted for fibrinogen showed that Ks was predicted by eosinophil count, peak thrombin generation, factor VIII, and soluble CD40 ligand, whereas eosinophil count, peak thrombin generation and antiplasmin predicted t50%.This study is the first to show that EGPA is associated with prothrombotic plasma fibrin clot phenotype, which may contribute to thromboembolic manifestations reported in this disease.

  1. 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.

  2. Automation scope at Roxboro generating station

    International Nuclear Information System (INIS)

    Ipakchi, A.; Chrisler, G.; Damesek, S.; Fields, E.W.; Cook, B.C.; Divakaruni, M.

    1991-01-01

    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

  3. 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.

  4. Aggregation of thrombin-derived C-terminal fragments as a previously undisclosed host defense mechanism

    DEFF Research Database (Denmark)

    Petrlova, Jitka; Hansen, Finja C; van der Plas, Mariena J A

    2017-01-01

    Effective control of endotoxins and bacteria is crucial for normal wound healing. During injury, the key enzyme thrombin is formed, leading to generation of fibrin. Here, we show that human neutrophil elastase cleaves thrombin, generating 11-kDa thrombin-derived C-terminal peptides (TCPs), which ...

  5. Automated Testing with Targeted Event Sequence Generation

    DEFF Research Database (Denmark)

    Jensen, Casper Svenning; Prasad, Mukul R.; Møller, Anders

    2013-01-01

    Automated software testing aims to detect errors by producing test inputs that cover as much of the application source code as possible. Applications for mobile devices are typically event-driven, which raises the challenge of automatically producing event sequences that result in high coverage....... Some existing approaches use random or model-based testing that largely treats the application as a black box. Other approaches use symbolic execution, either starting from the entry points of the applications or on specific event sequences. A common limitation of the existing approaches...... is that they often fail to reach the parts of the application code that require more complex event sequences. We propose a two-phase technique for automatically finding event sequences that reach a given target line in the application code. The first phase performs concolic execution to build summaries...

  6. Cerebellum engages in automation of verb-generation skill.

    Science.gov (United States)

    Yang, Zhi; Wu, Paula; Weng, Xuchu; Bandettini, Peter A

    2014-03-01

    Numerous studies have shown cerebellar involvement in item-specific association, a form of explicit learning. However, very few have demonstrated cerebellar participation in automation of non-motor cognitive tasks. Applying fMRI to a repeated verb-generation task, we sought to distinguish cerebellar involvement in learning of item-specific noun-verb association and automation of verb generation skill. The same set of nouns was repeated in six verb-generation blocks so that subjects practiced generating verbs for the nouns. The practice was followed by a novel block with a different set of nouns. The cerebellar vermis (IV/V) and the right cerebellar lobule VI showed decreased activation following practice; activation in the right cerebellar Crus I was significantly lower in the novel challenge than in the initial verb-generation task. Furthermore, activation in this region during well-practiced blocks strongly correlated with improvement of behavioral performance in both the well-practiced and the novel blocks, suggesting its role in the learning of general mental skills not specific to the practiced noun-verb pairs. Therefore, the cerebellum processes both explicit verbal associative learning and automation of cognitive tasks. Different cerebellar regions predominate in this processing: lobule VI during the acquisition of item-specific association, and Crus I during automation of verb-generation skills through practice.

  7. Next generation fluidized bed granulator automation.

    Science.gov (United States)

    Rantanen, J; Känsäkoski, M; Suhonen, J; Tenhunen, J; Lehtonen, S; Rajalahti, T; Mannermaa, J P; Yliruusi, J

    2000-05-06

    A system for fluidized bed granulator automation with in-line multichannel near infrared (NIR) moisture measurement and a unique air flow rate measurement design was assembled, and the information gained was investigated. The multivariate process data collected was analyzed using principal component analysis (PCA). The test materials (theophylline and microcrystalline cellulose) were granulated and the calibration behavior of the multichannel NIR set-up was evaluated against full Fourier Transform (FT) NIR spectra. Accurate and reliable process air flow rate measurement proved critical in controlling the granulation process. The process data describing the state of the process was projected in two dimensions, and the information from various trend charts was outlined simultaneously. The absorbence of test material at correction wavelengths (NIR region) and the nature of material-water interactions affected the detected in-line NIR water signal. This resulted in different calibration models for the test materials. Development of process analytical methods together with new data visualization algorithms creates new tools for in-process control of the fluidized bed granulation.

  8. Automated mass spectrum generation for new physics

    CERN Document Server

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

    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.

  9. Automated test data generation for branch testing using incremental ...

    Indian Academy of Sciences (India)

    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 ... The experimental results indicate that the proposed IGA search technique outperforms the other meta-heuristic search techniques in terms of memory usage and scalability.

  10. Superficial vein thrombosis, thrombin generation and activated protein C resistance as predictors of thromboembolic events in lupus and antiphospholipid patients. A prospective cohort study.

    Science.gov (United States)

    Zuily, Stéphane; Regnault, Véronique; Guillemin, Francis; Kaminsky, Pierre; Rat, Anne-Christine; Lecompte, Thomas; Wahl, Denis

    2013-07-01

    Predicting thrombosis in patients with systemic lupus erythematosus (SLE) and/or antiphospholipid antibodies (aPL) is still challenging. Our objective was to determine risk factors for thrombotic events including activated protein C (APC) resistance proven by a thrombin generation (TG) assay in patients with SLE and/or aPL. We performed a prospective cohort study in a French University Hospital and tertiary care center. Ninety-two consecutive patients with SLE and/or aPL without ongoing anticoagulant treatment were enrolled. The outcome was time to thrombotic event. We evaluated clinical and laboratory variables including APC sensitivity ratio (APCsr) determined by TG. An APCsr>90th percentile of a control population indicated APC resistance. Patients were followed-up for a median duration of 35 months (inter-quartile range: 26 to 62; 320 patient-years). Thrombosis during follow-up occurred in 18 patients. In univariate analysis, together with history of hypertension, superficial vein thrombosis (SVT) and arterial thrombosis, patients with both aPL and APC resistance had an increased risk for incident thromboembolic events (HR, 3.67 [95% confidence interval, 1.31 to 10.31]). In multivariate analysis, only history of hypertension (HR, 10.77 [95% confidence interval, 3.15 to 36.83]), SVT (HR, 7.45 [95% confidence interval, 2.25 to 24.66]) and arterial thrombosis (HR, 3.31 [95% confidence interval, 1.14 to 9.55]) remained independent risk factors. History of thrombosis including seemingly benign SVT have a higher predictive value for incident thrombotic events in SLE or aPL patients than APC resistance proven by TG. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. JWST Associations overview: automated generation of combined products

    Science.gov (United States)

    Alexov, Anastasia; Swade, Daryl; Bushouse, Howard; Diaz, Rosa; Eisenhamer, Jonathan; Hack, Warren; Kyprianou, Mark; Levay, Karen; Rahmani, Christopher; Swam, Mike; Valenti, Jeff

    2018-01-01

    We are presenting the design of the James Webb Space Telescope (JWST) Data Management System (DMS) automated processing of Associations. An Association captures the relationship between exposures and higher level data products, such as combined mosaics created from dithered and tiled observations. The astronomer’s intent is captured within the Proposal Planning System (PPS) and provided to DMS as candidate associations. These candidates are converted into Association Pools and Association Generator Tables that serve as input to automated processing which create the combined data products. Association Pools are generated to capture a list of exposures that could potentially form associations and provide relevant information about those exposures. The Association Generator using definitions on groupings creates one or more Association Tables from a single input Association Pool. Each Association Table defines a set of exposures to be combined and the ruleset of the combination to be performed; the calibration software creates Associated data products based on these input tables. The initial design produces automated Associations within a proposal. Additionally this JWST overall design is conducive to eventually produce Associations for observations from multiple proposals, similar to the Hubble Legacy Archive (HLA).

  12. Automation of steam generator services at public service electric & gas

    Energy Technology Data Exchange (ETDEWEB)

    Cruickshank, H.; Wray, J.; Scull, D. [Public Service Electric & Gas, Hancock`s Bridge, NJ (United States)

    1995-03-01

    Public Service Electric & Gas takes an aggressive approach to pursuing new exposure reduction techniques. Evaluation of historic outage exposure shows that over the last eight refueling outages, primary steam generator work has averaged sixty-six (66) person-rem, or, approximately tewenty-five percent (25%) of the general outage exposure at Salem Station. This maintenance evolution represents the largest percentage of exposure for any single activity. Because of this, primary steam generator work represents an excellent opportunity for the development of significant exposure reduction techniques. A study of primary steam generator maintenance activities demonstrated that seventy-five percent (75%) of radiation exposure was due to work activities of the primary steam generator platform, and that development of automated methods for performing these activities was worth pursuing. Existing robotics systems were examined and it was found that a new approach would have to be developed. This resulted in a joint research and development project between Westinghouse and Public Service Electric & Gas to develop an automated system of accomplishing the Health Physics functions on the primary steam generator platform. R.O.M.M.R.S. (Remotely Operated Managed Maintenance Robotics System) was the result of this venture.

  13. Recent developments in topical thrombins.

    Science.gov (United States)

    Kessler, Craig M; Ortel, Thomas L

    2009-07-01

    Managing blood loss is part of the surgeon's responsibility during surgical procedures, and a variety of therapeutic strategies are available to help accomplish this. Topical haemostatic agents are among the agents used to control surgical bleeding and locally arrest blood flow. Bovine thrombin is a commonly used topical haemostatic agent; however, its use has been associated with potential risks, including well-documented cases of antibody-mediated coagulopathy. This coagulopathy develops as a consequence of antibody formation directed against bovine thrombin, other bovine coagulation proteins, and their human orthologs. The fact that a coagulopathy can result in association with the use of bovine plasma-derived thrombin preparations prompted the FDA to require pharmaceutical companies to place a black-box warning in their prescribing information for products containing bovine plasma-derived thrombin. Recently, human plasma-derived thrombin and recombinant human thrombin have been approved by the FDA with the expectation that they will be less immunogenic than the bovine-derived product. In clinical studies, purified human plasma-derived thrombin and recombinant thrombin have demonstrated equivalent efficacy and safety, with improved immunogenicity profiles compared with bovine-derived thrombin agents. Well-designed and adequately powered clinical trials should be conducted to indicate whether human thrombin products would improve the risk-benefit and cost-benefit profiles for surgeries complicated by excessive bleeding.

  14. A Recommendation Algorithm for Automating Corollary Order Generation

    Science.gov (United States)

    Klann, Jeffrey; Schadow, Gunther; McCoy, JM

    2009-01-01

    Manual development and maintenance of decision support content is time-consuming and expensive. We explore recommendation algorithms, e-commerce data-mining tools that use collective order history to suggest purchases, to assist with this. In particular, previous work shows corollary order suggestions are amenable to automated data-mining techniques. Here, an item-based collaborative filtering algorithm augmented with association rule interestingness measures mined suggestions from 866,445 orders made in an inpatient hospital in 2007, generating 584 potential corollary orders. Our expert physician panel evaluated the top 92 and agreed 75.3% were clinically meaningful. Also, at least one felt 47.9% would be directly relevant in guideline development. This automated generation of a rough-cut of corollary orders confirms prior indications about automated tools in building decision support content. It is an important step toward computerized augmentation to decision support development, which could increase development efficiency and content quality while automatically capturing local standards. PMID:20351875

  15. Generative Representations for Computer-Automated Evolutionary Design

    Science.gov (United States)

    Hornby, Gregory S.

    2006-01-01

    With the increasing computational power of computers, software design systems are progressing from being tools for architects and designers to express their ideas to tools capable of creating designs under human guidance. One of the main limitations for these computer-automated design systems is the representation with which they encode designs. If the representation cannot encode a certain design, then the design system cannot produce it. To be able to produce new types of designs, and not just optimize pre-defined parameterizations, evolutionary design systems must use generative representations. Generative representations are assembly procedures, or algorithms, for constructing a design thereby allowing for truly novel design solutions to be encoded. In addition, by enabling modularity, regularity and hierarchy, the level of sophistication that can be evolved is increased. We demonstrate the advantages of generative representations on two different design domains: the evolution of spacecraft antennas and the evolution of 3D objects.

  16. Generative Representations for Computer-Automated Design Systems

    Science.gov (United States)

    Hornby, Gregory S.

    2004-01-01

    With the increasing computational power of Computers, software design systems are progressing from being tools for architects and designers to express their ideas to tools capable of creating designs under human guidance. One of the main limitations for these computer-automated design programs is the representation with which they encode designs. If the representation cannot encode a certain design, then the design program cannot produce it. Similarly, a poor representation makes some types of designs extremely unlikely to be created. Here we define generative representations as those representations which can create and reuse organizational units within a design and argue that reuse is necessary for design systems to scale to more complex and interesting designs. To support our argument we describe GENRE, an evolutionary design program that uses both a generative and a non-generative representation, and compare the results of evolving designs with both types of representations.

  17. Automated generation of burnup chain for reactor analysis applications

    International Nuclear Information System (INIS)

    Tran, Viet-Phu; Tran, Hoai-Nam; Yamamoto, Akio; Endo, Tomohiro

    2017-01-01

    This paper presents the development of an automated generation of burnup chain for reactor analysis applications. Algorithms are proposed to reevaluate decay modes, branching ratios and effective fission product (FP) cumulative yields of a given list of important FPs taking into account intermediate reactions. A new burnup chain is generated using the updated data sources taken from the JENDL FP decay data file 2011 and Fission yields data file 2011. The new burnup chain is output according to the format for the SRAC code system. Verification has been 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. Burnup calculations using the new burnup chain have also been performed based on UO 2 and MOX fuel pin cells and compared with a reference chain th2cm6fp193bp6T.

  18. Synergy between thrombin and serotonin in inducing vascular smooth muscle cell proliferation.

    Science.gov (United States)

    Pakala, R; Benedict, C

    1999-12-01

    Previous studies have indicated that apart from playing an important role in hemostasis and thrombosis, thrombin may also contribute to the development of postangioplasty restenosis caused by the stimulation of vascular smooth muscle cell (VSMC) proliferation. Because thrombin generation in vivo is accompanied by platelet activation and release of smooth muscle cell (SMC) growth factors such as serotonin, we examined the possible interaction between these two compounds on VSMC proliferation. Thrombin (0.01 to 100 nmol/L), thrombin receptor-activating peptide (0.1 to 1000 micromol/L), and serotonin (5HT; 0.1 to 1000 micromol/L) increased tritiated thymidine incorporation into the DNA of canine aortic VSMCs in a dose-dependent manner. When thrombin and 5HT were added together at sub-threshold concentrations, they acted synergistically in inducing tritiated thymidine incorporation. These findings were paralleled by a 90%+/-5% increase in the cell number at 48 hours, as compared with a 37%+/-2% increase with 50 micromol/L serotonin and a 13%+/-3% increase with 0.1 nmol/L thrombin. We also demonstrated that a brief exposure to thrombin (1 hour) is sufficient to show its potentiating effect on serotonin. The mitogenic effect of serotonin and its synergistic interaction with thrombin on VSMC proliferation was abolished by serotonin type 2 receptor antagonist LY281067. Similarly, gamma-hirudin--a direct thrombin inhibitor--blocked the mitogenic effect of thrombin and its synergistic interaction with serotonin. When LY281067 and gamma-hirudin were used together, they abolished the mitogenic effects of both the agonists. Because clot-bound active thrombin can escape inactivation by anti-thrombin, this thrombin may potentiate the mitogenic effect of serotonin and keep the SMCs in a proliferative state for a long period of time. These findings support the use of 5HT2 receptor antagonists in combination with thrombin inhibitors in the prevention of SMC proliferation after

  19. Loft: An Automated Mesh Generator for Stiffened Shell Aerospace Vehicles

    Science.gov (United States)

    Eldred, Lloyd B.

    2011-01-01

    Loft is an automated mesh generation code that is designed for aerospace vehicle structures. From user input, Loft generates meshes for wings, noses, tanks, fuselage sections, thrust structures, and so on. As a mesh is generated, each element is assigned properties to mark the part of the vehicle with which it is associated. This property assignment is an extremely powerful feature that enables detailed analysis tasks, such as load application and structural sizing. This report is presented in two parts. The first part is an overview of the code and its applications. The modeling approach that was used to create the finite element meshes is described. Several applications of the code are demonstrated, including a Next Generation Launch Technology (NGLT) wing-sizing study, a lunar lander stage study, a launch vehicle shroud shape study, and a two-stage-to-orbit (TSTO) orbiter. Part two of the report is the program user manual. The manual includes in-depth tutorials and a complete command reference.

  20. Automating Initial Guess Generation for High Fidelity Trajectory Optimization Tools

    Science.gov (United States)

    Villa, Benjamin; Lantoine, Gregory; Sims, Jon; Whiffen, Gregory

    2013-01-01

    Many academic studies in spaceflight dynamics rely on simplified dynamical models, such as restricted three-body models or averaged forms of the equations of motion of an orbiter. In practice, the end result of these preliminary orbit studies needs to be transformed into more realistic models, in particular to generate good initial guesses for high-fidelity trajectory optimization tools like Mystic. This paper reviews and extends some of the approaches used in the literature to perform such a task, and explores the inherent trade-offs of such a transformation with a view toward automating it for the case of ballistic arcs. Sample test cases in the libration point regimes and small body orbiter transfers are presented.

  1. Automating the Generation of Heterogeneous Aviation Safety Cases

    Science.gov (United States)

    Denney, Ewen W.; Pai, Ganesh J.; Pohl, Josef M.

    2012-01-01

    A safety case is a structured argument, supported by a body of evidence, which provides a convincing and valid justification that a system is acceptably safe for a given application in a given operating environment. This report describes the development of a fragment of a preliminary safety case for the Swift Unmanned Aircraft System. The construction of the safety case fragment consists of two parts: a manually constructed system-level case, and an automatically constructed lower-level case, generated from formal proof of safety-relevant correctness properties. We provide a detailed discussion of the safety considerations for the target system, emphasizing the heterogeneity of sources of safety-relevant information, and use a hazard analysis to derive safety requirements, including formal requirements. We evaluate the safety case using three classes of metrics for measuring degrees of coverage, automation, and understandability. We then present our preliminary conclusions and make suggestions for future work.

  2. Automated robust generation of compact 3D statistical shape models

    Science.gov (United States)

    Vrtovec, Tomaz; Likar, Bostjan; Tomazevic, Dejan; Pernus, Franjo

    2004-05-01

    Ascertaining the detailed shape and spatial arrangement of anatomical structures is important not only within diagnostic settings but also in the areas of planning, simulation, intraoperative navigation, and tracking of pathology. Robust, accurate and efficient automated segmentation of anatomical structures is difficult because of their complexity and inter-patient variability. Furthermore, the position of the patient during image acquisition, the imaging device and protocol, image resolution, and other factors induce additional variations in shape and appearance. Statistical shape models (SSMs) have proven quite successful in capturing structural variability. A possible approach to obtain a 3D SSM is to extract reference voxels by precisely segmenting the structure in one, reference image. The corresponding voxels in other images are determined by registering the reference image to each other image. The SSM obtained in this way describes statistically plausible shape variations over the given population as well as variations due to imperfect registration. In this paper, we present a completely automated method that significantly reduces shape variations induced by imperfect registration, thus allowing a more accurate description of variations. At each iteration, the derived SSM is used for coarse registration, which is further improved by describing finer variations of the structure. The method was tested on 64 lumbar spinal column CT scans, from which 23, 38, 45, 46 and 42 volumes of interest containing vertebra L1, L2, L3, L4 and L5, respectively, were extracted. Separate SSMs were generated for each vertebra. The results show that the method is capable of reducing the variations induced by registration errors.

  3. Automated Generation of Web Services for Visualization Toolkits

    Science.gov (United States)

    Jensen, P. A.; Yuen, D. A.; Erlebacher, G.; Bollig, E. F.; Kigelman, D. G.; Shukh, E. A.

    2005-12-01

    The recent explosion in the size and complexity of geophysical data and an increasing trend for collaboration across large geographical areas demand the use of remote, full featured visualization toolkits. As the scientific community shifts toward grid computing to handle these increased demands, new web services are needed to assemble powerful distributed applications. Recent research has established the possibility of converting toolkits such as VTK [1] and Matlab [2] into remote visualization services. We are investigating an automated system to allow these toolkits to export their functions as web services under the standardized protocols SOAP and WSDL using pre-existing software (gSOAP [3]) and a custom compiler for Tcl-based scripts. The compiler uses a flexible parser and type inferring mechanism to convert the Tcl into a C++ program that allows the desired Tcl procedures to be exported as SOAP-accessible functions and the VTK rendering window to be captured offscreen and encapsulated for forwarding through a web service. Classes for a client-side Java applet to access the rendering window remotely are also generated. We will use this system to demonstrate the streamlined generation of a standards-compliant web service (suitable for grid deployment) from a Tcl script for VTK. References: [1] The Visualization Toolkit, http://www.vtk.org [2] Matlab, http://www.mathworks.com [3] gSOAP, http://www.cs.fsu.edu/~engelen/soap.html

  4. 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

  5. Methodical Approaches to Creation of Dividing Automation at Industrial Enterprises with Generating Power Plants

    Directory of Open Access Journals (Sweden)

    E. V. Kalentionok

    2010-01-01

    Full Text Available The paper considers a problem pertaining to creation of dividing automation at industrial enterprises which have their own generating plants. Algorithms for action of dividing automation that permit to ensure minimum possible power non-balance while using generating plants for autonomous operation and possible parameters for its response are proposed in the paper.

  6. 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

  7. Performance Impact of Connectivity Restrictions and Increased Vulnerability Presence on Automated Attack Graph Generation

    National Research Council Canada - National Science Library

    Cullum, James; Irvine, Cynthia; Levin, Tim

    2007-01-01

    .... Although research has shown the effectiveness of automated attack graph generation tools in displaying potential attack paths in a network, research involving the performance of these tools has been limited...

  8. AutoDipole - Automated generation of dipole subtraction terms -

    Science.gov (United States)

    Hasegawa, K.; Moch, S.; Uwer, P.

    2010-10-01

    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 both massless 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. Program summaryProgram title: AutoDipole Catalogue identifier: AEGO_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGO_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 138 042 No. of bytes in distributed program, including test data, etc.: 1 117 665 Distribution format: tar.gz Programming language: Mathematica and Fortran Computer: Computers running Mathematica (version 7.0) Operating system: The package should work on every Linux system supported by Mathematica. Detailed tests have been performed on Scientific Linux as supported by DESY and CERN and on openSUSE and Debian. RAM: Depending on the complexity of the problem, recommended at least 128 MB RAM Classification: 11.5 External routines: MadGraph (including HELAS library) available under http://madgraph.hep.uiuc.edu/ or http://madgraph.phys.ucl.ac.be/ or http://madgraph.roma2.infn.it/. A copy of the tar file, MG_ME_SA_V4.4.30, is included in the AutoDipole distribution package. Nature of problem: Computation of next-to-leading order QCD corrections to scattering cross sections, regularization of real emission contributions. Solution method: Catani-Seymour subtraction method for massless and massive partons [1,2]; Numerical evaluation of subtracted matrix elements interfaced to MadGraph [3-5] (stand-alone version) using

  9. A fast, automated, semideterministic weight windows generator for MCNP

    International Nuclear Information System (INIS)

    Mickael, M.W.

    1995-01-01

    A fast automated method is developed to estimate particle importance in the Los Alamos Carlo code MCNP. It provides an automated and efficient way of predicting and setting up an important map for the weight windows technique. A short analog simulation is first performed to obtain effective group parameters based on the input description of the problem. A solution of the multigroup time-dependent adjoint diffusion equation is then used to estimate particle importance. At any point in space, time, and energy, the particle importance is determined, based on the calculated parameters, and used as the lower limit of the weight window. The method has been tested for neutron, photon, and coupled neutron-photon problems. Significant improvement in the simulation efficiency is obtained using this technique at no additional computer time and with no prior knowledge of the nature of the problem. Moreover, time and angular importance that are not available yet in MCNP are easily implemented in this method

  10. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Activation of human factor V by factor Xa and thrombin

    International Nuclear Information System (INIS)

    Monkovic, D.D.; Tracy, P.B.

    1990-01-01

    The activation of human factor V by factor Xa and thrombin was studied by functional assessment of cofactor activity and sodium dodecyl sulfate-polycarylamide gel electrophoresis followed by either autoradiography of 125 I-labeled factor V activation products or Western blot analyses of unlabeled factor V activation products. Cofactor activity was measured by the ability of the factor V/Va peptides to support the activation of prothrombin. The factor Xa catalyzed cleavage of factor V was observed to be time, phospholipid, and calcium ion dependent, yielding a cofactor with activity equal to that of thrombin-activated factor V (factor Va). The cleavage pattern differed markedly from the one observed in the bovine system. The factor Xa activated factor V subunits expressing cofactor activity were isolated and found to consist of peptides of M r 220,000 and 105,000. Although thrombin cleaved the M r 220,000 peptide to yield peptides previously shown to be products of thrombin activation, cofactor activity did not increase. N-Terminal sequence analysis confirmed that both factor Xa and thrombin cleave factor V at the same bond to generate the M r 220,000 peptide. The factor Xa dependent functional assessment of 125 I-labeled factor V coupled with densitometric analyses of the cleavage products indicated that the cofactor activity of factor Xa activated factor V closely paralleled the appearance of the M r 220,000 peptide. The data indicate that factor Xa is as efficient an enzyme toward factor V as thrombin

  12. Genetic algorithms in teaching artificial intelligence (automated generation of specific algebras)

    Science.gov (United States)

    Habiballa, Hashim; Jendryscik, Radek

    2017-11-01

    The problem of teaching essential Artificial Intelligence (AI) methods is an important task for an educator in the branch of soft-computing. The key focus is often given to proper understanding of the principle of AI methods in two essential points - why we use soft-computing methods at all and how we apply these methods to generate reasonable results in sensible time. We present one interesting problem solved in the non-educational research concerning automated generation of specific algebras in the huge search space. We emphasize above mentioned points as an educational case study of an interesting problem in automated generation of specific algebras.

  13. An Evaluation of Automated Code Generation with the PetriCode Approach

    DEFF Research Database (Denmark)

    Simonsen, Kent Inge

    2014-01-01

    Automated code generation is an important element of model driven development methodologies. We have previously proposed an approach for code generation based on Coloured Petri Net models annotated with textual pragmatics for the network protocol domain. In this paper, we present and evaluate three...

  14. EddyOne automated analysis of PWR/WWER steam generator tubes eddy current data

    International Nuclear Information System (INIS)

    Nadinic, B.; Vanjak, Z.

    2004-01-01

    INETEC Institute for Nuclear Technology developed software package called Eddy One which has option of automated analysis of bobbin coil eddy current data. During its development and on site use, many valuable lessons were learned which are described in this article. In accordance with previous, the following topics are covered: General requirements for automated analysis of bobbin coil eddy current data; Main approaches to automated analysis; Multi rule algorithms for data screening; Landmark detection algorithms as prerequisite for automated analysis (threshold algorithms and algorithms based on neural network principles); Field experience with Eddy One software; Development directions (use of artificial intelligence with self learning abilities for indication detection and sizing); Automated analysis software qualification; Conclusions. Special emphasis is given on results obtained on different types of steam generators, condensers and heat exchangers. Such results are then compared with results obtained by other automated software vendors giving clear advantage to INETEC approach. It has to be pointed out that INETEC field experience was collected also on WWER steam generators what is for now unique experience.(author)

  15. Automated Diagnosis and Classification of Steam Generator Tube Defects

    International Nuclear Information System (INIS)

    Garcia, Gabe V.

    2004-01-01

    A major cause of failure in nuclear steam generators is tube degradation. Tube defects are divided into seven categories, one of which is intergranular attack/stress corrosion cracking (IGA/SCC). Defects of this type usually begin on the outer surface of the tubes and propagate both inward and laterally. In many cases these defects occur at or near the tube support plates. Several different methods exist for the nondestructive evaluation of nuclear steam generator tubes for defect characterization

  16. Automated Diagnosis and Classification of Steam Generator Tube Defects

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Gabe V. Garcia

    2004-10-01

    A major cause of failure in nuclear steam generators is tube degradation. Tube defects are divided into seven categories, one of which is intergranular attack/stress corrosion cracking (IGA/SCC). Defects of this type usually begin on the outer surface of the tubes and propagate both inward and laterally. In many cases these defects occur at or near the tube support plates. Several different methods exist for the nondestructive evaluation of nuclear steam generator tubes for defect characterization.

  17. Towards Next Generation Rubrics: An Automated Assignment Feedback System

    Directory of Open Access Journals (Sweden)

    Nilupulee Nathawitharana

    2017-11-01

    Full Text Available As the use of blended learning environments and digital technologies become integrated into the higher education sector, rich technologies such as analytics have shown promise in facilitating teaching and learning. One popular application of analytics is Automated Writing Evaluation (AWE systems. Such systems can be used in a formative way; for example, by providing students with feedback on digitally submitted assignments. This paper presents work on the development of an AWE software tool for an Australian university using advanced text analytics techniques. The tool was designed to provide students with timely feedback on their initial assignment drafts, for revision and further improvement. Moreover, it could also assist academics in better understanding students’ assignment performance so as to inform future teaching activities. The paper provides details on the methodology used for development of the software, and presents the results obtained from the analysis of text-based assignments submitted in two subjects. The results are discussed, highlighting how the tool can provide practical value, followed by insights into existing challenges and possible future directions.

  18. Automating generation of textual class definitions from OWL to English.

    Science.gov (United States)

    Stevens, Robert; Malone, James; Williams, Sandra; Power, Richard; Third, Allan

    2011-05-17

    Text definitions for entities within bio-ontologies are a cornerstone of the effort to gain a consensus in understanding and usage of those ontologies. Writing these definitions is, however, a considerable effort and there is often a lag between specification of the main part of an ontology (logical descriptions and definitions of entities) and the development of the text-based definitions. The goal of natural language generation (NLG) from ontologies is to take the logical description of entities and generate fluent natural language. The application described here uses NLG to automatically provide text-based definitions from an ontology that has logical descriptions of its entities, so avoiding the bottleneck of authoring these definitions by hand. To produce the descriptions, the program collects all the axioms relating to a given entity, groups them according to common structure, realises each group through an English sentence, and assembles the resulting sentences into a paragraph, to form as 'coherent' a text as possible without human intervention. Sentence generation is accomplished using a generic grammar based on logical patterns in OWL, together with a lexicon for realising atomic entities. We have tested our output for the Experimental Factor Ontology (EFO) using a simple survey strategy to explore the fluency of the generated text and how well it conveys the underlying axiomatisation. Two rounds of survey and improvement show that overall the generated English definitions are found to convey the intended meaning of the axiomatisation in a satisfactory manner. The surveys also suggested that one form of generated English will not be universally liked; that intrusion of too much 'formal ontology' was not liked; and that too much explicit exposure of OWL semantics was also not liked. Our prototype tools can generate reasonable paragraphs of English text that can act as definitions. The definitions were found acceptable by our survey and, as a result, the

  19. UNICOS CPC6: automated code generation for process control applications

    International Nuclear Information System (INIS)

    Fernandez Adiego, B.; Blanco Vinuela, E.; Prieto Barreiro, I.

    2012-01-01

    The Continuous Process Control package (CPC) is one of the components of the CERN Unified Industrial Control System framework (UNICOS). As a part of this framework, UNICOS-CPC provides a well defined library of device types, a methodology and a set of tools to design and implement industrial control applications. The new CPC version uses the software factory UNICOS Application Builder (UAB) to develop CPC applications. The CPC component is composed of several platform oriented plug-ins (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 generator (based on PVSS) and the CPC wizard as a dedicated plug-in created to provide the user a friendly GUI (Graphical User Interface). A tool called UAB Bootstrap will manage the different UAB components, like CPC, and its dependencies with the resource packages. This tool guides the control system developer during the installation, update and execution of the UAB components. (authors)

  20. Generative Representations for the Automated Design of Modular Physical Robots

    Science.gov (United States)

    Hornby, Gregory S.; Lipson, Hod; Pollack, Jordan B.

    2003-01-01

    We will begin with a brief background of evolutionary robotics and related work, and demonstrate the scaling problem with our own prior results. Next we propose the use of an evolved generative representation as opposed to a non-generative representation. We describe this representation in detail as well as the evolutionary process that uses it. We then compare progress of evolved robots with and without the use of the grammar, and quantify the obtained advantage. Working two- dimensional and three-dimensional physical robots produced by the system are shown.

  1. 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 i...

  2. 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...

  3. 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...

  4. Automated generation of partial Markov chain from high level descriptions

    International Nuclear Information System (INIS)

    Brameret, P.-A.; Rauzy, A.; Roussel, J.-M.

    2015-01-01

    We propose an algorithm to generate partial Markov chains from high level implicit descriptions, namely AltaRica models. This algorithm relies on two components. First, a variation on Dijkstra's algorithm to compute shortest paths in a graph. Second, the definition of a notion of distance to select which states must be kept and which can be safely discarded. The proposed method solves two problems at once. First, it avoids a manual construction of Markov chains, which is both tedious and error prone. Second, up the price of acceptable approximations, it makes it possible to push back dramatically the exponential blow-up of the size of the resulting chains. We report experimental results that show the efficiency of the proposed approach. - Highlights: • We generate Markov chains from a higher level safety modeling language (AltaRica). • We use a variation on Dijkstra's algorithm to generate partial Markov chains. • Hence we solve two problems: the first problem is the tedious manual construction of Markov chains. • The second problem is the blow-up of the size of the chains, at the cost of decent approximations. • The experimental results highlight the efficiency of the method

  5. Bim Automation: Advanced Modeling Generative Process for Complex Structures

    Science.gov (United States)

    Banfi, F.; Fai, S.; Brumana, R.

    2017-08-01

    The new paradigm of the complexity of modern and historic structures, which are characterised by complex forms, morphological and typological variables, is one of the greatest challenges for building information modelling (BIM). Generation of complex parametric models needs new scientific knowledge concerning new digital technologies. These elements are helpful to store a vast quantity of information during the life cycle of buildings (LCB). The latest developments of parametric applications do not provide advanced tools, resulting in time-consuming work for the generation of models. This paper presents a method capable of processing and creating complex parametric Building Information Models (BIM) with Non-Uniform to NURBS) with multiple levels of details (Mixed and ReverseLoD) based on accurate 3D photogrammetric and laser scanning surveys. Complex 3D elements are converted into parametric BIM software and finite element applications (BIM to FEA) using specific exchange formats and new modelling tools. The proposed approach has been applied to different case studies: the BIM of modern structure for the courtyard of West Block on Parliament Hill in Ottawa (Ontario) and the BIM of Masegra Castel in Sondrio (Italy), encouraging the dissemination and interaction of scientific results without losing information during the generative process.

  6. Automated generation of compact models for fluidic microsystems

    Science.gov (United States)

    Turowski, Marek; Chen, Zhijian; Przekwas, Andrzej J.

    2000-04-01

    Simulation and design of microfluidic systems requires various level models: high-fidelity models for design and optimization of particular elements and devices as well as system-level models allowing for VLSI-scale simulation of such systems. For the latter purpose, reduced or compact models are necessary to make such system simulations computationally feasible. In this paper, we present a design methodology and practical approach for generation of compact models of microfluidic elements. In this procedure we use high-fidelity 3D simulations of the microfluidic devices to extract their characteristics for compact models, and subsequently, to validate the compact model behavior in various regimes of operation. The compact models are generated automatically in the formats that can be directly used in SPICE or SABER. As an example of a nonlinear fluidic device, the generation of compact model for 'Tesla valve' is described in detail. Tesla valve is one of the no-moving- parts valves used in micropumps in MEMS. Its principle of operation is based on the rectification of the fluid, so it may be considered as a 'fluidic diode'.

  7. Immunoassay of thyroid peroxidase autoantibodies: diagnostic performance in automated third generation methods. A multicentre evaluation.

    Science.gov (United States)

    D'Aurizio, Federica; Tozzoli, Renato; Villalta, Danilo; Pesce, Giampaola; Bagnasco, Marcello

    2015-02-01

    The use of automated immunometric methods for the detection of anti-thyroid peroxidase antibodies (TPOAb), the main serological marker of autoimmune thyroid diseases (AITD), has expanded in recent years. However, it is not known whether these new automated platforms have improved the diagnostic performance of TPOAb assays. The aim of this study was to evaluate the potential improvement of the inter-method agreement of current automated third generation systems, 12 years after a previous study, which had assessed the analytical variability between semi-automated second generation methods of TPOAb detection. Eight pools of sera from patients with chronic lymphocytic thyroiditis, exhibiting different TPOAb concentrations, were collected from routine laboratory diagnostics and distributed to seven companies throughout Italy. All automated third generation methods were calibrated against the Medical Research Council (MRC) reference preparation 66/387. The overall mean variability (CV) was 93.6% when results were expressed in part as arbitrary Units (U/mL) and in part as International Units (IU/mL). The conversion of all values in IU/mL resulted in a significant decrease of CV (49.8%). The CV expressed as COM (cut-off concentration multiples) was 64.0%. Agreement of qualitative results was 95.3% with a pronounced difference in the threshold values proposed by manufacturers (range 3.2-35.0 IU/mL). These findings confirm the improvement of harmonisation between different methods of automated third generation TPOAb assays. Nevertheless, further efforts should be made in the definition of the positive cut-off concentration to avoid misclassification of AITD patients as well as in a new international reference preparation and in the autoantigen purification modality.

  8. RADIOLOGICAL TIPS Percutaneous thrombin injection for ...

    African Journals Online (AJOL)

    pseudoaneurysm sac has a typical 'yin-yang' sign. The neck is normally seen posteriorly and is usually thin and longitudinal. A large neck diameter (e.g. >10 mm) is a relative contra-indication for thrombin injection because of a slightly higher risk of distal embolisation. There are several thrombin preparations available.

  9. Steam generator automated eddy current data analysis: A benchmarking study. Final report

    International Nuclear Information System (INIS)

    Brown, S.D.

    1998-12-01

    The eddy current examination of steam generator tubes is a very demanding process. Challenges include: complex signal analysis, massive amount of data to be reviewed quickly with extreme precision and accuracy, shortages of data analysts during peak periods, and the desire to reduce examination costs. One method to address these challenges is by incorporating automation into the data analysis process. Specific advantages, which automated data analysis has the potential to provide, include the ability to analyze data more quickly, consistently and accurately than can be performed manually. Also, automated data analysis can potentially perform the data analysis function with significantly smaller levels of analyst staffing. Despite the clear advantages that an automated data analysis system has the potential to provide, no automated system has been produced and qualified that can perform all of the functions that utility engineers demand. This report investigates the current status of automated data analysis, both at the commercial and developmental level. A summary of the various commercial and developmental data analysis systems is provided which includes the signal processing methodologies used and, where available, the performance data obtained for each system. Also, included in this report is input from seventeen research organizations regarding the actions required and obstacles to be overcome in order to bring automatic data analysis from the laboratory into the field environment. In order to provide assistance with ongoing and future research efforts in the automated data analysis arena, the most promising approaches to signal processing are described in this report. These approaches include: wavelet applications, pattern recognition, template matching, expert systems, artificial neural networks, fuzzy logic, case based reasoning and genetic algorithms. Utility engineers and NDE researchers can use this information to assist in developing automated data

  10. Automated Report Generation for Research Data Repositories: From i2b2 to PDF.

    Science.gov (United States)

    Thiemann, Volker S; Xu, Tingyan; Röhrig, Rainer; Majeed, Raphael W

    2017-01-01

    We developed an automated toolchain to generate reports of i2b2 data. It is based on free open source software and runs on a Java Application Server. It is sucessfully used in an ED registry project. The solution is highly configurable and portable to other projects based on i2b2 or compatible factual data sources.

  11. Automating the generation of finite element dynamical cores with Firedrake

    Science.gov (United States)

    Ham, David; Mitchell, Lawrence; Homolya, Miklós; Luporini, Fabio; Gibson, Thomas; Kelly, Paul; Cotter, Colin; Lange, Michael; Kramer, Stephan; Shipton, Jemma; Yamazaki, Hiroe; Paganini, Alberto; Kärnä, Tuomas

    2017-04-01

    The development of a dynamical core is an increasingly complex software engineering undertaking. As the equations become more complete, the discretisations more sophisticated and the hardware acquires ever more fine-grained parallelism and deeper memory hierarchies, the problem of building, testing and modifying dynamical cores becomes increasingly complex. Here we present Firedrake, a code generation system for the finite element method with specialist features designed to support the creation of geoscientific models. Using Firedrake, the dynamical core developer writes the partial differential equations in weak form in a high level mathematical notation. Appropriate function spaces are chosen and time stepping loops written at the same high level. When the programme is run, Firedrake generates high performance C code for the resulting numerics which are executed in parallel. Models in Firedrake typically take a tiny fraction of the lines of code required by traditional hand-coding techniques. They support more sophisticated numerics than are easily achieved by hand, and the resulting code is frequently higher performance. Critically, debugging, modifying and extending a model written in Firedrake is vastly easier than by traditional methods due to the small, highly mathematical code base. Firedrake supports a wide range of key features for dynamical core creation: A vast range of discretisations, including both continuous and discontinuous spaces and mimetic (C-grid-like) elements which optimally represent force balances in geophysical flows. High aspect ratio layered meshes suitable for ocean and atmosphere domains. Curved elements for high accuracy representations of the sphere. Support for non-finite element operators, such as parametrisations. Access to PETSc, a world-leading library of programmable linear and nonlinear solvers. High performance adjoint models generated automatically by symbolically reasoning about the forward model. This poster will present

  12. 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.

  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. Fully Automated Volumetric Modulated Arc Therapy Plan Generation for Prostate Cancer Patients

    International Nuclear Information System (INIS)

    Voet, Peter W.J.; Dirkx, Maarten L.P.; Breedveld, Sebastiaan; Al-Mamgani, Abrahim; Incrocci, Luca; Heijmen, Ben J.M.

    2014-01-01

    Purpose: To develop and evaluate fully automated volumetric modulated arc therapy (VMAT) treatment planning for prostate cancer patients, avoiding manual trial-and-error tweaking of plan parameters by dosimetrists. Methods and Materials: A system was developed for fully automated generation of VMAT plans with our commercial clinical treatment planning system (TPS), linked to the in-house developed Erasmus-iCycle multicriterial optimizer for preoptimization. For 30 randomly selected patients, automatically generated VMAT plans (VMAT auto ) were compared with VMAT plans generated manually by 1 expert dosimetrist in the absence of time pressure (VMAT man ). For all treatment plans, planning target volume (PTV) coverage and sparing of organs-at-risk were quantified. Results: All generated plans were clinically acceptable and had similar PTV coverage (V 95%  > 99%). For VMAT auto and VMAT man plans, the organ-at-risk sparing was similar as well, although only the former plans were generated without any planning workload. Conclusions: Fully automated generation of high-quality VMAT plans for prostate cancer patients is feasible and has recently been implemented in our clinic

  15. Automation of the process of generation of the students insurance, applying RFID and GPRS technologies

    Directory of Open Access Journals (Sweden)

    Nelson Barrera-Lombana

    2013-07-01

    Full Text Available This article presents the description of the design and implementation of a system which allows the fulfilment of a consultation service on various parameters to a web server using a GSM modem, exchanging information systems over the Internet (ISS and radio-frequency identification (RFID. The application validates for its use in automation of the process of generation of the student insurance, and hardware and software, developed by the Research Group in Robotics and Industrial Automation GIRAof UPTC, are used as a platform.

  16. Plasma centrifugation does not influence thrombin-antithrombin and plasmin-antiplasmin levels but determines platelet microparticles count.

    Science.gov (United States)

    Stępień, Ewa; Gruszczyński, Krzysztof; Kapusta, Przemysław; Kowalik, Artur; Wybrańska, Iwona

    2015-01-01

    Centrifugation is an essential step for plasma preparation to remove residual elements in plasma, especially platelets and platelet-derived microparticles (PMPs). Our working hypothesis was that centrifugation as a preanalytical step may influence some coagulation parameters. Healthy young men were recruited (N=17). For centrifugation, two protocols were applied: (A) the first centrifugation at 2500xg for 15 min and (B) at 2500xg for 20 min at room temperature with a light brake. In protocol (A), the second centrifugation was carried out at 2500xg for 15 min, whereas in protocol (B), the second centrifugation involved a 10 min spin at 13,000 x g. Thrombin-antithrombin (TAT) and plasmin-antiplasmin (PAP) complexes concentrations were determined by enzyme-linked immunosorbent assays. PMPs were stained with CD41 antibody and annexin V, and analyzed by flow cytometry method. Procoagulant activity was assayed by the Calibrated Automated Thrombogram method as a slope of thrombin formation (CAT velocity). Median TAT and PAP concentrations did not differ between the centrifugation protocols. The high speed centrifugation reduced the median (IQR) PMP count in plasma from 1291 (841-1975) to 573 (391-1010) PMP/µL (P=0.001), and CAT velocity from 2.01 (1.31-2.88) to 0.97 (0.82-1.73) nM/min (P=0.049). Spearman's rank correlation analysis showed correlation between TAT and PMPs in the protocol A plasma which was (rho=0.52, PCentrifugation protocols do not influence the markers of plasminogen (PAP) and thrombin (TAT) generation but they do affect the PMP count and procoagulant activity.

  17. Automated Generation of Technical Documentation and Provenance for Reproducible Research

    Science.gov (United States)

    Jolly, B.; Medyckyj-Scott, D.; Spiekermann, R.; Ausseil, A. G.

    2017-12-01

    Data provenance and detailed technical documentation are essential components of high-quality reproducible research, however are often only partially addressed during a research project. Recording and maintaining this information during the course of a project can be a difficult task to get right as it is a time consuming and often boring process for the researchers involved. As a result, provenance records and technical documentation provided alongside research results can be incomplete or may not be completely consistent with the actual processes followed. While providing access to the data and code used by the original researchers goes some way toward enabling reproducibility, this does not count as, or replace, data provenance. Additionally, this can be a poor substitute for good technical documentation and is often more difficult for a third-party to understand - particularly if they do not understand the programming language(s) used. We present and discuss a tool built from the ground up for the production of well-documented and reproducible spatial datasets that are created by applying a series of classification rules to a number of input layers. The internal model of the classification rules required by the tool to process the input data is exploited to also produce technical documentation and provenance records with minimal additional user input. Available provenance records that accompany input datasets are incorporated into those that describe the current process. As a result, each time a new iteration of the analysis is performed the documentation and provenance records are re-generated to provide an accurate description of the exact process followed. The generic nature of this tool, and the lessons learned during its creation, have wider application to other fields where the production of derivative datasets must be done in an open, defensible, and reproducible way.

  18. 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

    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 software implementing the IETF WebSocket protocol. This demonstrates the scalability of our approach to real...... 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...

  19. Thrombin impairs human endometrial endothelial angiogenesis; implications for progestin-only contraceptive-induced abnormal uterine bleeding.

    Science.gov (United States)

    Shapiro, John P; Guzeloglu-Kayisli, Ozlem; Kayisli, Umit A; Semerci, Nihan; Huang, S Joseph; Arlier, Sefa; Larsen, Kellie; Fadda, Paolo; Schatz, Frederick; Lockwood, Charles J

    2017-06-01

    Progestin-only contraceptives induce abnormal uterine bleeding, accompanied by prothrombin leakage from dilated endometrial microvessels and increased thrombin generation by human endometrial stromal cell (HESC)-expressed tissue factor. Initial studies of the thrombin-treated HESC secretome identified elevated levels of cleaved chondroitin sulfate proteoglycan 4 (CSPG4), impairing pericyte-endothelial interactions. Thus, we investigated direct and CSPG4-mediated effects of thrombin in eliciting abnormal uterine bleeding by disrupting endometrial angiogenesis. Liquid chromatography/tandem mass spectrometry, enzyme-linked immunosorbent assay (ELISA) and quantitative real-time-polymerase chain reaction (PCR) evaluated conditioned medium supernatant and cell lysates from control versus thrombin-treated HESCs. Pre- and post-Depo medroxyprogesterone acetate (DMPA)-administered endometria were immunostained for CSPG4. Proliferation, apoptosis and tube formation were assessed in human endometrial endothelial cells (HEECs) incubated with recombinant human (rh)-CSPG4 or thrombin or both. Thrombin induced CSPG4 protein expression in cultured HESCs as detected by mass spectrometry and ELISA (pabnormal uterine bleeding in DMPA users. Mass spectrometry analysis identified several HESC-secreted proteins regulated by thrombin. Therapeutic agents blocking angiogenic effects of thrombin in HESCs can prevent or minimize progestin-only contraceptive-induced abnormal uterine bleeding. Copyright © 2017. Published by Elsevier Inc.

  20. Thrombin and PAF stimulate formation of inositol triphosphate from similar pools of phosphatidylinositol-4,5-bisphosphate in platelets

    International Nuclear Information System (INIS)

    Shukla, S.D.; Franklin, C.C.

    1986-01-01

    During platelet activation phospholipase C cleaves phosphatidylinositol-4,5-bisphosphate (PIP 2 ) to generate diacylglycerol and inositol triphosphate (IP 3 ). Production of IP 3 was therefore used as a probe to differentiate between thrombin and platelet activating factor (PAF) sensitive pools of PIP 2 . Stimulation of [ 3 H]inositol labelled rabbit platelets (0.5 x 10 9 cells/ml containing 0.1 mM EGTA and 2 mM LiCl) with thrombin (1 U/ml) caused a maximum 3 to 10 fold increase in [ 3 H]IP 3 in 5 min. Treatment with PAF (1 x 10 -9 M) led to a maximum 3 to 5 fold increase in [ 3 H]IP 3 in 5 s followed by a decrease to basal level in 30 s. Addition of thrombin for 5 min followed by PAF for 5 s showed no further increase in [ 3 H]IP 3 over that obtained with thrombin alone. Various other sequential treatments with thrombin and PAF showed negligible cumulative effect. Simultaneous addition of thrombin and PAF showed a partial additive production of [ 3 H]IP 3 at short time periods but these levels never significantly exceeded those obtained by thrombin at 5 min or PAF at 5 s. It is concluded that in platelets thrombin and PAF (a) differentially activate PIP 2 -phosphodiesterase and (b) stimulate production of IP 3 from similar pools of PIP 2

  1. [Human thrombin: drug stability and stabilization].

    Science.gov (United States)

    Kolodzeĭskaia, M V; Sokolovskiĭ, V A; Volkov, G L

    2006-01-01

    Stabilization of enzymes is a key factor when using biocatalysis in practice. Each enzyme stability depends both on the structure of its molecule and on the effect of various environmental factors, thus, one of the methods of the enzyme stability preservation is the formation of optimal macromedium. Thus, water structure and enzyme hydration change in the presence of solvable additives that affects its stability and catalytic properties. The paper deals with a new method of stabilization of human thrombin developed by the authors. It is proposed to use some known organic-ligands which have ion group and different nonpolar hydrophobic groups instead of traditional additives (salts, aminoacids, polyols, polyethylene glycols etc.). Thrombin stabilization proceeds in the conditions something changed compared with traditional ones. Processes of thrombin stabilization by the above compound have been investigated, enzyme stability at different temperatures and long-term storage of diluted solutions of the preparation in different conditions have been studied. It has been established that rosselin and orange II are the most efficient ligands. Optimal finite concentrations of stabilizing agents make approximately 0.0012-0.0014 M which are rather low in the system thrombin-ligand. It has been found that diluted solutions of thrombin are more stable, than concentrated ones. In the latter case the process of autolysis is included that affects negatively the catalytic effect of the enzyme, as far as there occurs the change of thrombin molecule structure, especially of thrombin beta-chain sections, evoking conformational changes of some sites of its active centre. The experiments directed to increasing thrombin intensity in the presence of organic ligands rosselin and orange II are discussed in details. Special attention is given to autolytic method of thrombin inactivation. It is admitted on the basis of already obtained data that thrombin binding with organic ligands proceeds

  2. Monte Carlo generated spectra for QA/QC of automated NAA routine

    International Nuclear Information System (INIS)

    Jackman, K.R.; Biegalski, S.R.

    2007-01-01

    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. (author)

  3. Development of automated generation system of accidental operating procedures for a PWR

    International Nuclear Information System (INIS)

    Artaud, J.L.

    1991-06-01

    The aim of the ACACIA project is to develop an automated generation system of accident operating procedures for a PWR. This research and development study, common at CEA and EDF, has two objectives: at mean-dated the realization of a validation tool and a procedure generation; at long-dated the dynamic generation of real time procedures. This work is consecrated at the realization of 2 prototypes. These prototypes and the technics used are described in detail. The last chapter explores the perspectives given by this type of tool [fr

  4. The development of an automated sentence generator for the assessment of reading speed

    Directory of Open Access Journals (Sweden)

    Legge Gordon E

    2008-03-01

    Full Text Available Abstract Reading speed is an important outcome measure for many studies in neuroscience and psychology. Conventional reading speed tests have a limited corpus of sentences and usually require observers to read sentences aloud. Here we describe an automated sentence generator which can create over 100,000 unique sentences, scored using a true/false response. We propose that an estimate of the minimum exposure time required for observers to categorise the truth of such sentences is a good alternative to reading speed measures that guarantees comprehension of the printed material. Removing one word from the sentence reduces performance to chance, indicating minimal redundancy. Reading speed assessed using rapid serial visual presentation (RSVP of these sentences is not statistically different from using MNREAD sentences. The automated sentence generator would be useful for measuring reading speed with button-press response (such as within MRI scanners and for studies requiring many repeated measures of reading speed.

  5. Optimizing Decision Preparedness by Adapting Scenario Complexity and Automating Scenario Generation

    Science.gov (United States)

    Dunne, Rob; Schatz, Sae; Flore, Stephen M.; Nicholson, Denise

    2011-01-01

    Klein's recognition-primed decision (RPD) framework proposes that experts make decisions by recognizing similarities between current decision situations and previous decision experiences. Unfortunately, military personnel arQ often presented with situations that they have not experienced before. Scenario-based training (S8T) can help mitigate this gap. However, SBT remains a challenging and inefficient training approach. To address these limitations, the authors present an innovative formulation of scenario complexity that contributes to the larger research goal of developing an automated scenario generation system. This system will enable trainees to effectively advance through a variety of increasingly complex decision situations and experiences. By adapting scenario complexities and automating generation, trainees will be provided with a greater variety of appropriately calibrated training events, thus broadening their repositories of experience. Preliminary results from empirical testing (N=24) of the proof-of-concept formula are presented, and future avenues of scenario complexity research are also discussed.

  6. Fluorescence In Situ Hybridization (FISH Signal Analysis Using Automated Generated Projection Images

    Directory of Open Access Journals (Sweden)

    Xingwei Wang

    2012-01-01

    Full Text Available Fluorescence in situ hybridization (FISH tests provide promising molecular imaging biomarkers to more accurately and reliably detect and diagnose cancers and genetic disorders. Since current manual FISH signal analysis is low-efficient and inconsistent, which limits its clinical utility, developing automated FISH image scanning systems and computer-aided detection (CAD schemes has been attracting research interests. To acquire high-resolution FISH images in a multi-spectral scanning mode, a huge amount of image data with the stack of the multiple three-dimensional (3-D image slices is generated from a single specimen. Automated preprocessing these scanned images to eliminate the non-useful and redundant data is important to make the automated FISH tests acceptable in clinical applications. In this study, a dual-detector fluorescence image scanning system was applied to scan four specimen slides with FISH-probed chromosome X. A CAD scheme was developed to detect analyzable interphase cells and map the multiple imaging slices recorded FISH-probed signals into the 2-D projection images. CAD scheme was then applied to each projection image to detect analyzable interphase cells using an adaptive multiple-threshold algorithm, identify FISH-probed signals using a top-hat transform, and compute the ratios between the normal and abnormal cells. To assess CAD performance, the FISH-probed signals were also independently visually detected by an observer. The Kappa coefficients for agreement between CAD and observer ranged from 0.69 to 1.0 in detecting/counting FISH signal spots in four testing samples. The study demonstrated the feasibility of automated FISH signal analysis that applying a CAD scheme to the automated generated 2-D projection images.

  7. Automated calibration and control for polarization-resolved second harmonic generation on commercial microscopes.

    Science.gov (United States)

    Romijn, Elisabeth I; Finnøy, Andreas; Kumar, Rajesh; Lilledahl, Magnus B

    2018-01-01

    Polarization-resolved second harmonic generation (P-SHG) microscopy has evolved as a promising technique to reveal subresolution information about the structure and orientation of ordered biological macromolecules. To extend the adoption of the technique, it should be easily integrated onto commercial laser scanning microscopes. Furthermore, procedures for easy calibration and assessment of measurement accuracy are essential, and measurements should be fully automated to allow for analysis of large quantities of samples. In this paper we present a setup for P-SHG which is readily incorporated on commercial multiphoton microscopes. The entire system is completely automated which allows for rapid calibration through the freely available software and for automated imaging for different polarization measurements, including linear and circular polarization of the excitation beam. The results show that calibration settings are highly system dependent. We also show that the accuracy of the polarization control is easily quantified and that it varies between systems. The accuracy can be tuned by iterative alignment of optics or a more fine-grained calibration procedure. Images of real samples show that the red accuracy of the results is easily visualized with the automated setup. Through this system we believe that P-SHG could develop a wider adoption in biomedical applications.

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

    International Nuclear Information System (INIS)

    Both, J.P.; Nimal, J.C.; Vergnaud, T.

    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)

  9. CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

    Science.gov (United States)

    Velmeshev, Dmitry; Lally, Patrick; Magistri, Marco; Faghihi, Mohammad Ali

    2016-01-13

    Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers. To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app . We

  10. 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.

  11. A Solution Generator Algorithm for Decision Making based Automated Negotiation in the Construction Domain

    Directory of Open Access Journals (Sweden)

    Arazi Idrus

    2017-12-01

    Full Text Available In this paper, we present our work-in-progress of a proposed framework for automated negotiation in the construction domain. The proposed framework enables software agents to conduct negotiations and autonomously make value-based decisions. The framework consists of three main components which are, solution generator algorithm, negotiation algorithm, and conflict resolution algorithm. This paper extends the discussion on the solution generator algorithm that enables software agents to generate solutions and rank them from 1st to nth solution for the negotiation stage of the operation. The solution generator algorithm consists of three steps which are, review solutions, rank solutions, and form ranked solutions. For validation purpose, we present a scenario that utilizes the proposed algorithm to rank solutions. The validation shows that the algorithm is promising, however, it also highlights the conflict between different parties that needs further negotiation action.

  12. Advanced E-O test capability for Army Next-Generation Automated Test System (NGATS)

    Science.gov (United States)

    Errea, S.; Grigor, J.; King, D. F.; Matis, G.; McHugh, S.; McKechnie, J.; Nehring, B.

    2015-05-01

    The Future E-O (FEO) program was established to develop a flexible, modular, automated test capability as part of the Next Generation Automatic Test System (NGATS) program to support the test and diagnostic needs of currently fielded U.S. Army electro-optical (E-O) devices, as well as being expandable to address the requirements of future Navy, Marine Corps and Air Force E-O systems. Santa Barbara infrared (SBIR) has designed, fabricated, and delivered three (3) prototype FEO for engineering and logistics evaluation prior to anticipated full-scale production beginning in 2016. In addition to presenting a detailed overview of the FEO system hardware design, features and testing capabilities, the integration of SBIR's EO-IR sensor and laser test software package, IRWindows 4™, into FEO to automate the test execution, data collection and analysis, archiving and reporting of results is also described.

  13. 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.

  14. Generating Phenotypical Erroneous Human Behavior to Evaluate Human-automation Interaction Using Model Checking.

    Science.gov (United States)

    Bolton, Matthew L; Bass, Ellen J; Siminiceanu, Radu I

    2012-11-01

    Breakdowns in complex systems often occur as a result of system elements interacting in unanticipated ways. In systems with human operators, human-automation interaction associated with both normative and erroneous human behavior can contribute to such failures. Model-driven design and analysis techniques provide engineers with formal methods tools and techniques capable of evaluating how human behavior can contribute to system failures. This paper presents a novel method for automatically generating task analytic models encompassing both normative and erroneous human behavior from normative task models. The generated erroneous behavior is capable of replicating Hollnagel's zero-order phenotypes of erroneous action for omissions, jumps, repetitions, and intrusions. Multiple phenotypical acts can occur in sequence, thus allowing for the generation of higher order phenotypes. The task behavior model pattern capable of generating erroneous behavior can be integrated into a formal system model so that system safety properties can be formally verified with a model checker. This allows analysts to prove that a human-automation interactive system (as represented by the model) will or will not satisfy safety properties with both normative and generated erroneous human behavior. We present benchmarks related to the size of the statespace and verification time of models to show how the erroneous human behavior generation process scales. We demonstrate the method with a case study: the operation of a radiation therapy machine. A potential problem resulting from a generated erroneous human action is discovered. A design intervention is presented which prevents this problem from occurring. We discuss how our method could be used to evaluate larger applications and recommend future paths of development.

  15. Generating Phenotypical Erroneous Human Behavior to Evaluate Human-automation Interaction Using Model Checking

    Science.gov (United States)

    Bolton, Matthew L.; Bass, Ellen J.; Siminiceanu, Radu I.

    2012-01-01

    Breakdowns in complex systems often occur as a result of system elements interacting in unanticipated ways. In systems with human operators, human-automation interaction associated with both normative and erroneous human behavior can contribute to such failures. Model-driven design and analysis techniques provide engineers with formal methods tools and techniques capable of evaluating how human behavior can contribute to system failures. This paper presents a novel method for automatically generating task analytic models encompassing both normative and erroneous human behavior from normative task models. The generated erroneous behavior is capable of replicating Hollnagel’s zero-order phenotypes of erroneous action for omissions, jumps, repetitions, and intrusions. Multiple phenotypical acts can occur in sequence, thus allowing for the generation of higher order phenotypes. The task behavior model pattern capable of generating erroneous behavior can be integrated into a formal system model so that system safety properties can be formally verified with a model checker. This allows analysts to prove that a human-automation interactive system (as represented by the model) will or will not satisfy safety properties with both normative and generated erroneous human behavior. We present benchmarks related to the size of the statespace and verification time of models to show how the erroneous human behavior generation process scales. We demonstrate the method with a case study: the operation of a radiation therapy machine. A potential problem resulting from a generated erroneous human action is discovered. A design intervention is presented which prevents this problem from occurring. We discuss how our method could be used to evaluate larger applications and recommend future paths of development. PMID:23105914

  16. An Automated Microwave-Assisted Synthesis Purification System for Rapid Generation of Compound Libraries.

    Science.gov (United States)

    Tu, Noah P; Searle, Philip A; Sarris, Kathy

    2016-06-01

    A novel methodology for the synthesis and purification of drug-like compound libraries has been developed through the use of a microwave reactor with an integrated high-performance liquid chromatography-mass spectrometry (HPLC-MS) system. The strategy uses a fully automated synthesizer with a microwave as energy source and robotic components for weighing and dispensing of solid reagents, handling liquid reagents, capper/crimper of microwave reaction tube assemblies, and transportation. Crude reaction products were filtered through solid-phase extraction cartridges and injected directly onto a reverse-phase chromatography column via an injection valve. For multistep synthesis, crude products were passed through scavenger resins and reintroduced for subsequent reactions. All synthetic and purification steps were conducted under full automation with no handling or isolation of intermediates, to afford the desired purified products. This approach opens the way to highly efficient generation of drug-like compounds as part of a lead discovery strategy or within a lead optimization program. © 2015 Society for Laboratory Automation and Screening.

  17. Automated Breast Ultrasound for Ductal Pattern Reconstruction: Ground Truth File Generation and CADe Evaluation

    Science.gov (United States)

    Manousaki, D.; Panagiotopoulou, A.; Bizimi, V.; Haynes, M. S.; Love, S.; Kallergi, M.

    2017-11-01

    The purpose of this study was the generation of ground truth files (GTFs) of the breast ducts from 3D images of the Invenia™ Automated Breast Ultrasound System (ABUS) system (GE Healthcare, Little Chalfont, UK) and the application of these GTFs for the optimization of the imaging protocol and the evaluation of a computer aided detection (CADe) algorithm developed for automated duct detection. Six lactating, nursing volunteers were scanned with the ABUS before and right after breastfeeding their infants. An expert in breast ultrasound generated rough outlines of the milk-filled ducts in the transaxial slices of all image volumes and the final GTFs were created by using thresholding and smoothing tools in ImageJ. In addition, a CADe algorithm automatically segmented duct like areas and its results were compared to the expert’s GTFs by estimating true positive fraction (TPF) or % overlap. The CADe output differed significantly from the expert’s but both detected a smaller than expected volume of the ducts due to insufficient contrast (ducts were partially filled with milk), discontinuities, and artifacts. GTFs were used to modify the imaging protocol and improve the CADe method. In conclusion, electronic GTFs provide a valuable tool in the optimization of a tomographic imaging system, the imaging protocol, and the CADe algorithms. Their generation, however, is an extremely time consuming, strenuous process, particularly for multi-slice examinations, and alternatives based on phantoms or simulations are highly desirable.

  18. ATTEMPTS TO AUTOMATE THE PROCESS OF GENERATION OF ORTHOIMAGES OF OBJECTS OF CULTURAL HERITAGE

    Directory of Open Access Journals (Sweden)

    J. S. Markiewicz

    2015-02-01

    Full Text Available At present, digital documentation recorded in the form of raster or vector files is the obligatory way of inventorying historical objects. The orthoimage is a cartometric form of photographic presentation of information in the two-dimensional reference system. The paper will discuss the issue of automation of the orthoimage generation basing on the TLS data and digital images. At present attempts are made to apply modern technologies not only for the needs of surveys, but also during the data processing. This paper will present attempts aiming at utilisation of appropriate algorithms and the author’s application for automatic generation of the projection plane, for the needs of acquisition of intensity orthoimages from the TLS data. Such planes are defined manually in the majority of popular TLS data processing applications. A separate issue related to the RGB image generation is the orientation of digital images in relation to scans. It is important, in particular in such cases when scans and photographs are not taken simultaneously. This paper will present experiments concerning the utilisation of the SIFT algorithm for automatic matching of intensity orthoimages of the intensity and digital (RGB photographs. Satisfactory results of the process of automation, as well as in relation to the quality of resulting orthoimages have been obtained.

  19. Automation of labelling of Lipiodol with high-activity generator-produced {sup 188}Re

    Energy Technology Data Exchange (ETDEWEB)

    Lepareur, Nicolas, E-mail: n.lepareur@rennes.fnclcc.f [Service de Medecine Nucleaire, Centre Regional de Lutte Contre le Cancer Eugene Marquis, CS 44229, 35042 Rennes (France); INSERM U-991, Foie, Metabolismes et Cancer, 35033 Rennes (France); Universite Europeenne de Bretagne, Rennes (France); Ardisson, Valerie [Service de Medecine Nucleaire, Centre Regional de Lutte Contre le Cancer Eugene Marquis, CS 44229, 35042 Rennes (France); INSERM U-991, Foie, Metabolismes et Cancer, 35033 Rennes (France); Universite Europeenne de Bretagne, Rennes (France); Noiret, Nicolas [Universite Europeenne de Bretagne, Rennes (France); Ecole Nationale Superieure de Chimie de Rennes, UMR CNRS 6226, Chimie Organique et Supramoleculaire, Avenue du General Leclerc, CS 50837, 35708 Rennes Cedex 7 (France); Boucher, Eveline; Raoul, Jean-Luc [INSERM U-991, Foie, Metabolismes et Cancer, 35033 Rennes (France); Universite Europeenne de Bretagne, Rennes (France); Service d' Oncologie Digestive, Centre Regional de Lutte Contre le Cancer Eugene Marquis, CS 44229, 35042 Rennes (France); Clement, Bruno [INSERM U-991, Foie, Metabolismes et Cancer, 35033 Rennes (France); Garin, Etienne [Service de Medecine Nucleaire, Centre Regional de Lutte Contre le Cancer Eugene Marquis, CS 44229, 35042 Rennes (France); INSERM U-991, Foie, Metabolismes et Cancer, 35033 Rennes (France); Universite Europeenne de Bretagne, Rennes (France)

    2011-02-15

    This work describes optimisation of the kit formulation for labelling of Lipiodol with high-activity generator-produced rhenium-188. Radiochemical purity (RCP) was 92.52{+-}2.3% and extraction yield was 98.56{+-}1.2%. The synthesis has been automated with a TADDEO module (Comecer) giving a mean final yield of 52.68{+-}9.6%, and reducing radiation burden to the radiochemist by 80%. Radiolabelled Lipiodol ({sup 188}Re-SSS/Lipiodol) is stable for at least 7 days (RCP=91.07{+-}0.9%).

  20. Topical thrombin-related corneal calcification.

    Science.gov (United States)

    Kiratli, Hayyam; Irkeç, Murat; Alaçal, Sibel; Söylemezoğlu, Figen

    2006-09-01

    To report a highly unusual case of corneal calcification after brief intraoperative use of topical thrombin. A 44-year-old man underwent sclerouvectomy for ciliochoroidal leiomyoma, during which 35 UNIH/mL lyophilized bovine thrombin mixed with 9 mL of diluent containing 1500 mmol/mL calcium chloride was used. From the first postoperative day, corneal and anterior lenticular capsule calcifications developed, and corneal involvement slightly enlarged thereafter. A year later, 2 corneal punch biopsies confirmed calcification mainly in the Bowman layer. Topical treatment with 1.5% ethylenediaminetetraacetic acid significantly restored corneal clarity. Six months later, a standard extracapsular cataract extraction with intraocular lens placement improved visual acuity to 20/60. This case suggests that topical thrombin drops with elevated calcium concentrations may cause acute corneal calcification in Bowman layer and on the anterior lens capsule.

  1. PAR1 antagonists inhibit thrombin-induced platelet activation whilst leaving the PAR4-mediated response intact.

    Science.gov (United States)

    Judge, Heather M; Jennings, Lisa K; Moliterno, David J; Hord, Edward; Ecob, Rosemary; Tricoci, Pierluigi; Rorick, Tyrus; Kotha, Jayaprakash; Storey, Robert F

    2015-01-01

    Thrombin-induced platelet activation is initiated by PAR1 and PAR4 receptors. Vorapaxar, a PAR1 antagonist, has been assessed in patients with acute coronary syndromes (ACS) and stable atherosclerotic disease in addition to standard-of-care treatment. In clinical trials, vorapaxar has been observed to reduce the frequency of ischaemic events in some subgroups though in others has increased the frequency of bleeding events. Among patients undergoing CABG surgery, which is associated with excess thrombin generation, bleeding was not increased. The aim of these studies was to investigate the effects of selective PAR1 antagonism on thrombin-induced platelet activation in patients receiving vorapaxar or placebo in the TRACER trial and to explore the roles of PAR1 and PAR4 in thrombin-induced platelet activation in healthy volunteers. ACS patients receiving vorapaxar or placebo in the TRACER trial were studied at baseline and 4 hours, 1 and 4 months during drug administration. Thrombin-induced calcium mobilisation in platelet-rich plasma was assessed by flow cytometry. In vitro studies were performed in healthy volunteers using the PAR1 antagonist SCH79797 or PAR4 receptor desensitisation. Vorapaxar treatment significantly inhibited thrombin-induced calcium mobilisation, leaving a residual, delayed response. These findings were consistent with calcium mobilisation mediated via the PAR4 receptor and were reproduced in vitro using SCH79797. PAR4 receptor desensitization, in combination with SCH79797, completely inhibited thrombin-induced calcium mobilisation confirming that the residual calcium mobilisation was mediated via PAR4. In conclusion vorapaxar selectively antagonises the PAR1-mediated component of thrombin-induced platelet activation, leaving the PAR4-mediated response intact, which may explain why vorapaxar is well tolerated in patients undergoing CABG surgery since higher thrombin levels in this setting may override the effects of PAR1 antagonism through PAR4

  2. Automated system for generation of soil moisture products for agricultural drought assessment

    Science.gov (United States)

    Raja Shekhar, S. S.; Chandrasekar, K.; Sesha Sai, M. V. R.; Diwakar, P. G.; Dadhwal, V. K.

    2014-11-01

    Drought is a frequently occurring disaster affecting lives of millions of people across the world every year. Several parameters, indices and models are being used globally to forecast / early warning of drought and monitoring drought for its prevalence, persistence and severity. Since drought is a complex phenomenon, large number of parameter/index need to be evaluated to sufficiently address the problem. It is a challenge to generate input parameters from different sources like space based data, ground data and collateral data in short intervals of time, where there may be limitation in terms of processing power, availability of domain expertise, specialized models & tools. In this study, effort has been made to automate the derivation of one of the important parameter in the drought studies viz Soil Moisture. Soil water balance bucket model is in vogue to arrive at soil moisture products, which is widely popular for its sensitivity to soil conditions and rainfall parameters. This model has been encoded into "Fish-Bone" architecture using COM technologies and Open Source libraries for best possible automation to fulfill the needs for a standard procedure of preparing input parameters and processing routines. The main aim of the system is to provide operational environment for generation of soil moisture products by facilitating users to concentrate on further enhancements and implementation of these parameters in related areas of research, without re-discovering the established models. Emphasis of the architecture is mainly based on available open source libraries for GIS and Raster IO operations for different file formats to ensure that the products can be widely distributed without the burden of any commercial dependencies. Further the system is automated to the extent of user free operations if required with inbuilt chain processing for every day generation of products at specified intervals. Operational software has inbuilt capabilities to automatically

  3. Progestin and thrombin regulate tissue factor expression in human term decidual cells.

    Science.gov (United States)

    Lockwood, C J; Murk, W; Kayisli, U A; Buchwalder, L F; Huang, S-T; Funai, E F; Krikun, G; Schatz, F

    2009-06-01

    Perivascular cell membrane-bound tissue factor (TF) initiates hemostasis via thrombin generation. The identity and potential regulation of TF-expressing cells at the human maternal-fetal interface that confers hemostatic protection during normal and preterm delivery is unclear. The objective of the study were to identify TF-expressing cells at the maternal-fetal interface in term and preterm decidual sections by immunohistochemistry and evaluate progestin, thrombin, TNF-alpha, and IL-1beta effects on TF expression by cultured human term decidual cells (DCs). Serial placental sections were immunostained for TF. Leukocyte-free term DC monolayers were incubated with 10(-8) M estradiol (E2) or E2 plus 10(-7) M medroxyprogestrone acetate (MPA) +/- thrombin or TNF-alpha or IL-1beta. ELISA and Western blotting assessed TF in cell lysates. Quantitative real-time RT-PCR measured TF mRNA levels. Immunolocalized TF in DC membranes in preterm and term placental sections displayed higher Histologic Scores than villous mesenchymal cells (P term placental sections, DC-expressed TF exceeds that of other cell types at the maternal-fetal interface and is localized at the cell membranes in which it can bind to factor VII and meet the hemostatic demands of labor and delivery via thrombin formation. Unlike the general concept that TF is constitutive in cells that highly express it, MPA and thrombin significantly enhanced TF expression in term DC monolayers.

  4. An automated multidimensional thin film stretching device for the generation of anisotropic polymeric micro- and nanoparticles.

    Science.gov (United States)

    Meyer, Randall A; Meyer, Randall S; Green, Jordan J

    2015-08-01

    Anisotropic polymeric particles are of growing interest for biomaterials applications due to their unique properties. These include the ability for these particles to evade nonspecific cellular uptake and to have enhanced targeted cellular uptake and interaction. One of the most widely used methods for generating anisotropic polymeric particles is the thin film stretching procedure. Despite its theoretical simplicity, this procedure, as it has been implemented to date, can be difficult due to the inconsistent nature of the manual operation of machinery used to stretch the film. We have constructed an automated thin film stretcher for control over biomaterials via thin film stretching in 1D and 2D and as a result, have enabled precise generation of anisotropic polymeric particles. We demonstrate that this device can be utilized to produce anisotropic biodegradable particles of different size, shape, and material consistency. Furthermore, we show that this machine has enabled the scaled up and rapid production of anisotropic polymeric particles, including polymeric microparticles that mimic the shape of red blood cells. Further application of this automated thin film stretching device could allow for significant impact to diverse biomaterial and biomedical applications such as biomimetic particles for immunoengineering and long-circulating particles for controlled release of drugs. © 2015 Wiley Periodicals, Inc.

  5. Component-based modeling of systems for automated fault tree generation

    International Nuclear Information System (INIS)

    Majdara, Aref; Wakabayashi, Toshio

    2009-01-01

    One of the challenges in the field of automated fault tree construction is to find an efficient modeling approach that can support modeling of different types of systems without ignoring any necessary details. In this paper, we are going to represent a new system of modeling approach for computer-aided fault tree generation. In this method, every system model is composed of some components and different types of flows propagating through them. Each component has a function table that describes its input-output relations. For the components having different operational states, there is also a state transition table. Each component can communicate with other components in the system only through its inputs and outputs. A trace-back algorithm is proposed that can be applied to the system model to generate the required fault trees. The system modeling approach and the fault tree construction algorithm are applied to a fire sprinkler system and the results are presented

  6. 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.

  7. 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.

  8. 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.

  9. Application of a path sensitizing method on automated generation of test specifications for control software

    International Nuclear Information System (INIS)

    Morimoto, Yuuichi; Fukuda, Mitsuko

    1995-01-01

    An automated generation method for test specifications has been developed for sequential control software in plant control equipment. Sequential control software can be represented as sequential circuits. The control software implemented in a control equipment is designed from these circuit diagrams. In logic tests of VLSI's, path sensitizing methods are widely used to generate test specifications. But the method generates test specifications at a single time only, and can not be directly applied to sequential control software. The basic idea of the proposed method is as follows. Specifications of each logic operator in the diagrams are defined in the software design process. Therefore, test specifications of each operator in the control software can be determined from these specifications, and validity of software can be judged by inspecting all of the operators in the logic circuit diagrams. Candidates for sensitized paths, on which test data for each operator propagates, can be generated by the path sensitizing method. To confirm feasibility of the method, it was experimentally applied to control software in digital control equipment. The program could generate test specifications exactly, and feasibility of the method was confirmed. (orig.) (3 refs., 7 figs.)

  10. 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

  11. Automated panning and screening procedure on microplates for antibody generation from phage display libraries.

    Science.gov (United States)

    Turunen, Laura; Takkinen, Kristiina; Söderlund, Hans; Pulli, Timo

    2009-03-01

    Antibody phage display technology is well established and widely used for selecting specific antibodies against desired targets. Using conventional manual methods, it is laborious to perform multiple selections with different antigens simultaneously. Furthermore, manual screening of the positive clones requires much effort. The authors describe optimized and automated procedures of these processes using a magnetic bead processor for the selection and a robotic station for the screening step. Both steps are performed in a 96-well microplate format. In addition, adopting the antibody phage display technology to automated platform polyethylene glycol precipitation of the enriched phage pool was unnecessary. For screening, an enzyme-linked immunosorbent assay protocol suitable for a robotic station was developed. This system was set up using human gamma-globulin as a model antigen to select antibodies from a VTT naive human single-chain antibody (scFv) library. In total, 161 gamma-globulin-selected clones were screened, and according to fingerprinting analysis, 9 of the 13 analyzed clones were different. The system was further tested using testosterone bovine serum albumin (BSA) and beta-estradiol-BSA as antigens with the same library. In total, 1536 clones were screened from 4 rounds of selection with both antigens, and 29 different testosterone-BSA and 23 beta-estradiol-BSA binding clones were found and verified by sequencing. This automated antibody phage display procedure increases the throughput of generating wide panels of target-binding antibody candidates and allows the selection and screening of antibodies against several different targets in parallel with high efficiency.

  12. Inactivation of single-chain urokinase-type plasminogen activator by thrombin in human subjects

    NARCIS (Netherlands)

    Braat, E. A.; Levi, M. [=Marcel M.; Bos, R.; Haverkate, F.; Lassen, M. R.; de Maat, M. P.; Rijken, D. C.

    1999-01-01

    Thrombin cleaves single-chain urokinase-type plasminogen activator (scu-PA) into a virtually inactive two-chain form (tcu-PA/T), a process that may protect a blood clot from early fibrinolysis. It is not known under what circumstances tcu-PA/T can be generated in vivo. We have studied the occurrence

  13. Automated abdominal multi-organ segmentation with subject-specific atlas generation.

    Science.gov (United States)

    Wolz, Robin; Chu, Chengwen; Misawa, Kazunari; Fujiwara, Michitaka; Mori, Kensaku; Rueckert, Daniel

    2013-09-01

    A robust automated segmentation of abdominal organs can be crucial for computer aided diagnosis and laparoscopic surgery assistance. Many existing methods are specialized to the segmentation of individual organs and struggle to deal with the variability of the shape and position of abdominal organs. We present a general, fully-automated method for multi-organ segmentation of abdominal computed tomography (CT) scans. The method is based on a hierarchical atlas registration and weighting scheme that generates target specific priors from an atlas database by combining aspects from multi-atlas registration and patch-based segmentation, two widely used methods in brain segmentation. The final segmentation is obtained by applying an automatically learned intensity model in a graph-cuts optimization step, incorporating high-level spatial knowledge. The proposed approach allows to deal with high inter-subject variation while being flexible enough to be applied to different organs. We have evaluated the segmentation on a database of 150 manually segmented CT images. The achieved results compare well to state-of-the-art methods, that are usually tailored to more specific questions, with Dice overlap values of 94%, 93%, 70%, and 92% for liver, kidneys, pancreas, and spleen, respectively.

  14. 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 method was applied, combining support vector machine and multivariate generalized linear models to assess the early and late stages of fibrosis, respectively, based on these parameters. The verification cohort was used to verify the scoring method, and the area under the receiver operating characteristic curve was >0.82 for liver cirrhosis detection. Since no subjective gradings are needed, interobserver discrepancies could be avoided using this fully automated method.

  15. Automated facial recognition of manually generated clay facial approximations: Potential application in unidentified persons data repositories.

    Science.gov (United States)

    Parks, Connie L; Monson, Keith L

    2018-01-01

    This research examined how accurately 2D images (i.e., photographs) of 3D clay facial approximations were matched to corresponding photographs of the approximated individuals using an objective automated facial recognition system. Irrespective of search filter (i.e., blind, sex, or ancestry) or rank class (R 1 , R 10 , R 25 , and R 50 ) employed, few operationally informative results were observed. In only a single instance of 48 potential match opportunities was a clay approximation matched to a corresponding life photograph within the top 50 images (R 50 ) of a candidate list, even with relatively small gallery sizes created from the application of search filters (e.g., sex or ancestry search restrictions). Increasing the candidate lists to include the top 100 images (R 100 ) resulted in only two additional instances of correct match. Although other untested variables (e.g., approximation method, 2D photographic process, and practitioner skill level) may have impacted the observed results, this study suggests that 2D images of manually generated clay approximations are not readily matched to life photos by automated facial recognition systems. Further investigation is necessary in order to identify the underlying cause(s), if any, of the poor recognition results observed in this study (e.g., potential inferior facial feature detection and extraction). Additional inquiry exploring prospective remedial measures (e.g., stronger feature differentiation) is also warranted, particularly given the prominent use of clay approximations in unidentified persons casework. Copyright © 2017. Published by Elsevier B.V.

  16. Fully automated muscle quality assessment by Gabor filtering of second harmonic generation images

    Science.gov (United States)

    Paesen, Rik; Smolders, Sophie; Vega, José Manolo de Hoyos; Eijnde, Bert O.; Hansen, Dominique; Ameloot, Marcel

    2016-02-01

    Although structural changes on the sarcomere level of skeletal muscle are known to occur due to various pathologies, rigorous studies of the reduced sarcomere quality remain scarce. This can possibly be explained by the lack of an objective tool for analyzing and comparing sarcomere images across biological conditions. Recent developments in second harmonic generation (SHG) microscopy and increasing insight into the interpretation of sarcomere SHG intensity profiles have made SHG microscopy a valuable tool to study microstructural properties of sarcomeres. Typically, sarcomere integrity is analyzed by fitting a set of manually selected, one-dimensional SHG intensity profiles with a supramolecular SHG model. To circumvent this tedious manual selection step, we developed a fully automated image analysis procedure to map the sarcomere disorder for the entire image at once. The algorithm relies on a single-frequency wavelet-based Gabor approach and includes a newly developed normalization procedure allowing for unambiguous data interpretation. The method was validated by showing the correlation between the sarcomere disorder, quantified by the M-band size obtained from manually selected profiles, and the normalized Gabor value ranging from 0 to 1 for decreasing disorder. Finally, to elucidate the applicability of our newly developed protocol, Gabor analysis was used to study the effect of experimental autoimmune encephalomyelitis on the sarcomere regularity. We believe that the technique developed in this work holds great promise for high-throughput, unbiased, and automated image analysis to study sarcomere integrity by SHG microscopy.

  17. 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.

  18. Automated Generation of OCL Constraints: NL based Approach vs Pattern Based Approach

    Directory of Open Access Journals (Sweden)

    IMRAN SARWAR BAJWA

    2017-04-01

    Full Text Available This paper presents an approach used for automated generations of software constraints. In this model, the SBVR (Semantics of Business Vocabulary and Rules based semi-formal representation is obtained from the syntactic and semantic analysis of a NL (Natural Language (such as English sentence. A SBVR representation is easy to translate to other formal languages as SBVR is based on higher-order logic like other formal languages such as OCL (Object Constraint Language. The proposed model endows with a systematic and powerful system of incorporating NL knowledge on the formal languages. A prototype is constructed in Java (an Eclipse plug-in as a proof of the concept. The performance was tested for a few sample texts taken from existing research thesis reports and books

  19. 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. Copyright © 2015 Elsevier B.V. All rights

  20. 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

    1996-06-01

    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.

  1. Automated problem list generation and physicians perspective from a pilot study.

    Science.gov (United States)

    Devarakonda, Murthy V; Mehta, Neil; Tsou, Ching-Huei; Liang, Jennifer J; Nowacki, Amy S; Jelovsek, John Eric

    2017-09-01

    An accurate, comprehensive and up-to-date problem list can help clinicians provide patient-centered care. Unfortunately, problem lists created and maintained in electronic health records by providers tend to be inaccurate, duplicative and out of date. With advances in machine learning and natural language processing, it is possible to automatically generate a problem list from the data in the EHR and keep it current. In this paper, we describe an automated problem list generation method and report on insights from a pilot study of physicians' assessment of the generated problem lists compared to existing providers-curated problem lists in an institution's EHR system. The natural language processing and machine learning-based Watson 1 method models clinical thinking in identifying a patient's problem list using clinical notes and structured data. This pilot study assessed the Watson method and included 15 randomly selected, de-identified patient records from a large healthcare system that were each planned to be reviewed by at least two internal medicine physicians. The physicians created their own problem lists, and then evaluated the overall usefulness of their own problem lists (P), Watson generated problem lists (W), and the existing EHR problem lists (E) on a 10-point scale. The primary outcome was pairwise comparisons of P, W, and E. Six out of the 10 invited physicians completed 27 assessments of P, W, and E, and in process evaluated 732 Watson generated problems and 444 problems in the EHR system. As expected, physicians rated their own lists, P, highest. However, W was rated higher than E. Among 89% of assessments, Watson identified at least one important problem that physicians missed. Cognitive computing systems like this Watson system hold the potential for accurate, problem-list-centered summarization of patient records, potentially leading to increased efficiency, better clinical decision support, and improved quality of patient care. Copyright © 2017

  2. 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.

  3. Generating an Automated Test Suite by Variable Strength Combinatorial Testing for Web Services

    Directory of Open Access Journals (Sweden)

    Yin Li

    2016-09-01

    Full Text Available Testing Web Services has become the spotlight of software engineering as an important means to assure the quality of Web application. Due to lacking of graphic interface and source code, Web services need an automated testing method, which is an important part in efficiently designing and generating test suite. However, the existing testing methods may lead to the redundancy of test suite and the decrease of fault-detecting ability since it cannot handle scenarios where the strengths of the different interactions are not uniform. With the purpose of solving this problem, firstly the formal tree model based on WSDL is constructed and the actual interaction relationship of each node is made sufficient consideration into, then the combinatorial testing is proposed to generate variable strength combinatorial test suite based on One-test-at-a-time strategy. At last test cases are minimized according to constraint rules. The results show that compared with conventional random testing, the proposed approach can detect more errors with the same amount of test cases which turning out to be more ideal than existing ones in size.

  4. Automated planning target volume generation: an evaluation pitting a computer-based tool against human experts

    International Nuclear Information System (INIS)

    Ketting, Case H.; Austin-Seymour, Mary; Kalet, Ira; Jacky, Jon; Kromhout-Schiro, Sharon; Hummel, Sharon; Unger, Jonathan; Fagan, Lawrence M.; Griffin, Tom

    1997-01-01

    Purpose: Software tools are seeing increased use in three-dimensional treatment planning. However, the development of these tools frequently omits careful evaluation before placing them in clinical use. This study demonstrates the application of a rigorous evaluation methodology using blinded peer review to an automated software tool that produces ICRU-50 planning target volumes (PTVs). Methods and Materials: Seven physicians from three different institutions involved in three-dimensional treatment planning participated in the evaluation. Four physicians drew partial PTVs on nine test cases, consisting of four nasopharynx and five lung primaries. Using the same information provided to the human experts, the computer tool generated PTVs for comparison. The remaining three physicians, designated evaluators, individually reviewed the PTVs for acceptability. To exclude bias, the evaluators were blinded to the source (human or computer) of the PTVs they reviewed. Their scorings of the PTVs were statistically examined to determine if the computer tool performed as well as the human experts. Results: The computer tool was as successful as the human experts in generating PTVs. Failures were primarily attributable to insufficient margins around the clinical target volume and to encroachment upon critical structures. In a qualitative analysis, the human and computer experts displayed similar types and distributions of errors. Conclusions: Rigorous evaluation of computer-based radiotherapy tools requires comparison to current practice and can reveal areas for improvement before the tool enters clinical practice

  5. Automated Flight Dynamics Product Generation for the EOS AM-1 Spacecraft

    Science.gov (United States)

    Matusow, Carla

    1999-01-01

    As part of NASA's Earth Science Enterprise, the Earth Observing System (EOS) AM-1 spacecraft is designed to monitor long-term, global, environmental changes. Because of the complexity of the AM-1 spacecraft, the mission operations center requires more than 80 distinct flight dynamics products (reports). To create these products, the AM-1 Flight Dynamics Team (FDT) will use a combination of modified commercial software packages (e.g., Analytical Graphic's Satellite ToolKit) and NASA-developed software applications. While providing the most cost-effective solution to meeting the mission requirements, the integration of these software applications raises several operational concerns: (1) Routine product generation requires knowledge of multiple applications executing on variety of hardware platforms. (2) Generating products is a highly interactive process requiring a user to interact with each application multiple times to generate each product. (3) Routine product generation requires several hours to complete. (4) User interaction with each application introduces the potential for errors, since users are required to manually enter filenames and input parameters as well as run applications in the correct sequence. Generating products requires some level of flight dynamics expertise to determine the appropriate inputs and sequencing. To address these issues, the FDT developed an automation software tool called AutoProducts, which runs on a single hardware platform and provides all necessary coordination and communication among the various flight dynamics software applications. AutoProducts, autonomously retrieves necessary files, sequences and executes applications with correct input parameters, and deliver the final flight dynamics products to the appropriate customers. Although AutoProducts will normally generate pre-programmed sets of routine products, its graphical interface allows for easy configuration of customized and one-of-a-kind products. Additionally, Auto

  6. 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.

  7. Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.

    Science.gov (United States)

    Senger, Stefan; Bartek, Luca; Papadatos, George; Gaulton, Anna

    2015-12-01

    First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual processing and curation on such a large scale becomes even more challenging. An alternative approach better suited for this large corpus of documents is the automated extraction of chemical structures. A number of patent chemistry databases generated by using the latter approach are now available but little is known that can help to manage expectations when using them. This study aims to address this by comparing two such freely available sources, SureChEMBL and IBM SIIP (IBM Strategic Intellectual Property Insight Platform), with manually curated commercial databases. When looking at the percentage of chemical structures successfully extracted from a set of patents, using SciFinder as our reference, 59 and 51 % were also found in our comparison in SureChEMBL and IBM SIIP, respectively. When performing this comparison with compounds as starting point, i.e. establishing if for a list of compounds the databases provide the links between chemical structures and patents they appear in, we obtained similar results. SureChEMBL and IBM SIIP found 62 and 59 %, respectively, of the compound-patent pairs obtained from Reaxys. In our comparison of automatically generated vs. manually curated patent chemistry databases, the former successfully provided approximately 60 % of links between chemical structure and patents. It needs to be stressed that only a very limited number of patents and compound-patent pairs were used for our comparison. Nevertheless, our results will hopefully help to manage expectations of users of patent chemistry databases of this type and provide a useful framework for more studies like ours as well as guide future developments of the workflows used for the automated extraction of chemical structures from patents. The challenges we have encountered

  8. 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 

  9. Human Thrombin Injection for the Percutaneous Treatment of Iatrogenic Pseudoaneurysms

    International Nuclear Information System (INIS)

    Elford, Julian; Burrell, Christopher; Freeman, Simon; Roobottom, Carl

    2002-01-01

    Purpose: Thrombin injection is becoming well established for the percutaneous management of iatrogenic pseudoaneurysms. All the published series to date use bovine thrombin,and there have been reports of adverse immunologic effects following its use. Our study aimed to assess the efficacy of human thrombin injection for pseudoaneurysm occlusion. Methods:Fourteen patients with iatrogenic pseudoaneurysms underwent a color Doppler ultrasound examination to assess their suitability for percutaneous human thrombin injection. Human thrombin 1000 IU was then injected into the pseudoaneurysm sac under sterile conditions and with ultrasound guidance. A further color Doppler ultrasound examination was performed 24 hr later to confirm occlusion. Results: All 14 pseudoaneurysms were successfully occluded by human thrombin injection. In two cases a second injection of thrombin was required,but there were no other complications, and all pseudoaneurysms remained occluded at 24 hr. Conclusion: Ultrasound-guided human thrombin injection is simple to perform, effective and safe. We recommend that human thrombin becomes the agent of choice for percutaneous injection into iatrogenic pseudoaneurysms

  10. Thrombin induces macrophage migration inhibitory factor release and upregulation in urothelium: a possible contribution to bladder inflammation.

    Directory of Open Access Journals (Sweden)

    Pedro L Vera

    2010-12-01

    Full Text Available Macrophage migration inhibitory factor (MIF is a pro-inflammatory cytokine expressed by urothelial cells that mediates bladder inflammation. We investigated the effect of stimulation with thrombin, a Protease Activated Receptor-1 (PAR1 agonist, on MIF release and MIF mRNA upregulation in urothelial cells.MIF and PAR1 expression was examined in normal human immortalized urothelial cells (UROtsa using real-time RT-PCR, Western blotting and dual immunostaining. MIF and PAR1 immunostaining was also examined in rat urothelium. The effect of thrombin stimulation (100 nM on urothelial MIF release was examined in UROtsa cells (in vitro and in rats (in vivo. UROtsa cells were stimulated with thrombin, culture media were collected at different time points and MIF amounts were determined by ELISA. Pentobarbital anesthetized rats received intravesical saline (control, thrombin, or thrombin +2% lidocaine (to block nerve activity for 1 hr, intraluminal fluid was collected and MIF amounts determined by ELISA. Bladder or UROtsa MIF mRNA was measured using real time RT-PCR.UROtsa cells constitutively express MIF and PAR1 and immunostaining for both was observed in these cells and in the basal and intermediate layers of rat urothelium. Thrombin stimulation of urothelial cells resulted in a concentration- and time-dependent increase in MIF release both in vitro (UROtsa; 2.8-fold increase at 1 hr and in vivo (rat; 4.5-fold while heat-inactivated thrombin had no effect. In rats, thrombin-induced MIF release was reduced but not abolished by intravesical lidocaine treatment. Thrombin also upregulated MIF mRNA in UROtsa cells (3.3-fold increase and in the rat bladder (2-fold increase where the effect was reduced (1.4-fold by lidocaine treatment.Urothelial cells express both MIF and PAR1. Activation of urothelial PAR1 receptors, either by locally generated thrombin or proteases present in the urine, may mediate bladder inflammation by inducing urothelial MIF release and

  11. Conceptual Model of an Application for Automated Generation of Webpage Mobile Versions

    Directory of Open Access Journals (Sweden)

    Todor Rachovski

    2017-11-01

    Full Text Available Accessing webpages through various types of mobile devices with different screen sizes and using different browsers has put new demands on web developers. The main challenge is the development of websites with responsive design that is adaptable depending on the mobile device used. The article presents a conceptual model of an app for automated generation of mobile pages. It has five-layer architecture: database, database management layer, business logic layer, web services layer and a presentation layer. The database stores all the data needed to run the application. The database management layer uses an ORM model to convert relational data into an object-oriented format and control the access to them. The business logic layer contains components that perform the actual work on building a mobile version of the page, including parsing, building a hierarchical model of the page and a number of transformations. The web services layer provides external applications with access to lower-level functionalities, and the presentation layer is responsible for choosing and using the appropriate CSS. A web application that uses the proposed model was developed and experiments were conducted.

  12. 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.

  13. Agent-based Modeling Automated: Data-driven Generation of Innovation Diffusion Models

    NARCIS (Netherlands)

    Jensen, T.; Chappin, E.J.L.

    2016-01-01

    Simulation modeling is useful to gain insights into driving mechanisms of diffusion of innovations. This study aims to introduce automation to make identification of such mechanisms with agent-based simulation modeling less costly in time and labor. We present a novel automation procedure in which

  14. 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

  15. Object-Based Integration of Photogrammetric and LiDAR Data for Automated Generation of Complex Polyhedral Building Models

    Science.gov (United States)

    Kim, Changjae; Habib, Ayman

    2009-01-01

    This research is concerned with a methodology for automated generation of polyhedral building models for complex structures, whose rooftops are bounded by straight lines. The process starts by utilizing LiDAR data for building hypothesis generation and derivation of individual planar patches constituting building rooftops. Initial boundaries of these patches are then refined through the integration of LiDAR and photogrammetric data and hierarchical processing of the planar patches. Building models for complex structures are finally produced using the refined boundaries. The performance of the developed methodology is evaluated through qualitative and quantitative analysis of the generated building models from real data. PMID:22346722

  16. Thrombin-receptor antagonist vorapaxar in acute coronary syndromes

    DEFF Research Database (Denmark)

    Tricoci, Pierluigi; Huang, Zhen; Held, Claes

    2012-01-01

    Vorapaxar is a new oral protease-activated-receptor 1 (PAR-1) antagonist that inhibits thrombin-induced platelet activation.......Vorapaxar is a new oral protease-activated-receptor 1 (PAR-1) antagonist that inhibits thrombin-induced platelet activation....

  17. Translational Success Stories Development of Direct Thrombin Inhibitors

    NARCIS (Netherlands)

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

    2012-01-01

    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

  18. Hypersensitivity to thrombin of platelets from hypercholesterolemic rats

    International Nuclear Information System (INIS)

    Winocour, P.D.; Rand, M.L.; Kinlough-Rathbone, R.L.; Mustard, J.F.

    1986-01-01

    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 14 C-serotonin. In the presence of acetylsalicyclic acid (ASA) (to inhibit thromboxane A 2 (TXA 2 ) formation) and creatine phosphate/creatine phosphokinase (CP/CPK) (to remove released ADP), HC platelets aggregated more (26 +/- 1%) and released more 14 C (9.1 +/- 2.0%) than NC platelets (aggregation: 0%, p 14 C release: 1.5 +/- 0.5%, p 2 formation is involved in the hypersensitivity of HC platelets to thrombin. Total binding of 125 I-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 TXA 2 formation, the action of released ADP or increased thrombin binding

  19. Acidosis, magnesium and acetylsalicylic acid: Effects on thrombin

    Science.gov (United States)

    Borisevich, Nikolaj; Loznikova, Svetlana; Sukhodola, Aleksandr; Halets, Inessa; Bryszewska, Maria; Shcharbin, Dzmitry

    2013-03-01

    Thrombin, an enzyme from the hydrolase family, is the main component of the blood coagulation system. In ischemic stroke it acts as a serine protease that converts soluble fibrinogen into insoluble strands of fibrin forming blood clots in the brain. It has been found to phosphoresce at room temperature in the millisecond and microsecond ranges. The phosphorescence of thrombin was studied under physiological conditions, in acidosis (decrease of pH from 8.0 to 5.0) and on the addition of salts (magnesium sulfate and sodium chloride) and of acetylsalicylic acid, and its connection with thrombin function is discussed. Acidosis significantly increased the internal dynamics of thrombin. We propose that lactate-acidosis plays a protective role in stroke, preventing the formation of clots. The addition of NaCl and MgSO4 in different concentrations increased the internal dynamics of thrombin. Also, the addition of MgSO4 decreased thrombin-induced platelet aggregation. However, magnesium sulfate and acetylsalicylic acid in the therapeutic concentrations used for treatment of ischemic stroke had no effect on thrombin internal dynamics. The data obtained will help to elucidate the conformational stability of thrombin under conditions modulating lactate-acidosis and in the presence of magnesium sulfate.

  20. An automated graphics tool for comparative genomics: the Coulson plot generator.

    Science.gov (United States)

    Field, Helen I; Coulson, Richard M R; Field, Mark C

    2013-04-27

    Comparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under consideration. Frequently, genes can be grouped into small categories based on functional criteria, for example membership of a multimeric complex, participation in a metabolic or signaling pathway or shared sequence features and/or paralogy. These patterns of retention and loss are highly informative for the prediction of function, and hence possible biological context, and can provide great insights into the evolutionary history of cellular functions. However, representation of such information in a standard spreadsheet is a poor visual means from which to extract patterns within a dataset. We devised the Coulson Plot, a new graphical representation that exploits a matrix of pie charts to display comparative genomics data. Each pie is used to describe a complex or process from a separate taxon, and is divided into sectors corresponding to the number of proteins (subunits) in a complex/process. The predicted presence or absence of proteins in each complex are delineated by occupancy of a given sector; this format is visually highly accessible and makes pattern recognition rapid and reliable. A key to the identity of each subunit, plus hierarchical naming of taxa and coloring are included. A java-based application, the Coulson plot generator (CPG) automates graphic production, with a tab or comma-delineated text file as input and generating an editable portable document format or svg file. CPG software may be used to rapidly convert spreadsheet data to a graphical matrix pie chart format. The representation essentially retains all of the information from the spreadsheet but presents a graphically rich format making comparisons and identification of patterns significantly clearer. While the Coulson plot format is highly useful in comparative genomics, its

  1. Validation of Fully Automated VMAT Plan Generation for Library-Based Plan-of-the-Day Cervical Cancer Radiotherapy.

    Science.gov (United States)

    Sharfo, Abdul Wahab M; Breedveld, Sebastiaan; Voet, Peter W J; Heijkoop, Sabrina T; Mens, Jan-Willem M; Hoogeman, Mischa S; Heijmen, Ben J M

    2016-01-01

    To develop and validate fully automated generation of VMAT plan-libraries for plan-of-the-day adaptive radiotherapy in locally-advanced cervical cancer. Our framework for fully automated treatment plan generation (Erasmus-iCycle) was adapted to create dual-arc VMAT treatment plan libraries for cervical cancer patients. For each of 34 patients, automatically generated VMAT plans (autoVMAT) were compared to manually generated, clinically delivered 9-beam IMRT plans (CLINICAL), and to dual-arc VMAT plans generated manually by an expert planner (manVMAT). Furthermore, all plans were benchmarked against 20-beam equi-angular IMRT plans (autoIMRT). For all plans, a PTV coverage of 99.5% by at least 95% of the prescribed dose (46 Gy) had the highest planning priority, followed by minimization of V45Gy for small bowel (SB). Other OARs considered were bladder, rectum, and sigmoid. All plans had a highly similar PTV coverage, within the clinical constraints (above). After plan normalizations for exactly equal median PTV doses in corresponding plans, all evaluated OAR parameters in autoVMAT plans were on average lower than in the CLINICAL plans with an average reduction in SB V45Gy of 34.6% (plibraries has become feasible.

  2. 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.

  3. 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...

  4. Label-free aptamer biosensor for selective detection of thrombin

    Energy Technology Data Exchange (ETDEWEB)

    Na, Weidan; Liu, Xiaotong; Wang, Lei; Su, Xingguang, E-mail: suxg@jlu.edu.cn

    2015-10-29

    We fabricated a novel fluorescence biosensor for the selective detection of thrombin by using bovine serum albumin-capped CdS quantum dots (BSA-CdS QDs). Two kinds of designed DNA (DNA1 and DNA2) could bind to CdS QDs through the electrostatic interaction between DNA and Cd{sup 2+} on the surface of CdS QDs. The obtained DNA/BSA-CdS QDs kept stable in the solution with the fluorescence intensity obviously enhanced. Hairpin structure of DNA1contained two domains, one is the aptamer sequence of thrombin and the other is the complementary sequence of DNA2. When thrombin was added, it would bind to DNA1 and induce the hairpin structure of DNA1 changed into G-quadplex structure. Meanwhile, DNA2 would transfer from the surface of CdS QDs to DNA1 via hybridization, which resulted in the removal of DNA1 and DNA2 from the surface of CdS QDs, and led to the fluorescence intensity of CdS QDs reduced. Thus, the determination of thrombin could be achieved by monitoring the change of the fluorescence intensity of CdS QDs. The present method is simple and fast, and exhibits good selectivity for thrombin over other proteins. We have successfully detected thrombin in human serum samples with satisfactory results. - Highlights: • A novel strategy for the detection of thrombin was established based on BSA-CdS QDs. • DNA could serve as the co-ligands to stabilize CdS QDs and enhance the fluorescence intensity. • Thrombin could change the structure of DNA1 and quench the fluorescence of CdS QDs. • Thrombin in real sample was detected with satisfactory results.

  5. [Human thrombin: enzymatic properties, stability and standardization of preparation].

    Science.gov (United States)

    Kolodzeĭskaia, M V; Chernyshenko, T M

    2002-01-01

    The work deals with estimation of thrombin preparation having such features as: sedimentation activity 3000-3200 NIH un. per 1 mg of protein and 97% of active centres. The enzyme isolated has been estimated according to the amidolytic activity on synthetic substrates S-2160 and BAPNA being equal 5200 and 185 milli un/mg of protein, respectively. According to the electrophoresis in PAAG in the presence of Ds-Na the preparation is homogenous, its molecular mass is 36000. The fibrinogen sedimentation time dependence on the isolated thrombin concentration has been estimated as well as the comparative analysis with the thrombin of the firm "Sigma" with the previously calibrated activity using the international standartion (coded P4) has been conducted. The absence of proportionality between the substrate sedimentation time and the preparation concentration has been determined. It has been revealed, that if the experimental findings are presented in the units 1/t against the thrombin units NIH the right lines are received within the limits used. The defreezing and secondary freezing of the preparation preserved under -20 degrees C have been showed as rendering an essential effect on thrombin activity. In order of the enzyme stabilizing at preserving the thrombin isolated has been concentrated applying the amycon membranes (MWCo: 30,000). While applying the thrombin water-saline solution in the conditions selected the preparation has showed itself practically stable during a year without utilizing any admixtures. The essential effect on thrombin has been found from the side of 1% glycin, 0.5% PEG, 1% saccharose and so on. The thrombin isolated high functional homogeneity, its stability permit to recommend the preparation as an operative standard.

  6. Use of Automated Scoring Features to Generate Hypotheses Regarding Language-Based DIF

    Science.gov (United States)

    Shermis, Mark D.; Mao, Liyang; Mulholland, Matthew; Kieftenbeld, Vincent

    2017-01-01

    This study uses the feature sets employed by two automated scoring engines to determine if a "linguistic profile" could be formulated that would help identify items that are likely to exhibit differential item functioning (DIF) based on linguistic features. Sixteen items were administered to 1200 students where demographic information…

  7. Thrombin has biphasic effects on the nitric oxide-cGMP pathway in endothelial cells and contributes to experimental pulmonary hypertension.

    Directory of Open Access Journals (Sweden)

    Katrin F Nickel

    Full Text Available BACKGROUND: A potential role for coagulation factors in pulmonary arterial hypertension has been recently described, but the mechanism of action is currently not known. Here, we investigated the interactions between thrombin and the nitric oxide-cGMP pathway in pulmonary endothelial cells and experimental pulmonary hypertension. PRINCIPAL FINDINGS: Chronic treatment with the selective thrombin inhibitor melagatran (0.9 mg/kg daily via implanted minipumps reduced right ventricular hypertrophy in the rat monocrotaline model of experimental pulmonary hypertension. In vitro, thrombin was found to have biphasic effects on key regulators of the nitric oxide-cGMP pathway in endothelial cells (HUVECs. Acute thrombin stimulation led to increased expression of the cGMP-elevating factors endothelial nitric oxide synthase (eNOS and soluble guanylate cyclase (sGC subunits, leading to increased cGMP levels. By contrast, prolonged exposition of pulmonary endothelial cells to thrombin revealed a characteristic pattern of differential expression of the key regulators of the nitric oxide-cGMP pathway, in which specifically the factors contributing to cGMP elevation (eNOS and sGC were reduced and the cGMP-hydrolyzing PDE5 was elevated (qPCR and Western blot. In line with the differential expression of key regulators of the nitric oxide-cGMP pathway, a reduction of cGMP by prolonged thrombin stimulation was found. The effects of prolonged thrombin exposure were confirmed in endothelial cells of pulmonary origin (HPAECs and HPMECs. Similar effects could be induced by activation of protease-activated receptor-1 (PAR-1. CONCLUSION: These findings suggest a link between thrombin generation and cGMP depletion in lung endothelial cells through negative regulation of the nitric oxide-cGMP pathway, possibly mediated via PAR-1, which could be of relevance in pulmonary arterial hypertension.

  8. α-thrombin-induced inositol phosphate formation in G0-arrested and cycling hamster lung fibroblasts: evidence for a protein kinase C-mediated desensitization response

    International Nuclear Information System (INIS)

    L'allemain, G.; Paris, S.; Magnaldo, I.; Pouyssegur, J.

    1986-01-01

    In resting Chinese hamster fibroblasts (CCL39) α-thrombin rapidly induces the breakdown of phosphoinositides. Accumulation of inositol phosphates (IP), measured in the presence of Li + , is detectable within 5s (seconds) of thrombin stimulation. Formation of inositol tris- and bisphosphates slightly precedes that of inositol monophosphate, indicating that thrombin activates primarily the phospholipase C-mediated generation of inositol trisphosphate from phosphatidylinositol 4,5-bisphosphate. Initial rates of IP production increase with thrombin concentration, with no apparent saturability over the range 10 -4 -10 U/ml. Thrombin-induced phosphoinositide hydrolysis rapidly desensitizes (t/sub 1/2/ > 5 min), but a residual activity, corresponding to about 10% of the initial stimulation is sustained for at least 9 h, in contrast with the undetectable activity of G0-arrested cells. This apparent desensitization may be due to a feedback regulation by protein kinase C, since pretreatment with the phorbol ester 12-O-tetradecanoyl phorbol 13-acetate (TPA) markedly inhibits (by up to 70%) subsequent thrombin-induced inositol phosphate formation. This up regulation was found maximal in A51, a very well growth-arrested CCL39 derivative,and reduced or virtually abolished in two tumoral and growth factor-relaxed derivatives of CCL39. Although preliminary, this observation suggests that a persistent activation of phosphatidyl inositol breakdown might operate in variants selected for autonomous growth

  9. Purification and Characterization of Human Thrombin Activatable Fibrinolysis Inhibitor (TAFI)

    DEFF Research Database (Denmark)

    Christensen, Trine; Skottrup, Peter Durand; Valnickova, Zuzana

    Thrombin Activatable Fibrinolysis inhibitor (TAFI) is a basic carboxypeptidase, circulating in plasma as an enzymatic inactive precursor. TAFI shares ~40% overall sequence identity with pancreas Carboxypeptidase B (PCPB) with the activation peptide being less conserved. Following activation of TA...

  10. 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.

  11. Generation of orientation tools for automated zebrafish screening assays using desktop 3D printing

    OpenAIRE

    Wittbrodt, Jonas N.; Liebel, Urban; Gehrig, Jochen

    2014-01-01

    Background The zebrafish has been established as the main vertebrate model system for whole organism screening applications. However, the lack of consistent positioning of zebrafish embryos within wells of microtiter plates remains an obstacle for the comparative analysis of images acquired in automated screening assays. While technical solutions to the orientation problem exist, dissemination is often hindered by the lack of simple and inexpensive ways of distributing and duplicating tools. ...

  12. An automated procedure for calculating system matrices from perturbation data generated by an EAI Pacer and 100 hybrid computer system

    Science.gov (United States)

    Milner, E. J.; Krosel, S. M.

    1977-01-01

    Techniques are presented for determining the elements of the A, B, C, and D state variable matrices for systems simulated on an EAI Pacer 100 hybrid computer. An automated procedure systematically generates disturbance data necessary to linearize the simulation model and stores these data on a floppy disk. A separate digital program verifies this data, calculates the elements of the system matrices, and prints these matrices appropriately labeled. The partial derivatives forming the elements of the state variable matrices are approximated by finite difference calculations.

  13. Automated determination of size and morphology information from soot transmission electron microscope (TEM)-generated images

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Cheng; Chan, Qing N., E-mail: qing.chan@unsw.edu.au; Zhang, Renlin; Kook, Sanghoon; Hawkes, Evatt R.; Yeoh, Guan H. [UNSW, School of Mechanical and Manufacturing Engineering (Australia); Medwell, Paul R. [The University of Adelaide, Centre for Energy Technology (Australia)

    2016-05-15

    The thermophoretic sampling of particulates from hot media, coupled with transmission electron microscope (TEM) imaging, is a combined approach that is widely used to derive morphological information. The identification and the measurement of the particulates, however, can be complex when the TEM images are of low contrast, noisy, and have non-uniform background signal level. The image processing method can also be challenging and time consuming, when the samples collected have large variability in shape and size, or have some degree of overlapping. In this work, a three-stage image processing sequence is presented to facilitate time-efficient automated identification and measurement of particulates from the TEM grids. The proposed processing sequence is first applied to soot samples that were thermophoretically sampled from a laminar non-premixed ethylene-air flame. The parameter values that are required to be set to facilitate the automated process are identified, and sensitivity of the results to these parameters is assessed. The same analysis process is also applied to soot samples that were acquired from an externally irradiated laminar non-premixed ethylene-air flame, which have different geometrical characteristics, to assess the morphological dependence of the proposed image processing sequence. Using the optimized parameter values, statistical assessments of the automated results reveal that the largest discrepancies that are associated with the estimated values of primary particle diameter, fractal dimension, and prefactor values of the aggregates for the tested cases, are approximately 3, 1, and 10 %, respectively, when compared with the manual measurements.

  14. Automated determination of size and morphology information from soot transmission electron microscope (TEM)-generated images

    International Nuclear Information System (INIS)

    Wang, Cheng; Chan, Qing N.; Zhang, Renlin; Kook, Sanghoon; Hawkes, Evatt R.; Yeoh, Guan H.; Medwell, Paul R.

    2016-01-01

    The thermophoretic sampling of particulates from hot media, coupled with transmission electron microscope (TEM) imaging, is a combined approach that is widely used to derive morphological information. The identification and the measurement of the particulates, however, can be complex when the TEM images are of low contrast, noisy, and have non-uniform background signal level. The image processing method can also be challenging and time consuming, when the samples collected have large variability in shape and size, or have some degree of overlapping. In this work, a three-stage image processing sequence is presented to facilitate time-efficient automated identification and measurement of particulates from the TEM grids. The proposed processing sequence is first applied to soot samples that were thermophoretically sampled from a laminar non-premixed ethylene-air flame. The parameter values that are required to be set to facilitate the automated process are identified, and sensitivity of the results to these parameters is assessed. The same analysis process is also applied to soot samples that were acquired from an externally irradiated laminar non-premixed ethylene-air flame, which have different geometrical characteristics, to assess the morphological dependence of the proposed image processing sequence. Using the optimized parameter values, statistical assessments of the automated results reveal that the largest discrepancies that are associated with the estimated values of primary particle diameter, fractal dimension, and prefactor values of the aggregates for the tested cases, are approximately 3, 1, and 10 %, respectively, when compared with the manual measurements.

  15. P2X1 stimulation promotes thrombin receptor-mediated platelet aggregation.

    Science.gov (United States)

    Erhardt, J A; Toomey, J R; Douglas, S A; Johns, D G

    2006-04-01

    P2X1 receptors are ATP-gated channel demonstrated to be involved in multiple platelet responses, although in vitro analysis has been complicated by the effects of rapid desensitization. To further investigate potential roles of P2X1 receptors in platelet activation, the current study employed methods which maximally preserved P2X1 functionality. In preliminary in vivo studies, P2X1-deficiency reduced thrombus formation following the laser-induced, but not FeCl3-induced injury. Given the multiple potential mechanisms involved in thrombus formation in vivo, including tissue-factor/thrombin generation pathways, subsequent studies were designed to investigate the effects of P2X1 inhibition or stimulation on platelet activation in vitro; specifically, the interaction of P2X1 with thrombin receptor stimulation. Aggregation initiated by low/threshold levels of a protease-activated receptor (PAR)4 agonist was reduced in P2X1-deficient murine platelets, and inhibition of P2X1 in wild-type platelets similarly reduced PAR4-mediated aggregation. In human platelets, aggregation to low/threshold stimulation of PAR1 was inhibited with the P2X1 antagonist MRS2159. In addition, P2X1 stimulation primed human platelet responses, such that subsequent sub-threshold PAR1 responses were converted into significant aggregation. Selective ADP receptor inhibitors attenuated P2X1-mediated priming, suggesting that the synergy between P2X1 and sub-threshold PAR1 stimulation was in part because of enhanced granular release of ADP. Overall, the present study defines a novel interaction between platelet P2X1 and thrombin receptors, with P2X1 functioning to amplify aggregation responses at low levels of thrombin receptor stimulation.

  16. Aptamer/Protein Proximity Binding-Triggered Molecular Machine for Amplified Electrochemical Sensing of Thrombin.

    Science.gov (United States)

    Yang, Jianmei; Dou, Baoting; Yuan, Ruo; Xiang, Yun

    2017-05-02

    The development of convenient and sensitive methods without involving any enzymes or complex nanomaterials for the monitoring of proteins is of great significance in disease diagnostics. In this work, we describe the validation of a new aptamer/protein proximity binding-triggered molecular machinery amplification strategy for sensitive electrochemical assay of thrombin in complex serum samples. The sensing interface is prepared by self-assembly of three-stranded DNA complexes on the gold electrode. The association of two distinct functional aptamers with different sites of thrombin triggers proximity binding-induced displacement of one of the short single-stranded DNAs (ssDNAs) from the surface-immobilized three-stranded DNA complexes, exposing a prelocked toehold domain to hybridize with a methylene blue (MB)-tagged fuel ssDNA strand (MB-DNA). Subsequent toehold-mediated strand displacement by the MB-DNA leads to the release and recycling of the aptamer/protein complexes and the function of the molecular machine. Eventually, a large number of MB-DNA strands are captured by the sensor surface, generating drastically amplified electrochemical responses from the MB tags for sensitive detection of thrombin. Our signal amplified sensor is completely enzyme-free and shows a dynamic range from 5 pM to 1 nM with a detection limit of 1.7 pM. Such sensor also has a high specificity for thrombin assay in serum samples. By changing the affinity probe pairs, the developed sensor can be readily expanded as a more general platform for sensitive detection of different types of proteins.

  17. 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

    , one of the previously identified AEPs. We calculate the azeotropic lines using a numerical continuation method that solves the nonlinear azeotropic system of equations under a range of conditions and efficiently tracks entire azeotropic curves. We have integrated our strategy for calculating......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...

  18. Automated Gel Size Selection to Improve the Quality of Next-generation Sequencing Libraries Prepared from Environmental Water Samples.

    Science.gov (United States)

    Uyaguari-Diaz, Miguel I; Slobodan, Jared R; Nesbitt, Matthew J; Croxen, Matthew A; Isaac-Renton, Judith; Prystajecky, Natalie A; Tang, Patrick

    2015-04-17

    Next-generation sequencing of environmental samples can be challenging because of the variable DNA quantity and quality in these samples. High quality DNA libraries are needed for optimal results from next-generation sequencing. Environmental samples such as water may have low quality and quantities of DNA as well as contaminants that co-precipitate with DNA. The mechanical and enzymatic processes involved in extraction and library preparation may further damage the DNA. Gel size selection enables purification and recovery of DNA fragments of a defined size for sequencing applications. Nevertheless, this task is one of the most time-consuming steps in the DNA library preparation workflow. The protocol described here enables complete automation of agarose gel loading, electrophoretic analysis, and recovery of targeted DNA fragments. In this study, we describe a high-throughput approach to prepare high quality DNA libraries from freshwater samples that can be applied also to other environmental samples. We used an indirect approach to concentrate bacterial cells from environmental freshwater samples; DNA was extracted using a commercially available DNA extraction kit, and DNA libraries were prepared using a commercial transposon-based protocol. DNA fragments of 500 to 800 bp were gel size selected using Ranger Technology, an automated electrophoresis workstation. Sequencing of the size-selected DNA libraries demonstrated significant improvements to read length and quality of the sequencing reads.

  19. 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.

  20. Generation of orientation tools for automated zebrafish screening assays using desktop 3D printing.

    Science.gov (United States)

    Wittbrodt, Jonas N; Liebel, Urban; Gehrig, Jochen

    2014-05-01

    The zebrafish has been established as the main vertebrate model system for whole organism screening applications. However, the lack of consistent positioning of zebrafish embryos within wells of microtiter plates remains an obstacle for the comparative analysis of images acquired in automated screening assays. While technical solutions to the orientation problem exist, dissemination is often hindered by the lack of simple and inexpensive ways of distributing and duplicating tools. Here, we provide a cost effective method for the production of 96-well plate compatible zebrafish orientation tools using a desktop 3D printer. The printed tools enable the positioning and orientation of zebrafish embryos within cavities formed in agarose. Their applicability is demonstrated by acquiring lateral and dorsal views of zebrafish embryos arrayed within microtiter plates using an automated screening microscope. This enables the consistent visualization of morphological phenotypes and reporter gene expression patterns. The designs are refined versions of previously demonstrated devices with added functionality and strongly reduced production costs. All corresponding 3D models are freely available and digital design can be easily shared electronically. In combination with the increasingly widespread usage of 3D printers, this provides access to the developed tools to a wide range of zebrafish users. Finally, the design files can serve as templates for other additive and subtractive fabrication methods.

  1. Automated multiscale morphometry of muscle disease from second harmonic generation microscopy using tensor-based image processing.

    Science.gov (United States)

    Garbe, Christoph S; Buttgereit, Andreas; Schürmann, Sebastian; Friedrich, Oliver

    2012-01-01

    Practically, all chronic diseases are characterized by tissue remodeling that alters organ and cellular function through changes to normal organ architecture. Some morphometric alterations become irreversible and account for disease progression even on cellular levels. Early diagnostics to categorize tissue alterations, as well as monitoring progression or remission of disturbed cytoarchitecture upon treatment in the same individual, are a new emerging field. They strongly challenge spatial resolution and require advanced imaging techniques and strategies for detecting morphological changes. We use a combined second harmonic generation (SHG) microscopy and automated image processing approach to quantify morphology in an animal model of inherited Duchenne muscular dystrophy (mdx mouse) with age. Multiphoton XYZ image stacks from tissue slices reveal vast morphological deviation in muscles from old mdx mice at different scales of cytoskeleton architecture: cell calibers are irregular, myofibrils within cells are twisted, and sarcomere lattice disruptions (detected as "verniers") are larger in number compared to samples from healthy mice. In young mdx mice, such alterations are only minor. The boundary-tensor approach, adapted and optimized for SHG data, is a suitable approach to allow quick quantitative morphometry in whole tissue slices. The overall detection performance of the automated algorithm compares very well with manual "by eye" detection, the latter being time consuming and prone to subjective errors. Our algorithm outperfoms manual detection by time with similar reliability. This approach will be an important prerequisite for the implementation of a clinical image databases to diagnose and monitor specific morphological alterations in chronic (muscle) diseases. © 2011 IEEE

  2. A Novel Photoelectrochemical Biosensor for Tyrosinase and Thrombin Detection

    Science.gov (United States)

    Chen, Jiexia; Liu, Yifan; Zhao, Guang-Chao

    2016-01-01

    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. PMID:26805846

  3. 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.

  4. Mechanistic Modeling of the Effects of Acidosis on Thrombin Generation

    Science.gov (United States)

    2015-08-01

    The damage control sequence and underlying logic. Surg Clin North Am 1997;77:761–77 5. Waters JH, Miller LR, Clack S, Kim JV. Cause of metabolic ...1002–9 10. Ramaker AJ, Meyer P, van der Meer J, Struys MM, Lisman T, van Oeveren W, Hendriks HG. Effects of acidosis, alkalosis , hyperthermia and

  5. Lumbar model generator: a tool for the automated generation of a parametric scalable model of the lumbar spine.

    Science.gov (United States)

    Lavecchia, C E; Espino, D M; Moerman, K M; Tse, K M; Robinson, D; Lee, P V S; Shepherd, D E T

    2018-01-01

    Low back pain is a major cause of disability and requires the development of new devices to treat pathologies and improve prognosis following surgery. Understanding the effects of new devices on the biomechanics of the spine is crucial in the development of new effective and functional devices. The aim of this study was to develop a preliminary parametric, scalable and anatomically accurate finite-element model of the lumbar spine allowing for the evaluation of the performance of spinal devices. The principal anatomical surfaces of the lumbar spine were first identified, and then accurately fitted from a previous model supplied by S14 Implants (Bordeaux, France). Finally, the reconstructed model was defined according to 17 parameters which are used to scale the model according to patient dimensions. The developed model, available as a toolbox named the lumbar model generator, enables generating a population of models using subject-specific dimensions obtained from data scans or averaged dimensions evaluated from the correlation analysis. This toolbox allows patient-specific assessment, taking into account individual morphological variation. The models have applications in the design process of new devices, evaluating the biomechanics of the spine and helping clinicians when deciding on treatment strategies. © 2018 The Author(s).

  6. Oxidation State Specific Generation of Arsines from Methylated Arsenicals Based on L- Cysteine Treatment in Buffered Media for Speciation Analysis by Hydride Generation - Automated Cryotrapping - Gas Chromatography-Atomic Absorption Spectrometry with the Multiatomizer

    OpenAIRE

    Matoušek, Tomáš; Hernández-Zavala, Araceli; Svoboda, Milan; Langrová, Lenka; Adair, Blakely M.; Drobná, Zuzana; Thomas, David J.; Stýblo, Miroslav; Dědina, Jiří

    2008-01-01

    An automated system for hydride generation - cryotrapping- gas chromatography - atomic absorption spectrometry with the multiatomizer is described. Arsines are preconcentrated and separated in a Chromosorb filled U-tube. An automated cryotrapping unit, employing nitrogen gas formed upon heating in the detection phase for the displacement of the cooling liquid nitrogen, has been developed. The conditions for separation of arsines in a Chromosorb filled U-tube have been optimized. A complete se...

  7. 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

  8. 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.

  9. An Automated and Minimally Invasive Tool for Generating Autologous Viable Epidermal Micrografts

    Science.gov (United States)

    Osborne, Sandra N.; Schmidt, Marisa A.; Harper, John R.

    2016-01-01

    ABSTRACT OBJECTIVE: A new epidermal harvesting tool (CelluTome; Kinetic Concepts, Inc, San Antonio, Texas) created epidermal micrografts with minimal donor site damage, increased expansion ratios, and did not require the use of an operating room. The tool, which applies both heat and suction concurrently to normal skin, was used to produce epidermal micrografts that were assessed for uniform viability, donor-site healing, and discomfort during and after the epidermal harvesting procedure. DESIGN: This study was a prospective, noncomparative institutional review board–approved healthy human study to assess epidermal graft viability, donor-site morbidity, and patient experience. SETTING: These studies were conducted at the multispecialty research facility, Clinical Trials of Texas, Inc, San Antonio. PATIENTS: The participants were 15 healthy human volunteers. RESULTS: The average viability of epidermal micrografts was 99.5%. Skin assessment determined that 76% to 100% of the area of all donor sites was the same in appearance as the surrounding skin within 14 days after epidermal harvest. A mean pain of 1.3 (on a scale of 1 to 5) was reported throughout the harvesting process. CONCLUSIONS: Use of this automated, minimally invasive harvesting system provided a simple, low-cost method of producing uniformly viable autologous epidermal micrografts with minimal patient discomfort and superficial donor-site wound healing within 2 weeks. PMID:26765157

  10. An Automated and Minimally Invasive Tool for Generating Autologous Viable Epidermal Micrografts.

    Science.gov (United States)

    Osborne, Sandra N; Schmidt, Marisa A; Harper, John R

    2016-02-01

    A new epidermal harvesting tool (CelluTome; Kinetic Concepts, Inc, San Antonio, Texas) created epidermal micrografts with minimal donor site damage, increased expansion ratios, and did not require the use of an operating room. The tool, which applies both heat and suction concurrently to normal skin, was used to produce epidermal micrografts that were assessed for uniform viability, donor-site healing, and discomfort during and after the epidermal harvesting procedure. This study was a prospective, noncomparative institutional review board-approved healthy human study to assess epidermal graft viability, donor-site morbidity, and patient experience. These studies were conducted at the multispecialty research facility, Clinical Trials of Texas, Inc, San Antonio. The participants were 15 healthy human volunteers. The average viability of epidermal micrografts was 99.5%. Skin assessment determined that 76% to 100% of the area of all donor sites was the same in appearance as the surrounding skin within 14 days after epidermal harvest. A mean pain of 1.3 (on a scale of 1 to 5) was reported throughout the harvesting process. Use of this automated, minimally invasive harvesting system provided a simple, low-cost method of producing uniformly viable autologous epidermal micrografts with minimal patient discomfort and superficial donor-site wound healing within 2 weeks.

  11. Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

    International Nuclear Information System (INIS)

    Thompson, A.P.; Swiler, L.P.; Trott, C.R.; Foiles, S.M.; Tucker, G.J.

    2015-01-01

    We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum

  12. FULLY AUTOMATED GENERATION OF ACCURATE DIGITAL SURFACE MODELS WITH SUB-METER RESOLUTION FROM SATELLITE IMAGERY

    Directory of Open Access Journals (Sweden)

    J. Wohlfeil

    2012-07-01

    Full Text Available Modern pixel-wise image matching algorithms like Semi-Global Matching (SGM are able to compute high resolution digital surface models from airborne and spaceborne stereo imagery. Although image matching itself can be performed automatically, there are prerequisites, like high geometric accuracy, which are essential for ensuring the high quality of resulting surface models. Especially for line cameras, these prerequisites currently require laborious manual interaction using standard tools, which is a growing problem due to continually increasing demand for such surface models. The tedious work includes partly or fully manual selection of tie- and/or ground control points for ensuring the required accuracy of the relative orientation of images for stereo matching. It also includes masking of large water areas that seriously reduce the quality of the results. Furthermore, a good estimate of the depth range is required, since accurate estimates can seriously reduce the processing time for stereo matching. In this paper an approach is presented that allows performing all these steps fully automated. It includes very robust and precise tie point selection, enabling the accurate calculation of the images’ relative orientation via bundle adjustment. It is also shown how water masking and elevation range estimation can be performed automatically on the base of freely available SRTM data. Extensive tests with a large number of different satellite images from QuickBird and WorldView are presented as proof of the robustness and reliability of the proposed method.

  13. 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.

  14. Large-scale subject-specific cerebral arterial tree modeling using automated parametric mesh generation for blood flow simulation.

    Science.gov (United States)

    Ghaffari, Mahsa; Tangen, Kevin; Alaraj, Ali; Du, Xinjian; Charbel, Fady T; Linninger, Andreas A

    2017-12-01

    In this paper, we present a novel technique for automatic parametric mesh generation of subject-specific cerebral arterial trees. This technique generates high-quality and anatomically accurate computational meshes for fast blood flow simulations extending the scope of 3D vascular modeling to a large portion of cerebral arterial trees. For this purpose, a parametric meshing procedure was developed to automatically decompose the vascular skeleton, extract geometric features and generate hexahedral meshes using a body-fitted coordinate system that optimally follows the vascular network topology. To validate the anatomical accuracy of the reconstructed vasculature, we performed statistical analysis to quantify the alignment between parametric meshes and raw vascular images using receiver operating characteristic curve. Geometric accuracy evaluation showed an agreement with area under the curves value of 0.87 between the constructed mesh and raw MRA data sets. Parametric meshing yielded on-average, 36.6% and 21.7% orthogonal and equiangular skew quality improvement over the unstructured tetrahedral meshes. The parametric meshing and processing pipeline constitutes an automated technique to reconstruct and simulate blood flow throughout a large portion of the cerebral arterial tree down to the level of pial vessels. This study is the first step towards fast large-scale subject-specific hemodynamic analysis for clinical applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Horn fly (Diptera: Muscidae) saliva targets thrombin action in hemostasis.

    Science.gov (United States)

    Cupp, M S; Zhang, D; Cupp, E W

    2000-05-01

    The horn fly, Hematobia irritans (L.), is an important pest of livestock because the adult stage of both sexes are aggressive blood-feeders. Remarkably, even though horn fly adults feed recurrently on their hosts as ectoparasites, these flies lack the ADP-responsive antiplatelet aggregation and vasodilatory antihemostatic systems described for other blood-feeding Diptera. Horn fly salivary gland extracts do interfere with the normal coagulation process as demonstrated by the recalcification time assay. Using this as a baseline, the effects of saliva on recalcification time, activated partial thromboplastin time, prothrombin time, and thrombin time were measured to determine which arm(s) of the coagulation cascade might be impacted. Factor-deficient plasma assays also were used to measure possible perturbations in clotting. Gland-free saliva delayed the recalcification time as well as the activated partial thromboplastin time, prothrombin time, and thrombin time. Saliva also further delayed clotting times of plasmas deficient in factor V, factor VIII, and factor XIII, indicating that other factors in the coagulation cascade were inhibited. Although horn fly saliva did not alter the ability of deficient plasma reconstituted with factor X to clot, it did inhibit deficient plasma reconstituted with factor II (thrombin). Antithrombin activity in saliva was confirmed by its ability to interfere with thrombin hydrolysis of fibrinogen, its normal substrate, and by its inhibition of thrombin action on a chromagenic substrate that mimics the hydrolytic site of fibrinogen. Thus, horn fly saliva contains a factor that specifically targets thrombin, a key component in the coagulation cascade. While the biochemical mechanisms of inhibition may vary, this antihemostatic characteristic is shared with other zoophilic Diptera such as black flies, Simulium spp., and tsetse, Glossina morsitans morsitans Westwood, that feed on ungulates.

  16. Multiple active forms of thrombin. IV. Relative activities of meizothrombins

    International Nuclear Information System (INIS)

    Doyle, M.F.; Mann, K.G.

    1990-01-01

    The prothrombin activation intermediates meizothrombin and meizothrombin(desF1) (meizothrombin that has been autoproteolyzed to remove fragment 1) have been obtained in a relatively pure, active form with minimal autolysis, making them suitable for enzymatic characterization. When compared at equimolar concentrations, alpha-thrombin, fragment 1.2+ alpha-thrombin, meizothrombin(desF1), and meizothrombin have approximately 100, 100, 10, and 1% activity, respectively, toward the macromolecular substrates factor V, fibrinogen, and platelets. The difference in activity of these four enzymes cannot be attributed to alterations in the catalytic triad, as all four enzymes have nearly identical catalytic efficiency toward the chromogenic substrate S2238. Further, the ability of meizothrombin and meizothrombin(desF1) to activate protein C was 75% of the activity exhibited by alpha-thrombin or fragment 1.2+ alpha-thrombin. All four enzymes bind to thrombomodulin, as judged by the enhanced rate of protein C activation upon preincubation of the enzymes with thrombomodulin. The extent of rate enhancement varied, with meizothrombin/thrombomodulin exhibiting only 50% of the alpha-thrombin/thrombomodulin rate. This difference in rate is not due to a decreased affinity of the meizothrombin for thrombomodulin since the apparent dissociation constants for the alpha-thrombin-thrombomodulin complex and the meizothrombin-thrombomodulin complex are virtually identical. The difference in the observed rate is due in part to the higher Km for protein C exhibited by the meizothrombin-thrombomodulin complex. Incubation of the thrombomodulin-enzyme complex with phospholipid vesicles caused an increase in the protein C activation rates. The kinetic constants for protein C activation in the presence of phospholipid are virtually identical for these enzyme-thrombomodulin complexes

  17. Multiple active forms of thrombin. IV. Relative activities of meizothrombins

    Energy Technology Data Exchange (ETDEWEB)

    Doyle, M.F.; Mann, K.G. (Univ. of Vermont College of Medicine, Burlington (USA))

    1990-06-25

    The prothrombin activation intermediates meizothrombin and meizothrombin(desF1) (meizothrombin that has been autoproteolyzed to remove fragment 1) have been obtained in a relatively pure, active form with minimal autolysis, making them suitable for enzymatic characterization. When compared at equimolar concentrations, alpha-thrombin, fragment 1.2+ alpha-thrombin, meizothrombin(desF1), and meizothrombin have approximately 100, 100, 10, and 1% activity, respectively, toward the macromolecular substrates factor V, fibrinogen, and platelets. The difference in activity of these four enzymes cannot be attributed to alterations in the catalytic triad, as all four enzymes have nearly identical catalytic efficiency toward the chromogenic substrate S2238. Further, the ability of meizothrombin and meizothrombin(desF1) to activate protein C was 75% of the activity exhibited by alpha-thrombin or fragment 1.2+ alpha-thrombin. All four enzymes bind to thrombomodulin, as judged by the enhanced rate of protein C activation upon preincubation of the enzymes with thrombomodulin. The extent of rate enhancement varied, with meizothrombin/thrombomodulin exhibiting only 50% of the alpha-thrombin/thrombomodulin rate. This difference in rate is not due to a decreased affinity of the meizothrombin for thrombomodulin since the apparent dissociation constants for the alpha-thrombin-thrombomodulin complex and the meizothrombin-thrombomodulin complex are virtually identical. The difference in the observed rate is due in part to the higher Km for protein C exhibited by the meizothrombin-thrombomodulin complex. Incubation of the thrombomodulin-enzyme complex with phospholipid vesicles caused an increase in the protein C activation rates. The kinetic constants for protein C activation in the presence of phospholipid are virtually identical for these enzyme-thrombomodulin complexes.

  18. Steam generation process control and automation; Automacao e controle no processo de geracao de vapor

    Energy Technology Data Exchange (ETDEWEB)

    Souza Junior, Jose Cleodon de; Silva, Walmy Andre C.M. da [PETROBRAS S.A., Natal, RN (Brazil)

    2004-07-01

    This paper describes the implementation of the Supervisory Control and Data Acquisition System (SCADA) in the steam generation process for injection in heavy oil fields of the Alto do Rodrigues Production Asset, developed by PETROBRAS/E and P/UN-RNCE. This Asset is located in the northeastern region of Brazil, in Rio Grande do Norte State. It addresses to the steam generators for injection in oil wells and the upgrade project that installed remote terminal units and a new panel controlled by PLC, changed all the pneumatic transmitters by electronic and incorporated the steam quality and oxygen control, providing the remote supervision of the process. It also discusses the improvements obtained in the steam generation after the changes in the conception of the control and safety systems. (author)

  19. 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.

  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. Automated generation and ensemble-learned matching of X-ray absorption spectra

    Science.gov (United States)

    Zheng, Chen; Mathew, Kiran; Chen, Chi; Chen, Yiming; Tang, Hanmei; Dozier, Alan; Kas, Joshua J.; Vila, Fernando D.; Rehr, John J.; Piper, Louis F. J.; Persson, Kristin A.; Ong, Shyue Ping

    2018-03-01

    X-ray absorption spectroscopy (XAS) is a widely used materials characterization technique to determine oxidation states, coordination environment, and other local atomic structure information. Analysis of XAS relies on comparison of measured spectra to reliable reference spectra. However, existing databases of XAS spectra are highly limited both in terms of the number of reference spectra available as well as the breadth of chemistry coverage. In this work, we report the development of XASdb, a large database of computed reference XAS, and an Ensemble-Learned Spectra IdEntification (ELSIE) algorithm for the matching of spectra. XASdb currently hosts more than 800,000 K-edge X-ray absorption near-edge spectra (XANES) for over 40,000 materials from the open-science Materials Project database. We discuss a high-throughput automation framework for FEFF calculations, built on robust, rigorously benchmarked parameters. FEFF is a computer program uses a real-space Green's function approach to calculate X-ray absorption spectra. We will demonstrate that the ELSIE algorithm, which combines 33 weak "learners" comprising a set of preprocessing steps and a similarity metric, can achieve up to 84.2% accuracy in identifying the correct oxidation state and coordination environment of a test set of 19 K-edge XANES spectra encompassing a diverse range of chemistries and crystal structures. The XASdb with the ELSIE algorithm has been integrated into a web application in the Materials Project, providing an important new public resource for the analysis of XAS to all materials researchers. Finally, the ELSIE algorithm itself has been made available as part of veidt, an open source machine-learning library for materials science.

  2. Endotoxin, thrombin, and the Limulus amebocyte lysate test.

    Science.gov (United States)

    Yin, E T

    1975-09-01

    The Limulus amebocyte lysate, a proteinaceous composite isolated from the hemolymph cells of the horseshoe crab (Limulus polyphemus) is sensitive to picogram quantities of Gram-negative bacterial lipopolysaccharides. However, a controversy currently exists as to whether the Limulus amebocyte lysate is specifically sensitive to Gram-negative bacterial endotoxins as a result of a recent report that the blood coagulation protease, thrombin, can mimic endotoxins in the Limulus amebocyte lysate test. Experiments including those employing two highly purified fractions isolated from the Limulus lystae have provided us with evidence that thrombin per se is unable to mimic endotoxin.

  3. Automation of inspection methods for eddy current testing of steam generator tubes

    International Nuclear Information System (INIS)

    Meurgey, P.; Baumaire, A.

    1990-01-01

    Inspection of all the tubes of a steam generator when the reactor is stopped is required for some of these exchangers affected by stress corrosion cracking. Characterization of each crack, in each tube is made possible by the development of software for processing the signals from an eddy current probe. The ESTELLE software allows a rapid increase of tested tubes, more than 80,000 in 1989 [fr

  4. 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.

  5. Automated Generation of Traffic Incident Response Plan Based on Case-Based Reasoning and Bayesian Theory

    Directory of Open Access Journals (Sweden)

    Yongfeng Ma

    2014-01-01

    Full Text Available Traffic incident response plan, specifying response agencies and their responsibilities, can guide responders to take actions effectively and timely after traffic incidents. With a reasonable and feasible traffic incident response plan, related agencies will save many losses, such as humans and wealth. In this paper, how to generate traffic incident response plan automatically and specially was solved. Firstly, a well-known and approved method, Case-Based Reasoning (CBR, was introduced. Based on CBR, a detailed case representation and R5-cycle of CBR were developed. To enhance the efficiency of case retrieval, which was an important procedure, Bayesian Theory was introduced. To measure the performance of the proposed method, 23 traffic incidents caused by traffic crashes were selected and three indicators, Precision P, Recall R, and Indicator F, were used. Results showed that 20 of 23 cases could be retrieved effectively and accurately. The method is practicable and accurate to generate traffic incident response plans. The method will promote the intelligent generation and management of traffic incident response plans and also make Traffic Incident Management more scientific and effective.

  6. Temporal Dynamics of Health and Well-Being: A Crowdsourcing Approach to Momentary Assessments and Automated Generation of Personalized Feedback.

    Science.gov (United States)

    van der Krieke, Lian; Blaauw, Frank J; Emerencia, Ando C; Schenk, Hendrika M; Slaets, Joris P J; Bos, Elisabeth H; de Jonge, Peter; Jeronimus, Bertus F

    Recent developments in research and mobile health enable a quantitative idiographic approach in health research. The present study investigates the potential of an electronic diary crowdsourcing study in the Netherlands for (1) large-scale automated self-assessment for individual-based health promotion and (2) enabling research at both the between-persons and within-persons level. To illustrate the latter, we examined between-persons and within-persons associations between somatic symptoms and quality of life. A website provided the general Dutch population access to a 30-day (3 times a day) diary study assessing 43 items related to health and well-being, which gave participants personalized feedback. Associations between somatic symptoms and quality of life were examined with a linear mixed model. A total of 629 participants completed 28,430 assessments, with a mean (SD) of 45 (32) assessments per participant. Most participants (n = 517 [82%]) were women and 531 (84%) had high education. Almost 40% of the participants (n = 247) completed enough assessments (t = 68) to generate personalized feedback including temporal dynamics between well-being, health behavior, and emotions. Substantial between-person variability was found in the within-person association between somatic symptoms and quality of life. We successfully built an application for automated diary assessments and personalized feedback. The application was used by a sample of mainly highly educated women, which suggests that the potential of our intensive diary assessment method for large-scale health promotion is limited. However, a rich data set was collected that allows for group-level and idiographic analyses that can shed light on etiological processes and may contribute to the development of empirical-based health promotion solutions.

  7. TOWARD AUTOMATED FAÇADE TEXTURE GENERATION FOR 3D PHOTOREALISTIC CITY MODELLING WITH SMARTPHONES OR TABLET PCS

    Directory of Open Access Journals (Sweden)

    S. Wang

    2012-07-01

    Full Text Available 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.

  8. Human/autonomy collaboration for the automated generation of intelligence products

    Science.gov (United States)

    DiBona, Phil; Schlachter, Jason; Kuter, Ugur; Goldman, Robert

    2017-05-01

    Intelligence Analysis remains a manual process despite trends toward autonomy in information processing. Analysts need agile decision-­-support tools that can adapt to the evolving information needs of the mission, allowing the analyst to pose novel analytic questions. Our research enables the analysts to only provide a constrained English specification of what the intelligence product should be. Using HTN planning, the autonomy discovers, decides, and generates a workflow of algorithms to create the intelligence product. Therefore, the analyst can quickly and naturally communicate to the autonomy what information product is needed, rather than how to create it.

  9. Generating combinatorial test cases using Simplified Swarm Optimization (SSO algorithm for automated GUI functional testing

    Directory of Open Access Journals (Sweden)

    Bestoun S. Ahmed

    2014-12-01

    Full Text Available Graphical User Interface (GUI is the outer skin of programs that facilitate the interaction between the user and different type of computing devices. It is been used in different aspects ranging from normal computers, mobile device, to even very small device nowadays like watches. This interaction uses different tools and programming objects like images, text, buttons, checkboxes, etc. With this emergence of different types of GUIs, they become an essential component to be tested (if available in the software to ensure that the software meets the required quality by the user. In contrast to non-functional testing, function testing of GUI insures a proper interaction between the user and the application interface without dealing with the coding internals. In this paper, a strategy for GUI functional testing using Simplified Swarm Optimization (SSO is proposed. The SSO is used to generate an optimized test suite with the help of Event-Interaction Graph (EIG. The proposed strategy also manages and repairs the test suites by deleting the unnecessary event sequences that are not applicable. The proposed generation algorithm based on SSO has proved its effectiveness by evaluating it against other algorithms. In addition, the strategy is applied on a standard case study and proved its applicability in reality.

  10. Automated methodology for estimating waste streams generated from decommissioning contaminated facilities

    International Nuclear Information System (INIS)

    Toth, J.J.; King, D.A.; Humphreys, K.K.; Haffner, D.R.

    1994-01-01

    As part of the DOE Programmatic Environmental Impact Statement (PEIS), a viable way to determine aggregate waste volumes, cost, and direct labor hours for decommissioning and decontaminating facilities is required. In this paper, a methodology is provided for determining waste streams, cost and direct labor hours from remediation of contaminated facilities. The method is developed utilizing U.S. facility remediation data and information from several decommissioning programs, including reactor decommissioning projects. The method provides for rapid, consistent analysis for many facility types. Three remediation scenarios are considered for facility D ampersand D: unrestricted land use, semi-restricted land use, and restricted land use. Unrestricted land use involves removing radioactive components, decontaminating the building surfaces, and demolishing the remaining structure. Semi-restricted land use involves removing transuranic contamination and immobilizing the contamination on-site. Restricted land use involves removing the transuranic contamination and leaving the building standing. In both semi-restricted and restricted land use scenarios, verification of containment with environmental monitoring is required. To use the methodology, facilities are placed in a building category depending upon the level of contamination, construction design, and function of the building. Unit volume and unit area waste generation factors are used to calculate waste volumes and estimate the amount of waste generated in each of the following classifications: low-level, transuranic, and hazardous waste. Unit factors for cost and labor hours are also applied to the result to estimate D ampersand D cost and labor hours

  11. Rigidification of the autolysis loop enhances Na(+) binding to thrombin.

    Science.gov (United States)

    Pozzi, Nicola; Chen, Raymond; Chen, Zhiwei; Bah, Alaji; Di Cera, Enrico

    2011-11-01

    Binding of Na(+) to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na(+) is weak due to large heat capacity and enthalpy changes associated with binding, and the K(d)=80 mM ensures only 64% saturation of the site at the concentration of Na(+) in the blood (140 mM). Residues controlling Na(+) binding and activation have been identified. Yet, attempts to improve the interaction of Na(+) with thrombin and possibly increase catalytic activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human thrombin with the homologous rigid domain of the murine enzyme results in a drastic (up to 10-fold) increase in Na(+) affinity and a significant improvement in the catalytic activity of the enzyme. Rigidification of the autolysis loop abolishes the heat capacity change associated with Na(+) binding observed in the wild-type and also increases the stability of thrombin. These findings have general relevance to protein engineering studies of clotting proteases and trypsin-like enzymes. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Rigidification of the autolysis loop enhances Na+ binding to thrombin

    Science.gov (United States)

    Pozzi, Nicola; Chen, Raymond; Chen, Zhiwei; Bah, Alaji; Di Cera, Enrico

    2011-01-01

    Binding of Na+ to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na+ is weak due to large heat capacity and enthalpy changes associated with binding, and the Kd=80 mM ensures only 64% saturation of the site at the concentration of Na+ in the blood (140 mM). Residues controlling Na+ binding and activation have been identified. Yet, attempts to improve the interaction of Na+ with thrombin and possibly increase catalytic activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human thrombin with the homologous rigid domain of the murine enzyme results in a drastic (up to 10-fold) increase in Na+ affinity and a significant improvement in the catalytic activity of the enzyme. Rigidification of the autolysis loop abolishes the heat capacity change associated with Na+ binding observed in the wild-type and also increases the stability of thrombin. These findings have general relevance to protein engineering studies of clotting proteases and trypsin-like enzymes. PMID:21536369

  13. Tyrosine sulfation modulates activity of tick-derived thrombin inhibitors

    Science.gov (United States)

    Thompson, Robert E.; Liu, Xuyu; Ripoll-Rozada, Jorge; Alonso-García, Noelia; Parker, Benjamin L.; Pereira, Pedro José Barbosa; Payne, Richard J.

    2017-09-01

    Madanin-1 and chimadanin are two small cysteine-free thrombin inhibitors that facilitate blood feeding in the tick Haemaphysalis longicornis. Here, we report a post-translational modification—tyrosine sulfation—of these two proteins that is critical for potent anti-thrombotic and anticoagulant activity. Inhibitors produced in baculovirus-infected insect cells displayed heterogeneous sulfation of two tyrosine residues within each of the proteins. One-pot ligation-desulfurization chemistry enabled access to homogeneous samples of all possible sulfated variants of the proteins. Tyrosine sulfation of madanin-1 and chimadanin proved crucial for thrombin inhibitory activity, with the doubly sulfated variants three orders of magnitude more potent than the unmodified inhibitors. The three-dimensional structure of madanin-1 in complex with thrombin revealed a unique mode of inhibition, with the sulfated tyrosine residues binding to the basic exosite II of the protease. The importance of tyrosine sulfation within this family of thrombin inhibitors, together with their unique binding mode, paves the way for the development of anti-thrombotic drug leads based on these privileged scaffolds.

  14. Interaction of the 268-282 region of glycoprotein Ibalpha with the heparin-binding site of thrombin inhibits the enzyme activation of factor VIII.

    Science.gov (United States)

    De Cristofaro, R; De Filippis, V

    2003-01-01

    Activation of factor VIII (FVIII) by thrombin plays a fundamental role in the amplification of the coagulation cascade and takes place through specific proteolytic cleavages at Arg(372), Arg(740) and Arg(1689). Full FVIII activation requires cleavage at Arg(372), a process involving the alpha-thrombin exosite-II; referred to as heparin-binding site (HBS). The present study was aimed at investigating the effect of glycoprotein Ibalpha (GpIbalpha; 1-282 fragment) binding to thrombin HBS on FVIII activation. Similar experiments were also performed using a synthetic peptide modelled on the 268-282 sequence of GpIbalpha, and sulphated successfully at all tyrosine residues present along its sequence, at positions 276, 278 and 279. Both GpIbalpha 1-282 and the sulphated GpIb 268-282 peptides induced a progressive decrease (up to 70%) in activated FVIII generation, assessed by coagulation and FXa-generation assays. Furthermore, SDS/PAGE and Western-blot experiments showed that the specific appearance of the 44 kDa A2 domain on cleavage of the FVIII Arg(372)-Ser(373) peptide bond was delayed significantly in the presence of either GpIbalpha 1-282 or GpIb 268-282 peptide. Moreover, the effect of the latter on thrombin-mediated hydrolysis of a peptide having the sequence 341-376 of FVIII was investigated using reverse-phase HPLC. The k (cat)/ K (m) values of the FVIII 341-376 peptide hydrolysis by thrombin decreased linearly as a function of the GpIbalpha 268-282 peptide concentration, according to a competitive inhibition effect. Taken together, these experiments suggest that the sulphated 268-282 region of GpIbalpha binds to thrombin HBS, and is responsible for the inhibition of the Arg(372)-Ser(373) bond cleavage and activation of FVIII. PMID:12689334

  15. Thrombin induces rapid PAR1-mediated non-classical FGF1 release

    International Nuclear Information System (INIS)

    Duarte, Maria; Kolev, Vihren; Soldi, Raffaella; Kirov, Alexander; Graziani, Irene; Oliveira, Silvia Marta; Kacer, Doreen; Friesel, Robert; Maciag, Thomas; Prudovsky, Igor

    2006-01-01

    Thrombin induces cell proliferation and migration during vascular injury. We report that thrombin rapidly stimulated expression and release of the pro-angiogenic polypeptide fibroblast growth factor 1 (FGF1). Thrombin failed to induce FGF1 release from protease-activated receptor 1 (PAR1) null fibroblasts, indicating that this effect was dependent on PAR1. Similarly to thrombin, FGF1 expression and release were induced by TRAP, a specific oligopeptide agonist of PAR1. These results identify a novel aspect of the crosstalk between FGF and thrombin signaling pathways which both play important roles in tissue repair and angiogenesis

  16. MMS control system analysis using automated root-locus plot generation

    International Nuclear Information System (INIS)

    Hefler, J.W.

    1987-01-01

    Use of the Modular Modeling System (MMS) for control systems improvement has been impeded by the need to plot eigenvalues manually. This problem has been solved by an automatic eigenvalue plotting routine. A practical procedure for control systems analysis based upon automatically generated root-locus plots has been developed using the Advanced Continuous Simulation Language (ACSL)-based version of the Modular Modeling System. Examples are given of typical ACSL run-time statements. Actual root-locus and time history plots are shown for simple models (4 state variables). More complex models are discussed. The plots show the control systems response before and after the determination of tuning parameters using the methods described

  17. Automated WWER steam generator eddy current testing and plugging control system

    International Nuclear Information System (INIS)

    Gorecan, I.; Gortan, K.; Grzalja, I.

    2004-01-01

    The structural architecture of the system contains three main components which are described as follows: Manipulator Guidance System; Eddy Current Testing System; Plugging System. The manipulator system has the task to position the end-effectors to the desired tube position. When the final position is reached, the Eddy Current testing system performs data acquisition. In case defects are found, the plugging system performs tube plug installment. Each system is composed of 3 layers. The first layer is the hardware layer consisting of motors driving the effectors along with sensors needed to obtain the positioning data, pusher motors used to push the test probes into tubes of the WWER steam generator, and plugging hardware tool. The second layer is the control box performing basic monitoring and control routines as an interconnection between first and third layer. The highest layer is the control software, running on the PC, which is used as a human-machine-interface.(author)

  18. On random field Completely Automated Public Turing Test to Tell Computers and Humans Apart generation.

    Science.gov (United States)

    Kouritzin, Michael A; Newton, Fraser; Wu, Biao

    2013-04-01

    Herein, we propose generating CAPTCHAs through random field simulation and give a novel, effective and efficient algorithm to do so. Indeed, we demonstrate that sufficient information about word tests for easy human recognition is contained in the site marginal probabilities and the site-to-nearby-site covariances and that these quantities can be embedded directly into certain conditional probabilities, designed for effective simulation. The CAPTCHAs are then partial random realizations of the random CAPTCHA word. We start with an initial random field (e.g., randomly scattered letter pieces) and use Gibbs resampling to re-simulate portions of the field repeatedly using these conditional probabilities until the word becomes human-readable. The residual randomness from the initial random field together with the random implementation of the CAPTCHA word provide significant resistance to attack. This results in a CAPTCHA, which is unrecognizable to modern optical character recognition but is recognized about 95% of the time in a human readability study.

  19. CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data

    Directory of Open Access Journals (Sweden)

    Steve Davis

    2015-08-01

    Full Text Available The analysis of next-generation sequence (NGS data is often a fragmented step-wise process. For example, multiple pieces of software are typically needed to map NGS reads, extract variant sites, and construct a DNA sequence matrix containing only single nucleotide polymorphisms (i.e., a SNP matrix for a set of individuals. The management and chaining of these software pieces and their outputs can often be a cumbersome and difficult task. Here, we present CFSAN SNP Pipeline, which combines into a single package the mapping of NGS reads to a reference genome with Bowtie2, processing of those mapping (BAM files using SAMtools, identification of variant sites using VarScan, and production of a SNP matrix using custom Python scripts. We also introduce a Python package (CFSAN SNP Mutator that when given a reference genome will generate variants of known position against which we validate our pipeline. We created 1,000 simulated Salmonella enterica sp. enterica Serovar Agona genomes at 100× and 20× coverage, each containing 500 SNPs, 20 single-base insertions and 20 single-base deletions. For the 100× dataset, the CFSAN SNP Pipeline recovered 98.9% of the introduced SNPs and had a false positive rate of 1.04 × 10−6; for the 20× dataset 98.8% of SNPs were recovered and the false positive rate was 8.34 × 10−7. Based on these results, CFSAN SNP Pipeline is a robust and accurate tool that it is among the first to combine into a single executable the myriad steps required to produce a SNP matrix from NGS data. Such a tool is useful to those working in an applied setting (e.g., food safety traceback investigations as well as for those interested in evolutionary questions.

  20. Automated Kinematics Equations Generation and Constrained Motion Planning Resolution for Modular and Reconfigurable Robots

    Energy Technology Data Exchange (ETDEWEB)

    Pin, Francois G.; Love, Lonnie L.; Jung, David L.

    2004-03-29

    Contrary to the repetitive tasks performed by industrial robots, the tasks in most DOE missions such as environmental restoration or Decontamination and Decommissioning (D&D) can be characterized as ''batches-of-one'', in which robots must be capable of adapting to changes in constraints, tools, environment, criteria and configuration. No commercially available robot control code is suitable for use with such widely varying conditions. In this talk we present our development of a ''generic code'' to allow real time (at loop rate) robot behavior adaptation to changes in task objectives, tools, number and type of constraints, modes of controls or kinematics configuration. We present the analytical framework underlying our approach and detail the design of its two major modules for the automatic generation of the kinematics equations when the robot configuration or tools change and for the motion planning under time-varying constraints. Sample problems illustrating the capabilities of the developed system are presented.

  1. AN AUTOMATED METHOD FOR 3D ROOF OUTLINE GENERATION AND REGULARIZATION IN AIRBONE LASER SCANNER DATA

    Directory of Open Access Journals (Sweden)

    S. N. Perera

    2012-07-01

    Full Text Available In this paper, an automatic approach for the generation and regularization of 3D roof boundaries in Airborne Laser scanner data is presented. The workflow is commenced by segmentation of the point clouds. A classification step and a rule based roof extraction step are followed the planar segmentation. Refinement on roof extraction is performed in order to minimize the effect due to urban vegetation. Boundary points of the connected roof planes are extracted and fitted series of straight line segments. Each line is then regularized with respect to the dominant building orientation. We introduce the usage of cycle graphs for the best use of topological information. Ridge-lines and step-edges are basically extracted to recognise correct topological relationships among the roof faces. Inner roof corners are geometrically fitted based on the closed cycle graphs. Outer boundary is reconstructed using the same concept but with the outer most cycle graph. In here, union of the sub cycles is taken. Intermediate line segments (outer bounds are intersected to reconstruct the roof eave lines. Two test areas with two different point densities are tested with the developed approach. Performance analysis of the test results is provided to demonstrate the applicability of the method.

  2. Automated mask generation for PIV image analysis based on pixel intensity statistics

    Science.gov (United States)

    Masullo, Alessandro; Theunissen, Raf

    2017-06-01

    The measurement of displacements near the vicinity of surfaces involves advanced PIV algorithms requiring accurate knowledge of object boundaries. These data typically come in the form of a logical mask, generated manually or through automatic algorithms. The automatic detection of masks usually necessitates special features or reference points such as bright lines, high contrast objects, and sufficiently observable coherence between pixels. These are, however, not always present in experimental images necessitating a more robust and general approach. In this work, the authors propose a novel method for the automatic detection of static image regions which do not contain relevant information for the estimation of particle image displacements and can consequently be excluded or masked out. The method does not require any a priori knowledge of the static objects (i.e., contrast, brightness, or strong features) as it exploits statistical information from multiple PIV images. Based on the observation that the temporal variation in light intensity follows a completely different distribution for flow regions and object regions, the method utilizes a normality test and an automatic thresholding method on the retrieved probability to identify regions to be masked. The method is assessed through a Monte Carlo simulation with synthetic images and its performance under realistic imaging conditions is proven based on three experimental test cases.

  3. 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.

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

    Science.gov (United States)

    Johnson, Gregory R; Li, Jieyue; Shariff, Aabid; Rohde, Gustavo K; Murphy, Robert F

    2015-12-01

    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.

  5. Automated cloning methods.; TOPICAL

    International Nuclear Information System (INIS)

    Collart, F.

    2001-01-01

    Argonne has developed a series of automated protocols to generate bacterial expression clones by using a robotic system designed to be used in procedures associated with molecular biology. The system provides plate storage, temperature control from 4 to 37 C at various locations, and Biomek and Multimek pipetting stations. The automated system consists of a robot that transports sources from the active station on the automation system. Protocols for the automated generation of bacterial expression clones can be grouped into three categories (Figure 1). Fragment generation protocols are initiated on day one of the expression cloning procedure and encompass those protocols involved in generating purified coding region (PCR)

  6. Computational study of some benzamidine-based inhibitors of thrombin-like snake venom proteinases

    Science.gov (United States)

    Henriques, Elsa S.; Nascimento, Marco A. C.; Ramos, Maria João

    Pit viper venoms contain a number of serine proteinases that, despite their observed coagulant thrombin-like action in vitro, exhibit a paradoxical benign defibrinogenating (anticoagulant) action in vivo, with clinical applications in preventing thrombi and improved blood circulation. Considering that several benzamidine-based inhibitors, some highly selective to thrombin, also inhibit the enzymatic activity of such venombins, the modeling of their enzyme-inhibitor interactions could provide valuable information on the topological factors that determine the divergences in activity. The first step, and the object of the present study, was to derive the necessary set of parameters, consistent with the CHARMM force field, and to perform molecular dynamics (MD) simulations on a few selected representatives of the inhibitors in question under physiological conditions. Bonding and van der Waals parameters were derived by analogy to similar ones in the existing force field. Net atomic charges were obtained with a restrained fitting to the molecular electrostatic potential generated at B3LYP/6-31G(d) level. The parameters were refined to reproduce the available experimental geometries and crystal data, and the MD simulations of the free inhibitors in aqueous solution at 298 K provided an insightful description of their available conformational space.

  7. Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo.

    Science.gov (United States)

    Saravanan, Rathi; Adav, Sunil S; Choong, Yeu Khai; van der Plas, Mariena J A; Petrlova, Jitka; Kjellström, Sven; Sze, Siu Kwan; Schmidtchen, Artur

    2017-10-13

    The disease burden of failing skin repair and non-healing ulcers is extensive. There is an unmet need for new diagnostic approaches to better predict healing activity and wound infection. Uncontrolled and excessive protease activity, of endogenous or bacterial origin, has been described as a major contributor to wound healing impairments. Proteolytic peptide patterns could therefore correlate and "report" healing activity and infection. This work describes a proof of principle delineating a strategy by which peptides from a selected protein, human thrombin, are detected and attributed to proteolytic actions. With a particular focus on thrombin-derived C-terminal peptides (TCP), we show that distinct peptide patterns are generated in vitro by the human S1 peptidases human neutrophil elastase and cathepsin G, and the bacterial M4 peptidases Pseudomonas aeruginosa elastase and Staphylococcus aureus aureolysin, respectively. Corresponding peptide sequences were identified in wound fluids from acute and non-healing ulcers, and notably, one peptide, FYT21 (FYTHVFRLKKWIQKVIDQFGE), was only present in wound fluid from non-healing ulcers colonized by P. aeruginosa and S. aureus. Our result is a proof of principle pointing at the possibility of defining peptide biomarkers reporting distinct proteolytic activities, of potential implication for improved diagnosis of wound healing and infection.

  8. Feedback activation of factor XI by thrombin in plasma results in additional formation of thrombin that protects fibrin clots from fibrinolysis

    NARCIS (Netherlands)

    von dem Borne, P. A.; Meijers, J. C.; Bouma, B. N.

    1995-01-01

    Recently, an alternative pathway for factor XI activation has been described in which factor XI is activated by thrombin. Patients with a factor XI deficiency bleed mostly from tissues with high local fibrinolytic activity. Therefore, the role of thrombin-mediated factor XI activation in both fibrin

  9. 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.

  10. Automated Simulation Model Generation

    NARCIS (Netherlands)

    Huang, Y.

    2013-01-01

    One of today's challenges in the field of modeling and simulation is to model increasingly larger and more complex systems. Complex models take long to develop and incur high costs. With the advances in data collection technologies and more popular use of computer-aided systems, more data has become

  11. A second-generation device for automated training and quantitative behavior analyses of molecularly-tractable model organisms.

    Directory of Open Access Journals (Sweden)

    Douglas Blackiston

    2010-12-01

    Full Text Available A deep understanding of cognitive processes requires functional, quantitative analyses of the steps leading from genetics and the development of nervous system structure to behavior. Molecularly-tractable model systems such as Xenopus laevis and planaria offer an unprecedented opportunity to dissect the mechanisms determining the complex structure of the brain and CNS. A standardized platform that facilitated quantitative analysis of behavior would make a significant impact on evolutionary ethology, neuropharmacology, and cognitive science. While some animal tracking systems exist, the available systems do not allow automated training (feedback to individual subjects in real time, which is necessary for operant conditioning assays. The lack of standardization in the field, and the numerous technical challenges that face the development of a versatile system with the necessary capabilities, comprise a significant barrier keeping molecular developmental biology labs from integrating behavior analysis endpoints into their pharmacological and genetic perturbations. Here we report the development of a second-generation system that is a highly flexible, powerful machine vision and environmental control platform. In order to enable multidisciplinary studies aimed at understanding the roles of genes in brain function and behavior, and aid other laboratories that do not have the facilities to undergo complex engineering development, we describe the device and the problems that it overcomes. We also present sample data using frog tadpoles and flatworms to illustrate its use. Having solved significant engineering challenges in its construction, the resulting design is a relatively inexpensive instrument of wide relevance for several fields, and will accelerate interdisciplinary discovery in pharmacology, neurobiology, regenerative medicine, and cognitive science.

  12. 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.

  13. Thrombin preferentially induces autophagy in glia cells in the rat central nervous system.

    Science.gov (United States)

    Hu, Shukun; Wu, Gang; Ding, Xin; Zhang, Yi

    2016-09-06

    Autophagy widely occurs after intracerebral hemorrhage (ICH). In our previous study, we demonstrated that thrombin, a serine protease produced after hematoma, contributes to ICH-induced autophagy. However, whether thrombin plays a neuronal and/or astrocytic role in autophagy induction is largely unknown. Here, we examined the autophagic role of thrombin on neurons and glia cells, respectively. In vivo, we found that intracaudate injection of thrombin specifically elevated the astrocytic expression of beclin-1 and LC3, two autophagic markers, and promoted the formation of autophagic vacuoles within astrocytes rather than neurons in the ipsilateral basal ganglia. Consistent with this, thrombin enhanced the LC3-II level and increased the number of MDC-labeled autophagic vacuoles in cultured astrocytes. These results indicated that thrombin preferentially activated astrocytic autophagy after ICH, and therefore provided novel insights into the pathophysiological mechanisms and therapeutic targets for hemorrhage stroke and brain trauma. Copyright © 2016. Published by Elsevier Ireland Ltd.

  14. Thrombin Maybe Plays an Important Role in MK Differentiation into Platelets

    Directory of Open Access Journals (Sweden)

    Xiao-Lei Yang

    2016-01-01

    Full Text Available Objectives. After development and differentiation, megakaryocytes (MKs can produce platelets. As is well known, thrombopoietin (TPO can induce MKs to differentiate. The effect of thrombin on MKs differentiation is not clear. In this study, we used a human megakaryoblastic leukemia cell line (Meg-01 to assess the effect of thrombin on MKs differentiation. Methods. In order to interrogate the role of thrombin in Meg-01 cells differentiation, the changes of morphology, cellular function, and expression of diverse factors were analyzed. Results. The results show that thrombin suppresses Meg-01 cells proliferation and induces apoptosis and cell cycle arrest. Thrombin upregulates the expression of CD41b, which is one of the most important MK markers. Globin transcription factor 1 (GATA-1, an important transcriptional regulator, controls MK development and maturation. The expression of GATA-1 is also upregulated by thrombin in Meg-01 cells. The expression of B-cell lymphoma 2 (Bcl-2, an apoptosis-inhibitory protein, is downregulated by thrombin. Phosphorylated protein kinase B (p-AKT and phosphorylated extracellular signal-regulated kinase (p-ERK were upregulated by thrombin in Meg-01 cells. All the results are consistent with Meg-01 cells treated with TPO. Discussion and Conclusion. In conclusion, all these data indicate that thrombin maybe plays an important role in MK differentiation into platelets. However, whether the platelet-like particles are certainly platelets remains unknown.

  15. A chemiluminescence biosensor for the detection of thrombin based on the aptamer composites

    Science.gov (United States)

    Lin, Yanna; Li, Jianbo; Wang, Yanhui; Sun, Yuanling; Ding, Chaofan; Sun, Weiyan; Luo, Chuannan

    2018-03-01

    An efficient, rapid, simple and ultrasensitive chemiluminescence (CL) approach was proposed for thrombin detection based on the aptamer-thrombin recognition. The aptamer composites were synthesized in this work using graphene oxide (GO) as the backing material. The thrombin was adsorbed on the aptamer composites based on the aptamer-thrombin recognition. Thus, thrombin could be quantified by the difference value of the CL intensity between supernate of the sample and the mixture which composed of thrombin and coexisted substances. The CL intensity exhibits a stable response to thrombin over a concentration range from 2.5 × 10- 10 to 1 × 10- 9 mol·L- 1 with a detection limit as low as 8.3 × 10- 11 mol·L- 1, the relative standard deviation (RSD) was found to be 4.9% for 11 determinations of 1.25 × 10- 9 mol·L- 1 thrombin. Finally, the applicability of the method was verified by applying to serum samples. The recoveries were in the range of 90.3-101.0% with RSD of 2.6-3.2%.

  16. Probing the hirudin-thrombin interaction by incorporation of noncoded amino acids and molecular dynamics simulation

    NARCIS (Netherlands)

    De Filippis, [No Value; Colombo, G; Russo, [No Value; Spadari, B; Fontana, A

    2002-01-01

    Thrombin is a primary target for the development of novel anticoagulants, since It plays two important and opposite roles in hemostasis: procoagulant and anticoagulant. All thrombin functions are influenced by Na+ binding, which triggers the transition of this enzyme from an anticoagulant (slow)

  17. Three different signal amplification strategies for the impedimetric sandwich detection of thrombin

    Energy Technology Data Exchange (ETDEWEB)

    Ocaña, Cristina; Valle, Manel del, E-mail: manel.delvalle@uab.cat

    2016-03-17

    In this work, we report a comparative study on three highly specific amplification strategies for the ultrasensitive detection of thrombin with the use of aptamer sandwich protocol. The protocol consisted on the use of a first thrombin aptamer immobilized on the electrode surface, the recognition of thrombin protein, and the reaction with a second biotinylated thrombin aptamer forming the sandwich. Through the exposed biotin end, three variants have been tested to amplify the electrochemical impedance signal. The strategies included (a) silver enhancement treatment, (b) gold enhancement treatment and (c) insoluble product produced by the combination of the enzyme horseradish peroxidase (HRP) and 3-amino-9-ethylcarbazole (AEC). The properties of the sensing surface were probed by electrochemical impedance measurements in the presence of the ferrocyanide/ferricyanide redox marker. Insoluble product strategy and silver enhancement treatment resulted in the lowest detection limit (0.3 pM), while gold enhancement method resulted in the highest reproducibility, 8.8% RSD at the pM thrombin concentration levels. Results of silver and gold enhancement treatment also permitted direct inspection by scanning electron microscopy (SEM). - Highlights: • Aptasensor to detect thrombin reaching the femtomolar level. • Biosensing protocol employs two thrombin aptamers in a sandwich capture scheme. • Use of second biotinylated aptamer allows many amplification and detection variants. • Precipitation reaction provides the highest signal amplification of ca. 3 times. • Double recognition event improves remarkably selectivity for thrombin detection.

  18. Effects of Aerobic Capacity on Thrombin-Induced Hydrocephalus and White Matter Injury.

    Science.gov (United States)

    Ni, Wei; Gao, Feng; Zheng, Mingzhe; Koch, Lauren G; Britton, Steven L; Keep, Richard F; Xi, Guohua; Hua, Ya

    2016-01-01

    We have previously shown that intracerebral hemorrhage-induced brain injury is less in rats bred for high aerobic capacity (high capacity runners; HCR) compared with those bred for low aerobic capacity (low capacity runners; LCRs). Thrombin, an essential component in the coagulation cascade, is produced after cerebral hemorrhage. Intraventricular injection of thrombin causes significant hydrocephalus and white matter damage. In the present study, we examined the effect of exercise capacity on thrombin-induced hydrocephalus and white matter damage. Mid-aged (13-month-old) female LCRs (n = 13) and HCRs (n = 12) rats were used in this study. Rats received an intraventricular injection of thrombin (3 U, 50 μl). All rats underwent magnetic resonance imaging (MRI) at 24 h and were then euthanized for brain histology and Western blot. The mortalities were 20 % in LCRs and 33 % in HCRs after thrombin injection (p > 0.05). No rats died after saline injection. Intraventricular thrombin injection resulted in hydrocephalus and periventricular white matter damage as determined on MRI. In LCR rats, thrombin induced significant ventricle enlargement (23.0 ± 2.3 vs12.8 ± 1.9 mm(3) in LCR saline group; p hydrocephalus in rats with low aerobic capacity. A differential effect of thrombin may contribute to differences in the effects of cerebral hemorrhage with aerobic capacity.

  19. Open-Source Assisted Laboratory Automation through Graphical User Interfaces and 3D Printers: Application to Equipment Hyphenation for Higher-Order Data Generation.

    Science.gov (United States)

    Siano, Gabriel G; Montemurro, Milagros; Alcaráz, Mirta R; Goicoechea, Héctor C

    2017-10-17

    Higher-order data generation implies some automation challenges, which are mainly related to the hidden programming languages and electronic details of the equipment. When techniques and/or equipment hyphenation are the key to obtaining higher-order data, the required simultaneous control of them demands funds for new hardware, software, and licenses, in addition to very skilled operators. In this work, we present Design of Inputs-Outputs with Sikuli (DIOS), a free and open-source code program that provides a general framework for the design of automated experimental procedures without prior knowledge of programming or electronics. Basically, instruments and devices are considered as nodes in a network, and every node is associated both with physical and virtual inputs and outputs. Virtual components, such as graphical user interfaces (GUIs) of equipment, are handled by means of image recognition tools provided by Sikuli scripting language, while handling of their physical counterparts is achieved using an adapted open-source three-dimensional (3D) printer. Two previously reported experiments of our research group, related to fluorescence matrices derived from kinetics and high-performance liquid chromatography, were adapted to be carried out in a more automated fashion. Satisfactory results, in terms of analytical performance, were obtained. Similarly, advantages derived from open-source tools assistance could be appreciated, mainly in terms of lesser intervention of operators and cost savings.

  20. A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps.

    Science.gov (United States)

    Tan, Swee Jin; Phan, Huan; Gerry, Benjamin Michael; Kuhn, Alexandre; Hong, Lewis Zuocheng; Min Ong, Yao; Poon, Polly Suk Yean; Unger, Marc Alexander; Jones, Robert C; Quake, Stephen R; Burkholder, William F

    2013-01-01

    Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.

  1. 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.

  2. Thrombin contributes to protective immunity in pneumonia-derived sepsis via fibrin polymerization and platelet-neutrophil interactions

    NARCIS (Netherlands)

    Claushuis, T. A. M.; de Stoppelaar, S. F.; Stroo, I.; Roelofs, J. J. T. H.; Ottenhoff, R.; van der Poll, T.; van't Veer, C.

    2017-01-01

    Essentials Immunity and coagulation are linked during sepsis but the role of thrombin is not fully elucidated. We investigated the effect of thrombin inhibition on murine Klebsiella pneumosepsis outcome. Thrombin is crucial for survival and limiting bacterial growth in pneumonia derived sepsis.

  3. Enzyme binding selectivity prediction: alpha-thrombin vs trypsin inhibition.

    Science.gov (United States)

    Mlinsek, G; Novic, M; Kotnik, M; Solmajer, T

    2004-01-01

    In the present work we explore the possibility of an in-depth computational analysis of available experimental X-ray structures in the specific case of a series of alpha-thrombin and trypsin complexes with their respective inhibitors for the development of a novel scoring function based on molecular electrostatic potential computed at the contact surface in the enzyme-inhibitor molecular complex. We subsequently employ the chemometrical approach to determine which are the interactions in the large volume of data that determine the resulting experimental binding constant between ligand and receptor. The results of the model evaluated with molecules in the independent validation set show that a reasonable average error of 1.30 log units of the difference between experimental and calculated binding constants was achieved in the system thrombin-trypsin, which is comparable with those of methods from the literature. Furthermore, by a careful preparation of the Kohonen top layer in the artificial neural network approach that is normally perceived as a "black box device", we have been able to follow the implications of the structure of the inhibitor-enzyme complex for the inhibitor's binding constant. The method appears to be suitable for evaluation of selectivity in structurally similar enzymatic systems, which is currently an important problem in drug design. Copyright 2004 American Chemical Society

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

    International Nuclear Information System (INIS)

    Highsmith, R.F.; Gallaher, M.J.

    1986-01-01

    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 125 I-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

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

    Energy Technology Data Exchange (ETDEWEB)

    Highsmith, R.F.; Gallaher, M.J.

    1986-03-05

    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 /sup 125/I-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.

  6. Thrombin-Inhibiting Anticoagulant Liposomes: Development and Characterization.

    Science.gov (United States)

    Endreas, Wegderes; Brüßler, Jana; Vornicescu, Doru; Keusgen, Michael; Bakowsky, Udo; Steinmetzer, Torsten

    2016-02-04

    Many peptides and peptidomimetic drugs suffer from rapid clearance in vivo; this can be reduced by increasing their size through oligomerization or covalent conjugation with polymers. As proof of principle, an alternative strategy for drug oligomerization is described, in which peptidomimetic thrombin inhibitors are incorporated into the liposome surface. For this purpose, the inhibitor moieties were covalently coupled to a palmitic acid residue through a short bifunctionalized ethylene glycol spacer. These molecules were directly added to the lipid mixture used for liposome preparation. The obtained liposomes possess strong thrombin inhibitory potency in enzyme kinetic measurements and anticoagulant activity in plasma. Their strong potency and positive ζ potential indicate that large amounts of the benzamidine-derived inhibitors are located on the surface of the liposomes. This concept should be applicable to other drug molecules that suffer from rapid elimination and allow covalent modification with a suitable fatty acid residue. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Using Global Positioning Systems (GPS) and temperature data to generate time-activity classifications for estimating personal exposure in air monitoring studies: an automated method.

    Science.gov (United States)

    Nethery, Elizabeth; Mallach, Gary; Rainham, Daniel; Goldberg, Mark S; Wheeler, Amanda J

    2014-05-08

    Personal exposure studies of air pollution generally use self-reported diaries to capture individuals' time-activity data. Enhancements in the accuracy, size, memory and battery life of personal Global Positioning Systems (GPS) units have allowed for higher resolution tracking of study participants' locations. Improved time-activity classifications combined with personal continuous air pollution sampling can improve assessments of location-related air pollution exposures for health studies. Data was collected using a GPS and personal temperature from 54 children with asthma living in Montreal, Canada, who participated in a 10-day personal air pollution exposure study. A method was developed that incorporated personal temperature data and then matched a participant's position against available spatial data (i.e., road networks) to generate time-activity categories. The diary-based and GPS-generated time-activity categories were compared and combined with continuous personal PM2.5 data to assess the impact of exposure misclassification when using diary-based methods. There was good agreement between the automated method and the diary method; however, the automated method (means: outdoors = 5.1%, indoors other =9.8%) estimated less time spent in some locations compared to the diary method (outdoors = 6.7%, indoors other = 14.4%). Agreement statistics (AC1 = 0.778) suggest 'good' agreement between methods over all location categories. However, location categories (Outdoors and Transit) where less time is spent show greater disagreement: e.g., mean time "Indoors Other" using the time-activity diary was 14.4% compared to 9.8% using the automated method. While mean daily time "In Transit" was relatively consistent between the methods, the mean daily exposure to PM2.5 while "In Transit" was 15.9 μg/m3 using the automated method compared to 6.8 μg/m3 using the daily diary. Mean times spent in different locations as categorized by a GPS-based method were

  8. 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.

  9. 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

    of the thrombin receptor in growth-responsive CCL39 fibroblasts. Shc phosphorylation by thrombin or the thrombin receptor agonist peptide is maximal by 15 min and persists for > or = 2 h. Following thrombin stimulation, phosphorylated Shc is recruited to Grb2 complexes. One or more pertussis toxin......-insensitive proteins appear to mediate this effect, since (i) pertussis toxin pre-treatment of cells does not blunt the action of thrombin and (ii) Shc phosphorylation on tyrosine can be stimulated by the muscarinic m1 receptor. Shc phosphorylation does not appear to involve protein kinase C, since the addition of 4...

  10. AmeriFlux Data Processing: Integrating automated and manual data management across software technologies and an international network to generate timely data products

    Science.gov (United States)

    Christianson, D. S.; Beekwilder, N.; Chan, S.; Cheah, Y. W.; Chu, H.; Dengel, S.; O'Brien, F.; Pastorello, G.; Sandesh, M.; Torn, M. S.; Agarwal, D.

    2017-12-01

    AmeriFlux is a network of scientists who independently collect eddy covariance and related environmental observations at over 250 locations across the Americas. As part of the AmeriFlux Management Project, the AmeriFlux Data Team manages standardization, collection, quality assurance / quality control (QA/QC), and distribution of data submitted by network members. To generate data products that are timely, QA/QC'd, and repeatable, and have traceable provenance, we developed a semi-automated data processing pipeline. The new pipeline consists of semi-automated format and data QA/QC checks. Results are communicated via on-line reports as well as an issue-tracking system. Data processing time has been reduced from 2-3 days to a few hours of manual review time, resulting in faster data availability from the time of data submission. The pipeline is scalable to the network level and has the following key features. (1) On-line results of the format QA/QC checks are available immediately for data provider review. This enables data providers to correct and resubmit data quickly. (2) The format QA/QC assessment includes an automated attempt to fix minor format errors. Data submissions that are formatted in the new AmeriFlux FP-In standard can be queued for the data QA/QC assessment, often with minimal delay. (3) Automated data QA/QC checks identify and communicate potentially erroneous data via online, graphical quick views that highlight observations with unexpected values, incorrect units, time drifts, invalid multivariate correlations, and/or radiation shadows. (4) Progress through the pipeline is integrated with an issue-tracking system that facilitates communications between data providers and the data processing team in an organized and searchable fashion. Through development of these and other features of the pipeline, we present solutions to challenges that include optimizing automated with manual processing, bridging legacy data management infrastructure with

  11. The immobilization of a direct thrombin inhibitor to a polyurethane as a nonthrombogenic surface coating for extracorporeal circulation

    Science.gov (United States)

    Yu, Jane; Brisbois, Elizabeth; Handa, Hitesh; Annich, Gail; Meyerhoff, Mark; Bartlett, Robert; Major, Terry

    2016-01-01

    A biomaterial with both antithrombin and antiplatelet properties is the ideal surface for use in extracorporeal circulation (ECC) as it targets both fibrin generation and platelet adhesion. A hemocompatible surface coating avoids the need for systemic anticoagulation by providing a local anticoagulant effect at the polymer-blood interface. Previous work has demonstrated the potential use of argatroban, a direct thrombin inhibitor, as a nonthrombogenic material for extracorporeal devices. The work reported here focuses on the characterization of argatroban linked to a polyurethane-silicone polymer, CarboSil®. Chemical immobilization, the amount of argatroban, incubation times, and saturation point were evaluated to achieve maximal antithrombin activity at the polymer surface. Cross-linked polymer coatings reacted with 10 and 30 µmole of argatroban were prepared and tested. These coatings resulted in argatroban activity levels of 0.131 µM and 0.446 µM, respectively. After refining the cross-linking process, argatroban activity increased by approximately 3.6 fold. Maintenance of activity and leaching from the polymer surface were also evaluated. Using the refined process for linking argatroban to polymer, the resulting polymer was applied as a surface coating to the inner lumen of poly(vinyl chloride) ECC circuit tubing and its antithrombin effect evaluated using a 4 h rabbit ECC model. Following 4 h of blood exposure, the argatroban circuit demonstrated significantly less thrombus formation compared to the control CarboSil® coating with a 4.1 cm2 thrombus average area for the control coating compared to 1.2 cm2 for the argatroban coating (n=4). There was no significant change in thrombin time from baseline in plasma from animals in which the argatroban coated circuit was used, with a thrombin time of 16.2 s at t=0 and 14.5 s after 4 h. These results demonstrate the potential efficacy of immobilized argatroban as a hemocompatible biomaterial for extracorporeal

  12. Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics, thrombin and thermolysin inhibitors

    Science.gov (United States)

    Klebe, Gerhard; Mietzner, Thomas; Weber, Frank

    1994-12-01

    A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.

  13. The Organophosphate Paraoxon and Its Antidote Obidoxime Inhibit Thrombin Activity and Affect Coagulation In Vitro

    Science.gov (United States)

    Golderman, Valery; Shavit-Stein, Efrat; Tamarin, Ilia; Rosman, Yossi; Shrot, Shai; Rosenberg, Nurit

    2016-01-01

    Organophosphates (OPs) are potentially able to affect serine proteases by reacting with their active site. The potential effects of OPs on coagulation factors such as thrombin and on coagulation tests have been only partially characterized and potential interactions with OPs antidotes such as oximes and muscarinic blockers have not been addressed. In the current study, we investigated the in vitro interactions between coagulation, thrombin, the OP paraoxon, and its antidotes obidoxime and atropine. The effects of these substances on thrombin activity were measured in a fluorescent substrate and on coagulation by standard tests. Both paraoxon and obidoxime but not atropine significantly inhibited thrombin activity, and prolonged prothrombin time, thrombin time, and partial thromboplastin time. When paraoxon and obidoxime were combined, a significant synergistic effect was found on both thrombin activity and coagulation tests. In conclusion, paraoxon and obidoxime affect thrombin activity and consequently alter the function of the coagulation system. Similar interactions may be clinically relevant for coagulation pathways in the blood and possibly in the brain. PMID:27689805

  14. Oxidation state specific generation of arsines from methylated arsenicals based on L-cysteine treatment in buffered media for speciation analysis by hydride generation-automated cryotrapping-gas chromatography-atomic absorption spectrometry with the multiatomizer

    International Nuclear Information System (INIS)

    Matousek, Tomas; Hernandez-Zavala, Araceli; Svoboda, Milan; Langrova, Lenka; Adair, Blakely M.; Drobna, Zuzana; Thomas, David J.; Styblo, Miroslav; Dedina, Jiri

    2008-01-01

    An automated system for hydride generation-cryotrapping-gas chromatography-atomic absorption spectrometry with the multiatomizer is described. Arsines are preconcentrated and separated in a Chromosorb filled U-tube. An automated cryotrapping unit, employing nitrogen gas formed upon heating in the detection phase for the displacement of the cooling liquid nitrogen, has been developed. The conditions for separation of arsines in a Chromosorb filled U-tube have been optimized. A complete separation of signals from arsine, methylarsine, dimethylarsine, and trimethylarsine has been achieved within a 60 s reading window. The limits of detection for methylated arsenicals tested were 4 ng l -1 . Selective hydride generation is applied for the oxidation state specific speciation analysis of inorganic and methylated arsenicals. The arsines are generated either exclusively from trivalent or from both tri- and pentavalent inorganic and methylated arsenicals depending on the presence of L-cysteine as a prereductant and/or reaction modifier. A TRIS buffer reaction medium is proposed to overcome narrow optimum concentration range observed for the L-cysteine modified reaction in HCl medium. The system provides uniform peak area sensitivity for all As species. Consequently, the calibration with a single form of As is possible. This method permits a high-throughput speciation analysis of metabolites of inorganic arsenic in relatively complex biological matrices such as cell culture systems without sample pretreatment, thus preserving the distribution of tri- and pentavalent species

  15. Oxidation state specific generation of arsines from methylated arsenicals based on L-cysteine treatment in buffered media for speciation analysis by hydride generation-automated cryotrapping-gas chromatography-atomic absorption spectrometry with the multiatomizer

    Science.gov (United States)

    Matoušek, Tomáš; Hernández-Zavala, Araceli; Svoboda, Milan; Langrová, Lenka; Adair, Blakely M.; Drobná, Zuzana; Thomas, David J.; Stýblo, Miroslav; Dědina, Jiří

    2008-03-01

    An automated system for hydride generation-cryotrapping-gas chromatography-atomic absorption spectrometry with the multiatomizer is described. Arsines are preconcentrated and separated in a Chromosorb filled U-tube. An automated cryotrapping unit, employing nitrogen gas formed upon heating in the detection phase for the displacement of the cooling liquid nitrogen, has been developed. The conditions for separation of arsines in a Chromosorb filled U-tube have been optimized. A complete separation of signals from arsine, methylarsine, dimethylarsine, and trimethylarsine has been achieved within a 60 s reading window. The limits of detection for methylated arsenicals tested were 4 ng l - 1 . Selective hydride generation is applied for the oxidation state specific speciation analysis of inorganic and methylated arsenicals. The arsines are generated either exclusively from trivalent or from both tri- and pentavalent inorganic and methylated arsenicals depending on the presence of L-cysteine as a prereductant and/or reaction modifier. A TRIS buffer reaction medium is proposed to overcome narrow optimum concentration range observed for the L-cysteine modified reaction in HCl medium. The system provides uniform peak area sensitivity for all As species. Consequently, the calibration with a single form of As is possible. This method permits a high-throughput speciation analysis of metabolites of inorganic arsenic in relatively complex biological matrices such as cell culture systems without sample pretreatment, thus preserving the distribution of tri- and pentavalent species.

  16. Synergism between thrombin and adrenaline (epinephrine) in human platelets. Marked potentiation of inositol phospholipid metabolism.

    Science.gov (United States)

    Steen, V M; Tysnes, O B; Holmsen, H

    1988-01-01

    We have studied synergism between adrenaline (epinephrine) and low concentrations of thrombin in gel-filtered human platelets prelabelled with [32P]Pi. Suspensions of platelets, which did not contain added fibrinogen, were incubated at 37 degrees C to measure changes in the levels of 32P-labelled phosphatidylinositol 4,5-bisphosphate (PIP2), phosphatidylinositol 4-phosphate (PIP) and phosphatidate (PA), aggregation and dense-granule secretion after stimulation. Adrenaline alone (3.5-4.0 microM) did not cause a change in any parameter (phosphoinositide metabolism, aggregation and dense-granule secretion), but markedly enhanced the thrombin-induced responses over a narrow range of thrombin concentrations (0.03-0.08 units/ml). The thrombin-induced hydrolysis of inositol phospholipids by phospholipase C, which was measured as the formation of [32P]PA, was potentiated by adrenaline, as was the increase in the levels of [32P]PIP2 and [32P]PIP. The presence of adrenaline caused a shift to the left for the thrombin-induced changes in the phosphoinositide metabolism, without affecting the maximal levels of 32P-labelled compounds obtained. A similar shift by adrenaline in the dose-response relationship was previously demonstrated for thrombin-induced aggregation and dense-granule secretion. Also, the narrow range of concentrations of thrombin over which adrenaline potentiates thrombin-induced platelet responses is the same for changes in phosphoinositide metabolism and physiological responses (aggregation and dense-granule secretion). Our observations clearly indicate that adrenaline directly or indirectly influences thrombin-induced changes in phosphoinositide metabolism. PMID:2845924

  17. 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.

  18. 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

  19. 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

  20. 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...

  1. 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

    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 of the aptamers and thereby to maximize anticoagulant activity in functional assays. By judicious engineering...... of the DNA nanostructures, we have created a novel, functional DNA nanostructure, which is a multi-aptamer inhibitor with activity eightfold higher than free aptamer. Reversal of the thrombin inhibition was also achieved by the use of single-stranded DNA antidotes, thus enabling significant control over......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...

  2. Human Thrombin Detection Through a Sandwich Aptamer Microarray: Interaction Analysis in Solution and in Solid Phase

    Science.gov (United States)

    Sosic, Alice; Meneghello, Anna; Cretaio, Erica; Gatto, Barbara

    2011-01-01

    We have developed an aptamer-based microarray for human thrombin detection exploiting two non-overlapping DNA thrombin aptamers recognizing different exosites of the target protein. The 15-mer aptamer (TBA1) binds the fibrinogen-binding site, whereas the 29-mer aptamer (TBA2) binds the heparin binding domain. Extensive analysis on the complex formation between human thrombin and modified aptamers was performed by Electrophoresis Mobility Shift Assay (EMSA), in order to verify in solution whether the chemical modifications introduced would affect aptamers/protein recognition. The validated system was then applied to the aptamer microarray, using the solid phase system devised by the solution studies. Finally, the best procedure for Sandwich Aptamer Microarray (SAM) and the specificity of the sandwich formation for the developed aptasensor for human thrombin were optimized. PMID:22163703

  3. Impaired healing of cutaneous wounds and colonic anastomoses in mice lacking thrombin-activatable fibrinolysis inhibitor

    NARCIS (Netherlands)

    te Velde, E. A.; Wagenaar, G. T. M.; Reijerkerk, A.; Roose-Girma, M.; Borel Rinkes, I. H. M.; Voest, E. E.; Bouma, B. N.; Gebbink, M. F. B. G.; Meijers, J. C. M.

    2003-01-01

    Plasmin and other components of the plasminogen activation system play an important role in tissue repair by regulating extracellular matrix remodeling, including fibrin degradation. Thrombin-activatable fibrinolysis inhibitor (TAFI) is a procarboxypeptidase that, after activation, can attenuate

  4. Behaviour of homologous 125I fibrinogen after thrombin and ancrod infusion in rabbits

    International Nuclear Information System (INIS)

    Setter, R.

    1977-01-01

    The behaviour of radioactively labelled fibrinogen after infusion of thrombin or ancrod is investigated. Common factors and differences in the behaviour of fibrinogen after infusion of these two enzymes, which act proteolytically on the fibrinogen, are dealt with. Rabbits received an i.v. injection of homologous 125 I-fibrinogen 3 days before ancrod or thrombin infusion. On the day of the experiments, one group of animals received an ancrod infusion (1.5 U/kg body weight for 30 minutes), the other a thrombin infusion (600 U/kg body weight for 60 minutes). Intravenous ancrod and thrombin infusions lowered the fibrinogen level to 30% or 50% of the initial value due to intravascular coagulation. About 50% of the 125 I fibrinogen was transformed after ancrod exposure into a non-coagulating fraction of fibrinogen derivatives which produces no fibrinolytic decomposition products. (orig./AJ) [de

  5. Active but inoperable thrombin is accumulated in a plasma protein layer surrounding Streptococcus pyogenes

    NARCIS (Netherlands)

    Naudin, Clément; Hurley, Sinead M.; Malmström, Erik; Plug, Tom; Shannon, Oonagh; Meijers, Joost C. M.; Mörgelin, Matthias; Björck, Lars; Herwald, Heiko

    2015-01-01

    Activation of thrombin is a critical determinant in many physiological and pathological processes including haemostasis and inflammation. Under physiological conditions many of these functions are involved in wound healing or eradication of an invading pathogen. However, when activated systemically,

  6. Histopathology of Lesions in Swine Exposed to a Hemostatic Bandage Composed of Salmon Thrombin and Fibrinogen

    National Research Council Canada - National Science Library

    Szabo, Kathleen A; Flournoy, William S; Dorsey, Evelyn Sawyer ;David Simpson ;Gary Cadd ;Jennifer; Rothwell, Stephen W

    2006-01-01

    .... However, because of concern that these foreign proteins may induce an immune response in the patients, we investigated the inflammatory response in pigs exposed to salmon thrombin/fibrinogen dressings...

  7. Identification of berberine as a direct thrombin inhibitor from traditional Chinese medicine through structural, functional and binding studies

    Science.gov (United States)

    Wang, Xing; Zhang, Yuxin; Yang, Ying; Wu, Xia; Fan, Hantian; Qiao, Yanjiang

    2017-03-01

    Thrombin acts as a key enzyme in the blood coagulation cascade and represents a potential drug target for the treatment of several cardiovascular diseases. The aim of this study was to identify small-molecule direct thrombin inhibitors from herbs used in traditional Chinese medicine (TCM). A pharmacophore model and molecular docking were utilized to virtually screen a library of chemicals contained in compositions of traditional Chinese herbs, and these analyses were followed by in vitro bioassay validation and binding studies. Berberine (BBR) was first confirmed as a thrombin inhibitor using an enzymatic assay. The BBR IC50 value for thrombin inhibition was 2.92 μM. Direct binding studies using surface plasmon resonance demonstrated that BBR directly interacted with thrombin with a KD value of 16.39 μM. Competitive binding assay indicated that BBR could bind to the same argartroban/thrombin interaction site. A platelet aggregation assay demonstrated that BBR had the ability to inhibit thrombin-induced platelet aggregation in washed platelets samples. This study proved that BBR is a direct thrombin inhibitor that has activity in inhibiting thrombin-induced platelet aggregation. BBR may be a potential candidate for the development of safe and effective thrombin-inhibiting drugs.

  8. Thrombin and fibrinogen γ' impact clot structure by marked effects on intrafibrillar structure and protofibril packing.

    Science.gov (United States)

    Domingues, Marco M; Macrae, Fraser L; Duval, Cédric; McPherson, Helen R; Bridge, Katherine I; Ajjan, Ramzi A; Ridger, Victoria C; Connell, Simon D; Philippou, Helen; Ariëns, Robert A S

    2016-01-28

    Previous studies have shown effects of thrombin and fibrinogen γ' on clot structure. However, structural information was obtained using electron microscopy, which requires sample dehydration. Our aim was to investigate the role of thrombin and fibrinogen γ' in modulating fibrin structure under fully hydrated conditions. Fibrin fibers were studied using turbidimetry, atomic force microscopy, electron microscopy, and magnetic tweezers in purified and plasma solutions. Increased thrombin induced a pronounced decrease in average protofibril content per fiber, with a relatively minor decrease in fiber size, leading to the formation of less compact fiber structures. Atomic force microscopy under fully hydrated conditions confirmed that fiber diameter was only marginally decreased. Decreased protofibril content of the fibers produced by high thrombin resulted in weakened clot architecture as analyzed by magnetic tweezers in purified systems and by thromboelastometry in plasma and whole blood. Fibers produced with fibrinogen γ' showed reduced protofibril packing over a range of thrombin concentrations. High-magnification electron microscopy demonstrated reduced protofibril packing in γ' fibers and unraveling of fibers into separate protofibrils. Decreased protofibril packing was confirmed in plasma for high thrombin concentrations and fibrinogen-deficient plasma reconstituted with γ' fibrinogen. These findings demonstrate that, in fully hydrated conditions, thrombin and fibrinogen γ' have dramatic effects on protofibril content and that protein density within fibers correlates with strength of the fibrin network. We conclude that regulation of protofibril content of fibers is an important mechanism by which thrombin and fibrinogen γ' modulate fibrin clot structure and strength. © 2016 by The American Society of Hematology.

  9. Enzyme engineering: A synthetic biology approach for more effective library generation and automated high-throughput screening

    Science.gov (United States)

    Ebert, Maximilian C. C. J. C.; Mugford, Paul F.; Pelletier, Joelle N.

    2017-01-01

    The Golden Gate strategy entails the use of type IIS restriction enzymes, which cut outside of their recognition sequence. It enables unrestricted design of unique DNA fragments that can be readily and seamlessly recombined. Successfully employed in other synthetic biology applications, we demonstrate its advantageous use to engineer a biocatalyst. Hot-spots for mutations were individuated in three distinct regions of Candida antarctica lipase A (Cal-A), the biocatalyst chosen as a target to demonstrate the versatility of this recombination method. The three corresponding gene segments were subjected to the most appropriate method of mutagenesis (targeted or random). Their straightforward reassembly allowed combining products of different mutagenesis methods in a single round for rapid production of a series of diverse libraries, thus facilitating directed evolution. Screening to improve discrimination of short-chain versus long-chain fatty acid substrates was aided by development of a general, automated method for visual discrimination of the hydrolysis of varied substrates by whole cells. PMID:28178357

  10. Enzyme engineering: A synthetic biology approach for more effective library generation and automated high-throughput screening.

    Directory of Open Access Journals (Sweden)

    Daniela Quaglia

    Full Text Available The Golden Gate strategy entails the use of type IIS restriction enzymes, which cut outside of their recognition sequence. It enables unrestricted design of unique DNA fragments that can be readily and seamlessly recombined. Successfully employed in other synthetic biology applications, we demonstrate its advantageous use to engineer a biocatalyst. Hot-spots for mutations were individuated in three distinct regions of Candida antarctica lipase A (Cal-A, the biocatalyst chosen as a target to demonstrate the versatility of this recombination method. The three corresponding gene segments were subjected to the most appropriate method of mutagenesis (targeted or random. Their straightforward reassembly allowed combining products of different mutagenesis methods in a single round for rapid production of a series of diverse libraries, thus facilitating directed evolution. Screening to improve discrimination of short-chain versus long-chain fatty acid substrates was aided by development of a general, automated method for visual discrimination of the hydrolysis of varied substrates by whole cells.

  11. 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.

  12. Automated tube voltage selection for radiation dose and contrast medium reduction at coronary CT angiography using 3{sup rd} generation dual-source CT

    Energy Technology Data Exchange (ETDEWEB)

    Mangold, Stefanie [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); Eberhard-Karls University Tuebingen, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany); Wichmann, Julian L. [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Schoepf, U.J. [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); Medical University of South Carolina, Division of Cardiology, Department of Medicine, Charleston, SC (United States); Poole, Zachary B.; Varga-Szemes, Akos; De Cecco, Carlo N. [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); Canstein, Christian [Siemens Medical Solutions, Malvern, PA (United States); Caruso, Damiano [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); University of Rome ' ' Sapienza' ' , Department of Radiological Sciences, Oncology and Pathology, Rome (Italy); Bamberg, Fabian; Nikolaou, Konstantin [Eberhard-Karls University Tuebingen, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany)

    2016-10-15

    To investigate the relationship between automated tube voltage selection (ATVS) and body mass index (BMI) and its effect on image quality and radiation dose of coronary CT angiography (CCTA). We evaluated 272 patients who underwent CCTA with 3{sup rd} generation dual-source CT (DSCT). Prospectively ECG-triggered spiral acquisition was performed with automated tube current selection and advanced iterative reconstruction. Tube voltages were selected by ATVS (70-120 kV). BMI, effective dose (ED), and vascular attenuation in the coronary arteries were recorded. Signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were calculated. Five-point scales were used for subjective image quality analysis. Image quality was rated good to excellent in 98.9 % of examinations without significant differences for proximal and distal attenuation (all p ≥.0516), whereas image noise was rated significantly higher at 70 kV compared to ≥100 kV (all p <.0266). However, no significant differences were observed in SNR or CNR at 70-120 kV (all p ≥.0829). Mean ED at 70-120 kV was 1.5 ± 1.2 mSv, 2.4 ± 1.5 mSv, 3.6 ± 2.7 mSv, 5.9 ± 4.0 mSv, 7.9 ± 4.2 mSv, and 10.7 ± 4.1 mSv, respectively (all p ≤.0414). Correlation analysis showed a moderate association between tube voltage and BMI (r =.639). ATVS allows individual tube voltage adaptation for CCTA performed with 3{sup rd} generation DSCT, resulting in significantly decreased radiation exposure while maintaining image quality. (orig.)

  13. Automation synthesis modules review

    International Nuclear Information System (INIS)

    Boschi, S.; Lodi, F.; Malizia, C.; Cicoria, G.; Marengo, M.

    2013-01-01

    The introduction of 68 Ga labelled tracers has changed the diagnostic approach to neuroendocrine tumours and the availability of a reliable, long-lived 68 Ge/ 68 Ga generator has been at the bases of the development of 68 Ga radiopharmacy. The huge increase in clinical demand, the impact of regulatory issues and a careful radioprotection of the operators have boosted for extensive automation of the production process. The development of automated systems for 68 Ga radiochemistry, different engineering and software strategies and post-processing of the eluate were discussed along with impact of automation with regulations. - Highlights: ► Generators availability and robust chemistry boosted for the huge diffusion of 68Ga radiopharmaceuticals. ► Different technological approaches for 68Ga radiopharmaceuticals will be discussed. ► Generator eluate post processing and evolution to cassette based systems were the major issues in automation. ► Impact of regulations on the technological development will be also considered

  14. Development of a next-generation automated DICOM processing system in a PACS-less research environment.

    Science.gov (United States)

    Ziegler, Scott E

    2012-10-01

    The use of clinical imaging modalities within the pharmaceutical research space provides value and challenges. Typical clinical settings will utilize a Picture Archive and Communication System (PACS) to transmit and manage Digital Imaging and Communications in Medicine (DICOM) images generated by clinical imaging systems. However, a PACS is complex and provides many features that are not required within a research setting, making it difficult to generate a business case and determine the return on investment. We have developed a next-generation DICOM processing system using open-source software, commodity server hardware such as Apple Xserve®, high-performance network-attached storage (NAS), and in-house-developed preprocessing programs. DICOM-transmitted files are arranged in a flat file folder hierarchy easily accessible via our downstream analysis tools and a standard file browser. This next-generation system had a minimal construction cost due to the reuse of all the components from our first-generation system with the addition of a second server for a few thousand dollars. Performance metrics were gathered and the system was found to be highly scalable, performed significantly better than the first-generation system, is modular, has satisfactory image integrity, and is easier to maintain than the first-generation system. The resulting system is also portable across platforms and utilizes minimal hardware resources, allowing for easier upgrades and migration to smaller form factors at the hardware end-of-life. This system has been in production successfully for 8 months and services five clinical instruments and three pre-clinical instruments. This system has provided us with the necessary DICOM C-Store functionality, eliminating the need for a clinical PACS for day-to-day image processing.

  15. Synergy in thrombin-graphene sponge for improved hemostatic efficacy and facile utilization.

    Science.gov (United States)

    Li, Guofeng; Quan, Kecheng; Xu, CongCong; Deng, Bo; Wang, Xing

    2018-01-01

    Composites are attractive for its potential synergistic effects that can result in high-performance, but the synergy depends on subtle design. In this study, a hemostatic composite, a thrombin/cross-linked graphene sponge (TCGS), was developed through a facile gradient composite strategy. The porous structure of the CGS assures that the thrombin is stably embedded in the TCGS, avoiding a burst release but maintaining its bioactivity. In the synergy between proper thrombin stimulation and the fast absorption of the sponge, TCGS exhibits outstanding hemostatic performance, ultrafast bleeding cessation, within 100s, which is superior to both CGS and equal amounts of native thrombin. Lower or excessive thrombin dosages prolong the bleeding time. The study revealed that the balance between plasma absorption and thrombin stimulation at the interface is critical for improving hemostatic efficacy. TCGS is also highlighted for its biosafety and stability, even after 6 months of storage in environment. This potentially ultra-long shelf life is conducive to its practical applications. Therefore, TCGS not only provides a new strategy for developing a hemostatic composite but also provides a new method and understanding for the design of hemostatic materials. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Thrombin-induced microglial activation impairs hippocampal neurogenesis and spatial memory ability in mice.

    Science.gov (United States)

    Yang, Yuan; Zhang, Meikui; Kang, Xiaoni; Jiang, Chen; Zhang, Huan; Wang, Pei; Li, Jingjing

    2015-09-26

    To investigate the effects of microglia/macrophages activation induced by intrastriatal thrombin injection on dentate gyrus neurogenesis and spatial memory ability in mice. The male C57BL/6 mice were divided into 4 groups of 10: sham, intracerebral hemorrhage (ICH), ICH + hirudin (thrombin inhibitor), and ICH + indometacin (Indo, an anti-inflammation drug). ICH model was created by intrastriatal thrombin (1U) injection. BrdU (50 mg/kg) was administrated on the same day after surgery for 6 consecutive days. Motor functions were evaluated with rotarod and beam walking tests. The spatial memory deficit was measured with Morris water maze (MWM). Cell quantification was performed for doublecortin (DCX, immature neuron), BrdU (S-phase proliferating cell population) and CD68 (activated microglia/macrophage) immune-reactive cells. Microglia/macrophages activation induced by intrastriatal thrombin injection reduced hippocampal neurogenesis and impaired spatial memory ability, but did not affect the motor function at 3 and 5 days post-injury. Both hirudin and indometacin reduced microglia/macrophages activation, enhanced hippocampal neurogenesis, and improved spatial memory ability in mice. Microglia/macrophages activation induced by intrastriatal thrombin injection might be responsible for the spatial memory deficit. Targeting both thrombin and inflammation systems in acute phase of ICH might be important in alleviating the significant spatial memory deficits.

  17. Thrombin-Activatable Microbubbles as Potential Ultrasound Contrast Agents for the Detection of Acute Thrombosis.

    Science.gov (United States)

    Lux, Jacques; Vezeridis, Alexander M; Hoyt, Kenneth; Adams, Stephen R; Armstrong, Amanda M; Sirsi, Shashank R; Mattrey, Robert F

    2017-11-01

    Acute deep vein thrombosis (DVT) is the formation of a blood clot in the deep veins of the body that can lead to fatal pulmonary embolism. Acute DVT is difficult to distinguish from chronic DVT by ultrasound (US), the imaging modality of choice, and is therefore treated aggressively with anticoagulants, which can lead to internal bleeding. Here we demonstrate that conjugating perfluorobutane-filled (PFB-filled) microbubbles (MBs) with thrombin-sensitive activatable cell-penetrating peptides (ACPPs) could lead to the development of contrast agents that detect acute thrombosis with US imaging. Successful conjugation of ACPP to PFB-filled MBs was confirmed by fluorescence microscopy and flow cytometry. Fluorescein-labeled ACPP was used to evaluate the efficiency of thrombin-triggered cleavage by measuring the mean fluorescence intensity of ACPP-labeled MBs (ACPP-MBs) before and after incubation at 37 °C with thrombin. Lastly, control MBs and ACPP-MBs were infused through a tube containing a clot, and US contrast enhancement was measured with or without the presence of a thrombin inhibitor after washing the clot with saline. With thrombin activity, 91.7 ± 14.2% of the signal was retained after ACPP-MB infusion and washing, whereas only 16.7 ± 4% of the signal was retained when infusing ACPP-MBs in the presence of hirudin, a potent thrombin inhibitor.

  18. Active but inoperable thrombin is accumulated in a plasma protein layer surrounding Streptococcus pyogenes.

    Science.gov (United States)

    Naudin, Clément; Hurley, Sinead M; Malmström, Erik; Plug, Tom; Shannon, Oonagh; Meijers, Joost C M; Mörgelin, Matthias; Björck, Lars; Herwald, Heiko

    2015-10-01

    Activation of thrombin is a critical determinant in many physiological and pathological processes including haemostasis and inflammation. Under physiological conditions many of these functions are involved in wound healing or eradication of an invading pathogen. However, when activated systemically, thrombin can contribute to severe and life-threatening conditions by causing complications such as multiple multi-organ failure and disseminated intravascular coagulation. In the present study we investigated how the activity of thrombin is modulated when it is bound to the surface of Streptococcus pyogenes. Our data show that S. pyogenes bacteria become covered with a proteinaceous layer when incubated with human plasma, and that thrombin is a constituent of this layer. Though the coagulation factor is found attached to the bacteria with a functional active site, thrombin has lost its capacity to interact with its natural substrates and inhibitors. Thus, the interaction of bacteria with human plasma renders thrombin completely inoperable at the streptococcal surface. This could represent a host defense mechanism to avoid systemic activation of coagulation which could be otherwise induced when bacteria enter the circulation and cause systemic infection.

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

    Science.gov (United States)

    Ribeiro, David S M; Frigerio, Christian; Santos, João L M; Prior, João A V

    2012-07-20

    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 2.28×10(-6) mol L(-1) (r=0.9953; n=5) was verified. The determination rate was about 79 determinations per hour and the detection limit was about 8.69×10(-8) mol L(-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 relative deviations lower than 4.80%. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. TopoGen: A Network Topology Generation Architecture with application to automating simulations of Software Defined Networks

    CERN Document Server

    Laurito, Andres; The ATLAS collaboration

    2017-01-01

    Simulation is an important tool to validate the performance impact of control decisions in Software Defined Networks (SDN). Yet, the manual modeling of complex topologies that may change often during a design process can be a tedious error-prone task. We present TopoGen, a general purpose architecture and tool for systematic translation and generation of network topologies. TopoGen can be used to generate network simulation models automatically by querying information available at diverse sources, notably SDN controllers. The DEVS modeling and simulation framework facilitates a systematic translation of structured knowledge about a network topology into a formal modular and hierarchical coupling of preexisting or new models of network entities (physical or logical). TopoGen can be flexibly extended with new parsers and generators to grow its scope of applicability. This permits to design arbitrary workflows of topology transformations. We tested TopoGen in a network engineering project for the ATLAS detector ...

  1. TopoGen: A Network Topology Generation Architecture with application to automating simulations of Software Defined Networks

    CERN Document Server

    Laurito, Andres; The ATLAS collaboration

    2018-01-01

    Simulation is an important tool to validate the performance impact of control decisions in Software Defined Networks (SDN). Yet, the manual modeling of complex topologies that may change often during a design process can be a tedious error-prone task. We present TopoGen, a general purpose architecture and tool for systematic translation and generation of network topologies. TopoGen can be used to generate network simulation models automatically by querying information available at diverse sources, notably SDN controllers. The DEVS modeling and simulation framework facilitates a systematic translation of structured knowledge about a network topology into a formal modular and hierarchical coupling of preexisting or new models of network entities (physical or logical). TopoGen can be flexibly extended with new parsers and generators to grow its scope of applicability. This permits to design arbitrary workflows of topology transformations. We tested TopoGen in a network engineering project for the ATLAS detector ...

  2. An Automated Approach to the Generation of Structured Building Information Models from Unstructured 3d Point Cloud Scans

    DEFF Research Database (Denmark)

    Tamke, Martin; Evers, Henrik Leander; Wessel, Raoul

    2016-01-01

    In this paper we present and evaluate an approach for the automatic generation of building models in IFC BIM format from unstructured Point Cloud scans, as they result from 3dlaser scans of buildings. While the actual measurement process is relatively fast, 85% of the overall time are spend on th...

  3. An investigation on the relationship between the user model and graphic representations for the automated generation of multimedia presentations.

    NARCIS (Netherlands)

    K. Schwarz

    2004-01-01

    textabstractThis thesis investigates a possible solution to adapting an automatically generated presentation to an anonymous user. We will explore the field of User Modeling, specifically Adaptive Hypermedia, to find suitable methods. In our case study, we combine the methods we find to develop a

  4. Adenosine opposes thrombin-induced inhibition of intercellular calcium wave in corneal endothelial cells.

    Science.gov (United States)

    D'hondt, Catheleyne; Srinivas, Sangly P; Vereecke, Johan; Himpens, Bernard

    2007-04-01

    In corneal endothelial cells, intercellular Ca(2+) waves elicited by a mechanical stimulus involve paracrine intercellular communication, mediated by ATP release via connexin hemichannels, as well as gap junctional intercellular communication. Both mechanisms are inhibited by thrombin, which activates RhoA and hence results in myosin light chain phosphorylation. This study was conducted to examine the effects of adenosine, which is known to oppose thrombin-induced RhoA activation, thereby leading to myosin light chain dephosphorylation, on gap junctional intercellular communication and paracrine intercellular communication in cultured bovine corneal endothelial cells. An intercellular Ca(2+) wave was elicited by applying a mechanical stimulus to a single cell in a confluent monolayer. The area of Ca(2+) wave propagation was measured by [Ca(2+)](i) imaging using the fluorescent dye Fluo-4. Gap junctional intercellular communication was assessed by fluorescence recovery after photobleaching. Activity of hemichannels was determined by uptake of the hydrophilic dye Lucifer yellow in a Ca(2+)-free medium containing 2 mM EGTA. Adenosine triphosphate (ATP) release in response to mechanical stimulation was measured using the luciferin-luciferase technique. Gap26, a connexin mimetic peptide, was used to block hemichannels. Exposure to thrombin or TRAP-6 (a selective PAR-1 agonist) inhibited the Ca(2+) wave propagation by 70%. Pretreatment with adenosine prevented this inhibitory effect of thrombin. NECA (a potent A2B agonist) and forskolin, agents known to elevate cAMP in bovine corneal endothelial cells, also suppressed the effect of thrombin. The A1 receptor agonist CPA failed to inhibit the effect of thrombin. Similar to the effects on Ca(2+) wave propagation, adenosine prevented the thrombin-induced reduction in the fluorescence recovery during photobleaching experiments. Furthermore, pretreatment with adenosine prevented both thrombin and TRAP-6 from blocking the

  5. Automated generation of patient-tailored electronic care pathways by translating computer-interpretable guidelines into hierarchical task networks.

    Science.gov (United States)

    González-Ferrer, Arturo; ten Teije, Annette; Fdez-Olivares, Juan; Milian, Krystyna

    2013-02-01

    This paper describes a methodology which enables computer-aided support for the planning, visualization and execution of personalized patient treatments in a specific healthcare process, taking into account complex temporal constraints and the allocation of institutional resources. To this end, a translation from a time-annotated computer-interpretable guideline (CIG) model of a clinical protocol into a temporal hierarchical task network (HTN) planning domain is presented. The proposed method uses a knowledge-driven reasoning process to translate knowledge previously described in a CIG into a corresponding HTN Planning and Scheduling domain, taking advantage of HTNs known ability to (i) dynamically cope with temporal and resource constraints, and (ii) automatically generate customized plans. The proposed method, focusing on the representation of temporal knowledge and based on the identification of workflow and temporal patterns in a CIG, makes it possible to automatically generate time-annotated and resource-based care pathways tailored to the needs of any possible patient profile. The proposed translation is illustrated through a case study based on a 70 pages long clinical protocol to manage Hodgkin's disease, developed by the Spanish Society of Pediatric Oncology. We show that an HTN planning domain can be generated from the corresponding specification of the protocol in the Asbru language, providing a running example of this translation. Furthermore, the correctness of the translation is checked and also the management of ten different types of temporal patterns represented in the protocol. By interpreting the automatically generated domain with a state-of-art HTN planner, a time-annotated care pathway is automatically obtained, customized for the patient's and institutional needs. The generated care pathway can then be used by clinicians to plan and manage the patients long-term care. The described methodology makes it possible to automatically generate

  6. 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.

  7. On-line low and high frequency acoustic leak detection and location for an automated steam generator protection system

    International Nuclear Information System (INIS)

    Gaubatz, D.C.; Gluekler, E.L.

    1990-01-01

    Two on-line acoustic leak detection systems were operated and installed on a 76 MW hockey stick steam generator in the Sodium Components Test Installation (SCTI) at the Energy Technology Engineering Center (ETEC) in Southern California. The low frequency system demonstrated the capability to detect and locate leaks, both intentional and unintentional. No false alarms were issued during the two year test program even with adjacent blasting activities, pneumatic drilling, shuttle rocket engine testing nearby, scrams of the SCTI facility, thermal/hydraulic transient testing, and pump/control valve operations. For the high frequency system the capability to detect water into sodium reactions was established utilizing frequencies as high as 300 kHz. The high frequency system appeared to be sensitive to noise generated by maintenance work and system valve operations. Subsequent development work which is incomplete as of this date showed much more promise for the high frequency system. (author). 13 figs

  8. Distortions in processed signals and their application in electronic design - III: An automated generator of communication jamming signals

    International Nuclear Information System (INIS)

    Njau, E.C.

    1987-10-01

    We describe the design and operational features of a simple electronic circuit that is capable of automatically generating a narrow bandwidth jamming signal around each frequency signal received from target transmitters. It is noted that jamming based upon this circuit is fairly difficult to nullify using some of the conventional ''counter jamming'' strategies since in this case the jamming signals are flexibly locked onto the spectral components of the received signals. (author). 3 refs, 3 figs

  9. The myosin II ATPase inhibitor blebbistatin prevents thrombin-induced inhibition of intercellular calcium wave propagation in corneal endothelial cells.

    Science.gov (United States)

    Ponsaerts, Raf; D'hondt, Catheleyne; Bultynck, Geert; Srinivas, Sangly P; Vereecke, Johan; Himpens, Bernard

    2008-11-01

    Thrombin inhibits intercellular Ca(2+) wave propagation in bovine corneal endothelial cells (BCECs) through a mechanism dependent on myosin light chain (MLC) phosphorylation. In this study, blebbistatin, a selective myosin II ATPase inhibitor, was used to investigate whether the effect of thrombin is mediated by enhanced actomyosin contractility. BCECs were exposed to thrombin (2 U/mL) for 5 minutes. MLC phosphorylation was assayed by immunocytochemistry. Ca(2+) waves were visualized by confocal microscopy with Fluo-4AM. Fluorescence recovery after photobleaching (FRAP) was used to investigate intercellular communication (IC) via gap junctions. ATP release was measured by luciferin-luciferase assay. Lucifer yellow (LY) uptake was used to investigate hemichannel activity, and Fura-2 was used to assay thrombin- and ATP-mediated Ca(2+) responses. Pretreatment with blebbistatin (5 microM for 20 minutes) or its nitro derivative prevented the thrombin-induced inhibition of the Ca(2+) wave. Neither photo-inactivated blebbistatin nor the inactive enantiomers prevented the thrombin effect. Blebbistatin also prevented thrombin-induced inhibition of LY uptake, ATP release and FRAP, indicating that it prevented the thrombin effect on paracrine and gap junctional IC. In the absence of thrombin, blebbistatin had no significant effect on paracrine or gap junctional IC. The drug had no influence on MLC phosphorylation or on [Ca(2+)](i) transients in response to thrombin or ATP. Blebbistatin prevents the inhibitory effects of thrombin on intercellular Ca(2+) wave propagation. The findings demonstrate that myosin II-mediated actomyosin contractility plays a central role in thrombin-induced inhibition of gap junctional IC and of hemichannel-mediated paracrine IC.

  10. 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

  11. Computed tomography landmark-based semi-automated mesh morphing and mapping techniques: generation of patient specific models of the human pelvis without segmentation.

    Science.gov (United States)

    Salo, Zoryana; Beek, Maarten; Wright, David; Whyne, Cari Marisa

    2015-04-13

    Current methods for the development of pelvic finite element (FE) models generally are based upon specimen specific computed tomography (CT) data. This approach has traditionally required segmentation of CT data sets, which is time consuming and necessitates high levels of user intervention due to the complex pelvic anatomy. The purpose of this research was to develop and assess CT landmark-based semi-automated mesh morphing and mapping techniques to aid the generation and mechanical analysis of specimen-specific FE models of the pelvis without the need for segmentation. A specimen-specific pelvic FE model (source) was created using traditional segmentation methods and morphed onto a CT scan of a different (target) pelvis using a landmark-based method. The morphed model was then refined through mesh mapping by moving the nodes to the bone boundary. A second target model was created using traditional segmentation techniques. CT intensity based material properties were assigned to the morphed/mapped model and to the traditionally segmented target models. Models were analyzed to evaluate their geometric concurrency and strain patterns. Strains generated in a double-leg stance configuration were compared to experimental strain gauge data generated from the same target cadaver pelvis. CT landmark-based morphing and mapping techniques were efficiently applied to create a geometrically multifaceted specimen-specific pelvic FE model, which was similar to the traditionally segmented target model and better replicated the experimental strain results (R(2)=0.873). This study has shown that mesh morphing and mapping represents an efficient validated approach for pelvic FE model generation without the need for segmentation. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Organotin speciation in environmental matrices by automated on-line hydride generation-programmed temperature vaporization-capillary gas chromatography-mass spectrometry detection.

    Science.gov (United States)

    Serra, H; Nogueira, J M F

    2005-11-11

    In the present contribution, a new automated on-line hydride generation methodology was developed for dibutyltin and tributyltin speciation at the trace level, using a programmable temperature-vaporizing inlet followed by capillary gas chromatography coupled to mass spectrometry in the selected ion-monitoring mode acquisition (PTV-GC/MS(SIM)). The methodology involves a sequence defined by two running methods, the first one configured for hydride generation with sodium tetrahydroborate as derivatising agent and the second configured for speciation purposes, using a conventional autosampler and data acquisition controlled by the instrument's software. From the method-development experiments, it had been established that injector configuration has a great effect on the speciation of the actual methodology, particularly, the initial inlet temperature (-20 degrees C; He: 150 ml/min), injection volume (2 microl) and solvent characteristics using the solvent venting mode. Under optimized conditions, a remarkable instrumental performance including very good precision (RSD CRM 462, Nr. 330 dibutyltin: 68+/-12 ng/g; tributyltin: 54+/-15 ng/g on dry mass basis), using liquid-liquid extraction (LLE) and solid-phase extraction (SPE) sample enrichment and multiple injections (2 x 5 microl) for sensitivity enhancement. The methodology evidenced high reproducibility, is easy to work-up, sensitive and showed to be a suitable alternative to replace the currently dedicated analytical systems for organotin speciation in environmental matrices at the trace level.

  13. Development of a sandwich ELISA for the thrombin light chain identified by serum proteome analysis

    Directory of Open Access Journals (Sweden)

    Kazuyuki Sogawa

    2017-08-01

    Full Text Available We previously identified novel biomarker candidates in biliary tract cancer (BTC using serum proteome analysis. Among several candidates, we focused on thrombin light chain which is a 4204 Da peptide as the most promising biomarker for BTC. To move thrombin light chain toward potential diagnostic use, we developed an enzyme immunoassay that enables to measure serum thrombin light chain levels.Both one monoclonal antibody specific to the N-termini and one polyclonal antibody were used to develop a sandwich ELISA for thrombin light chain. The assay was evaluated by comparing the results with those obtained by the ClinProt™ system. Serum samples were obtained from 20 patients with BTC, 20 patients with BBTDs and 20 HVs using the ClinProt™ system and ELISA.The results of the established ELISA showed a positive correlation with the findings by ClinProt™ system (slope=0.3386, intercept=34.901, r2=0.9641. The performance of the ELISA was satisfactory in terms of recovery (97.9–102.5% and within-run (1.5–4.8% and between-day (1.9–6.7% reproducibility. Serum thrombin light chain levels were significantly greater in BTC (176.5±47.2 ng/mL than in BBTDs (128.6±17.4 ng/mL and HVs (127.6±16.0 ng/mL (p<0.001.The sandwich ELISA developed in this study will be useful for validation of the diagnostic significance of serum thrombin light chain levels in various cancers. Keywords: Thrombin light chain, Biliary tract cancer, Sandwich ELISA, Serum biomarker

  14. Construction of photoelectrochemical thrombin aptasensor via assembling multilayer of graphene-CdS nanocomposites.

    Science.gov (United States)

    Shangguan, Li; Zhu, Wei; Xue, Yanchun; Liu, Songqin

    2015-02-15

    A photoelectrochemical (PEC) aptasensor for highly sensitive and specific detection of thrombin was developed by using graphene–CdS nanocomposites multilayer as photoactive species and electroactive mediator hexaammineruthenium(III) chloride (Ru(NH(3))(6)(3+)) as signal enhancer. Graphene–CdS nanocomposites (G–CdS) were synthesized by one-pot reduction of oxide graphene and CdCl2 with thioacetamide. The photoactive multilayer was prepared by alternative assembly of the negatively charged 3-mercaptopropionic acid modified graphene–CdS nanocomposites (MPA-G–CdS) and the positively charged polyethylenimine (PEI) on ITO electrode. This layer-by-layer assembly method enhanced the stability and homogeneity of the photocurrent readout of G–CdS. Thrombin aptamer was covalently bound to the multilayer by using glutaraldehyde as cross-linking. Electroactive mediator (Ru(NH(3))(6)(3+)) could interact with the DNA phosphate backbone and thus facilitated the electron transfer between G–CdS multilayer and electrode and enhanced the photocurrent. Hybridizing of a long complementary DNA with thrombin aptamer could increase the adsorption amount of (Ru(NH(3))(6)(3+)), which in turn boosted the signal readout. In the presence of target thrombin, the affinity interaction between thrombin and its aptamer resulted in the long complementary DNA releasing from the G–CdS multilayer and decreasing of photocurrent signal. On the basis of G–CdS multilayer as the photoactive species, (Ru (NH(3))(6)(3+)) as an electroactive mediator, and aptamer as a recognition module, a high sensitive PEC aptasensor for thrombin detection was proposed. The thrombin aptasensor displayed a linear range from 2.0 pM to 600.0 pM and a detection limit of 1.0 pM. The present strategy provided a promising ideology for the future development of PEC biosensor. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Nanocomplexation of thrombin with cationic amylose derivative for improved stability and hemostatic efficacy

    Directory of Open Access Journals (Sweden)

    Zhuang B

    2015-01-01

    Full Text Available Baoxiong Zhuang,1,* Zhihua Li,1,* Jiadong Pang,2,* Wenbin Li,1 Pinbo Huang,1 Jie Wang,1 Yu Zhou,1 Qing Lin,1 Quanbo Zhou,1 Xiao Ye,1 Huilin Ye,1 Yimin Liu,1 Li-Ming Zhang,2 Rufu Chen1 1Department of Hepato-Pancreato-Billiary Surgery, Department of Medical Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China; 2DSAPM Lab and PCFM Lab, Institute of Polymer Science, Department of Polymer and Materials Science, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, People’s Republic of China *Authors share co-first authorship Abstract: As a topical hemostatic agent, thrombin has wide application for many surgical treatments. However, native thrombin always suffers from its physical and chemical instabilities. In this work, a nanocomplexation strategy was developed for modifying the stability and hemostatic efficacy of thrombin, in which a water-soluble cationic amylose derivative containing poly(l-lysine dendrons was prepared by a click reaction and then used to complex thrombin in an aqueous system. For resultant thrombin nanocomplexes, their morphology and particle size distribution were investigated. Their stabilities were studied in terms of activity retention percentages under different storage time, pH values, and illumination time. In addition, their ability to achieve in vitro fibrinogen and blood coagulation were evaluated. Via a rat hepatic hemorrhage model and a rat iliac artery hemorrhage model, these thrombin nanocomplexes were confirmed to have good tissue biocompatibility and in vivo hemostatic effectiveness. Keywords: thrombin, nanoparticles, amylose derivative, complexation, stability, hemostatic activity

  16. FAK phosphorylation plays a central role in thrombin-induced RPE cell migration.

    Science.gov (United States)

    Aguilar-Solis, E D; Lee-Rivera, I; Álvarez-Arce, A; López, E; López-Colomé, A M

    2017-08-01

    The migration of retinal pigment epithelial (RPE) cells is an important step in various pathologic conditions including subretinal neovascularization (SRN), proliferative vitreoretinopathy (PVR) and, importantly, as a consequence of retinal surgery. Therefore, the elucidation of the mechanisms underlying RPE trans-differentiation and migration is essential for devising effective treatments aimed to the prevention of these disorders. A common event in these pathologies is the alteration of the blood-retina barrier (BRB), which allows the interaction of RPE cells with thrombin, a pro-inflammatory protease contained in serum. Our previous work has demonstrated that thrombin induces RPE cell cytoskeletal remodeling and migration, hallmark processes in the development of PVR; however, the molecular mechanisms involved are still unclear. Cell migration requires the disassembly of focal adhesions induced by Focal Adhesion Kinase (FAK) phosphorylation, together with the formation of actin stress fibers. The aim of the present work was to identify thrombin-activated signaling pathways leading to FAK phosphorylation and to determine FAK participation in thrombin-induced RPE cell migration. Results demonstrate that the activation of PAR1 by thrombin induces FAK autophosphorylation at Y397 and the subsequent phosphorylation of Y576/577 within the activation loop. FAK phosphorylation was shown to be under the control of c/nPKC and PI3K/PKC-ζ, as well as by Rho/ROCK, since the inhibition of these pathways prevented thrombin-induced FAK phosphorylation and the consequent disassembly of focal adhesions, in parallel to FAK-dependent actin stress fiber formation and RPE cell migration. These findings demonstrate, for the first time, that thrombin stimulation of RPE cell transformation and migration are regulated by FAK tyrosine phosphorylation. Thus, targeting FAK phosphorylation may provide a strategical basis for PVR treatment. Copyright © 2017. Published by Elsevier Inc.

  17. An Automated Approach to the Generation of Structured Building Information Models from Unstructured 3d Point Cloud Scans

    DEFF Research Database (Denmark)

    Tamke, Martin; Evers, Henrik Leander; Wessel, Raoul

    2016-01-01

    In this paper we present and evaluate an approach for the automatic generation of building models in IFC BIM format from unstructured Point Cloud scans, as they result from 3dlaser scans of buildings. While the actual measurement process is relatively fast, 85% of the overall time are spend...... on the interpretation and transformation of the resulting Point Cloud data into information, which can be used in architectural and engineering design workflows. Our approach to tackle this problem, is in contrast to existing ones which work on the levels of points, based on the detection of building elements...

  18. Reenganche automático en circuitos de distribución con generación distribuida; Automatic reclosing in distribution circuits with distributed generation

    Directory of Open Access Journals (Sweden)

    Marta Bravo de las Casas

    2015-04-01

    Full Text Available Las redes de distribución han sido diseñadas tradicionalmente para que la potencia fluya en un solo sentido. La introducción de las unidades de generación distribuida hace que esta consideración ya no sea cierta, lo que traerá consigo nuevos retos para la operación y el diseño de estas redes. Una de las áreas afectadas en este sentido son la de las protecciones eléctricas, sobre todo la protección anti-aislamiento o separadora, y en especial cuando se utiliza reenganche automático, típico en las redes eléctricas de media tensión. El presente artículo realiza un estudio del reenganche automático en una subestación típica cubana que presenta generación distribuida fuel y diesel. Inicialmente se hace una breve revisión de la literatura y los resultados se presentan por medio de simulaciones en el software Matlab – Simulik (versión 7.4. La simulación confirma la existencia del problema y para ello se plantean las posibles soluciones. Distribution networks traditionally have been designed so that the power flows in one direction only. The introduction of distributed generation units makes this consideration is no longer true, which will bring new challenges for the operation and design of these networks. One of the areas affected in this regard are the electrical protections, especially the anti-isolating or separating, especially when automatic reclosing is used. The automatic reclosing is typical in middle voltage networks. In present article is carried out a study of automatic reclosing on a Cuban typical substation that presents distributed generation diesel and fuel. Initially a short review of the literature is made and the results are presented by means of the simulations from Matlab -Simulik (version 7.4 software. The simulation confirms the existence of this problem and possible solutions arise.

  19. Ethanol interferes with thrombin mediated changes in the morphology and cytoskeleton of human vascular endothelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Pratt, K.J.; Rubin, R.; Hoek, J.; Williams, S.K. (Thomas Jefferson Univ., Philadelphia, PA (United States))

    1991-03-15

    The effect of physiological concentrations of ethanol (EtOH) on the response of human vascular endothelial cells (EC) to thrombin was examined Treatment of EC with EtOH concentrations of 20-85mM for 2-10 min. produced no significant changes in the morphology of 3- and 4-day monolayers established on fibronectin coated polystyrene. When examined immunofluorescently no significantly changes in the microfilament or microtubule structures were seen. Exposure of EC monolayers to 0.5 and 1 U/ml of thrombin for 1-60 minutes causes a concentration and time dependent monolayer retraction, evidenced by a general decrease in cell size, increase in visible gaps in the monolayer and redistribution of the microtubule and microfilament networks. Pretreatment of EC monolayers with EtOH for 3-5 minutes prior to addition of thrombin prevents the changes seen with thrombin alone. Immunofluorescent examination of the microfilament and microtubule structures suggests than EtOH may act in part via the microtubule network, which appears to be disorganized/disrupted when the EC are exposed to EtOH and then thrombin. Colchicine studies show that EC which have been pretreated with EtOH respond to colchicine differently then cells which have not previously seen EtOH. These data suggest that EtOH may alter EC monolayer responsiveness either by indirect changes which are reflected in cytoskeletal disorganization or possibly by direct influence on the cytoskeleton.

  20. Bufadienolides from Kalanchoe daigremontiana as thrombin inhibitors-In vitro and in silico study.

    Science.gov (United States)

    Kolodziejczyk-Czepas, Joanna; Sieradzka, Malgorzata; Moniuszko-Szajwaj, Barbara; Pecio, Łukasz; Ponczek, Michal B; Nowak, Pawel; Stochmal, Anna

    2017-06-01

    Thrombin is an active plasma coagulation factor II, critical for the formation of fibrin clot during blood coagulation. For that reason, this protein is also a crucial target for different anti-thrombotic therapies. The work is based on in vitro evaluation of the inhibitory effect of bufadienolide-rich fraction, isolated from roots of Kalanchoe daigremontiana (1-50μg/ml) on enzymatic properties of a serine proteinase - thrombin. The efficacy of the inhibition of amidolytic activity of thrombin (measured as a hydrolysis of the chromogenic substrate S-2238, Chromogenix) attained about 10 and 66%, respectively. The IC 50 , established for the examined bufadienolide fraction was 2.79μg/ml, while the IC 50 calculated for argatroban (reference compound) was 0.78μg/ml. Linearization conducted using Lineweaver-Burk plot indicated that the K. daigremontiana fraction contains compounds that are uncompetitive inhibitors of thrombin. K. daigremontiana fraction was also able to reduce the proteolytic activity of thrombin towards its physiological substrate, i.e. fibrinogen. Additionally, this study is supported by in silico analysis of interactions of the most common compounds, identified in the examined in Kalanchoe extract to crystal structure of this enzyme. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Mohamed Ramadan El-Jade

    Full Text Available 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.

  2. An Automated Technique for Generating Georectified Mosaics from Ultra-High Resolution Unmanned Aerial Vehicle (UAV Imagery, Based on Structure from Motion (SfM Point Clouds

    Directory of Open Access Journals (Sweden)

    Christopher Watson

    2012-05-01

    Full Text Available Unmanned Aerial Vehicles (UAVs are an exciting new remote sensing tool capable of acquiring high resolution spatial data. Remote sensing with UAVs has the potential to provide imagery at an unprecedented spatial and temporal resolution. The small footprint of UAV imagery, however, makes it necessary to develop automated techniques to geometrically rectify and mosaic the imagery such that larger areas can be monitored. In this paper, we present a technique for geometric correction and mosaicking of UAV photography using feature matching and Structure from Motion (SfM photogrammetric techniques. Images are processed to create three dimensional point clouds, initially in an arbitrary model space. The point clouds are transformed into a real-world coordinate system using either a direct georeferencing technique that uses estimated camera positions or via a Ground Control Point (GCP technique that uses automatically identified GCPs within the point cloud. The point cloud is then used to generate a Digital Terrain Model (DTM required for rectification of the images. Subsequent georeferenced images are then joined together to form a mosaic of the study area. The absolute spatial accuracy of the direct technique was found to be 65–120 cm whilst the GCP technique achieves an accuracy of approximately 10–15 cm.

  3. Binding of poly(amidoamine), carbosilane, phosphorus and hybrid dendrimers to thrombin-Constants and mechanisms.

    Science.gov (United States)

    Shcharbin, Dzmitry; Pedziwiatr-Werbicka, Elzbieta; Vcherashniaya, Aliaksandra; Janaszewska, Anna; Marcinkowska, Monika; Goska, Piotr; Klajnert-Maculewicz, Barbara; Ionov, Maksim; Abashkin, Viktar; Ihnatsyeu-Kachan, Aliaksei; de la Mata, F Javier; Ortega, Paula; Gomez-Ramirez, Rafael; Majoral, Jean-Pierre; Bryszewska, Maria

    2017-07-01

    Thrombin is an essential part of the blood coagulation system; it is a serine protease that converts soluble fibrinogen into insoluble strands of fibrin, and catalyzes many other coagulation-related reactions. Absorption at its surface of small nanoparticles can completely change the biological properties of thrombin. We have analyzed the influence on thrombin of 3 different kinds of small nanoparticles: dendrimers (phosphorus-based, carbosilane based and polyamidoamine) and 2 hybrid systems containing carbosilane, viologen and phosphorus dendritic scaffolds in one single molecule, bearing different flexibility, size and surface charge. There was significant alteration in the rigidity of the rigid dendrimers in contrast to flexible dendrimers. These differences in their action are important in understanding interactions taking place at a bio-nanointerface. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Dabigatran reduces thrombin-induced platelet aggregation and activation in a dose-dependent manner

    DEFF Research Database (Denmark)

    Vinholt, Pernille Just; Nielsen, Christian; Söderström, Anna Cecilia

    2017-01-01

    of dabigatran fully inhibited platelet aggregation for thrombin up to 2 IU/mL, while dabigatran did not affect platelet aggregation by other agonists. Platelet activation (percentage of platelets positive for activated GPIIb/IIIa, CD63, P-selectin) was reduced after thrombin stimulation in samples...... with dabigatran levels ≥500 ng/mL. After stimulation with thrombin, the percentage of activated GPIIb/IIIa-positive platelets was 99.8 ± 0.2% without dabigatran, 14.7 ± 4.7% with 500 ng/mL dabigatran, and 4.2 ± 0.2% with 10,000 ng/mL dabigatran, both p 

  5. Pseudomonas aeruginosa elastase cleaves a C-terminal peptide from human thrombin that inhibits host inflammatory responses

    DEFF Research Database (Denmark)

    van der Plas, Mariena J A; Bhongir, Ravi K V; Kjellström, Sven

    2016-01-01

    Pseudomonas aeruginosa is an opportunistic pathogen known for its immune evasive abilities amongst others by degradation of a large variety of host proteins. Here we show that digestion of thrombin by P. aeruginosa elastase leads to the release of the C-terminal thrombin-derived peptide FYT21...

  6. The inactivation of single-chain urokinase-type plasminogen activator by thrombin in a plasma milieu : effect of thrombomodulin

    NARCIS (Netherlands)

    Braat, E.A.M.; Los, P.; Rijken, D.C.

    1998-01-01

    Thrombin cleaves single-chain urokinase-type plasminogen activator (scu- PA) into a virtually inactive two-chain form (tcu-PA/T), a process which may contribute to the maintenance of a fresh blood clot. We have examined the inactivation of scu-PA by thrombin in a plasma milieu to get more insight in

  7. The suicide substrate reaction between plasminogen activator inhibitor 1 acid thrombin is regulated by the cofactors vitronectin and heparin

    NARCIS (Netherlands)

    van Meijer, M.; Smilde, A.; Tans, G.; Nesheim, M. E.; Pannekoek, H.; Horrevoets, A. J.

    1997-01-01

    The interaction of thrombin with plasminogen activator inhibitor 1 (PAI-1) is shown to result in the simultaneous formation of both cleaved PAI-1 and a sodium dodecyl sulfate-stable thrombin-PAI-1 complex. The kinetics of this reaction can be described by a ''suicide substrate'' mechanism that

  8. 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 spontan......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...

  9. Percutaneous Thrombin Injection to Complete SMA Pseudoaneurysm Exclusion After Failing of Endograft Placement

    International Nuclear Information System (INIS)

    Szopinski, Piotr; Ciostek, Piotr; Pleban, Eliza; Iwanowski, Jaroslaw; Krol, Malgorzata Serafin-; Marianowska, Agnieszka; Noszczyk, Wojciech

    2005-01-01

    Visceral aneurysms are potentially life-threatening vascular lesions. Superior mesenteric artery (SMA) pseudoaneurysms are a rare but well-recognized complication of chronic pancreatitis. Open surgical repair of such an aneurysm, especially in patients after previous surgical treatment, might be dangerous and risky. Stent graft implantation makes SMA pseudoaneurysm exclusion possible and therefore avoids a major abdominal operation. Percutaneous direct thrombin injection is also one of the methods of treating aneurysms in this area. We report a first case of percutaneous ultrasound-guided thrombin injection to complete SMA pseudoaneurysm exclusion after an unsuccessful endograft placement. Six-month follow-up did not demonstrate any signs of aneurysm recurrence

  10. Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

    Science.gov (United States)

    Zhang, Jiang; Loo, Rachel R. Ogorzalek; Loo, Joseph A.

    2017-09-01

    Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH4OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin-TBA complex and 1 M NH4OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin-TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein-DNA complexes. [Figure not available: see fulltext.

  11. 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.

  12. Third-generation dual-source CT of the neck using automated tube voltage adaptation in combination with advanced modeled iterative reconstruction: evaluation of image quality and radiation dose

    International Nuclear Information System (INIS)

    Scholtz, Jan-Erik; Wichmann, Julian L.; Huesers, Kristina; Albrecht, Moritz H.; Beeres, Martin; Bauer, Ralf W.; Vogl, Thomas J.; Bodelle, Boris

    2016-01-01

    To evaluate image quality and radiation dose in third-generation dual-source computed tomography (DSCT) of the neck using automated tube voltage adaptation (TVA) with advanced modelled iterative reconstruction (ADMIRE) algorithm. One hundred and sixteen patients were retrospectively evaluated. Group A (n = 59) was examined on second-generation DSCT with automated TVA and filtered back projection. Group B (n = 57) was examined on a third-generation DSCT with automated TVA and ADMIRE. Age, body diameter, attenuation of several anatomic structures, noise, signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), radiation dose (CTDI vol ) and size-specific dose estimates (SSDE) were assessed. Diagnostic acceptability was rated by three readers. Age (p = 0.87) and body diameter (p = 0.075) did not differ significantly. Tube voltage in Group A was set automatically to 100 kV for all patients (n = 59), and to 70 kV (n = 2), 80 kV (n = 5), and 90 kV (n = 50) in Group B. Noise was reduced and CNR was increased significantly (p < 0.001). Diagnostic acceptability was rated high in both groups, with better ratings in Group B (p < 0.001). SSDE was reduced by 34 % in Group B (20.38 ± 1.63 mGy vs. 13.04 ± 1.50 mGy, p < 0.001). Combination of automated TVA and ADMIRE in neck CT using third-generation DSCT results in a substantial radiation dose reduction with low noise and increased CNR. (orig.)

  13. A sensitive bioimmunoassay for thrombin-cleaved two-chain urokinase-type plasminogen activator (abstract)

    NARCIS (Netherlands)

    Braat, E.A.M.; Nauland, U.; Dooijewaard, G.; Rijken, P.C.

    1996-01-01

    Thrombin cleaves single-chain urokinase-type plasminogen activator (scu-PA) into a virtually inactive two-chain form (tcu-PA/T). Little is known about the physiological importance of tcu-PA/T. To examine the occurrence of tcu-PA/T in vivo, we developed a sensitive and specific bioimmunoassay (BIA)

  14. EFFICACY OF THROMBIN FIBRIN GLUE AND SCLE ROSANT IN THE MANAGEMENT OF BLEEDI NG GASTRIC VARICES

    Directory of Open Access Journals (Sweden)

    Sanjay Gupta

    2015-01-01

    Full Text Available Gastric varices are noted in up to 20 % of patents with portal hypertension , and are more common in those with non - cirrhotic etiology 1 . They bleed at lower portal pressures , bleed more severely and are associated with higher rates of rebleed , encephalopathy and mortality 1,2,3 . Variceal obliteration using tissue adhesives such as N - butyl cyanoacrylate leading to plugging and thrombosis of the gastric varices is currently the first line management option for obliteration of the gastric varices 3 . Although various options have been proposed , gold standard for management of gastric variceal bleeds is yet to be defined. We theorized that injection of the gastric varices using thrombin based glue followed by injection of a sclerosant shall be effective in optimum sclerotherapy and eradication of gastric varices. MATERIAL AND METHODS : All patients presenting with gastric variceal bleed were offered sclerotherapy with Thrombin fibrin based glue and sclerosant (TFG/S . During the study period 18 patients were enrolled in the TGF/S group. 21 patients underwent variceal plugging with n - butyl cyanoacrylate (NBC . There was no significant difference in age/ sex , duration of bleed or time interval between onset of bleed and endotherapy. RESULTS: Patients undergoing endotherapy with TGF/S had less episodes of bleed , and greater eradication of varices. CONCLUSION: The results with thrombin / fibrin glue and sclerotherapy are highly encouraging. Well - designed trials need to be performed KEYWORDS:Gastric varices; Thrombin Sclerotherapy

  15. Inhibition of Src family kinases improves cognitive function after intraventricular hemorrhage or intraventricular thrombin.

    Science.gov (United States)

    Liu, Da Zhi; Waldau, Ben; Ander, Bradley P; Zhan, Xinhua; Stamova, Boryana; Jickling, Glen C; Lyeth, Bruce G; Sharp, Frank R

    2017-07-01

    Intraventricular hemorrhage causes spatial memory loss, but the mechanism remains unknown. Our recent studies demonstrated that traumatic brain injury activates Src family kinases, which cause spatial memory loss. To test whether the spatial memory loss was due to blood in the ventricles, which activated Src family kinases, we infused autologous whole blood or thrombin into the lateral ventricles of adult rats to model non-traumatic intraventricular hemorrhage. Hippocampal neuron loss was examined 1 day to 5 weeks later. Spatial memory function was assessed 29 to 33 days later using the Morris water maze. Five weeks after the ventricular injections of blood or thrombin, there was death of most hippocampal neurons and significant memory deficits compared with sham operated controls. These data show that intraventricular thrombin is sufficient to kill hippocampal neurons and produce spatial memory loss. In addition, systemic administration of the non-specific Src family kinase inhibitor PP2 or intraventricular injection of siRNA-Fyn, a Src family kinase family member, prevented hippocampal neuronal loss and spatial memory deficits following intraventricular hemorrhage. The data support the conclusions that thrombin mediates the hippocampal neuronal cell death and spatial memory deficits produced by intraventricular blood and that these can be blocked by non-specific inhibition of Src family kinases or by inhibiting Fyn.

  16. Rigidification of the autolysis loop enhances Na[superscript +] binding to thrombin

    Energy Technology Data Exchange (ETDEWEB)

    Pozzi, Nicola; Chen, Raymond; Chen, Zhiwei; Bah, Alaji; Di Cera, Enrico (St. Louis-MED)

    2011-09-20

    Binding of Na{sup +} to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na{sup +} is weak due to large heat capacity and enthalpy changes associated with binding, and the K{sub d} = 80 mM ensures only 64% saturation of the site at the concentration of Na{sup +} in the blood (140 mM). Residues controlling Na{sup +} binding and activation have been identified. Yet, attempts to improve the interaction of Na{sup +} with thrombin and possibly increase catalytic activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human thrombin with the homologous rigid domain of the murine enzyme results in a drastic (up to 10-fold) increase in Na{sup +} affinity and a significant improvement in the catalytic activity of the enzyme. Rigidification of the autolysis loop abolishes the heat capacity change associated with Na{sup +} binding observed in the wild-type and also increases the stability of thrombin. These findings have general relevance to protein engineering studies of clotting proteases and trypsin-like enzymes.

  17. Interactions between thrombin and natural products of Millettia speciosa Champ. using capillary zone electrophoresis.

    Science.gov (United States)

    Zhang, Shuyu; Yin, Ting; Ling, Xiaomei; Liang, Hong; Zhao, Yuying

    2008-08-01

    In Chinese medicine Suberect Spatholobus Stem is used to treat menoxenia, blood deficiency, numb paralyses, and so on. In folk, Millettia speciosa is often used as a substitute for Suberect Spatholobus Stem in some areas but it has not been reported whether M. speciosa is the eligible substitute for Suberect Spatholobus Stem or not till now. In this study, a capillary zone electrophoretic method was applied to determinate the interactions between natural products isolated from M. speciosa Champ. and thrombin for the first time. Both qualitative and quantitative characterizations of the molecule-enzyme binding were determined. Twenty ingredients were isolated from M. speciosa Champ. and the results showed that compared with positive and negative control, the compounds YT-1, YT-2, YT-3, YT-8, YT-9, YT-10, YT-11, YT-12, YT-14, YT-15, YT-16, and YT-20 interacted with thrombin while the other eight had no binding to thrombin. The binding constants of the interaction between compounds and thrombin were calculated by the Scatchard analysis formula. Because M. speciosa contains these compounds which have different levels of anticoagulant activity, it may be the eligible substitute for Suberect Spatholobus Stem.

  18. 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...

  19. Measuring Direct Thrombin Inhibitors With Routine and Dedicated Coagulation Assays Which Assay Is Helpful?

    NARCIS (Netherlands)

    Curvers, Joyce; van de Kerkhof, Daan; Stroobants, An K.; van den Dool, Erik-Jan; Scharnhorst, Volkher

    2012-01-01

    The use of direct thrombin inhibitors (DTIs) for prophylactic or therapeutic anticoagulation is increasing because of the predictable bioavailability and short half-life of these DTIs. However, in certain situations, indication of the concentration is warranted. We investigated the effects of 3 DTIs

  20. 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

  1. Automated Assessment in Massive Open Online Courses

    Science.gov (United States)

    Ivaniushin, Dmitrii A.; Shtennikov, Dmitrii G.; Efimchick, Eugene A.; Lyamin, Andrey V.

    2016-01-01

    This paper describes an approach to use automated assessments in online courses. Open edX platform is used as the online courses platform. The new assessment type uses Scilab as learning and solution validation tool. This approach allows to use automated individual variant generation and automated solution checks without involving the course…

  2. Competition-derived FRET-switching cationic conjugated polymer-Ir(III) complex probe for thrombin detection.

    Science.gov (United States)

    Du, Chunnuan; Hu, Yufang; Zhang, Qingqing; Guo, Zhiyong; Ge, Guoping; Wang, Sui; Zhai, Chunyang; Zhu, Mingshan

    2018-02-15

    A novel, label-free and convenient strategy for thrombin assay has been developed based on the fluorescence resonance energy transfer (FRET) from a cationic conjugated polymer (CCP) to Ir(III) complex. The energy donor (CCP) and acceptor (Ir(III) complex) were taken into close proximity through π-π stacking interaction and electrostatic interaction, leading to the occurrence of FRET. However, the introduction of the thrombin aptamer upset the status and blocked the FRET process, but afterwards the reappearance of FRET phenomenon was confirmed by the special binding interaction between aptamer and thrombin, thus achieving the quantitative detection of thrombin. This assay could detect thrombin as low concentration as about 0.05pM and provided a highly specific selectivity among other nonspecific proteins. Moreover, the strategy may allow our platform to provide similar sensitivity toward different targets in an aptamer-structure-independent manner. Furthermore, the assay can be used to detect thrombin in diluted real urine or serum samples with a satisfactory recovery, implying its great potential for rapid detection of thrombin in the clinic. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Affinity capillary electrophoresis with laser induced fluorescence detection for thrombin analysis using nuclease-resistant RNA aptamers.

    Science.gov (United States)

    Hao, Lihua; Bai, Yunlong; Wang, Hailin; Zhao, Qiang

    2016-12-09

    Aptamer affinity capillary electrophoresis coupled with laser-induced fluorescence (CE-LIF) combines the advantages of affinity aptamer, rapid CE separation, and high sensitivity detection. Here we reported an affinity CE-LIF assay for thrombin by using a fluorophore-labeled RNA aptamer containing 2'-fluoro modification in sugar rings of pyrimidine nucleotides (C and U) as affinity ligand. This RNA aptamer has high binding affinity, specificity and biostability. Thrombin at 0.2nM was successfully detected. This RNA aptamer allowed for the detection of thrombin spiked in diluted human serum sample due to the nuclease resistance. The RNA aptamer has comparable binding affinity to a 29-mer DNA aptamer for thrombin, and the binding site of the RNA aptamer on thrombin partially overlaps with the binding site of the 29-mer DNA aptamer on thrombin. It shows the nuclease-resistant RNA aptamers are promising in assays for thrombin. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Thrombin induces epithelial-mesenchymal transition and collagen production by retinal pigment epithelial cells via autocrine PDGF-receptor signaling.

    Science.gov (United States)

    Bastiaans, Jeroen; van Meurs, Jan C; van Holten-Neelen, Conny; Nagtzaam, Nicole M A; van Hagen, P Martin; Chambers, Rachel C; Hooijkaas, Herbert; Dik, Willem A

    2013-12-19

    De-differentiation of RPE cells into mesenchymal cells (epithelial-mesenchymal transition; EMT) and associated collagen production contributes to development of proliferative vitreoretinopathy (PVR). In patients with PVR, intraocular coagulation cascade activation occurs and may play an important initiating role. Therefore, we examined the effect of the coagulation proteins factor Xa and thrombin on EMT and collagen production by RPE cells. Retinal pigment epithelial cells were stimulated with factor Xa or thrombin and the effect on zonula occludens (ZO)-1, α-smooth muscle actin (α-SMA), collagen, and platelet-derived growth factor (PDGF)-B were determined by real-time quantitative-polymerase chain reaction (RQ-PCR), immunofluorescence microscopy, and HPLC and ELISA for collagen and PDGF-BB in culture supernatants, respectively. PDGF-receptor activation was determined by phosphorylation analysis and inhibition studies using the PDGF-receptor tyrosine kinase inhibitor AG1296. Thrombin reduced ZO-1 gene expression (P production of α-SMA and collagen increased. In contrast to thrombin, factor Xa hardly stimulated EMT by RPE. Thrombin clearly induced PDGF-BB production and PDGF-Rβ chain phosphorylation in RPE. Moreover, AG1296 significantly blocked the effect of thrombin on EMT and collagen production. Our findings demonstrate that thrombin is a potent inducer of EMT by RPE via autocrine activation of PDGF-receptor signaling. Coagulation cascade-induced EMT of RPE may thus contribute to the formation of fibrotic retinal membranes in PVR and should be considered as treatment target in PVR.

  5. Effects of fibrin, thrombin, and blood on breast capsule formation in a preclinical model.

    Science.gov (United States)

    Marques, Marisa; Brown, Spencer A; Cordeiro, Natália D S; Rodrigues-Pereira, Pedro; Cobrado, M Luís; Morales-Helguera, Aliuska; Lima, Nuno; Luís, André; Mendanha, Mário; Gonçalves-Rodrigues, Acácio; Amarante, José

    2011-03-01

    The root cause of capsular contracture (CC) associated with breast implants is unknown. Recent evidence points to the possible role of fibrin and bacteria in CC formation. The authors sought to determine whether fibrin, thrombin, and blood modulated the histological and microbiological outcomes of breast implant capsule formation in a rabbit model. The authors carried out a case-control study to assess the influence of fibrin, thrombin, and blood on capsule wound healing in a rabbit model. Eighteen New Zealand white rabbits received four tissue expanders. One expander acted as a control, whereas the other expander pockets received one of the following: fibrin glue, rabbit blood, or thrombin sealant. Intracapsular pressure/volume curves were compared among the groups, and histological and microbiological evaluations were performed (capsules, tissue expanders, rabbit skin, and air). The rabbits were euthanized at two or four weeks. At four weeks, the fibrin and thrombin expanders demonstrated significantly decreased intracapsular pressure compared to the control group. In the control and fibrin groups, mixed inflammation correlated with decreased intracapsular pressure, whereas mononuclear inflammation correlated with increased intracapsular pressure. The predominant isolate in the capsules, tissue expanders, and rabbit skin was coagulase-negative staphylococci. For fibrin and thrombin, both cultures that showed an organism other than staphylococci and cultures that were negative were associated with decreased intracapsular pressure, whereas cultures positive for staphylococci were associated with increased intracapsular pressure. Fibrin application during breast implantation may reduce rates of CC, but the presence of staphylococci is associated with increased capsule pressure even in the presence of fibrin, so care should be taken to avoid bacterial contamination.

  6. Effect of temperature on the association step in thrombin-fibrinogen interaction.

    Science.gov (United States)

    Picozzi, M; De Cristofaro, R

    1993-01-01

    Kinetics of fibrinopeptide A release by human alpha-thrombin at low fibrinogen concentration allowed us to measure the specificity constant, i.e. kcat/Km, for the interaction between the enzyme and human fibrinogen. A study of the dependence of the ratio kcat/Km upon the viscosity of the medium revealed that fibrinogen acts as a 'sticky' substrate, or, in other words, as a substrate that dissociates from the Michaelis complex with a rate comparable with that for acylation of the active site. These experiments allowed us also to compute for the first time the second-order rate constant for thrombin-fibrinogen association. A study of the temperature-dependence of the association rate, carried out over the temperature range spanning from 10 degrees C to 37 degrees C (pH 7.50; I0.15) permitted the estimation of the enthalpy and entropy of activation, delta H++ and delta S++, which were found to be equal to 5.69 +/- 0.77 kJ.mol-1 and -80.25 +/- 1.79 kJ.K-1.mol-1 respectively. In addition, the values of Km for thrombin-fibrinogen reaction were measured at different solution viscosities in order to derive the equilibrium dissociation constant, Ks, of this interaction. These experiments showed that the Ks values for thrombin-fibrinogen binding was equal to 1.8 microM at 25 degrees C. Altogether these results indicated that fibrinogen, though interacting with both the catalytic pocket and the fibrinogen recognition site on the thrombin molecule, dissociates from Michaelis complex with a rate comparable with that shown by amide substrates, which interact only with the catalytic site. PMID:8373370

  7. Process automation

    International Nuclear Information System (INIS)

    Moser, D.R.

    1986-01-01

    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

  8. Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule

    DEFF Research Database (Denmark)

    Aaldering, Lukas J.; Poongavanam, Vasanthanathan; Langkjær, Niels

    2017-01-01

    -modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G-quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding...... was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer-C3 introduction at the T7 loop position (TBA-SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling...

  9. Salmon and human thrombin differentially regulate radicular pain, glial-induced inflammation and spinal neuronal excitability through protease-activated receptor-1.

    Directory of Open Access Journals (Sweden)

    Jenell R Smith

    Full Text Available Chronic neck pain is a major problem with common causes including disc herniation and spondylosis that compress the spinal nerve roots. Cervical nerve root compression in the rat produces sustained behavioral hypersensitivity, due in part to the early upregulation of pro-inflammatory cytokines, the sustained hyperexcitability of neurons in the spinal cord and degeneration in the injured nerve root. Through its activation of the protease-activated receptor-1 (PAR1, mammalian thrombin can enhance pain and inflammation; yet at lower concentrations it is also capable of transiently attenuating pain which suggests that PAR1 activation rate may affect pain maintenance. Interestingly, salmon-derived fibrin, which contains salmon thrombin, attenuates nerve root-induced pain and inflammation, but the mechanisms of action leading to its analgesia are unknown. This study evaluates the effects of salmon thrombin on nerve root-mediated pain, axonal degeneration in the root, spinal neuronal hyperexcitability and inflammation compared to its human counterpart in the context of their enzymatic capabilities towards coagulation substrates and PAR1. Salmon thrombin significantly reduces behavioral sensitivity, preserves neuronal myelination, reduces macrophage infiltration in the injured nerve root and significantly decreases spinal neuronal hyperexcitability after painful root compression in the rat; whereas human thrombin has no effect. Unlike salmon thrombin, human thrombin upregulates the transcription of IL-1β and TNF-α and the secretion of IL-6 by cortical cultures. Salmon and human thrombins cleave human fibrinogen-derived peptides and form clots with fibrinogen with similar enzymatic activities, but salmon thrombin retains a higher enzymatic activity towards coagulation substrates in the presence of antithrombin III and hirudin compared to human thrombin. Conversely, salmon thrombin activates a PAR1-derived peptide more weakly than human thrombin. These

  10. Smashing the Stovepipe: Leveraging the GMSEC Open Architecture and Advanced IT Automation to Rapidly Prototype, Develop and Deploy Next-Generation Multi-Mission Ground Systems

    Science.gov (United States)

    Swenson, Paul

    2017-01-01

    Satellite/Payload Ground Systems - Typically highly-customized to a specific mission's use cases - Utilize hundreds (or thousands!) of specialized point-to-point interfaces for data flows / file transfers Documentation and tracking of these complex interfaces requires extensive time to develop and extremely high staffing costs Implementation and testing of these interfaces are even more cost-prohibitive, and documentation often lags behind implementation resulting in inconsistencies down the road With expanding threat vectors, IT Security, Information Assurance and Operational Security have become key Ground System architecture drivers New Federal security-related directives are generated on a daily basis, imposing new requirements on current / existing ground systems - These mandated activities and data calls typically carry little or no additional funding for implementation As a result, Ground System Sustaining Engineering groups and Information Technology staff continually struggle to keep up with the rolling tide of security Advancing security concerns and shrinking budgets are pushing these large stove-piped ground systems to begin sharing resources - I.e. Operational / SysAdmin staff, IT security baselines, architecture decisions or even networks / hosting infrastructure Refactoring these existing ground systems into multi-mission assets proves extremely challenging due to what is typically very tight coupling between legacy components As a result, many "Multi-Mission" ops. environments end up simply sharing compute resources and networks due to the difficulty of refactoring into true multi-mission systems Utilizing continuous integration / rapid system deployment technologies in conjunction with an open architecture messaging approach allows System Engineers and Architects to worry less about the low-level details of interfaces between components and configuration of systems GMSEC messaging is inherently designed to support multi-mission requirements, and

  11. 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

    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

  12. Binding of α2-macroglobulin-thrombin complexes and methylamine-treated α2-macroglobulin to human blood monocytes

    International Nuclear Information System (INIS)

    Straight, D.L.; Jakoi, L.; McKee, P.A.; Snyderman, R.

    1988-01-01

    The binding of α 2 -macroglobulin (α 2 M) to human peripheral blood monocytes was investigated. Monocytes, the precursors of tissue macrophages, were isolated from fresh blood by centrifugal elutriation or density gradient centrifugation. Binding studies were performed using 125 I-labeled α 2 M. Cells and bound ligand were separated from free ligand by rapid vacuum filtration. Nonlinear least-squares analysis of data obtained in direct binding studies at 0 0 C showed that monocytes bound the α 2 M-thrombin complex with a K/sub d/ 3.0 +- .09 nM and the monocyte had 1545 +- 153 sitescell. Thrombin alone did not compete for the site. Binding was divalent cation dependent. Direct binding studies also demonstrated that monocytes bound methylamine-treated α 2 M in a manner similar to α 2 M-thrombin. Competitive binding studies showed that α 2 M-thrombin and methylamine-treated α 2 M bound to the same sites on the monocyte. In contrast, native α 2 M did not compete with α 2 M-thrombin for the site. Studies done at 37 0 C suggested that after binding, the monocyte internalized and degraded α 2 M-thrombin and excreted the degradation products. Receptor turnover and degradation of α 2 M-thrombin complexes were blocked in monocytes treated with chloroquine, an inhibitor of lysosomal function. The results indicate that human monocytes have a divalent cation dependent, high-affinity binding site for α 2 M-thrombin and methylamine-treated α 2 M which may function to clear α 2 M-proteinase complexes from the circulation

  13. Plasmid-Mediated Resistance to Thrombin-Induced Platelet Microbicidal Protein in Staphylococci: Role of the qacA Locus

    OpenAIRE

    Kupferwasser, Leon Iri; Skurray, Ronald A.; Brown, Melissa H.; Firth, Neville; Yeaman, Michael R.; Bayer, Arnold S.

    1999-01-01

    Thrombin-induced platelet microbicidal protein 1 (tPMP-1) is a small, cationic peptide released from rabbit platelets following thrombin stimulation. In vitro resistance to this peptide among strains of Staphylococcus aureus correlates with the survival advantage of such strains at sites of endothelial damage in humans as well as in experimental endovascular infections. The mechanisms involved in the phenotypic resistance of S. aureus to tPMP-1 are not fully delineated. The plasmid-encoded st...

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

    DEFF Research Database (Denmark)

    Sciascia, Savino; Baldovino, Simone; Schreiber, Karen

    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...

  15. Addition of thrombin reduces the recovery of extracellular vesicles from blood plasma

    Directory of Open Access Journals (Sweden)

    Anush Arakelyan

    2016-10-01

    Full Text Available Extracellular vesicles (EVs are widely studied as a system of intercellular communication, as markers of various diseases, as well as a vehicle for delivery of various bioactive molecules to various cells. Investigation of EVs’ structure and function requires their isolation and precise quantification. However, in the current literature, there are significant discrepancies in the estimated numbers of EVs in different body fluids. In part, this discrepancy is due to the difference in EVs isolation protocols used by different investigators. A common protocol that includes ExoQuick ™ is often used to isolate EVs from body fluids and culture medium. Here, we show that in the case of isolation of EVs from blood, thrombin should be omitted from the protocol as clots formed due to the thrombin-triggered coagulation may entrap many EVs thus leading to the underestimation of their numbers.

  16. Addition of thrombin reduces the recovery of extracellular vesicles from blood plasma

    Science.gov (United States)

    Arakelyan, Anush; Fitzgerald, Wendy; Vagida, Murad; Vasilieva, Elena; Grivel, Jean-Charles

    2016-01-01

    Extracellular vesicles (EVs) are widely studied as a system of intercellular communication, as markers of various diseases, as well as a vehicle for delivery of various bioactive molecules to various cells. Investigation of EVs’ structure and function requires their isolation and precise quantification. However, in the current literature, there are significant discrepancies in the estimated numbers of EVs in different body fluids. In part, this discrepancy is due to the difference in EVs isolation protocols used by different investigators. A common protocol that includes ExoQuick™ is often used to isolate EVs from body fluids and culture medium. Here, we show that in the case of isolation of EVs from blood, thrombin should be omitted from the protocol as clots formed due to the thrombin-triggered coagulation may entrap many EVs thus leading to the underestimation of their numbers. PMID:28936260

  17. Inhibition of thermolysin and human alpha-thrombin by cobalt(III) Schiff base complexes.

    Science.gov (United States)

    Takeuchi, T; Böttcher, A; Quezada, C M; Meade, T J; Gray, H B

    1999-05-01

    Cobalt(III) Schiff base complexes have been shown to inhibit the replication of the ocular herpes virus. It is well known that these complexes have a high affinity for nitrogenous donors such as histidine residues, and it is possible that they bind to (and inhibit) an enzyme that is crucial to viral replication. In model studies, we have found that [Co(acacen)(NH3)2]+ is an effective irreversible inhibitor of thermolysin at millimolar concentrations; it also inhibits human alpha-thrombin. Axial ligand exchange with an active-site histidine is the proposed mechanism of inhibition. The activity of thermolysin and thrombin can be protected by binding a reversible inhibitor to the active site before addition of the cobalt(III) complex.

  18. Trypsin, Tryptase, and Thrombin Polarize Macrophages towards a Pro-Fibrotic M2a Phenotype.

    Directory of Open Access Journals (Sweden)

    Michael J V White

    Full Text Available For both wound healing and the formation of a fibrotic lesion, circulating monocytes enter the tissue and differentiate into fibroblast-like cells called fibrocytes and pro-fibrotic M2a macrophages, which together with fibroblasts form scar tissue. Monocytes can also differentiate into classically activated M1 macrophages and alternatively activated M2 macrophages. The proteases thrombin, which is activated during blood clotting, and tryptase, which is released by activated mast cells, potentiate fibroblast proliferation and fibrocyte differentiation, but their effect on macrophages is unknown. Here we report that thrombin, tryptase, and the protease trypsin bias human macrophage differentiation towards a pro-fibrotic M2a phenotype expressing high levels of galectin-3 from unpolarized monocytes, or from M1 and M2 macrophages, and that these effects appear to operate through protease-activated receptors. These results suggest that proteases can initiate scar tissue formation by affecting fibroblasts, fibrocytes, and macrophages.

  19. Gelatin-thrombin hemostatic matrix injection to salvage refractory post-renal graft biopsy bleed

    Directory of Open Access Journals (Sweden)

    V Jain

    2013-01-01

    Full Text Available Post-renal biopsy bleeding refractory to angioembolization usually requires graft nephrectomy as a life-saving measure. Gelatin-thrombin hemostatic matrix injection in the needle tract is a novel attempt to control bleeding in such cases and to salvage the allograft. We hereby describe two cases of post-graft biopsy bleed. Both these patients continued to bleed even after angioembolization. They were shifted to the operating room upon developing hypotension, having received multiple blood transfusions with the intention of performing graft nephrectomy to save their lives. However, bleeding was successfully controlled by using Gelatin-thrombin hemostatic matrix injection in the biopsy needle tract. Patients improved hemodynamically after the procedure. Graft function returned to normal in both the cases. At an average follow-up of 10.4 months, both the patients have shown stable graft functions.

  20. Thrombin effectuates therapeutic arteriogenesis in the rabbit hindlimb ischemia model: A quantitative analysis by computerized in vivo imaging

    International Nuclear Information System (INIS)

    Kagadis, George C.; Karnabatidis, Dimitrios; Katsanos, Konstantinos; Diamantopoulos, Athanassios; Samaras, Nikolaos; Maroulis, John; Siablis, Dimitrios; Nikiforidis, George C.

    2006-01-01

    We report on an experimental mammalian controlled study that documents arteriogenic capacity of thrombin and utilizes computerized algorithms to quantify the newly formed vessels. Hindlimb ischemia was surgically invoked in 10 New Zealand white rabbits. After quiescence of endogenous angiogenesis heterologous bovine thrombin was intramuscularly injected (1500 units) in one hindlimb per rabbit (Group T). Contralateral limbs were infused with normal saline (Group C). Digital subtraction angiography (DSA) of both limbs was performed after thrombin infusion by selective cannulation of the abdominal aorta and digital images were post-processed with computerized algorithms in order to enhance newly formed vessels. Total vessel area and total vessel length were quantified. In vivo functional evaluation included measurements of blood flow volume at the level of the external iliac artery by Doppler ultrasonography both at baseline and at 20 days after thrombin infusion. Total vessel area and length (in pixels) were 14,713+/-1023 and 5466+/-1327 in group T versus 12,015+/-2557 and 4598+/-1269 in group C (p=0.0062 and 0.1526, respectively). Blood flow volumes (ml/min) at baseline and at 20 days after thrombin infusion were 25.87+/-11.09 and 38.06+/-11.72 in group T versus 26.57+/-11.19 and 20.35+/-7.20 in group C (p=0.8898 and 0.0007, respectively). Intramuscular thrombin effectuates an arteriogenic response in the rabbit hindlimb ischemia model. Computerized algorithms may enable accurate quantification of the neovascularization outcome

  1. First Steps in the Direction of Synthetic, Allosteric, Direct Inhibitors of Thrombin and Factor Xa

    OpenAIRE

    Verghese, Jenson; Liang, Aiye; Sidhu, Preet Pal Singh; Hindle, Michael; Zhou, Qibing; Desai, Umesh R.

    2009-01-01

    Designing non-saccharide functional mimics of heparin is a major challenge. In this work, a library of small, aromatic molecules based on the sulfated DHP scaffold was synthesized and screened against thrombin and factor Xa. The results reveal that i) selected monomeric benzofuran derivatives inhibit the two enzymes, albeit weakly; ii) the two enzymes recognize different structural features in the benzofurans studied suggesting significant selectivity of recognition; and iii) the mechanism of...

  2. 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.

  3. Posttraumatic pseudoaneurysm of medial plantar artery in a child: treatment with percutaneous thrombin injection

    Directory of Open Access Journals (Sweden)

    Fabrício Neto Ladeira

    2014-03-01

    Full Text Available Pseudoaneurysms of the medial plantar artery are rare. The authors describe a case of a pseudoaneurysm of the medial plantar artery of a child who had suffered a penetrating laceration injury. Diagnosis can be confirmed using Doppler ultrasound and magnetic resonance angiography. As an alternative to the conventional surgery technique, percutaneous Doppler ultrasound-guided thrombin injection is a safe and effective treatment.

  4. Cleavage-based hybridization chain reaction for electrochemical detection of thrombin.

    Science.gov (United States)

    Chang, Yuanyuan; Chai, Yaqin; Xie, Shunbi; Yuan, Yali; Zhang, Juan; Yuan, Ruo

    2014-09-07

    In the present work, we constructed a new label-free "inter-sandwich" electrochemical aptasensor for thrombin (TB) detection by employing a cleavage-based hybridization chain reaction (HCR). The designed single-stranded DNA (defined as binding DNA), which contained the thrombin aptamer binding sequence, a DNAzyme cleavage site and a signal reporter sequence, was first immobilized on the electrode. In the absence of a target TB, the designed DNAzymes could combine with the thrombin aptamer binding sequence via complementary base pairing, and then Cu(2+) could cleave the binding DNA. In the presence of a target TB, TB could combine with the thrombin aptamer binding sequence to predominantly form an aptamer-protein complex, which blocked the DNAzyme cleavage site and prevented the binding DNA from being cleaved by Cu(2+)-dependent DNAzyme. As a result, the signal reporter sequence could leave the electrode surface to trigger HCR with the help of two auxiliary DNA single-strands, A1 and A2. Then, the electron mediator hexaammineruthenium (III) chloride ([Ru(NH3)6](3+)) was embedded into the double-stranded DNA (dsDNA) to produce a strong electrochemical signal for the quantitative measurement of TB. For further amplification of the electrochemical signal, graphene reduced by dopamine (PDA-rGO) was introduced as a platform in this work. With this strategy, the aptasensor displayed a wide linearity in the range of 0.0001 nM to 50 nM with a low detection limit of 0.05 pM. Moreover, the resulting aptasensor exhibited good specificity and acceptable reproducibility and stability. Because of these factors, the fabrication protocol proposed in this work may be extended to clinical application.

  5. In vitro pharmacological characterization of vorapaxar, a novel platelet thrombin receptor antagonist.

    Science.gov (United States)

    Hawes, Brian E; Zhai, Ying; Hesk, David; Wirth, Mark; Wei, Huijun; Chintala, Madhu; Seiffert, Dietmar

    2015-09-05

    Vorapaxar is a novel protease-activated receptor-1 (PAR1) antagonist recently approved for the reduction of thrombotic cardiovascular events in patients with a history of myocardial infarction or with peripheral arterial disease. The present study provides a comprehensive in vitro pharmacological characterization of vorapaxar interaction with the PAR1 receptor on human platelets. Similar studies were performed with a metabolite of vorapaxar (M20). Vorapaxar and M20 were competitive PAR1 antagonists that demonstrated concentration-dependent, saturable, specific, and slowly reversible binding to the receptor present on intact human platelets. The affinities of vorapaxar and M20 for the PAR1 receptor were in the low nanomolar range, as determined by saturation-, kinetic- and competitive binding studies. The calculated Kd and Ki values for vorapaxar increased in the presence of plasma, indicating a decrease in the free fraction available for binding to the PAR1 receptor on human platelets. Vorapaxar was also evaluated in functional assays using thrombin or a PAR1 agonist peptide (SFLLRN). Vorapaxar and M20 completely blocked thrombin-stimulated PAR1/β-arrestin association in recombinant cells and abolished thrombin-stimulated calcium influx in washed human platelets and vascular smooth muscle cells. Moreover, vorapaxar and M20 inhibited PAR1 agonist peptide-mediated platelet aggregation in human platelet rich plasma with a steep concentration response relationship. Vorapaxar exhibited high selectivity for inhibition of PAR1 over other platelet GPCRs. In conclusion, vorapaxar is a potent PAR1 antagonist exhibiting saturable, reversible, selective binding with slow off-rate kinetics and effectively inhibits thrombin's PAR1-mediated actions on human platelets. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. 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.

  7. 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.

  8. Alginate-calcium microsphere loaded with thrombin: a new composite biomaterial for hemostatic embolization.

    Science.gov (United States)

    Rong, Jing-jing; Liang, Ming; Xuan, Feng-qi; Sun, Jing-yang; Zhao, Li-jun; Zhen, Hui-zhen; Tian, Xiao-xiang; Liu, Dan; Zhang, Quan-yu; Peng, Cheng-fei; Yao, Tian-ming; Li, Fei; Wang, Xiao-zeng; Han, Ya-ling; Yu, Wei-ting

    2015-04-01

    To date, transcatheter arterial embolization (TAE) has become a standard treatment to control intracavitary bleeding as an alternative to surgery. Due to excellent biocompatibility and no residual in vivo, biodegradable materials are preferred in TAE. However, gelfoam is the only commercially available biodegradable embolic material used to treat blunt trauma of solid abdominal viscera until now, and controversial on its stability and reliability never stopped in the past five decades. In this study, a new biodegradable macromolecule material (thrombin-loaded alginate-calcium microspheres, TACMs) was prepared using electrostatic droplet techniques and a special method was developed for hemostatic embolization. Thrombin was successfully loaded into microspheres with high encapsulation efficiency and drug loading capacity. A burst release of TACMs was observed at early stage and sustained release later on, with the activity of thrombin preserved well. The strength of TACMs mixed thrombus, which was used as embolic agent, increased in a dose-dependent manner after TACMs were added. In addition, the TACMs were verified to be of no cytotoxicity and systemic toxicity, and biodegradable in vivo. Finally, the results of preliminary applications revealed that the TACMs could serve as an effective and promising embolic material for blunt trauma and hemorrhage of solid abdominal viscera. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Nanogravimetric and Optical Characterizations of Thrombin Interaction with a Self-Assembled Thiolated Aptamer

    Directory of Open Access Journals (Sweden)

    Jane Politi

    2016-01-01

    Full Text Available Efficient biorecognition of thrombin (TB, a serine protease with crucial role in physiological and pathological blood coagulation, is a hot topic in medical diagnostics. In this work, we investigate the ability of synthetic thrombin aptamer (TBA, immobilized on a gold substrate, to bind thrombin by two different label-free techniques: the quartz crystal microbalance (QCM and the spectroscopic ellipsometry (SE. By QCM characterization in the range from 20 to 110 nM, we demonstrate high specificity of TBA-TB interaction and determine affinity constant (Kd of 17.7±0.3 nM, system sensitivity of 0.42±0.03 Hz nM−1, and limit of detection (LOD of 240±20 pM. The interaction between TBA and TB is also investigated by SE, an all-optical method, by quantifying the thickness increase of the TBA film assembled on gold substrate. AFM characterization of TBA and TB molecules deposited on flat silicon surface is also supplied.

  10. Automated External Defibrillator

    Science.gov (United States)

    ... To Health Topics / Automated External Defibrillator Automated External Defibrillator Also known as What Is An automated external ... in survival. Training To Use an Automated External Defibrillator Learning how to use an AED and taking ...

  11. Library Automation.

    Science.gov (United States)

    Husby, Ole

    1990-01-01

    The challenges and potential benefits of automating university libraries are reviewed, with special attention given to cooperative systems. Aspects discussed include database size, the role of the university computer center, storage modes, multi-institutional systems, resource sharing, cooperative system management, networking, and intelligent…

  12. A label-free and high sensitive aptamer biosensor based on hyperbranched polyester microspheres for thrombin detection

    International Nuclear Information System (INIS)

    Sun, Chong; Han, Qiaorong; Wang, Daoying; Xu, Weimin; Wang, Weijuan; Zhao, Wenbo; Zhou, Min

    2014-01-01

    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

  13. 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.

  14. Bradykinin and thrombin stimulate release of arachidonic acid and formation of prostanoids in human periodontal ligament cells.

    Science.gov (United States)

    Marklund, M; Lerner, U H; Persson, M; Ransjö, M

    1994-06-01

    Previous reports have demonstrated the importance of prostaglandin formation in orthodontic tooth movement, but the mechanisms involved in the activation of prostaglandin biosynthesis in the periodontal ligament (PDL) are still unclear. There is, however, evidence that inflammatory reactions appear after application of orthodontic forces. In the present study, the effect of bradykinin (BK) and thrombin, two inflammatory mediators, on prostanoid biosynthesis in human PDL-cells was investigated. BK and thrombin caused a time-dependent burst of prostaglandin E2 (PGE2) formation (maximal effect after 2-5 min). The stimulatory actions of BK and thrombin on PGE2 biosynthesis were dose-dependent; seen in PDL-cells isolated from four different patients and abolished by the non-steroidal anti-inflammatory drug indomethacin. BK and thrombin also dose-dependently stimulated the biosynthesis of PGI2. BK agonists, with affinity to the B2 subtype of BK receptors, caused a significant increase of PGE2 biosynthesis in human PDL-cells. In contrast, BK agonists with affinity to BK-B1 receptors did not cause a burst of PGE2 biosynthesis. BK and BK-B2 receptor agonists as well as thrombin, but not BK-B1 receptor agonists, also significantly increased [3H] release in human PDL-cells prelabelled with [3H]-arachidonic acid, indicating that BK and thrombin stimulate prostanoid biosynthesis, at least partly, due to activation of phospholipase A2. These data show that BK via BK-B2 receptors, as well as thrombin, have the capacity to stimulate arachidonic acid release and subsequent prostanoid biosynthesis in human PDL-cells and thus may be implicated in the tissue reactions involved in orthodontic tooth movement.

  15. 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.

  16. The Science of Home Automation

    Science.gov (United States)

    Thomas, Brian Louis

    Smart home technologies and the concept of home automation have become more popular in recent years. This popularity has been accompanied by social acceptance of passive sensors installed throughout the home. The subsequent increase in smart homes facilitates the creation of home automation strategies. We believe that home automation strategies can be generated intelligently by utilizing smart home sensors and activity learning. In this dissertation, we hypothesize that home automation can benefit from activity awareness. To test this, we develop our activity-aware smart automation system, CARL (CASAS Activity-aware Resource Learning). CARL learns the associations between activities and device usage from historical data and utilizes the activity-aware capabilities to control the devices. To help validate CARL we deploy and test three different versions of the automation system in a real-world smart environment. To provide a foundation of activity learning, we integrate existing activity recognition and activity forecasting into CARL home automation. We also explore two alternatives to using human-labeled data to train the activity learning models. The first unsupervised method is Activity Detection, and the second is a modified DBSCAN algorithm that utilizes Dynamic Time Warping (DTW) as a distance metric. We compare the performance of activity learning with human-defined labels and with automatically-discovered activity categories. To provide evidence in support of our hypothesis, we evaluate CARL automation in a smart home testbed. Our results indicate that home automation can be boosted through activity awareness. We also find that the resulting automation has a high degree of usability and comfort for the smart home resident.

  17. Planificación automatizada del arranque de generadores para la restauración de sistemas eléctricos de potencia ;Generator Start-Up automated planning for electric power system restoration

    Directory of Open Access Journals (Sweden)

    Leonel Francisco Aleaga Loaiza

    2015-06-01

    Full Text Available La elección de la secuencia de arranque de los generadores afecta directamente a la capacidad de generación disponible en el proceso de restauración del sistema de potencia. En este artículo se utiliza un método basado en la planificación automatizada para calcular la secuencia de arranque de las unidades de generación en el proceso de restauración de sistemas eléctricos de potencia. Se presenta una formulación basada en acciones donde se involucran varios factores complejos tales como: la naturaleza combinatoria, el conocimiento de expertos, varias restricciones y condiciones cambiantes en el tiempo que deben cumplirse y la optimización de varios recursos numéricos. Los resultados de prueba sobre el sistema IEEE39-barras muestran que el método es muy eficiente en obtener planes precisos y optimizados para restaurar el sistema de generación utilizando un algoritmo de planificación automatizada basado en la búsqueda heurística con capacidades de razonamiento en tiempo continuo.The choice of generator startup sequence affects directly the available generation capacity in the power system restoration process. In this paper an automated planning based method is used to calculate the startup sequence generating units in the electric power system restoration process. An action-based formulation is presented where several complex factors are involved such us: the combinatorial nature, expert knowledge, several restrictions and changing conditions over time that must be met and the optimization of several numerical resources. The test result son theIEEE39-bus system show that the method is veryefficientto obtain accurate and optimized plans to restore the generation system using an automated planning algorithm based on heuristic search with capabilities of reasoning in continuous time.

  18. Factor VIII S373L: mutation at P1' site confers thrombin cleavage resistance, causing mild haemophilia A.

    Science.gov (United States)

    Johnson, D J; Pemberton, S; Acquila, M; Mori, P G; Tuddenham, E G; O'Brien, D P

    1994-04-01

    A novel CRM+ mutation, factor VIII position 373 serine to leucine substitution (FVIII 373-Leu) was identified during a survey of Factor VIII (FVIII) mutations. We have purified the variant protein from the patient's plasma in order to allow further characterisation of the molecule. The CRM+ plasma contained 120% Factor VIII antigen (FVIII:Ag) and 6% Factor VIII coagulant activity (FVIII:C). After purification the mutant FVIII was subjected to thrombin proteolysis, and was thereby activated 5.6-fold compared with 7-fold for wild type molecule. Subsequently, spontaneous inactivation of the mutant was much slower than noted for wild type FVIII. Western blot analysis using monoclonal antibodies demonstrated that thrombin cleavage of FVIII 373-Leu at positions 740 and 1689 were normal but that cleavage at position 372 was completely absent. Crystallographic coordinates of the active site of thrombin complexed to fibrinopeptide A were used to explore possible mechanistic reasons for the failure of thrombin to cleave the mutant FVIII at position 372. Steric hindrance between the mutant side chain and the side chain of the P1 residue was apparent. We conclude that the functional defect of FVIII 373-Leu results from the inability of thrombin to cleave the mutant at position 372-373, and propose that this is due to steric hindrance by the side chain of leucine 373, preventing correct formation of the enzyme substrate complex.

  19. 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.

  20. Protocol for obtaining platelet-rich plasma (PRP), platelet-poor plasma (PPP), and thrombin for autologous use.

    Science.gov (United States)

    Franco, Diogo; Franco, Talita; Schettino, Angélica Maria; Filho, João Medeiros Tavares; Vendramin, Fabiel Spani

    2012-10-01

    Plasma has been widely studied and used in many different situations to speed up healing with better tissue adherence and hemostasis. Research projects are now attempting to isolate platelet-rich plasma (PRP) and platelet-poor plasma (PPP), making better use of their properties, particularly during operations and for wounds that are slow to heal. In view of the wide diversity of industrial machines and extraction protocols, together with the variety of industrially produced biologic glues, this article suggests an option for obtaining PRP, PPP, and human thrombin for autologous use. A way of obtaining PRP, PPP, and thrombin is reproduced through a protocol defined and established by the authors. Autologous thrombin and plasma were obtained through the collection and successive centrifugation of ten whole blood samples, until the desired hemocomponents were isolated, followed by quantitative and qualitative analyses of the elements obtained. The mean platelet concentration obtained was 6.03 × 10(8) platelets/ml, with a mean thrombin concentration of 33.54 nM, both values compatible with reports in the literature when different protocols are applied. The protocol described is a good option for the preparation and application of PRP, PPP, and autologous thrombin, particularly as they can be obtained simultaneously, eliminating the possibilities of viral contamination and allergic reactions. Moreover, the cost of this procedure is low, it is easy to perform, and replicable. This journal requires that authors assign a level of evidence to each article.

  1. 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.

  2. Rapid and ultrasensitive detection of active thrombin based on the Vmh2 hydrophobin fused to a Green Fluorescent Protein.

    Science.gov (United States)

    Piscitelli, Alessandra; Pennacchio, Anna; Cicatiello, Paola; Politi, Jane; De Stefano, Luca; Giardina, Paola

    2017-01-15

    A fusion protein designed in order to combine the fluorescence emission of the Green Fluorescent Protein (GFP) with the adhesion ability of the class I hydrophobin Vmh2 was heterologously produced in the yeast Pichia pastoris. The Vmh2-GFP fusion protein has proven to be a smart and effective tool for the study of Vmh2 self-assembling. Since the two proteins were linked by the specific cutting site of the thrombin, the fusion protein was used as the active biological element in the realization of a thrombin biosensor. When the thrombin present in the target solution specifically hydrolyzed its cleavage sequence, a consequent decrease in the fluorescence intensity of the sample could be observed. The Vmh2-GFP based assay allowed quantification of thrombin in solution with a detection limit of 2.27aM. The specificity of the assay with respect to other proteases and proteins granted the measurement of thrombin added to healthy human plasma with same high sensitivity and a limit of detection of 2.3aM. Further advantages of the developed biosensor are the simplicity of its design and preparation, and the low requirements in terms of samples, reagents and time. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. A colorimetric aptamer biosensor based on cationic polythiophene derivative as peroxidase mimetics for the ultrasensitive detection of thrombin.

    Science.gov (United States)

    Liu, Mei; Li, Jiao; Li, Baoxin

    2017-12-01

    A colorimetric assay for the ultrasensitive determination of thrombin was presented, in which the cationic polythiophene derivative was used as catalyst of the 3,3',5,5'-tetramethylbenzidine (TMB)-H 2 O 2 reaction and the thrombin-binding aptamer (TBA) was used as inducing polymer's different conformation elements. It was found the cationic polythiophene derivative, poly[3-(3'-N,N,N-triethylamino-1'-propyloxy)-4-methyl-2,5-t-hiophene hydrochloride] (PMNT), can catalyze the oxidation reaction of TMB in the presence of H 2 O 2 to produce a blue color solution. The catalytic activity of PMNT on the TMB-H 2 O 2 reaction was closely relevant to the conformation of PMNT. The absorbance of TMB-H 2 O 2 was distinctly increased in the presence of TBA. With the addition of thrombin, TBA interacted with thrombin to form a G-quadruplex structure. The conformational change weakened the catalytic activity of PMNT and resulted in a decrease in the absorbance. The colorimetric sensor could detect thrombin down to 4pM with high selectivity against other interfering proteins. This work is not only of importance for a better understanding of the unique properties of cationic polythiophenes derivative but also have great potential for medical diagnostics and therapy for human health. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Thrombelastographic characterization of the thrombin-like activity of Crotalus simus and Bothrops asper venoms.

    Science.gov (United States)

    Nielsen, Vance G; Boyer, Leslie V; Redford, Daniel T; Ford, Paul

    2017-04-01

    : Annually, thousands suffer venomous snake-bite from Crotalus simus and Bothrops asper vipers in central and South America. The goals of the present study were to generally characterize the thrombin-like effects of venom from these snakes in human plasma with viscoelastic methods. Human plasma was exposed to the venom of three different C. simus subspecies and venoms obtained from B. asper vipers located in three different locations in Mexico. To characterize the factor X-activating and thrombin-like activity of these venoms, plasma (normal or factor XIII deficient) was pretreated with a variety of additives (e.g., heparin) in the absence or presence of calcium prior to exposure to 2.0 μg/ml of each viper's venom. These profiles were compared with plasma without venom that had contact activation of coagulation. Coagulation kinetics were determined with thrombelastography. All venoms had thrombin-like activity, with C. s. simus creating a slow growing, weak clot that was likely mediated by metalloproteinases. In contrast, B. asper venoms had rapid onset of coagulation and a high velocity of thrombus growth. Further, B. asper venom activity was calcium-independent, activated prothrombin, activated factor XIII, and independently polymerized fibrinogen. The viscoelastic methods used were able to differentiate subspecies of C. simus and specimens of B. asper, and provide insight into the mechanisms by which the venoms acted on plasma. These methods may be useful in the profiling of similar venoms and perhaps can assist in the assessment of interventions designed to treat envenomation (e.g., antivenom).

  5. 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.

  6. Diagnostic Accuracy of a Novel Chromogenic Direct Thrombin Inhibitor Assay: Clinical Experiences for Dabigatran Monitoring.

    Science.gov (United States)

    Poli, Sven; Härtig, Florian; Spencer, Charlotte; Ebner, Matthias; Birschmann, Ingvild; Kuhn, Joachim; Faix, Susanne; Ziemann, Ulf; Häring, Hans-Ulrich; Lehmann, Rainer; Peter, Andreas; Hörber, Sebastian

    2017-12-01

    Background Direct oral anticoagulants (DOACs) are increasingly replacing vitamin K antagonists (VKA) for clinical indications requiring long-term oral anticoagulation. In contrast to VKA, treatment with DOAC including dabigatran—the only direct thrombin inhibitor amongst them—does not require therapeutic drug monitoring. However, in case of treatment complications (e.g., major haemorrhage) and conditions requiring urgent surgery or thrombolytic therapy, information about actual DOAC plasma levels is needed to guide treatment decisions. Due to short reagent stability, limited accuracy at low dabigatran levels and high heparin sensitivity, the applicability of the widely used Hemoclot thrombin inhibitor (HTI) coagulation assay is limited in the emergency setting. Methods Dabigatran concentrations of 288 citrated plasma samples taken from 48 dabigatran-treated patients with drug concentrations of up to 300 ng/mL were measured with the chromogenic anti-IIa Biophen direct thrombin inhibitor (BDTI) assay and results compared with HTI using ultra performance liquid chromatography—tandem mass spectrometry as the reference method for measuring dabigatran plasma concentrations. Results BDTI results showed a very strong correlation with dabigatran concentrations (r = 0.965, p < 0.0001) as well as a low intra- and inter-assay variation of <5%. Compared with HTI, BDTI provides an improved on-board reagent stability of 72 hours, rapid turnaround times comparable to routine coagulation assays, high accuracy at low drug levels and reduced heparin sensitivity. Conclusion The BDTI is an ideal coagulation assay for the around-the-clock determination of dabigatran plasma levels in clinical routine including emergency situations.

  7. Thrombin-activatable fibrinolysis inhibitor influences disease severity in humans and mice with pneumococcal meningitis.

    Science.gov (United States)

    Mook-Kanamori, B B; Valls Serón, M; Geldhoff, M; Havik, S R; van der Ende, A; Baas, F; van der Poll, T; Meijers, J C M; P Morgan, B; Brouwer, M C; van de Beek, D

    2015-11-01

    Mortality and morbidity in patients with bacterial meningitis result from the proinflammatory response and dysregulation of coagulation and fibrinolysis. Thrombin-activatable fibrinolysis inhibitor (TAFI) is activated by free thrombin or thrombin in complex with thrombomodulin, and plays an antifibrinolytic role during fibrin clot degradation, but also has an anti-inflammatory role by inactivating proinflammatory mediators, such as complement activation products. To assess the role of TAFI in pneumococcal meningitis. We performed a prospective nationwide genetic association study in patients with bacterial meningitis, determined TAFI and complement levels in cerebrospinal fluid (CSF), and assessed the function of TAFI in a pneumococcal meningitis mouse model by using Cpb2 (TAFI) knockout mice. Polymorphisms (reference sequences: rs1926447 and rs3742264) in the CPB2 gene, coding for TAFI, were related to the development of systemic complications in patients with pneumococcal meningitis. Higher protein levels of TAFI in CSF were significantly associated with CSF complement levels (C3a, iC3b, and C5b-9) and with more systemic complications in patients with bacterial meningitis. The risk allele of rs1926447 (TT) was associated with higher levels of TAFI in CSF. In the murine model, consistent with the human data, Cpb2-deficient mice had decreased disease severity, as reflected by lower mortality, and attenuated cytokine levels and bacterial outgrowth in the systemic compartment during disease, without differences in the brain compartment, as compared with wild-type mice. These findings suggest that TAFI plays an important role during pneumococcal meningitis, which is likely to be mediated through inhibition of the complement system, and influences the occurrence of systemic complications and inflammation. © 2015 International Society on Thrombosis and Haemostasis.

  8. Renal function and plasma dabigatran level measured at trough by diluted thrombin time assay

    Directory of Open Access Journals (Sweden)

    Marta E. Martinuzzo

    2017-02-01

    Full Text Available Dabigatran etexilate (direct thrombin inhibitor is effective in preventing embolic stroke in patients with atrial fibrillation. It does not require laboratory control, but given the high renal elimination, its measurement in plasma is important in renal failure. The objectives of the study were to verify the analytical quality of the diluted thrombin time assay for measurement of dabigatran plasma concentration (cc, correlate cc with classic coagulation assays, prothrombin time (PT and activated partial thromboplastin time (APTT, and evaluate them according to the creatinine clearance (CLCr. Forty plasma samples of patients (34 consecutive and 6 suspected of drug accumulation receiving dabigatran at 150 (n = 19 or 110 (n = 21 mg/12 hours were collected. Blood samples were drawn at 10-14 hours of the last intake. Dabigatran concentration was determined by diluted thrombin time (HemosIl DTI, Instrumentation Laboratory (IL. PT and APTT (IL were performed on two fotooptical coagulometers, ACL TOP 300 and 500 (IL. DTI presented intra-assay coefficient of variation < 5.4% and inter-assay < 6%, linearity range 0-493 ng/ml. Patients' cc: median 83 (4-945 ng/ml. Individuals with CLCr in the lowest tertile (22.6-46.1 ml/min showed significantly higher median cc: 308 (49-945, compared to the average 72 (12-190 and highest tertile, 60 (4-118 ng/ml. Correlation between cc and APTT or PT were moderate, r2 = 0.59 and -0.66, p < 0.0001, respectively. DTI test allowed us to quantify plasma dabigatran levels, both in patients with normal or altered renal function, representing a useful tool in clinical situations such as renal failure, pre surgery or emergencies

  9. Differential proteolytic activation of factor VIII-von Willebrand factor complex by thrombin

    International Nuclear Information System (INIS)

    Hill-Eubanks, D.C.; Parker, C.G.; Lollar, P.

    1989-01-01

    Blood coagulation factor VIII (fVIII) is a plasma protein that is decreased or absent in hemophilia A. It is isolated as a mixture of heterodimers that contain a variably sized heavy chain and a common light chain. Thrombin catalyzes the activation of fVIII in a reaction that is associated with cleavages in both types of chain. The authors isolated a serine protease from Bothrops jararacussu snake venom that catalyzes thrombin-like heavy-chain cleavage but not light-chain cleavage in porcine fVIII as judged by NaDodSO 4 /PAGE and N-terminal sequence analysis. Using a plasma-free assay of the ability of activated 125 I-fVIII to function as a cofactor in the activation of factor X by factor IXa, they found that fVIII is activated by the venom enzyme. The venom enzyme-activated fVIII was isolated in stable form by cation-exchange HPLC. von Willebrand factor inhibited venom enzyme-activated fVIII but not thrombin-activated fVIII. These results suggest that the binding of fVIII to von Willebrand factor depends on the presence of an intact light chain and that activated fVIII must dissociate from von Willebrand factor to exert its cofactor effect. Thus, proteolytic activation of fVIII-von Willebrand factor complex appears to be differentially regulated by light-chain cleavage to dissociate the complex and heavy-chain cleavage to activate the cofactor function

  10. An improved method for the determination of trace levels of arsenic and antimony in geological materials by automated hydride generation-atomic absorption spectroscopy

    Science.gov (United States)

    Crock, J.G.; Lichte, F.E.

    1982-01-01

    An improved, automated method for the determination of arsenic and antimony in geological materials is described. After digestion of the material in sulfuric, nitric, hydrofluoric and perchloric acids, a hydrochloric acid solution of the sample is automatically mixed with reducing agents, acidified with additional hydrochloric acid, and treated with a sodium tetrahydroborate solution to form arsine and stibine. The hydrides are decomposed in a heated quartz tube in the optical path of an atomic absorption spectrometer. The absorbance peak height for arsenic or antimony is measured. Interferences that exist are minimized to the point where most geological materials including coals, soils, coal ashes, rocks and sediments can be analyzed directly without use of standard additions. The relative standard deviation of the digestion and the instrumental procedure is less than 2% at the 50 ??g l-1 As or Sb level. The reagent-blank detection limit is 0.2 ??g l-1 As or Sb. ?? 1982.

  11. First steps in the direction of synthetic, allosteric, direct inhibitors of thrombin and factor Xa.

    Science.gov (United States)

    Verghese, Jenson; Liang, Aiye; Sidhu, Preet Pal Singh; Hindle, Michael; Zhou, Qibing; Desai, Umesh R

    2009-08-01

    Designing non-saccharide functional mimics of heparin is a major challenge. In this work, a library of small, aromatic molecules based on the sulfated DHP scaffold was synthesized and screened against thrombin and factor Xa. The results reveal that (i) selected monomeric benzofuran derivatives inhibit the two enzymes, albeit weakly; (ii) the two enzymes recognize different structural features in the benzofurans studied suggesting significant selectivity of recognition; and (iii) the mechanism of inhibition is allosteric. The molecules represent the first allosteric small molecule inhibitors of the two enzymes.

  12. First Steps in the Direction of Synthetic, Allosteric, Direct Inhibitors of Thrombin and Factor Xa

    Science.gov (United States)

    Verghese, Jenson; Liang, Aiye; Sidhu, Preet Pal Singh; Hindle, Michael; Zhou, Qibing; Desai, Umesh R.

    2009-01-01

    Designing non-saccharide functional mimics of heparin is a major challenge. In this work, a library of small, aromatic molecules based on the sulfated DHP scaffold was synthesized and screened against thrombin and factor Xa. The results reveal that i) selected monomeric benzofuran derivatives inhibit the two enzymes, albeit weakly; ii) the two enzymes recognize different structural features in the benzofurans studied suggesting significant selectivity of recognition; and iii) the mechanism of inhibition is allosteric. The molecules represent the first allosteric small molecule inhibitors of the two enzymes. PMID:19540113

  13. The king is dead (warfarin): direct thrombin and factor Xa inhibitors: the next Diadochian War?

    Science.gov (United States)

    Diener, Hans-Christoph; Eikelboom, John; Granger, Christopher B; Hacke, Werner

    2012-02-01

    Atrial fibrillation is an important risk factor for stroke. New drugs for oral anticoagulation that do not exhibit the limitations of vitamin K antagonists like warfarin are under investigation. These include direct factor Xa inhibitors and direct thrombin-inhibitors. Recent studies provide promising results for apixaban, dabigatran, and rivaroxaban, including higher efficacy and significantly lower incidences of intracranial bleeds compared with warfarin. The new oral anticoagulants substances show similar results in secondary as in primary stroke prevention in patients with AF and will on the long run replace warfarin.

  14. Post-traumatic hepatic artery pseudoaneurysm treated with endovascular embolization and thrombin injection

    Science.gov (United States)

    Francisco, Lloret Estañ; Asunción, López Conesa; Antonio, Capel Alemán; Ricardo, Robles Campos; Manuel, Reus Pintado; Caridad, Marín Hernández

    2010-01-01

    Post-traumatic hepatic artery pseudoaneurysm is uncommon, appearing in approximately 1% of hepatic trauma cases. Most are extrahepatic (80%) and have a late onset. Although they are usually asymptomatic, they should always be treated becasue of the high risk of complications, especially breakage. Currently the treatment of choice is endovascular embolization with coils or the exclusion of the pseudoaneurysm using other intravascular devices. Recently there have been accounts of a treatment that combines embolization with coils and image-guided percutaneous human thrombin injection. We present a case of post-traumatic hepatic artery pseudoaneurysm that was successfully treated using this combined technique. PMID:21160978

  15. 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.

  16. 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; hide

    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.

  17. 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...

  18. Incidence of thromboembolic events after use of gelatin-thrombin-based hemostatic matrix during intracranial tumor surgery.

    Science.gov (United States)

    Gazzeri, Roberto; Galarza, Marcelo; Conti, Carlo; De Bonis, Costanzo

    2018-01-01

    Association between the use of hemostatic agents made from collagen/gelatin mixed with thrombin and thromboembolic events in patients undergoing tumor resection has been suggested. This study evaluates the relationship between flowable hemostatic matrix and deep vein thrombosis in a large cohort of patients treated for brain tumor removal. The authors conducted a retrospective, multicenter, clinical review of all craniotomies for tumor removal performed between 2013 and 2014. Patients were classified in three groups: group I (flowable gelatin hemostatic matrix with thrombin), group II (gelatin hemostatic without thrombin), and group III (classical hemostatic). A total of 932 patients were selected: tumor pathology included 441 gliomas, 296 meningiomas, and 195 metastases. Thromboembolic events were identified in 4.7% of patients in which gelatin matrix with thrombin was applied, in 8.4% of patients with gelatin matrix without thrombin, and in 3.6% of cases with classical methods of hemostasis. Patients with venous thromboembolism had an increased proportion of high-grade gliomas (7.2%). Patients receiving a greater dose than 10 ml gelatin hemostatic had a higher rate of thromboembolic events. Intracranial hematoma requiring reintervention occurred in 19 cases: 4.5% of cases of group III, while reoperation was performed in 1.3 and 1.6% of patients in which gelatin matrix with or without thrombin was applied. Gelatin matrix hemostat is an efficacious tool for neurosurgeons in cases of difficult intraoperative bleeding during cranial tumor surgery. This study may help to identify those patients at high risk for developing thromboembolism and to treat them accordingly.

  19. Heparin modulates chemokines in human endometrial stromal cells by interaction with tumor necrosis factor α and thrombin.

    Science.gov (United States)

    Spratte, Julia; Schönborn, Magdalena; Treder, Nora; Bornkessel, Frauke; Zygmunt, Marek; Fluhr, Herbert

    2015-05-01

    To study the impact of heparins on chemokines in decidualized human endometrial stromal cells (ESCs) in vitro. In vitro experiment. Research laboratory. Premenopausal women undergoing hysterectomy for benign reasons. ESCs were isolated from hysterectomy specimens, decidualized in vitro and incubated with unfractionated heparin and low-molecular-weight heparins (LMWHs) as well as tumor necrosis factor (TNF) α or thrombin with or without heparins. Chemokines CXCL1, CXCL5, CXCL8, CCL2, and CCL5 were measured with the use of ELISA, and CXCL5, CXCL8, CCL2, and CCL5 were detected with the use of real-time reverse-transcription polymerase chain reaction. Cell viability was determined with the use of a fluorometric assay. TNF-α and thrombin stimulated distinct patterns of chemokines in ESCs. Unfractionated heparin and LMWHs attenuated the TNF-α-mediated induction of CXCL8 and enhanced CXCL5, CCL2, and CCL5. The stimulating effect of thrombin on CXCL8 could be inhibited by heparin, whereas heparin had no impact on thrombin-induced CXCL1 and CCL2. Nuclear factor of transcription κB signaling mediated the effects of TNF-α. The effects of thrombin were mediated via extracellular signal-regulated protein kinases 1/2. Heparins have modulating effects on TNF-α- and thrombin-induced endometrial chemokines, which might have implications in the regulation of endometrial receptivity and early implantation. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  20. Role of Thrombin in Soluble Thrombomodulin-Induced Suppression of Peripheral HMGB1-Mediated Allodynia in Mice.

    Science.gov (United States)

    Tsujita, Ryuichi; Tsubota, Maho; Hayashi, Yusuke; Saeki, Haruka; Sekiguchi, Fumiko; Kawabata, Atsufumi

    2017-12-01

    High mobility group box 1 (HMGB1), a nuclear protein, once released into the extracellular space under pathological conditions, plays a pronociceptive role in redox-dependent distinct active forms, all-thiol HMGB1 (at-HMGB1) and disulfide HMGB1 (ds-HMGB1), that accelerate nociception through the receptor for advanced glycation endproducts (RAGE) and Toll-like receptor 4 (TLR4), respectively. Thrombomodulin (TM), an endothelial membrane protein, and soluble TM, known as TMα, promote thrombin-mediated activation of protein C and also sequester HMGB1, which might facilitate thrombin degradation of HMGB1. The present study aimed at clarifying the role of thrombin in TMα-induced suppression of peripheral HMGB1-dependent allodynia in mice. Thrombin-induced degradation of at-HMGB1 and ds-HMGB1 was accelerated by TMα in vitro. Intraplantar (i.pl.) injection of bovine thymus-derived HMGB1 in an unknown redox state, at-HMGB1, ds-HMGB1 or lipopolysaccharide (LPS), known to cause HMGB1 secretion, produced long-lasting mechanical allodynia in mice, as assessed by von Frey test. TMα, when preadministered i.pl., prevented the allodynia caused by bovine thymus-derived HMGB1, at-HMGB1, ds-HMGB1 or LPS, in a dose-dependent manner. The TMα-induced suppression of the allodynia following i.pl. at-HMGB1, ds-HMGB1 or LPS was abolished by systemic preadministration of argatroban, a thrombin-inhibiting agent, and accelerated by i.pl. co-administered thrombin. Our data clearly indicate that TMα is capable of promoting the thrombin-induced degradation of both at-HMGB1 and ds-HMGB1, and suppresses the allodynia caused by either HMGB1 in a thrombin-dependent manner. Considering the emerging role of HMGB1 in distinct pathological pain models, the present study suggests the therapeutic usefulness of TMα for treatment of intractable and/or persistent pain.

  1. Automation for the Nineties: A Review Article.

    Science.gov (United States)

    Whitney, Gretchen; Glogoff, Stuart

    1994-01-01

    Describes the technical, political, economic, and cultural environments of library automation. A review is then presented of five books covering wide-ranging library automation themes, including practical experiences; planning second-generation library systems; software, systems, and services; new roles for librarians; and the national network…

  2. High throughput protease profiling comprehensively defines active site specificity for thrombin and ADAMTS13.

    Science.gov (United States)

    Kretz, Colin A; Tomberg, Kärt; Van Esbroeck, Alexander; Yee, Andrew; Ginsburg, David

    2018-02-12

    We have combined random 6 amino acid substrate phage display with high throughput sequencing to comprehensively define the active site specificity of the serine protease thrombin and the metalloprotease ADAMTS13. The substrate motif for thrombin was determined by >6,700 cleaved peptides, and was highly concordant with previous studies. In contrast, ADAMTS13 cleaved only 96 peptides (out of >10 7 sequences), with no apparent consensus motif. However, when the hexapeptide library was substituted into the P3-P3' interval of VWF73, an exosite-engaging substrate of ADAMTS13, 1670 unique peptides were cleaved. ADAMTS13 exhibited a general preference for aliphatic amino acids throughout the P3-P3' interval, except at P2 where Arg was tolerated. The cleaved peptides assembled into a motif dominated by P3 Leu, and bulky aliphatic residues at P1 and P1'. Overall, the P3-P2' amino acid sequence of von Willebrand Factor appears optimally evolved for ADAMTS13 recognition. These data confirm the critical role of exosite engagement for substrates to gain access to the active site of ADAMTS13, and define the substrate recognition motif for ADAMTS13. Combining substrate phage display with high throughput sequencing is a powerful approach for comprehensively defining the active site specificity of proteases.

  3. 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.

  4. Thrombin activatable fibrinolysis inhibitor and other hemostatic parameters in patients with polycystic ovary syndrome.

    Science.gov (United States)

    Oral, Baha; Mermi, Betül; Dilek, Müfide; Alanoğlu, Güçhan; Sütçü, Recep

    2009-02-01

    To investigate the plasma levels of thrombin-activatable fibrinolysis inhibitor (TAFI) in women with polycystic ovary syndrome (PCOS) and its correlation with various metabolic, hormonal and hemostatic parameters. Forty-eight women with PCOS and 43 age- and BMI-matched ovulatory controls were recruited during a 20-month study period. Blood samples were drawn for all tests, which included plasma lipids and lipoproteins, reproductive hormones, glucose, insulin, TAFI antigen concentration, plasminogen activator inhibitor-1 (PAI-1) activity, fibrinogen concentration, thrombomodulin, thrombin-antithrombin (TAT) complexes, D-dimer, Protein C Antigen, Protein S Antigen, Antithrombin III (AT III) and activated protein C (APC) resistance. Plasma TAFI levels of PCOS patients were found to be significantly higher than in healthy controls (93.8%+/-30.6%vs. 79.8% +/- 22.4%, p < 0.05). Plasma levels of D-dimer, AT III, PAI-1 and thrombomodulin were also significantly higher in women with PCOS compared with healthy controls. All the other hemostatic parameters (including TAT complexes; Protein C; APC; and Protein S) were comparable between the two study groups. This study showed that plasma levels of TAFI, PAI-1, D-dimer, AT III and thrombomodulin were significantly increased in women with PCOS compared with age- and BMI-matched controls.

  5. FVIIa-sTF and Thrombin Inhibitory Activities of Compounds Isolated from Microcystis aeruginosa K-139.

    Science.gov (United States)

    Anas, Andrea Roxanne J; Mori, Akane; Tone, Mineka; Naruse, Chiaki; Nakajima, Anna; Asukabe, Hirohiko; Takaya, Yoshiaki; Imanishi, Susumu Y; Nishizawa, Tomoyasu; Shirai, Makoto; Harada, Ken-Ichi

    2017-08-30

    The rise of bleeding and bleeding complications caused by oral anticoagulant use are serious problems nowadays. Strategies that block the initiation step in blood coagulation involving activated factor VII-tissue factor (fVIIa-TF) have been considered. This study explores toxic Microcystis aeruginosa K-139, from Lake Kasumigaura, Ibaraki, Japan, as a promising cyanobacterium for isolation of fVIIa-sTF inhibitors. M. aeruginosa K-139 underwent reversed-phase solid-phase extraction (ODS-SPE) from 20% MeOH to MeOH elution with 40%-MeOH increments, which afforded aeruginosin K-139 in the 60% MeOH fraction; micropeptin K-139 and microviridin B in the MeOH fraction. Aeruginosin K-139 displayed an fVIIa-sTF inhibitory activity of ~166 µM, within a 95% confidence interval. Micropeptin K-139 inhibited fVIIa-sTF with EC 50 10.62 µM, which was more efficient than thrombin inhibition of EC 50 26.94 µM. The thrombin/fVIIa-sTF ratio of 2.54 in micropeptin K-139 is higher than those in 4-amidinophenylmethane sulfonyl fluoride (APMSF) and leupeptin, when used as positive controls. This study proves that M. aeruginosa K-139 is a new source of fVIIa-sTF inhibitors. It also opens a new avenue for micropeptin K-139 and related depsipeptides as fVIIa-sTF inhibitors.

  6. Thrombin-activatable fibrinolysis inhibitor is degraded by Salmonella enterica and Yersinia pestis.

    Science.gov (United States)

    Valls Serón, M; Haiko, J; DE Groot, P G; Korhonen, T K; Meijers, J C M

    2010-10-01

     Pathogenic bacteria modulate the host coagulation system to evade immune responses or to facilitate dissemination through extravascular tissues. In particular, the important bacterial pathogens Salmonella enterica and Yersinia pestis intervene with the plasminogen/fibrinolytic system. Thrombin-activatable fibrinolysis inhibitor (TAFI) has anti-fibrinolytic properties as the active enzyme (TAFIa) removes C-terminal lysine residues from fibrin, thereby attenuating accelerated plasmin formation.  Here, we demonstrate inactivation and cleavage of TAFI by homologous surface proteases, the omptins Pla of Y. pestis and PgtE of S. enterica. We show that omptin-expressing bacteria decrease TAFI activatability by thrombin-thrombomodulin and that the anti-fibrinolytic potential of TAFIa was reduced by recombinant Escherichia coli expressing Pla or PgtE. The functional impairment resulted from C-terminal cleavage of TAFI by the omptins.  Our results indicate that TAFI is degraded directly by the omptins PgtE of S. enterica and Pla of Y. pestis. This may contribute to the ability of PgtE and Pla to damage tissue barriers, such as fibrin, and thereby to enhance spread of S. enterica and Y. pestis during infection. © 2010 International Society on Thrombosis and Haemostasis.

  7. FVIIa-sTF and Thrombin Inhibitory Activities of Compounds Isolated from Microcystis aeruginosa K-139

    Directory of Open Access Journals (Sweden)

    Andrea Roxanne J. Anas

    2017-08-01

    Full Text Available The rise of bleeding and bleeding complications caused by oral anticoagulant use are serious problems nowadays. Strategies that block the initiation step in blood coagulation involving activated factor VII-tissue factor (fVIIa-TF have been considered. This study explores toxic Microcystis aeruginosa K-139, from Lake Kasumigaura, Ibaraki, Japan, as a promising cyanobacterium for isolation of fVIIa-sTF inhibitors. M. aeruginosa K-139 underwent reversed-phase solid-phase extraction (ODS-SPE from 20% MeOH to MeOH elution with 40%-MeOH increments, which afforded aeruginosin K-139 in the 60% MeOH fraction; micropeptin K-139 and microviridin B in the MeOH fraction. Aeruginosin K-139 displayed an fVIIa-sTF inhibitory activity of ~166 µM, within a 95% confidence interval. Micropeptin K-139 inhibited fVIIa-sTF with EC50 10.62 µM, which was more efficient than thrombin inhibition of EC50 26.94 µM. The thrombin/fVIIa-sTF ratio of 2.54 in micropeptin K-139 is higher than those in 4-amidinophenylmethane sulfonyl fluoride (APMSF and leupeptin, when used as positive controls. This study proves that M. aeruginosa K-139 is a new source of fVIIa-sTF inhibitors. It also opens a new avenue for micropeptin K-139 and related depsipeptides as fVIIa-sTF inhibitors.

  8. Autonomous Systems: Habitat Automation

    Data.gov (United States)

    National Aeronautics and Space Administration — The Habitat Automation Project Element within the Autonomous Systems Project is developing software to automate the automation of habitats and other spacecraft. This...

  9. An Automation Planning Primer.

    Science.gov (United States)

    Paynter, Marion

    1988-01-01

    This brief planning guide for library automation incorporates needs assessment and evaluation of options to meet those needs. A bibliography of materials on automation planning and software reviews, library software directories, and library automation journals is included. (CLB)

  10. Infection-Induced Thrombin Production: A Potential Novel Mechanism for Preterm Premature Rupture of Membranes (PPROM).

    Science.gov (United States)

    Feng, Liping; Allen, Terrence K; Marinello, William P; Murtha, Amy P

    2018-04-13

    Preterm premature rupture of membranes (PPROM) is a leading contributor to maternal and neonatal morbidity and mortality. Epidemiologic and experimental studies have demonstrated that thrombin causes fetal membrane weakening and subsequently PPROM. Although blood is suspected as the likely source of thrombin in fetal membranes and amniotic fluid of patients with PPROM, this has not been proven. Ureaplasma Parvum (U. parvum) is emerging as a pathogen involved in prematurity, including PPROM, but until now, prothrombin production directly induced by bacteria in fetal membranes has not been described. This study was designed to investigate whether U. parvum exposure can induce prothrombin production in fetal membranes cells. Primary fetal membrane cells (amnion epithelial, chorion trophoblast, and decidua stromal) or full-thickness fetal membrane tissue explants from elective, term, uncomplicated cesarean deliveries were harvested. Cells or tissue explants were infected with live U. parvum (1 x 10 5 , 1 x 10 6 , or 1 x 10 7 colony forming units (cfu)/ml) or lipopolysaccharide (Escherichia coli J5, L-5014, Sigma, 100 ng/ml or 1000 ng/ml) for 24 hours. Tissue explants were fixed for immunohistochemistry staining of thrombin/prothrombin. Fetal membrane cells were fixed for confocal immunofluorescent staining of the biomarkers of fetal membrane cell types and thrombin/prothrombin. Protein and mRNA were harvested from the cells and tissue explants for Western blot or qRT-PCR to quantify thrombin/prothrombin protein or mRNA production, respectively. Data are presented as mean values ± standard errors of mean. Data were analyzed using one-way ANOVA with post hoc Dunnett's test. Prothrombin production and localization was confirmed by Western blot and immunostainings in all primary fetal membrane cells and tissue explants. Immunofluorescence observations revealed a perinuclear localization of prothrombin in amnion epithelial cells. Localization of prothrombin in chorion and

  11. 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,...

  12. Effect of automated tube voltage selection, integrated circuit detector and advanced iterative reconstruction on radiation dose and image quality of 3rd generation dual-source aortic CT angiography: An intra-individual comparison.

    Science.gov (United States)

    Mangold, Stefanie; De Cecco, Carlo N; Wichmann, Julian L; Canstein, Christian; Varga-Szemes, Akos; Caruso, Damiano; Fuller, Stephen R; Bamberg, Fabian; Nikolaou, Konstantin; Schoepf, U Joseph

    2016-05-01

    To compare, on an intra-individual basis, the effect of automated tube voltage selection (ATVS), integrated circuit detector and advanced iterative reconstruction on radiation dose and image quality of aortic CTA studies using 2nd and 3rd generation dual-source CT (DSCT). We retrospectively evaluated 32 patients who had undergone CTA of the entire aorta with both 2nd generation DSCT at 120kV using filtered back projection (FBP) (protocol 1) and 3rd generation DSCT using ATVS, an integrated circuit detector and advanced iterative reconstruction (protocol 2). Contrast-to-noise ratio (CNR) was calculated. Image quality was subjectively evaluated using a five-point scale. Radiation dose parameters were recorded. All studies were considered of diagnostic image quality. CNR was significantly higher with protocol 2 (15.0±5.2 vs 11.0±4.2; pquality analysis revealed no significant differences for evaluation of attenuation (p=0.08501) but image noise was rated significantly lower with protocol 2 (p=0.0005). Mean tube voltage and effective dose were 94.7±14.1kV and 6.7±3.9mSv with protocol 2; 120±0kV and 11.5±5.2mSv with protocol 1 (pquality in comparison to 120kV imaging with FBP. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  13. Automated Clustering of Similar Amendments

    CERN Multimedia

    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.

  14. Automation 2017

    CERN Document Server

    Zieliński, Cezary; Kaliczyńska, Małgorzata

    2017-01-01

    This book consists of papers presented at Automation 2017, an international conference held in Warsaw from March 15 to 17, 2017. It discusses research findings associated with the concepts behind INDUSTRY 4.0, with a focus on offering a better understanding of and promoting participation in the Fourth Industrial Revolution. Each chapter presents a detailed analysis of a specific technical problem, in most cases followed by a numerical analysis, simulation and description of the results of implementing the solution in a real-world context. The theoretical results, practical solutions and guidelines presented are valuable for both researchers working in the area of engineering sciences and practitioners looking for solutions to industrial problems. .

  15. Marketing automation

    Directory of Open Access Journals (Sweden)

    TODOR Raluca Dania

    2017-01-01

    Full Text Available The automation of the marketing process seems to be nowadays, the only solution to face the major changes brought by the fast evolution of technology and the continuous increase in supply and demand. In order to achieve the desired marketing results, businessis have to employ digital marketing and communication services. These services are efficient and measurable thanks to the marketing technology used to track, score and implement each campaign. Due to the technical progress, the marketing fragmentation, demand for customized products and services on one side and the need to achieve constructive dialogue with the customers, immediate and flexible response and the necessity to measure the investments and the results on the other side, the classical marketing approached had changed continue to improve substantially.

  16. Development of Automated Procedures to Generate Reference Building Models for ASHRAE Standard 90.1 and India’s Building Energy Code and Implementation in OpenStudio

    Energy Technology Data Exchange (ETDEWEB)

    Parker, Andrew [National Renewable Energy Lab. (NREL), Golden, CO (United States); Haves, Philip [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Jegi, Subhash [International Institute of Information Technology, Hyderabad (India); Garg, Vishal [International Institute of Information Technology, Hyderabad (India); Ravache, Baptiste [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2017-09-14

    This paper describes a software system for automatically generating a reference (baseline) building energy model from the proposed (as-designed) building energy model. This system is built using the OpenStudio Software Development Kit (SDK) and is designed to operate on building energy models in the OpenStudio file format.

  17. Third-generation electrokinetically pumped sheath-flow nanospray interface with improved stability and sensitivity for automated capillary zone electrophoresis-mass spectrometry analysis of complex proteome digests.

    Science.gov (United States)

    Sun, Liangliang; Zhu, Guijie; Zhang, Zhenbin; Mou, Si; Dovichi, Norman J

    2015-05-01

    We have reported a set of electrokinetically pumped sheath flow nanoelectrospray interfaces to couple capillary zone electrophoresis with mass spectrometry. A separation capillary is threaded through a cross into a glass emitter. A side arm provides fluidic contact with a sheath buffer reservoir that is connected to a power supply. The potential applied to the sheath buffer drives electro-osmosis in the emitter to pump the sheath fluid at nanoliter per minute rates. Our first-generation interface placed a flat-tipped capillary in the emitter. Sensitivity was inversely related to orifice size and to the distance from the capillary tip to the emitter orifice. A second-generation interface used a capillary with an etched tip that allowed the capillary exit to approach within a few hundred micrometers of the emitter orifice, resulting in a significant increase in sensitivity. In both the first- and second-generation interfaces, the emitter diameter was typically 8 μm; these narrow orifices were susceptible to plugging and tended to have limited lifetime. We now report a third-generation interface that employs a larger diameter emitter orifice with very short distance between the capillary tip and the emitter orifice. This modified interface is much more robust and produces much longer lifetime than our previous designs with no loss in sensitivity. We evaluated the third-generation interface for a 5000 min (127 runs, 3.5 days) repetitive analysis of bovine serum albumin digest using an uncoated capillary. We observed a 10% relative standard deviation in peak area, an average of 160,000 theoretical plates, and very low carry-over (much less than 1%). We employed a linear-polyacrylamide (LPA)-coated capillary for single-shot, bottom-up proteomic analysis of 300 ng of Xenopus laevis fertilized egg proteome digest and identified 1249 protein groups and 4038 peptides in a 110 min separation using an LTQ-Orbitrap Velos mass spectrometer; peak capacity was ∼330. The

  18. Genetic variation in thrombin-activatable fibrinolysis inhibitor (TAFI) is associated with the risk of splanchnic vein thrombosis

    NARCIS (Netherlands)

    de Bruijne, Emile L. E.; Darwish Murad, Sarwa; de Maat, Moniek P. M.; Tanck, Michael W. T.; Haagsma, Elizabeth B.; van Hoek, Bart; Rosendaal, Frits R.; Janssen, Harry L. A.; Leebeek, Frank W. G.

    2007-01-01

    Splanchnic vein thrombosis (SVT) has been associated with a hypercoagulable state. Thrombin-activatable fibrinolysis inhibitor (TAFI) may contribute to a hypercoagulable state, and therefore we were interested in the role of TAFI in SVT. Since the disease is frequently associated with liver

  19. Genetic variation in thrombin-activatable fibrinolysis inhibitor (TAR) is associated with the risk of splanchnic vein thrombosis

    NARCIS (Netherlands)

    de Bruijne, Emile L. E.; Murad, Sarwa Darwish; de Maat, Moniek P. M.; Tanck, Michael W. T.; Haagsma, Elizabeth B.; van Hoeks, Bart; Rosendaal, Frits R.; Janssen, Harry L. A.; Leebeek, Frank W. G.

    Splanchnic vein thrombosis (SVT) has been associated with a hypercoagulable state. Thrombin-activatable fibrinolysis inhibitor (TAFI) may contribute to a hypercoagulable state, and therefore we were interested in the role of TAR in SVT. Since the disease is frequently associated with liver

  20. 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

    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

  1. Alkylation of phosphorothioated thrombin binding aptamers improves the selectivity of inhibition of tumor cell proliferation upon anticoagulation.

    Science.gov (United States)

    Yang, Xiantao; Zhu, Yuejie; Wang, Chao; Guan, Zhu; Zhang, Lihe; Yang, Zhenjun

    2017-07-01

    Recently, aptamers have been extensively researched for therapy and diagnostic applications. Thrombin-binding aptamer is a 15nt deoxyribonucleic acid screened by SELEX, it can specifically bind to thrombin and inhibit blood coagulation. Since it is also endowed with excellent antitumor activity, the intrinsic anticoagulation advantage converted to a main potential side effect for its further application in antiproliferative therapy. Site-specific alkylation was conducted through nucleophilic reaction of phosphorothioated TBAs using bromide reagents. Circular dichroism (CD) spectroscopy and surface plasmon resonance (SPR) measurements were used to evaluate anticoagulation activity, and a CCK-8 assay was used to determine cell proliferation activity. The CD spectra of the modified TBAs were weakened, and their affinity for thrombin was dramatically reduced, as reflected by the K D values. On the other hand, their inhibition of A549 cells was retained. Incorporation of different alkyls apparently disrupted the binding of TBA to thrombin while maintaining the antitumor activity. A new modification strategy was established for the use of TBA as a more selective antitumor agent. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. A sensitive bioimmunoassay for thrombin-cleaved two-chain urokinase-type plasminogen activator in human body fluids

    NARCIS (Netherlands)

    Braat, E.A.M.; Nauland, U.; Dooijewaard, G.; Rijken, D.C.

    1996-01-01

    Thrombin cleaves single-chain urokinase-type plasminogen activator (scu-PA) into a two-chain form (tcu-PA/T), which is virtually inactive in plasminogen activator assays. Little is known about the physiological importance of tcu-PA/T. To examine the occurrence of tcu-PA/T in vivo, we developed a

  3. Effect of the immobilisation of DNA aptamers on the detection of thrombin by means of surface plasmon resonance

    Czech Academy of Sciences Publication Activity Database

    Hianik, T.; Ostatná, V.; Vaisocherová, Hana; Homola, Jiří

    2008-01-01

    Roč. 391, č. 5 (2008), s. 1861-1869 ISSN 1618-2642 R&D Projects: GA AV ČR KAN200670701 Institutional research plan: CEZ:AV0Z20670512 Keywords : DNA aptamer * thrombin * dendrimers Subject RIV: EI - Biotechnology ; Bionics Impact factor: 3.328, year: 2008

  4. 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

  5. Effects of thrombin inhibition with melagatran on renal hemodynamics and function and liver integrity during early endotoxemia

    DEFF Research Database (Denmark)

    Nitescu, Nicoletta; Grimberg, Elisabeth; Ricksten, Sven-Erik

    2007-01-01

    Sepsis is associated with an activation of the coagulation system and multiorgan failure. The aim of the study was to examine the effects of selective thrombin inhibition with melagatran on renal hemodynamics and function, and liver integrity, during early endotoxemia. Endotoxemia was induced...

  6. Automation of a thermal expansion instrument

    Energy Technology Data Exchange (ETDEWEB)

    Holland, L.L.

    1979-03-01

    Automation of a thermal expansion instrument using a minicomputer system and with analog-to-digital converter inputs and flip-flop relay outputs is described. The necessary hardware link and the software were developed to allow equipment control, data acquisition, data reduction, and report generation by the minicomputer. The design of the automation allows non-programmers to run the experiment, reduce the data, and generate the report.

  7. aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data

    OpenAIRE

    Allen, Julie M; Huang, Daisie I; Cronk, Quentin C; Johnson, Kevin P

    2015-01-01

    Background Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome using de novo approaches can take days, even on a powerful computer, and these assemblies typically require data from a variety of genomic libraries. Here we describe software that will alleviate these issues by rapidly assembling genes from distantly related taxa using a sing...

  8. 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.

  9. Both Automation and Paper.

    Science.gov (United States)

    Purcell, Royal

    1988-01-01

    Discusses the concept of a paperless society and the current situation in library automation. Various applications of automation and telecommunications are addressed, and future library automation is considered. Automation at the Monroe County Public Library in Bloomington, Indiana, is described as an example. (MES)

  10. Personal experiences in direct ultrasound-guided injection of thrombin into the lumen of pseudoaneurysm as a method of treatment in case of iatrogenic femoral artery damage

    International Nuclear Information System (INIS)

    Slonina, J.; Zaleska-Dorobisz, U.; Malczewska, J.; Kozminska, U.; Sasiadek, M.; Obremska, M.; Agrawal, A.

    2010-01-01

    Background: Pseudoaneurysms constitute a quite common complication of procedures requiring puncture of the common femoral artery. The risk factors of the condition include: obesity, arterial hypertension, sex (more prevalent in males) as well as antithrombotic therapy. Material/Methods: The US-guided injection of thrombin into the pseudoaneurysm lumen was performed in patients referred from the Department of Invasive Cardiology who had undergone coronarography or coronary angioplasty. Pseudoaneurysms constituted the complication of common femoral artery canulation. After setting the diagnosis of pseudoaneurysm by means of Doppler ultrasound, patients with large pseudoaneurysms of volume exceeding 10 mm were qualified for thrombin injection. Generally, 33 patients underwent the treatment. In 3 cases - due to the presence of multiocular pseudoaneurysm - thrombin was administered twice. Results: Taking into account the safety of the procedure, ultimately 33 patients were qualified for thrombin administration, in whom aneurism of diameter exceeding 10 mm was diagnosed. In 3 patients with aneurysm of less than 10 mm, only a compression band was used prophylactically. In one case, because of a considerable oedema surrounding the tissue, as well as deep location of the aneurysm in the groin, thrombin treatment was not given due to technical reasons. In 30 cases, single administration of thrombin was effective and resulted in a complete thrombosis of the pseudoaneurism lumen within a couple of seconds following thrombin injection. In 3 patients with multicellular aneurysm, thrombin was given twice, resulting in a total obliteration of the pseudoaneurysm in two cases only. No complications were observed after the performed procedures. No recanalisation of pseudoaneurysms was demonstrated in follow-up examinations. Conclusions: 1. Direct thrombin injection into the pseudoaneurysm lumen can constitute an alternative method of treatment for open surgical techniques. 2. The

  11. Personal experiences in direct ultrasound-guided injection of thrombin into the lumen of pseudoaneurysm as a method of treatment in case of iatrogenic femoral artery damage

    International Nuclear Information System (INIS)

    Słonina, Joanna; Obremska, Marta; Zaleska-Dorobisz, Urszula; Agrawal, Anil; Malczewska, Joanna; Koźmińska, Urszula; Sąsiadek, Marek

    2010-01-01

    Pseudoaneurysms constitute a quite common complication of procedures requiring puncture of the common femoral artery. The risk factors of the condition include: obesity, arterial hypertension, sex (more prevalent in males) as well as antithrombotic therapy. The US-guided injection of thrombin into the pseudoaneurysm lumen was performed in patients referred from the Department of Invasive Cardiology who had undergone coronarography or coronary angioplasty. Pseudoaneurysms constituted the complication of common femoral artery canulation. After setting the diagnosis of pseudoaneurysm by means of Doppler ultrasound, patients with large pseudoaneurysms of volume exceeding 10 mm were qualified for thrombin injection. Generally, 33 patients underwent the treatment. In 3 cases – due to the presence of multiocular pseudoaneurysm – thrombin was administered twice. Taking into account the safety of the procedure, ultimately 33 patients were qualified for thrombin administration, in whom aneurism of diameter exceeding 10 mm was diagnosed. In 3 patients with aneurysm of less than 10mm, only a compression band was used prophylactically. In one case, because of a considerable oedema surrounding the tissue, as well as deep location of the aneurysm in the groin, thrombin treatment was not given due to technical reasons. In 30 cases, single administration of thrombin was effective and resulted in a complete thrombosis of the pseudoaneurism lumen within a couple of seconds following thrombin injection. In 3 patients with multicellular aneurysm, thrombin was given twice, resulting in a total obliteration of the pseudoaneurysm in two cases only. No complications were observed after the performed procedures. No recanalisation of pseudoaneurysms was demonstrated in follow-up examinations. 1. Direct thrombin injection into the pseudoaneurysm lumen can constitute an alternative method of treatment for open surgical techniques. 2. The procedure is highly effective, cheap and minimally

  12. iTRAQ quantitative proteomics-based identification of cell adhesion as a dominant phenotypic modulation in thrombin-stimulated human aortic endothelial cells.

    Science.gov (United States)

    Wang, Huang-Joe; Chen, Sung-Fang; Lo, Wan-Yu

    2015-05-01

    The phenotypic changes in thrombin-stimulated endothelial cells include alterations in permeability, cell shape, vasomotor tone, leukocyte trafficking, migration, proliferation, and angiogenesis. Previous studies regarding the pleotropic effects of thrombin on the endothelium used human umbilical vein endothelial cells (HUVECs)-cells derived from fetal tissue that does not exist in adults. Only a few groups have used screening approaches such as microarrays to profile the global effects of thrombin on endothelial cells. Moreover, the proteomic changes of thrombin-stimulated human aortic endothelial cells (HAECs) have not been elucidated. HAECs were stimulated with 2 units/mL thrombin for 5h and their proteome was investigated using isobaric tags for the relative and absolute quantification (iTRAQ) and the MetaCore(TM) software. A total of 627 (experiment A) and 622 proteins (experiment B) were quantified in the duplicated iTRAQ analyses. MetaCore(TM) pathway analysis identified cell adhesion as a dominant phenotype in thrombin-stimulated HAECs. Replicated iTRAQ data revealed that "Cell adhesion_Chemokines and adhesion," "Cell adhesion_Histamine H1 receptor signaling in the interruption of cell barrier integrity," and "Cell adhesion_Integrin-mediated cell adhesion and migration" were among the top 10 statistically significant pathways. The cell adhesion phenotype was verified by increased THP-1 adhesion to thrombin-stimulated HAECs. In addition, the expression of ICAM-1, VCAM-1, and SELE was significantly upregulated in thrombin-stimulated HAECs. Several regulatory pathways are altered in thrombin-stimulated HAECs, with cell adhesion being the dominant altered phenotype. Our findings show the feasibility of the iTRAQ technique for evaluating cellular responses to acute stimulation. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Diagnostic accuracy of coronary CT angiography using 3rd-generation dual-source CT and automated tube voltage selection: Clinical application in a non-obese and obese patient population

    International Nuclear Information System (INIS)

    Mangold, Stefanie; Wichmann, Julian L.; Schoepf, U.J.; Caruso, Damiano; Tesche, Christian; Steinberg, Daniel H.; Bayer, Richard R.; Varga-Szemes, Akos; Stubenrauch, Andrew C.; Biancalana, Matthew; De Cecco, Carlo N.; Nikolaou, Konstantin

    2017-01-01

    To investigate diagnostic accuracy of 3 rd -generation dual-source CT (DSCT) coronary angiography in obese and non-obese patients. We retrospectively analyzed 76 patients who underwent coronary CT angiography (CCTA) and invasive coronary angiography. Prospectively ECG-triggered acquisition was performed with automated tube voltage selection (ATVS). Patients were dichotomized based on body mass index in groups A (<30 kg/m 2 , n = 37) and B (≥30 kg/m 2 , n = 39) and based on tube voltage in groups C (<120 kV, n = 46) and D (120 kV, n = 30). Coronary arteries were assessed for significant stenoses (≥50 % luminal narrowing) and diagnostic accuracy was calculated. Per-patient overall sensitivity, specificity, positive predictive value, negative predictive value (NPV) and accuracy were 96.9 %, 95.5 %, 93.9 %, 97.7 % and 96.1 %, respectively. Sensitivity and NPV were lower in groups B and D compared to groups A and C, but no statistically significant differences were observed (group A vs. B: sensitivity, 100.0 % vs. 93.3 %, p = 0.9493; NPV, 100 % vs. 95.5 %, p = 0.9812; group C vs. D: sensitivity, 100.0 % vs. 92.3 %, p = 0.8462; NPV, 100.0 % vs. 94.1 %, p = 0.8285). CCTA using 3 rd -generation DSCT and (ATVS) provides high diagnostic accuracy in both non-obese and obese patients. (orig.)

  14. Diagnostic accuracy of coronary CT angiography using 3{sup rd}-generation dual-source CT and automated tube voltage selection: Clinical application in a non-obese and obese patient population

    Energy Technology Data Exchange (ETDEWEB)

    Mangold, Stefanie [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); Eberhard-Karls University Tuebingen, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany); Wichmann, Julian L. [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Schoepf, U.J. [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); Medical University of South Carolina, Division of Cardiology, Department of Medicine, Charleston, SC (United States); Caruso, Damiano [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); University of Rome ' ' Sapienza' ' , Department of Radiological Sciences, Oncology and Pathology, Rome (Italy); Tesche, Christian [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); Heart Centre Munich-Bogenhausen, Department of Cardiology, Munich (Germany); Steinberg, Daniel H.; Bayer, Richard R. [Medical University of South Carolina, Division of Cardiology, Department of Medicine, Charleston, SC (United States); Varga-Szemes, Akos; Stubenrauch, Andrew C.; Biancalana, Matthew; De Cecco, Carlo N. [Medical University of South Carolina, Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Charleston, SC (United States); Nikolaou, Konstantin [Eberhard-Karls University Tuebingen, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany)

    2017-06-15

    To investigate diagnostic accuracy of 3{sup rd}-generation dual-source CT (DSCT) coronary angiography in obese and non-obese patients. We retrospectively analyzed 76 patients who underwent coronary CT angiography (CCTA) and invasive coronary angiography. Prospectively ECG-triggered acquisition was performed with automated tube voltage selection (ATVS). Patients were dichotomized based on body mass index in groups A (<30 kg/m{sup 2}, n = 37) and B (≥30 kg/m{sup 2}, n = 39) and based on tube voltage in groups C (<120 kV, n = 46) and D (120 kV, n = 30). Coronary arteries were assessed for significant stenoses (≥50 % luminal narrowing) and diagnostic accuracy was calculated. Per-patient overall sensitivity, specificity, positive predictive value, negative predictive value (NPV) and accuracy were 96.9 %, 95.5 %, 93.9 %, 97.7 % and 96.1 %, respectively. Sensitivity and NPV were lower in groups B and D compared to groups A and C, but no statistically significant differences were observed (group A vs. B: sensitivity, 100.0 % vs. 93.3 %, p = 0.9493; NPV, 100 % vs. 95.5 %, p = 0.9812; group C vs. D: sensitivity, 100.0 % vs. 92.3 %, p = 0.8462; NPV, 100.0 % vs. 94.1 %, p = 0.8285). CCTA using 3{sup rd}-generation DSCT and (ATVS) provides high diagnostic accuracy in both non-obese and obese patients. (orig.)

  15. 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.

  16. 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.

  17. Comparison of Ultrasound-Guided Thrombin Injection of Iatrogenic Pseudoaneurysms Based on Neck Dimension.

    Science.gov (United States)

    Yang, Ethan Y; Tabbara, Marwan M; Sanchez, Priscila G; Abi-Chaker, Andrew M; Patel, Jaimin; Bornak, Arash; Jones, Keith M; Rey, Jorge

    2018-02-01

    Ultrasound-guided thrombin injection (UGTI) of femoral artery pseudoaneurysms after endovascular procedures is an effective therapy. There is controversy in the literature regarding injecting pseudoaneurysms with short and/or wide necks. This article reports our experience in UGTI of pseudoaneurysms in 1 hospital regarding the efficacy of this treatment in all pseudoaneurysms regardless of the size of the necks. A retrospective review of 46 patients diagnosed between 2011 and 2016 with groin pseudoaneurysms using established duplex ultrasound criteria. Mean age was 68 years (range 27-87). Ten pseudoaneurysms thrombosed spontaneously, 5 were thrombosed by ultrasound-guided compression, and 2 were treated surgically due to disqualifying criteria. In this retrospective review, we analyzed the remaining 29 pseudoaneurysms regarding the dimensions of their neck lengths and outcomes after attempting thrombin injection. The mean aneurysm neck length and width were 1.03 ± 0.9 cm and 0.30 ± 0.1 cm, respectively. All 29 patients were evaluated with respect to pseudoaneurysm size, neck length, neck width, and complexity. Successful treatment of 29 pseudoaneurysms (2 external iliac, 20 common femoral, 2 deep femoral, and 5 superficial femoral) with UGTI was achieved without complications in 100% of the cases, regardless of pseudoaneurysm size, neck dimensions, or complexity. Anticoagulation status did not affect the efficacy of the procedure. Nine of the 29 pseudoaneurysms (31.0%) had neck length less than 0.5 cm. This study demonstrates the safety and efficacy of UGTI in treating iatrogenic pseudoaneurysm in 29 of 29 patients, even in patients with pseudoaneurysm with short neck lengths. Our experiences support injecting all pseudoaneurysms irrespective of dimension. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. 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

  19. Visual automated macromolecular model building.

    Science.gov (United States)

    Langer, Gerrit G; Hazledine, Saul; Wiegels, Tim; Carolan, Ciaran; Lamzin, Victor S

    2013-04-01

    Automated model-building software aims at the objective interpretation of crystallographic diffraction data by means of the construction or completion of macromolecular models. Automated methods have rapidly gained in popularity as they are easy to use and generate reproducible and consistent results. However, the process of model building has become increasingly hidden and the user is often left to decide on how to proceed further with little feedback on what has preceded the output of the built model. Here, ArpNavigator, a molecular viewer tightly integrated into the ARP/wARP automated model-building package, is presented that directly controls model building and displays the evolving output in real time in order to make the procedure transparent to the user.

  20. Thrombostasin: purification, molecular cloning and expression of a novel anti-thrombin protein from horn fly saliva.

    Science.gov (United States)

    Zhang, D; Cupp, M S; Cupp, E W

    2002-03-01

    Thrombostasin (TS), a novel protein found in the saliva of Haematobia irritans (horn fly), was purified by high-performance liquid chromatography from the saliva of field-collected insects. This protein, which inhibits thrombin, accounts for anti-clotting activity in horn fly saliva [J. Med. Entomol. 37 (2000) 416] and is the first purified anti-hemostatic factor described from the Stomoxyinae, a large group of blood-feeding insects that are major pests of livestock world-wide. The purified TS had an apparent molecular weight of 16.7 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and revealed two isoelectric groups with isoelectric points (pIs) of approximately 4.6 and 4.8. Mass spectroscopy analysis, however, resulted in at least three major isoforms that range in mass from 9213 to 9274 Da. A 243-bp coding sequence was obtained from cDNA by using a degenerate primer deduced from the N-terminal sequence of the purified TS. The conceptual translation of the 243-bp sequence showed that the 81-amino-acid peptide, whose first 30 amino acids match those of the N-terminal sequence, had a predicted mass of 9213 Da with pI 4.14. A full-length TS cDNA was generated by rapid amplification of cDNA ends of the 5' and sequential polymerase chain reaction (PCR) amplification. It contained a 5'-end 12-bp segment preceding the putative ATG start codon, followed by a 54-bp sequence corresponding to a secretory signal and an additional 228-bp coding sequence preceding residues revealed by N-terminal sequencing of purified TS. The fidelity of the PCR-generated TS sequence was confirmed in genomic DNA and by biological activity of recombinant TS produced in a baculovirus expression system. Database comparisons revealed no homology between TS and other known molecules. Because of the paucity of other anti-hemostatic factors in horn fly saliva, TS may play a critical role in maintenance of the ectoparasitic lifestyle of horn flies.

  1. In vitro anti-inflammatory and anti-coagulant effects of antibiotics towards Platelet Activating Factor and thrombin

    Science.gov (United States)

    2011-01-01

    Background Sepsis is characterized as a systemic inflammatory response that results from the inability of the immune system to limit bacterial spread during an ongoing infection. In this condition the significant mediator of inflammation Platelet Activating Factor (PAF) and the coagulant factor thrombin are implicated. In animal models, treatment with PAF-antagonists or co-administration of antibiotics with recombinant-PAF-Acetylhydrolase (rPAF-AH) have exhibited promising results. In order to examine the putative anti-inflammatory and/or antithrombotic interactions between antibiotic treatment used in sepsis with PAF and/or thrombin, we studied the in vitro effects of these compounds towards PAF or/and thrombin related activities and towards PAF basic metabolic enzymes. Methods We assessed the inhibitory effect of these drugs against PAF or thrombin induced aggregation on washed rabbit platelets (WRPs) or rabbit Platelet Reach Plasma (rPRP) by evaluating their IC50 values. We also studied their effect on Cholinephosphotransferase of PAF (PAF-CPT)/Lyso-PAF-Acetyltransferase (Lyso-PAF-AT) of rabbit leukocytes (RLs), as well as on rabbit plasma-PAF-AH, the key enzymes of both de novo/remodelling PAF biosynthesis and PAF degradation, respectively. Results Several antibiotics inhibited PAF-induced platelet aggregation of both WRPs and rPRP in a concentration-depended manner, with clarithromycin, azithromycin and amikacin exhibiting the higher inhibitory effect, while when combined they synergistically inhibited PAF. Higher concentrations of all antibiotics tested were needed in order to inhibit PAF induced aggregation of rPRP, but also to inhibit thrombin induced aggregation of WRPs. Concentrations of these drugs similar to their IC50 values against PAF activity in WRPs, inhibited also in vitro PAF-CPT and Lyso-PAF-AT activities of rabbit leukocytes, while only clarithromycin and azithromycin increased rabbit plasma-PAF-AH activity. Conclusions These newly found

  2. Electrochemical and circular dichroism spectroscopic evidence of two types of interaction between [Ru(NH3)(6)](3+) and an elongated thrombin binding aptamer G-quadruplex

    Czech Academy of Sciences Publication Activity Database

    De Rache, A.; Kejnovská, Iva; Buess-Herman, C.; Doneux, T.

    2015-01-01

    Roč. 179, OCT 2015 (2015), s. 84-92 ISSN 0013-4686 Institutional support: RVO:68081707 Keywords : Biosensors * Thrombin binding aptamer * Hexaammineruthenium Subject RIV: BO - Biophysics Impact factor: 4.803, year: 2015

  3. Principles and methods for automated palynology.

    Science.gov (United States)

    Holt, K A; Bennett, K D

    2014-08-01

    Pollen grains are microscopic so their identification and quantification has, for decades, depended upon human observers using light microscopes: a labour-intensive approach. Modern improvements in computing and imaging hardware and software now bring automation of pollen analyses within reach. In this paper, we provide the first review in over 15 yr of progress towards automation of the part of palynology concerned with counting and classifying pollen, bringing together literature published from a wide spectrum of sources. We consider which attempts offer the most potential for an automated palynology system for universal application across all fields of research concerned with pollen classification and counting. We discuss what is required to make the datasets of these automated systems as acceptable as those produced by human palynologists, and present suggestions for how automation will generate novel approaches to counting and classifying pollen that have hitherto been unthinkable.

  4. 2-(2-Br-phenyl)-8-methoxy-benzoxazinone (HPW-RX2), a direct thrombin inhibitor with a suppressive effect on thromboxane formation in platelets.

    Science.gov (United States)

    Wu, Chin-Chung; Wang, Tsai-Wei; Wang, Wei-Ya; Hsieh, Pei-Wen; Wu, Yang-Chang

    2005-12-19

    2-(2-Br-phenyl)-8-methoxy-benzoxazinone (HPW-RX2), a newly synthetic benzoxazinone derivative, has previously been shown to inhibit rabbit platelet aggregation caused by thrombin and arachidonic acid. In the present study, the mechanism for the antiplatelet effect of HPW-RX2 was further investigated. In human platelets, HPW-RX2 concentration-dependently inhibited platelet aggregation, ATP release, P-selectin expression, and intracellular calcium mobilization caused by thrombin. In contrast, HPW-RX2 had no significant effect on either SFLLRN- or GYPGKF-induced platelet aggregation, indicating that HPW-RX2 did not interfere with platelet thrombin receptors. Moreover, HPW-RX2 inhibited the amidolytic activity of thrombin and prolonged the fibrinogen clotting time. These results suggest that the inhibitory effect of HPW-RX2 on thrombin-induced platelet aggregation is via direct inhibition of thrombin proteolytic activity. Besides the inhibition on thrombin, HPW-RX2 also prevented platelet aggregation, ATP release, and increase in [Ca2+]i caused by arachidonic acid and low concentration collagen. In a parallel manner, both arachidonic acid-induced thromboxane B2 and prostaglandin D2 formations were decreased in platelets treated with HPW-RX2. This indicates that HPW-RX2 is able to inhibit the arachidonic acid cascade at the cyclooxygenase level. This is the first report of a benzoxazinone derivative possessing both thrombin and cyclooxygenase inhibitory properties. The dual effect of HPW-RX2 might provide extra therapeutic benefits for treatment of arterial thrombosis.

  5. Host defense peptides of thrombin modulate inflammation and coagulation in endotoxin-mediated shock and Pseudomonas aeruginosa sepsis

    DEFF Research Database (Denmark)

    Kalle, Martina; Papareddy, Praveen; Kasetty, Gopinath

    2012-01-01

    Gram-negative sepsis is accompanied by a disproportionate innate immune response and excessive coagulation mainly induced by endotoxins released from bacteria. Due to rising antibiotic resistance and current lack of other effective treatments there is an urgent need for new therapies. We here...... present a new treatment concept for sepsis and endotoxin-mediated shock, based on host defense peptides from the C-terminal part of human thrombin, found to have a broad and inhibitory effect on multiple sepsis pathologies. Thus, the peptides abrogate pro-inflammatory cytokine responses to endotoxin...... sepsis, the peptide GKY25, while mediating a modest antimicrobial effect, significantly inhibited the pro-inflammatory response, decreased fibrin deposition and leakage in the lungs, as well as reduced mortality. Taken together, the capacity of such thrombin-derived peptides to simultaneously modulate...

  6. Label-free fluorescent detection of thrombin activity based on a recombinant enhanced green fluorescence protein and nickel ions immobilized nitrilotriacetic acid-coated magnetic nanoparticles.

    Science.gov (United States)

    Wang, Ming; Lei, Chunyang; Nie, Zhou; Guo, Manli; Huang, Yan; Yao, Shouzhuo

    2013-11-15

    Herein, a novel label-free fluorescent assay has been developed to detect the activity of thrombin and its inhibitor, based on a recombinant enhanced green fluorescence protein (EGFP) and Ni(2+) ions immobilized nitrilotriacetic acid-coated magnetic nanoparticles (Ni(2+)-NTA MNPs). The EGFP, containing a thrombin cleavage site and a hexahistidine sequence (His-tag) at its N-terminal, was adsorbed onto Ni(2+)-NTA MNPs through Ni(2+)-hexahistidine interaction, and dragged out of the solution by magnetic separation. Thrombin can selectively digest EGFP accompanied by His-tag peptide sequence leaving, and the resulting EGFP cannot be captured by Ni(2+)-NTA MNPs and kept in supernatant. Hence the fluorescence change of supernatant can clearly represent the activity of thrombin. Under optimized conditions, such assay showed a relatively low detection limit (3.0×10(-4) U mL(-1)), and was also used to detect the thrombin inhibitor, Hirudin, and further applied to detect thrombin activity in serum. Combined with the satisfactory reusability of Ni(2+)-NTA MNPs, our method presents a promising candidate for simple, sensitive, and cost-saving protease activity detecting and inhibitor screening. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. 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

  8. Automated electronic filter design

    CERN Document Server

    Banerjee, Amal

    2017-01-01

    This book describes a novel, efficient and powerful scheme for designing and evaluating the performance characteristics of any electronic filter designed with predefined specifications. The author explains techniques that enable readers to eliminate complicated manual, and thus error-prone and time-consuming, steps of traditional design techniques. The presentation includes demonstration of efficient automation, using an ANSI C language program, which accepts any filter design specification (e.g. Chebyschev low-pass filter, cut-off frequency, pass-band ripple etc.) as input and generates as output a SPICE(Simulation Program with Integrated Circuit Emphasis) format netlist. Readers then can use this netlist to run simulations with any version of the popular SPICE simulator, increasing accuracy of the final results, without violating any of the key principles of the traditional design scheme.

  9. An electrochemical aptasensor for thrombin detection based on direct electrochemistry of glucose oxidase using a functionalized graphene hybrid for amplification.

    Science.gov (United States)

    Bai, Lijuan; Yan, Bin; Chai, Yaqin; Yuan, Ruo; Yuan, Yali; Xie, Shunbi; Jiang, Liping; He, Ying

    2013-11-07

    In this work, we reported a new label-free electrochemical aptasensor for highly sensitive detection of thrombin using direct electron transfer of glucose oxidase (GOD) as a redox probe and a gold nanoparticle-polyaniline-graphene (Au-PANI-Gra) hybrid for amplification. The Au-PANI-Gra hybrid with large surface area provided a biocompatible sensing platform for the immobilization of GOD. GOD was encapsulated into the three-dimensional netlike (3-mercaptopropyl)trimethoxysilane (MPTS) to form the MPTS-GOD biocomposite, which not only retained the native functions and properties, but also exhibited tunable porosity, high thermal stability, and chemical inertness. With abundant thiol tail groups on MPTS, MPTS-GOD was able to chemisorb onto the surface of the Au-PANI-Gra modified electrode through the strong affinity of the Au-S bond. The electrochemical signal originated from GOD, avoiding the addition or labeling of other redox mediators. After immobilizing the thiolated thrombin binding aptamer through gold nanoparticles (AuNPs), GOD as a blocking reagent was employed to block the remaining active sites of the AuNPs and avoid the nonspecific adsorption. The proposed method avoided the labeling process of redox probes and increased the amount of electroactive GOD. The concentration of thrombin was monitored based on the decrease of current response through cyclic voltammetry (CV) in 0.1 M PBS (pH 7.4). With the excellent direct electron transfer of double layer GOD membranes, the resulting aptasensor exhibited high sensitivity for detection of thrombin with a wide linear range from 1.0 × 10(-12) to 3.0 × 10(-8) M. The proposed aptasensor also showed good stability, satisfactory reproducibility and high specificity, which provided a promising strategy for electrochemical aptamer-based detection of other biomolecules.

  10. The linkage between binding of the C-terminal domain of hirudin and amidase activity in human alpha-thrombin.

    OpenAIRE

    de Cristofaro, R; Rocca, B; Bizzi, B; Landolfi, R

    1993-01-01

    A method derived from the analysis of viscosity effects on the hydrolysis of the amide substrates D-phenylalanylpipecolyl-arginine-p-nitroaniline, tosylglycylprolylarginine-p-nitroanaline and cyclohexylglycylalanylarginine-p-nitroalanine by human alpha-thrombin was developed to dissect the Michaelis-Menten parameters Km and kcat into the individual rate constants of the binding, acylation and deacylation reactions. This method was used to analyse the effect of the C-terminal hirudin (residues...

  11. Autonomy and Automation

    Science.gov (United States)

    Shively, Jay

    2017-01-01

    A significant level of debate and confusion has surrounded the meaning of the terms autonomy and automation. Automation is a multi-dimensional concept, and we propose that Remotely Piloted Aircraft Systems (RPAS) automation should be described with reference to the specific system and task that has been automated, the context in which the automation functions, and other relevant dimensions. In this paper, we present definitions of automation, pilot in the loop, pilot on the loop and pilot out of the loop. We further propose that in future, the International Civil Aviation Organization (ICAO) RPAS Panel avoids the use of the terms autonomy and autonomous when referring to automated systems on board RPA. Work Group 7 proposes to develop, in consultation with other workgroups, a taxonomy of Levels of Automation for RPAS.

  12. An automated swimming respirometer

    DEFF Research Database (Denmark)

    STEFFENSEN, JF; JOHANSEN, K; BUSHNELL, PG

    1984-01-01

    An automated respirometer is described that can be used for computerized respirometry of trout and sharks.......An automated respirometer is described that can be used for computerized respirometry of trout and sharks....

  13. 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...

  14. Anti-thrombin III, Protein C, and Protein S deficiency in acute coronary syndrome

    Directory of Open Access Journals (Sweden)

    Dasnan Ismail

    2002-06-01

    Full Text Available The final most common pathway for the majority of coronary artery disease is occlusion of a coronary vessel. Under normal conditions, antithrombin III (AT III, protein C, and protein S as an active protein C cofactor, are natural anticoagulants (hemostatic control that balances procoagulant activity (thrombin antithrombin complex balance to prevent thrombosis. If the condition becomes unbalanced, natural anticoagulants and the procoagulants can lead to thrombosis. Thirty subjects with acute coronary syndrome (ACS were studied for the incidence of antithrombin III (AT III, protein C, and protein S deficiencies, and the result were compare to the control group. Among patients with ACS, the frequency of distribution of AT-III with activity < 75% were 23,3% (7 of 30, and only 6,7% ( 2 of 30 in control subject. No one of the 30 control subject have protein C activity deficient, in ACS with activity < 70% were 13,3% (4 of 30. Fifteen out of the 30 (50% control subjects had protein S activity deficiency, while protein S deficiency activity < 70% was found 73.3.% (22 out of 30. On linear regression, the deterministic coefficient of AT-III activity deficiency to the development ACS was 13,25 %, and the deterministic coefficient of protein C activity deficient to the development of ACS was 9,06 %. The cut-off point for AT-III without protein S deficiency expected to contribute to the development of vessel disease was 45%. On discriminant analysis, protein C activity deficiency posed a risk for ACS of 4,5 greater than non deficient subjects, and AT-III activity deficiency posed a risk for ACS of 3,5 times greater than non deficient subjects. On binary logistic regression, protein S activity acted only as a reinforcing factor of AT-III activity deficiency in the development of ACS. Protein C and AT III deficiency can trigger ACS, with determinant coefficients of 9,06% and 13,25% respectively. Low levels of protein C posed a greater risk of

  15. New Insights in Thrombin Inhibition Structure–Activity Relationships by Characterization of Octadecasaccharides from Low Molecular Weight Heparin

    Directory of Open Access Journals (Sweden)

    Pierre A. J. Mourier

    2017-03-01

    Full Text Available Low Molecular Weight Heparins (LMWH are complex anticoagulant drugs that mainly inhibit the blood coagulation cascade through indirect interaction with antithrombin. While inhibition of the factor Xa is well described, little is known about the polysaccharide structure inhibiting thrombin. In fact, a minimal chain length of 18 saccharides units, including an antithrombin (AT binding pentasaccharide, is mandatory to form the active ternary complex for LMWH obtained by alkaline β-elimination (e.g., enoxaparin. However, the relationship between structure of octadecasaccharides and their thrombin inhibition has not been yet assessed on natural compounds due to technical hurdles to isolate sufficiently pure material. We report the preparation of five octadecasaccharides by using orthogonal separation methods including size exclusion, AT affinity, ion pairing and strong anion exchange chromatography. Each of these octadecasaccharides possesses two AT binding pentasaccharide sequences located at various positions. After structural elucidation using enzymatic sequencing and NMR, in vitro aFXa and aFIIa were determined. The biological activities reveal the critical role of each pentasaccharide sequence position within the octadecasaccharides and structural requirements to inhibit thrombin. Significant differences in potency, such as the twenty-fold magnitude difference observed between two regioisomers, further highlights the importance of depolymerisation process conditions on LMWH biological activity.

  16. Knowledge engineering for design automation

    OpenAIRE

    Schotborgh, W.O.

    2009-01-01

    Engineering design teams face many challenges, one of which is the time pressure on the product creation process. A wide range of Information and Communications Technology solutions is available to relieve the time pressure and increase overall efficiency. A promising type of software is that which automates a design process and generates design candidates, based on specifications of required behavior. Visual presentation of multiple solutions in a “solution space” provides insight in the tre...

  17. 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.

  18. Automation in College Libraries.

    Science.gov (United States)

    Werking, Richard Hume

    1991-01-01

    Reports the results of a survey of the "Bowdoin List" group of liberal arts colleges. The survey obtained information about (1) automation modules in place and when they had been installed; (2) financing of automation and its impacts on the library budgets; and (3) library director's views on library automation and the nature of the…

  19. Dynamic affinity chromatography in the separation of sulfated lignins binding to thrombin

    Science.gov (United States)

    Liang, Aiye; Thakkar, Jay N.; Hindle, Michael; Desai, Umesh R.

    2013-01-01

    Sulfated low molecular weight lignins (LMWLs), a mixture of chemo-enzymatically prepared oligomers, have been found to be potent antagonists of coagulation. However, structures that induce anticoagulation remain unidentified. The highly polar sulfate groups on these molecules and the thousands of different structures present in these mixtures make traditional chromatographic resolution of sulfated LMWLs difficult. We performed dynamic thrombin affinity chromatography monitored using chromogenic substrate hydrolysis assay to isolate sulfated LMWL fractions that differed significantly in their biophysical and biochemical properties. Three fractions, I35, I55 and Peak II, were isolated from the starting complex mixture. Independent plasma clotting assays suggested that I35 possessed good anticoagulation potential (APTT = 4.2 μM; PT = 6.8 μM), while I55 and Peak II were approximately 10- and 100-fold less potent. The ESI-MS spectrum of this oligomeric fraction showed multiple peaks at 684.8, 610.6, 557.4, 541.4, 536.5, and 519.4 m/z, which most probably arise from variably functionalized (β-O4—β-β-linked trimers and/or a β-O4—β-O4-linked dimers. The first direct observation of these structures in sulfated LMWLs will greatly assist in the discovery of more potent sulfated LMWL-based anticoagulants. PMID:23122400

  20. Decrements in the thrombin activatable fibrinolysis inhibitor (TAFI) levels in association with orlistat treatment in obesity.

    Science.gov (United States)

    Guven, Gulay Sain; Kiliçaslan, Alpaslan; Oz, S Gul; Haznedaroglu, Ibrahim C; Kirazli, Serafettin; Aslan, Dilek; Sözen, Tümay

    2006-07-01

    Obesity and its associated metabolic complications can impair the physiologic regulation of fibrinolysis, leading to a hyper coagulable state. We aimed to assess circulating thrombin activatable fibrinolysis inhibitor (TAFI) levels in obese female patients and to test the effects of orlistat-induced weight loss on basal TAFI concentrations. Obese female outpatients age 18 and older, with a body mass index (BMI, calculated as weight in kilograms divided by the square of height in meters) of at least 30, were included into the study. Thirteen nonobese (median BMI, 22.60 kg/m(2)) age-matched females were taken as controls. Plasma TAFI levels were measured before orlistat administration and after 6 months of orlistat treatment in the obese group and only one measurement was done in the control group. Twenty-seven obese patients were recruited into the study. The median TAFI level of the control group was 124.00; this value was significantly lower than the basal TAFI level of the obese group (p < 0.001). TAFI levels after orlistat therapy were statistically significantly lower than basal TAFI levels (p < 0.001) in the obese group. Hemostatic abnormalities including TAFI alterations represent a link between obesity and vascular thrombosis. Effective interventions should be considered in improving the obesity-associated prothrombotic risk profile.

  1. Rapid hemostasis in a sheep model using particles that propel thrombin and tranexamic acid.

    Science.gov (United States)

    R Baylis, James; Finkelstein-Kulka, Andres; Macias-Valle, Luis; Manji, Jamil; Lee, Michael; Levchenko, Elina; Okpaleke, Christopher; Al-Salihi, Salahuddin; Javer, Amin; J Kastrup, Christian

    2017-04-01

    Bleeding during endoscopic sinus surgery and open surgeries can easily obstruct the surgeons' field of view and increase morbidity and risk of intraoperative complications. Intraoperative bleeding could potentially be addressed by a hemostatic agent that safely disperses itself through the escaping blood. We tested the safety and efficacy of a self-propelling formulation of thrombin and tranexamic acid (SPTT) in stopping bleeding in a paranasal sinus injury and in an open surgical carotid injury sheep model. Interventional animal study. SPTT was tested in the sinonasal space following endoscopic injury to the inferior turbinate of six sheep, and to the common carotid artery following open surgical injury in eight sheep. In the nasal cavity, bleeding time and local inflammation were measured and compared to plain gauze. Following carotid arteriotomy, successful hemostasis and markers of thrombosis and coagulopathy were compared to Floseal. SPTT significantly decreased bleeding times in the sinonasal space compared to plain gauze (mean difference = 3.8 minutes, P = .002). All of the carotid bleeds (100%) were successfully controlled with SPTT after 10 minutes of application under pressure, compared to 25% with Floseal. No adverse events were noted, and there was no evidence of thromboembolism. SPTT significantly reduced bleeding time in a sheep model of surgical sinus bleeding and successfully stopped bleeding following catastrophic carotid artery injury, with no adverse events observed. NA Laryngoscope, 127:787-793, 2017. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

  2. 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

    2016-04-05

    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.

  3. Noncoded amino acids in protein engineering: Structure-activity relationship studies of hirudin-thrombin interaction.

    Science.gov (United States)

    De Filippis, Vincenzo; Acquasaliente, Laura; Pontarollo, Giulia; Peterle, Daniele

    2018-01-01

    The advent of recombinant DNA technology allowed to site-specifically insert, delete, or mutate almost any amino acid in a given protein, significantly improving our knowledge of protein structure, stability, and function. Nevertheless, a quantitative description of the physical and chemical basis that makes a polypeptide chain to efficiently fold into a stable and functionally active conformation is still elusive. This mainly originates from the fact that nature combined, in a yet unknown manner, different properties (i.e., hydrophobicity, conformational propensity, polarizability, and hydrogen bonding capability) into the 20 standard natural amino acids, thus making difficult, if not impossible, to univocally relate the change in protein stability or function to the alteration of physicochemical properties caused by amino acid exchange(s). In this view, incorporation of noncoded amino acids with tailored side chains, allowing to finely tune the structure at a protein site, would facilitate to dissect the effects of a given mutation in terms of one or a few physicochemical properties, thus much expanding the scope of physical organic chemistry in the study of proteins. In this review, relevant applications from our laboratory will be presented on the use of noncoded amino acids in structure-activity relationships studies of hirudin binding to thrombin. © 2017 International Union of Biochemistry and Molecular Biology, Inc.

  4. Novel Bronchoscopic Management of Airway Bleeding With Absorbable Gelatin and Thrombin Slurry.

    Science.gov (United States)

    Peralta, A Rolando; Chawla, Mohit; Lee, Robert P

    2018-01-18

    Airway bleeding, either spontaneous or as a result of bronchoscopy, is associated with significant morbidity and mortality. Multiple bronchoscopic techniques are available to achieve complete hemostasis or as a bridge to definitive therapies. We report our experience on the feasibility of endobronchial instillation of an absorbable gelatin and thrombin slurry (GTS) for the treatment of spontaneous hemoptysis and procedure-related bleeding. We identified 13 cases in which GTS was used for endobronchial hemostasis when standard bronchoscopic measures like cold saline, epinephrine, and in some cases balloon occlusion were not successful. GTS was delivered through the working channel of the bronchoscope in 10 cases and through the distal port of a bronchial blocker in the remaining 3 cases. Median age was 69 years (range, 52 to 79 y). Eight cases corresponded to spontaneous hemoptysis and 5 cases to diagnostic or therapeutic procedures. Bleeding was considered severe in 9 (70%) cases. All but 1 case were associated with malignancy. Hemostasis was achieved in 10 (77%) cases by using standard measures in addition to GTS. No patient adverse events at 30 days or damage to the equipment were identified. Bronchoscopic instillation of an absorbable GTS is feasible and may be used in cases of spontaneous or procedure-related bleeding in addition to conventional measures. It can be delivered through the working channel of the bronchoscope or through the distal port available in some bronchial blockers. Controlled studies are necessary to determine the safety and efficacy of this novel technique.

  5. Acceleration of consolidation period by thrombin peptide 508 in tibial distraction osteogenesis in rats.

    Science.gov (United States)

    Cakarer, S; Olgac, V; Aksakalli, N; Tang, A; Keskin, C

    2010-12-01

    We aimed to find out whether a single local injection of two different doses of thrombin peptide 508 (TP508) could accelerate consolidation of bone in sites of tibial distraction osteogenesis in rats. Forty-eight adult male Sprague-Dawley rats were divided equally (n=16 in each group) into controls (given saline alone), and two experimental groups, given injections of TP508 10μg or 100 μg. The animals were killed on days 14 and 28 after distraction. Histomorphometric evaluation showed that the TP508 resulted in significantly larger areas of newly formed bone (pbone had formed in the group given TP508 100 μg than in the group given 10 μg, but the difference was not significant (p=0.8). However, the difference was significant at 4 weeks (p=0.03). These findings suggest that a single injection of TP508 given at the end of the distraction period increased the degree of consolidation. The higher dose was more effective at the later time point. Copyright © 2009 The British Association of Oral and Maxillofacial Surgeons. All rights reserved.

  6. Synergistic interactions of bradykinin, thrombin, interleukin 1 and tumor necrosis factor on prostanoid biosynthesis in human periodontal-ligament cells.

    Science.gov (United States)

    Ransjö, M; Marklund, M; Persson, M; Lerner, U H

    1998-04-01

    Prostaglandins are involved in force-induced orthodontic tooth movement. Bradykinin (BK) and thrombin are known to cause a significant time- and concentration-dependent burst of prostanoid biosynthesis in cultured human periodontal-ligament (PDL) cells. The aim now was to investigate interactive effects between interleukin 1 alpha, -beta (IL-1 alpha, -1 beta), tumour necrosis factor-alpha,-beta (TNF-alpha, -beta) and BK or thrombin on prostaglandin biosynthesis in human PDL cells. IL-1 alpha and -1 beta produced time- and concentration-dependent stimulation of prostanoid biosynthesis [prostaglandin (PG)E2 and 6-keto-PGF1alpha]. Synergistic stimulation of prostanoid biosynthesis was demonstrated when BK or thrombin were added together with IL-1 alpha or -1 beta. BK and IL-1 beta both significantly stimulated the release of [3H]arachidonic acid. No synergistic effect on [3H]arachidonic acid release was seen when BK and IL-1 beta were added simultaneously. These data suggest that the synergistic effect of BK and IL-1 beta on prostanoid biosynthesis is not due to interactions at the receptor level nor to enhanced release of arachidonic acid, but may be due to increased activity of cyclo-oxygenase. Also, TNF-alpha and -beta produced a concentration-dependent stimulation of PGE2 formation in cultured human PDL cells. Synergistic effects of BK and thrombin were demonstrated when PGE2 production was stimulated in combination with TNF-beta. In addition, a synergistic effect on the PGE2 response to IL-1 alpha or -1 beta was demonstrated when added in combination with TNF-alpha. These experiments demonstrate synergistic interactions between BK, thrombin, IL-1 and TNF on prostaglandin biosynthesis in cultured human PDL cells. The findings suggest that inflammatory mediators may act in concert in stimulating prostanoid production in response to pro-inflammatory stimuli. As an inflammatory reaction is seen in the periodontal ligament when teeth are orthodontically treated, this