WorldWideScience

Sample records for synthetic tp-agb models

  1. THE CONTRIBUTION OF TP-AGB STARS TO THE MID-INFRARED COLORS OF NEARBY GALAXIES

    Energy Technology Data Exchange (ETDEWEB)

    Chisari, Nora E. [Department of Astrophysical Sciences, Princeton University, 4 Ivy Lane, Princeton, NJ 08544 (United States); Kelson, Daniel D., E-mail: nchisari@astro.princeton.edu [Observatories of the Carnegie Institution of Science, 813 Santa Barbara St., Pasadena, CA 91101 (United States)

    2012-07-10

    We study the mid-infrared color space of 30 galaxies from the Spitzer Infrared Nearby Galaxies Survey (SINGS) survey for which Sloan Digital Sky Survey data are also available. We construct two-color maps for each galaxy and compare them to results obtained from combining Maraston evolutionary synthesis models, galactic thermally pulsating asymptotic giant branch (TP-AGB) colors, and smooth star formation histories. For most of the SINGS sample, the spatially extended mid-IR emission seen by Spitzer in normal galaxies is consistent with our simple model in which circumstellar dust from TP-AGB stars dominates at 8 and 24 {mu}m. There is a handful of exceptions that we identify as galaxies that have high star formation rates presumably with star formation histories that cannot be assumed to be smooth, or anemic galaxies, which were depleted of their H I at some point during their evolution and have very low ongoing star formation rates.

  2. THE CONTRIBUTION OF TP-AGB STARS TO THE MID-INFRARED COLORS OF NEARBY GALAXIES

    International Nuclear Information System (INIS)

    Chisari, Nora E.; Kelson, Daniel D.

    2012-01-01

    We study the mid-infrared color space of 30 galaxies from the Spitzer Infrared Nearby Galaxies Survey (SINGS) survey for which Sloan Digital Sky Survey data are also available. We construct two-color maps for each galaxy and compare them to results obtained from combining Maraston evolutionary synthesis models, galactic thermally pulsating asymptotic giant branch (TP-AGB) colors, and smooth star formation histories. For most of the SINGS sample, the spatially extended mid-IR emission seen by Spitzer in normal galaxies is consistent with our simple model in which circumstellar dust from TP-AGB stars dominates at 8 and 24 μm. There is a handful of exceptions that we identify as galaxies that have high star formation rates presumably with star formation histories that cannot be assumed to be smooth, or anemic galaxies, which were depleted of their H I at some point during their evolution and have very low ongoing star formation rates.

  3. A NEW GENERATION OF PARSEC-COLIBRI STELLAR ISOCHRONES INCLUDING THE TP-AGB PHASE

    International Nuclear Information System (INIS)

    Marigo, Paola; Aringer, Bernhard; Chen, Yang; Dussin, Marco; Nanni, Ambra; Pastorelli, Giada; Rodrigues, Thaíse S.; Trabucchi, Michele; Bladh, Sara; Montalbán, Josefina; Girardi, Léo; Bressan, Alessandro; Rosenfield, Philip; Dalcanton, Julianne; Groenewegen, Martin A. T.; Wood, Peter R.

    2017-01-01

    We introduce a new generation of PARSEC–COLIBRI stellar isochrones that includes a detailed treatment of the thermally pulsing asymptotic giant branch (TP-AGB) phase, covering a wide range of initial metallicities (0.0001 < Z i < 0.06). Compared to previous releases, the main novelties and improvements are use of new TP-AGB tracks and related atmosphere models and spectra for M and C-type stars; inclusion of the surface H+He+CNO abundances in the isochrone tables, accounting for the effects of diffusion, dredge-up episodes and hot-bottom burning; inclusion of complete thermal pulse cycles, with a complete description of the in-cycle changes in the stellar parameters; new pulsation models to describe the long-period variability in the fundamental and first-overtone modes; and new dust models that follow the growth of the grains during the AGB evolution, in combination with radiative transfer calculations for the reprocessing of the photospheric emission. Overall, these improvements are expected to lead to a more consistent and detailed description of properties of TP-AGB stars expected in resolved stellar populations, especially in regard to their mean photometric properties from optical to mid-infrared wavelengths. We illustrate the expected numbers of TP-AGB stars of different types in stellar populations covering a wide range of ages and initial metallicities, providing further details on the “C-star island” that appears at intermediate values of age and metallicity, and about the AGB-boosting effect that occurs at ages close to 1.6-Gyr for populations of all metallicities. The isochrones are available through a new dedicated web server.

  4. A NEW GENERATION OF PARSEC-COLIBRI STELLAR ISOCHRONES INCLUDING THE TP-AGB PHASE

    Energy Technology Data Exchange (ETDEWEB)

    Marigo, Paola; Aringer, Bernhard; Chen, Yang; Dussin, Marco; Nanni, Ambra; Pastorelli, Giada; Rodrigues, Thaíse S.; Trabucchi, Michele; Bladh, Sara; Montalbán, Josefina [Dipartimento di Fisica e Astronomia Galileo Galilei, Università di Padova, Vicolo dell’Osservatorio 3, I-35122 Padova (Italy); Girardi, Léo [Osservatorio Astronomico di Padova—INAF, Vicolo dell’Osservatorio 5, I-35122 Padova (Italy); Bressan, Alessandro [SISSA, via Bonomea 365, I-34136 Trieste (Italy); Rosenfield, Philip [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Dalcanton, Julianne [Department of Astronomy, University of Washington, Box 351580, Seattle, WA 98195 (United States); Groenewegen, Martin A. T. [Koninklijke Sterrenwacht van België, Ringlaan 3, B-1180 Brussels (Belgium); Wood, Peter R. [Research School of Astronomy and Astrophysics, Australian National University, Cotter Road, Weston Creek, ACT 2611 (Australia)

    2017-01-20

    We introduce a new generation of PARSEC–COLIBRI stellar isochrones that includes a detailed treatment of the thermally pulsing asymptotic giant branch (TP-AGB) phase, covering a wide range of initial metallicities (0.0001 < Z {sub i} < 0.06). Compared to previous releases, the main novelties and improvements are use of new TP-AGB tracks and related atmosphere models and spectra for M and C-type stars; inclusion of the surface H+He+CNO abundances in the isochrone tables, accounting for the effects of diffusion, dredge-up episodes and hot-bottom burning; inclusion of complete thermal pulse cycles, with a complete description of the in-cycle changes in the stellar parameters; new pulsation models to describe the long-period variability in the fundamental and first-overtone modes; and new dust models that follow the growth of the grains during the AGB evolution, in combination with radiative transfer calculations for the reprocessing of the photospheric emission. Overall, these improvements are expected to lead to a more consistent and detailed description of properties of TP-AGB stars expected in resolved stellar populations, especially in regard to their mean photometric properties from optical to mid-infrared wavelengths. We illustrate the expected numbers of TP-AGB stars of different types in stellar populations covering a wide range of ages and initial metallicities, providing further details on the “C-star island” that appears at intermediate values of age and metallicity, and about the AGB-boosting effect that occurs at ages close to 1.6-Gyr for populations of all metallicities. The isochrones are available through a new dedicated web server.

  5. THE CONTRIBUTION OF TP-AGB AND RHeB STARS TO THE NEAR-IR LUMINOSITY OF LOCAL GALAXIES: IMPLICATIONS FOR STELLAR MASS MEASUREMENTS OF HIGH-REDSHIFT GALAXIES

    International Nuclear Information System (INIS)

    Melbourne, J.; Williams, Benjamin F.; Dalcanton, Julianne J.; Rosenfield, Philip; Weisz, D.

    2012-01-01

    Using high spatial resolution Hubble Space Telescope WFC3 and Advanced Camera for Surveys imaging of resolved stellar populations, we constrain the contribution of thermally pulsing asymptotic giant branch (TP-AGB) stars and red helium burning (RHeB) stars to the 1.6 μm near-infrared (NIR) luminosities of 23 nearby galaxies, including dwarfs and spirals. The TP-AGB phase contributes as much as 17% of the integrated F160W flux, even when the red giant branch is well populated. The RHeB population contribution can match or even exceed the TP-AGB contribution, providing as much as 21% (18% after a statistical correction for foreground) of the integrated F160W light. We estimate that these two short-lived phases may account for up to 70% of the rest-frame NIR flux at higher redshift. The NIR mass-to-light (M/L) ratio should therefore be expected to vary significantly due to fluctuations in the star formation rate (SFR) over timescales from 25 Myr to several Gyr, an effect that may be responsible for some of the lingering scatter in NIR galaxy scaling relations such as the Tully-Fisher and metallicity-luminosity relations. We compare our observational results to predictions based on optically derived star formation histories and stellar population synthesis (SPS) models, including models based on the 2008 Padova isochrones (used in popular SPS programs) and the updated 2010 Padova isochrones, which shorten the lifetimes of low-mass (old) low-metallicity TP-AGB populations. The updated (2010) SPS models generally reproduce the expected numbers of TP-AGB stars in the sample; indeed, for 65% of the galaxies, the discrepancy between modeled and observed numbers is smaller than the measurement uncertainties. The weighted mean model/data number ratio for TP-AGB stars is 1.5 (1.4 with outliers removed) with a standard deviation of 0.5. The same SPS models, however, give a larger discrepancy in the F160W flux contribution from the TP-AGB stars, overpredicting the flux by a

  6. IRC +10 216 in 3D: morphology of a TP-AGB star envelope

    Science.gov (United States)

    Guélin, M.; Patel, N. A.; Bremer, M.; Cernicharo, J.; Castro-Carrizo, A.; Pety, J.; Fonfría, J. P.; Agúndez, M.; Santander-García, M.; Quintana-Lacaci, G.; Velilla Prieto, L.; Blundell, R.; Thaddeus, P.

    2018-02-01

    During their late pulsating phase, AGB stars expel most of their mass in the form of massive dusty envelopes, an event that largely controls the composition of interstellar matter. The envelopes, however, are distant and opaque to visible and NIR radiation: their structure remains poorly known and the mass-loss process poorly understood. Millimeter-wave interferometry, which combines the advantages of longer wavelength, high angular resolution and very high spectral resolution is the optimal investigative tool for this purpose. Mm waves pass through dust with almost no attenuation. Their spectrum is rich in molecular lines and hosts the fundamental lines of the ubiquitous CO molecule, allowing a tomographic reconstruction of the envelope structure. The circumstellar envelope IRC +10 216 and its central star, the C-rich TP-AGB star closest to the Sun, are the best objects for such an investigation. Two years ago, we reported the first detailed study of the CO(2-1) line emission in that envelope, made with the IRAM 30-m telescope. It revealed a series of dense gas shells, expanding at a uniform radial velocity. The limited resolution of the telescope (HPBW 11″) did not allow us to resolve the shell structure. We now report much higher angular resolution observations of CO(2-1), CO(1-0), CN(2-1) and C4H(24-23) made with the SMA, PdB and ALMA interferometers (with synthesized half-power beamwidths of 3″, 1″ and 0.3″, respectively). Although the envelope appears much more intricate at high resolution than with an 11″ beam, its prevailing structure remains a pattern of thin, nearly concentric shells. The average separation between the brightest CO shells is 16″ in the outer envelope, where it appears remarkably constant. Closer to the star (system with a period of 700 yr and a near face-on elliptical orbit. The companion fly-by triggers enhanced episodes of mass loss near periastron. The densification of the shell pattern observed in the central part of the

  7. Models for synthetic biology.

    Science.gov (United States)

    Kaznessis, Yiannis N

    2007-11-06

    Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biological molecules. What is new is the emphasis on system behavior. The objective is the design and construction of new biological devices and systems to deliver useful applications. Numerous synthetic gene circuits have been created in the past decade, including bistable switches, oscillators, and logic gates, and possible applications abound, including biofuels, detectors for biochemical and chemical weapons, disease diagnosis, and gene therapies. More than fifty years after the discovery of the molecular structure of DNA, molecular biology is mature enough for real quantification that is useful for biological engineering applications, similar to the revolution in modeling in chemistry in the 1950s. With the excitement that synthetic biology is generating, the engineering and biological science communities appear remarkably willing to cross disciplinary boundaries toward a common goal.

  8. Influence of the Outer Boundary Condition on models of AGB stars

    Science.gov (United States)

    Wagstaff, G.; Weiss, A.

    2018-04-01

    Current implementations of the stellar atmosphere typically derive boundary conditions for the interior model from either grey plane-parallel atmospheres or scaled solar atmospheres, neither of which can be considered to have appropriate underlying assumptions for the Thermally Pulsing Asymptotic Giant Branch (TP-AGB). This paper discusses the treatment and influence of the outer boundary condition within stellar evolution codes, and the resulting effects on the AGB evolution. The complex interaction of processes, such as the third dredge up and mass loss, governing the TP-AGB can be affected by varying the treatment of this boundary condition. Presented here are the results from altering the geometry, opacities and the implementation of a grid of MARCS/COMARCS model atmospheres in order to improve this treatment. Although there are changes in the TP-AGB evolution, observable quantities, such as the final core mass, are not significantly altered as a result of the change of atmospheric treatment. During the course of the investigation, a previously unseen phenomena in the AGB models was observed and further investigated. This is believed to be physical, although arising from specific conditions which make its presence unlikely. If it were present in stars, this phenomenon would increase the carbon-star lifetime above 10Myr and increase the final core mass by ˜0.1M⊙ in the narrow initial-mass range where it was observed (˜2 - 2.3M⊙).

  9. Cfd modeling of a synthetic jet actuator

    International Nuclear Information System (INIS)

    Dghim, Marouane; Ben Chiekh, Maher; Ben Nasrallah, Sassi

    2009-01-01

    Synthetic jet actuators show good promise as an enabling technology for innovative boundary layer flow control applied to external surfaces, like airplane wings, and to internal flows, like those occurring in a curved engine inlet. The appealing characteristics of a synthetic jet are zero-net-mass flux operation and an efficient control effect that takes advantages of unsteady fluid phenomena. The formation of a synthetic jet in a quiescent external air flow is only beginning to be understood and a rational understanding of these devices is necessary before they can be applied to the control of flows outside of the laboratory. The synthetic jet flow generated by a planar orifice is investigated here using computational approach. Computations of the 2D synthetic jet are performed with unsteady RANS modeled with the Realizable κ - ε turbulence model available in FLUENT environment. In this present work, the ability of the first order turbulence model, employed in our computations, to model the formation of the counter-rotating-vortex pair (CVP) that appears in the flow-field was investigated. Computational results were in good agreement with experimental measurements. The effectiveness of such control actuator was tested on separated boundary layer. Preliminary investigation were presented and discussed

  10. SYNTHETIC AGB EVOLUTION .1. A NEW MODEL

    NARCIS (Netherlands)

    GROENEWEGEN, MAT; DEJONG, T

    We have constructed a model to calculate in a synthetic way the evolution of stars on the asymptotic giant branch (AGB). The evolution is started at the first thermal pulse (TP) and is terminated when the envelope mass has been lost due to mass loss or when the core mass reaches the Chandrasekhar

  11. Agent-based modelling in synthetic biology.

    Science.gov (United States)

    Gorochowski, Thomas E

    2016-11-30

    Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. © 2016 The Author(s).

  12. Probing AGB nucleosynthesis via accurate Planetary Nebula abundances

    NARCIS (Netherlands)

    Marigo, P; Bernard-Salas, J; Pottasch, S. R.; Tielens, A. G. G. M.; Wesselius, P. R.

    2003-01-01

    The elemental abundances of ten planetary nebulae, derived with high accuracy including ISO and IUE spectra, are analysed with the aid of synthetic evolutionary models for the TP-AGB phase. The accuracy on the observed abundances is essential in order to make a reliable comparison with the models.

  13. Synthetic properties of models of globular clusters

    Energy Technology Data Exchange (ETDEWEB)

    Angeletti, L; Dolcetta, R; Giannone, P. (Rome Univ. (Italy). Osservatorio Astronomico)

    1980-05-01

    Synthetic and projected properties of models of globular clusters have been computed on the basis of stellar evolution and time changes of the dynamical cluster structure. Clusters with five and eight stellar groups (each group consisting of stars with the same mass) were studied. Mass loss from evolved stars was taken into account. Observational features were obtained at ages of 10-19 x 10/sup 9/ yr. The basic importance of the horizontal- and asymptotic-branch stars was pointed out. A comparison of the results with observed data of M3 is discussed with the purpose of obtaining general indications rather than a specific fit.

  14. Synthetic properties of models of globular clusters

    International Nuclear Information System (INIS)

    Angeletti, L.; Dolcetta, R.; Giannone, P.

    1980-01-01

    Synthetic and projected properties of models of globular clusters have been computed on the basis of stellar evolution and time changes of the dynamical cluster structure. Clusters with five and eight stellar groups (each group consisting of stars with the same mass) were studied. Mass loss from evolved stars was taken into account. Observational features were obtained at ages of 10-19 x 10 9 yr. The basic importance of the horizontal- and asymptotic-branch stars was pointed out. A comparison of the results with observed data of M3 is discussed with the purpose of obtaining general indications rather than a specific fit. (orig.)

  15. Synthetic quorum sensing in model microcapsule colonies

    Science.gov (United States)

    Shum, Henry; Balazs, Anna C.

    2017-08-01

    Biological quorum sensing refers to the ability of cells to gauge their population density and collectively initiate a new behavior once a critical density is reached. Designing synthetic materials systems that exhibit quorum sensing-like behavior could enable the fabrication of devices with both self-recognition and self-regulating functionality. Herein, we develop models for a colony of synthetic microcapsules that communicate by producing and releasing signaling molecules. Production of the chemicals is regulated by a biomimetic negative feedback loop, the “repressilator” network. Through theory and simulation, we show that the chemical behavior of such capsules is sensitive to both the density and number of capsules in the colony. For example, decreasing the spacing between a fixed number of capsules can trigger a transition in chemical activity from the steady, repressed state to large-amplitude oscillations in chemical production. Alternatively, for a fixed density, an increase in the number of capsules in the colony can also promote a transition into the oscillatory state. This configuration-dependent behavior of the capsule colony exemplifies quorum-sensing behavior. Using our theoretical model, we predict the transitions from the steady state to oscillatory behavior as a function of the colony size and capsule density.

  16. EARLY-TYPE GALAXIES AT z ∼ 1.3. II. MASSES AND AGES OF EARLY-TYPE GALAXIES IN DIFFERENT ENVIRONMENTS AND THEIR DEPENDENCE ON STELLAR POPULATION MODEL ASSUMPTIONS

    International Nuclear Information System (INIS)

    Raichoor, A.; Mei, S.; Huertas-Company, M.; Nakata, F.; Kodama, T.; Stanford, S. A.; Rettura, A.; Jee, M. J.; Holden, B. P.; Illingworth, G.; Postman, M.; White, R. L.; Rosati, P.; Blakeslee, J. P.; Demarco, R.; Eisenhardt, P.; Tanaka, M.

    2011-01-01

    We have derived masses and ages for 79 early-type galaxies (ETGs) in different environments at z ∼ 1.3 in the Lynx supercluster and in the GOODS/CDF-S field using multi-wavelength (0.6-4.5 μm; KPNO, Palomar, Keck, Hubble Space Telescope, Spitzer) data sets. At this redshift the contribution of the thermally pulsing asymptotic giant branch (TP-AGB) phase is important for ETGs, and the mass and age estimates depend on the choice of the stellar population model used in the spectral energy distribution fits. We describe in detail the differences among model predictions for a large range of galaxy ages, showing the dependence of these differences on age. Current models still yield large uncertainties. While recent models from Maraston and Charlot and Bruzual offer better modeling of the TP-AGB phase with respect to less recent Bruzual and Charlot models, their predictions do not often match. The modeling of this TP-AGB phase has a significant impact on the derived parameters for galaxies observed at high redshift. Some of our results do not depend on the choice of the model: for all models, the most massive galaxies are the oldest ones, independent of the environment. When using the Maraston and Charlot and Bruzual models, the mass distribution is similar in the clusters and in the groups, whereas in our field sample there is a deficit of massive (M ∼> 10 11 M sun ) ETGs. According to those last models, ETGs belonging to the cluster environment host on average older stars with respect to group and field populations. This difference is less significant than the age difference in galaxies of different masses.

  17. Quasi-Similarity Model of Synthetic Jets

    Czech Academy of Sciences Publication Activity Database

    Tesař, Václav; Kordík, Jozef

    2009-01-01

    Roč. 149, č. 2 (2009), s. 255-265 ISSN 0924-4247 R&D Projects: GA AV ČR IAA200760705; GA ČR GA101/07/1499 Institutional research plan: CEZ:AV0Z20760514 Keywords : jets * synthetic jets * similarity solution Subject RIV: BK - Fluid Dynamics Impact factor: 1.674, year: 2009 http://www.sciencedirect.com

  18. Synthetic

    Directory of Open Access Journals (Sweden)

    Anna Maria Manferdini

    2010-06-01

    Full Text Available Traditionally materials have been associated with a series of physical properties that can be used as inputs to production and manufacturing. Recently we witnessed an interest in materials considered not only as ‘true matter’, but also as new breeds where geometry, texture, tooling and finish are able to provoke new sensations when they are applied to a substance. These artificial materials can be described as synthetic because they are the outcome of various qualities that are not necessarily true to the original matter, but they are the combination of two or more parts, whether by design or by natural processes. The aim of this paper is to investigate the potential of architectural surfaces to produce effects through the invention of new breeds of artificial matter, using micro-scale details derived from Nature as an inspiration.

  19. Synthetic vision and memory model for virtual human - biomed 2010.

    Science.gov (United States)

    Zhao, Yue; Kang, Jinsheng; Wright, David

    2010-01-01

    This paper describes the methods and case studies of a novel synthetic vision and memory model for virtual human. The synthetic vision module simulates the biological / optical abilities and limitations of the human vision. The module is based on a series of collision detection between the boundary of virtual humans field of vision (FOV) volume and the surface of objects in a recreated 3D environment. The memory module simulates a short-term memory capability by employing a simplified memory structure (first-in-first-out stack). The synthetic vision and memory model has been integrated into a virtual human modelling project, Intelligent Virtual Modelling. The project aimed to improve the realism and autonomy of virtual humans.

  20. The use of synthetic input sequences in time series modeling

    International Nuclear Information System (INIS)

    Oliveira, Dair Jose de; Letellier, Christophe; Gomes, Murilo E.D.; Aguirre, Luis A.

    2008-01-01

    In many situations time series models obtained from noise-like data settle to trivial solutions under iteration. This Letter proposes a way of producing a synthetic (dummy) input, that is included to prevent the model from settling down to a trivial solution, while maintaining features of the original signal. Simulated benchmark models and a real time series of RR intervals from an ECG are used to illustrate the procedure

  1. Long Memory Models to Generate Synthetic Hydrological Series

    Directory of Open Access Journals (Sweden)

    Guilherme Armando de Almeida Pereira

    2014-01-01

    Full Text Available In Brazil, much of the energy production comes from hydroelectric plants whose planning is not trivial due to the strong dependence on rainfall regimes. This planning is accomplished through optimization models that use inputs such as synthetic hydrologic series generated from the statistical model PAR(p (periodic autoregressive. Recently, Brazil began the search for alternative models able to capture the effects that the traditional model PAR(p does not incorporate, such as long memory effects. Long memory in a time series can be defined as a significant dependence between lags separated by a long period of time. Thus, this research develops a study of the effects of long dependence in the series of streamflow natural energy in the South subsystem, in order to estimate a long memory model capable of generating synthetic hydrologic series.

  2. Yunnan-III models for evolutionary population synthesis

    Science.gov (United States)

    Zhang, F.; Li, L.; Han, Z.; Zhuang, Y.; Kang, X.

    2013-02-01

    We build the Yunnan-III evolutionary population synthesis (EPS) models by using the mesa stellar evolution code, BaSeL stellar spectra library and the initial mass functions (IMFs) of Kroupa and Salpeter, and present colours and integrated spectral energy distributions (ISEDs) of solar-metallicity stellar populations (SPs) in the range of 1 Myr to 15 Gyr. The main characteristic of the Yunnan-III EPS models is the usage of a set of self-consistent solar-metallicity stellar evolutionary tracks (the masses of stars are from 0.1 to 100 M⊙). This set of tracks is obtained by using the state-of-the-art mesa code. mesa code can evolve stellar models through thermally pulsing asymptotic giant branch (TP-AGB) phase for low- and intermediate-mass stars. By comparisons, we confirm that the inclusion of TP-AGB stars makes the V - K, V - J and V - R colours of SPs redder and the infrared flux larger at ages log(t/yr) ≳ 7.6 [the differences reach the maximum at log(t/yr) ˜ 8.6, ˜0.5-0.2 mag for colours, approximately two times for K-band flux]. We also find that the colour-evolution trends of Model with-TPAGB at intermediate and large ages are similar to those from the starburst99 code, which employs the Padova-AGB stellar library, BaSeL spectral library and the Kroupa IMF. At last, we compare the colours with the other EPS models comprising TP-AGB stars (such as CB07, M05, V10 and POPSTAR), and find that the B - V colour agrees with each other but the V-K colour shows a larger discrepancy among these EPS models [˜1 mag when 8 ≲ log(t/yr) ≲ 9]. The stellar evolutionary tracks, isochrones, colours and ISEDs can be obtained on request from the first author or from our website (http://www1.ynao.ac.cn/~zhangfh/). Using the isochrones, you can build your EPS models. Now the format of stellar evolutionary tracks is the same as that in the starburst99 code; you can put them into the starburst99 code and get the SP's results. Moreover, the colours involving other passbands

  3. Mathematical modeling of synthetic unit hydrograph case study: Citarum watershed

    Science.gov (United States)

    Islahuddin, Muhammad; Sukrainingtyas, Adiska L. A.; Kusuma, M. Syahril B.; Soewono, Edy

    2015-09-01

    Deriving unit hydrograph is very important in analyzing watershed's hydrologic response of a rainfall event. In most cases, hourly measures of stream flow data needed in deriving unit hydrograph are not always available. Hence, one needs to develop methods for deriving unit hydrograph for ungagged watershed. Methods that have evolved are based on theoretical or empirical formulas relating hydrograph peak discharge and timing to watershed characteristics. These are usually referred to Synthetic Unit Hydrograph. In this paper, a gamma probability density function and its variant are used as mathematical approximations of a unit hydrograph for Citarum Watershed. The model is adjusted with real field condition by translation and scaling. Optimal parameters are determined by using Particle Swarm Optimization method with weighted objective function. With these models, a synthetic unit hydrograph can be developed and hydrologic parameters can be well predicted.

  4. Synthetic LISA: Simulating time delay interferometry in a model LISA

    International Nuclear Information System (INIS)

    Vallisneri, Michele

    2005-01-01

    We report on three numerical experiments on the implementation of Time-Delay Interferometry (TDI) for LISA, performed with Synthetic LISA, a C++/Python package that we developed to simulate the LISA science process at the level of scientific and technical requirements. Specifically, we study the laser-noise residuals left by first-generation TDI when the LISA armlengths have a realistic time dependence; we characterize the armlength-measurement accuracies that are needed to have effective laser-noise cancellation in both first- and second-generation TDI; and we estimate the quantization and telemetry bitdepth needed for the phase measurements. Synthetic LISA generates synthetic time series of the LISA fundamental noises, as filtered through all the TDI observables; it also provides a streamlined module to compute the TDI responses to gravitational waves according to a full model of TDI, including the motion of the LISA array and the temporal and directional dependence of the armlengths. We discuss the theoretical model that underlies the simulation, its implementation, and its use in future investigations on system-characterization and data-analysis prototyping for LISA

  5. Basic science through engineering? Synthetic modeling and the idea of biology-inspired engineering.

    Science.gov (United States)

    Knuuttila, Tarja; Loettgers, Andrea

    2013-06-01

    Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their construction is typically combined with experiments on model organisms as well as mathematical modeling and simulation. What is especially interesting about this combinational modeling practice is that, apart from greater integration between these different epistemic activities, it has also led to the questioning of some central assumptions and notions on which synthetic biology is based. As a result synthetic biology is in the process of becoming more "biology inspired." Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Synthetic Domain Theory and Models of Linear Abadi & Plotkin Logic

    DEFF Research Database (Denmark)

    Møgelberg, Rasmus Ejlers; Birkedal, Lars; Rosolini, Guiseppe

    2008-01-01

    Plotkin suggested using a polymorphic dual intuitionistic/linear type theory (PILLY) as a metalanguage for parametric polymorphism and recursion. In recent work the first two authors and R.L. Petersen have defined a notion of parametric LAPL-structure, which are models of PILLY, in which one can...... reason using parametricity and, for example, solve a large class of domain equations, as suggested by Plotkin.In this paper, we show how an interpretation of a strict version of Bierman, Pitts and Russo's language Lily into synthetic domain theory presented by Simpson and Rosolini gives rise...... to a parametric LAPL-structure. This adds to the evidence that the notion of LAPL-structure is a general notion, suitable for treating many different parametric models, and it provides formal proofs of consequences of parametricity expected to hold for the interpretation. Finally, we show how these results...

  7. Evolving cell models for systems and synthetic biology.

    Science.gov (United States)

    Cao, Hongqing; Romero-Campero, Francisco J; Heeb, Stephan; Cámara, Miguel; Krasnogor, Natalio

    2010-03-01

    This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm's results as well as of the resulting evolved cell models.

  8. Solar Magnetic Carpet III: Coronal Modelling of Synthetic Magnetograms

    Science.gov (United States)

    Meyer, K. A.; Mackay, D. H.; van Ballegooijen, A. A.; Parnell, C. E.

    2013-09-01

    This article is the third in a series working towards the construction of a realistic, evolving, non-linear force-free coronal-field model for the solar magnetic carpet. Here, we present preliminary results of 3D time-dependent simulations of the small-scale coronal field of the magnetic carpet. Four simulations are considered, each with the same evolving photospheric boundary condition: a 48-hour time series of synthetic magnetograms produced from the model of Meyer et al. ( Solar Phys. 272, 29, 2011). Three simulations include a uniform, overlying coronal magnetic field of differing strength, the fourth simulation includes no overlying field. The build-up, storage, and dissipation of magnetic energy within the simulations is studied. In particular, we study their dependence upon the evolution of the photospheric magnetic field and the strength of the overlying coronal field. We also consider where energy is stored and dissipated within the coronal field. The free magnetic energy built up is found to be more than sufficient to power small-scale, transient phenomena such as nanoflares and X-ray bright points, with the bulk of the free energy found to be stored low down, between 0.5 - 0.8 Mm. The energy dissipated is currently found to be too small to account for the heating of the entire quiet-Sun corona. However, the form and location of energy-dissipation regions qualitatively agree with what is observed on small scales on the Sun. Future MHD modelling using the same synthetic magnetograms may lead to a higher energy release.

  9. KFUPM-KAUST Red Sea model: Digital viscoelastic depth model and synthetic seismic data set

    KAUST Repository

    Al-Shuhail, Abdullatif A.; Mousa, Wail A.; Alkhalifah, Tariq Ali

    2017-01-01

    The Red Sea is geologically interesting due to its unique structures and abundant mineral and petroleum resources, yet no digital geologic models or synthetic seismic data of the Red Sea are publicly available for testing algorithms to image and analyze the area's interesting features. This study compiles a 2D viscoelastic model of the Red Sea and calculates a corresponding multicomponent synthetic seismic data set. The models and data sets are made publicly available for download. We hope this effort will encourage interested researchers to test their processing algorithms on this data set and model and share their results publicly as well.

  10. KFUPM-KAUST Red Sea model: Digital viscoelastic depth model and synthetic seismic data set

    KAUST Repository

    Al-Shuhail, Abdullatif A.

    2017-06-01

    The Red Sea is geologically interesting due to its unique structures and abundant mineral and petroleum resources, yet no digital geologic models or synthetic seismic data of the Red Sea are publicly available for testing algorithms to image and analyze the area\\'s interesting features. This study compiles a 2D viscoelastic model of the Red Sea and calculates a corresponding multicomponent synthetic seismic data set. The models and data sets are made publicly available for download. We hope this effort will encourage interested researchers to test their processing algorithms on this data set and model and share their results publicly as well.

  11. A hierarchical stress release model for synthetic seismicity

    Science.gov (United States)

    Bebbington, Mark

    1997-06-01

    We construct a stochastic dynamic model for synthetic seismicity involving stochastic stress input, release, and transfer in an environment of heterogeneous strength and interacting segments. The model is not fault-specific, having a number of adjustable parameters with physical interpretation, namely, stress relaxation, stress transfer, stress dissipation, segment structure, strength, and strength heterogeneity, which affect the seismicity in various ways. Local parameters are chosen to be consistent with large historical events, other parameters to reproduce bulk seismicity statistics for the fault as a whole. The one-dimensional fault is divided into a number of segments, each comprising a varying number of nodes. Stress input occurs at each node in a simple random process, representing the slow buildup due to tectonic plate movements. Events are initiated, subject to a stochastic hazard function, when the stress on a node exceeds the local strength. An event begins with the transfer of excess stress to neighboring nodes, which may in turn transfer their excess stress to the next neighbor. If the event grows to include the entire segment, then most of the stress on the segment is transferred to neighboring segments (or dissipated) in a characteristic event. These large events may themselves spread to other segments. We use the Middle America Trench to demonstrate that this model, using simple stochastic stress input and triggering mechanisms, can produce behavior consistent with the historical record over five units of magnitude. We also investigate the effects of perturbing various parameters in order to show how the model might be tailored to a specific fault structure. The strength of the model lies in this ability to reproduce the behavior of a general linear fault system through the choice of a relatively small number of parameters. It remains to develop a procedure for estimating the internal state of the model from the historical observations in order to

  12. Surface characterisation of synthetic coal chars made from model compounds

    Energy Technology Data Exchange (ETDEWEB)

    Arenillas, A.; Pevida, C.; Rubiera, F.; Palacios, J.M.; Navarrete, R.; Denoyel, R.; Rouquerol, J.; Pis, J.J. [Instituto Nacional del Carbon, CSIC, Oviedo (Spain)

    2004-07-01

    Knowledge of surface properties is essential for understanding the reaction mechanisms involved in several coal conversion processes. However, due to the complexity and heterogeneity of coal this is rather difficult and the use of known model compounds could be a valuable tool. Single model compounds have been widely used, but they give a quite simplified picture. In this work a mixture of model compounds in a phenol-formaldehyde matrix was cured in order to create cross-linked structures. The obtained synthetic coal was pyrolysed in a fixed bed reactor, under helium atmosphere. The surface composition of the chars was evaluated by XPS, adsorption gravimetry of water vapour, temperature-programmed desorption and potentiometric titration. Texture was characterised by N{sub 2} and CO{sub 2} adsorption isotherms at 77 and 273 K, respectively, and immersion calorimetry in benzene. The results obtained from the different techniques were contrasted in order to give an overview of the surface properties (chemical and physical) of the samples studied. Chars obtained under the same operating conditions from a high volatile bituminous coal were used as a reference.

  13. Elastic properties of synthetic materials for soft tissue modeling

    International Nuclear Information System (INIS)

    Mansy, H A; Grahe, J R; Sandler, R H

    2008-01-01

    Mechanical models of soft tissue are useful for studying vibro-acoustic phenomena. They may be used for validating mathematical models and for testing new equipment and techniques. The objective of this study was to measure density and visco-elastic properties of synthetic materials that can be used to build such models. Samples of nine different materials were tested under dynamic (0.5 Hz) compressive loading conditions. The modulus of elasticity of the materials was varied, whenever possible, by adding a softener during manufacturing. The modulus was measured over a nine month period to quantify the effect of ageing and softener loss on material properties. Results showed that a wide range of the compression elasticity modulus (10 to 1400 kPa) and phase (3.5 0 -16.7 0 ) between stress and strain were possible. Some materials tended to exude softener over time, resulting in a weight loss and elastic properties change. While the weight loss under normal conditions was minimal in all materials (<3% over nine months), loss under accelerated weight-loss conditions can reach 59%. In the latter case an elasticity modulus increase of up to 500% was measured. Key advantages and limitations of candidate materials were identified and discussed

  14. Synthetic Pulse Dilation - PMT Model for high bandwidth gamma measurements

    Science.gov (United States)

    Geppert-Kleinrath, H.; Herrmann, H. W.; Kim, Y. H.; Zylstra, A. B.; Meaney, K. D.; Lopez, F. E.; Khater, H.; Horsfield, C. J.; Gales, S.; Leatherland, A.; Hilsabeck, T.; Kilkenny, J. D.; Hares, J. D.; Dymoke-Bradshaw, T.; Milnes, J.

    2017-10-01

    The Cherenkov mechanism used in Gas Cherenkov Detectors (GCD) is exceptionally fast. However, the temporal resolution of GCDs, such as the Gamma Reaction History diagnostic (GRH), is limited by the current state-of-the-art photomultiplier tube (PMT) to 100 ps. The new pulse dilation - PMT (PD-PMT) for NIF allows for a temporal resolution comparable to that of the gas cell, or of 10ps. Enhanced resolution will contribute to the quest for ignition in a crucial way through precision measurement of reaction history and areal density (ρ R) history, leading to better constrained models. Features such as onset of alpha heating, shock reverberations and burn truncation due to dynamically evolving failure modes will become visible for the first time. PD-PMT will be deployed on GCD-3 at NIF in 2018. Our synthetic PD-PMT model evaluates the capabilities of these future measurements, as well as minimum yield requirements for measurements performed in a well at 3.9 m from target chamber center (TCC), and within a diagnostic inserter at 0.2m from TCC.

  15. Evolution of thermally pulsing asymptotic giant branch stars. IV. Constraining mass loss and lifetimes of low mass, low metallicity AGB stars

    Energy Technology Data Exchange (ETDEWEB)

    Rosenfield, Philip; Dalcanton, Julianne J.; Weisz, Daniel; Williams, Benjamin F. [Department of Astronomy, University of Washington, Box 351580, Seattle, WA 98195 (United States); Marigo, Paola [Department of Physics and Astronomy G. Galilei, University of Padova, Vicolo dell' Osservatorio 3, I-35122 Padova (Italy); Girardi, Léo; Gullieuszik, Marco [Osservatorio Astronomico di Padova—INAF, Vicolo dell' Osservatorio 5, I-35122 Padova (Italy); Bressan, Alessandro [Astrophysics Sector, SISSA, Via Bonomea 265, I-34136 Trieste (Italy); Dolphin, Andrew [Raytheon Company, 1151 East Hermans Road, Tucson, AZ 85756 (United States); Aringer, Bernhard [Department of Astrophysics, University of Vienna, Turkenschanzstraße 17, A-1180 Wien (Austria)

    2014-07-20

    The evolution and lifetimes of thermally pulsating asymptotic giant branch (TP-AGB) stars suffer from significant uncertainties. In this work, we analyze the numbers and luminosity functions of TP-AGB stars in six quiescent, low metallicity ([Fe/H] ≲ –0.86) galaxies taken from the ACS Nearby Galaxy Survey Treasury sample, using Hubble Space Telescope (HST) photometry in both optical and near-infrared filters. The galaxies contain over 1000 TP-AGB stars (at least 60 per field). We compare the observed TP-AGB luminosity functions and relative numbers of TP-AGB and red giant branch (RGB) stars, N{sub TP-AGB}/N{sub RGB}, to models generated from different suites of TP-AGB evolutionary tracks after adopting star formation histories derived from the HST deep optical observations. We test various mass-loss prescriptions that differ in their treatments of mass loss before the onset of dust-driven winds (pre-dust). These comparisons confirm that pre-dust mass loss is important, since models that neglect pre-dust mass loss fail to explain the observed N{sub TP-AGB}/N{sub RGB} ratio or the luminosity functions. In contrast, models with more efficient pre-dust mass loss produce results consistent with observations. We find that for [Fe/H] ≲ –0.86, lower mass TP-AGB stars (M ≲ 1 M{sub ☉}) must have lifetimes of ∼0.5 Myr and higher masses (M ≲ 3 M{sub ☉}) must have lifetimes ≲ 1.2 Myr. In addition, assuming our best-fitting mass-loss prescription, we show that the third dredge-up has no significant effect on TP-AGB lifetimes in this mass and metallicity range.

  16. Neutron spectra and cross sections for ice and clathrate generated from the synthetic spectrum and synthetic model for molecular solids

    International Nuclear Information System (INIS)

    Petriw, S; Cantargi, F; Granada, R

    2006-01-01

    We present here a Synthetic Model for Molecular Solids, aimed at the description of the interaction of thermal neutrons with this kind of systems.Simple representations of the molecular dynamical modes are used, in order to produce a fair description of neutron scattering kernels and cross sections with a minimum set of input data. Using those spectra, we have generated thermal libraries for M C N P [es

  17. METABOLIC MODELLING IN THE DEVELOPMENT OF CELL FACTORIES BY SYNTHETIC BIOLOGY

    Directory of Open Access Journals (Sweden)

    Paula Jouhten

    2012-10-01

    Full Text Available Cell factories are commonly microbial organisms utilized for bioconversion of renewable resources to bulk or high value chemicals. Introduction of novel production pathways in chassis strains is the core of the development of cell factories by synthetic biology. Synthetic biology aims to create novel biological functions and systems not found in nature by combining biology with engineering. The workflow of the development of novel cell factories with synthetic biology is ideally linear which will be attainable with the quantitative engineering approach, high-quality predictive models, and libraries of well-characterized parts. Different types of metabolic models, mathematical representations of metabolism and its components, enzymes and metabolites, are useful in particular phases of the synthetic biology workflow. In this minireview, the role of metabolic modelling in synthetic biology will be discussed with a review of current status of compatible methods and models for the in silico design and quantitative evaluation of a cell factory.

  18. Antifouling Activity of Synthetic Alkylpyridinium Polymers Using the Barnacle Model

    Science.gov (United States)

    Piazza, Veronica; Dragić, Ivanka; Sepčić, Kristina; Faimali, Marco; Garaventa, Francesca; Turk, Tom; Berne, Sabina

    2014-01-01

    Polymeric alkylpyridinium salts (poly-APS) isolated from the Mediterranean marine sponge, Haliclona (Rhizoniera) sarai, effectively inhibit barnacle larva settlement and natural marine biofilm formation through a non-toxic and reversible mechanism. Potential use of poly-APS-like compounds as antifouling agents led to the chemical synthesis of monomeric and oligomeric 3-alkylpyridinium analogues. However, these are less efficient in settlement assays and have greater toxicity than the natural polymers. Recently, a new chemical synthesis method enabled the production of poly-APS analogues with antibacterial, antifungal and anti-acetylcholinesterase activities. The present study examines the antifouling properties and toxicity of six of these synthetic poly-APS using the barnacle (Amphibalanus amphitrite) as a model (cyprids and II stage nauplii larvae) in settlement, acute and sub-acute toxicity assays. Two compounds, APS8 and APS12-3, show antifouling effects very similar to natural poly-APS, with an anti-settlement effective concentration that inhibits 50% of the cyprid population settlement (EC50) after 24 h of 0.32 mg/L and 0.89 mg/L, respectively. The toxicity of APS8 is negligible, while APS12-3 is three-fold more toxic (24-h LC50: nauplii, 11.60 mg/L; cyprids, 61.13 mg/L) than natural poly-APS. This toxicity of APS12-3 towards nauplii is, however, 60-fold and 1200-fold lower than that of the common co-biocides, Zn- and Cu-pyrithione, respectively. Additionally, exposure to APS12-3 for 24 and 48 h inhibits the naupliar swimming ability with respective IC50 of 4.83 and 1.86 mg/L. PMID:24699112

  19. Antifouling Activity of Synthetic Alkylpyridinium Polymers Using the Barnacle Model

    Directory of Open Access Journals (Sweden)

    Veronica Piazza

    2014-04-01

    Full Text Available Polymeric alkylpyridinium salts (poly-APS isolated from the Mediterranean marine sponge, Haliclona (Rhizoniera sarai, effectively inhibit barnacle larva settlement and natural marine biofilm formation through a non-toxic and reversible mechanism. Potential use of poly-APS-like compounds as antifouling agents led to the chemical synthesis of monomeric and oligomeric 3-alkylpyridinium analogues. However, these are less efficient in settlement assays and have greater toxicity than the natural polymers. Recently, a new chemical synthesis method enabled the production of poly-APS analogues with antibacterial, antifungal and anti-acetylcholinesterase activities. The present study examines the antifouling properties and toxicity of six of these synthetic poly-APS using the barnacle (Amphibalanus amphitrite as a model (cyprids and II stage nauplii larvae in settlement, acute and sub-acute toxicity assays. Two compounds, APS8 and APS12-3, show antifouling effects very similar to natural poly-APS, with an anti-settlement effective concentration that inhibits 50% of the cyprid population settlement (EC50 after 24 h of 0.32 mg/L and 0.89 mg/L, respectively. The toxicity of APS8 is negligible, while APS12-3 is three-fold more toxic (24-h LC50: nauplii, 11.60 mg/L; cyprids, 61.13 mg/L than natural poly-APS. This toxicity of APS12-3 towards nauplii is, however, 60-fold and 1200-fold lower than that of the common co-biocides, Zn- and Cu-pyrithione, respectively. Additionally, exposure to APS12-3 for 24 and 48 h inhibits the naupliar swimming ability with respective IC50 of 4.83 and 1.86 mg/L.

  20. Techniques for Modeling Human Performance in Synthetic Environments: A Supplementary Review

    National Research Council Canada - National Science Library

    Ritter, Frank E; Shadbolt, Nigel R; Elliman, David; Young, Richard M; Gobet, Fernand; Baxter, Gordon D

    2003-01-01

    Selected recent developments and promising directions for improving the quality of models of human performance in synthetic environments are summarized, beginning with the potential uses and goals for behavioral models...

  1. A Statistical Approach For Modeling Tropical Cyclones. Synthetic Hurricanes Generator Model

    Energy Technology Data Exchange (ETDEWEB)

    Pasqualini, Donatella [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-05-11

    This manuscript brie y describes a statistical ap- proach to generate synthetic tropical cyclone tracks to be used in risk evaluations. The Synthetic Hur- ricane Generator (SynHurG) model allows model- ing hurricane risk in the United States supporting decision makers and implementations of adaptation strategies to extreme weather. In the literature there are mainly two approaches to model hurricane hazard for risk prediction: deterministic-statistical approaches, where the storm key physical parameters are calculated using physi- cal complex climate models and the tracks are usually determined statistically from historical data; and sta- tistical approaches, where both variables and tracks are estimated stochastically using historical records. SynHurG falls in the second category adopting a pure stochastic approach.

  2. Synthetic SAR Image Generation using Sensor, Terrain and Target Models

    DEFF Research Database (Denmark)

    Kusk, Anders; Abulaitijiang, Adili; Dall, Jørgen

    2016-01-01

    A tool to generate synthetic SAR images of objects set on a clutter background is described. The purpose is to generate images for training Automatic Target Recognition and Identification algorithms. The tool employs a commercial electromagnetic simulation program to calculate radar cross section...

  3. The pharmacokinetic profile of synthetic cathinones in a pregnancy model.

    Science.gov (United States)

    Strange, Lauren G; Kochelek, Kerri; Keasling, Robert; Brown, Stacy D; Pond, Brooks B

    2017-09-01

    In recent years, the abuse of synthetic cathinones or 'bath salts' has become a major public health concern. Although these compounds were initially sold legally and labeled "not for human consumption", the 'bath salts' are psychostimulants, with similar structures and pharmacologic mechanisms to cocaine, the amphetamines, and 3,4 methylendioxymethamphetamine (MDMA, Molly, or Ecstasy). The reported use of these substances by women of child-bearing age highlights the necessity of studies seeking to delineate risks of prenatal exposure. Three popular drugs of this type are methylone, mephedrone, and 3, 4-methylenedioxypyrovalerone (MDPV). Unfortunately, there is currently no information available on the teratogenicity of these compounds, or of the extent to which they cross the placenta. As such, the purpose of this study was to examine the pharmacokinetic profile of the 'bath salts' in a pregnancy model. Pregnant mice (E17.5 gestation) were injected intraperitoneally with a cocktail of 5mg/kg methylone, 10mg/kg mephedrone, and 3mg/kg (MDPV) dissolved in sterile saline. Maternal brain, maternal plasma, placenta, and fetal brain were collected at 30s, 1min, 5min, 10min, 15min, 30min, 1h, 2h, 4h, and 8h following injection. Methylone, mephedrone, and MDPV were extracted from tissue by solid phase extraction, and concentrations were determined using a previously validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. Interestingly, all 3 cathinones reached measurable concentrations in the placenta, as well as the fetal brain; in fact, for MDPV, the maximal concentration (Cmax) was highest in fetal brain, while mephedrone's highest Cmax value was achieved in placenta. Additionally, the total drug exposure for all 3 compounds (as represented by area under the curve, AUC) was higher in fetal matrices (placenta and fetal brain) than in maternal matrices (maternal brain and plasma), and the half-lives for the drugs were longer. Given the extensive

  4. Techniques for Modeling Human Performance in Synthetic Environments: A Supplementary Review

    National Research Council Canada - National Science Library

    Ritter, Frank E; Shadbolt, Nigel R; Elliman, David; Young, Richard M; Gobet, Fernand; Baxter, Gordon D

    2003-01-01

    ... architectures including hybrid architectures, and agent and Belief, Desires and Intentions (BDI) architectures. A list of projects with high payoff for modeling human performance in synthetic environments is provided as a conclusion.

  5. Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

    Science.gov (United States)

    Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

    2015-08-21

    In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

  6. Dynamics of synthetic drugs transmission model with psychological addicts and general incidence rate

    Science.gov (United States)

    Ma, Mingju; Liu, Sanyang; Xiang, Hong; Li, Jun

    2018-02-01

    Synthetic drugs are replacing traditional ones and becoming the main popular ones gradually, which have given rise to serious social issues in recent years. In this paper, a synthetic drugs transmission model with psychological addicts and general contact rate is proposed. The local and global stabilities are decided by the basic reproduction number R0. By analyzing the sensitivity of parameters, we obtain that controlling psychological addiction is better than drugs treatment. These results are verified by numerical simulations.

  7. Comparison between the reactivity of coal and synthetic coal models

    Energy Technology Data Exchange (ETDEWEB)

    A. Arenillas; C. Pevida; F. Rubiera; J.J. Pis [Instituto Nacional del Carbon, CSIC, Oviedo (Spain)

    2003-10-01

    A mixture of carbon compounds was pyrolysed under an inert atmosphere at different temperatures in a fixed bed reactor. The resultant chars were characterised in terms of texture and thermal behaviour. Textural characterisation of the chars was carried out by N{sub 2} and CO{sub 2} adsorption isotherms at -196 and 0{sup o}C, respectively. Char isothermal reactivity in air at 500{sup o}C, and in CO{sub 2} at 1000{sup o}C, was performed in a thermogravimetric analyser (TGA). Temperature-programmed combustion tests under 20% oxygen in argon were also performed in the TGA linked to a mass spectrometer (TGA/MS). The results showed that char textural properties do not always relate well to their reactivity. Not only do physical properties (e.g. surface area, porosity) but also chemical properties (e.g. active sites concentration and distribution) play an important role in the reaction of carbonaceous material and oxidant. On the other hand, in terms of chemical composition the chars obtained from the mixture of carbon compounds were very similar to the chars produced under the same experimental conditions by a high volatile bituminous coal. The fact that carbon compounds are well known makes it easier to obtain knowledge about the functional groups present in synthetic char, and to study the mechanisms of heterogeneous reactions such as the reduction of NO with carbon. 13 refs., 8 figs., 3 tabs.

  8. Modeling Vocal Fold Intravascular Flow using Synthetic Replicas

    Science.gov (United States)

    Terry, Aaron D.; Ricks, Matthew T.; Thomson, Scott L.

    2017-11-01

    Vocal fold vibration that is induced by air flowing from the lungs is believed to decrease blood flow through the vocal folds. This is important due to the critical role of blood flow in maintaining tissue health. However, the precise mechanical relationships between vocal fold vibration and blood perfusion remain understudied. A platform for studying liquid perfusion in a synthetic, life-size, self-oscillating vocal fold replica has recently been developed. The replicas are fabricated using molded silicone with material properties comparable to those of human vocal fold tissues and that include embedded microchannels through which liquid is perfused. The replicas are mounted on an air flow supply tube to initiate flow-induced vibration. A liquid reservoir is attached to the microchannel to cause liquid to perfuse through replica in the anterior-posterior direction. As replica vibration is initiated and amplitude increases, perfusion flow rate decreases. In this presentation, the replica design will be presented, along with data quantifying the relationships between parameters such as replica vibration amplitude, stiffness, microchannel diameter, and perfusion flow rate. This work was supported by Grant NIDCD R01DC005788 from the National Institutes of Health.

  9. Modelling biogas production of solid waste: application of the BGP model to a synthetic landfill

    Science.gov (United States)

    Rodrigo-Ilarri, Javier; Segura-Sobrino, Francisco

    2013-04-01

    Production of biogas as a result of the decomposition of organic matter included on solid waste landfills is still an issue to be understood. Reports on this matter are rarely included on the engineering construction projects of solid waste landfills despite it can be an issue of critical importance while operating the landfill and after its closure. This paper presents an application of BGP (Bio-Gas-Production) model to a synthetic landfill. The evolution in time of the concentrations of the different chemical compounds of biogas is studied. Results obtained show the impact on the air quality of different management alternatives which are usually performed in real landfills.

  10. Frequency Response of Synthetic Vocal Fold Models with Linear and Nonlinear Material Properties

    Science.gov (United States)

    Shaw, Stephanie M.; Thomson, Scott L.; Dromey, Christopher; Smith, Simeon

    2012-01-01

    Purpose: The purpose of this study was to create synthetic vocal fold models with nonlinear stress-strain properties and to investigate the effect of linear versus nonlinear material properties on fundamental frequency (F[subscript 0]) during anterior-posterior stretching. Method: Three materially linear and 3 materially nonlinear models were…

  11. White Dwarf Model Atmospheres: Synthetic Spectra for Super Soft Sources

    OpenAIRE

    Rauch, Thomas

    2011-01-01

    The T\\"ubingen NLTE Model-Atmosphere Package (TMAP) calculates fully metal-line blanketed white dwarf model atmospheres and spectral energy distributions (SEDs) at a high level of sophistication. Such SEDs are easily accessible via the German Astrophysical Virtual Observatory (GAVO) service TheoSSA. We discuss applications of TMAP models to (pre) white dwarfs during the hottest stages of their stellar evolution, e.g. in the parameter range of novae and super soft sources.

  12. White Dwarf Model Atmospheres: Synthetic Spectra for Supersoft Sources

    Science.gov (United States)

    Rauch, Thomas

    2013-01-01

    The Tübingen NLTE Model-Atmosphere Package (TMAP) calculates fully metal-line blanketed white dwarf model atmospheres and spectral energy distributions (SEDs) at a high level of sophistication. Such SEDs are easily accessible via the German Astrophysical Virtual Observatory (GAVO) service TheoSSA. We discuss applications of TMAP models to (pre) white dwarfs during the hottest stages of their stellar evolution, e.g. in the parameter range of novae and supersoft sources.

  13. New Approaches in Modeling Multiphase Flows and Dispersion in Turbulence, Fractal Methods and Synthetic Turbulence

    CERN Document Server

    Nicolleau, FCGA; Redondo, J-M

    2012-01-01

    This book contains a collection of the main contributions from the first five workshops held by Ercoftac Special Interest Group on Synthetic Turbulence Models (SIG42. It is intended as an illustration of the sig's activities and of the latest developments in the field. This volume investigates the use of Kinematic Simulation (KS) and other synthetic turbulence models for the particular application to environmental flows. This volume offers the best syntheses on the research status in KS, which is widely used in various domains, including Lagrangian aspects in turbulence mixing/stirring, partic

  14. A synthetic seismicity model for the Middle America Trench

    Science.gov (United States)

    Ward, Steven N.

    1991-01-01

    A novel iterative technique, based on the concept of fault segmentation and computed using 2D static dislocation theory, for building models of seismicity and fault interaction which are physically acceptable and geometrically and kinematically correct, is presented. The technique is applied in two steps to seismicity observed at the Middle America Trench. The first constructs generic models which randomly draw segment strengths and lengths from a 2D probability distribution. The second constructs predictive models in which segment lengths and strengths are adjusted to mimic the actual geography and timing of large historical earthquakes. Both types of models reproduce the statistics of seismicity over five units of magnitude and duplicate other aspects including foreshock and aftershock sequences, migration of foci, and the capacity to produce both characteristic and noncharacteristic earthquakes. Over a period of about 150 yr the complex interaction of fault segments and the nonlinear failure conditions conspire to transform an apparently deterministic model into a chaotic one.

  15. Synthetic Study on the Geological and Hydrogeological Model around KURT

    International Nuclear Information System (INIS)

    Park, Kyung Woo; Kim, Kyung Su; Koh, Yong Kwon; Choi, Jong Won

    2011-01-01

    To characterize the site specific properties of a study area for high-level radioactive waste disposal research in KAERI, the several geological investigations such as surface geological surveys and borehole drillings were carried out since 1997. Especially, KURT (KAERI Underground Research Tunnel) was constructed to understand the further study of geological environments in 2006. As a result, the first geological model of a study area was constructed by using the results of geological investigation. The objective of this research is to construct a hydrogeological model around KURT area on the basis of the geological model. Hydrogeological data which were obtained from in-situ hydraulic tests in the 9 boreholes were estimated to accomplish the objective. And, the hydrogeological properties of the 4 geological elements in the geological model, which were the subsurface weathering zone, the log angle fracture zone, the fracture zones and the bedrock were suggested. The hydrogeological model suggested in this study will be used as input parameters to carry out the groundwater flow modeling as a next step of the site characterization around KURT area

  16. Synthetic digital radiographs using exposure computer models of Voxels / EGS4 Phantoms

    International Nuclear Information System (INIS)

    Kenned, Roberto; Vieira, Jose W.; Lima, Fernando R.A.; Loureiro, Eduardo

    2008-01-01

    The objective of this work is to produce synthetic digital radiographs from synthetic phantoms with the use of a Computational Model of Exposition (MCE). The literature explains a model consisted on a phantom, a Monte Carlo code and an algorithm of a radioactive source. In this work it was used the FAX phantom (Female Adult voXel), besides the EGS4 system code Eletron Shower-range version 4) and an external source, similar to that used in diagnostic radiology. The implementation of MCE creates files with information on external energy deposited in the voxels of fantoma used, here called EnergiaPorVoxel.dat. These files along with the targeted phantom (fax.sgi) worked as data entry for the DIP software (Digital Imaging Processing) to build the synthetic phantoms based on energy and the effective dose. This way you can save each slice that is the stack of pictures of these phantoms synthetics, which have been called synthetic digital radiography. Using this, it is possible to use techniques of emphasis in space to increase the contrast or elineate contours between organs and tissues. The practical use of these images is not only to allow a planning of examinations performed in clinics and hospitals and reducing unnecessary exposure to patients by error of radiographic techniques. (author)

  17. Model of a synthetic wind speed time series generator

    DEFF Research Database (Denmark)

    Negra, N.B.; Holmstrøm, O.; Bak-Jensen, B.

    2008-01-01

    is described and some statistical issues (seasonal characteristics, autocorrelation functions, average values and distribution functions) are used for verification. The output of the model has been designed as input for sequential Monte Carlo simulation; however, it is expected that it can be used for other...... of the main elements to consider for this purpose is the model of the wind speed that is usually required as input. Wind speed measurements may represent a solution for this problem, but, for techniques such as sequential Monte Carlo simulation, they have to be long enough in order to describe a wide range...

  18. Generating synthetic wave climates for coastal modelling: a linear mixed modelling approach

    Science.gov (United States)

    Thomas, C.; Lark, R. M.

    2013-12-01

    Numerical coastline morphological evolution models require wave climate properties to drive morphological change through time. Wave climate properties (typically wave height, period and direction) may be temporally fixed, culled from real wave buoy data, or allowed to vary in some way defined by a Gaussian or other pdf. However, to examine sensitivity of coastline morphologies to wave climate change, it seems desirable to be able to modify wave climate time series from a current to some new state along a trajectory, but in a way consistent with, or initially conditioned by, the properties of existing data, or to generate fully synthetic data sets with realistic time series properties. For example, mean or significant wave height time series may have underlying periodicities, as revealed in numerous analyses of wave data. Our motivation is to develop a simple methodology to generate synthetic wave climate time series that can change in some stochastic way through time. We wish to use such time series in a coastline evolution model to test sensitivities of coastal landforms to changes in wave climate over decadal and centennial scales. We have worked initially on time series of significant wave height, based on data from a Waverider III buoy located off the coast of Yorkshire, England. The statistical framework for the simulation is the linear mixed model. The target variable, perhaps after transformation (Box-Cox), is modelled as a multivariate Gaussian, the mean modelled as a function of a fixed effect, and two random components, one of which is independently and identically distributed (iid) and the second of which is temporally correlated. The model was fitted to the data by likelihood methods. We considered the option of a periodic mean, the period either fixed (e.g. at 12 months) or estimated from the data. We considered two possible correlation structures for the second random effect. In one the correlation decays exponentially with time. In the second

  19. Active aeroelastic control aspects of an aircraft wing by using synthetic jet actuators : Modeling, simulations, experiments

    NARCIS (Netherlands)

    Donnell, K.O.; Schober, S.; Stolk, M.; Marzocca, P.; De Breuker, R.; Abdalla, M.; Nicolini, E.; Gürdal, Z.

    2007-01-01

    This paper discusses modeling, simulations and experimental aspects of active aeroelastic control on aircraft wings by using Synthetic Jet Actuators (SJAs). SJAs, a particular class of zero-net mass-flux actuators, have shown very promising results in numerous aeronautical applications, such as

  20. Comparison of Nonlinear Model Results Using Modified Recorded and Synthetic Ground Motions

    International Nuclear Information System (INIS)

    Spears, Robert E.; Wilkins, J. Kevin

    2011-01-01

    A study has been performed that compares results of nonlinear model runs using two sets of earthquake ground motion time histories that have been modified to fit the same design response spectra. The time histories include applicable modified recorded earthquake ground motion time histories and synthetic ground motion time histories. The modified recorded earthquake ground motion time histories are modified from time history records that are selected based on consistent magnitude and distance. The synthetic ground motion time histories are generated using appropriate Fourier amplitude spectrums, Arias intensity, and drift correction. All of the time history modification is performed using the same algorithm to fit the design response spectra. The study provides data to demonstrate that properly managed synthetic ground motion time histories are reasonable for use in nonlinear seismic analysis.

  1. Accurate, model-based tuning of synthetic gene expression using introns in S. cerevisiae.

    Directory of Open Access Journals (Sweden)

    Ido Yofe

    2014-06-01

    Full Text Available Introns are key regulators of eukaryotic gene expression and present a potentially powerful tool for the design of synthetic eukaryotic gene expression systems. However, intronic control over gene expression is governed by a multitude of complex, incompletely understood, regulatory mechanisms. Despite this lack of detailed mechanistic understanding, here we show how a relatively simple model enables accurate and predictable tuning of synthetic gene expression system in yeast using several predictive intron features such as transcript folding and sequence motifs. Using only natural Saccharomyces cerevisiae introns as regulators, we demonstrate fine and accurate control over gene expression spanning a 100 fold expression range. These results broaden the engineering toolbox of synthetic gene expression systems and provide a framework in which precise and robust tuning of gene expression is accomplished.

  2. Inference for multivariate regression model based on multiply imputed synthetic data generated via posterior predictive sampling

    Science.gov (United States)

    Moura, Ricardo; Sinha, Bimal; Coelho, Carlos A.

    2017-06-01

    The recent popularity of the use of synthetic data as a Statistical Disclosure Control technique has enabled the development of several methods of generating and analyzing such data, but almost always relying in asymptotic distributions and in consequence being not adequate for small sample datasets. Thus, a likelihood-based exact inference procedure is derived for the matrix of regression coefficients of the multivariate regression model, for multiply imputed synthetic data generated via Posterior Predictive Sampling. Since it is based in exact distributions this procedure may even be used in small sample datasets. Simulation studies compare the results obtained from the proposed exact inferential procedure with the results obtained from an adaptation of Reiters combination rule to multiply imputed synthetic datasets and an application to the 2000 Current Population Survey is discussed.

  3. Synthetic model for Doppler broadening of neutron absorption resonances in molecular fluids

    Energy Technology Data Exchange (ETDEWEB)

    Villanueva, Alejandro J., E-mail: villanueva@cab.cnea.gov.a [Comision Nacional de Energia Atomica, Centro Atomico Bariloche and Instituto Balseiro, 8400 S.C. de Bariloche (RN) (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas (Argentina); Granada, J.R. [Comision Nacional de Energia Atomica, Centro Atomico Bariloche and Instituto Balseiro, 8400 S.C. de Bariloche (RN) (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas (Argentina)

    2010-08-15

    A general and systematic approach expressed in modern language, accounting for molecular motion effects on Doppler Broadening of Neutron Absorption Resonances (DBNAR) is given the form of a new model. It relies on well validated hypothesis: The separability of atomic from nuclear degrees of freedom, the use of the Van Hove scattering formalism and the fact that a conceptually identical approach produced experimentally proved predictions when applied to DBNAR in solid systems. We treat the molecular internal degrees of freedom approximately as harmonic oscillators. As a second contribution of this work, a synthetic model is presented in order to make the more complete model mentioned above suitable for neutron calculation codes. This second synthetic model reduces to the exact expressions of the complete model in the low and high neutron energy regimes and provides a plausible transition in between. Numerical results are presented for a general hypothetical case to show its strengths and limitations. Also, both models are applied to a real case of the {sup 238}U 6.674 eV resonant effective broadened absorption cross-section in UF6 (uranium hexafluoride). A direct experimental validation of our models is still necessary for which a special high resolution neutron transmission experiment ought to be devised at low temperatures and pressures on a gaseous system. It is showed how the synthetic model can be used to make thermometric predictions in an improved fashion in comparison to the effective temperature gas model at low temperatures.

  4. Parametric Study of Synthetic-Jet-Based Flow Control on a Vertical Tail Model

    Science.gov (United States)

    Monastero, Marianne; Lindstrom, Annika; Beyar, Michael; Amitay, Michael

    2015-11-01

    Separation control over the rudder of the vertical tail of a commercial airplane using synthetic-jet-based flow control can lead to a reduction in tail size, with an associated decrease in drag and increase in fuel savings. A parametric, experimental study was undertaken using an array of finite span synthetic jets to investigate the sensitivity of the enhanced vertical tail side force to jet parameters, such as jet spanwise spacing and jet momentum coefficient. A generic wind tunnel model was designed and fabricated to fundamentally study the effects of the jet parameters at varying rudder deflection and model sideslip angles. Wind tunnel results obtained from pressure measurements and tuft flow visualization in the Rensselaer Polytechnic Subsonic Wind Tunnel show a decrease in separation severity and increase in model performance in comparison to the baseline, non-actuated case. The sensitivity to various parameters will be presented.

  5. Utilisation of transparent synthetic soil surrogates in geotechnical physical models: A review

    Directory of Open Access Journals (Sweden)

    Abideen Adekunle Ganiyu

    2016-08-01

    Full Text Available Efforts to obtain non-intrusive measurement of deformations and spatial flow within soil mass prior to the advent of transparent soils have perceptible limitations. The transparent soil is a two-phase medium composed of both the synthetic aggregate and fluid components of identical refractive indices aiming at attaining transparency of the resulting soil. The transparency facilitates real life visualisation of soil continuum in physical models. When applied in conjunction with advanced photogrammetry and image processing techniques, transparent soils enable the quantification of the spatial deformation, displacement and multi-phase flow in physical model tests. Transparent synthetic soils have been successfully employed in geotechnical model tests as soil surrogates based on the testing results of their geotechnical properties which replicate those of natural soils. This paper presents a review on transparent synthetic soils and their numerous applications in geotechnical physical models. The properties of the aggregate materials are outlined and the features of the various transparent clays and sands available in the literature are described. The merits of transparent soil are highlighted and the need to amplify its application in geotechnical physical model researches is emphasised. This paper will serve as a concise compendium on the subject of transparent soils for future researchers in this field.

  6. Synthetic environments

    Science.gov (United States)

    Lukes, George E.; Cain, Joel M.

    1996-02-01

    The Advanced Distributed Simulation (ADS) Synthetic Environments Program seeks to create robust virtual worlds from operational terrain and environmental data sources of sufficient fidelity and currency to interact with the real world. While some applications can be met by direct exploitation of standard digital terrain data, more demanding applications -- particularly those support operations 'close to the ground' -- are well-served by emerging capabilities for 'value-adding' by the user working with controlled imagery. For users to rigorously refine and exploit controlled imagery within functionally different workstations they must have a shared framework to allow interoperability within and between these environments in terms of passing image and object coordinates and other information using a variety of validated sensor models. The Synthetic Environments Program is now being expanded to address rapid construction of virtual worlds with research initiatives in digital mapping, softcopy workstations, and cartographic image understanding. The Synthetic Environments Program is also participating in a joint initiative for a sensor model applications programer's interface (API) to ensure that a common controlled imagery exploitation framework is available to all researchers, developers and users. This presentation provides an introduction to ADS and the associated requirements for synthetic environments to support synthetic theaters of war. It provides a technical rationale for exploring applications of image understanding technology to automated cartography in support of ADS and related programs benefitting from automated analysis of mapping, earth resources and reconnaissance imagery. And it provides an overview and status of the joint initiative for a sensor model API.

  7. A Canine Arthroscopic Anterior Cruciate Ligament Reconstruction Model for Study of Synthetic Augmentation of Tendon Allografts.

    Science.gov (United States)

    Cook, James L; Smith, Pat; Stannard, James P; Pfeiffer, Ferris; Kuroki, Keiichi; Bozynski, Chantelle C; Cook, Cristi

    2017-09-01

    Novel graft types, fixation methods, and means for augmenting anterior cruciate ligament (ACL) reconstructions require preclinical validation prior to safe and effective clinical application. The objective of this study was to describe and validate a translational canine model for all-inside arthroscopic complete ACL reconstruction using a quadriceps tendon allograft with internal brace (QTIB). With institutional approval, adult research hounds underwent complete transection of the native ACL followed by all-inside ACL reconstruction using the novel QTIB construct with suspensory fixation ( n  = 10). Contralateral knees were used as nonoperated controls ( n  = 10). Dogs were assessed over a 6-month period using functional, diagnostic imaging, gross, biomechanical, and histologic outcome measures required for preclinical animal models. Study results suggest that the novel QTIB construct used for complete ACL reconstruction can provide sustained knee stability and function without the development of premature osteoarthritis in a rigorous and valid preclinical model. The unique configuration of the QTIB construct-the combination of a tendon allograft with a synthetic suture tape internal brace-allowed for an effective biologic-synthetic load-sharing ACL construct. It prevented early failure, allowed for direct, four-zone graft-to-bone healing, and functional graft remodeling while avoiding problems noted with use of all-synthetic grafts. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  8. Smart-DS: Synthetic Models for Advanced, Realistic Testing: Distribution Systems and Scenarios

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, Venkat K [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Palmintier, Bryan S [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hodge, Brian S [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hale, Elaine T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Elgindy, Tarek [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Bugbee, Bruce [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Rossol, Michael N [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Lopez, Anthony J [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Krishnamurthy, Dheepak [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Vergara, Claudio [MIT; Domingo, Carlos Mateo [IIT Comillas; Postigo, Fernando [IIT Comillas; de Cuadra, Fernando [IIT Comillas; Gomez, Tomas [IIT Comillas; Duenas, Pablo [MIT; Luke, Max [MIT; Li, Vivian [MIT; Vinoth, Mohan [GE Grid Solutions; Kadankodu, Sree [GE Grid Solutions

    2017-08-09

    The National Renewable Energy Laboratory (NREL) in collaboration with Massachusetts Institute of Technology (MIT), Universidad Pontificia Comillas (Comillas-IIT, Spain) and GE Grid Solutions, is working on an ARPA-E GRID DATA project, titled Smart-DS, to create: 1) High-quality, realistic, synthetic distribution network models, and 2) Advanced tools for automated scenario generation based on high-resolution weather data and generation growth projections. Through these advancements, the Smart-DS project is envisioned to accelerate the development, testing, and adoption of advanced algorithms, approaches, and technologies for sustainable and resilient electric power systems, especially in the realm of U.S. distribution systems. This talk will present the goals and overall approach of the Smart-DS project, including the process of creating the synthetic distribution datasets using reference network model (RNM) and the comprehensive validation process to ensure network realism, feasibility, and applicability to advanced use cases. The talk will provide demonstrations of early versions of synthetic models, along with the lessons learnt from expert engagements to enhance future iterations. Finally, the scenario generation framework, its development plans, and co-ordination with GRID DATA repository teams to house these datasets for public access will also be discussed.

  9. Optimization of Soil Hydraulic Model Parameters Using Synthetic Aperture Radar Data: An Integrated Multidisciplinary Approach

    DEFF Research Database (Denmark)

    Pauwels, Valentijn; Balenzano, Anna; Satalino, Giuseppe

    2009-01-01

    It is widely recognized that Synthetic Aperture Radar (SAR) data are a very valuable source of information for the modeling of the interactions between the land surface and the atmosphere. During the last couple of decades, most of the research on the use of SAR data in hydrologic applications has...... that no direct relationships between the remote-sensing observations, more specifically radar backscatter values, and the parameter values can be derived. However, land surface models can provide these relationships. The objective of this paper is to retrieve a number of soil physical model parameters through...

  10. Multivariate synthetic streamflow generation using a hybrid model based on artificial neural networks

    Directory of Open Access Journals (Sweden)

    J. C. Ochoa-Rivera

    2002-01-01

    Full Text Available A model for multivariate streamflow generation is presented, based on a multilayer feedforward neural network. The structure of the model results from two components, the neural network (NN deterministic component and a random component which is assumed to be normally distributed. It is from this second component that the model achieves the ability to incorporate effectively the uncertainty associated with hydrological processes, making it valuable as a practical tool for synthetic generation of streamflow series. The NN topology and the corresponding analytical explicit formulation of the model are described in detail. The model is calibrated with a series of monthly inflows to two reservoir sites located in the Tagus River basin (Spain, while validation is performed through estimation of a set of statistics that is relevant for water resources systems planning and management. Among others, drought and storage statistics are computed and compared for both the synthetic and historical series. The performance of the NN-based model was compared to that of a standard autoregressive AR(2 model. Results show that NN represents a promising modelling alternative for simulation purposes, with interesting potential in the context of water resources systems management and optimisation. Keywords: neural networks, perceptron multilayer, error backpropagation, hydrological scenario generation, multivariate time-series..

  11. Numerical modeling of the radiative transfer in a turbid medium using the synthetic iteration.

    Science.gov (United States)

    Budak, Vladimir P; Kaloshin, Gennady A; Shagalov, Oleg V; Zheltov, Victor S

    2015-07-27

    In this paper we propose the fast, but the accurate algorithm for numerical modeling of light fields in the turbid media slab. For the numerical solution of the radiative transfer equation (RTE) it is required its discretization based on the elimination of the solution anisotropic part and the replacement of the scattering integral by a finite sum. The solution regular part is determined numerically. A good choice of the method of the solution anisotropic part elimination determines the high convergence of the algorithm in the mean square metric. The method of synthetic iterations can be used to improve the convergence in the uniform metric. A significant increase in the solution accuracy with the use of synthetic iterations allows applying the two-stream approximation for the regular part determination. This approach permits to generalize the proposed method in the case of an arbitrary 3D geometry of the medium.

  12. Characterization and three-dimensional reconstruction of synthetic bone model foams

    Energy Technology Data Exchange (ETDEWEB)

    Gómez, S. [Interdepartment Research Group for the Applied Scientific Collaboration (IRGASC), Division of Biomaterials and Bioengineering, Technical University of Catalonia (UPC), Avda. Diagonal 647, E-08028 Barcelona (Spain); Vlad, M.D. [Interdepartment Research Group for the Applied Scientific Collaboration (IRGASC), Division of Biomaterials and Bioengineering, Technical University of Catalonia (UPC), Avda. Diagonal 647, E-08028 Barcelona (Spain); Faculty of Medical Bioengineering, “Gr. T. Popa” University of Medicine and Pharmacy, Str. Kogalniceanu 9-13, 700454 Iasi (Romania); López, J. [Interdepartment Research Group for the Applied Scientific Collaboration (IRGASC), Division of Biomaterials and Bioengineering, Technical University of Catalonia (UPC), Avda. Diagonal 647, E-08028 Barcelona (Spain); Navarro, M. [Centre de Biotecnologia Animal i de Teràpia Gènica (CBATEG), Departament de Sanitat i d' Anatomia Animals, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Cerdanyola del Vallès (Spain); Fernández, E., E-mail: enrique.fernandez@upc.edu [Interdepartment Research Group for the Applied Scientific Collaboration (IRGASC), Division of Biomaterials and Bioengineering, Technical University of Catalonia (UPC), Avda. Diagonal 647, E-08028 Barcelona (Spain)

    2013-08-01

    Sawbones© open-cell foams with different porosity grades are being used as synthetic bone-like models for in vitro mechanical and infiltration experiments. However, a comprehensive characterization of these foams is not available and there is a lack of reliable information about them. For this reason two of these foams (Refs. 1522-505 and -507) have been characterized at the micro architectural level by scanning electron microscopy, computed tomography and image data analysis. BoneJ open software and ImageJ open software were used to obtain the characteristic histomorphometric parameters and the three dimensional virtual models of the foams. The results showed that both foams, while having different macro porosities, appeared undistinguishable at the micro scale. Moreover, the micro structural features resembled those of osteoporotic rather than healthy trabecular bone. It is concluded that Sawbones© foams behave reasonably as synthetic bone-like models. Consequently, their use is recommended for in vitro comparison purposes of both mechanical and infiltration testing performed in real vertebra. Finally, the virtual models obtained, which are available under request, can favour comparisons between future self-similar in vitro experiments and computer simulations. - Highlights: • Sawbones© model foams have been scanned by μ-CT. • Histomorphometric indices and 3D virtual models have been obtained. • The results will be of use to understand biocement vertebra infiltration studies.

  13. Characterization and three-dimensional reconstruction of synthetic bone model foams

    International Nuclear Information System (INIS)

    Gómez, S.; Vlad, M.D.; López, J.; Navarro, M.; Fernández, E.

    2013-01-01

    Sawbones© open-cell foams with different porosity grades are being used as synthetic bone-like models for in vitro mechanical and infiltration experiments. However, a comprehensive characterization of these foams is not available and there is a lack of reliable information about them. For this reason two of these foams (Refs. 1522-505 and -507) have been characterized at the micro architectural level by scanning electron microscopy, computed tomography and image data analysis. BoneJ open software and ImageJ open software were used to obtain the characteristic histomorphometric parameters and the three dimensional virtual models of the foams. The results showed that both foams, while having different macro porosities, appeared undistinguishable at the micro scale. Moreover, the micro structural features resembled those of osteoporotic rather than healthy trabecular bone. It is concluded that Sawbones© foams behave reasonably as synthetic bone-like models. Consequently, their use is recommended for in vitro comparison purposes of both mechanical and infiltration testing performed in real vertebra. Finally, the virtual models obtained, which are available under request, can favour comparisons between future self-similar in vitro experiments and computer simulations. - Highlights: • Sawbones© model foams have been scanned by μ-CT. • Histomorphometric indices and 3D virtual models have been obtained. • The results will be of use to understand biocement vertebra infiltration studies

  14. Evaluation of synthetic vascular grafts in a mouse carotid grafting model.

    Directory of Open Access Journals (Sweden)

    Alex H P Chan

    Full Text Available Current animal models for the evaluation of synthetic grafts are lacking many of the molecular tools and transgenic studies available to other branches of biology. A mouse model of vascular grafting would allow for the study of molecular mechanisms of graft failure, including in the context of clinically relevant disease states. In this study, we comprehensively characterise a sutureless grafting model which facilitates the evaluation of synthetic grafts in the mouse carotid artery. Using conduits electrospun from polycaprolactone (PCL we show the gradual development of a significant neointima within 28 days, found to be greatest at the anastomoses. Histological analysis showed temporal increases in smooth muscle cell and collagen content within the neointima, demonstrating its maturation. Endothelialisation of the PCL grafts, assessed by scanning electron microscopy (SEM analysis and CD31 staining, was near complete within 28 days, together replicating two critical aspects of graft performance. To further demonstrate the potential of this mouse model, we used longitudinal non-invasive tracking of bone-marrow mononuclear cells from a transgenic mouse strain with a dual reporter construct encoding both luciferase and green fluorescent protein (GFP. This enabled characterisation of mononuclear cell homing and engraftment to PCL using bioluminescence imaging and histological staining over time (7, 14 and 28 days. We observed peak luminescence at 7 days post-graft implantation that persisted until sacrifice at 28 days. Collectively, we have established and characterised a high-throughput model of grafting that allows for the evaluation of key clinical drivers of graft performance.

  15. Evaluation of synthetic vascular grafts in a mouse carotid grafting model.

    Science.gov (United States)

    Chan, Alex H P; Tan, Richard P; Michael, Praveesuda L; Lee, Bob S L; Vanags, Laura Z; Ng, Martin K C; Bursill, Christina A; Wise, Steven G

    2017-01-01

    Current animal models for the evaluation of synthetic grafts are lacking many of the molecular tools and transgenic studies available to other branches of biology. A mouse model of vascular grafting would allow for the study of molecular mechanisms of graft failure, including in the context of clinically relevant disease states. In this study, we comprehensively characterise a sutureless grafting model which facilitates the evaluation of synthetic grafts in the mouse carotid artery. Using conduits electrospun from polycaprolactone (PCL) we show the gradual development of a significant neointima within 28 days, found to be greatest at the anastomoses. Histological analysis showed temporal increases in smooth muscle cell and collagen content within the neointima, demonstrating its maturation. Endothelialisation of the PCL grafts, assessed by scanning electron microscopy (SEM) analysis and CD31 staining, was near complete within 28 days, together replicating two critical aspects of graft performance. To further demonstrate the potential of this mouse model, we used longitudinal non-invasive tracking of bone-marrow mononuclear cells from a transgenic mouse strain with a dual reporter construct encoding both luciferase and green fluorescent protein (GFP). This enabled characterisation of mononuclear cell homing and engraftment to PCL using bioluminescence imaging and histological staining over time (7, 14 and 28 days). We observed peak luminescence at 7 days post-graft implantation that persisted until sacrifice at 28 days. Collectively, we have established and characterised a high-throughput model of grafting that allows for the evaluation of key clinical drivers of graft performance.

  16. Wall modeled large eddy simulations of complex high Reynolds number flows with synthetic inlet turbulence

    International Nuclear Information System (INIS)

    Patil, Sunil; Tafti, Danesh

    2012-01-01

    Highlights: ► Large eddy simulation. ► Wall layer modeling. ► Synthetic inlet turbulence. ► Swirl flows. - Abstract: Large eddy simulations of complex high Reynolds number flows are carried out with the near wall region being modeled with a zonal two layer model. A novel formulation for solving the turbulent boundary layer equation for the effective tangential velocity in a generalized co-ordinate system is presented and applied in the near wall zonal treatment. This formulation reduces the computational time in the inner layer significantly compared to the conventional two layer formulations present in the literature and is most suitable for complex geometries involving body fitted structured and unstructured meshes. The cost effectiveness and accuracy of the proposed wall model, used with the synthetic eddy method (SEM) to generate inlet turbulence, is investigated in turbulent channel flow, flow over a backward facing step, and confined swirling flows at moderately high Reynolds numbers. Predictions are compared with available DNS, experimental LDV data, as well as wall resolved LES. In all cases, there is at least an order of magnitude reduction in computational cost with no significant loss in prediction accuracy.

  17. Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking

    Science.gov (United States)

    Tsvetkov, Vladimir B.; Serbin, Alexander V.

    2014-06-01

    In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 ( HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [ HR1]3 of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics ( MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]3 in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands-target interactions. Some newly MD-discovered aspects of the ligand's backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.

  18. Generation of synthetic Kinect depth images based on empirical noise model

    DEFF Research Database (Denmark)

    Iversen, Thorbjørn Mosekjær; Kraft, Dirk

    2017-01-01

    The development, training and evaluation of computer vision algorithms rely on the availability of a large number of images. The acquisition of these images can be time-consuming if they are recorded using real sensors. An alternative is to rely on synthetic images which can be rapidly generated....... This Letter describes a novel method for the simulation of Kinect v1 depth images. The method is based on an existing empirical noise model from the literature. The authors show that their relatively simple method is able to provide depth images which have a high similarity with real depth images....

  19. Synthetic Cognitive Apprenticeship Model – Possible Way to Enhance Students’ Metacognitive Skills

    Directory of Open Access Journals (Sweden)

    Jelena Suchanova

    2011-12-01

    Full Text Available The article presents the kaleidoscopic view on the concept of metacognition. There are a lot of implications showing the link between metacognitive skills, learning and teaching. Metacognitive skills such as self-direction, self-evaluation, and self-control, as well as orientation, planning, monitoring, testing, diagnosing, repairing, evaluation and reflection play an important role in facilitating the process of transition from teacher-centered environment to autonomous foreign language studies. Synthetic Cognitive Apprenticeship model is suggested as possible way to help students enhance their metacognitive skills thus becoming more prepared for autonomous foreign language studies.

  20. Generation of synthetic influent data for performing (micro) pollutant wastewater treatment modelling studies

    DEFF Research Database (Denmark)

    Snip, L. J. P.; Aymerich, I.; Flores-Alsina, X.

    2015-01-01

    The use of Activated Sludge Models (ASM) (Henze et al., 2000) is constantly growing and both industry and academia are increasingly applying these tools when performing wastewater treatment plant (WWTP) engineering studies. Besides describing the behaviour of traditional pollutants such as organic...... carbon (C), nitrogen(N) and phosphorus(P), ASM models have been successfully upgraded to predict the fate of different types of micro-pollutants (Benedetti et al., 2013). Indeed, the potential adverse effects of micro-pollutants in aquatic environments have been an object of intensive research during...... (Gernaey et al., 2011). This is an important point since realistic data representing the influent wastewater dynamics are crucial to accomplish any WWTP modelling project (Rieger et al., 2012). For this reason, model-based influent generators/synthetic data are an alternative that has recently gained...

  1. Attribute Synthetic Evaluation Model for the CBM Recoverability and Its Application

    Directory of Open Access Journals (Sweden)

    Xiao-gang Xia

    2015-01-01

    Full Text Available The coal-bed methane (CBM recoverability is the basic premise of CBM development practice; in order to effectively evaluate the CBM recoverability, the attribute synthetic evaluation model is established based on the theory and method of attribute mathematics. Firstly, five indexes are chosen to evaluate the recoverability through analyzing the influence factors of CBM, including seam thickness, gas saturation, permeability, reservoir pressure gradient, and hydrogeological conditions. Secondly, the attribute measurement functions of each index are constructed based on the attribute mathematics theory, and the calculation methods of the single index attribute measurement and the synthetic attribute measurement also are provided. Meanwhile, the weight of each index is given with the method of similar number and similar weight; the evaluation results also are determined by the confidence criterion reliability code. At last, according to the application results of the model in some coal target area of Fuxin and Hancheng mine, the evaluation results are basically consistent with the actual situation, which proves that the evaluation model can be used in the CBM recoverability prediction, and an effective method of the CBM recoverability evaluation is also provided.

  2. Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology

    Science.gov (United States)

    Toni, Tina; Tidor, Bruce

    2013-01-01

    Biological systems are inherently variable, with their dynamics influenced by intrinsic and extrinsic sources. These systems are often only partially characterized, with large uncertainties about specific sources of extrinsic variability and biochemical properties. Moreover, it is not yet well understood how different sources of variability combine and affect biological systems in concert. To successfully design biomedical therapies or synthetic circuits with robust performance, it is crucial to account for uncertainty and effects of variability. Here we introduce an efficient modeling and simulation framework to study systems that are simultaneously subject to multiple sources of variability, and apply it to make design decisions on small genetic networks that play a role of basic design elements of synthetic circuits. Specifically, the framework was used to explore the effect of transcriptional and post-transcriptional autoregulation on fluctuations in protein expression in simple genetic networks. We found that autoregulation could either suppress or increase the output variability, depending on specific noise sources and network parameters. We showed that transcriptional autoregulation was more successful than post-transcriptional in suppressing variability across a wide range of intrinsic and extrinsic magnitudes and sources. We derived the following design principles to guide the design of circuits that best suppress variability: (i) high protein cooperativity and low miRNA cooperativity, (ii) imperfect complementarity between miRNA and mRNA was preferred to perfect complementarity, and (iii) correlated expression of mRNA and miRNA – for example, on the same transcript – was best for suppression of protein variability. Results further showed that correlations in kinetic parameters between cells affected the ability to suppress variability, and that variability in transient states did not necessarily follow the same principles as variability in the steady

  3. A methodology to annotate systems biology markup language models with the synthetic biology open language.

    Science.gov (United States)

    Roehner, Nicholas; Myers, Chris J

    2014-02-21

    Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application to new projects, a problem exacerbated by a lack of engineering standards that combine descriptions of the structure and function of DNA. To address this need, this paper describes a methodology to connect the systems biology markup language (SBML) to the synthetic biology open language (SBOL), existing standards that describe biochemical models and DNA components, respectively. Our methodology involves first annotating SBML model elements such as species and reactions with SBOL DNA components. A graph is then constructed from the model, with vertices corresponding to elements within the model and edges corresponding to the cause-and-effect relationships between these elements. Lastly, the graph is traversed to assemble the annotating DNA components into a composite DNA component, which is used to annotate the model itself and can be referenced by other composite models and DNA components. In this way, our methodology can be used to build up a hierarchical library of models annotated with DNA components. Such a library is a useful input to any future genetic technology mapping algorithm that would automate the process of composing DNA components to satisfy a behavioral specification. Our methodology for SBML-to-SBOL annotation is implemented in the latest version of our genetic design automation (GDA) software tool, iBioSim.

  4. Modeling induced polarization effects in helicopter time domain electromagnetic data: Synthetic case studies

    DEFF Research Database (Denmark)

    Viezzoli, Andrea; Kaminskiy, Vladislav; Fiandaca, Gianluca

    2017-01-01

    constrained multiparametric inversion was evaluated, including recovery of chargeability distributions from shallow and deep targets based on analysis of induced polarization (IP) effects, simulated in airborne TDEM data. Different scenarios were studied, including chargeable targets associated...... processing and the effect of constraints, and a priori information. We have used a 1D layered earth model approximation and lateral constraints. Synthetic simulations were performed for several models and the corresponding Cole-Cole parameters. The possibility to recover these models by means of laterally...... the airborne electromagnetic is most sensitive (e.g., approximately 1 ms), it is possible to recover deep chargeable targets (to depths more than 130 m) in association with high electrical conductivity and in resistive environments. Furthermore, it was found that the recovery of a deep conductor, masked...

  5. Improved object optimal synthetic description, modeling, learning, and discrimination by GEOGINE computational kernel

    Science.gov (United States)

    Fiorini, Rodolfo A.; Dacquino, Gianfranco

    2005-03-01

    GEOGINE (GEOmetrical enGINE), a state-of-the-art OMG (Ontological Model Generator) based on n-D Tensor Invariants for n-Dimensional shape/texture optimal synthetic representation, description and learning, was presented in previous conferences elsewhere recently. Improved computational algorithms based on the computational invariant theory of finite groups in Euclidean space and a demo application is presented. Progressive model automatic generation is discussed. GEOGINE can be used as an efficient computational kernel for fast reliable application development and delivery in advanced biomedical engineering, biometric, intelligent computing, target recognition, content image retrieval, data mining technological areas mainly. Ontology can be regarded as a logical theory accounting for the intended meaning of a formal dictionary, i.e., its ontological commitment to a particular conceptualization of the world object. According to this approach, "n-D Tensor Calculus" can be considered a "Formal Language" to reliably compute optimized "n-Dimensional Tensor Invariants" as specific object "invariant parameter and attribute words" for automated n-Dimensional shape/texture optimal synthetic object description by incremental model generation. The class of those "invariant parameter and attribute words" can be thought as a specific "Formal Vocabulary" learned from a "Generalized Formal Dictionary" of the "Computational Tensor Invariants" language. Even object chromatic attributes can be effectively and reliably computed from object geometric parameters into robust colour shape invariant characteristics. As a matter of fact, any highly sophisticated application needing effective, robust object geometric/colour invariant attribute capture and parameterization features, for reliable automated object learning and discrimination can deeply benefit from GEOGINE progressive automated model generation computational kernel performance. Main operational advantages over previous

  6. A new Markov-chain-related statistical approach for modelling synthetic wind power time series

    International Nuclear Information System (INIS)

    Pesch, T; Hake, J F; Schröders, S; Allelein, H J

    2015-01-01

    The integration of rising shares of volatile wind power in the generation mix is a major challenge for the future energy system. To address the uncertainties involved in wind power generation, models analysing and simulating the stochastic nature of this energy source are becoming increasingly important. One statistical approach that has been frequently used in the literature is the Markov chain approach. Recently, the method was identified as being of limited use for generating wind time series with time steps shorter than 15–40 min as it is not capable of reproducing the autocorrelation characteristics accurately. This paper presents a new Markov-chain-related statistical approach that is capable of solving this problem by introducing a variable second lag. Furthermore, additional features are presented that allow for the further adjustment of the generated synthetic time series. The influences of the model parameter settings are examined by meaningful parameter variations. The suitability of the approach is demonstrated by an application analysis with the example of the wind feed-in in Germany. It shows that—in contrast to conventional Markov chain approaches—the generated synthetic time series do not systematically underestimate the required storage capacity to balance wind power fluctuation. (paper)

  7. A model for improving microbial biofuel production using a synthetic feedback loop

    Energy Technology Data Exchange (ETDEWEB)

    Dunlop, Mary; Keasling, Jay; Mukhopadhyay, Aindrila

    2011-07-14

    Cells use feedback to implement a diverse range of regulatory functions. Building synthetic feedback control systems may yield insight into the roles that feedback can play in regulation since it can be introduced independently of native regulation, and alternative control architectures can be compared. We propose a model for microbial biofuel production where a synthetic control system is used to increase cell viability and biofuel yields. Although microbes can be engineered to produce biofuels, the fuels are often toxic to cell growth, creating a negative feedback loop that limits biofuel production. These toxic effects may be mitigated by expressing efflux pumps that export biofuel from the cell. We developed a model for cell growth and biofuel production and used it to compare several genetic control strategies for their ability to improve biofuel yields. We show that controlling efflux pump expression directly with a biofuel-responsive promoter is a straight forward way of improving biofuel production. In addition, a feed forward loop controller is shown to be versatile at dealing with uncertainty in biofuel production rates.

  8. Effects of confinement on rock mass modulus: A synthetic rock mass modelling (SRM study

    Directory of Open Access Journals (Sweden)

    I. Vazaios

    2018-06-01

    Full Text Available The main objective of this paper is to examine the influence of the applied confining stress on the rock mass modulus of moderately jointed rocks (well interlocked undisturbed rock mass with blocks formed by three or less intersecting joints. A synthetic rock mass modelling (SRM approach is employed to determine the mechanical properties of the rock mass. In this approach, the intact body of rock is represented by the discrete element method (DEM-Voronoi grains with the ability of simulating the initiation and propagation of microcracks within the intact part of the model. The geometry of the pre-existing joints is generated by employing discrete fracture network (DFN modelling based on field joint data collected from the Brockville Tunnel using LiDAR scanning. The geometrical characteristics of the simulated joints at a representative sample size are first validated against the field data, and then used to measure the rock quality designation (RQD, joint spacing, areal fracture intensity (P21, and block volumes. These geometrical quantities are used to quantitatively determine a representative range of the geological strength index (GSI. The results show that estimating the GSI using the RQD tends to make a closer estimate of the degree of blockiness that leads to GSI values corresponding to those obtained from direct visual observations of the rock mass conditions in the field. The use of joint spacing and block volume in order to quantify the GSI value range for the studied rock mass suggests a lower range compared to that evaluated in situ. Based on numerical modelling results and laboratory data of rock testing reported in the literature, a semi-empirical equation is proposed that relates the rock mass modulus to confinement as a function of the areal fracture intensity and joint stiffness. Keywords: Synthetic rock mass modelling (SRM, Discrete fracture network (DFN, Rock mass modulus, Geological strength index (GSI, Confinement

  9. Calculation of the thermal neutron scattering kernel using the synthetic model. Pt. 2. Zero-order energy transfer kernel

    International Nuclear Information System (INIS)

    Drozdowicz, K.

    1995-01-01

    A comprehensive unified description of the application of Granada's Synthetic Model to the slow-neutron scattering by the molecular systems is continued. Detailed formulae for the zero-order energy transfer kernel are presented basing on the general formalism of the model. An explicit analytical formula for the total scattering cross section as a function of the incident neutron energy is also obtained. Expressions of the free gas model for the zero-order scattering kernel and for total scattering kernel are considered as a sub-case of the Synthetic Model. (author). 10 refs

  10. Nuclear Test Depth Determination with Synthetic Modelling: Global Analysis from PNEs to DPRK-2016

    Science.gov (United States)

    Rozhkov, Mikhail; Stachnik, Joshua; Baker, Ben; Epiphansky, Alexey; Bobrov, Dmitry

    2016-04-01

    Seismic event depth determination is critical for the event screening process at the International Data Center, CTBTO. A thorough determination of the event depth can be conducted mostly through additional special analysis because the IDC's Event Definition Criteria is based, in particular, on depth estimation uncertainties. This causes a large number of events in the Reviewed Event Bulletin to have depth constrained to the surface making the depth screening criterion not applicable. Further it may result in a heavier workload to manually distinguish between subsurface and deeper crustal events. Since the shape of the first few seconds of signal of very shallow events is very sensitive to the depth phases, cross correlation between observed and theoretic seismograms can provide a basis for the event depth estimation, and so an expansion to the screening process. We applied this approach mostly to events at teleseismic and partially regional distances. The approach was found efficient for the seismic event screening process, with certain caveats related mostly to poorly defined source and receiver crustal models which can shift the depth estimate. An adjustable teleseismic attenuation model (t*) for synthetics was used since this characteristic is not known for most of the rays we studied. We studied a wide set of historical records of nuclear explosions, including so called Peaceful Nuclear Explosions (PNE) with presumably known depths, and recent DPRK nuclear tests. The teleseismic synthetic approach is based on the stationary phase approximation with hudson96 program, and the regional modelling was done with the generalized ray technique by Vlastislav Cerveny modified to account for the complex source topography. The software prototype is designed to be used for the Expert Technical Analysis at the IDC. With this, the design effectively reuses the NDC-in-a-Box code and can be comfortably utilized by the NDC users. The package uses Geotool as a front-end for data

  11. Model prodrugs for the intestinal peptide transporter. a synthetic approach for coupling of hydroxy-containing compounds to dieptides

    DEFF Research Database (Denmark)

    Friedrichsen, G; Nielsen, Carsten Uhd; Steffansen, Bente

    2001-01-01

    The human peptide transporter, hPepT1, situated in the small intestine, may be exploited to increase absorption of drugs or model drugs by attaching them to a dipeptide, which is recognised by hPepT1. A synthetic protocol for this kind of model prodrugs was developed, in which model drugs...

  12. Use of VAP3D software for production and manipulation of synthetic radiographies of anthropomorphic models

    Energy Technology Data Exchange (ETDEWEB)

    Lima, Lindeval Fernandes de, E-mail: lindeval@dmat.ufrr.b [Universidade Federal de Roraima (DMAT/UFRR), Boa Vista, RR (Brazil). Dept. de Matematica; Centro Regional de Ciencias Nucleares (CRCN-NE/CNEN-PE), Recife, PE (Brazil); Vieira, Jose W. [Instituto Federal de Educacao, Ciencia e Tecnologia de Pernambuco (IFPE), Recife, PE (Brazil); Universidade de Pernambuco (EPP/UPE), Recife, PE (Brazil). Escola Politecnica de Pernambuco; Lima, Fernando R.A., E-mail: falima@cnen.gov.b [Centro Regional de Ciencias Nucleares (CRCN-NE/CNEN-PE), Recife, PE (Brazil); Leal Neto, Viriato [Universidade Federal de Pernambuco (DEN/UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear

    2011-07-01

    The Grupo de Dosimetria Numerica has developed exposure computational models (ECM) involving a Monte Carlo code and voxel phantoms to simulate various situations of internal and external exposure to ionizing radiation. Most analyses of the produced results are presented in tables and graphics formats. An alternative to this traditional way of analyzing results is to save voxels of Regions of Interest (ROI) of the phantom irradiated with information like the location of the voxel and the energy deposited in it during the simulation. Such information can be saved to a text file and later turned into 3D objects. In this paper the VAP3D software has been used to read text files produced in simulations using the ECM of DEN (Nuclear Energy Dept. - UFPE), converting them into binary files of the type RAW, and visualize them. In order to reflect the radiosensitivity of the organs and tissues suggested by ICRP-60, for conversion of text file to binary, of the energy deposited values are multiplied by the weighting factor of the tissue to which the voxel belongs. The result of the multiplication is normalized to the interval [0, 255]. The files transformed are referred herein as synthetic radiographies. In VAP3D software, it is possible to generate stacks from theses radiographies in transverse, sagittal and coronal directions. In order to illustrate the production of synthetic radiographies, some images are presented in this paper, and dosimetric results are obtained from a variety of ROIs of the phantoms of DEN for radiological exams. (author)

  13. Vaping Synthetic Cannabinoids: A Novel Preclinical Model of E-Cigarette Use in Mice

    Directory of Open Access Journals (Sweden)

    Timothy W Lefever

    2017-03-01

    Full Text Available Smoking is the most common route of administration for cannabis; however, vaping cannabis extracts and synthetic cannabinoids (“fake marijuana” in electronic cigarette devices has become increasingly popular. Yet, most animal models used to investigate biological mechanisms underlying cannabis use employ injection as the route of administration. This study evaluated a novel e-cigarette device that delivers aerosolized cannabinoids to mice. The effects of aerosolized and injected synthetic cannabinoids (CP 55,940, AB-CHMINACA, XLR-11, and JWH-018 in mice were compared in a battery of bioassays in which psychoactive cannabinoids produce characteristic effects. The most potent cannabinoids (CP 55,940 and AB-CHMINACA produced the full cannabinoid profile (ie, hypothermia, hypolocomotion, and analgesia, regardless of the route of administration. In contrast, aerosolized JWH-018 and XLR-11 did not produce the full profile of cannabimimetic effects. Results of time course analysis for hypothermia showed that aerosol exposure to CP 55,940 and AB-CHMINACA produced faster onset of effects and shorter duration of action than injection. The ability to administer cannabinoids to rodents using the most common route of administration among humans provides a method for collecting preclinical data with enhanced translational relevance.

  14. Analysing the Effects of Flood-Resilience Technologies in Urban Areas Using a Synthetic Model Approach

    Directory of Open Access Journals (Sweden)

    Reinhard Schinke

    2016-11-01

    Full Text Available Flood protection systems with their spatial effects play an important role in managing and reducing flood risks. The planning and decision process as well as the technical implementation are well organized and often exercised. However, building-related flood-resilience technologies (FReT are often neglected due to the absence of suitable approaches to analyse and to integrate such measures in large-scale flood damage mitigation concepts. Against this backdrop, a synthetic model-approach was extended by few complementary methodical steps in order to calculate flood damage to buildings considering the effects of building-related FReT and to analyse the area-related reduction of flood risks by geo-information systems (GIS with high spatial resolution. It includes a civil engineering based investigation of characteristic properties with its building construction including a selection and combination of appropriate FReT as a basis for derivation of synthetic depth-damage functions. Depending on the real exposition and the implementation level of FReT, the functions can be used and allocated in spatial damage and risk analyses. The application of the extended approach is shown at a case study in Valencia (Spain. In this way, the overall research findings improve the integration of FReT in flood risk management. They provide also some useful information for advising of individuals at risk supporting the selection and implementation of FReT.

  15. Vaping Synthetic Cannabinoids: A Novel Preclinical Model of E-Cigarette Use in Mice.

    Science.gov (United States)

    Lefever, Timothy W; Marusich, Julie A; Thomas, Brian F; Barrus, Daniel G; Peiper, Nicholas C; Kevin, Richard C; Wiley, Jenny L

    2017-01-01

    Smoking is the most common route of administration for cannabis; however, vaping cannabis extracts and synthetic cannabinoids ("fake marijuana") in electronic cigarette devices has become increasingly popular. Yet, most animal models used to investigate biological mechanisms underlying cannabis use employ injection as the route of administration. This study evaluated a novel e-cigarette device that delivers aerosolized cannabinoids to mice. The effects of aerosolized and injected synthetic cannabinoids (CP 55,940, AB-CHMINACA, XLR-11, and JWH-018) in mice were compared in a battery of bioassays in which psychoactive cannabinoids produce characteristic effects. The most potent cannabinoids (CP 55,940 and AB-CHMINACA) produced the full cannabinoid profile (ie, hypothermia, hypolocomotion, and analgesia), regardless of the route of administration. In contrast, aerosolized JWH-018 and XLR-11 did not produce the full profile of cannabimimetic effects. Results of time course analysis for hypothermia showed that aerosol exposure to CP 55,940 and AB-CHMINACA produced faster onset of effects and shorter duration of action than injection. The ability to administer cannabinoids to rodents using the most common route of administration among humans provides a method for collecting preclinical data with enhanced translational relevance.

  16. A new synthetic granular calcium phosphate compound induces new bone in a sinus lift rabbit model.

    Science.gov (United States)

    Trbakovic, Amela; Hedenqvist, Patricia; Mellgren, Torbjörn; Ley, Cecilia; Hilborn, Jöns; Ossipov, Dmitri; Ekman, Stina; Johansson, Carina B; Jensen-Waern, Marianne; Thor, Andreas

    2018-03-01

    The aim of this study was to investigate if a synthetic granular calcium phosphate compound (CPC) and a composite bisphosphonate-linked hyaluronic acid-calcium phosphate hydrogel (HABP·CaP) induced similar or more amount of bone as bovine mineral in a modified sinus lift rabbit model. Eighteen adult male New Zeeland White rabbits, received randomly one of the two test materials on a random side of the face, and bovine mineral as control on the contralateral side. In a sinus lift, the sinus mucosa was elevated and a titanium mini-implant was placed in the alveolar bone. Augmentation material (CPC, HABP·CaP or bovine bone) was applied in the space around the implant. The rabbits were euthanized three months after surgery and qualitative and histomorphometric evaluation were conducted. Histomorphometric evaluation included three different regions of interest (ROIs) and the bone to implant contact on each installed implant. Qualitative assessment (p = <.05), histomorphometric evaluations (p = < .01), and implant incorporation (p = <.05) showed that CPC and bovine mineral induced similar amount of bone and more than the HABP·CaP hydrogel. CPC induced similar amount of bone as bovine mineral and both materials induced more bone than HABP·CaP hydrogel. The CPC is suggested as a synthetic alternative for augmentations in the maxillofacial area. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Meta-stochastic simulation of biochemical models for systems and synthetic biology.

    Science.gov (United States)

    Sanassy, Daven; Widera, Paweł; Krasnogor, Natalio

    2015-01-16

    Stochastic simulation algorithms (SSAs) are used to trace realistic trajectories of biochemical systems at low species concentrations. As the complexity of modeled biosystems increases, it is important to select the best performing SSA. Numerous improvements to SSAs have been introduced but they each only tend to apply to a certain class of models. This makes it difficult for a systems or synthetic biologist to decide which algorithm to employ when confronted with a new model that requires simulation. In this paper, we demonstrate that it is possible to determine which algorithm is best suited to simulate a particular model and that this can be predicted a priori to algorithm execution. We present a Web based tool ssapredict that allows scientists to upload a biochemical model and obtain a prediction of the best performing SSA. Furthermore, ssapredict gives the user the option to download our high performance simulator ngss preconfigured to perform the simulation of the queried biochemical model with the predicted fastest algorithm as the simulation engine. The ssapredict Web application is available at http://ssapredict.ico2s.org. It is free software and its source code is distributed under the terms of the GNU Affero General Public License.

  18. BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

    Directory of Open Access Journals (Sweden)

    Thomas E Gorochowski

    Full Text Available Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.

  19. Information Theory Analysis of Cascading Process in a Synthetic Model of Fluid Turbulence

    Directory of Open Access Journals (Sweden)

    Massimo Materassi

    2014-02-01

    Full Text Available The use of transfer entropy has proven to be helpful in detecting which is the verse of dynamical driving in the interaction of two processes, X and Y . In this paper, we present a different normalization for the transfer entropy, which is capable of better detecting the information transfer direction. This new normalized transfer entropy is applied to the detection of the verse of energy flux transfer in a synthetic model of fluid turbulence, namely the Gledzer–Ohkitana–Yamada shell model. Indeed, this is a fully well-known model able to model the fully developed turbulence in the Fourier space, which is characterized by an energy cascade towards the small scales (large wavenumbers k, so that the application of the information-theory analysis to its outcome tests the reliability of the analysis tool rather than exploring the model physics. As a result, the presence of a direct cascade along the scales in the shell model and the locality of the interactions in the space of wavenumbers come out as expected, indicating the validity of this data analysis tool. In this context, the use of a normalized version of transfer entropy, able to account for the difference of the intrinsic randomness of the interacting processes, appears to perform better, being able to discriminate the wrong conclusions to which the “traditional” transfer entropy would drive.

  20. Synthetic Modeling of A Geothermal System Using Audio-magnetotelluric (AMT) and Magnetotelluric (MT)

    Science.gov (United States)

    Mega Saputra, Rifki; Widodo

    2017-04-01

    Indonesia has 40% of the world’s potential geothermal resources with estimated capacity of 28,910 MW. Generally, the characteristic of the geothermal system in Indonesia is liquid-dominated systems, which driven by volcanic activities. In geothermal exploration, electromagnetic methods are used to map structures that could host potential reservoirs and source rocks. We want to know the responses of a geothermal system using synthetic data of Audio-magnetotelluric (AMT) and Magnetotelluric (MT). Due to frequency range, AMT and MT data can resolve the shallow and deeper structure, respectively. 1-D models have been performed using AMT and MT data. The results indicate that AMT and MT data give detailed conductivity distribution of geothermal structure.

  1. Genetic interaction motif finding by expectation maximization – a novel statistical model for inferring gene modules from synthetic lethality

    Directory of Open Access Journals (Sweden)

    Ye Ping

    2005-12-01

    Full Text Available Abstract Background Synthetic lethality experiments identify pairs of genes with complementary function. More direct functional associations (for example greater probability of membership in a single protein complex may be inferred between genes that share synthetic lethal interaction partners than genes that are directly synthetic lethal. Probabilistic algorithms that identify gene modules based on motif discovery are highly appropriate for the analysis of synthetic lethal genetic interaction data and have great potential in integrative analysis of heterogeneous datasets. Results We have developed Genetic Interaction Motif Finding (GIMF, an algorithm for unsupervised motif discovery from synthetic lethal interaction data. Interaction motifs are characterized by position weight matrices and optimized through expectation maximization. Given a seed gene, GIMF performs a nonlinear transform on the input genetic interaction data and automatically assigns genes to the motif or non-motif category. We demonstrate the capacity to extract known and novel pathways for Saccharomyces cerevisiae (budding yeast. Annotations suggested for several uncharacterized genes are supported by recent experimental evidence. GIMF is efficient in computation, requires no training and automatically down-weights promiscuous genes with high degrees. Conclusion GIMF effectively identifies pathways from synthetic lethality data with several unique features. It is mostly suitable for building gene modules around seed genes. Optimal choice of one single model parameter allows construction of gene networks with different levels of confidence. The impact of hub genes the generic probabilistic framework of GIMF may be used to group other types of biological entities such as proteins based on stochastic motifs. Analysis of the strongest motifs discovered by the algorithm indicates that synthetic lethal interactions are depleted between genes within a motif, suggesting that synthetic

  2. Thermochemical Equilibrium Model of Synthetic Natural Gas Production from Coal Gasification Using Aspen Plus

    Directory of Open Access Journals (Sweden)

    Rolando Barrera

    2014-01-01

    Full Text Available The production of synthetic or substitute natural gas (SNG from coal is a process of interest in Colombia where the reserves-to-production ratio (R/P for natural gas is expected to be between 7 and 10 years, while the R/P for coal is forecasted to be around 90 years. In this work, the process to produce SNG by means of coal-entrained flow gasifiers is modeled under thermochemical equilibrium with the Gibbs free energy approach. The model was developed using a complete and comprehensive Aspen Plus model. Two typical technologies used in entrained flow gasifiers such as coal dry and coal slurry are modeled and simulated. Emphasis is put on interactions between the fuel feeding technology and selected energy output parameters of coal-SNG process, that is, energy efficiencies, power, and SNG quality. It was found that coal rank does not significantly affect energy indicators such as cold gas, process, and global efficiencies. However, feeding technology clearly has an effect on the process due to the gasifying agent. Simulations results are compared against available technical data with good accuracy. Thus, the proposed model is considered as a versatile and useful computational tool to study and optimize the coal to SNG process.

  3. Hydrologic modeling of Guinale River Basin using HEC-HMS and synthetic aperture radar

    Science.gov (United States)

    Bien, Ferdinand E.; Plopenio, Joanaviva C.

    2017-09-01

    This paper presents the methods and results of hydrologic modeling of Guinale river basin through the use of HEC-HMS software and Synthetic Aperture Radar Digital Elevation Model (SAR DEM). Guinale River Basin is located in the province of Albay, Philippines which is one of the river basins covered by the Ateneo de Naga University (ADNU) Phil-LiDAR 1. This research project was funded by the Department of Science and Technology (DOST) through the Philippine Council for Industry, Energy and Emerging Technology Research and Development (PCIEERD). Its objectives are to simulate the hydrologic model of Guinale River basin using HEC-HMS software and SAR DEM. Its basin covers an area of 165.395 sq.km. and the hydrologic model was calibrated using the storm event typhoon Nona (international name Melor). Its parameter had undergone a series of optimization processes of HEC-HMS software in order to produce an acceptable level of model efficiency. The Nash-Sutcliffe (E), Percent Bias and Standard Deviation Ratio were used to measure the model efficiency, giving values of 0.880, 0.260 and 0.346 respectively which resulted to a "very good" performance rating of the model. The flood inundation model was simulated using Legazpi Rainfall Intensity Duration Frequency Curves (RIDF) and HEC-RAS software developed by the US Army corps of Engineers (USACE). This hydrologic model will provide the Municipal Disaster Risk Reduction Management Office (MDRRMO), Local Government units (LGUs) and the community a tool for the prediction of runoff in the area.

  4. Removal of a synthetic organic chemical by PAC-UF systems. II: Model application.

    Science.gov (United States)

    Matsui, Y; Colas, F; Yuasa, A

    2001-02-01

    This paper describes several application potentials with a recently developed model for predicting the synthetic organic chemical (SOC) removal by powdered activated carbon (PAC) adsorption during ultrafiltration (UF) and discusses the removal mechanism. The model was successfully applied, without any modification, to dead-end mode operation as well as to cross-flow mode operation, validating the assumption of the internal diffusion control mechanism and the continuously-stirred-tank-reactor (CSTR) concept. Even when UF was operated in a cross-flow mode, PAC added was re-circulating in suspension for only a short time. Then, solute uptake took place mostly by PAC immobilized in membrane tubes not only for dead-end operation but also for cross-flow operation. Therefore, cross-flow operation did not have any advantage regarding the SOC mass transfer on PAC in UF loop over dead-end operation. The model simulation implied that pulse PAC addition at the beginning of filtration cycle resulted better SOC removal than continuous PAC addition. However, for the pulse PAC addition mode, the model predicted somewhat lower effluent SOC concentration than the observed values, and the benefit of pulse PAC application in terms of reducing SOC over its continuous dosage was not confirmed. Longer detention time of PAC dosed in a pulse than continuously dosed PAC could possibly further decrease internal diffusivity.

  5. Synthetic Earthquake Statistics From Physical Fault Models for the Lower Rhine Embayment

    Science.gov (United States)

    Brietzke, G. B.; Hainzl, S.; Zöller, G.

    2012-04-01

    As of today, seismic risk and hazard estimates mostly use pure empirical, stochastic models of earthquake fault systems tuned specifically to the vulnerable areas of interest. Although such models allow for reasonable risk estimates they fail to provide a link between the observed seismicity and the underlying physical processes. Solving a state-of-the-art fully dynamic description set of all relevant physical processes related to earthquake fault systems is likely not useful since it comes with a large number of degrees of freedom, poor constraints on its model parameters and a huge computational effort. Here, quasi-static and quasi-dynamic physical fault simulators provide a compromise between physical completeness and computational affordability and aim at providing a link between basic physical concepts and statistics of seismicity. Within the framework of quasi-static and quasi-dynamic earthquake simulators we investigate a model of the Lower Rhine Embayment (LRE) that is based upon seismological and geological data. We present and discuss statistics of the spatio-temporal behavior of generated synthetic earthquake catalogs with respect to simplification (e.g. simple two-fault cases) as well as to complication (e.g. hidden faults, geometric complexity, heterogeneities of constitutive parameters).

  6. Regional-scale geostatistical inverse modeling of North American CO2 fluxes: a synthetic data study

    Directory of Open Access Journals (Sweden)

    A. M. Michalak

    2010-07-01

    Full Text Available A series of synthetic data experiments is performed to investigate the ability of a regional atmospheric inversion to estimate grid-scale CO2 fluxes during the growing season over North America. The inversions are performed within a geostatistical framework without the use of any prior flux estimates or auxiliary variables, in order to focus on the atmospheric constraint provided by the nine towers collecting continuous, calibrated CO2 measurements in 2004. Using synthetic measurements and their associated concentration footprints, flux and model-data mismatch covariance parameters are first optimized, and then fluxes and their uncertainties are estimated at three different temporal resolutions. These temporal resolutions, which include a four-day average, a four-day-average diurnal cycle with 3-hourly increments, and 3-hourly fluxes, are chosen to help assess the impact of temporal aggregation errors on the estimated fluxes and covariance parameters. Estimating fluxes at a temporal resolution that can adjust the diurnal variability is found to be critical both for recovering covariance parameters directly from the atmospheric data, and for inferring accurate ecoregion-scale fluxes. Accounting for both spatial and temporal a priori covariance in the flux distribution is also found to be necessary for recovering accurate a posteriori uncertainty bounds on the estimated fluxes. Overall, the results suggest that even a fairly sparse network of 9 towers collecting continuous CO2 measurements across the continent, used with no auxiliary information or prior estimates of the flux distribution in time or space, can be used to infer relatively accurate monthly ecoregion scale CO2 surface fluxes over North America within estimated uncertainty bounds. Simulated random transport error is shown to decrease the quality of flux estimates in under-constrained areas at the ecoregion scale, although the uncertainty bounds remain realistic. While these synthetic

  7. Multi-sensor Cloud Retrieval Simulator and Remote Sensing from Model Parameters . Pt. 1; Synthetic Sensor Radiance Formulation; [Synthetic Sensor Radiance Formulation

    Science.gov (United States)

    Wind, G.; DaSilva, A. M.; Norris, P. M.; Platnick, S.

    2013-01-01

    In this paper we describe a general procedure for calculating synthetic sensor radiances from variable output from a global atmospheric forecast model. In order to take proper account of the discrepancies between model resolution and sensor footprint, the algorithm takes explicit account of the model subgrid variability, in particular its description of the probability density function of total water (vapor and cloud condensate.) The simulated sensor radiances are then substituted into an operational remote sensing algorithm processing chain to produce a variety of remote sensing products that would normally be produced from actual sensor output. This output can then be used for a wide variety of purposes such as model parameter verification, remote sensing algorithm validation, testing of new retrieval methods and future sensor studies.We show a specific implementation using the GEOS-5 model, the MODIS instrument and the MODIS Adaptive Processing System (MODAPS) Data Collection 5.1 operational remote sensing cloud algorithm processing chain (including the cloud mask, cloud top properties and cloud optical and microphysical properties products). We focus on clouds because they are very important to model development and improvement.

  8. Natural and Synthetic Biohydrogels Design, Characterization, Network Structure Imaging and Modeling

    Science.gov (United States)

    Marmorat, Clement

    Biocompatible hydrogels can be derived from materials that are naturally obtained, such as proteins or polysaccharides, or synthetic, such as poloxamers. In order to be classified as biocompatible, these water-swollen networks can not trigger a toxic response once introduced into a biological or physiological environment and, therefore, must be immunoneutral. Hyaluronic acid hydrogels can be great candidates for tissue engineering applications as long as the cross-linking chemistry and process does not affect the biocompatibility of the natural protein matrix. Thermoreversible hydrogels have the advantage of undergoing a sol/gel phase transition at specific temperatures. Thus, they are excellent candidates for biomedical applications such as drug delivery systems, wound healing coatings or cellular scaffolds. Although these hydrogels can be used in their natural form without further modification or chemical alteration, the original protein or polymer matrix is often strengthened by the use of a crosslinking agent to achieve a specific set of properties. In the case of gelatin fibril formation at low temperatures or the micellization of triblock copolymers in solution with temperature increase, the natural phase transition is modified when crosslinkers are introduced to alter the biohydrogels properties and, ultimately, disturb the system's equilibrium. By using spectroscopy techniques, rheology and cryo-imaging we investigated several biocompatible polymeric networks in their natural form as well as their engineered structures to better understand the mechanisms of gelation and artificial internal re-organization of the networks. Natural and synthetic biohydrogels were designed and their mechanical properties were characterized before imaging. Models that better describe the relationship between network configuration and resulting mechanical properties showed great agreement with experimental mesh size observations. Finally, a novel set of hybrid gels was developed

  9. A Synthetic Ecology Perspective: How Well Does Behavior of Model Organisms in the Laboratory Predict Microbial Activities in Natural Habitats?

    Science.gov (United States)

    Yu, Zheng; Krause, Sascha M B; Beck, David A C; Chistoserdova, Ludmila

    2016-01-01

    In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sediment for a few decades and have identified a number of species genetically equipped for this activity. We have also identified co-occurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. These findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.

  10. An Optimal DEM Reconstruction Method for Linear Array Synthetic Aperture Radar Based on Variational Model

    Directory of Open Access Journals (Sweden)

    Shi Jun

    2015-02-01

    Full Text Available Downward-looking Linear Array Synthetic Aperture Radar (LASAR has many potential applications in the topographic mapping, disaster monitoring and reconnaissance applications, especially in the mountainous area. However, limited by the sizes of platforms, its resolution in the linear array direction is always far lower than those in the range and azimuth directions. This disadvantage leads to the blurring of Three-Dimensional (3D images in the linear array direction, and restricts the application of LASAR. To date, the research on 3D SAR image enhancement has focused on the sparse recovery technique. In this case, the one-to-one mapping of Digital Elevation Model (DEM brakes down. To overcome this, an optimal DEM reconstruction method for LASAR based on the variational model is discussed in an effort to optimize the DEM and the associated scattering coefficient map, and to minimize the Mean Square Error (MSE. Using simulation experiments, it is found that the variational model is more suitable for DEM enhancement applications to all kinds of terrains compared with the Orthogonal Matching Pursuit (OMPand Least Absolute Shrinkage and Selection Operator (LASSO methods.

  11. The synthetic parasite-derived peptide GK1 increases survival in a preclinical mouse melanoma model.

    Science.gov (United States)

    Pérez-Torres, Armando; Vera-Aguilera, Jesús; Hernaiz-Leonardo, Juan Carlos; Moreno-Aguilera, Eduardo; Monteverde-Suarez, Diego; Vera-Aguilera, Carlos; Estrada-Bárcenas, Daniel

    2013-11-01

    The therapeutic efficacy of a synthetic parasite-derived peptide GK1, an immune response booster, was evaluated in a mouse melanoma model. This melanoma model correlates with human stage IIb melanoma, which is treated with wide surgical excision; a parallel study employing a surgical treatment was carried out as an instructive goal. C57BL/6 mice were injected subcutaneously in the flank with 2×10(5) B16-F10 murine melanoma cells. When the tumors reached 20 mm3, mice were separated into two different groups; the GK1 group, treated weekly with peritumoral injections of GK1 (10 μg/100 μL of sterile saline solution) and the control group, treated weekly with an antiseptic peritumoral injection of 100 μL of sterile saline solution without further intervention. All mice were monitored daily for clinical appearance, tumor size, and survival. Surgical treatment was performed in parallel when the tumor size was 20 mm3 (group A), 500 mm3 (group B), and >500 mm3 (group C). The GK1 peptide effectively increased the mean survival time by 9.05 days, corresponding to an increase of 42.58%, and significantly delayed tumor growth from day 3 to 12 of treatment. In addition, tumor necrosis was significantly increased (pcancers remains to be determined, and surgical removal remains a challenge for any new experimental treatment of melanoma in mouse models.

  12. On Signal Modeling of Moon-Based Synthetic Aperture Radar (SAR Imaging of Earth

    Directory of Open Access Journals (Sweden)

    Zhen Xu

    2018-03-01

    Full Text Available The Moon-based Synthetic Aperture Radar (Moon-Based SAR, using the Moon as a platform, has a great potential to offer global-scale coverage of the earth’s surface with a high revisit cycle and is able to meet the scientific requirements for climate change study. However, operating in the lunar orbit, Moon-Based SAR imaging is confined within a complex geometry of the Moon-Based SAR, Moon, and Earth, where both rotation and revolution have effects. The extremely long exposure time of Moon-Based SAR presents a curved moving trajectory and the protracted time-delay in propagation makes the “stop-and-go” assumption no longer valid. Consequently, the conventional SAR imaging technique is no longer valid for Moon-Based SAR. This paper develops a Moon-Based SAR theory in which a signal model is derived. The Doppler parameters in the context of lunar revolution with the removal of ‘stop-and-go’ assumption are first estimated, and then characteristics of Moon-Based SAR imaging’s azimuthal resolution are analyzed. In addition, a signal model of Moon-Based SAR and its two-dimensional (2-D spectrum are further derived. Numerical simulation using point targets validates the signal model and enables Doppler parameter estimation for image focusing.

  13. An Appraisal Model Based on a Synthetic Feature Selection Approach for Students’ Academic Achievement

    Directory of Open Access Journals (Sweden)

    Ching-Hsue Cheng

    2017-11-01

    Full Text Available Obtaining necessary information (and even extracting hidden messages from existing big data, and then transforming them into knowledge, is an important skill. Data mining technology has received increased attention in various fields in recent years because it can be used to find historical patterns and employ machine learning to aid in decision-making. When we find unexpected rules or patterns from the data, they are likely to be of high value. This paper proposes a synthetic feature selection approach (SFSA, which is combined with a support vector machine (SVM to extract patterns and find the key features that influence students’ academic achievement. For verifying the proposed model, two databases, namely, “Student Profile” and “Tutorship Record”, were collected from an elementary school in Taiwan, and were concatenated into an integrated dataset based on students’ names as a research dataset. The results indicate the following: (1 the accuracy of the proposed feature selection approach is better than that of the Minimum-Redundancy-Maximum-Relevance (mRMR approach; (2 the proposed model is better than the listing methods when the six least influential features have been deleted; and (3 the proposed model can enhance the accuracy and facilitate the interpretation of the pattern from a hybrid-type dataset of students’ academic achievement.

  14. Synthetic spectral analysis of a kinetic model for slow-magnetosonic waves in solar corona

    Energy Technology Data Exchange (ETDEWEB)

    Ruan, Wenzhi; He, Jiansen; Tu, Chuanyi; Wang, Linghua [School of Earth and Space Sciences, Peking University, Beijing, 100871, China, E-mail: jshept@gmail.com (China); Zhang, Lei [State Key Laboratory of Space Weather, Chinese Academy of Sciences, Beijing 100190 (China); Vocks, Christian [Leibniz-Institut für Astrophysik Potsdam, 14482, Potsdam (Germany); Marsch, Eckart [Institute for Experimental and Applied Physics, Christian-Albrechts-Universität zu Kiel, 24118 Kiel (Germany); Peter, Hardi [Max Plank Institut für Sonnensystemforschung, Justus-von-Liebig-Weg 3, 37077 Göttingen (Germany)

    2016-03-25

    We propose a kinetic model of slow-magnetosonic waves to explain various observational features associated with the propagating intensity disturbances (PIDs) occurring in the solar corona. The characteristics of slow mode waves, e.g, inphase oscillations of density, velocity, and thermal speed, are reproduced in this kinetic model. Moreover, the red-blue (R-B) asymmetry of the velocity distribution as self-consistently generated in the model is found to be contributed from the beam component, as a result of the competition between Landau resonance and Coulomb collisions. Furthermore, we synthesize the spectral lines and make the spectral analysis, based on the kinetic simulation data of the flux tube plasmas and the hypothesis of the surrounding background plasmas. It is found that the fluctuations of parameters of the synthetic spectral lines are basically consistent with the observations: (1) the line intensity, Doppler shift, and line width are fluctuating in phase; (2) the R-B asymmetry usually oscillate out of phase with the former three parameters; (3) the blueward asymmetry is more evident than the redward asymmetry in the R-B fluctuations. The oscillations of line parameters become weakened for the case with denser surrounding background plasmas. Similar to the observations, there is no doubled-frequency oscillation of the line width for the case with flux-tube plasmas flowing bulkly upward among the static background plasmas. Therefore, we suggest that the “wave + beam flow” kinetic model may be a viable interpretation for the PIDs observed in the solar corona.

  15. Synthetic biology, inspired by synthetic chemistry.

    Science.gov (United States)

    Malinova, V; Nallani, M; Meier, W P; Sinner, E K

    2012-07-16

    The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  16. Synthetic biology between challenges and risks: suggestions for a model of governance and a regulatory framework, based on fundamental rights.

    Science.gov (United States)

    Colussi, Ilaria Anna

    2013-01-01

    This paper deals with the emerging synthetic biology, its challenges and risks, and tries to design a model for the governance and regulation of the field. The model is called of "prudent vigilance" (inspired by the report about synthetic biology, drafted by the U.S. Presidential Commission on Bioethics, 2010), and it entails (a) an ongoing and periodically revised process of assessment and management of all the risks and concerns, and (b) the adoption of policies - taken through "hard law" and "soft law" sources - that are based on the principle of proportionality (among benefits and risks), on a reasonable balancing between different interests and rights at stake, and are oriented by a constitutional frame, which is represented by the protection of fundamental human rights emerging in the field of synthetic biology (right to life, right to health, dignity, freedom of scientific research, right to environment). After the theoretical explanation of the model, its operability is "checked", by considering its application with reference to only one specific risk brought up by synthetic biology - biosecurity risk, i.e. the risk of bioterrorism.

  17. Induction of hypospadias in a murine model by maternal exposure to synthetic estrogens

    International Nuclear Information System (INIS)

    Suk Kim, Kun; Torres, Carlos R.; Yucel, Selcuk; Raimondo, Kamakshi; Cunha, G.R.Gerald R.; Baskin, L.S.

    2004-01-01

    We tested the hypothesis that maternal exposure to synthetic estrogen can cause hypospadias in male offspring and defined the morphological changes in the disrupted urethral seam. Timed pregnant C57/6 mice were exposed to synthetic estrogens. The genital tubercles were examined for the presence of hypospadias using histology, three-dimensional computer reconstruction, and plastic cast injection molds of the urethra. Microscopic serial analysis confirmed the presence of hypospadias, which occurred in ∼50% of the synthetic-estrogen-treated male fetuses. No effect was seen in the female embryos. Plastic cast injection showed that affected males had a shorter total urethral length and loss of male anatomic features such as the prostatic utricle. Exposure to synthetic estrogens during pregnancy affects the normal development of the urethra in the mouse. We conclude that endocrine disrupters play an important role in genital tubercle anomalies

  18. Digital elevation model generation from satellite interferometric synthetic aperture radar: Chapter 5

    Science.gov (United States)

    Lu, Zhong; Dzurisin, Daniel; Jung, Hyung-Sup; Zhang, Lei; Lee, Wonjin; Lee, Chang-Wook

    2012-01-01

    An accurate digital elevation model (DEM) is a critical data set for characterizing the natural landscape, monitoring natural hazards, and georeferencing satellite imagery. The ideal interferometric synthetic aperture radar (InSAR) configuration for DEM production is a single-pass two-antenna system. Repeat-pass single-antenna satellite InSAR imagery, however, also can be used to produce useful DEMs. DEM generation from InSAR is advantageous in remote areas where the photogrammetric approach to DEM generation is hindered by inclement weather conditions. There are many sources of errors in DEM generation from repeat-pass InSAR imagery, for example, inaccurate determination of the InSAR baseline, atmospheric delay anomalies, and possible surface deformation because of tectonic, volcanic, or other sources during the time interval spanned by the images. This chapter presents practical solutions to identify and remove various artifacts in repeat-pass satellite InSAR images to generate a high-quality DEM.

  19. Toxicogenomic responses in rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to model chemicals and a synthetic mixture

    International Nuclear Information System (INIS)

    Finne, E.F.; Cooper, G.A.; Koop, B.F.; Hylland, K.; Tollefsen, K.E.

    2007-01-01

    As more salmon gene expression data has become available, the cDNA microarray platform has emerged as an appealing alternative in ecotoxicological screening of single chemicals and environmental samples relevant to the aquatic environment. This study was performed to validate biomarker gene responses of in vitro cultured rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to model chemicals, and to investigate effects of mixture toxicity in a synthetic mixture. Chemicals used for 24 h single chemical- and mixture exposures were 10 nM 17α-ethinylestradiol (EE2), 0.75 nM 2,3,7,8-tetrachloro-di-benzodioxin (TCDD), 100 μM paraquat (PQ) and 0.75 μM 4-nitroquinoline-1-oxide (NQO). RNA was isolated from exposed cells, DNAse treated and quality controlled before cDNA synthesis, fluorescent labelling and hybridisation to a 16k salmonid microarray. The salmonid 16k cDNA array identified differential gene expression predictive of exposure, which could be verified by quantitative real time PCR. More precisely, the responses of biomarker genes such as cytochrome p4501A and UDP-glucuronosyl transferase to TCDD exposure, glutathione reductase and gammaglutamyl cysteine synthetase to paraquat exposure, as well as vitellogenin and vitelline envelope protein to EE2 exposure validated the use of microarray applied to RNA extracted from in vitro exposed hepatocytes. The mutagenic compound NQO did not result in any change in gene expression. Results from exposure to a synthetic mixture of the same four chemicals, using identical concentrations as for single chemical exposures, revealed combined effects that were not predicted by results for individual chemicals alone. In general, the response of exposure to this mixture led to an average loss of approximately 60% of the transcriptomic signature found for single chemical exposure. The present findings show that microarray analyses may contribute to our mechanistic understanding of single contaminant mode of action as well as

  20. Toxicogenomic responses in rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to model chemicals and a synthetic mixture

    Energy Technology Data Exchange (ETDEWEB)

    Finne, E.F. [Norwegian Institute for Water Research, Gaustadalleen 21, N-0349 Oslo (Norway) and University of Oslo, Department of Biology, P.O. Box 1066, Blindern, N-0316 Oslo (Norway)]. E-mail: eivind.finne@niva.no; Cooper, G.A. [Centre for Biomedical Research, University of Victoria, BC V8P5C2 (Canada); Koop, B.F. [Centre for Biomedical Research, University of Victoria, BC V8P5C2 (Canada); Hylland, K. [Norwegian Institute for Water Research, Gaustadalleen 21, N-0349 Oslo (Norway); University of Oslo, Department of Biology, P.O. Box 1066, Blindern, N-0316 Oslo (Norway); Tollefsen, K.E. [Norwegian Institute for Water Research, Gaustadalleen 21, N-0349 Oslo (Norway)

    2007-03-10

    As more salmon gene expression data has become available, the cDNA microarray platform has emerged as an appealing alternative in ecotoxicological screening of single chemicals and environmental samples relevant to the aquatic environment. This study was performed to validate biomarker gene responses of in vitro cultured rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to model chemicals, and to investigate effects of mixture toxicity in a synthetic mixture. Chemicals used for 24 h single chemical- and mixture exposures were 10 nM 17{alpha}-ethinylestradiol (EE2), 0.75 nM 2,3,7,8-tetrachloro-di-benzodioxin (TCDD), 100 {mu}M paraquat (PQ) and 0.75 {mu}M 4-nitroquinoline-1-oxide (NQO). RNA was isolated from exposed cells, DNAse treated and quality controlled before cDNA synthesis, fluorescent labelling and hybridisation to a 16k salmonid microarray. The salmonid 16k cDNA array identified differential gene expression predictive of exposure, which could be verified by quantitative real time PCR. More precisely, the responses of biomarker genes such as cytochrome p4501A and UDP-glucuronosyl transferase to TCDD exposure, glutathione reductase and gammaglutamyl cysteine synthetase to paraquat exposure, as well as vitellogenin and vitelline envelope protein to EE2 exposure validated the use of microarray applied to RNA extracted from in vitro exposed hepatocytes. The mutagenic compound NQO did not result in any change in gene expression. Results from exposure to a synthetic mixture of the same four chemicals, using identical concentrations as for single chemical exposures, revealed combined effects that were not predicted by results for individual chemicals alone. In general, the response of exposure to this mixture led to an average loss of approximately 60% of the transcriptomic signature found for single chemical exposure. The present findings show that microarray analyses may contribute to our mechanistic understanding of single contaminant mode of action as

  1. Optimizing a Synthetic Signaling System, Using Mathematical Modeling to Direct Experimental Work

    Science.gov (United States)

    2014-09-05

    arsenic , toluene, lead, DDT, mercury, etc.). The synthetic signaling system then be used to trigger a phytoremediation process upon detection of these...transferred to soil and allowed to set seed. The T1 generation will yield plants heterozygous and homozygous for the synthetic signaling system, allowing...compounds, either by breaking them down or transporting them to the aerial tissue where they can be harvested and removed from the soil

  2. Conversion of Synthetic Aβ to In Vivo Active Seeds and Amyloid Plaque Formation in a Hippocampal Slice Culture Model.

    Science.gov (United States)

    Novotny, Renata; Langer, Franziska; Mahler, Jasmin; Skodras, Angelos; Vlachos, Andreas; Wegenast-Braun, Bettina M; Kaeser, Stephan A; Neher, Jonas J; Eisele, Yvonne S; Pietrowski, Marie J; Nilsson, K Peter R; Deller, Thomas; Staufenbiel, Matthias; Heimrich, Bernd; Jucker, Mathias

    2016-05-04

    The aggregation of amyloid-β peptide (Aβ) in brain is an early event and hallmark of Alzheimer's disease (AD). We combined the advantages of in vitro and in vivo approaches to study cerebral β-amyloidosis by establishing a long-term hippocampal slice culture (HSC) model. While no Aβ deposition was noted in untreated HSCs of postnatal Aβ precursor protein transgenic (APP tg) mice, Aβ deposition emerged in HSCs when cultures were treated once with brain extract from aged APP tg mice and the culture medium was continuously supplemented with synthetic Aβ. Seeded Aβ deposition was also observed under the same conditions in HSCs derived from wild-type or App-null mice but in no comparable way when HSCs were fixed before cultivation. Both the nature of the brain extract and the synthetic Aβ species determined the conformational characteristics of HSC Aβ deposition. HSC Aβ deposits induced a microglia response, spine loss, and neuritic dystrophy but no obvious neuron loss. Remarkably, in contrast to in vitro aggregated synthetic Aβ, homogenates of Aβ deposits containing HSCs induced cerebral β-amyloidosis upon intracerebral inoculation into young APP tg mice. Our results demonstrate that a living cellular environment promotes the seeded conversion of synthetic Aβ into a potent in vivo seeding-active form. In this study, we report the seeded induction of Aβ aggregation and deposition in long-term hippocampal slice cultures. Remarkably, we find that the biological activities of the largely synthetic Aβ aggregates in the culture are very similar to those observed in vivo This observation is the first to show that potent in vivo seeding-active Aβ aggregates can be obtained by seeded conversion of synthetic Aβ in a living (wild-type) cellular environment. Copyright © 2016 the authors 0270-6474/16/365084-10$15.00/0.

  3. A synthetic study on constaining a 2D density-dependent saltwater intrusion model using electrical imaging data

    DEFF Research Database (Denmark)

    Antonsson, Arni Valur; Nguyen, Frederic; Engesgaard, Peter Knudegaard

    of the synthetic model, basically a salinity distribution in the coastal aquifer, was converted to resistivity distribution by assuming a certain petrophysical relation between water salinity and electrical conductivity. The obtained resistivity distribution was then used when electrical data acquisition...... was simulated. By applying an advanced inversion approach, electrical images of resistivity were obtained and based on the assumed petrophysical model the salinity distribution was derived. A number of different intrusion simulations were conducted with the aim of assessing the applicability of the method under....... Compared to conventional methods, which only give (few) point information, electrical images can give data over large spatial distances but that can be of great value for groundwater modeling purposes. The aim of this study is to investigate in a synthetic way, the applicability of using electrical images...

  4. Open set recognition of aircraft in aerial imagery using synthetic template models

    Science.gov (United States)

    Bapst, Aleksander B.; Tran, Jonathan; Koch, Mark W.; Moya, Mary M.; Swahn, Robert

    2017-05-01

    Fast, accurate and robust automatic target recognition (ATR) in optical aerial imagery can provide game-changing advantages to military commanders and personnel. ATR algorithms must reject non-targets with a high degree of confidence in a world with an infinite number of possible input images. Furthermore, they must learn to recognize new targets without requiring massive data collections. Whereas most machine learning algorithms classify data in a closed set manner by mapping inputs to a fixed set of training classes, open set recognizers incorporate constraints that allow for inputs to be labelled as unknown. We have adapted two template-based open set recognizers to use computer generated synthetic images of military aircraft as training data, to provide a baseline for military-grade ATR: (1) a frequentist approach based on probabilistic fusion of extracted image features, and (2) an open set extension to the one-class support vector machine (SVM). These algorithms both use histograms of oriented gradients (HOG) as features as well as artificial augmentation of both real and synthetic image chips to take advantage of minimal training data. Our results show that open set recognizers trained with synthetic data and tested with real data can successfully discriminate real target inputs from non-targets. However, there is still a requirement for some knowledge of the real target in order to calibrate the relationship between synthetic template and target score distributions. We conclude by proposing algorithm modifications that may improve the ability of synthetic data to represent real data.

  5. Synthetic Botany.

    Science.gov (United States)

    Boehm, Christian R; Pollak, Bernardo; Purswani, Nuri; Patron, Nicola; Haseloff, Jim

    2017-07-05

    Plants are attractive platforms for synthetic biology and metabolic engineering. Plants' modular and plastic body plans, capacity for photosynthesis, extensive secondary metabolism, and agronomic systems for large-scale production make them ideal targets for genetic reprogramming. However, efforts in this area have been constrained by slow growth, long life cycles, the requirement for specialized facilities, a paucity of efficient tools for genetic manipulation, and the complexity of multicellularity. There is a need for better experimental and theoretical frameworks to understand the way genetic networks, cellular populations, and tissue-wide physical processes interact at different scales. We highlight new approaches to the DNA-based manipulation of plants and the use of advanced quantitative imaging techniques in simple plant models such as Marchantia polymorpha. These offer the prospects of improved understanding of plant dynamics and new approaches to rational engineering of plant traits. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  6. Altered vocal fold kinematics in synthetic self-oscillating models that employ adipose tissue as a lateral boundary condition.

    Science.gov (United States)

    Saidi, Hiba; Erath, Byron D.

    2015-11-01

    The vocal folds play a major role in human communication by initiating voiced sound production. During voiced speech, the vocal folds are set into sustained vibrations. Synthetic self-oscillating vocal fold models are regularly employed to gain insight into flow-structure interactions governing the phonation process. Commonly, a fixed boundary condition is applied to the lateral, anterior, and posterior sides of the synthetic vocal fold models. However, physiological observations reveal the presence of adipose tissue on the lateral surface between the thyroid cartilage and the vocal folds. The goal of this study is to investigate the influence of including this substrate layer of adipose tissue on the dynamics of phonation. For a more realistic representation of the human vocal folds, synthetic multi-layer vocal fold models have been fabricated and tested while including a soft lateral layer representative of adipose tissue. Phonation parameters have been collected and are compared to those of the standard vocal fold models. Results show that vocal fold kinematics are affected by adding the adipose tissue layer as a new boundary condition.

  7. Lagrangian modelling of ocean surface waves and synthetic aperture radar wave measurements

    Energy Technology Data Exchange (ETDEWEB)

    Fouques, Sebastien

    2005-07-01

    The present thesis is concerned with the estimation of the ocean wave spectrum from synthetic aperture radar imaging and the modelling of ocean surface waves using the Lagrangian formalism. The first part gives a short overview of the theories of ocean surface waves and synthetic aperture radar (SAR) whereas the second part consists of five independent publications. The first two articles investigate the influence of the radar backscatter model on the SAR imaging of ocean waves. In Article I, Monte Carlo simulations of SAR images of the ocean surface are carried out using a nonlinear backscatter model that include both specular reflection and Bragg scattering and the results are compared to simulations from the classical Hasselmann integral transform (Hasselmann and Hasselmann, 1991). It is shown that nonlinearities in the backscatter model strongly influence the imaging of range-travelling waves and that the former can suppress the range-splitting effect (Bruning et al., 1988). Furthermore, in Article II a database of Envisat-ASAR Wave Mode products co-located with directional wave spectra from the numerical model WAM and which contains range-travelling wave cases only, is set up. The WAM spectra are used as input to several ocean-to-SAR integral transforms, with various real aperture radar (RAR) models and the obtained SAR image cross-spectra are compared to the Envisat-ASAR observations. A first result is that the use of a linear backscatter model leads to a high proportion of non-physical negative backscatter values in the RAR image, as suggested by Schulz-Stellenfleth (2001). Then, a comparison between the observed SAR cross-spectra and the ones simulated through Hasselmann's integral transform reveals that only twenty percents of the observations show a range-splitting effect as strong as in the simulations. A much better agreement is obtained when using the integral transform by Schulz-Stellenfleth (2003), which is based on a nonlinear hackscatter model

  8. Numerical modeling of block structure dynamics: Application to the Vrancea region and study of earthquakes sequences in the synthetic catalogs

    International Nuclear Information System (INIS)

    Soloviev, A.A.; Vorobieva, I.A.

    1995-08-01

    A seismically active region is represented as a system of absolutely rigid blocks divided by infinitely thin plane faults. The interaction of the blocks along the fault planes and with the underlying medium is viscous-elastic. The system of blocks moves as a consequence of prescribed motion of boundary blocks and the underlying medium. When for some part of a fault plane the stress surpasses a certain strength level a stress-drop (''a failure'') occurs. It can cause a failure for other parts of fault planes. The failures are considered as earthquakes. As a result of the numerical simulation a synthetic earthquake catalogue is produced. This procedure is applied for numerical modeling of dynamics of the block structure approximating the tectonic structure of the Vrancea region. By numerical experiments the values of the model parameters were obtained which supplied the synthetic earthquake catalog with the space distribution of epicenters close to the real distribution of the earthquake epicenters in the Vrancea region. The frequency-magnitude relations (Gutenberg-Richter curves) obtained for the synthetic and real catalogs have some common features. The sequences of earthquakes arising in the model are studied for some artificial structures. It is found that ''foreshocks'', ''main shocks'', and ''aftershocks'' could be detected among earthquakes forming the sequences. The features of aftershocks, foreshocks, and catalogs of main shocks are analysed. (author). 5 refs, 12 figs, 16 tabs

  9. Optimization of Lead Removal via Napier Grass in Synthetic Brackish Water using Response Surface Model

    Science.gov (United States)

    Hongsawat, P.; Suttiarporn, P.; Wutsanthia, K.; Kongsiri, G.

    2018-03-01

    The efficiency of the lead (Pb) phytoremediation by Napier grass was studied on the plant’s growth and plant’s tolerance on the Pb toxicity in synthetic brackish water. It was found that the plant was high tolerance to high level of Pb concentration (10 mg/l) in synthetic brackish water. Which revealed on the possibilities of plant’s growth under the presence of Pb contaminated condition. According to the Pb removal efficiency, the highest one (88.63±4.9%) was found at 10 ppm Pb concentration, 0.3 g/l NaCl concentration during the period 45 day. However, this study investigated the optimum condition for lead (Pb) removal from synthetic brackish water using phytoremediation treatment with Napier grass through a Box-Behnken Design. Three operational variables, i.e. Pb concentration (1, 5.5, 10 mg/l), NaCl (0.1, 0.3, 0.5 g/l) and period time (7, 26, 45 day), were determined. The results were provided evidence that the highest Pb removal efficiency (93.56%) from synthetic brackish water via Napier grass was Pb and NaCl concentration at 10 mg/l and 0.5 g/l during 45 day.

  10. Synthetic Cannabinoids

    Directory of Open Access Journals (Sweden)

    Aslihan Okan Ibiloglu

    2017-09-01

    Full Text Available Synthetic cannabinoids which is a subgroup of cannabinoids are commonly used for recreational drug use throughout the whole world. Although both marijuana and synthetic cannabinoids stimulate the same receptors, cannabinoid receptor 1 (CB1 and cannabinoid receptor 2 (CB2, studies have shown that synthetic cannabinoids are much more potent than marijuana. The longer use of synthetic cannabinoids can cause severe physical and psychological symptoms that might even result in death, similar to many known illicit drugs. Main treatment options mostly involve symptom management and supportive care. The aim of this article is to discuss clinical and pharmacological properties of the increasingly used synthetic cannabinoids. [Psikiyatride Guncel Yaklasimlar - Current Approaches in Psychiatry 2017; 9(3.000: 317-328

  11. A preclinical evaluation of alternative synthetic biomaterials for fascial defect repair using a rat abdominal hernia model.

    Directory of Open Access Journals (Sweden)

    Daniela Ulrich

    Full Text Available Fascial defects are a common problem in the abdominal wall and in the vagina leading to hernia or pelvic organ prolapse that requires mesh enhancement to reduce operation failure. However, the long-term outcome of synthetic mesh surgery may be unsatisfactory due to post-surgical complications. We hypothesized that mesh fabricated from alternative synthetic polymers may evoke a different tissue response, and provide more appropriate mechanical properties for hernia repair. Our aim was to compare the in vivo biocompatibility of new synthetic meshes with a commercial mesh.We have fabricated 3 new warp-knitted synthetic meshes from different polymers with different tensile properties polyetheretherketone (PEEK, polyamide (PA and a composite, gelatin coated PA (PA+G. The rat abdominal hernia model was used to implant the meshes (25 × 35 mm, n = 24/ group. After 7, 30, 60, 90 days tissues were explanted for immunohistochemical assessment of foreign body reaction and tissue integration, using CD31, CD45, CD68, alpha-SMA antibodies. The images were analysed using an image analysis software program. Biomechanical properties were uniaxially evaluated using an Instron Tensile® Tester.This study showed that the new meshes induced complex differences in the type of foreign body reaction over the time course of implantation. The PA, and particularly the composite PA+G meshes, evoked a milder early inflammatory response, and macrophages were apparent throughout the time course. Our meshes led to better tissue integration and new collagen deposition, particularly with the PA+G meshes, as well as greater and sustained neovascularisation compared with the PP meshes.PA, PA+G and PEEK appear to be well tolerated and are biocompatible, evoking an overlapping and different host tissue response with time that might convey mechanical variations in the healing tissue. These new meshes comprising different polymers may provide an alternative option for future treatment

  12. Synthetic modeling chemistry of iron-sulfur clusters in nitric oxide signaling.

    Science.gov (United States)

    Fitzpatrick, Jessica; Kim, Eunsuk

    2015-08-18

    Nitric oxide (NO) is an important signaling molecule that is involved in many physiological and pathological functions. Iron-sulfur proteins are one of the main reaction targets for NO, and the [Fe-S] clusters within these proteins are converted to various iron nitrosyl species upon reaction with NO, of which dinitrosyl iron complexes (DNICs) are the most prevalent. Much progress has been made in identifying the origin of cellular DNIC generation. However, it is not well-understood which other products besides DNICs may form during [Fe-S] cluster degradation nor what effects DNICs and other degradation products can have once they are generated in cells. Even more elusive is an understanding of the manner by which cells cope with unwanted [Fe-S] modifications by NO. This Account describes our synthetic modeling efforts to identify cluster degradation products derived from the [2Fe-2S]/NO reaction in order to establish their chemical reactivity and repair chemistry. Our intent is to use the chemical knowledge that we generate to provide insight into the unknown biological consequences of cluster modification. Our recent advances in three different areas are described. First, new reaction conditions that lead to the formation of previously unrecognized products during the reaction of [Fe-S] clusters with NO are identified. Hydrogen sulfide (H2S), a gaseous signaling molecule, can be generated from the reaction between [2Fe-2S] clusters and NO in the presence of acid or formal H• (e(-)/H(+)) donors. In the presence of acid, a mononitrosyl iron complex (MNIC) can be produced as the major iron-containing product. Second, cysteine analogues can efficiently convert MNICs back to [2Fe-2S] clusters without the need for any other reagents. This reaction is possible for cysteine analogues because of their ability to labilize NO from MNICs and their capacity to undergo C-S bond cleavage, providing the necessary sulfide for [2Fe-2S] cluster formation. Lastly, unique dioxygen

  13. Application of Synthetic Polymeric Scaffolds in Breast Cancer 3D Tissue Cultures and Animal Tumor Models

    Directory of Open Access Journals (Sweden)

    Girdhari Rijal

    2017-01-01

    Full Text Available Preparation of three-dimensional (3D porous scaffolds from synthetic polymers is a challenge to most laboratories conducting biomedical research. Here, we present a handy and cost-effective method to fabricate polymeric hydrogel and porous scaffolds using poly(lactic-co-glycolic acid (PLGA or polycaprolactone (PCL. Breast cancer cells grown on 3D polymeric scaffolds exhibited distinct survival, morphology, and proliferation compared to those on 2D polymeric surfaces. Mammary epithelial cells cultured on PLGA- or PCL-coated slides expressed extracellular matrix (ECM proteins and their receptors. Estrogen receptor- (ER- positive T47D breast cancer cells are less sensitive to 4-hydroxytamoxifen (4-HT treatment when cultured on the 3D porous scaffolds than in 2D cultures. Finally, cancer cell-laden polymeric scaffolds support consistent tumor formation in animals and biomarker expression as seen in human native tumors. Our data suggest that the porous synthetic polymer scaffolds satisfy the basic requirements for 3D tissue cultures both in vitro and in vivo. The scaffolding technology has appealing potentials to be applied in anticancer drug screening for a better control of the progression of human cancers.

  14. Abundances in Planetary Nebulae: an Autopsy of Low and Intermediate Mass Stars

    Science.gov (United States)

    Buell, James Francis

    In this work we report on the results of synthetic thermally pulsing asymptotic giant branch models (TP-AGB) and compare the results to the abundance ratios in a sample of planetary nebulae. We use updated the input parameters for mass-loss, the stellar luminosity, and dredge-up. We calculated models with masses between 0.8 solar masses and 8 solar masses. We also calculated models with (Fe/H) between -2.5 and 0.3. The effect of the first, second, and third dredge-up as well as hot-bottom burning are reported on. The analysis of a sample of Galactic bulge and disk planetary nebulae is also reported on.

  15. Synthetic generation of myocardial blood-oxygen-level-dependent MRI time series via structural sparse decomposition modeling.

    Science.gov (United States)

    Rusu, Cristian; Morisi, Rita; Boschetto, Davide; Dharmakumar, Rohan; Tsaftaris, Sotirios A

    2014-07-01

    This paper aims to identify approaches that generate appropriate synthetic data (computer generated) for cardiac phase-resolved blood-oxygen-level-dependent (CP-BOLD) MRI. CP-BOLD MRI is a new contrast agent- and stress-free approach for examining changes in myocardial oxygenation in response to coronary artery disease. However, since signal intensity changes are subtle, rapid visualization is not possible with the naked eye. Quantifying and visualizing the extent of disease relies on myocardial segmentation and registration to isolate the myocardium and establish temporal correspondences and ischemia detection algorithms to identify temporal differences in BOLD signal intensity patterns. If transmurality of the defect is of interest pixel-level analysis is necessary and thus a higher precision in registration is required. Such precision is currently not available affecting the design and performance of the ischemia detection algorithms. In this work, to enable algorithmic developments of ischemia detection irrespective to registration accuracy, we propose an approach that generates synthetic pixel-level myocardial time series. We do this by 1) modeling the temporal changes in BOLD signal intensity based on sparse multi-component dictionary learning, whereby segmentally derived myocardial time series are extracted from canine experimental data to learn the model; and 2) demonstrating the resemblance between real and synthetic time series for validation purposes. We envision that the proposed approach has the capacity to accelerate development of tools for ischemia detection while markedly reducing experimental costs so that cardiac BOLD MRI can be rapidly translated into the clinical arena for the noninvasive assessment of ischemic heart disease.

  16. Three-dimensional coastal geomorphology deformation modelling using differential synthetic aperture interferometry

    Energy Technology Data Exchange (ETDEWEB)

    Marghany, Maged [Universiti Teknologi Malaysia, Skudai, Johor Bahru (Malaysia). Inst. for Science and Technology Geospatial (INSTeG)

    2012-06-15

    This work presents a new approach for three-dimensional (3D) coastal deformation simulation using differential synthetic aperture interferometry (DInSAR). In doing so, conventional InSAR procedures are implemented to three repeat passes of RADARSAT-1 SAR fine mode data (F1). Further, the DInSAR method is implemented with the phase unwrapping technique. Consequently, DInSAR is used to eliminate the phase decorrelation impact from the interferograms. The study shows the accurate performance of DInSAR with a root mean square error of 0.02 {+-} 0.21 m and 90% confidence intervals. In conclusion, the DInSAR technique produces an accurate 3D coastal geomorphology reconstruction. (orig.)

  17. Modeling climate change impacts on combined sewer overflow using synthetic precipitation time series.

    Science.gov (United States)

    Bendel, David; Beck, Ferdinand; Dittmer, Ulrich

    2013-01-01

    In the presented study climate change impacts on combined sewer overflows (CSOs) in Baden-Wuerttemberg, Southern Germany, were assessed based on continuous long-term rainfall-runoff simulations. As input data, synthetic rainfall time series were used. The applied precipitation generator NiedSim-Klima accounts for climate change effects on precipitation patterns. Time series for the past (1961-1990) and future (2041-2050) were generated for various locations. Comparing the simulated CSO activity of both periods we observe significantly higher overflow frequencies for the future. Changes in overflow volume and overflow duration depend on the type of overflow structure. Both values will increase at simple CSO structures that merely divide the flow, whereas they will decrease when the CSO structure is combined with a storage tank. However, there is a wide variation between the results of different precipitation time series (representative for different locations).

  18. Toxicity Assessments of Chalcone and Some Synthetic Chalcone Analogues in a Zebrafish Model

    Directory of Open Access Journals (Sweden)

    Ya-Ting Lee

    2014-01-01

    Full Text Available The aim of this study was to investigate the in vivo toxicities of some novel synthetic chalcones. Chalcone and four chalcone analogues 1a–d were evaluated using zebrafish embryos following antibody staining to visualize their morphological changes and muscle fiber alignment. Results showed that embryos treated with 3'-hydroxychalcone (compound 1b displayed a high percentage of muscle defects (96.6%, especially myofibril misalignment. Ultrastructural analysis revealed that compound 1b-treated embryos displayed many muscle defect phenotypes, including breakage and collapse of myofibrils, reduced cell numbers, and disorganized thick (myosin and thin (actin filaments. Taken together, our results provide in vivo evidence of the myotoxic effects of the synthesized chalcone analogues on developing zebrafish embryos.

  19. Characterisation of model compounds and a synthetic coal by TG/MS/FTIR to represent the pyrolysis behaviour of coal

    Energy Technology Data Exchange (ETDEWEB)

    Arenillas, A.; Pevida, C.; Rubiera, F.; Garcia, R.; Pis, J.J. [Instituto Nacional del Carbon, CSIC, Apartado 73, 33080 Oviedo (Spain)

    2004-06-01

    Coal pyrolysis is the initial, accompanying reaction of a number of coal conversion processes such as hydrogenation, combustion and gasification. However, because of the inherent complexity of coal composition, it is difficult to describe coal pyrolysis clearly. Single model compounds have been used before in order to provide additional insight into the complex processes that occur in the pyrolysis of coal. Yet the picture obtained is a simplified one and certain important aspects such as coal structure, interactions between different surface groups and cross-links are omitted. The approach used in this work involves the preparation of a synthetic coal, SC, with a known structure by curing a mixture of single, well-defined model compounds. By means of chemical characterisation, the SC was shown to contain the macroscopic features of a high volatile coal (proximate and ultimate analyses). FTIR characterisation revealed the presence of functional groups similar to those of coal in the structure of the SC. Temperature-programmed pyrolysis tests were performed in a thermobalance linked to a mass spectrometer and a Fourier transform infrared analyser (TG/MS/FTIR). The thermal behaviour of the synthetic coal (i.e., rate of mass loss and the evolution profiles of gaseous compounds during pyrolysis tests) is very similar to that of the high volatile bituminous coal which was used as a reference material. The great advantage of using SC lies in the fact that its composition and structure can be accurately determined and employed in subsequent applications in basic and mechanistic studies.

  20. Evolution, Nucleosynthesis, and Yields of AGB Stars at Different Metallicities. III. Intermediate-mass Models, Revised Low-mass Models, and the ph-FRUITY Interface

    Science.gov (United States)

    Cristallo, S.; Straniero, O.; Piersanti, L.; Gobrecht, D.

    2015-08-01

    We present a new set of models for intermediate-mass asymptotic giant branch (AGB) stars (4.0, 5.0, and 6.0 M⊙) at different metallicities (-2.15 ≤ [Fe/H] ≤ +0.15). This set integrates the existing models for low-mass AGB stars (1.3 ≤ M/M⊙ ≤ 3.0) already included in the FRUITY database. We describe the physical and chemical evolution of the computed models from the main sequence up to the end of the AGB phase. Due to less efficient third dredge up episodes, models with large core masses show modest surface enhancements. This effect is due to the fact that the interpulse phases are short and, therefore, thermal pulses (TPs) are weak. Moreover, the high temperature at the base of the convective envelope prevents it from deeply penetrating the underlying radiative layers. Depending on the initial stellar mass, the heavy element nucleosynthesis is dominated by different neutron sources. In particular, the s-process distributions of the more massive models are dominated by the 22Ne(α,n)25Mg reaction, which is efficiently activated during TPs. At low metallicities, our models undergo hot bottom burning and hot third dredge up. We compare our theoretical final core masses to available white dwarf observations. Moreover, we quantify the influence intermediate-mass models have on the carbon star luminosity function. Finally, we present the upgrade of the FRUITY web interface, which now also includes the physical quantities of the TP-AGB phase for all of the models included in the database (ph-FRUITY).

  1. EVOLUTION, NUCLEOSYNTHESIS, AND YIELDS OF AGB STARS AT DIFFERENT METALLICITIES. III. INTERMEDIATE-MASS MODELS, REVISED LOW-MASS MODELS, AND THE pH-FRUITY INTERFACE

    Energy Technology Data Exchange (ETDEWEB)

    Cristallo, S.; Straniero, O.; Piersanti, L.; Gobrecht, D. [INAF-Osservatorio Astronomico di Collurania, I-64100 Teramo (Italy)

    2015-08-15

    We present a new set of models for intermediate-mass asymptotic giant branch (AGB) stars (4.0, 5.0, and 6.0 M{sub ⊙}) at different metallicities (−2.15 ≤ [Fe/H] ≤ +0.15). This set integrates the existing models for low-mass AGB stars (1.3 ≤ M/M{sub ⊙} ≤ 3.0) already included in the FRUITY database. We describe the physical and chemical evolution of the computed models from the main sequence up to the end of the AGB phase. Due to less efficient third dredge up episodes, models with large core masses show modest surface enhancements. This effect is due to the fact that the interpulse phases are short and, therefore, thermal pulses (TPs) are weak. Moreover, the high temperature at the base of the convective envelope prevents it from deeply penetrating the underlying radiative layers. Depending on the initial stellar mass, the heavy element nucleosynthesis is dominated by different neutron sources. In particular, the s-process distributions of the more massive models are dominated by the {sup 22}Ne(α,n){sup 25}Mg reaction, which is efficiently activated during TPs. At low metallicities, our models undergo hot bottom burning and hot third dredge up. We compare our theoretical final core masses to available white dwarf observations. Moreover, we quantify the influence intermediate-mass models have on the carbon star luminosity function. Finally, we present the upgrade of the FRUITY web interface, which now also includes the physical quantities of the TP-AGB phase for all of the models included in the database (ph-FRUITY)

  2. Synthetic Rutile

    International Nuclear Information System (INIS)

    Burastero, J.

    1975-01-01

    This work is about the laboratory scale investigation of the conditions in the rutile synthetic production from one me nita in Aguas Dulces reservoir. The iron mineral is chlorinated and volatilized selectively leaving a residue enriched in titanium dioxide which can be used as a substitute of rutile mineral

  3. Mirror-Imaged Rapid Prototype Skull Model and Pre-Molded Synthetic Scaffold to Achieve Optimal Orbital Cavity Reconstruction.

    Science.gov (United States)

    Park, Sung Woo; Choi, Jong Woo; Koh, Kyung S; Oh, Tae Suk

    2015-08-01

    Reconstruction of traumatic orbital wall defects has evolved to restore the original complex anatomy with the rapidly growing use of computer-aided design and prototyping. This study evaluated a mirror-imaged rapid prototype skull model and a pre-molded synthetic scaffold for traumatic orbital wall reconstruction. A single-center retrospective review was performed of patients who underwent orbital wall reconstruction after trauma from 2012 to 2014. Patients were included by admission through the emergency department after facial trauma or by a tertiary referral for post-traumatic orbital deformity. Three-dimensional (3D) computed tomogram-based mirror-imaged reconstruction images of the orbit and an individually manufactured rapid prototype skull model by a 3D printing technique were obtained for each case. Synthetic scaffolds were anatomically pre-molded using the skull model as guide and inserted at the individual orbital defect. Postoperative complications were assessed and 3D volumetric measurements of the orbital cavity were performed. Paired samples t test was used for statistical analysis. One hundred four patients with immediate orbital defect reconstructions and 23 post-traumatic orbital deformity reconstructions were included in this study. All reconstructions were successful without immediate postoperative complications, although there were 10 cases with mild enophthalmos and 2 cases with persistent diplopia. Reoperations were performed for 2 cases of persistent diplopia and secondary touchup procedures were performed to contour soft tissue in 4 cases. Postoperative volumetric measurement of the orbital cavity showed nonsignificant volume differences between the damaged orbit and the reconstructed orbit (21.35 ± 1.93 vs 20.93 ± 2.07 cm(2); P = .98). This protocol was extended to severe cases in which more than 40% of the orbital frame was lost and combined with extensive soft tissue defects. Traumatic orbital reconstruction can be optimized and

  4. An in vitro Model for Oral Mixed Biofilms of Candida albicans and Streptococcus gordonii in Synthetic Saliva

    Directory of Open Access Journals (Sweden)

    Daniel eMontelongo-Jauregui

    2016-05-01

    Full Text Available As a member of the normal human oral microbiota, the fungus C. albicans is often found in association with Streptococcus gordonii, a member of dental plaque forming bacteria. Evidence suggests that S. gordonii serves as a facilitator of C. albicans adherence to dental tissues, which represents a clinically relevant problem, particularly for immunocompromised individuals that could subsequently develop fungal infections. In this study we describe the development of a relatively simple and economical in vitro model that allows for the growth of mixed bacterial/fungal biofilms in 96-well microtiter plates. We have applied this method to test and compare the growth characteristics of single and dual species biofilms in traditional microbiological media versus a synthetic saliva medium (basal medium mucin, BMM that more closely resembles physiological conditions within the oral cavity. Results indicated a synergistic effect for the formation of biofilms when both microorganisms were seeded together under all conditions tested. The structural and architectural features of the resulting biofilms were further characterized using scanning electron microscopy (SEM and confocal scanning laser microscopy (CSLM. We also performed drug susceptibility assays against single and mixed species biofilms using commonly used antifungals and antibacterial antibiotics, both in monotherapy and in combination therapy, for a direct comparison of resistance against antimicrobial treatment. As expected, mixed species biofilms displayed higher levels of resistance to antimicrobial treatment at every dose tested in both traditional media and BMM synthetic saliva, as compared to single-species biofilms.

  5. Simulation and thermodynamic modeling of the extraction of tocopherol from a synthetic mixture of tocopherol, squalene and CO2

    Directory of Open Access Journals (Sweden)

    M.F. Mendes

    2000-12-01

    Full Text Available Soybean oil is the most consumed vegetable oil in the world, representing 54% of the total world production. Brazil is the second country in the world that produces and export soybean seeds, almost 20%. One of the most important by-product of the soybean oil is the deodorizer distillate, commonly known as soybean sludge. This residue is rich in many high value compounds as tocopherols, squalene and sterols. Tocopherols are the major components in the deodorized distillated due to their characteristics as an antioxidant agent. So, the objective of this work is to study the concentration of tocopherols presented in this raw material, using the operational conditions obtained from the equilibrium data and using supercritical carbon dioxide as a solvent. The deodorizer distillate is a complex mixture of more than 200 components, so a synthetic mixture was chosen to represent the deodorizer distillate. The synthetic mixture used in this work is composed by tocopherols, fatty acids and squalene. The simulation was carried out using ASPEN+ simulator and the LCVM thermodynamic model was used to correlate the available equilibrium data.

  6. Kinetic Modeling of Synthetic Wastewater Treatment by the Moving-bed Sequential Continuous-inflow Reactor (MSCR

    Directory of Open Access Journals (Sweden)

    Mohammadreza Khani

    2016-11-01

    Full Text Available It was the objective of the present study to conduct a kinetic modeling of a Moving-bed Sequential Continuous-inflow Reactor (MSCR and to develop its best prediction model. For this purpose, a MSCR consisting of an aerobic-anoxic pilot 50 l in volume and an anaerobic pilot of 20 l were prepared. The MSCR was fed a variety of organic loads and operated at different hydraulic retention times (HRT using synthetic wastewater at input COD concentrations of 300 to 1000 mg/L with HRTs of 2 to 5 h. Based on the results and the best system operation conditions, the highest COD removal (98.6% was obtained at COD=500 mg/L. The three well-known first order, second order, and Stover-Kincannon models were utilized for the kinetic modeling of the reactor. Based on the kinetic analysis of organic removal, the Stover-Kincannon model was chosen for the kinetic modeling of the moving bed biofilm. Given its advantageous properties in the statisfactory prediction of organic removal at different organic loads, this model is recommended for the design and operation of MSCR systems.

  7. First and second order Markov chain models for synthetic generation of wind speed time series

    International Nuclear Information System (INIS)

    Shamshad, A.; Bawadi, M.A.; Wan Hussin, W.M.A.; Majid, T.A.; Sanusi, S.A.M.

    2005-01-01

    Hourly wind speed time series data of two meteorological stations in Malaysia have been used for stochastic generation of wind speed data using the transition matrix approach of the Markov chain process. The transition probability matrices have been formed using two different approaches: the first approach involves the use of the first order transition probability matrix of a Markov chain, and the second involves the use of a second order transition probability matrix that uses the current and preceding values to describe the next wind speed value. The algorithm to generate the wind speed time series from the transition probability matrices is described. Uniform random number generators have been used for transition between successive time states and within state wind speed values. The ability of each approach to retain the statistical properties of the generated speed is compared with the observed ones. The main statistical properties used for this purpose are mean, standard deviation, median, percentiles, Weibull distribution parameters, autocorrelations and spectral density of wind speed values. The comparison of the observed wind speed and the synthetically generated ones shows that the statistical characteristics are satisfactorily preserved

  8. Preparation of silver nanoparticles from synthetic and natural sources: remediation model for PAHs

    International Nuclear Information System (INIS)

    Abbasi, M.; Saeed, F.; Rafique, U.

    2013-01-01

    The emergence of nanoscience and technology is gaining popularity with an increasing demand for metal nanoparticles applicability in various areas such as electronics, catalysis, chemistry, energy and medicine. Metallic nanoparticles are traditionally synthesized by wet chemical techniques, where the chemicals used are quite often toxic and flammable. In this work, an attempt is made to compare the efficiency of two different synthesis methods and application of each for the remediation of poly aromatic hydrocarbons (PAHs). In this regard, silver nanoparticles are prepared by green and wet chemical method using plant extract of garlic (Allium sativum). The extract is known to reduce the metal during synthesis and acts as stabilizing ligand. These synthesized silver nanoparticles (Agp) and (AgW) were applied as adsorbents in synthetic batch mode experiments at varying parameters of pH and temperature. A concentration of 0.01mg/L of Phenanthrene, Anthracene, and Pyrene were induced at fixed dosage of 1mg/Kg of adsorbent. Residual concentration of each PAH was analyzed on UV-Visible spectrophotometer. The results indicated that both adsorbents follow the sequence of Phenanthrene>Pyrene>Anthracene with optimal removal of higher than 85 percentage in each case. A distinguishing privilege is attained by Agp adsorbent showing 3, 3 and 11 orders of magnitude higher efficiency than Agw. It may be attributed to more functional groups in the plant extract participating in binding of PAH to the surface. Each synthesized adsorbents was characterized by FTIR, SEM and EDX. The average particle size was determined to be of the order of 13-26 nm. The study concludes the use of alternate economical and green adsorbents for control of poly aromatic hydrocarbons (PAHs). (author)

  9. Preparation of Silver Nanoparticles from Synthetic and Natural Sources: Remediation Model for PAHs

    International Nuclear Information System (INIS)

    Abbasi, Maryam; Saeed, Fatima; Rafique, Uzaira

    2014-01-01

    The emergence of nanoscience and technology is gaining popularity with an increasing demand for metal nanoparticles applicability in various areas such as electronics, catalysis, chemistry, energy and medicine. Metallic nanoparticles are traditionally synthesized by wet chemical techniques, where the chemicals used are quite often toxic and flammable. In this work, an attempt is made to compare the efficiency of two different synthesis methods and application of each for the remediation of poly aromatic hydrocarbons (PAHs). In this regard, silver nanoparticles are prepared by green and wet chemical method using plant extract of garlic (Allium sativum). The extract is known to reduce the metal during synthesis and acts as stabilizing ligand. These synthesized silver nanoparticles (Agp) and (AgW) were applied as adsorbents in synthetic batch mode experiments at varying parameters of pH and temperature. A concentration of 0.01mg/L of Phenanthrene, Anthracene, and Pyrene were induced at fixed dosage of 1mg/Kg of adsorbent. Residual concentration of each PAH was analyzed on UV-Visible spectrophotometer. The results indicated that both adsorbents follow the sequence of Phenanthrene>Pyrene>Anthracene with optimal removal of higher than 85% in each case. A distinguishing privilege is attained by Agp adsorbent showing 3, 3 and 11 orders of magnitude higher efficiency than Agw. It may be attributed to more functional groups in the plant extract participating in binding of PAH to the surface. Each synthesized adsorbents was characterized by FTIR, SEM and EDX. The average particle size was determined to be of the order of 13-26 nm. The study concludes the use of alternate economical and green adsorbents for control of poly aromatic hydrocarbons (PAHs)

  10. Preparation of Silver Nanoparticles from Synthetic and Natural Sources: Remediation Model for PAHs

    Science.gov (United States)

    Abbasi, Maryam; Saeed, Fatima; Rafique, Uzaira

    2014-06-01

    The emergence of nanoscience and technology is gaining popularity with an increasing demand for metal nanoparticles applicability in various areas such as electronics, catalysis, chemistry, energy and medicine. Metallic nanoparticles are traditionally synthesized by wet chemical techniques, where the chemicals used are quite often toxic and flammable. In this work, an attempt is made to compare the efficiency of two different synthesis methods and application of each for the remediation of poly aromatic hydrocarbons (PAHs). In this regard, silver nanoparticles are prepared by green and wet chemical method using plant extract of garlic (Allium sativum). The extract is known to reduce the metal during synthesis and acts as stabilizing ligand. These synthesized silver nanoparticles (Agp) and (AgW) were applied as adsorbents in synthetic batch mode experiments at varying parameters of pH and temperature. A concentration of 0.01mg/L of Phenanthrene, Anthracene, and Pyrene were induced at fixed dosage of 1mg/Kg of adsorbent. Residual concentration of each PAH was analyzed on UV-Visible spectrophotometer. The results indicated that both adsorbents follow the sequence of Phenanthrene>Pyrene>Anthracene with optimal removal of higher than 85% in each case. A distinguishing privilege is attained by Agp adsorbent showing 3, 3 and 11 orders of magnitude higher efficiency than Agw. It may be attributed to more functional groups in the plant extract participating in binding of PAH to the surface. Each synthesized adsorbents was characterized by FTIR, SEM and EDX. The average particle size was determined to be of the order of 13-26 nm. The study concludes the use of alternate economical and green adsorbents for control of poly aromatic hydrocarbons (PAHs).

  11. In vivo tissue response and durability of five novel synthetic polymers in a rabbit model.

    Science.gov (United States)

    Sahin, E; Cingi, C; Eskiizmir, G; Altintoprak, N; Calli, A; Calli, C; Yilgör, I; Yilgör, E

    2016-04-01

    Alloplastic materials are frequently used in facial plastic surgeries such as rhinoplasty and nasal reconstruction. Unfortunately, the ideal alloplastic material has not been found. This experimental study evaluates the tissue response and durability of five novel polymers developed as an alloplastic material. In this experimental study involving a tertiary university hospital, six subcuticular pockets were formed at the back of 10 rabbits for the implantation of each polymer and sham group. Each pocket was excised with its adjacent tissue after three months, and collected for histopathological examination. Semi-quantitative examination including neovascularisation, inflammation, fibrosis, abscess formation, multinucleated foreign body giant cells was performed, and integrity of polymer was evaluated. A statistical comparison was performed. No statically significant difference was detected in neovascularisation, inflammation, fibrosis, abscess formation and multinucleated foreign body giant cells when a paired comparison between sham and polymer II, III and IV groups was performed individually. Nevertheless, the degree of fibrosis was less than sham group in polymer I (p = .027) and V (p = .018), although the other variables were almost similar. The integrity of polymers III (9 intact, 1 fragmented) and IV (8 intact, 2 absent) was better than the other polymers. These novel synthetic polymers could be considered as good candidates for clinical applicability. All polymers provided satisfactory results in terms of tissue response; however, fibrovascular integration was higher in polymers II, III and IV. In addition, the durability of polymer III and IV was better than the others. © Copyright by Società Italiana di Otorinolaringologia e Chirurgia Cervico-Facciale, Rome, Italy.

  12. Efficacy of a synthetic antimicrobial peptidomimetic versus vancomycin in a Staphylococcus epidermidis device-related murine peritonitis model

    DEFF Research Database (Denmark)

    Cavanagh, Jorunn Pauline; Granslo, Hildegunn Norbakken; Fredheim, Elizabeth Aarag

    2013-01-01

    Objectives Biofilm-forming Staphylococcus epidermidis is a prevalent cause of peritonitis during peritoneal dialysis. We compared the efficacy of a synthetic antimicrobial peptidomimetic (Ltx21) versus vancomycin in a murine model mimicking a device-related peritonitis. Methods Silicone implants......, pre-colonized with an S. epidermidis biofilm, were inserted into the peritoneal cavity of BALB/c mice. Three groups (36 mice in each) with pre-colonized implants received intraperitoneal treatment with Ltx21, vancomycin or placebo. Mice were euthanized on day 3 (n = 12), day 6 (n = 12) or day 8 (n...... = 12) post-implantation. Controls were mice with sterile implants (n = 18) and mice without surgery (n = 6). Bacterial reductions in cfu were analysed from implants and peritoneal fluid (PF). Inflammatory responses in serum and PF were measured. Results Vancomycin resulted in a stronger reduction...

  13. Convergence of regenerative medicine and synthetic biology to develop standardized and validated models of human diseases with clinical relevance.

    Science.gov (United States)

    Hutmacher, Dietmar Werner; Holzapfel, Boris Michael; De-Juan-Pardo, Elena Maria; Pereira, Brooke Anne; Ellem, Stuart John; Loessner, Daniela; Risbridger, Gail Petuna

    2015-12-01

    In order to progress beyond currently available medical devices and implants, the concept of tissue engineering has moved into the centre of biomedical research worldwide. The aim of this approach is not to replace damaged tissue with an implant or device but rather to prompt the patient's own tissue to enact a regenerative response by using a tissue-engineered construct to assemble new functional and healthy tissue. More recently, it has been suggested that the combination of Synthetic Biology and translational tissue-engineering techniques could enhance the field of personalized medicine, not only from a regenerative medicine perspective, but also to provide frontier technologies for building and transforming the research landscape in the field of in vitro and in vivo disease models. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  14. Improving Watershed-Scale Hydrodynamic Models by Incorporating Synthetic 3D River Bathymetry Network

    Science.gov (United States)

    Dey, S.; Saksena, S.; Merwade, V.

    2017-12-01

    Digital Elevation Models (DEMs) have an incomplete representation of river bathymetry, which is critical for simulating river hydrodynamics in flood modeling. Generally, DEMs are augmented with field collected bathymetry data, but such data are available only at individual reaches. Creating a hydrodynamic model covering an entire stream network in the basin requires bathymetry for all streams. This study extends a conceptual bathymetry model, River Channel Morphology Model (RCMM), to estimate the bathymetry for an entire stream network for application in hydrodynamic modeling using a DEM. It is implemented at two large watersheds with different relief and land use characterizations: coastal Guadalupe River basin in Texas with flat terrain and a relatively urban White River basin in Indiana with more relief. After bathymetry incorporation, both watersheds are modeled using HEC-RAS (1D hydraulic model) and Interconnected Pond and Channel Routing (ICPR), a 2-D integrated hydrologic and hydraulic model. A comparison of the streamflow estimated by ICPR at the outlet of the basins indicates that incorporating bathymetry influences streamflow estimates. The inundation maps show that bathymetry has a higher impact on flat terrains of Guadalupe River basin when compared to the White River basin.

  15. Using synthetic data to evaluate multiple regression and principal component analyses for statistical modeling of daily building energy consumption

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, T.A. (Energy Systems Lab., Texas A and M Univ., College Station, TX (United States)); Claridge, D.E. (Energy Systems Lab., Texas A and M Univ., College Station, TX (United States))

    1994-01-01

    Multiple regression modeling of monitored building energy use data is often faulted as a reliable means of predicting energy use on the grounds that multicollinearity between the regressor variables can lead both to improper interpretation of the relative importance of the various physical regressor parameters and to a model with unstable regressor coefficients. Principal component analysis (PCA) has the potential to overcome such drawbacks. While a few case studies have already attempted to apply this technique to building energy data, the objectives of this study were to make a broader evaluation of PCA and multiple regression analysis (MRA) and to establish guidelines under which one approach is preferable to the other. Four geographic locations in the US with different climatic conditions were selected and synthetic data sequence representative of daily energy use in large institutional buildings were generated in each location using a linear model with outdoor temperature, outdoor specific humidity and solar radiation as the three regression variables. MRA and PCA approaches were then applied to these data sets and their relative performances were compared. Conditions under which PCA seems to perform better than MRA were identified and preliminary recommendations on the use of either modeling approach formulated. (orig.)

  16. Forest height estimation from mountain forest areas using general model-based decomposition for polarimetric interferometric synthetic aperture radar images

    Science.gov (United States)

    Minh, Nghia Pham; Zou, Bin; Cai, Hongjun; Wang, Chengyi

    2014-01-01

    The estimation of forest parameters over mountain forest areas using polarimetric interferometric synthetic aperture radar (PolInSAR) images is one of the greatest interests in remote sensing applications. For mountain forest areas, scattering mechanisms are strongly affected by the ground topography variations. Most of the previous studies in modeling microwave backscattering signatures of forest area have been carried out over relatively flat areas. Therefore, a new algorithm for the forest height estimation from mountain forest areas using the general model-based decomposition (GMBD) for PolInSAR image is proposed. This algorithm enables the retrieval of not only the forest parameters, but also the magnitude associated with each mechanism. In addition, general double- and single-bounce scattering models are proposed to fit for the cross-polarization and off-diagonal term by separating their independent orientation angle, which remains unachieved in the previous model-based decompositions. The efficiency of the proposed approach is demonstrated with simulated data from PolSARProSim software and ALOS-PALSAR spaceborne PolInSAR datasets over the Kalimantan areas, Indonesia. Experimental results indicate that forest height could be effectively estimated by GMBD.

  17. Examples of modelling IP in AEM data: synthetic and real data

    DEFF Research Database (Denmark)

    Viezzoli, Andrea; Kaminskiy, Vladislav; Fiandaca, Gianluca

    There have been multiple evidences in the literature in the past several years of what has been referred to as IP effect in the Time Domain Airborne EM data (TDEM). This phenomenon is known to be responsible for incorrect inversion modelling of electrical resistivity, lower interpreted depth...... of investigation and lost information about chargeability of the subsurface as well as about other valuable parameters. Historically there have been many suggestions to account for the IP effect using the Cole-Cole model. In current paper we are showing the possibility to extract IP information from airborne TDEM...... with both high electrical conductivity and in resistive environments. Furthermore, modelling of IP effects allows corrected resistivity models. The Amakinskaya kimberlite pipe results highlight the relevance of chargeability for kimberlite exploration....

  18. Identification and synthetic modeling of factors affecting American black duck populations

    Science.gov (United States)

    Conroy, Michael J.; Miller, Mark W.; Hines, James E.

    2002-01-01

    We reviewed the literature on factors potentially affecting the population status of American black ducks (Anas rupribes). Our review suggests that there is some support for the influence of 4 major, continental-scope factors in limiting or regulating black duck populations: 1) loss in the quantity or quality of breeding habitats; 2) loss in the quantity or quality of wintering habitats; 3) harvest, and 4) interactions (competition, hybridization) with mallards (Anas platyrhychos) during the breeding and/or wintering periods. These factors were used as the basis of an annual life cycle model in which reproduction rates and survival rates were modeled as functions of the above factors, with parameters of the model describing the strength of these relationships. Variation in the model parameter values allows for consideration of scientific uncertainty as to the degree each of these factors may be contributing to declines in black duck populations, and thus allows for the investigation of the possible effects of management (e.g., habitat improvement, harvest reductions) under different assumptions. We then used available, historical data on black duck populations (abundance, annual reproduction rates, and survival rates) and possible driving factors (trends in breeding and wintering habitats, harvest rates, and abundance of mallards) to estimate model parameters. Our estimated reproduction submodel included parameters describing negative density feedback of black ducks, positive influence of breeding habitat, and negative influence of mallard densities; our survival submodel included terms for positive influence of winter habitat on reproduction rates, and negative influences of black duck density (i.e., compensation to harvest mortality). Individual models within each group (reproduction, survival) involved various combinations of these factors, and each was given an information theoretic weight for use in subsequent prediction. The reproduction model with highest

  19. SMART-DS: Synthetic Models for Advanced, Realistic Testing: Distribution Systems and Scenarios

    Energy Technology Data Exchange (ETDEWEB)

    Palmintier, Bryan: Hodge, Bri-Mathias

    2017-01-26

    This presentation provides a Smart-DS project overview and status update for the ARPA-e GRID DATA program meeting 2017, including distribution systems, models, and scenarios, as well as opportunities for GRID DATA collaborations.

  20. Chemical Reductive Transformations of Synthetic Organic Compounds. Probe Compound Studies and Mechanistic Modeling

    National Research Council Canada - National Science Library

    Peyton, Gary

    2001-01-01

    .... A kinetic model that was previously developed to describe the results of batch AOP treatment by H2O2/UV did not give satisfactory predictive results obtained when extended to describe flow experiments...

  1. Modeling Behavioral Experiment Interaction and Environmental Stimuli for a Synthetic C. elegans

    Directory of Open Access Journals (Sweden)

    Andoni Mujika

    2017-12-01

    Full Text Available This paper focusses on the simulation of the neural network of the Caenorhabditis elegans living organism, and more specifically in the modeling of the stimuli applied within behavioral experiments and the stimuli that is generated in the interaction of the C. elegans with the environment. To the best of our knowledge, all efforts regarding stimuli modeling for the C. elegansare focused on a single type of stimulus, which is usually tested with a limited subnetwork of the C. elegansneural system. In this paper, we follow a different approach where we model a wide-range of different stimuli, with more flexible neural network configurations and simulations in mind. Moreover, we focus on the stimuli sensation by different types of sensory organs or various sensory principles of the neurons. As part of this work, most common stimuli involved in behavioral assays have been modeled. It includes models for mechanical, thermal, chemical, electrical and light stimuli, and for proprioception-related self-sensed information exchange with the neural network. The developed models have been implemented and tested with the hardware-based Si elegans simulation platform.

  2. The eGo grid model: An open-source and open-data based synthetic medium-voltage grid model for distribution power supply systems

    Science.gov (United States)

    Amme, J.; Pleßmann, G.; Bühler, J.; Hülk, L.; Kötter, E.; Schwaegerl, P.

    2018-02-01

    The increasing integration of renewable energy into the electricity supply system creates new challenges for distribution grids. The planning and operation of distribution systems requires appropriate grid models that consider the heterogeneity of existing grids. In this paper, we describe a novel method to generate synthetic medium-voltage (MV) grids, which we applied in our DIstribution Network GeneratOr (DINGO). DINGO is open-source software and uses freely available data. Medium-voltage grid topologies are synthesized based on location and electricity demand in defined demand areas. For this purpose, we use GIS data containing demand areas with high-resolution spatial data on physical properties, land use, energy, and demography. The grid topology is treated as a capacitated vehicle routing problem (CVRP) combined with a local search metaheuristics. We also consider the current planning principles for MV distribution networks, paying special attention to line congestion and voltage limit violations. In the modelling process, we included power flow calculations for validation. The resulting grid model datasets contain 3608 synthetic MV grids in high resolution, covering all of Germany and taking local characteristics into account. We compared the modelled networks with real network data. In terms of number of transformers and total cable length, we conclude that the method presented in this paper generates realistic grids that could be used to implement a cost-optimised electrical energy system.

  3. The assessment of cold atmospheric plasma treatment of DNA in synthetic models of tissue fluid, tissue and cells

    Science.gov (United States)

    Szili, Endre J.; Gaur, Nishtha; Hong, Sung-Ha; Kurita, Hirofumi; Oh, Jun-Seok; Ito, Masafumi; Mizuno, Akira; Hatta, Akimitsu; Cowin, Allison J.; Graves, David B.; Short, Robert D.

    2017-07-01

    There is a growing literature database that demonstrates the therapeutic potential of cold atmospheric plasma (herein referred to as plasma). Given the breadth of proposed applications (e.g. from teeth whitening to cancer therapy) and vast gamut of plasma devices being researched, it is timely to consider plasma interactions with specific components of the cell in more detail. Plasma can produce highly reactive oxygen and nitrogen species (RONS) such as the hydroxyl radical (OH•), peroxynitrite (ONOO-) and superoxide (\\text{O}2- ) that would readily modify essential biomolecules such as DNA. These modifications could in principle drive a wide range of biological processes. Against this possibility, the reported therapeutic action of plasmas are not underpinned by a particularly deep knowledge of the potential plasma-tissue, -cell or -biomolecule interactions. In this study, we aim to partly address this issue by developing simple models to study plasma interactions with DNA, in the form of DNA-strand breaks. This is carried out using synthetic models of tissue fluid, tissue and cells. We argue that this approach makes experimentation simpler, more cost-effective and faster than compared to working with real biological materials and cells. Herein, a helium plasma jet source was utilised for these experiments. We show that the plasma jet readily induced DNA-strand breaks in the tissue fluid model and in the cell model, surprisingly without any significant poration or rupture of the phospholipid membrane. In the plasma jet treatment of the tissue model, DNA-strand breaks were detected in the tissue mass after pro-longed treatment (on the time-scale of minutes) with no DNA-strand breaks being detected in the tissue fluid model underneath the tissue model. These data are discussed in the context of the therapeutic potential of plasma.

  4. Riding Quality Model for Asphalt Pavement Monitoring Using Phase Array Type L-band Synthetic Aperture Radar (PALSAR

    Directory of Open Access Journals (Sweden)

    Kamiya Yoshikazu

    2010-11-01

    Full Text Available There are difficulties associated with near-real time or frequent pavement monitoring, because it is time consuming and costly. This study aimed to develop a binary logit model for the evaluation of highway riding quality, which could be used to monitor pavement conditions. The model was applied to investigate the influence of backscattering values of Phase Array type L-band Synthetic Aperture Radar (PALSAR. Training data obtained during 3–7 May 2007 was used in the development process, together with actual international roughness index (IRI values collected along a highway in Ayutthaya province, Thailand. The analysis showed that an increase in the backscattering value in the HH or the VV polarization indicated the poor condition of the pavement surface and, of the two, the HH polarization is more suitable for developing riding quality evaluation. The model developed was applied to analyze highway number 3467, to demonstrate its capability. It was found that the assessment accuracy of the prediction of the highway level of service was 97.00%. This is a preliminary study of the proposed technique and more intensive investigation must be carried out using ALOS/PALSAR images in various seasons.

  5. Creating Synthetic Coronal Observational Data From MHD Models: The Forward Technique

    Science.gov (United States)

    Rachmeler, Laurel A.; Gibson, Sarah E.; Dove, James; Kucera, Therese Ann

    2010-01-01

    We present a generalized forward code for creating simulated corona) observables off the limb from numerical and analytical MHD models. This generalized forward model is capable of creating emission maps in various wavelengths for instruments such as SXT, EIT, EIS, and coronagraphs, as well as spectropolari metric images and line profiles. The inputs to our code can be analytic models (of which four come with the code) or 2.5D and 3D numerical datacubes. We present some examples of the observable data created with our code as well as its functional capabilities. This code is currently available for beta-testing (contact authors), with the ultimate goal of release as a SolarSoft package

  6. Saccharomyces cerevisiae and S. kudriavzevii Synthetic Wine Fermentation Performance Dissected by Predictive Modeling.

    Science.gov (United States)

    Henriques, David; Alonso-Del-Real, Javier; Querol, Amparo; Balsa-Canto, Eva

    2018-01-01

    Wineries face unprecedented challenges due to new market demands and climate change effects on wine quality. New yeast starters including non-conventional Saccharomyces species, such as S. kudriavzevii , may contribute to deal with some of these challenges. The design of new fermentations using non-conventional yeasts requires an improved understanding of the physiology and metabolism of these cells. Dynamic modeling brings the potential of exploring the most relevant mechanisms and designing optimal processes more systematically. In this work we explore mechanisms by means of a model selection, reduction and cross-validation pipeline which enables to dissect the most relevant fermentation features for the species under consideration, Saccharomyces cerevisiae T73 and Saccharomyces kudriavzevii CR85. The pipeline involved the comparison of a collection of models which incorporate several alternative mechanisms with emphasis on the inhibitory effects due to temperature and ethanol. We focused on defining a minimal model with the minimum number of parameters, to maximize the identifiability and the quality of cross-validation. The selected model was then used to highlight differences in behavior between species. The analysis of model parameters would indicate that the specific growth rate and the transport of hexoses at initial times are higher for S. cervisiae T73 while S. kudriavzevii CR85 diverts more flux for glycerol production and cellular maintenance. As a result, the fermentations with S. kudriavzevii CR85 are typically slower; produce less ethanol but higher glycerol. Finally, we also explored optimal initial inoculation and process temperature to find the best compromise between final product characteristics and fermentation duration. Results reveal that the production of glycerol is distinctive in S. kudriavzevii CR85, it was not possible to achieve the same production of glycerol with S. cervisiae T73 in any of the conditions tested. This result brings the

  7. Saccharomyces cerevisiae and S. kudriavzevii Synthetic Wine Fermentation Performance Dissected by Predictive Modeling

    Directory of Open Access Journals (Sweden)

    David Henriques

    2018-02-01

    Full Text Available Wineries face unprecedented challenges due to new market demands and climate change effects on wine quality. New yeast starters including non-conventional Saccharomyces species, such as S. kudriavzevii, may contribute to deal with some of these challenges. The design of new fermentations using non-conventional yeasts requires an improved understanding of the physiology and metabolism of these cells. Dynamic modeling brings the potential of exploring the most relevant mechanisms and designing optimal processes more systematically. In this work we explore mechanisms by means of a model selection, reduction and cross-validation pipeline which enables to dissect the most relevant fermentation features for the species under consideration, Saccharomyces cerevisiae T73 and Saccharomyces kudriavzevii CR85. The pipeline involved the comparison of a collection of models which incorporate several alternative mechanisms with emphasis on the inhibitory effects due to temperature and ethanol. We focused on defining a minimal model with the minimum number of parameters, to maximize the identifiability and the quality of cross-validation. The selected model was then used to highlight differences in behavior between species. The analysis of model parameters would indicate that the specific growth rate and the transport of hexoses at initial times are higher for S. cervisiae T73 while S. kudriavzevii CR85 diverts more flux for glycerol production and cellular maintenance. As a result, the fermentations with S. kudriavzevii CR85 are typically slower; produce less ethanol but higher glycerol. Finally, we also explored optimal initial inoculation and process temperature to find the best compromise between final product characteristics and fermentation duration. Results reveal that the production of glycerol is distinctive in S. kudriavzevii CR85, it was not possible to achieve the same production of glycerol with S. cervisiae T73 in any of the conditions tested

  8. Durango: Scalable Synthetic Workload Generation for Extreme-Scale Application Performance Modeling and Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Carothers, Christopher D. [Rensselaer Polytechnic Institute (RPI); Meredith, Jeremy S. [ORNL; Blanco, Marc [Rensselaer Polytechnic Institute (RPI); Vetter, Jeffrey S. [ORNL; Mubarak, Misbah [Argonne National Laboratory; LaPre, Justin [Rensselaer Polytechnic Institute (RPI); Moore, Shirley V. [ORNL

    2017-05-01

    Performance modeling of extreme-scale applications on accurate representations of potential architectures is critical for designing next generation supercomputing systems because it is impractical to construct prototype systems at scale with new network hardware in order to explore designs and policies. However, these simulations often rely on static application traces that can be difficult to work with because of their size and lack of flexibility to extend or scale up without rerunning the original application. To address this problem, we have created a new technique for generating scalable, flexible workloads from real applications, we have implemented a prototype, called Durango, that combines a proven analytical performance modeling language, Aspen, with the massively parallel HPC network modeling capabilities of the CODES framework.Our models are compact, parameterized and representative of real applications with computation events. They are not resource intensive to create and are portable across simulator environments. We demonstrate the utility of Durango by simulating the LULESH application in the CODES simulation environment on several topologies and show that Durango is practical to use for simulation without loss of fidelity, as quantified by simulation metrics. During our validation of Durango's generated communication model of LULESH, we found that the original LULESH miniapp code had a latent bug where the MPI_Waitall operation was used incorrectly. This finding underscores the potential need for a tool such as Durango, beyond its benefits for flexible workload generation and modeling.Additionally, we demonstrate the efficacy of Durango's direct integration approach, which links Aspen into CODES as part of the running network simulation model. Here, Aspen generates the application-level computation timing events, which in turn drive the start of a network communication phase. Results show that Durango's performance scales well when

  9. Natural - synthetic - artificial!

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2010-01-01

    The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life.......The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life....

  10. Micromechanical models to guide the development of synthetic 'brick and mortar' composites

    NARCIS (Netherlands)

    Begley, M.R.; Philips, N.R.; Compton, B.G.; Wilbrink, D.V.; Ritchie, R.O.; Utz, M.

    2012-01-01

    This paper describes a micromechanical analysis of the uniaxial response of composites comprising elastic platelets (bricks) bonded together with thin elastic perfectly plastic layers (mortar). The model yields closed-form results for the spatial variation of displacements in the bricks as a

  11. Distribution of take-home opioid antagonist kits during a synthetic opioid epidemic in British Columbia, Canada: a modelling study

    Directory of Open Access Journals (Sweden)

    Michael A Irvine, PhD

    2018-05-01

    Full Text Available Summary: Background: Illicit use of high-potency synthetic opioids has become a global issue over the past decade. This misuse is particularly pronounced in British Columbia, Canada, where a rapid increase in availability of fentanyl and other synthetic opioids in the local illicit drug supply during 2016 led to a substantial increase in overdoses and deaths. In response, distribution of take-home naloxone (THN overdose prevention kits was scaled up (6·4-fold increase throughout the province. The aim of this study was to estimate the impact of the THN programme in terms of the number of deaths averted over the study period. Methods: We estimated the impact of THN kits on the ongoing epidemic among people who use illicit opioids in British Columbia and explored counterfactual scenarios for the provincial response. A Markov chain model was constructed explicitly including opioid-related deaths, fentanyl-related deaths, ambulance-attended overdoses, and uses of THN kits. The model was calibrated in a Bayesian framework incorporating population data between Jan 1, 2012, and Oct 31, 2016. Findings: 22 499 ambulance-attended overdoses and 2121 illicit drug-related deaths (677 [32%] deaths related to fentanyl were recorded in the study period, mostly since January, 2016. In the same period, 19 074 THN kits were distributed. We estimate that 298 deaths (95% credible interval [CrI] 91–474 were averted by the THN programme. Of these deaths, 226 (95% CrI 125–340 were averted in 2016, following a rapid scale-up in distribution of kits. We infer a rapid increase in fentanyl adulterant at the beginning of 2016, with an estimated 2·3 times (95% CrI 2·0–2·9 increase from 2015 to 2016. Counterfactual modelling indicated that an earlier scale-up of the programme would have averted an additional 118 deaths (95% CrI 64–207. Our model also indicated that the increase in deaths could parsimoniously be explained through a change in the fentanyl

  12. Synthetic Cannabinoids.

    Science.gov (United States)

    Mills, Brooke; Yepes, Andres; Nugent, Kenneth

    2015-07-01

    Synthetic cannabinoids (SCBs), also known under the brand names of "Spice," "K2," "herbal incense," "Cloud 9," "Mojo" and many others, are becoming a large public health concern due not only to their increasing use but also to their unpredictable toxicity and abuse potential. There are many types of SCBs, each having a unique binding affinity for cannabinoid receptors. Although both Δ-tetrahydrocannabinol (THC) and SCBs stimulate the same receptors, cannabinoid receptor 1 (CB1) and cannabinoid receptor 2 (CB2), studies have shown that SCBs are associated with higher rates of toxicity and hospital admissions than is natural cannabis. This is likely due to SCBs being direct agonists of the cannabinoid receptors, whereas THC is a partial agonist. Furthermore, the different chemical structures of SCBs found in Spice or K2 may interact in unpredictable ways to elicit previously unknown, and the commercial products may have unknown contaminants. The largest group of users is men in their 20s who participate in polydrug use. The most common reported toxicities with SCB use based on studies using Texas Poison Control records are tachycardia, agitation and irritability, drowsiness, hallucinations, delusions, hypertension, nausea, confusion, dizziness, vertigo and chest pain. Acute kidney injury has also been strongly associated with SCB use. Treatment mostly involves symptom management and supportive care. More research is needed to identify which contaminants are typically found in synthetic marijuana and to understand the interactions between different SBCs to better predict adverse health outcomes.

  13. Synthetic model of a new deoxybenzoin derivative from Deguelia hatschbachii A.M.G. Azevedo

    International Nuclear Information System (INIS)

    Magalhaes, A.F.; Magalhaes, E.G.; Trazzi, G.; Moraes, V.R. de S.

    2005-01-01

    In this paper we describe the synthesis of 2',4'-dimethoxy-8-(propyl-2-one)-deoxybenzoin, a new compound employed as a model for the comparison with the respective spectral data for 6',4-dihydroxy-3'-(3,3- dimethylallyl)-2 , 2 - dimethylchromene(5 , 6 : 5',4')-2'-methoxy-8-(propyl-2-one) deoxybenzoin, recently isolated from Deguelia hatschbachii A.M.G. Azevedo. Both compounds have a 'propyl-2-one' group attached to C-8 of the deoxybenzoin skeleton, for which there is no precedent in the literature. The Friedel-Crafts reaction of 1,3-dimethoxybenzene with phenylacetyl chloride furnished 2',4'-dimethoxydeoxybenzoin, that after reaction with allyl bromide gave 2',4'-dimethoxy-8-(allyl)-deoxybenzoin . Wacker oxidation gave the desired model compound in 15% overall yield. The corresponding spectral data reinforced the structure previously determined for the natural product. (author)

  14. sbml-diff: A Tool for Visually Comparing SBML Models in Synthetic Biology.

    Science.gov (United States)

    Scott-Brown, James; Papachristodoulou, Antonis

    2017-07-21

    We present sbml-diff, a tool that is able to read a model of a biochemical reaction network in SBML format and produce a range of diagrams showing different levels of detail. Each diagram type can be used to visualize a single model or to visually compare two or more models. The default view depicts species as ellipses, reactions as rectangles, rules as parallelograms, and events as diamonds. A cartoon view replaces the symbols used for reactions on the basis of the associated Systems Biology Ontology terms. An abstract view represents species as ellipses and draws edges between them to indicate whether a species increases or decreases the production or degradation of another species. sbml-diff is freely licensed under the three-clause BSD license and can be downloaded from https://github.com/jamesscottbrown/sbml-diff and used as a python package called from other software, as a free-standing command-line application, or online using the form at http://sysos.eng.ox.ac.uk/tebio/upload.

  15. Toward a synthetic economic systems modeling tool for sustainable exploitation of ecosystems.

    Science.gov (United States)

    Richardson, Colin; Courvisanos, Jerry; Crawford, John W

    2011-02-01

    Environmental resources that underpin the basic human needs of water, energy, and food are predicted to become in such short supply by 2050 that global security and the well-being of millions will be under threat. These natural commodities have been allowed to reach crisis levels of supply because of a failure of economic systems to sustain them. This is largely because there have been no means of integrating their exploitation into any economic model that effectively addresses ecological systemic failures in a way that provides an integrated ecological-economic tool that can monitor and evaluate market and policy targets. We review the reasons for this and recent attempts to address the problem while identifying outstanding issues. The key elements of a policy-oriented economic model that integrates ecosystem processes are described and form the basis of a proposed new synthesis approach. The approach is illustrated by an indicative case study that develops a simple model for rainfed and irrigated food production in the Murray-Darling basin of southeastern Australia. © 2011 New York Academy of Sciences.

  16. REE Partition Coefficients from Synthetic Diogenite-Like Enstatite and the Implications of Petrogenetic Modeling

    Science.gov (United States)

    Schwandt, C. S.; McKay, G. A.

    1996-01-01

    Determining the petrogenesis of eucrites (basaltic achondrites) and diogenites (orthopyroxenites) and the possible links between the meteorite types was initiated 30 years ago by Mason. Since then, most investigators have worked on this question. A few contrasting theories have emerged, with the important distinction being whether or not there is a direct genetic link between eucrites and diogenites. One theory suggests that diogenites are cumulates resulting from the fractional crystallization of a parent magma with the eucrites crystallizing, from the residual magma after separation from the diogenite cumulates. Another model proposes that diogenites are cumulates formed from partial melts derived from a source region depleted by the prior generation of eucrite melts. It has also been proposed that the diogenites may not be directly linked to the eucrites and that they are cumulates derived from melts that are more orthopyroxene normative than the eucrites. This last theory has recently received more analytical and experimental support. One of the difficulties with petrogenetic modeling is that it requires appropriate partition coefficients for modeling because they are dependent on temperature, pressure, and composition. For this reason, we set out to determine minor- and trace-element partition coefficients for diogenite-like orthopyroxene. We have accomplished this task and now have enstatite/melt partition coefficients for Al, Cr, Ti, La, Ce, Nd, Sm, Eu, Dy, Er, Yb, and La.

  17. Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma.

    Science.gov (United States)

    Smestad, John; Hamidi, Oksana; Wang, Lin; Holte, Molly Nelson; Khazal, Fatimah Al; Erber, Luke; Chen, Yue; Maher, L James

    2018-01-19

    Succinate dehydrogenase (SDH)-loss pheochromocytoma and paraganglioma (PPGL) are tumors driven by metabolic derangement. SDH loss leads to accumulation of intracellular succinate, which competitively inhibits dioxygenase enzymes, causing activation of pseudohypoxic signaling and hypermethylation of histones and DNA. The mechanisms by which these alterations lead to tumorigenesis are unclear, however. In an effort to fundamentally understand how SDH loss reprograms cell biology, we developed an immortalized mouse embryonic fibroblast cell line with conditional disruption of Sdhc and characterize the kinetics of Sdhc gene rearrangement, SDHC protein loss, succinate accumulation, and the resultant hypoproliferative phenotype. We further perform global transcriptomic, epigenomic, and proteomic characterization of changes resulting from SDHC loss, identifying specific perturbations at each biological level. We compare the observed patterns of epigenomic derangement to another previously-described immortalized mouse chromaffin cell model of SDHB loss, and compare both models to human SDH-loss tumors. Finally, we perform analysis of SDHC synthetic lethality with lactate dehydrogenase A (LDHA) and pyruvate carboxylase (PCX), which are important for regeneration of NAD+ and aspartate biosynthesis, respectively. Our data show that SDH-loss cells are selectively vulnerable to LDH genetic knock-down or chemical inhibition, suggesting that LDH inhibition may be an effective therapeutic strategy for SDH-loss PPGL.

  18. Complexation modeling of uranium and other actinides by organic compounds of natural or synthetic origin

    International Nuclear Information System (INIS)

    Bouby, M.

    1998-01-01

    The behaviour of nuclear wastes raises many questions, the answers of which require a precise knowledge of the physical, chemical and biological processes affecting the properties of the radio-elements present in the wastes. Three ways of research are approached. The results obtained give some elements of answer to these questions. The experimental methods that have been used are the neutron activation analysis, the UV-visible spectrophotometry, and the time-resolved laser spectro-fluorimetry. The analysis of the results has permitted to model part of the phenomena evidenced by using suitable ionic force correction models (Davies or MSA type) when chemical equilibria have been considered. The main results show: the bio-sorption capacities of Mycobacterium phlei microorganism with respect to UO 2 2+ and NpO 2+ cations such as: Q eq (UO 2 2+ ) = 60 and Q eq (NpO 2+ ) = 444 moles of cation per g of dry biomass; the retention capacities, in various leaching conditions, of this bacteria of the preliminarily adsorbed ions; the complexation properties of two siderophores with respect to UO 2 2+ , U 4+ and Th 4+ cations. One siderophore, Pyoverdine A, shows a selectiveness which is explained by the value of the thermodynamic equilibrium constant determined for each cation using the same model: K(UO 2 2+ ) 4+ ) 4+ ). The behaviour in highly acid environment (HCl and HClO 4 up to 12 M) of acylisoxazolone HPBI (1-phenyl-4-benzoyl-5-isoxazolone) and the value of its acidity thermodynamical constant (0.13 th 4 and CF 3 SO 3 H up to 12 M). It seems that a complexation between uranyl and the counter-ions present in the solution occurs. (J.S.)

  19. Evaluation of MODFLOW-LGR in Connection with a Synthetic Regional-Scale Model

    DEFF Research Database (Denmark)

    Vilhelmsen, Troels Norvin; Christensen, Steen; Mehl, Steffen

    2012-01-01

    flow problem more efficiently than the SN method. The MODFLOW-LGR results were compared with the results obtained using a globally coarse (GC) grid. The LGR simulations required one to two orders of magnitude longer run times than the GC model. However, the improvements of the numerical resolution...... around the buried valley substantially increased the accuracy of simulated heads and flows compared with the GC simulation. Accuracy further increased locally around the valley flanks when improving the geological resolution using the refined grid. Finally, comparing MODFLOW-LGR simulation...

  20. Mapping Offshore Winds Around Iceland Using Satellite Synthetic Aperture Radar and Mesoscale Model Simulations

    DEFF Research Database (Denmark)

    Hasager, Charlotte Bay; Badger, Merete; Nawri, Nikolai

    2015-01-01

    effects, gap flow, coastal barrier jets, and atmospheric gravity waves are not only observed in SAR, but are also modeled well from HARMONIE. Offshore meteorological observations are not available, but wind speed and wind direction measurements from coastal meteorological masts are found to compare well...... to nearby offshore locations observed by SAR. More than 2500 SAR scenes from the Envisat ASAR wide swathmode are used for wind energy resource estimation. The wind energy potential observed from satellite SAR shows high values above 1000 Wm −2 in coastal regions in the south, east, and west, with lower...

  1. Synthetic Brainbows

    KAUST Repository

    Wan, Y.

    2013-06-01

    Brainbow is a genetic engineering technique that randomly colorizes cells. Biological samples processed with this technique and imaged with confocal microscopy have distinctive colors for individual cells. Complex cellular structures can then be easily visualized. However, the complexity of the Brainbow technique limits its applications. In practice, most confocal microscopy scans use different florescence staining with typically at most three distinct cellular structures. These structures are often packed and obscure each other in rendered images making analysis difficult. In this paper, we leverage a process known as GPU framebuffer feedback loops to synthesize Brainbow-like images. In addition, we incorporate ID shuffing and Monte-Carlo sampling into our technique, so that it can be applied to single-channel confocal microscopy data. The synthesized Brainbow images are presented to domain experts with positive feedback. A user survey demonstrates that our synthetic Brainbow technique improves visualizations of volume data with complex structures for biologists.

  2. Length-scales of Slab-induced Asthenospheric Deformation from Geodynamic Modeling, Mantle Deformation Fabric, and Synthetic Shear Wave Splitting

    Science.gov (United States)

    Jadamec, M. A.; MacDougall, J.; Fischer, K. M.

    2017-12-01

    The viscosity structure of the Earth's interior is critically important, because it places a first order constraint on plate motion and mantle flow rates. Geodynamic models using a composite viscosity based on experimentally derived flow laws for olivine aggregates show that lateral viscosity variations emerge in the upper mantle due to the subduction dynamics. However, the length-scale of this transition is still not well understood. Two-dimensional numerical models of subduction are presented that investigate the effect of initial slab dip, maximum yield stress (slab strength), and viscosity formulation (Newtonian versus composite) on the emergent lateral viscosity variations in the upper-mantle and magnitude of slab-driven mantle flow velocity. Significant viscosity reductions occur in regions of large flow velocity gradients due to the weakening effect of the dislocation creep deformation mechanism. The dynamic reductions in asthenospheric viscosity (less than 1018 Pa s) occur within approximately 500 km from driving force of the slab, with peak flow velocities occurring in models with a lower yield stress (weaker slab) and higher stress exponent. This leads to a sharper definition of the rheological base of the lithosphere and implies lateral variability in tractions along the base of the lithosphere. As the dislocation creep mechanism also leads to mantle deformation fabric, we then examine the spatial variation in the LPO development in the asthenosphere and calculate synthetic shear wave splitting. The models show that olivine LPO fabric in the asthenosphere generally increases in alignment strength with increased proximity to the slab, but can be transient and spatially variable on small length scales. The vertical flow fields surrounding the slab tip can produce shear-wave splitting variations with back-azimuth that deviate from the predictions of uniform trench-normal anisotropy, a result that bears on the interpretation of complexity in shear

  3. Biogeochemical Responses and Feedbacks to Climate Change: Synthetic Meta-Analyses Relevant to Earth System Models

    Energy Technology Data Exchange (ETDEWEB)

    van Gestel, Natasja; Jan van Groenigen, Kees; Osenberg, Craig; Dukes, Jeffrey; Dijkstra, Paul

    2018-03-20

    This project examined the sensitivity of carbon in land ecosystems to environmental change, focusing on carbon contained in soil, and the role of carbon-nitrogen interactions in regulating ecosystem carbon storage. The project used a combination of empirical measurements, mathematical models, and statistics to partition effects of climate change on soil into processes enhancing soil carbon and processes through which it decomposes. By synthesizing results from experiments around the world, the work provided novel insight on ecological controls and responses across broad spatial and temporal scales. The project developed new approaches in meta-analysis using principles of element mass balance and large datasets to derive metrics of ecosystem responses to environmental change. The project used meta-analysis to test how nutrients regulate responses of ecosystems to elevated CO2 and warming, in particular responses of nitrogen fixation, critical for regulating long-term C balance.

  4. Turbulent transport modeling in the edge plasma of tokamaks: verification, validation, simulation and synthetic diagnostics

    International Nuclear Information System (INIS)

    Colin-Bellot, Clothilde

    2015-01-01

    The possibility to produce power by using magnetically confined fusion is a scientific and technological challenge. The perspective of ITER conveys strong signals to intensify modeling effort on magnetized fusion plasmas. The success of the fusion operation is conditioned by the quality of plasma confinement in the core of the reactor and by the control of plasma exhaust on the wall. Both phenomena are related to turbulent cross-field transport that is at the heart of the notion of magnetic confinement studies, particle and heat losses. The study of edge phenomena is therefore complicated by a particularly complex magnetic geometry.This calls for an improvement of our capacity to develop numerical tools able to reproduce turbulent transport properties reliable to predict particle and energy fluxes on the plasma facing components. This thesis introduces the TOKAM3X fluid model to simulate edge plasma turbulence. A special focus is made on the code Verification and the Validation. It is a necessary step before using a code as a predictive tool. Then new insights on physical properties of the edge plasma turbulence are explored. In particular, the poloidal asymmetries induced by turbulence and observed experimentally in the Low-Field-Side of the devices are investigated in details. Great care is dedicated to the reproduction of the MISTRAL base case which consists in changing the magnetic configuration and observing the impact on parallel flows in the poloidal plane. The simulations recover experimental measurements and provide new insights on the effect of the plasma-wall contact position location on the turbulent features, which were not accessible in experiments. (author) [fr

  5. Proton and metal ion binding to natural organic polyelectrolytes-I. Studies with synthetic model compounds

    Science.gov (United States)

    Marinsky, J.A.; Reddy, M.M.

    1984-01-01

    A unified physico-chemical model, based on a modified Henderson-Hasselbalch equation, for the analysis of ion complexation reactions involving charged polymeric systems is presented and verified. In this model pH = pKa+p(??Ka) + log(??/1 - ??) where Ka is the intrinsic acid dissociation constant of the ionizable functional groups on the polymer, ??Ka is the deviation of the intrinsic constant due to electrostatic interaction between the hydrogen ion and the polyanion, and alpha (??) is the polyacid degree of ionization. Using this approach pKa values for repeating acidic units of polyacrylic (PAA) and polymethacrylic (PMA) acids were found to be 4.25 ?? 0.03 and 4.8 ?? 0.1, respectively. The polyion electrostatic deviation term derived from the potentiometric titration data (i.e. p(??Ka)) is used to calculate metal ion concentration at the complexation site on the surface of the polyanion. Intrinsic cobalt-polycarboxylate binding constants (7.5 for PAA and 5.6 for PMA), obtained using this procedure, are consistent with the range of published binding constants for cobalt-monomer carboxylate complexes. In two phase systems incorporation of a Donnan membrane potential term allows determination of the intrinsic pKa of a cross-linked PMA gel, pKa = 4.83, in excellent agreement with the value obtained for the linear polyelectrolyte and the monomer. Similarly, the intrinsic stability constant for cobalt ion binding to a PMA-gel (??CoPMA+ = 11) was found to be in agreement with the linear polyelectrolyte analogue and the published data for cobalt-carboxylate monodentate complexes. ?? 1984.

  6. Complexation modelling of uranium and other actinides by organic compounds of natural or synthetic origin

    International Nuclear Information System (INIS)

    Bouby, M.

    1998-01-01

    The future of nuclear wastes raises a lot of questions. Their resolution require an accurate knowledge of the physical, chemical and biological processes which affect the properties of radioelements constituting the wastes. 3 research themes have been approached. The experimental methods used are: neutronic activation analysis, UV-visible spectrophotometry and time-resolved induced laser spectro-fluorimetry. A part of the phenomena has been modelled by ionic strength correction models (as Davies or MSA). The main results have revealed: 1)the bio-sorption capacities of the microorganism (Mycobacterium phlei) for UO 2 2+ and NpO 2+ (in conditions where the specific adsorption capacities Qe(UO 2 2+ )=60 and Qe(NpO 2+ )=444 moles cations/g dry biomass 2)the retention capacities, in various leaching conditions, by this bacteria of the ions initially adsorbed 3)the complexation properties of 2 siderophores for the cations UO 2 2+ , U 4+ and Th 4+ . The thermodynamical equilibrium constants were determined for one of the siderophore: the pyoverdine A; they were such that KUO 2 2+ ≤KU 4+ ≤KTh 4+ 4)in very acidic media (HCl and HClO 4 until 12 M), the behaviour of the acylisoxazolone HPBI (1-phenyl-4-benzoyl-5-isoxazolone) and the value of its acidity thermodynamical constant is such that 0.13≤KATh≤0.32 at 25 degrees Celsius 5)the variations of the fluorescence properties of the uranyl cation in terms of the acidity of the concentrated media (HClO 4 and CF 3 SO 3 H) in which they are in solution; it seems that a complexation between the uranyl ion and the counter-ions present in solution occur. (O.M.)

  7. Measurement needs guided by synthetic radar scans in high-resolution model output

    Science.gov (United States)

    Varble, A.; Nesbitt, S. W.; Borque, P.

    2017-12-01

    Microphysical and dynamical process interactions within deep convective clouds are not well understood, partly because measurement strategies often focus on statistics of cloud state rather than cloud processes. While processes cannot be directly measured, they can be inferred with sufficiently frequent and detailed scanning radar measurements focused on the life cycleof individual cloud regions. This is a primary goal of the 2018-19 DOE ARM Cloud, Aerosol, and Complex Terrain Interactions (CACTI) and NSF Remote sensing of Electrification, Lightning, And Mesoscale/microscale Processes with Adaptive Ground Observations (RELAMPAGO) field campaigns in central Argentina, where orographic deep convective initiation is frequent with some high-impact systems growing into the tallest and largest in the world. An array of fixed and mobile scanning multi-wavelength dual-polarization radars will be coupled with surface observations, sounding systems, multi-wavelength vertical profilers, and aircraft in situ measurements to characterize convective cloud life cycles and their relationship with environmental conditions. While detailed cloud processes are an observational target, the radar scan patterns that are most ideal for observing them are unclear. They depend on the locations and scales of key microphysical and dynamical processes operating within the cloud. High-resolution simulations of clouds, while imperfect, can provide information on these locations and scales that guide radar measurement needs. Radar locations are set in the model domain based on planned experiment locations, and simulatedorographic deep convective initiation and upscale growth are sampled using a number of different scans involving RHIs or PPIs with predefined elevation and azimuthal angles that approximately conform with radar range and beam width specifications. Each full scan pattern is applied to output atsingle model time steps with time step intervals that depend on the length of time

  8. Optimal decolorization and kinetic modeling of synthetic dyes by Pseudomonas strains.

    Science.gov (United States)

    Yu, J; Wang, X; Yue, P L

    2001-10-01

    Pseudomonas spp were isolated from an anaerobic-aerobic dyeing house wastewater treatment facility as the most active azo-dye degraders. Decolorization of azo dyes and non-azo dyes including anthraquinone, metal complex and indigo was compared with individual strains and a bacterial consortium consisting of the individual strain and municipal sludge (50 50wt). The consortium showed a significant improvement on decolorization of two recalcitrant non-azo dyes, but little effect on the dyes that the individual strains could degrade to a great or moderate extent. Decolorization of Acid violet 7 (monoazo) by a Pseudomonas strain GM3 was studied in detail under various conditions. The optimum decolorization activity was observed in a narrow pH range (7-8), a narrow temperature range (35-40 degrees C), and at the presence of organic and ammonium nitrogen. Nitrate had a severe inhibitory effect on azo dye decolorization: 10 mg/L led to 50% drop in decolorization activity and 1000 mg/L to complete activity depression. A kinetic model is established giving the dependence of decolorization rate on cell mass concentration (first-order) and dye concentration (half order). The rate increased with temperature from 10 to 35 C, which can be predicted by Arrhenius equation with the activation energy of 16.87 kcal/mol and the frequency factor of 1.49 x 10(11) (mg L)1/2/g DCM min.

  9. Micromechanical models to guide the development of synthetic ‘brick and mortar’ composites

    Science.gov (United States)

    Begley, Matthew R.; Philips, Noah R.; Compton, Brett G.; Wilbrink, David V.; Ritchie, Robert O.; Utz, Marcel

    2012-08-01

    This paper describes a micromechanical analysis of the uniaxial response of composites comprising elastic platelets (bricks) bonded together with thin elastic perfectly plastic layers (mortar). The model yields closed-form results for the spatial variation of displacements in the bricks as a function of constituent properties, which can be used to calculate the effective properties of the composite, including elastic modulus, strength and work-to-failure. Regime maps are presented which indicate critical stresses for failure of the bricks and mortar as a function of constituent properties and brick architecture. The solution illustrates trade-offs between elastic modulus, strength and dissipated work that are a result of transitions between various failure mechanisms associated with brick rupture and rupture of the interfaces. Detailed scaling relationships are presented with the goal of providing material developers with a straightforward means to identify synthesis targets that balance competing mechanical behaviors and optimize material response. Ashby maps are presented to compare potential brick and mortar composites with existing materials, and identify future directions for material development.

  10. Effect of variation of geometric parameters on the flow within a synthetic models of lower human airways

    Science.gov (United States)

    Espinosa Moreno, Andres Santiago; Duque Daza, Carlos Alberto

    2017-11-01

    The effects of variation of two geometric parameters, such as bifurcation angle and carina rounding radius, during the respiratory inhalation process, are studied numerically using two synthetic models of lower human airways. Laminar flow simulations were performed for six angles and three rounding radius, for 500, 1000, 1500 and 2000 for Reynolds numbers. Numerical results showed the existence of a direct relationship between the deformation of the velocity profiles (effect produced by the bifurcation) and the vortical structures observed through the secondary flow patterns. It is observed that the location of the vortices (and their related saddle point) is associated with the displacement of the velocity peak. On the other hand, increasing the angle and the rounding radius seems to bring about a growth of the pressure drop, which in turn displaces the distribution and peaks of the maximum shear stresses of the carina, that is, of the bifurcation point. Some physiological effects associated with the phenomena produced by these geometric variations are also discussed.

  11. Mathematical model for carbon dioxide evolution from the thermophilic composting of synthetic food wastes made of dog food

    International Nuclear Information System (INIS)

    Chang, J.I.; Tsai, J.J.; Wu, K.H.

    2005-01-01

    The impacts of the aeration and the agitation on the composting process of synthetic food wastes made of dog food were studied in a laboratory-scale reactor. Two major peaks of CO 2 evolution rate were observed. Each peak represented an independent stage of composting associated with the activities of thermophilic bacteria. CO 2 evolutions known to correlate well with microbial activities and reactor temperatures were fitted successfully to a modified Gompertz equation, which incorporated three biokinetic parameters, namely, CO 2 evolution potential, specific CO 2 evolution rate, and lag phase time. No parameters that describe the impact of operating variables are involved. The model is only valid for the specified experimental conditions and may look different with others. The effects of operating parameters such as aeration and agitation were studied statistically with multivariate regression technique. Contour plots were constructed using regression equations for the examination of the dependence of CO 2 evolution potentials on aeration and agitation. In the first stage, a maximum CO 2 evolution potential was found when the aeration rate and the agitation parameter were set at 1.75 l/kg solids-min and 0.35, respectively. In the second stage, a maximum existed when the aeration rate and the agitation parameter were set at 1.8 l/kg solids-min and 0.5, respectively. The methods presented here can also be applied for the optimization of large-scale composting facilities that are operated differently and take longer time

  12. Synthetic Astrobiology

    Science.gov (United States)

    Rothschild, Lynn J.

    2017-01-01

    "Are we alone?" is one of the primary questions of astrobiology, and whose answer defines our significance in the universe. Unfortunately, this quest is hindered by the fact that we have only one confirmed example of life, that of earth. While this is enormously helpful in helping to define the minimum envelope for life, it strains credulity to imagine that life, if it arose multiple times, has not taken other routes. To help fill this gap, our lab has begun using synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - as an enabling technology. One theme, the "Hell Cell" project, focuses on creating artificial extremophiles in order to push the limits for Earth life, and to understand how difficult it is for life to evolve into extreme niches. In another project, we are re-evolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids.

  13. Prevention of Prostate Cancer with Oleanane Synthetic Triterpenoid CDDO-Me in the TRAMP Mouse Model of Prostate Cancer

    International Nuclear Information System (INIS)

    Gao, Xiaohua; Deeb, Dorrah; Liu, Yongbo; Arbab, Ali S.; Divine, George W.; Dulchavsky, Scott A.; Gautam, Subhash C.

    2011-01-01

    2-Cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid (CDDO), a synthetic analog of oleanolic acid, and its C28 methyl ester derivative (CDDO-Me), have shown potent antitumorigenic activity against a wide range of cancer cell lines, including prostate cancer cells in vitro, and inhibited the development of liver and lung cancer in vivo. In the present study, we examined the efficacy of CDDO-Me in preventing the development and progression of prostate cancer in the transgenic adenocarinoma of the mouse prostate (TRAMP) model. CDDO-Me inhibited the growth of murine TRAMPC-1 prostate cancer cells by inducing apoptosis through the inhibition of antiapoptotic p-Akt, p-mTOR and NF-κB. Early intervention with CDDO-Me (7.5 mg/kg) initiated at five weeks of age for 20 wk inhibited the progression of the preneoplastic lesions (low-grade PIN and high-grade-PIN) to adenocarcinoma in the dorsolateral prostate (DLP) and ventral prostate (VP) lobes of TRAMP mice. Even delayed administration of CDDO-Me started at 12 wk of age for 12 wk inhibited the development of adenocarcimona of the prostate. Both early and late treatment with CDDO-Me inhibited the metastasis of tumor to the distant organs. Treatment with CDDO-Me inhibited the expression of prosurvival p-Akt and NF-κB in the prostate and knocking-down Akt in TRAMPC-1 tumor cells sensitized them to CDDO-Me. These findings indicated that Akt is a target for apoptoxicity in TRAMPC-1 cells in vitro and potentially a target of CDDO-Me for inhibition of prostate cancer in vivo

  14. ADEQUATE UV EXPOSURES FOR HEALTHY LIFE: IN SITU MONITORING AND MODEL CALCULATION OF THE VITAMIN-D-SYNTHETIC CAPACITY OF SUNLIGHT

    Directory of Open Access Journals (Sweden)

    Irina Terenetskaya

    2012-06-01

    Full Text Available Vitamin D which is formed upon UV solar radiation in human skin is essential in many physiological functions. To estimate beneficial vitamin-D-synthetic capacity of sunlight a bio-equivalent UV dosimeter that is based on the same molecular photochemistry from which vitamin D is photosynthesized in human skin has been developed. The examples of an in situ monitoring of the vitamin-D-synthetic capacity of sunlight using an in vitro model of vitamin D synthesis are presented, and various operational principles of the UV biodosimeter are discussed. In addition, reliable algorithm is presented for direct calculation of previtamin D3 accumulation using the photoreaction mathematical model with solar UV spectra as input data. Critical dependence of previtamin D3 accumulation on cloudiness and aerosols is demonstrated.

  15. Modeling L-band synthetic aperture radar observations through dielectric changes in soil moisture and vegetation over shrublands

    Science.gov (United States)

    L-band airborne synthetic aperture radar observations were made over California shrublands to better understand the effects by soil and vegetation parameters on backscatter. Temporal changes in radar backscattering coefficient (s0) of up to 3 dB were highly correlated to surface soil moisture but no...

  16. How Managed Care Affects Medicaid Utilization : A Synthetic Difference-in-Difference Zero-Inflated Count Model

    NARCIS (Netherlands)

    Freund, D.A.; Kniesner, T.J.; LoSasso, A.T.

    1996-01-01

    We develop a synthetic difference-in-differences statistical design to apply to experimental data for adult women living in Hennepin County, Minnesota, to estimate the impact of Medicaid managed care on various modes of medical care use.Because the outcomes of interest are utilization counts with

  17. The Development and Validation of an In Vitro Airway Model to Assess Realistic Airway Deposition and Drug Permeation Behavior of Orally Inhaled Products Across Synthetic Membranes.

    Science.gov (United States)

    Huynh, Bao K; Traini, Daniela; Farkas, Dale R; Longest, P Worth; Hindle, Michael; Young, Paul M

    2018-04-01

    Current in vitro approaches to assess lung deposition, dissolution, and cellular transport behavior of orally inhaled products (OIPs) have relied on compendial impactors to collect drug particles that are likely to deposit in the airway; however, the main drawback with this approach is that these impactors do not reflect the airway and may not necessarily represent drug deposition behavior in vivo. The aim of this article is to describe the development and method validation of a novel hybrid in vitro approach to assess drug deposition and permeation behavior in a more representative airway model. The medium-sized Virginia Commonwealth University (VCU) mouth-throat (MT) and tracheal-bronchial (TB) realistic upper airway models were used in this study as representative models of the upper airway. The TB model was modified to accommodate two Snapwell ® inserts above the first TB airway bifurcation region to collect deposited nebulized ciprofloxacin-hydrochloride (CIP-HCL) droplets as a model drug aerosol system. Permeation characteristics of deposited nebulized CIP-HCL droplets were assessed across different synthetic membranes using the Snapwell test system. The Snapwell test system demonstrated reproducible and discriminatory drug permeation profiles for already dissolved and nebulized CIP-HCL droplets through a range of synthetic permeable membranes under different test conditions. The rate and extent of drug permeation depended on the permeable membrane material used, presence of a stirrer in the receptor compartment, and, most importantly, the drug collection method. This novel hybrid in vitro approach, which incorporates a modified version of a realistic upper airway model, coupled with the Snapwell test system holds great potential to evaluate postairway deposition characteristics, such as drug permeation and particle dissolution behavior of OIPs. Future studies will expand this approach using a cell culture-based setup instead of synthetic membranes, within a

  18. Programming languages for synthetic biology.

    Science.gov (United States)

    Umesh, P; Naveen, F; Rao, Chanchala Uma Maheswara; Nair, Achuthsankar S

    2010-12-01

    In the backdrop of accelerated efforts for creating synthetic organisms, the nature and scope of an ideal programming language for scripting synthetic organism in-silico has been receiving increasing attention. A few programming languages for synthetic biology capable of defining, constructing, networking, editing and delivering genome scale models of cellular processes have been recently attempted. All these represent important points in a spectrum of possibilities. This paper introduces Kera, a state of the art programming language for synthetic biology which is arguably ahead of similar languages or tools such as GEC, Antimony and GenoCAD. Kera is a full-fledged object oriented programming language which is tempered by biopart rule library named Samhita which captures the knowledge regarding the interaction of genome components and catalytic molecules. Prominent feature of the language are demonstrated through a toy example and the road map for the future development of Kera is also presented.

  19. Fibrils from designed non-amyloid-related synthetic peptides induce AA-amyloidosis during inflammation in an animal model.

    Directory of Open Access Journals (Sweden)

    Per Westermark

    Full Text Available BACKGROUND: Mouse AA-amyloidosis is a transmissible disease by a prion-like mechanism where amyloid fibrils act by seeding. Synthetic peptides with no amyloid relationship can assemble into amyloid-like fibrils and these may have seeding capacity for amyloid proteins. PRINCIPAL FINDINGS: Several synthetic peptides, designed for nanotechnology, have been examined for their ability to produce fibrils with Congo red affinity and concomitant green birefringence, affinity for thioflavin S and to accelerate AA-amyloidosis in mice. It is shown that some amphiphilic fibril-forming peptides not only produced Congo red birefringence and showed affinity for thioflavin S, but they also shortened the lag phase for systemic AA-amyloidosis in mice when they were given intravenously at the time of inflammatory induction with silver nitride. Peptides, not forming amyloid-like fibrils, did not have such properties. CONCLUSIONS: These observations should caution researchers and those who work with synthetic peptides and their derivatives to be aware of the potential health concerns.

  20. Modeling the water use efficiency of soybean and maize plants under environmental stresses: application of a synthetic model of photosynthesis-transpiration based on stomatal behavior.

    Science.gov (United States)

    Yu, Gui-Rui; Wang, Qiu-Feng; Zhuang, Jie

    2004-03-01

    Understanding the variability of plant WUE and its control mechanism can promote the comprehension to the coupling relationship of water and carbon cycle in terrestrial ecosystem, which is the foundation for developing water-carbon coupling cycle model. In this paper, we made clear the differences of net assimilation rate, transpiration rate, and WUE between the two species by comparing the experiment data of soybean (Glycine max Merr.) and maize (Zea mays L.) plants under water and soil nutrient stresses. WUE of maize was about two and a half times more than that of soybean in the same weather conditions. Enhancement of water stresses led to the marked decrease of Am and Em of two species, but water stresses of some degree could improve WUE, and this effect was more obvious for soybean. WUE of the two species changed with psiL in a second-order curve relation, and the WUE at high fertilization was higher than that at low fertilization, this effect was especially obvious for maize. Moreover, according to the synthetic model of photosynthesis-transpiration based on stomatal behavior (SMPTSB) presented by Yu et al. (2001), the WUE model and its applicability were discussed with the data measured in this experiment. The WUE estimated by means of the model accorded well with the measured values. However, this model underestimated the WUE for maize slightly, thus further improvement on the original model was made in this study. Finally, by discussing some physiological factors controlling Am and WUE, we made clear the physiological explanation for differences of the relative contributions of stomata- and mesophyll processes to control of Am and WUE, and the applicability of WUE model between the two species. Because the requirement to stomatal conductance by unit change of net assimilation rate is different, the responses of opening-closing activity of stomata to environmental stresses are different between the two species. To obtain the same level of net assimilation

  1. Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking: anchors modified polyanions interference with the HIV-1 fusion mediator.

    Science.gov (United States)

    Tsvetkov, Vladimir B; Serbin, Alexander V

    2014-06-01

    In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 (HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [HR1]3 of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics (MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]3 in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands-target interactions. Some newly MD-discovered aspects of the ligand's backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.

  2. Plant synthetic biology.

    Science.gov (United States)

    Liu, Wusheng; Stewart, C Neal

    2015-05-01

    Plant synthetic biology is an emerging field that combines engineering principles with plant biology toward the design and production of new devices. This emerging field should play an important role in future agriculture for traditional crop improvement, but also in enabling novel bioproduction in plants. In this review we discuss the design cycles of synthetic biology as well as key engineering principles, genetic parts, and computational tools that can be utilized in plant synthetic biology. Some pioneering examples are offered as a demonstration of how synthetic biology can be used to modify plants for specific purposes. These include synthetic sensors, synthetic metabolic pathways, and synthetic genomes. We also speculate about the future of synthetic biology of plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Synthetic Cathinones ("Bath Salts")

    Science.gov (United States)

    ... Alcohol Club Drugs Cocaine Fentanyl Hallucinogens Inhalants Heroin Marijuana MDMA (Ecstasy/Molly) Methamphetamine Opioids Over-the-Counter Medicines Prescription Medicines Steroids (Anabolic) Synthetic Cannabinoids (K2/Spice) Synthetic Cathinones (Bath Salts) Tobacco/ ...

  4. Effect of screw position on single cycle to failure in bending and torsion of a locking plate-rod construct in a synthetic feline femoral gap model.

    Science.gov (United States)

    Niederhäuser, Simone K; Tepic, Slobodan; Weber, Urs T

    2015-05-01

    To evaluate the effect of screw position on strength and stiffness of a combination locking plate-rod construct in a synthetic feline femoral gap model. 30 synthetic long-bone models derived from beechwood and balsa wood. 3 constructs (2 locking plate-rod constructs and 1 locking plate construct; 10 specimens/construct) were tested in a diaphyseal bridge plating configuration by use of 4-point bending and torsion. Variables included screw position (near the fracture gap and far from the fracture gap) and application of an intramedullary pin. Constructs were tested to failure in each loading mode to determine strength and stiffness. Failure was defined as plastic deformation of the plate or breakage of the bone model or plate. Strength, yield angle, and stiffness were compared by use of a Wilcoxon test. Placement of screws near the fracture gap did not increase bending or torsional stiffness in the locking plate-rod constructs, assuming the plate was placed on the tension side of the bone. Addition of an intramedullary pin resulted in a significant increase in bending strength of the construct. Screw positioning did not have a significant effect on any torsion variables. Results of this study suggested that, in the investigated plate-rod construct, screw insertion adjacent to the fracture lacked mechanical advantages over screw insertion at the plate ends. For surgeons attempting to minimize soft tissue dissection, the decision to make additional incisions for screw placement should be considered with even more caution.

  5. Bone toughness at the molecular scale: A model for fracture toughness using crosslinked osteopontin on synthetic and biogenic mineral substrates.

    Science.gov (United States)

    Cavelier, S; Dastjerdi, A K; McKee, M D; Barthelat, F

    2018-05-01

    The most prominent structural components in bone are collagen and mineral. However, bone additionally contains a substantial amount of noncollagenous proteins (most notably of the SIBLING protein family), some of which may act as cohesive/adhesive "binders" for the composite hybrid collagen/mineral scaffolding, whether in the bulk phase of bone, or at its interfaces. One such noncollagenous protein - osteopontin (OPN) - appears to be critical to the deformability and fracture toughness of bone. In the present study, we used a reconstructed synthetic mineral-OPN-mineral interface, and a biogenic (natural tooth dentin) mineral/collagen-OPN-mineral/collagen interface, to measure the fracture toughness of OPN on mineralized substrates. We used this system to test the hypothesis that OPN crosslinking by the enzyme tissue transglutaminase 2 (TG2) that is found in bone enhances interfacial adhesion to increase the fracture toughness of bone. For this, we prepared double-cantilever beam substrates of synthetic pure hydroxyapatite mineral, and of narwhal dentin, and directly apposed them to one another under different intervening OPN/crosslinking conditions, and fracture toughness was tested using a miniaturized loading stage. The work-of-fracture of the OPN interface was measured for different OPN formulations (monomer vs. polymer), crosslinking states, and substrate composition. Noncrosslinked OPN provided negligible adhesion on pure hydroxyapatite, whereas OPN crosslinking (by the chemical crosslinker glutaraldehyde, and TG2 enzyme) provided strong interfacial adhesion for both hydroxyapatite and dentin using monomeric and polymeric OPN. Pre-coating of the substrate beams with monomeric OPN further improved the adhesive performance of the samples, likely by allowing effective binding of this nascent OPN form to mineral/matrix components, with this pre-attachment providing a protein layer for additional crosslinking between the substrates. Copyright © 2018 Elsevier Inc

  6. A framework of integrated hydrological and hydrodynamic models using synthetic rainfall for flash flood hazard mapping of ungauged catchments in tropical zones

    Directory of Open Access Journals (Sweden)

    W. Lohpaisankrit

    2016-05-01

    Full Text Available Flash flood hazard maps provide a scientific support to mitigate flash flood risk. The present study develops a practical framework with the help of integrated hydrological and hydrodynamic modelling in order to estimate the potential flash floods. We selected a small pilot catchment which has already suffered from flash floods in the past. This catchment is located in the Nan River basin, northern Thailand. Reliable meteorological and hydrometric data are missing in the catchment. Consequently, the entire upper basin of the main river was modelled with the help of the hydrological modelling system PANTA RHEI. In this basin, three monitoring stations are located along the main river. PANTA RHEI was calibrated and validated with the extreme flood events in June 2011 and July 2008, respectively. The results show a good agreement with the observed discharge data. In order to create potential flash flood scenarios, synthetic rainfall series were derived from temporal rainfall patterns based on the radar-rainfall observation and different rainfall depths from regional rainfall frequency analysis. The temporal rainfall patterns were characterized by catchment-averaged rainfall series selected from 13 rainstorms in 2008 and 2011 within the region. For regional rainfall frequency analysis, the well-known L-moments approach and related criteria were used to examine extremely climatic homogeneity of the region. According to the L-moments approach, Generalized Pareto distribution was recognized as the regional frequency distribution. The synthetic rainfall series were fed into the PANTA RHEI model. The simulated results from PANTA RHEI were provided to a 2-D hydrodynamic model (MEADFLOW, and various simulations were performed. Results from the integrated modelling framework are used in the ongoing study to regionalize and map the spatial distribution of flash flood hazards with four levels of flood severities. As an overall outcome, the presented framework

  7. A comparative study of two statistical approaches for the analysis of real seismicity sequences and synthetic seismicity generated by a stick-slip experimental model

    Science.gov (United States)

    Flores-Marquez, Leticia Elsa; Ramirez Rojaz, Alejandro; Telesca, Luciano

    2015-04-01

    The study of two statistical approaches is analyzed for two different types of data sets, one is the seismicity generated by the subduction processes occurred at south Pacific coast of Mexico between 2005 and 2012, and the other corresponds to the synthetic seismic data generated by a stick-slip experimental model. The statistical methods used for the present study are the visibility graph in order to investigate the time dynamics of the series and the scaled probability density function in the natural time domain to investigate the critical order of the system. This comparison has the purpose to show the similarities between the dynamical behaviors of both types of data sets, from the point of view of critical systems. The observed behaviors allow us to conclude that the experimental set up globally reproduces the behavior observed in the statistical approaches used to analyses the seismicity of the subduction zone. The present study was supported by the Bilateral Project Italy-Mexico Experimental Stick-slip models of tectonic faults: innovative statistical approaches applied to synthetic seismic sequences, jointly funded by MAECI (Italy) and AMEXCID (Mexico) in the framework of the Bilateral Agreement for Scientific and Technological Cooperation PE 2014-2016.

  8. Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project.

    Science.gov (United States)

    Sliva, Anna; Yang, Huanming; Boeke, Jef D; Mathews, Debra J H

    2015-08-01

    First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) PROJECT is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with this field of research and operate under a common set of principles. In this commentary, we survey the current ethics and regulatory landscape of synthetic biology and present the Sc2.0 Statement of Ethics and Governance to which all members of the project adhere. This statement focuses on four aspects of the Sc2.0 PROJECT: societal benefit, intellectual property, safety, and self-governance. We propose that such project-level agreements are an important, valuable, and flexible model of self-regulation for similar global, large-scale synthetic biology projects in order to maximize the benefits and minimize potential harms. Copyright © 2015 by the Genetics Society of America.

  9. Space Synthetic Biology Project

    Science.gov (United States)

    Howard, David; Roman, Monsi; Mansell, James (Matt)

    2015-01-01

    Synthetic biology is an effort to make genetic engineering more useful by standardizing sections of genetic code. By standardizing genetic components, biological engineering will become much more similar to traditional fields of engineering, in which well-defined components and subsystems are readily available in markets. Specifications of the behavior of those components and subsystems can be used to model a system which incorporates them. Then, the behavior of the novel system can be simulated and optimized. Finally, the components and subsystems can be purchased and assembled to create the optimized system, which most often will exhibit behavior similar to that indicated by the model. The Space Synthetic Biology project began in 2012 as a multi-Center effort. The purpose of this project was to harness Synthetic Biology principals to enable NASA's missions. A central target for application was to Environmental Control & Life Support (ECLS). Engineers from NASA Marshall Space Flight Center's (MSFC's) ECLS Systems Development Branch (ES62) were brought into the project to contribute expertise in operational ECLS systems. Project lead scientists chose to pursue the development of bioelectrochemical technologies to spacecraft life support. Therefore, the ECLS element of the project became essentially an effort to develop a bioelectrochemical ECLS subsystem. Bioelectrochemical systems exploit the ability of many microorganisms to drive their metabolisms by direct or indirect utilization of electrical potential gradients. Whereas many microorganisms are capable of deriving the energy required for the processes of interest (such as carbon dioxide (CO2) fixation) from sunlight, it is believed that subsystems utilizing electrotrophs will exhibit smaller mass, volume, and power requirements than those that derive their energy from sunlight. In the first 2 years of the project, MSFC personnel conducted modeling, simulation, and conceptual design efforts to assist the

  10. Utilizing Three-Dimensional Printing Technology to Assess the Feasibility of High-Fidelity Synthetic Ventricular Septal Defect Models for Simulation in Medical Education.

    Science.gov (United States)

    Costello, John P; Olivieri, Laura J; Krieger, Axel; Thabit, Omar; Marshall, M Blair; Yoo, Shi-Joon; Kim, Peter C; Jonas, Richard A; Nath, Dilip S

    2014-07-01

    The current educational approach for teaching congenital heart disease (CHD) anatomy to students involves instructional tools and techniques that have significant limitations. This study sought to assess the feasibility of utilizing present-day three-dimensional (3D) printing technology to create high-fidelity synthetic heart models with ventricular septal defect (VSD) lesions and applying these models to a novel, simulation-based educational curriculum for premedical and medical students. Archived, de-identified magnetic resonance images of five common VSD subtypes were obtained. These cardiac images were then segmented and built into 3D computer-aided design models using Mimics Innovation Suite software. An Objet500 Connex 3D printer was subsequently utilized to print a high-fidelity heart model for each VSD subtype. Next, a simulation-based educational curriculum using these heart models was developed and implemented in the instruction of 29 premedical and medical students. Assessment of this curriculum was undertaken with Likert-type questionnaires. High-fidelity VSD models were successfully created utilizing magnetic resonance imaging data and 3D printing. Following instruction with these high-fidelity models, all students reported significant improvement in knowledge acquisition (P 3D printing technology to create high-fidelity heart models with complex intracardiac defects. Furthermore, this tool forms the foundation for an innovative, simulation-based educational approach to teach students about CHD and creates a novel opportunity to stimulate their interest in this field. © The Author(s) 2014.

  11. Deposition and transport of linezolid mediated by a synthetic surfactant Synsurf® within a pressurized metered dose inhaler: a Calu-3 model

    Science.gov (United States)

    van Rensburg, Lyné; van Zyl, Johann M; Smith, Johan

    2018-01-01

    Background Previous studies in our laboratory demonstrated that a synthetic peptide containing lung surfactant enhances the permeability of chemical compounds through bronchial epithelium. The purpose of this study was to test two formulations of Synsurf® combined with linezolid as respirable compounds using a pressurized metered dose inhaler (pMDI). Methods Aerosolization efficiency of the surfactant-drug microparticles onto Calu-3 monolayers as an air interface culture was analyzed using a Next Generation Impactor™. Results The delivered particles and drug dose showed a high dependency from the preparation that was aerosolized. Scanning electron microscopy imaging allowed for visualization of the deposited particles, establishing them as liposomal-type structures (diameter 500 nm to 2 μm) with filamentous features. Conclusion The different surfactant drug combinations allow for an evaluation of the significance of the experimental model system, as well as assessment of the formulations providing a possible noninvasive, site-specific, delivery model via pMDI.

  12. Modelling of the plastic deformation and primary creep of metals coupled with DC in terms of the synthetic theory of irrecoverable deformation

    Science.gov (United States)

    Rusinko, Andrew; Varga, Peter

    2018-04-01

    The paper deals with modelling of the plastic and creep deformation of metals coupled with current. The passage of DC manifests itself in the increase in creep deformation and leads to primary creep time shortening. With plastic deformation, a short electric impulse results in the step-wise decrease of stress (stress-drop) on the stress-strain diagram. To catch these phenomena, we utilize the synthetic theory of recoverable deformation. The constitutive equation of this theory is supplemented by a term taking into account the intensity of DC. Further, we introduce DC intensity into the function governing transient creep. As a result, we predict the parameters of transient creep and calculate the stress-drop as a function of current intensity. The model results show good agreement with experimental data.

  13. Synthetic Peptides to Target Stringent Response-Controlled Virulence in a Pseudomonas aeruginosa Murine Cutaneous Infection Model

    Directory of Open Access Journals (Sweden)

    Daniel Pletzer

    2017-09-01

    Full Text Available Microorganisms continuously monitor their surroundings and adaptively respond to environmental cues. One way to cope with various stress-related situations is through the activation of the stringent stress response pathway. In Pseudomonas aeruginosa this pathway is controlled and coordinated by the activity of the RelA and SpoT enzymes that metabolize the small nucleotide secondary messenger molecule (pppGpp. Intracellular ppGpp concentrations are crucial in mediating adaptive responses and virulence. Targeting this cellular stress response has recently been the focus of an alternative approach to fight antibiotic resistant bacteria. Here, we examined the role of the stringent response in the virulence of P. aeruginosa PAO1 and the Liverpool epidemic strain LESB58. A ΔrelA/ΔspoT double mutant showed decreased cytotoxicity toward human epithelial cells, exhibited reduced hemolytic activity, and caused down-regulation of the expression of the alkaline protease aprA gene in stringent response mutants grown on blood agar plates. Promoter fusions of relA or spoT to a bioluminescence reporter gene revealed that both genes were expressed during the formation of cutaneous abscesses in mice. Intriguingly, virulence was attenuated in vivo by the ΔrelA/ΔspoT double mutant, but not the relA mutant nor the ΔrelA/ΔspoT complemented with either gene. Treatment of a cutaneous P. aeruginosa PAO1 infection with anti-biofilm peptides increased animal welfare, decreased dermonecrotic lesion sizes, and reduced bacterial numbers recovered from abscesses, resembling the phenotype of the ΔrelA/ΔspoT infection. It was previously demonstrated by our lab that ppGpp could be targeted by synthetic peptides; here we demonstrated that spoT promoter activity was suppressed during cutaneous abscess formation by treatment with peptides DJK-5 and 1018, and that a peptide-treated relA complemented stringent response double mutant strain exhibited reduced peptide

  14. Novel Synthetic, Host-defense Peptide Protects Against Organ Injury/Dysfunction in a Rat Model of Severe Hemorrhagic Shock.

    Science.gov (United States)

    Yamada, Noriaki; Martin, Lukas B; Zechendorf, Elisabeth; Purvis, Gareth S D; Chiazza, Fausto; Varrone, Barbara; Collino, Massimo; Shepherd, Joanna; Heinbockel, Lena; Gutsmann, Thomas; Correa, Wilmar; Brandenburg, Klaus; Marx, Gernot; Schuerholz, Tobias; Brohi, Karim; Thiemermann, Christoph

    2017-03-10

    To evaluate (1) levels of the host-defense/antimicrobial peptide LL-37 in patients with trauma and hemorrhagic shock (HS) and (2) the effects of a synthetic host-defense peptide; Pep19-4LF on multiple organ failure (MOF) associated with HS. HS is a common cause of death in severely injured patients. There is no specific therapy that reduces HS-associated MOF. (1) LL-37 was measured in 47 trauma/HS patients admitted to an urban major trauma center. (2) Male Wistar rats were submitted to HS (90 min, target mean arterial pressure: 27-32 mm Hg) or sham operation. Rats were treated with Pep19-4LF [66 (n = 8) or 333 μg/kg · h (n = 8)] or vehicle (n = 12) for 4 hours following resuscitation. Plasma LL-37 was 12-fold higher in patients with trauma/HS compared to healthy volunteers. HS rats treated with Pep19-4LF (high dose) had a higher mean arterial pressure at the end of the 4-hour resuscitation period (79 ± 4 vs 54 ± 5 mm Hg) and less renal dysfunction, liver injury, and lung inflammation than HS rats treated with vehicle. Pep19-4LF enhanced (kidney/liver) the phosphorylation of (1) protein kinase B and (2) endothelial nitric oxide synthase. Pep19-4LF attenuated the HS-induced (1) translocation of p65 from cytosol to nucleus, (2) phosphorylation of IκB kinase on Ser, and (3) phosphorylation of IκBα on Ser resulting in inhibition of nuclear factor kappa B and formation of proinflammatory cytokines. Pep19-4LF prevented the release of tumor necrosis factor alpha caused by heparan sulfate in human mononuclear cells by binding to this damage-associated molecular pattern. Trauma-associated HS results in release of LL-37. The synthetic host-defense/antimicrobial peptide Pep19-4LF attenuates the organ injury/dysfunction associated with HS.

  15. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

    Directory of Open Access Journals (Sweden)

    Jason Gunther Lomnitz

    2016-07-01

    Full Text Available Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1 enumeration of the repertoire of model phenotypes, (2 prediction of values for the parameters for any model phenotype and (3 analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3 and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between 3 stable states by transient stimulation through one of two input channels: a positive channel that increases

  16. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

    Science.gov (United States)

    Lomnitz, Jason G.; Savageau, Michael A.

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  17. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  18. Synthetic and Empirical Capsicum Annuum Image Dataset

    NARCIS (Netherlands)

    Barth, R.

    2016-01-01

    This dataset consists of per-pixel annotated synthetic (10500) and empirical images (50) of Capsicum annuum, also known as sweet or bell pepper, situated in a commercial greenhouse. Furthermore, the source models to generate the synthetic images are included. The aim of the datasets are to

  19. Biomechanical study: resistance comparison of posterior antiglide plate and lateral plate on synthetic bone models simulating Danis-Weber B malleolar fractures

    Directory of Open Access Journals (Sweden)

    Bruna Buscharino

    2013-06-01

    Full Text Available OBJECTIVE : The purpose of this study was to compare different positions of plates in lateral malleolar Danis-Weber B fractures on synthetic bone: a lateral plate and a posterior antiglide plate. METHODS : Short oblique fractures of distal fibula at the level of the syndesmosys were simulated with a fibular osteotomy in sixteen synthetic fibula bones (Synbone®. Eight fractures were fixed with lateral plating associated with an independent lag screw, and the other eight were fixed with posterior antiglide plating with a lag screw through the plate. A strain gage was installed at the center of each plate at the osteotomy site. Supination and external rotation forces were applied to each of the two groups at the bend. RESULTS : The lateral position plate group suffered more deformity in response to supination forces compared to the group with the posterior antiglide plate, but this result was not statistically significant. In the tests with external rotation forces, the posterior antiglide plating group had significantly higher resistance (p < 0.05. CONCLUSION : When subjected to external rotation forces, osteosynthesis with posterior antiglide plate models simulating type B fractures of the lateral malleolus of the ankle is more resistant than that of the neutralization plate.

  20. Complete synthetic seismograms based on a spherical self-gravitating Earth model with an atmosphere-ocean-mantle-core structure

    Science.gov (United States)

    Wang, Rongjiang; Heimann, Sebastian; Zhang, Yong; Wang, Hansheng; Dahm, Torsten

    2017-09-01

    A hybrid method is proposed to calculate complete synthetic seismograms based on a spherically symmetric and self-gravitating Earth with a multilayered structure of atmosphere, ocean, mantle, liquid core and solid core. For large wavelengths, a numerical scheme is used to solve the geodynamic boundary-value problem without any approximation on the deformation and gravity coupling. With decreasing wavelength, the gravity effect on the deformation becomes negligible and the analytical propagator scheme can be used. Many useful approaches are used to overcome the numerical problems that may arise in both analytical and numerical schemes. Some of these approaches have been established in the seismological community and the others are developed for the first time. Based on the stable and efficient hybrid algorithm, an all-in-one code QSSP is implemented to cover the complete spectrum of seismological interests. The performance of the code is demonstrated by various tests including the curvature effect on teleseismic body and surface waves, the appearance of multiple reflected, teleseismic core phases, the gravity effect on long period surface waves and free oscillations, the simulation of near-field displacement seismograms with the static offset, the coupling of tsunami and infrasound waves, and free oscillations of the solid Earth, the atmosphere and the ocean. QSSP is open source software that can be used as a stand-alone FORTRAN code or may be applied in combination with a Python toolbox to calculate and handle Green's function databases for efficient coding of source inversion problems.

  1. The synthetic progestin norgestrel modulates Nrf2 signaling and acts as an antioxidant in a model of retinal degeneration

    Directory of Open Access Journals (Sweden)

    Ashleigh M. Byrne

    2016-12-01

    Full Text Available Retinitis pigmentosa (RP is one of the most common retinal degenerative conditions affecting people worldwide, and is currently incurable. It is characterized by the progressive loss of photoreceptors, in which the death of rod cells leads to the secondary death of cone cells; the cause of eventual blindness. As rod cells die, retinal-oxygen metabolism becomes perturbed, leading to increased levels of reactive oxygen species (ROS and thus oxidative stress; a key factor in the secondary death of cones. In this study, norgestrel, an FDA-approved synthetic analog of progesterone, was found to be a powerful neuroprotective antioxidant, preventing light-induced ROS in photoreceptor cells, and subsequent cell death. Norgestrel also prevented light-induced photoreceptor morphological changes that were associated with ROS production, and that are characteristic of RP. Further investigation showed that norgestrel acts via post-translational modulation of the major antioxidant transcription factor Nrf2; bringing about its phosphorylation, subsequent nuclear translocation, and increased levels of its effector protein superoxide dismutase 2 (SOD2. In summary, these results demonstrate significant protection of photoreceptor cells from oxidative stress, and underscore the potential of norgestrel as a therapeutic option for RP.

  2. Evaluating and modeling biogas production from municipal fat, oil, and grease and synthetic kitchen waste in anaerobic co-digestions.

    Science.gov (United States)

    Li, Chenxi; Champagne, Pascale; Anderson, Bruce C

    2011-10-01

    The feasibility of using synthetic kitchen waste (KW) and fat, oil, and grease (FOG) as co-substrates in the anaerobic digestion of waste activated sludge (WAS) was investigated using two series of biochemical methane potential (BMP) tests. Ranges of ideal substrate to inoculum (S/I) ratio were determined for the FOG (0.25-0.75) and KW (0.80-1.26) as single substrates in the first experiment. The second experiment, which estimated the methane production performances of FOG and KW as co-substrates for WAS co-digestion, was conducted based on the optimal parameters selected from the results of the first experiment. Results indicated that co-digestions with FOG and KW enhanced methane production from 117±2.02 mL/gTVS (with only WAS) to 418±13.7 mL/gTVS and 324±4.11 mL/gTVS, respectively. FOG exhibited more biogas production than KW as co-substrate. Non-linear regression results showed that co-substrate addition shortened the lag phases of organic biodegradation from 81.8 (with only WAS) to 28.3 h with FOG and 3.90 h with KW. Copyright © 2011 Elsevier Ltd. All rights reserved.

  3. Transionospheric synthetic aperture imaging

    CERN Document Server

    Gilman, Mikhail; Tsynkov, Semyon

    2017-01-01

    This landmark monograph presents the most recent mathematical developments in the analysis of ionospheric distortions of SAR images and offers innovative new strategies for their mitigation. As a prerequisite to addressing these topics, the book also discusses the radar ambiguity theory as it applies to synthetic aperture imaging and the propagation of radio waves through the ionospheric plasma, including the anisotropic and turbulent cases. In addition, it covers a host of related subjects, such as the mathematical modeling of extended radar targets (as opposed to point-wise targets) and the scattering of radio waves off those targets, as well as the theoretical analysis of the start-stop approximation, which is used routinely in SAR signal processing but often without proper justification. The mathematics in this volume is clean and rigorous – no assumptions are hidden or ambiguously stated. The resulting work is truly interdisciplinary, providing both a comprehensive and thorough exposition of the field,...

  4. The STAGGER-grid: A grid of 3D stellar atmosphere models. V. Synthetic stellar spectra and broad-band photometry

    Science.gov (United States)

    Chiavassa, A.; Casagrande, L.; Collet, R.; Magic, Z.; Bigot, L.; Thévenin, F.; Asplund, M.

    2018-03-01

    Context. The surface structures and dynamics of cool stars are characterised by the presence of convective motions and turbulent flows which shape the emergent spectrum. Aims: We used realistic three-dimensional (3D) radiative hydrodynamical simulations from the STAGGER-grid to calculate synthetic spectra with the radiative transfer code OPTIM3D for stars with different stellar parameters to predict photometric colours and convective velocity shifts. Methods: We calculated spectra from 1000 to 200 000 Å with a constant resolving power of λ/Δλ = 20 000 and from 8470 and 8710 Å (Gaia Radial Velocity Spectrometer - RVS - spectral range) with a constant resolving power of λ/Δλ = 300 000. Results: We used synthetic spectra to compute theoretical colours in the Johnson-Cousins UBV (RI)C, SDSS, 2MASS, Gaia, SkyMapper, Strömgren systems, and HST-WFC3. Our synthetic magnitudes are compared with those obtained using 1D hydrostatic models. We showed that 1D versus 3D differences are limited to a small percent except for the narrow filters that span the optical and UV region of the spectrum. In addition, we derived the effect of the convective velocity fields on selected Fe I lines. We found the overall convective shift for 3D simulations with respect to the reference 1D hydrostatic models, revealing line shifts of between -0.235 and +0.361 km s-1. We showed a net correlation of the convective shifts with the effective temperature: lower effective temperatures denote redshifts and higher effective temperatures denote blueshifts. We conclude that the extraction of accurate radial velocities from RVS spectra need an appropriate wavelength correction from convection shifts. Conclusions: The use of realistic 3D hydrodynamical stellar atmosphere simulations has a small but significant impact on the predicted photometry compared with classical 1D hydrostatic models for late-type stars. We make all the spectra publicly available for the community through the POLLUX database

  5. Evolvable synthetic neural system

    Science.gov (United States)

    Curtis, Steven A. (Inventor)

    2009-01-01

    An evolvable synthetic neural system includes an evolvable neural interface operably coupled to at least one neural basis function. Each neural basis function includes an evolvable neural interface operably coupled to a heuristic neural system to perform high-level functions and an autonomic neural system to perform low-level functions. In some embodiments, the evolvable synthetic neural system is operably coupled to one or more evolvable synthetic neural systems in a hierarchy.

  6. [From synthetic biology to synthetic humankind].

    Science.gov (United States)

    Nouvel, Pascal

    2015-01-01

    In this paper, we propose an historical survey of the expression "synthetic biology" in order to identify its main philosophical components. The result of the analysis is then used to investigate the meaning of the notion of "synthetic man". It is shown that both notions share a common philosophical background that can be summed up by the short but meaningful assertion: "biology is technology". The analysis allows us to distinguish two notions that are often confused in transhumanist literature: the notion of synthetic man and the notion of renewed man. The consequences of this crucial distinction are discussed. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  7. Stereoscopy in cinematographic synthetic imagery

    Science.gov (United States)

    Eisenmann, Jonathan; Parent, Rick

    2009-02-01

    In this paper we present experiments and results pertaining to the perception of depth in stereoscopic viewing of synthetic imagery. In computer animation, typical synthetic imagery is highly textured and uses stylized illumination of abstracted material models by abstracted light source models. While there have been numerous studies concerning stereoscopic capabilities, conventions for staging and cinematography in stereoscopic movies have not yet been well-established. Our long-term goal is to measure the effectiveness of various cinematography techniques on the human visual system in a theatrical viewing environment. We would like to identify the elements of stereoscopic cinema that are important in terms of enhancing the viewer's understanding of a scene as well as providing guidelines for the cinematographer relating to storytelling. In these experiments we isolated stereoscopic effects by eliminating as many other visual cues as is reasonable. In particular, we aim to empirically determine what types of movement in synthetic imagery affect the perceptual depth sensing capabilities of our viewers. Using synthetic imagery, we created several viewing scenarios in which the viewer is asked to locate a target object's depth in a simple environment. The scenarios were specifically designed to compare the effectiveness of stereo viewing, camera movement, and object motion in aiding depth perception. Data were collected showing the error between the choice of the user and the actual depth value, and patterns were identified that relate the test variables to the viewer's perceptual depth accuracy in our theatrical viewing environment.

  8. Synergistic Synthetic Biology: Units in Concert

    International Nuclear Information System (INIS)

    Trosset, Jean-Yves; Carbonell, Pablo

    2013-01-01

    Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.

  9. Synergistic Synthetic Biology: Units in Concert

    Science.gov (United States)

    Trosset, Jean-Yves; Carbonell, Pablo

    2013-01-01

    Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications. PMID:25022769

  10. Future discharge drought across climate regions around the world modelled with a synthetic hydrological modelling approach forced by three general circulation models

    Science.gov (United States)

    Wanders, N.; Van Lanen, H. A. J.

    2015-03-01

    Hydrological drought characteristics (drought in groundwater and streamflow) likely will change in the 21st century as a result of climate change. The magnitude and directionality of these changes and their dependency on climatology and catchment characteristics, however, is uncertain. In this study a conceptual hydrological model was forced by downscaled and bias-corrected outcome from three general circulation models for the SRES A2 emission scenario (GCM forced models), and the WATCH Forcing Data set (reference model). The threshold level method was applied to investigate drought occurrence, duration and severity. Results for the control period (1971-2000) show that the drought characteristics of each GCM forced model reasonably agree with the reference model for most of the climate types, suggesting that the climate models' results after post-processing produce realistic outcomes for global drought analyses. For the near future (2021-2050) and far future (2071-2100) the GCM forced models show a decrease in drought occurrence for all major climates around the world and increase of both average drought duration and deficit volume of the remaining drought events. The largest decrease in hydrological drought occurrence is expected in cold (D) climates where global warming results in a decreased length of the snow season and an increased precipitation. In the dry (B) climates the smallest decrease in drought occurrence is expected to occur, which probably will lead to even more severe water scarcity. However, in the extreme climate regions (desert and polar), the drought analysis for the control period showed that projections of hydrological drought characteristics are most uncertain. On a global scale the increase in hydrological drought duration and severity in multiple regions will lead to a higher impact of drought events, which should motivate water resource managers to timely anticipate the increased risk of more severe drought in groundwater and streamflow

  11. Designing synthetic biology.

    Science.gov (United States)

    Agapakis, Christina M

    2014-03-21

    Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.

  12. The studies on the toxicity mechanism of environmentally hazardous natural (IAA) and synthetic (NAA) auxin--The experiments on model Arabidopsis thaliana and rat liver plasma membranes.

    Science.gov (United States)

    Hąc-Wydro, Katarzyna; Flasiński, Michał

    2015-06-01

    This paper concerns the studies towards membrane-damage effect of two auxins: indole-3-acetic acid - IAA and 1-naphthaleneacetic acid - NAA on plant (Arabidopsis thaliana) and animal (rat liver) model membranes. The foregoing auxins are plant growth regulators widely used in agriculture to control the quality of the crop. However, their accumulation in the environment makes them hazardous for the living organisms. The aim of our investigations was to compare the effect of natural (IAA) vs. synthetic (NAA) auxin on the organization of plant and animal model membranes and find a possible correlation between membrane-disturbing effect of these compounds and their toxicity. The collected data evidenced that auxins cause destabilization of membranes, decrease their condensation and weakens interactions of molecules. The alterations in the morphology of model systems were also noticed. The foregoing effects of auxins are concentration-dependent and additionally NAA was found to act on animal vs. plant membranes more selectively than IAA. Interestingly, both IAA and NAA induce the strongest disordering in model lipid system at the concentration, which is frequently reported as toxic to animal and plants. Based on the above findings it was proposed that membrane-damage effect induced by IAA and NAA may be important from the point of view of the mechanism of toxicity of these compounds and cannot be ignored in further investigations in this area. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Assessment of synthetic image fidelity

    Science.gov (United States)

    Mitchell, Kevin D.; Moorhead, Ian R.; Gilmore, Marilyn A.; Watson, Graham H.; Thomson, Mitch; Yates, T.; Troscianko, Tomasz; Tolhurst, David J.

    2000-07-01

    Computer generated imagery is increasingly used for a wide variety of purposes ranging from computer games to flight simulators to camouflage and sensor assessment. The fidelity required for this imagery is dependent on the anticipated use - for example when used for camouflage design it must be physically correct spectrally and spatially. The rendering techniques used will also depend upon the waveband being simulated, spatial resolution of the sensor and the required frame rate. Rendering of natural outdoor scenes is particularly demanding, because of the statistical variation in materials and illumination, atmospheric effects and the complex geometric structures of objects such as trees. The accuracy of the simulated imagery has tended to be assessed subjectively in the past. First and second order statistics do not capture many of the essential characteristics of natural scenes. Direct pixel comparison would impose an unachievable demand on the synthetic imagery. For many applications, such as camouflage design, it is important that nay metrics used will work in both visible and infrared wavebands. We are investigating a variety of different methods of comparing real and synthetic imagery and comparing synthetic imagery rendered to different levels of fidelity. These techniques will include neural networks (ICA), higher order statistics and models of human contrast perception. This paper will present an overview of the analyses we have carried out and some initial results along with some preliminary conclusions regarding the fidelity of synthetic imagery.

  14. Methods for preparing synthetic freshwaters.

    Science.gov (United States)

    Smith, E J; Davison, W; Hamilton-Taylor, J

    2002-03-01

    Synthetic solutions that emulate the major ion compositions of natural waters are useful in experiments aimed at understanding biogeochemical processes. Standard recipes exist for preparing synthetic analogues of seawater, with its relatively constant composition, but, due to the diversity of freshwaters, a range of compositions and recipes is required. Generic protocols are developed for preparing synthetic freshwaters of any desired composition. The major problems encountered in preparing hard and soft waters include dissolving sparingly soluble calcium carbonate, ensuring that the ionic components of each concentrated stock solution cannot form an insoluble salt and dealing with the supersaturation of calcium carbonate in many hard waters. For acidic waters the poor solubility of aluminium salts requires attention. These problems are overcome by preparing concentrated stock solutions according to carefully designed reaction paths that were tested using a combination of experiment and equilibrium modeling. These stock solutions must then be added in a prescribed order to prepare a final solution that is brought into equilibrium with the atmosphere. The example calculations for preparing hard, soft and acidic freshwater surrogates with major ion compositions the same as published analyses, are presented in a generalized fashion that should allow preparation of any synthetic freshwater according to its known analysis.

  15. Synthetic Image Generator Model; Application of View Angle Dependent Reflectivity Components and Performance Evaluation in the Visible Region

    Science.gov (United States)

    1993-02-01

    3.1.2. Modeling of Environment ....................... 6 3.1.3. Ray Tracing and Radiosity ..................... 8 3.2. Reflectivity Review...SIG modeling is dependent on proper treatment of its effects. 3.1.3 Ray Tracing and Radiosity Prior to reviewing reflectivity, a brief look is made of...methods of applying complex theoretical energy propagation algorithms. Two such methods are ray tracing and radiosity (Goral, et al, 1984). Ray tracing is a

  16. Reaction mechanism of coal liquefaction: hydrogenolysis of model compound using synthetic pyrite as catalysts. 7. Property change of synthetic pyrite catalyst with the time after production; Sekitan ekika hanno kiko (model kagobutsu no hanno). 7. Gosei ryukatetsu shokubai no keiji henka ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Ito, H.; Meno, H.; Uemaki, O.; Shibata, T.; Tsuji, T. [Hokkaido University, Sapporo (Japan)

    1996-10-28

    Reactions of various model compounds were investigated using synthetic pyrites for coal liquefaction. In this study, successive changes of the catalysts were investigated from the reactions of model compounds by using three different synthetic pyrites with the lapse of time after production. Benzyl phenyl ether, dibenzyl, and n-octylbenzene were used as model compounds. Reactions were conducted in an autoclave, into which sample, catalyst, decalin as solvent, and initial hydrogen pressure 10 MPa were charged. The autoclave was held at 450 or 475{degree}C of reaction temperature for 1 hour. The catalyst with a shorter lapse of time after production acted to hydrogen transfer, and inhibited the formation of condensation products due to the stabilization of decomposed fragment. It also acted to isomerization of materials by cutting alkyl side chains. When adding sulfur to the catalyst with longer lapse of time after production under these reaction conditions, it inhibited the formation of condensation products for the reaction of benzyl phenyl ether. However, it did not provide the effect for the reaction of n-octylbenzene. 5 refs., 3 figs.

  17. Modelling the effect of essential oil of betel leaf (Piper betle L.) on germination, growth, and apparent lag time of Penicillium expansum on semi-synthetic media.

    Science.gov (United States)

    Basak, Suradeep; Guha, Proshanta

    2015-12-23

    The current study aimed at characterizing the chemical components of betel leaf (Piper betle L. var. Tamluk Mitha) essential oil (BLEO) and modelling its effect on growth of Penicillium expansum on semi-synthetic medium. Gas chromatography-mass spectrophotometry (GC-MS) analysis of BLEO revealed the presence of different bioactive phenolic compounds in significant amounts. Among 46 different components identified, chavibetol (22.0%), estragole (15.8%), β-cubebene (13.6%), chavicol (11.8%), and caryophyllene (11.3%) were found to be the major compounds of BLEO. A disc diffusion and disc volatilization method were used to evaluate antifungal activity of the oil against a selected food spoilage mould. The logistic model was used to study the kinetics of spore germination. Prediction and validation of antifungal effect of BLEO was performed on semi-synthetic medium (apple juice agar) using predictive microbiological tools. The Baranyi and Roberts model was used to estimate maximum growth rate (μmax in mm/day) and apparent lag time (λ in days) of the mould. Secondary modelling was performed using a re-parameterized Monod-type equation based on cardinal values to study the effect of different BLEO concentration on estimated growth parameters. Emax (minimum concentration of oil at which mould growth was inhibited) and MIC (minimum inhibitory concentration of BLEO at which lag time is infinite) value of BLEO against P. expansum was estimated to be 0.56 and 0.74 μl/ml, respectively, which was found to be similar on potato dextrose agar (PDA) as well as apple juice agar (AJA) medium. The correlation between estimated growth parameters of the mould on both the media was obtained with satisfactory statistical indices (R(2) and RMSE). This study revealed inhibitory efficacy of BLEO on spore germination, mycelial growth and apparent lag time of P. expansum in a dose-dependent manner. Hence, BLEO has potential to be used as a natural food preservative. Copyright © 2015

  18. River discharge estimation from synthetic SWOT-type observations using variational data assimilation and the full Saint-Venant hydraulic model

    Science.gov (United States)

    Oubanas, Hind; Gejadze, Igor; Malaterre, Pierre-Olivier; Mercier, Franck

    2018-04-01

    The upcoming Surface Water and Ocean Topography satellite mission, to be launched in 2021, will measure river water surface elevation, slope and width, with an unprecedented level of accuracy for a remote sensing tool. This work investigates the river discharge estimation from synthetic SWOT observations, in the presence of strong uncertainties in the model inputs, i.e. the river bathymetry and bed roughness. The estimation problem is solved by a novel variant of the standard variational data assimilation, the '4D-Var' method, involving the full Saint-Venant 1.5D-network hydraulic model SIC2. The assimilation scheme simultaneously estimates the discharge, bed elevation and bed roughness coefficient and is designed to assimilate both satellite and in situ measurements. The method is tested on a 50 km-long reach of the Garonne River during a five-month period of the year 2010, characterized by multiple flooding events. First, the impact of the sampling frequency on discharge estimation is investigated. Secondly, discharge as well as the spatially distributed bed elevation and bed roughness coefficient are determined simultaneously. Results demonstrate feasibility and efficiency of the chosen combination of the estimation method and of the hydraulic model. Assimilation of the SWOT data results into an accurate estimation of the discharge at observation times, and a local improvement in the bed level and bed roughness coefficient. However, the latter estimates are not generally usable for different independent experiments.

  19. Functional imaging studies of emotion regulation: A synthetic review and evolving model of the cognitive control of emotion

    Science.gov (United States)

    Ochsner, Kevin N.; Silvers, Jennifer A.; Buhle, Jason T.

    2014-01-01

    This paper reviews and synthesizes functional imaging research that over the past decade has begun to offer new insights into the brain mechanisms underlying emotion regulation. Towards that end, the first section of the paper outlines a model of the processes and neural systems involved in emotion generation and regulation. The second section surveys recent research supporting and elaborating the model, focusing primarily on studies of the most commonly investigated strategy, which is known as reappraisal. At its core, the model specifies how prefrontal and cingulate control systems modulate activity in perceptual, semantic and affect systems as a function of one's regulatory goals, tactics, and the nature of the stimuli and emotions being regulated. This section also shows how the model can be generalized to understand the brain mechanisms underlying other emotion regulation strategies as well as a range of other allied phenomena. The third and last section considers directions for future research, including how basic models of emotion regulation can be translated to understand changes in emotion across the lifespan and in clinical disorders. PMID:23025352

  20. Predicting ion exchange resins decontamination factors. Experiments on synthetic primary coolant containing Ni, Co and Ag and modeling results

    International Nuclear Information System (INIS)

    Bachet, Martin; Schneider, Hélène; Jauberty, Loïc; Windt, Laurent De; Dieuleveult, Caroline de; Tevissen, Etienne

    2014-01-01

    Experiments performed under chemical and flow conditions representative of pressurized water reactors (PWR) primary fluid purification by ion exchange resins (Amberlite IRN9882) are modeled with the OPTIPUR code, considering 1D reactive transport in the mixed-bed column with convective/dispersive transport between beads and electro-diffusive transport within the boundary film around the beads. The effectiveness of the purification in these dilute conditions is highly related to film mass transfer restrictions, which are accounted for by adjustment of a common mass transfer coefficient (MTC) on the experimental initial leakage or modeling of species diffusion through the bead film by the Nernst-Planck equation. A detailed analysis of the modeling against experimental data shows that the Nernst-Planck approach with no adjustable parameters performs as well as, or better, than the MTC approach, particularly to simulate the chromatographic elution of silver by nickel and the subsequent enrichment of the solution in the former metal. (author)

  1. Modelling of the UO2 dissolution mechanisms in synthetic groundwater solutions. Dissolution experiments carried out under oxic conditions

    International Nuclear Information System (INIS)

    Cera, E.; Grive, M.; Bruno, J.; Ollila, K.

    2001-02-01

    The analytical data generated during the last three years within the 4th framework program of the European Community at VTT Chemical Technology concerning UO 2 dissolution under oxidising conditions have been modelled in the present work. The modelling work has been addressed to perform a kinetic study of the dissolution data generated by Ollila (1999) under oxidising conditions by using unirradiated uranium dioxide as solid sample. The average of the normalised UO 2 dissolution rates determined by using the initial dissolution data generated in all the experimental tests is (6.06 ± 3.64)* 10 -7 mol m -2 d -1 . This dissolution rate agrees with most of the dissolution rates reported in the literature under similar experimental conditions. The results obtained in this modelling exercise show that the same bicarbonate promoted oxidative dissolution processes operate for uranium dioxide, as a chemical analogue of the spent fuel matrix, independently of the composition of the aqueous solution used. (orig.)

  2. Synthetic horizontal branch models for globular clusters - the luminosity of the horizontal branch and the Oosterhoff effect

    International Nuclear Information System (INIS)

    Lee, Y.W.; Demarque, P.; Zinn, R.

    1987-01-01

    The variation of horizontal-branch (HB) luminosities with metal abundances is analyzed on the basis of HB models synthesized from theoretical HB evolutionary tracks. The focus is on the Oosterhoff effect, as related to period shifts in globular-cluster RR Lyr variables. The construction of the models and the Oosterhoff period groups is explained in detail, and the implications for globular-cluster ages are considered. The ratio of Delta M(bol) (RR) to Delta Fe/H for the HB is calculated as 0.24, slightly steeper than that found by Sandage (1981 and 1982). 35 references

  3. Air Dispersion Modeling for the INL Application for a Synthetic Minor Sitewide Air Quality Permit to Construct with a Facility Emission Cap Component

    Energy Technology Data Exchange (ETDEWEB)

    Sondrup, Andrus Jeffrey [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-10-01

    The Department of Energy Idaho Operations Office (DOE-ID) is applying for a synthetic minor, Sitewide, air quality permit to construct (PTC) with a facility emission cap (FEC) component from the Idaho Department of Environmental Quality (DEQ) for Idaho National Laboratory (INL) to limit its potential to emit to less than major facility limits for criteria air pollutants (CAPs) and hazardous air pollutants (HAPs) regulated under the Clean Air Act. This document is supplied as an appendix to the application, Idaho National Laboratory Application for a Synthetic Minor Sitewide Air Quality Permit to Construct with a Facility Emissions Cap Component, hereafter referred to as “permit application” (DOE-ID 2015). Air dispersion modeling was performed as part of the permit application process to demonstrate pollutant emissions from the INL will not cause a violation of any ambient air quality standards. This report documents the modeling methodology and results for the air dispersion impact analysis. All CAPs regulated under Section 109 of the Clean Air Act were modeled with the exception of lead (Pb) and ozone, which are not required to be modeled by DEQ. Modeling was not performed for toxic air pollutants (TAPs) as uncontrolled emissions did not exceed screening emission levels for carcinogenic and non-carcinogenic TAPs. Modeling for CAPs was performed with the EPA approved AERMOD dispersion modeling system (Version 14134) (EPA 2004a) and five years (2000-2004) of meteorological data. The meteorological data set was produced with the companion AERMET model (Version 14134) (EPA 2004b) using surface data from the Idaho Falls airport, and upper-air data from Boise International Airport supplied by DEQ. Onsite meteorological data from the Grid 3 Mesonet tower located near the center of the INL (north of INTEC) and supplied by the local National Oceanic and Atmospheric Administration (NOAA) office was used for surface wind directions and wind speeds. Surface data (i

  4. Synthetic Defects for Vibrothermography

    Science.gov (United States)

    Renshaw, Jeremy; Holland, Stephen D.; Thompson, R. Bruce; Eisenmann, David J.

    2010-02-01

    Synthetic defects are an important tool used for characterizing the performance of nondestructive evaluation techniques. Viscous material-filled synthetic defects were developed for use in vibrothermography (also known as sonic IR) as a tool to improve inspection accuracy and reliability. This paper describes how the heat-generation response of these VMF synthetic defects is similar to the response of real defects. It also shows how VMF defects can be applied to improve inspection accuracy for complex industrial parts and presents a study of their application in an aircraft engine stator vane.

  5. Synthetic biological networks

    International Nuclear Information System (INIS)

    Archer, Eric; Süel, Gürol M

    2013-01-01

    Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics. (review article)

  6. Optimization of Catalytic Ozonation Process for Formaldehyde Mineralization from Synthetic Wastewater by Fe/MgO Nanoparticles Synthesis by Sol-Gel Method by Response Surface Model

    Directory of Open Access Journals (Sweden)

    Ghorban Asgari

    2014-09-01

    Full Text Available Background: Design experiment stages of formalin mineralization process by center composition design (CCD cause ease of work, reducing the number of samples, increasing the accuracy of optimized conditions and the interaction parameters determined during the process. The aim of this study was optimization of catalytic ozonation process for formaldehyde mineralization from synthetic wastewater by Fe/MgO nanoparticles synthesis by sol-gel method by response surface model. Methods: This experimental study was conducted in a semi-batch reactor, using a RSM by taking 3 factors in the final stage of pH (7-9, reaction time (10-20 min and catalyst dose (1.1-1.3 g/L was investigated. Synthesis of nanoparticles was done by sol-gel method. The results were analyzed by Design Expert 7.0.1 software. Results: The results showed that the process was dependent on the parameters studied and changing each parameter, affected the process efficiency and other parameters. The optimum conditions predicted for the process was 86.51% of mineralization efficiency. Optimum condition included pH=8.82, reaction time of 20 minute and catalyst dose of 1.3 g/L. The correlation coefficient for the process was determined 0.91. Conclusion: Using a statistical model could reduce the number of experiments, the accuracy and the prediction process. The catalytic ozonation process has the ability to remove formaldehyde with high efficiency and the process was environmental friendly.

  7. Technical Assessment: Synthetic Biology

    Science.gov (United States)

    2015-01-01

    Pfizer, Bausch & Lomb, Coca - Cola , and other Fortune 500 companies 8 Data estimated by the... financial prize for ideas to drive forward the production of a sensor relying on synthetic organisms that can detect exposure to 500 specific chemicals

  8. Synthetic Constraint of Ecosystem C Models Using Radiocarbon and Net Primary Production (NPP) in New Zealand Grazing Land

    Science.gov (United States)

    Baisden, W. T.

    2011-12-01

    Time-series radiocarbon measurements have substantial ability to constrain the size and residence time of the soil C pools commonly represented in ecosystem models. Radiocarbon remains unique in the ability to constrain the large stabilized C pool with decadal residence times. Radiocarbon also contributes usefully to constraining the size and turnover rate of the passive pool, but typically struggles to constrain pools with residence times less than a few years. Overall, the number of pools and associated turnover rates that can be constrained depends upon the number of time-series samples available, the appropriateness of chemical or physical fractions to isolate unequivocal pools, and the utility of additional C flux data to provide additional constraints. In New Zealand pasture soils, we demonstrate the ability to constrain decadal turnover times with in a few years for the stabilized pool and reasonably constrain the passive fraction. Good constraint is obtained with two time-series samples spaced 10 or more years apart after 1970. Three or more time-series samples further improve the level of constraint. Work within this context shows that a two-pool model does explain soil radiocarbon data for the most detailed profiles available (11 time-series samples), and identifies clear and consistent differences in rates of C turnover and passive fraction in Andisols vs Non-Andisols. Furthermore, samples from multiple horizons can commonly be combined, yielding consistent residence times and passive fraction estimates that are stable with, or increase with, depth in different sites. Radiocarbon generally fails to quantify rapid C turnover, however. Given that the strength of radiocarbon is estimating the size and turnover of the stabilized (decadal) and passive (millennial) pools, the magnitude of fast cycling pool(s) can be estimated by subtracting the radiocarbon-based estimates of turnover within stabilized and passive pools from total estimates of NPP. In grazing

  9. Computational modeling for the angular reconstruction of monoenergetic neutron flux in non-multiplying slabs using synthetic diffusion approximation

    International Nuclear Information System (INIS)

    Mansur, Ralph S.; Barros, Ricardo C.

    2011-01-01

    We describe a method to determine the neutron scalar flux in a slab using monoenergetic diffusion model. To achieve this goal we used three ingredients in the computational code that we developed on the Scilab platform: a spectral nodal method that generates numerical solution for the one-speed slab-geometry fixed source diffusion problem with no spatial truncation errors; a spatial reconstruction scheme to yield detailed profile of the coarse-mesh solution; and an angular reconstruction scheme to yield approximately the neutron angular flux profile at a given location of the slab migrating in a given direction. Numerical results are given to illustrate the efficiency of the offered code. (author)

  10. Atmospheric observations and inverse modelling for quantifying emissions of point-source synthetic greenhouse gases in East Asia

    Science.gov (United States)

    Arnold, Tim; Manning, Alistair; Li, Shanlan; Kim, Jooil; Park, Sunyoung; Muhle, Jens; Weiss, Ray

    2017-04-01

    The fluorinated species carbon tetrafluoride (CF4; PFC-14), nitrogen trifluoride (NF3) and trifluoromethane (CHF3; HFC-23) are potent greenhouse gases with 100-year global warming potentials of 6,630, 16,100 and 12,400, respectively. Unlike the majority of CFC-replacements that are emitted from fugitive and mobile emission sources, these gases are mostly emitted from large single point sources - semiconductor manufacturing facilities (all three), aluminium smelting plants (CF4) and chlorodifluoromethane (HCFC-22) factories (HFC-23). In this work we show that atmospheric measurements can serve as a basis to calculate emissions of these gases and to highlight emission 'hotspots'. We use measurements from one Advanced Global Atmospheric Gases Experiment (AGAGE) long term monitoring sites at Gosan on Jeju Island in the Republic of Korea. This site measures CF4, NF3 and HFC-23 alongside a suite of greenhouse and stratospheric ozone depleting gases every two hours using automated in situ gas-chromatography mass-spectrometry instrumentation. We couple each measurement to an analysis of air history using the regional atmospheric transport model NAME (Numerical Atmospheric dispersion Modelling Environment) driven by 3D meteorology from the Met Office's Unified Model, and use a Bayesian inverse method (InTEM - Inversion Technique for Emission Modelling) to calculate yearly emission changes over seven years between 2008 and 2015. We show that our 'top-down' emission estimates for NF3 and CF4 are significantly larger than 'bottom-up' estimates in the EDGAR emissions inventory (edgar.jrc.ec.europa.eu). For example we calculate South Korean emissions of CF4 in 2010 to be 0.29±0.04 Gg/yr, which is significantly larger than the Edgar prior emissions of 0.07 Gg/yr. Further, inversions for several separate years indicate that emission hotspots can be found without prior spatial information. At present these gases make a small contribution to global radiative forcing, however, given

  11. River Flow Prediction for Future Climate Using Long Series of Multi-Site Synthetic Data and MIKE SHE Model

    Directory of Open Access Journals (Sweden)

    Kuchar Leszek

    2017-01-01

    Full Text Available A new simulation of daily flow for Kaczawa River, south-west Poland for extra long series of generated meteorological data (comparing to previous research and selected climate change scenarios are presented. The Representative Concentration Pathways (RCPs scenarios vs. SRES are introduced for simulations. The flow simulation in the river catchment is made using MIKE SHE hydrological model while the multisite data are generated by spatial weather generator SWGEN. Simulations are done for 2040 and 2060 while the simulations for the year 2000 are used as a background. The large number of new simulated series determined by the lead time, three climate change scenarios (RCP2.6 RCP4.5 and RCP6.0, and number of generated years (1000 for each case is equal to 7000 for a single station. Finally, Pdf function for flow is presented as well probability of exceedance of maximum flow.

  12. Modelling of the UO2 dissolution mechanisms in synthetic groundwater. Experiments carried out under anaerobic and reducing conditions

    International Nuclear Information System (INIS)

    Cera, E.; Grive, M.; Bruno, J.; Ollila, K.

    2000-07-01

    The experimental data generated under anaerobic and reducing conditions within the EU R and D programme 1996-1998 entitled 'Source term for performance assessment of spent fuel as a waste form' and published as a POSIVA report (Ollila, 1999) have been modelled in the present work. The dissolution data available, mainly U in the aqueous phase as a function of time and redox potentials have been used to elucidate the redox pairs controlling the redox potential of the systems studied. Dissolution experiments carried out under anaerobic conditions have shown the important role of the uranium system on buffering the redox capacity of these systems. In the presence of carbonates in the system, the redox control has been given by the UO 2 (c)/U(VI) aqueous redox couple while in absence of carbonates in the system, the redox control has been governed by the UO 2 (c)/UO 2+x transition. In addition dissolution rates have been satisfactorily modelled by assuming an oxidative dissolution mechanism consisting in an initial oxidation of the surface of the uranium dioxide, binding of the HCO 3 or H+ at the U(VI) sites of the oxidised surface layer and detachment of these surface complexes. The redox controls in the experiments carried out under reducing conditions have been exerted by the different reducing agents added in the systems. Therefore, the addition of Fe 2+ lead to a redox control exerted by the Fe 2+ /Fe(OH) 3 (s) redox pair, while the addition of sulphide lead to a different redox control governed by the HS/SO 3 2- redox pair. (orig.)

  13. Modelling of the UO{sub 2} dissolution mechanisms in synthetic groundwater. Experiments carried out under anaerobic and reducing conditions

    Energy Technology Data Exchange (ETDEWEB)

    Cera, E.; Grive, M.; Bruno, J. [EnvirosQuantiSci (Spain); Ollila, K. [VTT Chemical Technology, Espoo (Finland)

    2000-07-01

    The experimental data generated under anaerobic and reducing conditions within the EU R and D programme 1996-1998 entitled 'Source term for performance assessment of spent fuel as a waste form' and published as a POSIVA report (Ollila, 1999) have been modelled in the present work. The dissolution data available, mainly U in the aqueous phase as a function of time and redox potentials have been used to elucidate the redox pairs controlling the redox potential of the systems studied. Dissolution experiments carried out under anaerobic conditions have shown the important role of the uranium system on buffering the redox capacity of these systems. In the presence of carbonates in the system, the redox control has been given by the UO{sub 2}(c)/U(VI) aqueous redox couple while in absence of carbonates in the system, the redox control has been governed by the UO{sub 2}(c)/UO{sub 2+x} transition. In addition dissolution rates have been satisfactorily modelled by assuming an oxidative dissolution mechanism consisting in an initial oxidation of the surface of the uranium dioxide, binding of the HCO{sub 3} or H+ at the U(VI) sites of the oxidised surface layer and detachment of these surface complexes. The redox controls in the experiments carried out under reducing conditions have been exerted by the different reducing agents added in the systems. Therefore, the addition of Fe{sup 2+} lead to a redox control exerted by the Fe{sup 2+}/Fe(OH){sub 3}(s) redox pair, while the addition of sulphide lead to a different redox control governed by the HS/SO{sub 3}{sup 2-} redox pair. (orig.)

  14. Synthetic Sediments and Stochastic Groundwater Hydrology

    Science.gov (United States)

    Wilson, J. L.

    2002-12-01

    For over twenty years the groundwater community has pursued the somewhat elusive goal of describing the effects of aquifer heterogeneity on subsurface flow and chemical transport. While small perturbation stochastic moment methods have significantly advanced theoretical understanding, why is it that stochastic applications use instead simulations of flow and transport through multiple realizations of synthetic geology? Allan Gutjahr was a principle proponent of the Fast Fourier Transform method for the synthetic generation of aquifer properties and recently explored new, more geologically sound, synthetic methods based on multi-scale Markov random fields. Focusing on sedimentary aquifers, how has the state-of-the-art of synthetic generation changed and what new developments can be expected, for example, to deal with issues like conceptual model uncertainty, the differences between measurement and modeling scales, and subgrid scale variability? What will it take to get stochastic methods, whether based on moments, multiple realizations, or some other approach, into widespread application?

  15. Synthetic Secoisolariciresinol Diglucoside (LGM2605 Protects Human Lung in an Ex Vivo Model of Proton Radiation Damage

    Directory of Open Access Journals (Sweden)

    Anastasia Velalopoulou

    2017-11-01

    Full Text Available Radiation therapy for the treatment of thoracic malignancies has improved significantly by directing of the proton beam in higher doses on the targeted tumor while normal tissues around the tumor receive much lower doses. Nevertheless, exposure of normal tissues to protons is known to pose a substantial risk in long-term survivors, as confirmed by our work in space-relevant exposures of murine lungs to proton radiation. Thus, radioprotective strategies are being sought. We established that LGM2605 is a potent protector from radiation-induced lung toxicity and aimed in the current study to extend the initial findings of space-relevant, proton radiation-associated late lung damage in mice by looking at acute changes in human lung. We used an ex vivo model of organ culture where tissue slices of donor living human lung were kept in culture and exposed to proton radiation. We exposed donor human lung precision-cut lung sections (huPCLS, pretreated with LGM2605, to 4 Gy proton radiation and evaluated them 30 min and 24 h later for gene expression changes relevant to inflammation, oxidative stress, and cell cycle arrest, and determined radiation-induced senescence, inflammation, and oxidative tissue damage. We identified an LGM2605-mediated reduction of proton radiation-induced cellular senescence and associated cell cycle changes, an associated proinflammatory phenotype, and associated oxidative tissue damage. This is a first report on the effects of proton radiation and of the radioprotective properties of LGM2605 on human lung.

  16. Laser assisted removal of synthetic painting-conservation materials using UV radiation of ns and fs pulse duration: Morphological studies on model samples

    International Nuclear Information System (INIS)

    Pouli, P.; Nevin, A.; Andreotti, A.; Colombini, P.; Georgiou, S.; Fotakis, C.

    2009-01-01

    In an effort to establish the optimal parameters for the cleaning of complex layers of polymers (mainly based on acrylics, vinyls, epoxys known as Elvacite, Laropal, Paraloid B72, among others) applied during past conservation treatments on the surface of wall paintings, laser cleaning tests were performed with particular emphasis on the plausible morphological modifications induced in the remaining polymeric material. Pulse duration effects were studied using laser systems of different pulse durations (ns and fs) at 248 nm. Prior to tests on real fragments from the Monumental Cemetery in Pisa (Italy) which were coated with different polymers, attention was focused on the study of model samples consisting of analogous polymer films cast on quartz disks. Ultraviolet irradiation is strongly absorbed by the studied materials both in ns and fs irradiation regimes. However, it is demonstrated that ultrashort laser pulses result in reduced morphological alterations in comparison to ns irradiation. In addition, the dependence of the observed alterations on the chemical composition of the consolidation materials in both regimes was examined. Most importantly, it was shown that in this specific conservation problem, an optimum cleaning process may rely not only on the minimization of laser-induced morphological changes but also on the exploitation of the conditions that favour the disruption of the adhesion between the synthetic material and the painting.

  17. The anti-inflammatory effect of the synthetic antimicrobial peptide 19-2.5 in a murine sepsis model: a prospective randomized study

    Science.gov (United States)

    2013-01-01

    Introduction Increasing rates of multi-resistant bacteria are a major problem in the treatment of critically ill patients. Furthermore, conventional antibiotics lead to the release of bacterial derived membrane parts initiating pro-inflammatory cascades with potential harm to the patient. Antimicrobial peptides (AMP) may kill bacteria without releasing pro-inflammatory factors. Thus, we compared three newly developed synthetic anti-lipopolysaccharide peptides (SALPs) with a broader range of efficacy to suppress cytokine release in plasma and CD14 mRNA expression in organ tissue in a murine, polymicrobial sepsis model. Methods A randomized, experimental trial was conducted in an animal research facility. Male NMRI mice (n = 90; 8- to 12-weeks old) were randomized to the following six groups: (i) sham operation and parenteral vehicle (NaCl 0.9%) administration (sham); (ii) cecal ligation and puncture (CLP) and vehicle infusion (sepsis-control), (iii) CLP and polymyxin B infusion (polyB), or (iv to vi) CLP and infusion of three different synthetic antimicrobial peptides Peptide 19-2.5 (Pep2.5), Peptide 19-4 (Pep4) or Peptide 19-8 (Pep8). All animals underwent arterial and venous catheterization for hemodynamic monitoring 48 hours prior to CLP or sham-operation. Physical appearance and behavior (activity), plasma cytokine levels, and CD14 mRNA expression in heart, lung, liver, spleen and kidney tissue were determined 24 hours after CLP or sham operation. Results Only Pep2.5 significantly enhanced the activity after CLP, whereas none of the therapeutic regimens elevated the mean arterial pressure or heart rate. The strongly elevated IL-6, IL-10 and monocyte chemoattractant protein serum levels in septic animals were significantly reduced after Pep2.5 administration (P < 0.001, P < 0.001, and P < 0.001, respectively). Similarly, Pep2.5 significantly reduced the sepsis-induced CD14 mRNA expression in heart (P = 0.003), lung (P = 0.008), and spleen tissue (P = 0.009) but

  18. Calibrating a hydraulic model using water levels derived from time series high-resolution Radarsat-2 synthetic aperture radar images and elevation data

    Science.gov (United States)

    Trudel, M.; Desrochers, N.; Leconte, R.

    2017-12-01

    Knowledge of water extent (WE) and level (WL) of rivers is necessary to calibrate and validate hydraulic models and thus to better simulate and forecast floods. Synthetic aperture radar (SAR) has demonstrated its potential for delineating water bodies, as backscattering of water is much lower than that of other natural surfaces. The ability of SAR to obtain information despite cloud cover makes it an interesting tool for temporal monitoring of water bodies. The delineation of WE combined with a high-resolution digital terrain model (DTM) allows extracting WL. However, most research using SAR data to calibrate hydraulic models has been carried out using one or two images. The objectives of this study is to use WL derived from time series high resolution Radarsat-2 SAR images for the calibration of a 1-D hydraulic model (HEC-RAS). Twenty high-resolution (5 m) Radarsat-2 images were acquired over a 40 km reach of the Athabasca River, in northern Alberta, Canada, between 2012 and 2016, covering both low and high flow regimes. A high-resolution (2m) DTM was generated combining information from LIDAR data and bathymetry acquired between 2008 and 2016 by boat surveying. The HEC-RAS model was implemented on the Athabasca River to simulate WL using cross-sections spaced by 100 m. An image histogram thresholding method was applied on each Radarsat-2 image to derive WE. WE were then compared against each cross-section to identify those were the slope of the banks is not too abrupt and therefore amenable to extract WL. 139 observations of WL at different locations along the river reach and with streamflow measurements were used to calibrate the HEC-RAS model. The RMSE between SAR-derived and simulated WL is under 0.35 m. Validation was performed using in situ observations of WL measured in 2008, 2012 and 2016. The RMSE between the simulated water levels calibrated with SAR images and in situ observations is less than 0.20 m. In addition, a critical success index (CSI) was

  19. A Synthetic Teammate for UAV Applications: A Prospective Look

    National Research Council Canada - National Science Library

    Gluck, Kevin A; Ball, Jerry T; Gunzelmann, Glenn; Krusmark, Michael A; Lyon, Don R; Cooke, Nancy J

    2006-01-01

    ..., computational cognitive process modeling of aircraft maneuvering and reconnaissance missions, verbal interaction between human operators and synthetic entities, and the formal analysis of team skill...

  20. Philosophy of Systems and Synthetic Biology

    DEFF Research Database (Denmark)

    Green, Sara

    2017-01-01

    This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

  1. Synthetic biology analysed tools for discussion and evaluation

    CERN Document Server

    2016-01-01

    Synthetic biology is a dynamic, young, ambitious, attractive, and heterogeneous scientific discipline. It is constantly developing and changing, which makes societal evaluation of this emerging new science a challenging task, prone to misunderstandings. Synthetic biology is difficult to capture, and confusion arises not only regarding which part of synthetic biology the discussion is about, but also with respect to the underlying concepts in use. This book offers a useful toolbox to approach this complex and fragmented field. It provides a biological access to the discussion using a 'layer' model that describes the connectivity of synthetic or semisynthetic organisms and cells to the realm of natural organisms derived by evolution. Instead of directly reviewing the field as a whole, firstly our book addresses the characteristic features of synthetic biology that are relevant to the societal discussion. Some of these features apply only to parts of synthetic biology, whereas others are relevant to synthetic bi...

  2. Diagnostic Magnetic Resonance Imaging of Atherosclerosis in Apolipoprotein E Knockout Mouse Model Using Macrophage-Targeted Gadolinium-Containing Synthetic Lipopeptide Nanoparticles.

    Directory of Open Access Journals (Sweden)

    Zu T Shen

    Full Text Available Cardiovascular disease is the leading cause of death in Western cultures. The vast majority of cardiovascular events, including stroke and myocardial infarction, result from the rupture of vulnerable atherosclerotic plaques, which are characterized by high and active macrophage content. Current imaging modalities including magnetic resonance imaging (MRI aim to characterize anatomic and structural features of plaques rather than their content. Previously, we reported that macrophage-targeted delivery of gadolinium (Gd-based contrast agent (GBCA-HDL using high density lipoproteins (HDL-like particles significantly enhances the detection of plaques in an apolipoprotein (apo E knockout (KO mouse model, with an atherosclerotic wall/muscle normalized enhancement ratio (NER of 120% achieved. These particles are comprised of lipids and synthetic peptide fragments of the major protein of HDL, apo A-I, that contain a naturally occurring modification which targets the particles to macrophages. Targeted delivery minimizes the Gd dose and thus reduces the adverse effects of Gd. The aims of the current study were to test whether varying the GBCA-HDL particle shape and composition can further enhance atherosclerotic plaque MRI and control organ clearance of these agents. We show that the optimized GBCA-HDL particles are efficiently delivered intracellularly to and uptaken by both J774 macrophages in vitro and more importantly, by intraplaque macrophages in vivo, as evidenced by NER up to 160% and higher. This suggests high diagnostic power of our GBCA-HDL particles in the detection of vulnerable atherosclerotic plaques. Further, in contrast to discoidal, spherical GBCA-HDL exhibit hepatic clearance, which could further diminish adverse renal effects of Gd. Finally, activated macrophages are reliable indicators of any inflamed tissues and are implicated in other areas of unmet clinical need such as rheumatoid arthritis, sepsis and cancer, suggesting the

  3. What Are Synthetic Cannabinoids?

    Science.gov (United States)

    ... years, synthetic cannabinoid mixtures have been easy to buy in drug paraphernalia shops, novelty stores, gas stations, and over ... abuse, authorities have made it illegal to sell, buy, or possess some of ... use is that standard drug tests cannot easily detect many of the chemicals ...

  4. Synthetic Aperture Sequential Beamforming

    DEFF Research Database (Denmark)

    Kortbek, Jacob; Jensen, Jørgen Arendt; Gammelmark, Kim Løkke

    2008-01-01

    A synthetic aperture focusing (SAF) technique denoted Synthetic Aperture Sequential Beamforming (SASB) suitable for 2D and 3D imaging is presented. The technique differ from prior art of SAF in the sense that SAF is performed on pre-beamformed data contrary to channel data. The objective is to im......A synthetic aperture focusing (SAF) technique denoted Synthetic Aperture Sequential Beamforming (SASB) suitable for 2D and 3D imaging is presented. The technique differ from prior art of SAF in the sense that SAF is performed on pre-beamformed data contrary to channel data. The objective...... is to improve and obtain a more range independent lateral resolution compared to conventional dynamic receive focusing (DRF) without compromising frame rate. SASB is a two-stage procedure using two separate beamformers. First a set of Bmode image lines using a single focal point in both transmit and receive...... is stored. The second stage applies the focused image lines from the first stage as input data. The SASB method has been investigated using simulations in Field II and by off-line processing of data acquired with a commercial scanner. The performance of SASB with a static image object is compared with DRF...

  5. Building synthetic cellular organization

    OpenAIRE

    Polka, Jessica K.; Silver, Pamela A.

    2013-01-01

    The elaborate spatial organization of cells enhances, restricts, and regulates protein–protein interactions. However, the biological significance of this organization has been difficult to study without ways of directly perturbing it. We highlight synthetic biology tools for engineering novel cellular organization, describing how they have been, and can be, used to advance cell biology.

  6. Towards a synthetic chloroplast.

    Directory of Open Access Journals (Sweden)

    Christina M Agapakis

    2011-04-01

    Full Text Available The evolution of eukaryotic cells is widely agreed to have proceeded through a series of endosymbiotic events between larger cells and proteobacteria or cyanobacteria, leading to the formation of mitochondria or chloroplasts, respectively. Engineered endosymbiotic relationships between different species of cells are a valuable tool for synthetic biology, where engineered pathways based on two species could take advantage of the unique abilities of each mutualistic partner.We explored the possibility of using the photosynthetic bacterium Synechococcus elongatus PCC 7942 as a platform for studying evolutionary dynamics and for designing two-species synthetic biological systems. We observed that the cyanobacteria were relatively harmless to eukaryotic host cells compared to Escherichia coli when injected into the embryos of zebrafish, Danio rerio, or taken up by mammalian macrophages. In addition, when engineered with invasin from Yersinia pestis and listeriolysin O from Listeria monocytogenes, S. elongatus was able to invade cultured mammalian cells and divide inside macrophages.Our results show that it is possible to engineer photosynthetic bacteria to invade the cytoplasm of mammalian cells for further engineering and applications in synthetic biology. Engineered invasive but non-pathogenic or immunogenic photosynthetic bacteria have great potential as synthetic biological devices.

  7. Synthetic Metabolic Pathways

    DEFF Research Database (Denmark)

    topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Synthetic Metabolic Pathways: Methods and Protocols aims to ensure successful results in the further study...

  8. Results of the Simulator smart against synthetic signals using a model of reduced order of BWR with additive and multiplicative noise; Resultados del simulador smart frente a senales sinteticas utilizando un modelo de orden reducido de BWR con ruido aditivo y multiplicativo

    Energy Technology Data Exchange (ETDEWEB)

    Munoz-Cobo, J. L.; Montesino, M. E.; Pena, J.; Escriva, A.; Melara, J.

    2011-07-01

    Results of SMART-simulator front of synthetic signals with models of reduced order of BWR with additive and multiplicative noise Under the SMART project, which aims to monitor the signals Cofrentes nuclear plant, we have developed a signal generator of synthetics BWR that will allow together real signals of plant the validation of the monitor.

  9. Fault model of the 2017 Jiuzhaigou Mw 6.5 earthquake estimated from coseismic deformation observed using Global Positioning System and Interferometric Synthetic Aperture Radar data

    Science.gov (United States)

    Nie, Zhaosheng; Wang, Di-Jin; Jia, Zhige; Yu, Pengfei; Li, Liangfa

    2018-04-01

    On August 8, 2017, the Jiuzhaigou Mw 6.5 earthquake occurred in Sichuan province, southwestern China, along the eastern margin of the Tibetan Plateau. The epicenter is surrounded by the Minjiang, Huya, and Tazang Faults. As the seismic activity and tectonics are very complicated, there is controversy regarding the accurate location of the epicenter and the seismic fault of the Jiuzhaigou earthquake. To investigate these aspects, first, the coseismic deformation field was derived from Global Positioning System (GPS) and Interferometric Synthetic Aperture Radar (InSAR) measurements. Second, the fault geometry, coseismic slip model, and Coulomb stress changes around the seismic region were calculated using a homogeneous elastic half-space model. The coseismic deformation field derived from InSAR measurements shows that this event was mainly dominated by a left-lateral strike-slip fault. The maximal and minimal displacements were approximately 0.15 m and - 0.21 m, respectively, along line-of-sight observation. The whole deformation field follows a northwest-trending direction and is mainly concentrated west of the fault. The coseismic slip is 28 km along the strike and 18 km along the dip. It is dominated by a left-lateral strike-slip fault. The average and maximal fault slip is 0.18 and 0.85 m, respectively. The rupture did not fully reach the ground surface. The focal mechanism derived from GPS and InSAR data is consistent with the kinematics and geometry of the Huya Fault. Therefore, we conclude that the northern section or the Shuzheng segment of the Huya Fault is the seismogenic fault. The maximal fault slip is located at 33.25°N and 103.82°E at a depth of 11 km, and the release moment is approximately 6.635 × 1018 Nm, corresponding to a magnitude of Mw 6.49, which is consistent with results reported by the US Geological Survey, Global Centroid Moment Tensor, and other researchers. The coseismic Coulomb stress changes enhanced the stress on the northwest and

  10. Synthetic Scenarios from CMIP5 Model Simulations for Climate Change Impact Assessments in Managed Ecosystems and Water Resources: Case Study in South Asian Countries

    Science.gov (United States)

    Anandhi, A.; Omani, N.; Chaubey, I.; Horton, R.; Bader, D.; Nanjundiah, R. S.

    2017-01-01

    Increasing population, urbanization, and associated demand for food production compounded by climate change and variability have important implications for the managed ecosystems and water resources of a region. This is particularly true for south Asia, which supports one quarter of the global population, half of whom live below the poverty line. This region is largely dependent on monsoon precipitation for water. Given the limited resources of the developing countries in this region, the objective of our study was to empirically explore climate change in south Asia up to the year 2099 using monthly simulations from 35 global climate models (GCMs) participating in the fifth phase of the Climate Model Inter-comparison Project (CMIP5) for two future emission scenarios (representative concentration pathways RCP4.5 and RCP8.5) and provide a wide range of potential climate change outcomes. This was carried out using a three-step procedure: calculating the mean annual, monsoon, and non-monsoon precipitation and temperatures; estimating the percent change from historical conditions; and developing scenario funnels and synthetic scenarios. This methodology was applied for the entire south Asia region; however, the percent change information generated at 1.5deg grid scale can be used to generate scenarios at finer spatial scales. Our results showed a high variability in the future change in precipitation (-23% to 52%, maximum in the non-monsoon season) and temperature (0.8% to 2.1%) in the region. Temperatures in the region consistently increased, especially in the Himalayan region, which could have impacts including a faster retreat of glaciers and increased floods. It could also change rivers from perennial to seasonal, leading to significant challenges in water management. Increasing temperatures could further stress groundwater reservoirs, leading to withdrawal rates that become even more unsustainable. The high precipitation variability (with higher propensity for

  11. The Effect of Health Education based on Health Belief Model on Preventive Actions of Synthetic Drugs Dependence in Male Students of Kerman, Iran

    Directory of Open Access Journals (Sweden)

    Seyed Saeed Mazloomy Mahmoodabad

    2017-06-01

    Conclusion: Findings indicated that by increase of HBM components' average scores, the average score of synthetic drug dependence preventive actions increased too. Therefore, results of the research confirm the effect and efficiency of HBM in making preventive actions of drug dependence. 

  12. Synthetic Electric Microbial Biosensors

    Science.gov (United States)

    2017-06-10

    domains and DNA-binding domains into a single protein for deregulation of down stream genes of have been favored [10]. Initially experiments with... Germany DISTRIBUTION A. Approved for public release: distribution unlimited.   Talk title: “Synthetic biology based microbial biosensors for the...toolbox” in Heidelberg, Germany Poster title: “Anaerobic whole cell microbial biosensors” Link: http://phdsymposium.embl.org/#home   September, 2014

  13. BNN-20, a synthetic microneurotrophin, strongly protects dopaminergic neurons in the "weaver" mouse, a genetic model of dopamine-denervation, acting through the TrkB neurotrophin receptor.

    Science.gov (United States)

    Botsakis, Konstantinos; Mourtzi, Theodora; Panagiotakopoulou, Vasiliki; Vreka, Malamati; Stathopoulos, Georgios T; Pediaditakis, Iosif; Charalampopoulos, Ioannis; Gravanis, Achilleas; Delis, Foteini; Antoniou, Katerina; Zisimopoulos, Dimitrios; Georgiou, Christos D; Panagopoulos, Nikolaos T; Matsokis, Nikolaos; Angelatou, Fevronia

    2017-07-15

    Neurotrophic factors are among the most promising treatments aiming at slowing or stopping and even reversing Parkinson's disease (PD). However, in most cases, they cannot readily cross the human blood-brain-barrier (BBB). Herein, we propose as a therapeutic for PD the small molecule 17-beta-spiro-[5-androsten-17,2'-oxiran]-3beta-ol (BNN-20), a synthetic analogue of DHEA, which crosses the BBB and is deprived of endocrine side-effects. Using the "weaver" mouse, a genetic model of PD, which exhibits progressive dopaminergic neurodegeneration in the Substantia Nigra (SN), we have shown that long-term administration (P1-P21) of BNN-20 almost fully protected the dopaminergic neurons and their terminals, via i) a strong anti-apoptotic effect, probably mediated through the Tropomyosin receptor kinase B (TrkB) neurotrophin receptor's PI3K-Akt-NF-κB signaling pathway, ii) by exerting an efficient antioxidant effect, iii) by inducing significant anti-inflammatory activity and iv) by restoring Brain-Derived Neurotrophic Factor (BDNF) levels. By intercrossing "weaver" with NGL mice (dual GFP/luciferase-NF-κΒ reporter mice, NF-κΒ.GFP.Luc), we obtained Weaver/NGL mice that express the NF-κB reporter in all somatic cells. Acute BNN-20 administration to Weaver/NGL mice induced a strong NF-κB-dependent transcriptional response in the brain as detected by bioluminescence imaging, which was abolished by co-administration of the TrkB inhibitor ANA-12. This indicates that BNN-20 exerts its beneficial action (at least in part) through the TrkB-PI3K-Akt-NF-κB signaling pathway. These results could be of clinical relevance, as they suggest BNN-20 as an important neuroprotective agent acting through the TrkB neurotrophin receptor pathway, mimicking the action of the endogenous neurotrophin BDNF. Thus BNN-20 could be proposed for treatment of PD. Copyright © 2017. Published by Elsevier Ltd.

  14. [Comparative analysis of 3D data visibility of the prepared tooth finishing line on a synthetic jaw model, captured by international scanners in a laboratory conditions].

    Science.gov (United States)

    Ryakhovskiy, A N; Kostyukova, V V

    The aim of the study was to compare accuracy of digital impression's finishing line and the zone under it taken by different intraoral scanning systems. Parameters of comparison were: different level of the finishing line to the gingiva and width of sulcus after retraction. For this purpose two synthetic jaw models with prepared teeth were scanned using intraoral scanning systems: 3D Progress (MHT S.P.A., IT - MHT Optic Research AG, CH); True Definition (3M ESPE, USA); Trios (3Shape A/S, DNK); CEREC AC Bluecam, CEREC Omnicam (Sirona Dental System GmbH, DE); Planscan (Planmeca, FIN) (each n=10). Reference-scanning was done by ATOS Core (GOM mbH, DE). The resulting digital impressions were superimposed with the master-scan. The lowest measured deviations (trueness) for intraoral scanners, where the finishing line was 0.5 mm above gingiva were with scanner True Definition - 18.8±6.63 (on the finishing line) and 51.0±14.33 µm (0.3 mm under the finishing line). In conditions where finishing line was on the same level with gingiva, scanner Trios showed the best results: 17.0±3.96 and 52.7±6.52 µm. When the finishing line was 0.5 mm under gingiva, none of the testing scanners could visualize the zone 0.3 mm lower the finishing line. The best results for accuracy o the finishing line in that circumstances showed Trios: 15.1±5.05 µm. The optimum visualization of the finishing line and the zone under it was reached when the sulcus was 0.3 mm after retraction. Thus, the best accuracy was obtained with Trios: 10.3±2.69 (on the finishing line) and 57.2±13.58 µm (0.3 mm under finishing line). The results show that intraoral scanners also provide enough accuracy for indicating finishing line and the zone under it in different conditions of preparation and gingiva retraction. However, not all of the testing scanners can properly indicate finishing line and the zone under it when shoulder is below gingiva and the width of sulcus is less than 0.2 mm.

  15. A Mixed Green Micro-Algal Model (MAMO) – Model Identification And Calibration Using Synthetic Medium And Nutrient Rich Carbon Depleted Wastewater

    DEFF Research Database (Denmark)

    Sæbø, M.; Valverde Perez, Borja; Van Wagenen, Jonathan

    , ASM2d (Henze et al., 1999), and thus it also accounts for bacterial growth in the photobioreactor. We assess the factors, influencing algae growth and nutrient uptake, including macro-nutrient availability and light irradiance rate. Model parameters were estimated through microplate screenings...

  16. Goodness of Fit of Skills Assessment Approaches: Insights from Patterns of Real vs. Synthetic Data Sets

    Science.gov (United States)

    Beheshti, Behzad; Desmarais, Michel C.

    2015-01-01

    This study investigates the issue of the goodness of fit of different skills assessment models using both synthetic and real data. Synthetic data is generated from the different skills assessment models. The results show wide differences of performances between the skills assessment models over synthetic data sets. The set of relative performances…

  17. Opportunities in plant synthetic biology.

    Science.gov (United States)

    Cook, Charis; Martin, Lisa; Bastow, Ruth

    2014-05-01

    Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.

  18. Synthetic staggered architecture composites

    International Nuclear Information System (INIS)

    Dutta, Abhishek; Tekalur, Srinivasan Arjun

    2013-01-01

    Highlights: ► Composite design inspired by nature. ► Tuning microstructure via changing ceramic content and aspect ratio. ► Experimental display of structure–property correlationship in synthetic composites. - Abstract: Structural biocomposites (for example, nacre in seashells, bone, etc.) are designed according to the functional role they are delegated for. For instance, bone is primarily designed for withstanding time-dependent loading (for example, withstanding stresses while running, jumping, accidental fall) and hence the microstructure is designed primarily from enhanced toughness and moderate stiffness point of view. On the contrary, seashells (which lie in the abyss of oceans) apart from providing defense to the organism (it is hosting) against predatory attacks, are subjected to static loading (for example, enormous hydrostatic pressure). Hence, emphasis on the shell structure evolution is directed primarily towards providing enhanced stiffness. In order to conform between stiffness and toughness, nature precisely employs a staggered arrangement of inorganic bricks in a biopolymer matrix (at its most elementary level of architecture). Aspect ratio and content of ceramic bricks are meticulously used by nature to synthesize composites having varying degrees of stiffness, strength and toughness. Such an amazing capability of structure–property correlationship has rarely been demonstrated in synthetic composites. Therefore, in order to better understand the mechanical behavior of synthetic staggered composites, the problem becomes two-pronged: (a) synthesize composites with varying brick size and contents and (b) experimental investigation of the material response. In this article, an attempt has been made to synthesize and characterize staggered ceramic–polymer composites having varying aspect ratio and ceramic content using freeze-casting technique. This will in-turn help us in custom-design manufacture of hybrid bio-inspired composite materials

  19. Synthetic Aperture Ultrasound Imaging

    DEFF Research Database (Denmark)

    Jensen, Jørgen Arendt; Nikolov, Svetoslav; Gammelmark, Kim Løkke

    2006-01-01

    The paper describes the use of synthetic aperture (SA) imaging in medical ultrasound. SA imaging is a radical break with today's commercial systems, where the image is acquired sequentially one image line at a time. This puts a strict limit on the frame rate and the possibility of acquiring...... a sufficient amount of data for high precision flow estimation. These constrictions can be lifted by employing SA imaging. Here data is acquired simultaneously from all directions over a number of emissions, and the full image can be reconstructed from this data. The talk will demonstrate the many benefits...

  20. Transition in synthetic jets

    Czech Academy of Sciences Publication Activity Database

    Tesař, Václav; Kordík, Jozef

    2012-01-01

    Roč. 187, NOV 2012 (2012), s. 105-117 ISSN 0924-4247 R&D Projects: GA TA ČR(CZ) TA02020795; GA ČR(CZ) GPP101/12/P556; GA ČR(CZ) GCP101/11/J019 Institutional research plan: CEZ:AV0Z20760514 Keywords : turbulence * synthetic jet * transition * velocity spectra Subject RIV: BK - Fluid Dynamics Impact factor: 1.841, year: 2012 http://www. science direct.com/ science /article/pii/S0924424712005031

  1. Homogeneous nucleation of water in synthetic air

    NARCIS (Netherlands)

    Fransen, M.A.L.J.; Sachteleben, E.; Hruby, J.; Smeulders, D.M.J.; DeMott, P.J.; O'Dowd, C.D.

    2013-01-01

    Homogeneous nucleation rates for water vapor in synthetic air are measured by means of a Pulse-Expansion Wave Tube (PEWT). A comparison of the experimental nucleation rates with the Classical Nucleation Theory (CNT) shows that a more elaborated model is necessary to describe supercooled water

  2. Synthetic tsunamis along the Israeli coast.

    Science.gov (United States)

    Tobias, Joshua; Stiassnie, Michael

    2012-04-13

    The new mathematical model for tsunami evolution by Tobias & Stiassnie (Tobias & Stiassnie 2011 J. Geophys. Res. Oceans 116, C06026) is used to derive a synthetic tsunami database for the southern part of the Eastern Mediterranean coast. Information about coastal tsunami amplitudes, half-periods, currents and inundation levels is presented.

  3. CO2 Capture with Enzyme Synthetic Analogue

    Energy Technology Data Exchange (ETDEWEB)

    Cordatos, Harry

    2010-11-08

    Overview of an ongoing, 2 year research project partially funded by APRA-E to create a novel, synthetic analogue of carbonic anhydrase and incorporate it into a membrane for removal of CO2 from flue gas in coal power plants. Mechanism background, preliminary feasibility study results, molecular modeling of analogue-CO2 interaction, and program timeline are provided.

  4. Wind energy applications of synthetic aperture radar

    DEFF Research Database (Denmark)

    Badger, Merete

    Synthetic aperture radars (SAR), mounted on satellites or aircraft, have proven useful for ocean wind mapping. Wind speeds at the height 10 m may be retrieved from measurements of radar backscatter using empirical model functions. The resulting windfields are valuable in offshore wind energy plan...

  5. Mammalian synthetic biology for studying the cell.

    Science.gov (United States)

    Mathur, Melina; Xiang, Joy S; Smolke, Christina D

    2017-01-02

    Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. © 2017 Mathur et al.

  6. Engineering emergent multicellular behavior through synthetic adhesion

    Science.gov (United States)

    Glass, David; Riedel-Kruse, Ingmar

    In over a decade, synthetic biology has developed increasingly robust gene networks within single cells, but constructed very few systems that demonstrate multicellular spatio-temporal dynamics. We are filling this gap in synthetic biology's toolbox by developing an E. coli self-assembly platform based on modular cell-cell adhesion. We developed a system in which adhesive selectivity is provided by a library of outer membrane-displayed peptides with intra-library specificities, while affinity is provided by consistent expression across the entire library. We further provide a biophysical model to help understand the parameter regimes in which this tool can be used to self-assemble into cellular clusters, filaments, or meshes. The combined platform will enable future development of synthetic multicellular systems for use in consortia-based metabolic engineering, in living materials, and in controlled study of minimal multicellular systems. Stanford Bio-X Bowes Fellowship.

  7. Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project

    OpenAIRE

    Sliva, Anna; Yang, Huanming; Boeke, Jef D.; Mathews, Debra J. H.

    2015-01-01

    First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) Project is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with...

  8. Analog synthetic biology.

    Science.gov (United States)

    Sarpeshkar, R

    2014-03-28

    We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog-digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA-protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations.

  9. Synthetic lubricating oils

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez Jurado, J

    1953-01-01

    A yellow solid petroleum paraffin d/sup 60/ 0.808, I number 3.5, average molecular weight 350, chlorinated and condensed with benzene, xylene, or naphthalene by the Friedel and Crafts reaction, in the presence of anhydrous AlCl/sub 3/ or activated Al, gave synthetic lubricating oils. Xylene was the preferred aromatic compound, naphthalene required the use of less completely chlorinated paraffin, benzene produced resins difficult to remove and gave darker oils with excessive green fluorescence. Activated Al rather than anhydrous AlCl/sub 3/ gave darker oils with higher viscosity and Conradson C values. Tar from the low-temperature distillation of lignite, used as a source of a paraffin fraction melting 40/sup 0/ to 48/sup 0/ (chlorinated to 26.5 percent Cl) and an aromatic fraction, 45 percent aromatic compounds by volume (mainly polysubstituted benzenes), I number 10, was converted to a similar synthetic lubricant with the following properties: Kinematic viscosity at 210/sup 0/ F., 50.4 centistokes; viscosity index, 92; Conradson C, 1.5 percent; solidification point, 9/sup 0/; S, 0.41 percent.

  10. Coloring of synthetic fluorite

    International Nuclear Information System (INIS)

    Birsoy, R.

    1980-01-01

    A synthetic fluorite of the Harshaw Chemical Company is analyzed for rare earth elements, yttrium, and sodium. Samples of this fluorite are irradiated with X-rays, γ-rays, neutrons, electrons, protons, and α-particles at different energies, and their absorption spectra are analyzed. Analyzing the thermal bleaching of these radiation-coloured fluorites shows that both, impurities and radiation play a part in the coloration of synthetic fluorite. However, the main contribution comes from the radiation induced lattice defects. In the visible region spectra, the colour centre of the 5800 to 5900 A absorption band is probably mainly related with large aggregates of F-centres. The 5450 and the 5300 A absorption bands are mainly related to monovalent and divalent ion impurities and their association with lattice defects. The 3800 A absorption band seems to be related with F-centre aggregates. However, the contribution from the rare earth elements related complex color centres also plays some part for the production of this absorption band. These results indicate that the color centres of different origin can absorb light at the same wavelength. (author)

  11. Model-Based Discovery of Synthetic Agonists for the Zn2+-Sensing G-Protein-Coupled Receptor 39 (GPR39) Reveals Novel Biological Functions

    DEFF Research Database (Denmark)

    Frimurer, Thomas M.; Mende, Franziska; Graae, Anne-Sofie

    2017-01-01

    binding to other receptors with similar binding pockets to select iterative series of mini-libraries. These libraries were cherry-picked from all com. available synthetic compds. A total of only 520 compds. were tested in vitro, making this method broadly applicable for tool compd. development. The compds....... of the initial library were inactive when tested alone, but lead compds. were identified using Zn2 as an allosteric enhancer. Highly selective, highly potent Zn2-independent GPR39 agonists were found in subsequent mini-libraries. These agonists identified GPR39 as a novel regulator of gastric somatostatin...

  12. Current status of synthetic epikeratoplasty.

    Science.gov (United States)

    Thompson, K P; Hanna, K; Waring, G O; Gipson, I; Liu, Y; Gailitis, R P; Johnson-Wint, B; Green, K

    1991-01-01

    Many of the deficiencies with human tissue epikeratoplasty might be improved by the use of a suitable synthetic lenticule. Potential biomaterials for epikeratoplasty include collagen (types I, III, or IV), collagen-hydrogel copolymers, bioactive synthetics, and coated hydrogels. The biomaterial must be engineered to achieve strict specifications of optical clarity, support of epithelial migration and adhesion, permeability to solutes, and stability to corneal proteases. Attaching synthetic lenticules to the cornea without cutting Bowman's layer by adhesives, laser welding, or direct adhesion may also improve the efficacy of synthetic epikeratoplasty.

  13. Synthetic biology and occupational risk.

    Science.gov (United States)

    Howard, John; Murashov, Vladimir; Schulte, Paul

    2017-03-01

    Synthetic biology is an emerging interdisciplinary field of biotechnology that involves applying the principles of engineering and chemical design to biological systems. Biosafety professionals have done an excellent job in addressing research laboratory safety as synthetic biology and gene editing have emerged from the larger field of biotechnology. Despite these efforts, risks posed by synthetic biology are of increasing concern as research procedures scale up to industrial processes in the larger bioeconomy. A greater number and variety of workers will be exposed to commercial synthetic biology risks in the future, including risks to a variety of workers from the use of lentiviral vectors as gene transfer devices. There is a need to review and enhance current protection measures in the field of synthetic biology, whether in experimental laboratories where new advances are being researched, in health care settings where treatments using viral vectors as gene delivery systems are increasingly being used, or in the industrial bioeconomy. Enhanced worker protection measures should include increased injury and illness surveillance of the synthetic biology workforce; proactive risk assessment and management of synthetic biology products; research on the relative effectiveness of extrinsic and intrinsic biocontainment methods; specific safety guidance for synthetic biology industrial processes; determination of appropriate medical mitigation measures for lentiviral vector exposure incidents; and greater awareness and involvement in synthetic biology safety by the general occupational safety and health community as well as by government occupational safety and health research and regulatory agencies.

  14. Finding Hope in Synthetic Biology.

    Science.gov (United States)

    Takala, Tuija

    2017-04-01

    For some, synthetic biology represents great hope in offering possible solutions to many of the world's biggest problems, from hunger to sustainable development. Others remain fearful of the harmful uses, such as bioweapons, that synthetic biology can lend itself to, and most hold that issues of biosafety are of utmost importance. In this article, I will evaluate these points of view and conclude that although the biggest promises of synthetic biology are unlikely to become reality, and the probability of accidents is fairly substantial, synthetic biology could still be seen to benefit humanity by enhancing our ethical understanding and by offering a boost to world economy.

  15. Tissue Harmonic Synthetic Aperture Imaging

    DEFF Research Database (Denmark)

    Rasmussen, Joachim

    The main purpose of this PhD project is to develop an ultrasonic method for tissue harmonic synthetic aperture imaging. The motivation is to advance the field of synthetic aperture imaging in ultrasound, which has shown great potentials in the clinic. Suggestions for synthetic aperture tissue...... system complexity compared to conventional synthetic aperture techniques. In this project, SASB is sought combined with a pulse inversion technique for 2nd harmonic tissue harmonic imaging. The advantages in tissue harmonic imaging (THI) are expected to further improve the image quality of SASB...

  16. Life after the synthetic cell

    DEFF Research Database (Denmark)

    Rasmussen, Steen

    2010-01-01

    Nature asked eight synthetic-biology experts about the implications for science and society of the “synthetic cell” made by the J. Craig Venter Institute (JCVI). The institute's team assembled, modified and implanted a synthesized genome into a DNA-free bacterial shell to make a self-replicating ......Nature asked eight synthetic-biology experts about the implications for science and society of the “synthetic cell” made by the J. Craig Venter Institute (JCVI). The institute's team assembled, modified and implanted a synthesized genome into a DNA-free bacterial shell to make a self...

  17. Computational synthetic geometry

    CERN Document Server

    Bokowski, Jürgen

    1989-01-01

    Computational synthetic geometry deals with methods for realizing abstract geometric objects in concrete vector spaces. This research monograph considers a large class of problems from convexity and discrete geometry including constructing convex polytopes from simplicial complexes, vector geometries from incidence structures and hyperplane arrangements from oriented matroids. It turns out that algorithms for these constructions exist if and only if arbitrary polynomial equations are decidable with respect to the underlying field. Besides such complexity theorems a variety of symbolic algorithms are discussed, and the methods are applied to obtain new mathematical results on convex polytopes, projective configurations and the combinatorics of Grassmann varieties. Finally algebraic varieties characterizing matroids and oriented matroids are introduced providing a new basis for applying computer algebra methods in this field. The necessary background knowledge is reviewed briefly. The text is accessible to stud...

  18. Synthetic Aperture Compound Imaging

    DEFF Research Database (Denmark)

    Hansen, Jens Munk

    and the limiting factor is the amount of memory IO resources available. An equally high demand for memory throughput is found in the computer gaming industry, where a large part of the processing takes place on the graphics processing unit (GPU). Using the GPU, a framework for synthetic aperture imaging......Medical ultrasound imaging is used for many purposes, e.g. for localizing and classifying cysts, lesions, and other processes. Almost any mass is first observed using B-mode imaging and later classified using e.g. color flow, strain, or attenuation imaging. It is therefore important that the B......-mode images have high contrast. Like all imaging modalities, ultrasound is subject to a number of inherent artifacts that compromise image quality. The most prominent artifact is the degradation by coherent wave interference, known as “speckle”, which gives a granular appearance to an otherwise homogeneous...

  19. Radioimmunoassay of synthetic steroids

    Energy Technology Data Exchange (ETDEWEB)

    Raynaud, J -P; Bucourt, R; Salmon, J

    1975-12-01

    The sensitivity of a radioimmunoassay depends on the intrinsic association constant of the interaction between ligand and antibody. Its specificity depends on the position of the chain which forms the link with the antigen. Thus, an antibody specific of estradiol has been obtained by coupling estradiol to albumin via a chain at position 7. For synthetic steroids the structure of which is sufficiency different from that of natural hormones, the requirements for a sensitive assay method not involving chromatography are simply maximum affinity and positioning of the couple at a site which does not undergo metabolic attack. These criteria were used to develop assays for R 2858 and R 2453 which obviate the need to administer radioactive product in clinical pharmacology. Cross-reaction with structural analogs may be used to assay competitors. Thus, R 2323 antibody, highly specific for endogenous steroids, may be used to assay other trienes such as R 1697 (trenbolone) and R 2010 (norgestrienone).

  20. Synthetic fuels and fusion

    Energy Technology Data Exchange (ETDEWEB)

    Fillo, J A; Powell, J; Steinberg, M [Brookhaven National Lab., Upton, NY (USA)

    1981-03-01

    The decreasing availability of fossil fuels emphasizes the need to develop systems which will produce synthetic fuel to substitute for and supplement the natural supply. An important first step in the synthesis of liquid and gaseous fuels is the production of hydrogen. Thermonuclear fusion offers an inexhaustible source of energy for the production of hydrogen from water. Depending on design, electric generation efficiencies of approx. equal to 40-60% and hydrogen production efficiencies by high temperature electrolysis of approx. equal to 50-70% are projected for fusion reactors using high temperature blankets. Fusion/coal symbiotic systems appear economically promising for the first generation of commercial fusion synfuels plants. Coal production requirements and the environmental effects of large-scale coal usage would be greatly reduced by a fusion/coal system. In the long-term, there could be a gradual transition to an inexhaustible energy system based solely on fusion.

  1. Color profiles and stability of acylated and nonacylated anthocyanins as novel pigment sources in a lipstick model: A viable alternative to synthetic colorants.

    Science.gov (United States)

    Westfall, Alexandra; Giusti, Mónica

    Cosmetics, such as lipstick, can affect an individual's perception of attractiveness and morale. Consumer concern with the safety of synthetic colorants has made the need for alternative natural color sources increasingly urgent. Our goal was to evaluate the feasibility of anthocyanin (ACN) extracts as colorants in lipstick formulations. Lipstick formulations were colored with ACN-rich materials. Accelerated environmental testing typical of the cosmetic industry were used: incubation at 20°, 37°, and 45°C for 12 weeks and temperature abuse cycles between 20°/37°C or -20°/20°C. Color (CIELab) and total monomeric ACN (pH-differential) changes were monitored to determine shelf stability of the product. All formulations exhibited acceptable color for lipsticks. Shelf stability was determined to exceed 2 year based on the accelerated testing conditions. Formulations containing cyanidin as their main ACN were the most stable (elderberry, purple corn, and purple sweet potato). ACNs could be used as suitable alternatives to synthetic colorants in lipid-based topical formulations.

  2. Toxic influence of silver and uranium salts on activated sludge of wastewater treatment plants and synthetic activated sludge associates modeled on its pure cultures.

    Science.gov (United States)

    Tyupa, Dmitry V; Kalenov, Sergei V; Skladnev, Dmitry A; Khokhlachev, Nikolay S; Baurina, Marina M; Kuznetsov, Alexander Ye

    2015-01-01

    Toxic impact of silver and uranium salts on activated sludge of wastewater treatment facilities has been studied. Some dominating cultures (an active nitrogen fixer Agrobacterium tumifaciens (A.t) and micromyces such as Fusarium nivale, Fusarium oxysporum, and Penicillium glabrum) have been isolated and identified as a result of selection of the activated sludge microorganisms being steadiest under stressful conditions. For these cultures, the lethal doses of silver amounted 1, 600, 50, and 300 µg/l and the lethal doses of uranium were 120, 1,500, 1,000, and 1,000 mg/l, respectively. A.tumifaciens is shown to be more sensitive to heavy metals than micromyces. Synthetic granular activated sludge was formed on the basis of three cultures of the isolated micromyces steadiest against stress. Its granules were much more resistant to silver than the whole native activated sludge was. The concentration of silver causing 50 % inhibition of synthetic granular activated sludge growth reached 160-170 μg/l as far as for the native activated sludge it came only to 100-110 μg/l.

  3. Two approaches to forecast Ebola synthetic epidemics.

    Science.gov (United States)

    Champredon, David; Li, Michael; Bolker, Benjamin M; Dushoff, Jonathan

    2018-03-01

    We use two modelling approaches to forecast synthetic Ebola epidemics in the context of the RAPIDD Ebola Forecasting Challenge. The first approach is a standard stochastic compartmental model that aims to forecast incidence, hospitalization and deaths among both the general population and health care workers. The second is a model based on the renewal equation with latent variables that forecasts incidence in the whole population only. We describe fitting and forecasting procedures for each model and discuss their advantages and drawbacks. We did not find that one model was consistently better in forecasting than the other. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

  4. Designing synthetic RNA for delivery by nanoparticles

    International Nuclear Information System (INIS)

    Jedrzejczyk, Dominika; Pawlowska, Roza; Chworos, Arkadiusz; Gendaszewska-Darmach, Edyta

    2017-01-01

    The rapid development of synthetic biology and nanobiotechnology has led to the construction of various synthetic RNA nanoparticles of different functionalities and potential applications. As they occur naturally, nucleic acids are an attractive construction material for biocompatible nanoscaffold and nanomachine design. In this review, we provide an overview of the types of RNA and nucleic acid’s nanoparticle design, with the focus on relevant nanostructures utilized for gene-expression regulation in cellular models. Structural analysis and modeling is addressed along with the tools available for RNA structural prediction. The functionalization of RNA-based nanoparticles leading to prospective applications of such constructs in potential therapies is shown. The route from the nanoparticle design and modeling through synthesis and functionalization to cellular application is also described. For a better understanding of the fate of targeted RNA after delivery, an overview of RNA processing inside the cell is also provided. (topical review)

  5. Imaging with Synthetic Aperture Radar

    CERN Document Server

    Massonnet, Didier

    2008-01-01

    Describing a field that has been transformed by the recent availability of data from a new generation of space and airborne systems, the authors offer a synthetic geometrical approach to the description of synthetic aperture radar, one that addresses physicists, radar specialists, as well as experts in image processing.  

  6. Synthetic peptides for antibody production

    NARCIS (Netherlands)

    Zegers, N.D.

    1995-01-01

    Synthetic peptides are useful tools for the generation of antibodies. The use of antibodies as specific reagents in inununochemical assays is widely applied. In this chapter, the application of synthetic peptides for the generation of antibodies is described. The different steps that lead to the

  7. Synthetic peptides for antibody production

    NARCIS (Netherlands)

    N.D. Zegers (Netty)

    1995-01-01

    textabstractSynthetic peptides are useful tools for the generation of antibodies. The use of antibodies as specific reagents in inununochemical assays is widely applied. In this chapter, the application of synthetic peptides for the generation of antibodies is described. The different steps

  8. Synthetic biology and metabolic engineering.

    Science.gov (United States)

    Stephanopoulos, Gregory

    2012-11-16

    Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial synthesis of various products. As such, it deals with the engineering (design, construction, and optimization) of native as well as non-natural routes of product synthesis, aided in this task by the availability of synthetic DNA, the core enabling technology of synthetic biology. The two fields, however, only partially overlap in their interest in pathway engineering. While fabrication of biobricks, synthetic cells, genetic circuits, and nonlinear cell dynamics, along with pathway engineering, have occupied researchers in the field of synthetic biology, the sum total of these areas does not constitute a coherent definition of synthetic biology with a distinct intellectual foundation and well-defined areas of application. This paper reviews the origins of the two fields and advances two distinct paradigms for each of them: that of unit operations for metabolic engineering and electronic circuits for synthetic biology. In this context, metabolic engineering is about engineering cell factories for the biological manufacturing of chemical and pharmaceutical products, whereas the main focus of synthetic biology is fundamental biological research facilitated by the use of synthetic DNA and genetic circuits.

  9. The Ethics of Synthetic Biology

    DEFF Research Database (Denmark)

    Christiansen, Andreas

    The dissertation analyses and discusses a number of ethical issues that have been raised in connection with the development of synthetic biology. Synthetic biology is a set of new techniques for DNA-level design and construction of living beings with useful properties. The dissertation especially...

  10. Synthetic biology of polyketide synthases

    DEFF Research Database (Denmark)

    Yuzawa, Satoshi; Backman, Tyler W.H.; Keasling, Jay D.

    2018-01-01

    ). The modules are composed of enzymatic domains that share sequence and functional similarity across all known PKSs. We have used the nomenclature of synthetic biology to classify the enzymatic domains and modules as parts and devices, respectively, and have generated detailed lists of both. In addition, we...... realize the potential that synthetic biology approaches bring to this class of molecules....

  11. Post-Stroke Depression Modulation and in Vivo Antioxidant Activity of Gallic Acid and Its Synthetic Derivatives in a Murine Model System.

    Science.gov (United States)

    Nabavi, Seyed Fazel; Habtemariam, Solomon; Di Lorenzo, Arianna; Sureda, Antoni; Khanjani, Sedigheh; Nabavi, Seyed Mohammad; Daglia, Maria

    2016-04-28

    Gallic acid (3,4,5-trihydroxybenzoic acid, GA) is a plant secondary metabolite, which shows antioxidant activity and is commonly found in many plant-based foods and beverages. Recent evidence suggests that oxidative stress contributes to the development of many human chronic diseases, including cardiovascular and neurodegenerative pathologies, metabolic syndrome, type 2 diabetes and cancer. GA and its derivative, methyl-3-O-methyl gallate (M3OMG), possess physiological and pharmacological activities closely related to their antioxidant properties. This paper describes the antidepressive-like effects of intraperitoneal administration of GA and two synthetic analogues, M3OMG and P3OMG (propyl-3-O-methylgallate), in balb/c mice with post-stroke depression, a secondary form of depression that could be due to oxidative stress occurring during cerebral ischemia and the following reperfusion. Moreover, this study determined the in vivo antioxidant activity of these compounds through the evaluation of superoxide dismutase (SOD) and catalase (Cat) activity, thiobarbituric acid-reactive substances (TBARS) and reduced glutathione (GSH) levels in mouse brain. GA and its synthetic analogues were found to be active (at doses of 25 and 50 mg/kg) in the modulation of depressive symptoms and the reduction of oxidative stress, restoring normal behavior and, at least in part, antioxidant endogenous defenses, with M3OMG being the most active of these compounds. SOD, TBARS, and GSH all showed strong correlation with behavioral parameters, suggesting that oxidative stress is tightly linked to the pathological processes involved in stroke and PSD. As a whole, the obtained results show that the administration of GA, M3OMG and P3OMG induce a reduction in depressive symptoms and oxidative stress.

  12. Post-Stroke Depression Modulation and in Vivo Antioxidant Activity of Gallic Acid and Its Synthetic Derivatives in a Murine Model System

    Directory of Open Access Journals (Sweden)

    Seyed Fazel Nabavi

    2016-04-01

    Full Text Available Gallic acid (3,4,5-trihydroxybenzoic acid, GA is a plant secondary metabolite, which shows antioxidant activity and is commonly found in many plant-based foods and beverages. Recent evidence suggests that oxidative stress contributes to the development of many human chronic diseases, including cardiovascular and neurodegenerative pathologies, metabolic syndrome, type 2 diabetes and cancer. GA and its derivative, methyl-3-O-methyl gallate (M3OMG, possess physiological and pharmacological activities closely related to their antioxidant properties. This paper describes the antidepressive-like effects of intraperitoneal administration of GA and two synthetic analogues, M3OMG and P3OMG (propyl-3-O-methylgallate, in balb/c mice with post-stroke depression, a secondary form of depression that could be due to oxidative stress occurring during cerebral ischemia and the following reperfusion. Moreover, this study determined the in vivo antioxidant activity of these compounds through the evaluation of superoxide dismutase (SOD and catalase (Cat activity, thiobarbituric acid-reactive substances (TBARS and reduced glutathione (GSH levels in mouse brain. GA and its synthetic analogues were found to be active (at doses of 25 and 50 mg/kg in the modulation of depressive symptoms and the reduction of oxidative stress, restoring normal behavior and, at least in part, antioxidant endogenous defenses, with M3OMG being the most active of these compounds. SOD, TBARS, and GSH all showed strong correlation with behavioral parameters, suggesting that oxidative stress is tightly linked to the pathological processes involved in stroke and PSD. As a whole, the obtained results show that the administration of GA, M3OMG and P3OMG induce a reduction in depressive symptoms and oxidative stress.

  13. Synthetic Biology: Applications in the Food Sector.

    Science.gov (United States)

    Tyagi, Ashish; Kumar, Ashwani; Aparna, S V; Mallappa, Rashmi H; Grover, Sunita; Batish, Virender Kumar

    2016-08-17

    Synthetic biology also termed as "genomic alchemy" represents a powerful area of science that is based on the convergence of biological sciences with systems engineering. It has been fittingly described as "moving from reading the genetic code to writing it" as it focuses on building, modeling, designing and fabricating novel biological systems using customized gene components that result in artificially created genetic circuitry. The scientifically compelling idea of the technological manipulation of life has been advocated since long time. Realization of this idea has gained momentum with development of high speed automation and the falling cost of gene sequencing and synthesis following the completion of the human genome project. Synthetic biology will certainly be instrumental in shaping the development of varying areas ranging from biomedicine, biopharmaceuticals, chemical production, food and dairy quality monitoring, packaging, and storage of food and dairy products, bioremediation and bioenergy production, etc. However, potential dangers of using synthetic life forms have to be acknowledged and adoption of policies by the scientific community to ensure safe practice while making important advancements in the ever expanding field of synthetic biology is to be fully supported and implemented.

  14. Synthetic analog computation in living cells.

    Science.gov (United States)

    Daniel, Ramiz; Rubens, Jacob R; Sarpeshkar, Rahul; Lu, Timothy K

    2013-05-30

    A central goal of synthetic biology is to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnology applications. Digital logic has been used to build small-scale circuits, but other frameworks may be needed for efficient computation in the resource-limited environments of cells. Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated computational functions in living cells using just three transcription factors. Such synthetic analog gene circuits exploit feedback to implement logarithmically linear sensing, addition, ratiometric and power-law computations. The circuits exhibit Weber's law behaviour as in natural biological systems, operate over a wide dynamic range of up to four orders of magnitude and can be designed to have tunable transfer functions. Our circuits can be composed to implement higher-order functions that are well described by both intricate biochemical models and simple mathematical functions. By exploiting analog building-block functions that are already naturally present in cells, this approach efficiently implements arithmetic operations and complex functions in the logarithmic domain. Such circuits may lead to new applications for synthetic biology and biotechnology that require complex computations with limited parts, need wide-dynamic-range biosensing or would benefit from the fine control of gene expression.

  15. Elastic FWI for VTI media: A synthetic parameterization study

    KAUST Repository

    Kamath, Nishant; Tsvankin, Ilya; Diaz, Esteban

    2016-01-01

    A major challenge for multiparameter full-waveform inversion (FWI) is the inherent trade-offs (or cross-talk) between model parameters. Here, we perform FWI of multicomponent data generated for a synthetic VTI (transversely isotropic with a vertical

  16. Computing with synthetic protocells.

    Science.gov (United States)

    Courbet, Alexis; Molina, Franck; Amar, Patrick

    2015-09-01

    In this article we present a new kind of computing device that uses biochemical reactions networks as building blocks to implement logic gates. The architecture of a computing machine relies on these generic and composable building blocks, computation units, that can be used in multiple instances to perform complex boolean functions. Standard logical operations are implemented by biochemical networks, encapsulated and insulated within synthetic vesicles called protocells. These protocells are capable of exchanging energy and information with each other through transmembrane electron transfer. In the paradigm of computation we propose, protoputing, a machine can solve only one problem and therefore has to be built specifically. Thus, the programming phase in the standard computing paradigm is represented in our approach by the set of assembly instructions (specific attachments) that directs the wiring of the protocells that constitute the machine itself. To demonstrate the computing power of protocellular machines, we apply it to solve a NP-complete problem, known to be very demanding in computing power, the 3-SAT problem. We show how to program the assembly of a machine that can verify the satisfiability of a given boolean formula. Then we show how to use the massive parallelism of these machines to verify in less than 20 min all the valuations of the input variables and output a fluorescent signal when the formula is satisfiable or no signal at all otherwise.

  17. Toxoplasma gondii-derived synthetic peptides containing B- and T-cell epitopes from GRA2 protein are able to enhance mice survival in a model of experimental toxoplasmosis

    Directory of Open Access Journals (Sweden)

    Luciana Machado Bastos

    2016-06-01

    Full Text Available Toxoplasmosis is a zoonosis distributed all over the world, which the etiologic agent is an intracellular protozoan parasite, Toxoplasma gondii. This disease may cause abortions and severe diseases in many warm-blood hosts, including humans, particularly the immunocompromised patients. The parasite specialized secretory organelles, as micronemes, rhoptries and dense granules, are critical for the successful parasitism. The dense granule protein 2 (GRA2 is a parasite immunogenic protein secreted during infections and previous studies have been shown that this parasite component is crucial for the formation of intravacuolar membranous nanotubular network (MNN, as well as for secretion into the vacuole and spatial organization of the parasites within the vacuole. In the present study, we produced a monoclonal antibody to GRA2 (C3C5 mAb, isotype IgG2b, mapped the immunodominant epitope of the protein by phage display and built GRA2 synthetic epitopes to evaluate their ability to protect mice in a model of experimental infection. Our results showed that synthetic peptides for B- and T-cell epitopes are able to improve survival of immunized animals. In contrast with non-immunized animals, the immunized mice with both B- and T-cell epitopes had a better balance of cytokines and demonstrated higher levels of IL-10, IL-4 and IL-17 production, though similar levels of TNF-alpha and IL-6 were observed. The immunization with both B- and T-cell epitopes resulted in survival rate higher than 85% of the challenged mice. Overall, these results demonstrate that immunization with synthetic epitopes for both B- and T-cells from GRA2 protein can be more effective to protect against infection by T. gondii.

  18. Role playing with synthetic cultures: the evasive rules of the game

    NARCIS (Netherlands)

    Hofstede, G.J.

    2005-01-01

    This article sums up ten years of experience with over 1400 participants of simulation games using synthetic cultures. Synthetic cultures are scripts for role players. They are derived from the five dimensions of culture in Hofstede¿s model. Playing the synthetic cultures leads to dynamics that

  19. Robust synthetic biology design: stochastic game theory approach.

    Science.gov (United States)

    Chen, Bor-Sen; Chang, Chia-Hung; Lee, Hsiao-Ching

    2009-07-15

    Synthetic biology is to engineer artificial biological systems to investigate natural biological phenomena and for a variety of applications. However, the development of synthetic gene networks is still difficult and most newly created gene networks are non-functioning due to uncertain initial conditions and disturbances of extra-cellular environments on the host cell. At present, how to design a robust synthetic gene network to work properly under these uncertain factors is the most important topic of synthetic biology. A robust regulation design is proposed for a stochastic synthetic gene network to achieve the prescribed steady states under these uncertain factors from the minimax regulation perspective. This minimax regulation design problem can be transformed to an equivalent stochastic game problem. Since it is not easy to solve the robust regulation design problem of synthetic gene networks by non-linear stochastic game method directly, the Takagi-Sugeno (T-S) fuzzy model is proposed to approximate the non-linear synthetic gene network via the linear matrix inequality (LMI) technique through the Robust Control Toolbox in Matlab. Finally, an in silico example is given to illustrate the design procedure and to confirm the efficiency and efficacy of the proposed robust gene design method. http://www.ee.nthu.edu.tw/bschen/SyntheticBioDesign_supplement.pdf.

  20. Synthetic Biology and Personalized Medicine

    Science.gov (United States)

    Jain, K.K.

    2013-01-01

    Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell environment and enhance human health. Synthetic biology devices contribute not only to improve our understanding of disease mechanisms, but also provide novel diagnostic tools. Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs. The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already pointed out during a lecture delivered at Kuwait University in 2005. Of two approaches to synthetic biology, top-down and bottom-up, the latter is more relevant to the development of personalized medicines as it provides more flexibility in constructing a partially synthetic cell from basic building blocks for a desired task. PMID:22907209

  1. Synthetic Biology: Advancing Biological Frontiers by Building Synthetic Systems

    OpenAIRE

    Chen, Yvonne Yu-Hsuan; Galloway, Kate E; Smolke, Christina D

    2012-01-01

    Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.

  2. Moessbauer Studies of Stannous Fluoride Reactivity with Synthetic Tooth Enamel - A Model for the Tooth Cavity Protection Actions of Novel Dentifrices

    International Nuclear Information System (INIS)

    Denes, Georges; Muntasar, Abdualhafeed; Kozak, Kathy M.; Baig, Arif A.; White, Donald J.

    2002-01-01

    SnF 2 is an important toothpaste ingredient, added for the provision of clinical efficacy for hard and soft tissue diseases and in breath protection. Synthetic calcium hydroxyapatite powders were exposed to liquid supernates (25 w/w% toothpaste water slurries, centrifuged) of Crest Gum Care (registered) (SnF 2 ) dentifrice. One-minute treatments were followed by 3x water washing, centrifugation and lyophilization. Post treatment, powders were analyzed by Moessbauer spectroscopy with 0.5-1 gram of treated apatite powder. Results show that tooth mineral stannous fluoride interactions include: (1) formation of surface reaction products with both Sn(II) and Sn(IV) oxidation states; (2) Sn-F binding on mineral surfaces with no evidence of SnO. The surface binding is, however, not pure Sn-F but contains contributions of other ligands, probably oxygens from surface phosphates or hydroxyl groups. Results also suggest that surface reacted stannous tin is oxidized with time, even when bound as a layer on the tooth surface. This study demonstrates for the first time the presence of Sn-F on tooth enamel post treatment and the contribution of passivation to long term stannous chemistry on tooth surfaces. The study also illustrates the practical applications of the Moessbauer technique.

  3. Approaches to chemical synthetic biology.

    Science.gov (United States)

    Chiarabelli, Cristiano; Stano, Pasquale; Anella, Fabrizio; Carrara, Paolo; Luisi, Pier Luigi

    2012-07-16

    Synthetic biology is first represented in terms of two complementary aspects, the bio-engineering one, based on the genetic manipulation of extant microbial forms in order to obtain forms of life which do not exist in nature; and the chemical synthetic biology, an approach mostly based on chemical manipulation for the laboratory synthesis of biological structures that do not exist in nature. The paper is mostly devoted to shortly review chemical synthetic biology projects currently carried out in our laboratory. In particular, we describe: the minimal cell project, then the "Never Born Proteins" and lastly the Never Born RNAs. We describe and critically analyze the main results, emphasizing the possible relevance of chemical synthetic biology for the progress in basic science and biotechnology. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  4. Synthetic Biology for Specialty Chemicals.

    Science.gov (United States)

    Markham, Kelly A; Alper, Hal S

    2015-01-01

    In this review, we address recent advances in the field of synthetic biology and describe how those tools have been applied to produce a wide variety of chemicals in microorganisms. Here we classify the expansion of the synthetic biology toolbox into three different categories based on their primary function in strain engineering-for design, for construction, and for optimization. Next, focusing on recent years, we look at how chemicals have been produced using these new synthetic biology tools. Advances in producing fuels are briefly described, followed by a more thorough treatment of commodity chemicals, specialty chemicals, pharmaceuticals, and nutraceuticals. Throughout this review, an emphasis is placed on how synthetic biology tools are applied to strain engineering. Finally, we discuss organism and host strain diversity and provide a future outlook in the field.

  5. Is synthetic biology mechanical biology?

    Science.gov (United States)

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  6. Adaptive Synthetic Forces: Situation Awareness

    National Research Council Canada - National Science Library

    Hill, Randall

    2001-01-01

    ...: perception, comprehension, and prediction. Building on these ideas, we developed techniques for improving the situation awareness in synthetic helicopter pilots for the ModSAF military simulation by giving them more human-like perception...

  7. Economic Efficiency of Establishing Domestic Production of Synthetic Liquid Fuel

    Directory of Open Access Journals (Sweden)

    Kyzym Mykola O.

    2017-06-01

    Full Text Available The article notes a stable tendency to increasing the oil dependence of Ukraine, which creates a threat to the national economic security, and proves an expediency of establishing domestic production of synthetic liquid fuel. The technical, organizational and economic features of establishing synthetic liquid fuel production in Ukraine are presented. There proved a hypothesis on the expediency of organizing the production of synthetic liquid fuels based on steam-plasma coal gasification technology. The forecast resource cycle of the country until 2020 under conditions of developing this technology is modeled.

  8. Indole and synthetic derivative activate chaperone expression to reduce polyQ aggregation in SCA17 neuronal cell and slice culture models

    Directory of Open Access Journals (Sweden)

    Kung PJ

    2014-10-01

    Full Text Available Pin-Jui Kung,1,* Yu-Chen Tao,1,* Ho-Chiang Hsu,1 Wan-Ling Chen,1 Te-Hsien Lin,1 Donala Janreddy,2 Ching-Fa Yao,2 Kuo-Hsuan Chang,3 Jung-Yaw Lin,1 Ming-Tsan Su,1 Chung-Hsin Wu,1 Guey-Jen Lee-Chen,1 Hsiu-Mei Hsieh-Li1 1Department of Life Science, 2Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan; 3Department of Neurology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taipei, Taiwan *These authors contributed equally to this work Abstract: In spinocerebellar ataxia type 17 (SCA17, the expansion of a translated CAG repeat in the TATA box binding protein (TBP gene results in a long polyglutamine (polyQ tract in the TBP protein, leading to intracellular accumulation of aggregated TBP and cell death. The molecular chaperones act in preventing protein aggregation to ameliorate downstream harmful events. In this study, we used Tet-On SH-SY5Y cells with inducible SCA17 TBP/Q79-green fluorescent protein (GFP expression to test indole and synthetic derivative NC001-8 for neuroprotection. We found that indole and NC001-8 up-regulated chaperone expression to reduce polyQ aggregation in neuronal differentiated TBP/Q79 cells. The effects on promoting neurite outgrowth and on reduction of aggregation on Purkinje cells were also confirmed with cerebellar primary and slice cultures of SCA17 transgenic mice. Our results demonstrate how indole and derivative NC001-8 reduce polyQ aggregation to support their therapeutic potentials in SCA17 treatment. Keywords: spinocerebellar ataxia type 17, TATA box binding protein, polyQ aggregation, indole and derivative, therapeutics

  9. The construction of a decision tool to analyse local demand and local supply for GP care using a synthetic estimation model.

    Science.gov (United States)

    de Graaf-Ruizendaal, Willemijn A; de Bakker, Dinny H

    2013-10-27

    This study addresses the growing academic and policy interest in the appropriate provision of local healthcare services to the healthcare needs of local populations to increase health status and decrease healthcare costs. However, for most local areas information on the demand for primary care and supply is missing. The research goal is to examine the construction of a decision tool which enables healthcare planners to analyse local supply and demand in order to arrive at a better match. National sample-based medical record data of general practitioners (GPs) were used to predict the local demand for GP care based on local populations using a synthetic estimation technique. Next, the surplus or deficit in local GP supply were calculated using the national GP registry. Subsequently, a dynamic internet tool was built to present demand, supply and the confrontation between supply and demand regarding GP care for local areas and their surroundings in the Netherlands. Regression analysis showed a significant relationship between sociodemographic predictors of postcode areas and GP consultation time (F [14, 269,467] = 2,852.24; P 1,000 inhabitants in the Netherlands covering 97% of the total population. Confronting these estimated demand figures with the actual GP supply resulted in the average GP workload and the number of full-time equivalent (FTE) GP too much/too few for local areas to cover the demand for GP care. An estimated shortage of one FTE GP or more was prevalent in about 19% of the postcode areas with >1,000 inhabitants if the surrounding postcode areas were taken into consideration. Underserved areas were mainly found in rural regions. The constructed decision tool is freely accessible on the Internet and can be used as a starting point in the discussion on primary care service provision in local communities and it can make a considerable contribution to a primary care system which provides care when and where people need it.

  10. Research and application of a hybrid model based on dynamic fuzzy synthetic evaluation for establishing air quality forecasting and early warning system: A case study in China.

    Science.gov (United States)

    Xu, Yunzhen; Du, Pei; Wang, Jianzhou

    2017-04-01

    As the atmospheric environment pollution has been becoming more and more serious in China, it is highly desirable to develop a scientific and effective early warning system that plays a great significant role in analyzing and monitoring air quality. However, establishing a robust early warning system for warning the public in advance and ameliorating air quality is not only an extremely challenging task but also a public concerned problem for human health. Most previous studies are focused on improving the prediction accuracy, which usually ignore the significance of uncertainty information and comprehensive evaluation concerning air pollutants. Therefore, in this paper a novel robust early warning system was successfully developed, which consists of three modules: evaluation module, forecasting module and characteristics estimating module. In this system, a new dynamic fuzzy synthetic evaluation is proposed and applied to determine air quality levels and primary pollutants, which can be regarded as the research objectives; Moreover, to further mine and analyze the characteristics of air pollutants, four different distribution functions and interval forecasting method are also employed that can not only provide predictive range, confidence level and the other uncertain information of the pollutants future values, but also assist decision-makers in reducing and controlling the emissions of atmospheric pollutants. Case studies utilizing hourly PM 2.5 , PM 10 and SO 2 data collected from Tianjin and Shanghai in China are applied as illustrative examples to estimate the effectiveness and efficiency of the proposed system. Experimental results obviously indicated that the developed novel early warning system is much suitable for analyzing and monitoring air pollution, which can also add a novel viable option for decision-makers. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Synthetic Biology: Putting Synthesis into Biology

    Science.gov (United States)

    Liang, Jing; Luo, Yunzi; Zhao, Huimin

    2010-01-01

    The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

  12. Prospects for applying synthetic biology to toxicology

    DEFF Research Database (Denmark)

    Behrendorff, James Bruce Yarnton H; Gillam, Elizabeth M.J.

    2017-01-01

    The 30 years since the inception of Chemical Research in Toxicology, game-changing advances in chemical and molecular biology, the fundamental disciplines underpinning molecular toxicology, have been made. While these have led to important advances in the study of mechanisms by which chemicals...... damage cells and systems, there has been less focus on applying these advances to prediction, detection, and mitigation of toxicity. Over the last ∼15 years, synthetic biology, the repurposing of biological "parts" in systems engineered for useful ends, has been explored in other areas of the biomedical...... and life sciences, for such applications as detecting metabolites, drug discovery and delivery, investigating disease mechanisms, improving medical treatment, and producing useful chemicals. These examples provide models for the application of synthetic biology to toxicology, which, for the most part, has...

  13. Emotional Synthetic Forces

    National Research Council Canada - National Science Library

    Henninger, Amy

    2004-01-01

    .... To this end, researchers adopted an approach that promotes the emergence of behavior as a result of complex interactions between factors affecting emotions, integrated in a connectionist style model...

  14. Conserved synthetic peptides from the hemagglutinin of influenza viruses induce broad humoral and T-cell responses in a pig model.

    Directory of Open Access Journals (Sweden)

    Júlia Vergara-Alert

    Full Text Available Outbreaks involving either H5N1 or H1N1 influenza viruses (IV have recently become an increasing threat to cause potential pandemics. Pigs have an important role in this aspect. As reflected in the 2009 human H1N1 pandemia, they may act as a vehicle for mixing and generating new assortments of viruses potentially pathogenic to animals and humans. Lack of universal vaccines against the highly variable influenza virus forces scientists to continuously design vaccines à la carte, which is an expensive and risky practice overall when dealing with virulent strains. Therefore, we focused our efforts on developing a broadly protective influenza vaccine based on the Informational Spectrum Method (ISM. This theoretical prediction allows the selection of highly conserved peptide sequences from within the hemagglutinin subunit 1 protein (HA1 from either H5 or H1 viruses which are located in the flanking region of the HA binding site and with the potential to elicit broader immune responses than conventional vaccines. Confirming the theoretical predictions, immunization of conventional farm pigs with the synthetic peptides induced humoral responses in every single pig. The fact that the induced antibodies were able to recognize in vitro heterologous influenza viruses such as the pandemic H1N1 virus (pH1N1, two swine influenza field isolates (SwH1N1 and SwH3N2 and a H5N1 highly pathogenic avian virus, confirm the broad recognition of the antibodies induced. Unexpectedly, all pigs also showed T-cell responses that not only recognized the specific peptides, but also the pH1N1 virus. Finally, a partial effect on the kinetics of virus clearance was observed after the intranasal infection with the pH1N1 virus, setting forth the groundwork for the design of peptide-based vaccines against influenza viruses. Further insights into the understanding of the mechanisms involved in the protection afforded will be necessary to optimize future vaccine formulations.

  15. Meeting Report: Synthetic Biology Jamboree for Undergraduates

    Science.gov (United States)

    Campbell, A. Malcolm

    2005-01-01

    The field of synthetic biology (the name is derived from an analogy to synthetic chemistry) has recognized itself as a "field" only since about 2002. Synthetic biology has gotten some high-profile attention recently, but most people are not aware the field even exists. Synthetic biologists apply engineering principles to genomic circuits to…

  16. Synthetic biology, metaphors and responsibility.

    Science.gov (United States)

    McLeod, Carmen; Nerlich, Brigitte

    2017-08-29

    Metaphors are not just decorative rhetorical devices that make speech pretty. They are fundamental tools for thinking about the world and acting on the world. The language we use to make a better world matters; words matter; metaphors matter. Words have consequences - ethical, social and legal ones, as well as political and economic ones. They need to be used 'responsibly'. They also need to be studied carefully - this is what we want to do through this editorial and the related thematic collection. In the context of synthetic biology, natural and social scientists have become increasingly interested in metaphors, a wave of interest that we want to exploit and amplify. We want to build on emerging articles and books on synthetic biology, metaphors of life and the ethical and moral implications of such metaphors. This editorial provides a brief introduction to synthetic biology and responsible innovation, as well as a comprehensive review of literature on the social, cultural and ethical impacts of metaphor use in genomics and synthetic biology. Our aim is to stimulate an interdisciplinary and international discussion on the impact that metaphors can have on science, policy and publics in the context of synthetic biology.

  17. Content metamorphosis in synthetic holography

    International Nuclear Information System (INIS)

    Desbiens, Jacques

    2013-01-01

    A synthetic hologram is an optical system made of hundreds of images amalgamated in a structure of holographic cells. Each of these images represents a point of view on a three-dimensional space which makes us consider synthetic holography as a multiple points of view perspective system. In the composition of a computer graphics scene for a synthetic hologram, the field of view of the holographic image can be divided into several viewing zones. We can attribute these divisions to any object or image feature independently and operate different transformations on image content. In computer generated holography, we tend to consider content variations as a continuous animation much like a short movie. However, by composing sequential variations of image features in relation with spatial divisions, we can build new narrative forms distinct from linear cinematographic narration. When observers move freely and change their viewing positions, they travel from one field of view division to another. In synthetic holography, metamorphoses of image content are within the observer's path. In all imaging Medias, the transformation of image features in synchronisation with the observer's position is a rare occurrence. However, this is a predominant characteristic of synthetic holography. This paper describes some of my experimental works in the development of metamorphic holographic images.

  18. Control theory meets synthetic biology.

    Science.gov (United States)

    Del Vecchio, Domitilla; Dy, Aaron J; Qian, Yili

    2016-07-01

    The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building synthetic biomolecular circuits in living cells. In particular, we describe success stories that demonstrate how simple or more elaborate control design methods can be used to make the behaviour of synthetic genetic circuits within a single cell or across a cell population more reliable, predictable and robust to perturbations. The description especially highlights technical challenges that uniquely arise from the need to implement control designs within a new hardware setting, along with implemented or proposed solutions. Some engineering solutions employing complex feedback control schemes are also described, which, however, still require a deeper theoretical analysis of stability, performance and robustness properties. Overall, this paper should help synthetic biologists become familiar with feedback control concepts as they can be used in their application area. At the same time, it should provide some domain knowledge to control theorists who wish to enter the rising and exciting field of synthetic biology. © 2016 The Author(s).

  19. Synthetic tsunami waveform catalogs with kinematic constraints

    Science.gov (United States)

    Baptista, Maria Ana; Miranda, Jorge Miguel; Matias, Luis; Omira, Rachid

    2017-07-01

    In this study we present a comprehensive methodology to produce a synthetic tsunami waveform catalogue in the northeast Atlantic, east of the Azores islands. The method uses a synthetic earthquake catalogue compatible with plate kinematic constraints of the area. We use it to assess the tsunami hazard from the transcurrent boundary located between Iberia and the Azores, whose western part is known as the Gloria Fault. This study focuses only on earthquake-generated tsunamis. Moreover, we assume that the time and space distribution of the seismic events is known. To do this, we compute a synthetic earthquake catalogue including all fault parameters needed to characterize the seafloor deformation covering the time span of 20 000 years, which we consider long enough to ensure the representability of earthquake generation on this segment of the plate boundary. The computed time and space rupture distributions are made compatible with global kinematic plate models. We use the tsunami empirical Green's functions to efficiently compute the synthetic tsunami waveforms for the dataset of coastal locations, thus providing the basis for tsunami impact characterization. We present the results in the form of offshore wave heights for all coastal points in the dataset. Our results focus on the northeast Atlantic basin, showing that earthquake-induced tsunamis in the transcurrent segment of the Azores-Gibraltar plate boundary pose a minor threat to coastal areas north of Portugal and beyond the Strait of Gibraltar. However, in Morocco, the Azores, and the Madeira islands, we can expect wave heights between 0.6 and 0.8 m, leading to precautionary evacuation of coastal areas. The advantages of the method are its easy application to other regions and the low computation effort needed.

  20. Optical studies of high quality synthetic diamond

    International Nuclear Information System (INIS)

    Sharp, S.J.

    1999-01-01

    This thesis is concerned with the study of fundamental and defect induced optical properties of synthetic diamond grown using high pressure, high temperature (HPHT) synthesis or chemical vapour deposition (CVD). The primary technique used for investigation is cathodoluminescence (including imaging and decay-time measurements) in addition to other forms of optical spectroscopy. This thesis is timely in that the crystallinity and purity of synthetic diamond has increased ten fold over the last few years. The diamond exciton emission, which is easily quenched by the presence of defects, is studied in high quality samples in detail. In addition the ability now exists to engineer the isotopic content of synthetic diamond to a high degree of accuracy. The experimental chapters are divided as follows: Chapter 2: High resolution, low temperature spectra reveal a splitting of the free-exciton phonon recombination emission peaks and the bound-exciton zero phonon line. Included are measurements of the variation in intensity and decay-time as a function of temperature. Chapter 3: The shift in energy of the phonon-assisted free-exciton phonon replicas with isotopic content has been measured. The shift is in agreement with the results of interatomic force model for phonon scattering due to isotope disorder. Chapter 4: A study of the shift in energy with isotopic content of the diamond of the GR1 band due to the neutral vacancy has allowed a verification of the theoretical predictions due to the Jahn Teller effect. Chapter 5: The spatial distribution of the free-exciton luminescence is studied in HPHT synthetic and CVD diamond. A variation in intensity with distance from the surface is interpreted as a significant non-radiative loss of excitons to the surface. Chapter 6: The decay-times of all known self-interstitial related centres have been measured in order to calculate the concentration of these centres present in electron irradiated diamond. (author)

  1. Microfluidic Technologies for Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Sung Kuk Lee

    2011-06-01

    Full Text Available Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.

  2. Synthetic neurosteroids on brain protection

    Directory of Open Access Journals (Sweden)

    Mariana Rey

    2015-01-01

    Full Text Available Neurosteroids, like allopregnanolone and pregnanolone, are endogenous regulators of neuronal excitability. Inside the brain, they are highly selective and potent modulators of GABA A receptor activity. Their anticonvulsant, anesthetics and anxiolytic properties are useful for the treatments of several neurological and psychiatric disorders via reducing the risks of side effects obtained with the commercial drugs. The principal disadvantages of endogenous neurosteroids administration are their rapid metabolism and their low oral bioavailability. Synthetic steroids analogues with major stability or endogenous neurosteroids stimulation synthesis might constitute promising novel strategies for the treatment of several disorders. Numerous studies indicate that the 3α-hydroxyl configuration is the key for binding and activity, but modifications in the steroid nucleus may emphasize different pharmacophores. So far, several synthetic steroids have been developed with successful neurosteroid-like effects. In this work, we summarize the properties of various synthetic steroids probed in trials throughout the analysis of several neurosteroids-like actions.

  3. Identification of synthetic dynamic transfer-models and of their disturbances in the time-domain; Identifikation synthetischer dynamischer Uebertragungsmodelle und ihrer Stoerungen im Zeitbereich

    Energy Technology Data Exchange (ETDEWEB)

    Levenhagen, J.

    1998-12-31

    This thesis deals with a general approach to the identification of models for dynamic transfer-systems in the time-domain. Furthermore, a process is presented which will significantly detect particularly minute disturbances (anomalies) within a previously identified model. On the one hand, the identification is based on the knowledge of the system describing discrete input and output signals, and on the other on the assumption of a class of models transforming these into each other. If no information is available on the internal structure of the underlying system, the choice of the class of models to be adopted should imply as few restrictions as possible. The so-called extended Volterra-models meet this requirement quite well. The extraction, based on well-defined criteria, of an `optimal` model within the given class, represents a combinatorial optimization problem inside a binary modelling space. A genetic algorithm is used for its solution, which treats the models as individuals within populations of models. These individuals are rated in accordance with their ability to predict future system behaviour. Additionally, positive requirements can be formulated which, if not fulfilled, will lead to the elimination of the model concerned. A simple regression model is used to estimate the parameters of the genetic algorithm. However, auto-regressive features within the model cause biases; furthermore, statements on the distribution of parameters are not easily possible. Still, preliminary examinations suggest that the use of alternative and more complex estimation methods leads to comparative results, due to conditioning problems, and is therefore not justified. Automatic identification of disturbances is done by means of the distribution-free Kolmogoroff-Smirnoff test, the results of which can be depicted graphically by way of an appropriately adjusted quality control card. Finally, the efficiency of the proposed concept is tested in an exemplary manner on generated

  4. Synthetic biology as red herring.

    Science.gov (United States)

    Preston, Beth

    2013-12-01

    It has become commonplace to say that with the advent of technologies like synthetic biology the line between artifacts and living organisms, policed by metaphysicians since antiquity, is beginning to blur. But that line began to blur 10,000 years ago when plants and animals were first domesticated; and has been thoroughly blurred at least since agriculture became the dominant human subsistence pattern many millennia ago. Synthetic biology is ultimately only a late and unexceptional offshoot of this prehistoric development. From this perspective, then, synthetic biology is a red herring, distracting us from more thorough philosophical consideration of the most truly revolutionary human practice-agriculture. In the first section of this paper I will make this case with regard to ontology, arguing that synthetic biology crosses no ontological lines that were not crossed already in the Neolithic. In the second section I will construct a parallel case with regard to cognition, arguing that synthetic biology as biological engineering represents no cognitive advance over what was required for domestication and the new agricultural subsistence pattern it grounds. In the final section I will make the case with regard to human existence, arguing that synthetic biology, even if wildly successful, is not in a position to cause significant existential change in what it is to be human over and above the massive existential change caused by the transition to agriculture. I conclude that a longer historical perspective casts new light on some important issues in philosophy of technology and environmental philosophy. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. US Competitiveness in Synthetic Biology.

    Science.gov (United States)

    Gronvall, Gigi Kwik

    2015-01-01

    Synthetic biology is an emerging technical field that aims to make biology easier to engineer; the field has applications in strategically important sectors for the US economy. While the United States currently leads in synthetic biology R&D, other nations are heavily investing in order to boost their economies, which will inevitably diminish the US leadership position. This outcome is not entirely negative--additional investments will expand markets--but it is critical that the US government take steps to remain competitive: There are applications from which the US population and economy may benefit; there are specific applications with importance for national defense; and US technical leadership will ensure that US experts have a leading role in synthetic biology governance, regulation, and oversight. Measures to increase competitiveness in S&T generally are broadly applicable for synthetic biology and should be pursued. However, the US government will also need to take action on fundamental issues that will affect the field's development, such as countering anti-GMO (genetically modified organism) sentiments and anti-GMO legislation. The United States should maintain its regulatory approach so that it is the product that is regulated, not the method used to create a product. At the same time, the United States needs to ensure that the regulatory framework is updated so that synthetic biology products do not fall into regulatory gaps. Finally, the United States needs to pay close attention to how synthetic biology applications may be governed internationally, such as through the Nagoya Protocol of the Convention on Biological Diversity, so that beneficial applications may be realized.

  6. Developments in the Tools and Methodologies of Synthetic Biology

    Science.gov (United States)

    Kelwick, Richard; MacDonald, James T.; Webb, Alexander J.; Freemont, Paul

    2014-01-01

    Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a “body of knowledge” from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community. PMID:25505788

  7. SCScore: Synthetic Complexity Learned from a Reaction Corpus.

    Science.gov (United States)

    Coley, Connor W; Rogers, Luke; Green, William H; Jensen, Klavs F

    2018-02-26

    Several definitions of molecular complexity exist to facilitate prioritization of lead compounds, to identify diversity-inducing and complexifying reactions, and to guide retrosynthetic searches. In this work, we focus on synthetic complexity and reformalize its definition to correlate with the expected number of reaction steps required to produce a target molecule, with implicit knowledge about what compounds are reasonable starting materials. We train a neural network model on 12 million reactions from the Reaxys database to impose a pairwise inequality constraint enforcing the premise of this definition: that on average, the products of published chemical reactions should be more synthetically complex than their corresponding reactants. The learned metric (SCScore) exhibits highly desirable nonlinear behavior, particularly in recognizing increases in synthetic complexity throughout a number of linear synthetic routes.

  8. Cell-free synthetic biology for in vitro prototype engineering.

    Science.gov (United States)

    Moore, Simon J; MacDonald, James T; Freemont, Paul S

    2017-06-15

    Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. © 2017 The Author(s).

  9. Developments in the tools and methodologies of synthetic biology

    Directory of Open Access Journals (Sweden)

    Richard eKelwick

    2014-11-01

    Full Text Available Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices or systems. However, biological systems are generally complex and unpredictable and are therefore intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a ‘body of knowledge’ from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled and its functionality tested. At each stage of the design cycle an expanding repertoire of tools is being developed. In this review we highlight several of these tools in terms of their applications and benefits to the synthetic biology community.

  10. Synthetic Phage for Tissue Regeneration

    Directory of Open Access Journals (Sweden)

    So Young Yoo

    2014-01-01

    Full Text Available Controlling structural organization and signaling motif display is of great importance to design the functional tissue regenerating materials. Synthetic phage, genetically engineered M13 bacteriophage has been recently introduced as novel tissue regeneration materials to display a high density of cell-signaling peptides on their major coat proteins for tissue regeneration purposes. Structural advantages of their long-rod shape and monodispersity can be taken together to construct nanofibrous scaffolds which support cell proliferation and differentiation as well as direct orientation of their growth in two or three dimensions. This review demonstrated how functional synthetic phage is designed and subsequently utilized for tissue regeneration that offers potential cell therapy.

  11. Synthetic biology and its promises

    Directory of Open Access Journals (Sweden)

    José Manuel De Cózar Escalante

    2016-12-01

    Full Text Available Synthetic biology is a new science and emerging technology, or rather a technoscience, which converges with others such as nanotechnology, information technology, robotics, artificial intelligence and neuroscience. All have common features that could have highly concerning social and environmental impacts. With its ambitious goals of controlling complexity, redesigning and creating new living entities, synthetic biology perfectly exemplifies the new bioeconomic reality. This requires expanding the focus of the discussion beyond the limited comparative analysis of risks and benefits, to address uncertainties, reassign responsibilities and initiate a thorough social assessment of what is at stake.

  12. Development of a stratum corneum substitute for in vitro percutaneous penetration studies : a skin barrier model comprising synthetic stratum corneum lipids

    NARCIS (Netherlands)

    Jager, Miranda Wilhelmina de

    2006-01-01

    The research outlined in this thesis was focused on the development of a skin barrier model, which can substitute for stratum corneum in diffusion studies. This so-called stratum corneum substitute (SCS) was prepared with reconstituted SC lipids (cholesterol, free fatty acids and ceramides) on a

  13. Calibration and Validation of a Detailed Architectural Canopy Model Reconstruction for the Simulation of Synthetic Hemispherical Images and Airborne LiDAR Data

    Directory of Open Access Journals (Sweden)

    Magnus Bremer

    2017-02-01

    Full Text Available Canopy density measures such as the Leaf Area Index (LAI have become standardized mapping products derived from airborne and terrestrial Light Detection And Ranging (aLiDAR and tLiDAR, respectively data. A specific application of LiDAR point clouds is their integration into radiative transfer models (RTM of varying complexity. Using, e.g., ray tracing, this allows flexible simulations of sub-canopy light condition and the simulation of various sensors such as virtual hemispherical images or waveform LiDAR on a virtual forest plot. However, the direct use of LiDAR data in RTMs shows some limitations in the handling of noise, the derivation of surface areas per LiDAR point and the discrimination of solid and porous canopy elements. In order to address these issues, a strategy upgrading tLiDAR and Digital Hemispherical Photographs (DHP into plausible 3D architectural canopy models is suggested. The presented reconstruction workflow creates an almost unbiased virtual 3D representation of branch and leaf surface distributions, minimizing systematic errors due to the object–sensor relationship. The models are calibrated and validated using DHPs. Using the 3D models for simulations, their capabilities for the description of leaf density distributions and the simulation of aLiDAR and DHP signatures are shown. At an experimental test site, the suitability of the models, in order to systematically simulate and evaluate aLiDAR based LAI predictions under various scan settings is proven. This strategy makes it possible to show the importance of laser point sampling density, but also the diversity of scan angles and their quantitative effect onto error margins.

  14. Polar synthetic imaging

    Science.gov (United States)

    George, Jonathan K.

    2013-05-01

    In the search for low-cost wide spectrum imagers it may become necessary to sacrifice the expense of the focal plane array and revert to a scanning methodology. In many cases the sensor may be too unwieldy to physically scan and mirrors may have adverse effects on particular frequency bands. In these cases, photonic masks can be devised to modulate the incoming light field with a code over time. This is in essence code-division multiplexing of the light field into a lower dimension channel. In this paper a simple method for modulating the light field with masks of the Archimedes' spiral is presented and a mathematical model of the two-dimensional mask set is developed.

  15. Growth Modeling of Aspergillus niger Strains Isolated from Citrus Fruit as a Function of Temperature on a Synthetic Medium from Lime (Citrus latifolia T.) Pericarp.

    Science.gov (United States)

    Sandoval-Contreras, T; Marín, S; Villarruel-López, A; Gschaedler, A; Garrido-Sánchez, L; Ascencio, F

    2017-07-01

    Molds are responsible for postharvest spoilage of citrus fruits. The objective of this study was to evaluate the effect of temperature on growth rate and the time to visible growth of Aspergillus niger strains isolated from citrus fruits. The growth of these strains was studied on agar lime medium (AL) at different temperatures, and growth rate was estimated using the Baranyi and Roberts model (Int. J. Food Microbiol. 23:277-294, 1994). The Rosso et al. cardinal model with inflexion (L. Rosso, J. R. Lobry, S. Bajard, and J. P. Flandrois, J. Theor. Biol. 162:447-463, 1993) was used as a secondary model to describe the effect of temperature on growth rate and the lag phase. We hypothesized that the same model could be used to calculate the time for the mycelium to become visible (t v ) by substituting the lag phase (1/λ and 1/λ opt ) with the time to visible colony (1/t v -opt and 1/t v ), respectively, in the Rosso et al. High variability was observed at suboptimal conditions. Extremes of temperature of growth for A. niger seem to have a normal variability. For the growth rate and time t v , the model was satisfactorily compared with results of previous studies. An external validation was performed in lime fruits; the bias and accuracy factors were 1.3 and 1.5, respectively, for growth rate and 0.24 and 3.72, respectively, for the appearance time. The discrepancy may be due to the influence of external factors. A. niger grows significantly more slowly on lime fruit than in culture medium, probably because the nutrients are more easily available in medium than in fruits, where the peel consistency may be a physical barrier. These findings will help researchers understand the postharvest behavior of mold on lime fruits, host-pathogen interactions, and environmental conditions infecting fruit and also help them develop guidelines for future work in the field of predictive mycology to improve models for control of postharvest fungi.

  16. Where Synthetic Biology Meets ET

    Science.gov (United States)

    Rothschild, Lynn J.

    2016-01-01

    Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. And what about the limits for life? Can we create organisms that expand the envelope for life? In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

  17. Synthetic biology meets tissue engineering.

    Science.gov (United States)

    Davies, Jamie A; Cachat, Elise

    2016-06-15

    Classical tissue engineering is aimed mainly at producing anatomically and physiologically realistic replacements for normal human tissues. It is done either by encouraging cellular colonization of manufactured matrices or cellular recolonization of decellularized natural extracellular matrices from donor organs, or by allowing cells to self-organize into organs as they do during fetal life. For repair of normal bodies, this will be adequate but there are reasons for making unusual, non-evolved tissues (repair of unusual bodies, interface to electromechanical prostheses, incorporating living cells into life-support machines). Synthetic biology is aimed mainly at engineering cells so that they can perform custom functions: applying synthetic biological approaches to tissue engineering may be one way of engineering custom structures. In this article, we outline the 'embryological cycle' of patterning, differentiation and morphogenesis and review progress that has been made in constructing synthetic biological systems to reproduce these processes in new ways. The state-of-the-art remains a long way from making truly synthetic tissues, but there are now at least foundations for future work. © 2016 Authors; published by Portland Press Limited.

  18. Shock compression of synthetic opal

    International Nuclear Information System (INIS)

    Inoue, A; Okuno, M; Okudera, H; Mashimo, T; Omurzak, E; Katayama, S; Koyano, M

    2010-01-01

    Structural change of synthetic opal by shock-wave compression up to 38.1 GPa has been investigated by using SEM, X-ray diffraction method (XRD), Infrared (IR) and Raman spectroscopies. Obtained information may indicate that the dehydration and polymerization of surface silanole due to high shock and residual temperature are very important factors in the structural evolution of synthetic opal by shock compression. Synthetic opal loses opalescence by 10.9 and 18.4 GPa of shock pressures. At 18.4 GPa, dehydration and polymerization of surface silanole and transformation of network structure may occur simultaneously. The 4-membered ring of TO 4 tetrahedrons in as synthetic opal may be relaxed to larger ring such as 6-membered ring by high residual temperature. Therefore, the residual temperature may be significantly high at even 18.4 GPa of shock compression. At 23.9 GPa, opal sample recovered the opalescence. Origin of this opalescence may be its layer structure by shock compression. Finally, sample fuse by very high residual temperature at 38.1 GPa and the structure closes to that of fused SiO 2 glass. However, internal silanole groups still remain even at 38.1 GPa.

  19. Shock compression of synthetic opal

    Science.gov (United States)

    Inoue, A.; Okuno, M.; Okudera, H.; Mashimo, T.; Omurzak, E.; Katayama, S.; Koyano, M.

    2010-03-01

    Structural change of synthetic opal by shock-wave compression up to 38.1 GPa has been investigated by using SEM, X-ray diffraction method (XRD), Infrared (IR) and Raman spectroscopies. Obtained information may indicate that the dehydration and polymerization of surface silanole due to high shock and residual temperature are very important factors in the structural evolution of synthetic opal by shock compression. Synthetic opal loses opalescence by 10.9 and 18.4 GPa of shock pressures. At 18.4 GPa, dehydration and polymerization of surface silanole and transformation of network structure may occur simultaneously. The 4-membered ring of TO4 tetrahedrons in as synthetic opal may be relaxed to larger ring such as 6-membered ring by high residual temperature. Therefore, the residual temperature may be significantly high at even 18.4 GPa of shock compression. At 23.9 GPa, opal sample recovered the opalescence. Origin of this opalescence may be its layer structure by shock compression. Finally, sample fuse by very high residual temperature at 38.1 GPa and the structure closes to that of fused SiO2 glass. However, internal silanole groups still remain even at 38.1 GPa.

  20. Shock compression of synthetic opal

    Energy Technology Data Exchange (ETDEWEB)

    Inoue, A; Okuno, M; Okudera, H [Department of Earth Sciences, Kanazawa University Kanazawa, Ishikawa, 920-1192 (Japan); Mashimo, T; Omurzak, E [Shock Wave and Condensed Matter Research Center, Kumamoto University, Kumamoto, 860-8555 (Japan); Katayama, S; Koyano, M, E-mail: okuno@kenroku.kanazawa-u.ac.j [JAIST, Nomi, Ishikawa, 923-1297 (Japan)

    2010-03-01

    Structural change of synthetic opal by shock-wave compression up to 38.1 GPa has been investigated by using SEM, X-ray diffraction method (XRD), Infrared (IR) and Raman spectroscopies. Obtained information may indicate that the dehydration and polymerization of surface silanole due to high shock and residual temperature are very important factors in the structural evolution of synthetic opal by shock compression. Synthetic opal loses opalescence by 10.9 and 18.4 GPa of shock pressures. At 18.4 GPa, dehydration and polymerization of surface silanole and transformation of network structure may occur simultaneously. The 4-membered ring of TO{sub 4} tetrahedrons in as synthetic opal may be relaxed to larger ring such as 6-membered ring by high residual temperature. Therefore, the residual temperature may be significantly high at even 18.4 GPa of shock compression. At 23.9 GPa, opal sample recovered the opalescence. Origin of this opalescence may be its layer structure by shock compression. Finally, sample fuse by very high residual temperature at 38.1 GPa and the structure closes to that of fused SiO{sub 2} glass. However, internal silanole groups still remain even at 38.1 GPa.

  1. Programming Morphogenesis through Systems and Synthetic Biology.

    Science.gov (United States)

    Velazquez, Jeremy J; Su, Emily; Cahan, Patrick; Ebrahimkhani, Mo R

    2018-04-01

    Mammalian tissue development is an intricate, spatiotemporal process of self-organization that emerges from gene regulatory networks of differentiating stem cells. A major goal in stem cell biology is to gain a sufficient understanding of gene regulatory networks and cell-cell interactions to enable the reliable and robust engineering of morphogenesis. Here, we review advances in synthetic biology, single cell genomics, and multiscale modeling, which, when synthesized, provide a framework to achieve the ambitious goal of programming morphogenesis in complex tissues and organoids. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Protease-sensitive synthetic prions.

    Directory of Open Access Journals (Sweden)

    David W Colby

    2010-01-01

    Full Text Available Prions arise when the cellular prion protein (PrP(C undergoes a self-propagating conformational change; the resulting infectious conformer is designated PrP(Sc. Frequently, PrP(Sc is protease-resistant but protease-sensitive (s prions have been isolated in humans and other animals. We report here that protease-sensitive, synthetic prions were generated in vitro during polymerization of recombinant (rec PrP into amyloid fibers. In 22 independent experiments, recPrP amyloid preparations, but not recPrP monomers or oligomers, transmitted disease to transgenic mice (n = 164, denoted Tg9949 mice, that overexpress N-terminally truncated PrP. Tg9949 control mice (n = 174 did not spontaneously generate prions although they were prone to late-onset spontaneous neurological dysfunction. When synthetic prion isolates from infected Tg9949 mice were serially transmitted in the same line of mice, they exhibited sPrP(Sc and caused neurodegeneration. Interestingly, these protease-sensitive prions did not shorten the life span of Tg9949 mice despite causing extensive neurodegeneration. We inoculated three synthetic prion isolates into Tg4053 mice that overexpress full-length PrP; Tg4053 mice are not prone to developing spontaneous neurological dysfunction. The synthetic prion isolates caused disease in 600-750 days in Tg4053 mice, which exhibited sPrP(Sc. These novel synthetic prions demonstrate that conformational changes in wild-type PrP can produce mouse prions composed exclusively of sPrP(Sc.

  3. Yeast synthetic biology toolbox and applications for biofuel production.

    Science.gov (United States)

    Tsai, Ching-Sung; Kwak, Suryang; Turner, Timothy L; Jin, Yong-Su

    2015-02-01

    Yeasts are efficient biofuel producers with numerous advantages outcompeting bacterial counterparts. While most synthetic biology tools have been developed and customized for bacteria especially for Escherichia coli, yeast synthetic biological tools have been exploited for improving yeast to produce fuels and chemicals from renewable biomass. Here we review the current status of synthetic biological tools and their applications for biofuel production, focusing on the model strain Saccharomyces cerevisiae We describe assembly techniques that have been developed for constructing genes, pathways, and genomes in yeast. Moreover, we discuss synthetic parts for allowing precise control of gene expression at both transcriptional and translational levels. Applications of these synthetic biological approaches have led to identification of effective gene targets that are responsible for desirable traits, such as cellulosic sugar utilization, advanced biofuel production, and enhanced tolerance against toxic products for biofuel production from renewable biomass. Although an array of synthetic biology tools and devices are available, we observed some gaps existing in tool development to achieve industrial utilization. Looking forward, future tool development should focus on industrial cultivation conditions utilizing industrial strains. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

  4. Health Risk Behaviors With Synthetic Cannabinoids Versus Marijuana.

    Science.gov (United States)

    Clayton, Heather B; Lowry, Richard; Ashley, Carmen; Wolkin, Amy; Grant, Althea M

    2017-04-01

    Data are limited on the behavioral risk correlates of synthetic cannabinoid use. The purpose of this study was to compare the behavioral risk correlates of synthetic cannabinoid use with those among marijuana users. Data from the 2015 Youth Risk Behavior Survey, a cross-sectional survey conducted in a nationally representative sample of students in grades 9 through 12 ( N = 15 624), were used to examine the association between self-reported type of marijuana use (ie, never use of marijuana and synthetic cannabinoids, ever use of marijuana only, and ever use of synthetic cannabinoids) and self-report of 36 risk behaviors across 4 domains: substance use, injury/violence, mental health, and sexual health. Multivariable models were used to calculate adjusted prevalence ratios. Students who ever used synthetic cannabinoids had a significantly greater likelihood of engaging in each of the behaviors in the substance use and sexual risk domains compared with students who ever used marijuana only. Students who ever used synthetic cannabinoids were more likely than students who ever used marijuana only to have used marijuana before age 13 years, to have used marijuana ≥1 times during the past 30 days, and to have used marijuana ≥20 times during the past 30 days. Several injury/violence behaviors were more prevalent among students who ever used synthetic cannabinoids compared with students who ever used marijuana only. Health professionals and school-based substance use prevention programs should include strategies focused on the prevention of both synthetic cannabinoids and marijuana. Copyright © 2017 by the American Academy of Pediatrics.

  5. Brush border membrane vesicle and Caco-2 cell line: Two experimental models for evaluation of absorption enhancing effects of saponins, bile salts, and some synthetic surfactants

    Directory of Open Access Journals (Sweden)

    Eskandar Moghimipour

    2016-01-01

    Full Text Available The aim of this study was to investigate the influence of absorption enhancers in the uptake of hydrophilic compounds. The permeation of the two hydrophilic drug models gentamicin and 5 (6-carboxyfluorescein (CF across the brush border membrane vesicles and Caco-2 cell lines were evaluated using total saponins of Acanthophyllum squarrosum, Quillaja saponaria, sodium lauryl sulfate, sodium glycocholate, sodium taurodeoxycholate , and Tween 20 as absorption enhancers. Transepithelial electrical resistance (TEER measurement was utilized to assess the paracellular permeability of cell lines. Confocal laser scanning microscopy (CLSM was performed to obtain images of the distribution of CF in Caco-2 cells. These compounds were able to loosen tight junctions, thus increasing paracellular permeability. CLSM confirmed the effect of these absorption enhancers on CF transport across Caco-2 lines and increased the Caco-2 permeability via transcellular route. It was also confirmed that the decrease in TEER was transient and reversible after removal of permeation enhancers.

  6. Comparison of rSP-C surfactant with natural and synthetic surfactants after late treatment in a rat model of the acute respiratory distress syndrome

    Science.gov (United States)

    Häfner, Dietrich; Germann, Paul-Georg; Hauschke, Dieter

    1998-01-01

    In a previous paper we showed that an SP-C containing surfactant preparation has similar activity as bovine-derived surfactants in a rat lung lavage model of the adult respiratory distress syndrome. In this study surfactant was given ten minutes after the last lavage (early treatment). In the present investigation we were interested how different surfactant preparations behave when they are administered 1 h after the last lavage (late treatment). Four protein containing surfactants (rSP-C surfactant, bLES, Infasurf and Survanta) were compared with three protein-free surfactants (ALEC, Exosurf and the phospholipid (PL) mixture of the rSP-C surfactant termed PL surfactant) with respect to their ability to improve gas exchange in this more stringent model when surfactant is given one hour after the last lavage. For better comparison of the surfactants the doses were related to phospholipids. The surfactants were given at doses of 25, 50 and 100 mg kg−1 body weight. The surfactants were compared to an untreated control group that was only ventilated for the whole experimental period. Tracheotomized rats (8–12 per dose and surfactant) were pressure-controlled ventilated (Siemens Servo Ventilator 900C) with 100% oxygen at a respiratory rate of 30 breaths min−1, inspiration expiration ratio of 1 : 2, peak inspiratory pressure of 28 cmH2O at positive endexpiratory pressure (PEEP) of 8 cmH2O. Animals were ventilated for one hour after the last lavage and thereafter the surfactants were intratracheally instilled. During the whole experimental period the ventilation was not changed. Partial arterial oxygen pressures (PaO2, mmHg) at 30 min and 120 min after treatment were used for statistical comparison. All protein containing surfactants caused a dose-dependent increase of the reduced PaO2 values at 30 min after treatment. The protein-free surfactants showed only weak dose-dependent increase in PaO2 values at this time. This difference between the

  7. Antibacterial Evaluation of Synthetic Thiazole Compounds In Vitro and In Vivo in a Methicillin-Resistant Staphylococcus aureus (MRSA) Skin Infection Mouse Model.

    Science.gov (United States)

    Mohammad, Haroon; Cushman, Mark; Seleem, Mohamed N

    2015-01-01

    The emergence of community-associated methicillin-resistant Staphylococcus aureus (MRSA), including strains resistant to current antibiotics, has contributed to an increase in the number of skin infections reported in humans in recent years. New therapeutic options are needed to counter this public health challenge. The aim of the present study was to examine the potential of thiazole compounds synthesized by our research group to be used topically to treat MRSA skin and wound infections. The broth microdilution method confirmed that the lead thiazole compound and four analogues are capable of inhibiting MRSA growth at concentrations as low as 1.3 μg/mL. Additionally, three compounds exhibited a synergistic relationship when combined with the topical antibiotic mupirocin against MRSA in vitro via the checkerboard assay. Thus the thiazole compounds have potential to be used alone or in combination with mupirocin against MRSA. When tested against human keratinocytes, four derivatives of the lead compound demonstrated an improved toxicity profile (were found to be non-toxic up to a concentration of 20 μg/mL). Utilizing a murine skin infection model, we confirmed that the lead compound and three analogues exhibited potent antimicrobial activity in vivo, with similar capability as the antibiotic mupirocin, as they reduced the burden of MRSA present in skin wounds by more than 90%. Taken altogether, the present study provides important evidence that these thiazole compounds warrant further investigation for development as novel topical antimicrobials to treat MRSA skin infections.

  8. An Approach for a Synthetic CTL Vaccine Design against Zika Flavivirus Using Class I and Class II Epitopes Identified by Computer Modeling

    Directory of Open Access Journals (Sweden)

    Edecio Cunha-Neto

    2017-06-01

    Full Text Available The threat posed by severe congenital abnormalities related to Zika virus (ZKV infection during pregnancy has turned development of a ZKV vaccine into an emergency. Recent work suggests that the cytotoxic T lymphocyte (CTL response to infection is an important defense mechanism in response to ZKV. Here, we develop the rationale and strategy for a new approach to developing cytotoxic T lymphocyte (CTL vaccines for ZKV flavivirus infection. The proposed approach is based on recent studies using a protein structure computer model for HIV epitope selection designed to select epitopes for CTL attack optimized for viruses that exhibit antigenic drift. Because naturally processed and presented human ZKV T cell epitopes have not yet been described, we identified predicted class I peptide sequences on ZKV matching previously identified DNV (Dengue class I epitopes and by using a Major Histocompatibility Complex (MHC binding prediction tool. A subset of those met the criteria for optimal CD8+ attack based on physical chemistry parameters determined by analysis of the ZKV protein structure encoded in open source Protein Data File (PDB format files. We also identified candidate ZKV epitopes predicted to bind promiscuously to multiple HLA class II molecules that could provide help to the CTL responses. This work suggests that a CTL vaccine for ZKV may be possible even if ZKV exhibits significant antigenic drift. We have previously described a microsphere-based CTL vaccine platform capable of eliciting an immune response for class I epitopes in mice and are currently working toward in vivo testing of class I and class II epitope delivery directed against ZKV epitopes using the same microsphere-based vaccine.

  9. Catalysts for synthetic liquid fuels

    Energy Technology Data Exchange (ETDEWEB)

    Bruce, L.A.; Turney, T.W.

    1987-12-01

    Fischer-Tropsch catalysts have been designed, characterized and tested for the selective production of hydrocarbons suitable as synthetic liquid transport fuels from synthesis gas (i.e., by the reduction of carbon monoxide with hydrogen). It was found that hydrocarbons in the middle distillate range, or suitable for conversion to that range, could be produced over several of the new catalyst systems. The various catalysts examined included: (1) synthetic cobalt clays, mainly cobalt chlorites; (2) cobalt hydrotalcites; (3) ruthenium metal supported on rare earth oxides of high surface area; and (4) a novel promoted cobalt catalyst. Active and selective catalysts have been obtained, in each category. With the exception of the clays, reproducibility of catalyst performance has been good. Catalysts in groups 2 and 4 have exhibited very high activity, with long lifetimes and easy regeneration.

  10. Design Automation in Synthetic Biology.

    Science.gov (United States)

    Appleton, Evan; Madsen, Curtis; Roehner, Nicholas; Densmore, Douglas

    2017-04-03

    Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior. In synthetic biology, these tools are called bio-design automation (BDA) tools. In this review, we discuss the BDA tools areas-specify, design, build, test, and learn-and introduce the existing software tools designed to solve problems in these areas. We then detail the functionality of some of these tools and show how they can be used together to create the desired behavior of two types of modern synthetic genetic regulatory networks. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  11. Synthetic biology character and impact

    CERN Document Server

    Pade, Christian; Wigger, Henning; Gleich, Arnim

    2015-01-01

    Synthetic Biology is already an object of intensive debate. However, to a great extent the discussion to date has been concerned with fundamental ethical, religious and philosophical questions. By contrast, based on an investigation of the field’s scientific and technological character, this book focuses on new functionalities provided by synthetic biology and explores the associated opportunities and risks. Following an introduction to the subject and a discussion of the most central paradigms and methodologies, the book provides an overview of the structure of this field of science and technology. It informs the reader about the current stage of development, as well as topical problems and potential opportunities in important fields of application. But not only the science itself is in focus. In order to investigate its broader impact, ecological as well as ethical implications will be considered, paving the way for a discussion of responsibilities in the context of a field at a transitional crossroads be...

  12. Synthetic greenhouse gases under control

    International Nuclear Information System (INIS)

    Horisberger, B.; Karlaganis, G.

    2003-01-01

    This article discusses new Swiss regulations on the use of synthetic materials that posses a considerable greenhouse-warming potential. Synthetic materials such as hydro-chlorofluorocarbons HCFCs, perfluoride-hydrocarbons and sulphur hexafluoride have, in recent years, replaced chlorofluorocarbons CFCs, which were banned on account of their ozone depletion characteristics. The use of these persistent substances is now being limited to applications where more environment-friendly alternatives are not available. The measures decreed in the legislation, which include a general ban on HCFCs as of 2004 and a ban on the export of installations and equipment that use ozone-depleting refrigerants are described. Details on the legislation's effects on the Swiss refrigeration industry are listed and discussed

  13. Synthetic LDL as targeted drug delivery vehicle

    Science.gov (United States)

    Forte, Trudy M [Berkeley, CA; Nikanjam, Mina [Richmond, CA

    2012-08-28

    The present invention provides a synthetic LDL nanoparticle comprising a lipid moiety and a synthetic chimeric peptide so as to be capable of binding the LDL receptor. The synthetic LDL nanoparticle of the present invention is capable of incorporating and targeting therapeutics to cells expressing the LDL receptor for diseases associated with the expression of the LDL receptor such as central nervous system diseases. The invention further provides methods of using such synthetic LDL nanoparticles.

  14. Vibrational spectrum of synthetic carnotite

    Energy Technology Data Exchange (ETDEWEB)

    Baran, E J; Botto, I L [La Plata Univ. Nacional (Argentina). Facultad de Ciencias Exactas

    1976-05-01

    The infrared and laser-Raman spectra of synthetic carnotite, K/sub 2/((UO/sub 2/)/sub 2/V/sub 2/O/sub 8/), are reported and discussed. Force constants for the terminal V-O bonds as well as for the UO/sub 2//sup 2 +/ ions are evaluated. From the spectroscopic data, a U-O bond length of 1.81 A is estimated for the uranyl ion in this compound.

  15. Designer Drugs: A Synthetic Catastrophe

    OpenAIRE

    Fratantonio, James; Andrade, Lawrence; Febo, Marcelo

    2015-01-01

    Synthetic stimulants can cause hallucinations, aggressive behaviors, death and are sometimes legal. These substances are sold as plant food and bath salts that are "Not for Human Consumption", therefore skirting the 1986 Federal Analogue Act and giving a false pretense of safety. Studies have proved that these substances are toxic, have a high abuse potential, and are becoming extremely prevalent in the United States. This creates a dilemma for law enforcement agents, hospitals, and substance...

  16. Hydrogen speciation in synthetic quartz

    Science.gov (United States)

    Aines, R.D.; Kirby, S.H.; Rossman, G.R.

    1984-01-01

    The dominant hydrogen impurity in synthetic quartz is molecular H2O. H-OH groups also occur, but there is no direct evidence for the hydrolysis of Si-O-Si bonds to yield Si-OH HO-Si groups. Molecular H2O concentrations in the synthetic quartz crystals studied range from less than 10 to 3,300 ppm (H/Si), and decrease smoothly by up to an order of magnitude with distance away from the seed. OH- concentrations range from 96 to 715 ppm, and rise smoothly with distance away from the seed by up to a factor of three. The observed OH- is probably all associated with cationic impurities, as in natural quartz. Molecular H2O is the dominant initial hydrogen impurity in weak quartz. The hydrolytic weakening of quartz may be caused by the transformation H2O + Si-O-Si ??? 2SiOH, but this may be a transitory change with the SiOH groups recombining to form H2O, and the average SiOH concentration remaining very low. Synthetic quartz is strengthened when the H2O is accumulated into fluid inclusions and cannot react with the quartz framework. ?? 1984 Springer-Verlag.

  17. Synthetic triphones from trajectory-based feature distributions

    CSIR Research Space (South Africa)

    Badenhorst, J

    2015-11-01

    Full Text Available we reconstruct models for unseen transitions. In the current study, we restrict ourselves to triphone modelling, and aim to generate synthetic triphones from seen diphones. If this is possible, the same approach should be applicable to larger contexts... are applied in a similar fashion. Using trajectory models for the same goal, builds on prior work analysing co-articulation trajectories [7], [8], [9] as well as various studies on trajectory modelling for ASR purposes [10], [11], [12], [13]. Particularly...

  18. Characterization of synthetic peptides by mass spectrometry

    DEFF Research Database (Denmark)

    Prabhala, Bala Krishna; Mirza, Osman Asghar; Højrup, Peter

    2015-01-01

    Mass spectrometry (MS) is well suited for analysis of the identity and purity of synthetic peptides. The sequence of a synthetic peptide is most often known, so the analysis is mainly used to confirm the identity and purity of the peptide. Here, simple procedures are described for MALDI......-TOF-MS and LC-MS of synthetic peptides....

  19. A standard-enabled workflow for synthetic biology

    KAUST Repository

    Myers, Chris J.

    2017-06-15

    A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

  20. Predicting Translation Initiation Rates for Designing Synthetic Biology

    International Nuclear Information System (INIS)

    Reeve, Benjamin; Hargest, Thomas; Gilbert, Charlie; Ellis, Tom

    2014-01-01

    In synthetic biology, precise control over protein expression is required in order to construct functional biological systems. A core principle of the synthetic biology approach is a model-guided design and based on the biological understanding of the process, models of prokaryotic protein production have been described. Translation initiation rate is a rate-limiting step in protein production from mRNA and is dependent on the sequence of the 5′-untranslated region and the start of the coding sequence. Translation rate calculators are programs that estimate protein translation rates based on the sequence of these regions of an mRNA, and as protein expression is proportional to the rate of translation initiation, such calculators have been shown to give good approximations of protein expression levels. In this review, three currently available translation rate calculators developed for synthetic biology are considered, with limitations and possible future progress discussed.

  1. Synthetic Biology of Cyanobacteria: Unique Challenges and Opportunities

    Directory of Open Access Journals (Sweden)

    Bertram M Berla

    2013-08-01

    Full Text Available Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria’s potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli. While these organisms may in many cases be more difficult to work with as ‘chassis’ strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a ‘green E. coli’. In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria. We review classical and recently developed methods for constructing targeted mutants in various cyanobacterial strains, and offer perspective on what genetic tools might most greatly expand the ability to engineer new functions in such strains. Similarly, we review what genetic parts are most needed for the development of cyanobacterial synthetic biology. Finally, we highlight recent methods to construct genome-scale models of cyanobacterial metabolism and to use those models to measure properties of autotrophic metabolism. Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.

  2. SYNTHETIC EDUCATIONAL ENVIRONMENT – A FOOTPACE TO NEW EDUCATION

    Directory of Open Access Journals (Sweden)

    Olga P. Pinchuk

    2017-09-01

    Full Text Available The article studies the problems of introducing a synthetic learning environment in the practice of education. The modern views on the essence of the learning environment and its new forms based on information and communication technologies are analyzed. Particular attention is paid to a range of issues that are united in the English-language publications as a "synthetic environment", which is considered in two aspects – artificial environment and synthetic as is formed due to the synthesis of the real physical world and the results of simulation and modeling. There are considered issues of trends in usage of game-based learning and modeling as cognitive technologies, as well as of social networks as a synthetic environment of social development. Conclusions are drawn: synthetic learning environment becomes an independent subject of learning through the expansion of its content and didactic power, transformation of the individual as a recipient of knowledge into the synthesizing element of the educational process in the metaverse.

  3. Investigation of PVdF active diaphragms for synthetic jets

    Science.gov (United States)

    Bailo, Kelly C.; Brei, Diann E.; Calkins, Frederick T.

    2000-06-01

    Current research has shown that aircraft can gain significant aerodynamic performance benefits by employing active flow control (AFC). One of the enabling technologies of AFC is the synthetic jet. Synthetic jets, also known as zero-net-mass flux actuators, act as bi-directional pumps injecting high momentum air into the local aerodynamic flow. Previous work has concentrated on high frequency synthetic jets based on piezoelectric active diaphragms such as Thunder actuators. Low frequency synthetic jets present a unique challenge requiring large displacements, which current technology has difficulty meeting. Boeing is investigating novel shaped low frequency synthetic jets that can modify the flow over fixed aircraft wings. This paper present the initial study of two promising active diaphragm concepts: a crescent shape and an opposing bender shape. These active diaphragms were numerically modeled utilizing the general-purpose finite element code ABAQUS. Using the ABAQUS results, the dynamic volume change within each jet was calculated and incorporated into an analytical linear Bernoulli model to predict the velocities and pressures at the nozzle. Simulations were performed to determine trends to assist in selection of prototype configurations. Prototypes of both diaphragm concepts were constructed from polyvinylidene fluoride and experimentally tested at Boeing with promising results.

  4. Transient Calibration of a Variably-Saturated Groundwater Flow Model By Iterative Ensemble Smoothering: Synthetic Case and Application to the Flow Induced During Shaft Excavation and Operation of the Bure Underground Research Laboratory

    Science.gov (United States)

    Lam, D. T.; Kerrou, J.; Benabderrahmane, H.; Perrochet, P.

    2017-12-01

    The calibration of groundwater flow models in transient state can be motivated by the expected improved characterization of the aquifer hydraulic properties, especially when supported by a rich transient dataset. In the prospect of setting up a calibration strategy for a variably-saturated transient groundwater flow model of the area around the ANDRA's Bure Underground Research Laboratory, we wish to take advantage of the long hydraulic head and flowrate time series collected near and at the access shafts in order to help inform the model hydraulic parameters. A promising inverse approach for such high-dimensional nonlinear model, and which applicability has been illustrated more extensively in other scientific fields, could be an iterative ensemble smoother algorithm initially developed for a reservoir engineering problem. Furthermore, the ensemble-based stochastic framework will allow to address to some extent the uncertainty of the calibration for a subsequent analysis of a flow process dependent prediction. By assimilating the available data in one single step, this method iteratively updates each member of an initial ensemble of stochastic realizations of parameters until the minimization of an objective function. However, as it is well known for ensemble-based Kalman methods, this correction computed from approximations of covariance matrices is most efficient when the ensemble realizations are multi-Gaussian. As shown by the comparison of the updated ensemble mean obtained for our simplified synthetic model of 2D vertical flow by using either multi-Gaussian or multipoint simulations of parameters, the ensemble smoother fails to preserve the initial connectivity of the facies and the parameter bimodal distribution. Given the geological structures depicted by the multi-layered geological model built for the real case, our goal is to find how to still best leverage the performance of the ensemble smoother while using an initial ensemble of conditional multi

  5. A Canadian refiner's perspective of synthetic crudes

    International Nuclear Information System (INIS)

    Halford, T.L.; McIntosh, A.P.; Rasmussen

    1997-01-01

    Some of the factors affecting a refiner's choice of crude oil include refinery hardware, particularly gas oil crackers, products slate and product specifications, crude availability, relative crude price and crude quality. An overview of synthetic crude, the use of synthetic crude combined with other crudes and a comparison of synthetic crude with conventional crude oil was given. The two main users of synthetic crude are basically two groups of refiners, those large groups who use synthetic crude combined with other crudes, and a smaller group who run synthetic crude on specially designed units as a sole feed. The effects of changes in fuel legislation were reviewed. It was predicted that the changes will have a mixed impact on the value of synthetic crude, but low sulphur diesel regulations and gasoline sulphur regulations will make current synthetic crudes attractive. The big future change with a negative impact will be diesel cetane increases to reduce engine emissions. This will reduce synthetic crude attractiveness due to distillate yields and quality and high gas oil yields. Similarly, any legislation limiting aromatics in diesel fuel will also make synthetic crudes less attractive. Problems experienced by refiners with hardware dedicated to synthetic crude (salt, naphthenic acid, fouling, quality variations) were also reviewed. 3 tabs

  6. Understanding Biological Regulation Through Synthetic Biology.

    Science.gov (United States)

    Bashor, Caleb J; Collins, James J

    2018-03-16

    Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function. Expected final online publication date for the Annual Review of Biophysics Volume 47 is May 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  7. Synthetic biology: Emerging bioengineering in Indonesia

    Science.gov (United States)

    Suhandono, Sony

    2017-05-01

    The development of synthetic biology will shape the new era of science and technology. It is an emerging bioengineering technique involving genetic engineering which can alter the phenotype and behavior of the cell or the new product. Synthetic biology may produce biomaterials, drugs, vaccines, biosensors, and even a recombinant secondary metabolite used in herbal and complementary medicine, such as artemisinin, a malaria drug which is usually extracted from the plant Artemisia annua. The power of synthetic biology has encouraged scientists in Indonesia, and is still in early development. This paper also covers some research from an Indonesian research institute in synthetic biology such as observing the production of bio surfactants and the enhanced production of artemisinin using a transient expression system. Synthetic biology development in Indonesia may also be related to the iGEM competition, a large synthetic biology research competition which was attended by several universities in Indonesia. The application of synthetic biology for drug discovery will be discussed.

  8. Printability of Synthetic Papers by Electrophotography

    Directory of Open Access Journals (Sweden)

    Rozália Szentgyörgyvölgyi

    2010-04-01

    Full Text Available This paper deals with the printability of synthetic papers by the electrophotography technique. Prints of cmyk colour fields from 20% to 100% raster tone values were printed on three types of synthetic papers (one film synthetic paper and two fiber synthetic papers. The investigation of the appearance included densitometric measurement of the cmyk prints. The results have shown differences in the optical density and optical tone value between cmyk prints made on various synthetic papers. The highest optical density and the increase of the optical tone value were observed on the film synthetic paper, where cmyk prints were more saturated. The highest abrasion resistance of cmyk prints was obtained from the fibre synthetic paper.

  9. BrisSynBio: a BBSRC/EPSRC-funded Synthetic Biology Research Centre.

    Science.gov (United States)

    Sedgley, Kathleen R; Race, Paul R; Woolfson, Derek N

    2016-06-15

    BrisSynBio is the Bristol-based Biotechnology and Biological Sciences Research Council (BBSRC)/Engineering and Physical Sciences Research Council (EPSRC)-funded Synthetic Biology Research Centre. It is one of six such Centres in the U.K. BrisSynBio's emphasis is on rational and predictive bimolecular modelling, design and engineering in the context of synthetic biology. It trains the next generation of synthetic biologists in these approaches, to facilitate translation of fundamental synthetic biology research to industry and the clinic, and to do this within an innovative and responsible research framework. © 2016 The Author(s).

  10. Reconstruction of recycling flux from synthetic camera images, evaluated for the Wendelstein 7-X startup limiter

    Science.gov (United States)

    Frerichs, H.; Effenberg, F.; Feng, Y.; Schmitz, O.; Stephey, L.; Reiter, D.; Börner, P.; The W7-X Team

    2017-12-01

    The interpretation of spectroscopic measurements in the edge region of high-temperature plasmas can be guided by modeling with the EMC3-EIRENE code. A versatile synthetic diagnostic module, initially developed for the generation of synthetic camera images, has been extended for the evaluation of the inverse problem in which the observable photon flux is related back to the originating particle flux (recycling). An application of this synthetic diagnostic to the startup phase (inboard) limiter in Wendelstein 7-X (W7-X) is presented, and reconstruction of recycling from synthetic observation of \\renewcommand{\

  11. Synthetic Aperture Vector Flow Imaging

    DEFF Research Database (Denmark)

    Villagómez Hoyos, Carlos Armando

    The main objective of this project was to continue the development of a synthetic aperture vector flow estimator. This type of estimator is capable of overcoming two of the major limitations in conventional ultrasound systems: 1) the inability to scan large region of interest with high temporal......, this thesis showed that novel information can be obtained with vector velocity methods providing quantitative estimates of blood flow and insight into the complexity of the hemodynamics dynamics. This could give the clinician a new tool in assessment and treatment of a broad range of diseases....

  12. Synthetic Biology Guides Biofuel Production

    Directory of Open Access Journals (Sweden)

    Michael R. Connor

    2010-01-01

    Full Text Available The advancement of microbial processes for the production of renewable liquid fuels has increased with concerns about the current fuel economy. The development of advanced biofuels in particular has risen to address some of the shortcomings of ethanol. These advanced fuels have chemical properties similar to petroleum-based liquid fuels, thus removing the need for engine modification or infrastructure redesign. While the productivity and titers of each of these processes remains to be improved, progress in synthetic biology has provided tools to guide the engineering of these processes through present and future challenges.

  13. Adsorption of polar aromatic hydrocarbons on synthetic calcite

    DEFF Research Database (Denmark)

    Madsen, Lene; Grahl-Madsen, Laila; Grøn, Christian

    1996-01-01

    The wettability of hydrocarbon reservoirs depends on how and to what extent the organic compounds are adsorbed onto the surfaces of calcite, quartz and clay. A model system of synthetic call cite, cyclohexane and the three probe molecules: benzoic acid, benzyl alcohol and benzylamine, have been...

  14. Calibration of the TUD Ku-band Synthetic Aperture Radiometer

    DEFF Research Database (Denmark)

    Laursen, Brian; Skou, Niels

    1995-01-01

    The TUD Synthetic Aperture Radiometer is a 2-channel demonstration model that can simulate a thinned aperture radiometer having an unfilled aperture consisting of several small antenna elements. Aperture synthesis obtained by interferometric measurements using the antenna elements in pairs, follo...

  15. Antiangiogenic effects of synthetic analogs of curcumin in vivo ...

    African Journals Online (AJOL)

    The active compound curcumin is isolated from the spice turmeric. Curcumin, curcuminoids and their synthetic analogs have been shown to inhibit the progression of cancer in animal models. In colon and skin carcinogenesis the genetic changes engross different genes, but curcumin is effective in preventing ...

  16. Role of catalysis in sustainable production of synthetic elastomers

    Indian Academy of Sciences (India)

    productions, the impact of synthetic elastomer business cannot be overlooked. The need of ... Keywords. Elastomers; catalysis; tyres and automobiles; mechanism; manufacturing process. 1. ..... level fractional factorial design model was also developed to ..... Polybutadiene can be manufactured by a number of pro- cesses ...

  17. Modified signed-digit trinary addition using synthetic wavelet filter

    Science.gov (United States)

    Iftekharuddin, K. M.; Razzaque, M. A.

    2000-09-01

    The modified signed-digit (MSD) number system has been a topic of interest as it allows for parallel carry-free addition of two numbers for digital optical computing. In this paper, harmonic wavelet joint transform (HWJT)-based correlation technique is introduced for optical implementation of MSD trinary adder implementation. The realization of the carry-propagation-free addition of MSD trinary numerals is demonstrated using synthetic HWJT correlator model. It is also shown that the proposed synthetic wavelet filter-based correlator shows high performance in logic processing. Simulation results are presented to validate the performance of the proposed technique.

  18. The PLOS ONE Synthetic Biology Collection: Six Years and Counting

    Science.gov (United States)

    Peccoud, Jean; Isalan, Mark

    2012-01-01

    Since it was launched in 2006, PLOS ONE has published over fifty articles illustrating the many facets of the emerging field of synthetic biology. This article reviews these publications by organizing them into broad categories focused on DNA synthesis and assembly techniques, the development of libraries of biological parts, the use of synthetic biology in protein engineering applications, and the engineering of gene regulatory networks and metabolic pathways. Finally, we review articles that describe enabling technologies such as software and modeling, along with new instrumentation. In order to increase the visibility of this body of work, the papers have been assembled into the PLOS ONE Synthetic Biology Collection (www.ploscollections.org/synbio). Many of the innovative features of the PLOS ONE web site will help make this collection a resource that will support a lively dialogue between readers and authors of PLOS ONE synthetic biology papers. The content of the collection will be updated periodically by including relevant articles as they are published by the journal. Thus, we hope that this collection will continue to meet the publishing needs of the synthetic biology community. PMID:22916228

  19. Varieties of noise: analogical reasoning in synthetic biology.

    Science.gov (United States)

    Knuuttila, Tarja; Loettgers, Andrea

    2014-12-01

    The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice.

  20. Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria.

    Science.gov (United States)

    Tan, Gao-Yi; Liu, Tiangang

    2017-01-01

    Natural products (NPs) and their derivatives are widely used as frontline treatments for many diseases. Actinobacteria spp. are used to produce most of NP antibiotics and have also been intensively investigated for NP production, derivatization, and discovery. However, due to the complicated transcriptional and metabolic regulation of NP biosynthesis in Actinobacteria, especially in the cases of genome mining and heterologous expression, it is often difficult to rationally and systematically engineer synthetic pathways to maximize biosynthetic efficiency. With the emergence of new tools and methods in metabolic engineering, the synthetic pathways of many chemicals, such as fatty acids and biofuels, in model organisms (e.g. Escherichia coli ), have been refactored to realize precise and flexible control of production. These studies also offer a promising approach for synthetic pathway refactoring in Actinobacteria. In this review, the great potential of Actinobacteria as a microbial cell factory for biosynthesis of NPs is discussed. To this end, recent progress in metabolic engineering of NP synthetic pathways in Actinobacteria are summarized and strategies and perspectives to rationally and systematically refactor synthetic pathways in Actinobacteria are highlighted. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  1. CLIMABR parte I: modelo para a geração de séries sintéticas de precipitação CLIMABR part I: model for generation of synthetic series of precipitation

    Directory of Open Access Journals (Sweden)

    Vicente de P. S. de Oliveira

    2005-09-01

    Full Text Available Na área agrícola tem-se muitos dos estudos relativos à precipitação buscando avaliar os efeitos advindos da sua ocorrência no escoamento superficial; neste caso, é imprescindível o conhecimento não apenas das informações relativas à lâmina precipitada, à duração e intensidade das chuvas mas, também, ao perfil da precipitação. Objetivou-se, através do presente trabalho, mostrar o desenvolvimento de um modelo denominado CLIMABR, para a geração de séries sintéticas de precipitação, para as condições climáticas encontradas no Estado do Rio de Janeiro; para isto, utilizaram-se dados pluviométricos e pluviográficos de 11 estações da Fundação Superintendência Estadual de Rios e Lagoas - SERLA, e da Companhia LIGHT - Serviços de Eletricidade S.A. Na série sintética gerada obtiveram-se os valores mensais da probabilidade de um dia ser chuvoso tendo sido o anterior também chuvoso P(W/W e da probabilidade de um dia ser chuvoso tendo sido o anterior seco P(W/D; o número de dias chuvosos (NW e a precipitação total diária (P ocorrida nesses dias, além de outras informações relativas ao perfil de precipitação. A comparação dos dados gerados pelo CLIMABR com os dados observados mostrou um bom desempenho do modelo para a estimativa destas variáveis.In the agricultural area, many studies related to precipitation have tried to evaluate the effects resulting from its occurrence in surface runoff. In this case the knowledge of not only the information relative to precipitation, its duration and intensity of the rains, but, also the profile of the precipitation is of great importance. With this objective, the present work was carried out to develop a model called CLIMABR, for the generation of synthetic precipitation series and of the instantaneous profile associated to these for the climatic conditions of the State of Rio de Janeiro. Pluviometric and pluviographic data from eleven stations of the Funda

  2. Synthetic polyester-hydrolyzing enzymes from thermophilic actinomycetes.

    Science.gov (United States)

    Wei, Ren; Oeser, Thorsten; Zimmermann, Wolfgang

    2014-01-01

    Thermophilic actinomycetes produce enzymes capable of hydrolyzing synthetic polyesters such as polyethylene terephthalate (PET). In addition to carboxylesterases, which have hydrolytic activity predominantly against PET oligomers, esterases related to cutinases also hydrolyze synthetic polymers. The production of these enzymes by actinomycetes as well as their recombinant expression in heterologous hosts is described and their catalytic activity against polyester substrates is compared. Assays to analyze the enzymatic hydrolysis of synthetic polyesters are evaluated, and a kinetic model describing the enzymatic heterogeneous hydrolysis process is discussed. Structure-function and structure-stability relationships of actinomycete polyester hydrolases are compared based on molecular dynamics simulations and recently solved protein structures. In addition, recent progress in enhancing their activity and thermal stability by random or site-directed mutagenesis is presented. © 2014 Elsevier Inc. All rights reserved.

  3. Synthetic Biology with Cytochromes P450 Using Photosynthetic Chassis

    DEFF Research Database (Denmark)

    Gnanasekaran, Thiyagarajan

    , this modern field of synthetic biology is completely dependent on the nature of the chassis - the host organisms - for its endeavor. Of all the chassis, photosynthetic organisms such as cyanobacteria and plants gains special attention due to the remarkable amount of sunlight that is striking the Earth...... in cyanobacteria and plant chloroplasts for the purpose of light driven synthesis of bioactive compounds by using synthetic biology approaches. As model pathways, in this thesis, the pathway involved in the synthesis of the cyanogenic glucoside dhurrin from Sorghum bicolor, and the pathway involved......Synthetic biology is a rapidly growing engineering discipline in biology. It aims at building novel biological systems that do not exist in nature by selecting the interchangeable standardized biological parts that are already available in the nature, and assembling them in a specific order. Today...

  4. Tracking the emergence of synthetic biology.

    Science.gov (United States)

    Shapira, Philip; Kwon, Seokbeom; Youtie, Jan

    2017-01-01

    Synthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research, innovation, and policy interest in recent years. This paper contributes to efforts to delineate this emerging domain by presenting a newly constructed bibliometric definition of synthetic biology. Our approach is dimensioned from a core set of papers in synthetic biology, using procedures to obtain benchmark synthetic biology publication records, extract keywords from these benchmark records, and refine the keywords, supplemented with articles published in dedicated synthetic biology journals. We compare our search strategy with other recent bibliometric approaches to define synthetic biology, using a common source of publication data for the period from 2000 to 2015. The paper details the rapid growth and international spread of research in synthetic biology in recent years, demonstrates that diverse research disciplines are contributing to the multidisciplinary development of synthetic biology research, and visualizes this by profiling synthetic biology research on the map of science. We further show the roles of a relatively concentrated set of research sponsors in funding the growth and trajectories of synthetic biology. In addition to discussing these analyses, the paper notes limitations and suggests lines for further work.

  5. DNA recognition by synthetic constructs.

    Science.gov (United States)

    Pazos, Elena; Mosquera, Jesús; Vázquez, M Eugenio; Mascareñas, José L

    2011-09-05

    The interaction of transcription factors with specific DNA sites is key for the regulation of gene expression. Despite the availability of a large body of structural data on protein-DNA complexes, we are still far from fully understanding the molecular and biophysical bases underlying such interactions. Therefore, the development of non-natural agents that can reproduce the DNA-recognition properties of natural transcription factors remains a major and challenging goal in chemical biology. In this review we summarize the basics of double-stranded DNA recognition by transcription factors, and describe recent developments in the design and preparation of synthetic DNA binders. We mainly focus on synthetic peptides that have been designed by following the DNA interaction of natural proteins, and we discuss how the tools of organic synthesis can be used to make artificial constructs equipped with functionalities that introduce additional properties to the recognition process, such as sensing and controllability. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Synthetic Biology of Polyhydroxyalkanoates (PHA).

    Science.gov (United States)

    Meng, De-Chuan; Chen, Guo-Qiang

    Microbial polyhydroxyalkanoates (PHA) are a family of biodegradable and biocompatible polyesters which have been extensively studied using synthetic biology and metabolic engineering methods for improving production and for widening its diversity. Synthetic biology has allowed PHA to become composition controllable random copolymers, homopolymers, and block copolymers. Recent developments showed that it is possible to establish a microbial platform for producing not only random copolymers with controllable monomers and their ratios but also structurally defined homopolymers and block copolymers. This was achieved by engineering the genome of Pseudomonas putida or Pseudomonas entomophiles to weaken the β-oxidation and in situ fatty acid synthesis pathways, so that a fatty acid fed to the bacteria maintains its original chain length and structures when incorporated into the PHA chains. The engineered bacterium allows functional groups in a fatty acid to be introduced into PHA, forming functional PHA, which, upon grafting, generates endless PHA variety. Recombinant Escherichia coli also succeeded in producing efficiently poly(3-hydroxypropionate) or P3HP, the strongest member of PHA. Synthesis pathways of P3HP and its copolymer P3HB3HP of 3-hydroxybutyrate and 3-hydroxypropionate were assembled respectively to allow their synthesis from glucose. CRISPRi was also successfully used to manipulate simultaneously multiple genes and control metabolic flux in E. coli to obtain a series of copolymer P3HB4HB of 3-hydroxybutyrate (3HB) and 4-hydroxybutyrate (4HB). The bacterial shapes were successfully engineered for enhanced PHA accumulation.

  7. Vectoring of parallel synthetic jets

    Science.gov (United States)

    Berk, Tim; Ganapathisubramani, Bharathram; Gomit, Guillaume

    2015-11-01

    A pair of parallel synthetic jets can be vectored by applying a phase difference between the two driving signals. The resulting jet can be merged or bifurcated and either vectored towards the actuator leading in phase or the actuator lagging in phase. In the present study, the influence of phase difference and Strouhal number on the vectoring behaviour is examined experimentally. Phase-locked vorticity fields, measured using Particle Image Velocimetry (PIV), are used to track vortex pairs. The physical mechanisms that explain the diversity in vectoring behaviour are observed based on the vortex trajectories. For a fixed phase difference, the vectoring behaviour is shown to be primarily influenced by pinch-off time of vortex rings generated by the synthetic jets. Beyond a certain formation number, the pinch-off timescale becomes invariant. In this region, the vectoring behaviour is determined by the distance between subsequent vortex rings. We acknowledge the financial support from the European Research Council (ERC grant agreement no. 277472).

  8. Synthetic membrane-targeted antibiotics.

    Science.gov (United States)

    Vooturi, S K; Firestine, S M

    2010-01-01

    Antimicrobial resistance continues to evolve and presents serious challenges in the therapy of both nosocomial and community-acquired infections. The rise of resistant strains like methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Staphylococcus aureus (VRSA) and vancomycin-resistant enterococci (VRE) suggests that antimicrobial resistance is an inevitable evolutionary response to antimicrobial use. This highlights the tremendous need for antibiotics against new bacterial targets. Agents that target the integrity of bacterial membrane are relatively novel in the clinical armamentarium. Daptomycin, a lipopeptide is a classical example of membrane-bound antibiotic. Nature has also utilized this tactic. Antimicrobial peptides (AMPs), which are found in all kingdoms, function primarily by permeabilizing the bacterial membrane. AMPs have several advantages over existing antibiotics including a broad spectrum of activity, rapid bactericidal activity, no cross-resistance with the existing antibiotics and a low probability for developing resistance. Currently, a small number of peptides have been developed for clinical use but therapeutic applications are limited because of poor bioavailability and high manufacturing cost. However, their broad specificity, potent activity and lower probability for resistance have spurred the search for synthetic mimetics of antimicrobial peptides as membrane-active antibiotics. In this review, we will discuss the different classes of synthetic membrane-bound antibiotics published since 2004.

  9. Synthetic vision display evaluation studies

    Science.gov (United States)

    Regal, David M.; Whittington, David H.

    1994-01-01

    The goal of this research was to help us understand the display requirements for a synthetic vision system for the High Speed Civil Transport (HSCT). Four experiments were conducted to examine the effects of different levels of perceptual cue complexity in displays used by pilots in a flare and landing task. Increased levels of texture mapping of terrain and runway produced mixed results, including harder but shorter landings and a lower flare initiation altitude. Under higher workload conditions, increased texture resulted in an improvement in performance. An increase in familiar size cues did not result in improved performance. Only a small difference was found between displays using two patterns of high resolution texture mapping. The effects of increased perceptual cue complexity on performance was not as strong as would be predicted from the pilot's subjective reports or from related literature. A description of the role of a synthetic vision system in the High Speed Civil Transport is provide along with a literature review covering applied research related to perceptual cue usage in aircraft displays.

  10. Synthetic Stromgren photometry for F dwarf stars

    Science.gov (United States)

    Bell, R. A.

    1988-01-01

    Recent synthetic spectrum and color calculations for cool dwarf star models are tested by comparison with observation. The accuracy of the computed dependence of the thermal colors B-V and b-y on effective temperature is examined, and H-beta indices are presented and compared with observed values. The accuracy of the predictions of the Stromgren uvby system metal-abundance indicator m1 and luminosity indicator c1 are tested. A new calibration of the c1, b-y diagram in terms of absolute magnitudes is given, making use of recent calculations of stellar isochrones. Observations of very metal-poor subdwarfs are used to study the accuracy of the isochrones. The c1, b-y diagram of the subdwarfs is compared with that of the turnoff-region stars in the very metal-poor globular cluster NGC 6397.

  11. Dissolution studies of synthetic soddyite and uranophane

    International Nuclear Information System (INIS)

    Casas, I.; Perez, I.; Torrero, E.; Bruno, J.; Cera, E.; Duro, L.

    1997-09-01

    The dissolution of synthetically obtained soddyite and uranophane has been studied in solutions of low ionic strength. These are the likely final phases of the oxidative alternation pathway of uranium dioxide. The thermodynamic and kinetic dissolution properties of these phases have been determined at different bicarbonate concentrations. The solubilities determined in the experiments with soddyite correspond fairly well to the theoretical model calculated with a log K 0 s0 =3.9±0.7. For uranophane, the best fitting was obtained for a log K 0 s0 =11.7±0.6. The dissolution rate in the presence of bicarbonate gave for soddyite an average value of 6.8(±4.4) 10 -10 mol m -2 s -1 . For uranophane, under the same experimental conditions, the following dissolution rate equation has been derived: r 0 (mol m -2 s -1 )=10 -9±2. [HCO 3 - ] 0.69±0.09 2

  12. Synthetic and Virtual Environmental Media (SAVEM)

    International Nuclear Information System (INIS)

    Booth, F. H. K.; Decker, K. M.; Bath, R. J.; Bottrell, D. W.; Wright, K. L.

    2002-01-01

    The Synthetic and Virtual Environmental Media (SAVEM) Program, developed at the DOE Environmental Measurements Laboratory, responds directly to issues of improved data quality, increased regulatory confidence, analytical laboratory waste minimization, pollution prevention, worker safety/radiation exposure risk reduction, and environmental stewardship. The SAVEM radiochemistry information analysis system uses digitally generated spectra to accurately model gamma-ray emission characteristics of radiological samples. A digital virtual sample can be specified that has the characteristics of any environmental media such as soil, sediment, or vegetation, and which exhibits the spectral characteristics of more than 2,000 gamma-emitting nuclides. The SAVEM system can duplicate the characteristics of 2,361 individual radionuclides with 47,902 gamma lines

  13. Toward the First Data Acquisition Standard in Synthetic Biology.

    Science.gov (United States)

    Sainz de Murieta, Iñaki; Bultelle, Matthieu; Kitney, Richard I

    2016-08-19

    This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine. A data model is described which has been specifically developed for synthetic biology. The model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data. DICOM-SB also includes services orientated toward the automatic exchange of data and information between modalities and repositories. DICOM-SB has been developed in the context of systematic design in synthetic biology, which is based on the engineering principles of modularity, standardization, and characterization. The systematic design approach utilizes the design, build, test, and learn design cycle paradigm. DICOM-SB has been designed to be compatible with and complementary to other standards in synthetic biology, including SBOL. In this regard, the software provides effective interoperability. The new standard has been tested by experiments and data exchange between Nanyang Technological University in Singapore and Imperial College London.

  14. Synthetic socioeconomic based domestic wastewater hydrographs for small arid communities

    KAUST Repository

    Elnakar, H.

    2012-06-04

    A model was developed to predict synthetic socioeconomic based domestic wastewater hydrographs for the small arid communities. The model predicts the flow hydrograph for random weekdays and weekends based on the specific socioeconomic characteristics of the community. The main socioeconomic characteristics are the composition of the community, the different user behaviours in using water appliances, and the unit discharges of such appliances. Use patterns of water appliances are assumed to vary for the various members of the community and the type of day. Each community is composed of several social categories such as the employee, working woman, stay home woman, stay home child, students etc. The use patterns account for the stochastic nature of use in terms of number of uses, duration of the use and times of use in the day. Randomly generated hydrographs are generated for weekdays and weekends along with synthetic hydrographs of non-exceedance. The model was verified for a small residential compound in Sharm El Shiekh - Egypt using 11 days of flow measurements performed in summer. The synthetic hydrographs based on assumed water use patterns of the various members of the community compared reasonably with the measured hydrographs. Synthetic hydrographs can be derived for a community under consideration to reflect its socioeconomic conditions and thus can be used to generate probability based peaking factors to be used in the design of sewerage systems pumping facilities, and treatment plants. © 201 WIT Press.

  15. Synthetic socioeconomic based domestic wastewater hydrographs for small arid communities

    KAUST Repository

    Elnakar, H.; Imam, E.; Nassar, K.

    2012-01-01

    A model was developed to predict synthetic socioeconomic based domestic wastewater hydrographs for the small arid communities. The model predicts the flow hydrograph for random weekdays and weekends based on the specific socioeconomic characteristics of the community. The main socioeconomic characteristics are the composition of the community, the different user behaviours in using water appliances, and the unit discharges of such appliances. Use patterns of water appliances are assumed to vary for the various members of the community and the type of day. Each community is composed of several social categories such as the employee, working woman, stay home woman, stay home child, students etc. The use patterns account for the stochastic nature of use in terms of number of uses, duration of the use and times of use in the day. Randomly generated hydrographs are generated for weekdays and weekends along with synthetic hydrographs of non-exceedance. The model was verified for a small residential compound in Sharm El Shiekh - Egypt using 11 days of flow measurements performed in summer. The synthetic hydrographs based on assumed water use patterns of the various members of the community compared reasonably with the measured hydrographs. Synthetic hydrographs can be derived for a community under consideration to reflect its socioeconomic conditions and thus can be used to generate probability based peaking factors to be used in the design of sewerage systems pumping facilities, and treatment plants. © 201 WIT Press.

  16. Word selection affects perceptions of synthetic biology

    Directory of Open Access Journals (Sweden)

    Tonidandel Scott

    2011-07-01

    Full Text Available Abstract Members of the synthetic biology community have discussed the significance of word selection when describing synthetic biology to the general public. In particular, many leaders proposed the word "create" was laden with negative connotations. We found that word choice and framing does affect public perception of synthetic biology. In a controlled experiment, participants perceived synthetic biology more negatively when "create" was used to describe the field compared to "construct" (p = 0.008. Contrary to popular opinion among synthetic biologists, however, low religiosity individuals were more influenced negatively by the framing manipulation than high religiosity people. Our results suggest that synthetic biologists directly influence public perception of their field through avoidance of the word "create".

  17. Creating biological nanomaterials using synthetic biology

    International Nuclear Information System (INIS)

    Rice, MaryJoe K; Ruder, Warren C

    2014-01-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

  18. Creating biological nanomaterials using synthetic biology.

    Science.gov (United States)

    Rice, MaryJoe K; Ruder, Warren C

    2014-02-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  19. Synthetic approaches to uniform polymers.

    Science.gov (United States)

    Ali, Monzur; Brocchini, Steve

    2006-12-30

    Uniform polymers are characterised by a narrow molecular weight distribution (MWD). Uniformity is also defined by chemical structure in respect of (1) monomer orientation, sequence and stereo-regularity, (2) polymer shape and morphology and (3) chemical functionality. The function of natural polymers such as polypeptides and polynucleotides is related to their conformational structure (e.g. folded tertiary structure). This is only possible because of their high degree of uniformity. While completely uniform synthetic polymers are rare, polymers with broad structure and MWD are widely used in medicine and the biomedical sciences. They are integral components in final dosage forms, drug delivery systems (DDS) and in implantable devices. Increasingly uniform polymers are being used to develop more complex medicines (e.g. delivery of biopharmaceuticals, enhanced formulations or DDS's for existing actives). In addition to the function imparted by any new polymer it will be required to meet stringent specifications in terms of cost containment, scalability, biocompatibility and performance. Synthetic polymers with therapeutic activity are also being developed to exploit their polyvalent properties, which is not possible with low molecular weight molecules. There is need to utilise uniform polymers for applications where the polymer may interact with the systemic circulation, tissues or cellular environment. There are also potential applications (e.g. stimuli responsive coatings) where uniform polymers may be used for their more defined property profile. While it is not yet practical to prepare synthetic polymers to the same high degree of uniformity as proteins, nature also effectively utilises many polymers with lower degrees of uniformity (e.g. polysaccharides, poly(amino acids), polyhydroxyalkanoates). In recent years it has become possible to prepare with practical experimental protocols sufficient quantities of polymers that display many aspects of uniformity. This

  20. Synthetic Lipoproteins as Carriers for Drug Delivery.

    Science.gov (United States)

    Huang, Gangliang; Liu, Yang; Huang, Hualiang

    2016-01-01

    Synthetic lipoprotein is an effective carrier of targeted delivery for drugs. It has the very small size, good biocompatibility, suitable half-life, and specific lipoprotein receptorbinding capacity. Compared with the traditional natural lipoprotein, synthetic lipoprotein not only retains the original biological characteristics and functions, but also exhibits the excellent characteristics in drug delivery. Herein, the advantages, development, applications, and prospect of synthetic lipoproteins as drug carriers were summarized.

  1. Geo synthetic-reinforced Pavement systems

    International Nuclear Information System (INIS)

    Zornberg, J. G.

    2014-01-01

    Geo synthetics have been used as reinforcement inclusions to improve pavement performance. while there are clear field evidence of the benefit of using geo synthetic reinforcements, the specific conditions or mechanisms that govern the reinforcement of pavements are, at best, unclear and have remained largely unmeasured. Significant research has been recently conducted with the objectives of: (i) determining the relevant properties of geo synthetics that contribute to the enhanced performance of pavement systems, (ii) developing appropriate analytical, laboratory and field methods capable of quantifying the pavement performance, and (iii) enabling the prediction of pavement performance as a function of the properties of the various types of geo synthetics. (Author)

  2. Veterans Affairs Suicide Prevention Synthetic Dataset

    Data.gov (United States)

    Department of Veterans Affairs — The VA's Veteran Health Administration, in support of the Open Data Initiative, is providing the Veterans Affairs Suicide Prevention Synthetic Dataset (VASPSD). The...

  3. Synthetic biology assemblies for sustainable space exploration

    Data.gov (United States)

    National Aeronautics and Space Administration — The work utilized synthetic biology to create sustainable food production processes by developing technology to efficiently convert inedible crop waste to...

  4. Synthetic biology of antimicrobial discovery

    Science.gov (United States)

    Zakeri, Bijan; Lu, Timothy K.

    2012-01-01

    Antibiotic discovery has a storied history. From the discovery of penicillin by Sir Alexander Fleming to the relentless quest for antibiotics by Selman Waksman, the stories have become like folklore, used to inspire future generations of scientists. However, recent discovery pipelines have run dry at a time when multidrug resistant pathogens are on the rise. Nature has proven to be a valuable reservoir of antimicrobial agents, which are primarily produced by modularized biochemical pathways. Such modularization is well suited to remodeling by an interdisciplinary approach that spans science and engineering. Herein, we discuss the biological engineering of small molecules, peptides, and non-traditional antimicrobials and provide an overview of the growing applicability of synthetic biology to antimicrobials discovery. PMID:23654251

  5. Preparation of synthetic standard minerals

    International Nuclear Information System (INIS)

    Herrick, C.C.; Bustamante, S.J.; Charls, R.W.; Cowan, R.E.; Hakkila, E.A.; Hull, D.E.; Olinger, B.W.; Roof, R.B.; Sheinberg, H.; Herrick, G.C.

    1978-01-01

    A number of techniques for synthetic mineral preparations have been examined. These techniques include hot-pressing in graphite dies at moderate pressures, high-pressure, high-temperature synthesis in a piston and cylinder apparatus, isostatic pressing under helium gas pressures, hydrous mineral preparations using water as the pressure medium, explosion-generated shock waves, and radiofrequency heating. Minerals suitable for equation-of-state studies (three-inch, high-density discs), for thermodynamic property determinations (low-density powders) and for microprobe standards (fusion-cast microbeads) have been prepared. Mechanical stress-strain calculations in the piston-cylinder apparatus have been initiated and their integration with thermal stress calculations is currently under investigation

  6. Synthetic biology of antimicrobial discovery.

    Science.gov (United States)

    Zakeri, Bijan; Lu, Timothy K

    2013-07-19

    Antibiotic discovery has a storied history. From the discovery of penicillin by Sir Alexander Fleming to the relentless quest for antibiotics by Selman Waksman, the stories have become like folklore used to inspire future generations of scientists. However, recent discovery pipelines have run dry at a time when multidrug-resistant pathogens are on the rise. Nature has proven to be a valuable reservoir of antimicrobial agents, which are primarily produced by modularized biochemical pathways. Such modularization is well suited to remodeling by an interdisciplinary approach that spans science and engineering. Herein, we discuss the biological engineering of small molecules, peptides, and non-traditional antimicrobials and provide an overview of the growing applicability of synthetic biology to antimicrobials discovery.

  7. Synthetic biology: a utilitarian perspective.

    Science.gov (United States)

    Smith, Kevin

    2013-10-01

    I examine the positive and negative features of synthetic biology ('SynBio') from a utilitarian ethical perspective. The potential beneficial outcomes from SynBio in the context of medicine are substantial; however it is not presently possible to predict precise outcomes due to the nascent state of the field. Potential negative outcomes from SynBio also exist, including iatrogenesis and bioterrorism; however it is not yet possible to quantify these risks. I argue that the application of a 'precautionary' approach to SynBio is ethically fraught, as is the notion that SynBio-associated knowledge ought to be restricted. I conclude that utilitarians ought to support a broadly laissez-faire stance in respect of SynBio. © 2013 John Wiley & Sons Ltd.

  8. Synthetic biology: engineering molecular computers

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    Complicated systems cannot survive the rigors of a chaotic environment, without balancing mechanisms that sense, decide upon and counteract the exerted disturbances. Especially so with living organisms, forced by competition to incredible complexities, escalating also their self-controlling plight. Therefore, they compute. Can we harness biological mechanisms to create artificial computing systems? Biology offers several levels of design abstraction: molecular machines, cells, organisms... ranging from the more easily-defined to the more inherently complex. At the bottom of this stack we find the nucleic acids, RNA and DNA, with their digital structure and relatively precise interactions. They are central enablers of designing artificial biological systems, in the confluence of engineering and biology, that we call Synthetic biology. In the first part, let us follow their trail towards an overview of building computing machines with molecules -- and in the second part, take the case study of iGEM Greece 201...

  9. Microorganism Utilization for Synthetic Milk

    Science.gov (United States)

    Morford, Megan A.; Khodadad, Christina L.; Caro, Janicce I.; Spencer, LaShelle E.; Richards, Jeffery T.; Strayer, Richard F.; Birmele, Michele N.; Wheeler, Raymond M.

    2014-01-01

    A desired architecture for long duration spaceflight, like aboard the International Space Station or for future missions to Mars, is to provide a supply of fresh food crops for the astronauts. However, some crops can create a high proportion of inedible plant waste. The main goal of the Synthetic Biology project, Cow in a Column, was to produce the components of milk (sugar, lipid, protein) from inedible plant waste by utilizing microorganisms (fungi, yeast, bacteria). Of particular interest was utilizing the valuable polysaccharide, cellulose, found in plant waste, to naturally fuel-through microorganism cellular metabolism- the creation of sugar (glucose), lipid (milk fat), and protein (casein) in order to produce a synthetic edible food product. Environmental conditions such as pH, temperature, carbon source, aeration, and choice microorganisms were optimized in the laboratory and the desired end-products, sugars and lipids, were analyzed. Trichoderma reesei, a known cellulolytic fungus, was utilized to drive the production of glucose, with the intent that the produced glucose would serve as the carbon source for milk fat production and be a substitute for the milk sugar lactose. Lipid production would be carried out by Rhodosporidium toruloides, yeast known to accumulate those lipids that are typically found in milk fat. Results showed that glucose and total lipid content were below what was expected during this phase of experimentation. In addition, individual analysis of six fatty acids revealed that the percentage of each fatty acid was lower than naturally produced bovine milk. Overall, this research indicates that microorganisms could be utilized to breakdown inedible solid waste to produce useable products. For future work, the production of the casein protein for milk would require the development of a genetically modified organism, which was beyond the scope of the original project. Additional trials would be needed to further refine the required

  10. Synthetic vision and memory for autonomous virtual humans

    OpenAIRE

    PETERS, CHRISTOPHER; O'SULLIVAN, CAROL ANN

    2002-01-01

    PUBLISHED A memory model based on ?stage theory?, an influential concept of memory from the field of cognitive psychology, is presented for application to autonomous virtual humans. The virtual human senses external stimuli through a synthetic vision system. The vision system incorporates multiple modes of vision in order to accommodate a perceptual attention approach. The memory model is used to store perceived and attended object information at different stages in a filtering...

  11. THE ACS NEARBY GALAXY SURVEY TREASURY. IX. CONSTRAINING ASYMPTOTIC GIANT BRANCH EVOLUTION WITH OLD METAL-POOR GALAXIES

    International Nuclear Information System (INIS)

    Girardi, Leo; Williams, Benjamin F.; Gilbert, Karoline M.; Rosenfield, Philip; Dalcanton, Julianne J.; Marigo, Paola; Boyer, Martha L.; Dolphin, Andrew; Weisz, Daniel R.; Skillman, Evan; Melbourne, Jason; Olsen, Knut A. G.; Seth, Anil C.

    2010-01-01

    In an attempt to constrain evolutionary models of the asymptotic giant branch (AGB) phase at the limit of low masses and low metallicities, we have examined the luminosity functions and number ratios between AGB and red giant branch (RGB) stars from a sample of resolved galaxies from the ACS Nearby Galaxy Survey Treasury. This database provides Hubble Space Telescope optical photometry together with maps of completeness, photometric errors, and star formation histories for dozens of galaxies within 4 Mpc. We select 12 galaxies characterized by predominantly metal-poor populations as indicated by a very steep and blue RGB, and which do not present any indication of recent star formation in their color-magnitude diagrams. Thousands of AGB stars brighter than the tip of the RGB (TRGB) are present in the sample (between 60 and 400 per galaxy), hence, the Poisson noise has little impact in our measurements of the AGB/RGB ratio. We model the photometric data with a few sets of thermally pulsing AGB (TP-AGB) evolutionary models with different prescriptions for the mass loss. This technique allows us to set stringent constraints on the TP-AGB models of low-mass, metal-poor stars (with M sun , [Fe/H]∼ sun . This is also in good agreement with recent observations of white dwarf masses in the M4 old globular cluster. These constraints can be added to those already derived from Magellanic Cloud star clusters as important mileposts in the arduous process of calibrating AGB evolutionary models.

  12. A systematic design method for robust synthetic biology to satisfy design specifications.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chih-Hung

    2009-06-30

    Synthetic biology is foreseen to have important applications in biotechnology and medicine, and is expected to contribute significantly to a better understanding of the functioning of complex biological systems. However, the development of synthetic gene networks is still difficult and most newly created gene networks are non-functioning due to intrinsic parameter uncertainties, external disturbances and functional variations of intra- and extra-cellular environments. The design method for a robust synthetic gene network that works properly in a host cell under these intrinsic parameter uncertainties and external disturbances is the most important topic in synthetic biology. In this study, we propose a stochastic model that includes parameter fluctuations and external disturbances to mimic the dynamic behaviors of a synthetic gene network in the host cell. Then, based on this stochastic model, four design specifications are introduced to guarantee that a synthetic gene network can achieve its desired steady state behavior in spite of parameter fluctuations, external disturbances and functional variations in the host cell. We propose a systematic method to select a set of appropriate design parameters for a synthetic gene network that will satisfy these design specifications so that the intrinsic parameter fluctuations can be tolerated, the external disturbances can be efficiently filtered, and most importantly, the desired steady states can be achieved. Thus the synthetic gene network can work properly in a host cell under intrinsic parameter uncertainties, external disturbances and functional variations. Finally, a design procedure for the robust synthetic gene network is developed and a design example is given in silico to confirm the performance of the proposed method. Based on four design specifications, a systematic design procedure is developed for designers to engineer a robust synthetic biology network that can achieve its desired steady state behavior

  13. Stress-Strain Relationship of Synthetic Fiber Reinforced Concrete Columns

    Directory of Open Access Journals (Sweden)

    Rosidawani

    2017-01-01

    Full Text Available Many empirical confinement models for normal and high strength concrete have been developed. Nevertheless, reported studies in the term of confinement of fiber reinforced concrete are limited. Whereas, the use of fiber reinforced concrete in structural elements has become the subject of the research and has indicated positive experiences. Since the stress-strain relationship of concrete in compression is required for analysis of structural members, the study of the stress-strain relationship for synthetic fiber reinforced concrete is substantial. The aim of the study is to examine the capabilities of the various models available in the literature to predict the actual experimental behavior of synthetic fiber reinforced high-strength concrete columns. The experimental data used are the results of the circular column specimens with the spiral spacing and the volume fraction of synthetic fiber as the test variables. The axial stress-strain curves from the tests are then compared with the various models of confinement from the literature. The performance index of each model is measured by using the coefficient of variation (COV concept of stress and strain behavior parameter. Among the confinement models, Cusson model shows the closest valid value of the coefficient of variation.

  14. TinkerCell: modular CAD tool for synthetic biology

    Science.gov (United States)

    Chandran, Deepak; Bergmann, Frank T; Sauro, Herbert M

    2009-01-01

    Background Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. Using a CAD application, it would be possible to construct models using available biological "parts" and directly generate the DNA sequence that represents the model, thus increasing the efficiency of design and construction of synthetic networks. Results An application named TinkerCell has been developed in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various third-party C and Python programs that are hosted by TinkerCell via an extensive C and Python application programming interface (API). TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at . Conclusion An ideal CAD application for engineering biological systems would provide features such as: building and simulating networks, analyzing robustness of networks, and searching databases for components that meet the design criteria. At the current state of synthetic biology, there are no established methods for measuring robustness or identifying components that fit a design. The same is true for databases of biological parts. TinkerCell's flexible modeling framework allows it to cope with changes in the field. Such changes may involve the way parts are characterized or the way synthetic networks are modeled and analyzed computationally. TinkerCell can readily

  15. TinkerCell: modular CAD tool for synthetic biology

    Directory of Open Access Journals (Sweden)

    Bergmann Frank T

    2009-10-01

    Full Text Available Abstract Background Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD is necessary in order to bridge the gap between computational modeling and biological data. Using a CAD application, it would be possible to construct models using available biological "parts" and directly generate the DNA sequence that represents the model, thus increasing the efficiency of design and construction of synthetic networks. Results An application named TinkerCell has been developed in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various third-party C and Python programs that are hosted by TinkerCell via an extensive C and Python application programming interface (API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at http://www.tinkercell.com. Conclusion An ideal CAD application for engineering biological systems would provide features such as: building and simulating networks, analyzing robustness of networks, and searching databases for components that meet the design criteria. At the current state of synthetic biology, there are no established methods for measuring robustness or identifying components that fit a design. The same is true for databases of biological parts. TinkerCell's flexible modeling framework allows it to cope with changes in the field. Such changes may involve the way parts are characterized or the way synthetic networks are modeled

  16. Pareto Optimal Design for Synthetic Biology.

    Science.gov (United States)

    Patanè, Andrea; Santoro, Andrea; Costanza, Jole; Carapezza, Giovanni; Nicosia, Giuseppe

    2015-08-01

    Recent advances in synthetic biology call for robust, flexible and efficient in silico optimization methodologies. We present a Pareto design approach for the bi-level optimization problem associated to the overproduction of specific metabolites in Escherichia coli. Our method efficiently explores the high dimensional genetic manipulation space, finding a number of trade-offs between synthetic and biological objectives, hence furnishing a deeper biological insight to the addressed problem and important results for industrial purposes. We demonstrate the computational capabilities of our Pareto-oriented approach comparing it with state-of-the-art heuristics in the overproduction problems of i) 1,4-butanediol, ii) myristoyl-CoA, i ii) malonyl-CoA , iv) acetate and v) succinate. We show that our algorithms are able to gracefully adapt and scale to more complex models and more biologically-relevant simulations of the genetic manipulations allowed. The Results obtained for 1,4-butanediol overproduction significantly outperform results previously obtained, in terms of 1,4-butanediol to biomass formation ratio and knock-out costs. In particular overproduction percentage is of +662.7%, from 1.425 mmolh⁻¹gDW⁻¹ (wild type) to 10.869 mmolh⁻¹gDW⁻¹, with a knockout cost of 6. Whereas, Pareto-optimal designs we have found in fatty acid optimizations strictly dominate the ones obtained by the other methodologies, e.g., biomass and myristoyl-CoA exportation improvement of +21.43% (0.17 h⁻¹) and +5.19% (1.62 mmolh⁻¹gDW⁻¹), respectively. Furthermore CPU time required by our heuristic approach is more than halved. Finally we implement pathway oriented sensitivity analysis, epsilon-dominance analysis and robustness analysis to enhance our biological understanding of the problem and to improve the optimization algorithm capabilities.

  17. PTBS segmentation scheme for synthetic aperture radar

    Science.gov (United States)

    Friedland, Noah S.; Rothwell, Brian J.

    1995-07-01

    The Image Understanding Group at Martin Marietta Technologies in Denver, Colorado has developed a model-based synthetic aperture radar (SAR) automatic target recognition (ATR) system using an integrated resource architecture (IRA). IRA, an adaptive Markov random field (MRF) environment, utilizes information from image, model, and neighborhood resources to create a discrete, 2D feature-based world description (FBWD). The IRA FBWD features are peak, target, background and shadow (PTBS). These features have been shown to be very useful for target discrimination. The FBWD is used to accrue evidence over a model hypothesis set. This paper presents the PTBS segmentation process utilizing two IRA resources. The image resource (IR) provides generic (the physics of image formation) and specific (the given image input) information. The neighborhood resource (NR) provides domain knowledge of localized FBWD site behaviors. A simulated annealing optimization algorithm is used to construct a `most likely' PTBS state. Results on simulated imagery illustrate the power of this technique to correctly segment PTBS features, even when vehicle signatures are immersed in heavy background clutter. These segmentations also suppress sidelobe effects and delineate shadows.

  18. Study of seed for synthetical quartz

    International Nuclear Information System (INIS)

    Suzuki, C.K.; Torikai, D.

    1988-01-01

    Natural quartz blocks for seed (synthetic quartz technology) were studied by using various characterization techniques, such as X-ray topography, optical micrography, inspectoscopy, polariscopy and conoscopy, and etching. One of the most commonly found defect is the electrical or Dauphine twin. In The present research, we have developed a methodology to obtain a highly perfect seed for the synthetic quartz industries. (author) [pt

  19. Synthetic biology: programming cells for biomedical applications.

    Science.gov (United States)

    Hörner, Maximilian; Reischmann, Nadine; Weber, Wilfried

    2012-01-01

    The emerging field of synthetic biology is a novel biological discipline at the interface between traditional biology, chemistry, and engineering sciences. Synthetic biology aims at the rational design of complex synthetic biological devices and systems with desired properties by combining compatible, modular biological parts in a systematic manner. While the first engineered systems were mainly proof-of-principle studies to demonstrate the power of the modular engineering approach of synthetic biology, subsequent systems focus on applications in the health, environmental, and energy sectors. This review describes recent approaches for biomedical applications that were developed along the synthetic biology design hierarchy, at the level of individual parts, of devices, and of complex multicellular systems. It describes how synthetic biological parts can be used for the synthesis of drug-delivery tools, how synthetic biological devices can facilitate the discovery of novel drugs, and how multicellular synthetic ecosystems can give insight into population dynamics of parasites and hosts. These examples demonstrate how this new discipline could contribute to novel solutions in the biopharmaceutical industry.

  20. Metal immobilization in soils using synthetic zeolites

    NARCIS (Netherlands)

    Osté, L.A.; Lexmond, T.M.; Riemsdijk, van W.H.

    2002-01-01

    In situ immobilization of heavy metals in contaminated soils is a technique to improve soil quality. Synthetic zeolites are potentially useful additives to bind heavy metals. This study selected the most effective zeolite in cadmium and zinc binding out of six synthetic zeolites (mordenite-type,

  1. Synthetic aperture radar: principles and applications

    International Nuclear Information System (INIS)

    Khan, N.A.; Yahya, K.M.

    2003-01-01

    In this paper an introduction to synthetic aperture radar is presented. Synthetic aperture radar is a relatively new remote sensing platform and the technology has matured a lot in the last two decades. This paper introduces the concepts behind SAR principles as well as the major areas where this new technology has shown additional information. (author)

  2. Opportunities for microfluidic technologies in synthetic biology

    OpenAIRE

    Gulati, Shelly; Rouilly, Vincent; Niu, Xize; Chappell, James; Kitney, Richard I.; Edel, Joshua B.; Freemont, Paul S.; deMello, Andrew J.

    2009-01-01

    We introduce microfluidics technologies as a key foundational technology for synthetic biology experimentation. Recent advances in the field of microfluidics are reviewed and the potential of such a technological platform to support the rapid development of synthetic biology solutions is discussed.

  3. Steel desulphurization with synthetic slag

    Directory of Open Access Journals (Sweden)

    Heput, T.

    2007-02-01

    Full Text Available Generally speaking, sulphur is considered a harmful element for steel quality, reason why all the technological steps are being taken in order to eliminate it from the metal bath. This paper deals with the influence of the chemical composition, on the slag quantity and of the bath stirring condition upon the desulphurization process in the casting ladle by treatment with synthetic slag. The experiments were made at an open-hearth plant with the steel tapping in two ladles (the desulphurization was made with synthetic slag at one ladle while the other one was considered standard and at the electric steel plant and for the synthetic slag formation a mix was used, made, according to several receipts, of: lime (50-75%, fluorine (0-17%, bauxite (0-32% and aluminous slag (8-22%. The data were processed in the calculation programs EXCEL and MATLAB, which resulted in a series of correlations between the desulphurization degree and the chemical composition of the slag, respectively the slag quantity both for the charges bubbled with Argon and the unbubbled ones.

    En general, el azufre es considerado un elemento nocivo para la calidad del acero y, por eso, en la práctica, se toman todas las medidas de orden tecnológico para su eliminación del baño metálico. En este trabajo se analiza la influencia de la composición química, de la cantidad de escoria y del estado de agitación del baño sobre el proceso de desulfuración en la cuchara para fundir por tratamiento con escoria sintética. Los experimentos se han realizado en una acería evacuando el acero en dos ollas (en una cuchara se efectuó la desulfuración con escoria sintética y a la otra se consideró como patrón y en un acería eléctrica y para la formación de la escoria sintética se utilizó una mezcla producida según muchas recetas, formada por: cal (50-75%, fluorina (0-17%, bauxita (0-32% y escoria aluminosa (8-22%. Los datos han sido procesados en los programas de c

  4. Synthetic biology: an emerging engineering discipline.

    Science.gov (United States)

    Cheng, Allen A; Lu, Timothy K

    2012-01-01

    Over the past decade, synthetic biology has emerged as an engineering discipline for biological systems. Compared with other substrates, biology poses a unique set of engineering challenges resulting from an incomplete understanding of natural biological systems and tools for manipulating them. To address these challenges, synthetic biology is advancing from developing proof-of-concept designs to focusing on core platforms for rational and high-throughput biological engineering. These platforms span the entire biological design cycle, including DNA construction, parts libraries, computational design tools, and interfaces for manipulating and probing synthetic circuits. The development of these enabling technologies requires an engineering mindset to be applied to biology, with an emphasis on generalizable techniques in addition to application-specific designs. This review aims to discuss the progress and challenges in synthetic biology and to illustrate areas where synthetic biology may impact biomedical engineering and human health.

  5. Mammalian synthetic biology: emerging medical applications.

    Science.gov (United States)

    Kis, Zoltán; Pereira, Hugo Sant'Ana; Homma, Takayuki; Pedrigi, Ryan M; Krams, Rob

    2015-05-06

    In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON-OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug discovery, drug delivery, receptor-activating gene circuits and mammalian biomanufacturing processes. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  6. Mass Spectrometric Analysis of Synthetic Organic Pigments.

    Science.gov (United States)

    Sugaya, Naeko; Takahashi, Mitsuko; Sakurai, Katsumi; Tanaka, Nobuko; Okubo, Ichiro; Kawakami, Tsuyoshi

    2018-04-18

    Though synthetic organic colorants are used in various applications nowadays, there is the concern that impurities by-produced during the manufacturing and degradation products in some of these colorants are persistent organic pollutants and carcinogens. Thus, it is important to identify the synthetic organic colorants in various products, such as commercial paints, ink, cosmetics, food, textile, and plastics. Dyes, which are soluble in water and other solvents, could be analyzed by chromatographic methods. In contrast, it is difficult to analyze synthetic organic pigments by these methods because of their insolubility. This review is an overview of mass spectrometric analysis of synthetic organic pigments by various ionization methods. We highlight a recent study of textile samples by atmospheric pressure solid analysis probe MS. Furthermore, the mass spectral features of synthetic organic pigments and their separation from other components such as paint media and plasticizers are discussed.

  7. Annotating novel genes by integrating synthetic lethals and genomic information

    Directory of Open Access Journals (Sweden)

    Faty Mahamadou

    2008-01-01

    Full Text Available Abstract Background Large scale screening for synthetic lethality serves as a common tool in yeast genetics to systematically search for genes that play a role in specific biological processes. Often the amounts of data resulting from a single large scale screen far exceed the capacities of experimental characterization of every identified target. Thus, there is need for computational tools that select promising candidate genes in order to reduce the number of follow-up experiments to a manageable size. Results We analyze synthetic lethality data for arp1 and jnm1, two spindle migration genes, in order to identify novel members in this process. To this end, we use an unsupervised statistical method that integrates additional information from biological data sources, such as gene expression, phenotypic profiling, RNA degradation and sequence similarity. Different from existing methods that require large amounts of synthetic lethal data, our method merely relies on synthetic lethality information from two single screens. Using a Multivariate Gaussian Mixture Model, we determine the best subset of features that assign the target genes to two groups. The approach identifies a small group of genes as candidates involved in spindle migration. Experimental testing confirms the majority of our candidates and we present she1 (YBL031W as a novel gene involved in spindle migration. We applied the statistical methodology also to TOR2 signaling as another example. Conclusion We demonstrate the general use of Multivariate Gaussian Mixture Modeling for selecting candidate genes for experimental characterization from synthetic lethality data sets. For the given example, integration of different data sources contributes to the identification of genetic interaction partners of arp1 and jnm1 that play a role in the same biological process.

  8. Strategy revealing phenotypic differences among synthetic oscillator designs.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2014-09-19

    Considerable progress has been made in identifying and characterizing the component parts of genetic oscillators, which play central roles in all organisms. Nonlinear interaction among components is sufficiently complex that mathematical models are required to elucidate their elusive integrated behavior. Although natural and synthetic oscillators exhibit common architectures, there are numerous differences that are poorly understood. Utilizing synthetic biology to uncover basic principles of simpler circuits is a way to advance understanding of natural circadian clocks and rhythms. Following this strategy, we address the following questions: What are the implications of different architectures and molecular modes of transcriptional control for the phenotypic repertoire of genetic oscillators? Are there designs that are more realizable or robust? We compare synthetic oscillators involving one of three architectures and various combinations of the two modes of transcriptional control using a methodology that provides three innovations: a rigorous definition of phenotype, a procedure for deconstructing complex systems into qualitatively distinct phenotypes, and a graphical representation for illuminating the relationship between genotype, environment, and the qualitatively distinct phenotypes of a system. These methods provide a global perspective on the behavioral repertoire, facilitate comparisons of alternatives, and assist the rational design of synthetic gene circuitry. In particular, the results of their application here reveal distinctive phenotypes for several designs that have been studied experimentally as well as a best design among the alternatives that has yet to be constructed and tested.

  9. Science with Synthetic Stellar Surveys

    Science.gov (United States)

    Sanderson, Robyn Ellyn

    2018-04-01

    A new generation of observational projects is poised to revolutionize our understanding of the resolved stellar populations of Milky-Way-like galaxies at an unprecedented level of detail, ushering in an era of precision studies of galaxy formation. In the Milky Way itself, astrometric, spectroscopic and photometric surveys will measure three-dimensional positions and velocities and numerous chemical abundances for stars from the disk to the halo, as well as for many satellite dwarf galaxies. In the Local Group and beyond, HST, JWST and eventually WFIRST will deliver pristine views of resolved stars. The groundbreaking scale and dimensionality of this new view of resolved stellar populations in galaxies challenge us to develop new theoretical tools to robustly compare these surveys to simulated galaxies, in order to take full advantage of our new ability to make detailed predictions for stellar populations within a cosmological context. I will describe a framework for generating realistic synthetic star catalogs and mock surveys from state-of-the-art cosmological-hydrodynamical simulations, and present several early scientific results from, and predictions for, resolved stellar surveys of our Galaxy and its neighbors.

  10. Synthetic mimics of antimicrobial peptides.

    Science.gov (United States)

    Som, Abhigyan; Vemparala, Satyavani; Ivanov, Ivaylo; Tew, Gregory N

    2008-01-01

    Infectious diseases and antibiotic resistance are now considered the most imperative global healthcare problem. In the search for new treatments, host defense, or antimicrobial, peptides have attracted considerable attention due to their various unique properties; however, attempts to develop in vivo therapies have been severely limited. Efforts to develop synthetic mimics of antimicrobial peptides (SMAMPs) have increased significantly in the last decade, and this review will focus primarily on the structural evolution of SMAMPs and their membrane activity. This review will attempt to make a bridge between the design of SMAMPs and the fundamentals of SMAMP-membrane interactions. In discussions regarding the membrane interaction of SMAMPs, close attention will be paid to the lipid composition of the bilayer. Despite many years of study, the exact conformational aspects responsible for the high selectivity of these AMPs and SMAMPs toward bacterial cells over mammalian cells are still not fully understood. The ability to design SMAMPs that are potently antimicrobial, yet nontoxic to mammalian cells has been demonstrated with a variety of molecular scaffolds. Initial animal studies show very good tissue distribution along with more than a 4-log reduction in bacterial counts. The results on SMAMPs are not only extremely promising for novel antibiotics, but also provide an optimistic picture for the greater challenge of general proteomimetics.

  11. Synthetic sustained gene delivery systems.

    Science.gov (United States)

    Agarwal, Ankit; Mallapragada, Surya K

    2008-01-01

    Gene therapy today is hampered by the need of a safe and efficient gene delivery system that can provide a sustained therapeutic effect without cytotoxicity or unwanted immune responses. Bolus gene delivery in solution results in the loss of delivered factors via lymphatic system and may cause undesired effects by the escape of bioactive molecules to distant sites. Controlled gene delivery systems, acting as localized depot of genes, provide an extended sustained release of genes, giving prolonged maintenance of the therapeutic level of encoded proteins. They also limit the DNA degradation in the nuclease rich extra-cellular environment. While attempts have been made to adapt existing controlled drug delivery technologies, more novel approaches are being investigated for controlled gene delivery. DNA encapsulated in nano/micro spheres of polymers have been administered systemically/orally to be taken up by the targeted tissues and provide sustained release once internalized. Alternatively, DNA entrapped in hydrogels or scaffolds have been injected/implanted in tissues/cavities as platforms for gene delivery. The present review examines these different modalities for sustained delivery of viral and non-viral gene-delivery vectors. Design parameters and release mechanisms of different systems made with synthetic or natural polymers are presented along with their prospective applications and opportunities for continuous development.

  12. Online professionalism: A synthetic review.

    Science.gov (United States)

    Chretien, Katherine C; Tuck, Matthew G

    2015-04-01

    The rise of social media has increased connectivity and blurred personal and professional boundaries, bringing new challenges for medical professionalism. Whether traditional professionalism principles apply to the online social media space remains unknown. The purpose of this synthetic literature review was to characterize the original peer-reviewed research studies published between 1 January 2000-1 November 2014 on online professionalism, to assess methodologies and approaches used, and to provide insights to guide future studies in this area. The investigators searched three databases and performed manual searches of bibliographies to identify the 32 studies included. Most studies originated in the USA. Cross-sectional surveys and analyses of publicly available online content were the most common methodologies employed. Studies covered the general areas of use and privacy, assessment of unprofessional online behaviours, consensus-gathering of what constitutes unprofessional or inappropriate online behaviours, and education and policies. Studies were of variable quality; only around half of survey studies had response rates of 50% or greater. Medical trainees were the most common population studied. Future directions for research include public perspectives of online professionalism, impact on patient trust, and how to use social media productively as medical professionals.

  13. Industrial systems biology and its impact on synthetic biology of yeast cell factories.

    Science.gov (United States)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-06-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  14. Angular dependence of spin transfer torque on magnetic tunnel junctions with synthetic ferrimagnetic free layer

    International Nuclear Information System (INIS)

    Ichimura, M; Hamada, T; Imamura, H; Takahashi, S; Maekawa, S

    2010-01-01

    Based on a spin-polarized free-electron model, spin and charge transports are analyzed in magnetic tunnel junctions with synthetic ferrimagnetic layers in the ballistic regime, and the spin transfer torque is derived. We characterize the synthetic ferrimagnetic free layer by extending an arbitrary direction of magnetizations of the two free layers forming the synthetic ferrimagnetic free layer. The synthetic ferrimagnetic configuration exerts the approximately optimum torque for small magnetization angle of the first layer relative to that of the pinned layer. For approximately anti-parallel magnetization of the first layer to that of the pinned layer, the parallel magnetization of two magnetic layers is favorable for magnetization reversal rather than the synthetic ferrimagnetic configuration.

  15. Industrial systems biology and its impact on synthetic biology of yeast cell factories

    DEFF Research Database (Denmark)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-01-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

  16. Synthetic circuit designs for earth terraformation.

    Science.gov (United States)

    Solé, Ricard V; Montañez, Raúl; Duran-Nebreda, Salva

    2015-07-18

    Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of counterbalancing these effects involve geoengineering, sustainable practices and carbon sequestration, among others. None of these scenarios seems powerful enough to achieve the desired restoration of safe boundaries. We hypothesize that synthetic organisms with the appropriate engineering design could be used to safely prevent declines in some stressed ecosystems and help improving carbon sequestration. Such schemes would include engineering mutualistic dependencies preventing undesired evolutionary processes. We hypothesize that some particular design principles introduce unescapable constraints to the engineered organisms that act as effective firewalls. Testing this designed organisms can be achieved by using controlled bioreactor models, with single and heterogeneous populations, and accurate computational models including different scales (from genetic constructs and metabolic pathways to population dynamics). Our hypothesis heads towards a future anthropogenic action that should effectively act as Terraforming processes. It also implies a major challenge in the existing biosafety policies, since we suggest release of modified organisms as potentially necessary strategy for success.

  17. Synthetic Biology: Mapping the Scientific Landscape

    Science.gov (United States)

    Oldham, Paul; Hall, Stephen; Burton, Geoff

    2012-01-01

    This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved. Debates under the Convention are likely to focus on a possible moratorium on the field release of synthetic organisms, cells or genomes. Based on the empirical evidence we propose that guidance could be provided to funding agencies to respect the letter and spirit of the Convention on Biological Diversity in making research investments. Building on the recommendations of the United States Presidential Commission for the Study of Bioethical Issues we demonstrate that it is possible to promote independent and transparent monitoring of developments in synthetic biology using modern information tools. In particular, public and policy understanding and engagement with synthetic biology can be enhanced through the use of online interactive tools. As a step forward in this process we make existing data on the scientific literature on synthetic biology available in an online interactive workbook so that researchers, policy makers and civil society can explore the data and draw conclusions for themselves. PMID:22539946

  18. The Role of Synthetic Reconstruction Tests in Seismic Tomography

    Science.gov (United States)

    Rawlinson, N.; Spakman, W.

    2015-12-01

    Synthetic reconstruction tests are widely used in seismic tomography as a means for assessing the robustness of solutions produced by linear or iterative non-linear inversion schemes. The most common test is the so-called checkerboard resolution test, which uses an alternating pattern of high and low wavespeeds (or some other seismic property such as attenuation). However, checkerboard tests have a number of limitations, including that they (1) only provide indirect evidence of quantitative measures of reliability such as resolution and uncertainty; (2) give a potentially misleading impression of the range of scale-lengths that can be resolved; (3) don't give a true picture of the structural distortion or smearing caused by the data coverage; and (4) result in an inverse problem that is biased towards an accurate reconstruction. The widespread use of synthetic reconstruction tests in seismic tomography is likely to continue for some time yet, so it is important to implement best practice where possible. The goal here is to provide a general set of guidelines, derived from the underlying theory and illustrated by a series of numerical experiments, on their implementation in seismic tomography. In particular, we recommend (1) using a sparse distribution of spikes, rather than the more conventional tightly-spaced checkerboard; (2) using the identical data coverage (e.g. geometric rays) for the synthetic model that was computed for the observation-based model; (3) carrying out multiple tests using anomalies of different scale length; (4) exercising caution when analysing synthetic recovery tests that use anomaly patterns that closely mimic the observation-based model; (5) investigating the trade-off between data noise levels and the minimum wavelength of recovered structure; (6) where possible, test the extent to which preconditioning (e.g. identical parameterization for input and output models) influences the recovery of anomalies.

  19. Specifications of Standards in Systems and Synthetic Biology.

    Science.gov (United States)

    Schreiber, Falk; Bader, Gary D; Golebiewski, Martin; Hucka, Michael; Kormeier, Benjamin; Le Novère, Nicolas; Myers, Chris; Nickerson, David; Sommer, Björn; Waltemath, Dagmar; Weise, Stephan

    2015-09-04

    Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation). Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/. So far the different standards were published and made accessible through the standards’ web- pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated specifications.

  20. Evaluation of synthetic linear motor-molecule actuation energetics

    OpenAIRE

    Brough, Branden; Northrop, Brian H.; Schmidt, Jacob J.; Tseng, Hsian-Rong; Houk, Kendall N.; Stoddart, J. Fraser; Ho, Chih-Ming

    2006-01-01

    By applying atomic force microscope (AFM)-based force spectroscopy together with computational modeling in the form of molecular force-field simulations, we have determined quantitatively the actuation energetics of a synthetic motor-molecule. This multidisciplinary approach was performed on specifically designed, bistable, redox-controllable [2]rotaxanes to probe the steric and electrostatic interactions that dictate their mechanical switching at the single-molecule level. The fusion of expe...

  1. The Core Mass Growth and Stellar Lifetime of Thermally Pulsing Asymptotic Giant Branch Stars

    Science.gov (United States)

    Kalirai, Jason S.; Marigo, Paola; Tremblay, Pier-Emmanuel

    2014-02-01

    We establish new constraints on the intermediate-mass range of the initial-final mass relation, and apply the results to study the evolution of stars on the thermally pulsing asymptotic giant branch (TP-AGB). These constraints derive from newly discovered (bright) white dwarfs in the nearby Hyades and Praesepe star clusters, including a total of 18 high signal-to-noise ratio measurements with progenitor masses of M initial = 2.8-3.8 M ⊙. We also include a new analysis of existing white dwarfs in the older NGC 6819 and NGC 7789 star clusters, M initial = 1.6 and 2.0 M ⊙. Over this range of initial masses, stellar evolutionary models for metallicity Z initial = 0.02 predict the maximum growth of the core of TP-AGB stars. By comparing the newly measured remnant masses to the robust prediction of the core mass at the first thermal pulse on the AGB (i.e., from stellar interior models), we establish several findings. First, we show that the stellar core mass on the AGB grows rapidly from 10% to 30% for stars with M initial = 1.6 to 2.0 M ⊙. At larger masses, the core-mass growth decreases steadily to ~10% at M initial = 3.4 M ⊙, after which there is a small hint of a upturn out to M initial = 3.8 M ⊙. These observations are in excellent agreement with predictions from the latest TP-AGB evolutionary models in Marigo et al. We also compare to models with varying efficiencies of the third dredge-up and mass loss, and demonstrate that the process governing the growth of the core is largely the stellar wind, while the third dredge-up plays a secondary, but non-negligible role. Based on the new white dwarf measurements, we perform an exploratory calibration of the most popular mass-loss prescriptions in the literature, as well as of the third dredge-up efficiency as a function of the stellar mass. Finally, we estimate the lifetime and the integrated luminosity of stars on the TP-AGB to peak at t ~ 3 Myr and E = 1.2 × 1010 L ⊙ yr for M initial ~ 2 M ⊙ (t ~ 2 Myr

  2. The core mass growth and stellar lifetime of thermally pulsing asymptotic giant branch stars

    International Nuclear Information System (INIS)

    Kalirai, Jason S.; Tremblay, Pier-Emmanuel; Marigo, Paola

    2014-01-01

    We establish new constraints on the intermediate-mass range of the initial-final mass relation, and apply the results to study the evolution of stars on the thermally pulsing asymptotic giant branch (TP-AGB). These constraints derive from newly discovered (bright) white dwarfs in the nearby Hyades and Praesepe star clusters, including a total of 18 high signal-to-noise ratio measurements with progenitor masses of M initial = 2.8-3.8 M ☉ . We also include a new analysis of existing white dwarfs in the older NGC 6819 and NGC 7789 star clusters, M initial = 1.6 and 2.0 M ☉ . Over this range of initial masses, stellar evolutionary models for metallicity Z initial = 0.02 predict the maximum growth of the core of TP-AGB stars. By comparing the newly measured remnant masses to the robust prediction of the core mass at the first thermal pulse on the AGB (i.e., from stellar interior models), we establish several findings. First, we show that the stellar core mass on the AGB grows rapidly from 10% to 30% for stars with M initial = 1.6 to 2.0 M ☉ . At larger masses, the core-mass growth decreases steadily to ∼10% at M initial = 3.4 M ☉ , after which there is a small hint of a upturn out to M initial = 3.8 M ☉ . These observations are in excellent agreement with predictions from the latest TP-AGB evolutionary models in Marigo et al. We also compare to models with varying efficiencies of the third dredge-up and mass loss, and demonstrate that the process governing the growth of the core is largely the stellar wind, while the third dredge-up plays a secondary, but non-negligible role. Based on the new white dwarf measurements, we perform an exploratory calibration of the most popular mass-loss prescriptions in the literature, as well as of the third dredge-up efficiency as a function of the stellar mass. Finally, we estimate the lifetime and the integrated luminosity of stars on the TP-AGB to peak at t ∼ 3 Myr and E = 1.2 × 10 10 L ☉ yr for M initial ∼ 2 M

  3. The core mass growth and stellar lifetime of thermally pulsing asymptotic giant branch stars

    Energy Technology Data Exchange (ETDEWEB)

    Kalirai, Jason S.; Tremblay, Pier-Emmanuel [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Marigo, Paola, E-mail: jkalirai@stsci.edu, E-mail: paola.marigo@unipd.it, E-mail: ptremblay@lsw.uni-heidelberg.de [Department of Physics and Astronomy, University of Padova, Vicolo dell' Osservatorio 3, I-35122 Padova (Italy)

    2014-02-10

    We establish new constraints on the intermediate-mass range of the initial-final mass relation, and apply the results to study the evolution of stars on the thermally pulsing asymptotic giant branch (TP-AGB). These constraints derive from newly discovered (bright) white dwarfs in the nearby Hyades and Praesepe star clusters, including a total of 18 high signal-to-noise ratio measurements with progenitor masses of M {sub initial} = 2.8-3.8 M {sub ☉}. We also include a new analysis of existing white dwarfs in the older NGC 6819 and NGC 7789 star clusters, M {sub initial} = 1.6 and 2.0 M {sub ☉}. Over this range of initial masses, stellar evolutionary models for metallicity Z {sub initial} = 0.02 predict the maximum growth of the core of TP-AGB stars. By comparing the newly measured remnant masses to the robust prediction of the core mass at the first thermal pulse on the AGB (i.e., from stellar interior models), we establish several findings. First, we show that the stellar core mass on the AGB grows rapidly from 10% to 30% for stars with M {sub initial} = 1.6 to 2.0 M {sub ☉}. At larger masses, the core-mass growth decreases steadily to ∼10% at M {sub initial} = 3.4 M {sub ☉}, after which there is a small hint of a upturn out to M {sub initial} = 3.8 M {sub ☉}. These observations are in excellent agreement with predictions from the latest TP-AGB evolutionary models in Marigo et al. We also compare to models with varying efficiencies of the third dredge-up and mass loss, and demonstrate that the process governing the growth of the core is largely the stellar wind, while the third dredge-up plays a secondary, but non-negligible role. Based on the new white dwarf measurements, we perform an exploratory calibration of the most popular mass-loss prescriptions in the literature, as well as of the third dredge-up efficiency as a function of the stellar mass. Finally, we estimate the lifetime and the integrated luminosity of stars on the TP-AGB to peak at t

  4. Synthetic Biology: game changer in intelectual property

    Directory of Open Access Journals (Sweden)

    Laurens Landeweerd

    2016-12-01

    Full Text Available Synthetic biology can be considered a game changer that plays an important role in the current NBIC, or BINC convergence of nano-, bio-, info and cognitive sciences. Although most synthetic biology experts are unaware of it, the field appeals to the imagination in its adherence to targets that were usually associated with premodern alchemist science. This paper elaborates several aspects of synthetic biology as well as its consequences for long held notions of intellectual property and the ontological categories of scientific discovery on the one hand and engineering on the other, the distinction between natural and artificial, the grown and the made.

  5. Defining the Synthetic Biology Supply Chain

    Energy Technology Data Exchange (ETDEWEB)

    Frazar, Sarah L.; Hund, Gretchen E.; Bonheyo, George T.; Diggans, James; Bartholomew, Rachel A.; Gehrig, Lindsey; Greaves, Mark

    2017-08-01

    In this article, a team of experts in synthetic biology, data analytics, and national security describe the overall supply chain surrounding synthetic biology. The team analyzes selected interactions within that network to better understand the risks raised by synthetic biology and identifies opportunities for risk mitigation. To introduce the concept, the article will briefly describe how an understanding of supply chains has been important in promoting nuclear nonproliferation objectives. The article concludes by assessing the structure and networks identified in the supply chains to reveal potential opportunities for future biodefense research and development; options for additional information exchange; and means to interdict, detect, or deter suspicious activity.

  6. [Smart therapeutics based on synthetic gene circuits].

    Science.gov (United States)

    Peng, Shuguang; Xie, Zhen

    2017-03-25

    Synthetic biology has an important impact on biology research since its birth. Applying the thought and methods that reference from electrical engineering, synthetic biology uncovers many regulatory mechanisms of life systems, transforms and expands a series of biological components. Therefore, it brings a wide range of biomedical applications, including providing new ideas for disease diagnosis and treatment. This review describes the latest advances in the field of disease diagnosis and therapy based on mammalian cell or bacterial synthetic gene circuits, and provides new ideas for future smart therapy design.

  7. Establishment and application of fuzzy synthetic evaluating model for choice of cooperation partnership%合作伙伴选择模糊综合评价模型的建立与应用

    Institute of Scientific and Technical Information of China (English)

    徐金河; 陈智强

    2017-01-01

    At present , to obtain sustainable development , application-oriented universities need to adhere to the "combination of work and study and school -enterprise cooperation"n and find satisfactory enterprise co-operation partnership to achieve mutual benefit for both sides , thus stabilizing the school -enterprise cooperation for a long time.Drawing on the supply chain management thoughts , this paper constructs the cooperative rela-tionship between schools and enterprises in the talent training supply chain of application -oriented universities to make sure the relationship between the school and the enterprise will be sincerely cooperative , benefit sharing and co-governing .In order to scientifically select the enterprise partners in application -oriented universities talent training supply chain , this article uses four first -class indicators-corporate credibility , business input , school-enterprise compatibility and school -enterprise matching degree , which are highly valued by scholars domestically and abroad , 12 secondary indicators such as enterprise operation situation and Theil unbalanced in -dex and fuzzy synthetic evaluating model to select satisfactory enterprise cooperation partners .Finally, the article proposes that only through the trust mechanism , power mechanism , and the monitoring and evaluation mechanism can a long and stable school -enterprise partnership in the talent training supply chain of application -oriented university be established .%当前应用型大学要获得可持续发展,就需要坚持"工学结合、校企合作",寻找满意的企业合作伙伴,双方达到互利互惠,校企合作关系才能长久稳定.本文借鉴供应链管理思想来构建应用型大学人才培养供应链中校企合作关系,目的是把校企关系打造成精诚合作、利益共享与共同治理关系;为了科学地选择应用型大学人才培养供应链中企业合作伙伴,文章通过深受国内外学

  8. A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials

    Directory of Open Access Journals (Sweden)

    Rosalind A. Le Feuvre

    2018-06-01

    Full Text Available Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials, where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal. Keywords: Synthetic biology, Materials, Biological materials, Biomaterials, Advanced materials

  9. [Progress in synthetic biology of "973 Funding Program" in China].

    Science.gov (United States)

    Chen, Guoqiang; Wang, Ying

    2015-06-01

    This paper reviews progresses made in China from 2011 in areas of "Synthetic Biology" supported by State Basic Research 973 Program. Till the end of 2014, 9 "synthetic biology" projects have been initiated with emphasis on "microbial manufactures" with the 973 Funding Program. Combined with the very recent launch of one project on "mammalian cell synthetic biology" and another on "plant synthetic biology", Chinese "synthetic biology" research reflects its focus on "manufactures" while not giving up efforts on "synthetic biology" of complex systems.

  10. Solution dynamics of synthetic and natural polyelectrolytes

    Science.gov (United States)

    Krause, Wendy E.

    Polyelectrolytes are abundant in nature and essential to life, and used extensively in industry. This work discussed two polyelectrolytes: sodium poly(2-acrylamido-2-methylpropanesulfonate) (NaPAMS), synthetic polyelectrolyte, and sodium hyaluronate (NaHA), a glycosaminoglycan. Rheological data of NaPAMS solutions of variable chain length and concentration were reported. A strong dependence of viscosity eta on chain length: eta ˜ M2.4 was found. The comparison of the rheological data with two proposed scaling theories (Dobrynin 1995, Witten 1987) forces the conclusion that neither theory is correct. A possible interpretation of the viscosity data falling between the predictions of the two scaling theories is that some chain rigidity may persist beyond the correlation length. A sample model for the conductivity of semidilute polyelectrolytes with no added salt was presented. The model correctly describes the logarithmic decrease of specific conductance observed for many polyelectrolytes at low concentration (below ca. 10-2M), and is in good agreement with data from NaPAMS solutions. NaHA in phosphate buffered saline behaves as a typical polyelectrolyte in the high-salt limit, as Newtonian viscosities are observed over a wide range of shear rates. There is no evidence of intermolecular hydrogen bonding causing gel formation in NaHA solutions without protein present. The viscosity of 3 mg/mL NaHA was measured in the presence of the selected anti-inflammatory agents. Of the seven additives investigated only (D)-penicillamine significantly altered the rheology of HA. (D)-Penicillamine dramatically reduced the viscosity of HA, probably by disrupting intramolecular hydrogen bonding. The plasma proteins albumin and gamma-globulins bind to HA in solution to form a weak reversible gel. The rheology and osmotic pressure of the simple model for synovial fluid, consisting of 3mg/mL NaHA, 11 mg/mL albumin, and 7 mg/mL gamma-globulins in phosphate buffered saline, were studied

  11. Dataset reporting the perceiver identification rates of basic emotions expressed by male, female and ambiguous gendered walkers in full-light, point-light and synthetically modelled point-light walkers.

    Science.gov (United States)

    Halovic, Shaun; Kroos, Christian

    2017-12-01

    This data set describes the experimental data collected and reported in the research article "Walking my way? Walker gender and display format confounds the perception of specific emotions" (Halovic and Kroos, in press) [1]. The data set represent perceiver identification rates for different emotions (happiness, sadness, anger, fear and neutral), as displayed by full-light, point-light and synthetic point-light walkers. The perceiver identification scores have been transformed into H t rates, which represent proportions/percentages of correct identifications above what would be expected by chance. This data set also provides H t rates separately for male, female and ambiguously gendered walkers.

  12. CRISPR and the Rebirth of Synthetic Biology

    NARCIS (Netherlands)

    Heidari, Raheleh; Shaw, David Martin; Elger, Bernice Simone

    Emergence of novel genome engineering technologies such as clustered regularly interspaced short palindromic repeat (CRISPR) has refocused attention on unresolved ethical complications of synthetic biology. Biosecurity concerns, deontological issues and human right aspects of genome editing have

  13. Thermodynamic Analysis of Ionic Compounds: Synthetic Applications.

    Science.gov (United States)

    Yoder, Claude H.

    1986-01-01

    Shows how thermodynamic cycles can be used to understand trends in heats of formation and aqueous solubilities and, most importantly, how they may be used to choose synthetic routes to new ionic compounds. (JN)

  14. Synthetic biology platform technologies for antimicrobial applications.

    Science.gov (United States)

    Braff, Dana; Shis, David; Collins, James J

    2016-10-01

    The growing prevalence of antibiotic resistance calls for new approaches in the development of antimicrobial therapeutics. Likewise, improved diagnostic measures are essential in guiding the application of targeted therapies and preventing the evolution of therapeutic resistance. Discovery platforms are also needed to form new treatment strategies and identify novel antimicrobial agents. By applying engineering principles to molecular biology, synthetic biologists have developed platforms that improve upon, supplement, and will perhaps supplant traditional broad-spectrum antibiotics. Efforts in engineering bacteriophages and synthetic probiotics demonstrate targeted antimicrobial approaches that can be fine-tuned using synthetic biology-derived principles. Further, the development of paper-based, cell-free expression systems holds promise in promoting the clinical translation of molecular biology tools for diagnostic purposes. In this review, we highlight emerging synthetic biology platform technologies that are geared toward the generation of new antimicrobial therapies, diagnostics, and discovery channels. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Defining the Synthetic Biology Supply Chain.

    Science.gov (United States)

    Frazar, Sarah L; Hund, Gretchen E; Bonheyo, George T; Diggans, James; Bartholomew, Rachel A; Gehrig, Lindsey; Greaves, Mark

    Several recent articles have described risks posed by synthetic biology and spurred vigorous discussion in the scientific, commercial, and government communities about how to best detect, prevent, regulate, and respond to these risks. The Pacific Northwest National Laboratory's (PNNL) deep experience working with dual-use technologies for the nuclear industry has shown that analysis of supply chains can reveal security vulnerabilities and ways to mitigate security risk without hindering beneficial research and commerce. In this article, a team of experts in synthetic biology, data analytics, and national security describe the overall supply chain surrounding synthetic biology to illustrate new insights about the effectiveness of current regulations, the possible need for different screening approaches, and new technical solutions that could help identify or mitigate risks in the synthetic biology supply chain.

  16. Long synthetic nanotubes from calix[4]arenes.

    Science.gov (United States)

    Organo, Voltaire G; Sgarlata, Valentina; Firouzbakht, Farhood; Rudkevich, Dmitry M

    2007-01-01

    We report the synthesis and encapsulation properties of long (up to 5 nm) molecular nanotubes 1-4, which are based on calix[4]arenes and can be filled with multiple nitrosonium (NO(+)) ions upon reaction with NO(2)/N(2)O(4) gases. These are among the largest nanoscale molecular containers prepared to date and can entrap up to five guests. The structure and properties of tubular complexes 1(NO(+))(2)-4(NO(+))(5) were studied by UV/Vis, FTIR, and (1)H NMR spectroscopy in solution, and also by molecular modeling. Entrapment of NO(+) in 1(NO(+))(2)-4(NO(+))(5) is reversible, and addition of [18]crown-6 quickly recovers starting tubes 1-4. The FTIR and titration data revealed enhanced binding of NO(+) in longer tubes, which may be due to cooperativity. The described nanotubes may serve as materials for storing and converting NO(x) and also offer a promise to further develop supramolecular chemistry of molecular containers. These findings also open wider perspectives towards applications of synthetic nanotubes as alternatives to carbon nanotubes.

  17. Electrolytic conductivity of synthetic organomineral complexes

    Directory of Open Access Journals (Sweden)

    Ksiezopolska Alicja

    2005-01-01

    Full Text Available The mechanism of the formation of organomineral complexes in soils is very complex and still little known. Examination of the complexes in unaltered form, as isolated from the soil, is very difficult due to the dispersing effect of all extraction agents which break the complexes up, destroying their natural properties. It is much easier to perform most of the tests on preparations of organomineral complexes obtained under laboratory conditions. This paper is concerned with model research on the formation of synthetic complexes of humic acids with minerals: Na-montmorillonite, mica, kaolinite at various pH values (3-7 and in the presence of aluminum ions. The aim of the research was to develop an optimum reaction of suspension for the synthesis of organomineral complexes, to study the role of aluminum ions, and to attempt to determine the degree of their complexity on the basis of the electrolytic conductivity (EC. An important influence of the suspension pH value on the value of EC was observed. The greatest correlation was found in the organomineral preparations with kaolinite and with aluminum (r = 0.93***. Generally, it can be stated that the degree of reaction of humic acids with minerals depended most of all on the type of mineral, on the pH value, and on the presence of aluminum.

  18. Synthetic Sling Failure - Evaluations and Recommendations

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, C. S. [Washington River Protection Solutions, Richland, WA (United States); Mackey, Thomas C. [Washington River Protection Solutions, Richland, WA (United States)

    2009-10-26

    The information and evaluations provided in this report were compiled to address the recurring problem of synthetic sling failure. As safety is the number one priority in all work aspects, a solution must be devised to prevent accidents from occurring. A total of thirteen cases regarding synthetic sling failure were evaluated in order to determine their causes, effects, and preventative measures. From the collected data, it was found that all cases in which the synthetic sling contacted the edge of its load resulted in sling failure. It is required that adequate synthetic sling protection devices be used to protect slings in any lift where the sling comes in direct contact with the edge or corner of its load. However, there are no consensus codes or standards stating the type, material, or purpose of the type of protective device used to protect the sling from being cut. Numerous industry standards and codes provide vague descriptions on how to protect synthetic slings. Without a clear, concise statement of how to protect synthetic slings, it is common for inadequate materials and sling protection devices to be used in an attempt to meet the intent of these requirements. The use of an inadequate sling protection device is the main cause of synthetic sling failure in all researched cases. Commercial sling protection devices come in many shapes and sizes, and have a variety of names, as well as advertised uses. 'Abrasion pads' and 'wear protectors' are two different names for products with the same intended purpose. There is no distinguishable way to determine the extent of sling protection which these devices will provide, or what specific scenarios they are made for. This creates room for error in a field where error is unacceptable. This report provides a recommended action for hoisting and rigging activities which require synthetic slings to contact a load, as well as recommended changes to industry standards which will benefit overall

  19. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

    Science.gov (United States)

    Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

    2014-06-01

    The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

  20. Synthetic Biology and the Translational Imperative.

    Science.gov (United States)

    Heidari Feidt, Raheleh; Ienca, Marcello; Elger, Bernice Simone; Folcher, Marc

    2017-12-18

    Advances at the interface between the biological sciences and engineering are giving rise to emerging research fields such as synthetic biology. Harnessing the potential of synthetic biology requires timely and adequate translation into clinical practice. However, the translational research enterprise is currently facing fundamental obstacles that slow down the transition of scientific discoveries from the laboratory to the patient bedside. These obstacles including scarce financial resources and deficiency of organizational and logistic settings are widely discussed as primary impediments to translational research. In addition, a number of socio-ethical considerations inherent in translational research need to be addressed. As the translational capacity of synthetic biology is tightly linked to its social acceptance and ethical approval, ethical limitations may-together with financial and organizational problems-be co-determinants of suboptimal translation. Therefore, an early assessment of such limitations will contribute to proactively favor successful translation and prevent the promising potential of synthetic biology from remaining under-expressed. Through the discussion of two case-specific inventions in synthetic biology and their associated ethical implications, we illustrate the socio-ethical challenges ahead in the process of implementing synthetic biology into clinical practice. Since reducing the translational lag is essential for delivering the benefits of basic biomedical research to society at large and promoting global health, we advocate a moral obligation to accelerating translational research: the "translational imperative."

  1. Synthetic biology era: Improving antibiotic's world.

    Science.gov (United States)

    Guzmán-Trampe, Silvia; Ceapa, Corina D; Manzo-Ruiz, Monserrat; Sánchez, Sergio

    2017-06-15

    The emergence of antibiotic-resistant pathogen microorganisms is problematic in the context of the current spectrum of available medication. The poor specificity and the high toxicity of some available molecules have made imperative the search for new strategies to improve the specificity and to pursue the discovery of novel compounds with increased bioactivity. Using living cells as platforms, synthetic biology has counteracted this problem by offering novel pathways to create synthetic systems with improved and desired functions. Among many other biotechnological approaches, the advances in synthetic biology have made it possible to design and construct novel biological systems in order to look for new drugs with increased bioactivity. Advancements have also been made in the redesigning of RNA and DNA molecules in order to engineer antibiotic clusters for antibiotic overexpression. As for the production of these antibacterial compounds, yeasts and filamentous fungi as well as gene therapy are utilized to enhance protein solubility. Specific delivery is achieved by creating chimeras using plant genes into bacterial hosts. Some of these synthetic systems are currently in clinical trials, proving the proficiency of synthetic biology in terms of both pharmacological activities as well as an increase in the biosafety of treatments. It is possible that we may just be seeing the tip of the iceberg, and synthetic biology applications will overpass expectations beyond our present knowledge. Copyright © 2017. Published by Elsevier Inc.

  2. Synthetic cannabis and acute ischemic stroke.

    Science.gov (United States)

    Bernson-Leung, Miya E; Leung, Lester Y; Kumar, Sandeep

    2014-01-01

    An association between marijuana use and stroke has been previously reported. However, the health risks of newer synthetic cannabinoid compounds are less well known. We describe 2 cases that introduce a previously unreported association between synthetic cannabis use and ischemic stroke in young adults. A 22-year-old woman presented with dysarthria, left hemiplegia, and left hemianesthesia within hours of first use of synthetic cannabis. She was healthy and without identified stroke risk factors other than oral contraceptive use and a patent foramen ovale without venous thromboses. A 26-year-old woman presented with nonfluent aphasia, left facial droop, and left hemianesthesia approximately 12 hours after first use of synthetic cannabis. Her other stroke risk factors included migraine with aura, oral contraceptive use, smoking, and a family history of superficial thrombophlebitis. Both women were found to have acute, large-territory infarctions of the right middle cerebral artery. Our 2 cases had risk factors for ischemic stroke but were otherwise young and healthy and the onset of their deficits occurred within hours after first-time exposure to synthetic cannabis. Synthetic cannabis use is an important consideration in the investigation of stroke in young adults. Copyright © 2014 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  3. Intelligent Entity Behavior Within Synthetic Environments. Chapter 3

    Science.gov (United States)

    Kruk, R. V.; Howells, P. B.; Siksik, D. N.

    2007-01-01

    This paper describes some elements in the development of realistic performance and behavior in the synthetic entities (players) which support Modeling and Simulation (M&S) applications, particularly military training. Modern human-in-the-loop (virtual) training systems incorporate sophisticated synthetic environments, which provide: 1. The operational environment, including, for example, terrain databases; 2. Physical entity parameters which define performance in engineered systems, such as aircraft aerodynamics; 3. Platform/system characteristics such as acoustic, IR and radar signatures; 4. Behavioral entity parameters which define interactive performance, including knowledge/reasoning about terrain, tactics; and, 5. Doctrine, which combines knowledge and tactics into behavior rule sets. The resolution and fidelity of these model/database elements can vary substantially, but as synthetic environments are designed to be compose able, attributes may easily be added (e.g., adding a new radar to an aircraft) or enhanced (e.g. Amending or replacing missile seeker head/ Electronic Counter Measures (ECM) models to improve the realism of their interaction). To a human in the loop with synthetic entities, their observed veridicality is assessed via engagement responses (e.g. effect of countermeasures upon a closing missile), as seen on systems displays, and visual (image) behavior. The realism of visual models in a simulation (level of detail as well as motion fidelity) remains a challenge in realistic articulation of elements such as vehicle antennae and turrets, or, with human figures; posture, joint articulation, response to uneven ground. Currently the adequacy of visual representation is more dependant upon the quality and resolution of the physical models driving those entities than graphics processing power per Se. Synthetic entities in M&S applications traditionally have represented engineered systems (e.g. aircraft) with human-in-the-loop performance

  4. Suppression of atherosclerosis by synthetic REV-ERB agonist

    Energy Technology Data Exchange (ETDEWEB)

    Sitaula, Sadichha [Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458 (United States); Billon, Cyrielle [Department of Pharmacological & Physiological Science, Saint Louis University School of Medicine, St. Louis, MO 63104 (United States); Kamenecka, Theodore M.; Solt, Laura A. [Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458 (United States); Burris, Thomas P., E-mail: burristp@slu.edu [Department of Pharmacological & Physiological Science, Saint Louis University School of Medicine, St. Louis, MO 63104 (United States)

    2015-05-08

    The nuclear receptors for heme, REV-ERBα and REV-ERBβ, play important roles in the regulation of metabolism and inflammation. Recently it was demonstrated that reduced REV-ERBα expression in hematopoetic cells in LDL receptor null mice led to increased atherosclerosis. We sought to determine if synthetic REV-ERB agonists that we have developed might have the ability to suppress atherosclerosis in this model. A previously characterized synthetic REV-ERB agonist, SR9009, was used to determine if activation of REV-ERB activity would affect atherosclerosis in LDL receptor deficient mice. Atherosclerotic plaque size was significantly reduced (p < 0.05) in mice administered SR9009 (100 mg/kg) for seven weeks compared to control mice (n = 10 per group). SR9009 treatment of bone marrow-derived mouse macrophages (BMDM) reduced the polarization of BMDMs to proinflammatory M1 macrophage while increasing the polarization of BMDMs to anti-inflammatory M2 macrophages. Our results suggest that pharmacological targeting of REV-ERBs may be a viable therapeutic option for treatment of atherosclerosis. - Highlights: • Synthetic REV-ERB agonist treatment reduced atherosclerosis in a mouse model. • Pharmacological activation of REV-ERB decreased M1 macrophage polarization. • Pharmacological activation of REV-ERB increased M2 macrophage polarization.

  5. A standard-enabled workflow for synthetic biology.

    Science.gov (United States)

    Myers, Chris J; Beal, Jacob; Gorochowski, Thomas E; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

    2017-06-15

    A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  6. Micro-Raman spectroscopy of natural and synthetic indigo samples.

    Science.gov (United States)

    Vandenabeele, Peter; Moens, Luc

    2003-02-01

    In this work indigo samples from three different sources are studied by using Raman spectroscopy: the synthetic pigment and pigments from the woad (Isatis tinctoria) and the indigo plant (Indigofera tinctoria). 21 samples were obtained from 8 suppliers; for each sample 5 Raman spectra were recorded and used for further chemometrical analysis. Principal components analysis (PCA) was performed as data reduction method before applying hierarchical cluster analysis. Linear discriminant analysis (LDA) was implemented as a non-hierarchical supervised pattern recognition method to build a classification model. In order to avoid broad-shaped interferences from the fluorescence background, the influence of 1st and 2nd derivatives on the classification was studied by using cross-validation. Although chemically identical, it is shown that Raman spectroscopy in combination with suitable chemometric methods has the potential to discriminate between synthetic and natural indigo samples.

  7. Plant synthetic biology for molecular engineering of signalling and development.

    Science.gov (United States)

    Nemhauser, Jennifer L; Torii, Keiko U

    2016-03-02

    Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions.

  8. Survey of Approaches to Generate Realistic Synthetic Graphs

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Seung-Hwan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Sangkeun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Powers, Sarah S [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Shankar, Mallikarjun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Imam, Neena [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-10-01

    A graph is a flexible data structure that can represent relationships between entities. As with other data analysis tasks, the use of realistic graphs is critical to obtaining valid research results. Unfortunately, using the actual ("real-world") graphs for research and new algorithm development is difficult due to the presence of sensitive information in the data or due to the scale of data. This results in practitioners developing algorithms and systems that employ synthetic graphs instead of real-world graphs. Generating realistic synthetic graphs that provide reliable statistical confidence to algorithmic analysis and system evaluation involves addressing technical hurdles in a broad set of areas. This report surveys the state of the art in approaches to generate realistic graphs that are derived from fitted graph models on real-world graphs.

  9. A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials.

    Science.gov (United States)

    Le Feuvre, Rosalind A; Scrutton, Nigel S

    2018-06-01

    Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials , where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal.

  10. Studies on the specificity of immunological reactions of synthetic and natural Thomsen-Friedenreich antigens

    International Nuclear Information System (INIS)

    Hoeppner, W.

    1982-01-01

    A number of derivatives of disaccharide β-D-Gal-(1,3)-D-GalNAc, the carbohydrate component of T-antigen, and four different synthetic antigens having this disaccharide structure have been investigated. The immunological reactions with native human antibodies and rabbit immune antibodies have been studied in the haemagglutination inhibition test and in RIA. The findings are relevant to the use of synthetic carbohydrate antigens as model substances for immunological studies. (orig./MG) [de

  11. Synthetic bedding and wheeze in childhood.

    Science.gov (United States)

    Ponsonby, Anne-Louise; Dwyer, Terence; Kemp, Andrew; Cochrane, Jennifer; Couper, David; Carmichael, Allan

    2003-01-01

    The reasons for the increase in childhood asthma over time are unclear. The indoor environment is of particular concern. An adverse role for synthetic bedding on asthma development in childhood has been suggested by cross-sectional studies that have found an association between synthetic pillow use and childhood wheeze. Prospective data on infant bedding have not been available. Bedding data at 1 month of age were available from an infant survey for children who were participating in a 1995 follow-up study (N = 863; 78% traced). The 1995 follow-up was embedded in a larger cross-sectional survey involving 6,378 seven year olds in Tasmania (N = 92% of eligible). Outcome measures included respiratory symptoms as defined in the International Study of Asthma and Allergies in Childhood protocol. Frequent wheeze was defined as more than 12 wheeze episodes over the past year compared with no wheeze. Synthetic pillow use at 1 month of age was associated with frequent wheeze at age 7 (adjusted relative risk [aRR] = 2.5; 95% confidence interval [CI] = 1.2-5.5) independent of childhood exposure. Current synthetic pillow and quilt use was strongly associated with frequent wheeze (aRR = 5.2; CI = 1.3-20.6). Substantial trends were evident for an association of increasing number of synthetic bedding items with frequent wheeze and with increasing wheeze frequency. Among children with asthma, the age of onset of asthma occurred earlier if synthetic bedding was used in infancy. In this cohort, synthetic bedding was strongly and consistently associated with frequent childhood wheeze. The association did not appear to be attributable to bedding choice as part of an asthma management strategy.

  12. Distal hindlimb kinematics of galloping Thoroughbred racehorses on dirt and synthetic racetrack surfaces.

    Science.gov (United States)

    Symons, J E; Garcia, T C; Stover, S M

    2014-03-01

    The effect of racetrack surface (dirt or synthetic) on distal hindlimb kinematics of racehorses running at competition speeds is not known. To compare distal hindlimb and hoof kinematics during stance of breezing (unrestrained gallop) racehorses between dirt and synthetic surfaces. Two-dimensional kinematic video analysis of 5 Thoroughbred racehorses galloping at high speeds (12-17 m/s) on a dirt racetrack and a synthetic racetrack. The positions of kinematic markers applied to the left hindlimb were recorded at 500 Hz. Position, velocity and acceleration of joint angles and hoof translation during stance were calculated in the sagittal plane. Peak translational and angular kinematic values were compared between the dirt and synthetic race surfaces using mixed model analyses of covariance. Maximum and heel-strike metatarsophalangeal (fetlock) angles were greater (Pdirt surface than on the synthetic surface. Maximum fetlock angle occurred earlier during stance on the dirt surface (Pdirt surface (Pdirt surface than on a synthetic surface. Synthetic race surfaces may mitigate risk of injury to hindlimb fetlock structures by reducing fetlock hyperextension and associated strains in fetlock support structures. Differences in hoof slide may contribute to different distal hindlimb kinematics between surfaces. © 2013 EVJ Ltd.

  13. Shape analysis of isoseismals based on empirical and synthetic data

    International Nuclear Information System (INIS)

    Molchan, G.; Panza, G.F.

    2000-11-01

    We present an attempt to compare modeled ground motion acceleration fields with macroseismic observations. Two techniques for the representation of the observed intensities by isoseismals, a smoothing technique and one which visualizes the local uncertainty of an isoseismal, are tested with synthetic and observed data. We show how noise in the data and irregularities in the distribution of observation sites affect the resolution of the isoseismal's shape. In addition to ''standard'' elongated shapes, we identify cross-like patterns in the macroseismic observations for two Italian earthquakes of strike-slip type; similar patterns are displayed by the theoretical peak acceleration fields calculated assuming the point source models given in the literature. (author)

  14. 21 CFR 73.1200 - Synthetic iron oxide.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Synthetic iron oxide. 73.1200 Section 73.1200 Food... COLOR ADDITIVES EXEMPT FROM CERTIFICATION Drugs § 73.1200 Synthetic iron oxide. (a) Identity. (1) The color additive synthetic iron oxide consists of any one or any combination of synthetically prepared...

  15. 21 CFR 73.200 - Synthetic iron oxide.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Synthetic iron oxide. 73.200 Section 73.200 Food... COLOR ADDITIVES EXEMPT FROM CERTIFICATION Foods § 73.200 Synthetic iron oxide. (a) Identity. (1) The color additive synthetic iron oxide consists of any one or any combination of synthetically prepared...

  16. 21 CFR 172.888 - Synthetic petroleum wax.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Synthetic petroleum wax. 172.888 Section 172.888... CONSUMPTION Multipurpose Additives § 172.888 Synthetic petroleum wax. Synthetic petroleum wax may be safely used in or on foods in accordance with the following conditions: (a) Synthetic petroleum wax is a...

  17. Artificial magnetic-field quenches in synthetic dimensions

    Science.gov (United States)

    Yılmaz, F.; Oktel, M. Ö.

    2018-02-01

    Recent cold atom experiments have realized models where each hyperfine state at an optical lattice site can be regarded as a separate site in a synthetic dimension. In such synthetic ribbon configurations, manipulation of the transitions between the hyperfine levels provide direct control of the hopping in the synthetic dimension. This effect was used to simulate a magnetic field through the ribbon. Precise control over the hopping matrix elements in the synthetic dimension makes it possible to change this artificial magnetic field much faster than the time scales associated with atomic motion in the lattice. In this paper, we consider such a magnetic-flux quench scenario in synthetic dimensions. Sudden changes have not been considered for real magnetic fields as such changes in a conducting system would result in large induced currents. Hence we first study the difference between a time varying real magnetic field and an artificial magnetic field using a minimal six-site model. This minimal model clearly shows the connection between gauge dependence and the lack of on-site induced scalar potential terms. We then investigate the dynamics of a wave packet in an infinite two- or three-leg ladder following a flux quench and find that the gauge choice has a dramatic effect on the packet dynamics. Specifically, a wave packet splits into a number of smaller packets moving with different velocities. Both the weights and the number of packets depend on the implemented gauge. If an initial packet, prepared under zero flux in an n -leg ladder, is quenched to Hamiltonian with a vector potential parallel to the ladder, it splits into at most n smaller wave packets. The same initial wave packet splits into up to n2 packets if the vector potential is implemented to be along the rungs. Even a trivial difference in the gauge choice such as the addition of a constant to the vector potential produces observable effects. We also calculate the packet weights for arbitrary initial and

  18. Synthetic biology and the technicity of biofuels.

    Science.gov (United States)

    Mackenzie, Adrian

    2013-06-01

    The principal existing real-world application of synthetic biology is biofuels. Several 'next generation biofuel' companies-Synthetic Genomics, Amyris and Joule Unlimited Technologies-claim to be using synthetic biology to make biofuels. The irony of this is that highly advanced science and engineering serves the very mundane and familiar realm of transport. Despite their rather prosaic nature, biofuels could offer an interesting way to highlight the novelty of synthetic biology from several angles at once. Drawing on the French philosopher of technology and biology Gilbert Simondon, we can understand biofuels as technical objects whose genesis involves processes of concretisation that negotiate between heterogeneous geographical, biological, technical, scientific and commercial realities. Simondon's notion of technicity, the degree of concretisation of a technical object, usefully conceptualises this relationality. Viewed in terms of technicity, we might understand better how technical entities, elements, and ensembles are coming into being in the name of synthetic biology. The broader argument here is that when we seek to identify the newness of disciplines, their newness might be less epistemic and more logistic. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  19. WISB: Warwick Integrative Synthetic Biology Centre.

    Science.gov (United States)

    McCarthy, John

    2016-06-15

    Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary 'build to apply' and 'build to understand' approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. © 2016 The Author(s).

  20. Synthetic cathinones: a new public health problem.

    Science.gov (United States)

    Karila, Laurent; Megarbane, Bruno; Cottencin, Olivier; Lejoyeux, Michel

    2015-01-01

    New psychoactive substances (NPS) have completely modified the drug scene and the current landscape of addiction. Synthetic substances, such as substituted or synthetic cathinones, also known as « legal highs », are often produced and used to mimic the effects of controlled drugs such as cocaine, methylenedioxymethamphetamine (MDMA, ecstasy), and methamphetamine. The overwhelming majority of synthetic cathinones are produced in China and South East Asian countries. The Internet has emerged as the new marketplace for NPS, playing a major role in providing information on acquisition, synthesis, extraction, identification, and substance use. All these compounds are intentionally mislabeled and sold on-line under slang terms such as bath salts, plant food, plant feeders and research chemicals. They are sometimes labeled « not for human use » or « not tested for hazards or toxicity ». The rapid spread of NPS forces member countries of the European Union to adapt their response to the potential new dangers that may cause. To date, not only health actors but also the general public need to be clearly informed and aware of dangers resulting from NPS spread and use. Here, we review the major clinical effects of synthetic cathinones to highlight their impact on public health. A literature search was conducted from 2009 to 2014 based on PubMed, Google Scholar, Erowid, and governmental websites, using the following keywords alone or in combination: "new psychoactive substances", "synthetic cathinones", "substituted cathinones", "mephedrone", "methylone", "MDPV", "4-MEC", "addiction", and "substance use disorder".