Science.gov

Sample records for synthetic model systems

  1. A system model and inversion for synthetic aperture radar imaging.

    PubMed

    Soumekh, M

    1992-01-01

    A system model and its corresponding inversion for synthetic aperture radar (SAR) imaging are presented. The system model incorporates the spherical nature of a radar's radiation pattern at far field. The inverse method based on this model performs a spatial Fourier transform (Doppler processing) on the recorded signals with respect to the available coordinates of a translational radar (SAR) or target (inverse SAR). It is shown that the transformed data provide samples of the spatial Fourier transform of the target's reflectivity function. The inverse method can be modified to incorporate deviations of the radar's motion from its prescribed straight line path. The effects of finite aperture on resolution, reconstruction, and sampling constraints for the imaging problem are discussed.

  2. Rigid Biological Systems as Models for Synthetic Composites

    NASA Astrophysics Data System (ADS)

    Mayer, George

    2005-11-01

    Advances that have been made in understanding the mechanisms underlying the mechanical behavior of a number of biological materials (namely mollusk shells and sponge spicules) are discussed here. Attempts at biomimicry of the structure of a nacreous layer of a mollusk shell have shown reasonable success. However, they have revealed additional issues that must be addressed if new synthetic composite materials that are based on natural systems are to be constructed. Some of the important advantages and limitations of copying from nature are also described here.

  3. Evolvable synthetic neural system

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed

    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).

  5. MSW to synthetic natural gas: System modeling and thermodynamics assessment.

    PubMed

    Zhu, Lin; Zhang, Le; Fan, Junming; Jiang, Peng; Li, Luling

    2016-02-01

    To achieve environmental-friendly and energy-efficiency synthetic natural gas (SNG) production routing from municipal solid waste (MSW), a MSW-to-SNG process is unprecedentedly presented in this work, of which the designed configuration is developed and simulated with the aid of Aspen Plus. In addition, sensitivity analyses on major operation parameters, such as equivalence volume ratio (ER), steam-to-MSW mass ratio (S/M) and methanation pressure, are performed with the discussion of process efficiencies and SNG quality. In parallel, the comparison analysis is considered by adopting various MSW material. In this work, the composition of SNG mainly consists of 87.7% CH4, 2.9% CO2, 2.3% H2 and 7.1% N2. And lower heating value (LHV) together with Wobbe index of SNG are separately 31.66MJ/Nm(3) and 45.90MJ/Nm(3). Moreover, the wood-to-SNG, MSW-to-SNG and coal-to-SNG processes are carried out to demonstrate the superiority of the MSW-to-SNG process. The results reveal that the MSW-to-SNG process is a promising option to dispose MSW environmentally, meanwhile converting MSW to the valuable SNG.

  6. MSW to synthetic natural gas: System modeling and thermodynamics assessment.

    PubMed

    Zhu, Lin; Zhang, Le; Fan, Junming; Jiang, Peng; Li, Luling

    2016-02-01

    To achieve environmental-friendly and energy-efficiency synthetic natural gas (SNG) production routing from municipal solid waste (MSW), a MSW-to-SNG process is unprecedentedly presented in this work, of which the designed configuration is developed and simulated with the aid of Aspen Plus. In addition, sensitivity analyses on major operation parameters, such as equivalence volume ratio (ER), steam-to-MSW mass ratio (S/M) and methanation pressure, are performed with the discussion of process efficiencies and SNG quality. In parallel, the comparison analysis is considered by adopting various MSW material. In this work, the composition of SNG mainly consists of 87.7% CH4, 2.9% CO2, 2.3% H2 and 7.1% N2. And lower heating value (LHV) together with Wobbe index of SNG are separately 31.66MJ/Nm(3) and 45.90MJ/Nm(3). Moreover, the wood-to-SNG, MSW-to-SNG and coal-to-SNG processes are carried out to demonstrate the superiority of the MSW-to-SNG process. The results reveal that the MSW-to-SNG process is a promising option to dispose MSW environmentally, meanwhile converting MSW to the valuable SNG. PMID:26525970

  7. Synthetical Reliability Analysis Model of CNC Software System

    NASA Astrophysics Data System (ADS)

    Xu, Yue; Xia, Yinjie; Wan, Yi

    CNC technology is the core of advanced manufacturing technology, and CNC software system is the very important part of numerical control system. The entire CNC system will not work normally, once the potential failure makes the software invalid. As to the current study of CNC sysytem, in use of the FAULT glitch tree, established a glitch tree for the CNC system; find the minimum cut sets with Fussed method and then according to the probability of several common glitches, make quantitative analysis in the reliability of the CNC system so that scientific ways can be provided for the reliability design, maintenance and management of the CNC system.

  8. Synthetic Vision Systems

    NASA Technical Reports Server (NTRS)

    Prinzel, L.J.; Kramer, L.J.

    2009-01-01

    A synthetic vision system is an aircraft cockpit display technology that presents the visual environment external to the aircraft using computer-generated imagery in a manner analogous to how it would appear to the pilot if forward visibility were not restricted. The purpose of this chapter is to review the state of synthetic vision systems, and discuss selected human factors issues that should be considered when designing such displays.

  9. Synthetic Visibility System

    NASA Technical Reports Server (NTRS)

    1989-01-01

    Test pilot Lee Person evaluates a Synthetic Visibility System - in essence, two helmet-mounted eyepieces connected to video cameras that swivel in response to head movements. Photograph published in Winds of Change, 75th Anniversary NASA publication (page 113), by James Schultz.

  10. A new approach to thermodynamic modelling of peridotite melting in synthetic and natural systems

    NASA Astrophysics Data System (ADS)

    Smith, P. M.; McKenzie, D. P.

    2002-12-01

    Parameterisations of peridotite melting have been very important in understanding magma generation in various tectonic settings. Most have made simplifying assumptions that limit their applicability. As the available experimental data set and computer power increase rapidly an accurate model of (near) fractional melting over a range of P, T and source composition is becoming a realistic possibility. We are developing software for a new thermodynamic model of peridotite melting, with the principal aim that the scheme can easily accommodate new data as it becomes available. Numerous previous thermodynamic models exist for synthetic systems with limited components. Often these cover a very wide composition space but are limited to 1-atm. In contrast, the widely used models of Ghiorso and Sack (1995; MELTS) and Ghiorso (1998; pMELTS) for the natural system extend over a wide range of pressures and concentrate on a relatively restricted range of compositions. Our intermediate approach is for peridotite melting only but the calibration is suitable for synthetic and natural systems. Although simultaneous modelling of synthetic and natural systems may not be possible, calibration of systems with fewer components should give useful estimates of parameters for the natural system. The software we present here has several features designed to overcome known problems with MELTS and pMELTS, as well as difficulties encountered in previous work in CMAS (Smith and Holland 1999; AGU abstract) and also to make maximum use of the data and error estimates. A `forward' model calculates P, T, and composition of coexisting phases for a given set of parameters by optimising the fit to the bulk composition subject to a set of energy and mass balance constraints. Interaction parameters for phases that exhibit solution are derived by minimising the misfit between calculated and observed P, T, and composition (the `inverse' model). Pure phase end-member data may be varied, if necessary, and

  11. New synthetic technology for the construction of N-hydroxyindoles and synthesis of nocathiacin I model systems

    PubMed Central

    Nicolaou, K. C.; Estrada, Anthony A.; Freestone, Graeme C.; Lee, Sang Hyup; Alvarez-Mico, Xavier

    2009-01-01

    A new synthetic method providing expedient access to a wide range of polyfunctionalized N-hydroxyindoles (IV) is reported. These unique constructs are assembled by nucleophilic additions to in situ generated α,β-unsaturated nitrones (III) through carbon–carbon and carbon–heteroatom bond formation. The new synthetic technology was applied to the synthesis of nocathiacin I (1) model systems (2 and 3a–c) containing the N-hydroxyindole structural motif. PMID:20606766

  12. BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology

    PubMed Central

    Gorochowski, Thomas E.; Matyjaszkiewicz, Antoni; Todd, Thomas; Oak, Neeraj; Kowalska, Kira; Reid, Stephen; Tsaneva-Atanasova, Krasimira T.

    2012-01-01

    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. PMID:22936991

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

    PubMed

    Gorochowski, Thomas E; Matyjaszkiewicz, Antoni; Todd, Thomas; Oak, Neeraj; Kowalska, Kira; Reid, Stephen; Tsaneva-Atanasova, Krasimira T; Savery, Nigel J; Grierson, Claire S; di Bernardo, Mario

    2012-01-01

    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. PMID:22936991

  14. Synthetic gene networks in plant systems.

    PubMed

    Junker, Astrid; Junker, Björn H

    2012-01-01

    Synthetic biology methods are routinely applied in the plant field as in other eukaryotic model systems. Several synthetic components have been developed in plants and an increasing number of studies report on the assembly into functional synthetic genetic circuits. This chapter gives an overview of the existing plant genetic networks and describes in detail the application of two systems for inducible gene expression. The ethanol-inducible system relies on the ethanol-responsive interaction of the AlcA transcriptional activator and the AlcR receptor resulting in the transcription of the gene of interest (GOI). In comparison, the translational fusion of GOI and the glucocorticoid receptor (GR) domain leads to the dexamethasone-dependent nuclear translocation of the GOI::GR protein. This chapter contains detailed protocols for the application of both systems in the model plants potato and Arabidopsis, respectively.

  15. Using synthetic model systems to understand charge separation and spin dynamics in photosynthetic reaction centers.

    SciTech Connect

    Wasielewski, M. R.

    1998-08-27

    Our current work in modeling reaction center dynamics has resulted in the observation of each major spin-dependent photochemical pathway that is observed in reaction centers. The development of new, simpler model systems has permitted us to probe deeply into the mechanistic issues that drive these dynamics. Based on these results we have returned to biomimetic chlorophyll-based electron donors to mimic these dynamics. Future studies will focus on the details of electronic structure and energetic of both the donor-acceptor molecules and their surrounding environment that dictate the mechanistic pathways and result in efficient photosynthetic charge separation.

  16. Synthetic population system user guide

    SciTech Connect

    Roberts, D.J.

    1998-03-01

    The Los Alamos National Laboratory (LANL) TRansportation Analysis SIMulatiuon System (TRANSIMS) synthetic population system (SYN) is designed to produce populations (family households, non-family households, and group quarters) that are statistically equivalent to actual populations when compared at the level of block group or higher. The methodology used by this system is described in a report entitled Creating Synthetic Baseline Populations. The inputs to the system are US Census Bureau data (STF3A and PUMS) and MABLE/GEOCORR data. Census Bureau STF3A and PUMS data formats are commonly used and are available on CD-ROM from the Census Bureau. These data inputs will not be described in any detail in this guide. The primary function of MABLE/GEOCORR data is to cross-reference STF3 block group data to PUMS areas. The outputs of the system are files that contain family household, non-family household, and group quarters data in the form of household and person records. SYN will run on a variety of Unix platforms.

  17. Performance evaluation of an on-site volume reduction system with synthetic urine using a water transport model.

    PubMed

    Pahore, Muhammad Masoom; Ito, Ryusei; Funamizu, Naoyuki

    2011-07-01

    The parameters of a model of the transport of water from a wet cloth sheet to the air, developed for deionized water, to establish design procedures of an on-site volume reduction system, were identified for high salt concentrations present in synthetic urine. The results showed that the water penetration was affected neither by the salts, urea or creatinine present in the synthetic urine nor by the salts accumulated on the surface of the vertical gauze sheet. However, the saturated vapour pressure decreased, leading to reduction in the evaporation rate, which occurred as a result of the salts accumulating on the surface of the vertical gauze sheet. Furthermore, a steady-state evaporation condition was established, illustrating salts falling back to the tank from the vertical gauze sheet. Accordingly, the existing design procedure was amended by incorporating the calculation procedure for the saturated vapour pressure using Raoult's law. Subsequently, the effective evaporation area of the vertical gauze sheet was estimated using the amended deign procedures to assess feasibility. This estimation showed that the arid, tropical, temperate and cold climates are suitable for the operation of this system, which require requires a small place at household level for 80% volume reduction of 10 L of urine per day for 12 hours' operation in the daytime. PMID:21882549

  18. Online updating of synthetic vision system databases

    NASA Astrophysics Data System (ADS)

    Simard, Philippe

    In aviation, synthetic vision systems render artificial views of the world (using a database of the world and pose information) to support navigation and situational awareness in low visibility conditions. The database needs to be periodically updated to ensure its consistency with reality, since it reflects at best a nominal state of the environment. This thesis presents an approach for automatically updating the geometry of synthetic vision system databases and 3D models in general. The approach is novel in that it profits from all of the available prior information: intrinsic/extrinsic camera parameters and geometry of the world. Geometric inconsistencies (or anomalies) between the model and reality are quickly localized; this localization serves to significantly reduce the complexity of the updating problem. Given a geometric model of the world, a sample image and known camera motion, a predicted image can be generated based on a differential approach. Model locations where predictions do not match observations are assumed to be incorrect. The updating is then cast as an optimization problem where differences between observations and predictions are minimized. To cope with system uncertainties, a mechanism that automatically infers their impact on prediction validity is derived. This method not only renders the anomaly detection process robust but also prevents the overfitting of the data. The updating framework is examined at first using synthetic data and further tested in both a laboratory environment and using a helicopter in flight. Experimental results show that the algorithm is effective and robust across different operating conditions.

  19. Designing and encoding models for synthetic biology

    PubMed Central

    Endler, Lukas; Rodriguez, Nicolas; Juty, Nick; Chelliah, Vijayalakshmi; Laibe, Camille; Li, Chen; Le Novère, Nicolas

    2009-01-01

    A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis. Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. There has been a concomitant increase in the number of software tools and standards, thereby facilitating model exchange and reuse. We give here an overview of the model creation and analysis processes as well as some software tools in common use. Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization. Evaluation of simulation results and validation of the model close the systems biology ‘loop’. PMID:19364720

  20. Targeting of Synthetic Gene Delivery Systems

    PubMed Central

    2003-01-01

    Safe, efficient, and specific delivery of therapeutic genes remains an important bottleneck for the development of gene therapy. Synthetic, nonviral systems have a unique pharmaceutical profile with potential advantages for certain applications. Targeting of the synthetic vector improves the specificity of gene medicines through a modulation of the carriers' biodistribution, thus creating a dose differential between healthy tissue and the target site. The biodistribution of current carrier systems is being influenced to a large extent by intrinsic physicochemical characteristics, such as charge and size. Consequently, such nonspecific interactions can interfere with specific targeting, for example, by ligands. Therefore, a carrier complex should ideally be inert, that is, free from intrinsic properties that would bias its distribution away from the target site. Strategies such as coating of DNA carrier complexes with hydrophilic polymers have been used to mask some of these intrinsic targeting effects and avoid nonspecific interactions. Preexisting endogenous ligand-receptor interactions have frequently been used for targeting to certain cell types or tumours. Recently exogenous ligands have been derived from microorganisms or, like antibodies or phage-derived peptides, developed de novo. In animal models, such synthetic vectors have targeted remote sites such as a tumour. Furthermore, the therapeutic proof of the concept has been demonstrated for fitting combinations of synthetic vectors and therapeutic gene. PMID:12721518

  1. Photocatalytic Systems with Flavinium Salts: From Photolyase Models to Synthetic Tool for Cyclobutane Ring Opening.

    PubMed

    Hartman, Tomáš; Cibulka, Radek

    2016-08-01

    Two new photocatalytic systems based on flavinium species formed in situ by protonation of riboflavin-tetraacetate (1) with triflic acid or prepared in advance via alloxazine quaternization are presented as effective tools for oxidative cyclobutane ring [2 + 2] cycloreversion using visible light. The system with 1,3-dimethyl-8-trifluoromethylalloxazinium perchlorate (2c) was found to be superior allowing an acid-free mild procedure, which results in the opening of cyclobutanes with high oxidation potential (up to 2.14 V) and/or with sensitive groups (e.g., furan) without side reactions. PMID:27415962

  2. Synthetic molecular systems based on porphyrins as models for the study of energy transfer in photosynthesis

    NASA Astrophysics Data System (ADS)

    Konovalova, Nadezhda V.; Evstigneeva, Rima P.; Luzgina, Valentina N.

    2001-11-01

    The published data on the synthesis and photochemical properties of porphyrin-based molecular ensembles which represent models of natural photosynthetic light-harvesting complexes are generalised and systematised. The dependence of the transfer of excitation energy on the distance between donor and acceptor components, their mutual arrangement, electronic and environmental factors are discussed. Two mechanisms of energy transfer reactions, viz., 'through space' and 'through bond', are considered. The bibliography includes 96 references.

  3. Using X-band Weather Radar Measurements to Monitor the Integrity of Digital Elevation Models for Synthetic Vision Systems

    NASA Technical Reports Server (NTRS)

    Young, Steve; UijtdeHaag, Maarten; Sayre, Jonathon

    2003-01-01

    Synthetic Vision Systems (SVS) provide pilots with displays of stored geo-spatial data representing terrain, obstacles, and cultural features. As comprehensive validation is impractical, these databases typically have no quantifiable level of integrity. Further, updates to the databases may not be provided as changes occur. These issues limit the certification level and constrain the operational context of SVS for civil aviation. Previous work demonstrated the feasibility of using a realtime monitor to bound the integrity of Digital Elevation Models (DEMs) by using radar altimeter measurements during flight. This paper describes an extension of this concept to include X-band Weather Radar (WxR) measurements. This enables the monitor to detect additional classes of DEM errors and to reduce the exposure time associated with integrity threats. Feature extraction techniques are used along with a statistical assessment of similarity measures between the sensed and stored features that are detected. Recent flight-testing in the area around the Juneau, Alaska Airport (JNU) has resulted in a comprehensive set of sensor data that is being used to assess the feasibility of the proposed monitor technology. Initial results of this assessment are presented.

  4. Using X-band weather radar measurements to monitor the integrity of digital elevation models for synthetic vision systems

    NASA Astrophysics Data System (ADS)

    Young, Steven D.; Uijt de Haag, Maarten; Sayre, Jonathon

    2003-09-01

    Synthetic Vision Systems (SVS) provide pilots with displays of stored geo-spatial data representing terrain, obstacles, and cultural features. As comprehensive validation is impractical, these databases typically have no quantifiable level of integrity. Futher, updates to the databases may not be provided as changes occur. These issues limit the certification level and constrain the operational context of SVS for civil aviation. Previous work demonstrated the feasibility of using a real-time monitor to bound the integrity of Digital Elevation Models (DEMs) by using radar altimeter measurements during flight. This paper describes an extension of this concept to include X-band Weather Radar (WxR) measurements. This enables the monitor to detect additional classes of DEM errors and to reduce the exposure time associated with integrity threats. Feature extraction techniques are used along with a statistical assessment of similarity measures between the sensed and stored features that are detected. Recent flight-testing in the area around Juneau, Alaska Airport (JNU) has resulted in a comprehensive set of sensor data that is being used to assess the feasibility of the proposed monitor technology. Initial results of this assessment are presented.

  5. Protoplaneary Dynamics Uncovered through Synthetic Spectral Modeling

    NASA Astrophysics Data System (ADS)

    Kronberg, Martin

    2010-01-01

    One of the key problems in planetary formation research is to determine the properties and dynamics of protoplaneary accretion disks where all planetary formation occurs. An increasingly useful probe into these systems is near infrared spectroscopy of ro-vibrational CO emission. The goal of the study is to develop techniques that utilize synthetic spectra generated via a modeling algorithm fitted to actual spectral data gathered from protoplanetary systems to determine specific properties of the system. We currently have a working algorithm which generates synthetic spectra based upon a number of degenerate parameters. In order to generate the best fit given the degenerate nature of the parameters we are developing a Monte Carlo algorithm that will determine local as well as absolute minima in a ten dimensional surface plot. Once this is completed we will utilize two CONDOR clusters to generate fits for hundreds of known protoplanetary systems.The result will be the largest, most descriptive database of protoplanetary systems, an essential tool for planetary and stellar researchers. This project was funded by a partnership between the National Science Foundation (NSF AST-0552798), Research Experiences for Undergraduates (REU), and the Department of Defense (DoD) ASSURE (Awards to Stimulate and Support Undergraduate Research Experiences) programs.

  6. High-fidelity synthetic IR imaging model

    NASA Astrophysics Data System (ADS)

    Wegener, Michael; Drake, Richard

    2000-07-01

    This paper describes a High Fidelity Synthetic IR Imaging Model which attempts to generate accurate static images as would be seen by a defined IR sensor given the target type and the atmospheric conditions. The model attempts to be quite general in its accommodation of physical processes yet maintain radiometric accuracy. Its main application are to assist in the validation of real-time IR scene generation software, and as a tool which can be used for range performance studies of electro-optical systems. The software model allows facet modeling of targets including temperature profiles and material properties. LOWTRAN/MODTRAN is used to provide atmospheric data for transmittance and self-radiation. Optical systems are described in terms of their transmittance and point spread function, both as functions of wavelength, and a self radiation term having temperature and material properties. At each wavelength desired the model generates descriptions of the flux distribution falling on the focal plane of the sensor system. The flux from different sources is added together to form the total flux distribution on the focal plane. Pixels on the focal plane are modeled by groups of facets with associated material properties allowing the shape and wavelength sensitivity to be expressed. The raw pixel output is obtained by integrating the flux distribution over the component facets and across wavelengths. Following non-uniformity modeling a convolution is applied which models readout smearing. Bandlimited noise is then added. The model is also able to generate and apply a matched filter to the output image. The model is designed to use common commercial software tools such as Multigen for target modeling and Open GL for the rendering. The model currently executes on Silicon Graphics hardware.

  7. Systems approaches for synthetic biology: a pathway toward mammalian design

    PubMed Central

    Rekhi, Rahul; Qutub, Amina A.

    2013-01-01

    We review methods of understanding cellular interactions through computation in order to guide the synthetic design of mammalian cells for translational applications, such as regenerative medicine and cancer therapies. In doing so, we argue that the challenges of engineering mammalian cells provide a prime opportunity to leverage advances in computational systems biology. We support this claim systematically, by addressing each of the principal challenges to existing synthetic bioengineering approaches—stochasticity, complexity, and scale—with specific methods and paradigms in systems biology. Moreover, we characterize a key set of diverse computational techniques, including agent-based modeling, Bayesian network analysis, graph theory, and Gillespie simulations, with specific utility toward synthetic biology. Lastly, we examine the mammalian applications of synthetic biology for medicine and health, and how computational systems biology can aid in the continued development of these applications. PMID:24130532

  8. Synthetic biology of minimal living cells: primitive cell models and semi-synthetic cells

    PubMed Central

    2010-01-01

    This article summarizes a contribution presented at the ESF 2009 Synthetic Biology focused on the concept of the minimal requirement for life and on the issue of constructive (synthetic) approaches in biological research. The attempts to define minimal life within the framework of autopoietic theory are firstly described, and a short report on the development of autopoietic chemical systems based on fatty acid vesicles, which are relevant as primitive cell models is given. These studies can be used as a starting point for the construction of more complex systems, firstly being inspired by possible origins of life scenarioes (and therefore by considering primitive functions), then by considering an approach based on modern biomacromolecular-encoded functions. At this aim, semi-synthetic minimal cells are defined as those man-made vesicle-based systems that are composed of the minimal number of genes, proteins, biomolecules and which can be defined as living. Recent achievements on minimal sized semi-synthetic cells are then discussed, and the kind of information obtained is recognized as being distinctively derived by a constructive approach. Synthetic biology is therefore a fundamental tool for gaining basic knowledge about biosystems, and it should not be confined at all to the engineering side. PMID:21886680

  9. Synthetic immunology: modulating the human immune system.

    PubMed

    Geering, Barbara; Fussenegger, Martin

    2015-02-01

    Humans have manipulated the immune system to dampen or boost the immune response for thousands of years. As our understanding of fundamental immunology and biotechnological methodology accumulates, we can capitalize on this combined knowledge to engineer biological devices with the aim of rationally manipulating the immune response. We address therapeutic approaches based on the principles of synthetic immunology that either ameliorate disorders of the immune system by interfering with the immune response, or improve diverse pathogenic conditions by exploiting immune cell effector functions. We specifically highlight synthetic proteins investigated in preclinical and clinical trials, summarize studies that have used engineered immune cells, and finish with a discussion of possible future therapeutic concepts.

  10. Flight Testing an Integrated Synthetic Vision System

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Arthur, Jarvis J., III; Bailey, Randall E.; Prinzel, Lawrence J., III

    2005-01-01

    NASA's Synthetic Vision Systems (SVS) project is developing technologies with practical applications to eliminate low visibility conditions as a causal factor to civil aircraft accidents while replicating the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. A major thrust of the SVS project involves the development/demonstration of affordable, certifiable display configurations that provide intuitive out-the-window terrain and obstacle information with advanced pathway guidance for transport aircraft. The SVS concept being developed at NASA encompasses the integration of tactical and strategic Synthetic Vision Display Concepts (SVDC) with Runway Incursion Prevention System (RIPS) alerting and display concepts, real-time terrain database integrity monitoring equipment (DIME), and Enhanced Vision Systems (EVS) and/or improved Weather Radar for real-time object detection and database integrity monitoring. A flight test evaluation was jointly conducted (in July and August 2004) by NASA Langley Research Center and an industry partner team under NASA's Aviation Safety and Security, Synthetic Vision System project. A Gulfstream GV aircraft was flown over a 3-week period in the Reno/Tahoe International Airport (NV) local area and an additional 3-week period in the Wallops Flight Facility (VA) local area to evaluate integrated Synthetic Vision System concepts. The enabling technologies (RIPS, EVS and DIME) were integrated into the larger SVS concept design. This paper presents experimental methods and the high level results of this flight test.

  11. Flight testing an integrated synthetic vision system

    NASA Astrophysics Data System (ADS)

    Kramer, Lynda J.; Arthur, Jarvis J., III; Bailey, Randall E.; Prinzel, Lawrence J., III

    2005-05-01

    NASA's Synthetic Vision Systems (SVS) project is developing technologies with practical applications to eliminate low visibility conditions as a causal factor to civil aircraft accidents while replicating the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. A major thrust of the SVS project involves the development/demonstration of affordable, certifiable display configurations that provide intuitive out-the-window terrain and obstacle information with advanced pathway guidance for transport aircraft. The SVS concept being developed at NASA encompasses the integration of tactical and strategic Synthetic Vision Display Concepts (SVDC) with Runway Incursion Prevention System (RIPS) alerting and display concepts, real-time terrain database integrity monitoring equipment (DIME), and Enhanced Vision Systems (EVS) and/or improved Weather Radar for real-time object detection and database integrity monitoring. A flight test evaluation was jointly conducted (in July and August 2004) by NASA Langley Research Center and an industry partner team under NASA's Aviation Safety and Security, Synthetic Vision System project. A Gulfstream G-V aircraft was flown over a 3-week period in the Reno/Tahoe International Airport (NV) local area and an additional 3-week period in the Wallops Flight Facility (VA) local area to evaluate integrated Synthetic Vision System concepts. The enabling technologies (RIPS, EVS and DIME) were integrated into the larger SVS concept design. This paper presents experimental methods and the high level results of this flight test.

  12. Synthetic computational models of selective attention.

    PubMed

    Raffone, Antonino

    2006-11-01

    Computational modeling plays an important role to understand the mechanisms of attention. In this framework, synthetic computational models can uniquely contribute to integrate different explanatory levels and neurocognitive findings, with special reference to the integration of attention and awareness processes. Novel combined experimental and computational investigations can lead to important insights, as in the revived domain of neural correlates of attention- and awareness-related meditation states and traits.

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

    PubMed Central

    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

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

    PubMed

    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

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

    PubMed

    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

  16. Towards synthetic molecular motors: a model elastic-network study

    NASA Astrophysics Data System (ADS)

    Sarkar, Amartya; Flechsig, Holger; Mikhailov, Alexander S.

    2016-04-01

    Protein molecular motors play a fundamental role in biological cells and development of their synthetic counterparts is a major challenge. Here, we show how a model motor system with the operation mechanism resembling that of muscle myosin can be designed at the concept level, without addressing the implementation aspects. The model is constructed as an elastic network, similar to the coarse-grained descriptions used for real proteins. We show by numerical simulations that the designed synthetic motor can operate as a deterministic or Brownian ratchet and that there is a continuous transition between such two regimes. The motor operation under external load, approaching the stall condition, is also analysed.

  17. Theoretical Modelling of Synthetic Molecular Motors

    NASA Astrophysics Data System (ADS)

    Barbu, Corina; Sofo, Jorge; Crespi, Vincent

    2004-03-01

    Synthetic molecular motors with sizes of few nanometers offer prospects to control molecular-scale mechanical motion. Motors with electric dipoles designed into their structure can undergo conformational changes in response to an external electric field and thereby, in principle, perform mechanical work. The synthetic rotary motor of our interest consists of a molecular caltrop with a three-legged base for attachment to a substrate and a molecular shaft functionalized with a molecular rotor at the upper end. Both the static dipole and the electric field-induced dipole of the molecular rotor are relevant to producing rotation. Also, the combination of external electrostatic torque and the internal thermal fluctuations must be sufficient to overcome any rotational barriers on experimentally relevant timescales. Density functional theory calculations at the B3LYP/TZV level coupled to analytical modelling reveal the dynamical response of the motor.

  18. Synthetic Vision Systems - Operational Considerations Simulation Experiment

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Williams, Steven P.; Bailey, Randall E.; Glaab, Louis J.

    2007-01-01

    Synthetic vision is a computer-generated image of the external scene topography that is generated from aircraft attitude, high-precision navigation information, and data of the terrain, obstacles, cultural features, and other required flight information. A synthetic vision system (SVS) enhances this basic functionality with real-time integrity to ensure the validity of the databases, perform obstacle detection and independent navigation accuracy verification, and provide traffic surveillance. Over the last five years, NASA and its industry partners have developed and deployed SVS technologies for commercial, business, and general aviation aircraft which have been shown to provide significant improvements in terrain awareness and reductions in the potential for Controlled-Flight-Into-Terrain incidents/accidents compared to current generation cockpit technologies. It has been hypothesized that SVS displays can greatly improve the safety and operational flexibility of flight in Instrument Meteorological Conditions (IMC) to a level comparable to clear-day Visual Meteorological Conditions (VMC), regardless of actual weather conditions or time of day. An experiment was conducted to evaluate SVS and SVS-related technologies as well as the influence of where the information is provided to the pilot (e.g., on a Head-Up or Head-Down Display) for consideration in defining landing minima based upon aircraft and airport equipage. The "operational considerations" evaluated under this effort included reduced visibility, decision altitudes, and airport equipage requirements, such as approach lighting systems, for SVS-equipped aircraft. Subjective results from the present study suggest that synthetic vision imagery on both head-up and head-down displays may offer benefits in situation awareness; workload; and approach and landing performance in the visibility levels, approach lighting systems, and decision altitudes tested.

  19. Synthetic vision systems: operational considerations simulation experiment

    NASA Astrophysics Data System (ADS)

    Kramer, Lynda J.; Williams, Steven P.; Bailey, Randall E.; Glaab, Louis J.

    2007-04-01

    Synthetic vision is a computer-generated image of the external scene topography that is generated from aircraft attitude, high-precision navigation information, and data of the terrain, obstacles, cultural features, and other required flight information. A synthetic vision system (SVS) enhances this basic functionality with real-time integrity to ensure the validity of the databases, perform obstacle detection and independent navigation accuracy verification, and provide traffic surveillance. Over the last five years, NASA and its industry partners have developed and deployed SVS technologies for commercial, business, and general aviation aircraft which have been shown to provide significant improvements in terrain awareness and reductions in the potential for Controlled-Flight-Into-Terrain incidents / accidents compared to current generation cockpit technologies. It has been hypothesized that SVS displays can greatly improve the safety and operational flexibility of flight in Instrument Meteorological Conditions (IMC) to a level comparable to clear-day Visual Meteorological Conditions (VMC), regardless of actual weather conditions or time of day. An experiment was conducted to evaluate SVS and SVS-related technologies as well as the influence of where the information is provided to the pilot (e.g., on a Head-Up or Head-Down Display) for consideration in defining landing minima based upon aircraft and airport equipage. The "operational considerations" evaluated under this effort included reduced visibility, decision altitudes, and airport equipage requirements, such as approach lighting systems, for SVS-equipped aircraft. Subjective results from the present study suggest that synthetic vision imagery on both head-up and head-down displays may offer benefits in situation awareness; workload; and approach and landing performance in the visibility levels, approach lighting systems, and decision altitudes tested.

  20. Synthetic Microbes As Drug Delivery Systems

    PubMed Central

    2015-01-01

    Synthetic cell therapy is a field that has broad potential for future applications in human disease treatment. Next generation therapies will consist of engineered bacterial strains capable of diagnosing disease, producing and delivering therapeutics, and controlling their numbers to meet containment and safety concerns. A thorough understanding of the microbial ecology of the human body and the interaction of the microbes with the immune system will benefit the choice of an appropriate chassis that engrafts stably and interacts productively with the resident community in specific body niches. PMID:25079685

  1. Crop monitoring & yield forecasting system based on Synthetic Aperture Radar (SAR) and process-based crop growth model: Development and validation in South and South East Asian Countries

    NASA Astrophysics Data System (ADS)

    Setiyono, T. D.

    2014-12-01

    Accurate and timely information on rice crop growth and yield helps governments and other stakeholders adapting their economic policies and enables relief organizations to better anticipate and coordinate relief efforts in the wake of a natural catastrophe. Such delivery of rice growth and yield information is made possible by regular earth observation using space-born Synthetic Aperture Radar (SAR) technology combined with crop modeling approach to estimate yield. Radar-based remote sensing is capable of observing rice vegetation growth irrespective of cloud coverage, an important feature given that in incidences of flooding the sky is often cloud-covered. The system allows rapid damage assessment over the area of interest. Rice yield monitoring is based on a crop growth simulation and SAR-derived key information, particularly start of season and leaf growth rate. Results from pilot study sites in South and South East Asian countries suggest that incorporation of SAR data into crop model improves yield estimation for actual yields. Remote-sensing data assimilation into crop model effectively capture responses of rice crops to environmental conditions over large spatial coverage, which otherwise is practically impossible to achieve. Such improvement of actual yield estimates offers practical application such as in a crop insurance program. Process-based crop simulation model is used in the system to ensure climate information is adequately captured and to enable mid-season yield forecast.

  2. Southern San Andreas-San Jacinto fault system slip rates estimated from earthquake cycle models constrained by GPS and interferometric synthetic aperture radar observations

    NASA Astrophysics Data System (ADS)

    Lundgren, Paul; Hetland, Eric A.; Liu, Zhen; Fielding, Eric J.

    2009-02-01

    We use ground geodetic and interferometric synthetic aperture radar satellite observations across the southern San Andreas (SAF)-San Jacinto (SJF) fault systems to constrain their slip rates and the viscosity structure of the lower crust and upper mantle on the basis of periodic earthquake cycle, Maxwell viscoelastic, finite element models. Key questions for this system are the SAF and SJF slip rates, the slip partitioning between the two main branches of the SJF, and the dip of the SAF. The best-fitting models generally have a high-viscosity lower crust (η = 1021 Pa s) overlying a lower-viscosity upper mantle (η = 1019 Pa s). We find considerable trade-offs between the relative time into the current earthquake cycle of the San Jacinto fault and the upper mantle viscosity. With reasonable assumptions for the relative time in the earthquake cycle, the partition of slip is fairly robust at around 24-26 mm/a for the San Jacinto fault system and 16-18 mm/a for the San Andreas fault. Models for two subprofiles across the SAF-SJF systems suggest that slip may transfer from the western (Coyote Creek) branch to the eastern (Clark-Superstition hills) branch of the SJF from NW to SE. Across the entire system our best-fitting model gives slip rates of 2 ± 3, 12 ± 9, 12 ± 9, and 17 ± 3 mm/a for the Elsinore, Coyote Creek, Clark, and San Andreas faults, respectively, where the large uncertainties in the slip rates for the SJF branches reflect the large uncertainty in the slip rate partitioning within the SJF system.

  3. A Property-Driven Methodology for Formal Analysis of Synthetic Biology Systems.

    PubMed

    Konur, Savas; Gheorghe, Marian

    2015-01-01

    This paper proposes a formal methodology to analyse bio-systems, in particular synthetic biology systems. An integrative analysis perspective combining different model checking approaches based on different property categories is provided. The methodology is applied to the synthetic pulse generator system and several verification experiments are carried out to demonstrate the use of our approach to formally analyse various aspects of synthetic biology systems.

  4. Network benchmarking: a happy marriage between systems and synthetic biology.

    PubMed

    Minty, Jeremy J; Varedi K, S Marjan; Nina Lin, Xiaoxia

    2009-03-27

    In their new Cell paper, Cantone et al. (2009) present exciting results on constructing and utilizing a small synthetic gene regulatory network in yeast that draws from two rapidly developing fields of systems and synthetic biology.

  5. Synthetic calibration of a Rainfall-Runoff Model

    USGS Publications Warehouse

    Thompson, David B.; Westphal, Jerome A.; ,

    1990-01-01

    A method for synthetically calibrating storm-mode parameters for the U.S. Geological Survey's Precipitation-Runoff Modeling System is described. Synthetic calibration is accomplished by adjusting storm-mode parameters to minimize deviations between the pseudo-probability disributions represented by regional regression equations and actual frequency distributions fitted to model-generated peak discharge and runoff volume. Results of modeling storm hydrographs using synthetic and analytic storm-mode parameters are presented. Comparisons are made between model results from both parameter sets and between model results and observed hydrographs. Although mean storm runoff is reproducible to within about 26 percent of the observed mean storm runoff for five or six parameter sets, runoff from individual storms is subject to large disparities. Predicted storm runoff volume ranged from 2 percent to 217 percent of commensurate observed values. Furthermore, simulation of peak discharges was poor. Predicted peak discharges from individual storm events ranged from 2 percent to 229 percent of commensurate observed values. The model was incapable of satisfactorily executing storm-mode simulations for the study watersheds. This result is not considered a particular fault of the model, but instead is indicative of deficiencies in similar conceptual models.

  6. Synthetic approach to designing optical alignment systems.

    PubMed

    Whang, A J; Gallagher, N C

    1988-08-15

    The objective of this study is twofold: to design reticle patterns with desirable alignment properties; to build an automatic alignment system using these patterns. We design such reticle patterns via a synthetic approach; the resultant patterns, so-called pseudonoise arrays, are binary and their autocorrelation functions are bilevel. Both properties are desirable in optical alignment. Besides, these arrays have attractive signal-to-noise ratio performance when employed in alignment. We implement the pseudonoise array as a 2-D cross-grating structure of which the grating period is much less than the wavelength of impinging light used for alignment. The short grating period feature, together with the use of polarized light, enables us to perform essentially 2-D optical alignment in one dimension. This alignment separability allows us to build a system that performs alignment automatically according to a simple 1-D algorithm. PMID:20539412

  7. Specifications of Standards in Systems and Synthetic Biology.

    PubMed

    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.

  8. Specifications of Standards in Systems and Synthetic Biology.

    PubMed

    Schreiber, Falk; Bader, Gary D; Golebiewski, Martin; Hucka, Michael; Kormeier, Benjamin; Le Novère, Nicolas; Myers, Chris; Nickerson, David; Sommer, Björn; Waltemath, Dagmar; Weise, Stephan

    2015-01-01

    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. PMID

  9. Synthetic organisms and self-designing systems

    SciTech Connect

    Dress, W.B.

    1989-01-01

    This paper examines the need for complex, adaptive solutions to certain types of complex problems typified by the Strategic Defense System and NASA's Space Station and Mars Rover. Since natural systems have evolved with capabilities of intelligent behavior in complex, dynamic situations, it is proposed that biological principles be identified and abstracted for application to certain problems now facing industry defense, and space exploration. Two classes of artificial neural networks are presented/endash/a non-adaptive network used as a genetically determined ''retina,'' and a frequency-coded network as an adaptive ''brain.'' The role of a specific environment coupled with a system of artificial neural networks having simulated sensors and effectors is seen as an ecosystem. Evolution of synthetic organisms within this ecosystem provides a powerful optimization methodology for creating intelligent systems able to function successfully in any desired environment. A complex software system involving a simulation of an environment and a program designed to cope with that environment are presented. Reliance on adaptive systems, as found in nature, is only part of the proposed answer, though an essential one. The second part of the proposed method makes use of an additional biological metaphor/endash/that of natural selection/endash/to solve the dynamic optimization problems that every intelligent system eventually faces. A third area of concern in developing an adaptive, intelligent system is that of real-time computing. It is recognized that many of the problems now being explored in this area have their parallels in biological organisms, and many of the performance issues facing artificial neural networks may find resolution in the methodology of real-time computing. 30 refs., 4 figs.

  10. A synthetic aperture acoustic prototype system

    NASA Astrophysics Data System (ADS)

    Luke, Robert H.; Bishop, Steven S.; Chan, Aaron M.; Gugino, Peter M.; Donzelli, Thomas P.; Soumekh, Mehrdad

    2015-05-01

    A novel quasi-monostatic system operating in a side-scan synthetic aperture acoustic (SAA) imaging mode is presented. This research project's objectives are to explore the military utility of outdoor continuous sound imaging of roadside foliage and target detection. The acoustic imaging method has several military relevant advantages such as being immune to RF jamming, superior spatial resolution as compared to 0.8-2.4 GHz ground penetrating radar (GPR), capable of standoff side and forward-looking scanning, and relatively low cost, weight and size when compared to GPR technologies. The prototype system's broadband 2-17 kHz LFM chirp transceiver is mounted on a manned all-terrain vehicle. Targets are positioned within the acoustic main beam at slant ranges of two to seven meters and on surfaces such as dirt, grass, gravel and weathered asphalt and with an intervening metallic chain link fence. Acoustic image reconstructions and signature plots result in means for literal interpretation and quantifiable analyses.

  11. Insights Into the P-To-Q Conversion in the Catalytic Cycle of Methane Monooxygenase From a Synthetic Model System

    SciTech Connect

    Xue, G.; Fiedler, A.T.; Martinho, M.; Munck, E.; Que, L.; Jr.

    2009-05-28

    For the catalytic cycle of soluble methane monooxygenase (sMMO), it has been proposed that cleavage of the O-O bond in the ({mu}-peroxo)diiron(III) intermediate P gives rise to the diiron(IV) intermediate Q with an Fe{sub 2}({mu}-O){sub 2} diamond core, which oxidizes methane to methanol. As a model for this conversion, ({mu}-oxo) diiron(III) complex 1 ([Fe{sup III}{sub 2}({mu}-O)({mu}-O{sub 2}H{sub 3})(L){sub 2}]{sup 3+}, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) has been treated consecutively with one eq of H{sub 2}O{sub 2} and one eq of HClO{sub 4} to form 3 ([Fe{sup IV}{sub 2}({mu}-O){sub 2}(L){sub 2}]{sup 4+}). In the course of this reaction a new species, 2, can be observed before the protonation step; 2 gives rise to a cationic peak cluster by ESI-MS at m/z 1,399, corresponding to the [Fe{sub 2}O{sub 3}L{sub 2}H](OTf){sub 2}{sup +} ion in which 1 oxygen atom derives from 1 and the other two originate from H{sub 2}O{sub 2}. Moessbauer studies of 2 reveal the presence of two distinct, exchange coupled iron(IV) centers, and EXAFS fits indicate a short Fe-O bond at 1.66 {angstrom} and an Fe-Fe distance of 3.32 {angstrom}. Taken together, the spectroscopic data point to an HO-Fe{sup IV}-O-Fe{sup IV} = O core for 2. Protonation of 2 results in the loss of H{sub 2}O and the formation of 3. Isotope labeling experiments show that the [Fe{sup IV}{sub 2}({mu}-O){sub 2}] core of 3 can incorporate both oxygen atoms from H{sub 2}O{sub 2}. The reactions described here serve as the only biomimetic precedent for the conversion of intermediates P to Q in the sMMO reaction cycle and shed light on how a peroxodiiron(III) unit can transform into an [Fe{sup IV}{sub 2}({mu}-O){sub 2}] core.

  12. Towards a whole-cell modeling approach for synthetic biology

    NASA Astrophysics Data System (ADS)

    Purcell, Oliver; Jain, Bonny; Karr, Jonathan R.; Covert, Markus W.; Lu, Timothy K.

    2013-06-01

    Despite rapid advances over the last decade, synthetic biology lacks the predictive tools needed to enable rational design. Unlike established engineering disciplines, the engineering of synthetic gene circuits still relies heavily on experimental trial-and-error, a time-consuming and inefficient process that slows down the biological design cycle. This reliance on experimental tuning is because current modeling approaches are unable to make reliable predictions about the in vivo behavior of synthetic circuits. A major reason for this lack of predictability is that current models view circuits in isolation, ignoring the vast number of complex cellular processes that impinge on the dynamics of the synthetic circuit and vice versa. To address this problem, we present a modeling approach for the design of synthetic circuits in the context of cellular networks. Using the recently published whole-cell model of Mycoplasma genitalium, we examined the effect of adding genes into the host genome. We also investigated how codon usage correlates with gene expression and find agreement with existing experimental results. Finally, we successfully implemented a synthetic Goodwin oscillator in the whole-cell model. We provide an updated software framework for the whole-cell model that lays the foundation for the integration of whole-cell models with synthetic gene circuit models. This software framework is made freely available to the community to enable future extensions. We envision that this approach will be critical to transforming the field of synthetic biology into a rational and predictive engineering discipline.

  13. Modeling and Experimentation on a Two-dimensional Synthetic jet

    NASA Astrophysics Data System (ADS)

    Wang, Yunfei; Mohseni, Kamran

    2007-11-01

    Hotwire anemometry is employed in order to investigate the spatial development of a two-dimensional synthetic jet. Flow velocity at various locations downstream from a slit is measured. A self similar behavior in the measured velocity is observed. An analytical model for a steady synthetic jet is developed that accurately matches the experimental data. As observed by other groups, the two-dimensional synthetic jet spreads at a rate higher than a continuous jet. This rate is accurately predicted by our model. It is identified that the main difference between a continuous jet and a synthetic jet is the higher value of the virtual viscosity (eddy viscosity) in a synthetic jet. This is attributed to the pulsate nature of a synthetic jet that makes it more susceptible to turbulence.

  14. Engineering coherence among excited states in synthetic heterodimer systems.

    PubMed

    Hayes, Dugan; Griffin, Graham B; Engel, Gregory S

    2013-06-21

    The design principles that support persistent electronic coherence in biological light-harvesting systems are obscured by the complexity of such systems. Some electronic coherences in these systems survive for hundreds of femtoseconds at physiological temperatures, suggesting that coherent dynamics may play a role in photosynthetic energy transfer. Coherent effects may increase energy transfer efficiency relative to strictly incoherent transfer mechanisms. Simple, tractable, manipulable model systems are required in order to probe the fundamental physics underlying these persistent electronic coherences, but to date, these quantum effects have not been observed in small molecules. We have engineered a series of rigid synthetic heterodimers that can serve as such a model system and observed quantum beating signals in their two-dimensional electronic spectra consistent with the presence of persistent electronic coherences.

  15. Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems.

    PubMed

    Konur, Savas; Gheorghe, Marian; Dragomir, Ciprian; Mierla, Laurentiu; Ipate, Florentin; Krasnogor, Natalio

    2015-01-16

    Computational models are perceived as an attractive alternative to mathematical models (e.g., ordinary differential equations). These models incorporate a set of methods for specifying, modeling, testing, and simulating biological systems. In addition, they can be analyzed using algorithmic techniques (e.g., formal verification). This paper shows how formal verification is utilized in systems and synthetic biology through qualitative vs quantitative analysis. Here, we choose two well-known case studies: quorum sensing in P. aeruginosas and pulse generator. The paper reports verification analysis of two systems carried out using some model checking tools, integrated to the Infobiotics Workbench platform, where system models are based on stochastic P systems.

  16. Exploring Synthetic and Systems Biology at the University of Edinburgh.

    PubMed

    Fletcher, Liz; Rosser, Susan; Elfick, Alistair

    2016-06-15

    The Centre for Synthetic and Systems Biology ('SynthSys') was originally established in 2007 as the Centre for Integrative Systems Biology, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). Today, SynthSys embraces an extensive multidisciplinary community of more than 200 researchers from across the University with a common interest in synthetic and systems biology. Our research is broad and deep, addressing a diversity of scientific questions, with wide ranging impact. We bring together the power of synthetic biology and systems approaches to focus on three core thematic areas: industrial biotechnology, agriculture and the environment, and medicine and healthcare. In October 2015, we opened a newly refurbished building as a physical hub for our new U.K. Centre for Mammalian Synthetic Biology funded by the BBSRC/EPSRC/MRC as part of the U.K. Research Councils' Synthetic Biology for Growth programme.

  17. Metabolic modelling in the development of cell factories by synthetic biology

    PubMed Central

    Jouhten, Paula

    2012-01-01

    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. PMID:24688669

  18. Bridging the gap between systems biology and synthetic biology

    PubMed Central

    Liu, Di; Hoynes-O’Connor, Allison; Zhang, Fuzhong

    2013-01-01

    Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics, and metabolomics, aiming to fill the gap between systems and synthetic biology. PMID:23898328

  19. Bridging the gap between systems biology and synthetic biology.

    PubMed

    Liu, Di; Hoynes-O'Connor, Allison; Zhang, Fuzhong

    2013-01-01

    Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics, and metabolomics, aiming to fill the gap between systems and synthetic biology.

  20. Synthetic thrombus model for in vitro studies of laser thrombolysis

    SciTech Connect

    Hermes, R.E.; Trajkovska, K.

    1998-07-01

    Laser thrombolysis is the controlled ablation of a thrombus (blood clot) blockage in a living arterial system. Theoretical modeling of the interaction of laser light with thrombi relies on the ability to perform in vitro experiments with well characterized surrogate materials. A synthetic thrombus formulation may offer more accurate results when compared to in vivo clinical experiments. The authors describe the development of new surrogate materials based on formulations incorporating chick egg, guar gum, modified food starch, and a laser light absorbing dye. The sound speed and physical consistency of the materials were very close to porcine (arterial) and human (venous) thrombi. Photographic and videotape recordings of pulsed dye laser ablation experiments under various experimental conditions were used to evaluate the new material as compared to in vitro tests with human (venous) thrombus. The characteristics of ablation and mass removal were similar to that of real thrombi, and therefore provide a more realistic model for in vitro laser thrombolysis when compared to gelatin.

  1. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing

    NASA Astrophysics Data System (ADS)

    Garcia-Ojalvo, Jordi; Elowitz, Michael B.; Strogatz, Steven H.

    2004-07-01

    Diverse biochemical rhythms are generated by thousands of cellular oscillators that somehow manage to operate synchronously. In fields ranging from circadian biology to endocrinology, it remains an exciting challenge to understand how collective rhythms emerge in multicellular structures. Using mathematical and computational modeling, we study the effect of coupling through intercell signaling in a population of Escherichia coli cells expressing a synthetic biological clock. Our results predict that a diverse and noisy community of such genetic oscillators interacting through a quorum-sensing mechanism should self-synchronize in a robust way, leading to a substantially improved global rhythmicity in the system. As such, the particular system of coupled genetic oscillators considered here might be a good candidate to provide the first quantitative example of a synchronization transition in a population of biological oscillators.

  2. A Heritable Recombination system for synthetic Darwinian evolution in yeast.

    PubMed

    Romanini, Dante W; Peralta-Yahya, Pamela; Mondol, Vanessa; Cornish, Virginia W

    2012-12-21

    Genetic recombination is central to the generation of molecular diversity and enhancement of evolutionary fitness in living systems. Methods such as DNA shuffling that recapitulate this diversity mechanism in vitro are powerful tools for engineering biomolecules with useful new functions by directed evolution. Synthetic biology now brings demand for analogous technologies that enable the controlled recombination of beneficial mutations in living cells. Thus, here we create a Heritable Recombination system centered around a library cassette plasmid that enables inducible mutagenesis via homologous recombination and subsequent combination of beneficial mutations through sexual reproduction in Saccharomyces cerevisiae. Using repair of nonsense codons in auxotrophic markers as a model, Heritable Recombination was optimized to give mutagenesis efficiencies of up to 6% and to allow successive repair of different markers through two cycles of sexual reproduction and recombination. Finally, Heritable Recombination was employed to change the substrate specificity of a biosynthetic enzyme, with beneficial mutations in three different active site loops crossed over three continuous rounds of mutation and selection to cover a total sequence diversity of 10(13). Heritable Recombination, while at an early stage of development, breaks the transformation barrier to library size and can be immediately applied to combinatorial crossing of beneficial mutations for cell engineering, adding important features to the growing arsenal of next generation molecular biology tools for synthetic biology. PMID:23412545

  3. Industrial systems biology and its impact on synthetic biology of yeast cell factories.

    PubMed

    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.

  4. SIFT vehicle recognition with semi-synthetic model database

    NASA Astrophysics Data System (ADS)

    Price, Rebecca L.; Rovito, Todd V.

    2012-06-01

    Object recognition is an important problem that has many applications that are of interest to the United States Air Force (USAF). Recently the USAF released its update to Technology Horizons, a report that is designed to guide the science and technology direction of the Air Force. Technology Horizons specifically calls out for the need to use autonomous systems in essentially all aspects of Air Force operations [1]. Object recognition is a key enabler to autonomous exploitation of intelligence, surveillance, and reconnaissance (ISR) data which might make the automatic searching of millions of hours of video practical. In particular this paper focuses on vehicle recognition with Lowe's Scale-invariant feature transform (SIFT) using a model database that was generated with semi-synthetic data. To create the model database we used a desktop laser scanner to create a high resolution 3D facet model. Then the 3D facet model was imported into LuxRender, a physics accurate ray tracing tool, and several views were rendered to create a model database. SIFT was selected because the algorithm is invariant to scale, noise, and illumination making it possible to create a model database of only a hundred original viewing locations which keeps the size of the model database reasonable.

  5. Developing a synthetic signal transduction system in plants.

    PubMed

    Morey, Kevin J; Antunes, Mauricio S; Albrecht, Kirk D; Bowen, Tessa A; Troupe, Jared F; Havens, Keira L; Medford, June I

    2011-01-01

    One area of focus in the emerging field of plant synthetic biology is the manipulation of systems involved in sensing and response to environmental signals. Sensing and responding to signals, including ligands, typically involves biological signal transduction. Plants use a wide variety of signaling systems to sense and respond to their environment. One of these systems, a histidine kinase (HK) based signaling system, lends itself to manipulation using the tools of synthetic biology. Both plants and bacteria use HKs to relay signals, which in bacteria can involve as few as two proteins (two-component systems or TCS). HK proteins are evolutionarily conserved between plants and bacteria and plant HK components have been shown to be functional in bacteria. We found that this conservation also applies to bacterial HK components which can function in plants. This conservation of function led us to hypothesize that synthetic HK signaling components can be designed and rapidly tested in bacteria. These novel HK signaling components form the foundation for a synthetic signaling system in plants, but typically require modifications such as codon optimization and proper targeting to allow optimal function. We describe the process and methodology of producing a synthetic signal transduction system in plants. We discovered that the bacterial response regulator (RR) PhoB shows HK-dependent nuclear translocation in planta. Using this discovery, we engineered a partial synthetic pathway in which a synthetic promoter (PlantPho) is activated using a plant-adapted PhoB (PhoB-VP64) and the endogenous HK-based cytokinin signaling pathway. Building on this work, we adapted an input or sensing system based on bacterial chemotactic binding proteins and HKs, resulting in a complete eukaryotic signal transduction system. Input to our eukaryotic signal transduction system is provided by a periplasmic binding protein (PBP), ribose-binding protein (RBP). RBP interacts with the membrane

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

    PubMed

    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. PMID:20467105

  7. Synthetic aperture radar autofocus based on a bilinear model.

    PubMed

    Liu, Kuang-Hung; Wiesel, Ami; Munson, David C

    2012-05-01

    Autofocus algorithms are used to restore images in nonideal synthetic aperture radar imaging systems. In this paper, we propose a bilinear parametric model for the unknown image and the nuisance phase parameters and derive an efficient maximum-likelihood autofocus (MLA) algorithm. In the special case of a simple image model and a narrow range of look angles, MLA coincides with the successful multichannel autofocus (MCA). MLA can be interpreted as a generalization of MCA to a larger class of models with a larger range of look angles. We analyze its advantages over previous extensions of MCA in terms of identifiability conditions and noise sensitivity. As a byproduct, we also propose numerical approximations to the difficult constant modulus quadratic program that lies at the core of these algorithms. We demonstrate the superior performance of our proposed methods using computer simulations in both the correct and mismatched system models. MLA performs better than other methods, both in terms of the mean squared error and visual quality of the restored image.

  8. Design and mathematical modelling of a synthetic symbiotic ecosystem.

    PubMed

    Kambam, P K R; Henson, M A; Sun, L

    2008-01-01

    Artificial microbial ecosystems have been increasingly used to understand principles of ecology. These systems offer unique capabilities to mimic a variety of ecological interactions that otherwise would be difficult to study experimentally in a reasonable period of time. However, the elucidation of the genetic bases for these interactions remains a daunting challenge. To address this issue, we have designed and analysed a synthetic symbiotic ecosystem in which the genetic nature of the microbial interactions is defined explicitly. A mathematical model of the gene regulatory network in each species and their interaction through quorum sensing mediated intercellular signalling was derived to investigate the effect of system components on cooperative behaviour. Dynamic simulation and bifurcation analysis showed that the designed system admits a stable coexistence steady state for sufficiently large initial cell concentrations of the two species. The steady-state fraction of each species could be altered by varying model parameters associated with gene transcription and signalling molecule synthesis rates. The design also admitted a stable steady state corresponding to extinction of the two species for low initial cell concentrations and stable periodic solutions over certain domains of parameter space. The mathematical analysis was shown to provide insights into natural microbial ecosystems and to allow identification of molecular targets for engineering system behaviour.

  9. Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

    PubMed Central

    Lewis, Daniel D.; Villarreal, Fernando D.; Wu, Fan; Tan, Cheemeng

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems. PMID:25538941

  10. Synthetic biology outside the cell: linking computational tools to cell-free systems.

    PubMed

    Lewis, Daniel D; Villarreal, Fernando D; Wu, Fan; Tan, Cheemeng

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

  11. The Application of Lidar to Synthetic Vision System Integrity

    NASA Technical Reports Server (NTRS)

    Campbell, Jacob L.; UijtdeHaag, Maarten; Vadlamani, Ananth; Young, Steve

    2003-01-01

    One goal in the development of a Synthetic Vision System (SVS) is to create a system that can be certified by the Federal Aviation Administration (FAA) for use at various flight criticality levels. As part of NASA s Aviation Safety Program, Ohio University and NASA Langley have been involved in the research and development of real-time terrain database integrity monitors for SVS. Integrity monitors based on a consistency check with onboard sensors may be required if the inherent terrain database integrity is not sufficient for a particular operation. Sensors such as the radar altimeter and weather radar, which are available on most commercial aircraft, are currently being investigated for use in a real-time terrain database integrity monitor. This paper introduces the concept of using a Light Detection And Ranging (LiDAR) sensor as part of a real-time terrain database integrity monitor. A LiDAR system consists of a scanning laser ranger, an inertial measurement unit (IMU), and a Global Positioning System (GPS) receiver. Information from these three sensors can be combined to generate synthesized terrain models (profiles), which can then be compared to the stored SVS terrain model. This paper discusses an initial performance evaluation of the LiDAR-based terrain database integrity monitor using LiDAR data collected over Reno, Nevada. The paper will address the consistency checking mechanism and test statistic, sensitivity to position errors, and a comparison of the LiDAR-based integrity monitor to a radar altimeter-based integrity monitor.

  12. Synthetic testing of the Pacific Northwest earthquake early warning system

    NASA Astrophysics Data System (ADS)

    Crowell, B. W.; Schmidt, D. A.; Bodin, P.; Vidale, J. E.; Gomberg, J. S.; Jamison, D.; Minson, S. E.; Hartog, J. R.; Kress, V. C.; Malone, S. D.; Usher, M.

    2014-12-01

    The Cascadia subduction zone poses one of the greatest risks for a megaquake in the continental United States and, because of this, the Pacific Northwest Seismic Network (PNSN) at the University of Washington is building a joint seismic and geodetic earthquake early warning system. Our two-stage approach to earthquake early warning includes: (1) detection and initial characterization using strong-motion and broadband data from the PNSN with the ElarmS package, and (2) geodetic modeling modules using GPS data from the Pacific Northwest Geodetic Array (PANGA) and combined seismogeodetic (GPS + strong-motion) data. Because of Cascadia's relatively low seismicity rate and the paucity of data from plate boundary earthquakes, we have prioritized the development of a test system and the creation of several large simulated events. The test system permits us to: (1) replay segments of actual seismic waveform data recorded from the PNSN and neighboring networks to represent both earthquakes and noise conditions, and (2) broadcast synthetic data into the system to simulate signals we anticipate from earthquakes for which we have no actual ground motion recordings. The test system lets us also simulate various error conditions (latent and/or out-of-sequence data, telemetry drop-outs, etc.) and to explore how best to mitigate them. Here, we report on the performance of the joint early warning system and the geodetic modeling modules in a simulated real-time mode using simulated 5-Hz displacements from plausible Cascadian earthquake scenarios. The simulations are created using the FK integration method for hypothetical source models for a wide array of possible faulting types and magnitudes. The results show that the geodetic modeling modules are able to properly characterize the simulated events, and we discuss the limitations with respect to latency, network architecture, and earthquake location throughout the Pacific Northwest.

  13. Enhanced/Synthetic Vision Systems for Advanced Flight Decks

    NASA Technical Reports Server (NTRS)

    Kaiser, Mary K.; Jenkins, James; Statler, Irving C. (Technical Monitor)

    1994-01-01

    One of the most challenging arenas for enhanced and synthetic vision systems is the flight deck. Here, pilots must perform active and supervisory control behaviors based on imagery generated in real time or transduced from imaging sensors. Although enhanced and synthetic vision technologies have been used in military vehicles for more than two decades, they have only recently been considered for civilian transport aircraft. In this paper we discuss the human performance issues still to be resolved for these systems, and consider the special constraints that must be considered for their use in the transport domain.

  14. Kapitza problem for the magnetic moments of synthetic antiferromagnetic systems

    SciTech Connect

    Dzhezherya, Yu. I.; Demishev, K. O.; Korenivskii, V. N.

    2012-08-15

    The dynamics of magnetization in synthetic antiferromagnetic systems with the magnetic dipole coupling in a rapidly oscillating field has been examined. It has been revealed that the system can behave similar to the Kapitza pendulum. It has been shown that an alternating magnetic field can be efficiently used to control the magnetic state of a cell of a synthetic antiferromagnet. Analytical relations have been obtained between the parameters of such an antiferromagnet and an external magnetic field at which certain quasistationary states are implemented.

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

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

    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.

  16. Synthetic biology: advancing the design of diverse genetic systems

    PubMed Central

    Wang, Yen-Hsiang; Wei, Kathy Y.; Smolke, Christina D.

    2013-01-01

    A main objective of synthetic biology is to make the process of designing genetically-encoded biological systems more systematic, predictable, robust, scalable, and efficient. The examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from a simple genetic switch to search-and-destroy systems. While significant advances in synthesis capabilities support the potential for the implementation of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Synthetic biology offers much promise in developing systems to address challenges faced in manufacturing, the environment and sustainability, and health and medicine, but the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems. PMID:23413816

  17. Transfer of Instrument Training and the Synthetic Flight Training System.

    ERIC Educational Resources Information Center

    Caro, Paul W.

    One phase of an innovative flight training program, its development, and initial administration is described in this paper. The operational suitability test activities related to a determination of the transfer of instrument training value of the Army's Synthetic Flight Training System (SFTS) Device 2B24. Sixteen active Army members of an Officer…

  18. Directed evolution and synthetic biology applications to microbial systems.

    PubMed

    Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

    2016-06-01

    Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. PMID:27054950

  19. Synthetic gauge flux and Weyl points in acoustic systems

    NASA Astrophysics Data System (ADS)

    Xiao, Meng; Chen, Wen-Jie; He, Wen-Yu; Chan, C. T.

    We consider acoustic systems comprising a honeycomb lattice in the xy plane and periodic along the z direction. As kz is a good quantum number here, for each fixed kz, this system can be treated as a reduced two-dimensional system. By engineering the interlayer coupling in the z-direction, we show that we can realize effective inversion symmetry breaking and synthetic staggered gauge flux in the reduced two-dimensional system. The realizations of chiral edge states for fixed values of kz are direct consequences of the staggered gauge flux. And we then show that the synthetic gauge flux is closely related to the Weyl points in the three-dimensional band structure. This work was supported by the Hong Kong Research Grants Council (Grant No. AoE/P-02/12).

  20. A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

    PubMed

    Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

    2016-06-17

    Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

  1. Experiments with the Mesoscale Atmospheric Simulation System (MASS) using the synthetic relative humidity

    NASA Technical Reports Server (NTRS)

    Chang, Chia-Bo

    1994-01-01

    This study is intended to examine the impact of the synthetic relative humidity on the model simulation of mesoscale convective storm environment. The synthetic relative humidity is derived from the National Weather Services surface observations, and non-conventional sources including aircraft, radar, and satellite observations. The latter sources provide the mesoscale data of very high spatial and temporal resolution. The synthetic humidity data is used to complement the National Weather Services rawinsonde observations. It is believed that a realistic representation of initial moisture field in a mesoscale model is critical for the model simulation of thunderstorm development, and the formation of non-convective clouds as well as their effects on the surface energy budget. The impact will be investigated based on a real-data case study using the mesoscale atmospheric simulation system developed by Mesoscale Environmental Simulations Operations, Inc. The mesoscale atmospheric simulation system consists of objective analysis and initialization codes, and the coarse-mesh and fine-mesh dynamic prediction models. Both models are a three dimensional, primitive equation model containing the essential moist physics for simulating and forecasting mesoscale convective processes in the atmosphere. The modeling system is currently implemented at the Applied Meteorology Unit, Kennedy Space Center. Two procedures involving the synthetic relative humidity to define the model initial moisture fields are considered. It is proposed to perform several short-range (approximately 6 hours) comparative coarse-mesh simulation experiments with and without the synthetic data. They are aimed at revealing the model sensitivities should allow us both to refine the specification of the observational requirements, and to develop more accurate and efficient objective analysis schemes. The goal is to advance the MASS (Mesoscal Atmospheric Simulation System) modeling expertise so that the model

  2. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    PubMed Central

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  3. Enhanced and synthetic vision system (ESVS) flight demonstration

    NASA Astrophysics Data System (ADS)

    Sanders-Reed, John N.; Bernier, Ken; Güell, Jeff

    2008-04-01

    Boeing has developed and flight demonstrated a distributed aperture enhanced and synthetic vision system for integrated situational awareness. The system includes 10 sensors, 2 simultaneous users with head mounted displays (one via a wireless remote link), and intelligent agents for hostile fire detection, ground moving target detection and tracking, and stationary personnel and vehicle detection. Flight demonstrations were performed in 2006 and 2007 on a MD-530 "Little Bird" helicopter.

  4. Scaling Reversible Adhesion in Synthetic and Biological Systems

    NASA Astrophysics Data System (ADS)

    Bartlett, Michael; Irschick, Duncan; Crosby, Alfred

    2013-03-01

    High capacity, easy release polymer adhesives, as demonstrated by a gecko's toe, present unique opportunities for synthetic design. However, without a framework that connects biological and synthetic adhesives from basic nanoscopic features to macroscopic systems, synthetic mimics have failed to perform favorably at large length scales. Starting from an energy balance, we develop a scaling approach to understand unstable interfacial fracture over multiple length scales. The simple theory reveals that reversibly adhesive polymers do not rely upon fibrillar features but require contradicting attributes: maximum compliance normal to the substrate and minimum compliance in the loading direction. We use this counterintuitive criterion to create reversible, easy release adhesives at macroscopic sizes (100 cm2) with unprecedented force capacities on the order of 3000 N. Importantly, we achieve this without fibrillar features, supporting our predictions and emphasizing the importance of subsurface anatomy in biological adhesive systems. Our theory describes adhesive force capacity as a function of material properties and geometry and is supported by over 1000 experiments, spanning both synthetic and biological adhesives, with agreement over 14 orders of magnitude in adhesive force.

  5. Convex model-based synthetic aperture radar processing

    NASA Astrophysics Data System (ADS)

    Knight, Chad P.

    The use of radar often conjures up images of small blobs on a screen. But current synthetic aperture radar (SAR) systems are able to generate near-optical quality images with amazing benefits compared to optical sensors. These SAR sensors work in all weather conditions, day or night, and provide many advanced capabilities to detect and identify targets of interest. These amazing abilities have made SAR sensors a work-horse in remote sensing, and military applications. SAR sensors are ranging instruments that operate in a 3D environment, but unfortunately the results and interpretation of SAR images have traditionally been done in 2D. Three-dimensional SAR images could provide improved target detection and identification along with improved scene interpretability. As technology has increased, particularly regarding our ability to solve difficult optimization problems, the 3D SAR reconstruction problem has gathered more interest. This dissertation provides the SAR and mathematical background required to pose a SAR 3D reconstruction problem. The problem is posed in a way that allows prior knowledge about the target of interest to be integrated into the optimization problem when known. The developed model is demonstrated on simulated data initially in order to illustrate critical concepts in the development. Then once comprehension is achieved the processing is applied to actual SAR data. The 3D results are contrasted against the current "gold-standard." The results are shown as 3D images demonstrating the improvement regarding scene interpretability that this approach provides.

  6. JAK/STAT signalling--an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology.

    PubMed

    Blätke, Mary Ann; Dittrich, Anna; Rohr, Christian; Heiner, Monika; Schaper, Fred; Marwan, Wolfgang

    2013-06-01

    Mathematical models of molecular networks regulating biological processes in cells or organisms are most frequently designed as sets of ordinary differential equations. Various modularisation methods have been applied to reduce the complexity of models, to analyse their structural properties, to separate biological processes, or to reuse model parts. Taking the JAK/STAT signalling pathway with the extensive combinatorial cross-talk of its components as a case study, we make a natural approach to modularisation by creating one module for each biomolecule. Each module consists of a Petri net and associated metadata and is organised in a database publically accessible through a web interface (). The Petri net describes the reaction mechanism of a given biomolecule and its functional interactions with other components including relevant conformational states. The database is designed to support the curation, documentation, version control, and update of individual modules, and to assist the user in automatically composing complex models from modules. Biomolecule centred modules, associated metadata, and database support together allow the automatic creation of models by considering differential gene expression in given cell types or under certain physiological conditions or states of disease. Modularity also facilitates exploring the consequences of alternative molecular mechanisms by comparative simulation of automatically created models even for users without mathematical skills. Models may be selectively executed as an ODE system, stochastic, or qualitative models or hybrid and exported in the SBML format. The fully automated generation of models of redesigned networks by metadata-guided modification of modules representing biomolecules with mutated function or specificity is proposed. PMID:23443149

  7. Millimeter Wave Synthetic Aperture Imaging System with a Unique Rotary Scanning System

    NASA Technical Reports Server (NTRS)

    Ghasr, M. T.; Case, J. T.; McClanahan, A. D.; Abou-Khousa, M.; Guinn, K.; Kharkovsky, S.; Zoughi, R.; Afaki-Beni, A.; DePaulis, F.; Pommerenke, D.

    2008-01-01

    This is the video that accompanies the "Millimeter Wave Synthetic Aperture Imaging System with a Unique Rotary Scanning System" presentation. It shows the operation of the scanning system, and reviews the results of the scanning of a sample.

  8. Waveform Inversion of Synthetic Ocean Models in the Laplace Domain

    NASA Astrophysics Data System (ADS)

    Rosado, H.; Blacic, T. M.; Jun, H.; Shin, C.

    2014-12-01

    In seismic oceanography, the processed images show where small temperature changes (as little as 0.03°C) occur, although they do not give absolute temperatures. To get a 2-D temperature map, the data must be inverted for sound speed, which is then converted to temperature using equations of state. Full waveform inversion requires a starting model that is iteratively updated until the residuals converge. Global search algorithms such as Genetic Algorithm do not require a starting model close to the true model, but are computationally exhausting. Local search inversion is less expensive, but requires a reasonably accurate starting model. Unfortunately, most marine seismic data has little associated hydrographic data and so it is difficult to create starting models close enough to the true model for convergence throughout the target area. In addition, the band-limited nature of seismic data makes it inherently challenging to extract the long wavelength sound speed trend directly from seismic data. Laplace domain inversion (LDI) developed by Changsoo Shin and colleagues requires only a rudimentary starting model to produce smooth background sound speed models without requiring prior information about the medium. It works by transforming input data to the Laplace domain, and then examining the zero frequency component of the damped wavefield to extract a smooth sound speed model - basically, removing higher frequency fluctuations to expose background trends. This ability to use frequencies below those effectively propagated by the seismic source is what enables LDI to produce the smooth background trend from the data. We applied LDI to five synthetic data sets based on simplified models of oceanographic features. Using LDI, we were able to recover smoothed versions of our synthetic models, showing the viability of the method for creating sound speed profiles suitable for use as starting models for other methods of inversion that output more detailed models.

  9. Synthetic membranes and membrane processes with counterparts in biological systems

    NASA Astrophysics Data System (ADS)

    Matson, Stephen L.

    1996-02-01

    Conventional synthetic membranes, fashioned for the most part from rather unremarkable polymeric materials, are essentially passive structures that achieve various industrial and biomedical separations through simple and selective membrane permeation processes. Indeed, simplicity of membrane material, structure, and function has long been perceived as a virtue of membranes relative to other separation processes with which they compete. The passive membrane separation processes -- exemplified by micro- and ultrafiltration, dialysis, reverse osmosis, and gas permeation -- differ from one another primarily in terms of membrane morphology or structure (e.g., porous, gel-type, and nonporous) and the permeant transport mechanism and driving force (e.g., diffusion, convection, and 'solution/diffusion'). The passive membrane separation processes have in common the fact that interaction between permeant and membrane material is typically weak and physicochemical in nature; indeed, it is frequently an objective of membrane materials design to minimize interaction between permeant and membrane polymer, since such strategies can minimize membrane fouling. As a consequence, conventional membrane processes often provide only modest separation factors or permselectivities; that is, they are more useful in performing 'group separations' (i.e., the separation of different classes of material) than they are in fractionating species within a given class. It has long been recognized within the community of membrane technologists that biological membrane structures and their components are extraordinarily sophisticated and powerful as compared to their synthetic counterparts. Moreover, biomembranes and related biological systems have been 'designed' according to a very different paradigm -- one that frequently maximizes and capitalizes on extraordinarily strong and biochemically specific interactions between components of the membrane and species interacting with them. Thus, in recent

  10. Crew and Display Concepts Evaluation for Synthetic / Enhanced Vision Systems

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Kramer, Lynda J.; Prinzel, Lawrence J., III

    2006-01-01

    NASA s Synthetic Vision Systems (SVS) project is developing technologies with practical applications that strive to eliminate low-visibility conditions as a causal factor to civil aircraft accidents and replicate the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. Enhanced Vision System (EVS) technologies are analogous and complementary in many respects to SVS, with the principle difference being that EVS is an imaging sensor presentation, as opposed to a database-derived image. The use of EVS in civil aircraft is projected to increase rapidly as the Federal Aviation Administration recently changed the aircraft operating rules under Part 91, revising the flight visibility requirements for conducting operations to civil airports. Operators conducting straight-in instrument approach procedures may now operate below the published approach minimums when using an approved EVS that shows the required visual references on the pilot s Head-Up Display. An experiment was conducted to evaluate the complementary use of SVS and EVS technologies, specifically focusing on new techniques for integration and/or fusion of synthetic and enhanced vision technologies and crew resource management while operating under the newly adopted FAA rules which provide operating credit for EVS. Overall, the experimental data showed that significant improvements in SA without concomitant increases in workload and display clutter could be provided by the integration and/or fusion of synthetic and enhanced vision technologies for the pilot-flying and the pilot-not-flying.

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

    PubMed Central

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

    2016-01-01

    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. PMID:27136579

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

    PubMed

    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.

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

    PubMed

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

    2016-01-01

    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. PMID:27136579

  14. Lighting system with thermal management system having point contact synthetic jets

    DOEpatents

    Arik, Mehmet; Weaver, Stanton Earl; Kuenzler, Glenn Howard; Wolfe, Jr, Charles Franklin; Sharma, Rajdeep

    2016-08-30

    Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system includes a plurality of synthetic jets. The synthetic jets are arranged within the lighting system such that they are secured at contact points.

  15. Lighting system with thermal management system having point contact synthetic jets

    DOEpatents

    Arik, Mehmet; Weaver, Stanton Earl; Kuenzler, Glenn Howard; Wolfe, Jr., Charles Franklin; Sharma, Rajdeep

    2016-08-23

    Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system includes a plurality of synthetic jets. The synthetic jets are arranged within the lighting system such that they are secured at contact points.

  16. Lighting system with thermal management system having point contact synthetic jets

    DOEpatents

    Arik, Mehmet; Weaver, Stanton Earl; Kuenzler, Glenn Howard; Wolfe, Jr., Charles Franklin; Sharma, Rajdeep

    2013-12-10

    Lighting system having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system includes a plurality of synthetic jets. The synthetic jets are arranged within the lighting system such that they are secured at contact points.

  17. Synthetic immunosurveillance systems: nanodevices to monitor physiological events.

    PubMed

    Woappi, Yvon L; Jangiti, Rahul; Singh, Om V

    2014-11-15

    The field of nanotechnology has recently seen vast advancements in its applications for therapeutic strategy. This technological revolution has led way to nanomedicine, which spurred the development of clever drug delivery designs and ingenious nanovehicles for the monitoring of cellular events in vivo. The clinical implementations of this technology are innumerable and have demonstrated utility as diagnostic tools and fortifying machineries for the mammalian immune system. Recently engineered viral vectors and multi-subunit packaging RNAs have verified stable enough for long-term existence in the physiological environment and therefore reveal unique potential as artificial immunosurveillance devices. Physiological and pathological events recorded by nanodevices could help develop "biocatalogs" of patients' infection history, frequency of disease, and much more. In this article, we introduce a novel design concept for a multilayer synthetic immune network parallel to the natural immune system; an artificial network of continuously patrolling nanodevices incorporated in the blood and lymphatic systems, and adapted for molecular event recording, anomaly detection, drug delivery, and gene silencing. We also aim to discuss the approaches and advances recently reported in nanomedicine, especially as it pertains to promising viral and RNA-based nanovehicles and their prospective applications for the development of a synthetic immunosurveillance system (SIS). Alternative suggestions and limitations of these technologies are also discussed.

  18. Comparison of different synthetic 5-min rainfall time series regarding their suitability for urban drainage modelling

    NASA Astrophysics Data System (ADS)

    van der Heijden, Sven; Callau Poduje, Ana; Müller, Hannes; Shehu, Bora; Haberlandt, Uwe; Lorenz, Manuel; Wagner, Sven; Kunstmann, Harald; Müller, Thomas; Mosthaf, Tobias; Bárdossy, András

    2015-04-01

    For the design and operation of urban drainage systems with numerical simulation models, long, continuous precipitation time series with high temporal resolution are necessary. Suitable observed time series are rare. As a result, intelligent design concepts often use uncertain or unsuitable precipitation data, which renders them uneconomic or unsustainable. An expedient alternative to observed data is the use of long, synthetic rainfall time series as input for the simulation models. Within the project SYNOPSE, several different methods to generate synthetic precipitation data for urban drainage modelling are advanced, tested, and compared. The presented study compares four different approaches of precipitation models regarding their ability to reproduce rainfall and runoff characteristics. These include one parametric stochastic model (alternating renewal approach), one non-parametric stochastic model (resampling approach), one downscaling approach from a regional climate model, and one disaggregation approach based on daily precipitation measurements. All four models produce long precipitation time series with a temporal resolution of five minutes. The synthetic time series are first compared to observed rainfall reference time series. Comparison criteria include event based statistics like mean dry spell and wet spell duration, wet spell amount and intensity, long term means of precipitation sum and number of events, and extreme value distributions for different durations. Then they are compared regarding simulated discharge characteristics using an urban hydrological model on a fictitious sewage network. First results show a principal suitability of all rainfall models but with different strengths and weaknesses regarding the different rainfall and runoff characteristics considered.

  19. The NASA/JPL Airborne Synthetic Aperture Radar System

    NASA Technical Reports Server (NTRS)

    Lou, Yunling; Kim,Yunjin; vanZyl, Jakob

    1996-01-01

    In this paper we will briefly describe the instrument characteristics, the evolution of various radar modes, the instrument performance and improvement in the knowledge of the positioning and attitude information of the NASA/JPL airborne synthetic aperture radar (SAR). This system operates in the fully polarimetric mode in the P, L, and C band simultaneously or in the interferometric mode in both the L and C band simultaneously. We also summarize the progress of the data processing effort, especially in the interferometry processing and we address the issue of processing and calibrating the cross-track interferometry data.

  20. Phase correction system for automatic focusing of synthetic aperture radar

    DOEpatents

    Eichel, Paul H.; Ghiglia, Dennis C.; Jakowatz, Jr., Charles V.

    1990-01-01

    A phase gradient autofocus system for use in synthetic aperture imaging accurately compensates for arbitrary phase errors in each imaged frame by locating highlighted areas and determining the phase disturbance or image spread associated with each of these highlight areas. An estimate of the image spread for each highlighted area in a line in the case of one dimensional processing or in a sector, in the case of two-dimensional processing, is determined. The phase error is determined using phase gradient processing. The phase error is then removed from the uncorrected image and the process is iteratively performed to substantially eliminate phase errors which can degrade the image.

  1. Quantitative statistical assessment of conditional models for synthetic aperture radar.

    PubMed

    DeVore, Michael D; O'Sullivan, Joseph A

    2004-02-01

    Many applications of object recognition in the presence of pose uncertainty rely on statistical models-conditioned on pose-for observations. The image statistics of three-dimensional (3-D) objects are often assumed to belong to a family of distributions with unknown model parameters that vary with one or more continuous-valued pose parameters. Many methods for statistical model assessment, for example the tests of Kolmogorov-Smirnov and K. Pearson, require that all model parameters be fully specified or that sample sizes be large. Assessing pose-dependent models from a finite number of observations over a variety of poses can violate these requirements. However, a large number of small samples, corresponding to unique combinations of object, pose, and pixel location, are often available. We develop methods for model testing which assume a large number of small samples and apply them to the comparison of three models for synthetic aperture radar images of 3-D objects with varying pose. Each model is directly related to the Gaussian distribution and is assessed both in terms of goodness-of-fit and underlying model assumptions, such as independence, known mean, and homoscedasticity. Test results are presented in terms of the functional relationship between a given significance level and the percentage of samples that wold fail a test at that level. PMID:15376934

  2. Vibratory responses of synthetic, self-oscillating vocal fold models

    PubMed Central

    Murray, Preston R.; Thomson, Scott L.

    2012-01-01

    The flow-induced responses of four self-oscillating synthetic vocal fold models are compared. All models were life-sized and fabricated using flexible silicone compounds with material properties comparable to those of human vocal fold tissue. Three of the models had two layers of different stiffness to represent the body–cover grouping of vocal fold tissue. Two of the two-layer models were based on the “M5” geometry [Scherer et al., J. Acoust. Soc. Am. 109, 1616–1630 (2001)], while the third was based on magnetic resonance imaging data. The fourth model included several layers, including a thin epithelial layer, an exceedingly flexible superficial lamina propria layer, a ligament layer that included an anteriorly–posteriorly oriented fiber to restrict vertical motion, and a body layer. Measurements were performed with these models in full larynx and hemilarynx configurations. Data included onset pressure, vibration frequency, glottal flow rate, maximum glottal width, and medial surface motion, the latter two of which were acquired using high-speed imaging techniques. The fourth, multi-layer model exhibited onset pressure, frequency, and medial surface motion traits that are comparable to published human vocal fold data. Importantly, the model featured an alternating convergent–divergent glottal profile and mucosal wave-like motion, characteristics which are important markers of human vocal fold vibration. PMID:23145623

  3. Statistical assessment of model fit for synthetic aperture radar data

    NASA Astrophysics Data System (ADS)

    DeVore, Michael D.; O'Sullivan, Joseph A.

    2001-08-01

    Parametric approaches to problems of inference from observed data often rely on assumed probabilistic models for the data which may be based on knowledge of the physics of the data acquisition. Given a rich enough collection of sample data, the validity of those assumed models can be assessed in a statistical hypothesis testing framework using any of a number of goodness-of-fit tests developed over the last hundred years for this purpose. Such assessments can be used both to compare alternate models for observed data and to help determine the conditions under which a given model breaks down. We apply three such methods, the (chi) 2 test of Karl Pearson, Kolmogorov's goodness-of-fit test, and the D'Agostino-Pearson test for normality, to quantify how well the data fit various models for synthetic aperture radar (SAR) images. The results of these tests are used to compare a conditionally Gaussian model for complex-valued SAR pixel values, a conditionally log-normal model for SAR pixel magnitudes, and a conditionally normal model for SAR pixel quarter-power values. Sample data for these tests are drawn from the publicly released MSTAR dataset.

  4. Image processing in an enhanced and synthetic vision system

    NASA Astrophysics Data System (ADS)

    Mueller, Rupert M.; Palubinskas, Gintautas; Gemperlein, Hans

    2002-07-01

    'Synthetic Vision' and 'Sensor Vision' complement to an ideal system for the pilot's situation awareness. To fuse these two data sets the sensor images are first segmented by a k-means algorithm and then features are extracted by blob analysis. These image features are compared with the features of the projected airport data using fuzzy logic in order to identify the runway in the sensor image and to improve the aircraft navigation data. This process is necessary due to inaccurate input data i.e. position and attitude of the aircraft. After identifying the runway, obstacles can be detected using the sensor image. The extracted information is presented to the pilot's display system and combined with the appropriate information from the MMW radar sensor in a subsequent fusion processor. A real time image processing procedure is discussed and demonstrated with IR measurements of a FLIR system during landing approaches.

  5. Synthetic vision and emotion calculation in intelligent virtual human modeling.

    PubMed

    Zhao, Y; Kang, J; Wright, D K

    2007-01-01

    The virtual human technique can already provide vivid and believable human behaviour in more and more scenarios. Virtual humans are expected to replace real humans in hazardous situations to undertake tests and feed back valuable information. This paper will introduce a virtual human with a novel collision-based synthetic vision, short-term memory model and a capability to implement emotion calculation and decision making. The virtual character based on this model can 'see' what is in its field of view (FOV) and remember those objects. After that, a group of affective computing equations have been introduced. These equations have been implemented into a proposed emotion calculation process to enlighten emotion for virtual intelligent humans. PMID:17487108

  6. Enhanced/Synthetic Vision Systems - Human factors research and implications for future systems

    NASA Technical Reports Server (NTRS)

    Foyle, David C.; Ahumada, Albert J.; Larimer, James; Sweet, Barbara T.

    1992-01-01

    This paper reviews recent human factors research studies conducted in the Aerospace Human Factors Research Division at NASA Ames Research Center related to the development and usage of Enhanced or Synthetic Vision Systems. Research discussed includes studies of field of view (FOV), representational differences of infrared (IR) imagery, head-up display (HUD) symbology, HUD advanced concept designs, sensor fusion, and sensor/database fusion and evaluation. Implications for the design and usage of Enhanced or Synthetic Vision Systems are discussed.

  7. Gene gymnastics: Synthetic biology for baculovirus expression vector system engineering.

    PubMed

    Vijayachandran, Lakshmi S; Thimiri Govinda Raj, Deepak B; Edelweiss, Evelina; Gupta, Kapil; Maier, Josef; Gordeliy, Valentin; Fitzgerald, Daniel J; Berger, Imre

    2013-01-01

    Most essential activities in eukaryotic cells are catalyzed by large multiprotein assemblies containing up to ten or more interlocking subunits. The vast majority of these protein complexes are not easily accessible for high resolution studies aimed at unlocking their mechanisms, due to their low cellular abundance and high heterogeneity. Recombinant overproduction can resolve this bottleneck and baculovirus expression vector systems (BEVS) have emerged as particularly powerful tools for the provision of eukaryotic multiprotein complexes in high quality and quantity. Recently, synthetic biology approaches have begun to make their mark in improving existing BEVS reagents by de novo design of streamlined transfer plasmids and by engineering the baculovirus genome. Here we present OmniBac, comprising new custom designed reagents that further facilitate the integration of heterologous genes into the baculovirus genome for multiprotein expression. Based on comparative genome analysis and data mining, we herein present a blueprint to custom design and engineer the entire baculovirus genome for optimized production properties using a bottom-up synthetic biology approach. PMID:23328086

  8. Synthetic event-related potentials: a computational bridge between neurolinguistic models and experiments.

    PubMed

    Barrès, Victor; Simons, Arthur; Arbib, Michael

    2013-01-01

    that mediate the relation between the brain's inputs, outputs, and internal states in executing a specific task. The neural networks used for Synthetic ERP must include neuroanatomically realistic placement and orientation of the cortical pyramidal neurons. These constraints pose exciting challenges for future work in neural network modeling that is applicable to systems and cognitive neuroscience.

  9. Synthetic vision system flight test results and lessons learned

    NASA Technical Reports Server (NTRS)

    Radke, Jeffrey

    1993-01-01

    Honeywell Systems and Research Center developed and demonstrated an active 35 GHz Radar Imaging system as part of the FAA/USAF/Industry sponsored Synthetic Vision System Technology Demonstration (SVSTD) Program. The objectives of this presentation are to provide a general overview of flight test results, a system level perspective that encompasses the efforts of the SVSTD and Augmented VIsual Display (AVID) programs, and more importantly, provide the AVID workshop participants with Honeywell's perspective on the lessons that were learned from the SVS flight tests. One objective of the SVSTD program was to explore several known system issues concerning radar imaging technology. The program ultimately resolved some of these issues, left others open, and in fact created several new concerns. In some instances, the interested community has drawn improper conclusions from the program by globally attributing implementation specific issues to radar imaging technology in general. The motivation for this presentation is therefore to provide AVID researchers with a better understanding of the issues that truly remain open, and to identify the perceived issues that are either resolved or were specific to Honeywell's implementation.

  10. Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants.

    PubMed

    Hill, Camilla Beate; Czauderna, Tobias; Klapperstück, Matthias; Roessner, Ute; Schreiber, Falk

    2015-01-01

    Life on earth depends on dynamic chemical transformations that enable cellular functions, including electron transfer reactions, as well as synthesis and degradation of biomolecules. Biochemical reactions are coordinated in metabolic pathways that interact in a complex way to allow adequate regulation. Biotechnology, food, biofuel, agricultural, and pharmaceutical industries are highly interested in metabolic engineering as an enabling technology of synthetic biology to exploit cells for the controlled production of metabolites of interest. These approaches have only recently been extended to plants due to their greater metabolic complexity (such as primary and secondary metabolism) and highly compartmentalized cellular structures and functions (including plant-specific organelles) compared with bacteria and other microorganisms. Technological advances in analytical instrumentation in combination with advances in data analysis and modeling have opened up new approaches to engineer plant metabolic pathways and allow the impact of modifications to be predicted more accurately. In this article, we review challenges in the integration and analysis of large-scale metabolic data, present an overview of current bioinformatics methods for the modeling and visualization of metabolic networks, and discuss approaches for interfacing bioinformatics approaches with metabolic models of cellular processes and flux distributions in order to predict phenotypes derived from specific genetic modifications or subjected to different environmental conditions.

  11. Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants

    PubMed Central

    Hill, Camilla Beate; Czauderna, Tobias; Klapperstück, Matthias; Roessner, Ute; Schreiber, Falk

    2015-01-01

    Life on earth depends on dynamic chemical transformations that enable cellular functions, including electron transfer reactions, as well as synthesis and degradation of biomolecules. Biochemical reactions are coordinated in metabolic pathways that interact in a complex way to allow adequate regulation. Biotechnology, food, biofuel, agricultural, and pharmaceutical industries are highly interested in metabolic engineering as an enabling technology of synthetic biology to exploit cells for the controlled production of metabolites of interest. These approaches have only recently been extended to plants due to their greater metabolic complexity (such as primary and secondary metabolism) and highly compartmentalized cellular structures and functions (including plant-specific organelles) compared with bacteria and other microorganisms. Technological advances in analytical instrumentation in combination with advances in data analysis and modeling have opened up new approaches to engineer plant metabolic pathways and allow the impact of modifications to be predicted more accurately. In this article, we review challenges in the integration and analysis of large-scale metabolic data, present an overview of current bioinformatics methods for the modeling and visualization of metabolic networks, and discuss approaches for interfacing bioinformatics approaches with metabolic models of cellular processes and flux distributions in order to predict phenotypes derived from specific genetic modifications or subjected to different environmental conditions. PMID:26557642

  12. Modeling human response errors in synthetic flight simulator domain

    NASA Technical Reports Server (NTRS)

    Ntuen, Celestine A.

    1992-01-01

    This paper presents a control theoretic approach to modeling human response errors (HRE) in the flight simulation domain. The human pilot is modeled as a supervisor of a highly automated system. The synthesis uses the theory of optimal control pilot modeling for integrating the pilot's observation error and the error due to the simulation model (experimental error). Methods for solving the HRE problem are suggested. Experimental verification of the models will be tested in a flight quality handling simulation.

  13. Comparison of different synthetic 5-min rainfall time series on the results of rainfall runoff simulations in urban drainage modelling

    NASA Astrophysics Data System (ADS)

    Krämer, Stefan; Rohde, Sophia; Schröder, Kai; Belli, Aslan; Maßmann, Stefanie; Schönfeld, Martin; Henkel, Erik; Fuchs, Lothar

    2015-04-01

    The design of urban drainage systems with numerical simulation models requires long, continuous rainfall time series with high temporal resolution. However, suitable observed time series are rare. As a result, usual design concepts often use uncertain or unsuitable rainfall data, which renders them uneconomic or unsustainable. An expedient alternative to observed data is the use of long, synthetic rainfall time series as input for the simulation models. Within the project SYNOPSE, several different methods to generate synthetic rainfall data as input for urban drainage modelling are advanced, tested, and compared. Synthetic rainfall time series of three different precipitation model approaches, - one parametric stochastic model (alternating renewal approach), one non-parametric stochastic model (resampling approach), one downscaling approach from a regional climate model-, are provided for three catchments with different sewer system characteristics in different climate regions in Germany: - Hamburg (northern Germany): maritime climate, mean annual rainfall: 770 mm; combined sewer system length: 1.729 km (City center of Hamburg), storm water sewer system length (Hamburg Harburg): 168 km - Brunswick (Lower Saxony, northern Germany): transitional climate from maritime to continental, mean annual rainfall: 618 mm; sewer system length: 278 km, connected impervious area: 379 ha, height difference: 27 m - Friburg in Brisgau (southern Germany): Central European transitional climate, mean annual rainfall: 908 mm; sewer system length: 794 km, connected impervious area: 1 546 ha, height difference 284 m Hydrodynamic models are set up for each catchment to simulate rainfall runoff processes in the sewer systems. Long term event time series are extracted from the - three different synthetic rainfall time series (comprising up to 600 years continuous rainfall) provided for each catchment and - observed gauge rainfall (reference rainfall) according national hydraulic design

  14. EFFECTIVENESS OF THE VIDEOARTHROSCOPY LEARNING PROCESS IN SYNTHETIC SHOULDER MODELS

    PubMed Central

    Dal Molin, Fabio Farina; Mothes, Fernando Carlos; Feder, Marta Goldman

    2015-01-01

    Objectives: The authors evaluate the learning of the videoarthroscopic technique, using the video surgery simulator SAM® (Shoulder Arthroscopy Model). Methods: Twenty medical residents in Orthepaedics, without prior knowledge of the arthroscopic technique, were evaluated before and after training. The tasks consisted of positioning, in holes that simulated portals, four surgical threads attached to an anchor placed in the anatomical neck of the humerus in the synthetic model. Time, number of movements, number of attempts, amount of errors and comparison between the two phases of training before and after - were observed and noted. Results: The data was submitted to statistical analysis, and a significant difference was found in the comparison of the variables before and after the training. Conclusion: The result of this study enables us to conclude that training in the videoarthroscopic technique using the video surgery simulator SAM enables the surgeon to execute essential tasks involved in these techniques, in less time, making less mistakes, and developing the ability to deal better with the videoarthrocopic image. PMID:27027086

  15. Modeling synthetic radar image from a digital terrain model

    NASA Astrophysics Data System (ADS)

    Durand, Philippe; Jaupi, Luan; Ghorbanzadeh, Dariush; Rudant, Jean Paul

    2015-03-01

    In this paper we propose to simulate SAR radar images that can be acquired by aircraft or satellite. This corresponds to a real problematic, in fact, an airborne radar data acquisition campaign, was conducted in the south east of France. We want to estimate the geometric deformations that a digital terrain model can be subjected. By extrapolation, this construction should also allow to understand the image distortion if a plane is replaced by a satellite. This manipulation allow to judge the relevance of a space mission to quantify geological and geomorphological data. The radar wave is an electromagnetic wave, they have the advantage of overcoming atmospheric conditions since more wavelength is large is better crossing the cloud layer. Therefore imaging radar provides continuous monitoring.

  16. QSAR and pharmacophore modeling of natural and synthetic antimalarial prodiginines.

    PubMed

    Singh, Baljinder; Vishwakarma, Ram A; Bharate, Sandip B

    2013-09-01

    Prodiginines are a family of linear and cyclic oligopyrrole red-pigmented compounds possessing antibacterial, anticancer and immunosuppressive activities and are produced by actinomycetes and other eubacteria. Recently, prodiginines have been reported to possess potent in vitro as well as in vivo antimalarial activity against chloroquine sensitive D6 and multi-drug resistant Dd2 strains of Plasmodium falciparum. In the present paper, a QSAR and pharmacophore modeling for a series of natural and synthetic prodiginines was performed to find out structural features which are crucial for antimalarial activity against these D6 and Dd2 Plasmodium strains. The study indicated that inertia moment 2 length, Kier Chi6 (path) index, kappa 3 index and Wiener topological index plays important role in antimalarial activity against D6 strain whereas descriptors inertia moment 2 length, ADME H-bond donors, VAMP polarization XX component and VAMP quadpole XZ component play important role in antimalarial activity against Dd2 strain. Furthermore, a five-point pharmacophore (ADHRR) model with one H-bond acceptor (A), one H-bond donor (D), one hydrophobic group (H) and two aromatic rings (R) as pharmacophore features was developed for D6 strain by PHASE module of Schrodinger suite. Similarly a six-point pharmacophore AADDRR was developed for Dd2 strain activity. All developed QSAR models showed good correlation coefficient (r² > 0.7), higher F value (F >20) and excellent predictive power (Q² > 0.6). Developed models will be highly useful for predicting antimalarial activity of new compounds and could help in designing better molecules with enhanced antimalarial activity. Furthermore, calculated ADME properties indicated drug-likeness of prodiginines.

  17. A Machine Reading System for Assembling Synthetic Paleontological Databases

    PubMed Central

    Peters, Shanan E.; Zhang, Ce; Livny, Miron; Ré, Christopher

    2014-01-01

    Many aspects of macroevolutionary theory and our understanding of biotic responses to global environmental change derive from literature-based compilations of paleontological data. Existing manually assembled databases are, however, incomplete and difficult to assess and enhance with new data types. Here, we develop and validate the quality of a machine reading system, PaleoDeepDive, that automatically locates and extracts data from heterogeneous text, tables, and figures in publications. PaleoDeepDive performs comparably to humans in several complex data extraction and inference tasks and generates congruent synthetic results that describe the geological history of taxonomic diversity and genus-level rates of origination and extinction. Unlike traditional databases, PaleoDeepDive produces a probabilistic database that systematically improves as information is added. We show that the system can readily accommodate sophisticated data types, such as morphological data in biological illustrations and associated textual descriptions. Our machine reading approach to scientific data integration and synthesis brings within reach many questions that are currently underdetermined and does so in ways that may stimulate entirely new modes of inquiry. PMID:25436610

  18. Synthetic mitochondria as therapeutics against systemic aging: a hypothesis.

    PubMed

    Tang, Bor Luen

    2015-02-01

    We hypothesize herein that synthetic mitochondria, engineered, or reprogrammed to be more energetically efficient and to have mildly elevated levels of reactive oxygen species (ROS) production, would be an effective form of therapeutics against systemic aging. The free radical and mitochondria theories of aging hold that mitochondria-generated ROS underlies chronic organelle, cell and tissues damages that contribute to systemic aging. More recent findings, however, collectively suggest that while acute and massive ROS generation during events such as tissue injury is indeed detrimental, subacute stresses, and chronic elevation in ROS production may instead induce a state of mitochondrial hormesis (or "mitohormesis") that could extend lifespan. Mitohormesis appears to be a convergent mechanism for several known anti-aging signaling pathways. Importantly, mitohormetic signaling could also occur in a non-cell autonomous manner, with its induction in neurons affecting gut cells, for example. Technologies are outlined that could lead towards testing of the hypothesis, which include genetic and epigenetic engineering of the mitochondria, as well as intercellular transfer of mitochondria from transplanted helper cells to target tissues.

  19. Terahertz interferometric synthetic aperture tomography for confocal imaging systems.

    PubMed

    Heimbeck, M S; Marks, D L; Brady, D; Everitt, H O

    2012-04-15

    Terahertz (THz) interferometric synthetic aperture tomography (TISAT) for confocal imaging within extended objects is demonstrated by combining attributes of synthetic aperture radar and optical coherence tomography. Algorithms recently devised for interferometric synthetic aperture microscopy are adapted to account for the diffraction-and defocusing-induced spatially varying THz beam width characteristic of narrow depth of focus, high-resolution confocal imaging. A frequency-swept two-dimensional TISAT confocal imaging instrument rapidly achieves in-focus, diffraction-limited resolution over a depth 12 times larger than the instrument's depth of focus in a manner that may be easily extended to three dimensions and greater depths.

  20. Synthetic fluorescent probes for studying copper in biological systems

    PubMed Central

    Cotruvo, Joseph A.; Aron, Allegra T.; Ramos-Torres, Karla M.; Chang, Christopher J.

    2015-01-01

    The potent redox activity of copper is required for sustaining life. Mismanagement of its cellular pools, however, can result in oxidative stress and damage connected to aging, neurodegenerative diseases, and metabolic disorders. Therefore, copper homeostasis is tightly regulated by cells and tissues. Whereas copper and other transition metal ions are commonly thought of as static cofactors buried within protein active sites, emerging data points to the presence of additional loosely bound, labile pools that can participate in dynamic signalling pathways. Against this backdrop, we review advances in sensing labile copper pools and understanding their functions using synthetic fluorescent indicators. Following brief introductions to cellular copper homeostasis and considerations in sensor design, we survey available fluorescent copper probes and evaluate their properties in the context of their utility as effective biological screening tools. We emphasize the need for combined chemical and biological evaluation of these reagents, as well as the value of complementing probe data with other techniques for characterizing the different pools of metal ions in biological systems. This holistic approach will maximize the exciting opportunities for these and related chemical technologies in the study and discovery of novel biology of metals. PMID:25692243

  1. Simulation assessment of synthetic vision system concepts for UAV operations

    NASA Astrophysics Data System (ADS)

    Calhoun, Gloria L.; Draper, Mark H.; Ruff, Heath A.; Nelson, Jeremy T.; Lefebvre, Austen T.

    2006-05-01

    The Air Force Research Laboratory's Human Effectiveness Directorate supports research addressing human factors associated with Unmanned Aerial Vehicle (UAV) operator control stations. One research thrust explores the value of combining synthetic vision data with live camera video presented on a UAV control station display. Information is constructed from databases (e.g., terrain, etc.), as well as numerous information updates via networked communication with other sources. This information is overlaid conformal, in real time, onto the dynamic camera video image display presented to operators. Synthetic vision overlay technology is expected to improve operator situation awareness by highlighting elements of interest within the video image. Secondly, it can assist the operator in maintaining situation awareness of an environment if the video datalink is temporarily degraded. Synthetic vision overlays can also serve to facilitate intuitive communications of spatial information between geographically separated users. This paper discusses results from a high-fidelity UAV simulation evaluation of synthetic symbology overlaid on a (simulated) live camera display. Specifically, the effects of different telemetry data update rates for synthetic visual data were examined for a representative sensor operator task. Participants controlled the zoom and orientation of the camera to find and designate targets. The results from both performance and subjective data demonstrated the potential benefit of an overlay of synthetic symbology for improving situation awareness, reducing workload, and decreasing time required to designate points of interest. Implications of symbology update rate are discussed, as well as other human factors issues.

  2. Determining resolvability of mantle plumes with synthetic seismic modeling

    NASA Astrophysics Data System (ADS)

    Maguire, R.; Van Keken, P. E.; Ritsema, J.; Fichtner, A.; Goes, S. D. B.

    2014-12-01

    Hotspot volcanism in locations such as Hawaii and Iceland is commonly thought to be associated with plumes rising from the deep mantle. In theory these dynamic upwellings should be visible in seismic data due to their reduced seismic velocity and their effect on mantle transition zone thickness. Numerous studies have attempted to image plumes [1,2,3], but their deep mantle origin remains unclear. In addition, a debate continues as to whether lower mantle plumes are visible in the form of body wave travel time delays, or whether such delays will be erased due to wavefront healing. Here we combine geodynamic modeling of mantle plumes with synthetic seismic waveform modeling in order to quantitatively determine under what conditions mantle plumes should be seismically visible. We model compressible plumes with phase changes at 410 km and 670 km, and a viscosity reduction in the upper mantle. These plumes thin from greater than 600 km in diameter in the lower mantle, to 200 - 400 km in the upper mantle. Plume excess potential temperature is 375 K, which maps to seismic velocity reductions of 4 - 12 % in the upper mantle, and 2 - 4 % in the lower mantle. Previous work that was limited to an axisymmetric spherical geometry suggested that these plumes would not be visible in the lower mantle [4]. Here we extend this approach to full 3D spherical wave propagation modeling. Initial results using a simplified cylindrical plume conduit suggest that mantle plumes with a diameter of 1000 km or greater will retain a deep mantle seismic signature. References[1] Wolfe, Cecily J., et al. "Seismic structure of the Iceland mantle plume." Nature 385.6613 (1997): 245-247. [2] Montelli, Raffaella, et al. "Finite-frequency tomography reveals a variety of plumes in the mantle." Science 303.5656 (2004): 338-343. [3] Schmandt, Brandon, et al. "Hot mantle upwelling across the 660 beneath Yellowstone." Earth and Planetary Science Letters 331 (2012): 224-236. [4] Hwang, Yong Keun, et al

  3. Model-Based Information Extraction From Synthetic Aperture Radar Signals

    NASA Astrophysics Data System (ADS)

    Matzner, Shari A.

    2011-07-01

    Synthetic aperture radar (SAR) is a remote sensing technology for imaging areas of the earth's surface. SAR has been successfully used for monitoring characteristics of the natural environment such as land cover type and tree density. With the advent of higher resolution sensors, it is now theoretically possible to extract information about individual structures such as buildings from SAR imagery. This information could be used for disaster response and security-related intelligence. SAR has an advantage over other remote sensing technologies for these applications because SAR data can be collected during the night and in rainy or cloudy conditions. This research presents a model-based method for extracting information about a building -- its height and roof slope -- from a single SAR image. Other methods require multiple images or ancillary data from specialized sensors, making them less practical. The model-based method uses simulation to match a hypothesized building to an observed SAR image. The degree to which a simulation matches the observed data is measured by mutual information. The success of this method depends on the accuracy of the simulation and on the reliability of the mutual information similarity measure. Electromagnetic theory was applied to relate a building's physical characteristics to the features present in a SAR image. This understanding was used to quantify the precision of building information contained in SAR data, and to identify the inputs needed for accurate simulation. A new SAR simulation technique was developed to meet the accuracy and efficiency requirements of model-based information extraction. Mutual information, a concept from information theory, has become a standard for measuring the similarity between medical images. Its performance in the context of matching a simulation image to a SAR image was evaluated in this research, and it was found to perform well under certain conditions. The factors that affect its performance

  4. Mimicry of the radical pair and triplet states in photosynthetic reaction centers with a synthetic model

    SciTech Connect

    Hasharoni, K.; Levanon, H.; Greenfield, S.R.; Gosztola, D.J.; Svec, W.A.; Wasiclewski, M.R. |

    1995-08-02

    Supramolecular systems synthesized to model the photosynthetic reaction center (RC) are designed to mimic several key properties of the RC protein. Thus far, most RC models fulfill only a subset of these criteria, with very few reports employing time-resolved electron paramagnetic resonance spectroscopy (TREPR). We now report TREPR results on a photosynthetic model system (1) in a nematic liquid crystal (LC) that does not contain the natural pigments, yet closely mimics the spin dynamics of triplet state formation found only in photosynthetic RCs. The design of supermolecule 1 follows criteria established for promoting high quantum yield charge separation in glassy media. The observation of this triplet state in 1 by TREPR demonstrates that most of the electronic states found in the primary photochemistry of photosynthetic RCs can be mimicked successfully in synthetic models interacting with LCs. 12 refs., 3 figs.

  5. EXPOSURE ANALYSIS MODELING SYSTEM (EXAMS): USER MANUAL AND SYSTEM DOCUMENTATION

    EPA Science Inventory

    The Exposure Analysis Modeling System, first published in 1982 (EPA-600/3-82-023), provides interactive computer software for formulating aquatic ecosystem models and rapidly evaluating the fate, transport, and exposure concentrations of synthetic organic chemicals - pesticides, ...

  6. Antifouling activity of synthetic alkylpyridinium polymers using the barnacle model.

    PubMed

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

    2014-04-01

    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

  7. Apparatus, systems, and methods for ultrasound synthetic aperature focusing

    DOEpatents

    Schuster, George J.; Crawford, Susan L.; Doctor, Steven R.; Harris, Robert V.

    2005-04-12

    One form of the present invention is a technique for interrogating a sample with ultrasound which includes: generating ultrasonic energy data corresponding to a volume of a sample and performing a synthetic aperture focusing technique on the ultrasonic energy data. The synthetic aperture focusing technique includes: defining a number of hyperbolic surfaces which extend through the volume at different depths and a corresponding number of multiple element accumulation vectors, performing a focused element calculation procedure for a group of vectors which are representative of the interior of a designated aperture, performing another focused element calculation procedure for vectors corresponding to the boundary of the aperture, and providing an image corresponding to features of the sample in accordance with the synthetic aperture focusing technique.

  8. High-resolution imaging with a real-time synthetic aperture ultrasound system: a phantom study

    NASA Astrophysics Data System (ADS)

    Huang, Lianjie; Labyed, Yassin; Simonetti, Francesco; Williamson, Michael; Rosenberg, Robert; Heintz, Philip; Sandoval, Daniel

    2011-03-01

    It is difficult for ultrasound to image small targets such as breast microcalcifications. Synthetic aperture ultrasound imaging has recently developed as a promising tool to improve the capabilities of medical ultrasound. We use two different tissueequivalent phantoms to study the imaging capabilities of a real-time synthetic aperture ultrasound system for imaging small targets. The InnerVision ultrasound system DAS009 is an investigational system for real-time synthetic aperture ultrasound imaging. We use the system to image the two phantoms, and compare the images with those obtained from clinical scanners Acuson Sequoia 512 and Siemens S2000. Our results show that synthetic aperture ultrasound imaging produces images with higher resolution and less image artifacts than Acuson Sequoia 512 and Siemens S2000. In addition, we study the effects of sound speed on synthetic aperture ultrasound imaging and demonstrate that an accurate sound speed is very important for imaging small targets.

  9. Question 7: Construction of a Semi-Synthetic Minimal Cell: A Model for Early Living Cells

    NASA Astrophysics Data System (ADS)

    Murtas, Giovanni

    2007-10-01

    Using a Synthetic Biology approach we are building a semi-synthetic minimal cell. This represents an exercise to shape a minimal-cell model system recalling the simplicity of early living cells in early evolution. We have recently introduced into liposome compartments a minimal set of enzymes named “Puresystem” (PS) synthesizing EGFP proteins. To establish reproduction of the shell compartment with a minimal set of genes we have cloned the genes for the Fatty Acid Synthase (FAS) type I enzymes. These FAS genes introduced into liposomes, translated into FAS enzymes by PS and in the presence of precursors produce fatty acids. The resulting release of fatty acid molecules within liposome vesicles should promote vesicle growth and reproduction. The core reproduction of a minimal cell corresponding to the replication of the minimal genome will require a few genes for the DNA replication and the PS, and a minimum set of genes for the synthesis of t-RNAs. In future the reconstruction of a minimal ribosome will bring the number of genes for ribosomal proteins from 54 of an existing minimal genome down to 30 20 genes. A Synthetic Biology approach could bring the number of essential genes for a minimal cell down to 100 or less.

  10. 78 FR 5557 - Twenty-First Meeting: RTCA Special Committee 213, Enhanced Flight Vision Systems/Synthetic Vision...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-25

    ... Systems/Synthetic Vision Systems (EFVS/SVS) AGENCY: Federal Aviation Administration (FAA), U.S. Department... Systems/Synthetic Vision Systems (EFVS/SVS). SUMMARY: The FAA is issuing this notice to advise the public.../Synthetic Vision Systems (EFVS/SVS). DATES: The meeting will be held February 5-7, 2013 from 9:00...

  11. Functional fusion of living systems with synthetic electrode interfaces

    PubMed Central

    Staufer, Oskar; Weber, Sebastian; Bengtson, C Peter; Bading, Hilmar; Spatz, Joachim P

    2016-01-01

    Summary The functional fusion of “living” biomaterial (such as cells) with synthetic systems has developed into a principal ambition for various scientific disciplines. In particular, emerging fields such as bionics and nanomedicine integrate advanced nanomaterials with biomolecules, cells and organisms in order to develop novel strategies for applications, including energy production or real-time diagnostics utilizing biomolecular machineries “perfected” during billion years of evolution. To date, hardware–wetware interfaces that sample or modulate bioelectric potentials, such as neuroprostheses or implantable energy harvesters, are mostly based on microelectrodes brought into the closest possible contact with the targeted cells. Recently, the possibility of using electrochemical gradients of the inner ear for technical applications was demonstrated using implanted electrodes, where 1.12 nW of electrical power was harvested from the guinea pig endocochlear potential for up to 5 h (Mercier, P.; Lysaght, A.; Bandyopadhyay, S.; Chandrakasan, A.; Stankovic, K. Nat. Biotech. 2012, 30, 1240–1243). More recent approaches employ nanowires (NWs) able to penetrate the cellular membrane and to record extra- and intracellular electrical signals, in some cases with subcellular resolution (Spira, M.; Hai, A. Nat. Nano. 2013, 8, 83–94). Such techniques include nanoelectric scaffolds containing free-standing silicon NWs (Robinson, J. T.; Jorgolli, M.; Shalek, A. K.; Yoon, M. H.; Gertner, R. S.; Park, H. Nat Nanotechnol. 2012, 10, 180–184) or NW field-effect transistors (Qing, Q.; Jiang, Z.; Xu, L.; Gao, R.; Mai, L.; Lieber, C. Nat. Nano. 2013, 9, 142–147), vertically aligned gallium phosphide NWs (Hällström, W.; Mårtensson, T.; Prinz, C.; Gustavsson, P.; Montelius, L.; Samuelson, L.; Kanje, M. Nano Lett. 2007, 7, 2960–2965) or individually contacted, electrically active carbon nanofibers. The latter of these approaches is capable of recording electrical

  12. Functional fusion of living systems with synthetic electrode interfaces.

    PubMed

    Staufer, Oskar; Weber, Sebastian; Bengtson, C Peter; Bading, Hilmar; Spatz, Joachim P; Rustom, Amin

    2016-01-01

    The functional fusion of "living" biomaterial (such as cells) with synthetic systems has developed into a principal ambition for various scientific disciplines. In particular, emerging fields such as bionics and nanomedicine integrate advanced nanomaterials with biomolecules, cells and organisms in order to develop novel strategies for applications, including energy production or real-time diagnostics utilizing biomolecular machineries "perfected" during billion years of evolution. To date, hardware-wetware interfaces that sample or modulate bioelectric potentials, such as neuroprostheses or implantable energy harvesters, are mostly based on microelectrodes brought into the closest possible contact with the targeted cells. Recently, the possibility of using electrochemical gradients of the inner ear for technical applications was demonstrated using implanted electrodes, where 1.12 nW of electrical power was harvested from the guinea pig endocochlear potential for up to 5 h (Mercier, P.; Lysaght, A.; Bandyopadhyay, S.; Chandrakasan, A.; Stankovic, K. Nat. Biotech. 2012, 30, 1240-1243). More recent approaches employ nanowires (NWs) able to penetrate the cellular membrane and to record extra- and intracellular electrical signals, in some cases with subcellular resolution (Spira, M.; Hai, A. Nat. Nano. 2013, 8, 83-94). Such techniques include nanoelectric scaffolds containing free-standing silicon NWs (Robinson, J. T.; Jorgolli, M.; Shalek, A. K.; Yoon, M. H.; Gertner, R. S.; Park, H. Nat Nanotechnol. 2012, 10, 180-184) or NW field-effect transistors (Qing, Q.; Jiang, Z.; Xu, L.; Gao, R.; Mai, L.; Lieber, C. Nat. Nano. 2013, 9, 142-147), vertically aligned gallium phosphide NWs (Hällström, W.; Mårtensson, T.; Prinz, C.; Gustavsson, P.; Montelius, L.; Samuelson, L.; Kanje, M. Nano Lett. 2007, 7, 2960-2965) or individually contacted, electrically active carbon nanofibers. The latter of these approaches is capable of recording electrical responses from oxidative events

  13. Functional fusion of living systems with synthetic electrode interfaces.

    PubMed

    Staufer, Oskar; Weber, Sebastian; Bengtson, C Peter; Bading, Hilmar; Spatz, Joachim P; Rustom, Amin

    2016-01-01

    The functional fusion of "living" biomaterial (such as cells) with synthetic systems has developed into a principal ambition for various scientific disciplines. In particular, emerging fields such as bionics and nanomedicine integrate advanced nanomaterials with biomolecules, cells and organisms in order to develop novel strategies for applications, including energy production or real-time diagnostics utilizing biomolecular machineries "perfected" during billion years of evolution. To date, hardware-wetware interfaces that sample or modulate bioelectric potentials, such as neuroprostheses or implantable energy harvesters, are mostly based on microelectrodes brought into the closest possible contact with the targeted cells. Recently, the possibility of using electrochemical gradients of the inner ear for technical applications was demonstrated using implanted electrodes, where 1.12 nW of electrical power was harvested from the guinea pig endocochlear potential for up to 5 h (Mercier, P.; Lysaght, A.; Bandyopadhyay, S.; Chandrakasan, A.; Stankovic, K. Nat. Biotech. 2012, 30, 1240-1243). More recent approaches employ nanowires (NWs) able to penetrate the cellular membrane and to record extra- and intracellular electrical signals, in some cases with subcellular resolution (Spira, M.; Hai, A. Nat. Nano. 2013, 8, 83-94). Such techniques include nanoelectric scaffolds containing free-standing silicon NWs (Robinson, J. T.; Jorgolli, M.; Shalek, A. K.; Yoon, M. H.; Gertner, R. S.; Park, H. Nat Nanotechnol. 2012, 10, 180-184) or NW field-effect transistors (Qing, Q.; Jiang, Z.; Xu, L.; Gao, R.; Mai, L.; Lieber, C. Nat. Nano. 2013, 9, 142-147), vertically aligned gallium phosphide NWs (Hällström, W.; Mårtensson, T.; Prinz, C.; Gustavsson, P.; Montelius, L.; Samuelson, L.; Kanje, M. Nano Lett. 2007, 7, 2960-2965) or individually contacted, electrically active carbon nanofibers. The latter of these approaches is capable of recording electrical responses from oxidative events

  14. 77 FR 2342 - Seventeenth Meeting: RTCA Special Committee 213, Enhanced Flight Vision/Synthetic Vision Systems...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-17

    ... Federal Aviation Administration Seventeenth Meeting: RTCA Special Committee 213, Enhanced Flight Vision... Transportation (DOT). ACTION: Notice of RTCA Special Committee 213, Enhanced Flight Vision/ Synthetic Vision... meeting of RTCA Special Committee 213, Enhanced Flight Vision/Synthetic Vision Systems (EFVS/SVS)....

  15. Millimeter Wave Synthetic Aperture Imaging System with a Unique Rotary Scanning System

    NASA Technical Reports Server (NTRS)

    Ghasr, M. T.; Pommerenke, D.; Case, J. T.; McClanahan, A. D.; Afaki-Beni, A.; Abou-Khousa, M.; Guinn, K.; DePaulis, F.; Kharkovsky, S.; Zoughi, R.

    2008-01-01

    In recent years, millimeter wave imaging techniques, using synthetic aperture focusing and holographical approaches, have shown tremendous potential for nondestructive testing applications, involving materials and structures used in space vehicles, including the space shuttle external fuel tank spray on foam insulation and its acreage heat tiles. The ability of signals at millimeter wave frequencies (30 - 300 GHz) to easily penetrate inside of low loss dielectric materials, their relatively small wavelengths, and the possibility of detecting coherent (magnitude and phase) reflections make them suitable for high resolution synthetic aperture focused imaging the interior of such materials and structures. To accommodate imaging requirements, commonly a scanning system is employed that provides for a raster scan of the desired structure. However, most such scanners, although simple in design and construction, are inherently slow primarily due to the need to stop and start at the beginning and end of each scan line. To this end, a millimeter wave synthetic aperture focusing system including a custom-designed transceiver operating at 35 - 45 GHz (Q-band) and unique and complex rotary scanner was designed and developed. The rotary scanner is capable of scanning an area with approximately 80 cm in diameter in less than 10 minutes at step sizes of 3 mm and smaller. The transceiver is capable of producing accurate magnitude and phase of reflected signal from the structure under test. Finally, a synthetic aperture focusing algorithm was developed that translates this rotary-obtained magnitude and phase into a synthetic aperture focusing image of inspected structures. This paper presents the design of the transceiver and the rotary scanning system along with showing several images obtained with this system from various complicated structures.

  16. Perception of synthetic speech produced automatically by rule: Intelligibility of eight text-to-speech systems.

    PubMed

    Greene, Beth G; Logan, John S; Pisoni, David B

    1986-03-01

    We present the results of studies designed to measure the segmental intelligibility of eight text-to-speech systems and a natural speech control, using the Modified Rhyme Test (MRT). Results indicated that the voices tested could be grouped into four categories: natural speech, high-quality synthetic speech, moderate-quality synthetic speech, and low-quality synthetic speech. The overall performance of the best synthesis system, DECtalk-Paul, was equivalent to natural speech only in terms of performance on initial consonants. The findings are discussed in terms of recent work investigating the perception of synthetic speech under more severe conditions. Suggestions for future research on improving the quality of synthetic speech are also considered. PMID:23225916

  17. Synthetic and Enhanced Vision System for Altair Lunar Lander

    NASA Technical Reports Server (NTRS)

    Prinzell, Lawrence J., III; Kramer, Lynda J.; Norman, Robert M.; Arthur, Jarvis J., III; Williams, Steven P.; Shelton, Kevin J.; Bailey, Randall E.

    2009-01-01

    Past research has demonstrated the substantial potential of synthetic and enhanced vision (SV, EV) for aviation (e.g., Prinzel & Wickens, 2009). These augmented visual-based technologies have been shown to significantly enhance situation awareness, reduce workload, enhance aviation safety (e.g., reduced propensity for controlled flight -into-terrain accidents/incidents), and promote flight path control precision. The issues that drove the design and development of synthetic and enhanced vision have commonalities to other application domains; most notably, during entry, descent, and landing on the moon and other planetary surfaces. NASA has extended SV/EV technology for use in planetary exploration vehicles, such as the Altair Lunar Lander. This paper describes an Altair Lunar Lander SV/EV concept and associated research demonstrating the safety benefits of these technologies.

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

    SciTech Connect

    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.

  19. Hardware system concept For student's space synthetic aperture radar (ESA SSETI-ESMO project)

    NASA Astrophysics Data System (ADS)

    Dawidowicz, Bartek; Filipek, Tomasz; Piotrkowski, Michał

    2006-02-01

    In this paper a concept of a cheap, lightweight, low power satellite radar for Moon's surface mapping is presented. This radar is designed to work in two modes: two-dimensional imaging (Synthetic Aperture Radar - SAR) and three-dimensional imaging (Interferometric Synthetic Aperture Radar - IfSAR). The proposed radar system performs the functions both of a radar system and a high data rate communication system. This enables costs and weight reduction which is very important in space applications.

  20. Sensor fusion display evaluation using information integration models in enhanced/synthetic vision applications

    NASA Technical Reports Server (NTRS)

    Foyle, David C.

    1993-01-01

    Based on existing integration models in the psychological literature, an evaluation framework is developed to assess sensor fusion displays as might be implemented in an enhanced/synthetic vision system. The proposed evaluation framework for evaluating the operator's ability to use such systems is a normative approach: The pilot's performance with the sensor fusion image is compared to models' predictions based on the pilot's performance when viewing the original component sensor images prior to fusion. This allows for the determination as to when a sensor fusion system leads to: poorer performance than one of the original sensor displays, clearly an undesirable system in which the fused sensor system causes some distortion or interference; better performance than with either single sensor system alone, but at a sub-optimal level compared to model predictions; optimal performance compared to model predictions; or, super-optimal performance, which may occur if the operator were able to use some highly diagnostic 'emergent features' in the sensor fusion display, which were unavailable in the original sensor displays.

  1. Porphyrin-quinone compounds as synthetic models of the reaction centre in photosynthesis

    NASA Astrophysics Data System (ADS)

    Borovkov, V. V.; Evstigneeva, Rima P.; Strekova, L. N.; Filippovich, E. I.

    1989-06-01

    Data on the synthesis, steric structure, and photochemical properties of porphyrin-quinone compounds as synthetic models of the reaction centre in photosynthesis are examined and described systematically. The bibliography includes 113 references.

  2. Evaluation Digital Elevation Model Generated by Synthetic Aperture Radar Data

    NASA Astrophysics Data System (ADS)

    Makineci, H. B.; Karabörk, H.

    2016-06-01

    Digital elevation model, showing the physical and topographical situation of the earth, is defined a tree-dimensional digital model obtained from the elevation of the surface by using of selected an appropriate interpolation method. DEMs are used in many areas such as management of natural resources, engineering and infrastructure projects, disaster and risk analysis, archaeology, security, aviation, forestry, energy, topographic mapping, landslide and flood analysis, Geographic Information Systems (GIS). Digital elevation models, which are the fundamental components of cartography, is calculated by many methods. Digital elevation models can be obtained terrestrial methods or data obtained by digitization of maps by processing the digital platform in general. Today, Digital elevation model data is generated by the processing of stereo optical satellite images, radar images (radargrammetry, interferometry) and lidar data using remote sensing and photogrammetric techniques with the help of improving technology. One of the fundamental components of remote sensing radar technology is very advanced nowadays. In response to this progress it began to be used more frequently in various fields. Determining the shape of topography and creating digital elevation model comes the beginning topics of these areas. It is aimed in this work , the differences of evaluation of quality between Sentinel-1A SAR image ,which is sent by European Space Agency ESA and Interferometry Wide Swath imaging mode and C band type , and DTED-2 (Digital Terrain Elevation Data) and application between them. The application includes RMS static method for detecting precision of data. Results show us to variance of points make a high decrease from mountain area to plane area.

  3. Technical Challenges in the Development of a NASA Synthetic Vision System Concept

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Parrish, Russell V.; Kramer, Lynda J.; Harrah, Steve; Arthur, J. J., III

    2002-01-01

    Within NASA's Aviation Safety Program, the Synthetic Vision Systems Project is developing display system concepts to improve pilot terrain/situation awareness by providing a perspective synthetic view of the outside world through an on-board database driven by precise aircraft positioning information updating via Global Positioning System-based data. This work is aimed at eliminating visibility-induced errors and low visibility conditions as a causal factor to civil aircraft accidents, as well as replicating the operational benefits of clear day flight operations regardless of the actual outside visibility condition. Synthetic vision research and development activities at NASA Langley Research Center are focused around a series of ground simulation and flight test experiments designed to evaluate, investigate, and assess the technology which can lead to operational and certified synthetic vision systems. The technical challenges that have been encountered and that are anticipated in this research and development activity are summarized.

  4. Evaluating the Effects of Dimensionality in Advanced Avionic Display Concepts for Synthetic Vision Systems

    NASA Technical Reports Server (NTRS)

    Alexander, Amy L.; Prinzel, Lawrence J., III; Wickens, Christopher D.; Kramer, Lynda J.; Arthur, Jarvis J.; Bailey, Randall E.

    2007-01-01

    Synthetic vision systems provide an in-cockpit view of terrain and other hazards via a computer-generated display representation. Two experiments examined several display concepts for synthetic vision and evaluated how such displays modulate pilot performance. Experiment 1 (24 general aviation pilots) compared three navigational display (ND) concepts: 2D coplanar, 3D, and split-screen. Experiment 2 (12 commercial airline pilots) evaluated baseline 'blue sky/brown ground' or synthetic vision-enabled primary flight displays (PFDs) and three ND concepts: 2D coplanar with and without synthetic vision and a dynamic multi-mode rotatable exocentric format. In general, the results pointed to an overall advantage for a split-screen format, whether it be stand-alone (Experiment 1) or available via rotatable viewpoints (Experiment 2). Furthermore, Experiment 2 revealed benefits associated with utilizing synthetic vision in both the PFD and ND representations and the value of combined ego- and exocentric presentations.

  5. Fate of synthetic organic chemicals in soil-groundwater systems.

    PubMed

    Pancorbo, O C; Varney, T C

    1986-04-01

    Land disposal of municipal, industrial and agricultural wastes often leads to soil and groundwater contamination with synthetic organic chemicals. In this review, the fate of such organics in soils and the subsurface environment is discussed. In particular, the biodegradation of organic compounds in soils and the subsurface region, as well as the sorption of these compounds to soils is emphasized. Due to the disastrous impact of groundwater contamination on a community and the great cost of restoring a contaminated aquifer, a case is made for concentrating future efforts on isolating potential sources of groundwater contamination and instituting appropriate control measures.

  6. Synthetic Quorum Sensing and Induced Aggregation in Model Microcapsule Colonies with Repressilator Feedback

    NASA Astrophysics Data System (ADS)

    Shum, Henry; Yashin, Victor; Balazs, Anna

    We model a system of synthetic microcapsules that communicate chemically by releasing nanoparticles or signaling molecules. These signaling species bind to receptors on the shells of capsules and modulate the target shell's permeability, thereby controlling nanoparticle release from the target capsule. Using the repressilator regulatory network motif, whereby three species suppress the production of the next in a cyclic fashion, we show that large amplitude oscillations in nanoparticle release can emerge when many capsules are close together. This exemplifies quorum sensing, which is the ability of cells to gauge their population density and collectively initiate a new behavior once a critical density is reached. We present a physically realizable model in which the oscillations exhibited in crowded populations induce aggregation of the microcapsules, mimicking complex biological behavior of the slime mold Dictyostelium discoideum with only simple, synthetic components. We also show that the clusters can be dispersed and reformed repeatedly and controllably by addition of chemical stimuli, demonstrating possible applications in creating reconfigurable or programmable materials.

  7. Autonomous system for initializing synthetic aperture radar seeker acquisition

    SciTech Connect

    Hamilton, P.C.

    1993-08-03

    A method is described of guiding a missile having an active seeker including a synthetic aperture radar operating in a squint mode to a target aircraft having a search radar therein the maximum range of active seeker acquisition being within said missile's maneuver capability to intercept, and the maximum range of active seeker acquisition not exceeding the capability of the active seeker, said method comprising the steps of: launching said missile in response to detection of the search radar; implementing a passive seeker mode of operation to passively guide said missile towards said target aircraft in a manner to avoid detection of said missile by said target aircraft; transferring from said passive seeker mode to an active seeker mode in response to detected shutdown of said search radar; maneuvering said missile to execute a turn angle away from said target aircraft such that the search field of said synthetic aperture radar sweeps through an entire target uncertainty volume, said turn angle being within a first preselected limit and a second preselected limit such that said target aircraft does not cross over said missile's terminal flight path; and intercepting said target aircraft within a lethal range of said missile.

  8. Cotton crop spectral imaging analysis: a web-based hyperspectral synthetic imagery simulation system

    NASA Astrophysics Data System (ADS)

    Alarcon, Vladimir J.; Sassenrath, Gretchen F.

    2004-11-01

    The development of spectral libraries for specific vegetation species and soils is useful for identifying different physiological or physical-chemical characteristics. Usually, spectral libraries are provided as a data-base add-in of current commercial software used for analyzing hyperspectral imagery. The use of those databases requires installation of the software in the user"s machine for either visualizing or using the spectral libraries. There are also spectral libraries available on the web but the data is static and partitioned by spectrum of vegetation or soil because the size of the files of actual hyperspectral images precludes it"s publication on the web. In this paper, a web-based simulation environment for generating hyperspectral synthetic imagery of cotton plots is presented. The system was developed using Java and is based on a previous synthetic imagery program1. The mathematical and numerical formulation of the model is briefly sketched. The core computing components of the simulation environment were written in C for their computational efficiency. The emerging Java Native Interface (JNI) technique and standard Java techniques were used to design a user-friendly simulator. The simulation system provides interactive user control and real time visualization of the resulting hyperspectral image through standard web browsers. It shows potential for providing web-based hyperspectral libraries, in the form of images, for public use.

  9. Synthetic Model of the Oxygen-Evolving Center: Photosystem II under the Spotlight.

    PubMed

    Yu, Yang; Hu, Cheng; Liu, Xiaohong; Wang, Jiangyun

    2015-09-21

    The oxygen-evolving center (OEC) in photosystem II catalyzes a water splitting reaction. Great efforts have already been made to artificially synthesize the OEC, in order to elucidate the structure-function relationship and the mechanism of the reaction. Now, a new synthetic model makes the best mimic yet of the OEC. This recent study opens up the possibility to study the mechanism of photosystem II and photosynthesis in general for applications in renewable energy and synthetic biology.

  10. System for synthetic vision and augmented reality in future flight decks

    NASA Astrophysics Data System (ADS)

    Behringer, Reinhold; Tam, Clement K.; McGee, Joshua H.; Sundareswaran, Venkataraman; Vassiliou, Marius S.

    2000-06-01

    Rockwell Science Center is investigating novel human-computer interface techniques for enhancing the situational awareness in future flight decks. One aspect is to provide intuitive displays which provide the vital information and the spatial awareness by augmenting the real world with an overlay of relevant information registered to the real world. Such Augmented Reality (AR) techniques can be employed during bad weather scenarios to permit flying in Visual Flight Rules (VFR) in conditions which would normally require Instrumental Flight Rules (IFR). These systems could easily be implemented on heads-up displays (HUD). The advantage of AR systems vs. purely synthetic vision (SV) systems is that the pilot can relate the information overlay to real objects in the world, whereas SV systems provide a constant virtual view, where inconsistencies can hardly be detected. The development of components for such a system led to a demonstrator implemented on a PC. A camera grabs video images which are overlaid with registered information, Orientation of the camera is obtained from an inclinometer and a magnetometer, position is acquired from GPS. In a possible implementation in an airplane, the on-board attitude information can be used for obtaining correct registration. If visibility is sufficient, computer vision modules can be used to fine-tune the registration by matching visual clues with database features. Such technology would be especially useful for landing approaches. The current demonstrator provides a frame-rate of 15 fps, using a live video feed as background and an overlay of avionics symbology in the foreground. In addition, terrain rendering from a 1 arc sec. digital elevation model database can be overlaid to provide synthetic vision in case of limited visibility. For true outdoor testing (on ground level), the system has been implemented on a wearable computer.

  11. Synthetic Jets for Heat Transfer Augmentation in Microelectronics Systems

    NASA Astrophysics Data System (ADS)

    Arik, Mehmet; Tamdogan, Enes

    Rapid progress in science and information technology, growing manufacturing activities and increase in globalization have boosted the demand for advanced electronics devices. Moreover, increase in microprocessor power dissipation coupled with the reduction in feature sizes due to manufacturing process improvements have resulted in continuously increasing heat fluxes. Thus, ever increasing heat fluxes have required the development of novel, reliable and affordable thermal management technologies. Although some of those proposed solutions for high flux cooling problems based on liquid cooling methods such as spray and evaporative cooling; air cooling is still commonly preferred due to its availability, reliability, easiness and low cost. Therefore, over the last decade microfluidics devices such as synthetic jets have been investigated as an alternative to conventional air moving devices, and have been shown as highly effective for cooling of electronics in compact thermal real estates...

  12. Systems-Level Synthetic Biology for Advanced Biofuel Production

    SciTech Connect

    Ruffing, Anne; Jensen, Travis J.; Strickland, Lucas Marshall; Meserole, Stephen; Tallant, David

    2015-03-01

    Cyanobacteria have been shown to be capable of producing a variety of advanced biofuels; however, product yields remain well below those necessary for large scale production. New genetic tools and high throughput metabolic engineering techniques are needed to optimize cyanobacterial metabolisms for enhanced biofuel production. Towards this goal, this project advances the development of a multiple promoter replacement technique for systems-level optimization of gene expression in a model cyanobacterial host: Synechococcus sp. PCC 7002. To realize this multiple-target approach, key capabilities were developed, including a high throughput detection method for advanced biofuels, enhanced transformation efficiency, and genetic tools for Synechococcus sp. PCC 7002. Moreover, several additional obstacles were identified for realization of this multiple promoter replacement technique. The techniques and tools developed in this project will help to enable future efforts in the advancement of cyanobacterial biofuels.

  13. Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality

    PubMed Central

    Jacunski, Alexandra; Dixon, Scott J.; Tatonetti, Nicholas P.

    2015-01-01

    Synthetic lethality is a genetic interaction wherein two otherwise nonessential genes cause cellular inviability when knocked out simultaneously. Drugs can mimic genetic knock-out effects; therefore, our understanding of promiscuous drugs, polypharmacology-related adverse drug reactions, and multi-drug therapies, especially cancer combination therapy, may be informed by a deeper understanding of synthetic lethality. However, the colossal experimental burden in humans necessitates in silico methods to guide the identification of synthetic lethal pairs. Here, we present SINaTRA (Species-INdependent TRAnslation), a network-based methodology that discovers genome-wide synthetic lethality in translation between species. SINaTRA uses connectivity homology, defined as biological connectivity patterns that persist across species, to identify synthetic lethal pairs. Importantly, our approach does not rely on genetic homology or structural and functional similarity, and it significantly outperforms models utilizing these data. We validate SINaTRA by predicting synthetic lethality in S. pombe using S. cerevisiae data, then identify over one million putative human synthetic lethal pairs to guide experimental approaches. We highlight the translational applications of our algorithm for drug discovery by identifying clusters of genes significantly enriched for single- and multi-drug cancer therapies. PMID:26451775

  14. Synthetic biodegradable hydrogel delivery of demineralized bone matrix for bone augmentation in a rat model

    PubMed Central

    Kinard, Lucas A.; Dahlin, Rebecca L.; Lam, Johnny; Lu, Steven; Lee, Esther J.; Kasper, F. Kurtis; Mikos, Antonios G.

    2014-01-01

    There exists a strong clinical need for a more capable and robust method to achieve bone augmentation, and a system with fine-tuned delivery of demineralized bone matrix (DBM) has potential to meet that need. As such, the objective of the present study was to investigate a synthetic biodegradable hydrogel for the delivery of DBM for bone augmentation in a rat model. Oligo(poly(ethylene glycol) fumarate) (OPF) constructs were designed and fabricated by varying the content of rat-derived DBM particles (either 1:3, 1:1, or 3:1 DBM:OPF weight ratio on a dry basis) and using two DBM particle size ranges (50–150 or 150–250 μm). The physical properties of the constructs and the bioactivity of the DBM were evaluated. Select formulations (1:1 and 3:1 with 50–150 μm DBM) were evaluated in vivo compared to an empty control to investigate the effect of DBM dose and construct properties on bone augmentation. Overall, 3:1 constructs with higher DBM content achieved the greatest volume of bone augmentation exceeding 1:1 constructs and empty implants by 3-fold and 5-fold, respectively. As such, we have established that a synthetic, biodegradable hydrogel can function as a carrier for DBM, and that the volume of bone augmentation achieved by the constructs correlated directly to DBM dose. PMID:25046637

  15. Synthetic nanoparticles camouflaged with biomimetic erythrocyte membranes for reduced reticuloendothelial system uptake

    NASA Astrophysics Data System (ADS)

    Rao, Lang; Xu, Jun-Hua; Cai, Bo; Liu, Huiqin; Li, Ming; Jia, Yan; Xiao, Liang; Guo, Shi-Shang; Liu, Wei; Zhao, Xing-Zhong

    2016-02-01

    Suppression of the reticuloendothelial system (RES) uptake is one of the most challenging tasks in nanomedicine. Coating stratagems using polymers, such as poly(ethylene glycol) (PEG), have led to great success in this respect. Nevertheless, recent observations of immunological response toward these synthetic polymers have triggered a search for better alternatives. In this work, natural red blood cell (RBC) membranes are camouflaged on the surface of Fe3O4 nanoparticles for reducing the RES uptake. In vitro macrophage uptake, in vivo biodistribution and pharmacokinetic studies demonstrate that the RBC membrane is a superior alternative to the current gold standard PEG for nanoparticle ‘stealth’. Furthermore, we systematically investigate the in vivo potential toxicity of RBC membrane-coated nanoparticles by blood biochemistry, whole blood panel examination and histology analysis based on animal models. The combination of synthetic nanoparticles and natural cell membranes embodies a novel and biomimetic nanomaterial design strategy and presents a compelling property of functional materials for a broad range of biomedical applications.

  16. Synthetic nanoparticles camouflaged with biomimetic erythrocyte membranes for reduced reticuloendothelial system uptake.

    PubMed

    Rao, Lang; Xu, Jun-Hua; Cai, Bo; Liu, Huiqin; Li, Ming; Jia, Yan; Xiao, Liang; Guo, Shi-Shang; Liu, Wei; Zhao, Xing-Zhong

    2016-02-26

    Suppression of the reticuloendothelial system (RES) uptake is one of the most challenging tasks in nanomedicine. Coating stratagems using polymers, such as poly(ethylene glycol) (PEG), have led to great success in this respect. Nevertheless, recent observations of immunological response toward these synthetic polymers have triggered a search for better alternatives. In this work, natural red blood cell (RBC) membranes are camouflaged on the surface of Fe3O4 nanoparticles for reducing the RES uptake. In vitro macrophage uptake, in vivo biodistribution and pharmacokinetic studies demonstrate that the RBC membrane is a superior alternative to the current gold standard PEG for nanoparticle 'stealth'. Furthermore, we systematically investigate the in vivo potential toxicity of RBC membrane-coated nanoparticles by blood biochemistry, whole blood panel examination and histology analysis based on animal models. The combination of synthetic nanoparticles and natural cell membranes embodies a novel and biomimetic nanomaterial design strategy and presents a compelling property of functional materials for a broad range of biomedical applications.

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

    NASA Astrophysics Data System (ADS)

    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.

  18. Comparison of naturally and synthetically baited spruce beetle trapping systems in the central Rocky Mountains.

    PubMed

    Hansen, E M; Vandygriff, J C; Cain, R J; Wakarchuk, D

    2006-04-01

    We compared naturally baited trapping systems to synthetically baited funnel traps and fallen trap trees for suppressing preoutbreak spruce beetle, Dendroctonus rufipennis Kirby, populations. Lures for the traps were fresh spruce (Picea spp.) bolts or bark sections, augmented by adding female spruce beetles to create secondary attraction. In 2003, we compared a naturally baited system ("bolt trap") with fallen trap trees and with synthetically baited funnel traps. Trap performance was evaluated by comparing total beetle captures and spillover of attacks into nearby host trees. Overall, the trap systems did not significantly differ in spruce beetle captures, although bolt traps caught 6 to 7 times more beetles than funnel traps during the first 4 wk of testing. Funnel traps with synthetic lures had significantly more spillover than either trap trees or bolt traps. The study was repeated in 2004 with modifications including an enhanced blend synthetic lure. Again, trap captures were generally similar among naturally and synthetically baited traps, but naturally baited traps had significantly less spillover. Although relatively labor-intensive, the bolt trap could be used to suppress preoutbreak beetle populations, especially when spillover is undesirable. Our work provides additional avenues for management of spruce beetles and suggests that currently used synthetic lures can be improved. PMID:16686135

  19. Using synthetic models to simulate aging of Cu contamination in soils.

    PubMed

    Proffit, S; Marin, B; Cances, B; Ponthieu, M; Sayen, S; Guillon, E

    2015-05-01

    The Bureau Commun de Référence (BCR) sequential extraction scheme and micro-synchrotron-based X-ray fluorescence (μ-SXRF) analysis were used to determine the Cu fractionation in a calcareous vineyard soil and a synthetic soil (mixture of seven constituents: calcite, birnessite, ferrihydrite, goethite, lignocellulosic residue, kaolinite, and quartz) at different Cu contamination rates (190, 1270, and 6350 mg kg(-1) of Cu) and aging times (1, 30, 92, and 181 days). The Cu distribution in the spiked vineyard and synthetic soils was different from the original vineyard one and was influenced by the loading level. The newly added Cu was preferentially present in the acid soluble fraction. Aging of the contaminated vineyard and synthetic soils during 6 months led to the redistribution of Cu from the weakly bound acid soluble fraction to the strongly bound reducible one. The evolution with time could satisfactorily be simulated by the Elovich diffusion model for the synthetic soils. It was less significant as less marked in the contaminated vineyard soil than in the synthetic one, even though the trends observed in both were similar. This study supported the hypothesis that "simple" synthetic models could be used to approach the Cu fractionation and its evolution with time in vineyard soils.

  20. Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides.

    PubMed

    Schilter, David; Camara, James M; Huynh, Mioy T; Hammes-Schiffer, Sharon; Rauchfuss, Thomas B

    2016-08-10

    Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications. PMID:27353631

  1. Studies of synthetic protein models designed for biomolecular materials applications and model ion channels via molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zou, Hongling

    MD simulation has become an established and powerful tool to study large macromolecular systems including proteins in explicit solvent. Here simulation is applied to two types of synthetic protein models developed for biomolecular materials applications and for understanding complex biological problems, respectively. The simulation work presented in this thesis aims to facilitate the interpretation of experimental data and to provide detailed structural and dynamic information of protein models inaccessible by experiments. Several synthetic protein models have been investigated in this thesis. Firstly, the structure and dynamics of a de novo designed amphiphilic 4-alpha-helix bundle protein model capable of binding biological metallo-porphyrin cofactors are examined. The simulation results are in agreement with the experimental structural determinations available at lower resolution and limited dimension. Then the work proceeds to incorporate a more comprehensive nonbiological conjugated chromophore into this peptide model. The results show that the protein module plays an important role in controlling the chromophore's conformation and dynamics that are critical to optimize its functionality. Secondly, based on the success of the first work, simulation is utilized to test the viability and help improve the design of two computational designed multi-metalloporphyrins binding protein assemblies, which have different structural features and potential applications. Thirdly, the protein model idea is applied to study the mechanism of the general anesthetic binding as well. The simplified model allows for more sophisticated physical techniques, such as infrared spectroscopy, to be used. MD simulation correctly predicts the infrared frequency shift of the vibrational probes at the binding site in the presence of anesthetics. It also provides the interpretation to the experimental results and reveals the nature of the weak bonding between anesthetics and the model ion

  2. Human vision simulation for evaluation of enhanced and synthetic vision systems

    NASA Astrophysics Data System (ADS)

    Doll, Theodore J.; Home, Richard; Cooke, Kevin J.; Wasilewski, Anthony A.; Sheerin, David T.; Hetzler, Morris C.

    2003-09-01

    One of the key problems in developing Enhanced and Synthetic Vision Systems is evaluating their effectiveness in enhancing human visual performance. A validated simulation of human vision would provide a means of avoiding costly and time-consuming testing of human observers. We describe an image-based simulation of human visual search, detection, and identification, and efforts to further validate and refine this simulation. One of the advantages of an image-based simulation is that it can predict performance for exactly the same visual stimuli seen by human operators. This makes it possible to assess aspects of the imagery, such as particular types and amounts of background clutter and sensor distortions, that are not usually considered in non-image based models. We present two validation studies - one showing that the simulation accurately predicts human color discrimination, and a second showing that it produces probabilities of detection (Pd's) that closely match Blackwell-type human threshold data.

  3. Flight Test Comparison Between Enhanced Vision (FLIR) and Synthetic Vision Systems

    NASA Technical Reports Server (NTRS)

    Arthur, Jarvis J., III; Kramer, Lynda J.; Bailey, Randall E.

    2005-01-01

    Limited visibility and reduced situational awareness have been cited as predominant causal factors for both Controlled Flight Into Terrain (CFIT) and runway incursion accidents. NASA s Synthetic Vision Systems (SVS) project is developing practical application technologies with the goal of eliminating low visibility conditions as a causal factor to civil aircraft accidents while replicating the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. A major thrust of the SVS project involves the development/demonstration of affordable, certifiable display configurations that provide intuitive out-the-window terrain and obstacle information with advanced pathway guidance. A flight test evaluation was conducted in the summer of 2004 by NASA Langley Research Center under NASA s Aviation Safety and Security, Synthetic Vision System - Commercial and Business program. A Gulfstream G-V aircraft, modified and operated under NASA contract by the Gulfstream Aerospace Corporation, was flown over a 3-week period at the Reno/Tahoe International Airport and an additional 3-week period at the NASA Wallops Flight Facility to evaluate integrated Synthetic Vision System concepts. Flight testing was conducted to evaluate the performance, usability, and acceptance of an integrated synthetic vision concept which included advanced Synthetic Vision display concepts for a transport aircraft flight deck, a Runway Incursion Prevention System, an Enhanced Vision Systems (EVS), and real-time Database Integrity Monitoring Equipment. This paper focuses on comparing qualitative and subjective results between EVS and SVS display concepts.

  4. Flight test comparison between enhanced vision (FLIR) and synthetic vision systems

    NASA Astrophysics Data System (ADS)

    Arthur, Jarvis J., III; Kramer, Lynda J.; Bailey, Randall E.

    2005-05-01

    Limited visibility and reduced situational awareness have been cited as predominant causal factors for both Controlled Flight Into Terrain (CFIT) and runway incursion accidents. NASA"s Synthetic Vision Systems (SVS) project is developing practical application technologies with the goal of eliminating low visibility conditions as a causal factor to civil aircraft accidents while replicating the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. A major thrust of the SVS project involves the development/demonstration of affordable, certifiable display configurations that provide intuitive out-the-window terrain and obstacle information with advanced pathway guidance. A flight test evaluation was conducted in the summer of 2004 by NASA Langley Research Center under NASA's Aviation Safety and Security, Synthetic Vision System - Commercial and Business program. A Gulfstream G-V aircraft, modified and operated under NASA contract by the Gulfstream Aerospace Corporation, was flown over a 3-week period at the Reno/Tahoe International Airport and an additional 3-week period at the NASA Wallops Flight Facility to evaluate integrated Synthetic Vision System concepts. Flight testing was conducted to evaluate the performance, usability, and acceptance of an integrated synthetic vision concept which included advanced Synthetic Vision display concepts for a transport aircraft flight deck, a Runway Incursion Prevention System, an Enhanced Vision Systems (EVS), and real-time Database Integrity Monitoring Equipment. This paper focuses on comparing qualitative and subjective results between EVS and SVS display concepts.

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

    ERIC Educational Resources Information Center

    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…

  6. Sonophotolytic degradation of synthetic pharmaceutical wastewater: statistical experimental design and modeling.

    PubMed

    Ghafoori, Samira; Mowla, Amir; Jahani, Ramtin; Mehrvar, Mehrab; Chan, Philip K

    2015-03-01

    The merits of the sonophotolysis as a combination of sonolysis (US) and photolysis (UV/H2O2) are investigated in a pilot-scale external loop airlift sonophotoreactor for the treatment of a synthetic pharmaceutical wastewater (SPWW). In the first part of this study, the multivariate experimental design is carried out using Box-Behnken design (BBD). The effluent is characterized by the total organic carbon (TOC) percent removal as a surrogate parameter. The results indicate that the response of the TOC percent removal is significantly affected by the synergistic effects of the linear term of H2O2 dosage and ultrasound power with the antagonistic effect of quadratic term of H2O2 dosage. The statistical analysis of the results indicates a satisfactory prediction of the system behavior by the developed model. In the second part of this study, a novel rigorous mathematical model for the sonophotolytic process is developed to predict the TOC percent removal as a function of time. The mathematical model is based on extensively accepted sonophotochemical reactions and the rate constants in advanced oxidation processes. A good agreement between the model predictions and experimental data indicates that the proposed model could successfully describe the sonophotolysis of the pharmaceutical wastewater.

  7. Development of piezoelectric-based membranes for synthetic jet actuators: experiments and modeling

    NASA Astrophysics Data System (ADS)

    Housley, Kevin W.; Clingman, Dan J.; Amitay, Michael

    2016-04-01

    A mathematical model was developed to represent the behavior of circular piezoelectric bimorphs in a synthetic jet actuator. Synthetic jet actuators are popular active flow control devices whose application is being widely explored in aerodynamics. The material properties were matched to those of PZT-5A mounted on a substrate. The actuator's geometry consisted of a cylindrical cavity of low height to diameter aspect ratio. A bimorph formed one of the cylinder's bases. The ingestion/expulsion orifice for the synthetic jet actuator was placed in the edge of the cavity so as to allow for either the present single bimorph or future dual bimorph configurations. Simply supported and rigidly supported boundary conditions were assessed around the circumference of the bimorph. The potential of alternate mode shapes occurring in the bimorphs during operation of the synthetic jet was evaluated. A limited parametric study was conducted varying the thickness of the piezoelectric wafers used in the bimorphs and the geometry of the cavity and orifice. Results were obtained for the displacement of the center of the bimorph's surface and the peak velocity of the air being ingested and expulsed through the orifice. These results were compared to values obtained through a mathematical model. Experimental data present in literature were also compared. The mathematical model was seen to have considerable potential for predicting the performance of synthetic jet actuators and their resonant frequencies but failed to capture the effects of acoustic coupling with the cavity, which is a topic of future research.

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

    NASA Technical Reports Server (NTRS)

    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.

  9. Coins as intermediate targets: reconstructive analysis with synthetic body models.

    PubMed

    Thali, Michael J; Kneubuehl, Beat P; Rodriguez, William R; Smirniotopoulos, James G; Richardson, A Charles; Fowler, David; Godwin, Michael; Jurrus, Aaron; Fletcher, Douglas; Mallak, Craig

    2009-06-01

    The phenomenon of intermediate targets is well known in wound ballistics. In forensic science, models are used to reconstruct injury patterns to answer questions regarding the dynamic formation of these unusual injuries. Soft-tissue substitutes or glycerin soap and ordnance gelatin have been well established. Recently, based on previous experiences with artificial bone, a skull-brain model was developed. The goal of this study was to create and analyze a model-supported reconstruction of a real forensic case with a coin as an intermediate target. It was possible not only to demonstrate the "bullet-coin interaction," but also to recreate the wound pattern found in the victim. This case demonstrates that by using ballistic models, gunshot cases can be reproduced simply and economically, without coming into conflict with ethical guidelines. PMID:19465807

  10. Coins as intermediate targets: reconstructive analysis with synthetic body models.

    PubMed

    Thali, Michael J; Kneubuehl, Beat P; Rodriguez, William R; Smirniotopoulos, James G; Richardson, A Charles; Fowler, David; Godwin, Michael; Jurrus, Aaron; Fletcher, Douglas; Mallak, Craig

    2009-06-01

    The phenomenon of intermediate targets is well known in wound ballistics. In forensic science, models are used to reconstruct injury patterns to answer questions regarding the dynamic formation of these unusual injuries. Soft-tissue substitutes or glycerin soap and ordnance gelatin have been well established. Recently, based on previous experiences with artificial bone, a skull-brain model was developed. The goal of this study was to create and analyze a model-supported reconstruction of a real forensic case with a coin as an intermediate target. It was possible not only to demonstrate the "bullet-coin interaction," but also to recreate the wound pattern found in the victim. This case demonstrates that by using ballistic models, gunshot cases can be reproduced simply and economically, without coming into conflict with ethical guidelines.

  11. Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae.

    PubMed

    Rantasalo, Anssi; Czeizler, Elena; Virtanen, Riitta; Rousu, Juho; Lähdesmäki, Harri; Penttilä, Merja; Jäntti, Jussi; Mojzita, Dominik

    2016-01-01

    This work describes the development and characterization of a modular synthetic expression system that provides a broad range of adjustable and predictable expression levels in S. cerevisiae. The system works as a fixed-gain transcription amplifier, where the input signal is transferred via a synthetic transcription factor (sTF) onto a synthetic promoter, containing a defined core promoter, generating a transcription output signal. The system activation is based on the bacterial LexA-DNA-binding domain, a set of modified, modular LexA-binding sites and a selection of transcription activation domains. We show both experimentally and computationally that the tuning of the system is achieved through the selection of three separate modules, each of which enables an adjustable output signal: 1) the transcription-activation domain of the sTF, 2) the binding-site modules in the output promoter, and 3) the core promoter modules which define the transcription initiation site in the output promoter. The system has a novel bidirectional architecture that enables generation of compact, yet versatile expression modules for multiple genes with highly diversified expression levels ranging from negligible to very strong using one synthetic transcription factor. In contrast to most existing modular gene expression regulation systems, the present system is independent from externally added compounds. Furthermore, the established system was minimally affected by the several tested growth conditions. These features suggest that it can be highly useful in large scale biotechnology applications. PMID:26901642

  12. Investigation of the synthetic experiment system of machine equipment fault diagnosis

    NASA Astrophysics Data System (ADS)

    Liu, Hongyu; Xu, Zening; Yu, Xiaoguang

    2008-12-01

    The invention and manufacturing of the synthetic experiment system of machine equipment fault diagnosis filled in the blank of this kind of experiment equipment in China and obtained national practical new type patent. By the motor speed regulation system, machine equipment fault imitation system, measuring and monitoring system and analysis and diagnosis system of the synthetic experiment system, students can regulate motor speed arbitrarily, imitate multi-kinds of machine equipment parts fault, collect the signals of acceleration, speed, displacement, force and temperature and make multi-kinds of time field, frequency field and figure analysis. The application of the synthetic experiment system in our university's teaching practice has obtained good effect on fostering professional eligibility in measuring, monitoring and fault diagnosis of machine equipment. The synthetic experiment system has the advantages of short training time, quick desirable result and low test cost etc. It suits for spreading in university extraordinarily. If the systematic software was installed in portable computer, user can fulfill measuring, monitoring, signal processing and fault diagnosis on multi-kinds of field machine equipment conveniently. Its market foreground is very good.

  13. Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae

    PubMed Central

    Rantasalo, Anssi; Czeizler, Elena; Virtanen, Riitta; Rousu, Juho; Lähdesmäki, Harri; Penttilä, Merja

    2016-01-01

    This work describes the development and characterization of a modular synthetic expression system that provides a broad range of adjustable and predictable expression levels in S. cerevisiae. The system works as a fixed-gain transcription amplifier, where the input signal is transferred via a synthetic transcription factor (sTF) onto a synthetic promoter, containing a defined core promoter, generating a transcription output signal. The system activation is based on the bacterial LexA-DNA-binding domain, a set of modified, modular LexA-binding sites and a selection of transcription activation domains. We show both experimentally and computationally that the tuning of the system is achieved through the selection of three separate modules, each of which enables an adjustable output signal: 1) the transcription-activation domain of the sTF, 2) the binding-site modules in the output promoter, and 3) the core promoter modules which define the transcription initiation site in the output promoter. The system has a novel bidirectional architecture that enables generation of compact, yet versatile expression modules for multiple genes with highly diversified expression levels ranging from negligible to very strong using one synthetic transcription factor. In contrast to most existing modular gene expression regulation systems, the present system is independent from externally added compounds. Furthermore, the established system was minimally affected by the several tested growth conditions. These features suggest that it can be highly useful in large scale biotechnology applications. PMID:26901642

  14. Validating high-resolution California coastal flood modeling with Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR)

    NASA Astrophysics Data System (ADS)

    O'Neill, A.

    2015-12-01

    The Coastal Storm Modeling System (CoSMoS) is a numerical modeling scheme used to predict coastal flooding due to sea level rise and storms influenced by climate change, currently in use in central California and in development for Southern California (Pt. Conception to the Mexican border). Using a framework of circulation, wave, analytical, and Bayesian models at different geographic scales, high-resolution results are translated as relevant hazards projections at the local scale that include flooding, wave heights, coastal erosion, shoreline change, and cliff failures. Ready access to accurate, high-resolution coastal flooding data is critical for further validation and refinement of CoSMoS and improved coastal hazard projections. High-resolution Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) provides an exceptional data source as appropriately-timed flights during extreme tides or storms provide a geographically-extensive method for determining areas of inundation and flooding extent along expanses of complex and varying coastline. Landward flood extents are numerically identified via edge-detection in imagery from single flights, and can also be ascertained via change detection using additional flights and imagery collected during average wave/tide conditions. The extracted flooding positions are compared against CoSMoS results for similar tide, water level, and storm-intensity conditions, allowing for robust testing and validation of CoSMoS and providing essential feedback for supporting regional and local model improvement.

  15. Development of a Synthetic Adaptive Neuro-Fuzzy Prediction Model for Tumor Motion Tracking in External Radiotherapy by Evaluating Various Data Clustering Algorithms.

    PubMed

    Ghorbanzadeh, Leila; Torshabi, Ahmad Esmaili; Nabipour, Jamshid Soltani; Arbatan, Moslem Ahmadi

    2016-04-01

    In image guided radiotherapy, in order to reach a prescribed uniform dose in dynamic tumors at thorax region while minimizing the amount of additional dose received by the surrounding healthy tissues, tumor motion must be tracked in real-time. Several correlation models have been proposed in recent years to provide tumor position information as a function of time in radiotherapy with external surrogates. However, developing an accurate correlation model is still a challenge. In this study, we proposed an adaptive neuro-fuzzy based correlation model that employs several data clustering algorithms for antecedent parameters construction to avoid over-fitting and to achieve an appropriate performance in tumor motion tracking compared with the conventional models. To begin, a comparative assessment is done between seven nuero-fuzzy correlation models each constructed using a unique data clustering algorithm. Then, each of the constructed models are combined within an adaptive sevenfold synthetic model since our tumor motion database has high degrees of variability and that each model has its intrinsic properties at motion tracking. In the proposed sevenfold synthetic model, best model is selected adaptively at pre-treatment. The model also updates the steps for each patient using an automatic model selectivity subroutine. We tested the efficacy of the proposed synthetic model on twenty patients (divided equally into two control and worst groups) treated with CyberKnife synchrony system. Compared to Cyberknife model, the proposed synthetic model resulted in 61.2% and 49.3% reduction in tumor tracking error in worst and control group, respectively. These results suggest that the proposed model selection program in our synthetic neuro-fuzzy model can significantly reduce tumor tracking errors. Numerical assessments confirmed that the proposed synthetic model is able to track tumor motion in real time with high accuracy during treatment. PMID:25765021

  16. Interactions between model bacterial membranes and synthetic antimicrobials.

    NASA Astrophysics Data System (ADS)

    Yang, Lihua; Mishra, Abhijit; Som, Abhigyan; Tew, Gregory N.; Wong, Gerard C. L.

    2006-03-01

    Antimicrobial peptides comprise a key component of innate immunity for a wide range of multicellular organisms. It has been shown that natural antimicrobial peptides and their analogs can permeate bacterial membranes selectively. There are a number of proposed models for this action, but the detailed molecular mechanism of the induced membrane permeation remains unclear. We investigate interactions between model bacterial membranes and a prototypical family of phenylene ethynylene-based antimicrobials with controllable hydrophilic and hydrophobic volume fractions, controllable charge placement. Preliminary results from synchrotron small angle x-ray scattering (SAXS) results will be presented.

  17. Electromagnetic-acoustic-transducer synthetic-aperture system for thick-weld inspection

    NASA Astrophysics Data System (ADS)

    Fortunko, C. M.; Schramm, R. E.; Moulder, J. C.; McColskey, J. D.

    1984-05-01

    A system is described based on electromagnetic acoustic transducers (EMATs) as an approach to automated nondestructive evaluation of thick weldments. Applications include a new type of ultrasonic inspection system for thick, butt welds used in ship construction. A minicomputer controlled transducer positioned and acquired the digitized ultrasonic waveforms for synthetic aperture processing. The synthetic aperture technique further improved signal quality and yielded flaw localization through the weld thickness. Details include the design of the transducers and electronics, as well as the mechanical positioner, signal processing algorithms, and complete computer program listings.

  18. Comparison of model and human observer performance in FFDM, DBT, and synthetic mammography

    NASA Astrophysics Data System (ADS)

    Ikejimba, Lynda; Glick, Stephen J.; Samei, Ehsan; Lo, Joseph Y.

    2016-03-01

    Reader studies are important in assessing breast imaging systems. The purpose of this work was to assess task-based performance of full field digital mammography (FFDM), digital breast tomosynthesis (DBT), and synthetic mammography (SM) using different phantom types, and to determine an accurate observer model for human readers. Images were acquired on a Hologic Selenia Dimensions system with a uniform and anthropomorphic phantom. A contrast detail insert of small, low-contrast disks was created using an inkjet printer with iodine-doped ink and inserted in the phantoms. The disks varied in diameter from 210 to 630 μm, and in contrast from 1.1% contrast to 2.2% in regular increments. Human and model observers performed a 4-alternative forced choice experiment. The models were a non-prewhitening matched filter with eye model (NPWE) and a channelized Hotelling observer with either Gabor channels (Gabor-CHO) or Laguerre-Gauss channels (LG-CHO). With the given phantoms, reader scores were higher in FFDM and DBT than SM. The structure in the phantom background had a bigger impact on outcome for DBT than for FFDM or SM. All three model observers showed good correlation with humans in the uniform background, with ρ between 0.89 and 0.93. However, in the structured background, only the CHOs had high correlation, with ρ=0.92 for Gabor-CHO, 0.90 for LG-CHO, and 0.77 for NPWE. Because results of any analysis can depend on the phantom structure, conclusions of modality performance may need to be taken in the context of an appropriate model observer and a realistic phantom.

  19. Generating a Dynamic Synthetic Population – Using an Age-Structured Two-Sex Model for Household Dynamics

    PubMed Central

    Namazi-Rad, Mohammad-Reza; Mokhtarian, Payam; Perez, Pascal

    2014-01-01

    Generating a reliable computer-simulated synthetic population is necessary for knowledge processing and decision-making analysis in agent-based systems in order to measure, interpret and describe each target area and the human activity patterns within it. In this paper, both synthetic reconstruction (SR) and combinatorial optimisation (CO) techniques are discussed for generating a reliable synthetic population for a certain geographic region (in Australia) using aggregated- and disaggregated-level information available for such an area. A CO algorithm using the quadratic function of population estimators is presented in this paper in order to generate a synthetic population while considering a two-fold nested structure for the individuals and households within the target areas. The baseline population in this study is generated from the confidentialised unit record files (CURFs) and 2006 Australian census tables. The dynamics of the created population is then projected over five years using a dynamic micro-simulation model for individual- and household-level demographic transitions. This projection is then compared with the 2011 Australian census. A prediction interval is provided for the population estimates obtained by the bootstrapping method, by which the variability structure of a predictor can be replicated in a bootstrap distribution. PMID:24733522

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

    NASA Astrophysics Data System (ADS)

    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

  1. A synthetic ecology perspective: How well does behavior of model organisms in the laboratory predict microbial activities in natural habitats?

    DOE PAGESBeta

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

    2016-06-15

    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 sedimentmore » for a few decades and have identified a number of species genetically equipped for this activity. We have also identified cooccurring 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. Furthermore, these findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.« less

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

    PubMed Central

    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. PMID:27379075

  3. Current Challenges for Modeling Enzyme Active Sites by Biomimetic Synthetic Diiron Complexes

    PubMed Central

    Friedle, Simone; Reisner, Erwin; Lippard, Stephen J.

    2010-01-01

    This tutorial review describes recent progress in modeling the active sites of carboxylate-rich non-heme diiron enzymes that activate dioxygen to carry out several key reactions in nature. The chemistry of soluble methane monooxygenase, which catalyzes the selective oxidation of methane to methanol, is of particular interest for (bio)technological applications. Novel synthetic diiron complexes that mimic structural, and, to a lesser extent, functional features of these diiron enzymes are discussed. The chemistry of the enzymes is also briefly summarized. A particular focus of this review is on models that mimic characteristics of the diiron systems that were previously not emphasized, including systems that contain (i) aqua ligands, (ii) different substrates tethered to the ligand framework, (iii) dendrimers attached to carboxylates to mimic the protein environment, (iv) two N-donors in a syn-orientation with respect to the iron-iron vector, and (v) a N-rich ligand environment capable of accessing oxygenated high-valent diiron intermediates. PMID:20485834

  4. Web-based software tool for constraint-based design specification of synthetic biological systems.

    PubMed

    Oberortner, Ernst; Densmore, Douglas

    2015-06-19

    miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).

  5. Web-based software tool for constraint-based design specification of synthetic biological systems.

    PubMed

    Oberortner, Ernst; Densmore, Douglas

    2015-06-19

    miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ). PMID:25426642

  6. Development of a simple radiation system based on synthetic mats

    NASA Astrophysics Data System (ADS)

    Abel, K.; Hampel, A.; Kerber, W.; Percornik, D.; Sattler, K.

    1985-11-01

    Possibilities to use the physical effect of passive radiation cooling economically for space cooling in arid areas were investigated. Development of emitter layer configurations (coatings); computer models for optimization of the heat exchangers; and determination of design features for practical realization were studied. Practical tests prove that an economically feasible approach is possible with simple components.

  7. Co-culture systems and technologies: taking synthetic biology to the next level.

    PubMed

    Goers, Lisa; Freemont, Paul; Polizzi, Karen M

    2014-07-01

    Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions. PMID:24829281

  8. Co-culture systems and technologies: taking synthetic biology to the next level.

    PubMed

    Goers, Lisa; Freemont, Paul; Polizzi, Karen M

    2014-07-01

    Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions.

  9. Synthetic Modeling of Autonomous Learning with a Chaotic Neural Network

    NASA Astrophysics Data System (ADS)

    Funabashi, Masatoshi

    We investigate the possible role of intermittent chaotic dynamics called chaotic itinerancy, in interaction with nonsupervised learnings that reinforce and weaken the neural connection depending on the dynamics itself. We first performed hierarchical stability analysis of the Chaotic Neural Network model (CNN) according to the structure of invariant subspaces. Irregular transition between two attractor ruins with positive maximum Lyapunov exponent was triggered by the blowout bifurcation of the attractor spaces, and was associated with riddled basins structure. We secondly modeled two autonomous learnings, Hebbian learning and spike-timing-dependent plasticity (STDP) rule, and simulated the effect on the chaotic itinerancy state of CNN. Hebbian learning increased the residence time on attractor ruins, and produced novel attractors in the minimum higher-dimensional subspace. It also augmented the neuronal synchrony and established the uniform modularity in chaotic itinerancy. STDP rule reduced the residence time on attractor ruins, and brought a wide range of periodicity in emerged attractors, possibly including strange attractors. Both learning rules selectively destroyed and preserved the specific invariant subspaces, depending on the neuron synchrony of the subspace where the orbits are situated. Computational rationale of the autonomous learning is discussed in connectionist perspective.

  10. Design Optimization Tool for Synthetic Jet Actuators Using Lumped Element Modeling

    NASA Technical Reports Server (NTRS)

    Gallas, Quentin; Sheplak, Mark; Cattafesta, Louis N., III; Gorton, Susan A. (Technical Monitor)

    2005-01-01

    The performance specifications of any actuator are quantified in terms of an exhaustive list of parameters such as bandwidth, output control authority, etc. Flow-control applications benefit from a known actuator frequency response function that relates the input voltage to the output property of interest (e.g., maximum velocity, volumetric flow rate, momentum flux, etc.). Clearly, the required performance metrics are application specific, and methods are needed to achieve the optimal design of these devices. Design and optimization studies have been conducted for piezoelectric cantilever-type flow control actuators, but the modeling issues are simpler compared to synthetic jets. Here, lumped element modeling (LEM) is combined with equivalent circuit representations to estimate the nonlinear dynamic response of a synthetic jet as a function of device dimensions, material properties, and external flow conditions. These models provide reasonable agreement between predicted and measured frequency response functions and thus are suitable for use as design tools. In this work, we have developed a Matlab-based design optimization tool for piezoelectric synthetic jet actuators based on the lumped element models mentioned above. Significant improvements were achieved by optimizing the piezoceramic diaphragm dimensions. Synthetic-jet actuators were fabricated and benchtop tested to fully document their behavior and validate a companion optimization effort. It is hoped that the tool developed from this investigation will assist in the design and deployment of these actuators.

  11. The NASA/JPL Airborne Synthetic Aperture Radar System

    NASA Technical Reports Server (NTRS)

    Kim, Yun-Jin; Lou, Yun-Ling; vanZyl, Jakob

    1996-01-01

    The NASA/JPL airborne SAR (AIRSAR) system operates in the fully polarimetric mode at P-, L- and C-band simultaneously or in the interferometric mode in both L- and C-band simultaneously. The system became operational in late 1987 and flew its first mission aboard a DC-8 aircraft operated by NASA's Ames Research Center in Mountain View, California. Since then, the AIRSAR has flown missions every year and acquired images in North, Central and South America, Europe and Australia. In this paper, we will briefly describe the instrument characteristics, the evolution of the various radar modes, the instrument performance, and improvement in the knowledge of the positioning and attitude information of the radar. In addition, we will summarize the progress of the data processing effort especially in the interferometry processing. Finally, we will address the issue of processing and calibrating the cross-track interferometry (XTI) data.

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

    SciTech Connect

    Robert E. Spears; J. Kevin Wilkins

    2011-11-01

    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.

  13. Assessment of synthetic winds through spectral modelling, rainflow count analysis and statistics of increments

    NASA Astrophysics Data System (ADS)

    Beyer, Hans Georg; Chougule, Abhijit

    2016-04-01

    While wind energy industry growing rapidly and siting of wind turbines onshore as well as offshore is increasing, many wind engineering model tools have been developed for the assessment of loads on wind turbines due to varying wind speeds. In order to have proper wind turbine design and performance analysis, it is important to have an accurate representation of the incoming wind field. To ease the analysis, tools for the generation of synthetic wind fields have been developed, e.g the widely used TurbSim procedure. We analyse respective synthetic data sets on one hand in view of the similarity of the spectral characteristics of measured and synthetic sets. In addition, second order characteristics with direct relevance to load assessment as given by the statistics of increments and rainflow count results are inspected.

  14. Synthetic ECG Generation and Bayesian Filtering Using a Gaussian Wave-Based Dynamical Model

    PubMed Central

    Sayadi, Omid; Shamsollahi, Mohammad B.; Clifford, Gari D.

    2011-01-01

    In this paper, we describe a Gaussian wave-based state space to model the temporal dynamics of electrocardiogram (ECG) signals. It is shown that this model may be effectively used for generating synthetic ECGs as well as separate characteristic waves (CWs) such as the atrial and ventricular complexes. The model uses separate state variables for each CW, i.e. P, QRS and T, and hence is capable of generating individual synthetic CWs as well as realistic ECG signals. The model is therefore useful for generating arrhythmias. Simulations of sinus bradycardia, sinus tachycardia, ventricular flutter, atrial fibrillation, and ventricular tachycardia are presented. In addition, discrete versions of the equations are presented for a model-based Bayesian framework for denoising. This framework, together with an extended Kalman filter (EKF) and extended Kalman smoother (EKS), were used for denoising the ECG for both normal rhythms and arrhythmias. For evaluating the denoising performance the signal-to-noise ratio (SNR) improvement of the filter outputs and clinical parameter stability were studied. The results demonstrate superiority over a wide range of input SNRs, achieving a maximum 12.7 dB improvement. Results indicate that preventing clinically relevant distortion of the ECG is sensitive to the number of model parameters. Models are presented which do not exhibit such distortions. The approach presented in this paper may therefore serve as an effective framework for synthetic ECG generation and model-based filtering of noisy ECG recordings. PMID:20720288

  15. Synthetic polyion-counterion transport systems in polymersomes and gels.

    PubMed

    Montenegro, Javier; Braun, Jörg; Fischer-Onaca, Ozana; Meier, Wolfgang; Matile, Stefan

    2011-10-01

    Transport across the membranes of polymersomes remains difficult in part due to the great thickness of the polymer bilayers. Here, we report that dynamic polyion-counterion transport systems are active in fluorogenic polymersomes composed of poly(dimethylsiloxane)-b-poly(2-methyloxazoline) (PDMS-PMOXA). These results suggest that counterion-activated calf-thymus DNA can act as cation carrier that moves not only across lipid bilayer and bulk chloroform membranes but also across the "plastic" membranes of polymersomes. Compared to egg yolk phosophatidylcholine (EYPC) lipsosomes, activities and activator scope in PDMS-PMOXA polymersomes are clearly reduced. Embedded in agar gel matrices, fluorogenic PDMS-PMOXA polymersomes respond reliably to polyion-counterion transporters, with high contrast, high stability and preserved selectivity. Compared to standard EYPC liposomes, it cannot be said that PDMS-PMOXA polymersomes are better. However, they are different, and this difference could be interesting for the development of sensing devices.

  16. Genome-scale engineering for systems and synthetic biology

    PubMed Central

    Esvelt, Kevin M; Wang, Harris H

    2013-01-01

    Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targeted gene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering. PMID:23340847

  17. Synthetic 3D multicellular systems for drug development.

    PubMed

    Rimann, Markus; Graf-Hausner, Ursula

    2012-10-01

    Since the 1970s, the limitations of two dimensional (2D) cell culture and the relevance of appropriate three dimensional (3D) cell systems have become increasingly evident. Extensive effort has thus been made to move cells from a flat world to a 3D environment. While 3D cell culture technologies are meanwhile widely used in academia, 2D culture technologies are still entrenched in the (pharmaceutical) industry for most kind of cell-based efficacy and toxicology tests. However, 3D cell culture technologies will certainly become more applicable if biological relevance, reproducibility and high throughput can be assured at acceptable costs. Most recent innovations and developments clearly indicate that the transition from 2D to 3D cell culture for industrial purposes, for example, drug development is simply a question of time.

  18. Synthetic vision system for improving unmanned aerial vehicle operator situation awareness

    NASA Astrophysics Data System (ADS)

    Calhoun, Gloria L.; Draper, Mark H.; Abernathy, Michael F.; Patzek, Michael; Delgado, Francisco

    2005-05-01

    The Air Force Research Laboratory's Human Effectiveness Directorate (AFRL/HE) supports research addressing human factors associated with Unmanned Aerial Vehicle (UAV) operator control stations. Recent research, in collaboration with Rapid Imaging Software, Inc., has focused on determining the value of combining synthetic vision data with live camera video presented on a UAV control station display. Information is constructed from databases (e.g., terrain, cultural features, pre-mission plan, etc.), as well as numerous information updates via networked communication with other sources (e.g., weather, intel). This information is overlaid conformal, in real time, onto the dynamic camera video image display presented to operators. Synthetic vision overlay technology is expected to improve operator situation awareness by highlighting key spatial information elements of interest directly onto the video image, such as threat locations, expected locations of targets, landmarks, emergency airfields, etc. Also, it may help maintain an operator"s situation awareness during periods of video datalink degradation/dropout and when operating in conditions of poor visibility. Additionally, this technology may serve as an intuitive means of distributed communications between geographically separated users. This paper discusses the tailoring of synthetic overlay technology for several UAV applications. Pertinent human factors issues are detailed, as well as the usability, simulation, and flight test evaluations required to determine how best to combine synthetic visual data with live camera video presented on a ground control station display and validate that a synthetic vision system is beneficial for UAV applications.

  19. Modern synthetic tools toward the preparation of sophisticated phthalocyanine-based photoactive systems.

    PubMed

    Ragoussi, Maria-Eleni; Torres, Tomás

    2014-10-01

    Phthalocyanines are ideal components in a variety of electronic applications due to their extraordinary photophysical characteristics combined with their synthetic versatility and robustness. They have attracted substantial attention in recent decades and are now established building blocks of sophisticated molecular materials. Synthetically, a great deal of this progress is attributed to the use of modern synthetic tools, which gave rise to phthalocyanine-based systems that could not have been envisaged in the past. In particular, Pd-catalyzed cross-coupling reactions, together with other transition-metal-catalyzed procedures, "click" chemistry, and ruthenium metathesis have been employed extensively en route to an abundant range of elaborate phthalocyanine mono- and multicomponent photoactive architectures. Herein, we describe the synthesis of a selection of key examples that are representative in certain optoelectronic applications.

  20. Flight Test Evaluation of Situation Awareness Benefits of Integrated Synthetic Vision System Technology f or Commercial Aircraft

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence J., III; Kramer, Lynda J.; Arthur, Jarvis J., III

    2005-01-01

    Research was conducted onboard a Gulfstream G-V aircraft to evaluate integrated Synthetic Vision System concepts during flight tests over a 6-week period at the Wallops Flight Facility and Reno/Tahoe International Airport. The NASA Synthetic Vision System incorporates database integrity monitoring, runway incursion prevention alerting, surface maps, enhanced vision sensors, and advanced pathway guidance and synthetic terrain presentation. The paper details the goals and objectives of the flight test with a focus on the situation awareness benefits of integrating synthetic vision system enabling technologies for commercial aircraft.

  1. Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory.

    PubMed

    Nikolaev, Evgeni V; Sontag, Eduardo D

    2016-04-01

    biochemically-detailed and biologically-relevant model that we developed. Another novel feature of our approach is that our theorems on exponential stability of steady states for homogeneous or mixed populations are valid independently of the number N of cells in the population, which is usually very large (N ≫ 1) and unknown. We prove that the exponential stability depends on relative proportions of each type of state only. While monotone systems theory has been used previously for systems biology analysis, the current work illustrates its power for synthetic biology design, and thus has wider significance well beyond the application to the important problem of coordination of toggle switches.

  2. Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory

    PubMed Central

    Nikolaev, Evgeni V.

    2016-01-01

    analysis, performed for a biochemically-detailed and biologically-relevant model that we developed. Another novel feature of our approach is that our theorems on exponential stability of steady states for homogeneous or mixed populations are valid independently of the number N of cells in the population, which is usually very large (N ≫ 1) and unknown. We prove that the exponential stability depends on relative proportions of each type of state only. While monotone systems theory has been used previously for systems biology analysis, the current work illustrates its power for synthetic biology design, and thus has wider significance well beyond the application to the important problem of coordination of toggle switches. PMID:27128344

  3. Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory.

    PubMed

    Nikolaev, Evgeni V; Sontag, Eduardo D

    2016-04-01

    biochemically-detailed and biologically-relevant model that we developed. Another novel feature of our approach is that our theorems on exponential stability of steady states for homogeneous or mixed populations are valid independently of the number N of cells in the population, which is usually very large (N ≫ 1) and unknown. We prove that the exponential stability depends on relative proportions of each type of state only. While monotone systems theory has been used previously for systems biology analysis, the current work illustrates its power for synthetic biology design, and thus has wider significance well beyond the application to the important problem of coordination of toggle switches. PMID:27128344

  4. Robust model matching design methodology for a stochastic synthetic gene network.

    PubMed

    Chen, Bor-Sen; Chang, Chia-Hung; Wang, Yu-Chao; Wu, Chih-Hung; Lee, Hsiao-Ching

    2011-03-01

    Synthetic biology has shown its potential and promising applications in the last decade. However, many synthetic gene networks cannot work properly and maintain their desired behaviors due to intrinsic parameter variations and extrinsic disturbances. In this study, the intrinsic parameter uncertainties and external disturbances are modeled in a non-linear stochastic gene network to mimic the real environment in the host cell. Then a non-linear stochastic robust matching design methodology is introduced to withstand the intrinsic parameter fluctuations and to attenuate the extrinsic disturbances in order to achieve a desired reference matching purpose. To avoid solving the Hamilton-Jacobi inequality (HJI) in the non-linear stochastic robust matching design, global linearization technique is used to simplify the design procedure by solving a set of linear matrix inequalities (LMIs). As a result, the proposed matching design methodology of the robust synthetic gene network can be efficiently designed with the help of LMI toolbox in Matlab. Finally, two in silico design examples of the robust synthetic gene network are given to illustrate the design procedure and to confirm the robust model matching performance to achieve the desired behavior in spite of stochastic parameter fluctuations and environmental disturbances in the host cell. PMID:21215760

  5. Synthetic cellularity based on non-lipid micro-compartments and protocell models.

    PubMed

    Li, Mei; Huang, Xin; Tang, T-Y Dora; Mann, Stephen

    2014-10-01

    This review discusses recent advances in the design and construction of protocell models based on the self-assembly or microphase separation of non-lipid building blocks. We focus on strategies involving partially hydrophobic inorganic nanoparticles (colloidosomes), protein-polymer globular nano-conjugates (proteinosomes), amphiphilic block copolymers (polymersomes), and stoichiometric mixtures of oppositely charged biomolecules and polyelectrolytes (coacervates). Developments in the engineering of membrane functionality to produce synthetic protocells with gated responses and control over multi-step reactions are described. New routes to protocells comprising molecularly crowded, cytoskeletal-like hydrogel interiors, as well as to the construction of hybrid protocell models are also highlighted. Together, these strategies enable a wide range of biomolecular and synthetic components to be encapsulated, regulated and processed within the micro-compartmentalized volume, and suggest that the development of non-lipid micro-ensembles offers an approach that is complementary to protocell models based on phospholipid or fatty acid vesicles. PMID:24952153

  6. [Application of systems biology and synthetic biology in strain improvement for biofuel production].

    PubMed

    Zhao, Xinqing; Bai, Fengwu; Li, Yin

    2010-07-01

    Biofuels are renewable and environmentally friendly, but high production cost makes them economically not competitive, and the development of robust strains is thus one of the prerequisites. In this article, strain improvement studies based on the information from systems biology studies are reviewed, with a focus on their applications on stress tolerance improvement. Furthermore, the contribution of systems biology, synthetic biology and metabolic engineering in strain development for biofuel production is discussed, with an expectation for developing more robust strains for biofuel production.

  7. Ensemble Modeling of Hepatic Fatty Acid Metabolism with a Synthetic Glyoxylate Shunt

    PubMed Central

    Dean, Jason T.; Rizk, Matthew L.; Tan, Yikun; Dipple, Katrina M.; Liao, James C.

    2010-01-01

    Abstract The liver plays a central role in maintaining whole body metabolic and energy homeostasis by consuming and producing glucose and fatty acids. Glucose and fatty acids compete for hepatic substrate oxidation with regulation ensuring glucose is oxidized preferentially. Increasing fatty acid oxidation is expected to decrease lipid storage in the liver and avoid lipid-induced insulin-resistance. To increase hepatic lipid oxidation in the presence of glucose, we previously engineered a synthetic glyoxylate shunt into human hepatocyte cultures and a mouse model and showed that this synthetic pathway increases free fatty acid β-oxidation and confers resistance to diet-induced obesity in the mouse model. Here we used ensemble modeling to decipher the effects of perturbations to the hepatic metabolic network on fatty acid oxidation and glucose uptake. Despite sampling of kinetic parameters using the most fundamental elementary reaction models, the models based on current metabolic regulation did not readily describe the phenotype generated by glyoxylate shunt expression. Although not conclusive, this initial negative result prompted us to probe unknown regulations, and malate was identified as inhibitor of hexokinase 2 expression either through direct or indirect actions. This regulation allows the explanation of observed phenotypes (increased fatty acid degradation and decreased glucose consumption). Moreover, the result is a function of pyruvate-carboxylase, mitochondrial pyruvate transporter, citrate transporter protein, and citrate synthase activities. Some subsets of these flux ratios predict increases in fatty acid and decreases in glucose uptake after glyoxylate expression, whereas others predict no change. Altogether, this work defines the possible biochemical space where the synthetic shunt will produce the desired phenotype and demonstrates the efficacy of ensemble modeling for synthetic pathway design. PMID:20409457

  8. Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

    PubMed Central

    Aziz, Ramy K.; Monk, Jonathan M.; Lewis, Robert M.; In Loh, Suh; Mishra, Arti; Abhay Nagle, Amrita; Satyanarayana, Chitkala; Dhakshinamoorthy, Saravanakumar; Luche, Michele; Kitchen, Douglas B.; Andrews, Kathleen A.; Fong, Nicole L.; Li, Howard J.; Palsson, Bernhard O.; Charusanti, Pep

    2015-01-01

    Mathematical models of metabolism from bacterial systems biology have proven their utility across multiple fields, for example metabolic engineering, growth phenotype simulation, and biological discovery. The usefulness of the models stems from their ability to compute a link between genotype and phenotype, but their ability to accurately simulate gene-gene interactions has not been investigated extensively. Here we assess how accurately a metabolic model for Escherichia coli computes one particular type of gene-gene interaction, synthetic lethality, and find that the accuracy rate is between 25% and 43%. The most common failure modes were incorrect computation of single gene essentiality and biological information that was missing from the model. Moreover, we performed virtual and biological screening against several synthetic lethal pairs to explore whether two-compound formulations could be found that inhibit the growth of Gram-negative bacteria. One set of molecules was identified that, depending on the concentrations, inhibits E. coli and S. enterica serovar Typhimurium in an additive or antagonistic manner. These findings pinpoint specific ways in which to improve the predictive ability of metabolic models, and highlight one potential application of systems biology to drug discovery and translational medicine. PMID:26531810

  9. Testing 3D landform quantification methods with synthetic drumlins in a real digital elevation model

    NASA Astrophysics Data System (ADS)

    Hillier, John K.; Smith, Mike J.

    2012-06-01

    Metrics such as height and volume quantifying the 3D morphology of landforms are important observations that reflect and constrain Earth surface processes. Errors in such measurements are, however, poorly understood. A novel approach, using statistically valid ‘synthetic' landscapes to quantify the errors is presented. The utility of the approach is illustrated using a case study of 184 drumlins observed in Scotland as quantified from a Digital Elevation Model (DEM) by the ‘cookie cutter' extraction method. To create the synthetic DEMs, observed drumlins were removed from the measured DEM and replaced by elongate 3D Gaussian ones of equivalent dimensions positioned randomly with respect to the ‘noise' (e.g. trees) and regional trends (e.g. hills) that cause the errors. Then, errors in the cookie cutter extraction method were investigated by using it to quantify these ‘synthetic' drumlins, whose location and size is known. Thus, the approach determines which key metrics are recovered accurately. For example, mean height of 6.8 m is recovered poorly at 12.5 ± 0.6 (2σ) m, but mean volume is recovered correctly. Additionally, quantification methods can be compared: A variant on the cookie cutter using an un-tensioned spline induced about twice (× 1.79) as much error. Finally, a previously reportedly statistically significant (p = 0.007) difference in mean volume between sub-populations of different ages, which may reflect formational processes, is demonstrated to be only 30-50% likely to exist in reality. Critically, the synthetic DEMs are demonstrated to realistically model parameter recovery, primarily because they are still almost entirely the original landscape. Results are insensitive to the exact method used to create the synthetic DEMs, and the approach could be readily adapted to assess a variety of landforms (e.g. craters, dunes and volcanoes).

  10. A Synthetic Self-Oscillating Vocal Fold Model Platform for Studying Augmentation Injection

    PubMed Central

    Murray, Preston R.; Thomson, Scott L.; Smith, Marshall E.

    2013-01-01

    Objective Design and evaluate a platform for studying the mechanical effects of augmentation injections using synthetic self-oscillating vocal fold models. Study Design Basic science. Methods Life-sized, synthetic, multi-layer, self-oscillating vocal fold models were created that simulated bowing via volumetric reduction of the body layer relative to that of a normal, unbowed model. Material properties of the layers were unchanged. Models with varying degrees of bowing were created and paired with normal models. Following initial acquisition of data (onset pressure, vibration frequency, flow rate, and high-speed image sequences), bowed models were injected with silicone that had material properties similar to those used in augmentation procedures. Three different silicone injection quantities were tested: sufficient to close the glottal gap, insufficient to close the glottal gap, and excess silicone to create convex bowing of the bowed model. The above-mentioned metrics were again taken and compared. Pre- and post-injection high-speed image sequences were acquired using a hemilarynx setup, from which medial surface dynamics were quantified. Results The models vibrated with mucosal wave-like motion and at onset pressures and frequencies typical of human phonation. The models successfully exhibited various degrees of bowing which were then mitigated by injecting filler material. The models showed general pre- to post-injection decreases in onset pressure, flow rate, and open quotient, and a corresponding increase in vibration frequency. Conclusion The model may be useful in further explorations of the mechanical consequences of augmentation injections. PMID:24476985

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

    PubMed Central

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

    2014-01-01

    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 during anterior-posterior stretching. Method Three materially linear and three materially nonlinear models were created and stretched up to 10 mm in 1 mm increments. Phonation onset pressure (Pon) and fundamental frequency (F0) at Pon were recorded for each length. Measurements were repeated as the models were relaxed in 1 mm increments back to their resting lengths, and tensile tests were conducted to determine the stress-strain responses of linear versus nonlinear models. Results Nonlinear models demonstrated a more substantial frequency response than did linear models and a more predictable pattern of F0 increase with respect to increasing length (although range was inconsistent across models). Pon generally increased with increasing vocal fold length for nonlinear models, whereas for linear models, Pon decreased with increasing length. Conclusions Nonlinear synthetic models appear to more accurately represent the human vocal folds than linear models, especially with respect to F0 response. PMID:22271874

  12. Sender-receiver systems and applying information theory for quantitative synthetic biology.

    PubMed

    Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

    2015-02-01

    Sender-receiver (S-R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S-R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning.

  13. Sender–receiver systems and applying information theory for quantitative synthetic biology

    PubMed Central

    Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

    2015-01-01

    Sender–receiver (S–R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S–R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning. PMID:25282688

  14. The G-FAST Geodetic Earthquake Early Warning System: Operational Performance and Synthetic Testing

    NASA Astrophysics Data System (ADS)

    Crowell, B. W.; Schmidt, D. A.; Bodin, P.; Vidale, J. E.; Melbourne, T. I.; Santillan, V. M.

    2015-12-01

    The G-FAST (Geodetic First Approximation of Size and TIming) earthquake early warning module is part of a joint seismic and geodetic earthquake early warning system currently under development at the Pacific Northwest Seismic Network (PNSN). Our two-stage approach to earthquake early warning includes: (1) initial detection and characterization from PNSN strong-motion and broadband data with the ElarmS package within ShakeAlert, and then (2) modeling of GPS data from the Pacific Northwest Geodetic Array (PANGA). The two geodetic modeling modules are (1) a fast peak-ground-displacement magnitude and depth estimate and (2) a CMT-based finite fault inversion that utilizes coseismic offsets to compute earthquake extent, slip and magnitude. The seismic and geodetic source estimates are then combined in a decision module currently under development. In this presentation, we first report on the operational performance during the first several months that G-FAST has been live with respect to magnitude estimates, timing information, and stability. Secondly, we report on the performance of the G-FAST test system using simulated displacements from plausible Cascadian earthquake scenarios. The test system permits us to: (1) replay segments of actual seismic waveform data recorded from the PNSN and neighboring networks to investigate both earthquakes and noise conditions, and (2) broadcast synthetic data into the system to simulate signals we anticipate from earthquakes for which we have no actual ground motion recordings. The test system lets us also simulate various error conditions (latent and/or out-of-sequence data, telemetry drop-outs, etc.) in order to explore how best to mitigate them. For example, we show for a replay of the 2001 M6.8 Nisqually earthquake that telemetry drop-outs create the largest variability and biases in magnitude and depth estimates whereas latency only causes some variability towards the beginning of the recordings before quickly stabilizing

  15. Therapeutic Effect of a Synthetic RORα/γ Agonist in an Animal Model of Autism

    PubMed Central

    2015-01-01

    Autism is a developmental disorder of the nervous system associated with impaired social communication and interactions as well excessive repetitive behaviors. There are no drug therapies that directly target the pathology of this disease. The retinoic acid receptor-related orphan receptor α (RORα) is a nuclear receptor that has been demonstrated to have reduced expression in many individuals with autism spectrum disorder (ASD). Several genes that have been shown to be downregulated in individuals with ASD have also been identified as putative RORα target genes. Utilizing a synthetic RORα/γ agonist, SR1078, that we identified previously, we demonstrate that treatment of BTBR mice (a model of autism) with SR1078 results in reduced repetitive behavior. Furthermore, these mice display increased expression of ASD-associated RORα target genes in both the brains of the BTBR mice and in a human neuroblastoma cell line treated with SR1078. These data suggest that pharmacological activation of RORα may be a method for treatment of autism. PMID:26625251

  16. Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

    PubMed Central

    Bilitchenko, Lesia; Liu, Adam; Cheung, Sherine; Weeding, Emma; Xia, Bing; Leguia, Mariana; Anderson, J. Christopher; Densmore, Douglas

    2011-01-01

    Background Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts. Results We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively. Conclusions Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly. PMID:21559524

  17. A synthetic vision system using directionally selective motion detectors to recognize collision.

    PubMed

    Yue, Shigang; Rind, F Claire

    2007-01-01

    Reliably recognizing objects approaching on a collision course is extremely important. A synthetic vision system is proposed to tackle the problem of collision recognition in dynamic environments. The system combines the outputs of four whole-field motion-detecting neurons, each receiving inputs from a network of neurons employing asymmetric lateral inhibition to suppress their responses to one direction of motion. An evolutionary algorithm is then used to adjust the weights between the four motion-detecting neurons to tune the system to detect collisions in two test environments. To do this, a population of agents, each representing a proposed synthetic visual system, either were shown images generated by a mobile Khepera robot navigating in a simplified laboratory environment or were shown images videoed outdoors from a moving vehicle. The agents had to cope with the local environment correctly in order to survive. After 400 generations, the best agent recognized imminent collisions reliably in the familiar environment where it had evolved. However, when the environment was swapped, only the agent evolved to cope in the robotic environment still signaled collision reliably. This study suggests that whole-field direction-selective neurons, with selectivity based on asymmetric lateral inhibition, can be organized into a synthetic vision system, which can then be adapted to play an important role in collision detection in complex dynamic scenes.

  18. A synthetic vision system using directionally selective motion detectors to recognize collision.

    PubMed

    Yue, Shigang; Rind, F Claire

    2007-01-01

    Reliably recognizing objects approaching on a collision course is extremely important. A synthetic vision system is proposed to tackle the problem of collision recognition in dynamic environments. The system combines the outputs of four whole-field motion-detecting neurons, each receiving inputs from a network of neurons employing asymmetric lateral inhibition to suppress their responses to one direction of motion. An evolutionary algorithm is then used to adjust the weights between the four motion-detecting neurons to tune the system to detect collisions in two test environments. To do this, a population of agents, each representing a proposed synthetic visual system, either were shown images generated by a mobile Khepera robot navigating in a simplified laboratory environment or were shown images videoed outdoors from a moving vehicle. The agents had to cope with the local environment correctly in order to survive. After 400 generations, the best agent recognized imminent collisions reliably in the familiar environment where it had evolved. However, when the environment was swapped, only the agent evolved to cope in the robotic environment still signaled collision reliably. This study suggests that whole-field direction-selective neurons, with selectivity based on asymmetric lateral inhibition, can be organized into a synthetic vision system, which can then be adapted to play an important role in collision detection in complex dynamic scenes. PMID:17355187

  19. A synthetic gene drive system for local, reversible modification and suppression of insect populations.

    PubMed

    Akbari, Omar S; Matzen, Kelly D; Marshall, John M; Huang, Haixia; Ward, Catherine M; Hay, Bruce A

    2013-04-22

    Replacement of wild insect populations with genetically modified individuals unable to transmit disease provides a self-perpetuating method of disease prevention but requires a gene drive mechanism to spread these traits to high frequency. Drive mechanisms requiring that transgenes exceed a threshold frequency in order to spread are attractive because they bring about local but not global replacement, and transgenes can be eliminated through dilution of the population with wild-type individuals. These features are likely to be important in many social and regulatory contexts. Here we describe the first creation of a synthetic threshold-dependent gene drive system, designated maternal-effect lethal underdominance (UD(MEL)), in which two maternally expressed toxins, located on separate chromosomes, are each linked with a zygotic antidote able to rescue maternal-effect lethality of the other toxin. We demonstrate threshold-dependent replacement in single- and two-locus configurations in Drosophila. Models suggest that transgene spread can often be limited to local environments. They also show that in a population in which single-locus UD(MEL) has been carried out, repeated release of wild-type males can result in population suppression, a novel method of genetic population manipulation.

  20. Implementing a shadow detection algorithm for synthetic vision systems in reconfigurable hardware

    NASA Astrophysics Data System (ADS)

    Ladeji-Osias, Jumoke; Theobalds, Andre; Nare, Otsebele; Wandji, Theirry; Scott, Craig; Nyarko, Kofi

    2006-05-01

    The integrity monitor for synthetic vision systems provides pilots with a consistency check between stored Digital Elevation Models (DEM) and real-time sensor data. This paper discusses the implementation of the Shadow Detection and Extraction (SHADE) algorithm in reconfigurable hardware to increase the efficiency of the design. The SHADE algorithm correlates data from a weather radar and DEM to determine occluded regions of the flight path terrain. This process of correlating the weather radar and DEM data occurs in two parallel threads which are then fed into a disparity checker. The DEM thread is broken up into four main sub-functions: 1) synchronization and translation of GPS coordinates of aircraft to the weather radar, 2) mapping range bins to coordinates and computing depression angles, 3) mapping state assignments to range bins, and 4) shadow region edge detection. This correlation must be done in realtime; therefore, a hardware implementation is ideal due to the amount of data that is to be processed. The hardware of choice is the field programmable gate array because of programmability, reusability, and computational ability. Assigning states to each range bin is the most computationally intensive process and it is implemented as a finite state machine (FSM). Results of this work are focused on the implementation of the FSM.

  1. Cosmo Cassette: A Microfluidic Microgravity Microbial System For Synthetic Biology Unit Tests and Satellite Missions

    NASA Technical Reports Server (NTRS)

    Berliner, Aaron J.

    2013-01-01

    Although methods in the design-build-test life cycle of the synthetic biology field have grown rapidly, the expansion has been non-uniform. The design and build stages in development have seen innovations in the form of biological CAD and more efficient means for building DNA, RNA, and other biological constructs. The testing phase of the cycle remains in need of innovation. Presented will be both a theoretical abstraction of biological measurement and a practical demonstration of a microfluidics-based platform for characterizing synthetic biological phenomena. Such a platform demonstrates a design of additive manufacturing (3D printing) for construction of a microbial fuel cell (MFC) to be used in experiments carried out in space. First, the biocompatibility of the polypropylene chassis will be demonstrated. The novel MFCs will be cheaper, and faster to make and iterate through designs. The novel design will contain a manifold switchingdistribution system and an integrated in-chip set of reagent reservoirs fabricated via 3D printing. The automated nature of the 3D printing yields itself to higher resolution switching valves and leads to smaller sized payloads, lower cost, reduced power and a standardized platform for synthetic biology unit tests on Earth and in space. It will be demonstrated that the application of unit testing in synthetic biology will lead to the automatic construction and validation of desired constructs. Unit testing methodologies offer benefits of preemptive problem identification, change of facility, simplicity of integration, ease of documentation, and separation of interface from implementation, and automated design.

  2. Seismic reflection mapping of discontinuous sandstone bodies. Part I: synthetic modeling studying

    SciTech Connect

    Dobecki, T.L.

    1980-06-01

    Utilizing depth models consistent with the size, velocity, and density of observed sandstone channels in the upper Cretaceous Mesa Verde and Tertiary Wasatch formations, the synthetic seismic response of such channel lenses has been computed. By varying the lens thickness, depth, number, and separation, it was possible to observe the net effect on the seismic response and, in turn, how these affects might influence interpretation of field data.

  3. Phenolic mediators enhance the manganese peroxidase catalyzed oxidation of recalcitrant lignin model compounds and synthetic lignin.

    PubMed

    Nousiainen, Paula; Kontro, Jussi; Manner, Helmiina; Hatakka, Annele; Sipilä, Jussi

    2014-11-01

    Fungal oxidative enzymes, such as peroxidases and laccases, are the key catalysts in lignin biodegradation in vivo, and consequently provide an important source for industrial ligninolytic biocatalysts. Recently, it has been shown that some syringyl-type phenolics have potential as industrial co-oxidants or mediators, in laccase-catalyzed modification of lignocellulosic material. We have now studied the effect of such mediators with ligninolytic peroxidases on oxidation of the most recalcitrant lignin model compounds. We found that they are able to enhance the manganese peroxidase (MnP) catalyzed oxidation reactions of small non-phenolic compounds, veratryl alcohol and veratrylglycerol β-guaiacyl ether (adlerol), which are not usually oxidized by manganese peroxidases alone. In these experiments we compared two peroxidases from white-rot fungi, MnP from Phlebia sp. Nf b19 and versatile peroxidase (VP) from Bjerkandera adusta under two oxidation conditions: (i) the Mn(III) initiated mediated oxidation by syringyl compounds and (ii) the system involving MnP-dependent lipid peroxidation, both with production of (hydrogen) peroxides in situ to maintain the peroxidase catalytic cycle. It was found that both peroxidases produced α-carbonyl oxidation product of veratryl alcohol in clearly higher yields in reactions mediated by phenoxy radicals than in lipid-peroxyl radical system. The oxidation of adlerol, on the other hand, was more efficient in lipid-peroxidation-system. VP was more efficient than MnP in the oxidation of veratryl alcohol and showed its lignin peroxidase type activity in the reaction conditions indicated by some cleavage of Cα-Cβ-bond of adlerol. Finally, the mediator assisted oxidation conditions were applied in the oxidation of synthetic lignin (DHP) and the structural analysis of the oxidized polymers showed clear modifications in the polymer outcome, e.g. the oxidation resulted in reduced amount of aliphatic hydroxyls indicated by (31)P NMR.

  4. Phenolic mediators enhance the manganese peroxidase catalyzed oxidation of recalcitrant lignin model compounds and synthetic lignin.

    PubMed

    Nousiainen, Paula; Kontro, Jussi; Manner, Helmiina; Hatakka, Annele; Sipilä, Jussi

    2014-11-01

    Fungal oxidative enzymes, such as peroxidases and laccases, are the key catalysts in lignin biodegradation in vivo, and consequently provide an important source for industrial ligninolytic biocatalysts. Recently, it has been shown that some syringyl-type phenolics have potential as industrial co-oxidants or mediators, in laccase-catalyzed modification of lignocellulosic material. We have now studied the effect of such mediators with ligninolytic peroxidases on oxidation of the most recalcitrant lignin model compounds. We found that they are able to enhance the manganese peroxidase (MnP) catalyzed oxidation reactions of small non-phenolic compounds, veratryl alcohol and veratrylglycerol β-guaiacyl ether (adlerol), which are not usually oxidized by manganese peroxidases alone. In these experiments we compared two peroxidases from white-rot fungi, MnP from Phlebia sp. Nf b19 and versatile peroxidase (VP) from Bjerkandera adusta under two oxidation conditions: (i) the Mn(III) initiated mediated oxidation by syringyl compounds and (ii) the system involving MnP-dependent lipid peroxidation, both with production of (hydrogen) peroxides in situ to maintain the peroxidase catalytic cycle. It was found that both peroxidases produced α-carbonyl oxidation product of veratryl alcohol in clearly higher yields in reactions mediated by phenoxy radicals than in lipid-peroxyl radical system. The oxidation of adlerol, on the other hand, was more efficient in lipid-peroxidation-system. VP was more efficient than MnP in the oxidation of veratryl alcohol and showed its lignin peroxidase type activity in the reaction conditions indicated by some cleavage of Cα-Cβ-bond of adlerol. Finally, the mediator assisted oxidation conditions were applied in the oxidation of synthetic lignin (DHP) and the structural analysis of the oxidized polymers showed clear modifications in the polymer outcome, e.g. the oxidation resulted in reduced amount of aliphatic hydroxyls indicated by (31)P NMR. PMID

  5. Synthetic environments

    NASA Astrophysics Data System (ADS)

    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.

  6. Database integrity monitoring for synthetic vision systems using machine vision and SHADE

    NASA Astrophysics Data System (ADS)

    Cooper, Eric G.; Young, Steven D.

    2005-05-01

    In an effort to increase situational awareness, the aviation industry is investigating technologies that allow pilots to visualize what is outside of the aircraft during periods of low-visibility. One of these technologies, referred to as Synthetic Vision Systems (SVS), provides the pilot with real-time computer-generated images of obstacles, terrain features, runways, and other aircraft regardless of weather conditions. To help ensure the integrity of such systems, methods of verifying the accuracy of synthetically-derived display elements using onboard remote sensing technologies are under investigation. One such method is based on a shadow detection and extraction (SHADE) algorithm that transforms computer-generated digital elevation data into a reference domain that enables direct comparison with radar measurements. This paper describes machine vision techniques for making this comparison and discusses preliminary results from application to actual flight data.

  7. Database Integrity Monitoring for Synthetic Vision Systems Using Machine Vision and SHADE

    NASA Technical Reports Server (NTRS)

    Cooper, Eric G.; Young, Steven D.

    2005-01-01

    In an effort to increase situational awareness, the aviation industry is investigating technologies that allow pilots to visualize what is outside of the aircraft during periods of low-visibility. One of these technologies, referred to as Synthetic Vision Systems (SVS), provides the pilot with real-time computer-generated images of obstacles, terrain features, runways, and other aircraft regardless of weather conditions. To help ensure the integrity of such systems, methods of verifying the accuracy of synthetically-derived display elements using onboard remote sensing technologies are under investigation. One such method is based on a shadow detection and extraction (SHADE) algorithm that transforms computer-generated digital elevation data into a reference domain that enables direct comparison with radar measurements. This paper describes machine vision techniques for making this comparison and discusses preliminary results from application to actual flight data.

  8. Enhanced Flight Vision Systems and Synthetic Vision Systems for NextGen Approach and Landing Operations

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Williams, Steven P.; Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Shelton, Kevin J.

    2013-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory standards and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility approach and landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O'Hare environment. Various scenarios tested the potential for using EFVS to conduct approach, landing, and roll-out operations in visibility as low as 1000 feet runway visual range (RVR). Also, SVS was tested to evaluate the potential for lowering decision heights (DH) on certain instrument approach procedures below what can be flown today. Expanding the portion of the visual segment in which EFVS can be used in lieu of natural vision from 100 feet above the touchdown zone elevation to touchdown and rollout in visibilities as low as 1000 feet RVR appears to be viable as touchdown performance was acceptable without any apparent workload penalties. A lower DH of 150 feet and/or possibly reduced visibility minima using SVS appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  9. Synthetic 3D modeling of active regions and simulation of their multi-wavelength emission

    NASA Astrophysics Data System (ADS)

    Nita, Gelu M.; Fleishman, Gregory; Kuznetsov, Alexey A.; Loukitcheva, Maria A.; Viall, Nicholeen M.; Klimchuk, James A.; Gary, Dale E.

    2015-04-01

    To facilitate the study of solar active regions, we have created a synthetic modeling framework that combines 3D magnetic structures obtained from magnetic extrapolations with simplified 1D thermal models of the chromosphere, transition region, and corona. To handle, visualize, and use such synthetic data cubes to compute multi-wavelength emission maps and compare them with observations, we have undertaken a major enhancement of our simulation tools, GX_Simulator (ftp://sohoftp.nascom.nasa.gov/solarsoft/packages/gx_simulator/), developed earlier for modeling emission from flaring loops. The greatly enhanced, object-based architecture, which now runs on Windows, Mac, and UNIX platform, offers important new capabilities that include the ability to either import 3D density and temperature distribution models, or to assign to each individual voxel numerically defined coronal or chromospheric temperature and densities, or coronal Differential Emission Measure distributions. Due to these new capabilities, the GX_Simulator can now apply parametric heating models involving average properties of the magnetic field lines crossing a given voxel volume, as well as compute and investigate the spatial and spectral properties of radio (to be compared with VLA or EOVSA data), (sub-)millimeter (ALMA), EUV (AIA/SDO), and X-ray (RHESSI) emission calculated from the model. The application integrates shared-object libraries containing fast free-free, gyrosynchrotron, and gyroresonance emission codes developed in FORTRAN and C++, and soft and hard X-ray and EUV codes developed in IDL. We use this tool to model and analyze an active region and compare the synthetic emission maps obtained in different wavelengths with observations.This work was partially supported by NSF grants AGS-1250374, AGS-1262772, NASA grant NNX14AC87G, the Marie Curie International Research Staff Exchange Scheme "Radiosun" (PEOPLE-2011-IRSES-295272), RFBR grants 14-02-91157, 15-02-01089, 15-02-03717, 15

  10. Rewiring Cells: Synthetic biology as a tool to interrogate the organizational principles of living systems

    PubMed Central

    Bashor, Caleb J.; Horwitz, Andrew A.; Peisajovich, Sergio G.; Lim, Wendell A.

    2010-01-01

    The living cell is an incredibly complex entity, and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent, we have yet to decode how these parts are organized to yield complex physiological function. Classically, we have learned about the organization of cellular networks by perturbing them through genetic or chemical means. The emerging discipline of synthetic biology offers an additional, powerful way to study systems. By rearranging the parts that comprise existing networks, we can gain valuable insight into the hierarchical logic of the networks and identify the modular building blocks that evolution uses to generate innovative function. Additionally, by building minimal “toy” networks, one can systematically explore the relationship between network space (linkages and parameters) and functional space (the system's physiological behavior). Here, we outline recent work that uses synthetic biology approaches to investigate the organization and function of cellular networks, and describe a vision for a synthetic biology toolkit that could be used to interrogate the design principles of diverse systems. PMID:20192780

  11. A Hybrid Synthetic Vision System for the Tele-operation of Unmanned Vehicles

    NASA Technical Reports Server (NTRS)

    Delgado, Frank; Abernathy, Mike

    2004-01-01

    A system called SmartCam3D (SC3D) has been developed to provide enhanced situational awareness for operators of a remotely piloted vehicle. SC3D is a Hybrid Synthetic Vision System (HSVS) that combines live sensor data with information from a Synthetic Vision System (SVS). By combining the dual information sources, the operators are afforded the advantages of each approach. The live sensor system provides real-time information for the region of interest. The SVS provides information rich visuals that will function under all weather and visibility conditions. Additionally, the combination of technologies allows the system to circumvent some of the limitations from each approach. Video sensor systems are not very useful when visibility conditions are hampered by rain, snow, sand, fog, and smoke, while a SVS can suffer from data freshness problems. Typically, an aircraft or satellite flying overhead collects the data used to create the SVS visuals. The SVS data could have been collected weeks, months, or even years ago. To that extent, the information from an SVS visual could be outdated and possibly inaccurate. SC3D was used in the remote cockpit during flight tests of the X-38 132 and 131R vehicles at the NASA Dryden Flight Research Center. SC3D was also used during the operation of military Unmanned Aerial Vehicles. This presentation will provide an overview of the system, the evolution of the system, the results of flight tests, and future plans. Furthermore, the safety benefits of the SC3D over traditional and pure synthetic vision systems will be discussed.

  12. A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology.

    PubMed

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-07-12

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homogeneous DBNs fail to model the non-stationarity and time-varying nature of the gene regulatory processes. Various authors have therefore recently proposed combining DBNs with multiple changepoint processes to obtain time varying dynamic Bayesian networks (TV-DBNs). However, TV-DBNs are not without problems. Gene expression time series are typically short, which leaves the model over-flexible, leading to over-fitting or inflated inference uncertainty. In the present paper, we introduce a Bayesian regularization scheme that addresses this difficulty. Our approach is based on the rationale that changes in gene regulatory processes appear gradually during an organism's life cycle or in response to a changing environment, and we have integrated this notion in the prior distribution of the TV-DBN parameters. We have extensively tested our regularized TV-DBN model on synthetic data, in which we have simulated short non-homogeneous time series produced from a system subject to gradual change. We have then applied our method to real-world gene expression time series, measured during the life cycle of Drosophila melanogaster, under artificially generated constant light condition in Arabidopsis thaliana, and from a synthetically designed strain of Saccharomyces cerevisiae exposed to a changing environment.

  13. Synthetic, Multi-Layer, Self-Oscillating Vocal Fold Model Fabrication

    PubMed Central

    Murray, Preston R.; Thomson, Scott L.

    2011-01-01

    Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing material properties 1. Normal voice production relies on healthy tissue and vocal folds, and occurs as a result of complex coupling between aerodynamic, structural dynamic, and acoustic physical phenomena. Voice disorders affect up to 7.5 million annually in the United States alone 2 and often result in significant financial, social, and other quality-of-life difficulties. Understanding the physics of voice production has the potential to significantly benefit voice care, including clinical prevention, diagnosis, and treatment of voice disorders. Existing methods for studying voice production include in vivo experimentation using human and animal subjects, in vitro experimentation using excised larynges and synthetic models, and computational modeling. Owing to hazardous and difficult instrument access, in vivo experiments are severely limited in scope. Excised larynx experiments have the benefit of anatomical and some physiological realism, but parametric studies involving geometric and material property variables are limited. Further, they are typically only able to be vibrated for relatively short periods of time (typically on the order of minutes). Overcoming some of the limitations of excised larynx experiments, synthetic vocal fold models are emerging as a complementary tool for studying voice production. Synthetic models can be fabricated with systematic changes to geometry and material properties, allowing for the study of healthy and unhealthy human phonatory aerodynamics, structural dynamics, and acoustics. For example, they have been used to study left-right vocal fold asymmetry 3,4, clinical instrument development 5, laryngeal aerodynamics 6-9, vocal fold contact pressure 10, and subglottal acoustics 11 (a more comprehensive list can be found in Kniesburges et al. 12) Existing synthetic vocal fold models

  14. Synthetic, multi-layer, self-oscillating vocal fold model fabrication.

    PubMed

    Murray, Preston R; Thomson, Scott L

    2011-01-01

    Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing material properties. Normal voice production relies on healthy tissue and vocal folds, and occurs as a result of complex coupling between aerodynamic, structural dynamic, and acoustic physical phenomena. Voice disorders affect up to 7.5 million annually in the United States alone and often result in significant financial, social, and other quality-of-life difficulties. Understanding the physics of voice production has the potential to significantly benefit voice care, including clinical prevention, diagnosis, and treatment of voice disorders. Existing methods for studying voice production include in vivo experimentation using human and animal subjects, in vitro experimentation using excised larynges and synthetic models, and computational modeling. Owing to hazardous and difficult instrument access, in vivo experiments are severely limited in scope. Excised larynx experiments have the benefit of anatomical and some physiological realism, but parametric studies involving geometric and material property variables are limited. Further, they are typically only able to be vibrated for relatively short periods of time (typically on the order of minutes). Overcoming some of the limitations of excised larynx experiments, synthetic vocal fold models are emerging as a complementary tool for studying voice production. Synthetic models can be fabricated with systematic changes to geometry and material properties, allowing for the study of healthy and unhealthy human phonatory aerodynamics, structural dynamics, and acoustics. For example, they have been used to study left-right vocal fold asymmetry, clinical instrument development, laryngeal aerodynamics, vocal fold contact pressure, and subglottal acoustics (a more comprehensive list can be found in Kniesburges et al.) Existing synthetic vocal fold models, however, have either

  15. Generation of topographic terrain models utilizing synthetic aperture radar and surface level data

    NASA Technical Reports Server (NTRS)

    Imhoff, Marc L. (Inventor)

    1991-01-01

    Topographical terrain models are generated by digitally delineating the boundary of the region under investigation from the data obtained from an airborne synthetic aperture radar image and surface elevation data concurrently acquired either from an airborne instrument or at ground level. A set of coregistered boundary maps thus generated are then digitally combined in three dimensional space with the acquired surface elevation data by means of image processing software stored in a digital computer. The method is particularly applicable for generating terrain models of flooded regions covered entirely or in part by foliage.

  16. Synthetic aperture imaging using a semi-analytic model for the transmit beams

    NASA Astrophysics Data System (ADS)

    Hansen, Jens M.; Nikolov, Svetoslav I.

    2015-03-01

    Many modern high-end scanners use some form for coherent synthesis of image lines by combining beams acquired with different transmissions, such as retrospective dynamic transmit focusing (Acuson / Siemens), nSIGHT (Philips), and Zone imaging (Zonare). There are two major strategies described in the literature to uniformly focus both transmit and receive beams throughout the field of view - using virtual sources, and by applying spatial matched filtration. The virtual source model is precise, when the transmit is either strongly focused (f-number ~ 1, 2) or images are formed using circular or spherical waves. The spatial matched filtration can be used also with weakly focused transmissions, but requires the measurement and storage of the response of point targets within the limits of the transmit beam. This paper presents a semi-analytic model for the transmitted field, which can be applied to synthetic transmit imaging. The model is more precise than the virtual source concept, does not require the measurement of the transmit field as matched filtration methods do, and can be applied to both strongly and weakly focused transmissions. Furthermore, the model is applicable to tissue harmonic and contrast enhanced ultrasound imaging. The paper presents the development of the model using the principles of diffraction, and its validation using computer simulations and measurements on a phantom. Finally, the model is demonstrated for synthetic aperture tissue harmonic in-vivo imaging.

  17. Investigations Into Early Magnitude Estimation From Predominant Period, Using Synthetic Rupture Models

    NASA Astrophysics Data System (ADS)

    Hildyard, M.; Rietbrock, A.

    2007-12-01

    Considerable interest has been shown in a method for estimating predominant period in the time domain (TpMax), first proposed by Nakamura (1988) and currently being developed for other early warning systems (e.g. Lockman and Allen, BSSA, 2005). Issues still exist as to the causes of the scatter evident in empirical work, and how effective the method is for characterising large events whose time to rupture is longer than the few seconds desired to estimate the magnitude. Our work on applying this method to an aftershock dataset motivated us to investigate the method through the use of synthetic rupture models. The rupture model we use prescribes a stress-drop with a prescribed rise-time over a small patch of the fault surface. This stress-drop is propagated to other patches of the fault according to a prescribed rupture rate. The same finite difference model geometry and fault patch size was then used to model events ranging from magnitude 3.7 to 7.2. Moment Magnitude was calculated directly by integrating the resultant slip on the fault, and TpMax was calculated from seismograms recorded on surface 50 km from the centre of the fault. The initial modelling used a homogenous stress drop, rise-time, and rupture rate. A dataset of 165 events, showed a significant increasing relationship between the TpMax calculation and magnitude. Isolating similar events initiating at the same point on the fault, gave a near straight-line trend. Scatter in the relationship is shown to result from variations in the position, initiation point, stress drop, rise time, and rupture velocity. Low frequency filtering was found to significantly affect the TpMax calculations and trends. Without filtering, the relationship saturated from just after magnitude 6, as the time to rupture becomes longer than the window used to calculate TpMax. However, low frequency filtering actually reduces the time to reach a maximum in the calculation, and this can cause the increasing trend to continue into

  18. Synthetic Genomics and Synthetic Biology Applications Between Hopes and Concerns

    PubMed Central

    König, Harald; Frank, Daniel; Heil, Reinhard; Coenen, Christopher

    2013-01-01

    New organisms and biological systems designed to satisfy human needs are among the aims of synthetic genomics and synthetic biology. Synthetic biology seeks to model and construct biological components, functions and organisms that do not exist in nature or to redesign existing biological systems to perform new functions. Synthetic genomics, on the other hand, encompasses technologies for the generation of chemically-synthesized whole genomes or larger parts of genomes, allowing to simultaneously engineer a myriad of changes to the genetic material of organisms. Engineering complex functions or new organisms in synthetic biology are thus progressively becoming dependent on and converging with synthetic genomics. While applications from both areas have been predicted to offer great benefits by making possible new drugs, renewable chemicals or clean energy, they have also given rise to concerns about new safety, environmental and socio-economic risks – stirring an increasingly polarizing debate. Here we intend to provide an overview on recent progress in biomedical and biotechnological applications of synthetic genomics and synthetic biology as well as on arguments and evidence related to their possible benefits, risks and governance implications. PMID:23997647

  19. Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance.

    PubMed

    Kalluri, Udaya C; Yin, Hengfu; Yang, Xiaohan; Davison, Brian H

    2014-12-01

    Fine-tuning plant cell wall properties to render plant biomass more amenable to biofuel conversion is a colossal challenge. A deep knowledge of the biosynthesis and regulation of plant cell wall and a high-precision genome engineering toolset are the two essential pillars of efforts to alter plant cell walls and reduce biomass recalcitrance. The past decade has seen a meteoric rise in use of transcriptomics and high-resolution imaging methods resulting in fresh insights into composition, structure, formation and deconstruction of plant cell walls. Subsequent gene manipulation approaches, however, commonly include ubiquitous mis-expression of a single candidate gene in a host that carries an intact copy of the native gene. The challenges posed by pleiotropic and unintended changes resulting from such an approach are moving the field towards synthetic biology approaches. Synthetic biology builds on a systems biology knowledge base and leverages high-precision tools for high-throughput assembly of multigene constructs and pathways, precision genome editing and site-specific gene stacking, silencing and/or removal. Here, we summarize the recent breakthroughs in biosynthesis and remodelling of major secondary cell wall components, assess the impediments in obtaining a systems-level understanding and explore the potential opportunities in leveraging synthetic biology approaches to reduce biomass recalcitrance.

  20. Analysis of Microbe-Associated Molecular Pattern-Responsive Synthetic Promoters with the Parsley Protoplast System.

    PubMed

    Kanofsky, Konstantin; Lehmeyer, Mona; Schulze, Jutta; Hehl, Reinhard

    2016-01-01

    Plants recognize pathogens by microbe-associated molecular patterns (MAMPs) and subsequently induce an immune response. The regulation of gene expression during the immune response depends largely on cis-sequences conserved in promoters of MAMP-responsive genes. These cis-sequences can be analyzed by constructing synthetic promoters linked to a reporter gene and by testing these constructs in transient expression systems. Here, the use of the parsley (Petroselinum crispum) protoplast system for analyzing MAMP-responsive synthetic promoters is described. The synthetic promoter consists of four copies of a potential MAMP-responsive cis-sequence cloned upstream of a minimal promoter and the uidA reporter gene. The reporter plasmid contains a second reporter gene, which is constitutively expressed and hence eliminates the requirement of a second plasmid used as a transformation control. The reporter plasmid is transformed into parsley protoplasts that are elicited by the MAMP Pep25. The MAMP responsiveness is validated by comparing the reporter gene activity from MAMP-treated and untreated cells and by normalizing reporter gene activity using the constitutively expressed reporter gene.

  1. Analysis of Microbe-Associated Molecular Pattern-Responsive Synthetic Promoters with the Parsley Protoplast System.

    PubMed

    Kanofsky, Konstantin; Lehmeyer, Mona; Schulze, Jutta; Hehl, Reinhard

    2016-01-01

    Plants recognize pathogens by microbe-associated molecular patterns (MAMPs) and subsequently induce an immune response. The regulation of gene expression during the immune response depends largely on cis-sequences conserved in promoters of MAMP-responsive genes. These cis-sequences can be analyzed by constructing synthetic promoters linked to a reporter gene and by testing these constructs in transient expression systems. Here, the use of the parsley (Petroselinum crispum) protoplast system for analyzing MAMP-responsive synthetic promoters is described. The synthetic promoter consists of four copies of a potential MAMP-responsive cis-sequence cloned upstream of a minimal promoter and the uidA reporter gene. The reporter plasmid contains a second reporter gene, which is constitutively expressed and hence eliminates the requirement of a second plasmid used as a transformation control. The reporter plasmid is transformed into parsley protoplasts that are elicited by the MAMP Pep25. The MAMP responsiveness is validated by comparing the reporter gene activity from MAMP-treated and untreated cells and by normalizing reporter gene activity using the constitutively expressed reporter gene. PMID:27557767

  2. Crew and display concepts evaluation for synthetic/enhanced vision systems

    NASA Astrophysics Data System (ADS)

    Bailey, Randall E.; Kramer, Lynda J.; Prinzel, Lawrence J., III

    2006-05-01

    NASA's Synthetic Vision Systems (SVS) project is developing technologies with practical applications that strive to eliminate low-visibility conditions as a causal factor to civil aircraft accidents and replicate the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. Enhanced Vision System (EVS) technologies are analogous and complementary in many respects to SVS, with the principle difference being that EVS is an imaging sensor presentation, as opposed to a database-derived image. The use of EVS in civil aircraft is projected to increase rapidly as the Federal Aviation Administration recently changed the aircraft operating rules under Part 91, revising the flight visibility requirements for conducting operations to civil airports. Operators conducting straight-in instrument approach procedures may now operate below the published approach minimums when using an approved EVS that shows the required visual references on the pilot's Head-Up Display. An experiment was conducted to evaluate the complementary use of SVS and EVS technologies, specifically focusing on new techniques for integration and/or fusion of synthetic and enhanced vision technologies and crew resource management while operating under the newly adopted FAA rules which provide operating credit for EVS. Overall, the experimental data showed that significant improvements in SA without concomitant increases in workload and display clutter could be provided by the integration and/or fusion of synthetic and enhanced vision technologies for the pilot-flying and the pilot-not-flying.

  3. A red light-controlled synthetic gene expression switch for plant systems.

    PubMed

    Müller, Konrad; Siegel, David; Rodriguez Jahnke, Fernando; Gerrer, Katrin; Wend, Sabrina; Decker, Eva L; Reski, Ralf; Weber, Wilfried; Zurbriggen, Matias D

    2014-07-01

    On command control of gene expression in time and space is required for the comprehensive analysis of key plant cellular processes. Even though some chemical inducible systems showing satisfactory induction features have been developed, they are inherently limited in terms of spatiotemporal resolution and may be associated with toxic effects. We describe here the first synthetic light-inducible system for the targeted control of gene expression in plants. For this purpose, we applied an interdisciplinary synthetic biology approach comprising mammalian and plant cell systems to customize and optimize a split transcription factor based on the plant photoreceptor phytochrome B and one of its interacting factors (PIF6). Implementation of the system in transient assays in tobacco protoplasts resulted in strong (95-fold) induction in red light (660 nm) and could be instantaneously returned to the OFF state by subsequent illumination with far-red light (740 nm). Capitalizing on this toggle switch-like characteristic, we demonstrate that the system can be kept in the OFF state in the presence of 740 nm-supplemented white light, opening up perspectives for future application of the system in whole plants. Finally we demonstrate the system's applicability in basic research, by the light-controlled tuning of auxin signalling networks in N. tabacum protoplasts, as well as its biotechnological potential for the chemical-inducer free production of therapeutic proteins in the moss P. patens.

  4. Gulf Coast Subsidence: Integration of Geodesy, Geophysical Modeling, and Interferometric Synthetic Aperture Radar Observations

    NASA Astrophysics Data System (ADS)

    Blom, R. G.; Chapman, B. D.; Deese, R.; Dokka, R. K.; Fielding, E. J.; Hawkins, B.; Hensley, S.; Ivins, E. R.; Jones, C. E.; Kent, J. D.; Liu, Z.; Lohman, R.; Zheng, Y.

    2012-12-01

    The vulnerability of the US Gulf Coast has received increased attention in the years since hurricanes Katrina and Rita. Agencies responsible for the long-term protection of lives and infrastructure require precise estimates of future subsidence and sea level rise. A quantitative, geophysically based methodology can provide such estimates by incorporating geological data, geodetic measurements, geophysical models of non-elastic mechanical behavior at depth, and geographically comprehensive deformation monitoring made possible with measurements from Interferometric Synthetic Aperture Radar (InSAR). To be effective, results must be available to user agencies in a format suitable for integration within existing decision-support processes. Work to date has included analysis of historical and continuing ground-based geodetic measurements. These reveal a surprising degree of complexity, including regions that are subsiding at rates faster than those considered for hurricane protection planning of New Orleans and other coastal communities (http://www.mvn.usace.army.mil/pdf/hps_verticalsettlement.pdf) as well as Louisiana's coastal restoration strategies (http://www.coast2050.gov/2050reports.htm) (Dokka, 2011, J. Geophys. Res., 116, B06403, doi:10.1029/2010JB008008). Traditional geodetic measurements provide precise information at single points, while InSAR observations provide geographically comprehensive measurements of surface deformation at lower vertical precision. Available InSAR data sources include X-, C- and L-band satellite, and NASA/JPL airborne UAVSAR L-band data. The Gulf Coast environment is very challenging for InSAR techniques, especially with systems not designed for interferometry. For example, the shorter wavelength C-band data decorrelates over short time periods requiring more elaborate time-series analysis techniques, with which we've had some success. Meanwhile, preliminary analysis of limited L-Band ALOS/PALSAR satellite data show promise

  5. Three-dimensional pure deflagration models with nucleosynthesis and synthetic observables for Type Ia supernovae

    NASA Astrophysics Data System (ADS)

    Fink, Michael; Kromer, Markus; Seitenzahl, Ivo R.; Ciaraldi-Schoolmann, Franco; Röpke, Friedrich K.; Sim, Stuart A.; Pakmor, Rüdiger; Ruiter, Ashley J.; Hillebrandt, Wolfgang

    2014-02-01

    We investigate whether pure deflagration models of Chandrasekhar-mass carbon-oxygen white dwarf stars can account for one or more subclass of the observed population of Type Ia supernova (SN Ia) explosions. We compute a set of 3D full-star hydrodynamic explosion models, in which the deflagration strength is parametrized using the multispot ignition approach. For each model, we calculate detailed nucleosynthesis yields in a post-processing step with a 384 nuclide nuclear network. We also compute synthetic observables with our 3D Monte Carlo radiative transfer code for comparison with observations. For weak and intermediate deflagration strengths (energy release Enuc ≲ 1.1 × 1051 erg), we find that the explosion leaves behind a bound remnant enriched with 3 to 10 per cent (by mass) of deflagration ashes. However, we do not obtain the large kick velocities recently reported in the literature. We find that weak deflagrations with Enuc ˜ 0.5 × 1051 erg fit well both the light curves and spectra of 2002cx-like SNe Ia, and models with even lower explosion energies could explain some of the fainter members of this subclass. By comparing our synthetic observables with the properties of SNe Ia, we can exclude the brightest, most vigorously ignited models as candidates for any observed class of SN Ia: their B - V colours deviate significantly from both normal and 2002cx-like SNe Ia and they are too bright to be candidates for other subclasses.

  6. Comparison of Single Channel Potassium Current in Biological and Synthetic Systems --- Dependence on Voltage

    NASA Astrophysics Data System (ADS)

    Siwy, Zuzanna; Mercik, Szymon; Weron, Karina; Spohr, Reimar; Wolf, Alexander; Grzywna, Zbigniew

    2000-05-01

    The influence of an external field on an ion current pattern in biological and synthetic systems was investigated. The patch clamp recordings of potassium current through a big conductance locust potassium channel (BK-channel) and a track-etched polyethylene terephthalate membrane were examined by the power spectrum, fractal analysis and relative dispersion analysis. A similar dependence of potassium current behaviour on the external voltage in both systems was found. The generalized dimension formalism is redefined to make it applicable to the analysis of time series.

  7. Synthetic Biology and Microbial Fuel Cells: Towards Self-Sustaining Life Support Systems

    NASA Technical Reports Server (NTRS)

    Hogan, John Andrew

    2014-01-01

    NASA ARC and the J. Craig Venter Institute (JCVI) collaborated to investigate the development of advanced microbial fuels cells (MFCs) for biological wastewater treatment and electricity production (electrogenesis). Synthetic biology techniques and integrated hardware advances were investigated to increase system efficiency and robustness, with the intent of increasing power self-sufficiency and potential product formation from carbon dioxide. MFCs possess numerous advantages for space missions, including rapid processing, reduced biomass and effective removal of organics, nitrogen and phosphorus. Project efforts include developing space-based MFC concepts, integration analyses, increasing energy efficiency, and investigating novel bioelectrochemical system applications

  8. A digital system to produce imagery from SAR data. [Synthetic Aperture Radar

    NASA Technical Reports Server (NTRS)

    Wu, C.

    1976-01-01

    This paper describes a digital processing algorithm and its associated system design for producing images from Synthetic Aperture Radar (SAR) data. The proposed system uses the Fast Fourier Transform (FFT) approach to perform the two-dimensional correlation process. The range migration problem, which is often a major obstacle to efficient processing, can be alleviated by approximating the locus of echoes from a point target by several linear segments. SAR data corresponding to each segment is correlated separately, and the results are coherently summed to produce full-resolution images. This processing approach exhibits greatly improved computation efficiency relative to conventional digital processing methods.

  9. Probabilistic and Non-probabilistic Synthetic Reliability Model for Space Structures

    NASA Astrophysics Data System (ADS)

    Hong, Dongpao; Hu, Xiao; Zhang, Jing

    2016-07-01

    As an alternative to reliability analysis, the non-probabilistic model is an effective supplement when the interval information exists. We describe the uncertain parameters of the structures with interval variables, and establish a non-probabilistic reliability model of structures. Then, we analyze the relation between the typical interference mode and the reliability according to the structure stress-strength interference model, and propose a new measure of structure non-probabilistic reliability. Furthermore we describe other uncertain parameters with random variables when probabilistic information also exists. For the complex structures including both random variables and interval variables, we propose a probabilistic and non-probabilistic synthetic reliability model. The illustrative example shows that the presented model is feasible for structure reliability analysis and design.

  10. Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource

    PubMed Central

    King, Elizabeth G.; Merkes, Chris M.; McNeil, Casey L.; Hoofer, Steven R.; Sen, Saunak; Broman, Karl W.; Long, Anthony D.; Macdonald, Stuart J.

    2012-01-01

    Genetic dissection of complex, polygenic trait variation is a key goal of medical and evolutionary genetics. Attempts to identify genetic variants underlying complex traits have been plagued by low mapping resolution in traditional linkage studies, and an inability to identify variants that cumulatively explain the bulk of standing genetic variation in genome-wide association studies (GWAS). Thus, much of the heritability remains unexplained for most complex traits. Here we describe a novel, freely available resource for the Drosophila community consisting of two sets of recombinant inbred lines (RILs), each derived from an advanced generation cross between a different set of eight highly inbred, completely resequenced founders. The Drosophila Synthetic Population Resource (DSPR) has been designed to combine the high mapping resolution offered by multiple generations of recombination, with the high statistical power afforded by a linkage-based design. Here, we detail the properties of the mapping panel of >1600 genotyped RILs, and provide an empirical demonstration of the utility of the approach by genetically dissecting alcohol dehydrogenase (ADH) enzyme activity. We confirm that a large fraction of the variation in this classic quantitative trait is due to allelic variation at the Adh locus, and additionally identify several previously unknown modest-effect trans-acting QTL (quantitative trait loci). Using a unique property of multiparental linkage mapping designs, for each QTL we highlight a relatively small set of candidate causative variants for follow-up work. The DSPR represents an important step toward the ultimate goal of a complete understanding of the genetics of complex traits in the Drosophila model system. PMID:22496517

  11. Synthetic vision as an integrated element of an enhanced vision system

    NASA Astrophysics Data System (ADS)

    Jennings, Chad W.; Alter, Keith W.; Barrows, Andrew K.; Bernier, Ken L.; Guell, Jeff J.

    2002-07-01

    Enhanced Vision Systems (EVS) and Synthetic Vision Systems (SVS) have the potential to allow vehicle operators to benefit from the best that various image sources have to offer. The ability to see in all directions, even in reduced visibility conditions, offers considerable benefits for operational effectiveness and safety. Nav3D and The Boeing Company are conducting development work on an Enhanced Vision System with an integrated Synthetic Vision System. The EVS consists of several imaging sensors that are digitally fused together to give a pilot a better view of the outside world even in challenging visual conditions. The EVS is limited however to provide imagery within the viewing frustum of the imaging sensors. The SVS can provide a rendered image of an a priori database in any direction that the pilot chooses to look and thus can provide information of terrain and flight path that are outside the purview of the EVS. Design concepts of the system will be discussed. In addition the ground and flight testing of the system will be described.

  12. Comparison of synthetic membranes in the development of an in vitro feeding system for Dermanyssus gallinae.

    PubMed

    Harrington, D W J; Guy, J H; Robinson, K; Sparagano, O A E

    2010-04-01

    Although artificial feeding models for the poultry red mite (Dermanyssus gallinae) most frequently use biological membranes consisting of day-old chick skin, there are ethical considerations associated with the use of skin. The few studies reported in the literature that have investigated the use of synthetic membranes to feed D. gallinae in vitro have reported limited success. The current study describes an investigation into the use of synthetic membranes made from either Nescofilm or rayon and silicone, used either alone or in combination with different feather or skin extracts, as well as the use of capillary tubes. In all, 12 different treatments were used, and the feeding rate of D. gallinae was compared to that of day-old chick skin. Allowing mites to feed on a membrane consisting of Nescofilm with a skin extract resulted in the highest proportion of mites feeding (32.3%), which was not significantly different to the feeding rate of mites on day-old chick skin (38.8%). This study confirms that synthetic membranes can be used to feed D. gallinae artificially. Further optimization of the membrane and mite storage conditions is still necessary, but the study demonstrates a proof of concept.

  13. Fused enhanced and synthetic vision system (EVS/SVS) for low-visibility operations

    NASA Astrophysics Data System (ADS)

    Tiana, Carlo; Hennessy, Robert; Alter, Keith; Jennings, Chad

    2007-04-01

    We present an Integrated Multisensor Synthetic Imaging System (IMSIS) developed for low-visibility, low-level operations, tailored to Army rotorcraft. IMSIS optimally avails itself of a variety of image-information sources: FLIR, mm-Wave RADAR and synthetic imagery are all presented to the flying crew in real time, on a fused display. Synthetic imagery is validated in real time by a 3D terrain sensing radar, to ensure that the a priori stored database is valid, and to eliminate any possible aircraft positioning errors with respect to the database. Extensive human factor evaluations were performed on the fused display concept. All pilots agreed that IMSIS would be a valuable asset in reduced visibility conditions and that the validated SVS display was rated nearly as flyable as a good FLIR display. The pilots also indicated that the ability to select and fuse terrain information sources was an important feature. IMSIS increases situational awareness at night and in all weather conditions, while considerably reducing pilot workload compared to separately monitoring each sensor and enhancing low-level flight safety by updating the terrain in real time. While specifically designed for helicopter low-level flight and navigation, it can aid hover and touchdown and landing for both fixed and rotary wing platforms as well as aid navigation even in non-airborne domains.

  14. Modeling and training emotional talking faces of virtual actors in synthetic movies

    NASA Astrophysics Data System (ADS)

    Karunaratne, Savant; Yan, Hong

    2000-05-01

    This paper presents an overview of a virtual actor system composed of several subsystems designed to automate some of these animation tasks. Our emphasis is on the facial animation of virtual actors. The paper specifically details the situations processor component of the framework, which is a major building block in the automatic virtual actor system. An expert system using a fuzzy knowledge-based control system is used to realize the automated system. Fuzzy linguistic rules are used to train virtual actors to know the appropriate emotions and gestures to use in different situations of a synthetic movie, the higher level parameters of which are provided by human directors. Theories of emotion, personality, dialogue, and acting, as well as empirical evidence is incorporated into our framework and knowledge bases to produce promising results.

  15. Aspects of Synthetic Vision Display Systems and the Best Practices of the NASA's SVS Project

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Kramer, Lynda J.; Jones, Denise R.; Young, Steven D.; Arthur, Jarvis J.; Prinzel, Lawrence J.; Glaab, Louis J.; Harrah, Steven D.; Parrish, Russell V.

    2008-01-01

    NASA s Synthetic Vision Systems (SVS) Project conducted research aimed at eliminating visibility-induced errors and low visibility conditions as causal factors in civil aircraft accidents while enabling the operational benefits of clear day flight operations regardless of actual outside visibility. SVS takes advantage of many enabling technologies to achieve this capability including, for example, the Global Positioning System (GPS), data links, radar, imaging sensors, geospatial databases, advanced display media and three dimensional video graphics processors. Integration of these technologies to achieve the SVS concept provides pilots with high-integrity information that improves situational awareness with respect to terrain, obstacles, traffic, and flight path. This paper attempts to emphasize the system aspects of SVS - true systems, rather than just terrain on a flight display - and to document from an historical viewpoint many of the best practices that evolved during the SVS Project from the perspective of some of the NASA researchers most heavily involved in its execution. The Integrated SVS Concepts are envisagements of what production-grade Synthetic Vision systems might, or perhaps should, be in order to provide the desired functional capabilities that eliminate low visibility as a causal factor to accidents and enable clear-day operational benefits regardless of visibility conditions.

  16. Site-Directed Mutagenesis to Improve Sensitivity of a Synthetic Two-Component Signaling System.

    PubMed

    Olshefsky, Audrey; Shehata, Laila; Kuldell, Natalie

    2016-01-01

    Two-component signaling (2CS) systems enable bacterial cells to respond to changes in their local environment, often using a membrane-bound sensor protein and a cytoplasmic responder protein to regulate gene expression. Previous work has shown that Escherichia coli's natural EnvZ/OmpR 2CS could be modified to construct a light-sensing bacterial photography system. The resulting bacterial photographs, or "coliroids," rely on a phosphotransfer reaction between Cph8, a synthetic version of EnvZ that senses red light, and OmpR. Gene expression changes can be visualized through upregulation of a LacZ reporter gene by phosphorylated OmpR. Unfortunately, basal LacZ expression leads to a detectable reporter signal even when cells are grown in the light, diminishing the contrast of the coliroids. We performed site-directed mutagenesis near the phosphotransfer site of Cph8 to isolate mutants with potentially improved image contrast. Five mutants were examined, but only one of the mutants, T541S, increased the ratio of dark/light gene expression, as measured by β-galactosidase activity. The ratio changed from 2.57 fold in the starting strain to 5.59 in the T541S mutant. The ratio decreased in the four other mutant strains we examined. The phenotype observed in the T541S mutant strain may arise because the serine sidechain is chemically similar but physically smaller than the threonine sidechain. This may minimally change the protein's local structure, but may be less sterically constrained when compared to threonine, resulting in a higher probability of a phosphotransfer event. Our initial success pairing synthetic biology and site-directed mutagenesis to optimize the bacterial photography system's performance encourages us to imagine further improvements to the performance of this and other synthetic systems, especially those based on 2CS signaling. PMID:26799494

  17. Flow-induced vibratory response of idealized versus magnetic resonance imaging-based synthetic vocal fold models.

    PubMed

    Pickup, Brian A; Thomson, Scott L

    2010-09-01

    Recent vocal fold vibration studies have used models defined using idealized geometry. Although these models exhibit important similarities with human vocal fold vibration, some aspects of their motion are less than realistic. In this report it is demonstrated that more realistic motion may be obtained when using geometry derived from magnetic resonance imaging (MRI) data. The dynamic response of both idealized and MRI-based synthetic vocal fold models are presented. MRI-based model improvements include evidence of mucosal wave-like motion and less vertical movement. Limitations of the MRI-based model are discussed and suggestions for further synthetic model development are offered.

  18. Concept of operations for the use of Synthetic Vision System (SVS) display during precision instrument approach

    NASA Astrophysics Data System (ADS)

    Domino, David A.

    2007-04-01

    Synthetic Vision Systems (SVS) create images for display in the cockpit from the information contained in databases of terrain, obstacles and cultural features like runways and taxiways, and the known own-ship position in space. Displays are rendered egocentrically, from the point of view of the pilot. Certified synthetic vision systems, however, do not yet qualify for operational credit in any domain, other than to provide enhanced situation awareness. It is not known at this time whether the information provided by the system is sufficiently robust to substitute for natural vision in a specific application. In this paper an operations concept is described for the use of SVS information during a precision instrument approach in lieu of visual contact with a runway approach light system. It proposes an operation within the existing framework of regulations, and identifies specific areas that may require additional research data to support certification of the proposed operational credit. The larger purpose is to set out an example application and intended function which will require the elaboration and resolution of operational and human performance concerns. To this end, issues in several categories are identified.

  19. Crystal chemistry of natural and synthetic trioctahedral micas: Exploring the limits of geometric crystal chemical models

    NASA Astrophysics Data System (ADS)

    Mercier, Patrick H. J.

    Seventy-five synthetic powder trioctahedral mica samples (between Mg, Co, Ni, and Fe end members, with different degrees of oxidation, vacancy and Al/Si contents, and including an OH/F substitution series) were studied by room-temperature powder X-ray diffraction. The iron-bearing samples were studied by 57Fe Mossbauer spectroscopy. Subsets of the samples were also characterized by scanning electron microscopy combined with energy dispersive spectroscopy, optical microscopy, X-ray fluorescence spectroscopy, and gas chromatography. Lattice parameters (refined under the 1M stacking polytype, space group C2/m) were determined for all powder samples and iron site populations ([4]Fe 3+, [6]Fe2+, and [6]Fe 2+) were obtained from Mossbauer spectroscopy. The relation (c/a)cosbeta* = 113 was found to hold exactly (within experimental error) for all synthetic powders whereas it does not hold in general for synthetic and natural 1M single-crystals. The above relation is predicted to hold for geometric home-octahedral sheets (having equal M1 and M2 site bond lengths) and not to hold for geometric meso-octahedral sheets (having unequal M1 and M2 site bond lengths). The counter-rotation of the M2 site of 1M single-crystals exactly (within experimental error) follows the geometric meso-octahedral sheet model, which, assuming a uniform octahedral sheet height and site-specific M1 and M2 bond lengths, predicts site-specific flattening angles and a counter-rotation angle for the M2 site which is uniquely determined by the bond length difference between the M1 and M2 sites. A geometric meso-octahedral 2:1 layer silicate was shown to require corrugated tetrahedral sheets composed of bond-distorted tetrahedra. Key geometric meso-octahedral distortions in 1M single-crystals were identified and elucidated: (i) intra-layer top-bottom displacements within a TOT layer; and (ii) a tetrahedral bending angle between the apical bond and the pyramidal base formed by the three basal bonds. Plots

  20. Site-Directed Mutagenesis to Improve Sensitivity of a Synthetic Two-Component Signaling System

    PubMed Central

    Kuldell, Natalie

    2016-01-01

    Two-component signaling (2CS) systems enable bacterial cells to respond to changes in their local environment, often using a membrane-bound sensor protein and a cytoplasmic responder protein to regulate gene expression. Previous work has shown that Escherichia coli’s natural EnvZ/OmpR 2CS could be modified to construct a light-sensing bacterial photography system. The resulting bacterial photographs, or “coliroids,” rely on a phosphotransfer reaction between Cph8, a synthetic version of EnvZ that senses red light, and OmpR. Gene expression changes can be visualized through upregulation of a LacZ reporter gene by phosphorylated OmpR. Unfortunately, basal LacZ expression leads to a detectable reporter signal even when cells are grown in the light, diminishing the contrast of the coliroids. We performed site-directed mutagenesis near the phosphotransfer site of Cph8 to isolate mutants with potentially improved image contrast. Five mutants were examined, but only one of the mutants, T541S, increased the ratio of dark/light gene expression, as measured by β-galactosidase activity. The ratio changed from 2.57 fold in the starting strain to 5.59 in the T541S mutant. The ratio decreased in the four other mutant strains we examined. The phenotype observed in the T541S mutant strain may arise because the serine sidechain is chemically similar but physically smaller than the threonine sidechain. This may minimally change the protein’s local structure, but may be less sterically constrained when compared to threonine, resulting in a higher probability of a phosphotransfer event. Our initial success pairing synthetic biology and site-directed mutagenesis to optimize the bacterial photography system’s performance encourages us to imagine further improvements to the performance of this and other synthetic systems, especially those based on 2CS signaling. PMID:26799494

  1. Nnuclear uptake and retention of a synthetic progestin in the cardiovascular system of the baboon

    SciTech Connect

    Sheridan, P.J.; McGill, H.C. Jr.

    1984-06-01

    It has long been known that there is a sexual dimorphism in the incidence of coronary heart disease. This observation, together with more recent reports of increased cardiovascular disease associated with the use of oral contraceptives, led to a search for steroid receptors in the cardiovascular system. In this study the nuclear uptake and retention of a synthetic progestin was examined in the cardiovascular system of the baboons. Long term oophorectomized baboons were primed with estradiol benzoate for 3 days before the experiment (50 micrograms/kg, im) and adrenalectomized 2 days before the experiment. On the day of the experiment, the animals were injected under anesthesia with 2.5 micrograms/kg BW (/sup 3/H)ORG 2058 (16 alpha-ethyl-21-hydroxy-19-nor-(6,7-/sup 3/H)pregn-4-ene-3,20-dione) or with (/sup 3/H) ORG 2058 plus a 1000-fold excess of unlabeled progesterone (control). One hour after the injection, the animals were rapidly exsanguinated, and parts of the cardiovascular system were removed and processed for autoradiography. Localization of the synthetic progestin was found in nuclei of between 25-75% of all smooth muscle cells of the media of all arteries examined and to a lesser extent in the nuclei of the fibroblasts and others cells of the adventitia. Localization of the synthetic progestin in the heart was limited to approximately 1% of the myocardial cells and less than 5% of interstitial cell nuclei. The pattern of localization found differs from that for estrogen and androgen and suggests the possible presence of estrogen-independent progesterone receptors in smooth muscle cells of the media of the aorta and coronary arteries.

  2. New Synthetic Biology Tools to Track Microbial Dynamics in the Earth System

    NASA Astrophysics Data System (ADS)

    Silberg, J. J.; Masiello, C. A.; Cheng, H. Y.

    2015-12-01

    Microbes drive processes in the Earth system far exceeding their physical scale, mediating significant fluxes in the global C and N cycles. The tools of synthetic biology have the potential to significantly improve our understanding of microbes' role in the Earth system; however, these tools have not yet seen wide laboratory use because synthetically "programmed" microbes typically report by fluorescing (expressing green fluorescent protein), making them challenging to deploy into many Earth materials, the majority of which are not transparent and are heterogeneous (soils, sediments, and biomass). We are developing a new suite of biosensors that report instead by releasing gases. We will provide an overview of the use of gas-reporting biosensors in biogeochemistry and will report the development of the systematics of these sensors. These sensors will make tractable the testing of gene expression hypotheses derived from metagenomics data. Examples of processes that could be tracked non-invasively with gas sensors include coordination of biofilm formation, nitrification, rhizobial infection of plant roots, and at least some forms of methanogenesis, all of which are managed by an easily-engineered cell-cell communication system. Another relatively simple process to track with gas sensors is horizontal gene transfer. Successful development of gas biosensors for Earth science applications will require addressing issues including: engineering the intensity and selectivity of microbial gas production to maximize the signal to noise using the tools of synthetic biology; normalizing the gas reporter signal to cell population size, since the number of cells and gene expression both contribute to gas production; managing gas diffusion effects on signal shape; and developing multiple gases that can be used in parallel to report on multiple biological processes in parallel. We will report on progress addressing each of these issues.

  3. In vivo visualization of robotically implemented synthetic tracked aperture ultrasound (STRATUS) imaging system using curvilinear array

    NASA Astrophysics Data System (ADS)

    Zhang, Haichong K.; Aalamifar, Fereshteh; Boctor, Emad M.

    2016-04-01

    Synthetic aperture for ultrasound is a technique utilizing a wide aperture in both transmit and receive to enhance the ultrasound image quality. The limitation of synthetic aperture is the maximum available aperture size limit determined by the physical size of ultrasound probe. We propose Synthetic-Tracked Aperture Ultrasound (STRATUS) imaging system to overcome the limitation by extending the beamforming aperture size through ultrasound probe tracking. With a setup involving a robotic arm, the ultrasound probe is moved using the robotic arm, while the positions on a scanning trajectory are tracked in real-time. Data from each pose are synthesized to construct a high resolution image. In previous studies, we have demonstrated the feasibility through phantom experiments. However, various additional factors such as real-time data collection or motion artifacts should be taken into account when the in vivo target becomes the subject. In this work, we build a robot-based STRATUS imaging system with continuous data collection capability considering the practical implementation. A curvilinear array is used instead of a linear array to benefit from its wider capture angle. We scanned human forearms under two scenarios: one submerged the arm in the water tank under 10 cm depth, and the other directly scanned the arm from the surface. The image contrast improved 5.51 dB, and 9.96 dB for the underwater scan and the direct scan, respectively. The result indicates the practical feasibility of STRATUS imaging system, and the technique can be potentially applied to the wide range of human body.

  4. Applicability of artificial neural networks for obtaining velocity models from synthetic seismic data

    NASA Astrophysics Data System (ADS)

    Baronian, C.; Riahi, M. A.; Lucas, C.

    2009-07-01

    Seismic velocity analysis is a crucial part of seismic data processing and interpretation which has been practiced using different methods. In contrast to time consuming and complicated numerical methods, artificial neural networks (ANNs) are found to be of potential applicability. ANN ability to establish a relationship between an input and output space is considered to be appropriate for mapping seismic velocity corresponding to travel times picked from seismograms. Accordingly a preliminary attempt is made to evaluate the applicability of ANNs to determine velocity and dips of dipping layered earth models corresponding to travel time data. The study is based on synthetic data generated using inverse modeling approach for three earth models. The models include a three-layer structure with same dips and same directions, a three-layer model with different dips and same directions, as well as a two-layer model with different dips and directions. An ANN structure is designed in three layers, namely, input, output, and hidden ones. The training and testing process of the ANN is successfully accomplished using the synthetic data. The evaluation of the applicability of the trained ANN to unknown data sets indicates that the ANN can satisfactorily compute velocity and dips corresponding to travel times. The error intervals between the desired and calculated velocity and dips are shown to be acceptably small in all cases. The applicability of the trained ANN in extrapolating is also evaluated using a number of data outside of the range already known to ANN. The results indicate that the trained ANN acceptably approximates the velocity and dips. Furthermore, the trained ANN is also evaluated in terms of capability of handling deficiency in input data where acceptable results were also achieved in velocity and dip calculations. Generally, this study shows that velocity analysis using ANNs can promisingly tackle the challenge of retrieving an initial velocity model from the

  5. Synthetic Biology and the U.S. Biotechnology Regulatory System: Challenges and Options

    SciTech Connect

    Carter, Sarah R.; Rodemeyer, Michael; Garfinkel, Michele S.; Friedman, Robert M.

    2014-05-01

    Synthetic Biology and the U.S. Biotechnology Regulatory System: Challenges and Options Sarah R. Carter, Ph.D., J. Craig Venter Institute; Michael Rodemeyer, J.D., University of Virginia; Michele S. Garfinkel, Ph.D., EMBO; Robert M. Friedman, Ph.D., J. Craig Venter Institute In recent years, a range of genetic engineering techniques referred to as “synthetic biology” has significantly expanded the tool kit available to scientists and engineers, providing them with far greater capabilities to engineer organisms than previous techniques allowed. The field of synthetic biology includes the relatively new ability to synthesize long pieces of DNA from chemicals, as well as improved methods for genetic manipulation and design of genetic pathways to achieve more precise control of biological systems. These advances will help usher in a new generation of genetically engineered microbes, plants, and animals. The JCVI Policy Center team, along with researchers at the University of Virginia and EMBO, examined how well the current U.S. regulatory system for genetically engineered products will handle the near-term introduction of organisms engineered using synthetic biology. In particular, the focus was on those organisms intended to be used or grown directly in the environment, outside of a contained facility. The study concludes that the U.S. regulatory agencies have adequate legal authority to address most, but not all, potential environmental, health and safety concerns posed by these organisms. Such near-term products are likely to represent incremental changes rather than a marked departure from previous genetically engineered organisms. However, the study also identified two key challenges for the regulatory system, which are detailed in the report. First, USDA’s authority over genetically engineered plants depends on the use of an older engineering technique that is no longer necessary for many applications. The shift to synthetic biology and other newer genetic

  6. Ion mobility-mass spectrometry strategies for untargeted systems, synthetic, and chemical biology

    PubMed Central

    May, Jody C.; Goodwin, Cody R.; McLean, John A.

    2014-01-01

    Contemporary strategies that concentrate on only one or a handful of molecular targets limits the utility of the information gained for diagnostic and predictive purposes. Recent advances in the sensitivity, speed, and precision of measurements obtained from ion mobility coupled to mass spectrometry (IM-MS) have accelerated the utility of IM-MS in untargeted, discovery-driven studies in biology. Perhaps most evident is the impact that such wide-scale discovery capabilities have yielded in the areas of systems, synthetic, and chemical biology, where the need for comprehensive, hypothesis-driving studies from multidimensional and unbiased data is required. PMID:25462629

  7. Computational approaches to metabolic engineering utilizing systems biology and synthetic biology.

    PubMed

    Fong, Stephen S

    2014-08-01

    Metabolic engineering modifies cellular function to address various biochemical applications. Underlying metabolic engineering efforts are a host of tools and knowledge that are integrated to enable successful outcomes. Concurrent development of computational and experimental tools has enabled different approaches to metabolic engineering. One approach is to leverage knowledge and computational tools to prospectively predict designs to achieve the desired outcome. An alternative approach is to utilize combinatorial experimental tools to empirically explore the range of cellular function and to screen for desired traits. This mini-review focuses on computational systems biology and synthetic biology tools that can be used in combination for prospective in silico strain design.

  8. Alaskan flight trials of a synthetic vision system for instrument landings of a piston twin aircraft

    NASA Astrophysics Data System (ADS)

    Barrows, Andrew K.; Alter, Keith W.; Jennings, Chad W.; Powell, J. D.

    1999-07-01

    Stanford University has developed a low-cost prototype synthetic vision system and flight tested it onboard general aviation aircraft. The display aids pilots by providing an 'out the window' view, making visualization of the desired flight path a simple task. Predictor symbology provides guidance on straight and curved paths presented in a 'tunnel- in-the-sky' format. Based on commodity PC hardware to achieve low cost, the Tunnel Display system uses differential GPS (typically from Stanford prototype Wide Area Augmentation System hardware) for positioning and GPS-aided inertial sensors for attitude determination. The display has been flown onboard Piper Dakota and Beechcraft Queen Air aircraft at several different locations. This paper describes the system, its development, and flight trials culminating with tests in Alaska during the summer of 1998. Operational experience demonstrated the Tunnel Display's ability to increase flight- path following accuracy and situational awareness while easing the task instrument flying.

  9. Synthetic Ultrashort Cationic Lipopeptides Induce Systemic Plant Defense Responses against Bacterial and Fungal Pathogens ▿

    PubMed Central

    Brotman, Yariv; Makovitzki, Arik; Shai, Yechiel; Chet, Ilan; Viterbo, Ada

    2009-01-01

    A new family of synthetic, membrane-active, ultrashort lipopeptides composed of only four amino acids linked to fatty acids was tested for the ability to induce systemic resistance and defense responses in plants. We found that two peptides wherein the third residue is a d-enantiomer (italic), C16-KKKK and C16-KLLK, can induce medium alkalinization of tobacco suspension-cultured cells and expression of defense-related genes in cucumber and Arabidopsis seedlings. Moreover, these compounds can prime systemic induction of antimicrobial compounds in cucumber leaves similarly to the plant-beneficial fungus Trichoderma asperellum T203 and provide systemic protection against the phytopathogens Botrytis cinerea B05, Pseudomonas syringae pv. lachrimans, and P. syringae pv. tomato DC3000. Thus, short cationic lipopeptides are a new category of compounds with potentially high utility in the induction of systemic resistance in plants. PMID:19542326

  10. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories.

    PubMed

    Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Arruda, Letícia Magalhães; Silva-Rocha, Rafael

    2016-04-01

    Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech applications. In this sense, progress in this field has been marked by the utilization of high-throughput techniques to gain deep understanding of the molecular machinery controlling the physiology of these organisms, starting thus the Systems Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized promoters in order to construct new expression systems with enhanced performance under the conditions of interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact in the final performance of the process of interest. We expect to provide here some new directions to drive future research directed to the construction of high-performance, engineered fungal strains working as microbial cell factories.

  11. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories.

    PubMed

    Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Arruda, Letícia Magalhães; Silva-Rocha, Rafael

    2016-04-01

    Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech applications. In this sense, progress in this field has been marked by the utilization of high-throughput techniques to gain deep understanding of the molecular machinery controlling the physiology of these organisms, starting thus the Systems Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized promoters in order to construct new expression systems with enhanced performance under the conditions of interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact in the final performance of the process of interest. We expect to provide here some new directions to drive future research directed to the construction of high-performance, engineered fungal strains working as microbial cell factories. PMID:27226765

  12. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories

    PubMed Central

    Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Arruda, Letícia Magalhães; Silva-Rocha, Rafael

    2016-01-01

    Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech applications. In this sense, progress in this field has been marked by the utilization of high-throughput techniques to gain deep understanding of the molecular machinery controlling the physiology of these organisms, starting thus the Systems Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized promoters in order to construct new expression systems with enhanced performance under the conditions of interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact in the final performance of the process of interest. We expect to provide here some new directions to drive future research directed to the construction of high-performance, engineered fungal strains working as microbial cell factories. PMID:27226765

  13. Evaluation of Synthetic Self-Oscillating Models of the Vocal Folds

    NASA Astrophysics Data System (ADS)

    Hubler, Elizabeth P.; Weiland, Kelley S.; Hancock, Adrienne B.; Plesniak, Michael W.

    2013-11-01

    Approximately 30% of people will suffer from a voice disorder at some point in their lives. The probability doubles for those who rely heavily on their voice, such as teachers and singers. Synthetic vocal fold (VF) models are fabricated and evaluated experimentally in a vocal tract simulator to replicate physiological conditions. Pressure measurements are acquired along the vocal tract and high-speed images are captured at varying flow rates during VF oscillation to facilitate understanding of the characteristics of healthy and damaged VFs. The images are analyzed using a videokymography line-scan technique that has been used to examine VF motion and mucosal wave dynamics in vivo. Clinically relevant parameters calculated from the volume-velocity output of a circumferentially-vented mask (Rothenberg mask) are compared to patient data. This study integrates speech science with engineering and flow physics to overcome current limitations of synthetic VF models to properly replicate normal phonation in order to advance the understanding of resulting flow features, progression of pathological conditions, and medical techniques. Supported by the GW Institute for Biomedical Engineering (GWIBE) and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  14. Synthetic Astrobiology

    NASA Technical Reports Server (NTRS)

    Rothschild, Lynn J.

    2015-01-01

    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. 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.

  15. Synthetic Astrobiology

    NASA Technical Reports Server (NTRS)

    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.

  16. Awareness and Detection of Traffic and Obstacles Using Synthetic and Enhanced Vision Systems

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.

    2012-01-01

    Research literature are reviewed and summarized to evaluate the awareness and detection of traffic and obstacles when using Synthetic Vision Systems (SVS) and Enhanced Vision Systems (EVS). The study identifies the critical issues influencing the time required, accuracy, and pilot workload associated with recognizing and reacting to potential collisions or conflicts with other aircraft, vehicles and obstructions during approach, landing, and surface operations. This work considers the effect of head-down display and head-up display implementations of SVS and EVS as well as the influence of single and dual pilot operations. The influences and strategies of adding traffic information and cockpit alerting with SVS and EVS were also included. Based on this review, a knowledge gap assessment was made with recommendations for ground and flight testing to fill these gaps and hence, promote the safe and effective implementation of SVS/EVS technologies for the Next Generation Air Transportation System

  17. Attribute Assignment to a Synthetic Population in Support of Agent-Based Disease Modeling

    PubMed Central

    Cajka, James C.; Cooley, Philip C.; Wheaton, William D.

    2010-01-01

    Communicable-disease transmission models are useful for the testing of prevention and intervention strategies. Agent-based models (ABMs) represent a new and important class of the many types of disease transmission models in use. Agent-based disease models benefit from their ability to assign disease transmission probabilities based on characteristics shared by individual agents. These shared characteristics allow ABMs to apply transmission probabilities when agents come together in geographic space. Modeling these types of social interactions requires data, and the results of the model largely depend on the quality of these input data. We initially generated a synthetic population for the United States, in support of the Models of Infectious Disease Agent Study. Subsequently, we created shared characteristics to use in ABMs. The specific goals for this task were to assign the appropriately aged populations to schools, workplaces, and public transit. Each goal presented its own challenges and problems; therefore, we used different techniques to create each type of shared characteristic. These shared characteristics have allowed disease models to more realistically predict the spread of disease, both spatially and temporally. PMID:22577617

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

    NASA Astrophysics Data System (ADS)

    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

  19. Terrain Portrayal for Synthetic Vision Systems Head-Down Displays Evaluation Results: Compilation of Pilot Transcripts

    NASA Technical Reports Server (NTRS)

    Hughes, Monica F.; Glaab, Louis J.

    2007-01-01

    The Terrain Portrayal for Head-Down Displays (TP-HDD) simulation experiment addressed multiple objectives involving twelve display concepts (two baseline concepts without terrain and ten synthetic vision system (SVS) variations), four evaluation maneuvers (two en route and one approach maneuver, plus a rare-event scenario), and three pilot group classifications. The TP-HDD SVS simulation was conducted in the NASA Langley Research Center's (LaRC's) General Aviation WorkStation (GAWS) facility. The results from this simulation establish the relationship between terrain portrayal fidelity and pilot situation awareness, workload, stress, and performance and are published in the NASA TP entitled Terrain Portrayal for Synthetic Vision Systems Head-Down Displays Evaluation Results. This is a collection of pilot comments during each run of the TP-HDD simulation experiment. These comments are not the full transcripts, but a condensed version where only the salient remarks that applied to the scenario, the maneuver, or the actual research itself were compiled.

  20. Sorption and mineral-promoted transformation of synthetic hormone growth promoters in soil systems.

    PubMed

    Qu, Shen; Kolodziej, Edward P; Cwiertny, David M

    2014-12-24

    This work examines the fate of synthetic growth promoters (trenbolone acetate, melengestrol acetate, and zeranol) in sterilized soil systems, focusing on their sorption to organic matter and propensity for mineral-promoted reactions. In organic-rich soil matrices (e.g., Pahokee Peat), the extent and reversibility of sorption did not generally correlate with compound hydrophobicity (e.g., K(ow) values), suggesting that specific binding interactions (e.g., potentially hydrogen bonding through C17 hydroxyl groups for the trenbolone and melengestrol families) can also contribute to uptake. In soils with lower organic carbon contents (1-5.9% OC), evidence supports sorption occurring in parallel with surface reaction on inorganic mineral phases. Subsequent experiments with pure mineral phases representative of those naturally abundant in soil (e.g., iron, silica, and manganese oxides) suggest that growth promoters are prone to mineral-promoted oxidation, hydrolysis, and/or nucleophilic (e.g., H2O or OH(-)) addition reactions. Although reaction products remain unidentified, this study shows that synthetic growth promoters can undergo abiotic transformation in soil systems, a previously unidentified fate pathway with implications for their persistence and ecosystem effects in the subsurface.

  1. [Mechanical characteristics of synthetic polyelectrolyte gel as a physical model of the cytoskeleton].

    PubMed

    Shkliar, T F; Toropova, O A; Safronov, A P; Pollack, G H; Bliakhman, F A

    2011-01-01

    A physical model of the cytoskeleton based on synthetic polyelectrolyte hydrogel of polymethacrylic acid has been proposed. From the physicochemical point of view, the structures of polyelectrolyte gel and the cytoskeleton show a high degree of similarity. It was shown that polyelectrolyte gel can shorten and produce mechanical stress in response to changes in the composition of the surrounding solution. The mechanical properties of the model gel were evaluated: Young modulus (2-6 kPa), stress relaxation time (0.1-1 s), and apparent viscosity (0.3-3 kPa x s). The viscoelastic properties of the gel depend on the degree of its swelling. It has been demonstrated that the mechanical properties of gels of polymethacrylic acid are close to those of biological objects.

  2. Natural and synthetic podolactones with potential use as natural herbicide models.

    PubMed

    Macías, F A; Simonet, A M; Pacheco, P C; Barrero, A F; Cabrera, E; Jiménez-González, D

    2000-07-01

    A collection of 11 natural and synthetic podolactones have been tested as allelochemicals in a range between 10(-4) and 10(-9) M, and their potential use as natural herbicide models is discussed. Their effects on the germination and growth of the dicots Lactuca sativa (cv. Nigra and cv. Roman), Lepidium sativum, and Lycopersicon esculentum and the monocots Allium cepa, Hordeum vulgare, and Triticum aestivum as standard target species have been studied. An important inhibitory effect on the germination and growth of all tested species (average = 90%) was produced by compounds 9-11 at 10(-4) M. The specific structural requirements related to their activities are studied. On the basis of these results, their use as potential natural herbicide models is proposed. PMID:10898656

  3. Forward induced seismic hazard assessment: application to a synthetic seismicity catalogue from hydraulic stimulation modelling

    NASA Astrophysics Data System (ADS)

    Hakimhashemi, Amir Hossein; Yoon, Jeoung Seok; Heidbach, Oliver; Zang, Arno; Grünthal, Gottfried

    2014-07-01

    The M w 3.2-induced seismic event in 2006 due to fluid injection at the Basel geothermal site in Switzerland was the starting point for an ongoing discussion in Europe on the potential risk of hydraulic stimulation in general. In particular, further development of mitigation strategies of induced seismic events of economic concern became a hot topic in geosciences and geoengineering. Here, we present a workflow to assess the hazard of induced seismicity in terms of occurrence rate of induced seismic events. The workflow is called Forward Induced Seismic Hazard Assessment (FISHA) as it combines the results of forward hydromechanical-numerical models with methods of time-dependent probabilistic seismic hazard assessment. To exemplify FISHA, we use simulations of four different fluid injection types with various injection parameters, i.e. injection rate, duration and style of injection. The hydromechanical-numerical model applied in this study represents a geothermal reservoir with preexisting fractures where a routine of viscous fluid flow in porous media is implemented from which flow and pressure driven failures of rock matrix and preexisting fractures are simulated, and corresponding seismic moment magnitudes are computed. The resulting synthetic catalogues of induced seismicity, including event location, occurrence time and magnitude, are used to calibrate the magnitude completeness M c and the parameters a and b of the frequency-magnitude relation. These are used to estimate the time-dependent occurrence rate of induced seismic events for each fluid injection scenario. In contrast to other mitigation strategies that rely on real-time data or already obtained catalogues, we can perform various synthetic experiments with the same initial conditions. Thus, the advantage of FISHA is that it can quantify hazard from numerical experiments and recommend a priori a stimulation type that lowers the occurrence rate of induced seismic events. The FISHA workflow is rather

  4. Synthetic biology with artificially expanded genetic information systems. From personalized medicine to extraterrestrial life.

    PubMed

    Benner, Steven A; Hutter, Daniel; Sismour, A Michael

    2003-01-01

    Over 15 years ago, the Benner group noticed that the DNA alphabet need not be limited to the four standard nucleotides known in natural DNA. Rather, twelve nucleobases forming six base pairs joined by mutually exclusive hydrogen bonding patterns are possible within the geometry of the Watson-Crick pair (Fig. 1). Synthesis and studies on these compounds have brought us to the threshold of a synthetic biology, an artificial chemical system that does basic processes needed for life (in particular, Darwinian evolution), but with unnatural chemical structures. At the same time, the artificial genetic information systems (AEGIS) that we have developed have been used in FDA-approved commercial tests for managing HIV and hepatitis C infections in individual patients, and in a tool that seeks the virus for severe acute respiratory syndrome (SARS). AEGIS also supports the next generation of robotic probes to search for genetic molecules on Mars, Europa, and elsewhere where NASA probes will travel.

  5. Communication-induced multistability and multirhythmicity in a synthetic multicellular system

    NASA Astrophysics Data System (ADS)

    Yi, Qizhi; Zhou, Tianshou

    2011-05-01

    Traditionally, the main role of cell-to-cell communication was thought of as synchronizing a population of cells, thereby coordinating cellular behavior. Here we show that cell density, which quantifies cellular communication, can induce multistability and multirhythmicity in a synthetic multicellular system, where individual oscillators are a combination of repressillator and hysteresis-based oscillators and are coupled through a quorum-sensing mechanism. Specifically, for moderately small cell densities, the coupled system can exhibit multistability including stable homogenous and inhomogeneous steady states. For moderately large cell densities, it has the potential to generate multirhythmicity including multimode oscillations such as an in-phase periodic solution, antiphase periodic solution, asymmetric periodic solution, mixed-mode oscillations, coexistence of periodic orbits of several different modes, and bursting oscillations such as periodic bursting, torus quasiperiodic bursting, and chaotic bursting. Such versatility of cell-to-cell communication would be beneficial for cells or organisms to live in diversely changeable environments.

  6. Comparison of Two Synthetic Bone Graft Products in a Rabbit Posterolateral Fusion Model

    PubMed Central

    Fredericks, Douglas; Petersen, Emily B.; Watson, Nicole; Grosland, Nicole; Gibson-Corley, Katherine; Smucker, Joseph

    2016-01-01

    Background The drawbacks of iliac crest autograft as graft material for spine fusion are well reported. Despite continued modifications to improve bone healing capacity, the efficacy of synthetic graft materials as stand-alone replacements remains uncertain. The rabbit posterolateral fusion model is an established environment for testing of fusion concepts. It offers the opportunity to obtain radiographic, biomechanical and histological data on novel fusion materials. The objective of this study was to compare the spine fusion capability of two synthetic bone graft products in an established rabbit posterolateral spine fusion (PLF) model: Signafuse® Bioactive Bone Graft Putty and Actifuse® ABX. Methods Bilateral intertransverse spine fusion was performed at the L5-L6 transverse processes (TPs) of New Zealand White rabbits using either Signafuse or Actifuse ABX as the bone graft material. Bone remodeling and spine fusion were assessed at 6 and 12 weeks using radiographic, biomechanical and histological endpoints. Results Fusion rate by manual palpation at 6 weeks was greater for Signafuse (33%) compared to Actifuse ABX (0%), and equivalent in both groups at 12 weeks (50%). Biomechanical fusion rate based on flexion-extension data was 80% in Signafuse group and 44% for Actifuse ABX. Histology revealed a normal healing response in both groups. MicroCT and histomorphometric data at 6 weeks showed greater new bone formation in the Signafuse group compared to Actifuse ABX (p <0.05), with no differences detected at 12 weeks. Histological fusion scores were greater in the Signafuse group at 6 and 12 weeks, indicated by higher degree structural remodeling and tendency towards complete bridging of the fusion bed compared to the Actifuse ABX group. Conclusion Confirmed by several metrics, Signafuse outperformed Actifuse ABX as a standalone synthetic bone graft in an established PLF model, demonstrating greater rates of bone remodeling and spine fusion. The combination of 45

  7. Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

    PubMed Central

    Cai, Yizhi; Lux, Matthew W.; Adam, Laura; Peccoud, Jean

    2009-01-01

    Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology. PMID:19816554

  8. Constraining shallow seismic event depth via synthetic modeling for Expert Technical Analysis at the IDC

    NASA Astrophysics Data System (ADS)

    Stachnik, J.; Rozhkov, M.; Baker, B.; Bobrov, D.; Friberg, P. A.

    2015-12-01

    Depth of event is an important criterion of seismic event screening at the International Data Center, CTBTO. However, a thorough determination of the event depth can be conducted mostly through 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. When the true origin depth is greater than that reasonable for a nuclear test (3 km based on existing observations), this may result in a heavier workload to manually distinguish between shallow and deep events. Also, IDC depth criterion is not applicable to the events with the small t(pP-P) travel time difference, which is the case of the nuclear test. Since the shape of the first few seconds of signal of very shallow events is very sensitive to the presence of the depth phase, cross correlation between observed and theoretic seismogram can provide an estimate for the depth of the event, and so provide an expansion to the screening process. We exercised this approach mostly with events at teleseismic and partially regional distances. We found that such approach can be very efficient for the seismic event screening process, with certain caveats related mostly to the poorly defined crustal models at source and receiver which can shift the depth estimate. We used adjustable t* teleseismic attenuation model for synthetics since this characteristic is not determined 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 Robert Herrmann's hudson96 program, and the regional modelling was done with the generalized ray technique by Vlastislav Cerveny modified to the complex source topography.

  9. Phase and extraction equilibria in water-polyethyleneglycol ethers of monoethanolamides of synthetic fatty acid-ammonium chloride systems

    NASA Astrophysics Data System (ADS)

    Lesnov, A. E.; Golovkina, A. V.; Kudryashova, O. S.; Denisova, S. A.

    2016-08-01

    Phase equilibria in layering systems of water, polyethyleneglycol ethers of monoethanolamides of synthetic fatty acids (SFAs) (synthamide-5), and ammonium chloride are studied. The possibility of using such systems for the liquid extraction of metal ions is evaluated. The effect the nature of salting-out agents has on the processes of segregation of the systems has been considered.

  10. Study of Synthetic Vision Systems (SVS) and Velocity-vector Based Command Augmentation System (V-CAS) on Pilot Performance

    NASA Technical Reports Server (NTRS)

    Liu, Dahai; Goodrich, Ken; Peak, Bob

    2006-01-01

    This study investigated the effects of synthetic vision system (SVS) concepts and advanced flight controls on single pilot performance (SPP). Specifically, we evaluated the benefits and interactions of two levels of terrain portrayal, guidance symbology, and control-system response type on SPP in the context of lower-landing minima (LLM) approaches. Performance measures consisted of flight technical error (FTE) and pilot perceived workload. In this study, pilot rating, control type, and guidance symbology were not found to significantly affect FTE or workload. It is likely that transfer from prior experience, limited scope of the evaluation task, specific implementation limitations, and limited sample size were major factors in obtaining these results.

  11. Prediction of Antimicrobial Activity of Synthetic Peptides by a Decision Tree Model

    PubMed Central

    Lira, Felipe; Perez, Pedro S.; Baranauskas, José A.

    2013-01-01

    Antimicrobial resistance is a persistent problem in the public health sphere. However, recent attempts to find effective substitutes to combat infections have been directed at identifying natural antimicrobial peptides in order to circumvent resistance to commercial antibiotics. This study describes the development of synthetic peptides with antimicrobial activity, created in silico by site-directed mutation modeling using wild-type peptides as scaffolds for these mutations. Fragments of antimicrobial peptides were used for modeling with molecular modeling computational tools. To analyze these peptides, a decision tree model, which indicated the action range of peptides on the types of microorganisms on which they can exercise biological activity, was created. The decision tree model was processed using physicochemistry properties from known antimicrobial peptides available at the Antimicrobial Peptide Database (APD). The two most promising peptides were synthesized, and antimicrobial assays showed inhibitory activity against Gram-positive and Gram-negative bacteria. Colossomin C and colossomin D were the most inhibitory peptides at 5 μg/ml against Staphylococcus aureus and Escherichia coli. The methods described in this work and the results obtained are useful for the identification and development of new compounds with antimicrobial activity through the use of computational tools. PMID:23455341

  12. Particle oxidation model of synthetic FeS and sediment acid-volatile sulfide

    SciTech Connect

    Toro, D.M. di |; Mahony, J.D.; Gonzalez, A.M.

    1996-12-01

    A model is proposed for the kinetics of the oxidation of acid-volatile sulfide (AVS). It is based on a surface oxidation reaction that erodes the particle surface until the particle disappears. A monodisperse particle size distribution is assumed with a reaction rate that is proportional to the surface area remaining and a dimensional exponent that related the surface area to the particle volume. The model is fit to time course data from a number of experiments conducted using synthetic FeS at various pHs, oxygen concentrations, and ionic strengths. The reaction rate constants are modeled using a surface complexation model. It is based upon the formation of two activated surface complexes with molecular oxygen, one of which is charged. The complexation model provides a good fit to the variation of the reaction rate constant with respect to O{sub 2}, pH, temperature, and ionic strength. The dimensional exponent {nu} increases with pH from values characteristic of plates and needles to values reflecting more spherical particles, presumably due to coagulation. However the increase in {nu} with respect to O{sub 2} at high concentrations is unexplained.

  13. Towards a compendium of essential genes – From model organisms to synthetic lethality in cancer cells

    PubMed Central

    Zhan, Tianzuo; Boutros, Michael

    2016-01-01

    Abstract Essential genes are defined by their requirement to sustain life in cells or whole organisms. The systematic identification of essential gene sets not only allows insights into the fundamental building blocks of life, but may also provide novel therapeutic targets in oncology. The discovery of essential genes has been tightly linked to the development and deployment of various screening technologies. Here, we describe how gene essentiality was addressed in different eukaryotic model organisms, covering a range of organisms from yeast to mouse. We describe how increasing knowledge of evolutionarily divergent genomes facilitate identification of gene essentiality across species. Finally, the impact of gene essentiality and synthetic lethality on cancer research and the clinical translation of screening results are highlighted. PMID:26627871

  14. 3-D synthetic aperture processing on high-frequency wide-beam microwave systems

    NASA Astrophysics Data System (ADS)

    Cristofani, Edison; Brook, Anna; Vandewal, Marijke

    2012-06-01

    The use of High-Frequency MicroWaves (HFMW) for high-resolution imagery has gained interest over the last years. Very promising in-depth applications can be foreseen for composite non-metal, non-polarized materials, widely used in the aeronautic and aerospace industries. Most of these materials present a high transparency in the HFMW range and, therefore, defects, delaminations or occlusions within the material can be located. This property can be exploited by applying 3-D HFMW imaging where conventional focused imaging systems are typically used but a different approach such as Synthetic Aperture (SA) radar can be addressed. This paper will present an end-to-end 3-D imagery system for short-range, non-destructive testing based on a frequency-modulated continuous-wave HFMWsensor operating at 100 GHz, implying no health concerns to the human body as well as relatively low cost and limited power requirements. The sensor scans the material while moving sequentially in every elevation plane following a 2-D grid and uses a significantly wide beam antenna for data acquisition, in contrast to focused systems. Collected data must be coherently combined using a SA algorithm to form focused images. Range-independent, synthetically improved cross-range resolutions are remarkable added values of SA processing. Such algorithms can be found in the literature and operate in the time or frequency domains, being the former computationally impractical and the latter the best option for in-depth 3-D imaging. A balanced trade-off between performance and image focusing quality is investigated for several SA algorithms.

  15. Design of a perspective flight guidance display for a synthetic vision system

    NASA Astrophysics Data System (ADS)

    Gross, Martin; Mayer, Udo; Kaufhold, Rainer

    1998-07-01

    Adverse weather conditions affect flight safety as well as productivity of the air traffic industry. The problem becomes evident in the airport area (Taxiing, takeoff, approach and landing). The productivity of the air traffic industry goes down because the resources of the airport can not be used optimally. Canceled and delayed flights lead directly to additional costs for the airlines. Against the background of aggravated problems due to a predicted increasing air traffic the European Union launched the project AWARD (All Weather ARrival and Departure) in June 1996. Eleven European aerospace companies and research institutions are participating. The project will be finished by the end of 1999. Subject of AWARD is the development of a Synthetic Vision System (based on database and navigation) and an Enhanced Vision System (based on sensors like FLIR and MMWR). Darmstadt University of Technology is responsible for the development of the SVS prototype. The SVS application is depending on precise navigation, databases for terrain and flight relevant information, and a flight guidance display. The objective is to allow landings under CAT III a/b conditions independently from CAT III ILS airport installations. One goal of SVS is to enhance the situation awareness of pilots during all airport area operations by designing an appropriate man-machine- interface for the display. This paper describes the current state of the research and development of the Synthetic Vision System being developed in AWARD. The paper describes which methodology was used to identify the information that should be displayed. Human factors which influenced the basic design of the SVS are portrayed and some of the planned activities for the flight simulation tests are summarized.

  16. A constant stress-drop model for producing broadband synthetic seismograms: Comparison with the next generation attenuation relations

    USGS Publications Warehouse

    Frankel, A.

    2009-01-01

    Broadband (0.1-20 Hz) synthetic seismograms for finite-fault sources were produced for a model where stress drop is constant with seismic moment to see if they can match the magnitude dependence and distance decay of response spectral amplitudes found in the Next Generation Attenuation (NGA) relations recently developed from strong-motion data of crustal earthquakes in tectonically active regions. The broadband synthetics were constructed for earthquakes of M 5.5, 6.5, and 7.5 by combining deterministic synthetics for plane-layered models at low frequencies with stochastic synthetics at high frequencies. The stochastic portion used a source model where the Brune stress drop of 100 bars is constant with seismic moment. The deterministic synthetics were calculated using an average slip velocity, and hence, dynamic stress drop, on the fault that is uniform with magnitude. One novel aspect of this procedure is that the transition frequency between the deterministic and stochastic portions varied with magnitude, so that the transition frequency is inversely related to the rise time of slip on the fault. The spectral accelerations at 0.2, 1.0, and 3.0 sec periods from the synthetics generally agreed with those from the set of NGA relations for M 5.5-7.5 for distances of 2-100 km. At distances of 100-200 km some of the NGA relations for 0.2 sec spectral acceleration were substantially larger than the values of the synthetics for M 7.5 and M 6.5 earthquakes because these relations do not have a term accounting for Q. At 3 and 5 sec periods, the synthetics for M 7.5 earthquakes generally had larger spectral accelerations than the NGA relations, although there was large scatter in the results from the synthetics. The synthetics showed a sag in response spectra at close-in distances for M 5.5 between 0.3 and 0.7 sec that is not predicted from the NGA relations.

  17. Modeling Parallel System Workloads with Temporal Locality

    NASA Astrophysics Data System (ADS)

    Minh, Tran Ngoc; Wolters, Lex

    In parallel systems, similar jobs tend to arrive within bursty periods. This fact leads to the existence of the locality phenomenon, a persistent similarity between nearby jobs, in real parallel computer workloads. This important phenomenon deserves to be taken into account and used as a characteristic of any workload model. Regrettably, this property has received little if any attention of researchers and synthetic workloads used for performance evaluation to date often do not have locality. With respect to this research trend, Feitelson has suggested a general repetition approach to model locality in synthetic workloads [6]. Using this approach, Li et al. recently introduced a new method for modeling temporal locality in workload attributes such as run time and memory [14]. However, with the assumption that each job in the synthetic workload requires a single processor, the parallelism has not been taken into account in their study. In this paper, we propose a new model for parallel computer workloads based on their result. In our research, we firstly improve their model to control locality of a run time process better and then model the parallelism. The key idea for modeling the parallelism is to control the cross-correlation between the run time and the number of processors. Experimental results show that not only the cross-correlation is controlled well by our model, but also the marginal distribution can be fitted nicely. Furthermore, the locality feature is also obtained in our model.

  18. Reach scale floodplain inundation dynamics observed using airborne synthetic aperture radar imagery: Data analysis and modelling

    NASA Astrophysics Data System (ADS)

    Bates, Paul D.; Wilson, Matthew D.; Horritt, Matthew S.; Mason, David C.; Holden, Nick; Currie, Anthony

    2006-08-01

    SummaryIn this paper, we use an airborne synthetic aperture radar to map river flood inundation synoptically at fine spatial resolution (1.2 m) along a ˜16 km reach of the River Severn, west-central England. Images were obtained at four times through a large flood event between 8th and 17th November 2000 and processed using a statistical active contour algorithm to yield the flood shoreline at each time. Intersection of these data with a high vertical accuracy survey of floodplain topography obtained from airborne laser altimetry permitted the calculation of dynamic changes in inundated area, total reach storage and rates of reach dewatering. In addition, comparison of the data to gauged flow rates, the measured floodplain topography and map data giving the location of embankments and drainage channels on the floodplain yields new insights into the factors controlling the development of inundation patterns at a variety of scales. Finally, the data were used to assess the performance of a simple two-dimensional flood inundation model, LISFLOOD-FP, and allows us, for the first time, to validate the dynamic performance of the model. This process is shown to give new information into structural weaknesses of the model and suggests possible future developments, including the incorporation of a better description of floodplain hydrological processes in the hydraulic model to represent more accurately the dewatering of the floodplain.

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

    NASA Astrophysics Data System (ADS)

    Ruan, Wenzhi; He, Jiansen; Zhang, Lei; Vocks, Christian; Marsch, Eckart; Tu, Chuanyi; Peter, Hardi; Wang, Linghua

    2016-03-01

    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.

  20. Validation analysis of the thermal and radiometric integrity of RIT's synthetic image generation model, DIRSIG

    NASA Astrophysics Data System (ADS)

    Mason, John E.; Schott, John R.; Rankin-Parobek, Donna

    1994-06-01

    The digital imaging and remote sensing laboratory's image generation model (DIRSIG) was validated in the long wave infrared (LWIR, 8 - 13.3 micrometers ) and midwife infrared (MWIR, 3 - 5 micrometers ) pass bands. Truth data was collected for all components of the thermal and radiometric submodels including a complete set of meteorological and radiometric data. Truth temperatures were collected using a bank of thermistors and truth radiance images were collected with calibrated InSb (MWIR) and HgCdTe (LWIR) detectors. Sensor spectral response functions were also included in the radiometric analysis. Relative error contributions to the total temperature/radiance digital count were investigated for each component in the multi-spectral model. Largest contributions were found to be wind speed, air temperature, visible emissivity, and fractional sky exposure for the thermal model and atmospheric transmission, temperature, and emissivity for the radiance model. An overall comparison of truth and synthetic images yields rms errors of as low as 1.8 degree(s)C actual temperature and 5 degree(s)C (LWIR) and 6 degree(s)C (MWIR) apparent temperature.

  1. Synthetic and Thermodynamic Investigations of Ancillary Ligand Influence on Catalytic Organometallic Systems. Final Report

    SciTech Connect

    Nolan, Steven

    2003-03-20

    During the grant period we have been involved in synthesizing and experimentally determining solution enthalpy values associated with partially fluorinated ligands. This has lead to the publication of manuscripts dealing with synthetic, calorimetric and catalytic behavior of partially fluorinated ligands. The collaboration with Los Alamos researchers has lead to the publication of catalytic results in sc CO{sub 2} which have proven very interesting. Furthermore, we have also examined ligands that behave as phosphine mimics. The N-heterocyclic carbenes have been explored as alternatives for tertiary phosphines and have resulted in the design and construction of efficient palladium and nickel system capable of performing C-C and C-N cross coupling reactions. The initial studies in this areas were made possible by exploratory work conducted under the DOE/EPSCoR grant.

  2. Polymerase Interactions with Wobble Mismatches in Synthetic Genetic Systems and Their Evolutionary Implications.

    PubMed

    Winiger, Christian B; Kim, Myong-Jung; Hoshika, Shuichi; Shaw, Ryan W; Moses, Jennifer D; Matsuura, Mariko F; Gerloff, Dietlind L; Benner, Steven A

    2016-07-19

    In addition to completing the Watson-Crick nucleobase matching "concept" (big pairs with small, hydrogen bond donors pair with hydrogen bond acceptors), artificially expanded genetic information systems (AEGIS) also challenge DNA polymerases with a complete set of mismatches, including wobble mismatches. Here, we explore wobble mismatches with AEGIS with DNA polymerase 1 from Escherichia coli. Remarkably, we find that the polymerase tolerates an AEGIS:standard wobble that has the same geometry as the G:T wobble that polymerases have evolved to exclude but excludes a wobble geometry that polymerases have never encountered in natural history. These results suggest certain limits to "structural analogy" and "evolutionary guidance" as tools to help synthetic biologists expand DNA alphabets. PMID:27347689

  3. Transition of Attention in Terminal Area NextGen Operations Using Synthetic Vision Systems

    NASA Technical Reports Server (NTRS)

    Ellis, Kyle K. E.; Kramer, Lynda J.; Shelton, Kevin J.; Arthur, Shelton, J. J., III; Prinzel, Lance J., III; Norman, Robert M.

    2011-01-01

    This experiment investigates the capability of Synthetic Vision Systems (SVS) to provide significant situation awareness in terminal area operations, specifically in low visibility conditions. The use of a Head-Up Display (HUD) and Head-Down Displays (HDD) with SVS is contrasted to baseline standard head down displays in terms of induced workload and pilot behavior in 1400 RVR visibility levels. Variances across performance and pilot behavior were reviewed for acceptability when using HUD or HDD with SVS under reduced minimums to acquire the necessary visual components to continue to land. The data suggest superior performance for HUD implementations. Improved attentional behavior is also suggested for HDD implementations of SVS for low-visibility approach and landing operations.

  4. On Brucella pathogenesis: looking for the unified challenge in systems and synthetic biology.

    PubMed

    Chiliveru, Srikanth; Appari, Mahesh; Suravajhala, Prashanth

    2015-06-01

    Brucellosis is a zoonotic infection transmitted to humans from infected animals and is one of the widely spread zoonoses. Recently, six species were recognized within the genus Brucella wherein B. melitensis, B. suis and B. abortus are considered virulent for humans. While these species differ phenotypically by their pattern of metabolic activities, there has been an imperative need to understand pathogenesis of Brucella species. It has been foreseen that creating a human vaccine for Brucellosis would entail decreased dose of antibiotics. However the emerging role of Brucella pathogenesis still centers on isolation of the organism and various diagnostic tests thereby leading to varying strategies of treatment cycle. In view of disease heterogeneity, we focus systems and synthetic biology challenges that might improve our understanding the Brucella pathogenesis.

  5. Feature discrimination and detection probability in synthetic aperture radar imaging system

    NASA Technical Reports Server (NTRS)

    Lipes, R. G.; Butman, S. A.

    1977-01-01

    Images obtained using synthetic aperture radar (SAR) systems can only represent the intensities of resolution cells in the scene of interest probabilistically since radar receiver noise and Rayleigh scattering of the transmitted radiation are always present. Consequently, when features to be identified differ only by their contribution to the mean power of the radar return, discrimination can be treated by detection theory. In this paper, we develop a 'sufficient statistic' for discriminating between competing features and compare it with some suboptimal methods frequently used. Discrimination is measured by probability of detection error and depends on number of samples or 'looks', signal-to-noise ratio (SNR), and ratio of mean power returns from the competing features. Our results show discrimination and image quality rapidly saturate with SNR (very small improvement for SNR not less than 10 dB) but continue to improve with increasing number of looks.

  6. Modulation of endothelial cell adhesion to synthetic vascular grafts using biotinylated fibronectin in a dual ligand protein system

    NASA Astrophysics Data System (ADS)

    Anamelechi, Charles Chibuzor

    Over half a million coronary artery bypass operations are performed annually in the US yielding an annual health care cost of over 16 billion dollars. Only five percent of bypasses are repeat operations in spite of the procedures prevalence. Patients facing repeat coronary artery bypass operations often lack transplantable autologous arteries or veins, necessitating the use of substitutes. Unfortunately, synthetic small diameter vascular grafts have unacceptable patency rates, primarily due to lumenal thrombus formation and intimal thickening. Endothelial cells (EC) mediate the anti-thrombotic activity in healthy blood vessels, and due to the scarcity of suitable autologous vascular replacement, EC-seeded small diameter synthetic vascular grafts represent a clear, immediate, and practical solution. The fundamental goal of this project was to optimize the dual ligand (DL) system on synthetic vascular graft (SVG) surrogates to show enhanced cell adhesion, retention, and native functionality compared to fibronectin alone. Initially, two SVG surrogates were identified through characterization by x-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and 125I radiolabeling. The first modification to the DL system involved direct biotinylation of fibronectin (bFN) as a replacement for co-adsorption of FN with biotinylated bovine serum albumin (bBSA). This was analyzed with a Langmuir model using surface plasmon resonance (SPR) spectroscopy to verify the binding affinity of bFN and ELISA to detect the availability of the RGD binding motif post biotinylation. The second major change in this project examined cell binding and formation of focal adhesion after shifting from direct incubation of HUVECs with RGD-SA to sequentially adsorbing bFN(9) and RGD-SA prior to introducing unmodified HUVECs. These experiments were conducted under static seeding conditions. Next, dynamic cell seeding onto the sequentially adsorbed protein surface was examined as a function

  7. Can Effective Synthetic Vision System Displays be Implemented on Limited Size Display Spaces?

    NASA Technical Reports Server (NTRS)

    Comstock, J. Raymond, Jr.; Glaab, Lou J.; Prinzel, Lance J.; Elliott, Dawn M.

    2004-01-01

    The Synthetic Vision Systems (SVS) element of the NASA Aviation Safety Program is striving to eliminate poor visibility as a causal factor in aircraft accidents, and to enhance operational capabilities of all types or aircraft. To accomplish these safety and situation awareness improvements, the SVS concepts are designed to provide a clear view of the world ahead through the display of computer generated imagery derived from an onboard database of terrain, obstacle and airport information. An important issue for the SVS concept is whether useful and effective Synthetic Vision System (SVS) displays can be implemented on limited size display spaces as would be required to implement this technology on older aircraft with physically smaller instrument spaces. In this study, prototype SVS displays were put on the following display sizes: (a) size "A' (e.g. 757 EADI), (b) form factor "D" (e.g. 777 PFD), and (c) new size "X" (Rectangular flat-panel, approximately 20 x 25 cm). Testing was conducted in a high-resolution graphics simulation facility at NASA Langley Research Center. Specific issues under test included the display size as noted above, the field-of-view (FOV) to be shown on the display and directly related to FOV is the degree of minification of the displayed image or picture. Using simulated approaches with display size and FOV conditions held constant no significant differences by these factors were found. Preferred FOV based on performance was determined by using approaches during which pilots could select FOV. Mean preference ratings for FOV were in the following order: (1) 30 deg., (2) Unity, (3) 60 deg., and (4) 90 deg., and held true for all display sizes tested. Limitations of the present study and future research directions are discussed.

  8. Synthetic models of the active site of catechol oxidase: mechanistic studies.

    PubMed

    Koval, Iryna A; Gamez, Patrick; Belle, Catherine; Selmeczi, Katalin; Reedijk, Jan

    2006-09-01

    The ability of copper proteins to process dioxygen at ambient conditions has inspired numerous research groups to study their structural, spectroscopic and catalytic properties. Catechol oxidase is a type-3 copper enzyme usually encountered in plant tissues and in some insects and crustaceans. It catalyzes the conversion of a large number of catechols into the respective o-benzoquinones, which subsequently auto-polymerize, resulting in the formation of melanin, a dark pigment thought to protect a damaged tissue from pathogens. After the report of the X-ray crystal structure of catechol oxidase a few years earlier, a large number of publications devoted to the biomimetic modeling of its active site appeared in the literature. This critical review (citing 114 references) extensively discusses the synthetic models of this enzyme, with a particular emphasis on the different approaches used in the literature to study the mechanism of the catalytic oxidation of the substrate (catechol) by these compounds. These are the studies on the substrate binding to the model complexes, the structure-activity relationship, the kinetic studies of the catalytic oxidation of the substrate and finally the substrate interaction with (per)oxo-dicopper adducts. The general overview of the recognized types of copper proteins and the detailed description of the crystal structure of catechol oxidase, as well as the proposed mechanisms of the enzymatic cycle are also presented. PMID:16936929

  9. Synthetic plant defense elicitors

    PubMed Central

    Bektas, Yasemin; Eulgem, Thomas

    2015-01-01

    To defend themselves against invading pathogens plants utilize a complex regulatory network that coordinates extensive transcriptional and metabolic reprogramming. Although many of the key players of this immunity-associated network are known, the details of its topology and dynamics are still poorly understood. As an alternative to forward and reverse genetic studies, chemical genetics-related approaches based on bioactive small molecules have gained substantial popularity in the analysis of biological pathways and networks. Use of such molecular probes can allow researchers to access biological space that was previously inaccessible to genetic analyses due to gene redundancy or lethality of mutations. Synthetic elicitors are small drug-like molecules that induce plant defense responses, but are distinct from known natural elicitors of plant immunity. While the discovery of some synthetic elicitors had already been reported in the 1970s, recent breakthroughs in combinatorial chemical synthesis now allow for inexpensive high-throughput screens for bioactive plant defense-inducing compounds. Along with powerful reverse genetics tools and resources available for model plants and crop systems, comprehensive collections of new synthetic elicitors will likely allow plant scientists to study the intricacies of plant defense signaling pathways and networks in an unparalleled fashion. As synthetic elicitors can protect crops from diseases, without the need to be directly toxic for pathogenic organisms, they may also serve as promising alternatives to conventional biocidal pesticides, which often are harmful for the environment, farmers and consumers. Here we are discussing various types of synthetic elicitors that have been used for studies on the plant immune system, their modes-of-action as well as their application in crop protection. PMID:25674095

  10. Enhanced and synthetic vision system for autonomous all weather approach and landing

    NASA Astrophysics Data System (ADS)

    Korn, Bernd R.

    2007-04-01

    Within its research project ADVISE-PRO (Advanced visual system for situation awareness enhancement - prototype, 2003 - 2006) that will be presented in this contribution, DLR has combined elements of Enhanced Vision and Synthetic Vision to one integrated system to allow all low visibility operations independently from the infrastructure on ground. The core element of this system is the adequate fusion of all information that is available on-board. This fusion process is organized in a hierarchical manner. The most important subsystems are a) the sensor based navigation which determines the aircraft's position relative to the runway by automatically analyzing sensor data (MMW, IR, radar altimeter) without using neither (D)GPS nor precise knowledge about the airport geometry, b) an integrity monitoring of navigation data and terrain data which verifies on-board navigation data ((D)GPS + INS) with sensor data (MMW-Radar, IR-Sensor, Radar altimeter) and airport / terrain databases, c) an obstacle detection system and finally d) a consistent description of situation and respective HMI for the pilot.

  11. A New Titanium-Bearing Calcium Aluminosilicate Phase. 1; Meteoritic Occurrences and Formation in Synthetic Systems

    NASA Technical Reports Server (NTRS)

    Paque, Julie M.; Beckett, John R.; Barber, David J.; Stolper, Edward M.

    1994-01-01

    A new titanium-bearing calcium aluminosilicate mineral has been identified in coarse-grained calcium-aluminum-rich inclusions (CAIs) from carbonaceous chondrites. The formula for this phase, which we have temporarily termed "UNK," is Ca3Ti(AlTi)2(Si,Al)3O14, and it is present in at least 8 of the 20 coarse-grained CAIs from the Allende CV3 chondrite examined as part of this project. The phase occurs in Types A and B1 inclusions as small tabular crystals oriented along two mutually perpendicular planes in melilite. UNK crystallizes from melts in dynamic crystallization experiments conducted in air from four bulk compositions modeled after Types A, B1, B2 and C inclusions. Cooling rates resulting in crystallization of UNK ranged from 0.5 to 200 C/h from maximum (initial) temperatures of 1375 to 1580 C. Only below 1190 C does UNK itself begin to crystallize. To first order, the presence or absence of UNK from individual experiments can be understood in terms of the compositions of residual melts and nucleation probabilities. Compositions of synthetic and meteoritic LINK are very similar in terms of major oxides, differing only in the small amounts of trivalent Ti (7-13% of total Ti) in meteoritic samples. UNK crystallized from the Type A analog is similar texturally to that found in CAls, although glass, which is typically associated with synthetic UN& is not observed in meteoritic occurrences. A low Ti end-member of UNK ("Si-UNK") with a composition new that of Ca3Al2Si4O14 was produced in a few samples from the Type B1 analog. This phase has not been found in the meteoritic inclusions.

  12. The biomechanics of the T2 femoral nailing system: a comparison of synthetic femurs withfinite element analysis.

    PubMed

    Bougherara, H; Zdero, R; Miric, M; Shah, S; Hardisty, M; Zalzal, P; Schemitsch, E H

    2009-04-01

    Intramedullary nails are commonly used to repair femoral fractures. Fractures in normal healthy bone often occur in the young during motor vehicle accidents. Although clinically beneficial, bone refracture and implant failure persist. Large variations in human femur quality and geometry have motivated recent experimental use of synthetic femurs that mimic human tissue and the development of increasingly sophisticated theoretical models. Four synthetic femurs were fitted with a T2 femoral nailing system (Stryker, Mahwah, New Jersey, USA). The femurs were not fractured in order to simulate post-operative perfect union. Six configurations were created: retrograde nail with standard locking (RS), retrograde nail with advanced locking 'off' (RA-off), retrograde nail with advanced locking 'on' (RA-on), antegrade nail with standard locking (AS), antegrade nail with advanced locking 'off' (AA-off), and antegrade nail with advanced locking 'on' (AA-on). Strain gauges were placed on the medial side of femurs. A 580 N axial load was applied, and the stiffness was measured. Strains were recorded and compared with results from a three-dimensional finite element (FE) model. Experimental axial stiffnesses for RA-off (771.3 N/mm) and RA-on (681.7 N/mm) were similar to intact human cadaveric femurs from previous literature (757 + 264 N/mm). Conversely, experimental axial stiffnesses for AS (1168.8N/mm), AA-off (1135.3N/mm), AA-on (1152.1 N/mm), and RS (1294.0 N/mm) were similar to intact synthetic femurs from previous literature (1290 +/- 30 N/mm). There was better agreement between experimental and FE analysis strains for RS (average percentage difference, 11.6 per cent), RA-on (average percentage difference, 11.1 per cent), AA-off (average percentage difference, 13.4 per cent), and AA-on (average percentage difference, 16.0 per cent), than for RA-off (average percentage difference, 33.5 per cent) and AS (average percentage difference, 32.6 per cent). FE analysis was more

  13. Analysis of properties of synthetic mineral microparticles for retention and drainage system

    NASA Astrophysics Data System (ADS)

    Lee, Sa Yong

    Over the past 20 years there has been a revolution involving the use of nano- or macro-sized particles as a component of drainage and retention systems during the manufacture of paper. More recently a group of patented technologies called Synthetic Mineral Microparticles (SMM) has been invented and developed. This system has potential to further promote the drainage of water and retention of fine particles during papermaking. Prior research, as well as our own preliminary research showed that the SMM system has advantages in both of drainage and retention, compared with montmorillonite (bentonite), which is one of the most popular materials presently used in this kind of application. In spite of the demonstrated advantages of this SMM system, the properties and activity of SMM particles in the aqueous state have not been elucidated yet. To help understand the molecular mechanisms involved in SMM technology, streaming current and potentiometric titration were employed to characterize the charge behavior of SMM, depending on the synthetic conditions, which included variation of the Al/Si ratio, partial neutralization of Al species, salt addition and shear rate. Surface area of SMM and the distribution of SMM particle size were investigated with scanning electron microscopy in order to elucidate the relationship between the morphology and coagulation behavior of SMM, versus the pre-stated synthetic conditions, as well as to estimate the optimal conditions to produce SMM as a retention and drainage aid for use during papermaking. Through the streaming current titration experiments it was found that pH variation, caused by the change of Al/Si ratio and partial neutralization of aluminum's acidity, profoundly affects the charge properties of SMM. These effects can be attributed to the variation of Al-ion speciation and the influence ionizable groups on the Si-containing particle surfaces. The relationship between Al/Si ratio and isoelectric pH, measured by potentiometric

  14. Synthetic and Enhanced Vision Systems for NextGen (SEVS) Simulation and Flight Test Performance Evaluation

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Kramer, Lynda J.; Ellis,Kyle K.; Rehfeld, Sherri A.

    2012-01-01

    The Synthetic and Enhanced Vision Systems for NextGen (SEVS) simulation and flight tests are jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA). The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SEVS operational and system-level performance capabilities. Nine test flights (38 flight hours) were conducted over the summer and fall of 2011. The evaluations were flown in Gulfstream.s G450 flight test aircraft outfitted with the SEVS technology under very low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 ft to 2400 ft visibility) into various airports from Louisiana to Maine. In-situ flight performance and subjective workload and acceptability data were collected in collaboration with ground simulation studies at LaRC.s Research Flight Deck simulator.

  15. Large Hybrid Energy Systems for Making Low CO2 Load-Following Power and Synthetic Fuel

    SciTech Connect

    Robert S. Cherry; Richard D. Boardman; Steven Aumeier

    2012-02-01

    Hybrid energy systems using nuclear heat sources can economically produce load-following electrical power by exploiting the surplus generation capacity available at night or seasonally to make synthetic fuel. Vehicle fuel is the only current energy use large enough to absorb all the energy capacity that might be diverted from the power industry, and its ease of storage obviates problems with discontinuous synfuel production. The potential benefits and challenges of synfuels integration are illustrated by the production of methanol from natural gas (as a source of carbon) using steam from a light water nuclear power reactor which is assumed to be available in accord with a year's worth of power demand data. Methanol's synthesis process is easily adapted to using 300 C heat from a light water reactor and this simple compound can be further processed into gasoline, biodiesel, or dimethyl ether, fuels which can be used with the current vehicle fleet. A supplemental feed to the methanol process of natural gas (for energy) allows operation at constant full rate when the nuclear heat is being used to produce electrical power. The higher capital costs of such a system are offset by a lower cost of heat and power production from a large base load type of plant and by reduced costs associated with much lower CO2 emissions. Other less tangible economic benefits of this and similar hybrid systems include better use of natural resource for fuels and greater energy services security from the domestic production of vehicle fuel.

  16. Functional characterization and structural modeling of synthetic polyester-degrading hydrolases from Thermomonospora curvata

    PubMed Central

    2014-01-01

    Thermomonospora curvata is a thermophilic actinomycete phylogenetically related to Thermobifida fusca that produces extracellular hydrolases capable of degrading synthetic polyesters. Analysis of the genome of T. curvata DSM43183 revealed two genes coding for putative polyester hydrolases Tcur1278 and Tcur0390 sharing 61% sequence identity with the T. fusca enzymes. Mature proteins of Tcur1278 and Tcur0390 were cloned and expressed in Escherichia coli TOP10. Tcur1278 and Tcur0390 exhibited an optimal reaction temperature against p-nitrophenyl butyrate at 60°C and 55°C, respectively. The optimal pH for both enzymes was determined at pH 8.5. Tcur1278 retained more than 80% and Tcur0390 less than 10% of their initial activity following incubation for 60 min at 55°C. Tcur0390 showed a higher hydrolytic activity against poly(ε-caprolactone) and polyethylene terephthalate (PET) nanoparticles compared to Tcur1278 at reaction temperatures up to 50°C. At 55°C and 60°C, hydrolytic activity against PET nanoparticles was only detected with Tcur1278. In silico modeling of the polyester hydrolases and docking with a model substrate composed of two repeating units of PET revealed the typical fold of α/β serine hydrolases with an exposed catalytic triad. Molecular dynamics simulations confirmed the superior thermal stability of Tcur1278 considered as the main reason for its higher hydrolytic activity on PET. PMID:25405080

  17. Communication system modeling

    NASA Technical Reports Server (NTRS)

    Holland, L. D.; Walsh, J. R., Jr.; Wetherington, R. D.

    1971-01-01

    This report presents the results of work on communications systems modeling and covers three different areas of modeling. The first of these deals with the modeling of signals in communication systems in the frequency domain and the calculation of spectra for various modulations. These techniques are applied in determining the frequency spectra produced by a unified carrier system, the down-link portion of the Command and Communications System (CCS). The second modeling area covers the modeling of portions of a communication system on a block basis. A detailed analysis and modeling effort based on control theory is presented along with its application to modeling of the automatic frequency control system of an FM transmitter. A third topic discussed is a method for approximate modeling of stiff systems using state variable techniques.

  18. A Program for Calculating and Plotting Synthetic Common-Source Seismic-Reflection Traces for Multilayered Earth Models.

    ERIC Educational Resources Information Center

    Ramananantoandro, Ramanantsoa

    1988-01-01

    Presented is a description of a BASIC program to be used on an IBM microcomputer for calculating and plotting synthetic seismic-reflection traces for multilayered earth models. Discusses finding raypaths for given source-receiver offsets using the "shooting method" and calculating the corresponding travel times. (Author/CW)

  19. Synthetic receptors as models for alkali metal cation- binding sites in proteins

    NASA Astrophysics Data System (ADS)

    de Wall, Stephen L.; Meadows, Eric S.; Barbour, Leonard J.; Gokel, George W.

    2000-06-01

    The alkali metal cations Na+ and K+ have several important physiological roles, including modulating enzyme activity. Recent work has suggested that alkali metal cations may be coordinated by systems, such as the aromatic amino acid side chains. The ability of K+ to interact with an aromatic ring has been assessed by preparing a family of synthetic receptors that incorporate the aromatic side chains of phenylalanine, tyrosine, and tryptophan. Thesereceptors are constructed around a diaza-18-crown-6 scaffold, which serves as the primary binding site for an alkali metal cation. The ability of the aromatic rings to coordinate a cation was determined by crystallizing each of the receptors in the presence of K+ and by solving the solid state structures. In all cases, complexation of K+ by the pi system was observed. When possible, the structures of the unbound receptors also were determined for comparison. Further proof that the aromatic ring makes an energetically favorable interaction with the cation was obtained by preparing a receptor in which the arene was perfluorinated. Fluorination of the arene reverses the electrostatics, but the aromaticity is maintained. The fluorinated arene rings do not coordinate the cation in the solid state structure of the K+ complex. Thus, the results of the predicted electrostatic reversal were confirmed. Finally, the biological implications of the alkali metal cation-pi interaction are addressed.

  20. MineSeis -- A MATLAB GUI program to calculate synthetic seismograms from a linear, multi-shot blast source model

    SciTech Connect

    Yang, X.

    1998-12-31

    Modeling ground motions from multi-shot, delay-fired mining blasts is important to the understanding of their source characteristics such as spectrum modulation. MineSeis is a MATLAB{reg_sign} (a computer language) Graphical User Interface (GUI) program developed for the effective modeling of these multi-shot mining explosions. The program provides a convenient and interactive tool for modeling studies. Multi-shot, delay-fired mining blasts are modeled as the time-delayed linear superposition of identical single shot sources in the program. These single shots are in turn modeled as the combination of an isotropic explosion source and a spall source. Mueller and Murphy`s (1971) model for underground nuclear explosions is used as the explosion source model. A modification of Anandakrishnan et al.`s (1997) spall model is developed as the spall source model. Delays both due to the delay-firing and due to the single-shot location differences are taken into account in calculating the time delays of the superposition. Both synthetic and observed single-shot seismograms can be used to construct the superpositions. The program uses MATLAB GUI for input and output to facilitate user interaction with the program. With user provided source and path parameters, the program calculates and displays the source time functions, the single shot synthetic seismograms and the superimposed synthetic seismograms. In addition, the program provides tools so that the user can manipulate the results, such as filtering, zooming and creating hard copies.

  1. Novel bio-synthetic hybrid materials and coculture systems for musculoskeletal tissue engineering

    NASA Astrophysics Data System (ADS)

    Lee, Hyeseung Janice

    Tissue Engineering is a truly exciting field of this age, trying to regenerate and repair impaired tissues. Unlike the old artificial implants, tissue engineering aims at making a long-term functional biological replacement. One strategy for such tissue engineering requires the following three components: cells, scaffolds, and soluble factors. Cells are cultured in a three-dimensional (3D) scaffold with medium containing various soluble factors. Once a tissue is developed in vitro, then it is implanted in vivo. The overall goal of this thesis was to develop novel bio-synthetic hybrid scaffolds and coculture system for musculoskeletal tissue engineering. The most abundant cartilage extracellular matrix (ECM) components are collagen and glycosaminoglycan (GAG), which are the natural scaffold for chondrocytes. As two different peptides, collagen mimetic peptide (CMP) and hyaluronic acid binding peptide (HABPep) were previously shown to bind to collagen and hyaluronic acid (HA) of GAG, respectively, it was hypothesized that immobilizing CMP and HABP on 3D scaffold would results in an interaction between ECM components and synthetic scaffolds via peptide-ECM bindings. CMP or HABPep-conjugated photopolymerizable poly(ethylene oxide) diacrylate (PEODA) hydrogels were synthesized and shown to retain encapsulated collagen or HA, respectively. This result supported that conjugated CMP and HABPep can interact with collagen and HA, respectively, and can serve as biological linkers in 3D synthetic hydrogels. When chondrocytes or mesenchymal stem cells (MSCs) were seeded, cells in CMP-conjugated scaffolds produced significantly more amount of type II collagen and GAG, compared to those in control scaffolds. Moreover, MSCs cultured in CMP-conjugated scaffolds exhibited lower level of hypertrophic markers, cbfa-1 and type X collagen. These results demonstrated that enhanced interaction between collagen and scaffold via CMP improves chondrogenesis of chondrocytes and MSCs and

  2. Detection of aquifer system compaction and land subsidence using interferometric synthetic aperture radar, Antelope Valley, Mojave Desert, California

    USGS Publications Warehouse

    Galloway, D.L.; Hudnut, K.W.; Ingebritsen, S.E.; Phillips, S.P.; Peltzer, G.; Rogez, F.; Rosen, P.A.

    1998-01-01

    Interferometric synthetic aperture radar (InSAR) has great potential to detect and quantify land subsidence caused by aquifer system compaction. InSAR maps with high spatial detail and resolution of range displacement (??10 mm in change of land surface elevation) were developed for a groundwater basin (~103 km2) in Antelope Valley, California, using radar data collected from the ERS-1 satellite. These data allow comprehensive comparison between recent (1993-1995) subsidence patterns and those detected historically (1926-1992) by more traditional methods. The changed subsidence patterns are generally compatible with recent shifts in land and water use. The InSAR-detected patterns are generally consistent with predictions based on a coupled model of groundwater flow and aquifer system compaction. The minor inconsistencies may reflect our imperfect knowledge of the distribution and properties of compressible sediments. When used in conjunction with coincident measurements of groundwater levels and other geologic information, InSAR data may be useful for constraining parameter estimates in simulations of aquifer system compaction.

  3. Synthetic Output by Simulation. An Introductory Paper.

    ERIC Educational Resources Information Center

    Mason, Thomas R.

    Simulation is the process of synthetically manipulating the variables in a model of a system for the purpose of understanding, experimenting with, and predicting the behavior of that system. Many different models are now being developed by university administrators to aid them in making decisions. Simulation models have been developed for…

  4. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

    PubMed Central

    He, Fei; Murabito, Ettore; Westerhoff, Hans V.

    2016-01-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways. PMID:27075000

  5. Concept of Operations for Commercial and Business Aircraft Synthetic Vision Systems. 1.0

    NASA Technical Reports Server (NTRS)

    Williams Daniel M.; Waller, Marvin C.; Koelling, John H.; Burdette, Daniel W.; Capron, William R.; Barry, John S.; Gifford, Richard B.; Doyle, Thomas M.

    2001-01-01

    A concept of operations (CONOPS) for the Commercial and Business (CaB) aircraft synthetic vision systems (SVS) is described. The CaB SVS is expected to provide increased safety and operational benefits in normal and low visibility conditions. Providing operational benefits will promote SVS implementation in the Net, improve aviation safety, and assist in meeting the national aviation safety goal. SVS will enhance safety and enable consistent gate-to-gate aircraft operations in normal and low visibility conditions. The goal for developing SVS is to support operational minima as low as Category 3b in a variety of environments. For departure and ground operations, the SVS goal is to enable operations with a runway visual range of 300 feet. The system is an integrated display concept that provides a virtual visual environment. The SVS virtual visual environment is composed of three components: an enhanced intuitive view of the flight environment, hazard and obstacle defection and display, and precision navigation guidance. The virtual visual environment will support enhanced operations procedures during all phases of flight - ground operations, departure, en route, and arrival. The applications selected for emphasis in this document include low visibility departures and arrivals including parallel runway operations, and low visibility airport surface operations. These particular applications were selected because of significant potential benefits afforded by SVS.

  6. Dynamic Tunnel Usability Study: Format Recommendations for Synthetic Vision System Primary Flight Displays

    NASA Technical Reports Server (NTRS)

    Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Kramer, Lynda J.; Bailey, Randall E.

    2006-01-01

    A usability study evaluating dynamic tunnel concepts has been completed under the Aviation Safety and Security Program, Synthetic Vision Systems Project. The usability study was conducted in the Visual Imaging Simulator for Transport Aircraft Systems (VISTAS) III simulator in the form of questionnaires and pilot-in-the-loop simulation sessions. Twelve commercial pilots participated in the study to determine their preferences via paired comparisons and subjective rankings regarding the color, line thickness and sensitivity of the dynamic tunnel. The results of the study showed that color was not significant in pilot preference paired comparisons or in pilot rankings. Line thickness was significant for both pilot preference paired comparisons and in pilot rankings. The preferred line/halo thickness combination was a line width of 3 pixels and a halo of 4 pixels. Finally, pilots were asked their preference for the current dynamic tunnel compared to a less sensitive dynamic tunnel. The current dynamic tunnel constantly gives feedback to the pilot with regard to path error while the less sensitive tunnel only changes as the path error approaches the edges of the tunnel. The tunnel sensitivity comparison results were not statistically significant.

  7. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering.

    PubMed

    He, Fei; Murabito, Ettore; Westerhoff, Hans V

    2016-04-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways.

  8. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering.

    PubMed

    He, Fei; Murabito, Ettore; Westerhoff, Hans V

    2016-04-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways. PMID:27075000

  9. Predicting the performance of system for the co-production of Fischer-Tropsch synthetic liquid and power from coal

    SciTech Connect

    Wang, X.; Xiao, Y.; Xu, S.; Guo, Z.

    2008-01-15

    A co-production system based on Fischer-Tropsch (FT) synthesis reactor and gas turbine was simulated and analyzed. Syngas from entrained bed coal gasification was used as feedstock of the low-temperature slurry phase Fischer-Tropsch reactor. Raw synthetic liquid produced was fractioned and upgraded to diesel, gasoline, and liquid petrol gas (LPG). Tail gas composed of unconverted syngas and FT light components was fed to the gas turbine. Supplemental fuel (NG, or refinery mine gas) might be necessary, which was dependent on gas turbine capacity expander through flow capacity, etc. FT yield information was important to the simulation of this co-production system. A correlation model based on Mobil's two step pilot plant was applied. User models that can predict product yields and cooperate with other units were embedded into Aspen plus simulation. Performance prediction of syngas fired gas turbine was the other key of this system. The increase in mass flow through the turbine affects the match between compressor and turbine operating conditions. The calculation was carried out by GS software developed by Politecnico Di Milano and Princeton University. Various cases were investigated to match the FT synthesis island, power island, and gasification island in co-production systems. Effects of CO{sub 2} removal/LPG recovery, co-firing, and CH{sub 4} content variation were studied. Simulation results indicated that more than 50% of input energy was converted to electricity and FT products. Total yield of gasoline, diesel, and LPG was 136-155 g/N m{sup 3} (CO+H{sub 2}). At coal feed of 21.9 kg/s, net electricity exported to the grid was higher than 100 MW. Total production of diesel and gasoline (and LPG) was 118,000 t (134,000 t)/year. Under the economic analysis conditions assumed in this paper the co-production system was economically feasible.

  10. Mathematical circulatory system model

    NASA Technical Reports Server (NTRS)

    Lakin, William D. (Inventor); Stevens, Scott A. (Inventor)

    2010-01-01

    A system and method of modeling a circulatory system including a regulatory mechanism parameter. In one embodiment, a regulatory mechanism parameter in a lumped parameter model is represented as a logistic function. In another embodiment, the circulatory system model includes a compliant vessel, the model having a parameter representing a change in pressure due to contraction of smooth muscles of a wall of the vessel.

  11. Multidimensional Signal Processing Techniques for Disturbance Mitigation in Synthetic Aperture Systems

    NASA Astrophysics Data System (ADS)

    Edussooriya, Chamira Udaya Shantha

    In this thesis, multidimensional signal processing techniques to mitigate disturbances in synthetic aperture systems such as radio telescopes are investigated. Here, two computationally efficient three-dimensional (3D) spatio-temporal (ST) finite impulse response (FIR) cone filter bank structures are proposed. Furthermore, a strategy is proposed to design 3D ST FIR frustum filter banks, having double-frustum-shaped passbands oriented along the temporal axis, derived from appropriate 3D ST FIR cone filter banks. Both types of cone and frustum filter banks are almost alias free and provide near-perfect reconstruction. In the proposed cone and frustum filter banks, both temporal and spatial filtering operations can be carried out at a significantly lower rate compared to previously reported 3D ST FIR cone filter banks implying lower power consumption. Furthermore, the proposed cone and frustum filter banks require a significantly lower computational complexity than previously reported 3D ST FIR cone and frustum filter banks. Importantly, this is achieved without deteriorating the improvement in signal-to-interference-plus-noise ratio. A theoretical analysis of brightness distribution (BD) errors caused by parameter perturbations and mismatches among the transfer functions of receivers employed in synthetic aperture systems is presented. First, the BD errors caused by perturbations in the transfer functions of low noise amplifiers (LNAs) and anti-aliasing filters (AAFs) are considered, and the characteristics of the additive BD error and its effects on synthesized BDs are thoroughly analyzed. Second, the conditions that should be satisfied by the transfer functions of digital beamformers to eliminate the BD errors caused by their phase responses are examined. The sufficient condition to eliminate the BD errors is that the transfer functions are matched, and, interestingly, the phase responses are not necessary to be linear. Furthermore, the BD errors caused by typical

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

    PubMed

    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.

  13. Deep source model for Nevado del Ruiz Volcano, Colombia, constrained by interferometric synthetic aperture radar observations

    NASA Astrophysics Data System (ADS)

    Lundgren, P.; Samsonov, S. V.; López, C. M.; Ordoñez, M.

    2015-12-01

    Nevado del Ruiz (NRV) is part of a large volcano complex in the northern Andes of Colombia with a large glacier that erupted in 1985, generating a lahar killing over 23,000 people in the city of Armero and 2,000 people in the town of Chinchina. NRV is the most active volcano in Colombia and since 2012 has generated small eruptions, with no casualties, and constant gas and ash emissions. Interferometric synthetic aperture radar (InSAR) observations from ascending and descending track RADARSAT-2 data show a large (>20 km) wide inflation pattern apparently starting in late 2011 to early 2012 and continuing to the time of this study in early 2015 at a LOS rate of over 3-4 cm/yr (Fig. 1). Volcano pressure volume models for both a point source (Mogi) and a spheroidal (Yang) source find solutions over 14 km beneath the surface, or 10 km below sea level, and centered 10 km to the SW of Nevado del Ruiz volcano. The spheroidal source has a roughly horizontal long axis oriented parallel to the Santa Isabel - Nevado del Ruiz volcanic line and perpendicular to the ambient compressive stress direction. Its solution provides a statistically significant improvement in fit compared to the point source, though consideration of spatially correlated noise sources may diminish this significance. Stress change computations do not favor one model over the other but show that propagating dikes would become trapped in sills, leading to a more complex pathway to the surface and possibly explaining the significant lateral distance between the modeled sources and Nevado del Ruiz volcano.

  14. Modular Modeling System Model Builder

    SciTech Connect

    McKim, C.S.; Matthews, M.T.

    1996-12-31

    The latest release of the Modular Modeling System (MMS) Model Builder adds still more time-saving features to an already powerful MMS dynamic-simulation tool set. The Model Builder takes advantage of 32-bit architecture within the Microsoft Windows 95/NT{trademark} Operating Systems to better integrate a mature library of power-plant components. In addition, the MMS Library of components can now be modified and extended with a new tool named MMS CompGen{trademark}. The MMS Model Builder allows the user to quickly build a graphical schematic representation for a plant by selecting from a library of predefined power plant components to dynamically simulate their operation. In addition, each component has a calculation subroutine stored in a dynamic-link library (DLL), which facilitates the determination of a steady-state condition and performance of routine calculations for the component. These calculations, termed auto-parameterization, help avoid repetitive and often tedious hand calculations for model initialization. In striving to meet the needs for large models and increase user productivity, the MMS Model Builder has been completely revamped to make power plant model creation and maintainability easier and more efficient.

  15. Synthetic photometry for M and K giants and stellar evolution: hydrostatic dust-free model atmospheres and chemical abundances

    NASA Astrophysics Data System (ADS)

    Aringer, B.; Girardi, L.; Nowotny, W.; Marigo, P.; Bressan, A.

    2016-04-01

    Based on a grid of hydrostatic spherical COMARCS models for cool stars, we have calculated observable properties of these objects, which will be mainly used in combination with stellar evolution tracks and population synthesis tools. The high-resolution opacity sampling and low-resolution convolved spectra as well as bolometric corrections for a large number of filter systems are made electronically available. We exploit those data to study the effect of mass, C/O ratio and nitrogen abundance on the photometry of K and M giants. Depending on effective temperature, surface gravity and the chosen wavelength ranges, variations of the investigated parameters cause very weak to moderate and, in the case of C/O values close to 1, even strong shifts of the colours. For the usage with stellar evolution calculations, they will be treated as correction factors applied to the results of an interpolation in the main quantities. When we compare the synthetic photometry to observed relations and to data from the Galactic bulge, we find in general a good agreement. Deviations appear for the coolest giants showing pulsations, mass-loss and dust shells, which cannot be described by hydrostatic models.

  16. Performance modeling of nonconcentrating solar detoxification systems

    SciTech Connect

    March, M.; Martin, A.; Saltiel, C.

    1995-03-01

    A detailed simulation model is developed for predicting the performance of solar detoxification systems. Concentration profiles are determined via a method of lines approach during sunlight hours for acquired and synthetic (simulating clear and cloudy days) ultraviolet radiation intensity data. Verification of the model is performed with comparison against indoor laboratory and outdoor field test results. Simulations are performed over a range of design parameters to examine system sensitivity. Discussions are focused on the determination of optimal sizing and operating conditions. 17 refs., 8 figs.

  17. Experimental phase densities and interfacial tensions for a CO[sub 2]/synthetic-oil and a CO[sub 2]/reservoir-oil system

    SciTech Connect

    Gasem, K.A.M.; Dickson, K.B.; Shaver, R.D.; Robinson, R.L. Jr. )

    1993-08-01

    Experimental data are presented for equilibrium vapor and liquid densities and interfacial tensions (IFT's) for two multi-component mixtures. Data are presented at 120 and 150 F for a CO[sub 2]/synthetic-oil (containing the n-paraffins, methane to tetradecane) and at 130 F for a CO[sub 2]/recombined-reservoir-oil system. In both systems, measurements include the near-critical region, where IFT's become very low. These data should be useful in developing and testing models to predict phase behavior and IFT's for CO[sub 2] EOR operations.

  18. Optimal waveform-based clutter suppression algorithm for recursive synthetic aperture radar imaging systems

    NASA Astrophysics Data System (ADS)

    Zhu, Binqi; Gao, Yesheng; Wang, Kaizhi; Liu, Xingzhao

    2016-04-01

    A computational method for suppressing clutter and generating clear microwave images of targets is proposed in this paper, which combines synthetic aperture radar (SAR) principles with recursive method and waveform design theory, and it is suitable for SAR for special applications. The nonlinear recursive model is introduced into the SAR operation principle, and the cubature Kalman filter algorithm is used to estimate target and clutter responses in each azimuth position based on their previous states, which are both assumed to be Gaussian distributions. NP criteria-based optimal waveforms are designed repeatedly as the sensor flies along its azimuth path and are used as the transmitting signals. A clutter suppression filter is then designed and added to suppress the clutter response while maintaining most of the target response. Thus, with fewer disturbances from the clutter response, we can generate the SAR image with traditional azimuth matched filters. Our simulations show that the clutter suppression filter significantly reduces the clutter response, and our algorithm greatly improves the SINR of the SAR image based on different clutter suppression filter parameters. As such, this algorithm may be preferable for special target imaging when prior information on the target is available.

  19. Synthetic biology in plastids.

    PubMed

    Scharff, Lars B; Bock, Ralph

    2014-06-01

    Plastids (chloroplasts) harbor a small gene-dense genome that is amenable to genetic manipulation by transformation. During 1 billion years of evolution from the cyanobacterial endosymbiont to present-day chloroplasts, the plastid genome has undergone a dramatic size reduction, mainly as a result of gene losses and the large-scale transfer of genes to the nuclear genome. Thus the plastid genome can be regarded as a naturally evolved miniature genome, the gradual size reduction and compaction of which has provided a blueprint for the design of minimum genomes. Furthermore, because of the largely prokaryotic genome structure and gene expression machinery, the high transgene expression levels attainable in transgenic chloroplasts and the very low production costs in plant systems, the chloroplast lends itself to synthetic biology applications that are directed towards the efficient synthesis of green chemicals, biopharmaceuticals and other metabolites of commercial interest. This review describes recent progress with the engineering of plastid genomes with large constructs of foreign or synthetic DNA, and highlights the potential of the chloroplast as a model system in bottom-up and top-down synthetic biology approaches.

  20. Mimicry of the radical pair and triplet states in photosynthetic reaction centers with a synthetic model

    SciTech Connect

    Wasielewski, M.R.; Greenfield, S.R.; Svec, W.A.

    1997-08-01

    Results are presented on a photosynthetic model system that closely mimics the spin dynamics of triplet state formation found in photosynthetic reaction centers. This research will make it possible to design new models to probe the mechanism of the primary events of photosynthesis.

  1. Synthetic vision systems: the effects of guidance symbology, display size, and field of view.

    PubMed

    Alexander, Amy L; Wickens, Christopher D; Hardy, Thomas J

    2005-01-01

    Two experiments conducted in a high-fidelity flight simulator examined the effects of guidance symbology, display size, and geometric field of view (GFOV) within a synthetic vision system (SVS). In Experiment 1, 18 pilots flew highlighted and low-lighted tunnel-in-the-sky displays, as well as a less cluttered follow-me aircraft (FMA), through a series of curved approaches over rugged terrain. The results revealed that both tunnels supported better flight path tracking and lower workload levels than did the FMA because of the availability of more preview information. Increasing tunnel intensity had no benefit on tracking and, in fact, degraded traffic awareness because of clutter and attentional tunneling. In Experiment 2, 24 pilots flew a lowlighted tunnel configured according to different display sizes (small or large) and GFOVs (30 degrees or 60 degrees). Measures of flight path tracking and terrain awareness generally favored the 60 degrees GFOV; however, there were no effects of display size. Actual or potential applications of this research include understanding the impact of SVS properties on flight path tracking, traffic and terrain awareness, workload, and the allocation of attention. PMID:16553060

  2. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    DOEpatents

    Craig, George D.; Glass, Robert; Rupp, Bernhard

    1997-01-01

    A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

  3. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    DOEpatents

    Craig, G.D.; Glass, R.; Rupp, B.

    1997-01-28

    A method is disclosed for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10{sup 6}V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved. 2 figs.

  4. Synthetic double-stranded RNA enhances airway inflammation and remodelling in a rat model of asthma.

    PubMed

    Takayama, Satoshi; Tamaoka, Meiyo; Takayama, Koji; Okayasu, Kaori; Tsuchiya, Kimitake; Miyazaki, Yasunari; Sumi, Yuki; Martin, James G; Inase, Naohiko

    2011-10-01

    Respiratory viral infections are frequently associated with exacerbations of asthma. Double-stranded RNA (dsRNA) produced during viral infections may be one of the stimuli for exacerbation. We aimed to assess the potential effect of dsRNA on certain aspects of chronic asthma through the administration of polyinosine-polycytidylic acid (poly I:C), synthetic dsRNA, to a rat model of asthma. Brown Norway rats were sensitized to ovalbumin and challenged three times to evoke airway remodelling. The effect of poly I:C on the ovalbumin-induced airway inflammation and structural changes was assessed from bronchoalveolar lavage fluid and histological findings. The expression of cytokines and chemokines was evaluated by real-time quantitative reverse transcription PCR and ELISA. Ovalbumin-challenged animals showed an increased number of total cells and eosinophils in bronchoalveolar lavage fluid compared with PBS-challenged controls. Ovalbumin-challenged animals treated with poly I:C showed an increased number of total cells and neutrophils in bronchoalveolar lavage fluid compared with those without poly I:C treatment. Ovalbumin-challenged animals showed goblet cell hyperplasia, increased airway smooth muscle mass, and proliferation of both airway epithelial cells and airway smooth muscle cells. Treatment with poly I:C enhanced these structural changes. Among the cytokines and chemokines examined, the expression of interleukins 12 and 17 and of transforming growth factor-β(1) in ovalbumin-challenged animals treated with poly I:C was significantly increased compared with those of the other groups. Double-stranded RNA enhanced airway inflammation and remodelling in a rat model of bronchial asthma. These observations suggest that viral infections may promote airway remodelling.

  5. Modeling of geothermal systems

    SciTech Connect

    Bodvarsson, G.S.; Pruess, K.; Lippmann, M.J.

    1985-03-01

    During the last decade the use of numerical modeling for geothermal resource evaluation has grown significantly, and new modeling approaches have been developed. In this paper we present a summary of the present status in numerical modeling of geothermal systems, emphasizing recent developments. Different modeling approaches are described and their applicability discussed. The various modeling tasks, including natural-state, exploitation, injection, multi-component and subsidence modeling, are illustrated with geothermal field examples. 99 refs., 14 figs.

  6. BINARY STAR SYNTHETIC PHOTOMETRY AND DISTANCE DETERMINATION USING BINSYN

    SciTech Connect

    Linnell, Albert P.; DeStefano, Paul; Hubeny, Ivan E-mail: pdestefa@uw.edu

    2013-09-15

    This paper extends synthetic photometry to components of binary star systems. The paper demonstrates accurate recovery of single star photometric properties for four photometric standards, Vega, Sirius, GD153, and HD209458, ranging over the HR diagram, when their model synthetic spectra are placed in fictitious binary systems and subjected to synthetic photometry processing. Techniques for photometric distance determination have been validated for all four photometric standards.

  7. Binary Star Synthetic Photometry and Distance Determination Using BINSYN

    NASA Astrophysics Data System (ADS)

    Linnell, Albert P.; DeStefano, Paul; Hubeny, Ivan

    2013-09-01

    This paper extends synthetic photometry to components of binary star systems. The paper demonstrates accurate recovery of single star photometric properties for four photometric standards, Vega, Sirius, GD153, and HD209458, ranging over the HR diagram, when their model synthetic spectra are placed in fictitious binary systems and subjected to synthetic photometry processing. Techniques for photometric distance determination have been validated for all four photometric standards.

  8. System Advisor Model

    2010-03-01

    The System Advisor Model (SAM) is a performance and economic model designed to facilitate decision making for people involved in the renewable energy industry, ranging from project managers and engineers to incentive program designers, technology developers, and researchers.

  9. Multiple-input multiple-output synthetic aperture ladar system for wide-range swath with high azimuth resolution.

    PubMed

    Tang, Yu; Qin, Bao; Yan, Yun; Xing, Mengdao

    2016-02-20

    For the trade-off between the high azimuth resolution and the wide-range swath in the single-input single-output synthetic aperture ladar (SAL) system, the range swath of the SAL system is restricted to a narrow range, this paper proposes a multiple-input multiple-output (MIMO) synthetic aperture ladar system. The MIMO system adopts a low pulse repetition frequency (PRF) to avoid a range ambiguity for the wide-range swath and in azimuth adopts the multi-channel method to achieve azimuth high resolution from the unambiguous azimuth wide-spectrum signal, processed through adaptive digital beam-forming technology. Simulations and analytical results are presented.

  10. Bergman Clusters, Multiple Bonds, and Defect Planes: Synthetic Outcomes of Chemical Frustration in Ternary Intermetallic Systems

    NASA Astrophysics Data System (ADS)

    Hadler, Amelia Beth

    Intermetallics crystallize in a variety of complex structures, many of which show unusual bonding or intriguing properties. Understanding what factors drive this structural chemistry would be a valuable step towards designing new intermetallics with specific structures or properties. One pathway towards understanding and predicting the structures of complex intermetallics is chemical frustration, a design tool which harnesses competition between incompatible bonding or packing modes to induce complexity in ternary intermetallic systems. The research outlined in this thesis focuses on developing chemical frustration through exploratory synthesis in ternary systems designed to induce frustration between the tetrahedral close packing of many intermetallics and the simple cubic packing seen for ionic salts or elemental metals. Syntheses in three systems yielded six new ternary intermetallics, four of which crystallize in novel structure types. Three were discovered in the Ca-Cu-Cd system: Ca5Cu2Cd and Ca2Cu 2Cd9, which adopt ternary variants of binary structures, and Ca10Cu2Cd27, which crystallizes in a new structure built from Bergman clusters. All three structures can be traced to electronic packing frustration induced by the similar electronegativities but different metallic radii of Cu and Cd. The Gd-Fe-C system yielded the new carbometalate Gd13Fe 10C13 and an oxycarbide derivative. These phases crystallize in structures built from Gd tricapped trigonal prisms interpenetrated by an Fe-C network. Theoretical analyses reveal that Fe-Fe and Fe-C multiple bonding is found throughout this network. A theoretical investigation of similar carbides uncovers additional metal-metal, metal-carbon, and carbon-carbon multiple bonding. This unusual bonding stabilizes the carbides by satisfying preferred electron counts for their transition metal sites. One new phase, Mg4.5Pd5Ge1.5, was found in the Mg-Pd-Ge system. Its structure is closely related to the CsCl-type structure of

  11. DOUBLE-DETONATION SUB-CHANDRASEKHAR SUPERNOVAE: SYNTHETIC OBSERVABLES FOR MINIMUM HELIUM SHELL MASS MODELS

    SciTech Connect

    Kromer, M.; Sim, S. A.; Fink, M.; Roepke, F. K.; Seitenzahl, I. R.; Hillebrandt, W.

    2010-08-20

    In the double-detonation scenario for Type Ia supernovae, it is suggested that a detonation initiates in a shell of helium-rich material accreted from a companion star by a sub-Chandrasekhar-mass white dwarf. This shell detonation drives a shock front into the carbon-oxygen white dwarf that triggers a secondary detonation in the core. The core detonation results in a complete disruption of the white dwarf. Earlier studies concluded that this scenario has difficulties in accounting for the observed properties of Type Ia supernovae since the explosion ejecta are surrounded by the products of explosive helium burning in the shell. Recently, however, it was proposed that detonations might be possible for much less massive helium shells than previously assumed (Bildsten et al.). Moreover, it was shown that even detonations of these minimum helium shell masses robustly trigger detonations of the carbon-oxygen core (Fink et al.). Therefore, it is possible that the impact of the helium layer on observables is less than previously thought. Here, we present time-dependent multi-wavelength radiative transfer calculations for models with minimum helium shell mass and derive synthetic observables for both the optical and {gamma}-ray spectral regions. These differ strongly from those found in earlier simulations of sub-Chandrasekhar-mass explosions in which more massive helium shells were considered. Our models predict light curves that cover both the range of brightnesses and the rise and decline times of observed Type Ia supernovae. However, their colors and spectra do not match the observations. In particular, their B - V colors are generally too red. We show that this discrepancy is mainly due to the composition of the burning products of the helium shell of the Fink et al. models which contain significant amounts of titanium and chromium. Using a toy model, we also show that the burning products of the helium shell depend crucially on its initial composition. This leads us

  12. The Synthetic Parasite-Derived Peptide GK1 Increases Survival in a Preclinical Mouse Melanoma Model

    PubMed Central

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

    2013-01-01

    Abstract Purpose 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. Experimental Design C57BL/6 mice were injected subcutaneously in the flank with 2×105 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). Results 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 (p<0.05) in the treated mice. The overall survival rates obtained with surgical treatment at 6 months were 83.33% for group A, 40% for group B, and 0% for group C, with significant differences (p<0.05) among the groups. Conclusions The GK1 peptide demonstrated therapeutic properties in a mouse melanoma model, as treatment resulted in a significant increase in the mean survival time of the treated animals (42.58%). The potential for GK1 to be used as a primary or adjuvant component of chemotherapeutic cocktails for the treatment of experimental and human cancers remains to be determined, and surgical removal remains a challenge for any new experimental treatment of melanoma in mouse models. PMID:23841709

  13. Numerical validation of a synthetic cell-based model of blood coagulation.

    PubMed

    Pavlova, J; Fasano, A; Janela, J; Sequeira, A

    2015-09-01

    In Fasano et al. (2012) a new reduced mathematical model for blood coagulation was proposed, incorporating biochemical and mechanical actions of blood flow and including platelets activity. The model was characterized by a considerable simplification of the differential system associated to the biochemical network and it incorporated the role of blood slip at the vessel wall as an extra source of activated platelets. The purpose of this work is to check the validity of the reduced mathematical model, using as a benchmark the model presented in Anand et al. (2008), and to investigate the importance of the blood slip velocity in the blood coagulation process.

  14. Hybrid Energy System Modeling in Modelica

    SciTech Connect

    William R. Binder; Christiaan J. J. Paredis; Humberto E. Garcia

    2014-03-01

    In this paper, a Hybrid Energy System (HES) configuration is modeled in Modelica. Hybrid Energy Systems (HES) have as their defining characteristic the use of one or more energy inputs, combined with the potential for multiple energy outputs. Compared to traditional energy systems, HES provide additional operational flexibility so that high variability in both energy production and consumption levels can be absorbed more effectively. This is particularly important when including renewable energy sources, whose output levels are inherently variable, determined by nature. The specific HES configuration modeled in this paper include two energy inputs: a nuclear plant, and a series of wind turbines. In addition, the system produces two energy outputs: electricity and synthetic fuel. The models are verified through simulations of the individual components, and the system as a whole. The simulations are performed for a range of component sizes, operating conditions, and control schemes.

  15. Short-Period Normal-mode Synthetics and Fr{é}chet kernels for Spherically Symmetric Earth Models

    NASA Astrophysics Data System (ADS)

    Yang, H.; Zhao, L.; Hung, S.

    2007-12-01

    Determination of three dimensional multiscale Earth structures requires high-quality seismic data and accurate synthetic waveforms. To extract and interpret the full waveform information from widely available broadband data, we need to be able to calculate complete broadband synthetic seismograms. Normal-mode theory provides the exact solutions to the wave equation in spherically symmetric Earth models, and the efficiency afforded by the usage of precalculated eigenfunction databases makes normal-mode summation the preferred approach for calculating long-period synthetic seismograms in 1-D reference models. In this study, we extend the normal-mode summation to short period by attacking the problems encountered in computing normal-mode eigenfrequencies and eigenfunctions at higher frequencies. Flexible radial sampling scheme based on the WKBJ approximation is adopted to ensure the accuracy of the secular equation when the radial eigenfunctions are highly oscillatory. This allows us to compute accurate normal-mode eigenfunctions up to much higher frequencies (~ 1Hz for Spheroidal and ~ 2Hz for Toroidal modes). Although errors can still be large for certain modes, they are almost all inner-core shear modes, and numerical experiments show that they have no contribution to seismograms on the surface. In contrast, omitting only 0.1% mantle modes at random can lead to noisy synthetics. The capability to compute normal modes up to high frequencies enables us to obtain accurate and complete synthetic seismograms that can be used to both extract waveform information from all seismic phases and to compute their full-wave Fr{é}chet kernels, which opens up possibilities in global and regional high-resolution tomography as well as studies on the seismic structure in the deep mantle and the inner core.

  16. Synthetic Active Site Model of the [NiFeSe] Hydrogenase

    PubMed Central

    Wombwell, Claire; Reisner, Erwin

    2015-01-01

    A dinuclear synthetic model of the [NiFeSe] hydrogenase active site and a structural, spectroscopic and electrochemical analysis of this complex is reported. [NiFe(‘S2Se2’)(CO)3] (H2‘S2Se2’=1,2-bis(2-thiabutyl-3,3-dimethyl-4-selenol)benzene) has been synthesized by reacting the nickel selenolate complex [Ni(‘S2Se2’)] with [Fe(CO)3bda] (bda=benzylideneacetone). X-ray crystal structure analysis confirms that [NiFe(‘S2Se2’)(CO)3] mimics the key structural features of the enzyme active site, including a doubly bridged heterobimetallic nickel and iron center with a selenolate terminally coordinated to the nickel center. Comparison of [NiFe(‘S2Se2’)(CO)3] with the previously reported thiolate analogue [NiFe(‘S4’)(CO)3] (H2‘S4’=H2xbsms=1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) showed that the selenolate groups in [NiFe(‘S2Se2’)(CO)3] give lower carbonyl stretching frequencies in the IR spectrum. Electrochemical studies of [NiFe(‘S2Se2’)(CO)3] and [NiFe(‘S4’)(CO)3] demonstrated that both complexes do not operate as homogenous H2 evolution catalysts, but are precursors to a solid deposit on an electrode surface for H2 evolution catalysis in organic and aqueous solution. PMID:25847470

  17. Synthetic cluster models of biological and heterogeneous manganese catalysts for O2 evolution.

    PubMed

    Tsui, Emily Y; Kanady, Jacob S; Agapie, Theodor

    2013-12-16

    Artificial photosynthesis has emerged as an important strategy toward clean and renewable fuels. Catalytic oxidation of water to O2 remains a significant challenge in this context. A mechanistic understanding of currently known heterogeneous and biological catalysts at a molecular level is highly desirable for fundamental reasons as well as for the rational design of practical catalysts. This Award Article discusses recent efforts in synthesizing structural models of the oxygen-evolving complex of photosystem II. These structural motifs are also related to heterogeneous mixed-metal oxide catalysts. A stepwise synthetic methodology was developed toward achieving the structural complexity of the targeted active sites. A geometrically restricted multinucleating ligand, but with labile coordination modes, was employed for the synthesis of low-oxidation-state trimetallic species. These precursors were elaborated to site-differentiated tetrametallic complexes in high oxidation states. This methodology has allowed for structure-reactivity studies that have offered insight into the effects of different components of the clusters. Mechanistic aspects of oxygen-atom transfer and incorporation from water have been interrogated. Significantly, a large and systematic effect of redox-inactive metals on the redox properties of these clusters was discovered. With the pKa value of the redox-inactive metal-aqua complex as a measure of the Lewis acidity, structurally analogous clusters display a linear dependence between the reduction potential and acidity; each pKa unit shifts the potential by ca. 90 mV. Implications for the function of the biological and heterogeneous catalysts are discussed. PMID:24328344

  18. Potentiometric titrations of five synthetic tetraacids as models for indigenous C80 tetraacids.

    PubMed

    Sundman, Ola; Nordgård, Erland L; Grimes, Brian; Sjöblom, Johan

    2010-02-01

    The acid/base properties, critical micelle concentrations (cmcs), and pH-dependent solubility of five synthetic tetraacids have been studied at several ionic strengths (20-600 mM NaCl) and in the pH range of 1.5-11 using high precision potentiometric titrations, tensiometer measurements, and UV spectroscopy, respectively. The molecular weight of the tetraacids ranged between 478 and 983 g/mol. The potentiometric titration data was evaluated in terms of thermodynamic equilibrium models, developed in the light of relevant solubility data, Langmuir monolayer compressions and cmc of the different tetraacids. The results indicate that for two of the tetraacids, called BP5 and BP7, two chemical forms fully dominate the speciation of the monomers; the insoluble fully protonated form, and the soluble fully deprotonated form. The partly protonated species, only play a very minor role in the speciation of these tetraacids. For the other tetraacids the results are more complicated; for the smallest tetraacid, called BP1, all species seem to play important roles, and for the most hydrophobic, BP10, the formation of micelles and aggregates severely complicates the evaluation of the speciation. For the tetraacid BP3 one of the partly deprotonated forms seems to be important, thus confirming the structure to properties relationship. In spite of the complicated micelle formation chemistry, and although not actually measured, the acid/base properties for the monomers of BP10 were interpreted by means of surface charge densities of the micellar aggregates. The modeling indicates an increase of the aggregation number of the micelle upon acidification, a result of formation of mixed micelles incorporating the fully protonated and deprotonated species. An intrinsic pK(a) of 5.4 for BP5 was used to model the monomer pK(a) of BP10, and corresponded well with a monolayer acidity constant pK(s)(a) of 5.5 obtained from surface collapse pressures of Langmuir monolayers as a function of pH.

  19. Small synthetic hyaluronan disaccharides afford neuroprotection in brain ischemia-related models.

    PubMed

    Egea, J; Parada, E; Gómez-Rangel, V; Buendia, I; Negredo, P; Montell, E; Ruhí, R; Vergés, J; Roda, J M; García, A G; López, M G

    2014-04-18

    High molecular weight (HMW) glycosaminoglycanes of the extracellular matrix have been implicated in tissue repair. The aim of this study was to evaluate if small synthetic hyaluronan disaccharides with different degrees of sulfation (methyl 2-acetamido-2-deoxy-3-O-(β-d-glucopyranosyluronic acid)-O-sulfo-α-d-glucopyranoside, sodium salt (di0S), methyl 2-acetamido-2-deoxy-3-O-(β-d-glucopyranosyluronic acid)-6-di-O-sulfo-α-d-glucopyranoside, disodium salt (di6S) and methyl 2-acetamido-2-deoxy-3-O-(β-d-glucopyranosyluronic acid)-4,6-di-O-sulfo-α-d-glucopyranoside, trisodium salt (di4,6S)) could improve cell survival in in vitro and in vivo brain ischemia-related models. Rat hippocampal slices subjected to oxygen and glucose deprivation and a photothrombotic stroke model in mice were used. The three hyaluran disaccharides, incubated during the oxygen and glucose deprivation (15min) and re-oxygenation periods (120min), reduced cell death of hippocampal slices measured as 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide reduction, being the most potent di4,6S; in contrast, high molecular hyaluronan was ineffective. The protective actions of di4,6S against oxygen and glucose deprivation were related to activation of the PI3K/Akt survival pathway, reduction of p65 translocation to the nucleus, inhibition of inducible nitric oxide oxidase induction and reactive oxygen species production, and to an increase in glutathione levels. Administered 1h post-stroke, di4,6S reduced cerebral infarct size and improved motor activity in the beam walk test. In conclusion, di4,6S affords neuroprotection in in vitro and in vivo models of ischemic neuronal damage. Our results suggest that its neuroprotective effect could be exerted through its capability to reduce oxidative stress during ischemia. Its small molecular size makes it a more potential druggable drug to target the brain as compared with its HMW parent compound hyaluronan. PMID:24486437

  20. Small synthetic hyaluronan disaccharides afford neuroprotection in brain ischemia-related models.

    PubMed

    Egea, J; Parada, E; Gómez-Rangel, V; Buendia, I; Negredo, P; Montell, E; Ruhí, R; Vergés, J; Roda, J M; García, A G; López, M G

    2014-04-18

    High molecular weight (HMW) glycosaminoglycanes of the extracellular matrix have been implicated in tissue repair. The aim of this study was to evaluate if small synthetic hyaluronan disaccharides with different degrees of sulfation (methyl 2-acetamido-2-deoxy-3-O-(β-d-glucopyranosyluronic acid)-O-sulfo-α-d-glucopyranoside, sodium salt (di0S), methyl 2-acetamido-2-deoxy-3-O-(β-d-glucopyranosyluronic acid)-6-di-O-sulfo-α-d-glucopyranoside, disodium salt (di6S) and methyl 2-acetamido-2-deoxy-3-O-(β-d-glucopyranosyluronic acid)-4,6-di-O-sulfo-α-d-glucopyranoside, trisodium salt (di4,6S)) could improve cell survival in in vitro and in vivo brain ischemia-related models. Rat hippocampal slices subjected to oxygen and glucose deprivation and a photothrombotic stroke model in mice were used. The three hyaluran disaccharides, incubated during the oxygen and glucose deprivation (15min) and re-oxygenation periods (120min), reduced cell death of hippocampal slices measured as 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide reduction, being the most potent di4,6S; in contrast, high molecular hyaluronan was ineffective. The protective actions of di4,6S against oxygen and glucose deprivation were related to activation of the PI3K/Akt survival pathway, reduction of p65 translocation to the nucleus, inhibition of inducible nitric oxide oxidase induction and reactive oxygen species production, and to an increase in glutathione levels. Administered 1h post-stroke, di4,6S reduced cerebral infarct size and improved motor activity in the beam walk test. In conclusion, di4,6S affords neuroprotection in in vitro and in vivo models of ischemic neuronal damage. Our results suggest that its neuroprotective effect could be exerted through its capability to reduce oxidative stress during ischemia. Its small molecular size makes it a more potential druggable drug to target the brain as compared with its HMW parent compound hyaluronan.

  1. MLS: Airplane system modeling

    NASA Technical Reports Server (NTRS)

    Thompson, A. D.; Stapleton, B. P.; Walen, D. B.; Rieder, P. F.; Moss, D. G.

    1981-01-01

    Analysis, modeling, and simulations were conducted as part of a multiyear investigation of the more important airplane-system-related items of the microwave landing system (MLS). Particular emphasis was placed upon the airplane RF system, including the antenna radiation distribution, the cabling options from the antenna to the receiver, and the overall impact of the airborne system gains and losses upon the direct-path signal structure. In addition, effort was expended toward determining the impact of the MLS upon the airplane flight management system and developing the initial stages of a fast-time MLS automatic control system simulation model. Results ot these studies are presented.

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

    NASA Astrophysics Data System (ADS)

    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.

  3. A comparison of spatial sampling techniques enabling first principles modeling of a synthetic aperture RADAR imaging platform

    NASA Astrophysics Data System (ADS)

    Gartley, Michael; Goodenough, Adam; Brown, Scott; Kauffman, Russel P.

    2010-04-01

    Simulation of synthetic aperture radar (SAR) imagery may be approached in many different ways. One method treats a scene as a radar cross section (RCS) map and simply evaluates the radar equation, convolved with a system impulse response to generate simulated SAR imagery. Another approach treats a scene as a series of primitive geometric shapes, for which a closed form solution for the RCS exists (such as boxes, spheres and cylinders), and sums their contribution at the antenna level by again solving the radar equation. We present a ray-tracing approach to SAR image simulation that treats a scene as a series of arbitrarily shaped facetized objects, each facet potentially having a unique radio frequency optical property and time-varying location and orientation. A particle based approach, as compared to a wave based approach, presents a challenge for maintaining coherency of sampled scene points between pulses that allows the reconstruction of an exploitable image from the modeled complex phase history. We present a series of spatial sampling techniques and their relative success at producing accurate phase history data for simulations of spotlight, stripmap and SAR-GMTI collection scenarios.

  4. A synthetic homing endonuclease-based gene drive system in the human malaria mosquito.

    PubMed

    Windbichler, Nikolai; Menichelli, Miriam; Papathanos, Philippos Aris; Thyme, Summer B; Li, Hui; Ulge, Umut Y; Hovde, Blake T; Baker, David; Monnat, Raymond J; Burt, Austin; Crisanti, Andrea

    2011-05-12

    Genetic methods of manipulating or eradicating disease vector populations have long been discussed as an attractive alternative to existing control measures because of their potential advantages in terms of effectiveness and species specificity. The development of genetically engineered malaria-resistant mosquitoes has shown, as a proof of principle, the possibility of targeting the mosquito's ability to serve as a disease vector. The translation of these achievements into control measures requires an effective technology to spread a genetic modification from laboratory mosquitoes to field populations. We have suggested previously that homing endonuclease genes (HEGs), a class of simple selfish genetic elements, could be exploited for this purpose. Here we demonstrate that a synthetic genetic element, consisting of mosquito regulatory regions and the homing endonuclease gene I-SceI, can substantially increase its transmission to the progeny in transgenic mosquitoes of the human malaria vector Anopheles gambiae. We show that the I-SceI element is able to invade receptive mosquito cage populations rapidly, validating mathematical models for the transmission dynamics of HEGs. Molecular analyses confirm that expression of I-SceI in the male germline induces high rates of site-specific chromosomal cleavage and gene conversion, which results in the gain of the I-SceI gene, and underlies the observed genetic drive. These findings demonstrate a new mechanism by which genetic control measures can be implemented. Our results also show in principle how sequence-specific genetic drive elements like HEGs could be used to take the step from the genetic engineering of individuals to the genetic engineering of populations.

  5. Prefiltering synthetic images for projection in hardware-in-the-loop systems

    NASA Astrophysics Data System (ADS)

    Flynn, David S.; Sieglinger, Breck A.; Coker, Charles F.

    1997-07-01

    A challenging problem associated with performing hardware- in-the-loop tests of imaging infrared seekers is projecting images that are spatially realistic. The problem is complicated by the fact that the targets may be small and unresolved at acquisition and grow to fill the field of view during the final guidance updates. Although characteristics of the projection system are usually thought of as determining the spatial realism, the imagery used to drive the projector is also important. For a pixelized projector, the driving imagery must be sampled at a rate determined by the sample spacing of the pixels in the projector. If the scenes contain important information that is small compared to the projector pixel spacing (that is, if they have important information at high spatial frequencies), then information may be lost in the sampling process if the images are not adequately bandlimited. This bandlimiting can be accomplished by prefiltering the scenes. At acquisition, targets are usually small; thus, prefiltering is necessary to preserve information about the target. Without such prefiltering, for example, infinitesimally small targets would never be seen unless they just happened to be at the exact location where the scene is sampled for a projector pixel. This paper reports the results of a study of various filters that might be used for prefiltering synthetic imagery generated to drive projectors in the KHILS facility. Projector and seeker characteristics typical of the KHILS facility were adopted for the study. Since the radiance produced by projectors is always positive, filters that can produce negative values were not considered. Figures of merit were defined based on the sensor-measured quantities such as radiant intensity, centroid, and spot size. The performance of prefilters of various shapes and sizes and for typical projector and seeker characteristics will be reported.

  6. Integrated Workforce Modeling System

    NASA Technical Reports Server (NTRS)

    Moynihan, Gary P.

    2000-01-01

    There are several computer-based systems, currently in various phases of development at KSC, which encompass some component, aspect, or function of workforce modeling. These systems may offer redundant capabilities and/or incompatible interfaces. A systems approach to workforce modeling is necessary in order to identify and better address user requirements. This research has consisted of two primary tasks. Task 1 provided an assessment of existing and proposed KSC workforce modeling systems for their functionality and applicability to the workforce planning function. Task 2 resulted in the development of a proof-of-concept design for a systems approach to workforce modeling. The model incorporates critical aspects of workforce planning, including hires, attrition, and employee development.

  7. Overembedding Method for Modeling Nonstationary Systems

    SciTech Connect

    Verdes, P.F.

    2006-03-24

    We propose a general overembedding method for modeling and prediction of nonstationary systems. It basically enlarges the standard time-delay-embedding space by inclusion of the (unknown) slow driving signal, which is estimated simultaneously with the intrinsic stationary dynamics. Our method can be implemented with any modeling tool. Using, in particular, artificial neural networks, its application to both synthetic and real-world time series shows that it is highly efficient, leading to much more accurate results and longer prediction horizons than other existing overembedding methods in the literature.

  8. Synthetic cannabinoids: In silico prediction of the cannabinoid receptor 1 affinity by a quantitative structure-activity relationship model.

    PubMed

    Paulke, Alexander; Proschak, Ewgenij; Sommer, Kai; Achenbach, Janosch; Wunder, Cora; Toennes, Stefan W

    2016-03-14

    The number of new synthetic psychoactive compounds increase steadily. Among the group of these psychoactive compounds, the synthetic cannabinoids (SCBs) are most popular and serve as a substitute of herbal cannabis. More than 600 of these substances already exist. For some SCBs the in vitro cannabinoid receptor 1 (CB1) affinity is known, but for the majority it is unknown. A quantitative structure-activity relationship (QSAR) model was developed, which allows the determination of the SCBs affinity to CB1 (expressed as binding constant (Ki)) without reference substances. The chemically advance template search descriptor was used for vector representation of the compound structures. The similarity between two molecules was calculated using the Feature-Pair Distribution Similarity. The Ki values were calculated using the Inverse Distance Weighting method. The prediction model was validated using a cross validation procedure. The predicted Ki values of some new SCBs were in a range between 20 (considerably higher affinity to CB1 than THC) to 468 (considerably lower affinity to CB1 than THC). The present QSAR model can serve as a simple, fast and cheap tool to get a first hint of the biological activity of new synthetic cannabinoids or of other new psychoactive compounds.

  9. Applicability of cranial models in urethane resin and foam as a substitute for bone: are synthetic materials reliable?

    PubMed

    Muccino, Enrico; Porta, Davide; Magli, Francesca; Cigada, Alfredo; Sala, Remo; Gibelli, Daniele; Cattaneo, Cristina

    2013-09-01

    As literature is poor in functional synthetic cranial models, in this study, synthetic handmade models of cranial vaults were produced in two different materials (a urethane resin and a self-hardening foam), from multiple bone specimens (eight original cranial vaults: four human and four swine), in order to test their resemblance to bone structure in behavior, during fracture formation. All the vaults were mechanically tested with a 2-kg impact weight and filmed with a high-speed camera. Fracture patterns were homogeneous in all swine vaults and heterogeneous in human vaults, with resin fractures more similar to bone fractures. Mean fracture latency time extrapolated by videos were of 0.75 msec (bone), 1.5 msec (resin), 5.12 msec (foam) for human vaults and of 0.625 msec (bone), 1.87 msec (resin), 3.75 msec (foam) for swine vaults. These data showed that resin models are more similar to bone than foam reproductions, but that synthetic material may behave quite differently from bone as concerns fracture latency times.

  10. Biodegradation of perchlorate from real and synthetic effluent by Proteobacterium ARJR SMBS in a stirred tank bioreactor system.

    PubMed

    Raj, J R Anoop; Muruganandam, L

    2013-01-01

    The present work is a laboratory-scale study of perchlorate degradation using Proteobacterium ARJR SMBS in a stirred tank bioreactor (STBR). Anaerobically grown cultures of ARJR SMBS exposed to a variety of ClO4(-) levels within the range 30 to 150 mg L(-1) under anoxic conditions have been studied. The chloride released was measured and the average value found to be 43.55 mg L(-1). The average daily value of perchlorate degradation rate in this system was 17.24 mg L(-1) at optimum pH 7.5 and 0.25% NaCl salinity. The mixed liquor suspension solids of the system gradually increased from 0.025-0.156 g L(-1) during the operating period of 55 days. Mass balance indicated that the chloride produced was 0.45 mole per mole of perchlorate. The salinity of the system varied from 2.50-18.46 g L(-1), dependent primarily upon the inlet perchlorate concentration. The degradation mechanism, which obeyed a first-order substrate-utilizing kinetic model, allowed the growth rates and the half-saturation constants to be determined. The maximum observed anoxic growth rates (0.83-1.2 h(-1)) for ARJR SMBS in a synthetic effluent (SE) were considerably higher than in real effluent (RE) (0.45-0.59 h(-1)). The biomass yield of ARJR SMBS in STBR was higher in SE (1 +/- 0.4 mg L(-1)) than in RE (1 +/- 0.1 mg L(-1)). From the experimental findings, the uptake of perchlorate by the bacterium is suggested to be a non-interfacially-based mechanism. Under steady state operating condition the performance of the reactor was comparatively lower for RE than for SE but still offers significant control over the degradation of perchlorate under full-scale conditions.

  11. Effects of Water in Synthetic Lubricant Systems and Clathrate Formation: A Literature Search and Review

    SciTech Connect

    Rohatgi, Ngoc Dung T.

    2001-08-08

    An extensive literature search and a confidential survey were critically analyzed to determine the effects of water on the stability of hydrofluorocarbon/synthetic lubricant systems and to identify key areas requiring further investigation. Following are highlights from the analysis: Clathrate hydrates are solid solutions formed when water molecules are linked through hydrogen bonding creating cavities that can enclose various guest molecules from hydrate formers, such as hydrofluorocarbons R-32, R-125, R-134a, R-407C and R-410A. The four methods for preventing clathrate formation were drying the gas, heating it, reducing its pressure, or using inhibitors. The hydrolysis of polyolester lubricants was mostly acid-catalyzed and its reaction rate constant typically followed the Arrhenius equation of an activated process. Hydrolytic stability improved with hindered molecular structures, and with the presence of acid catcher additives and desiccants. Water vapor can effect the adsorption of long-chain fatty acids and the chemistry of formation of protective oxide film. However, these effects on lubrication can be either positive or negative. Fifty to sixty percent of the moisture injected into an air-conditioning system remained in the refrigerant and the rest mixed with the compressor oil. In an automotive air-conditioning system using R-134a, ice would form at 0 C evaporating temperature when the water content in the vapor refrigerant on the low-pressure side was more than 350 ppm. Moisture would cause the embrittlement of polyethylene terephthalate and the hydrolysis of polyesters, but would reduce the effect of amine additives on fluoroelastomer rubbers. The reactions of water with refrigerants and lubricants would cause formicary and large-pit corrosion in copper tubes, as well as copper plating and sludge formation. Moreover, blockage of capillary tubes increased rapidly in the presence of water. Twenty-four companies responded to the survey. From the responses

  12. Shuttle Imaging Radar-C mission operations - Technology test bed for Earth Observing System synthetic aperture radar

    NASA Technical Reports Server (NTRS)

    Trimble, J. P.; Collins, C. E.

    1992-01-01

    The mission operations for the Space Radar Lab (SRL), particularly in the areas of real-time replanning and science activity coordination, are presented. The two main components of SRL are the Shuttle Imaging Radar-C and the X-Band Synthetic Aperture Radar. The Earth Observing System SAR will be a multispectral, multipolarization radar satellite that will provide information over an entire decade, permitting scientists to monitor large-scale changes in the earth's environment over a long period of time.

  13. Model-Based Systems

    NASA Technical Reports Server (NTRS)

    Frisch, Harold P.

    2007-01-01

    Engineers, who design systems using text specification documents, focus their work upon the completed system to meet Performance, time and budget goals. Consistency and integrity is difficult to maintain within text documents for a single complex system and more difficult to maintain as several systems are combined into higher-level systems, are maintained over decades, and evolve technically and in performance through updates. This system design approach frequently results in major changes during the system integration and test phase, and in time and budget overruns. Engineers who build system specification documents within a model-based systems environment go a step further and aggregate all of the data. They interrelate all of the data to insure consistency and integrity. After the model is constructed, the various system specification documents are prepared, all from the same database. The consistency and integrity of the model is assured, therefore the consistency and integrity of the various specification documents is insured. This article attempts to define model-based systems relative to such an environment. The intent is to expose the complexity of the enabling problem by outlining what is needed, why it is needed and how needs are being addressed by international standards writing teams.

  14. Synthetic virus-like particles prepared via protein corona formation enable effective vaccination in an avian model of coronavirus infection.

    PubMed

    Chen, Hui-Wen; Huang, Chen-Yu; Lin, Shu-Yi; Fang, Zih-Syun; Hsu, Chen-Hsuan; Lin, Jung-Chen; Chen, Yuan-I; Yao, Bing-Yu; Hu, Che-Ming J

    2016-11-01

    The ongoing battle against current and rising viral infectious threats has prompted increasing effort in the development of vaccine technology. A major thrust in vaccine research focuses on developing formulations with virus-like features towards enhancing antigen presentation and immune processing. Herein, a facile approach to formulate synthetic virus-like particles (sVLPs) is demonstrated by exploiting the phenomenon of protein corona formation induced by the high-energy surfaces of synthetic nanoparticles. Using an avian coronavirus spike protein as a model antigen, sVLPs were prepared by incubating 100 nm gold nanoparticles in a solution containing an optimized concentration of viral proteins. Following removal of free proteins, antigen-laden particles were recovered and showed morphological semblance to natural viral particles under nanoparticle tracking analysis and transmission electron microscopy. As compared to inoculation with free proteins, vaccination with the sVLPs showed enhanced lymphatic antigen delivery, stronger antibody titers, increased splenic T-cell response, and reduced infection-associated symptoms in an avian model of coronavirus infection. Comparison to a commercial whole inactivated virus vaccine also showed evidence of superior antiviral protection by the sVLPs. The study demonstrates a simple yet robust method in bridging viral antigens with synthetic nanoparticles for improved vaccine application; it has practical implications in the management of human viral infections as well as in animal agriculture.

  15. Synthetic virus-like particles prepared via protein corona formation enable effective vaccination in an avian model of coronavirus infection.

    PubMed

    Chen, Hui-Wen; Huang, Chen-Yu; Lin, Shu-Yi; Fang, Zih-Syun; Hsu, Chen-Hsuan; Lin, Jung-Chen; Chen, Yuan-I; Yao, Bing-Yu; Hu, Che-Ming J

    2016-11-01

    The ongoing battle against current and rising viral infectious threats has prompted increasing effort in the development of vaccine technology. A major thrust in vaccine research focuses on developing formulations with virus-like features towards enhancing antigen presentation and immune processing. Herein, a facile approach to formulate synthetic virus-like particles (sVLPs) is demonstrated by exploiting the phenomenon of protein corona formation induced by the high-energy surfaces of synthetic nanoparticles. Using an avian coronavirus spike protein as a model antigen, sVLPs were prepared by incubating 100 nm gold nanoparticles in a solution containing an optimized concentration of viral proteins. Following removal of free proteins, antigen-laden particles were recovered and showed morphological semblance to natural viral particles under nanoparticle tracking analysis and transmission electron microscopy. As compared to inoculation with free proteins, vaccination with the sVLPs showed enhanced lymphatic antigen delivery, stronger antibody titers, increased splenic T-cell response, and reduced infection-associated symptoms in an avian model of coronavirus infection. Comparison to a commercial whole inactivated virus vaccine also showed evidence of superior antiviral protection by the sVLPs. The study demonstrates a simple yet robust method in bridging viral antigens with synthetic nanoparticles for improved vaccine application; it has practical implications in the management of human viral infections as well as in animal agriculture. PMID:27552321

  16. A constructed wetland model for synthetic reactive dye wastewater treatment by narrow-leaved cattails (Typha angustifolia Linn.).

    PubMed

    Nilratnisakorn, S; Thiravetyan, P; Nakbanpote, W

    2009-01-01

    Textile wastewater is contaminated by reactive dye causing unattractive levels of wastewater color, high pH and high salt content when discharged into public water systems. Decolorization of textile wastewater by plant, phytoremediation, is an alternative, sustainable method which is suitable for long term operation. Narrow-leaved cattails are one species of wetland plant with efficiency for decolorizing and remediating textile wastewater. In addition, chemical oxygen demand (COD) can be lowered and dye residue can be removed. The plant also showed a good salt tolerance even after being exposed to a salt solution for 15 days. The narrow-leaved cattails were set up in a constructed wetland model with a vertical flow system operating from bottom to top for synthetic reactive dye wastewater (SRDW) removal. Narrow-leaved cattails could achieve the removal of SRDW at approximately 0.8 g(SRDW) m(-2) day(-1). Decolorization of SRDW by this plant was approximately 60%. The advantage of this method is that it is suitable for textile wastewater management and improvement of wetland. These plants could lower COD, remove dye, sodium and total dissolved solids (TDS) whereas other biological and chemical methods could not remove TDS and dye in the same time. These results suggested that the spongy cell structure of this plant has the ability to absorb large amounts of water and nutrients. Physico-chemical analysis revealed increasing amounts of sulfur, silicon, iron and calcium in the plant leafs and roots after exposure to wastewater. Proteins or amide groups in the plant might help in textile dye removal. Regarding decolorization, this plant accumulates dye in the intercellular space and still grows in this SRDW condition. Hence, it can be noted here that narrow-leaved cattails are efficient for textile dye wastewater treatment.

  17. A constructed wetland model for synthetic reactive dye wastewater treatment by narrow-leaved cattails (Typha angustifolia Linn.).

    PubMed

    Nilratnisakorn, S; Thiravetyan, P; Nakbanpote, W

    2009-01-01

    Textile wastewater is contaminated by reactive dye causing unattractive levels of wastewater color, high pH and high salt content when discharged into public water systems. Decolorization of textile wastewater by plant, phytoremediation, is an alternative, sustainable method which is suitable for long term operation. Narrow-leaved cattails are one species of wetland plant with efficiency for decolorizing and remediating textile wastewater. In addition, chemical oxygen demand (COD) can be lowered and dye residue can be removed. The plant also showed a good salt tolerance even after being exposed to a salt solution for 15 days. The narrow-leaved cattails were set up in a constructed wetland model with a vertical flow system operating from bottom to top for synthetic reactive dye wastewater (SRDW) removal. Narrow-leaved cattails could achieve the removal of SRDW at approximately 0.8 g(SRDW) m(-2) day(-1). Decolorization of SRDW by this plant was approximately 60%. The advantage of this method is that it is suitable for textile wastewater management and improvement of wetland. These plants could lower COD, remove dye, sodium and total dissolved solids (TDS) whereas other biological and chemical methods could not remove TDS and dye in the same time. These results suggested that the spongy cell structure of this plant has the ability to absorb large amounts of water and nutrients. Physico-chemical analysis revealed increasing amounts of sulfur, silicon, iron and calcium in the plant leafs and roots after exposure to wastewater. Proteins or amide groups in the plant might help in textile dye removal. Regarding decolorization, this plant accumulates dye in the intercellular space and still grows in this SRDW condition. Hence, it can be noted here that narrow-leaved cattails are efficient for textile dye wastewater treatment. PMID:19759459

  18. Continuous wave synthetic low-coherence wind sensing Lidar: motionless measurement system with subsequent numerical range scanning.

    PubMed

    Brinkmeyer, Ernst; Waterholter, Thomas

    2013-01-28

    A continuous wave (CW) Lidar system for detection of scattering from atmospheric aerosol particles is presented which is useful in particular for remote sensing of wind velocities. It is based on a low-coherence interferometric setup powered by a synthetic broadband laser source with Gaussian power density spectrum. The laser bandwidth is electronically adjustable and determines the spatial resolution which is independent of range. The Lidar system has no moving parts. The location to be resolved can be shifted numerically after the measurement meaning that a single measurement already contains the full range information. The features of constant resolution and numerical range scanning are in sharp contrast to ordinary CW Lidar systems.

  19. 2D full wave modeling for a synthetic Doppler backscattering diagnostic

    SciTech Connect

    Hillesheim, J. C.; Schmitz, L.; Kubota, S.; Rhodes, T. L.; Carter, T. A.; Holland, C.

    2012-10-15

    Doppler backscattering (DBS) is a plasma diagnostic used in tokamaks and other magnetic confinement devices to measure the fluctuation level of intermediate wavenumber (k{sub {theta}}{rho}{sub s}{approx} 1) density fluctuations and the lab frame propagation velocity of turbulence. Here, a synthetic DBS diagnostic is described, which has been used for comparisons between measurements in the DIII-D tokamak and predictions from nonlinear gyrokinetic simulations. To estimate the wavenumber range to which a Gaussian beam would be sensitive, a ray tracing code and a 2D finite difference, time domain full wave code are used. Experimental density profiles and magnetic geometry are used along with the experimental antenna and beam characteristics. An example of the effect of the synthetic diagnostic on the output of a nonlinear gyrokinetic simulation is presented.

  20. 2D full wave modeling for a synthetic Doppler backscattering diagnostica)

    NASA Astrophysics Data System (ADS)

    Hillesheim, J. C.; Holland, C.; Schmitz, L.; Kubota, S.; Rhodes, T. L.; Carter, T. A.

    2012-10-01

    Doppler backscattering (DBS) is a plasma diagnostic used in tokamaks and other magnetic confinement devices to measure the fluctuation level of intermediate wavenumber (kθρs ˜ 1) density fluctuations and the lab frame propagation velocity of turbulence. Here, a synthetic DBS diagnostic is described, which has been used for comparisons between measurements in the DIII-D tokamak and predictions from nonlinear gyrokinetic simulations. To estimate the wavenumber range to which a Gaussian beam would be sensitive, a ray tracing code and a 2D finite difference, time domain full wave code are used. Experimental density profiles and magnetic geometry are used along with the experimental antenna and beam characteristics. An example of the effect of the synthetic diagnostic on the output of a nonlinear gyrokinetic simulation is presented.

  1. Proposed data model for the next version of the synthetic biology open language.

    PubMed

    Roehner, Nicholas; Oberortner, Ernst; Pocock, Matthew; Beal, Jacob; Clancy, Kevin; Madsen, Curtis; Misirli, Goksel; Wipat, Anil; Sauro, Herbert; Myers, Chris J

    2015-01-16

    While the first version of the Synthetic Biology Open Language (SBOL) has been adopted by several academic and commercial genetic design automation (GDA) software tools, it only covers a limited number of the requirements for a standardized exchange format for synthetic biology. In particular, SBOL Version 1.1 is capable of representing DNA components and their hierarchical composition via sequence annotations. This proposal revises SBOL Version 1.1, enabling the representation of a wider range of components with and without sequences, including RNA components, protein components, small molecules, and molecular complexes. It also introduces modules to instantiate groups of components on the basis of their shared function and assert molecular interactions between components. By increasing the range of structural and functional descriptions in SBOL and allowing for their composition, the proposed improvements enable SBOL to represent and facilitate the exchange of a broader class of genetic designs.

  2. Commercial Flight Crew Decision-Making during Low-Visibility Approach Operations Using Fused Synthetic/Enhanced Vision Systems

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Prinzel, Lawrence J., III

    2007-01-01

    NASA is investigating revolutionary crew-vehicle interface technologies that strive to proactively overcome aircraft safety barriers that would otherwise constrain the full realization of the next-generation air transportation system. A fixed-based piloted simulation experiment was conducted to evaluate the complementary use of Synthetic and Enhanced Vision technologies. Specific focus was placed on new techniques for integration and/or fusion of Enhanced and Synthetic Vision and its impact within a two-crew flight deck on the crew's decision-making process during low-visibility approach and landing operations. Overall, the experimental data showed that significant improvements in situation awareness, without concomitant increases in workload and display clutter, could be provided by the integration and/or fusion of synthetic and enhanced vision technologies for the pilot-flying and the pilot-not-flying. During non-normal operations, the ability of the crew to handle substantial navigational errors and runway incursions were neither improved nor adversely impacted by the display concepts. The addition of Enhanced Vision may not, unto itself, provide an improvement in runway incursion detection without being specifically tailored for this application. Existing enhanced vision system procedures were effectively used in the crew decision-making process during approach and missed approach operations but having to forcibly transition from an excellent FLIR image to natural vision by 100 ft above field level was awkward for the pilot-flying.

  3. Natural-Synthetic Hybrid Polymers Developed via Electrospinning: The Effect of PET in Chitosan/Starch System

    PubMed Central

    Espíndola-González, Adolfo; Martínez-Hernández, Ana Laura; Fernández-Escobar, Francisco; Castaño, Victor Manuel; Brostow, Witold; Datashvili, Tea; Velasco-Santos, Carlos

    2011-01-01

    Chitosan is an amino polysaccharide found in nature, which is biodegradable, nontoxic and biocompatible. It has versatile features and can be used in a variety of applications including films, packaging, and also in medical surgery. Recently a possibility to diversify chitosan properties has emerged by combining it with synthetic materials to produce novel natural-synthetic hybrid polymers. We have studied structural and thermophysical properties of chitosan + starch + poly(ethylene terephthalate) (Ch + S + PET) fibers developed via electrospinning. Properties of these hybrids polymers are compared with extant chitosan containing hybrids synthesized by electrospinning. Molecular interactions and orientation in the fibers are analyzed by infrared and Raman spectroscopies respectively, morphology by scanning electron microscopy and thermophysical properties by thermogravimetric analysis and differential scanning calorimetry. Addition of PET to Ch + S systems results in improved thermal stability at elevated temperatures. PMID:21673930

  4. Canister Model, Systems Analysis

    1993-09-29

    This packges provides a computer simulation of a systems model for packaging nuclear waste and spent nuclear fuel in canisters. The canister model calculates overall programmatic cost, number of canisters, and fuel and waste inventories for the Idaho Chemical Processing Plant (other initial conditions can be entered).

  5. Flexible system modeling

    SciTech Connect

    Maragno, M.; Schmid, C.; Schmieg, M.

    1995-04-01

    Stability analysis calculations are typically based on predefined system models, where, in the majority of cases, the well known IEEE definitions for controllers, prime movers, and other associated devices and functions are in use. for planning purposes, this approach might be acceptable, since predefined sets of parameters will allow a favorable and reasonable behavior of the analyzed system to be achieved, thus representing the possibly implementable system behavior. However, this approach is often also applied for system operation analysis purposes, for which typical IEEE models are applicable only in few cases. In quite a number of cases, even manufacturers who perform highly accurate system modeling studies have been asked to deliver block diagrams and parameters according to a list of available IEEE models. Utilities and consultants with an in-depth knowledge and tradition of conducting system operation performance and optimization studies have frequently requested adequate and accurate procedures and tools to tackle this special field of power system analysis appropriately. This need to solve complex operation analysis and special component planning problems has prompted the development of adequate methods and tools at DIgSILENT Systems in cooperation with FICHTNER C.E. This article focuses on various possibilities to approach this problem and to report on the applied strategies and methods. Comprehensive examples are given to demonstrate the capabilities of the implemented procedures.

  6. Microwave-assisted regeneration of synthetic zeolite used in tritium removal systems

    SciTech Connect

    Tanaka, M.; Takayama, S.; Sano, S.

    2015-03-15

    The regeneration process using synthetic honeycomb type 5A zeolite under microwave irradiation was experimentally investigated using a single-mode cavity at 2.46 GHz. In order to investigate the effect of electromagnetic fields, inductive heating by a magnetic field was applied to synthetic zeolite containing water. Because the microwave energy absorbed in the sample was less than 15 W, the zeolite sample was only heated to a temperature of 71 C. degrees. Water desorption was observed based on the increased temperature of the zeolite sample and the thermogravimetric curve that indicated a single step phenomenon. As a result, the regeneration process of zeolite was not complete over a period of 6000 s. A comparison of dielectric heating by an electric field with inductive heating by a magnetic field showed that the regeneration process by microwave irradiation was particularly beneficial in dielectric heating. (authors)

  7. Studies of Cell-Mediated Immunity Against Immune Disorders Using Synthetic Peptides and Rotating Bioreactor System

    NASA Technical Reports Server (NTRS)

    Sastry, Jagannadha K.

    1997-01-01

    Our proposed experiments included: (1) immunzing mice with synthetic peptides; (2) preparing spleen and lymph node cells; (3) growing them under conventional conditions as well as in the rotatory vessel in appropriate medium reconstituting with synthetic peptides and/or cytokines as needed; and (4) comparing at regular time intervals the specific CTL activity as well as helper T-cell activity (in terms of both proliferative responses and cytokine production) using established procedures in my laboratory. We further proposed that once we demonstrated the merit of rotatory vessel technology to achieve desired results, these studies would be expanded to include immune cells from non-human primates (rhesus monkeys and chimpanzees) and also humans. We conducted a number of experiments to determine CTL induction by the synthetic peptides corresponding to antigenic proteins in HIV and HPV in different mouse strains that express MHC haplotypes H-2b or H-2d. We immunized mice with 100 ug of the synthetic peptide, suspended in sterile water, and emulsified in CFA (1:1). The immune lymph node cells obtained after 7 days were restimulated by culturing in T25 flask, HARV-10, or STLV-50, in the presence of the peptide at 20 ug/ml. The results from the 5'Cr-release assay consistently revealed complete abrogation of CTL activity of cells grown in the bioreactors (both HARV and STLV), while significant antigen-specific CTL activity was observed with cells cultured in tissue culture flasks. Thus, overall the data we generated in this study proved the usefulness of the NASA-developed developed technology for understanding the known immune deficiency during space travel. Additionally, this ex vivo microgravity technology since it mimics effectively the in vivo situation, it is also useful in understanding immune disorders in general. Thus, our proposed studies in TMC-NASA contract round II application benefit from data generated in this TMC-NASA contract round I study.

  8. Building synthetic memory

    PubMed Central

    Inniss, Mara C.; Silver, Pamela A.

    2013-01-01

    Synopsis Cellular memory – conversion of a transient signal into a sustained response – is a common feature of biological systems. Synthetic biologists aim to understand and reengineer such systems in a reliable and predictable manner. Synthetic memory circuits have been designed and built in vitro and in vivo based on diverse mechanisms such as oligonucleotide hybridization, recombination, transcription, phosphorylation, and RNA editing. Thus far, building these circuits has helped us explore the basic principles required for stable memory and ask novel biological questions. Here we discuss strategies for building synthetic memory circuits, their use as research tools, and future applications of these devices in medicine and industry. PMID:24028965

  9. Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC

    PubMed Central

    Aziz, Ramy K.; Khaw, Valerie L.; Monk, Jonathan M.; Brunk, Elizabeth; Lewis, Robert; Loh, Suh I.; Mishra, Arti; Nagle, Amrita A.; Satyanarayana, Chitkala; Dhakshinamoorthy, Saravanakumar; Luche, Michele; Kitchen, Douglas B.; Andrews, Kathleen A.; Palsson, Bernhard Ø.; Charusanti, Pep

    2015-01-01

    Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100–200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics. PMID:26441892

  10. Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.

    PubMed

    Aziz, Ramy K; Khaw, Valerie L; Monk, Jonathan M; Brunk, Elizabeth; Lewis, Robert; Loh, Suh I; Mishra, Arti; Nagle, Amrita A; Satyanarayana, Chitkala; Dhakshinamoorthy, Saravanakumar; Luche, Michele; Kitchen, Douglas B; Andrews, Kathleen A; Palsson, Bernhard Ø; Charusanti, Pep

    2015-01-01

    Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.

  11. Modeling of arsenic adsorption kinetics of synthetic and contaminated groundwater on natural laterite.

    PubMed

    Maiti, Abhijit; Sharma, Himanshu; Basu, Jayanta Kumar; De, Sirshendu

    2009-12-30

    A simple shrinking core model is applied to predict the adsorption kinetics of arsenite and arsenate species onto natural laterite (NL) in a stirred tank adsorber. The proposed model is a two-resistance model, in which two unknown parameters, external mass transfer coefficient (K(f)) and pore diffusion coefficient (D(e)) are estimated by comparing the simulation concentration profile with the experimental data using a nonlinear optimization technique. The model is applied under various operating conditions, e.g., initial arsenic concentration, NL dose, NL particle size, temperature, stirring speed, etc. Estimated values of D(e) and K(f) are found to be in the range of 2.2-2.6 x 10(-11)m(2)/s and 1.0-1.4 x 10(-6)m/s at 305K for different operating conditions, respectively. D(e) and K(f) values are found to be increasing with temperature and stirrer speed, respectively. Calculated values of Biot numbers indicate that both external mass transfer and pore diffusion are important during the adsorption. The model is also applied satisfactorily to predict the arsenic adsorption kinetics of arsenic contaminated groundwater-NL system and can be used to scale up. PMID:19717233

  12. Modeling of arsenic adsorption kinetics of synthetic and contaminated groundwater on natural laterite.

    PubMed

    Maiti, Abhijit; Sharma, Himanshu; Basu, Jayanta Kumar; De, Sirshendu

    2009-12-30

    A simple shrinking core model is applied to predict the adsorption kinetics of arsenite and arsenate species onto natural laterite (NL) in a stirred tank adsorber. The proposed model is a two-resistance model, in which two unknown parameters, external mass transfer coefficient (K(f)) and pore diffusion coefficient (D(e)) are estimated by comparing the simulation concentration profile with the experimental data using a nonlinear optimization technique. The model is applied under various operating conditions, e.g., initial arsenic concentration, NL dose, NL particle size, temperature, stirring speed, etc. Estimated values of D(e) and K(f) are found to be in the range of 2.2-2.6 x 10(-11)m(2)/s and 1.0-1.4 x 10(-6)m/s at 305K for different operating conditions, respectively. D(e) and K(f) values are found to be increasing with temperature and stirrer speed, respectively. Calculated values of Biot numbers indicate that both external mass transfer and pore diffusion are important during the adsorption. The model is also applied satisfactorily to predict the arsenic adsorption kinetics of arsenic contaminated groundwater-NL system and can be used to scale up.

  13. Critical Infrastructure Modeling System

    2004-10-01

    The Critical Infrastructure Modeling System (CIMS) is a 3D modeling and simulation environment designed to assist users in the analysis of dependencies within individual infrastructure and also interdependencies between multiple infrastructures. Through visual cuing and textual displays, a use can evaluate the effect of system perturbation and identify the emergent patterns that evolve. These patterns include possible outage areas from a loss of power, denial of service or access, and disruption of operations. Method ofmore » Solution: CIMS allows the user to model a system, create an overlay of information, and create 3D representative images to illustrate key infrastructure elements. A geo-referenced scene, satellite, aerial images or technical drawings can be incorporated into the scene. Scenarios of events can be scripted, and the user can also interact during run time to alter system characteristics. CIMS operates as a discrete event simulation engine feeding a 3D visualization.« less

  14. Visual cues in low-level flight - Implications for pilotage, training, simulation, and enhanced/synthetic vision systems

    NASA Technical Reports Server (NTRS)

    Foyle, David C.; Kaiser, Mary K.; Johnson, Walter W.

    1992-01-01

    This paper reviews some of the sources of visual information that are available in the out-the-window scene and describes how these visual cues are important for routine pilotage and training, as well as the development of simulator visual systems and enhanced or synthetic vision systems for aircraft cockpits. It is shown how these visual cues may change or disappear under environmental or sensor conditions, and how the visual scene can be augmented by advanced displays to capitalize on the pilot's excellent ability to extract visual information from the visual scene.

  15. The validity of the one-dimensional fluid model of electrical breakdown in synthetic air at low pressure

    NASA Astrophysics Data System (ADS)

    Jovanović, A. P.; Stankov, M. N.; Marković, V. Lj.; Stamenković, S. N.

    2013-12-01

    In this letter the validity of the fluid model used to simulate the electrical breakdown in air at low pressure is discussed. The new method for the determination of the ionization source term for the mixed gases is proposed. Paschen's curve obtained by the fluid model is compared to the available experimental data. The electron and ions density profiles calculated by the fluid model are presented. Based on Ohm's law, the current and voltage waveforms are calculated and compared to the ones measured by the oscilloscope in the synthetic-air filled tube with stainless-steel electrodes. It is shown that the one-dimensional fluid model can be used for modeling the electrical breakdown at pd values higher than Paschen's minimum and to determine stationary values of electron and ions densities.

  16. Time-domain inflow boundary condition for turbulence-airfoil interaction noise prediction using synthetic turbulence modeling

    NASA Astrophysics Data System (ADS)

    Kim, Daehwan; Heo, Seung; Cheong, Cheolung

    2015-03-01

    The present paper deals with development of the synthetic turbulence inflow boundary condition (STIBC) to predict inflow broadband noise generated by interaction between turbulence and an airfoil/a cascade of airfoils in the time-domain. The STIBC is derived by combining inflow boundary conditions that have been successfully applied in external and internal computational aeroacoustics (CAA) simulations with a synthetic turbulence model. The random particle mesh (RPM) method based on a digital filter is used as the synthetic turbulence model. Gaussian and Liepmann spectra are used to define the filters for turbulence energy spectra. The linearized Euler equations are used as governing equations to evaluate the suitability of the STIBC in time-domain CAA simulations. First, the velocity correlations and energy spectra of the synthesized turbulent velocities are compared with analytic ones. The comparison results reveal that the STIBC can reproduce a turbulent velocity field satisfying the required statistical characteristics of turbulence. Particularly, the Liepmann filter representing a non-Gaussian filter is shown to be effectively described by superposing the Gaussian filters. Each Gaussian filter has a different turbulent kinetic energy and integral length scale. Second, two inflow noise problems are numerically solved using the STIBC: the turbulence-airfoil interaction and the turbulence-a cascade of airfoils interaction problems. The power spectrum of noise due to an isolated flat plate airfoil interacting with incident turbulence is predicted, and its result is successfully validated against Amiet's analytic model (Amiet, 1975) [4]. The prediction results of the upstream and downstream acoustic power spectra from a cascade of flat plates are then compared with Cheong's analytic model (Cheong et al., 2006) [30]. These comparisons are also in excellent agreement. On the basis of these illustrative computation results, the STIBC is expected to be applied to

  17. Synthetic battery cycling techniques

    NASA Technical Reports Server (NTRS)

    Leibecki, H.; Thaller, L. H.

    1982-01-01

    The group of techniques that as a class are referred to as synthetic battery cycling are described with reference to spacecraft battery systems. Synthetic battery cycling makes use of the capability of computer graphics to illustrate some of the basic characteristics of operation of individual electrodes within an operating electrochemical cell. It can also simulate the operation of an entire string of cells that are used as the energy storage subsystem of a power system.

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

    PubMed

    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

  19. Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models.

    PubMed

    Chowdhury, Ratul; Chowdhury, Anupam; Maranas, Costas D

    2015-01-01

    Essentiality (ES) and Synthetic Lethality (SL) information identify combination of genes whose deletion inhibits cell growth. This information is important for both identifying drug targets for tumor and pathogenic bacteria suppression and for flagging and avoiding gene deletions that are non-viable in biotechnology. In this study, we performed a comprehensive ES and SL analysis of two important eukaryotic models (S. cerevisiae and CHO cells) using a bilevel optimization approach introduced earlier. Information gleaned from this study is used to propose specific model changes to remedy inconsistent with data model predictions. Even for the highly curated Yeast 7.11 model we identified 50 changes (metabolic and GPR) leading to the correct prediction of an additional 28% of essential genes and 36% of synthetic lethals along with a 53% reduction in the erroneous identification of essential genes. Due to the paucity of mutant growth phenotype data only 12 changes were made for the CHO 1.2 model leading to an additional correctly predicted 11 essential and eight non-essential genes. Overall, we find that CHO 1.2 was 76% less accurate than the Yeast 7.11 metabolic model in predicting essential genes. Based on this analysis, 14 (single and double deletion) maximally informative experiments are suggested to improve the CHO cell model by using information from a mouse metabolic model. This analysis demonstrates the importance of single and multiple knockout phenotypes in assessing and improving model reconstructions. The advent of techniques such as CRISPR opens the door for the global assessment of eukaryotic models. PMID:26426067

  20. Modeling Sustainable Food Systems

    NASA Astrophysics Data System (ADS)

    Allen, Thomas; Prosperi, Paolo

    2016-05-01

    The processes underlying environmental, economic, and social unsustainability derive in part from the food system. Building sustainable food systems has become a predominating endeavor aiming to redirect our food systems and policies towards better-adjusted goals and improved societal welfare. Food systems are complex social-ecological systems involving multiple interactions between human and natural components. Policy needs to encourage public perception of humanity and nature as interdependent and interacting. The systemic nature of these interdependencies and interactions calls for systems approaches and integrated assessment tools. Identifying and modeling the intrinsic properties of the food system that will ensure its essential outcomes are maintained or enhanced over time and across generations, will help organizations and governmental institutions to track progress towards sustainability, and set policies that encourage positive transformations. This paper proposes a conceptual model that articulates crucial vulnerability and resilience factors to global environmental and socio-economic changes, postulating specific food and nutrition security issues as priority outcomes of food systems. By acknowledging the systemic nature of sustainability, this approach allows consideration of causal factor dynamics. In a stepwise approach, a logical application is schematized for three Mediterranean countries, namely Spain, France, and Italy.

  1. Modeling Sustainable Food Systems.

    PubMed

    Allen, Thomas; Prosperi, Paolo

    2016-05-01

    The processes underlying environmental, economic, and social unsustainability derive in part from the food system. Building sustainable food systems has become a predominating endeavor aiming to redirect our food systems and policies towards better-adjusted goals and improved societal welfare. Food systems are complex social-ecological systems involving multiple interactions between human and natural components. Policy needs to encourage public perception of humanity and nature as interdependent and interacting. The systemic nature of these interdependencies and interactions calls for systems approaches and integrated assessment tools. Identifying and modeling the intrinsic properties of the food system that will ensure its essential outcomes are maintained or enhanced over time and across generations, will help organizations and governmental institutions to track progress towards sustainability, and set policies that encourage positive transformations. This paper proposes a conceptual model that articulates crucial vulnerability and resilience factors to global environmental and socio-economic changes, postulating specific food and nutrition security issues as priority outcomes of food systems. By acknowledging the systemic nature of sustainability, this approach allows consideration of causal factor dynamics. In a stepwise approach, a logical application is schematized for three Mediterranean countries, namely Spain, France, and Italy.

  2. Development of a GPS-aided motion measurement, pointing, and stabilization system for a Synthetic Aperture Radar. [Global Positioning System (GPS)

    SciTech Connect

    Fellerhoff, J.R.; Kohler, S.M.

    1991-01-01

    An advanced Synthetic Aperture Radar Motion Compensation System has been developed by Sandia National Laboratories (SNL). The system includes a miniaturized high accuracy ring laser gyro inertial measurement unit, a three axis gimbal pointing and stabilization assembly, a differential Global Positioning System (GPS) navigation aiding system, and a pilot guidance system. The system provides several improvements over previous SNL motion compensation systems and is capable of antenna stabilization to less than 0.01 degrees RMS and absolute position measurement to less than 5.0 meters RMS. These accuracies have been demonstrated in recent flight testing aboard a DHC-6-300 Twin Otter'' aircraft.

  3. A fast and inexpensive procedure for the isolation of synthetic cannabinoids from 'Spice' products using a flash chromatography system.

    PubMed

    Moosmann, Bjoern; Kneisel, Stefan; Wohlfarth, Ariane; Brecht, Volker; Auwärter, Volker

    2013-05-01

    In the age of the Internet, the variety of drugs offered online is constantly increasing, and new drugs emerge every month. One group of drugs showing such an enormous increase is that of synthetic cannabinoids. Since their first identification in 'herbal mixtures', new structural modifications continue to appear on the market. In order to keep up with this process, toxicological screening methods need to be up to date. This can become extremely difficult if no reference material is available. In this article, a fast and effective way to extract and purify synthetic cannabinoids from 'herbal mixtures' is presented. This method opens a new opportunity for a timely reaction by obtaining reference material straight out of the 'herbal mixtures' ordered via the Internet. Isolation was carried out on a flash chromatography system with gradient elution on a C18 column using methanol and 0.55 % formic acid as mobile phases. The obtained purity of all compounds exceeded 99 %. In addition to the isolation of single compounds, the method proved to be suitable for the separation of various synthetic cannabinoids in one mixture, including the diastereomers cis- and trans-CP-47,497-C8. This approach for obtaining pure standards of new drugs proved to be effective, inexpensive and much quicker than waiting for the substances to be commercially available as reference material.

  4. Integrated Operation of INL HYTEST System and High-Temperature Steam Electrolysis for Synthetic Natural Gas Production

    SciTech Connect

    Carl Marcel Stoots; Lee Shunn; James O'Brien

    2010-06-01

    The primary feedstock for synthetic fuel production is syngas, a mixture of carbon monoxide and hydrogen. Current hydrogen production technologies rely upon fossil fuels and produce significant quantities of greenhouse gases as a byproduct. This is not a sustainable means of satisfying future hydrogen demands, given the current projections for conventional world oil production and future targets for carbon emissions. For the past six years, the Idaho National Laboratory has been investigating the use of high-temperature steam electrolysis (HTSE) to produce the hydrogen feedstock required for synthetic fuel production. High-temperature electrolysis water-splitting technology, combined with non-carbon-emitting energy sources, can provide a sustainable, environmentally-friendly means of large-scale hydrogen production. Additionally, laboratory facilities are being developed at the INL for testing hybrid energy systems composed of several tightly-coupled chemical processes (HYTEST program). The first such test involved the coupling of HTSE, CO2 separation membrane, reverse shift reaction, and methanation reaction to demonstrate synthetic natural gas production from a feedstock of water and either CO or a simulated flue gas containing CO2. This paper will introduce the initial HTSE and HYTEST testing facilities, overall coupling of the technologies, testing results, and future plans.

  5. Test of simultaneous synthetic DNA tracer injections for the estimation of the englacial and subglacial drainage system structure of Storglaciären, northern Sweden

    NASA Astrophysics Data System (ADS)

    Dahlke, H. E.; Leung, S.; Lyon, S. W.; Sharma, A. N.; Walter, M. T.; Williamson, A.

    2013-12-01

    Storglaciären glacier, located in the sub-arctic Tarfala catchment, in northern Sweden is one of the world's longest continuously monitored glaciers which provides a unique research platform for the long-term assessment of glacier and ice sheet processes. For example, small mountain glacier hydrological knowledge of the subglacial water distribution at the ice-bed interface has been applied to ice sheets to predict basal sliding processes. Basal sliding promoted by hydraulic jacking is an important glacial-velocity control that is dependent on the subglacial flow pathways' morphology. Thus, understanding subglacial water distribution and drainage system structure and morphology is crucial for modeling ice masses' flow. In order to estimate subglacial drainage system structure and morphology dye tracing experiments are widely employed. Tracer experiments provide quantitative parameters for any input location including tracer transit velocity, dispersivity, recovery and storage. However, spatial data coverage is limited by the finite number of tracers available for simultaneous tracing. In the presented study we test the use of synthetic DNA tracers for the assessment of the englacial and subglacial drainage system structure of Storglaciären. The synthetic DNA tracer is composed of polylactic acid (PLA) microspheres into which short strands of synthetic DNA and paramagnetic iron oxide nanoparticles are incorporated (Sharma et al., 2012, Environmental Science & Technology). Because the DNA sequences can be randomly combined the synthetic DNA tracer provides an enormous number of unique tracers (approximately 1.61 x 1060). Thus, these synthetic tracers have the advantage that multiple (>10) experiments can be conducted simultaneously, allowing a greater information gain within a shorter measurement period. Quantities of a certain DNA strand can be detected using biotechnology tools such as polymerase chain reaction (PCR) and quantitative PCR (qPCR). During the 2013

  6. Using state-of-the-art hydrodynamic models to generate synthetic data cubes for imaging spectral sensing applications

    NASA Astrophysics Data System (ADS)

    Kao, Jim; Smith, William S.; Smith, Barham W.; Borel, Christoph C.

    2002-01-01

    An airborne IR hyperspectral imaging sensor based on the Fourier transform spectrometer technique has been used for studying atmospheric gaseous plumes under the auspice of U.S. Department of Energy. Model generated synthetic data of spectral intensity associated withe the plume and the surface background is useful in terms of performing trade studies as well as testing new algorithms. To cope with the highly turbulent and transient atmospheric boundary layer where plume emissions and evolution are embedded, we have used a high-resolution (at the scale of 1 m) time-dependent Napier-Stoke atmospheric hydrodynamic code, HIGRAD, to replace the Gaussian/multi-fractal approach in the original package of the Los Alamos End-to-End Modeling of Imaging Spectral Sensing Applications (EMISSA). The output from HIGRAD is then used for calculations of radiance reaching the sensor through the Fast Atmospheric Signature Code (FASCODE) with a spectral resolution of 1 cm-1 or less. The modeled plume structure in concentrations and associated plume images in radiance bear great resemblance to the contrast model for its capability in quantifying the column densities of chemical species. The synthetic data produced through our approach proves to be effective in evaluation our understanding of the thermal infrared imaging process.

  7. Distributed fuzzy system modeling

    SciTech Connect

    Pedrycz, W.; Chi Fung Lam, P.; Rocha, A.F.

    1995-05-01

    The paper introduces and studies an idea of distributed modeling treating it as a new paradigm of fuzzy system modeling and analysis. This form of modeling is oriented towards developing individual (local) fuzzy models for specific modeling landmarks (expressed as fuzzy sets) and determining the essential logical relationships between these local models. The models themselves are implemented in the form of logic processors being regarded as specialized fuzzy neural networks. The interaction between the processors is developed either in an inhibitory or excitatory way. In more descriptive way, the distributed model can be sought as a collection of fuzzy finite state machines with their individual local first or higher order memories. It is also clarified how the concept of distributed modeling narrows down a gap between purely numerical (quantitative) models and the qualitative ones originated within the realm of Artificial Intelligence. The overall architecture of distributed modeling is discussed along with the detailed learning schemes. The results of extensive simulation experiments are provided as well. 17 refs.

  8. Synthetic approaches to the bicyclo[2.2.2]diazaoctane ring system common to the paraherquamides, stephacidins and related prenylated indole alkaloids.

    PubMed

    Miller, Kenneth A; Williams, Robert M

    2009-11-01

    The bicyclo[2.2.2]diazaoctane ring system is common to a number of highly biologically active secondary metabolites isolated from numerous species of fungi. In this tutorial review, we describe the varied synthetic approaches that have been employed to construct this ring system in the course of recent total synthesis endeavors, and this review should be of interest to synthetic organic chemists and natural product chemists. Detailed herein are a number of synthetic disconnections including intramolecular S(N)2' cyclizations, biomimetic Diels-Alder reactions, radical cyclizations, and cationic cascade reactions. PMID:19847349

  9. icpTOF: a new way for the detection of synthetic nanoparticles in environmental systems

    NASA Astrophysics Data System (ADS)

    Borovinskaya, Olga; Tanner, Martin; Böhme, Steffi; Gondikas, Andreas

    2016-04-01

    they have entered the real ecosystem. Besides, element ratios of single particles can be used as a specific merit for the identification of synthetic nanoparticles in the presence of naturally occurring particulate background [4]. In addition to higher mass resolving power, the instrument is equipped with a collision/reaction cell, which helps to improve detection limits for elements suffering from interferences (e.g. Fe, Ti, P, S). The icpTOF performance will be shown in combination with different sample introduction systems, including novel discrete microdroplet introduction. The single droplet introduction approach enables particle quantification without particulate reference materials and significantly simplifies the analysis. The advantages of fast simultaneous detection for the characterization of multi-component nanoparticles in environmental media will be demonstrated on several studies. [1] Nanoscience and Nanotechnologies: Nanoscience and nanotechnologies: opportunities and uncertainties, Final Report. Royal Society: London, 2004 [2] Degueldre et al. (2003), Coll. Surf. A, 217, 137-142. [3] Borovinskaya et al. (2014), Anal. Chem, 86, 8142-8148. [4] Von der Kammer et al. (2012), Env. Tox. and Chem., 31, 32-49.

  10. Synthetic oils

    NASA Technical Reports Server (NTRS)

    Hatton, R. E.

    1973-01-01

    Synthetic lubricants are discussed by chemical class and their general strengths and weaknesses in terms of lubrication properties are analyzed. Comparative ratings are given for 14 chemical classes and are used as a guide for lubricant selection. The effects of chemical structure on the properties of the lubricant are described with special emphasis on thermal stability. The diversity of synthetic lubricants which is provided by the wide range of properties permits many applications, some of which are reported.

  11. The derivation of a sub-canopy digital terrain model of a flooded forest using synthetic aperture radar

    NASA Technical Reports Server (NTRS)

    Imhoff, Marc Lee; Gesch, Dean B.

    1990-01-01

    Synthetic aperture radar data from the Shuttle Imaging Radar-B Mission were combined with the tide surface information to create a digital terrain model for a 70-km by 40-km section of the Mouths of the Ganges forests in southern Bangladesh. The dominance of the interaction phenomenon (canopy to surface or surface to canopy reflection) in flooded forests was exploited to create sub-canopy flood boundary maps for two different tide times. The boundary maps were digitally combined in x, y, z space with tide elevation models created from tide gauge data gridding the survey site and used as input to interpolation routines to create a terrain model. The end product represents a significant step in our ability to characterize the topography and hydrology of wetland ecosystems. The model derived here can be used for simulating tidal flow and nutrient transport from the forest to the marine habitat.

  12. Hybrid PET/CT for noninvasive pharmacokinetic evaluation of dynamic PolyConjugates, a synthetic siRNA delivery system.

    PubMed

    Mudd, Sarah R; Trubetskoy, Vladimir S; Blokhin, Andrei V; Weichert, Jamey P; Wolff, Jon A

    2010-07-21

    Positron emission tomography/computed tomography (PET/CT) hybrid imaging can be used to gain insights into a synthetic siRNA delivery system targeted to the liver. Either siRNA or the delivery vehicle was labeled with (64)Cu via 1, 4, 7, 10- tetraazacyclododecane- 1, 4, 7, 10- tetraacetic acid (DOTA) chelation. This study confirmed that the siRNA delivery system was successfully targeted to the liver. Incorporation of the siRNA into the delivery system protected the siRNA from renal filtration long enough so that the siRNA could be delivered to the liver. PET/CT imaging was important for confirming biodistribution and for determining differences in the distribution of labeled siRNA, siRNA incorporated into the delivery system, and the delivery system without siRNA.

  13. Distributed generation systems model

    SciTech Connect

    Barklund, C.R.

    1994-12-31

    A slide presentation is given on a distributed generation systems model developed at the Idaho National Engineering Laboratory, and its application to a situation within the Idaho Power Company`s service territory. The objectives of the work were to develop a screening model for distributed generation alternatives, to develop a better understanding of distributed generation as a utility resource, and to further INEL`s understanding of utility concerns in implementing technological change.

  14. Climate system modeling program

    SciTech Connect

    1995-12-31

    The Climate System Modeling Project is a component activity of NSF's Climate Modeling, Analysis and Prediction Program, supported by the Atmospheric Sciences Program, Geosciences Directorate. Its objective is to accelerate progress toward reliable prediction of global and regional climate changes in the decades ahead. CSMP operates through workshops, support for post-docs and graduate students and other collaborative activities designed to promote interdisciplinary and strategic work in support of the overall objective (above) and specifically in three areas, (1) Causes of interdecadal variability in the climate system, (2) Interactions of regional climate forcing with global processes, and (3) Scientific needs of climate assessment.

  15. Saga of synthetic rubber

    SciTech Connect

    Solo, R.A.

    1980-04-01

    The proposal to establish an Energy Mobilization Board and a synthetic fuels industry is reminiscent of World War II efforts to produce synthetic rubber. To avoid the mistakes made in the earlier effort, Mr. Solo suggests that the synthetic-fuel program should (1) use a more-successful technological development project as a model; (2) commit public funding and not rely on profit-oriented private enterprise; and (3) avoid entrusting social planning to single-purpose entities that have not been sensitive to social values. (DCK)

  16. Modeling the earth system

    SciTech Connect

    Ojima, D.

    1992-12-31

    The 1990 Global Change Institute (GCI) on Earth System Modeling is the third of a series organized by the Office for Interdisciplinary Earth Studies to look in depth at particular issues critical to developing a better understanding of the earth system. The 1990 GCI on Earth System Modeling was organized around three themes: defining critical gaps in the knowledge of the earth system, developing simplified working models, and validating comprehensive system models. This book is divided into three sections that reflect these themes. Each section begins with a set of background papers offering a brief tutorial on the subject, followed by working group reports developed during the institute. These reports summarize the joint ideas and recommendations of the participants and bring to bear the interdisciplinary perspective that imbued the institute. Since the conclusion of the 1990 Global Change Institute, research programs, nationally and internationally, have moved forward to implement a number of the recommendations made at the institute, and many of the participants have maintained collegial interactions to develop research projects addressing the needs identified during the two weeks in Snowmass.

  17. The mechanisms of subharmonic tone generation in a synthetic larynx model.

    PubMed

    Kniesburges, Stefan; Lodermeyer, Alexander; Becker, Stefan; Traxdorf, Maximilian; Döllinger, Michael

    2016-06-01

    The sound spectra obtained in a synthetic larynx exhibited subharmonic tones that are characteristic for diplophonia. Although the generation of subharmonics is commonly associated with asymmetrically oscillating vocal folds, the synthetic elastic vocal folds showed symmetrical oscillations. The amplitudes of the subharmonics decreased with an increasing lateral diameter of the supraglottal channel, which indicates a strong dependence of the supraglottal boundary conditions. Investigations of the supraglottal flow field revealed small cycle-to-cycle variations of the static pressure in the region of the pulsatile glottal jet as the origin of the first subharmonic tone. It is located at half the fundamental frequency of the vocal fold oscillation. A principle component analysis of the supraglottal flow field with the fully developed glottal jet revealed a large recirculation area in the second spatial eigenvector which deflected the glottal jet slightly in a perpendicular direction of the jet axis. The rotation direction of the recirculation area changed with different oscillation cycles between clockwise and counterclockwise. As both directions were uniformly distributed across all acquired oscillation cycles, a cycle-wise change can be assumed. It is concluded that acoustic subharmonics are generated by small fluctuations of the glottal jet location favored by small lateral diameters of the supraglottal channel. PMID:27369142

  18. Autofocusing circular synthetic aperture sonar imagery using phase corrections modeled as generalized cones.

    PubMed

    Marston, Timothy M; Kennedy, Jermaine L; Marston, Philip L

    2014-08-01

    Circular synthetic aperture sonar (CSAS) is a coherent aperture synthesis technique that utilizes backscattered acoustic information from an encircled scene to generate information rich, high-resolution imagery. The aperture length required for image synthesis is much longer than in its linear synthetic aperture sonar counterpart and can result in challenging phase delay and navigation estimation constraints. Residual uncorrected phase errors manifest as focus aberrations in reconstructed CSAS imagery. This paper demonstrates that phase error in image patches can be approximated as an aspect variant linear phase shift representable as a generalized cone in wave-number space. If the geometry of the generalized cone is known, it can be applied as the spectral phase of an inverse filter for aberration correction. A method is derived for reconstructing the error cone geometry from independent estimates of its local curvatures, which are found via a series of one-dimensional line searches that maximize the focus of CSAS sub-aperture images. This approach is applied to real and simulated CSAS data containing aperture distortions, and the results successfully demonstrate estimation and correction of the underlying focus aberrations.

  19. On modeling and controlling intelligent systems

    SciTech Connect

    Dress, W.B.

    1993-11-01

    The aim of this paper is to show how certain diverse and advanced techniques of information processing and system theory might be integrated into a model of an intelligent, complex entity capable of materially enhancing an advanced information management system. To this end, we first examine the notion of intelligence and ask whether a semblance thereof can arise in a system consisting of ensembles of finite-state automata. Our goal is to find a functional model of intelligence in an information-management setting that can be used as a tool. The purpose of this tool is to allow us to create systems of increasing complexity and utility, eventually reaching the goal of an intelligent information management system that provides and anticipates needed data and information. We base our attempt on the ideas of general system theory where the four topics of system identification, modeling, optimization, and control provide the theoretical framework for constructing a complex system that will be capable of interacting with complex systems in the real world. These four key topics are discussed within the purview of cellular automata, neural networks, and evolutionary programming. This is a report of ongoing work, and not yet a success story of a synthetic intelligent system.

  20. A female pelvic bone shape model for air/bone separation in support of synthetic CT generation for radiation therapy

    NASA Astrophysics Data System (ADS)

    Liu, Lianli; Cao, Yue; Fessler, Jeffrey A.; Jolly, Shruti; Balter, James M.

    2016-01-01

    Separating bone from air in MR data is one of the major challenges in using MR images to derive synthetic CT. The problem is further complicated when the anatomic regions filled with air are altered across scans due to air mobility, for instance, in pelvic regions, thereby the air regions estimated using an ultrashort echo time (UTE) sequence are invalid in other image series acquired for multispectral classification. This study aims to develop and investigate a female pelvic bone shape model to identify low intensity regions in MRI where air is unlikely to be present in support of synthetic CT generation without UTE imaging. CT scans of 30 patients were collected for the study, 17 of them also have corresponding MR scans. The shape model was built from the CT dataset, where the reference image was aligned to each of the training images using B-spline deformable registration. Principal component analysis was performed on B-spline coefficients for a compact model where shape variance was described by linear combination of principal modes. The model was applied to identify pelvic bone in MR images by deforming the corresponding MR data of the reference image to target MR images, where the search space of the deformation process was constrained within the subspace spanned by principal modes. The local minima in the search space were removed effectively by the shape model, thus supporting an efficient binary search for the optimal solution. We evaluated the model by its efficacy in identifying bone voxels and excluding air regions. The model was tested across the 17 patients that have corresponding MR scans using a leave-one-out cross validation. A simple model using the first leading principal mode only was found to achieve reasonable accuracy, where an averaged 87% of bone voxels were correctly identified. Finally dilation of the optimally fit bone mask by 5 mm was found to cover 96% of bone voxels while minimally impacting the overlap with air (below 0.4%).

  1. MineSeis -- A MATLAB{reg_sign} GUI program to calculate synthetic seismograms from a linear, multi-shot blast source model

    SciTech Connect

    Yang, X.

    1998-04-01

    Large scale (up to 5 kt) chemical blasts are routinely conducted by mining and quarry industries around the world to remove overburden or to fragment rocks. Because of their ability to trigger the future International Monitoring System (IMS) of the Comprehensive Test Ban Treaty (CTBT), these blasts are monitored and studied by verification seismologists for the purpose of discriminating them from possible clandestine nuclear tests. One important component of these studies is the modeling of ground motions from these blasts with theoretical and empirical source models. The modeling exercises provide physical bases to regional discriminants and help to explain the observed signal characteristics. The program MineSeis has been developed to implement the synthetic seismogram modeling of multi-shot blast sources with the linear superposition of single shot sources. Single shot sources used in the modeling are the spherical explosion plus spall model mentioned here. Mueller and Murphy`s (1971) model is used as the spherical explosion model. A modification of Anandakrishnan et al.`s (1997) spall model is developed for the spall component. The program is implemented with the MATLAB{reg_sign} Graphical User Interface (GUI), providing the user with easy, interactive control of the calculation.

  2. A synthetic system for expression of components of a bacterial microcompartment.

    PubMed

    Sargent, Frank; Davidson, Fordyce A; Kelly, Ciarán L; Binny, Rachelle; Christodoulides, Natasha; Gibson, David; Johansson, Emelie; Kozyrska, Katarzyna; Lado, Lucia Licandro; Maccallum, Jane; Montague, Rachel; Ortmann, Brian; Owen, Richard; Coulthurst, Sarah J; Dupuy, Lionel; Prescott, Alan R; Palmer, Tracy

    2013-11-01

    In general, prokaryotes are considered to be single-celled organisms that lack internal membrane-bound organelles. However, many bacteria produce proteinaceous microcompartments that serve a similar purpose, i.e. to concentrate specific enzymic reactions together or to shield the wider cytoplasm from toxic metabolic intermediates. In this paper, a synthetic operon encoding the key structural components of a microcompartment was designed based on the genes for the Salmonella propanediol utilization (Pdu) microcompartment. The genes chosen included pduA, -B, -J, -K, -N, -T and -U, and each was shown to produce protein in an Escherichia coli chassis. In parallel, a set of compatible vectors designed to express non-native cargo proteins was also designed and tested. Engineered hexa-His tags allowed isolation of the components of the microcompartments together with co-expressed, untagged, cargo proteins. Finally, an in vivo protease accessibility assay suggested that a PduD-GFP fusion could be protected from proteolysis when co-expressed with the synthetic microcompartment operon. This work gives encouragement that it may be possible to harness the genes encoding a non-native microcompartment for future biotechnological applications.

  3. A Short Review of Chemical Reaction Database Systems, Computer-Aided Synthesis Design, Reaction Prediction and Synthetic Feasibility.

    PubMed

    Warr, Wendy A

    2014-06-01

    This article is the text for a pedagogical lecture to be given at the Strasbourg Summer School in Chemoinformatics in June 2104. It covers a very wide range of reaction topics including structure and reaction representation, reaction centers, atom-to-atom mapping, reaction retrieval systems, computer-aided synthesis design, retrosynthesis, reaction prediction and synthetic feasibility. In the time available the coverage of each topic can only be cursory; the main usefulness of this article to the research community is the extensive bibliography.

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

    NASA Astrophysics Data System (ADS)

    Lohpaisankrit, Worapong; Meon, Günter; Tingsanchali, Tawatchai

    2016-05-01

    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 can be applied in

  5. Electronic Education System Model.

    ERIC Educational Resources Information Center

    Cloete, Elsabe

    2001-01-01

    Discusses electronic learning efforts and problems in implementing computers in schools. Defines and describes an electronic educational system model that was developed to assist the designers of different electronic learning settings to plan and successfully implement a specific learning situation, with the focus on the individual requirements of…

  6. Synthetic guide star generation

    DOEpatents

    Payne, Stephen A.; Page, Ralph H.; Ebbers, Christopher A.; Beach, Raymond J.

    2004-03-09

    A system for assisting in observing a celestial object and providing synthetic guide star generation. A lasing system provides radiation at a frequency at or near 938 nm and radiation at a frequency at or near 1583 nm. The lasing system includes a fiber laser operating between 880 nm and 960 nm and a fiber laser operating between 1524 nm and 1650 nm. A frequency-conversion system mixes the radiation and generates light at a frequency at or near 589 nm. A system directs the light at a frequency at or near 589 nm toward the celestial object and provides synthetic guide star generation.

  7. Synthetic guide star generation

    DOEpatents

    Payne, Stephen A [Castro Valley, CA; Page, Ralph H [Castro Valley, CA; Ebbers, Christopher A [Livermore, CA; Beach, Raymond J [Livermore, CA

    2008-06-10

    A system for assisting in observing a celestial object and providing synthetic guide star generation. A lasing system provides radiation at a frequency at or near 938 nm and radiation at a frequency at or near 1583 nm. The lasing system includes a fiber laser operating between 880 nm and 960 nm and a fiber laser operating between 1524 nm and 1650 nm. A frequency-conversion system mixes the radiation and generates light at a frequency at or near 589 nm. A system directs the light at a frequency at or near 589 nm toward the celestial object and provides synthetic guide star generation.

  8. Modified ADM1 for modelling an UASB reactor laboratory plant treating starch wastewater and synthetic substrate load tests.

    PubMed

    Hinken, L; Huber, M; Weichgrebe, D; Rosenwinkel, K-H

    2014-11-01

    A laboratory plant consisting of two UASB reactors was used for the treatment of industrial wastewater from the wheat starch industry. Several load tests were carried out with starch wastewater and the synthetic substrates glucose, acetate, cellulose, butyrate and propionate to observe the impact of changing loads on gas yield and effluent quality. The measurement data sets were used for calibration and validation of the Anaerobic Digestion Model No. 1 (ADM1). For a precise simulation of the detected glucose degradation during load tests with starch wastewater and glucose, it was necessary to incorporate the complete lactic acid fermentation into the ADM1, which contains the formation and degradation of lactate and a non-competitive inhibition function. The modelling results of both reactors based on the modified ADM1 confirm an accurate calculation of the produced gas and the effluent concentrations. Especially, the modelled lactate effluent concentrations for the load cases are similar to the measurements and justified by literature.

  9. Automated analysis of short responses in an interactive synthetic tutoring system for introductory physics

    NASA Astrophysics Data System (ADS)

    Nakamura, Christopher M.; Murphy, Sytil K.; Christel, Michael G.; Stevens, Scott M.; Zollman, Dean A.

    2016-06-01

    Computer-automated assessment of students' text responses to short-answer questions represents an important enabling technology for online learning environments. We have investigated the use of machine learning to train computer models capable of automatically classifying short-answer responses and assessed the results. Our investigations are part of a project to develop and test an interactive learning environment designed to help students learn introductory physics concepts. The system is designed around an interactive video tutoring interface. We have analyzed 9 with about 150 responses or less. We observe for 4 of the 9 automated assessment with interrater agreement of 70% or better with the human rater. This level of agreement may represent a baseline for practical utility in instruction and indicates that the method warrants further investigation for use in this type of application. Our results also suggest strategies that may be useful for writing activities and questions that are more appropriate for automated assessment. These strategies include building activities that have relatively few conceptually distinct ways of perceiving the physical behavior of relatively few physical objects. Further success in this direction may allow us to promote interactivity and better provide feedback in online learning systems. These capabilities could enable our system to function more like a real tutor.

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

    USGS Publications Warehouse

    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.

  11. Anisotropic organization and microscopic manipulation of self-assembling synthetic porphyrin microrods that mimic chlorosomes: bacterial light-harvesting systems.

    PubMed

    Chappaz-Gillot, Cyril; Marek, Peter L; Blaive, Bruno J; Canard, Gabriel; Bürck, Jochen; Garab, Gyozo; Hahn, Horst; Jávorfi, Tamás; Kelemen, Loránd; Krupke, Ralph; Mössinger, Dennis; Ormos, Pál; Reddy, Chilla Malla; Roussel, Christian; Steinbach, Gábor; Szabó, Milán; Ulrich, Anne S; Vanthuyne, Nicolas; Vijayaraghavan, Aravind; Zupcanova, Anita; Balaban, Teodor Silviu

    2012-01-18

    Being able to control in time and space the positioning, orientation, movement, and sense of rotation of nano- to microscale objects is currently an active research area in nanoscience, having diverse nanotechnological applications. In this paper, we demonstrate unprecedented control and maneuvering of rod-shaped or tubular nanostructures with high aspect ratios which are formed by self-assembling synthetic porphyrins. The self-assembly algorithm, encoded by appended chemical-recognition groups on the periphery of these porphyrins, is the same as the one operating for chlorosomal bacteriochlorophylls (BChl's). Chlorosomes, rod-shaped organelles with relatively long-range molecular order, are the most efficient naturally occurring light-harvesting systems. They are used by green photosynthetic bacteria to trap visible and infrared light of minute intensities even at great depths, e.g., 100 m below water surface or in volcanic vents in the absence of solar radiation. In contrast to most other natural light-harvesting systems, the chlorosomal antennae are devoid of a protein scaffold to orient the BChl's; thus, they are an attractive goal for mimicry by synthetic chemists, who are able to engineer more robust chromophores to self-assemble. Functional devices with environmentally friendly chromophores-which should be able to act as photosensitizers within hybrid solar cells, leading to high photon-to-current conversion efficiencies even under low illumination conditions-have yet to be fabricated. The orderly manner in which the BChl's and their synthetic counterparts self-assemble imparts strong diamagnetic and optical anisotropies and flow/shear characteristics to their nanostructured assemblies, allowing them to be manipulated by electrical, magnetic, or tribomechanical forces. PMID:22148684

  12. Synthetic microbial ecosystems for biotechnology.

    PubMed

    Pandhal, Jagroop; Noirel, Josselin

    2014-06-01

    Most highly controlled and specific applications of microorganisms in biotechnology involve pure cultures. Maintaining single strain cultures is important for industry as contaminants can reduce productivity and lead to longer "down-times" during sterilisation. However, microbes working together provide distinct advantages over pure cultures. They can undertake more metabolically complex tasks, improve efficiency and even expand applications to open systems. By combining rapidly advancing technologies with ecological theory, the use of microbial ecosystems in biotechnology will inevitably increase. This review provides insight into the use of synthetic microbial communities in biotechnology by applying the engineering paradigm of measure, model, manipulate and manufacture, and illustrate the emerging wider potential of the synthetic ecology field. Systems to improve biofuel production using microalgae are also discussed.

  13. Modelling resonant planetary systems

    NASA Astrophysics Data System (ADS)

    Emel'yanenko, V.

    2012-09-01

    Many discovered multi-planet systems are in meanmotion resonances. The aim of this work is to study dynamical processes leading to the formation of resonant configurations on the basis of a unified model described earlier [1]. The model includes gravitational interactions of planets and migration of planets due to the presence of a gas disc. For the observed systems 24 Sex, HD 37124, HD 73526, HD 82943, HD 128311, HD 160691, Kepler 9, NN Ser with planets moving in the 2:1 resonance, it is shown that the capture in this resonance occurs at very wide ranges of parameters of both type I and type II migration. Conditions of migration leading to the formation of the resonant systems HD 45364 и HD 200964 (3:2 and 4:3, respectively) are obtained. Formation scenarios are studied for the systems HD 102272, HD 108874, HD 181433, HD 202206 with planets in high order resonances. We discuss also how gravitational interactions of planets and planetesimal discs lead to the breakup of resonant configurations and the formation of systems similar to the 47 UMa system.

  14. Synthetic peptide models for the redox-active disulfide loop of glutaredoxin. Conformational studies

    SciTech Connect

    Kishore, R.; Raghothama, S.; Balaram, P.

    1988-04-05

    Two cyclic peptide disulfides have been synthesized as models for the 14-membered redox-active disulfide loop glutaredoxin. /sup 1/H NMR studies at 270 MHz in chloroform solutions establish a type I ..beta..-turn conformation for the Pro-X segment in both peptides, stabilized by a 4 ..-->.. 1 hydrogen bond between the Cys(1) CO and Cys(4) NH groups. Nuclear Overhauser effects establish that the aromatic ring in the X = Phe peptide is oriented over the central peptide unit. In dimethyl sulfoxide solutions two conformational species are observed in slow exchange on the NMR time scale, for both peptides. These are assigned to type I and type II ..beta..-turn structures with -Pro-Tyr(Phe)-as the corner resides. The structural assignments are based on correlation of NMR parameters with model 14-membered cyclic cystine peptides with Pro-X spacers. Circular dichroism studies based on the -S-S-n-sigma* transition suggest a structural change in the disulfide bridge with changing solvent polarity, establishing conformational coupling between the peptide backbone and the disulfide linkage in these systems.

  15. Synthetic peptides.

    PubMed

    Francis, M J

    1996-01-01

    Efforts to produce more stable and defined vaccines have concentrated on studying, in detail, the immune response to many infectious diseases in order to identify the antigenic sites on the pathogens that are involved in stimulating protective immumty. Armed with this knowledge, it is possible to mimic such sites by producing short chains of amino acids (peptides) and to use these as the basis for novel vaccines. The earliest documented work on peptide immunization is actually for a plant virus, tobacco mosaic virus. In 1963, Anderer (1) demonstrated that rabbit antibodies to an isolated hexapeptide fragment from the virus-coat protein coupled to bovine serum albumm would neutralize the infectious vn-us in culture. Two years later, he used a synthetically produced copy of the same peptide to confirm this observation. This was pioneering work, and it was over 10 years before the next example of a peptide that elicited antivirus antibody appeared following work by Sela and his colleagues (2) on a virus, MS2 bacteriophage, which infects bacteria. The emergence of more accessible techniques for sequencing proteins in 1977, coupled with the ability to synthesize readily peptides already developed in 1963, heralded a decade of intensive research into experimental peptide vaccines. The first demonstration that peptides could elicit protective immunity in vivo, in addition to neutralizing activity in vitro, was obtained using a peptide from the VP1 coat protein of foot-and-mouth disease virus (FMDV) in 1982, with the guinea pig as a laboratory animal model (3, 4). PMID:21359696

  16. Synthetic Catalysts for CO2 Storage: Catalytic Improvement of Solvent Capture Systems

    SciTech Connect

    2010-08-15

    IMPACCT Project: LLNL is designing a process to pull CO2 out of the exhaust gas of coal-fired power plants so it can be transported, stored, or utilized elsewhere. Human lungs rely on an enzyme known as carbonic anhydrase to help separate CO2 from our blood and tissue as part of the normal breathing process. LLNL is designing a synthetic catalyst with the same function as this enzyme. The catalyst can be used to quickly capture CO2 from coal exhaust, just as the natural enzyme does in our lungs. LLNL is also developing a method of encapsulating chemical solvents in permeable microspheres that will greatly increase the speed of binding of CO2. The goal of the project is an industry-ready chemical vehicle that can withstand the harsh environments found in exhaust gas and enable new, simple process designs requiring less capital investment.

  17. Synthetic Jets

    NASA Technical Reports Server (NTRS)

    Milanovic, Ivana M.

    2003-01-01

    Current investigation of synthetic jets and synthetic jets in cross-flow examined the effects of orifice geometry and dimensions, momentum-flux ratio, cluster of orifices, pitch and yaw angles as well as streamwise development of the flow field. This comprehensive study provided much needed experimental information related to the various control strategies. The results of the current investigation on isolated and clustered synthetic jets with and without cross-flow will be further analyzed and documented in detail. Presentations at national conferences and publication of peer- reviewed journal articles are also expected. Projected publications will present both the mean and turbulent properties of the flow field, comparisons made with the data available in an open literature, as well as recommendations for the future work.

  18. The combination of the histone deacetylase inhibitor vorinostat and synthetic triterpenoids reduces tumorigenesis in mouse models of cancer

    PubMed Central

    Liby, Karen T.

    2013-01-01

    Novel drugs and drug combinations are needed for the chemoprevention and treatment of cancer. We show that the histone deacetylase inhibitor vorinostat [suberoylanilide hydroxamic acid (SAHA)] and the methyl ester or ethyl amide derivatives of the synthetic triterpenoid 2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid (CDDO-Me and CDDO-Ea, respectively) cooperated to inhibit the de novo synthesis of nitric oxide in RAW 264.7 macrophage-like cells and in primary mouse peritoneal macrophages. Additionally, SAHA enhanced the ability of synthetic triterpenoids to delay formation of estrogen receptor-negative mammary tumors in MMTV-polyoma middle T (PyMT) mice. CDDO-Me (50mg/kg diet) and SAHA (250mg/kg diet) each significantly delayed the initial development of tumors by 4 (P < 0.001) and 2 (P < 0.05) weeks, respectively, compared with the control group in the time required to reach 50% tumor incidence. CDDO-Ea (400mg/kg diet), as a single agent, did not delay tumor development. The combination of either triterpenoid with SAHA was significantly more potent than the individual drugs for delaying tumor development, with a 7 week (P < 0.001) delay before 50% tumor incidence was reached. SAHA, alone and in combination with CDDO-Me, also significantly (P < 0.05) inhibited the infiltration of tumor-associated macrophages into the mammary glands of PyMT mice and levels of the chemokine macrophage colony-stimulating factor in primary PyMT tumor cells. In addition, SAHA and the synthetic triterpenoids cooperated to suppress secreted levels of the pro-angiogenic factor matrix metalloproteinase-9. Similar results were observed in mouse models of pancreatic and lung cancer. At concentrations that were anti-inflammatory, SAHA had no effect on histone acetylation. These studies suggest that both SAHA and triterpenoids effectively delay tumorigenesis, thereby demonstrating a promising, novel drug combination for chemoprevention. PMID:23042302

  19. Continuous wave synthetic low-coherence wind sensing Lidar: motionless measurement system with subsequent numerical range scanning.

    PubMed

    Brinkmeyer, Ernst; Waterholter, Thomas

    2013-01-28

    A continuous wave (CW) Lidar system for detection of scattering from atmospheric aerosol particles is presented which is useful in particular for remote sensing of wind velocities. It is based on a low-coherence interferometric setup powered by a synthetic broadband laser source with Gaussian power density spectrum. The laser bandwidth is electronically adjustable and determines the spatial resolution which is independent of range. The Lidar system has no moving parts. The location to be resolved can be shifted numerically after the measurement meaning that a single measurement already contains the full range information. The features of constant resolution and numerical range scanning are in sharp contrast to ordinary CW Lidar systems. PMID:23389172

  20. NEP systems model

    NASA Astrophysics Data System (ADS)

    George, Jeffrey A.

    A new nuclear electric propulsion (NEP) systems analysis code is discussed. The new code is modular and consists of a driver code and various subsystem models. The code models five different subsystems: (1) reactor/shield; (2) power conversion; (3) heat rejection; (4) power management and distribution (PMAD); and (5) thrusters. The code optimizes for the following design criteria: minimum mass; minimum radiator area; and low mass/low area. The code also optimizes the following parameters: separation distance; temperature ratio; pressure ratio; and transmission frequency. The discussion is presented in vugraph form.

  1. Modelling robot construction systems

    NASA Technical Reports Server (NTRS)

    Grasso, Chris

    1990-01-01

    TROTER's are small, inexpensive robots that can work together to accomplish sophisticated construction tasks. To understand the issues involved in designing and operating a team of TROTER's, the robots and their components are being modeled. A TROTER system that features standardized component behavior is introduced. An object-oriented model implemented in the Smalltalk programming language is described and the advantages of the object-oriented approach for simulating robot and component interactions are discussed. The presentation includes preliminary results and a discussion of outstanding issues.

  2. Numerical modeling on the source parameter scaling relations and synthetic surface deformation of episodic slow slip events in subduction zones

    NASA Astrophysics Data System (ADS)

    Liu, Y.

    2013-12-01

    moment-duration relation may be dependent on friction parameters and pore pressure condition. We also compute the resulted surface deformation (synthetic GPS time series) due to the spatiotemporal evolution of slip velocity on the subduction fault. Preliminary modeling results show that the along-strike segmentation in Cascadia SSEs may result from the slip velocity variation as SSEs propagate along the trench. Comparison between the spectra of modeled synthetic displacement and the Plate Boundary Observatory GPS time series along Cascadia will be conducted, to determine the detection threshold of the synthetic signal.

  3. Opportunities in plant synthetic biology.

    PubMed

    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.

  4. Opportunities in plant synthetic biology.

    PubMed

    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. PMID:24502956

  5. Validation of model-based estimates (synthetic estimates) of the prevalence of risk factors for coronary heart disease for wards in England.

    PubMed

    Scarborough, Peter; Allender, Steven; Rayner, Mike; Goldacre, Michael

    2009-06-01

    Several sets of model-based estimates (synthetic estimates) of the prevalence of risk factors for coronary heart disease for small areas in England have been developed. These have been used in policy documents to indicate which areas are in need of intervention. In general, these models have not been subjected to validity assessment. This paper describes a validity assessment of 16 sets of synthetic estimates, by comparison of the models with national, regional and local survey-based estimates, and local mortality rate estimates. Model-based estimates of the prevalence of smoking, low fruit and vegetable consumption, obesity, hypertension and raised cholesterol are found to be valid.

  6. Piloted Simulation of Various Synthetic Vision Systems Terrain Portrayal and Guidance Symbology Concepts for Low Altitude En-Route Scenario

    NASA Technical Reports Server (NTRS)

    Takallu, M. A.; Glaab, L. J.; Hughes, M. F.; Wong, D. T.; Bartolone, A. P.

    2008-01-01

    In support of the NASA Aviation Safety Program's Synthetic Vision Systems Project, a series of piloted simulations were conducted to explore and quantify the relationship between candidate Terrain Portrayal Concepts and Guidance Symbology Concepts, specific to General Aviation. The experiment scenario was based on a low altitude en route flight in Instrument Metrological Conditions in the central mountains of Alaska. A total of 18 general aviation pilots, with three levels of pilot experience, evaluated a test matrix of four terrain portrayal concepts and six guidance symbology concepts. Quantitative measures included various pilot/aircraft performance data, flight technical errors and flight control inputs. The qualitative measures included pilot comments and pilot responses to the structured questionnaires such as perceived workload, subjective situation awareness, pilot preferences, and the rare event recognition. There were statistically significant effects found from guidance symbology concepts and terrain portrayal concepts but no significant interactions between them. Lower flight technical errors and increased situation awareness were achieved using Synthetic Vision Systems displays, as compared to the baseline Pitch/Roll Flight Director and Blue Sky Brown Ground combination. Overall, those guidance symbology concepts that have both path based guidance cue and tunnel display performed better than the other guidance concepts.

  7. Development of a Synthetic Oxytetracycline-Inducible Expression System for Streptomycetes Using de Novo Characterized Genetic Parts.

    PubMed

    Wang, Weishan; Yang, Tongjian; Li, Yihong; Li, Shanshan; Yin, Shouliang; Styles, Kathryn; Corre, Christophe; Yang, Keqian

    2016-07-15

    Precise control of gene expression using exogenous factors is of great significance. To develop ideal inducible expression systems for streptomycetes, new genetic parts, oxytetracycline responsive repressor OtrR, operator otrO, and promoter otrBp from Streptomyces rimosus, were selected de novo and characterized in vivo and in vitro. OtrR showed strong affinity to otrO (KD = 1.7 × 10(-10) M) and oxytetracycline induced dissociation of the OtrR/DNA complex in a concentration-dependent manner. On the basis of these genetic parts, a synthetic inducible expression system Potr* was optimized. Induction of Potr* with 0.01-4 μM of oxytetracycline triggered a wide-range expression level of gfp reporter gene in different Streptomyces species. Benchmarking Potr* against the widely used constitutive promoters ermE* and kasOp* revealed greatly enhanced levels of expression when Potr* was fully induced. Finally, Potr* was used as a tool to activate and optimize the expression of the silent jadomycin biosynthetic gene cluster in Streptomyces venezuelae. Altogether, the synthetic Potr* presents a new versatile tool for fine-tuning gene expression in streptomycetes.

  8. Synthetic earthquake catalogs simulating seismic activity in the Corynth Gulf, Greece, fault system

    NASA Astrophysics Data System (ADS)

    Console, R.; Carluccio, R.; Papadimitriou, E. E.; Karakostas, V. G.

    2014-12-01

    The characteristic earthquake hypothesis is the basis of time-dependent modeling of earthquake recurrence on major faults, using the renewal process methodology. However, the characteristic earthquake hypothesis is not strongly supported by observational data. Few fault segments have long historical or paleoseismic records of individually dated ruptures, and when data and parameter uncertainties are allowed for, the form of the recurrence-distribution is difficult to establish. This is the case, for instance, of the Corinth gulf fault system, for which documents about strong earthquakes exist for at least two thousand years, but they can be considered complete for magnitudes > 6.0 only for the latest 300 years, during which only few characteristic earthquakes are reported for single fault segments. The use of a physics-based earthquake simulator has allowed the production of catalogs lasting 100,000 years and containing more than 500,000 events of magnitudes > 4.0. The main features of our simulation algorithm are (1) the imposition of an average slip rate released by earthquakes to every single segment recognized in the investigated fault system, (2) the interaction between earthquake sources, (3) a self-organized earthquake magnitude distribution, and (4) the effect of minor earthquakes in redistributing stress. The application of our simulation algorithm to the Corinth gulf fault system has shown realistic features in time, space and magnitude behavior of the seismicity. These features include long-term periodicity of strong earthquakes, short-term clustering of both strong and smaller events, and a realistic earthquake magnitude distribution departing from the Gutenberg-Richter distribution in the higher magnitude range.

  9. Tuning the dials of Synthetic Biology

    PubMed Central

    Arpino, James A. J.; Hancock, Edward J.; Anderson, James; Barahona, Mauricio; Stan, Guy-Bart V.; Polizzi, Karen

    2013-01-01

    Synthetic Biology is the ‘Engineering of Biology’ – it aims to use a forward-engineering design cycle based on specifications, modelling, analysis, experimental implementation, testing and validation to modify natural or design new, synthetic biology systems so that they behave in a predictable fashion. Motivated by the need for truly plug-and-play synthetic biological components, we present a comprehensive review of ways in which the various parts of a biological system can be modified systematically. In particular, we review the list of ‘dials’ that are available to the designer and discuss how they can be modelled, tuned and implemented. The dials are categorized according to whether they operate at the global, transcriptional, translational or post-translational level and the resolution that they operate at. We end this review with a discussion on the relative advantages and disadvantages of some dials over others. PMID:23704788

  10. Comparison of Experimental and Model Data for the Evaporation of a Synthetic Topopah Spring Tuff Pore Water, Yucca Mountain, NV

    SciTech Connect

    Alai, M; Sutton, M; Carroll, S

    2003-10-14

    The evaporation of a range of synthetic pore water solutions representative of the potential high-level-nuclear-waste repository at Yucca Mountain, NV is being investigated. The motivation of this work is to understand and predict the range of brine compositions that may contact the waste containers from evaporation of pore waters, because these brines could form corrosive thin films on the containers and impact their long-term integrity. A relatively complex synthetic Topopah Spring Tuff pore water was progressively concentrated by evaporation in a closed vessel, heated to 95 C in a series of sequential experiments. Periodic samples of the evaporating solution were taken to determine the evolving water chemistry. According to chemical divide theory at 25 C and 95 C our starting solution should evolve towards a high pH carbonate brine. Results at 95 C show that this solution evolves towards a complex brine that contains about 99 mol% Na{sup +} for the cations, and 71 mol% Cl{sup -}, 18 mol% {Sigma}CO{sub 2}(aq), 9 mol% SO{sub 4}{sup 2-} for the anions. Initial modeling of the evaporating solution indicates precipitation of aragonite, halite, silica, sulfate and fluoride phases. The experiments have been used to benchmark the use of the EQ3/6 geochemical code in predicting the evolution of carbonate-rich brines during evaporation.

  11. Combinatorial biosynthesis of cyclic lipopeptide antibiotics: a model for synthetic biology to accelerate the evolution of secondary metabolite biosynthetic pathways.

    PubMed

    Baltz, Richard H

    2014-10-17

    Nonribosomal peptide synthetases (NRPSs) are giant multi-enzymes that carry out sequencial assembly line couplings of amino acids to generate linear or cyclic peptides. NRPSs are composed of repeating enzyme domains with modular organization to activate and couple specific amino acids in a particular order. From a synthetic biology perspective, they can be considered as peptide assembly machines composed of devices to couple fatty acids to l-amino acids, l-amino acids to l-amino acids, and d-amino acids to l-amino acids. The coupling devices are composed of specific parts that contain two or more enzyme domains that can be exchanged combinatorially to generate novel peptide assembly machines to produce novel peptides. The potent lipopeptide antibiotics daptomycin and A54145E have identical cyclic depsipeptide ring structures and stereochemistry but have divergent amino acid sequences. As their biosynthetic gene clusters are derived from an ancient ancestral lipopetide pathway, these lipopeptides provided an attractive model to develop combinatorial biosynthesis to generate antibiotics superior to daptomycin. These studies on combinatorial biosynthesis have helped generate guidelines for the successful assembly of NRPS parts and devices that can be used to generate novel lipopeptide structures and have established a basis for future synthetic biology studies to further develop combinatorial biosynthesis as a robust approach to natural product drug discovery.

  12. An In Vitro Model for Oral Mixed Biofilms of Candida albicans and Streptococcus gordonii in Synthetic Saliva

    PubMed Central

    Montelongo-Jauregui, Daniel; Srinivasan, Anand; Ramasubramanian, Anand K.; Lopez-Ribot, Jose L.

    2016-01-01

    As a member of the normal human oral microbiota, the fungus Candida 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 and confocal scanning laser microscopy. 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. PMID:27242712

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

    PubMed

    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.

  14. Experimental measurements and mathematical modeling of biological noise arising from transcriptional and translational regulation of basic synthetic gene circuits.

    PubMed

    Bandiera, Lucia; Pasini, Alice; Pasotti, Lorenzo; Zucca, Susanna; Mazzini, Giuliano; Magni, Paolo; Giordano, Emanuele; Furini, Simone

    2016-04-21

    The small number of molecules, unevenly distributed within an isogenic cell population, makes gene expression a noisy process, and strategies have evolved to deal with this variability in protein concentration and to limit its impact on cellular behaviors. As translational efficiency has a major impact on biological noise, a possible strategy to control noise is to regulate gene expression processes at the post-transcriptional level. In this study, fluctuations in the concentration of a green fluorescent protein were compared, at the single cell level, upon transformation of an isogenic bacterial cell population with synthetic gene circuits implementing either a transcriptional or a post-transcriptional control of gene expression. Experimental measurements showed that protein variability is lower under post-transcriptional control, when the same average protein concentrations are compared. This effect is well reproduced by stochastic simulations, supporting the hypothesis that noise reduction is due to the control mechanism acting on the efficiency of translation. Similar strategies are likely to play a role in noise reduction in natural systems and to be useful for controlling noise in synthetic biology applications.

  15. Collective operations in a file system based execution model

    DOEpatents

    Shinde, Pravin; Van Hensbergen, Eric

    2013-02-12

    A mechanism is provided for group communications using a MULTI-PIPE synthetic file system. A master application creates a multi-pipe synthetic file in the MULTI-PIPE synthetic file system, the master application indicating a multi-pipe operation to be performed. The master application then writes a header-control block of the multi-pipe synthetic file specifying at least one of a multi-pipe synthetic file system name, a message type, a message size, a specific destination, or a specification of the multi-pipe operation. Any other application participating in the group communications then opens the same multi-pipe synthetic file. A MULTI-PIPE file system module then implements the multi-pipe operation as identified by the master application. The master application and the other applications then either read or write operation messages to the multi-pipe synthetic file and the MULTI-PIPE synthetic file system module performs appropriate actions.

  16. Collective operations in a file system based execution model

    DOEpatents

    Shinde, Pravin; Van Hensbergen, Eric

    2013-02-19

    A mechanism is provided for group communications using a MULTI-PIPE synthetic file system. A master application creates a multi-pipe synthetic file in the MULTI-PIPE synthetic file system, the master application indicating a multi-pipe operation to be performed. The master application then writes a header-control block of the multi-pipe synthetic file specifying at least one of a multi-pipe synthetic file system name, a message type, a message size, a specific destination, or a specification of the multi-pipe operation. Any other application participating in the group communications then opens the same multi-pipe synthetic file. A MULTI-PIPE file system module then implements the multi-pipe operation as identified by the master application. The master application and the other applications then either read or write operation messages to the multi-pipe synthetic file and the MULTI-PIPE synthetic file system module performs appropriate actions.

  17. Leachability of chemical constituents in soil–plant systems irrigated with synthetic graywater.

    PubMed

    Negahban-Azar, Masoud; Sharvelle, Sybil E; Qian, Yaling; Shogbon, Alicia

    2013-04-01

    Over recent years, reuse of graywater for irrigation has become increasingly widespread internationally. While this practice is rapidly growing, there remain unanswered questions with respect to impacts to environmental quality and human health. The objective of this research was to determine the leachability of graywater constituents after applied to soil through a set of controlled greenhouse experiments. Four plant species including bermudagrass, tall fescue, Meyer Lemon and Emerald Gaiety Euonymus were included in the study. Three replicate columns for each species were set up and irrigated either with synthetic graywater or potable water for a 17 month duration. Leachate quality was assessed for dissolved organic carbon, nitrate, ammonium, total phosphorous, boron, sodium adsorption ratio, conductivity, surfactants, and total dissolved solids. The same constituents and also organic matter were measured in soil samples collected at the end of experiments. Phosphorus did not leach through the 50 cm deep soil columns. Salts, including boron, showed potential to leach through graywater irrigated soil. A portion of the applied nitrogen was assimilated by plants, but leaching of nitrogen was still observed as documented by statistically higher nitrogen in leachate collected from graywater-irrigated columns compared to potable water-irrigated columns (P ≤ 0.05). A low percentage of surfactants added to columns leached through (7 ± 6% on average) and a mass balance on surfactant parent compounds showed that 92–96% of added surfactants were biodegraded. PMID:23653909

  18. Extended tracking of the microbial community structure and dynamics in an industrial synthetic metalworking fluid system.

    PubMed

    Kapoor, Renuka; Selvaraju, Suresh B; Yadav, Jagjit S

    2014-03-01

    Understanding of the occupational exposure risk scenario and disease etiology associated with industrial metalworking fluids (MWFs) requires knowledge of the development and composition of their microbial diversity in relation to the underlying fluid management factors. In this study, a managed synthetic MWF operation freshly recharged following the dumping, cleaning, and recharge (DCR) process was tracked in real time for microbial community changes over a period of 1.25 years (65 weeks). The recharged fluid developed very high bacterial counts (viable and nonviable) fairly quickly after the DCR process, indicating its inadequacy. Genus-/group-specific real-time qPCR confirmed the prevalence of six potentially pathogenic/immunogenic microbial genera/groups, viz. pseudomonads, enterics, mycobacteria, legionellae, actinomycetes, and fungi. Selective culturing revealed Acinetobacter and Bacillus as the most frequently isolated Gram-negative and Gram-positive genera, respectively, in addition to the presence of fungi and actinomycetes. Endotoxin perturbations (< 1000 to > 100000 EU mL⁻¹) coincided with temporal increases in Gram-negative bacteria and/or periodic biocide additions. PCR-DGGE-sequencing revealed an expanded estimated bacterial richness (up to 23 bands per sample). Of the 16 dominant bacterial phylotypes identified, the majority were detected for the first time in MWF. Interestingly, the study revealed a crucial role for MWF brand, among other fluid factors, in modulating the community structure and dynamics. PMID:24256434

  19. Fatal attraction: synthetic musk fragrances compromise multixenobiotic defense systems in mussels.

    PubMed

    Luckenbach, Till; Corsi, Ilaria; Epel, David

    2004-01-01

    We studied interactions of nitromusk compounds musk ketone and musk xylene and polycyclic musks Galaxolide trade mark (HHCB), Celestolide trade mark (ADBI), Tetralide trade mark (AHTN), and Traseolide trade mark (AITI) with multixenobiotic resistance (mxr) transporters in gill tissue of the marine mussel Mytilus californianus (Conrad, 1837). A competitive substrate transport test with rhodamine B was used to assay modulation of transport activity by musks. All tested musks inhibited the transport activity in the low microm range as indicated by increased accumulation of rhodamine B in the tissue. Compared to known substrates of mxr transporters, the effective concentration range was similar to quinidine and about 100 times higher than verapamil. Musk ketone and musk xylene also inhibited efflux of rhodamine B from gill tissue which was loaded with the dye and subsequently incubated with these compounds. Synthetic musk compounds are persistent environmental pollutants in aquatic environments with a high potential to bioaccumulate. As potent inhibitors of mxr transporters they may also play a role as chemosensitizers that enable toxic mxr substrates to accumulate in cells of aquatic organisms.

  20. Efficient Enzymatic Preparation of (13) N-Labelled Amino Acids: Towards Multipurpose Synthetic Systems.

    PubMed

    da Silva, Eunice S; Gómez-Vallejo, Vanessa; Baz, Zuriñe; Llop, Jordi; López-Gallego, Fernando

    2016-09-12

    Nitrogen-13 can be efficiently produced in biomedical cyclotrons in different chemical forms, and its stable isotopes are present in the majority of biologically active molecules. Hence, it may constitute a convenient alternative to Fluorine-18 and Carbon-11 for the preparation of positron-emitter-labelled radiotracers; however, its short half-life demands for the development of simple, fast, and efficient synthetic processes. Herein, we report the one-pot, enzymatic and non-carrier-added synthesis of the (13) N-labelled amino acids l-[(13) N]alanine, [(13) N]glycine, and l-[(13) N]serine by using l-alanine dehydrogenase from Bacillus subtilis, an enzyme that catalyses the reductive amination of α-keto acids by using nicotinamide adenine dinucleotide (NADH) as the redox cofactor and ammonia as the amine source. The integration of both l-alanine dehydrogenase and formate dehydrogenase from Candida boidinii in the same reaction vessel to facilitate the in situ regeneration of NADH during the radiochemical synthesis of the amino acids allowed a 50-fold decrease in the concentration of the cofactor without compromising reaction yields. After optimization of the experimental conditions, radiochemical yields were sufficient to carry out in vivo imaging studies in small rodents. PMID:27515007

  1. An automated lung nodule detection system for CT images using synthetic minority oversampling

    NASA Astrophysics Data System (ADS)

    Mehre, Shrikant A.; Mukhopadhyay, Sudipta; Dutta, Anirvan; Harsha, Nagam Chaithan; Dhara, Ashis Kumar; Khandelwal, Niranjan

    2016-03-01

    Pulmonary nodules are a potential manifestation of lung cancer, and their early detection can remarkably enhance the survival rate of patients. This paper presents an automated pulmonary nodule detection algorithm for lung CT images. The algorithm utilizes a two-stage approach comprising nodule candidate detection followed by reduction of false positives. The nodule candidate detection involves thresholding, followed by morphological opening. The geometrical features at this stage are selected from properties of nodule size and compactness, and lead to reduced number of false positives. An SVM classifier is used with a radial basis function kernel. The data imbalance, due to uneven distribution of nodules and non-nodules as a result of the candidate detection stage, is proposed to be addressed by oversampling of minority class using Synthetic Minority Over-sampling Technique (SMOTE), and over-imposition of its misclassification penalty. Experiments were performed on 97 CT scans of a publically-available (LIDC-IDRI) database. Performance is evaluated in terms of sensitivity and false positives per scan (FP/scan). Results indicate noteworthy performance of the proposed approach (nodule detection sensitivity after 4-fold cross-validation is 92.91% with 3 FP/scan). Comparative analysis also reflects a comparable and often better performance of the proposed setup over some of the existing techniques.

  2. The Role of Galectin-1 in Cancer Progression, and Synthetic Multivalent Systems for the Study of Galectin-1.

    PubMed

    Cousin, Jonathan M; Cloninger, Mary J

    2016-01-01

    This review discusses the role of galectin-1 in the tumor microenvironment. First, the structure and function of galectin-1 are discussed. Galectin-1, a member of the galectin family of lectins, is a functionally dimeric galactoside-binding protein. Although galectin-1 has both intracellular and extracellular functions, the defining carbohydrate-binding role occurs extracellularly. In this review, the extracellular roles of galectin-1 in cancer processes are discussed. In particular, the importance of multivalent interactions in galectin-1 mediated cellular processes is reviewed. Multivalent interactions involving galectin-1 in cellular adhesion, mobility and invasion, tumor-induced angiogenesis, and apoptosis are presented. Although the mechanisms of action of galectin-1 in these processes are still not well understood, the overexpression of galectin-1 in cancer progression indicates that the role of galectin-1 is significant. To conclude this review, synthetic frameworks that have been used to modulate galectin-1 processes are reviewed. Small molecule oligomers of carbohydrates, carbohydrate-functionalized pseudopolyrotaxanes, cyclodextrins, calixarenes, and glycodendrimers are presented. These synthetic multivalent systems serve as important tools for studying galectin-1 mediated cancer cellular functions. PMID:27649167

  3. The Role of Galectin-1 in Cancer Progression, and Synthetic Multivalent Systems for the Study of Galectin-1.

    PubMed

    Cousin, Jonathan M; Cloninger, Mary J

    2016-01-01

    This review discusses the role of galectin-1 in the tumor microenvironment. First, the structure and function of galectin-1 are discussed. Galectin-1, a member of the galectin family of lectins, is a functionally dimeric galactoside-binding protein. Although galectin-1 has both intracellular and extracellular functions, the defining carbohydrate-binding role occurs extracellularly. In this review, the extracellular roles of galectin-1 in cancer processes are discussed. In particular, the importance of multivalent interactions in galectin-1 mediated cellular processes is reviewed. Multivalent interactions involving galectin-1 in cellular adhesion, mobility and invasion, tumor-induced angiogenesis, and apoptosis are presented. Although the mechanisms of action of galectin-1 in these processes are still not well understood, the overexpression of galectin-1 in cancer progression indicates that the role of galectin-1 is significant. To conclude this review, synthetic frameworks that have been used to modulate galectin-1 processes are reviewed. Small molecule oligomers of carbohydrates, carbohydrate-functionalized pseudopolyrotaxanes, cyclodextrins, calixarenes, and glycodendrimers are presented. These synthetic multivalent systems serve as important tools for studying galectin-1 mediated cancer cellular functions.

  4. The Role of Galectin-1 in Cancer Progression, and Synthetic Multivalent Systems for the Study of Galectin-1

    PubMed Central

    Cousin, Jonathan M.; Cloninger, Mary J.

    2016-01-01

    This review discusses the role of galectin-1 in the tumor microenvironment. First, the structure and function of galectin-1 are discussed. Galectin-1, a member of the galectin family of lectins, is a functionally dimeric galactoside-binding protein. Although galectin-1 has both intracellular and extracellular functions, the defining carbohydrate-binding role occurs extracellularly. In this review, the extracellular roles of galectin-1 in cancer processes are discussed. In particular, the importance of multivalent interactions in galectin-1 mediated cellular processes is reviewed. Multivalent interactions involving galectin-1 in cellular adhesion, mobility and invasion, tumor-induced angiogenesis, and apoptosis are presented. Although the mechanisms of action of galectin-1 in these processes are still not well understood, the overexpression of galectin-1 in cancer progression indicates that the role of galectin-1 is significant. To conclude this review, synthetic frameworks that have been used to modulate galectin-1 processes are reviewed. Small molecule oligomers of carbohydrates, carbohydrate-functionalized pseudopolyrotaxanes, cyclodextrins, calixarenes, and glycodendrimers are presented. These synthetic multivalent systems serve as important tools for studying galectin-1 mediated cancer cellular functions. PMID:27649167

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

    NASA Astrophysics Data System (ADS)

    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).

  6. Phase-locked flow field analysis in a synthetic human larynx model

    NASA Astrophysics Data System (ADS)

    Lodermeyer, Alexander; Becker, Stefan; Döllinger, Michael; Kniesburges, Stefan

    2015-04-01

    The fluid flow within a human larynx plays an essential role in the fluid-structure-acoustic interaction during voice production. This study addresses the flow field downstream of aerodynamically driven, synthetic vocal folds. In order to quantitatively investigate the supraglottal formation of the flow field within one oscillation cycle of the vocal folds, a phase-locked PIV technique is introduced. The pseudo-time-resolved measurement results were averaged for each phase angle. When including a supraglottal channel, the jet was deflected from the centerline of the supraglottal channel and changed the direction of deflection in different cycles. The result is a bistable flow field. Therefore, a sorting method based on the mean cyclic supraglottal pressure difference was introduced. For both states of the flow field, a recirculation area was detected, interacting with the arising glottal jet in every oscillation cycle. This interaction could be identified as the major cause for supraglottal jet deflection, and the sense of rotation of the recirculation area defined the direction of deflection. The asymmetric structure of the flow field was caused by the geometric boundary condition, i.e., due to the present supraglottal channel. An additional key factor was found to be the contact between the two vocal folds in each oscillation cycle which interrupted the jet flow periodically. Removing the supraglottal channel resulted in a symmetric jet location. When avoiding vocal fold contact, the bistable behavior vanished and the jet was steadily deflected to one lateral side. In the present study, it cannot be confirmed that the Coanda effect is responsible for the deflection.

  7. 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.

    PubMed

    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.

  8. Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system.

    PubMed

    Sun, Zachary Z; Yeung, Enoch; Hayes, Clarmyra A; Noireaux, Vincent; Murray, Richard M

    2014-06-20

    Accelerating the pace of synthetic biology experiments requires new approaches for rapid prototyping of circuits from individual DNA regulatory elements. However, current testing standards require days to weeks due to cloning and in vivo transformation. In this work, we first characterized methods to protect linear DNA strands from exonuclease degradation in an Escherichia coli based transcription-translation cell-free system (TX-TL), as well as mechanisms of degradation. This enabled the use of linear DNA PCR products in TX-TL. We then compared expression levels and binding dynamics of different promoters on linear DNA and plasmid DNA. We also demonstrated assembly technology to rapidly build circuits entirely in vitro from separate parts. Using this strategy, we prototyped a four component genetic switch in under 8 h entirely in vitro. Rapid in vitro assembly has future applications for prototyping multiple component circuits if combined with predictive computational models.

  9. Multitemporal L- and C-Band Synthetic Aperture Radar To Highlight Differences in Water Status Among Boreal Forest and Wetland Systems in the Yukon Flats, Interior Alaska

    USGS Publications Warehouse

    Balser, Andrew W.; Wylie, Bruce K.

    2010-01-01

    Tracking landscape-scale water status in high-latitude boreal systems is indispensible to understanding the fate of stored and sequestered carbon in a climate change scenario. Spaceborne synthetic aperture radar (SAR) imagery provides critical information for water and moisture status in Alaskan boreal environments at the landscape scale. When combined with results from optical sensor analyses, a complementary picture of vegetation, biomass, and water status emerges. Whereas L-band SAR showed better inherent capacity to map water status, C-band had much more temporal coverage in this study. Analysis through the use of L- and C-band SARs combined with Landsat Enhanced Thematic Mapper Plus (ETM+) enables landscape stratification by vegetation and by seasonal and interannual hydrology. Resultant classifications are highly relevant to biogeochemistry at the landscape scale. These results enhance our understanding of ecosystem processes relevant to carbon balance and may be scaled up to inform regional carbon flux estimates and better parameterize general circulation models (GCMs).

  10. On reduction of risks in UXO and mine detection using remote sensing systems and related synthetic image simulation

    NASA Astrophysics Data System (ADS)

    Bostater, Charles R., Jr.

    2005-06-01

    It is important to understand remote sensing systems and associated platforms in the context of autonomous or semi-autonomous designs for (robotic & mechatronics) that may be affect the motion control or stabilization aspects of the imagery, scan lines or fixed points scanned. This need can be most easily conceived as being related to the reduction of risks associated with false detection as well as the risks associated with hardware and software failure and risks associated with the actual operation of sensor and platform in dangerous environments. Thus safety is ultimately our concern when it comes to risk assessment. This paper will describe (a) remote sensing systems, (b) platforms (fixed and mobile, as well as to demonstrate (c) the value of thinking in terms of scalability as well as modularity in the design and application of new systems and (d) creation of synthetic signatures obtained for detection of targets in the aquatic environment. New systems - sensing systems as well as autonomous or semiautonomous robotic and mechatronic systems will be essential to secure domestic preparedness for humanitarian reasons as well as for demining and UXO detection. These same systems hold tremendous value, if thoughtfully designed for other applications which include environmental monitoring and surveillance.

  11. System of systems modeling and analysis.

    SciTech Connect

    Campbell, James E.; Anderson, Dennis James; Longsine, Dennis E.; Shirah, Donald N.

    2005-01-01

    This report documents the results of an LDRD program entitled 'System of Systems Modeling and Analysis' that was conducted during FY 2003 and FY 2004. Systems that themselves consist of multiple systems (referred to here as System of Systems or SoS) introduce a level of complexity to systems performance analysis and optimization that is not readily addressable by existing capabilities. The objective of the 'System of Systems Modeling and Analysis' project was to develop an integrated modeling and simulation environment that addresses the complex SoS modeling and analysis needs. The approach to meeting this objective involved two key efforts. First, a static analysis approach, called state modeling, has been developed that is useful for analyzing the average performance of systems over defined use conditions. The state modeling capability supports analysis and optimization of multiple systems and multiple performance measures or measures of effectiveness. The second effort involves time simulation which represents every system in the simulation using an encapsulated state model (State Model Object or SMO). The time simulation can analyze any number of systems including cross-platform dependencies and a detailed treatment of the logistics required to support the systems in a defined mission.

  12. Towards a Data-Optimized Coronal Magnetic Field Model (DOC-FM): Synthetic Test Beds and Multiwavelength Forward Modeling

    NASA Astrophysics Data System (ADS)

    Gibson, S. E.; Dalmasse, K.; Fan, Y.; Fineschi, S.; MacKay, D.; Rempel, M.; White, S. M.

    2015-12-01

    Understanding the physical state of the solar corona is key to deciphering the origins of space weather as well as to realistically representing the environment to be navigated by missions such as Solar Orbiter and Solar Probe Plus. However, inverting solar coronal observations to reconstruct this physical state -- and in particular the three-dimensional coronal magnetic field - is complicated by limited lines of sight and by projection effects. On the other hand, the sensitivity of multiwavelength observations to different physical mechanisms implies a potential for simultaneous probing of different parts of the coronal plasma. In order to study this complementarity, and to ultimately establish an optimal set of observations for constraining the three-dimensional coronal magnetic field, we are developing a suite of representative simulations to act as diagnostic test beds. We will present three such test beds: a coronal active region, a quiescent prominence, and a global corona. Each fully define the physical state of density, temperature, and vector magnetic field in three dimensions throughout the simulation domain. From these test beds, and using the FORWARD SolarSoft IDL codes, we will create a broad range of synthetic data. Radio observables will include intensity and circular polarization (including gyroresonance effects) and Faraday rotation for a range of frequencies. Infrared and visible forbidden line diagnostics of Zeeman and saturated Hanle effects will yield full Stokes vector (I, Q, U, V) synthetic data, and UV permitted line Hanle diagnostics will yield intensity and linear polarization. In addition, we will synthesize UV and SXR imager data, UV/EUV spectrometric data, and white light brightness and polarized brightness. All of these synthetic data, along with the "ground truth" physical state of the simulations from which they are derived, will be made available to the community for the purpose of testing coronal inversion techniques.

  13. Savannah woody structure modelling and mapping using multi-frequency (X-, C- and L-band) Synthetic Aperture Radar data

    NASA Astrophysics Data System (ADS)

    Naidoo, Laven; Mathieu, Renaud; Main, Russell; Kleynhans, Waldo; Wessels, Konrad; Asner, Gregory; Leblon, Brigitte

    2015-07-01

    Structural parameters of the woody component in African savannahs provide estimates of carbon stocks that are vital to the understanding of fuelwood reserves, which is the primary source of energy for 90% of households in South Africa (80% in Sub-Saharan Africa) and are at risk of over utilisation. The woody component can be characterised by various quantifiable woody structural parameters, such as tree cover, tree height, above ground biomass (AGB) or canopy volume, each been useful for different purposes. In contrast to the limited spatial coverage of ground-based approaches, remote sensing has the ability to sense the high spatio-temporal variability of e.g. woody canopy height, cover and biomass, as well as species diversity and phenological status - a defining but challenging set of characteristics typical of African savannahs. Active remote sensing systems (e.g. Light Detection and Ranging - LiDAR; Synthetic Aperture Radar - SAR), on the other hand, may be more effective in quantifying the savannah woody component because of their ability to sense within-canopy properties of the vegetation and its insensitivity to atmosphere and clouds and shadows. Additionally, the various components of a particular target's structure can be sensed differently with SAR depending on the frequency or wavelength of the sensor being utilised. This study sought to test and compare the accuracy of modelling, in a Random Forest machine learning environment, woody above ground biomass (AGB), canopy cover (CC) and total canopy volume (TCV) in South African savannahs using a combination of X-band (TerraSAR-X), C-band (RADARSAT-2) and L-band (ALOS PALSAR) radar datasets. Training and validation data were derived from airborne LiDAR data to evaluate the SAR modelling accuracies. It was concluded that the L-band SAR frequency was more effective in the modelling of the CC (coefficient of determination or R2 of 0.77), TCV (R2 of 0.79) and AGB (R2 of 0.78) metrics in Southern African

  14. Influence of supraglottal structures on the glottal jet exiting a two-layer synthetic, self-oscillating vocal fold model

    PubMed Central

    Drechsel, James S.; Thomson, Scott L.

    2008-01-01

    A synthetic two-layer, self-oscillating, life-size vocal fold model was used to study the influence of the vocal tract and false folds on the glottal jet. The model vibrated at frequencies, pressures, flow rates, and amplitudes consistent with human phonation, although some differences in behavior between the model and the human vocal folds are noted. High-speed images of model motion and flow visualization were acquired. Phase-locked ensemble-averaged glottal jet velocity measurements using particle image velocimetry (PIV) were acquired with and without an idealized vocal tract, with and without false folds. PIV data were obtained with varying degrees of lateral asymmetric model positioning. Glottal jet velocity magnitudes were consistent with those measured using excised larynges. A starting vortex was observed in all test cases. The false folds interfered with the starting vortex, and in some cases vortex shedding from the false folds was observed. In asymmetric cases without false folds, the glottal jet tended to skew toward the nearest wall; with the false folds, the opposite trend was observed. rms velocity calculations showed the jet shear layer and laminar core. The rms velocities were higher in the vocal tract cases compared to the open jet and false fold cases. PMID:18537394

  15. Prenatal Synthetic Glucocorticoid Treatment Changes DNA Methylation States in Male Organ Systems: Multigenerational Effects

    PubMed Central

    Crudo, Ariann; Petropoulos, Sophie; Moisiadis, Vasilis G.; Iqbal, Majid; Kostaki, Alisa; Machnes, Ziv; Szyf, Moshe

    2012-01-01

    Prenatal synthetic glucocorticoids (sGC) are administered to pregnant women at risk of delivering preterm, approximately 10% of all pregnancies. Animal studies have demonstrated that offspring exposed to elevated glucocorticoids, either by administration of sGC or as a result of maternal stress, are at increased risk of developing behavioral, endocrine, and metabolic abnormalities. DNA methylation is a covalent modification of DNA that plays a critical role in long-lasting programming of gene expression. Here we tested the hypothesis that prenatal sGC treatment has both acute and long-term effects on DNA methylation states in the fetus and offspring and that these effects extend into a subsequent generation. Pregnant guinea pigs were treated with sGC in late gestation, and methylation analysis by luminometric methylation assay was undertaken in organs from fetuses and offspring across two generations. Expression of genes that modify the epigenetic state were measured by quantitative real-time PCR. Results indicate that there are organ-specific developmental trajectories of methylation in the fetus and newborn. Furthermore, these trajectories are substantially modified by intrauterine exposure to sGC. These sGC-induced changes in DNA methylation remain into adulthood and are evident in the next generation. Furthermore, prenatal sGC exposure alters the expression of several genes encoding proteins that modulate the epigenetic state. Several of these changes are long lasting and are also present in the next generation. These data support the hypothesis that prenatal sGC exposure leads to broad changes in critical components of the epigenetic machinery and that these effects can pass to the next generation. PMID:22564977

  16. Model systems for single molecule polymer dynamics

    PubMed Central

    Latinwo, Folarin

    2012-01-01

    Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of “ideal” and “real” chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force–extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer–monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of “real” polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena. PMID:22956980

  17. Forward Modeling of Synthetic EUV/SXR Emission from Solar Coronal Active Regions: Case of AR 11117

    NASA Astrophysics Data System (ADS)

    Airapetian, V. S.; Allred, J.

    2015-01-01

    Recent progress in obtaining high spatial resolution images of the solar corona in the extreme-ultraviolet (EUV) with Hinode, TRACE, SDO and recent Hi-C missions and soft X-ray (SXR) bands opened a new avenue in understanding the solar coronal heating, the major goal of solar physics. The data from EUV/SXR missions suggest that solar corona is a non-uniform environment structured into active regions (AR) represented by bundles magnetic loops heated to temperatures exceeding 5 MK. Any viable coronal heating model should be capable of reproducing EUV and SXR emission from coronal active regions well as dynamic activity. Measurements of emission measures (EM) for ARs provide clues to time dependence of the heating mechanism: static versus impulsive. While static equilibrium coronal loop models are successful in reproducing SXR emission within an AR, they cannot adequately predict the bright EUV loops. Meantime, impulsive heating is capable in reproducing both EUV and SXR loop emission. The major goal of this paper is to construct realistic synthetic EM images of specific solar corona active region, AR 11117 by using our 1D fully non-linear time-dependent single-fluid hydrodynamic code. We first construct a magnetic skeleton for the entire active region using the HMI/SDO magnetogram for AR 11117 and populate magnetic field lines with plasma. We then parametrically specify impulsive heating of individual strands (flux tubes) comprising coronal loops. Next, we simulated the response of the entire active region (with LOS projection effects) to the heating function (volumetric heating rate) scaled with magnetic field and spatial scale parameters and find the best match between synthetic and actual (reconstructed) DEMs obtained by SDO.

  18. Inhibition of Lux quorum-sensing system by synthetic N-acyl-L-homoserine lactone analogous.

    PubMed

    Wang, Wenzhao; Morohoshi, Tomohiro; Ikeda, Tsukasa; Chen, Liang

    2008-12-01

    In the present study, we investigated the inhibition of the Lux quorum-sensing system by N-acyl cyclopentylamine (Cn-CPA). The Lux quorum-sensing system regulates luminescence gene expression in Vibrio fischeri. We have already reported on the synthesis of Cn-CPA and their abilities as inhibitors of the quorum-sensing systems in Pseudomonas aeruginosa and Serratia marcescens. In the case of Pseudomonas aeruginosa (Las and Rhl quorum-sensing system) and Serratia marcescens (Spn quorum-sensing system), specific Cn-CPA with a particular acyl chain length showed the strongest inhibitory effect. In the case of the Lux quorum-sensing system, it was found that several kinds of Cn-CPA with a range from C5 to C10 showed similar strong inhibitory effects. Moreover, the inhibitory effect of Cn-CPA on the Lux quorum-sensing system was stronger than that of halogenated furanone, a natural quorum-sensing inhibitor.

  19. Synthetic battery cycling techniques

    NASA Technical Reports Server (NTRS)

    Leibecki, H. F.; Thaller, L. H.

    1982-01-01

    Synthetic battery cycling makes use of the fast growing capability of computer graphics to illustrate some of the basic characteristics of operation of individual electrodes within an operating electrochemical cell. It can also simulate the operation of an entire string of cells that are used as the energy storage subsystem of a power system. The group of techniques that as a class have been referred to as Synthetic Battery Cycling is developed in part to try to bridge the gap of understanding that exists between single cell characteristics and battery system behavior.

  20. [Interactions between synthetic drugs used in treatment of selected central nervous system disorders and dietary supplements and herbal drugs].

    PubMed

    Zabłocka-Słowińska, Katarzyna; Jawna, Katarzyna; Biernat, Jadwiga

    2013-01-01

    The risk of interaction between dietary supplements, herbal drugs and synthetic drugs increases when patients are treated chronically, e.g. due to impairment of central nervous system (CNS)--depression, psychotic disorders, Parkinson's and Alzheimer's diseases. On the basis of scientific literature, there was shown that simultaneous intake of antidepressants, antipsychotic drugs and herbal drugs or dietary supplements containing: St. John's wort, valerian root, ginkgo biloba leaf, hops, and food ingredients: dietary fiber or folic acid, may lead to interactions. Dietary fiber supplementation should be applied carefully during treatment of Parkinson's disease and in case of Alzheimer disease treatment--supplements containing ginkgo biloba leaf can increase the risk of interaction. Knowledge of these interactions is essential in effective treatment of this illness. However this area of science should be verified constantly due to growing number of new products registered as a supplements--often with complex composition. PMID:23885542

  1. Waveform modelling using locked-mode synthetic and differential seismograms: application to determination of the structure of Mexico

    USGS Publications Warehouse

    Gomberg, J.S.; Masters, T. Guy

    1988-01-01

    We have developed algorithms for modelling seismic waveforms to constrain regional Earth structure. The seismogram is represented as a sum of locked-mode travelling waves in a layered medium. This representation is convenient as it allows us to model structures with slowly varying heterogeneity and to construct differential seismograms. Describes the techniques we have implemented that enable us to compute synthetic and differential seismograms in an efficient and stable manner. The computational methods are sufficiently rapid that many modes can be included and in some cases the entire seismogram may be modified. These algorithms are applied to model a set of seismograms of southern Mexican earthquakes recorded in northern Mexico. The frequency bandwidth of these data is centred at 0.067 Hz and we demonstrate that even at these relatively high frequencies, many features of the seismogram can be successfully modelled. Our results suggest that the structure within the recording array in northern Mexico is resolvably different from that to the south. We find that the average shear velocity of the lower lithosphere of southern Mexico is very low, approximately 4.3 km s-1. If the low-velocity region is confined to the Trans Mexican Volcanic Belt, the shear velocities between 20-80 km depth are approximately 3.3 km s-1. This may be correlated with partial melt and is consistent with the active volcanism and high heat flow found in the region. -Authors

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

    USGS Publications Warehouse

    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

  3. Synthetic promoters consisting of defined cis-acting elements link multiple signaling pathways to probenazole-inducible system * #

    PubMed Central

    Zhu, Zheng; Gao, Jiong; Yang, Jin-xiao; Wang, Xiao-yan; Ren, Guo-dong; Ding, Yu-long; Kuai, Ben-ke

    2015-01-01

    Probenazole (3-allyloxy-1,2-benzisothiazole-1,1-dioxide, PBZ), the active component of Oryzemate, could induce systemic acquired resistance (SAR) in plants through the induction of salicylic acid (SA) biosynthesis. As a widely used chemical inducer, PBZ is a good prospect for establishing a new chemical-inducible system. We first designed artificially synthetic promoters with tandem copies of a single type of cis-element (SARE, JERE, GCC, GST1, HSRE, and W-box) that could mediate the expression of the β-glucuronidase (GUS) reporter gene in plants upon PBZ treatment. Then we combined different types of elements in order to improve inducibility in the PBZ-inducible system. On the other hand, we were surprised to find that the cis-elements, which are responsive to jasmonic acid (JA) and ethylene, also responded to PBZ, implying that SA, JA, and ethylene pathways also would play important roles in PBZ’s action. Further analysis demonstrated that PBZ also induced early events of innate immunity via a signaling pathway in which Ca2+ influx and mitogen-activated protein kinase (MAPK) activity were involved. We constructed synthesized artificial promoters to establish a PBZ chemical-inducible system, and preliminarily explored SA, JA, ethylene, calcium, and MAPK signaling pathways via PBZ-inducible system, which could provide an insight for in-depth study. PMID:25845359

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

    USGS Publications Warehouse

    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

  5. An Evaluation of Kinetic Models in the Biodesulfurization of Synthetic Oil by Rhodococcus erythropolis ATCC 4277.

    PubMed

    Maass, D; Mayer, D A; Moritz, D E; Oliveira, D; de Souza, A A Ulson; Souza, S M A Guelli

    2015-10-01

    Biodesulfurization is an eco-friendly technology applied in the removal of sulfur from fossil fuels. This technology is based on the use of microorganisms as biocatalysts to convert the recalcitrant sulfur compounds into others easily treatable, as sulfides. Despite it has been studied during the last decades, there are some unsolved questions, as per example the kinetic model which appropriately describes the biodesulfurization globally. In this work, different kinetic models were tested to a batch desulfurization process using dibenzothiophene (DBT) as a model compound, n-dodecane as organic solvent, and Rhodococcus erythropolis ATCC 4277 as biocatalyst. The models were solved by ODE45 function in the MATLAB. Monod model was capable to describe the biodesulfurization process predicting all experimental data with a very good fitting. The coefficients of determination achieved to organic phase concentrations of 20, 80, and 100 % (v/v) were 0.988, 0.995, and 0.990, respectively. R. erythropolis ATCC 4277 presented a good affinity with the substrate (DBT) since the coefficients of saturation obtained to reaction medium containing 20, 80, and 100 % (v/v) were 0.034, 0.07, and 0.116, respectively. This kinetic evaluation provides an improvement in the development of biodesulfurization technology because it showed that a simple model is capable to describe the throughout process. PMID:26201481

  6. A General, Synthetic Model for Predicting Biodiversity Gradients from Environmental Geometry.

    PubMed

    Gross, Kevin; Snyder-Beattie, Andrew

    2016-10-01

    Latitudinal and elevational biodiversity gradients fascinate ecologists, and have inspired dozens of explanations. The geometry of the abiotic environment is sometimes thought to contribute to these gradients, yet evaluations of geometric explanations are limited by a fragmented understanding of the diversity patterns they predict. This article presents a mathematical model that synthesizes multiple pathways by which environmental geometry can drive diversity gradients. The model characterizes species ranges by their environmental niches and limits on range sizes and places those ranges onto the simplified geometries of a sphere or cone. The model predicts nuanced and realistic species-richness gradients, including latitudinal diversity gradients with tropical plateaus and mid-latitude inflection points and elevational diversity gradients with low-elevation diversity maxima. The model also illustrates the importance of a mid-environment effect that augments species richness at locations with intermediate environments. Model predictions match multiple empirical biodiversity gradients, depend on ecological traits in a testable fashion, and formally synthesize elements of several geometric models. Together, these results suggest that previous assessments of geometric hypotheses should be reconsidered and that environmental geometry may play a deeper role in driving biodiversity gradients than is currently appreciated.

  7. A General, Synthetic Model for Predicting Biodiversity Gradients from Environmental Geometry.

    PubMed

    Gross, Kevin; Snyder-Beattie, Andrew

    2016-10-01

    Latitudinal and elevational biodiversity gradients fascinate ecologists, and have inspired dozens of explanations. The geometry of the abiotic environment is sometimes thought to contribute to these gradients, yet evaluations of geometric explanations are limited by a fragmented understanding of the diversity patterns they predict. This article presents a mathematical model that synthesizes multiple pathways by which environmental geometry can drive diversity gradients. The model characterizes species ranges by their environmental niches and limits on range sizes and places those ranges onto the simplified geometries of a sphere or cone. The model predicts nuanced and realistic species-richness gradients, including latitudinal diversity gradients with tropical plateaus and mid-latitude inflection points and elevational diversity gradients with low-elevation diversity maxima. The model also illustrates the importance of a mid-environment effect that augments species richness at locations with intermediate environments. Model predictions match multiple empirical biodiversity gradients, depend on ecological traits in a testable fashion, and formally synthesize elements of several geometric models. Together, these results suggest that previous assessments of geometric hypotheses should be reconsidered and that environmental geometry may play a deeper role in driving biodiversity gradients than is currently appreciated. PMID:27622881

  8. An Evaluation of Kinetic Models in the Biodesulfurization of Synthetic Oil by Rhodococcus erythropolis ATCC 4277.

    PubMed

    Maass, D; Mayer, D A; Moritz, D E; Oliveira, D; de Souza, A A Ulson; Souza, S M A Guelli

    2015-10-01

    Biodesulfurization is an eco-friendly technology applied in the removal of sulfur from fossil fuels. This technology is based on the use of microorganisms as biocatalysts to convert the recalcitrant sulfur compounds into others easily treatable, as sulfides. Despite it has been studied during the last decades, there are some unsolved questions, as per example the kinetic model which appropriately describes the biodesulfurization globally. In this work, different kinetic models were tested to a batch desulfurization process using dibenzothiophene (DBT) as a model compound, n-dodecane as organic solvent, and Rhodococcus erythropolis ATCC 4277 as biocatalyst. The models were solved by ODE45 function in the MATLAB. Monod model was capable to describe the biodesulfurization process predicting all experimental data with a very good fitting. The coefficients of determination achieved to organic phase concentrations of 20, 80, and 100 % (v/v) were 0.988, 0.995, and 0.990, respectively. R. erythropolis ATCC 4277 presented a good affinity with the substrate (DBT) since the coefficients of saturation obtained to reaction medium containing 20, 80, and 100 % (v/v) were 0.034, 0.07, and 0.116, respectively. This kinetic evaluation provides an improvement in the development of biodesulfurization technology because it showed that a simple model is capable to describe the throughout process.

  9. Geometric and electronic structures of the synthetic Mn₄CaO₄ model compound mimicking the photosynthetic oxygen-evolving complex.

    PubMed

    Shoji, Mitsuo; Isobe, Hiroshi; Shen, Jian-Ren; Yamaguchi, Kizashi

    2016-04-28

    Water oxidation by photosystem II (PSII) converts light energy into chemical energy with the concomitant production of molecular oxygen, both of which are indispensable for sustaining life on Earth. This reaction is catalyzed by an oxygen-evolving complex (OEC) embedded in the huge PSII complex, and its mechanism remains elusive in spite of the extensive studies of the geometric and electronic structures. In order to elucidate the water-splitting mechanism, synthetic approaches have been extensively employed to mimic the native OEC. Very recently, a synthetic complex [Mn4CaO4(Bu(t)COO)8(py)(Bu(t)COOH)2] (1) closely mimicking the structure of the native OEC was obtained. In this study, we extensively examined the geometric, electronic and spin structures of 1 using the density functional theory method. Our results showed that the geometric structure of 1 can be accurately reproduced by theoretical calculations, and revealed many similarities in the ground valence and spin states between 1 and the native OEC. We also revealed two different valence states in the one-electron oxidized state of 1 (corresponding to the S2 state), which lie in the lower and higher ground spin states (S = 1/2 and S = 5/2), respectively. One remarkable difference between 1 and the native OEC is the presence of a non-negligible antiferromagnetic interaction between the Mn1 and Mn4 sites, which slightly influenced their ground spin structures (spin alignments). The major reason causing the difference can be attributed to the short Mn1-O5 and Mn1-Mn4 distances in 1. The introduction of the missing O4 atom and the reorientation of the Ca coordinating ligands improved the Mn1-O5 and Mn1-Mn4 distances comparable to the native OEC. These modifications will therefore be important for the synthesis of further advanced model complexes more closely mimicking the native OEC beyond 1.

  10. Influence of asymmetric stiffness on the structural and aerodynamic response of synthetic vocal fold models.

    PubMed

    Pickup, B A; Thomson, S L

    2009-10-16

    The influence of asymmetric vocal fold stiffness on voice production was evaluated using life-sized, self-oscillating vocal fold models with an idealized geometry based on the human vocal folds. The models were fabricated using flexible, materially-linear silicone compounds with Young's modulus values comparable to that of vocal fold tissue. The models included a two-layer design to simulate the vocal fold layered structure. The respective Young's moduli of elasticity of the "left" and "right" vocal fold models were varied to create asymmetric conditions. High-speed videokymography was used to measure maximum vocal fold excursion, vibration frequency, and left-right phase shift, all of which were significantly influenced by asymmetry. Onset pressure, a measure of vocal effort, increased with asymmetry. Particle image velocimetry (PIV) analysis showed significantly greater skewing of the glottal jet in the direction of the stiffer vocal fold model. Potential applications to various clinical conditions are mentioned, and suggestions for future related studies are presented.

  11. Influence of Asymmetric Stiffness on the Structural and Aerodynamic Response of Synthetic Vocal Fold Models

    PubMed Central

    Pickup, B.A.; Thomson, S.L.

    2012-01-01

    The influence of asymmetric vocal fold stiffness on voice production was evaluated using life-sized, self-oscillating vocal fold models with an idealized geometry based on the human vocal folds. The models were fabricated using flexible, materially-linear silicone compounds with Young’s modulus values comparable to that of vocal fold tissue. The models included a two-layer design to simulate the vocal fold layered structure. The respective Young’s moduli of elasticity of the “left” and “right” vocal fold models were varied to create asymmetric conditions. High-speed videokymography was used to measure maximum vocal fold excursion, vibration frequency, and left-right phase shift, all of which were significantly influenced by asymmetry. Onset pressure, a measure of vocal effort, increased with asymmetry. Particle image velocimetry (PIV) analysis showed significantly greater skewing of the glottal jet in the direction of the stiffer vocal fold model. Potential applications to various clinical conditions are mentioned, and suggestions for future related studies are presented. PMID:19664777

  12. A Reduced-Order Model For Zero-Mass Synthetic Jet Actuators

    NASA Technical Reports Server (NTRS)

    Yamaleev, Nail K.; Carpenter, Mark H.; Vatsa, Veer S.

    2007-01-01

    Accurate details of the general performance of fluid actuators is desirable over a range of flow conditions, within some predetermined error tolerance. Designers typically model actuators with different levels of fidelity depending on the acceptable level of error in each circumstance. Crude properties of the actuator (e.g., peak mass rate and frequency) may be sufficient for some designs, while detailed information is needed for other applications (e.g., multiple actuator interactions). This work attempts to address two primary objectives. The first objective is to develop a systematic methodology for approximating realistic 3-D fluid actuators, using quasi-1-D reduced-order models. Near full fidelity can be achieved with this approach at a fraction of the cost of full simulation and only a modest increase in cost relative to most actuator models used today. The second objective, which is a direct consequence of the first, is to determine the approximate magnitude of errors committed by actuator model approximations of various fidelities. This objective attempts to identify which model (ranging from simple orifice exit boundary conditions to full numerical simulations of the actuator) is appropriate for a given error tolerance.

  13. Synthetic Diagnostic for the Evaluation of New Microwave Imaging Reflectometry System for Large Tokomaks - DIII-D and KSTAR

    NASA Astrophysics Data System (ADS)

    Lei, Li Juan

    Microwave Imaging Reflectometry (MIR) systems have been used as diagnostic tools for characterization of fluctuating plasma density in large tokamaks. Such a technique has been implemented on the TEXTOR device [H. Park, et al., Review of Scientific Instruments, 2004] and is being continued on DIII-D and KSTAR. To develop a new MIR system for density fluctuation measurements for DIII-D and KSTAR, one requires an understanding of how to preserve phase information. The current design for an MIR optical system makes use of design tools in free space, which is great for evaluation of port access but not provide significant information when it comes to the plasma region. This thesis describes a numerical study of MIR in the presence of turbulent fluctuations by evaluating the effectiveness in coupling the reflection layer in the full wave region and the detector array in free space with respect to fluctuation levels. A synthetic diagnostic tool making use of 2D full-wave diffractive simulation in full plasma geometry is applied to couple an optical imaging system with different optical arrangements.

  14. A Reduced Power Digital Electronics System for a Digital Beamforming Space Exploration Synthetic Aperture Radar

    NASA Astrophysics Data System (ADS)

    Carter, L. M.; Rincon, R. F.; Novak, M.

    2016-10-01

    We will discuss design of an orbital P-band (70 cm wavelength) digital beamforming radar system that is modular and can be used for imaging polarimetry of Earth and rocky planets and moons, as well as asteroids and comets.

  15. Generation of synthetic influent data to perform (micro)pollutant wastewater treatment modelling studies.

    PubMed

    Snip, L J P; Flores-Alsina, X; Aymerich, I; Rodríguez-Mozaz, S; Barceló, D; Plósz, B G; Corominas, Ll; Rodriguez-Roda, I; Jeppsson, U; Gernaey, K V

    2016-11-01

    The use of process models to simulate the fate of micropollutants in wastewater treatment plants is constantly growing. However, due to the high workload and cost of measuring campaigns, many simulation studies lack sufficiently long time series representing realistic wastewater influent dynamics. In this paper, the feasibility of the Benchmark Simulation Model No. 2 (BSM2) influent generator is tested to create realistic dynamic influent (micro)pollutant disturbance scenarios. The presented set of models is adjusted to describe the occurrence of three pharmaceutical compounds and one of each of its metabolites with samples taken every 2-4h: the anti-inflammatory drug ibuprofen (IBU), the antibiotic sulfamethoxazole (SMX) and the psychoactive carbamazepine (CMZ). Information about type of excretion and total consumption rates forms the basis for creating the data-defined profiles used to generate the dynamic time series. In addition, the traditional influent characteristics such as flow rate, ammonium, particulate chemical oxygen demand and temperature are also modelled using the same framework with high frequency data. The calibration is performed semi-automatically with two different methods depending on data availability. The 'traditional' variables are calibrated with the Bootstrap method while the pharmaceutical loads are estimated with a least squares approach. The simulation results demonstrate that the BSM2 influent generator can describe the dynamics of both traditional variables and pharmaceuticals. Lastly, the study is complemented with: 1) the generation of longer time series for IBU following the same catchment principles; 2) the study of the impact of in-sewer SMX biotransformation when estimating the average daily load; and, 3) a critical discussion of the results, and the future opportunities of the presented approach balancing model structure/calibration procedure complexity versus predictive capabilities.

  16. Struvite precipitation under changing ionic conditions in synthetic wastewater: Experiment and modeling.

    PubMed

    Lee, Sang-Hun; Kumar, Rahul; Jeon, Byong-Hun

    2016-07-15

    A computational model was developed and applied to investigate struvite precipitation under different pH levels and ionic concentrations. Ionic species, including ammonium (NH4(+)), hydrogen phosphate (HPO4(2-)), magnesium (Mg(2+)), calcium (Ca(2+)), and struvite, were incorporated into the proposed model. The unknown kinetic coefficients of struvite were identified from the experimental data. In this study, the kinetics of struvite precipitation, which combined the ionic reactions (NH4(+)/NH3 and HPO4(2-)/H2PO4(-)) on the basis of pseudo-equilibrium conditions was parameterized. The experiments for model verification were conducted at a constant initial Mg/P ratio with changing ionic concentrations at pH levels of 8.7 and 9.7. The batch experiments showed high struvite precipitation (>90% for 300mg-NL(-1) and 100mg-PL(-1)). The presence of Ca(2+) (Ca(2+)/Mg(2+) >0.5) in the reactors interfered with the formation and growth of struvite. The decrease in the pH level with the struvite precipitation verified the simulation data. The model also confirmed the optimal ionic conditions in order to maximize the struvite precipitation (300mg-PL(-1), and N/P molar ratio >7). The model responding to the ionic conditions provided good prediction of the decrease in the pH levels and the positive role of the nitrogen levels for struvite precipitation. High nitrogen concentrations provided high P removal due to pH buffering and crystal purity.

  17. Struvite precipitation under changing ionic conditions in synthetic wastewater: Experiment and modeling.

    PubMed

    Lee, Sang-Hun; Kumar, Rahul; Jeon, Byong-Hun

    2016-07-15

    A computational model was developed and applied to investigate struvite precipitation under different pH levels and ionic concentrations. Ionic species, including ammonium (NH4(+)), hydrogen phosphate (HPO4(2-)), magnesium (Mg(2+)), calcium (Ca(2+)), and struvite, were incorporated into the proposed model. The unknown kinetic coefficients of struvite were identified from the experimental data. In this study, the kinetics of struvite precipitation, which combined the ionic reactions (NH4(+)/NH3 and HPO4(2-)/H2PO4(-)) on the basis of pseudo-equilibrium conditions was parameterized. The experiments for model verification were conduct