Science.gov

Sample records for synthetic model systems

  1. Model selection in systems and synthetic biology.

    PubMed

    Kirk, Paul; Thorne, Thomas; Stumpf, Michael P H

    2013-08-01

    Developing mechanistic models has become an integral aspect of systems biology, as has the need to differentiate between alternative models. Parameterizing mathematical models has been widely perceived as a formidable challenge, which has spurred the development of statistical and optimisation routines for parameter inference. But now focus is increasingly shifting to problems that require us to choose from among a set of different models to determine which one offers the best description of a given biological system. We will here provide an overview of recent developments in the area of model selection. We will focus on approaches that are both practical as well as build on solid statistical principles and outline the conceptual foundations and the scope for application of such methods in systems biology. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. 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.

  3. 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.

  4. Models for synthetic biology

    PubMed Central

    Kaznessis, Yiannis N

    2007-01-01

    Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biological molecules. What is new is the emphasis on system behavior. The objective is the design and construction of new biological devices and systems to deliver useful applications. Numerous synthetic gene circuits have been created in the past decade, including bistable switches, oscillators, and logic gates, and possible applications abound, including biofuels, detectors for biochemical and chemical weapons, disease diagnosis, and gene therapies. More than fifty years after the discovery of the molecular structure of DNA, molecular biology is mature enough for real quantification that is useful for biological engineering applications, similar to the revolution in modeling in chemistry in the 1950s. With the excitement that synthetic biology is generating, the engineering and biological science communities appear remarkably willing to cross disciplinary boundaries toward a common goal. PMID:17986347

  5. 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.

  6. 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).

  7. 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.

  8. 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.

  9. EOID System Model Validation, Metrics, and Synthetic Clutter Generation

    DTIC Science & Technology

    2003-09-30

    Our long-term goal is to accurately predict the capability of the current generation of laser-based underwater imaging sensors to perform Electro ... Optic Identification (EOID) against relevant targets in a variety of realistic environmental conditions. The models will predict the impact of

  10. Noise and Oscillations in Biological Systems: Multidisciplinary Approach Between Experimental Biology, Theoretical Modelling and Synthetic Biology

    NASA Astrophysics Data System (ADS)

    Ullner, E.; Ares, S.; Morelli, L. G.; Oates, A. C.; Jülicher, F.; Nicola, E.; Heussen, R.; Whitmore, D.; Blyuss, K.; Fryett, M.; Zakharova, A.; Koseska, A.; Nene, N. R.; Zaikin, A.

    2012-10-01

    Rapid progress of experimental biology has provided a huge flow of quantitative data, which can be analyzed and understood only through the application of advanced techniques recently developed in theoretical sciences. On the other hand, synthetic biology enabled us to engineer biological models with reduced complexity. In this review we discuss that a multidisciplinary approach between this sciences can lead to deeper understanding of the underlying mechanisms behind complex processes in biology. Following the mini symposia "Noise and oscillations in biological systems" on Physcon 2011 we have collected different research examples from theoretical modeling, experimental and synthetic biology.

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

    DTIC Science & Technology

    2014-09-05

    design plant based genetic circuits enables researchers to engineer control of gene expression beyond overexpression or knockouts. These circuits can...of synthetic components Synthetic promoters and other synthetic genetic components offer several advantages in plant synthetic biology. First...through plant hormone pathways like auxin and through the multitude of proteins they interact with. Engineering a signaling system using genetic

  12. 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.

  13. A Model of a Synthetic Biological Communication Interface between Mammalian Cells and Mechatronic Systems.

    PubMed

    Heyde, Keith C; Ruder, Warren C

    2016-12-01

    The creation of communication interfaces between abiotic and biotic systems represents a significant research challenge. In this work, we design and model a system linking the biochemical signaling pathways of mammalian cells to the actions of a mobile robotic prosthesis. We envision this system as a robotic platform carrying an optically monitored bioreactor that harbors mammalian cells. The cellular, optical signal is captured by an onboard fluorescent microscope and converted into an electronic signal. We first present a design for the overall cell-robot system, with a specific focus on the design of the synthetic gene networks needed for the system. We use these synthetic networks to encode motion commands within the cell's endogenous, oscillatory calcium signaling pathways. We then describe a potential system whereby this oscillatory signal could be outputted and monitored as a change in cellular fluorescence. Next, we use the changes resulting from the synthetic biological modifications as new parameters in a simulation of a well-established mathematical model for intracellular calcium signaling. The resulting signal is processed in the frequency domain, with specific frequencies activating cognate robot motion subroutines.

  14. A Model of a Synthetic Biological Communication Interface between Mammalian Cells and Mechatronic Systems.

    PubMed

    Heyde, Keith Cameron; Ruder, Warren Christopher

    2016-10-25

    The creation of communication interfaces between abiotic and biotic systems represents a significant research challenge. In this work, we design and model a system linking the biochemical signaling pathways of mammalian cells to the actions of a mobile robotic prosthesis. We envision this system as a robotic platform carrying an optically monitored bioreactor that harbors mammalian cells. The cellular, optical signal is captured by an onboard fluorescent microscope and converted into an electronic signal. We first present a design for the overall cellrobot system, with a specific focus on the design of the synthetic gene networks needed for the system. We use these synthetic networks to encode motion commands within the cell's endogenous, oscillatory calcium signaling pathways. We then describe a potential system whereby this oscillatory signal could be outputted and monitored as a change in cellular fluorescence. Next, we use the changes resulting from the synthetic biological modifications as new parameters in a simulation of a wellestablished mathematical model for intracellular calcium signaling. The resulting signal is processed in the frequency domain, with specific frequencies activating cognate robot motion subroutines.

  15. Modeling Transport Through Synthetic Nanopores

    PubMed Central

    Aksimentiev, Aleksei; Brunner, Robert K.; Cruz-Chú, Eduardo; Comer, Jeffrey; Schulten, Klaus

    2011-01-01

    Nanopores in thin synthetic membranes have emerged as convenient tools for high-throughput single-molecule manipulation and analysis. Because of their small sizes and their ability to selectively transport solutes through otherwise impermeable membranes, nanopores have numerous potential applications in nanobiotechnology. For most applications, properties of the nanopore systems have to be characterize at the atomic level, which is currently beyond the limit of experimental methods. Molecular dynamics (MD) simulations can provide the desired information, however several technical challenges have to be met before this method can be applied to synthetic nanopore systems. Here, we highlight our recent work on modeling synthetic nanopores of the most common types. First, we describe a novel graphical tool for setting up all-atom systems incorporating inorganic materials and biomolecules. Next, we illustrate the application of the MD method for silica, silicon nitride, and polyethylene terephthalate nanopores. Following that, we describe a method for modeling synthetic surfaces using a bias potential. Future directions for tool development and nanopore modeling are briefly discussed at the end of this article. PMID:21909347

  16. Multiscale models for synthetic biology.

    PubMed

    Kaznessis, Yiannis N

    2009-01-01

    Reacting systems away from the thermodynamic limit cannot be accurately modeled with ordinary differential equations. These continuous-deterministic modeling formalisms, traditionally developed and used by chemical engineers can be distinctly false if the number of molecules of reacting chemical species is very small, or if reaction events are very rare. Then stochastic-discrete representations are appropriate. Importantly, in cases where in a network of reactions there are some parts that must be modeled discretely and stochastically, yet others can be modeled continuously and deterministically, the need for development of multiscale models emerges naturally. In computational synthetic biology, such cases arise often. In this work we present the development of multiscale models for synthetic biology applications, demonstrating accuracy, computational efficiency and utility.

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

    NASA Astrophysics Data System (ADS)

    Mega Saputra, Rifki; Widodo

    2017-04-01

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

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

    SciTech Connect

    Hodge, Bri-Mathias; Palmintier, Bryan

    2016-03-03

    This presentation provides an overview of full-scale, high-quality, synthetic distribution system data set(s) for testing distribution automation algorithms, distributed control approaches, ADMS capabilities, and other emerging distribution technologies.

  19. Synthetic quantum systems

    NASA Astrophysics Data System (ADS)

    Cahill, Reginald T.

    2002-10-01

    So far proposed quantum computers use fragile and environmentally sensitive natural quantum systems. Here we explore the new notion that synthetic quantum systems suitable for quantum computation may be fabricated from smart nanostructures using topological excitations of a stochastic neural-type network that can mimic natural quantum systems. These developments are a technological application of process physics which is an information theory of reality in which space and quantum phenomena are emergent, and so indicates the deep origins of quantum phenomena. Analogous complex stochastic dynamical systems have recently been proposed within neurobiology to deal with the emergent complexity of biosystems, particularly the biodynamics of higher brain function. The reasons for analogous discoveries in fundamental physics and neurobiology are discussed.

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

    PubMed

    Roehner, Nicholas; Myers, Chris J

    2014-02-21

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

  1. The Pan-STARRS Synthetic Solar System Model and its Applications

    NASA Astrophysics Data System (ADS)

    Grav, Tommy; Jedicke, R.; Denneau, L.; Holman, M. J.; Spahr, T.; Pan-STARRS Moving Object Processing System Team

    2007-12-01

    We present here the Pan-STARRS Moving Object Processing System (MOPS) Solar System Model (SSM) comprising of synthetic populations of objects inside Earth's orbit (IEOs), near Earth objects (NEOs - Athens, Apollos and Amors), the main belt asteroids (MBAs), Trojans of all planets from Venus through Neptune, Centaurs, trans-Neptnuian objects (classical, resonant and scattered TNOs), and short and long period comets (SPCs and LPCs). All of these populations are complete to a minimum of R=24.5, corresponding to approximately the expected limiting magnitude for Pan-STARRS' ability to detect moving objects.The only exception to this rule being the NEOs, which are complete to H=25 (corresponding to objects of about 50m in diameter). The PS SSM is an integral part of the MOPS and will be utilized to test and characterize the PS1 survey and subsequent processing.

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

    PubMed

    Sanassy, Daven; Widera, Paweł; Krasnogor, Natalio

    2015-01-16

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

  3. 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.

  4. A 4DVAR System for the Navy Coastal Ocean Model. Part 1: System Description and Assimilation of Synthetic Observations in Monterey Bay

    DTIC Science & Technology

    2014-06-01

    A 4DVAR System for the Navy Coastal Ocean Model . Part I: System Description and Assimilation of Synthetic Observations in Monterey Bay* HANS NGODOCK...ABSTRACT A 4D variational data assimilation systemwas developed for assimilating ocean observations with the Navy Coastal Ocean Model . It is described in...Navy Coastal Ocean Model (NCOM). NCOM is an opera- tional ocean model (primarily at the Naval Oceano- graphic Office) that has been validated (Martin

  5. Agent-based modelling in synthetic biology

    PubMed Central

    2016-01-01

    Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. PMID:27903820

  6. 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.

  7. 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.

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

    PubMed

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

    2011-02-01

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

  9. Agent-based modelling in synthetic biology.

    PubMed

    Gorochowski, Thomas E

    2016-11-30

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

  10. 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

  11. A Unique Model Platform for C4 Plant Systems and Synthetic Biology

    DTIC Science & Technology

    2015-12-10

    ABSTRACT We are developing Setaria viridis as a C4 model to accelerate metabolic engineering of key C4 crop species. A genome scale metabolic...14. ABSTRACT We are developing Setaria viridis as a C4 model to accelerate metabolic engineering of key C4 crop species. A genome scale metabolic...Performance: 3 June 2014 – 2 June 2015 Abstract: We are developing Setaria viridis as a C4 model to accelerate metabolic engineering of key C4 crop

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. [Combinatorial optimization of synthetic biological systems].

    PubMed

    Gu, Qun; Li, Yifan; Chen, Tao

    2013-08-01

    A major challenge in synthetic biology is to engineer complex biological systems with novel functions. Due to the inherent complexity of biological systems, it is often difficult to rationally design every component in a synthetic gene network to achive an optimal performance. Combinatorial engineering is an important solution to this problem and can greatly facilitate the construction of novel biological functions. Here, we review methods and techniques developed in recent years for combinatorial optimization of synthetic biological systems, including methods for fine-tuning pathway components, strategies for systematically optimization of metabolic pathways, and techniques for introducing multiplex genome wide perturbations.

  17. Tunable promoters in synthetic and systems biology.

    PubMed

    Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

    2012-01-01

    Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression levels using libraries of synthetic promoters now exist.

  18. 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.

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

    PubMed

    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.

  20. A Synthetic Model of Mass Persuasion.

    ERIC Educational Resources Information Center

    Kneupper, Charles W.; Underwood, Willard A.

    Mass persuasion involves a message production process which significantly alters or reinforces an attitude, belief, or action of the members of a large, heterogeneous audience. A synthetic communication model for mass persuasion has been constructed which incorporates aspects of several models created to describe the process of effective…

  1. Realistic synthetic observations from radiative transfer models

    NASA Astrophysics Data System (ADS)

    Koepferl, Christine; Robitaille, Thomas

    2013-07-01

    When modeling young stars and star-forming regions throughout the Galaxy, it is important to correctly treat the limitations of the data such as finite resolution and sensitivity. In order to study these effects, and to make radiative transfer models directly comparable to real observations, we have developed a Python package that allows post-processing the output of the 3-d Monte Carlo Radiative Transfer code HYPERION (Robitaille 2011 A&A 536, A79, see poster 2S001). With this package, realistic synthetic observations can be generated, modeling the effects of convolution with arbitrary PSFs, transmission curves, finite pixel resolution, noise and reddening. Pipelines can be written to compute synthetic observations that simulate observatories such as the Spitzer Space Telescope or the Herschel Space Observatory. In this poster we describe the package and present examples of such synthetic observations.

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

    PubMed

    Stano, Pasquale

    2010-09-01

    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.

  3. 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

  4. Synthetic biology: advancing biological frontiers by building synthetic systems.

    PubMed

    Chen, Yvonne Y; Galloway, Kate E; Smolke, Christina D

    2012-02-20

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

  5. Synthetic biology: advancing biological frontiers by building synthetic systems

    PubMed Central

    2012-01-01

    Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field. PMID:22348749

  6. 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.

  7. 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.

  8. How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology.

    PubMed

    Gonze, Didier; Abou-Jaoudé, Wassim; Ouattara, Djomangan Adama; Halloy, José

    2011-01-01

    The recent advance of genetic studies and the rapid accumulation of molecular data, together with the increasing performance of computers, led researchers to design more and more detailed mathematical models of biological systems. Many modeling approaches rely on ordinary differential equations (ODE) which are based on standard enzyme kinetics. Michaelis-Menten and Hill functions are indeed commonly used in dynamical models in systems and synthetic biology because they provide the necessary nonlinearity to make the dynamics nontrivial (i.e., limit-cycle oscillations or multistability). For most of the systems modeled, the actual molecular mechanism is unknown, and the enzyme equations should be regarded as phenomenological. In this chapter, we discuss the validity and accuracy of these approximations. In particular, we focus on the validity of the Michaelis-Menten function for open systems and on the use of Hill kinetics to describe transcription rates of regulated genes. Our discussion is illustrated by numerical simulations of prototype systems, including the Repressilator (a genetic oscillator) and the Toggle Switch model (a bistable system). We systematically compare the results obtained with the compact version (based on Michaelis-Menten and Hill functions) with its corresponding developed versions (based on "elementary" reaction steps and mass action laws). We also discuss the use of compact approaches to perform stochastic simulations (Gillespie algorithm). On the basis of these results, we argue that using compact models is suitable to model qualitatively biological systems.

  9. Synthetic Flight Training System Study

    DTIC Science & Technology

    1983-12-23

    System Component Development Program (VSCDP) as a baseline. In addition, the study investiqated commonality issues of such subsystems as motion...Combat Development Command issued the first in a series of what are now entitled Training Device Requirements (TDR) documents for the development of the...study’s basic issues of visual technology application and commonality are analyzed. The study focuses on approximately five prinicpal organizations

  10. Miniature synthetic-aperture radar system

    NASA Astrophysics Data System (ADS)

    Stockton, Wayne; Stromfors, Richard D.

    1990-11-01

    Loral Defense Systems-Arizona has developed a high-performance synthetic-aperture radar (SAR) for small aircraft and unmanned aerial vehicle (UAV) reconnaissance applications. This miniature radar, called Miniature Synthetic-Aperture Radar (MSAR), is packaged in a small volume and has low weight. It retains key features of large SAR systems, including high-resolution imaging and all-weather operation. The operating frequency of MSAR can optionally be selected to provide foliage penetration capability. Many imaging radar configurations can be derived using this baseline system. MSAR with a data link provides an attractive UAV sensor. MSAR with a real-time image formation processor is well suited to installations where onboard processing and immediate image analysis are required. The MSAR system provides high-resolution imaging for short-to-medium range reconnaissance applications.

  11. Synthetic Ecology of Microbes: Mathematical Models and Applications.

    PubMed

    Zomorrodi, Ali R; Segrè, Daniel

    2016-02-27

    As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.

  12. 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

  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. Synthetic quantitative MRI through relaxometry modelling.

    PubMed

    Callaghan, Martina F; Mohammadi, Siawoosh; Weiskopf, Nikolaus

    2016-12-01

    Quantitative MRI (qMRI) provides standardized measures of specific physical parameters that are sensitive to the underlying tissue microstructure and are a first step towards achieving maps of biologically relevant metrics through in vivo histology using MRI. Recently proposed models have described the interdependence of qMRI parameters. Combining such models with the concept of image synthesis points towards a novel approach to synthetic qMRI, in which maps of fundamentally different physical properties are constructed through the use of biophysical models. In this study, the utility of synthetic qMRI is investigated within the context of a recently proposed linear relaxometry model. Two neuroimaging applications are considered. In the first, artefact-free quantitative maps are synthesized from motion-corrupted data by exploiting the over-determined nature of the relaxometry model and the fact that the artefact is inconsistent across the data. In the second application, a map of magnetization transfer (MT) saturation is synthesized without the need to acquire an MT-weighted volume, which directly leads to a reduction in the specific absorption rate of the acquisition. This feature would be particularly important for ultra-high field applications. The synthetic MT map is shown to provide improved segmentation of deep grey matter structures, relative to segmentation using T1 -weighted images or R1 maps. The proposed approach of synthetic qMRI shows promise for maximizing the extraction of high quality information related to tissue microstructure from qMRI protocols and furthering our understanding of the interrelation of these qMRI parameters. © 2016 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

  15. Synthetic quantitative MRI through relaxometry modelling

    PubMed Central

    Mohammadi, Siawoosh; Weiskopf, Nikolaus

    2016-01-01

    Abstract Quantitative MRI (qMRI) provides standardized measures of specific physical parameters that are sensitive to the underlying tissue microstructure and are a first step towards achieving maps of biologically relevant metrics through in vivo histology using MRI. Recently proposed models have described the interdependence of qMRI parameters. Combining such models with the concept of image synthesis points towards a novel approach to synthetic qMRI, in which maps of fundamentally different physical properties are constructed through the use of biophysical models. In this study, the utility of synthetic qMRI is investigated within the context of a recently proposed linear relaxometry model. Two neuroimaging applications are considered. In the first, artefact‐free quantitative maps are synthesized from motion‐corrupted data by exploiting the over‐determined nature of the relaxometry model and the fact that the artefact is inconsistent across the data. In the second application, a map of magnetization transfer (MT) saturation is synthesized without the need to acquire an MT‐weighted volume, which directly leads to a reduction in the specific absorption rate of the acquisition. This feature would be particularly important for ultra‐high field applications. The synthetic MT map is shown to provide improved segmentation of deep grey matter structures, relative to segmentation using T 1‐weighted images or R 1 maps. The proposed approach of synthetic qMRI shows promise for maximizing the extraction of high quality information related to tissue microstructure from qMRI protocols and furthering our understanding of the interrelation of these qMRI parameters. PMID:27753154

  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. Synthetic bounds for semi-Markov reliability models

    NASA Technical Reports Server (NTRS)

    White, A. L.

    1985-01-01

    Upper and lower bounds are derived for the probability of failure for a class of highly reliable process control computers. The bounds are synthetic in the sense that the descriptions of component failure and system recovery are assumed to be obtained from different sources. The reliability model is constructed under the assumption that the processes are independent.

  18. Simpson's paradox in a synthetic microbial system.

    PubMed

    Chuang, John S; Rivoire, Olivier; Leibler, Stanislas

    2009-01-09

    The maintenance of "public" or "common good" producers is a major question in the evolution of cooperation. Because nonproducers benefit from the shared resource without bearing its cost of production, they may proliferate faster than producers. We established a synthetic microbial system consisting of two Escherichia coli strains of common-good producers and nonproducers. Depending on the population structure, which was varied by forming groups with different initial compositions, an apparently paradoxical situation could be attained in which nonproducers grew faster within each group, yet producers increased overall. We show that a simple way to generate the variance required for this effect is through stochastic fluctuations via population bottlenecks. The synthetic approach described here thus provides a way to study generic mechanisms of natural selection.

  19. 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.

  20. 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.

  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. Mammalian Synthetic Biology: Engineering Biological Systems.

    PubMed

    Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

    2017-06-21

    The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

  4. 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.

  5. 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.

  6. Identifying biases in deterioration models using synthetic sewer data.

    PubMed

    Scheidegger, A; Maurer, M

    2012-01-01

    The assessment and validation of sewer deterioration models is difficult because reliable data are missing. This makes it hard to find the most suitable model for a particular application. A network condition simulator (NetCoS) is used to generate synthetic sewer data for defined test scenarios. Thereby, the deterioration and replacement of pipes, the expansion of the sewer network, and classification errors are considered. Based on such synthetic data, deterioration models are calibrated and their results compared with the predefined scenario. While this approach is not capable of proving that a model performs correctly on a real application, it highlights the strengths and weaknesses of a model. The influence of condition classification errors and the age of the sewer system is investigated for two deterioration models. The results show, that classification errors can introduce substantial biases in the parameter estimation of the Markov model while in comparison the applied cohort model is fairly robust. Young sewer systems with fewer pipes in bad condition states on the other hand, have a very strong influence on the parameter uncertainties of the cohort model while the Markov model proved to be less sensitive.

  7. 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.

  8. 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.

  9. 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.

  10. Building synthetic systems to learn nature's design principles.

    PubMed

    Davidson, Eric A; Windram, Oliver P F; Bayer, Travis S

    2012-01-01

    Evolution undoubtedly shapes the architecture of biological systems, yet it is unclear which features of regulatory, metabolic, and signalling circuits have adaptive significance and how the architecture of these circuits constrains or promotes evolutionary processes, such as adaptation to new environments. Experimentally rewiring circuits using genetic engineering and constructing novel circuits in living cells allows direct testing and validation of hypotheses in evolutionary systems biology. Building synthetic genetic systems enables researchers to explore regions of the genotype-phenotype and fitness landscapes that may be inaccessible to more traditional analysis. Here, we review the strategies that allow synthetic systems to be constructed and how evolutionary design principles have advanced these technologies. We also describe how building small genetic regulatory systems can provide insight on the trade-offs that constrain adaptation and can shape the structure of biological networks. In the future, the possibility of building biology de novo at the genome scale means that increasingly sophisticated models of the evolutionary dynamics of networks can be proposed and validated, and will allow us to recreate ancestral systems in the lab. This interplay between evolutionary systems theory and engineering design may illuminate the fundamental limits of performance, robustness, and evolvability of living systems.

  11. 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.

  12. Computational models for synthetic marine infrared clutter

    NASA Astrophysics Data System (ADS)

    Constantikes, Kim T.; Zysnarski, Adam H.

    1996-06-01

    The next generation of ship defense missiles will need to engage stealthy, passive, sea-skimming missiles. Detection and guidance will occur against a background of sea surface and horizon which can present significant clutter problems for infrared seekers, particularly when targets are comparatively dim. We need a variety of sea clutter models: statistical image models for signal processing algorithm design, clutter occurrence models for systems effectiveness assessment, and constructive image models for synthesizing very large field-of-view (FOV) images with high spatial and temporal resolution. We have implemented and tested such a constructive model. First principle models of water waves and light transport provide a computationally intensive clutter model implemented as a raytracer. Our models include sea, sky, and solar radiance; reflectance; attenuating atmospheres; constructive solid geometry targets; target and water wave dynamics; and simple sensor image formation.

  13. 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.

  14. Computational Modeling And Analysis Of Synthetic Jets

    NASA Technical Reports Server (NTRS)

    Mittal, Rajat; Cattafesta, Lou

    2005-01-01

    In the last report we focused on the study of 3D synthetic jets of moderate jet aspect-ratio. Jets in quiescent and cross-flow cases were investigated. Since most of the synthetic jets in practical applications are found to be of large aspect ratio, the focus was shifted to studying synthetic jets of large aspect ratio. In the current year, further progress has been made by studying jets of aspect ratio 8 and infinity. Some other aspects of the jet, like the vorticity flux is looked into apart from analyzing the vortex dynamics, velocity profiles and the other dynamical characteristics of the jet which allows us to extract some insight into the effect of these modifications on the jet performance. Also, efforts were made to qualitatively validate the simulated results with the NASA Langley test cases at higher jet Reynolds number for the quiescent jet case.

  15. Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development.

    PubMed

    Paddon, Chris J; Keasling, Jay D

    2014-05-01

    Recent developments in synthetic biology, combined with continued progress in systems biology and metabolic engineering, have enabled the engineering of microorganisms to produce heterologous molecules in a manner that was previously unfeasible. The successful synthesis and recent entry of semi-synthetic artemisinin into commercial production is the first demonstration of the potential of synthetic biology for the development and production of pharmaceutical agents. In this Review, we describe the metabolic engineering and synthetic biology approaches that were used to develop this important antimalarial drug precursor. This not only demonstrates the incredible potential of the available technologies but also illuminates how lessons learned from this work could be applied to the production of other pharmaceutical agents.

  16. Engineering of synthetic intercellular communication systems.

    PubMed

    Bacchus, William; Fussenegger, Martin

    2013-03-01

    The introduction of synthetic devices that provide precise fine-tuning of transgene expression has revolutionized the field of biology. The design and construction of sophisticated and reliable genetic control circuits have increased dramatically in complexity in recent years. The norm when creating such circuits is to program the whole network in a single cell. Although this has been greatly successful, the time will soon come when the capacity of a single cell is no longer adequate. Therefore, synthetic biology-inspired research has started to shift towards a multicellular approach in which specialized cells are constructed and then interconnected, enabling the creation of higher-order networks that do not face the same limitations as single cells. This approach is conceptually appealing in many respects. The fact that overall workload can be easily divided between cells eliminates the problem of limited program capacity of a single cell. Furthermore, engineering of specialized cells will enable a plug-and-play approach in which cells are combined into multicellular consortia depending on the requested task. Recent advances in synthetic biology to implement intercellular communication and multicellular consortia have demonstrated an impressive arsenal of new devices with novel functions that are unprecedented even in engineered single cells. Engineering of such devices have been achieved in bacteria, yeast and mammalian cells, all of which is covered in this review. The introduction of synthetic intercellular communication into the cell engineering toolbox will open up new frontiers and will greatly contribute to the future success of synthetic biology and its clinical applications. Copyright © 2012 Elsevier Inc. All rights reserved.

  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. Synthetic Biology: Engineering Living Systems from Biophysical Principles.

    PubMed

    Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

    2017-03-28

    Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  19. Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects.

    PubMed

    Liu, Yanfeng; Shin, Hyun-dong; Li, Jianghua; Liu, Long

    2015-02-01

    Metabolic engineering facilitates the rational development of recombinant bacterial strains for metabolite overproduction. Building on enormous advances in system biology and synthetic biology, novel strategies have been established for multivariate optimization of metabolic networks in ensemble, spatial, and dynamic manners such as modular pathway engineering, compartmentalization metabolic engineering, and metabolic engineering guided by genome-scale metabolic models, in vitro reconstitution, and systems and synthetic biology. Herein, we summarize recent advances in novel metabolic engineering strategies. Combined with advancing kinetic models and synthetic biology tools, more efficient new strategies for improving cellular properties can be established and applied for industrially important biochemical production.

  20. 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

  1. Mechanistically Consistent Reduced Models of Synthetic Gene Networks

    PubMed Central

    Mier-y-Terán-Romero, Luis; Silber, Mary; Hatzimanikatis, Vassily

    2013-01-01

    Designing genetic networks with desired functionalities requires an accurate mathematical framework that accounts for the essential mechanistic details of the system. Here, we formulate a time-delay model of protein translation and mRNA degradation by systematically reducing a detailed mechanistic model that explicitly accounts for the ribosomal dynamics and the cleaving of mRNA by endonucleases. We exploit various technical and conceptual advantages that our time-delay model offers over the mechanistic model to probe the behavior of a self-repressing gene over wide regions of parameter space. We show that a heuristic time-delay model of protein synthesis of a commonly used form yields a notably different prediction for the parameter region where sustained oscillations occur. This suggests that such heuristics can lead to erroneous results. The functional forms that arise from our systematic reduction can be used for every system that involves transcription and translation and they could replace the commonly used heuristic time-delay models for these processes. The results from our analysis have important implications for the design of synthetic gene networks and stress that such design must be guided by a combination of heuristic models and mechanistic models that include all relevant details of the process. PMID:23663853

  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.

  3. Systems and synthetic biology for the biotechnological application of cyanobacteria.

    PubMed

    Hagemann, Martin; Hess, Wolfgang R

    2017-08-23

    Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. Their evolutionary relation to plastids in eukaryotic phototrophs and their increasing utilization as green cell factories initiated the use of systems biology approaches early on. For select model strains, extensive 'omics' data sets have been generated, and genome-wide models have been elucidated. Moreover, the results obtained may be used for the optimization of cyanobacterial metabolism, which can direct the biotechnological production of biofuels or chemical feedstock. Synthetic biology approaches permit the rational construction of novel metabolic pathways that are based on the combination of multiple enzymatic activities of different origins. In addition, the manipulation of whole metabolic networks by CRISPR-based and sRNA-based technologies with multiple parallel targets will further stimulate the use of cyanobacteria for diverse applications in basic research and biotechnology. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. 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.

  5. Synthetic modelling of acoustical propagation applied to seismic oceanography experiments

    NASA Astrophysics Data System (ADS)

    Kormann, Jean; Cobo, Pedro; Biescas, Berta; Sallarés, Valentí; Papenberg, Cord; Recuero, Manuel; Carbonell, Ramón

    2010-03-01

    Recent work shows that multichannel seismic (MCS) systems provide detailed information on the oceans' finestructure. The aim of this paper is to analyze if high order numerical algorithms are suitable to accurately model the extremely weak wavefield scattered by the oceans' finestructures. For this purpose, we generate synthetic shot records along a coincident seismic and oceanographic profile acquired across a Mediterranean salt lens in the Gulf of Cadiz. We apply a 2D finite-difference time-domain propagation model, together with second-order Complex Frequency Shifted Perfectly Matched Layers at the numerical boundaries, using as reference a realistic sound speed map with the lateral resolution of the seismic data. We show that our numerical propagator creates an acoustical image of the ocean finestructures including the salt lens that reproduces with outstanding detail the real acquired one.

  6. Wildfire simulation using LES with synthetic-velocity SGS models

    NASA Astrophysics Data System (ADS)

    McDonough, J. M.; Tang, Tingting

    2016-11-01

    Wildland fires are becoming more prevalent and intense worldwide as climate change leads to warmer, drier conditions; and large-eddy simulation (LES) is receiving increasing attention for fire spread predictions as computing power continues to improve (see, e.g.,). We report results from wildfire simulations over general terrain employing implicit LES for solution of the incompressible Navier-Stokes (N.-S.) and thermal energy equations with Boussinesq approximation, altered with Darcy, Forchheimer and Brinkman extensions, to represent forested regions as porous media with varying (in both space and time) porosity and permeability. We focus on subgrid-scale (SGS) behaviors computed with a synthetic-velocity model, a discrete dynamical system, based on the poor man's N.-S. equations and investigate the ability of this model to produce fire whirls (tornadoes of fire) at the (unresolved) SGS level. Professor, Mechanical Engineering and Mathematics.

  7. 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.

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

    PubMed Central

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

    2004-01-01

    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. PMID:15256602

  9. A resource dependent protein synthesis model for evaluating synthetic circuits.

    PubMed

    Halter, Wolfgang; Montenbruck, Jan Maximilian; Tuza, Zoltan A; Allgöwer, Frank

    2017-03-09

    Reliable in silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the Ribosome Flow Model and among other things describes the movement of RNA-polymerase and ribosomes on mRNA and DNA templates, respectively. By analyzing the convergence properties of this model based upon geometric considerations, we present additional insights into the dynamic mechanisms of the process of protein synthesis. Further, we demonstrate how this model can be used to evaluate the performance of synthetic gene circuits under different loading scenarios.

  10. 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

  11. Alternative Watson-Crick Synthetic Genetic Systems.

    PubMed

    Benner, Steven A; Karalkar, Nilesh B; Hoshika, Shuichi; Laos, Roberto; Shaw, Ryan W; Matsuura, Mariko; Fajardo, Diego; Moussatche, Patricia

    2016-11-01

    In its "grand challenge" format in chemistry, "synthesis" as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work.

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

    PubMed

    Xu, Yunzhen; Du, Pei; Wang, Jianzhou

    2017-04-01

    As the atmospheric environment pollution has been becoming more and more serious in China, it is highly desirable to develop a scientific and effective early warning system that plays a great significant role in analyzing and monitoring air quality. However, establishing a robust early warning system for warning the public in advance and ameliorating air quality is not only an extremely challenging task but also a public concerned problem for human health. Most previous studies are focused on improving the prediction accuracy, which usually ignore the significance of uncertainty information and comprehensive evaluation concerning air pollutants. Therefore, in this paper a novel robust early warning system was successfully developed, which consists of three modules: evaluation module, forecasting module and characteristics estimating module. In this system, a new dynamic fuzzy synthetic evaluation is proposed and applied to determine air quality levels and primary pollutants, which can be regarded as the research objectives; Moreover, to further mine and analyze the characteristics of air pollutants, four different distribution functions and interval forecasting method are also employed that can not only provide predictive range, confidence level and the other uncertain information of the pollutants future values, but also assist decision-makers in reducing and controlling the emissions of atmospheric pollutants. Case studies utilizing hourly PM2.5, PM10 and SO2 data collected from Tianjin and Shanghai in China are applied as illustrative examples to estimate the effectiveness and efficiency of the proposed system. Experimental results obviously indicated that the developed novel early warning system is much suitable for analyzing and monitoring air pollution, which can also add a novel viable option for decision-makers. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. 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.

  14. 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.

  15. Informing biological design by integration of systems and synthetic biology.

    PubMed

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

  16. Informing Biological Design by Integration of Systems and Synthetic Biology

    PubMed Central

    Smolke, Christina D.; Silver, Pamela A.

    2011-01-01

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. PMID:21414477

  17. Contextualizing context for synthetic biology – identifying causes of failure of synthetic biological systems

    PubMed Central

    Cardinale, Stefano; Arkin, Adam Paul

    2012-01-01

    Despite the efforts that bioengineers have exerted in designing and constructing biological processes that function according to a predetermined set of rules, their operation remains fundamentally circumstantial. The contextual situation in which molecules and single-celled or multi-cellular organisms find themselves shapes the way they interact, respond to the environment and process external information. Since the birth of the field, synthetic biologists have had to grapple with contextual issues, particularly when the molecular and genetic devices inexplicably fail to function as designed when tested in vivo. In this review, we set out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues. PMID:22649052

  18. 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.

  19. Synthetic and systems biology for microbial production of commodity chemicals.

    PubMed

    Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J; Keasling, Jay D; Martín, Héctor García

    2016-01-01

    The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.

  20. Synthetic and systems biology for microbial production of commodity chemicals

    SciTech Connect

    Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J.; Keasling, Jay D.; Martín, Héctor Garcia

    2016-04-07

    The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.

  1. Synthetic and systems biology for microbial production of commodity chemicals

    PubMed Central

    Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J; Keasling, Jay D; Martín, Héctor García

    2016-01-01

    The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering. PMID:28725470

  2. Spectral characterization and discrimination of synthetic fibers with near-infrared hyperspectral imaging system.

    PubMed

    Jin, Xiaoke; Memon, Hafeezullah; Tian, Wei; Yin, Qinli; Zhan, Xiaofang; Zhu, Chengyan

    2017-04-20

    Synthetic fibers account for about half of all fiber usage, with applications in every textile field. The phenomenon of fiber composition not matching the label harms consumer interests and impedes market development. Hyperspectral imaging technology as a potential technique can be utilized to discriminate mass synthetic fibers rapidly and nondestructively and achieves the functions that traditional Fourier transform infrared instruments do not have. On the basis of investigating the impact of dope-dyeing and wrapping processes on spectra, the spectral features (from 900 to 2500 nm) of six categories of synthetic fibers were extracted with a hyperspectral imaging system. A principal component analysis-linear discriminant analysis model was developed to discriminate the chemical content of fibers in different colors and structures, which showed 100% discrimination accuracy. Results demonstrated the feasibility of a hyperspectral imaging system in synthetic fiber discrimination. Therefore, this method offers a more convenient alternative for textile industry on-site discrimination.

  3. A SEASAT-A synthetic aperture imaging radar system

    NASA Technical Reports Server (NTRS)

    Jordan, R. L.; Rodgers, D. H.

    1975-01-01

    The SEASAT, a synthetic aperture imaging radar system is the first radar system of its kind designed for the study of ocean wave patterns from orbit. The basic requirement of this system is to generate continuous radar imagery with a 100 km swath with 25m resolution from an orbital altitude of 800 km. These requirements impose unique system design problems. The end to end data system described including interactions of the spacecraft, antenna, sensor, telemetry link, and data processor. The synthetic aperture radar system generates a large quantity of data requiring the use of an analog link with stable local oscillator encoding. The problems associated in telemetering the radar information with sufficient fidelity to synthesize an image on the ground is described as well as the selected solutions to the problems.

  4. 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

  5. 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.

  6. 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…

  7. Antenna dimensions of synthetic aperture radar systems on satellites

    NASA Technical Reports Server (NTRS)

    Richter, K. R.

    1973-01-01

    Design of a synthetic aperture radar (SAR) for a satellite must take into account the limitation in weight and dimensions of the antenna. The lower limits of the antenna area are derived from the conditions of unambiguity of the SAR system. This result is applied to estimate the antenna requirements for SARs on satellites in circular orbits of various altitudes around Earth and Venus.

  8. Innovation at the intersection of synthetic and systems biology.

    PubMed

    Lanza, Amanda M; Crook, Nathan C; Alper, Hal S

    2012-10-01

    The promises of modern biotechnology hinge upon the hope that we can understand microscopic cellular complexity and in doing so create novel function. In this regard, the fields of systems and synthetic biology are important for accelerating both our understanding of biological systems and our ability to quantitatively engineer cells. At the nexus of these two fields is a unique synergy that can help attain these goals. Thus, the next greatest advances in biology and biotechnology are arising at the intersection of the top-down systems approach and the bottom-up synthetic approach. Collectively, these developments enable the precise control of cellular state for systems studies and the discovery of novel parts, control strategies, and interactions for the design of robust synthetic function. This review seeks to highlight this activity as well as provide a perspective for future directions. Combining these efforts can provide novel insights into cellular function and lead to robust, novel synthetic design. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. Ambiguities in spaceborne synthetic aperture radar systems

    NASA Technical Reports Server (NTRS)

    Li, F. K.; Johnson, W. T. K.

    1983-01-01

    An examination of aspects of spaceborne SAR time delay and Doppler ambiguities has led to the formulation of an accurate method for the evaluation of the ratio of ambiguity intensities to that of the signal, which has been applied to the nominal SAR system on Seasat. After discussing the variation of this ratio as a function of orbital latitude and attitude control error, it is shown that the detailed range migration-azimuth phase history of an ambiguity is different from that of a signal, so that the images of ambiguities are dispersed. Seasat SAR dispersed images are presented, and their dispersions are eliminated through an adjustment of the processing parameters. A method is also presented which uses a set of multiple pulse repetition sequences to determine the Doppler centroid frequency absolute values for SARs with high carrier frequencies and poor attitude measurements.

  10. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Incorporation of polarization into the DIRSIG synthetic image generation model

    NASA Astrophysics Data System (ADS)

    Meyers, Jason P.; Schott, John R.; Brown, Scott D.

    2002-11-01

    The Digital Imaging and Remote Sensing Synthetic Image Generation (DIRSIG) model uses a quantitative first principles approach to generate synthetic hyperspectral imagery. This paper presents the methods used to add modeling of polarization phenomenology. The radiative transfer equations were modified to use Stokes vectors for the radiance values and Mueller matrices for the energy-matter interactions. The use of Stokes vectors enables a full polarimetric characterization of the illumination and sensor reaching radiances. The bi-directional reflectance distribution function (BRDF) module was rewritten and modularized to accommodate a variety of polarized and unpolarized BRDF models. Two new BRDF models based on Torrance-Sparrow and Beard-Maxwell were added to provide polarized BRDF estimations. The sensor polarization characteristics are modeled using Mueller matrix transformations on a per pixel basis. All polarized radiative transfer calculations are performed spectrally to preserve the hyperspectral capabilities of DIRSIG. Integration over sensor bandpasses is handled by the sensor module.

  12. Generalized radial flow in synthetic flow systems.

    PubMed

    Bowman, Dale O; Roberts, Randall M; Holt, Robert M

    2013-01-01

    Traditional analysis methods used to determine hydraulic properties from pumping tests work well in many porous media aquifers, but they often do not work in heterogeneous and fractured-rock aquifers, producing non-plausible and erroneous results. The generalized radial flow model developed by Barker (1988) can reveal information about heterogeneity characteristics and aquifer geometry from pumping test data by way of a flow dimension parameter. The physical meaning of non-integer flow dimensions has long been a subject of debate and research. We focus on understanding and interpreting non-radial flow through high permeability conduits within fractured aquifers. We develop and simulate flow within idealized non-radial flow conduits and expand on this concept by simulating pumping in non-fractal random fields with specific properties that mimic persistent sub-radial flow responses. Our results demonstrate that non-integer flow dimensions can arise from non-fractal geometries within aquifers. We expand on these geometric concepts and successfully simulate pumping in random fields that mimic well-test responses seen in the Culebra Dolomite above the Waste Isolation Pilot Plant. © 2012, The Author(s). Groundwater © 2012, National Ground Water Association.

  13. Study on key techniques for synthetic aperture ladar system

    NASA Astrophysics Data System (ADS)

    Cao, Changqing; Zeng, Xiaodong; Feng, Zhejun; Zhang, Wenrui; Su, Lei

    2008-03-01

    The spatial resolution of a conventional imaging LADAR system is constrained by the diffraction limit of the telescope aperture. The purpose of this work is to investigate Synthetic Aperture Imaging LADAR (SAIL), which employs aperture synthesis with coherent laser radar to overcome the diffraction limit and achieve fine-resolution, long range, two-dimensional imaging with modest aperture diameters. Because of many advantages, LADAR based on synthetic aperture theory is becoming research hotspot and practicality. Synthetic Aperture LADAR (SAL) technology satisfies the critical need for reliable, long-range battlefield awareness. An image that takes radar tens of seconds to produce can be produced in a few thousands of a second at optical frequencies. While radar waves respond to macroscopic features such as corners, edges, and facets, laser waves interact with microscopic surface characteristics, which results in imagery that appears more familiar and is more easily interpreted. SAL could provide high resolution optical/infrared imaging. In the present paper we have tried to answer three questions: (1) the process of collecting the samples over the large "synthetic" aperture; (2) differences between SAR and SAL; (3) the key techniques for SAL system. The principle and progress of SAL are introduced and a typical SAL system is described. Beam stabilization, chirp laser, and heterodyne detection, which are among the most challenging aspects of SAL, are discussed in detail.

  14. Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

    PubMed

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-10-11

    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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. A dynamical model for generating synthetic Phonocardiogram signals

    PubMed Central

    Almasi, Ali; Shamsollahi, Mohammad-Bagher; Senhadji, Lotfi

    2011-01-01

    In this paper we introduce a dynamical model for Phonocardiogram (PCG) signal which is capable of generating realistic synthetic PCG signals. This model is based on PCG morphology and consists of three ordinary differential equations and can represent various morphologies of normal PCG signals. Beat-to-beat variation in PCG morphology is significant so model parameters vary from beat to beat. This model is inspired of Electrocardiogram (ECG) dynamical model proposed by McSharry et al. and can be employed to assess biomedical signal processing techniques. PMID:22255630

  20. Synthetic and systems biology for microbial production of commodity chemicals

    DOE PAGES

    Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J.; ...

    2016-04-07

    The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges startmore » at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.« less

  1. 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.

  2. Kappa rule-based modeling in synthetic biology.

    PubMed

    Wilson-Kanamori, John; Danos, Vincent; Thomson, Ty; Honorato-Zimmer, Ricardo

    2015-01-01

    Rule-based modeling, an alternative to traditional reaction-based modeling, allows us to intuitively specify biological interactions while abstracting from the underlying combinatorial complexity. One such rule-based modeling formalism is Kappa, which we introduce to readers in this chapter. We discuss the application of Kappa to three modeling scenarios in synthetic biology: a unidirectional switch based on nitrosylase induction in Saccharomyces cerevisiae, the repressilator in Escherichia coli formed from BioBrick parts, and a light-mediated extension to said repressilator developed by the University of Edinburgh team during iGEM 2010. The second and third scenarios in particular form a case-based introduction to the Kappa BioBrick Framework, allowing us to systematically address the modeling of devices and circuits based on BioBrick parts in Kappa. Through the use of these examples, we highlight the ease with which Kappa can model biological interactions both at the genetic and the protein-protein interaction level, resulting in detailed stochastic models accounting naturally for transcriptional and translational resource usage. We also hope to impart the intuitively modular nature of the modeling processes involved, supported by the introduction of visual representations of Kappa models. Concluding, we explore future endeavors aimed at making modeling of synthetic biology more user-friendly and accessible, taking advantage of the strengths of rule-based modeling in Kappa.

  3. 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.

  4. Synthetic Fluorophores for Visualizing Biomolecules in Living Systems

    PubMed Central

    Martynov, V. I.; Pakhomov, A. A.; Popova, N. V.; Deyev, I. E.; Petrenko, A. G.

    2016-01-01

    The last decade has witnessed significant advance in the imaging of living systems using fluorescent markers. This progress has been primarily associated with the discovery of different spectral variants of fluorescent proteins. However, the fluorescent protein technology has its own limitations and, in some cases, the use of low-molecular-weight fluorophores is preferable. In this review, we describe the arsenal of synthetic fluorescent tools that are currently in researchers’ hands and span virtually the entire spectrum, from the UV to visible and, further, to the near-infrared region. An overview of recent advances in site-directed introduction of synthetic fluorophores into target cellular objects is provided. Application of these fluorescent probes to the solution of a wide range of biological problems, in particular, to the determination of local ion concentrations and pH in living systems, is discussed. PMID:28050265

  5. Numerical modeling of active separation control by synthetic jets

    NASA Astrophysics Data System (ADS)

    Aram, Shawn

    Zero-Net Mass-Flux (ZNMF) actuators or synthetic jet actuators are versatile micro scale devices with numerous applications in the field of fluid mechanics. The primary focus of the current work is to use time-accurate simulations to study the interaction of these jets with cross flows and to optimize their performance for the control of boundary layer separation. This study consists of four parts. In the first part, a class of phenomenology-based models is proposed to reproduce the flow associated with synthetic jets in grazing flows and simplify the task of ZNMF-based flow control simulations. The proposed models have a non-uniform jet velocity profile with only two spatial degrees of freedom and a uniform slip velocity on the slot-flow boundary. A comparison of key integral quantities associated with the momentum, energy and vorticity fluxes shows that the models with a non-uniform jet velocity during the expulsion phase and uniform jet velocity during the ingestion phase can predict these quantities with good accuracy, whereas a simple plug flow model with a zero slip and uniform jet velocity under-predicts these three quantities during the expulsion phase. Based on our initial analysis, three of the simplest models are selected for further study, including an assessment of their performance for a canonical separated flow at different forcing frequencies. A key finding is that a simple plug-flow type model can predict incorrect trends for separation reduction with the jet frequency. A preliminary attempt is also made to provide empirical closure to these models. The effect of synthetic jets orientation on its interaction with a zero pressure gradient laminar boundary layer is explored in the second part. A rectangular slot is chosen in this study and streamwise and spanwise orientations of this slot are examined. The orientation of the slot is found to have a significant impact on its interaction with the boundary layer. The dominant feature in the streamwise

  6. A digital calibration method for synthetic aperture radar systems

    NASA Technical Reports Server (NTRS)

    Larson, Richard W.; Jackson, P. L.; Kasischke, Eric S.

    1988-01-01

    A basic method to calibrate imagery from synthetic aperture radar (SAR) systems is presented. SAR images are calibrated by monitoring all the terms of the radar equation. This procedure includes the use of both external (calibrated reference reflectors) and internal (system-generated calibration signals) sources to monitor the total SAR system transfer function. To illustrate the implementation of the procedure, two calibrated SAR images (X-band, 3.2-cm wavelength) are presented, along with the radar cross-section measurements of specific scenes within each image. The sources of error within the SAR image calibration procedure are identified.

  7. 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

  8. 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.

  9. A New PAMPA Model Proposed on the Basis of a Synthetic Phospholipid Membrane

    PubMed Central

    Yu, Hui; Wang, Qi; Sun, Ying; Shen, Ming; Li, He; Duan, Yourong

    2015-01-01

    The purpose of this work was to investigate the synthetic phospholipid dependence of permeability measured by parallel artificial membrane permeability assay (PAMPA) method. Three phospholipids with hydrophobic groups of different lengths and phosphorylcholine as the hydrophilic group were concisely synthesized. Ten model drug molecules were selected because of their distinct human fraction absorbed (%FA) values and various pKa characteristics. In vitro drug permeation experiments were designed to determine the effect of the incubation time (4–20 h), pH gradient (4.6–9.32) and carbon chain length (8, 10, 12) on the drug permeability through the synthetic phospholipid membrane in the PAMPA system. The results showed that intensive and significant synthetic phospholipids dependence of permeability influenced by the length of lipid’s hydrophobic carbon chain. The effective permeability constant (Pe) of each drug increased rapidly with time, then decreased slightly after reaching the maximum; the pH gradient changed the drug permeability according to the pH-partition hypothesis for drugs with diverse pKa values; and longer hydrophobic chains in the synthetic phospholipid membrane improved the drug permeability, as observed for all test drugs at almost all incubation time points. This newly proposed PAMPA model considered the synthetic phospholipid membrane and showed good Pe-%FA correlation for the passive transport of drugs, making it a helpful supplementary method for PAMPA systems. PMID:25647086

  10. Engineering the Feedback Dynamics of in vitro Synthetic Biological Systems

    NASA Astrophysics Data System (ADS)

    Bishop, Joshua D.

    Building a biochemical system from scratch that rivals a living cell in ability to robustly perform many complex tasks in response to environmental signals is beyond the state-of-the- art. However, feedback is clearly a principle widely employed by cells---as it is by engineers---to enable robust dynamical behaviors, although a limited system-level understanding of feedback regulation and dynamical behavior in biochemical contexts hampers our ability to engineer such systems. Studying simple feedback systems in a rich, yet fully synthetic, biochemical context---like that provided by DNA nanotechnology---may therefore lead to a new state-of-the-art for synthetic biological systems. This thesis, in keeping with this philosophy, describes basic efforts in engineering bio- chemical feedback control systems in the form of simple, in vitro, nucleic-acid-based devices. I describe two such devices, which provide basic test-beds for engineering feedback dynamics in vitro. The first device is a DNA nanomotor, previously described in the literature, that is built from and operated by nucleic acid components, and that I modify by the introduction of a protein enzyme to improve the performance of the device in experimental tests. The second device I design and build from nucleic acid components and two protein enzymes to regulate the free quantity of an RNA molecule, which in turn can be used to dynamically drive the operation of other nucleic-acid-based systems---such as the first device---in a robust manner.

  11. 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.

  12. 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.

  13. 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.

  14. Engineering plant metabolism into microbes: from systems biology to synthetic biology.

    PubMed

    Xu, Peng; Bhan, Namita; Koffas, Mattheos A G

    2013-04-01

    Plant metabolism represents an enormous repository of compounds that are of pharmaceutical and biotechnological importance. Engineering plant metabolism into microbes will provide sustainable solutions to produce pharmaceutical and fuel molecules that could one day replace substantial portions of the current fossil-fuel based economy. Metabolic engineering entails targeted manipulation of biosynthetic pathways to maximize yields of desired products. Recent advances in Systems Biology and the emergence of Synthetic Biology have accelerated our ability to design, construct and optimize cell factories for metabolic engineering applications. Progress in predicting and modeling genome-scale metabolic networks, versatile gene assembly platforms and delicate synthetic pathway optimization strategies has provided us exciting opportunities to exploit the full potential of cell metabolism. In this review, we will discuss how systems and synthetic biology tools can be integrated to create tailor-made cell factories for efficient production of natural products and fuel molecules in microorganisms.

  15. 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.

  16. 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

  17. 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.

  18. Synthetic-gauge-field-induced Dirac semimetal state in an acoustic resonator system

    NASA Astrophysics Data System (ADS)

    Yang, Zhaoju; Gao, Fei; Shi, Xihang; Zhang, Baile

    2016-12-01

    Recently, a proposal of synthetic gauge field in reduced two-dimensional (2D) system from three-dimensional (3D) acoustic structure shows an analogue of the gapped Haldane model with fixed k z , and achieves the gapless Weyl semimetal phase in 3D momentum space. Here, extending this approach of synthetic gauge flux, we propose a reduced square lattice of acoustic resonators, which exhibits Dirac nodes with broken effective time-reversal symmetry. Protected by an additional hidden symmetry, these Dirac nodes with quantized values of topological charge are characterized by nonzero winding number and the finite structure exhibits flat edge modes that cannot be destroyed by perturbations.

  19. Nonlinear inversion for arbitrarily-oriented anisotropic models: Synthetic testing

    NASA Astrophysics Data System (ADS)

    Bremner, P. M.; Panning, M. P.

    2010-12-01

    We present an implementation of new 3-D finite-frequency kernels, based on the Born approximation, for inversion of a synthetic surface wave dataset. The kernels are formulated based on a hexagonal symmetry with an arbitrary orientation. Numerical tests are performed to achieve a robust inversion scheme. Nonlinear inversion schemes are examined for adequate recovery of three input models to include: isotropic, anisotropic, and both anisotropic and isotropic input models. Output models from inversions of calculated synthetic data are compared against these input models to test for accurate reproduction of input model features, and the resolution of those features. The focus of this study is on inverting for structure beneath western North America. The synthetic dataset consists of collected seismic waveforms of 128 earthquake mechanisms, of magnitude 6-7 from Dec 2006 to Feb 2009, from the IRIS database. Events were selected to correlate with USArray deployments, and to have as complete an azimuthal coverage as possible. The events occurred within a circular region of radius 150° centered about 44° lat, -110° lon (an arbitrary location within USArray coverage). The seismograms have been calculated within a simplified version of PREM in which the crust and 220 km discontinuity have been removed, dubbed PREM LIGHT, utilizing a spectral element code (SEM) coupled to a normal mode solution. The mesh consists of a 3-D heterogeneous outer shell, representing the upper mantle above 400 km depth, coupled to a spherically symmetric inner sphere. The SEM solves the weak formulation of the seismic wave equation in the outer shell, and uses normal mode summation methods for the inner sphere. To validate the results of the SEM, seismograms are benchmarked against seismograms calculated with a 1-D normal mode summation. From the synthetic dataset, multi-taper fundamental mode surface wave phase delay measurements are taken. The orthogonal 2.5π spheroidal wave function

  20. Ferritin nanocontainers that self-direct in synthetic polymer systems

    NASA Astrophysics Data System (ADS)

    Sengonul, Merih C.

    Currently, there are many approaches to introduce functionality into synthetic polymers. Among these, for example, are copolymerization, grafting, and blending methods. However, modifications made by such methods also change the thermodynamics and rheological properties of the polymer system of interest, and each new modification often requires a costly reoptimization of polymer processing. Such a reoptimalization would not be necessary if new functionality could be introduced via a container whose external surface is chemically and physically tuned to interact with the parent polymer. The contents of the container could then be changed without changing other important properties of the parent polymer. In this context this thesis project explores an innovative nanocontainer platform which can be introduced into phase-separating homopolymer blends. Ferritin is a naturally existing nanocontainer that can be used synthetically to package and selectively transport functional moieties to a particular phase that is either in the bulk or on the surface of a homopolymer blend system. The principal focus of this work centers on modifying the surface of wild ferritin to: (1) render modified ferritin soluble in a non-aqueous solvent; and (2) impart it with self-directing properties when exposed to a homopolymer blend surface or incorporated into the bulk of a homopolymer blend. Wild ferritin is water soluble, and this research project successfully modified wild ferritin by grafting either amine-functional poly(ethylene glycol) (PEG) or short-chain alkanes to carbodiimide activated carboxylate groups on ferritin's surface. Such modified ferritin is soluble in dichloromethane (DCM). Modification was confirmed by ion-exchange chromatography, zeta-potential measurements, and electrospray mass spectroscopy. FT-IR was used to quantify the extent of PEGylation of the reaction products through area ratios of the -C-O-C asymmetric stretching vibration of the grafted PEG chains to the

  1. 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.

  2. Molten salt parabolic trough system with synthetic oil preheating

    NASA Astrophysics Data System (ADS)

    Yuasa, Minoru; Hino, Koichi

    2017-06-01

    Molten salt parabolic trough system (MSPT), which can heat the heat transfer fluid (HTF) to 550 °C has a better performance than a synthetic oil parabolic trough system (SOPT), which can heat the HTF to 400 °C or less. The utilization of HTF at higher temperature in the parabolic trough system is able to realize the design of a smaller size of storage tank and higher heat to electricity conversion efficiency. However, with MSPT there is a great amount of heat loss at night so it is necessary to circulate the HTF at a high temperature of about 290 °C in order to prevent solidification. A new MSPT concept with SOPT preheating (MSSOPT) has been developed to reduce the heat loss at night. In this paper, the MSSOPT system, its performance by steady state analysis and annual performance analysis are introduced.

  3. Hierarchical model-based interferometric synthetic aperture radar image registration

    NASA Astrophysics Data System (ADS)

    Wang, Yang; Huang, Haifeng; Dong, Zhen; Wu, Manqing

    2014-01-01

    With the rapid development of spaceborne interferometric synthetic aperture radar technology, classical image registration methods are incompetent for high-efficiency and high-accuracy masses of real data processing. Based on this fact, we propose a new method. This method consists of two steps: coarse registration that is realized by cross-correlation algorithm and fine registration that is realized by hierarchical model-based algorithm. Hierarchical model-based algorithm is a high-efficiency optimization algorithm. The key features of this algorithm are a global model that constrains the overall structure of the motion estimated, a local model that is used in the estimation process, and a coarse-to-fine refinement strategy. Experimental results from different kinds of simulated and real data have confirmed that the proposed method is very fast and has high accuracy. Comparing with a conventional cross-correlation method, the proposed method provides markedly improved performance.

  4. Synthetic-Eddy Method for Urban Atmospheric Flow Modelling

    NASA Astrophysics Data System (ADS)

    Pavlidis, D.; Gorman, G. J.; Gomes, J. L. M. A.; Pain, C. C.; Apsimon, H.

    2010-08-01

    The computational fluid dynamics code Fluidity, with anisotropic mesh adaptivity, is used as a multi-scale obstacle-accommodating meteorological model. A novel method for generating realistic inlet boundary conditions based on the view of turbulence as a superposition of synthetic eddies is adopted. It is able to reproduce prescribed first-order and second-order one-point statistics and turbulence length scales. The aim is to simulate an urban boundary layer. The model is validated against two standard benchmark tests: a plane channel flow numerical simulation and a flow past a cube physical simulation. The performed large-eddy simulations are in good agreement with both reference models giving confidence that the model can be used to successfully simulate urban atmospheric flows.

  5. 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.

  6. Model verification: synthetic single pattern simulations using seismic reflection data

    SciTech Connect

    Ramirez, Abelardo; Dyer, Kathleen; White, Donald; Hao, Yue; Yang, Xianjin

    2010-07-09

    During Phase 1 of the Weyburn Project (2000-2004), 4D reflection seismic data were used to map CO2 migration within the Midale reservoir, while an extensive fluid sampling program documented the geochemical evolution triggered by CO2-brine-oilmineral interactions. The aim of this task (3b.11) is to exploit these existing seismic and geochemical data sets, augmented by CO2/H2O injection and HC/H2O production data toward optimizing the reservoir model and thereby improving site characterization and dependent predictions of long-term CO2 storage in the Weyburn-Midale reservoir. Our current project activities have concentrated on completing and testing a stochastic inversion method that will identify reservoir models that optimize agreement between the observed and predicted seismic response. This report describes the results of a validation test that uses synthetic seismic data to identify optimal porosity/permeability distributions within the reservoir. The report partially fulfills deliverable D3: “Model verification: synthetic single pattern simulations” in the project’s statement of work. A future deliverable will describe verification activities related to the geochemical inversion algorithm.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. [Recent researches of synthetic mercury sulfide in traditional medicine system].

    PubMed

    Chen, Chao-jun; Wu, Shi-kui; Wang, Yi-bo; Hou, Jin-feng; Ma, Lei; Sun, Xiao-yan

    2012-10-01

    Herein, the synthesis, component, microstructure and pharmacological and toxicology researches of the Synthetic Mercury Sulfide (S-HgS) a kind of common drug in Chinese, Mongolia, Tibetan medicine, and Indian medicine system were summarized. The similar cognition about mercury toxicity & pharmacological action from some Asian regions was analyzed, and it can supply some useful direction for the traditional Asian medicine system. Recent literatures both domestic and abroad were summarized and analyzed. S-HgS is the basis of Vermilion, Mongolia-Vermilion, Zuotai, and Ras-sindoor. Athough the processes of synthesis are very different, but the microstructure and pharmacological & toxicology of S-HgS is similar. S-HgS has a far-ranging application,and unique curative effect. New technology such as nanotechnology can be used for improving the advancement of traditional Asian medicine.

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

    PubMed

    Knuuttila, Tarja; Loettgers, Andrea

    2013-06-01

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

  13. Spectral classification of stars using synthetic model atmospheres

    NASA Astrophysics Data System (ADS)

    Bertone, E.; Buzzoni, A.

    2001-09-01

    We devised a straightforward procedure to derive the atmospheric fundamental parameters of stars across the different MK spectral types by comparing mid-resolution spectroscopic observations with theoretical grids of synthetic spectra. The results of a preliminary experiment, by matching the Gunn & Stryker (1983) and Jacoby et al. (1984) spectrophotometric atlases with the Kurucz (1995) models, are briefly discussed. For stars in the A-K spectral range, effective temperature is obtained within a 1-2% relative uncertainty (at 2-sigma confidence level). This value raises to 4-5% for the hottest stars in the samples (O-B spectral types). A poorer fit is obtained throughout for stars cooler than 4000 K mainly due to the limiting input physics in the Kurucz models.

  14. Optical design of a synthetic aperture ladar antenna system

    NASA Astrophysics Data System (ADS)

    Cao, Changqing; Zeng, Xiaodong; Zhao, Xiaoyan; Liu, Huanhuan; Man, Xiangkun

    2008-03-01

    The spatial resolution of a conventional imaging LADAR system is constrained by the diffraction limit of the telescope aperture. The purpose of this work is to investigate Synthetic Aperture Imaging LADAR (SAIL), which employs aperture synthesis with coherent laser radar to overcome the diffraction limit and achieve fine-resolution, long range, two-dimensional imaging with modest aperture diameters. According to the demands of the Synthetic Aperture LADAR (SAL), the key techniques are analyzed briefly. The preliminary design of the optical antenna is also introduced in this paper. We investigate the design method and relevant problems of efficient optical antenna that are required in SAL. The design is pursued on the basis of the same method as is used at microwave frequency. The method is based on numerical analysis and the error values obtained by present manufacturing technology. According to the requirement to SAL with the trial of little size, light mass, low cost and high image quality, the result by ZEMAX will result.

  15. 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.

  16. Rewiring and dosing of systems modules as a design approach for synthetic mammalian signaling networks.

    PubMed

    Kämpf, Michael M; Engesser, Raphael; Busacker, Moritz; Hörner, Maximilian; Karlsson, Maria; Zurbriggen, Matias D; Fussenegger, Martin; Timmer, Jens; Weber, Wilfried

    2012-06-01

    Modularly structured signaling networks coordinate the fate and function of complex biological systems. Each component in the network performs a discrete computational operation, but when connected to each other intricate functionality emerges. Here we study such an architecture by connecting auxin signaling modules and inducible protein biotinylation systems with transcriptional control systems to construct synthetic mammalian high-detect, low-detect and band-detect networks that translate overlapping gradients of inducer molecules into distinct gene expression patterns. Guided by a mathematical model we apply fundamental computational operations like conjunction or addition to rewire individual building blocks to qualitatively and quantitatively program the way the overall network interprets graded input signals. The design principles described in this study might serve as a conceptual blueprint for the development of next-generation mammalian synthetic gene networks in fundamental and translational research.

  17. Study of method for synthetic precipitation data for ungauged sites using quantitative precipitation model

    NASA Astrophysics Data System (ADS)

    Bae, Hyo-Jun; Oh, Jai-Ho

    2017-08-01

    A method was developed to estimate a synthetic precipitation record for ungauged sites using irregular coarse observations. The proposed synthetic precipitation data were produced with ultrahigh hourly resolution on a regular 1 × 1 km grid. The proposed method was used to analyze selected real-time observational data collected in South Korea from 2010 to the end of 2014. The observed precipitation data were measured using the Automatic Weather System and Automated Synoptic Observing System. The principal objective of the proposed method was to estimate the additional effects of orography on precipitation introduced by ultrahigh- resolution (1 × 1 km) topography provided by a digital elevation model. The Global Forecast System analysis of the National Centers for Environmental Prediction was used for the upper-atmospheric conditions, necessary for estimating the orographic effects. Precipitation data from 48 of the more than 600 observation sites used in the study, which matched the grid points of the synthetic data, were not included in the synthetic data estimation. Instead, these data were used to evaluate the proposed method by direct comparison with the real observations at these sites. A bias score was investigated by comparison of the synthetic precipitation data with the observations. In this comparison, the number of Hit, False, Miss, and Correct results for 2010-2014 was 74738, 25778, 7544, and 367981, respectively. In the Hit cases, the bias score was 1.22 and the correlation coefficient was 0.74. The means of the differences between the synthetic data and the observations were 0.3, -3.9, -14.4, and -34.9 mm h-1 and the root mean square errors (RMSEs) were 2.7, 8.3, 19.3, and 39.6 mm h-1 for the categories of 0.5-10.0, 10.0-30.0, 30.0-50.0, and 50.0-100.0 mm h-1, respectively. In addition, in each range, the 60% difference between the synthetic precipitation data and the observation data was -1.5 to +1.5, -5.0 to +5.0, -17.0 to +17.0, and -33.0 to +33

  18. 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.

  19. Cosmic non-TEM radiation and synthetic feed array sensor system in ASIC mixed signal technology

    NASA Astrophysics Data System (ADS)

    Centureli, F.; Scotti, G.; Tommasino, P.; Trifiletti, A.; Romano, F.; Cimmino, R.; Saitto, A.

    2014-08-01

    The paper deals with the opportunity to introduce "Not strictly TEM waves" Synthetic detection Method (NTSM), consisting in a Three Axis Digital Beam Processing (3ADBP), to enhance the performances of radio telescope and sensor systems. Current Radio Telescopes generally use the classic 3D "TEM waves" approximation Detection Method, which consists in a linear tomography process (Single or Dual axis beam forming processing) neglecting the small z component. The Synthetic FEED ARRAY three axis Sensor SYSTEM is an innovative technique using a synthetic detection of the generic "NOT strictly TEM Waves radiation coming from the Cosmo, which processes longitudinal component of Angular Momentum too. Than the simultaneous extraction from radiation of both the linear and quadratic information component, may reduce the complexity to reconstruct the Early Universe in the different requested scales. This next order approximation detection of the observed cosmologic processes, may improve the efficacy of the statistical numerical model used to elaborate the same information acquired. The present work focuses on detection of such waves at carrier frequencies in the bands ranging from LF to MMW. The work shows in further detail the new generation of on line programmable and reconfigurable Mixed Signal ASIC technology that made possible the innovative Synthetic Sensor. Furthermore the paper shows the ability of such technique to increase the Radio Telescope Array Antenna performances.

  20. The role of regulation in the origin and synthetic modelling of minimal cognition.

    PubMed

    Bich, Leonardo; Moreno, Alvaro

    2016-10-01

    In this paper we address the question of minimal cognition by investigating the origin of some crucial cognitive properties from the very basic organisation of biological systems. More specifically, we propose a theoretical model of how a system can distinguish between specific features of its interaction with the environment, which is a fundamental requirement for the emergence of minimal forms of cognition. We argue that the appearance of this capacity is grounded in the molecular domain, and originates from basic mechanisms of biological regulation. In doing so, our aim is to provide a theoretical account that can also work as a possible conceptual bridge between Synthetic Biology and Artificial Intelligence. In fact, we argue, Synthetic Biology can contribute to the study of minimal cognition (and therefore to a minimal AI), by providing a privileged approach to the study of these mechanisms by means of artificial systems.

  1. Exploring the properties of the DDO system using synthetic colors

    NASA Astrophysics Data System (ADS)

    Tripicco, Michael J.; Bell, R. A.

    1991-08-01

    The properties of the David Dunlap Observatory (DDO) system (which uses bandpasses centered at about 3450, 3800, 4180, 4250, 4500, 4850, and 5150 A, referred to as 35, 38, 41, 42, 45, 48, and 51 filters) are explored by applying synthetic colors. Using DDO colors for a sample of stars for which spectrophotometric data were reported by Gunn and Stryker (1983), the correctness of the transmission profiles of the filters was established. It is shown that the presence of MgH lines in the 48 bandpass is an important reason why cool dwarfs and giants are separated in the C(45-48) vs C(42-45) diagram. It was found that including SiH lines in the spectra improved the agreement between observed and computed C(41-45) colors for dwarfs.

  2. 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.

  3. Literature Evidence on Live Animal Versus Synthetic Models for Training and Assessing Trauma Resuscitation Procedures.

    PubMed

    Hart, Danielle; McNeil, Mary Ann; Hegarty, Cullen; Rush, Robert; Chipman, Jeffery; Clinton, Joseph; Reihsen, Troy; Sweet, Robert

    2016-01-01

    There are many models currently used for teaching and assessing performance of trauma-related airway, breathing, and hemorrhage procedures. Although many programs use live animal (live tissue [LT]) models, there is a congressional effort to transition to the use of nonanimal- based methods (i.e., simulators, cadavers) for military trainees. We examined the existing literature and compared the efficacy, acceptability, and validity of available models with a focus on comparing LT models with synthetic systems. Literature and Internet searches were conducted to examine current models for seven core trauma procedures. We identified 185 simulator systems. Evidence on acceptability and validity of models was sparse. We found only one underpowered study comparing the performance of learners after training on LT versus simulator models for tube thoracostomy and cricothyrotomy. There is insufficient data-driven evidence to distinguish superior validity of LT or any other model for training or assessment of critical trauma procedures.

  4. Synthetic aperture radar modeling for the Watchkeeper tactical UAV program

    NASA Astrophysics Data System (ADS)

    Jolly, Alistair D.; Thompson, Peter

    2002-07-01

    Critical to the performance of any synthetic aperture radar (SAR) system is accurate compensation for aircraft motion during the imaging aperture. This is thought to be particularly important for Unmanned Aerial Vehicles (UAVs) operating in poor weather conditions where the aircraft may be subject to pronounced turbulence effects. This paper presents some initial findings of an investigation into the effects of aircraft motion on SAR azimuth point spread function for given levels of motion spectrum suppression as supplied by the radar's motion compensation processing. With validation, this approach will allow indicative levels of SAR performance to be estimated over a wide range of operating conditions and hence provides a useful source of advice when considering procurement options.

  5. Model-based detection of synthetic bat echolocation calls using an energy threshold detector for initialization.

    PubMed

    Skowronski, Mark D; Fenton, M Brock

    2008-05-01

    Detection of echolocation calls is fundamental to quantitative analysis of bat acoustic signals. Automated methods of detection reduce the subjectivity of hand labeling of calls and speed up the detection process in an accurate and repeatable manner. A model-based detector was initialized using a baseline energy threshold detector, removing the need for hand labels to train the model, and shown to be superior to the baseline detector using synthetic calls in two experiments: (1) an artificial environment and (2) a field playback setting. Synthetic calls using a piecewise exponential frequency modulation function from five hypothetical species were employed to control the signal-to-noise ratio (SNR) in each experiment and to provide an absolute ground truth to judge detector performance. The model-based detector outperformed the baseline detector by 2.5 dB SNR in the artificial environment and 1.5 dB SNR in the field playback setting. Atmospheric absorption was measured for the synthetic calls, and 1.5 dB increased the effective detection radius by between 1 and 7 m depending on species. The results demonstrate that hand labels are not necessary for training detection models and that model-based detectors significantly increase the range of detection for a recording system.

  6. Modeling atmospheric precipitation impact on synthetic aperture radar imagery at X and Ka bands

    NASA Astrophysics Data System (ADS)

    Mori, Saverio; Polverari, Federica; Pulvirenti, Luca; Montopoli, Mario; Pierdicca, Nazzareno; Marzano, Frank S.

    2014-10-01

    Spaceborne synthetic aperture radars (SARs) operating at X-band and above allow observations of Earth surface at very high spatial resolution. Moreover, recent polarimetric SARs enable the complete characterization of target scattering and extinction properties. Nowadays several spaceborne X-band SAR systems are operative, and plans exist for systems operating at higher frequency bands (i.e. Ku, Ka and W). Although higher frequencies may have interesting and distinctive applications, atmospheric effects, especially in precipitating conditions, may affect the surface SAR response in both the signal amplitude and its phase, as assessed by numerous works in the last years. A valid tool to analyze and characterize the SAR response in these conditions is represented by forward modeling, where a known synthetic scenario, which is described by user-selected surface and atmospheric conditions, is considered. Thus, the SAR echoes corresponding to the synthetic scenarios are simulated using electromagnetic models. In this work a 3-D realistic polarimetric SAR response numerical simulator is presented. The proposed model framework accounts for the SAR slant observing geometry and it is able to characterize the polarimetric response both in amplitude and phase. In this work we have considered both X and Ka bands, thus exploring the atmospheric effects for the present and future polarimetric systems. The atmospheric conditions are simulated using the System for Atmospheric Modeling (SAM) which is an high-resolution mesoscale model. SAM is used to define the three-dimensional distribution of hydrometeors which are among the inputs used in the Hydrometeor Ensemble Scattering Simulator (HESS) T-Matrix which allow simulating the SAR signal due to the atmospheric component. The SAR surface component is, instead, simulated by a Semi Empirical Model (SEM) for bare-soils conditions and SEAWIND2 two-scale model for ocean surfaces. The proposed methodology has been applied in this work

  7. Standard virtual biological parts: a repository of modular modeling components for synthetic biology.

    PubMed

    Cooling, M T; Rouilly, V; Misirli, G; Lawson, J; Yu, T; Hallinan, J; Wipat, A

    2010-04-01

    Fabrication of synthetic biological systems is greatly enhanced by incorporating engineering design principles and techniques such as computer-aided design. To this end, the ongoing standardization of biological parts presents an opportunity to develop libraries of standard virtual parts in the form of mathematical models that can be combined to inform system design. We present an online Repository, populated with a collection of standardized models that can readily be recombined to model different biological systems using the inherent modularity support of the CellML 1.1 model exchange format. The applicability of this approach is demonstrated by modeling gold-medal winning iGEM machines. The Repository is available online as part of http://models.cellml.org. We hope to stimulate the worldwide community to reuse and extend the models therein, and contribute to the Repository of Standard Virtual Parts thus founded. Systems Model architecture information for the Systems Model described here, along with an additional example and a tutorial, is also available as Supplementary information. The example Systems Model from this manuscript can be found at http://models.cellml.org/workspace/bugbuster. The Template models used in the example can be found at http://models.cellml.org/workspace/SVP_Templates200906.

  8. Synthetic Cannabinoids and Their Effects on the Cardiovascular System.

    PubMed

    Von Der Haar, Jonathan; Talebi, Soheila; Ghobadi, Farzaneh; Singh, Shailinder; Chirurgi, Roger; Rajeswari, Pingle; Kalantari, Hossein; Hassen, Getaw Worku

    2016-02-01

    In the past couple of years, there has been an outbreak of synthetic cannabinoid (SC) use in major cities in the United States. Patients can present with various symptoms affecting the central nervous and cardiovascular systems. The effects of endocannabinoid on contractility and Ca(2+) signaling have been shown through both cannabinoid receptors and a direct effect on ion channels. These effects result in abnormalities in ionotropy, chronotropy, and conduction. Here we report on two cases of SC abuse and abnormalities in the cardiovascular system. These cases raise concerns about the adverse effects of SCs and the possibility of QTc prolongation and subsequent complications when using antipsychotic medication in the presence of SC abuse. WHY SHOULD AN EMERGENCY PHYSICIAN BE AWARE OF THIS?: Given the rise in SC use and the potential effect on the cardiovascular system, physicians need to be mindful of potential cardiac complications, such as QTc prolongation and torsade de pointe, especially when administering medications that have the potential to cause QTc prolongation. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. 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

  10. 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

  11. Effect of the ventricular folds in a synthetic larynx model.

    PubMed

    Kniesburges, Stefan; Birk, Veronika; Lodermeyer, Alexander; Schützenberger, Anne; Bohr, Christopher; Becker, Stefan

    2017-04-11

    Within the human larynx, the ventricular folds serve primarily as a protecting valve during swallowing. They are located directly above the sound-generating vocal folds. During normal phonation, the ventricular folds are passive structures that are not excited to periodical oscillations. However, the impact of the ventricular folds on the phonation process has not yet been finally clarified. An experimental synthetic human larynx model was used to investigate the effect of the ventricular folds on the phonation process. The model includes self-oscillating vocal fold models and allows the comparison of the pressure distribution at multiple locations in the larynx for configurations with and without ventricular folds. The results indicate that the ventricular folds increase the efficiency of the phonation process by reducing the phonation threshold level of the pressure below the vocal folds. Two effects caused by the ventricular folds could be identified as reasons: (1) a decrease in the mean pressure level in the region between vocal and ventricular folds (ventricles) and (2) an increase in the glottal flow resistance. The reason for the first effect is a reduction of the pressure level in the ventricles due to the jet entrainment and the low static pressure in the glottal jet. The second effect results from an increase in the glottal flow resistance that enhances the aerodynamic energy transfer into the vocal folds. This effect reduces the onset threshold of the pressure difference across the glottis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Design and evaluation of a gastroretentive drug delivery system for metformin HCl using synthetic and semi-synthetic polymers.

    PubMed

    Meka, Venkata Srikanth; Gorajana, Adinaravyana; Dharmanlingam, Senthil Rajan; Kolapalli, Venkata Ramana Murthy

    2013-12-01

    The aim of the present research was to prepare and evaluate a gastroretentive drug delivery system for metformin HCl, using synthetic and semi-synthetic polymers. The floating approach was applied for preparing gastroretentive tablets (GRT) and these tablets were manufactured by the direct compression method. The drug delivery system comprises of synthetic and semi-synthetic polymers such as polyethylene oxide and Carboxymethyl ethyl cellulose (CMEC) as release-retarding polymers. GRT were evaluated for physico-chemical properties like weight variation, hardness, assay friability, in vitro floating behaviour, swelling studies, in vitro dissolution studies and rate order kinetics. Based upon the drug release and floating properties, two formulations (MP04 & MC03) were selected as optimized formulations. The optimized formulations MP04 and MC03 followed zero order rate kinetics, with non-Fickian diffusion and first order rate kinetics with erosion mechanism, respectively. The optimized formulation was characterised with FTIR studies and it was observed that there was no interaction between the drug and polymers.

  13. 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.

  14. Synthetic Tumor Networks for Screening Drug Delivery Systems

    PubMed Central

    Prabhakarpandian, Balabhaskar; Shen, Ming-Che; Nichols, Joseph B.; Garson, Charles J.; Mills, Ivy R.; Matar, Majed M.; Fewell, Jason G.; Pant, Kapil

    2015-01-01

    Tumor drug delivery is a complex phenomenon affected by several elements in addition to drug or delivery vehicle’s physico-chemical properties. A key factor is tumor microvasculature with complex effects including convective transport, high interstitial pressure and enhanced vascular permeability due to the presence of “leaky vessels”. Current in vitro models of the tumor microenvironment for evaluating drug delivery are oversimplified and, as a result, show poor correlation with in vivo performance. In this study, we report on the development of a novel microfluidic platform that models the tumor microenvironment more accurately, with physiologically and morphologically realistic microvasculature including endothelial cell lined leaky capillary vessels along with 3D solid tumors. Endothelial cells and 3D spheroids of cervical tumor cells were co-cultured in the networks. Drug vehicle screening was demonstrated using GFP gene delivery by different formulations of nanopolymers. The synthetic tumor network was successful in predicting in vivo delivery efficiencies of the drug vehicles. The developed assay will have critical applications both in basic research, where it can be used to develop next generation delivery vehicles, and in drug discovery where it can be used to study drug transport and delivery efficacy in realistic tumor microenvironment, thereby enabling drug compound and/or delivery vehicle screening. PMID:25599856

  15. New synthetic substrates of mammalian nucleotide excision repair system

    PubMed Central

    Evdokimov, Alexey; Petruseva, Irina; Tsidulko, Aleksandra; Koroleva, Ludmila; Serpokrylova, Inna; Silnikov, Vladimir; Lavrik, Olga

    2013-01-01

    DNA probes for the studies of damaged strand excision during the nucleotide excision repair (NER) have been designed using the novel non-nucleosidic phosphoramidite reagents that contain N-[6-(9-antracenylcarbamoyl)hexanoyl]-3-amino-1,2-propandiol (nAnt) and N-[6-(5(6)-fluoresceinylcarbamoyl)hexanoyl]-3-amino-1,2-propandiol (nFlu) moieties. New lesion-imitating adducts being inserted into DNA show good substrate properties in NER process. Modified extended linear nFlu– and nAntr–DNA are suitable for estimation of specific excision activity catalysed with mammalian whole-cell extracts. The following substrate activity range was revealed for the model 137-bp linear double-stranded DNA: nAnt–DNA ≈ nFlu–DNA > Chol–DNA (Chol–DNA—legitimate NER substrate that contains non-nucleoside fragment bearing cholesterol residue). In vitro assay shows that modified DNA can be a useful tool to study NER activity in whole-cell extracts. The developed approach should be of general use for the incorporation of NER-sensitive distortions into model DNAs. The new synthetic extended linear DNA containing bulky non-nucleoside modifications will be useful for NER mechanism study and for applications. PMID:23609543

  16. Investigation of Sorption Mass Transfer Models Using Synthetic Soils

    DTIC Science & Technology

    1996-12-01

    distributions of two or more materials and sizes. We tested the ability of the model to simulate the behavior of these systems and to fit system...for groundwater pollutants and improved clean-up operations are possible. New models developed for this purpose require rigorous testing using media of...be made to test model validity. Research Obiectives: The purpose of this experimental study is to test a theory that relates sorption rate to geometry

  17. A machine reading system for assembling synthetic paleontological databases.

    PubMed

    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.

  18. 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

  19. 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.

  20. 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

  1. Transient ejection phase modeling of a Plasma Synthetic Jet actuator

    NASA Astrophysics Data System (ADS)

    Laurendeau, F.; Chedevergne, F.; Casalis, G.

    2014-12-01

    For several years, a promising Plasma Synthetic Jet actuator for high-speed flow control has been under development at ONERA. So far, its confined geometry and small space-time scales at play have prevented its full experimental characterization. Complementary accurate numerical simulations are then considered in this study in order to provide a complete aerothermodynamic description of the actuator. Two major obstacles have to be overcome with this approach: the modeling of the energy deposited by the electric arc and the accurate computation of the transient response of the cavity generating the pulsed jet. To solve the first problem, an Euler solver coupled with an electric circuit model was used to evaluate the energy deposition in the cavity. Such a coupling is performed by considering the electric field between the two electrodes. The second issue was then addressed by injecting these source terms in large Eddy simulations of the entire actuator. Aerodynamic results were finally compared with Schlieren visualizations. Using the proposed methodology, the temporal evolution of the jet front is remarkably well predicted.

  2. Modelling the future Israel EEWS performance using synthetic catalogue

    NASA Astrophysics Data System (ADS)

    Pinsky, V.

    2017-10-01

    In 2012 June, Israel government decided about building an Earthquake Early Warning System (EEWS) in the country. The network configuration suggested was to be a staggered line of ˜100 stations along the regional main faults: Dead Sea fault and Carmel fault and additional ˜22 stations spread over the country. The EEWS alarm system should have to utilize two approaches: the P-wave-based algorithm combined with the S-threshold method. The former utilizes first wave arrivals to several closest stations for prompt location and the three initial seconds of the waveform data for magnitude estimation. The latter issues alarm when the surface shaking (velocity or acceleration) exceeds the relatively high threshold corresponding to a magnitude 5 earthquake at a short distance of about 10 km at least for the two neighbouring stations. For each of the approaches and for a reasonable combination of them, we simulate the EEWS performance based on a synthetic catalogue. The input seismicity parameters for the processing are extracted from the real instrumental catalogue. Using a general ground-motion prediction equations for peak ground accelaration, τc and Pd we then evaluate how false and missed alarm rates depend on the corresponding thresholds. Practically, in turn, these dependencies approve choosing initial thresholds for the EEWS providing suitable false and missed alarms rates.

  3. 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.

  4. 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, ...

  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. Synthetic Scene Generation of Stennis Target Range for the Calibration of Remote Sensing Systems

    NASA Technical Reports Server (NTRS)

    Cao, Chang-Yong; Blonski, Slawomir; Ryan, Robert; Gasser, Gerald; Zanoni, Vicki; Jenner, Jeff

    1999-01-01

    The validation and verification (V&V) target range developed at Stennis Space Center is a useful tool for the calibration of remote sensing systems. In this paper, we present an algorithm for generating synthetic scenes or digital models of this target range. The atmospheric radiative transfer code Modtran 4 is used in simulating at-sensor radiance for a given sensor. Software is developed to generate the scene with different spatial and spectral resolutions using the at-sensor radiance values. Synthetic scenes provide a cost-effective way for in-flight validation for the spatial and radiometric accuracy of the data. Other applications include mission planning, sensor simulation, and trade-off analysis in sensor design. The radiometric and spatial accuracy of the simulation is evaluated by comparing simulated scenes with AVIRIS acquired values.

  7. Kinetics of an anaerobic moving bed reactor system treating synthetic milk wastewater.

    PubMed

    Ramakant; Satyanarayan, Shanta; Kaul, S N

    2002-10-01

    In the present study, anaerobic moving bed reactor called anaerobic rotating biological contactor treating synthetic milk wastewater operated at different organic loading rates and different hydraulic retention times, were evaluated to determine kinetic parameters for the substrate, biomass and biogas based on various models. The maximum substrate loading rate and half velocity constant were evaluated as 5.71 kgCOD/m3 x d and 1178 mg/L respectively by using Lineweaver-Burke plot. Maximum substrate removal efficiency and critical hydraulic retention time were compared with modified Young and McCarty model and the model is best fitted for the study. The complete removal of substrate cannot be expected due to presence of metabolic refractory material produced within the reactor system from influent system. Kinetic constants for maximum specific growth rate and decay coefficient were compared with the modified Monod model. Kornegay and Andrews model were used to evaluate the area capacity constant and half velocity constant. Kinetic constants for maximum specific gas production rate and proportionality constant were evaluated using Stover model. The gas production and quality are dependent on the substrate removal and substrate loading rate. The kinetic relationships derived from lab-scale experiment provided good estimates of the performance of pilot- and full-scale anaerobic rotating biological contactor packed with fibrous nylon pads and treating synthetic milk wastewater in terms of the effluent chemical oxygen demand concentrations and specific biogas production rates.

  8. 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

  9. Analytic model and frequency characteristics of plasma synthetic jet actuator

    NASA Astrophysics Data System (ADS)

    Zong, Hao-hua; Wu, Yun; Li, Ying-hong; Song, Hui-min; Zhang, Zhi-bo; Jia, Min

    2015-02-01

    This paper reports a novel analytic model of a plasma synthetic jet actuator (PSJA), considering both the heat transfer effect and the inertia of the throat gas. Both the whole cycle characteristics and the repetitive working process of PSJA can be predicted with this model. The frequency characteristics of a PSJA with 87 mm3 volume and different orifice diameters are investigated based on the analytic model combined with experiments. In the repetitive working mode, the actuator works initially in the transitional stage with 20 cycles and then in the dynamic balanced stage. During the transitional stage, major performance parameters of PSJA experience stepped growth, while during the dynamic balanced stage, these parameters are characterized by periodic variation. With a constant discharge energy of 6.9 mJ, there exists a saturated frequency of 4 kHz/6 kHz for an orifice diameter of 1 mm/1.5 mm, at which the time-averaged total pressure of the pulsed jet reaches a maximum. Between 0.5 mm and 1.5 mm, a larger orifice diameter leads to a higher saturated frequency due to the reduced jet duration time. As the actuation frequency increases, both the time-averaged cavity temperature and the peak jet velocity initially increase and then remain almost unchanged at 1600 K and 280 m/s, respectively. Besides, with increasing frequency, the mechanical energy incorporated in single pulsed jet, the expelled mass per pulse, and the time-averaged density in the cavity, decline in a stair stepping way, which is caused by the intermittent decrease of refresh stage duration in one period.

  10. Identification of line-specific strategies for improving carotenoid production in synthetic maize through data-driven mathematical modeling.

    PubMed

    Comas, Jorge; Benfeitas, Rui; Vilaprinyo, Ester; Sorribas, Albert; Solsona, Francesc; Farré, Gemma; Berman, Judit; Zorrilla, Uxue; Capell, Teresa; Sandmann, Gerhard; Zhu, Changfu; Christou, Paul; Alves, Rui

    2016-09-01

    Plant synthetic biology is still in its infancy. However, synthetic biology approaches have been used to manipulate and improve the nutritional and health value of staple food crops such as rice, potato and maize. With current technologies, production yields of the synthetic nutrients are a result of trial and error, and systematic rational strategies to optimize those yields are still lacking. Here, we present a workflow that combines gene expression and quantitative metabolomics with mathematical modeling to identify strategies for increasing production yields of nutritionally important carotenoids in the seed endosperm synthesized through alternative biosynthetic pathways in synthetic lines of white maize, which is normally devoid of carotenoids. Quantitative metabolomics and gene expression data are used to create and fit parameters of mathematical models that are specific to four independent maize lines. Sensitivity analysis and simulation of each model is used to predict which gene activities should be further engineered in order to increase production yields for carotenoid accumulation in each line. Some of these predictions (e.g. increasing Zmlycb/Gllycb will increase accumulated β-carotenes) are valid across the four maize lines and consistent with experimental observations in other systems. Other predictions are line specific. The workflow is adaptable to any other biological system for which appropriate quantitative information is available. Furthermore, we validate some of the predictions using experimental data from additional synthetic maize lines for which no models were developed.

  11. 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.

  12. 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

  13. 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.

  14. 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.

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

    PubMed Central

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

    2014-01-01

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

  16. 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

    2014-04-02

    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.

  17. Inclusion of sensor noise in radiometric models for generation of synthetic longwave infrared images

    NASA Astrophysics Data System (ADS)

    Schott, John R.; Salvaggio, Carl

    1987-01-01

    A radiometric model has been developed for modeling the effects of self emission, reflection of downwelled radiance, atmospheric transmission and path radiance on the radiance reaching an airborne or satellite sensing system. The model, which incorporates LOWTRAN 6, includes angular emissivity effects and will account for either specular or diffuse reflectance from targets and backgrounds. The model has been refined to facilitate its use in generating primitive synthetic images to study LWIR phenomena. In particular, various types of sensor related noise have been included in the imaging process. Images are presented simulating the effects of target-to-background contrast as a function of view angle, range, emissivity variation, and atmospheric effects. The potential for use of LWIR models in sensor and algorithm development is discussed.

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

    PubMed Central

    Toni, Tina; Tidor, Bruce

    2013-01-01

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

  19. Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology.

    PubMed

    Toni, Tina; Tidor, Bruce

    2013-01-01

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

  20. Background character research for synthetical performance of thermal imaging systems

    NASA Astrophysics Data System (ADS)

    Chen, Song-lin; Wang, Ji-hui; Wang, Xiao-wei; Jin, Wei-qi

    2014-05-01

    Background is assumed to be uniform usually for evaluating the performance of thermal imaging systems, however the impact of background cannot be ignored for target acquisition in reality, background character is important research content for thermal imaging technology. A background noise parameter 𝜎 was proposed in MRTD model and used to describe background character. Background experiments were designed, and some typical backgrounds (namely lawn background, concrete pavement background, trees background and snow background) character were analyzed by 𝜎. MRTD including 𝜎 was introduced into MRTD-Channel Width (CW) model, the impact of above typical backgrounds for target information quantity were analyzed by MRTD-CW model with background character. Target information quantity for different backgrounds was calculated by MRTD-CW, and compared with that of TTP model. A target acquisition performance model based on MRTD-CW with background character will be research in the future.

  1. 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.

  2. 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

  3. 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

  4. Rectification in synthetic conical nanopores: a one-dimensional Poisson-Nernst-Planck model.

    PubMed

    Kosińska, I D; Goychuk, I; Kostur, M; Schmid, G; Hänggi, P

    2008-03-01

    Ion transport in biological and synthetic nanochannels is characterized by phenomena such as ion current fluctuations and rectification. Recently, it has been demonstrated that nanofabricated synthetic pores can mimic transport properties of biological ion channels [P. Yu. Apel, Nucl. Instrum Methods Phys. Res. B 184, 337 (2001); Z. Siwy, Europhys. Lett. 60, 349 (2002)]. Here, the ion current rectification is studied within a reduced one-dimensional (1D) Poisson-Nernst-Planck (PNP) model of synthetic nanopores. A conical channel of a few nm to a few hundred nm in diameter, and of a few mum long is considered in the limit where the channel length considerably exceeds the Debye screening length. The rigid channel wall is assumed to be weakly charged. A one-dimensional reduction of the three-dimensional problem in terms of corresponding entropic effects is put forward. The ion transport is described by the nonequilibrium steady-state solution of the 1D Poisson-Nernst-Planck system within a singular perturbation treatment. An analytic formula for the approximate rectification current in the lowest order perturbation theory is derived. A detailed comparison between numerical results and the singular perturbation theory is presented. The crucial importance of the asymmetry in the potential jumps at the pore ends on the rectification effect is demonstrated. This so constructed 1D theory is shown to describe well the experimental data in the regime of small-to-moderate electric currents.

  5. 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.

  6. A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches.

    PubMed

    Cantone, Irene; Marucci, Lucia; Iorio, Francesco; Ricci, Maria Aurelia; Belcastro, Vincenzo; Bansal, Mukesh; Santini, Stefania; di Bernardo, Mario; di Bernardo, Diego; Cosma, Maria Pia

    2009-04-03

    Systems biology approaches are extensively used to model and reverse engineer gene regulatory networks from experimental data. Conversely, synthetic biology allows "de novo" construction of a regulatory network to seed new functions in the cell. At present, the usefulness and predictive ability of modeling and reverse engineering cannot be assessed and compared rigorously. We built in the yeast Saccharomyces cerevisiae a synthetic network, IRMA, for in vivo "benchmarking" of reverse-engineering and modeling approaches. The network is composed of five genes regulating each other through a variety of regulatory interactions; it is negligibly affected by endogenous genes, and it is responsive to small molecules. We measured time series and steady-state expression data after multiple perturbations. These data were used to assess state-of-the-art modeling and reverse-engineering techniques. A semiquantitative model was able to capture and predict the behavior of the network. Reverse engineering based on differential equations and Bayesian networks correctly inferred regulatory interactions from the experimental data.

  7. 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). DATES...

  8. Design of a Ku band Instrumentation Synthetic Aperture Radar System

    DTIC Science & Technology

    2015-10-14

    small form-factor Ku band Synthetic Aperture Radar (SAR) for use on aerial drones . Group 105 have also been using this radar as an instrumentation...to 40 m/s based off of the speed of a predator drone . Parameter Value Speed of Light 299720000 m/s Center Frequency 16.75 GHz Wavelength 0.0179 m

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

    SciTech Connect

    Pasqualini, Donatella

    2016-05-11

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

  10. Synthetic wind speed scenarios generation for probabilistic analysis of hybrid energy systems

    SciTech Connect

    Chen, Jun; Rabiti, Cristian

    2016-11-25

    Hybrid energy systems consisting of multiple energy inputs and multiple energy outputs have been proposed to be an effective element to enable ever increasing penetration of clean energy. In order to better understand the dynamic and probabilistic behavior of hybrid energy systems, this paper proposes a model combining Fourier series and autoregressive moving average (ARMA) to characterize historical weather measurements and to generate synthetic weather (e.g., wind speed) data. In particular, Fourier series is used to characterize the seasonal trend in historical data, while ARMA is applied to capture the autocorrelation in residue time series (e.g., measurements minus seasonal trends). The generated synthetic wind speed data is then utilized to perform probabilistic analysis of a particular hybrid energy system con guration, which consists of nuclear power plant, wind farm, battery storage, natural gas boiler, and chemical plant. As a result, requirements on component ramping rate, economic and environmental impacts of hybrid energy systems, and the effects of deploying different sizes of batteries in smoothing renewable variability, are all investigated.

  11. Synthetic wind speed scenarios generation for probabilistic analysis of hybrid energy systems

    DOE PAGES

    Chen, Jun; Rabiti, Cristian

    2016-11-25

    Hybrid energy systems consisting of multiple energy inputs and multiple energy outputs have been proposed to be an effective element to enable ever increasing penetration of clean energy. In order to better understand the dynamic and probabilistic behavior of hybrid energy systems, this paper proposes a model combining Fourier series and autoregressive moving average (ARMA) to characterize historical weather measurements and to generate synthetic weather (e.g., wind speed) data. In particular, Fourier series is used to characterize the seasonal trend in historical data, while ARMA is applied to capture the autocorrelation in residue time series (e.g., measurements minus seasonal trends).more » The generated synthetic wind speed data is then utilized to perform probabilistic analysis of a particular hybrid energy system con guration, which consists of nuclear power plant, wind farm, battery storage, natural gas boiler, and chemical plant. As a result, requirements on component ramping rate, economic and environmental impacts of hybrid energy systems, and the effects of deploying different sizes of batteries in smoothing renewable variability, are all investigated.« less

  12. A fully synthetic lung model for wound-ballistic experiments-First results.

    PubMed

    Bolliger, S A; Poschmann, S A; Thali, M J; Eggert, S

    2017-06-01

    Today, synthetic models have all but replaced animal and corpse models in examining damage to soft-tissues and skeletal structures by ballistic trauma. As, however, non-solid organs such as the lungs, have not been able to be replaced by a fully synthetic model we attempted to create such a model. 20% ordnance gelatine was frothed with a household mixer and cooled to stable foam. Several of these foam blocks were then stuck together with liquid gelatine and placed between 10% gelatine blocks. As controls, we embedded pig lungs in gelatine and compared the wound channels seen in computed tomography created upon shooting with 9mm Luger. The fully synthetic models displayed radiological and physical densities comparable to real lungs. The wound profile characteristics of the fully synthetic lung models were very similar to the semisynthetic swine-gelatine models regarding the permanent wound cavity. Furthermore, in both semi- and fully synthetic models we detected a ring surrounding the permanent wound channel, most likely representing the remnants of the temporary wound cavity. Our results indicate that this fully synthetic lung model is a viable substitute for ballistic experiments on lungs. We believe that further research on the temporary wound channel in lungs is possible with this model in order to provide more insight into the effect of ballistic trauma to the lungs not seen otherwise. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2017-09-01

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

  14. Enhancing the Analytic Utility of the Synthetic Theater Operations Research Model (STORM)

    DTIC Science & Technology

    2014-12-01

    Operations Research Model ( STORM ) 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER...SYNTHETIC THEATER OPERATIONS RESEARCH MODEL ( STORM ) Mary L. McDonald Stephen C. Upton Christian N. Seymour Thomas W. Lucas Susan M. Sanchez...Force and Marine Corps, use the Synthetic Theater Operations Research Model ( STORM ) to assess risk in an integrated, campaign setting. Ultimately

  15. 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.

  16. 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.

  17. Valence tautomerism in synthetic models of cytochrome P450

    PubMed Central

    Das, Pradip Kumar; Samanta, Subhra; McQuarters, Ashley B.; Lehnert, Nicolai

    2016-01-01

    CytP450s have a cysteine-bound heme cofactor that, in its as-isolated resting (oxidized) form, can be conclusively described as a ferric thiolate species. Unlike the native enzyme, most synthetic thiolate-bound ferric porphyrins are unstable in air unless the axial thiolate ligand is sterically protected. Spectroscopic investigations on a series of synthetic mimics of cytP450 indicate that a thiolate-bound ferric porphyrin coexists in organic solutions at room temperature (RT) with a thiyl-radical bound ferrous porphyrin, i.e., its valence tautomer. The ferric thiolate state is favored by greater enthalpy and is air stable. The ferrous thiyl state is favored by entropy, populates at RT, and degrades in air. These ground states can be reversibly interchanged at RT by the addition or removal of water to the apolar medium. It is concluded that hydrogen bonding and local electrostatics protect the resting oxidized cytP450 active site from degradation in air by stabilizing the ferric thiolate ground state in contrast to its synthetic analogs. PMID:27302948

  18. 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.

  19. Interferometric synthetic aperture radar and the Data Collection System Digital Terrain Elevation Demonstration

    NASA Astrophysics Data System (ADS)

    Heidelbach, Robert; Bolus, R.; Chadwick, J.

    1994-08-01

    Digital Terrain Elevations (DTE) that can be rapidly generated, and that have better fidelity and accuracy than Digital Terrain Elevation Data (DTED) Levels 1 or 2, would be extremely beneficial to Department of Defense (DOD) military operations, civil works programs, and various commercial applications. As a result, the Advanced Research Projects Agency (ARPA), along with the U.S. Army Topographic Engineering Center (TEC), are developing an Interferometric Synthetic Aperture Radar (IFSAR) elevation mapping capability. This system, the Interferometric Synthetic Aperture Radar for Digital Radar Elevations (IFSARE), is capable of collecting and providing data in all weather (reasonable), in day or night scenarios, and where obscurants are present. The IFSARE, which is currently undergoing Integration and Test, will allow for rapid on-line automatic processing of the collected digital radar data into DTE and high quality imagery. The prime contractor is the Environmental Research Institute of Michigan (ERIM). This paper addresses the proof of concept for civil works applications by analyzing a data set taken by the Wright Labs/ERIM Data Collection System (DCS). The objective was to demonstrate the capability of an IFSAR system to provide high fidelity, fine resolution DTE that can be employed in hydraulic models of the Mississippi River watershed. The demonstration was sponsored by ARPA and TEC.

  20. 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.

  1. 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.

  2. Prospects for Applying Synthetic Biology to Toxicology: Future Opportunities and Current Limitations for the Repurposing of Cytochrome P450 Systems.

    PubMed

    Behrendorff, James B Y H; Gillam, Elizabeth M J

    2017-01-17

    The 30 years since the inception of Chemical Research in Toxicology, game-changing advances in chemical and molecular biology, the fundamental disciplines underpinning molecular toxicology, have been made. While these have led to important advances in the study of mechanisms by which chemicals damage cells and systems, there has been less focus on applying these advances to prediction, detection, and mitigation of toxicity. Over the last ∼15 years, synthetic biology, the repurposing of biological "parts" in systems engineered for useful ends, has been explored in other areas of the biomedical and life sciences, for such applications as detecting metabolites, drug discovery and delivery, investigating disease mechanisms, improving medical treatment, and producing useful chemicals. These examples provide models for the application of synthetic biology to toxicology, which, for the most part, has not yet benefited from such approaches. In this perspective, we review the synthetic biology approaches that have been applied to date and speculate on possible short to medium term and "blue sky" aspirations for synthetic biology, particularly in clinical and environmental toxicology. Finally, we point out key hurdles that must be overcome for the full potential of synthetic biology to be realized.

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

    SciTech Connect

    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 sediment 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.

  4. [System biology and synthetic biology modify drug discovery and development].

    PubMed

    Haiech, Jacques; Ranjeva, Raoul; Kilhoffer, Marie-Claude

    2012-02-01

    Life Sciences are built on observations. Right now, a more systemic approach allowing to integrate the different organizational levels in Biology is emerging. Such an approach uses a set of technologies and strategies allowing to build models that appear to be more and more predictive (omics, bioinformatics, integrative biology, computational biology…). Those models accelerate the rational development of new therapies avoiding an engineering based only on trials and errors. This approach both holistic and predictive radically modifies the discovery and development modalities used today in health industries. Moreover, because of the apparition of new jobs at the interface of disciplines, of private and public sectors and of life sciences and engineering sciences, this implies to rethink the training programs in both their contents and their pedagogical tools.

  5. Synthetic benchmark for modeling flow in 3D fractured media

    NASA Astrophysics Data System (ADS)

    de Dreuzy, Jean-Raynald; Pichot, Géraldine; Poirriez, Baptiste; Erhel, Jocelyne

    2013-01-01

    Intensity and localization of flows in fractured media have promoted the development of a large range of different modeling approaches including Discrete Fracture Networks, pipe networks and equivalent continuous media. While benchmarked usually within site studies, we propose an alternative numerical benchmark based on highly-resolved Discrete Fracture Networks (DFNs) and on a stochastic approach. Test cases are built on fractures of different lengths, orientations, aspect ratios and hydraulic apertures, issuing the broad ranges of topological structures and hydraulic properties classically observed. We present 18 DFN cases, with 10 random simulations by case. These 180 DFN structures are provided and fully documented. They display a representative variety of the configurations that challenge the numerical methods at the different stages of discretization, mesh generation and system solving. Using a previously assessed mixed hybrid finite element method (Erhel et al., 2009a), we systematically provide reference flow and head solutions. Because CPU and memory requirements stem mainly from system solving, we study direct and iterative sparse linear solvers. We show that the most cpu-time efficient method is a direct multifrontal method for small systems, while conjugate gradient preconditioned by algebraic multrigrid is more relevant at larger sizes. Available results can be used further as references for building up alternative numerical and physical models in both directions of improving accuracy and efficiency.

  6. ADSORPTION STUDIES IN A SYNTHETIC RUBBER LATEX-OVALBUMIN SYSTEM

    PubMed Central

    Williams, H. B.; Choppin, A. R.

    1950-01-01

    1. Adsorption of ovalbumin on the latex surface was in excess of the quantity required to produce coverage of the surface over most of the protein concentrations range which was investigated. 2. "S" shaped isothermals which probably indicated multilayer adsorption were obtained. 3. The quantity of ovalbumin required to produce a constant surface charge density on the latex particle surface was a function of the pH, and a theory of active centers on the latex particles has been suggested. 4. A shift in the isoelectric point from that of native ovalbumin has been observed for the protein when adsorbed on a synthetic latex. PMID:14824490

  7. 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.

  8. 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.

  9. Synthetic approaches to RBC mimicry and oxygen carrier systems.

    PubMed

    Modery-Pawlowski, Christa L; Tian, Lewis L; Pan, Victor; Sen Gupta, Anirban

    2013-04-08

    Whole blood or red blood cell (RBC) transfusions are highly significant, clinically, for blood replacement therapies in traumatic injuries, presurgical conditions, and anemias. However, natural RBC-based products suffer from limited shelf life due to pathological contamination and also present risks of refractoriness, graft-versus-host disease, immunosuppression, and acute lung injury. These issues can be only partially resolved by pathogen reduction technologies, serological blood testing, leukoreduction, and specialized storage; hence, they severely affect the efficacy and safety of the blood products. Consequently, there is a significant interest in synthetic RBC analogues that can mimic its oxygen-transport properties while allowing convenient manufacture, reproducibility, long shelf life, and reduced biological risks. To this end, the current Review provides a comprehensive description and discussion of the various research approaches and current state-of-the-art in synthetically mimicking RBC's oxygen-carrying biochemical properties, as well as the biophysical parameters (shape, size and mechanical modulus) that influence RBCs' hemodynamic transport properties in blood flow.

  10. Two sides of the same coin? The (techno)epistemic cultures of systems and synthetic biology.

    PubMed

    Kastenhofer, Karen

    2013-06-01

    Systems and synthetic biology both emerged around the turn of this century as labels for new research approaches. Although their disciplinary status as well as their relation to each other is rarely discussed in depth, now and again the idea is invoked that both approaches represent 'two sides of the same coin'. The following paper focuses on this general notion and compares it with empirical findings concerning the epistemic cultures prevalent in the two contexts. Drawing on interviews with researchers from both fields, on participatory observation in conferences and courses and on documentary analysis, this paper delineates differences and similarities, incompatibilities and blurred boundaries. By reconstructing systems and synthetic biology's epistemic cultures, this paper argues that they represent two 'communities of vision', encompassing heterogeneous practices. Understanding the relation of the respective visions of understanding nature and engineering life is seen as indispensible for the characterisation of (techno)science in more general terms. Depending on the conceptualisation of understanding and construction (or: science and engineering), related practices such as in silico modelling for enhancing understanding or enabling engineering can either be seen as incommensurable or 'two sides of one coin'. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Advances in de novo strain design using integrated systems and synthetic biology tools.

    PubMed

    Ng, Chiam Yu; Khodayari, Ali; Chowdhury, Anupam; Maranas, Costas D

    2015-10-01

    Recent efforts in expanding the range of biofuel and biorenewable molecules using microbial production hosts have focused on the introduction of non-native pathways in model organisms and the bio-prospecting of non-model organisms with desirable features. Current challenges lie in the assembly and coordinated expression of the (non-)native pathways and the elimination of competing pathways and undesirable regulation. Several systems and synthetic biology approaches providing contrasting top-down and bottom-up strategies, respectively, have been developed. In this review, we discuss recent advances in both in silico and experimental approaches for metabolic pathway design and engineering, with a critical assessment of their merits and remaining challenges. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. 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.

  13. Significant antitumor effect of a synthetic lipid A analogue, DT-5461, on murine syngeneic tumor models.

    PubMed

    Kumazawa, E; Tohgo, A; Soga, T; Kusama, T; Osada, Y

    1992-01-01

    The antitumor effect of a synthetic lipid A analogue, DT-5461, was investigated using syngeneic tumor models in mice. Intravenous injection of DT-5461 into mice transplanted with solid tumors of MethA fibrosarcoma, MH134 hepatoma, MM46 mammary carcinoma, Lewis lung carcinoma (3LL), and colon adenocarcinomas 26 and 38 resulted in significant reductions in the weight of all tumors except Colon 26, with marked hemorrhagic necrosis of tumor tissues. Efficacy was almost equal to that of an Escherichia coli-type synthetic lipid A (compound 506), and also to those of some chemotherapeutics including Adriamycin, mitomycin C, fluorouracil and cisplatin. Furthermore, DT-5461 was more effective than other immunotherapeutics, including picibanil (OK-432) and lentinan. However, its antitumor effects were inferior to those of Adriamycin or OK-432 against the malignant ascites caused by intraperitoneal inoculation with MethA or with MH134 cells; life span was not prolonged by either intraperitoneal or intravenous administration. In addition, although DT-5461 showed direct inhibitory effects on the in vitro growth of MethA or MH134, these were much weaker than those of Adriamycin. These findings clearly indicated that DT-5461 with systemic administration is a highly effective antitumor agent on solid tumors, and suggest that the antitumor effect of DT-5461 with potent necrotizing activity might derive from indirect mechanisms related to the activation of host immune systems and not to the weak direct cytotoxicity.

  14. 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...

  15. 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.

  16. Systemic Antibacterial Activity of Novel Synthetic Cyclic Peptides

    PubMed Central

    Dartois, Véronique; Sanchez-Quesada, Jorge; Cabezas, Edelmira; Chi, Ellen; Dubbelde, Chad; Dunn, Carrie; Granja, Juan; Gritzen, Colleen; Weinberger, Dana; Ghadiri, M. Reza; Parr, Thomas R.

    2005-01-01

    Cyclic peptides with an even number of alternating d,l-α-amino acid residues are known to self-assemble into organic nanotubes. Such peptides previously have been shown to be stable upon protease treatment, membrane active, and bactericidal and to exert antimicrobial activity against Staphylococcus aureus and other gram-positive bacteria. The present report describes the in vitro and in vivo pharmacology of selected members of this cyclic peptide family. The intravenous (i.v.) efficacy of six compounds with MICs of less than 12 μg/ml was tested in peritonitis and neutropenic-mouse thigh infection models. Four of the six peptides were efficacious in vivo, with 50% effective doses in the peritonitis model ranging between 4.0 and 6.7 mg/kg against methicillin-sensitive S. aureus (MSSA). In the thigh infection model, the four peptides reduced the bacterial load 2.1 to 3.0 log units following administration of an 8-mg/kg i.v. dose. Activity against methicillin-resistant S. aureus was similar to MSSA. The murine pharmacokinetic profile of each compound was determined following i.v. bolus injection. Interestingly, those compounds with poor efficacy in vivo displayed a significantly lower maximum concentration of the drug in serum and a higher volume of distribution at steady state than compounds with good therapeutic properties. S. aureus was unable to easily develop spontaneous resistance upon prolonged exposure to the peptides at sublethal concentrations, in agreement with the proposed interaction with multiple components of the bacterial membrane canopy. Although additional structure-activity relationship studies are required to improve the therapeutic window of this class of antimicrobial peptides, our results suggest that these amphipathic cyclic d,l-α-peptides have potential for systemic administration and treatment of otherwise antibiotic-resistant infections. PMID:16048940

  17. Neglected disease - african sleeping sickness: recent synthetic and modeling advances.

    PubMed

    Paliwal, Sarvesh K; Verma, Ankita Narayan; Paliwal, Shailendra

    2011-01-01

    Human African Trypanosomiasis (HAT) also called sleeping sickness is caused by subspecies of the parasitic hemoflagellate Trypanosoma brucei that mostly occurs in sub-Saharan Africa. The current chemotherapy of the human trypanosomiases relies on only six drugs, five of which have been developed more than 30 years ago, have undesirable toxic side effects and most of them show drug-resistance. Though development of new anti-trypanosomal drugs seems to be a priority area research in this area has lagged far behind. The given review mainly focus upon the recent synthetic and computer based approaches made by various research groups for the development of newer anti-trypanosomal analogues which may have improved efficacy and oral bioavailability than the present ones. The given paper also attempts to investigate the relationship between the various physiochemical parameters and anti-trypanosomal activity that may be helpful in development of potent anti-trypanosomal agents against sleeping sickness.

  18. 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.

  19. Improving the Analysis Capabilities of the Synthetic Theater Operations Research Model (STORM)

    DTIC Science & Technology

    2014-09-01

    the Chief of Naval Operations, Capability Analysis and Assessment Division (OPNAV N81), along with other DOD organizations, utilizes the Synthetic...Capability Analysis and Assessment Division (OPNAV N81), along with other DOD organizations, utilizes the Synthetic Theater Operations Research Model...Navy’s Assessment Division, adopted STORM as its primary campaign analysis tool due to its stochastic nature, which provides analysts the ability to

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Fast algorithm for a three-dimensional synthetic model of intermittent turbulence

    NASA Astrophysics Data System (ADS)

    Malara, Francesco; Di Mare, Francesca; Nigro, Giuseppina; Sorriso-Valvo, Luca

    2016-11-01

    Synthetic turbulence models are useful tools that provide realistic representations of turbulence, necessary to test theoretical results, to serve as background fields in some numerical simulations, and to test analysis tools. Models of one-dimensional (1D) and 3D synthetic turbulence previously developed still required large computational resources. A "wavelet-based" model of synthetic turbulence, able to produce a field with tunable spectral law, intermittency, and anisotropy, is presented here. The rapid algorithm introduced, based on the classic p -model of intermittent turbulence, allows us to reach a broad spectral range using a modest computational effort. The model has been tested against the standard diagnostics for intermittent turbulence, i.e., the spectral analysis, the scale-dependent statistics of the field increments, and the multifractal analysis, all showing an excellent response.

  5. Geometrical exponents of contour loops on synthetic multifractal rough surfaces: multiplicative hierarchical cascade p model.

    PubMed

    Hosseinabadi, S; Rajabpour, M A; Movahed, M Sadegh; Allaei, S M Vaez

    2012-03-01

    In this paper, we study many geometrical properties of contour loops to characterize the morphology of synthetic multifractal rough surfaces, which are generated by multiplicative hierarchical cascading processes. To this end, two different classes of multifractal rough surfaces are numerically simulated. As the first group, singular measure multifractal rough surfaces are generated by using the p model. The smoothened multifractal rough surface then is simulated by convolving the first group with a so-called Hurst exponent, H*. The generalized multifractal dimension of isoheight lines (contours), D(q), correlation exponent of contours, x(l), cumulative distributions of areas, ξ, and perimeters, η, are calculated for both synthetic multifractal rough surfaces. Our results show that for both mentioned classes, hyperscaling relations for contour loops are the same as that of monofractal systems. In contrast to singular measure multifractal rough surfaces, H* plays a leading role in smoothened multifractal rough surfaces. All computed geometrical exponents for the first class depend not only on its Hurst exponent but also on the set of p values. But in spite of multifractal nature of smoothened surfaces (second class), the corresponding geometrical exponents are controlled by H*, the same as what happens for monofractal rough surfaces.

  6. 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.

  7. Interaction of a synthetic antimicrobial peptide with a model bilayer platform mimicking bacterial membranes.

    PubMed

    Niu, Lifang; Wohland, Thorsten; Knoll, Wolfgang; Köper, Ingo

    2017-08-31

    Tethered bimolecular lipid membranes are solid supported membrane systems, which provide a versatile model platform for the study of many membrane related processes. Here, such an architecture has been used to study the interaction of the small synthetic antimicrobial peptide, V4, with membranes of various mixed lipid compositions, including membranes containing bacterial lipids. By investigating the binding of the peptide using a range of surface analytical techniques such as surface plasmon resonance and surface plasmon field-enhanced fluorescence spectroscopy as well as electrochemical impedance spectroscopy, a clear preference of the peptide for negatively charged membranes over zwitterionic ones has been shown. Additionally, the interactions seemed to indicate a cooperative behavior for the peptide binding to a membrane.

  8. Resonance-based low-frequency synthetic jet actuator modeling, design, and testing

    NASA Astrophysics Data System (ADS)

    Gravatt, Lynn; Flatau, Alison

    2006-03-01

    Synthetic Jet Actuators have been the topic of extensive study in the aerospace industry because of their ability to actively control flow over aerodynamic surfaces without discrete control surfaces such as a flap. One challenge has been to develop a low frequency, lightweight actuator that can provide large displacements. This study will discuss the modeling, design, manufacture, and testing of a bimorph piezo-composite actuator that will provide such displacements at low frequencies. The design employs two opposing benders that provide a piston-type motion. The initial goals of this study were to achieve 30 m/s out of the slot while maintaining the mechanical resonant frequency of the system at about 100 Hz.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Synthetic aperture LADAR at 1550 nm: system demonstration, imaging processing and experimental result

    NASA Astrophysics Data System (ADS)

    Li, Guangzuo; Wang, Ran; Wang, Peisi; Zhang, Keshu; Wu, Yirong

    2016-10-01

    In this manuscript, we propose and experimentally demonstrate our synthetic aperture LADAR (SAL) system. The system could obtain imageries in a few milliseconds with resolution of 5 cm from a long distance. Fine resolution in the range dimension was obtained by transmitting LADAR signal with large bandwidth. While in the cross-range dimension, the large synthetic aperture diameter provided fine resolution. By employing continuous translational motion of SAL system, a large aperture diameter was obtained through synthetic aperture processing. So the diffraction limit of real aperture diameter was overcome and finer resolution was achieved. Indoor and outdoor experiments were both performed and the corresponding results were showed. Results validated the feasibility of our system and processing algorithm.

  14. Reactions of Trimethylaluminium: Modelling the Chemical Degradation of Synthetic Lubricants.

    PubMed

    Slaughter, Jonathan; Peel, Andrew J; Wheatley, Andrew E H

    2017-01-01

    In investigating and seeking to mimic the reactivity of trimethylaluminium (TMA) with synthetic, ester-based lubricating oils, the reaction of methyl propionate 1 was explored with 1, 2 and 3 equivalents of the organoaluminium reagent. Spectroscopic analysis points to the formation of the adduct 1(TMA) accompanied only by the low level 1:1 production of Me2 AlOCEtMe2 2 and Me2 AlOMe 3 when an equimolar amount of TMA is applied. The deployment of excess TMA favours reaction to give 2 and 3 over 1(TMA) adduct formation and spectroscopy reveals that in hydrocarbon solution substitution product 2 traps unreacted TMA to yield 2(TMA). The (1) H NMR spectroscopic observation of two Al-Me signals not attributable to free TMA and in the ratio 1:4 suggests the formation of a previously only postulated, symmetrical metallacycle in Me4 Al2 (μ(2) -Me)(μ(2) -OCEtMe2 ). In the presence of 3, 2(TMA) undergoes thermally induced exchange to yield Me4 Al2 (μ(2) -OMe)(μ(2) -OCEtMe2 ) 4 and TMA. The reaction of methyl phenylacetate 5 with TMA allows isolation of the crystalline product Me2 AlOCBnMe2 (TMA) 6(TMA), which allows the first observation of the Me4 Al2 (μ(2) -Me)(μ(2) -OR) motif in the solid state. Distances of 2.133(3) Å (Al-Mebridging ) and 1.951 Å (mean Al-Meterminal ) are recorded. The abstraction of TMA from 6(TMA) by the introduction of Et2 O has yielded 6, which exists as a dimer. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  15. 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.

  16. 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…

  17. 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…

  18. Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

    PubMed

    Craig, Thomas; Holland, Richard; D'Amore, Rosalinda; Johnson, James R; McCue, Hannah V; West, Anthony; Zulkower, Valentin; Tekotte, Hille; Cai, Yizhi; Swan, Daniel; Davey, Robert P; Hertz-Fowler, Christiane; Hall, Anthony; Caddick, Mark

    2017-09-13

    This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture. Hence, it enables highly configurable task-based workflows and supports data capture from project inception to completion. As such, in addition to it supporting synthetic biology it is ideal for many laboratory environments with multiple projects and users. The system is deployed as a web application through Docker and is provided under a permissive MIT license. It is freely available for download at https://leaflims.github.io .

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. A synthetic seismicity model for the Middle America Trench

    NASA Technical Reports Server (NTRS)

    Ward, Steven N.

    1991-01-01

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

  4. Liposomes containing lipid A: an effective, safe, generic adjuvant system for synthetic vaccines.

    PubMed

    Alving, Carl R; Rao, Mangala; Steers, Nicholas J; Matyas, Gary R; Mayorov, Alexander V

    2012-06-01

    Liposomes containing monophosphoryl lipid A (MPLA) have previously exhibited considerable potency and safety in human trials with a variety of candidate vaccines, including vaccines to malaria, HIV-1 and several different types of cancer. The long history of research and development of MPLA and liposomal MPLA as vaccine adjuvants reveals that there are numerous opportunities for creation and development of generic (nonproprietary) adjuvant system formulations with these materials that are not only highly potent and safe, but also readily available as native materials or as synthetic compounds. They are easily manufactured as potentially inexpensive and easy to use adjuvant systems and might be effective even with synthetic peptides as antigens.

  5. 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.

  6. The SIR-C/X-SAR synthetic aperture radar system

    NASA Technical Reports Server (NTRS)

    Jordan, Rolando L.; Huneycutt, Bryan L.; Werner, Marian

    1991-01-01

    SIR-C/X-SAR, a three-frequency radar to be flown on the Space Shuttle in September 1993, is described. The SIR-C system is a two-frequency radar operating at 1250 MHz (L-band) and 5300 MHz (C-band), and is designed to get four-polarization radar imagery at multiple surface angles. The X-SAR system is an X-band imaging radar operating at 9600 MHz. The discussion covers the mission concept; system design; hardware; RF electronics; digital electronics; command, timing, and telemetry; and testing.

  7. NEMESYS: Next Generation Models of Synthetic Urban Areas

    DTIC Science & Technology

    2004-12-01

    Network of aqueducts Sewer and drainage systems Subway tunnels Utility corridors Cellars Civil defense shelters Hand-dug tunnels (older cities) Catacombs...below surface level) What Network of aqueducts Sewer and drainage systems Cellars Civil defense shelters Hand-dug tunnels (older cities) Catacombs

  8. SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs

    PubMed Central

    Weeding, Emma; Houle, Jason

    2010-01-01

    Modeling tools can play an important role in synthetic biology the same way modeling helps in other engineering disciplines: simulations can quickly probe mechanisms and provide a clear picture of how different components influence the behavior of the whole. We present a brief review of available tools and present SynBioSS Designer. The Synthetic Biology Software Suite (SynBioSS) is used for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS consists of three distinct components: the Desktop Simulator, the Wiki, and the Designer. SynBioSS Designer takes as input molecular parts involved in gene expression and regulation (e.g. promoters, transcription factors, ribosome binding sites, etc.), and automatically generates complete networks of reactions that represent transcription, translation, regulation, induction and degradation of those parts. Effectively, Designer uses DNA sequences as input and generates networks of biomolecular reactions as output. In this paper we describe how Designer uses universal principles of molecular biology to generate models of any arbitrary synthetic biological system. These models are useful as they explain biological phenotypic complexity in mechanistic terms. In turn, such mechanistic explanations can assist in designing synthetic biological systems. We also discuss, giving practical guidance to users, how Designer interfaces with the Registry of Standard Biological Parts, the de facto compendium of parts used in synthetic biology applications. PMID:20639523

  9. SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs.

    PubMed

    Weeding, Emma; Houle, Jason; Kaznessis, Yiannis N

    2010-07-01

    Modeling tools can play an important role in synthetic biology the same way modeling helps in other engineering disciplines: simulations can quickly probe mechanisms and provide a clear picture of how different components influence the behavior of the whole. We present a brief review of available tools and present SynBioSS Designer. The Synthetic Biology Software Suite (SynBioSS) is used for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS consists of three distinct components: the Desktop Simulator, the Wiki, and the Designer. SynBioSS Designer takes as input molecular parts involved in gene expression and regulation (e.g. promoters, transcription factors, ribosome binding sites, etc.), and automatically generates complete networks of reactions that represent transcription, translation, regulation, induction and degradation of those parts. Effectively, Designer uses DNA sequences as input and generates networks of biomolecular reactions as output. In this paper we describe how Designer uses universal principles of molecular biology to generate models of any arbitrary synthetic biological system. These models are useful as they explain biological phenotypic complexity in mechanistic terms. In turn, such mechanistic explanations can assist in designing synthetic biological systems. We also discuss, giving practical guidance to users, how Designer interfaces with the Registry of Standard Biological Parts, the de facto compendium of parts used in synthetic biology applications.

  10. A synthetic aperture radar-based model to assess historical changes in lowland floodplain hydroperiod

    NASA Astrophysics Data System (ADS)

    Townsend, Philip A.; Foster, Jane R.

    2002-07-01

    The hydrology of riparian wetlands worldwide has been altered extensively owing to the construction and operation of dams. We developed a model for the Roanoke River floodplain (United States) to simulate flood extent and duration based on a power law correlation between inundation area A, as mapped from synthetic aperture radar (SAR) imagery, and river discharge Q. Model fit was 0.955 for the upper portion of the study area and 0.789 for the tidally influenced lower section. We then compared hydroperiod simulated for predam (1912-1949) and postdam (1965-1995) periods. Topographically wet areas are now flooded longer than before damming, and dry areas are now drier. Similarly, hydrologically wet years experience longer floods, whereas the driest years are drier. Most importantly, spring hydroperiod regimes are now wetter than prior to damming. Our results suggest that the intermediate zone of the hydrologic gradient has been squeezed to either wetter or drier conditions. The model presented represents a simple but effective empirical method to simulate hydroperiod regimes at the landscape scale in large lowland systems where the data necessary to develop more complex physical models are not available.

  11. 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.

  12. 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.

  13. Integration of Analytic and Synthetic Biosystem Models and Data

    DTIC Science & Technology

    2005-06-01

    environment akin to the Electrical Engineering SPICE modeling and simulation package, in which an open environment and standards-based modularity enable an...the Electrical Engineering SPICE modeling and simulation package, in which an open environment and standards-based modularity enable an enormous...was based on the following perceived requirements (excerpted from the white paper): • Heterogeneous Data Access. The Bio- SPICE DMI must support

  14. Cell-Based Biohybrid Drug Delivery Systems: The Best of the Synthetic and Natural Worlds.

    PubMed

    Banskota, Samagya; Yousefpour, Parisa; Chilkoti, Ashutosh

    2017-01-01

    The goal of drug delivery is to deliver therapeutics to the site of disease while reducing unwanted side effects. In recent years, a diverse variety of synthetic nano and microparticles have been developed as drug delivery systems. The success of these systems for drug delivery lies in their ability to overcome biological barriers such as the blood-brain barrier, to evade immune clearance and avoid nonspecific biodistribution. This Review provides an overview of recent advances in the design of biohybrid drug delivery systems, which combine cells with synthetic systems to overcome some of these biological hurdles. Examples include eukaryotic cells, such as stem cells, red blood cells, immune cells, platelets, and cancer cells that are used to carry drug-loaded synthetic particles. Synthetic particles can also be cloaked with naturally derived cell membranes and thereby evade immune clearance, exhibit prolonged systemic circulation, and target specific tissues by capitalizing on the interaction/homing tendency of certain cells and their membrane components to particular tissues. Different designs of cell-based biohybrid systems and their applications, as well as their promise and limitations, are discussed herein. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. 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 ).

  16. The RAPIDD Ebola forecasting challenge: Model description and synthetic data generation.

    PubMed

    Ajelli, Marco; Zhang, Qian; Sun, Kaiyuan; Merler, Stefano; Fumanelli, Laura; Chowell, Gerardo; Simonsen, Lone; Viboud, Cecile; Vespignani, Alessandro

    2017-09-20

    The Ebola forecasting challenge organized by the Research and Policy for Infectious Disease Dynamics (RAPIDD) program of the Fogarty International Center relies on synthetic disease datasets generated by numerical simulations of a highly detailed spatially-structured agent-based model. We discuss here the architecture and technical steps of the challenge, leading to datasets that mimic as much as possible the data collection, reporting, and communication process experienced in the 2014-2015 West African Ebola outbreak. We provide a detailed discussion of the model's definition, the epidemiological scenarios' construction, synthetic patient database generation and the data communication platform used during the challenge. Finally we offer a number of considerations and takeaways concerning the extension and scalability of synthetic challenges to other infectious diseases. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed

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

    2014-07-06

    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.

  19. Interface Reactions and Synthetic Reaction of Composite Systems

    PubMed Central

    Park, Joon Sik; Kim, Jeong Min

    2010-01-01

    Interface reactions in composite systems often determine their overall properties, since product phases usually formed at interfaces during composite fabrication processing make up a large portion of the composites. Since most composite materials represent a ternary or higher order materials system, many studies have focused on analyses of diffusion phenomena and kinetics in multicomponent systems. However, the understanding of the kinetic behavior increases the complexity, since the kinetics of each component during interdiffusion reactions need to be defined for interpreting composite behaviors. From this standpoint, it is important to clarify the interface reactions for producing compatible interfaces with desired product phases. A thermodynamic evaluation such as a chemical potential of involving components can provide an understanding of the diffusion reactions, which govern diffusion pathways and product phase formation. A strategic approach for designing compatible interfaces is discussed in terms of chemical potential diagrams and interface morphology, with some material examples.

  20. 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

  1. 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.

  2. Backus Effect on a Perpendicular Errors in Harmonic Models of Real vs. Synthetic Data

    NASA Technical Reports Server (NTRS)

    Voorhies, C. V.; Santana, J.; Sabaka, T.

    1999-01-01

    Measurements of geomagnetic scalar intensity on a thin spherical shell alone are not enough to separate internal from external source fields; moreover, such scalar data are not enough for accurate modeling of the vector field from internal sources because of unmodeled fields and small data errors. Spherical harmonic models of the geomagnetic potential fitted to scalar data alone therefore suffer from well-understood Backus effect and perpendicular errors. Curiously, errors in some models of simulated 'data' are very much less than those in models of real data. We analyze select Magsat vector and scalar measurements separately to illustrate Backus effect and perpendicular errors in models of real scalar data. By using a model to synthesize 'data' at the observation points, and by adding various types of 'noise', we illustrate such errors in models of synthetic 'data'. Perpendicular errors prove quite sensitive to the maximum degree in the spherical harmonic expansion of the potential field model fitted to the scalar data. Small errors in models of synthetic 'data' are found to be an artifact of matched truncation levels. For example, consider scalar synthetic 'data' computed from a degree 14 model. A degree 14 model fitted to such synthetic 'data' yields negligible error, but amplifies 4 nT (rmss) added noise into a 60 nT error (rmss); however, a degree 12 model fitted to the noisy 'data' suffers a 492 nT error (rmms through degree 12). Geomagnetic measurements remain unaware of model truncation, so the small errors indicated by some simulations cannot be realized in practice. Errors in models fitted to scalar data alone approach 1000 nT (rmss) and several thousand nT (maximum).

  3. A System for Drawing Synthetic Images of Forested Landscapes

    Treesearch

    Timothy P. McDonald

    1997-01-01

    A software package for drawing images of forested landscapes was developed. Programs included in the system convert topographic and stand polygon information output from a GIS into a form that can be read by a general-purpose ray-tracing renderer. Other programs generate definitions for surface features, mainly trees but ground surface textural properties as well. The...

  4. [Hannover synthetic moulages. A singular collection of dermatologic teaching models].

    PubMed

    Schnalke, T

    1987-12-01

    Dermatological moulages rapidly lost their importance during the 1950s. The disadvantages of the classical moulage materials, plaster of Paris and wax, are pointed out. In the 1960s and 1970s modern plastics were introduced to moulage technology at the Linden Dermatological Clinic in Hannover. Silicon-caoutchouc and Vestolit-PVC were the substances used. This paper describes how the Hannover collection of plastic models was assembled and presents its current status. Wax and plastic models are set against each other in the illustrations.

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

    DOE PAGES

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

    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

  6. Directed-energy Models for Distributed, Synthetic Environments

    DTIC Science & Technology

    2010-01-01

    JDMS Original article Journal of Defense Modeling and Simulation: Applications, Methodology, Technology XX(X) 1 –12 © 2010 The Society for...response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and... reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information

  7. Advanced Neural Network Modeling of Synthetic Jet Flow Fields

    DTIC Science & Technology

    2006-03-01

    The purpose of this research was to continue development of a neural network -based, lumped deterministic source term (LDST) approximation module for...main exploration involved the grid sensitivity of the neural network model. A second task was originally planned on the portability of the approach to

  8. Planetary Probe Entry Atmosphere Estimation Using Synthetic Air Data System

    NASA Technical Reports Server (NTRS)

    Karlgaard, Chris; Schoenenberger, Mark

    2017-01-01

    This paper develops an atmospheric state estimator based on inertial acceleration and angular rate measurements combined with an assumed vehicle aerodynamic model. The approach utilizes the full navigation state of the vehicle (position, velocity, and attitude) to recast the vehicle aerodynamic model to be a function solely of the atmospheric state (density, pressure, and winds). Force and moment measurements are based on vehicle sensed accelerations and angular rates. These measurements are combined with an aerodynamic model and a Kalman-Schmidt filter to estimate the atmospheric conditions. The new method is applied to data from the Mars Science Laboratory mission, which landed the Curiosity rover on the surface of Mars in August 2012. The results of the new estimation algorithm are compared with results from a Flush Air Data Sensing algorithm based on onboard pressure measurements on the vehicle forebody. The comparison indicates that the new proposed estimation method provides estimates consistent with the air data measurements, without the use of pressure measurements. Implications for future missions such as the Mars 2020 entry capsule are described.

  9. Development of a Synthetic Earth Gravity Model by 3D mass optimisation based on forward modelling

    NASA Astrophysics Data System (ADS)

    Fellner, J. J.; Kuhn, M.; Featherstone, W. E.

    2012-01-01

    Several previous Synthetic Earth Gravity Model (SEGM) simulations are based on existing information about the Earth's internal mass distribution. However, currently available information is insufficient to model the Earth's anomalous gravity field on a global scale. The low-frequency information is missing when modelling only topography, bathymetry and crust (including the Mohorovičić discontinuity), but the inclusion of information on the mantle and core does not seem to significantly improve this situation. This paper presents a method to determine a more realistic SEGM by considering simulated 3D mass distributions within the upper mantle as a proxy for all unmodelled masses within the Earth. The aim is to improve an initial SEGM based on forward gravity modelling of the topography, bathymetry and crust such that the missing low-frequency information is now included. The simulated 3D mass distribution has been derived through an interactive and iterative mass model optimisation algorithm, which minimises geoid height differences with respect to a degree-360 spherical harmonic expansion of the EGM2008 global external gravity field model. We present the developed optimisation algorithm by applying it to the development of a global SEGM that gives a reasonably close fit to EGM2008, and certainly closer than a SEGM based only on the topography, bathymetry and crust.

  10. Temperature-responsive copolymeric hydrogel systems synthetized by ionizing radiation

    NASA Astrophysics Data System (ADS)

    López-Barriguete, Jesús Eduardo; Bucio, Emilio

    2017-06-01

    Eight different systems of hydrogel copolymers with diverse temperature responsiveness were prepared to elaborate membranes for their biomedical application. The hydrogels were synthesized using poly(N-isopropylacrylamide) (PNIPAAm) and poly(N-vinylcaprolactam) (PNVCL), which have a low critical solution temperature (LCST) close to that of the human body temperature. The networks were synthesized using gamma radiation at a dose rate of 11.2 kGy h-1, and dose of 50 kGy. The LCST of each system was measured by differential scanning calorimetry (DSC). The effect of using hydrophilic monomers of acrylic acid (AAc), methacrylic acid (MAAc), dimethyl acrylamide (DMAAm), and hydroxyethyl methacrylate (HEMA) for the copolymerization on the critical point was evaluated. Five viable systems were obtained, with the best hydrogel being that of poly(NIPAAm-co-DMAAm), which an LCST at 39.8 °C. All the samples were characterized by FTIR-ATR, DSC, TGA, X-Ray Diffraction, and SEM. The proportion of monomers during the formation of the copolymers was decisive in the displacement of the LCST.

  11. 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

  12. Synthetic model of the gravitational wave background from evolving binary compact objects

    NASA Astrophysics Data System (ADS)

    Dvorkin, Irina; Uzan, Jean-Philippe; Vangioni, Elisabeth; Silk, Joseph

    2016-11-01

    Modeling the stochastic gravitational wave background from various astrophysical sources is a key objective in view of upcoming observations with ground- and space-based gravitational wave observatories such as Advanced LIGO, VIRGO, eLISA, and the pulsar timing array. We develop a synthetic model framework that follows the evolution of single and binary compact objects in an astrophysical context. We describe the formation and merger rates of binaries, the evolution of their orbital parameters with time, and the spectrum of emitted gravitational waves at different stages of binary evolution. Our approach is modular and allows us to test and constrain different ingredients of the model, including stellar evolution, black hole formation scenarios, and the properties of binary systems. We use this framework in the context of a particularly well-motivated astrophysical setup to calculate the gravitational wave background from several types of sources, including inspiraling stellar-mass binary black holes that have not merged during a Hubble time. We find that this signal, albeit weak, has a characteristic shape that can help constrain the properties of binary black holes in a way complementary to observations of the background from merger events. We discuss possible applications of our framework in the context of other gravitational wave sources, such as supermassive black holes.

  13. Modeling and Simulation of Synthetic Aperture Radars in Matlab

    DTIC Science & Technology

    2013-06-01

    was done optically by utilizing Fourier optics methods including a coherent laser and a carefully positioned system of lenses to determine the... Fourier transform of the data collected and stored on film. It was the limitations posed by optical processing that prompted research into digital... Fourier Optics : Third Edition. Englewood, CO: Roberts & Company Publishers, 2005. [4] A. W. Love. In memory of Carl A. Wiley. IEEE Antennas and

  14. The mechanics of neutrophils: synthetic modeling of three experiments.

    PubMed

    Herant, Marc; Marganski, William A; Dembo, Micah

    2003-05-01

    Much experimental data exist on the mechanical properties of neutrophils, but so far, they have mostly been approached within the framework of liquid droplet models. This has two main drawbacks: 1), It treats the cytoplasm as a single phase when in reality, it is a composite of cytosol and cytoskeleton; and 2), It does not address the problem of active neutrophil deformation and force generation. To fill these lacunae, we develop here a comprehensive continuum-mechanical paradigm of the neutrophil that includes proper treatment of the membrane, cytosol, and cytoskeleton components. We further introduce two models of active force production: a cytoskeletal swelling force and a polymerization force. Armed with these tools, we present computer simulations of three classic experiments: the passive aspiration of a neutrophil into a micropipette, the active extension of a pseudopod by a neutrophil exposed to a local stimulus, and the crawling of a neutrophil inside a micropipette toward a chemoattractant against a varying counterpressure. Principal results include: 1), Membrane cortical tension is a global property of the neutrophil that is affected by local area-increasing shape changes. We argue that there exists an area dilation viscosity caused by the work of unfurling membrane-storing wrinkles and that this viscosity is responsible for much of the regulation of neutrophil deformation. 2), If there is no swelling force of the cytoskeleton, then it must be endowed with a strong cohesive elasticity to prevent phase separation from the cytosol during vigorous suction into a capillary tube. 3), We find that both swelling and polymerization force models are able to provide a unifying fit to the experimental data for the three experiments. However, force production required in the polymerization model is beyond what is expected from a simple short-range Brownian ratchet model. 4), It appears that, in the crawling of neutrophils or other amoeboid cells inside a micropipette

  15. The Mechanics of Neutrophils: Synthetic Modeling of Three Experiments

    PubMed Central

    Herant, Marc; Marganski, William A.; Dembo, Micah

    2003-01-01

    Much experimental data exist on the mechanical properties of neutrophils, but so far, they have mostly been approached within the framework of liquid droplet models. This has two main drawbacks: 1), It treats the cytoplasm as a single phase when in reality, it is a composite of cytosol and cytoskeleton; and 2), It does not address the problem of active neutrophil deformation and force generation. To fill these lacunae, we develop here a comprehensive continuum-mechanical paradigm of the neutrophil that includes proper treatment of the membrane, cytosol, and cytoskeleton components. We further introduce two models of active force production: a cytoskeletal swelling force and a polymerization force. Armed with these tools, we present computer simulations of three classic experiments: the passive aspiration of a neutrophil into a micropipette, the active extension of a pseudopod by a neutrophil exposed to a local stimulus, and the crawling of a neutrophil inside a micropipette toward a chemoattractant against a varying counterpressure. Principal results include: 1), Membrane cortical tension is a global property of the neutrophil that is affected by local area-increasing shape changes. We argue that there exists an area dilation viscosity caused by the work of unfurling membrane-storing wrinkles and that this viscosity is responsible for much of the regulation of neutrophil deformation. 2), If there is no swelling force of the cytoskeleton, then it must be endowed with a strong cohesive elasticity to prevent phase separation from the cytosol during vigorous suction into a capillary tube. 3), We find that both swelling and polymerization force models are able to provide a unifying fit to the experimental data for the three experiments. However, force production required in the polymerization model is beyond what is expected from a simple short-range Brownian ratchet model. 4), It appears that, in the crawling of neutrophils or other amoeboid cells inside a micropipette

  16. Digital computer simulation of synthetic aperture systems and images

    NASA Astrophysics Data System (ADS)

    Camporeale, Claudio; Galati, Gaspare

    1991-06-01

    Digital computer simulation is a powerful tool for the design, the mission planning and the image quality analysis of advanced SAR Systems. 'End-to-end' simulators describe the whole process of the SAR imaging including the generation of the coherent echoes and their processing and allow, unlike the 'product simulators', to evaluate the effects of the various impairments on the final image. The main disadvantage of the 'end-to-end' approach, as described in this paper, is the heavy computation burden; therefore, a new type of simulator is presented, attempting to reduce the burden but presenting a greater degree of completeness and realism than the SAR product simulators, already existing.

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

    Treesearch

    E. Matthew Hansen; Jim C. Vandygriff; Robert J. Cain; David Wakarchuk

    2006-01-01

    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...

  18. [New polymer-drug systems based on natural and synthetic polymers].

    PubMed

    Racoviţă, Stefania; Vasiliu, Silvia; Foia, Liliana

    2010-01-01

    The great versatility of polymers makes them very useful in the biomedical and pharmaceutical fields. The combination of natural and synthetic polymers leads to new materials with tailored functional properties. The aim of this work consists in the preparation of new drug delivery system based on chitosan (natural polymer) and polybetaines (synthetic polymers), by a simple process, well known in the literature as complex coacervation methods. Also, the adsorption and release studies of two antibiotics as well as the preservation of their bactericidal capacities were performed.

  19. Dynamic visual image modeling for 3D synthetic scenes in agricultural engineering

    NASA Astrophysics Data System (ADS)

    Gao, Li; Yan, Juntao; Li, Xiaobo; Ji, Yatai; Li, Xin

    The dynamic visual image modeling for 3D synthetic scenes by using dynamic multichannel binocular visual image based on the mobile self-organizing network. Technologies of 3D modeling synthetic scenes have been widely used in kinds of industries. The main purpose of this paper is to use multiple networks of dynamic visual monitors and sensors to observe an unattended area, to use the advantages of mobile network in rural areas for improving existing mobile network information service further and providing personalized information services. The goal of displaying is to provide perfect representation of synthetic scenes. Using low-power dynamic visual monitors and temperature/humidity sensor or GPS installed in the node equipment, monitoring data will be sent at scheduled time. Then through the mobile self-organizing network, 3D model is rebuilt by synthesizing the returned images. On this basis, we formalize a novel algorithm for multichannel binocular visual 3D images based on fast 3D modeling. Taking advantage of these low prices mobile, mobile self-organizing networks can get a large number of video from where is not suitable for human observation or unable to reach, and accurately synthetic 3D scene. This application will play a great role in promoting its application in agriculture.

  20. A synthetic model for the oxygen-evolving complex in Sr(2+)-containing photosystem II.

    PubMed

    Chen, Changhui; Zhang, Chunxi; Dong, Hongxing; Zhao, Jingquan

    2014-08-25

    A novel heterometallic MnSr complex containing the Mn3SrO4 cuboidal moiety and all types of μ-O(2-) moieties observed in the oxygen-evolving complex (OEC) in Sr(2+)-containing photosystem II (PSII) has been synthesized and characterized, which provides a new synthetic model of the OEC.

  1. Comparisons of Historical versus Synthetic Weather Inputs to Watershed Models and their Effect on Pollutant Loads

    USDA-ARS?s Scientific Manuscript database

    Synthetic weather generators are important for continuous-simulation of agricultural watersheds for risk analyses of downstream water quality. Many watersheds are sparsely or totally ungauged and daily weather must either be transposed or augmented. Since water quality models must recognize runoff...

  2. 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.

  3. Spectral distribution of UV-B irradiance derived by synthetic model compared with simulation results of TUV and ground measurements

    NASA Astrophysics Data System (ADS)

    Wang, Xinli; Gao, Wei; Slusser, James R.; Davis, John; Gao, Zhiqiang; Scott, Gwen; Olson, Becky; Krotkov, Nickolay; Xu, Min; Liang, Xin-Zhong

    2006-08-01

    Multifilter rotating shadowband radiometers are deployed in the United States, Canada, and New Zealand by the USDA (United States Department of Agriculture) UV-B (ultraviolet-B) Monitoring and Research Program to measure UV-B irradiances at seven discrete wavelengths. A synthetic model is used to construct the continuous spectral distribution, from which irradiance integrals can be performed for various purposes. The derived spectral data are posted for public use through a web accessible database. Although the synthetic model has been validated with a certain data set, few works have been seen to compare the results of the synthetic model with simulations of other widely accepted models such as TUV. Through this comparison the validation of the synthetic model can be further confirmed and alternative techniques for constructing spectral irradiances from discrete narrowband measurements can also be explored. In this study the data from the USDA UV-B Monitoring and Research Program are used to evaluate the synthetic model and to explore the capability of the TUV model for constructing continuous spectra from discrete measurements. Simulations of the TUV model are compared with discrete measurements, erythema-weighted broadband measurements, and the results of the synthetic model. Good agreements between derived results by using TUV model and the synthetic model with measurements in general further confirm the validation of the synthetic model. Generally, the spectral irradiances constructed by using synthetic model are lower than those by using the TUV model at very shorter wavelengths (<301 nm) and at the wavelengths of 315-342 nm, but are higher at other wavelengths. The ratio of erythemal doses derived by using the TUV simulation to broadband measurements varies between 0.87-1.02. Constructed erythemal doses by using the TUV simulation are closer to broadband measurements than those obtained by using the synthetic model. These results suggest that the TUV model

  4. 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.

  5. 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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. 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

  7. Evolutionary adaptation of phenotypic plasticity in a synthetic microbial system

    NASA Astrophysics Data System (ADS)

    Tans, Sander

    2010-03-01

    While phenotypic plasticity -the capability to respond to the environment- is vital to organisms, tests of its adaptation have remained indecisive because constraints and selection in variable environments are unknown and entangled. We show that one can determine the phenotype-fitness landscape that specifies selection on plasticity, by uncoupling the environmental cue and stress in a genetically engineered microbial system. Evolutionary trajectories revealed genetic constraints in a regulatory protein, which imposed cross-environment trade-offs that favored specialization. However, depending on the synchronicity and amplitude of the applied cue and stress variations, adaptation could break constraints, resolve trade-offs, and evolve optimal phenotypes that exhibit qualitatively altered (inverse) responses to the cue. Our results provide a first step to explain the adaptive origins of complex behavior in heterogeneous environments.

  8. 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.

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

    PubMed

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

    2011-10-07

    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.

  10. 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.

  11. Erythrocytes-based synthetic delivery systems: transition from conventional to novel engineering strategies.

    PubMed

    Bhateria, Manisha; Rachumallu, Ramakrishna; Singh, Rajbir; Bhatta, Rabi Sankar

    2014-08-01

    Erythrocytes (red blood cells [RBCs]) and artificial or synthetic delivery systems such as liposomes, nanoparticles (NPs) are the most investigated carrier systems. Herein, progress made from conventional approach of using RBC as delivery systems to novel approach of using synthetic delivery systems based on RBC properties will be reviewed. We aim to highlight both conventional and novel approaches of using RBCs as potential carrier system. Conventional approaches which include two main strategies are: i) directly loading therapeutic moieties in RBCs; and ii) coupling them with RBCs whereas novel approaches exploit structural, mechanical and biological properties of RBCs to design synthetic delivery systems through various engineering strategies. Initial attempts included coupling of antibodies to liposomes to specifically target RBCs. Knowledge obtained from several studies led to the development of RBC membrane derived liposomes (nanoerythrosomes), inspiring future application of RBC or its structural features in other attractive delivery systems (hydrogels, filomicelles, microcapsules, micro- and NPs) for even greater potential. In conclusion, this review dwells upon comparative analysis of various conventional and novel engineering strategies in developing RBC based drug delivery systems, diversifying their applications in arena of drug delivery. Regardless of the challenges in front of us, RBC based delivery systems offer an exciting approach of exploiting biological entities in a multitude of medical applications.

  12. Water quality assessment of the Li Canal using a functional fuzzy synthetic evaluation model.

    PubMed

    Feng, Yan; Ling, Liu

    2014-07-01

    Through introducing functional data analysis (FDA) theory into the conventional fuzzy synthetic evaluation (FSE) method, the functional fuzzy synthetic evaluation (FFSE) model is established. FFSE keeps the property of the conventional FSE that the fuzziness in the water quality condition can be suitably measured. Furthermore, compared with FSE, FFSE has the following advantages: (1) FFSE requires fewer conditions for observation, for example, pollutants can be monitored at different times, and missing data is accepted; (2) the dynamic variation of the water quality condition can be represented more comprehensively and intuitively. The procedure of FFSE is discussed and the water quality of the Li Canal in 2012 is evaluated as an illustration. The synthetic classification of the Li Canal is "II" in January, February and July, and "I" in other months, which can satisfy the requirement of the Chinese South-to-North Water Diversion Project.

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

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

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

  14. 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.

  15. 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.

  16. Glottal jet measurements in synthetic, MRI-based human vocal fold models

    NASA Astrophysics Data System (ADS)

    Thomson, Scott; Pickup, Brian; Gollnick, Paul

    2007-11-01

    Human vocal fold vibration generates a time-varying elliptically-shaped glottal jet that produces sound in speech. Improved understanding of glottal jet dynamics can yield insight into voice production mechanisms and improve the diagnosis and treatment of voice disorders. Experiments using recently developed life-sized synthetic models of the vocal folds are presented. The fabrication process of converting MRI images to synthetic models is described. The process allows for varying the Young's modulus of the models, allowing for asymmetric conditions to be created by casting opposing vocal folds using materials of different stiffness. The models are shown to oscillate at frequencies, pressures, and flow rates typical of human speech. Phase-locked particle image velocimetry (PIV) results are presented which characterize the glottal jet, including jet direction, vortical structures, and turbulence levels. Results are shown for symmetric and asymmetric vocal fold models. The degree of material asymmetry required to cause significant asymmetry in the glottal jet is reported.

  17. VLSI system for synthetic aperture radar /SAR/ processing

    NASA Technical Reports Server (NTRS)

    Cohen, D.; Tyree, V.

    1979-01-01

    The paper discusses an SAR problem based on actual requirements set forth by NASA for a spaceborne application. The requirements for high resolution and high quality necessitate a data sampling rate of 7.5 MHz. For each data value 1,025 4-bit complex multiply + add operations are needed, which is equivalent to 7.7 GHz complex multiply + add operation rate. Since this rate is much too high for general purpose systems, a special-purpose device was sought. This paper discusses two architectures based on parallel operation of 1,025 identical cells, each of which is capable of performing arithmetic, storage, and several control operations. The operation rate in each device is only 7.5 MHz, which is quite manageable, especially with the help of a substantial degree of pipelining. A computational-mathematical analysis is used as a primary tool for evaluating the design and some of its tradeoffs. Two different approaches are discussed and compared; both are based on having 1,025 identical cells working in parallel, but differ in their dual approaches to the flow of data.

  18. Synthetic Multivariate Models to Accommodate Unmodeled Interfering Components During Quantitative Spectral Analyses

    SciTech Connect

    Haaland, David M.

    1999-07-14

    The analysis precision of any multivariate calibration method will be severely degraded if unmodeled sources of spectral variation are present in the unknown sample spectra. This paper describes a synthetic method for correcting for the errors generated by the presence of unmodeled components or other sources of unmodeled spectral variation. If the spectral shape of the unmodeled component can be obtained and mathematically added to the original calibration spectra, then a new synthetic multivariate calibration model can be generated to accommodate the presence of the unmodeled source of spectral variation. This new method is demonstrated for the presence of unmodeled temperature variations in the unknown sample spectra of dilute aqueous solutions of urea, creatinine, and NaCl. When constant-temperature PLS models are applied to spectra of samples of variable temperature, the standard errors of prediction (SEP) are approximately an order of magnitude higher than that of the original cross-validated SEPs of the constant-temperature partial least squares models. Synthetic models using the classical least squares estimates of temperature from pure water or variable-temperature mixture sample spectra reduce the errors significantly for the variable temperature samples. Spectrometer drift adds additional error to the analyte determinations, but a method is demonstrated that can minimize the effect of drift on prediction errors through the measurement of the spectra of a small subset of samples during both calibration and prediction. In addition, sample temperature can be predicted with high precision with this new synthetic model without the need to recalibrate using actual variable-temperature sample data. The synthetic methods eliminate the need for expensive generation of new calibration samples and collection of their spectra. The methods are quite general and can be applied using any known source of spectral variation and can be used with any multivariate

  19. Synthetic ECG generation and Bayesian filtering using a Gaussian wave-based dynamical model.

    PubMed

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

    2010-10-01

    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 and extended Kalman smoother, was 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.

  20. 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

  1. 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

  2. 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.

  3. Measurement and modeling of CO₂ solubility in natural and synthetic formation brines for CO₂ sequestration.

    PubMed

    Zhao, Haining; Dilmore, Robert; Allen, Douglas E; Hedges, Sheila W; Soong, Yee; Lvov, Serguei N

    2015-02-03

    CO2 solubility data in the natural formation brine, synthetic formation brine, and synthetic NaCl+CaCl2 brine were collected at the pressures from 100 to 200 bar, temperatures from 323 to 423 K. Experimental results demonstrate that the CO2 solubility in the synthetic formation brines can be reliably represented by that in the synthetic NaCl+CaCl2 brines. We extended our previously developed model (PSUCO2) to calculate CO2 solubility in aqueous mixed-salt solution by using the additivity rule of the Setschenow coefficients of the individual ions (Na(+), Ca(2+), Mg(2+), K(+), Cl(-), and SO4(2-)). Comparisons with previously published models against the experimental data reveal a clear improvement of the proposed PSUCO2 model. Additionally, the path of the maximum gradient of the CO2 solubility contours divides the P-T diagram into two distinct regions: in Region I, the CO2 solubility in the aqueous phase decreases monotonically in response to increased temperature; in region II, the behavior of the CO2 solubility is the opposite of that in Region I as the temperature increases.

  4. Advanced synthetic image generation models and their application to multi/hyperspectral algorithm development

    NASA Astrophysics Data System (ADS)

    Schott, John R.; Brown, Scott D.; Raqueno, Rolando V.; Gross, Harry N.; Robinson, Gary

    1999-01-01

    The need for robust image data sets for algorithm development and testing has prompted the consideration of synthetic imagery as a supplement to real imagery. The unique ability of synthetic image generation (SIG) tools to supply per-pixel truth allows algorithm writers to test difficult scenarios that would require expensive collection and instrumentation efforts. In addition, SIG data products can supply the user with `actual' truth measurements of the entire image area that are not subject to measurement error thereby allowing the user to more accurately evaluate the performance of their algorithm. Advanced algorithms place a high demand on synthetic imagery to reproduce both the spectro-radiometric and spatial character observed in real imagery. This paper describes a synthetic image generation model that strives to include the radiometric processes that affect spectral image formation and capture. In particular, it addresses recent advances in SIG modeling that attempt to capture the spatial/spectral correlation inherent in real images. The model is capable of simultaneously generating imagery from a wide range of sensors allowing it to generate daylight, low-light-level and thermal image inputs for broadband, multi- and hyper-spectral exploitation algorithms.

  5. Optogenetic characterization methods overcome key challenges in synthetic and systems biology.

    PubMed

    Olson, Evan J; Tabor, Jeffrey J

    2014-07-01

    Systems biologists aim to understand how organism-level processes, such as differentiation and multicellular development, are encoded in DNA. Conversely, synthetic biologists aim to program systems-level biological processes, such as engineered tissue growth, by writing artificial DNA sequences. To achieve their goals, these groups have adapted a hierarchical electrical engineering framework that can be applied in the forward direction to design complex biological systems or in the reverse direction to analyze evolved networks. Despite much progress, this framework has been limited by an inability to directly and dynamically characterize biological components in the varied contexts of living cells. Recently, two optogenetic methods for programming custom gene expression and protein localization signals have been developed and used to reveal fundamentally new information about biological components that respond to those signals. This basic dynamic characterization approach will be a major enabling technology in synthetic and systems biology.

  6. A molecular rheostat maintains ATP levels to drive a synthetic biochemistry system.

    PubMed

    Opgenorth, Paul H; Korman, Tyler P; Iancu, Liviu; Bowie, James U

    2017-09-01

    Synthetic biochemistry seeks to engineer complex metabolic pathways for chemical conversions outside the constraints of the cell. Establishment of effective and flexible cell-free systems requires the development of simple systems to replace the intricate regulatory mechanisms that exist in cells for maintaining high-energy cofactor balance. Here we describe a simple rheostat that regulates ATP levels by controlling the flow down either an ATP-generating or non-ATP-generating pathway according to the free-phosphate concentration. We implemented this concept for the production of isobutanol from glucose. The rheostat maintains adequate ATP concentrations even in the presence of ATPase contamination. The final system including the rheostat produced 24.1 ± 1.8 g/L of isobutanol from glucose in 91% theoretical yield with an initial productivity of 1.3 g/L/h. The molecular rheostat concept can be used in the design of continuously operating, self-sustaining synthetic biochemistry systems.

  7. [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.

  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. Synthetic vision in the cockpit: 3D systems for general aviation

    NASA Astrophysics Data System (ADS)

    Hansen, Andrew J.; Rybacki, Richard M.; Smith, W. Garth

    2001-08-01

    Synthetic vision has the potential to improve safety in aviation through better pilot situational awareness and enhanced navigational guidance. The technological advances enabling synthetic vision are GPS based navigation (position and attitude) systems and efficient graphical systems for rendering 3D displays in the cockpit. A benefit for military, commercial, and general aviation platforms alike is the relentless drive to miniaturize computer subsystems. Processors, data storage, graphical and digital signal processing chips, RF circuitry, and bus architectures are at or out-pacing Moore's Law with the transition to mobile computing and embedded systems. The tandem of fundamental GPS navigation services such as the US FAA's Wide Area and Local Area Augmentation Systems (WAAS) and commercially viable mobile rendering systems puts synthetic vision well with the the technological reach of general aviation. Given the appropriate navigational inputs, low cost and power efficient graphics solutions are capable of rendering a pilot's out-the-window view into visual databases with photo-specific imagery and geo-specific elevation and feature content. Looking beyond the single airframe, proposed aviation technologies such as ADS-B would provide a communication channel for bringing traffic information on-board and into the cockpit visually via the 3D display for additional pilot awareness. This paper gives a view of current 3D graphics system capability suitable for general aviation and presents a potential road map following the current trends.

  10. 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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  13. Assessment of synthetic winds through spectral modeling and validation using FAST

    NASA Astrophysics Data System (ADS)

    Chougule, A.; Kandukuri, S. T.; Beyer, H. G.

    2016-09-01

    In this paper, we analyse the simulated and measured wind data with respect to their spectral characteristics and their effect on wind turbine loads. The synthetic data is generated from a stochastic full-field turbulent wind simulator - TurbSim for neutral stability conditions. We first investigate a model for velocity spectra and, a coherence model, by comparing the model results with the measurements. In the second part we analyse the synthetic data via spectra and coherence for two cases; without and with adding coherent events. Finally, we compare wind turbine loads calculated by using FAST simulation of 5 MW reference wind turbine on the basis of simulated and measured data for the given mean wind speed.

  14. Sources of error in a helmet-mounted enhanced and synthetic vision system

    NASA Astrophysics Data System (ADS)

    Jennings, Sion A.; Craig, Greg; Link, Norah K.

    2002-08-01

    Head-up displays (HUDs) or helmet-mounted displays (HMDs) that provide pilots with world-referenced symbology or imagery require critical alignment and minimal time delays. In this paper, some aspects of system accuracy and latency will be discussed in the context of the Enhanced and Synthetic Vision System (ESVS), which is displayed on an HMD. In a joint program, the Canadian Department of National Defence (DND), CAE Inc., CMC Electronics, and the Flight Research Laboratory of the National Research Council of Canada integrated and flight-tested an enhanced and synthetic vision system. The goal of the program was to examine the potential of the ESVS concept for search and rescue operations. Despite obvious misalignments between the enhanced and synthetic images, the current system demonstrated the potential of ESVS systems with most of the test pilots able to navigate at low altitude in low visibility in an area without prepared navigation aids. The flight tests highlighted the system potential- the synthetic imagery provided continuous virtual VFR conditions, while the enhanced sensor generally provided more accurate spatial data and obstacle avoidance information. The ESVS program finished with the first helicopter flight test of both enhanced and synthetic visual displays presented on an HMD. While this milestone was successfully achieved, there is clearly a need for improved technology and further research to implement safe and effective ESVS systems. The system alignment was found to be a complex and perplexing issue. It was not possible to align the system within the precise tolerances generally accepted for HUD-equipped aircraft and, in fact, errors that were an order of magnitude greater than the recommendations were common. Errors built up in such a way that the system developers needed to develop an interim alignment solution and pilots were forced to deal with relatively large angular offsets. This was less than optimal, but proved to be sufficient for

  15. Synthetic Botany.

    PubMed

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

    2017-07-05

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

  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. 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).

  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. 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.

  1. 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

  2. Frequency response of synthetic vocal fold models with linear and nonlinear material properties.

    PubMed

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

    2012-10-01

    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 (F0) during anterior-posterior stretching. Three materially linear and 3 materially nonlinear models were created and stretched up to 10 mm in 1-mm increments. Phonation onset pressure (Pon) and 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. 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. Nonlinear synthetic models appear to more accurately represent the human vocal folds than do linear models, especially with respect to F0 response.

  3. 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

  4. 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

  5. Integrative systems and synthetic biology of cell-matrix adhesion sites.

    PubMed

    Zamir, Eli

    2016-09-02

    The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.

  6. Integrative systems and synthetic biology of cell-matrix adhesion sites

    PubMed Central

    Zamir, Eli

    2016-01-01

    ABSTRACT The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them. PMID:26853318

  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. A synthetic Earth Gravity Model Designed Specifically for Testing Regional Gravimetric Geoid Determination Algorithms

    NASA Astrophysics Data System (ADS)

    Baran, I.; Kuhn, M.; Claessens, S. J.; Featherstone, W. E.; Holmes, S. A.; Vaníček, P.

    2006-04-01

    A synthetic [simulated] Earth gravity model (SEGM) of the geoid, gravity and topography has been constructed over Australia specifically for validating regional gravimetric geoid determination theories, techniques and computer software. This regional high-resolution (1-arc-min by 1-arc-min) Australian SEGM (AusSEGM) is a combined source and effect model. The long-wavelength effect part (up to and including spherical harmonic degree and order 360) is taken from an assumed errorless EGM96 global geopotential model. Using forward modelling via numerical Newtonian integration, the short-wavelength source part is computed from a high-resolution (3-arc-sec by 3-arc-sec) synthetic digital elevation model (SDEM), which is a fractal surface based on the GLOBE v1 DEM. All topographic masses are modelled with a constant mass-density of 2,670 kg/m3. Based on these input data, gravity values on the synthetic topography (on a grid and at arbitrarily distributed discrete points) and consistent geoidal heights at regular 1-arc-min geographical grid nodes have been computed. The precision of the synthetic gravity and geoid data (after a first iteration) is estimated to be better than 30 μ Gal and 3 mm, respectively, which reduces to 1 μ Gal and 1 mm after a second iteration. The second iteration accounts for the changes in the geoid due to the superposed synthetic topographic mass distribution. The first iteration of AusSEGM is compared with Australian gravity and GPS-levelling data to verify that it gives a realistic representation of the Earth’s gravity field. As a by-product of this comparison, AusSEGM gives further evidence of the north south-trending error in the Australian Height Datum. The freely available AusSEGM-derived gravity and SDEM data, included as Electronic Supplementary Material (ESM) with this paper, can be used to compute a geoid model that, if correct, will agree to in 3 mm with the AusSEGM geoidal heights, thus offering independent verification of theories

  9. 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.

  10. 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.

  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. 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

  13. 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.

  14. 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.

  15. Synthetic lethal screening in the mammalian central nervous system identifies Gpx6 as a modulator of Huntington's disease.

    PubMed

    Shema, Reut; Kulicke, Ruth; Cowley, Glenn S; Stein, Rachael; Root, David E; Heiman, Myriam

    2015-01-06

    Huntington's disease, the most common inherited neurodegenerative disease, is characterized by a dramatic loss of deep-layer cortical and striatal neurons, as well as morbidity in midlife. Human genetic studies led to the identification of the causative gene, huntingtin. Recent genomic advances have also led to the identification of hundreds of potential interacting partners for huntingtin protein and many hypotheses as to the molecular mechanisms whereby mutant huntingtin leads to cellular dysfunction and death. However, the multitude of possible interacting partners and cellular pathways affected by mutant huntingtin has complicated efforts to understand the etiology of this disease, and to date no curative therapeutic exists. To address the general problem of identifying the disease-phenotype contributing genes from a large number of correlative studies, here we develop a synthetic lethal screening methodology for the mammalian central nervous system, called SLIC, for synthetic lethal in the central nervous system. Applying SLIC to the study of Huntington's disease, we identify the age-regulated glutathione peroxidase 6 (Gpx6) gene as a modulator of mutant huntingtin toxicity and show that overexpression of Gpx6 can dramatically alleviate both behavioral and molecular phenotypes associated with a mouse model of Huntington's disease. SLIC can, in principle, be used in the study of any neurodegenerative disease for which a mouse model exists, promising to reveal modulators of neurodegenerative disease in an unbiased fashion, akin to screens in simpler model organisms.

  16. Use of Two-Component Signal Transduction Systems in the Construction of Synthetic Genetic Networks

    PubMed Central

    Ninfa, Alexander J.

    2012-01-01

    Summary of Recent Advances Two-component signal transduction systems are a common type of signaling system in prokaryotes; the typical cell has dozens of systems regulating aspects of physiology and controlling responses to environmental conditions. In this review, I consider how these systems may be useful for engineering novel cell functions. Examples of successful incorporation of two-component systems into engineered systems are noted, and features of the systems that favor or hinder potential future use of these signaling systems for synthetic biology applications are discussed. The focus will be on the engineering of novel couplings of sensory functions to signaling outputs. Recent successes in this area are noted, such as the development of light-sensitive transmitter proteins and chemotactic receptors responsive to nitrate. PMID:20149718

  17. Use of two-component signal transduction systems in the construction of synthetic genetic networks.

    PubMed

    Ninfa, Alexander J

    2010-04-01

    Two-component signal transduction systems are a common type of signaling system in prokaryotes; the typical cell has dozens of systems regulating aspects of physiology and controlling responses to environmental conditions. In this review, I consider how these systems may be useful for engineering novel cell functions. Examples of successful incorporation of two-component systems into engineered systems are noted, and features of the systems that favor or hinder potential future use of these signaling systems for synthetic biology applications are discussed. The focus will be on the engineering of novel couplings of sensory functions to signaling outputs. Recent successes in this area are noted, such as the development of light-sensitive transmitter proteins and chemotactic receptors responsive to nitrate. Copyright 2010 Elsevier Ltd. All rights reserved.

  18. A Reduced-Order Model for Efficient Simulation of Synthetic Jet Actuators

    NASA Technical Reports Server (NTRS)

    Yamaleev, Nail K.; Carpenter, Mark H.

    2003-01-01

    A new reduced-order model of multidimensional synthetic jet actuators that combines the accuracy and conservation properties of full numerical simulation methods with the efficiency of simplified zero-order models is proposed. The multidimensional actuator is simulated by solving the time-dependent compressible quasi-1-D Euler equations, while the diaphragm is modeled as a moving boundary. The governing equations are approximated with a fourth-order finite difference scheme on a moving mesh such that one of the mesh boundaries coincides with the diaphragm. The reduced-order model of the actuator has several advantages. In contrast to the 3-D models, this approach provides conservation of mass, momentum, and energy. Furthermore, the new method is computationally much more efficient than the multidimensional Navier-Stokes simulation of the actuator cavity flow, while providing practically the same accuracy in the exterior flowfield. The most distinctive feature of the present model is its ability to predict the resonance characteristics of synthetic jet actuators; this is not practical when using the 3-D models because of the computational cost involved. Numerical results demonstrating the accuracy of the new reduced-order model and its limitations are presented.

  19. Maritime surveillance with synthetic aperture radar (SAR) and automatic identification system (AIS) onboard a microsatellite constellation

    NASA Astrophysics Data System (ADS)

    Peterson, E. H.; Zee, R. E.; Fotopoulos, G.

    2012-11-01

    New developments in small spacecraft capabilities will soon enable formation-flying constellations of small satellites, performing cooperative distributed remote sensing at a fraction of the cost of traditional large spacecraft missions. As part of ongoing research into applications of formation-flight technology, recent work has developed a mission concept based on combining synthetic aperture radar (SAR) with automatic identification system (AIS) data. Two or more microsatellites would trail a large SAR transmitter in orbit, each carrying a SAR receiver antenna and one carrying an AIS antenna. Spaceborne AIS can receive and decode AIS data from a large area, but accurate decoding is limited in high traffic areas, and the technology relies on voluntary vessel compliance. Furthermore, vessel detection amidst speckle in SAR imagery can be challenging. In this constellation, AIS broadcasts of position and velocity are received and decoded, and used in combination with SAR observations to form a more complete picture of maritime traffic and identify potentially non-cooperative vessels. Due to the limited transmit power and ground station downlink time of the microsatellite platform, data will be processed onboard the spacecraft. Herein we present the onboard data processing portion of the mission concept, including methods for automated SAR image registration, vessel detection, and fusion with AIS data. Georeferencing in combination with a spatial frequency domain method is used for image registration. Wavelet-based speckle reduction facilitates vessel detection using a standard CFAR algorithm, while leaving sufficient detail for registration of the filtered and compressed imagery. Moving targets appear displaced from their actual position in SAR imagery, depending on their velocity and the image acquisition geometry; multiple SAR images acquired from different locations are used to determine the actual positions of these targets. Finally, a probabilistic inference

  20. 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

  1. A new approach to compensate the geometric distortion in the synthetic aperture ultrasonic imaging system.

    PubMed

    He, Xiaonian; Liu, Weixiang; Chen, Siping; Qin, Zhengdi

    2015-01-01

    In the field of ultrasonic imaging technology, the problem of geometric distortion is often encountered, especially in the ultrasonic near-field. In this study, a new approach is proposed to compensate for geometric distortion in the synthetic aperture ultrasonic imaging system. This approach is based on the synthetic aperture ultrasonic holographic B-scan (UHB) imaging system, which is a combination of ultrasonic holography based on the backward propagation principle and the conventional B-scan technique. To solve the geometric distortion problem, the operation of the spatial compression and resampling in the frequency domain are introduced. The main advantage of the approach is that the real holographic value can be calculated without distortion by using the spatial interpolation function after the spatial frequency compression. After the compensation for geometric distortion is performed, the synthetic aperture technique based on the backward propagation principle is then applied in the process of the two-dimensional numerical imaging reconstruction. Both the simulation and measurement experiment show that the approach is promising. The geometric distortion that is dependent on the wave front angle can be effectively compensated. The spatial resolution is practically uniform throughout the depth range and close to the theoretical limit in the experiments.

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

    PubMed Central

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

    2014-01-01

    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. PMID:25363806

  3. 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.

  4. 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. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

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

    DOE PAGES

    Kalluri, Udaya C.; Yin, Hengfu; Yang, Xiaohan; ...

    2014-01-01

    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 thatmore » 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. Finally, 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.« less

  6. Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems.

    PubMed

    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 disrupting them through genetic or chemical means. The emerging discipline of synthetic biology offers an additional, powerful approach 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. In addition, by building minimal toy networks, one can systematically explore the relationship between network structure and function. 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.

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

    PubMed

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

    2015-07-27

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

  8. Simulation of synthetic aperture imaging ladar (SAIL) for three-dimensional target model

    NASA Astrophysics Data System (ADS)

    Yi, Ning; Wu, Zhen-Sen

    2010-11-01

    In conventional imaging laser radar, the resolution of target is constrained by the diffraction-limited, which includes the beamwidth of the laser in the target plane and the telescope's aperture. Synthetic aperture imaging Ladar (SAIL) is an imaging technique which employs aperture synthesis with coherent laser radar, the resolution is determined by the total frequency spread of the source and is independent of range, so can achieve fine resolution in long range. Ray tracing is utilized here to obtain two-dimensional scattering properties from three-dimensional geometric model of actual target, and range-doppler algorithm is used for synthetic aperture process in laser image simulation. The results show that the SAIL can support better resolution.

  9. Synthetic genes specifying periodic polymers modelled on the repetitive domain of wheat gliadins: conception and expression.

    PubMed

    Elmorjani, K; Thiévin, M; Michon, T; Popineau, Y; Hallet, J N; Guéguen, J

    1997-10-09

    In order to optimise new polypeptide based biomaterials, we developed a procedure for producing homoblock polypeptides using recombinant DNA technology. Synthetic genes encoding periodic polypeptides modelled on the consensus sequence of wheat gliadins (a family of wheat storage proteins) were devised to be expressed in Escherichia coli. The construction strategy followed allows the construction of three genes encoding 8, 16, and 32 copies of the PQQPY module. The optimal expression conditions in the enterobacteria were established and a convenient purification procedure was shown to be useful in recovery of sizable amounts of strictly periodic polypeptides. The identities of the synthesized polypeptides were assessed using positive cross reactions to antibodies raised against a synthetic decapeptide (PQQPYPQQPA) and amino acid composition was determined as well.

  10. 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

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

    PubMed

    Murray, Preston R; Thomson, Scott L

    2011-12-02

    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

  12. Synthetic genomics and synthetic biology applications between hopes and concerns.

    PubMed

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

    2013-03-01

    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.

  13. 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

  14. NLTE models for synthetic spectra of type IA supernovae. The influence of line blocking.

    NASA Astrophysics Data System (ADS)

    Pauldrach, A. W. A.; Duschinger, M.; Mazzali, P. A.; Puls, J.; Lennon, M.; Miller, D. L.

    1996-08-01

    A method to compute a NLTE model of the atmosphere of a type Ia supernova (SN Ia) near maximum light is presented. The determination of the level populations is carried out using detailed atomic models, and including all important contributions to the rate equations: Thomson scattering, bound-free (from ground and excited levels) and free-free opacities, line absorption and emission processes. Dielectronic recombination is included. The spherical radiation transfer is solved at up to 400 frequency points and 41 depth points. Finally, a synthetic spectrum is computed using a formal integral solution of the transfer equation based on a spatial microgrid. It is found that the SN atmosphere is electron scattering-dominated, and that the high velocity of the apparent photosphere (~8000km/s) is due to the pseudo-continuum opacity created by the thick line forest which blocks the flux in the UV and optical part of the spectrum. Increasingly more sophisticated treatments of the process of flux blocking in the UV (line blocking) are discussed. The necessity of treating the far-UV flux correctly is demonstrated. Line blocking in the region 800-1300A reduces the photoionization from the excited levels of several important ions (e.g. Fe II, Co II, Si II, Ca II), thus decreasing the overall degree of ionization. This effect is clearly seen in the synthetic emergent spectra. Synthetic spectra obtained with the various methods adopted for line blocking are shown, and compared to one another. When line blocking is properly treated, the synthetic spectrum reproduces well the spectrum of the `normal' SN Ia 1992A from the UV to the near-IR.

  15. 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

  16. 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.

  17. Finite difference time domain electroacoustic model for synthetic jet actuators including nonlinear flow resistance.

    PubMed

    Kooijman, Gerben; Ouweltjes, Okke

    2009-04-01

    A lumped element electroacoustic model for a synthetic jet actuator is presented. The model includes the nonlinear flow resistance associated with flow separation and employs a finite difference scheme in the time domain. As opposed to more common analytical frequency domain electroacoustic models, in which the nonlinear resistance can only be considered as a constant, it allows the calculation of higher harmonics, i.e., distortion components, generated as a result of this nonlinear resistance. Model calculations for the time-averaged momentum flux of the synthetic jet as well as the radiated sound power spectrum are compared to experimental results for various configurations. It is shown that a significantly improved prediction of the momentum flux-and thus flow velocity-of the jet is obtained when including the nonlinear resistance. Here, the current model performs slightly better than an analytical model. For the power spectrum of radiated sound, a reasonable agreement is obtained when assuming a plausible slight asymmetry in the nonlinear resistance. However, results suggest that loudspeaker nonlinearities play a significant role as well in the generation of the first few higher harmonics.

  18. Expression optimization and synthetic gene networks in cell-free systems.

    PubMed

    Karig, David K; Iyer, Sukanya; Simpson, Michael L; Doktycz, Mitchel J

    2012-04-01

    Synthetic biology offers great promise to a variety of applications through the forward engineering of biological function. Most efforts in this field have focused on employing living cells, yet cell-free approaches offer simpler and more flexible contexts. Here, we evaluate cell-free regulatory systems based on T7 promoter-driven expression by characterizing variants of TetR and LacI repressible T7 promoters in a cell-free context and examining sequence elements that determine expression efficiency. Using the resulting constructs, we then explore different approaches for composing regulatory systems, leading to the implementation of inducible negative feedback in Escherichia coli extracts and in the minimal PURE system, which consists of purified proteins necessary for transcription and translation. Despite the fact that negative feedback motifs are common and essential to many natural and engineered systems, this simple building block has not previously been implemented in a cell-free context. As a final step, we then demonstrate that the feedback systems developed using our cell-free approach can be implemented in live E. coli as well, illustrating the potential for using cell-free expression to fast track the development of live cell systems in synthetic biology. Our quantitative cell-free component characterizations and demonstration of negative feedback embody important steps on the path to harnessing biological function in a bottom-up fashion.

  19. 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

  20. Full Waveform 3D Synthetic Seismic Algorithm for 1D Layered Anelastic Models

    NASA Astrophysics Data System (ADS)

    Schwaiger, H. F.; Aldridge, D. F.; Haney, M. M.

    2007-12-01

    Numerical calculation of synthetic seismograms for 1D layered earth models remains a significant aspect of amplitude-offset investigations, surface wave studies, microseismic event location approaches, and reflection interpretation or inversion processes. Compared to 3D finite-difference algorithms, memory demand and execution time are greatly reduced, enabling rapid generation of seismic data within workstation or laptop computational environments. We have developed a frequency-wavenumber forward modeling algorithm adapted to realistic 1D geologic media, for the purpose of calculating seismograms accurately and efficiently. The earth model consists of N layers bounded by two halfspaces. Each layer/halfspace is a homogeneous and isotropic anelastic (attenuative and dispersive) solid, characterized by a rectangular relaxation spectrum of absorption mechanisms. Compressional and shear phase speeds and quality factors are specified at a particular reference frequency. Solution methodology involves 3D Fourier transforming the three coupled, second- order, integro-differential equations for particle displacements to the frequency-horizontal wavenumber domain. An analytic solution of the resulting ordinary differential system is obtained. Imposition of welded interface conditions (continuity of displacement and stress) at all interfaces, as well as radiation conditions in the two halfspaces, yields a system of 6(N+1) linear algebraic equations for the coefficients in the ODE solution. An optimized inverse 2D Fourier transform to the space domain gives the seismic wavefield on a horizontal plane. Finally, three-component seismograms are obtained by accumulating frequency spectra at designated receiver positions on this plane, followed by a 1D inverse FFT from angular frequency ω to time. Stress-free conditions may be applied at the top or bottom interfaces, and seismic waves are initiated by force or moment density sources. Examples reveal that including attenuation

  1. 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.

  2. 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.

  3. Developing an Automated Machine Learning Marine Oil Spill Detection System with Synthetic Aperture Radar

    NASA Astrophysics Data System (ADS)

    Pinales, J. C.; Graber, H. C.; Hargrove, J. T.; Caruso, M. J.

    2016-02-01

    Previous studies have demonstrated the ability to detect and classify marine hydrocarbon films with spaceborne synthetic aperture radar (SAR) imagery. The dampening effects of hydrocarbon discharges on small surface capillary-gravity waves renders the ocean surface "radar dark" compared with the standard wind-borne ocean surfaces. Given the scope and impact of events like the Deepwater Horizon oil spill, the need for improved, automated and expedient monitoring of hydrocarbon-related marine anomalies has become a pressing and complex issue for governments and the extraction industry. The research presented here describes the development, training, and utilization of an algorithm that detects marine oil spills in an automated, semi-supervised manner, utilizing X-, C-, or L-band SAR data as the primary input. Ancillary datasets include related radar-borne variables (incidence angle, etc.), environmental data (wind speed, etc.) and textural descriptors. Shapefiles produced by an experienced human-analyst served as targets (validation) during the training portion of the investigation. Training and testing datasets were chosen for development and assessment of algorithm effectiveness as well as optimal conditions for oil detection in SAR data. The algorithm detects oil spills by following a 3-step methodology: object detection, feature extraction, and classification. Previous oil spill detection and classification methodologies such as machine learning algorithms, artificial neural networks (ANN), and multivariate classification methods like partial least squares-discriminant analysis (PLS-DA) are evaluated and compared. Statistical, transform, and model-based image texture techniques, commonly used for object mapping directly or as inputs for more complex methodologies, are explored to determine optimal textures for an oil spill detection system. The influence of the ancillary variables is explored, with a particular focus on the role of strong vs. weak wind forcing.

  4. Flow Physics of Synthetic Jet Interactions on a Sweptback Model with a Control Surface

    NASA Astrophysics Data System (ADS)

    Monastero, Marianne; Amitay, Michael

    2016-11-01

    Active flow control using synthetic jets can be used on aerodynamic surfaces to improve performance and increase fuel efficiency. The flowfield resulting from the interaction of the jets with a separated crossflow with a spanwise component must be understood to determine actuator spacing for aircraft integration. The current and previous work showed adjacent synthetic jets located upstream of a control surface hingeline on a sweptback model interact with each other under certain conditions. Whether these interactions are constructive or destructive is dependent on the spanwise spacing of the jets, the severity of separation over the control surface, and the magnitude of the spanwise flow. Measuring and understanding the detailed flow physics of the flow structures emanating from the synthetic jet orifices and their interactions with adjacent jets of varying spacings is the focus of this work. Wind tunnel experiments were conducted at the Rensselaer Polytechnic Institute Subsonic Wind Tunnel using stereo particle image velocimetry (SPIV) and pressure measurements to study the effect that varying the spanwise spacing has on the overall performance. Initial SPIV data gave insight into defining and understanding the mechanisms behind the beneficial or detrimental jets interactions.

  5. 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.

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

    PubMed Central

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

    2017-01-01

    Current animal models for the evaluation of synthetic grafts are lacking many of the molecular tools and transgenic studies available to other branches of biology. A mouse model of vascular grafting would allow for the study of molecular mechanisms of graft failure, including in the context of clinically relevant disease states. In this study, we comprehensively characterise a sutureless grafting model which facilitates the evaluation of synthetic grafts in the mouse carotid artery. Using conduits electrospun from polycaprolactone (PCL) we show the gradual development of a significant neointima within 28 days, found to be greatest at the anastomoses. Histological analysis showed temporal increases in smooth muscle cell and collagen content within the neointima, demonstrating its maturation. Endothelialisation of the PCL grafts, assessed by scanning electron microscopy (SEM) analysis and CD31 staining, was near complete within 28 days, together replicating two critical aspects of graft performance. To further demonstrate the potential of this mouse model, we used longitudinal non-invasive tracking of bone-marrow mononuclear cells from a transgenic mouse strain with a dual reporter construct encoding both luciferase and green fluorescent protein (GFP). This enabled characterisation of mononuclear cell homing and engraftment to PCL using bioluminescence imaging and histological staining over time (7, 14 and 28 days). We observed peak luminescence at 7 days post-graft implantation that persisted until sacrifice at 28 days. Collectively, we have established and characterised a high-throughput model of grafting that allows for the evaluation of key clinical drivers of graft performance. PMID:28355300

  7. 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.

  8. Coherence estimation in synthetic aperture radar data based on speckle noise modeling.

    PubMed

    López-Martínez, Carlos; Pottier, Eric

    2007-02-01

    In the past we proposed a multidimensional speckle noise model to which we now include systematic phase variation effects. This extension makes it possible to define what is believed to be a novel coherence model able to identify the different sources of bias when coherence is estimated on multidimensional synthetic radar aperture (SAR) data. On the one hand, low coherence biases are basically due to the complex additive speckle noise component of the Hermitian product of two SAR images. On the other hand, the availability of the coherence model permits us to quantify the bias due to topography when multilook filtering is considered, permitting us to establish the conditions upon which information may be estimated independently of topography. Based on the coherence model, two coherence estimation approaches, aiming to reduce the different biases, are proposed. Results with simulated and experimental polarimetric and interferometric SAR data illustrate and validate both, the coherence model and the coherence estimation algorithms.

  9. Distributed and collaborative synthetic environments

    NASA Technical Reports Server (NTRS)

    Bajaj, Chandrajit L.; Bernardini, Fausto

    1995-01-01

    Fast graphics workstations and increased computing power, together with improved interface technologies, have created new and diverse possibilities for developing and interacting with synthetic environments. A synthetic environment system is generally characterized by input/output devices that constitute the interface between the human senses and the synthetic environment generated by the computer; and a computation system running a real-time simulation of the environment. A basic need of a synthetic environment system is that of giving the user a plausible reproduction of the visual aspect of the objects with which he is interacting. The goal of our Shastra research project is to provide a substrate of geometric data structures and algorithms which allow the distributed construction and modification of the environment, efficient querying of objects attributes, collaborative interaction with the environment, fast computation of collision detection and visibility information for efficient dynamic simulation and real-time scene display. In particular, we address the following issues: (1) A geometric framework for modeling and visualizing synthetic environments and interacting with them. We highlight the functions required for the geometric engine of a synthetic environment system. (2) A distribution and collaboration substrate that supports construction, modification, and interaction with synthetic environments on networked desktop machines.

  10. Design and performance of a small-animal imaging system using synthetic collimation

    NASA Astrophysics Data System (ADS)

    Havelin, R. J.; Miller, B. W.; Barrett, H. H.; Furenlid, L. R.; Murphy, J. M.; Dwyer, R. M.; Foley, M. J.

    2013-05-01

    This work outlines the design and construction of a single-photon emission computed tomography imaging system based on the concept of synthetic collimation. A focused multi-pinhole collimator is constructed using rapid-prototyping and casting techniques. The collimator projects the centre of the field of view (FOV) through 46 pinholes when the detector is adjacent to the collimator, with the number reducing towards the edge of the FOV. The detector is then moved further from the collimator to increase the magnification of the system. The object distance remains constant, and each new detector distance is a new system configuration. The level of overlap of the pinhole projections increases as the system magnification increases, but the number of projections subtended by the detector is reduced. There is no rotation in the system; a single tomographic angle is used in each system configuration. Image reconstruction is performed using maximum-likelihood expectation-maximization and an experimentally measured system matrix. The system matrix is measured for each configuration on a coarse grid, using a point source. The pinholes are individually identified and tracked, and a Gaussian fit is made to each projection. The coefficients of these fits are used to interpolate the system matrix. The system is validated experimentally with a hot-rod phantom. The Fourier crosstalk matrix is also measured to provide an estimate of the average spatial resolution along each axis over the entire FOV. The 3D synthetic-collimator image is formed by estimating the activity distribution within the FOV and summing the activities in the voxels along the axis perpendicular to the collimator face.

  11. 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.

  12. Development of a unique 3D interaction model of endogenous and synthetic peripheral benzodiazepine receptor ligands

    NASA Astrophysics Data System (ADS)

    Cinone, Nunzia; Höltje, Hans-Dieter; Carotti, Angelo

    2000-11-01

    Different classes of Peripheral-type Benzodiazepine Receptor (PBR) ligands were examined and common structural elements were detected and used to develop a rational binding model based on energetically allowed ligand conformations. Two lipophilic regions and one electrostatic interaction site are essential features for high affinity ligand binding, while a further lipophilic region plays an important modulator role. A comparative molecular field analysis, performed over 130 PBR ligands by means of the GRID/GOLPE methodology, led to a PLS model with both high fitting and predictive values (r2 = 0.898, Q2 = 0.761). The outcome from the 3D QSAR model and the GRID interaction fields computed on the putative endogenous PBR ligands DBI (Diazepam Binding Inhibitor) and TTN (Tetracontatetraneuropeptide) was used to identify the amino acids most probably involved in PBR binding. Three amino acids, bearing lipophilic side chains, were detected in DBI (Phe49, Leu47 and Met46) and in TTN (Phe33, Leu31 and Met30) as likely residues underlying receptor binding. Moreover, a qualitative comparison of the molecular electrostatic potentials of DBI, TTN and selected synthetic ligands indicated also similar electronic properties. Convergent results from the modeling studies of synthetic and endogenous ligands suggest a common binding mode to PBRs. This may help the rational design of new high affinity PBR ligands.

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

    PubMed

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

    2013-08-01

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

  14. Single channel conductance modeling of the peptide alamethicin in synthetically formed bilayers

    NASA Astrophysics Data System (ADS)

    Creasy, M. Austin; Leo, Donald J.

    2011-04-01

    Bilayers are synthetically made cell membranes that are used to study cell membrane properties and make functional devices that incorporate inherent properties of the cell membranes. Lipids and proteins are two of the main components of a cell membrane. Lipids provide the structure of the membrane in the form of two leaflets or layers that are held together by the amphiphilic interaction between the lipids and water. Proteins are made from a combination of amino acids and the properties of these proteins are dependent on the amino acid sequence. Some proteins are antibiotics and can easily self insert into the membrane of a cell or into a synthetically formed bilayer. The peptide alamethicin is one such antibiotic that easily inserts into a bilayer and changes the conductance properties of the bilayer. Analytical models of the conductance change with respect to the potential and other variables across the bilayer follows the nonlinear conductance changes seen with the incorporation of the peptide in a bilayer. The individual channels formed by the peptide have been studied and the peptide has several discrete conductance levels. These discrete levels have been shown to be dependent on the potential across the bilayer and several other variables including the lipid variety. The conductance level for a single channel can change with time in a probabilistic fashion. This paper will model these discrete conductance levels of the peptide alamethicin and the model of the single channel conductance will be used to model the cumulative effect of multiple channels within a bilayer.

  15. 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.

  16. 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

  17. 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.

  18. The nuclear uptake and retention of a synthetic progestin in the cardiovascular system of the baboon.

    PubMed

    Sheridan, P J; McGill, H C

    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 we examined the nuclear uptake and retention of a synthetic progestin 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 [3H]ORG 2058 (16 alpha-ethyl-21-hydroxy-19-nor-[6,7-3H]pregn-4-ene-3,20-dione) or with [3H] 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.

  19. 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.

  20. Synthetic peptides as tools for diagnosis and therapeutic strategies to treat systemic lupus erythematous.

    PubMed

    Muller, Sylviane

    2012-09-01

    Synthetic peptides can advantageously replace cognate proteins in solid-phase assays designed to help diagnosing autoimmune diseases. They can also represent essential tools for the discovery, pre-clinical and pharmaceutical development of therapeutics designed to attenuate these multifactorial and polymorphic diseases. We comment here on the peptide P140 able to delay the development of lupus in mouse models that spontaneously develop the disease and that has been evaluated in multicenter double-blind phase IIb clinical trials including lupus patients. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology.

    PubMed

    Sun, Zachary Z; Hayes, Clarmyra A; Shin, Jonghyeon; Caschera, Filippo; Murray, Richard M; Noireaux, Vincent

    2013-09-16

    Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform. This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environment for synthetic biology. To achieve the latter goal, cell-free expression systems that preserve endogenous Escherichia coli transcription-translation mechanisms are able to more accurately reflect in vivo cellular dynamics than those based on T7 RNA polymerase transcription. We describe the preparation and execution of an efficient endogenous E. coli based transcription-translation (TX-TL) cell-free expression system that can produce equivalent amounts of protein as T7-based systems at a 98% cost reduction to similar commercial systems. The preparation of buffers and crude cell extract are described, as well as the execution of a three tube TX-TL reaction. The entire protocol takes five days to prepare and yields enough material for up to 3000 single reactions in one preparation. Once prepared, each reaction takes under 8 hr from setup to data collection and analysis. Mechanisms of regulation and transcription exogenous to E. coli, such as lac/tet repressors and T7 RNA polymerase, can be supplemented. Endogenous properties, such as mRNA and DNA degradation rates, can also be adjusted. The TX-TL cell-free expression system has been demonstrated for large-scale circuit assembly, exploring biological phenomena, and expression of proteins under both T7- and endogenous promoters. Accompanying mathematical models are available. The resulting system has unique applications in synthetic biology as a prototyping environment, or "TX-TL biomolecular breadboard."

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

    NASA Astrophysics Data System (ADS)

    Tsvetkov, Vladimir B.; Serbin, Alexander V.

    2014-06-01

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

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

    PubMed Central

    Pickup, Brian A.; Thomson, Scott L.

    2010-01-01

    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. PMID:20815428

  4. 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

  5. Synthetic Scene Generation of the Stennis V and V Target Range for the Calibration of Remote Sensing Systems

    NASA Technical Reports Server (NTRS)

    Cao, Chang-Yong; Blonski, Slawomir; Ryan, Robert; Gasser, Jerry; Zanoni, Vicki

    1999-01-01

    The verification and validation (V&V) target range developed at Stennis Space Center is a useful test site for the calibration of remote sensing systems. In this paper, we present a simple algorithm for generating synthetic radiance scenes or digital models of this target range. The radiation propagation for the target in the solar reflective and thermal infrared spectral regions is modeled using the atmospheric radiative transfer code MODTRAN 4. The at-sensor, in-band radiance and spectral radiance for a given sensor at a given altitude is predicted. Software is developed to generate scenes with different spatial and spectral resolutions using the simulated at-sensor radiance values. The radiometric accuracy of the simulation is evaluated by comparing simulated with AVIRIS acquired radiance values. The results show that in general there is a good match between AVIRIS sensor measured and MODTRAN predicted radiance values for the target despite the fact that some anomalies exist. Synthetic scenes provide a cost-effective way for in-flight validation of the spatial and radiometric accuracy of the data. Other applications include mission planning, sensor simulation, and trade-off analysis in sensor design.

  6. Synthetic biology for therapeutic applications.

    PubMed

    Abil, Zhanar; Xiong, Xiong; Zhao, Huimin

    2015-02-02

    Synthetic biology is a relatively new field with the key aim of designing and constructing biological systems with novel functionalities. Today, synthetic biology devices are making their first steps in contributing new solutions to a number of biomedical challenges, such as emerging bacterial antibiotic resistance and cancer therapy. This review discusses some synthetic biology approaches and applications that were recently used in disease mechanism investigation and disease modeling, drug discovery and production, as well as vaccine development and treatment of infectious diseases, cancer, and metabolic disorders.

  7. Synthetic Biology for Therapeutic Applications

    PubMed Central

    2015-01-01

    Synthetic biology is a relatively new field with the key aim of designing and constructing biological systems with novel functionalities. Today, synthetic biology devices are making their first steps in contributing new solutions to a number of biomedical challenges, such as emerging bacterial antibiotic resistance and cancer therapy. This review discusses some synthetic biology approaches and applications that were recently used in disease mechanism investigation and disease modeling, drug discovery and production, as well as vaccine development and treatment of infectious diseases, cancer, and metabolic disorders. PMID:25098838

  8. 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

  9. Statistical-physical model for foliage clutter in ultra-wideband synthetic aperture radar images.

    PubMed

    Banerjee, Amit; Chellappa, Rama

    2003-01-01

    Analyzing foliage-penetrating (FOPEN) ultra-wideband synthetic aperture radar (SAR) images is a challenging problem owing to the noisy and impulsive nature of foliage clutter. Indeed, many target-detection algorithms for FOPEN SAR data are characterized by high false-alarm rates. In this work, a statistical-physical model for foliage clutter is proposed that explains the presence of outliers in the data and suggests the use of symmetric alpha-stable (SalphaS) distributions for accurate clutter modeling. Furthermore, with the use of general assumptions of the noise sources and propagation conditions, the proposed model relates the parameters of the SalphaS model to physical parameters such as the attenuation coefficient and foliage density.

  10. Synthetic ultrashort cationic lipopeptides induce systemic plant defense responses against bacterial and fungal pathogens.

    PubMed

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

    2009-08-01

    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.

  11. 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.

  12. Effects of synthetic androgens on liver function using the rabbit as a model.

    PubMed

    Hild, Sheri Ann; Attardi, Barbara J; Koduri, Sailaja; Till, Bruce A; Reel, Jerry R

    2010-01-01

    The objective of this study was to determine whether the rabbit was a suitable model to test new synthetic androgens for potential liver toxicity within a short dosing interval. Adult male rabbits were dosed orally daily on days 0-13 with 17α-methyltestosterone (MT) as a positive control and testosterone (T) as a negative control to validate this model. Synthetic androgens tested were: 7α-methyl-19-nortestosterone (MENT), dimethandrolone-undecanoate (DMAU), and 11β-methyl-19-nortestosterone-17β-dodecylcarbonate (11β-MNTDC). Serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma glutamyl transpeptidase (GGT), and sorbitol dehydrogenase (SDH), as well as clearance of intravenous injected bromsulfonphthalein (BSP) from serum on days 0, 7, and 14, were determined. As expected, T (10 mg/kg/d) did not adversely affect BSP retention or serum liver enzymes. MT (10 mg/kg/d) increased BSP retention, and AST, ALT, GGT, and SDH levels, indicating that this model could detect androgens known to be hepatotoxic. DMAU and MENT (10 mg/kg/d) increased BSP retention and all 4 serum liver enzymes as well, but the effects were less than those observed with MT at the same dose. All parameters returned to baseline 2 weeks after cessation of dosing. 11β-MNTDC at 10 mg/kg/d did not have an effect on BSP retention or liver enzymes, but a slight increase in serum GGT levels was observed in rabbits treated with 25 mg/kg/d. For the androgens that exhibited liver toxicity at 10 mg/kg/d (MT, DMAU, and MENT), a no-observed-effect level of 1 mg/kg/d was established. Overall ranking of the synthetic androgens from most to least hepatotoxic on the basis of percent BSP retention was: MT & DMAU > MENT > 11β-MNTDC. Hence, the rabbit appears to be a promising model for detection of potential liver toxicity by synthetic androgens using BSP clearance and serum liver enzyme levels as early indicators of injury.

  13. Effects of Synthetic Androgens on Liver Function Using the Rabbit as a Model*†

    PubMed Central

    Hild, Sheri Ann; Attardi, Barbara J.; Koduri, Sailaja; Till, Bruce A.; Reel, Jerry R.

    2010-01-01

    The objective of this study was to determine if the rabbit was a suitable model to test new synthetic androgens for potential liver toxicity within a short dosing interval. Adult male rabbits were dosed orally daily on days 0–13 with 17α-methyltestosterone (MT), as a positive control, and testosterone (T), as a negative control, to validate this model. Synthetic androgens tested were: 7α-methyl-19-nortestosterone (MENT), dimethandrolone-undecanoate (DMAU), and 11β-methyl-19-nortestosterone-17β-dodecylcarbonate (11β-MNTDC). Serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma glutamyl transpeptidase (GGT), and sorbitol dehydrogenase (SDH), as well as clearance of intravenous injected bromsulfonphthalein (BSP) from serum on days 0, 7 and 14, were determined. As expected, T (10 mg/kg/day) did not adversely affect BSP retention or serum liver enzymes. MT (10 mg/kg/day) increased BSP retention, and AST, ALT, GGT, and SDH levels indicating that this model could detect androgens known to be hepatotoxic. DMAU and MENT (10 mg/kg/day), increased BSP retention, and all 4 serum liver enzymes as well, but the effects were less than those observed with MT at the same dose. All parameters returned to baseline 2 weeks after cessation of dosing. 11β-MNTDC at 10 mg/kg/day did not have an effect on BSP retention or liver enzymes, but a slight increase in serum GGT levels was observed in rabbits treated with 25 mg/kg/day. For the androgens that exhibited liver toxicity at 10 mg/kg/day (MT, DMAU, and MENT), a no observed effect level (NOEL) of 1 mg/kg/day was established. Overall ranking of the synthetic androgens from most to least hepatotoxic based on %BSP retention was: MT ≫ DMAU > MENT > 11β-MNTDC. Hence, the rabbit appears to be a promising model for detection of potential liver toxicity by synthetic androgens using BSP clearance and serum liver enzyme levels as early indicators of injury. PMID:20378929

  14. A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes.

    PubMed

    Gorochowski, Thomas E; Avcilar-Kucukgoze, Irem; Bovenberg, Roel A L; Roubos, Johannes A; Ignatova, Zoya

    2016-07-15

    Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here, we develop a minimal model of ribosome allocation dynamics capturing the demands on translation when expressing a synthetic construct together with endogenous genes required for the maintenance of cell physiology. Critically, it contains three key variables related to design parameters of the synthetic construct covering transcript abundance, translation initiation rate, and elongation time. We show that model-predicted changes in ribosome allocation closely match experimental shifts in synthetic protein expression rate and cellular growth. Intriguingly, the model is also able to accurately infer transcript levels and translation times after further exposure to additional ambient stress. Our results demonstrate that a simple model of resource allocation faithfully captures the redistribution of protein synthesis resources when faced with the burden of synthetic gene expression and environmental stress. The tractable nature of the model makes it a versatile tool for exploring the guiding principles of efficient heterologous expression and the indirect interactions that can arise between synthetic circuits and their host chassis because of competition for shared translational resources.

  15. 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.

  16. 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

  17. Synthetic aperture radar image segmentation based on edge-region active contour model

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Wen, Xianbin; Xu, Haixia; Meng, Qingxia

    2016-07-01

    An energy functional is proposed based on an edge-region active contour model for synthetic aperture radar (SAR) image segmentation. The proposed energy functional not only has a desirable property to process inhomogeneous regions in SAR images, but also shows satisfactory convergence speed. Our proposed energy functional consists of two main energy terms: an edge-region term and a regularization term. The edge-region term is derived from a Gamma model and gradient term model, which can process the speckle noises and drive the motion of the curves toward desired locations. The regularization term is not only able to maintain a desired shape of the evolution curves but also has a strong smoothing curve effect and avoid the occurrence of small, isolated regions in the final segmentation. Finally, the gradient descent flow method is introduced for minimizing our energy functional. A desirable feature of the proposed method is that it is not sensitive to the contour initialization. Compared with other methods, experimental results show that the proposed approach has promising edge detection results on the synthetic and real SAR images.

  18. 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

  19. Lures for red palm weevil trapping systems: aggregation pheromone and synthetic kairomone.

    PubMed

    Vacas, Sandra; Melita, Ourania; Michaelakis, Antonios; Milonas, Panagiotis; Minuz, Roxana; Riolo, Paola; Abbass, Mohamed Kamal; Lo Bue, Paolo; Colazza, Stefano; Peri, Ezio; Soroker, Victoria; Livne, Yaara; Primo, Jaime; Navarro-Llopis, Vicente

    2017-01-01

    The optimisation of the lure is essential for the implementation of trapping systems to control insect pests. In this work, the response of the red palm weevil (RPW), Rhynchophorus ferrugineus Olivier, to increasing emission rates of its aggregation pheromone (ferrugineol) and the efficacy of a convenient synthetic kairomone based on fermentation odours (ethyl acetate and ethanol) have been evaluated in different years and locations along the Mediterranean basin. In general, although capture data and emission had noticeable variability among locations, significantly fewer RPW were captured in pyramidal Picusan® traps with the lowest ferrugineol emission rates tested (0.6-3.8 mg day(-1) ). Captures increased rapidly with ferrugineol emission up to 4-5 mg day(-1) ; then, higher emission rates did not improve or reduce captures, up to the highest emission rate tested of 50.9 mg day(-1) . Thus, there is no evidence of an optimum release rate corresponding to a maximum of RPW catches. Traps baited with the synthetic kairomone (1:3 ethyl acetate/ethanol) captured 1.4-2.2 times more total weevils than traps baited only with ferrugineol. Moreover, in most of the locations, the synthetic blend was at least as effective as the local coattractants used (plant material + molasses). Ferrugineol emission rate can vary in a wide range without significantly affecting RPW response. Coattractants based on fermenting compounds, ethyl acetate and ethanol, are able to improve the attractant level of ferrugineol and could be employed to replace non-standardised natural kairomones in RPW trapping systems after further optimisation of their proportions and doses. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  20. The design, computer modeling, solution structure, and biological evaluation of synthetic analogs of bryostatin 1

    PubMed Central

    Wender, Paul A.; DeBrabander, Jef; Harran, Patrick G.; Jimenez, Juan-Miguel; Koehler, Michael F. T.; Lippa, Blaise; Park, Cheol-Min; Siedenbiedel, Carsten; Pettit, George R.

    1998-01-01

    The bryostatins are a unique family of emerging cancer chemotherapeutic candidates isolated from marine bryozoa. Although the biochemical basis for their therapeutic activity is not known, these macrolactones exhibit high affinities for protein kinase C (PKC) isozymes, compete for the phorbol ester binding site on PKC, and stimulate kinase activity in vitro and in vivo. Unlike the phorbol esters, they are not first-stage tumor promoters. The design, computer modeling, NMR solution structure, PKC binding, and functional assays of a unique class of synthetic bryostatin analogs are described. These analogs (7b, 7c, and 8) retain the putative recognition domain of the bryostatins but are simplified through deletions and modifications in the C4-C14 spacer domain. Computer modeling of an analog prototype (7a) indicates that it exists preferentially in two distinct conformational classes, one in close agreement with the crystal structure of bryostatin 1. The solution structure of synthetic analog 7c was determined by NMR spectroscopy and found to be very similar to the previously reported structures of bryostatins 1 and 10. Analogs 7b, 7c, and 8 bound strongly to PKC isozymes with Ki = 297, 3.4, and 8.3 nM, respectively. Control 7d, like the corresponding bryostatin derivative, exhibited weak PKC affinity, as did the derivative, 9, lacking the spacer domain. Like bryostatin, acetal 7c exhibited significant levels of in vitro growth inhibitory activity (1.8–170 ng/ml) against several human cancer cell lines, providing an important step toward the development of simplified, synthetically accessible analogs of the bryostatins. PMID:9618462

  1. Comparative evaluation of rivastigmine permeation from a transdermal system in the Franz cell using synthetic membranes and pig ear skin with in vivo-in vitro correlation.

    PubMed

    Simon, Alice; Amaro, Maria Inês; Healy, Anne Marie; Cabral, Lucio Mendes; de Sousa, Valeria Pereira

    2016-10-15

    In the present study, in vitro permeation experiments in a Franz diffusion cell were performed using different synthetic polymeric membranes and pig ear skin to evaluate a rivastigmine (RV) transdermal drug delivery system. In vitro-in vivo correlations (IVIVC) were examined to determine the best model membrane. In vitro permeation studies across different synthetic membranes and skin were performed for the Exelon(®) Patch (which contains RV), and the results were compared. Deconvolution of bioavailability data using the Wagner-Nelson method enabled the fraction of RV absorbed to be determined and a point-to-point IVIVC to be established. The synthetic membrane, Strat-M™, showed a RV permeation profile similar to that obtained with pig ear skin (R(2)=0.920). Studies with Strat-M™ resulted in a good and linear IVIVC (R(2)=0.991) when compared with other synthetic membranes that showed R(2) values less than 0.90. The R(2) for pig ear skin was 0.982. Strat-M™ membrane was the only synthetic membrane that adequately simulated skin barrier performance and therefore it can be considered to be a suitable alternative to human or animal skin in evaluating transdermal drug transport, potentially reducing the number of studies requiring human or animal samples. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Evaluation of radar backscattering models using L- and C-band synthetic aperture radar data

    NASA Astrophysics Data System (ADS)

    Tao, Liangliang; Li, Jing; Jiang, Jinbao; He, Shi; Cai, Qingkong; Chen, Xi

    2015-01-01

    Five surface backscattering models, including Oh, integral equation model (IEM), advanced integral equation model (AIEM), Dubois, and Shi models are selected to evaluate and reproduce synthetic aperture radar backscatter coefficients based on radar configuration and ground measurements at L- and C-bands. Regardless of bands or polarizations, the Oh model can attain a better performance among the five models with a root mean square error (RMSE) of about 2 dB, with the only exception being the AIEM and Shi models in VV polarization at the C-band. The Dubois model overestimates the radar signal and an underestimation is produced using the Shi model. The estimation accuracy of AIEM is significantly higher than that of IEM. Meanwhile, the performance of the scattering models in 0 to 7.6 cm is better than that in 0 to 20 cm. The frequency distribution of soil moisture over the field site approximates the normal distribution. Nevertheless, the estimated accuracy is not satisfactory for the inversion of AIEM. A site-specific calibration parameter is used at the C-band and improves the backscatter prediction for the AIEM. After calibration, the mean differences between the AIEM and RADARSAT-2 are nearly -1 dB with RMSEs of about 1 dB in the HH and VV polarizations. This work indicates that effective calibration factors can significantly improve the estimation accuracy and precisely implement soil moisture retrieval.

  3. 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

  4. Continuous system modeling

    NASA Technical Reports Server (NTRS)

    Cellier, Francois E.

    1991-01-01

    A comprehensive and systematic introduction is presented for the concepts associated with 'modeling', involving the transition from a physical system down to an abstract description of that system in the form of a set of differential and/or difference equations, and basing its treatment of modeling on the mathematics of dynamical systems. Attention is given to the principles of passive electrical circuit modeling, planar mechanical systems modeling, hierarchical modular modeling of continuous systems, and bond-graph modeling. Also discussed are modeling in equilibrium thermodynamics, population dynamics, and system dynamics, inductive reasoning, artificial neural networks, and automated model synthesis.

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

    NASA Astrophysics Data System (ADS)

    Fiorini, Rodolfo A.; Dacquino, Gianfranco

    2005-03-01

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

  6. 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.

  7. [Microbial model Halobacterium salinarum in screening of synthetic analogues of antibiotic turbomycin A with anticancer activity].

    PubMed

    Trenin, A S; Tsvigun, E A; Bychkova, O P; Lavrenov, S N

    2013-01-01

    The microbial test-system based on cultivation of Halobacterium salinarum developed earlier for screening inhibitors of sterol biosynthesis and proposed for screening anticancer antibiotics, proved to be efficient in revealing anticancer compounds among derivatives of tris(1-alkylindol-3-yl)methylium, synthetic analogues of antibiotic turbomycin A. Most of the methane sulfonate and chloride salts of such compounds, investigated with the help of the H. salinarum test-system, showed no activity (MIC>32 mcM), while several derivatives, containing N-butyl or N-pentyl substituents were rather active against the bacterial strain. The MICs of them against H. salinarum were 8 mcM for total and 1 mcM for partial inhibition of the bacterial growth. The results of the study correlated with the results of other investigations that revealed anticancer activity of such compounds in tumor cell cultures. Therefore, the H. salinarum test-system demonstrated its availability for screening compounds with anticancer activity.

  8. 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).

  9. 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.

  10. 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.

  11. Dynamic Changes in Local Protein Synthetic Machinery in Regenerating Central Nervous System Axons after Spinal Cord Injury.

    PubMed

    Sachdeva, Rahul; Farrell, Kaitlin; McMullen, Mary-Katharine; Twiss, Jeffery L; Houle, John D

    2016-01-01

    Intra-axonal localization of mRNAs and protein synthesis machinery (PSM) endows neurons with the capacity to generate proteins locally, allowing precise spatiotemporal regulation of the axonal response to extracellular stimuli. A number of studies suggest that this local translation is a promising target to enhance the regenerative capacity of damaged axons. Using a model of central nervous system (CNS) axons regenerating into intraspinal peripheral nerve grafts (PNGs) we established that adult regenerating CNS axons contain several different mRNAs and protein synthetic machinery (PSM) components in vivo. After lower thoracic level spinal cord transection, ascending sensory axons regenerate into intraspinal PNGs but axon growth is stalled when they reach the distal end of the PNG (3 versus 7 weeks after grafting, resp.). By immunofluorescence with optical sectioning of axons by confocal microscopy, the total and phosphorylated forms of PSMs are significantly lower in stalled compared with actively regenerating axons. Reinjury of these stalled axons increased axonal localization of the PSM proteins, indicative of possible priming for a subcellular response to axotomy. These results suggest that axons downregulate protein synthetic capacity as they cease growing, yet they retain the ability to upregulate PSM after a second injury.

  12. Dynamic Changes in Local Protein Synthetic Machinery in Regenerating Central Nervous System Axons after Spinal Cord Injury

    PubMed Central

    Sachdeva, Rahul; Farrell, Kaitlin; McMullen, Mary-Katharine; Twiss, Jeffery L.; Houle, John D.

    2016-01-01

    Intra-axonal localization of mRNAs and protein synthesis machinery (PSM) endows neurons with the capacity to generate proteins locally, allowing precise spatiotemporal regulation of the axonal response to extracellular stimuli. A number of studies suggest that this local translation is a promising target to enhance the regenerative capacity of damaged axons. Using a model of central nervous system (CNS) axons regenerating into intraspinal peripheral nerve grafts (PNGs) we established that adult regenerating CNS axons contain several different mRNAs and protein synthetic machinery (PSM) components in vivo. After lower thoracic level spinal cord transection, ascending sensory axons regenerate into intraspinal PNGs but axon growth is stalled when they reach the distal end of the PNG (3 versus 7 weeks after grafting, resp.). By immunofluorescence with optical sectioning of axons by confocal microscopy, the total and phosphorylated forms of PSMs are significantly lower in stalled compared with actively regenerating axons. Reinjury of these stalled axons increased axonal localization of the PSM proteins, indicative of possible priming for a subcellular response to axotomy. These results suggest that axons downregulate protein synthetic capacity as they cease growing, yet they retain the ability to upregulate PSM after a second injury. PMID:27375904

  13. 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

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

    PubMed

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

    2010-09-01

    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.

  15. 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

  16. 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.

  17. 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; Goodric, 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.

  18. 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.

  19. Flight tests of a helmet-mounted display synthetic visibility system

    NASA Technical Reports Server (NTRS)

    Yenni, Kenneth R.

    1990-01-01

    A short flight test program was conducted using the NASA Langley Research Center's B737 Advanced Transport Operating Systems (ATOPS) research airplane to determine if pilots could land a transport category airplane under visual meteorological conditions (VMC) by reference to a synthetic visibility system. No external guidance was to be used. The program was undertaken jointly by NASA and the McDonnel-Douglas Corporation. The airplane was fitted with forward-looking television cameras fixed in the nose. Inputs from the television cameras were mixed with internally generated symbology and displayed to the pilot on helmet-mounted eyepieces. The pilot task was to execute a visual approach and landing. Two NASA and two McDonnel-Douglas engineering test pilots participated in the program completing over 200 landings in a 32-hour test program. Landings accomplished with the helmet-mounted display (HMD) were compared with visual landings for each pilot.

  20. Synthetic Vision System Commercial Aircraft Flight Deck Display Technologies for Unusual Attitude Recovery

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence J., III; Ellis, Kyle E.; Arthur, Jarvis J.; Nicholas, Stephanie N.; Kiggins, Daniel

    2017-01-01

    A Commercial Aviation Safety Team (CAST) study of 18 worldwide loss-of-control accidents and incidents determined that the lack of external visual references was associated with a flight crew's loss of attitude awareness or energy state awareness in 17 of these events. Therefore, CAST recommended development and implementation of virtual day-Visual Meteorological Condition (VMC) display systems, such as synthetic vision systems, which can promote flight crew attitude awareness similar to a day-VMC environment. This paper describes the results of a high-fidelity, large transport aircraft simulation experiment that evaluated virtual day-VMC displays and a "background attitude indicator" concept as an aid to pilots in recovery from unusual attitudes. Twelve commercial airline pilots performed multiple unusual attitude recoveries and both quantitative and qualitative dependent measures were collected. Experimental results and future research directions under this CAST initiative and the NASA "Technologies for Airplane State Awareness" research project are described.

  1. Synthetic aperture radar image processing techniques for damage detection of FRP-concrete systems

    NASA Astrophysics Data System (ADS)

    Yu, Tzuyang

    2017-04-01

    Electromagnetic imaging enables researchers and engineers to assess the surface and subsurface condition of concrete structures using radar and microwave sensors. Among existing radar imaging methods, synthetic aperture radar (SAR) imaging offers flexible resolution for various purposes in condition assessment. In this paper, two novel SAR image processing techniques are reported for the subsurface condition assessment of FRP(fiber reinforced polymer)-strengthened concrete systems; mathematical morphology (MM) and the K-R-I transform. Glass FRP (GFRP) and carbon CFRP (CFRP) strengthened concrete cylinders are used as examples. From our experimental results, it is found that both techniques are capable of quantifying SAR images for condition assessment. It is also found that Euler's number and the coefficient of correlation of K-R-I curves of SAR images can be used for monitoring subsurface changes in FRP-concrete systems.

  2. 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.

  3. [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.

  4. A model for forming airborne synthetic aperture radar images of underground targets

    SciTech Connect

    Doerry, A.W.

    1994-01-01

    Synthetic Aperture Radar (SAR) from an airborne platform has been proposed for imaging targets beneath the earth`s surface. The propagation of the radar`s energy within the ground, however, is much different than in the earth`s atmosphere. The result is signal refraction, echo delay, propagation losses, dispersion, and volumetric scattering. These all combine to make SAR image formation from an airborne platform much more challenging than a surface imaging counterpart. This report treats the ground as a lossy dispersive half-space, and presents a model for the radar echo based on measurable parameters. The model is then used to explore various imaging schemes, and image properties. Dynamic range is discussed, as is the impact of loss on dynamic range. Modified window functions are proposed to mitigate effects of sidelobes of shallow targets overwhelming deeper targets.

  5. Identifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis

    PubMed Central

    Senthivel, Vivek Raj; Sturrock, Marc; Piedrafita, Gabriel; Isalan, Mark

    2016-01-01

    Nonlinear responses to signals are widespread natural phenomena that affect various cellular processes. Nonlinearity can be a desirable characteristic for engineering living organisms because it can lead to more switch-like responses, similar to those underlying the wiring in electronics. Steeper functions are described as ultrasensitive, and can be applied in synthetic biology by using various techniques including receptor decoys, multiple co-operative binding sites, and sequential positive feedbacks. Here, we explore the inherent non-linearity of a biological signaling system to identify functions that can potentially be exploited using cell genome engineering. For this, we performed genome-wide transcription profiling to identify genes with ultrasensitive response functions to Hepatocyte Growth Factor (HGF). We identified 3,527 genes that react to increasing concentrations of HGF, in Madin-Darby canine kidney (MDCK) cells, grown as cysts in 3D collagen cell culture. By fitting a generic Hill function to the dose-responses of these genes we obtained a measure of the ultrasensitivity of HGF-responsive genes, identifying a subset with higher apparent Hill coefficients (e.g. MMP1, TIMP1, SNORD75, SNORD86 and ERRFI1). The regulatory regions of these genes are potential candidates for future engineering of synthetic mammalian gene circuits requiring nonlinear responses to HGF signalling. PMID:27982133

  6. The Monitoring Case of Ground-Based Synthetic Aperture Radar with Frequency Modulated Continuous Wave System

    NASA Astrophysics Data System (ADS)

    Zhang, H. Y.; Zhai, Q. P.; Chen, L.; Liu, Y. J.; Zhou, K. Q.; Wang, Y. S.; Dou, Y. D.

    2017-09-01

    The features of the landslide geological disaster are wide distribution, variety, high frequency, high intensity, destructive and so on. It has become a natural disaster with harmful and wide range of influence. The technology of ground-based synthetic aperture radar is a novel deformation monitoring technology developed in recent years. The features of the technology are large monitoring area, high accuracy, long distance without contact and so on. In this paper, fast ground-based synthetic aperture radar (Fast-GBSAR) based on frequency modulated continuous wave (FMCW) system is used to collect the data of Ma Liuzui landslide in Chongqing. The device can reduce the atmospheric errors caused by rapidly changing environment. The landslide deformation can be monitored in severe weather conditions (for example, fog) by Fast-GBSAR with acquisition speed up to 5 seconds per time. The data of Ma Liuzui landslide in Chongqing are analyzed in this paper. The result verifies that the device can monitor landslide deformation under severe weather conditions.

  7. Synthetic jets based on micro magneto mechanical systems for aerodynamic flow control

    NASA Astrophysics Data System (ADS)

    Gimeno, L.; Talbi, A.; Viard, R.; Merlen, A.; Pernod, P.; Preobrazhensky, V.

    2010-07-01

    A magneto-mechanical micro-actuator providing an axisymmetric synthetic microjet for active flow control was designed, fabricated and characterized. The micro-actuator consists of an enclosed cavity with a small orifice in one face and a high flexible elastomeric (PDMS) membrane in the opposite one. The membrane vibration is achieved using a magnetic actuation chosen for its capacity for providing large out of plane displacements and forces necessary for the performances aimed for. The paper presents first numerical simulations of the flow performed during the design process in order to identify a general jet formation criterion and optimize the device's performances. The fabrication process of this micro-magneto-mechanical system (MMMS) is then briefly described. The full size of the device, including packaging and actuation, does not exceed 1 cm3. The evaluation of the performances of the synthetic jet with 600 µm orifice was performed. The results show that the optimum working point is in the frequency range 400-700 Hz which is in accordance with the frequency response of the magnet-membrane mechanical resonator. In this frequency range, the microjet reaches maximum speeds ranging from 25 m s-1 to 55 m s-1 for an electromagnetic power consumption of 500 mW. Finally the axial velocity transient and stream-wise behaviours in the near and far fields are reported and discussed.

  8. Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast

    PubMed Central

    McIsaac, R. Scott; Oakes, Benjamin L.; Wang, Xin; Dummit, Krysta A.; Botstein, David; Noyes, Marcus B.

    2013-01-01

    A general method for the dynamic control of single gene expression in eukaryotes, with no off-target effects, is a long-sought tool for molecular and systems biologists. We engineered two artificial transcription factors (ATFs) that contain Cys2His2 zinc-finger DNA-binding domains of either the mouse transcription factor Zif268 (9 bp of specificity) or a rationally designed array of four zinc fingers (12 bp of specificity). These domains were expressed as fusions to the human estrogen receptor and VP16 activation domain. The ATFs can rapidly induce a single gene driven by a synthetic promoter in response to introduction of an otherwise inert hormone with no detectable off-target effects. In the absence of inducer, the synthetic promoter is inactive and the regulated gene product is not detected. Following addition of inducer, transcripts are induced >50-fold within 15 min. We present a quantitative characterization of these ATFs and provide constructs for making their implementation straightforward. These new tools allow for the elucidation of regulatory network elements dynamically, which we demonstrate with a major metabolic regulator, Gcn4p. PMID:23275543

  9. Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.

    PubMed

    McIsaac, R Scott; Oakes, Benjamin L; Wang, Xin; Dummit, Krysta A; Botstein, David; Noyes, Marcus B

    2013-02-01

    A general method for the dynamic control of single gene expression in eukaryotes, with no off-target effects, is a long-sought tool for molecular and systems biologists. We engineered two artificial transcription factors (ATFs) that contain Cys(2)His(2) zinc-finger DNA-binding domains of either the mouse transcription factor Zif268 (9 bp of specificity) or a rationally designed array of four zinc fingers (12 bp of specificity). These domains were expressed as fusions to the human estrogen receptor and VP16 activation domain. The ATFs can rapidly induce a single gene driven by a synthetic promoter in response to introduction of an otherwise inert hormone with no detectable off-target effects. In the absence of inducer, the synthetic promoter is inactive and the regulated gene product is not detected. Following addition of inducer, transcripts are induced >50-fold within 15 min. We present a quantitative characterization of these ATFs and provide constructs for making their implementation straightforward. These new tools allow for the elucidation of regulatory network elements dynamically, which we demonstrate with a major metabolic regulator, Gcn4p.

  10. Impact of synthetic abyssal hill roughness on resolved motions in numerical global ocean tide models

    NASA Astrophysics Data System (ADS)

    Timko, Patrick G.; Arbic, Brian K.; Goff, John A.; Ansong, Joseph K.; Smith, Walter H. F.; Melet, Angélique; Wallcraft, Alan J.

    2017-04-01

    Global models of seafloor topography have incomplete and inconsistent resolution at horizontal wavelengths less than about 10-20 km, notably due to their inability to resolve abyssal hills in areas unsurveyed by ships (that is, about 90% of the global seafloor). We investigated the impact of this unresolved bottom roughness on global numerical simulations of the HYbrid Coordinate Ocean Model (HYCOM) that are forced exclusively by the M2 and K1 internal tides. Simulations were run with horizontal resolutions of 0.08° and 0.04°, 10 isopycnal layers in the vertical direction, and two versions of bathymetry: one derived from the SRTM30_PLUS global bathymetry model, and one merging SRTM30_PLUS with a synthetic fractal surface simulating the expected roughness of abyssal hills in the 2-10 km horizontal wavelength band. Power spectra of the two bathymetry versions diverge at wavenumbers of order 4*10-4 radians/m and higher (wavelengths of order 15 km and lower), with more pronounced differences evident on the 0.04° grid, as the 0.08° grid has a more limited ability to capture bathymetric details at the abyssal hill scale. Our simulations show an increase in the amount of kinetic and potential energy in higher vertical modes, especially in the 0.04° simulation, when the synthetic roughness is added. Adding abyssal hills to the 0.04° simulation increases the M2 kinetic energy for modes 3 and 4 by 12-18% and the potential energy by 5 - 15%. Adding abyssal hills to the 0.08° simulation yields a reduced, though still measurable, impact on simulated baroclinic tidal energies. Baroclinic tidal energy conversion rates increase by up to 16% in regions of high roughness, and by up to 3.4% in the global integral. The 3.4% increase in global conversion rates in the numerical simulations is less than the 10% increase computed from a linear analysis on a 0.008° grid because of the resolution limitations of the numerical simulations. The results obtained in the present study

  11. An Integrated Navigation System using GPS Carrier Phase for Real-Time Airborne Synthetic Aperture Radar (SAR)

    SciTech Connect

    Fellerhoff, J. Rick; Kim, Theodore J.; Kohler, Stewart M.

    1999-06-24

    A Synthetic Aperture Radar (SAR) requires accu- rate measurement of the motion of the imaging plat- form to produce well-focused images with minimal absolute position error. The motion measurement (MoMeas) system consists of a inertial measurement unit (IMU) and a P-code GPS receiver that outputs corrected ephemeris, L1 & L2 pseudoranges, and L1 & L2 carrier phase measurements. The unknown initial carrier phase biases to the GPS satellites are modeled as states in an extended Kalman filter and the resulting integrated navigation solution has po- sition errors that change slowly with time. Position error drifts less than 1- cm/sec have been measured from the SAR imagery for various length apertures.

  12. Evaluation of terrain models for the geocoding and terrain correction, of synthetic aperture radar (SAR) images

    USGS Publications Warehouse

    Wivell, C. E.; Steinwand, Daniel R.; Kelly, G. G.; Meyer, D.J.

    1992-01-01

    The variability of the resolutions and the presence of artifacts cause inaccurate correction of the terrain-induced geometric distortions in synthetic-aperture radar (SAR) images. To quantify the effects of these inaccuracies on SAR terrain correction, corrections of a Seasat SAR image were performed using a 1 degrees US Geological Survey (USGS) terrain model, a 7.5-min USGS terrain model, and a terrain model derived from stereoimagery acquired from SPOT. Geometric verifications of the corrected imagery showed that the resolution of the 1 degrees terrain model is not adequate to resolve many features in the Seasat image. Geometric verifications of images corrected with the two higher resolution terrain models showed localized errors as large as 52 m for mountain peaks. However, comparison of data corrected with those models shows that both produce results that differ by less than the resolution of either of them. Periodic artifacts observed in the terrain models translated to ground range differences of 18 m, which are well below the resolution of the SAR imagery.

  13. Chosen results of field tests of synthetic aperture radar system installed on board UAV

    NASA Astrophysics Data System (ADS)

    Kaniewski, Piotr; Komorniczak, Wojciech; Lesnik, Czeslaw; Cyrek, Jacek; Serafin, Piotr; Labowski, Michal; Wajszczyk, Bronislaw

    2017-04-01

    The paper presents a synthetic information on a UAV-based radar terrain imaging system, its purpose, structure and working principle as well as terrain images obtained from flight experiments. A SAR technology demonstrator has been built as a result of a research project conducted by the Military University of Technology and WB Electronics S.A. under the name WATSAR. The developed system allows to obtain high resolution radar images, both in on-line and off-line modes, independently of the light conditions over the observed area. The software developed for the system allows to determine geographic coordinates of the imaged objects with high accuracy. Four LFM-CW radar sensors were built during the project: two for S band and two for Ku band, working with different signal bandwidths. Acquired signals were processed with the TDC algorithm, which allowed for a number of analyses in order to evaluate the performance of the system. The impact of the navigational corrections on a SAR image quality was assessed as well. The research methodology of the in-flight experiments of the system is presented in the paper. The projects results show that the developed system may be implemented as an aid to tactical C4ISR systems.

  14. From Initial Models of Seismicity, Structure and Noise to Synthetic Seismograms for Mars

    NASA Astrophysics Data System (ADS)

    Ceylan, Savas; van Driel, Martin; Euchner, Fabian; Khan, Amir; Clinton, John; Krischer, Lion; Böse, Maren; Stähler, Simon; Giardini, Domenico

    2017-06-01

    The InSight mission will land a single seismic station on Mars in November 2018, and the resultant seismicity catalog will be a key component for studies aiming to understand the interior structure of the planet. Here, we present a preliminary version of the web services that will be used to distribute the event and station metadata in practice, employing synthetic seismograms generated for Mars using a catalog of expected seismicity. Our seismicity catalog consists of 120 events with double-couple source mechanisms only. We also provide Green's functions databases for a total of 16 structural models, which are constructed to reflect one-dimensional thin (30 km) and thick (80 km) Martian crust with varying seismic wave speeds and densities, combined with two different profiles for temperature and composition for the mantle. Both the Green's functions databases and the precomputed seismograms are accessible online. These new utilities allow the researchers to either download the precomputed synthetic waveforms directly, or produce customized data sets using any desired source mechanism and event distribution via our servers.

  15. [Application of entropy-weight TOPSIS model in synthetical quality evaluation of Angelica sinensis growing in Gansu Province].

    PubMed

    Gu, Zhi-rong; Wang, Ya-li; Sun, Yu-jing; Dind, Jun-xia

    2014-09-01

    To investigate the establishment and application methods of entropy-weight TOPSIS model in synthetical quality evaluation of traditional Chinese medicine with Angelica sinensis growing in Gansu Province as an example. The contents of ferulic acid, 3-butylphthalide, Z-butylidenephthalide, Z-ligustilide, linolic acid, volatile oil, and ethanol soluble extractive were used as an evaluation index set. The weights of each evaluation index were determined by information entropy method. The entropyweight TOPSIS model was established to synthetically evaluate the quality of Angelica sinensis growing in Gansu Province by Euclid closeness degree. The results based on established model were in line with the daodi meaning and the knowledge of clinical experience. The established model was simple in calculation, objective, reliable, and can be applied to synthetical quality evaluation of traditional Chinese medicine.

  16. Dual State/Rainfall Correction via Soil Moisture Assimilation for Improved Hydrologic Prediction - A Synthetic Study Using the VIC Model in the Arkansas-Red River Basin

    NASA Astrophysics Data System (ADS)

    Mao, Y.; Crow, W. T.; Nijssen, B.

    2016-12-01

    Accurate streamflow prediction based on hydrologic models requires accurate antecedent soil moisture conditions as well as realistic rainfall estimates. If soil moisture measurements are available, they presumably contain information about both. With the growing availability of satellite-based precipitation and soil moisture products, data assimilation techniques have been used to enhance both antecedent soil moisture states and rainfall to achieve more accurate streamflow prediction. One such approach is a dual state/rainfall correction framework, which assimilates soil moisture measurements into both hydrologic model states and rainfall estimates simultaneously to enhance pre-storm soil moisture conditions and within-storm rainfall totals.To date such approaches have only been applied to deterministic hydrologic prediction within relatively small (< 10,000 km2) hydrologic basins. In this study, we conducted a synthetic experiment in the 500,000 km2 Arkansas-Red River basin in the central United States, in which we applied such a dual system to a semi-distributed hydrologic model, the Variable Infiltration Capacity (VIC) model, at a sub-daily time step for multiple years at 1/8 degree resolution. We considered a VIC model realization as synthetic "truth" and added noise to the simulated true state to create synthetic soil moisture measurements. We then used a separate VIC realization, based on modified forcings and model states, as the "open-loop" results (i.e., baseline model run prior to any assimilation) into which the synthetic soil moisture measurements were assimilated. For the state correction part in the dual system, the synthetic measurements were assimilated into the open-loop states using an ensemble Kalman filtering (EnKF) approach, resulting in an ensemble of updated antecedent states. Separately, the soil moisture data was also assimilated into a simple water balance model using EnKF to obtain an ensemble of corrected rainfall estimates. The

  17. 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.

  18. A model to estimate the methane generation rate constant in sanitary landfills using fuzzy synthetic evaluation.

    PubMed

    Garg, Anurag; Achari, Gopal; Joshi, Ramesh C

    2006-08-01

    This paper presents a model using fuzzy synthetic evaluation to estimate the methane generation rate constant, k, for landfills. Four major parameters, precipitation, temperature, waste composition and landfill depth were used as inputs to the model. Whereas, these parameters are known to impact the methane generation, mathematical relationships between them and the methane generation rate constant required to estimate methane generation in landfills, are not known. In addition, the spatial variations of k within a landfill combined with the necessity of site-specific information to estimate its value, makes k one of the most elusive parameters in the accurate prediction of methane generation within a landfill. In this paper, a fuzzy technique was used to develop a model to predict the methane generation rate constant. The model was calibrated and verified using k values from 42 locations. Data from 10 sites were used to calibrate the model and the rest were used to verify it. The model predictions are reasonably accurate. A sensitivity analysis was also conducted to investigate the effect of uncertainty in the input parameters on the generation rate constant.

  19. Effect of Synthetic Jet Actuator Spacing on the Performance Enhancement of a Vertical Tail Model

    NASA Astrophysics Data System (ADS)

    Monastero, Marianne; Rathay, Nicholas; Whalen, Edward; Amitay, Michael

    2014-11-01

    The use of synthetic-jet-based active flow control to augment the side force produced by vertical tail models through rudder separation control was experimentally investigated in the Rensselaer Polytechnic Institute Subsonic Wind Tunnel. Increasing the side force generated by the vertical tail may lead to a reduction in tail size and, therefore, less drag and fuel consumption. Stereo particle image velocimetry and aerodynamic load data were acquired with a focus on the effect of non-dimensional spacing between jets on the resulting flowfield and forces for a 1/19th scale model based on a Boeing 767 commercial airplane. For some rudder deflections, differing results with active flow control were found when force data for the 1/19th scale model were compared to force data obtained on a larger, 1/9th scale model. Actuator spacing was varied and individual jet momentum coefficient was held constant for these experiments. These results show the need for more fundamental testing to understand why jets are beneficial or detrimental to the augmented side force and how those effects scale-up. A new model was designed to enable a fundamental study of the effect on the flowfield of various jet and model parameters such as sweep angle, jets spacing, rudder chord extent, and rudder deflection.

  20. Exploring hydrogeological controls on river and groundwater vulnerability to droughts using synthetic models

    NASA Astrophysics Data System (ADS)

    Carlier, Claire; Wirth, Stefanie B.; Cochand, Fabien; Hunkeler, Daniel; Brunner, Philip

    2017-04-01

    Characterising the vulnerability of watersheds to droughts is essential to guarantee water supply under changing climatic conditions. Numerous studies have analysed watershed processes under dry conditions focusing on surface flows. However, hydrological catchment dynamics, and especially river low-flows, are strongly dependent on the surrounding hydrogeological settings. We thus propose an integrated quantification of the impact of prolonged dry periods on both surface water and groundwater. To achieve this, we consider various catchment properties representative of a wide range of geological and topographical environments. The relationship between these physical parameters and low-flow dynamics in a catchment is highly complex, and no straightforward correlation can be obtained by analysing easily measurable catchment properties such as slope or main geological units. A modelling approach is therefore developed to systematically and independently quantify the control mechanisms of catchment parameters on river and groundwater dynamics. The physically based numerical model HydroGeoSphere is used, which simulates surface water and groundwater in a fully coupled way. More than 200 synthetic models are designed with systematically varying geometrical parameters such as river and hill slopes, as well as hydraulic conductivities and porosities of the main geological units. A clear correlation between the porous storage volume in a catchment and the resilience to drought of both streamflow and groundwater is observed. An attempt to link these results to real watersheds is made by analysing the flows, the geology and the hydrogeological properties of a selection of catchments. The validation of the synthetic results with observations will allow the development of drought sensitivity indicators applicable to both groundwater and river low-flows based solely on watershed physical properties.

  1. 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

  2. A novel view of modelling interactions between synthetic and biological polymers via docking

    NASA Astrophysics Data System (ADS)

    Tsvetkov, Vladimir B.; Serbin, Alexander V.

    2012-12-01

    Multipoint interactions between synthetic and natural polymers provide a promising platform for many topical applications, including therapeutic blockage of virus-specific targets. Docking may become a useful tool for modelling of such interactions. However, the rigid docking cannot be correctly applied to synthetic polymers with flexible chains. The application of flexible docking to these polymers as whole macromolecule ligands is also limited by too many possible conformations. We propose to solve this problem via stepwise flexible docking. Step 1 is docking of separate polymer components: (1) backbone units ( BU), multi-repeated along the chain, and (2) side groups ( SG) consisting of functionally active elements ( SG F ) and bridges ( SG B ) linking SG F with BU. At this step, probable binding sites locations and binding energies for the components are scored. Step 2 is docking of component-integrating models: [ BU] m , SG = SG F -SG B , BU-SG, BU-BU( SG) -BU, BU( SG) -[ BU] m -BU( SG), and [ BU var ( SG var )] m . Every modelling level yields new information, including how the linkage of various components influences on the ligand—target contacts positioning, orientation, and binding energy in step-by-step approximation to polymeric ligand motifs. Step 3 extrapolates the docking results to real-scale macromolecules. This approach has been demonstrated by studying the interactions between hetero-SG modified anionic polymers and the N-heptad repeat region tri-helix core of the human immunodeficiency virus type 1 ( HIV-1) envelope glycoprotein gp41, the key mediator of HIV-1 fusion during virus entry. The docking results are compared to real polymeric compounds, acting as HIV-1 entry inhibitors in vitro. This study clarifies the optimal macromolecular design for the viral fusion inhibition and drug resistance prevention.

  3. A novel view of modelling interactions between synthetic and biological polymers via docking.

    PubMed

    Tsvetkov, Vladimir B; Serbin, Alexander V

    2012-12-01

    Multipoint interactions between synthetic and natural polymers provide a promising platform for many topical applications, including therapeutic blockage of virus-specific targets. Docking may become a useful tool for modelling of such interactions. However, the rigid docking cannot be correctly applied to synthetic polymers with flexible chains. The application of flexible docking to these polymers as whole macromolecule ligands is also limited by too many possible conformations. We propose to solve this problem via stepwise flexible docking. Step 1 is docking of separate polymer components: (1) backbone units (BU), multi-repeated along the chain, and (2) side groups (SG) consisting of functionally active elements (SG(F)) and bridges (SG(B)) linking SG(F) with BU. At this step, probable binding sites locations and binding energies for the components are scored. Step 2 is docking of component-integrating models: [BU](m), SG = SG(F)-SG(B), BU-SG, BU-BU(SG)-BU, BU(SG)-[BU](m)-BU(SG), and [BU(var)(SG(var))](m). Every modelling level yields new information, including how the linkage of various components influences on the ligand-target contacts positioning, orientation, and binding energy in step-by-step approximation to polymeric ligand motifs. Step 3 extrapolates the docking results to real-scale macromolecules. This approach has been demonstrated by studying the interactions between hetero-SG modified anionic polymers and the N-heptad repeat region tri-helix core of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp41, the key mediator of HIV-1 fusion during virus entry. The docking results are compared to real polymeric compounds, acting as HIV-1 entry inhibitors in vitro. This study clarifies the optimal macromolecular design for the viral fusion inhibition and drug resistance prevention.

  4. 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.

  5. Design and Application of an Object Oriented Graphical Database Management System for Synthetic Environments

    DTIC Science & Technology

    1991-12-01

    development of the Database Generation System was also successful. In addition to providing an excellent platform for testing GDMS funtionality , it proved to...Format Several geometries are available for modeling objects in three- space. Procedural models, fractals, grammar -based models, particle systems

  6. Full-color autostereoscopic 3D display system using color-dispersion-compensated synthetic phase holograms.

    PubMed

    Choi, Kyongsik; Kim, Hwi; Lee, Byoungho

    2004-10-18

    A novel full-color autostereoscopic three-dimensional (3D) display system has been developed using color-dispersion-compensated (CDC) synthetic phase holograms (SPHs) on a phase-type spatial light modulator. To design the CDC phase holograms, we used a modified iterative Fourier transform algorithm with scaling constants and phase quantization level constraints. We obtained a high diffraction efficiency (~90.04%), a large signal-to-noise ratio (~9.57dB), and a low reconstruction error (~0.0011) from our simulation results. Each optimized phase hologram was synthesized with each CDC directional hologram for red, green, and blue wavelengths for full-color autostereoscopic 3D display. The CDC SPHs were composed and modulated by only one phase-type spatial light modulator. We have demonstrated experimentally that the designed CDC SPHs are able to generate full-color autostereoscopic 3D images and video frames very well, without any use of glasses.

  7. 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.

  8. Gene brushes on a chip: From crowding and the search problem to synthetic systems

    NASA Astrophysics Data System (ADS)

    Bar-Ziv, Roy

    2009-03-01

    We assemble DNA polymer brushes coding for entire genes on a surface by means of a new photolithographic approach. The gene density can be controlled from dilute to high density where the local concentration -- Megabase pairs per micron cubed -- is comparable to that in a bacterium. The gene brush, therefore, emulates the crowded medium of the cell, allowing us to study DNA transactions in vitro under native conditions. We find that transcription/translation from these gene brushes is highly sensitive to DNA density, orientation and composition. As a step towards multi-gene synthetic systems, we integrated on a chip two spatially separated gene brushes, and implemented a two-stage transcription/translation cascade.

  9. 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.

  10. Development of GRAS strains for nutraceutical production using systems and synthetic biology approaches: advances and prospects.

    PubMed

    Liu, Long; Guan, Ningzi; Li, Jianghua; Shin, Hyun-Dong; Du, Guocheng; Chen, Jian

    2017-03-01

    Nutraceuticals are food substances with medical and health benefits for humans. Limited by complicated procedures, high cost, low yield, insufficient raw materials, resource waste, and environment pollution, chemical synthesis and extraction are being replaced by microbial synthesis of nutraceuticals. Many microbial strains that are generally regarded as safe (GRAS) have been identified and developed for the synthesis of nutraceuticals, and significant nutraceutical production by these strains has been achieved. In this review, we systematically summarize recent advances in nutraceutical research in terms of physiological effects on health, potential applications, drawbacks of traditional production processes, characteristics of production strains, and progress in microbial fermentation. Recent advances in systems and synthetic biology techniques have enabled comprehensive understanding of GRAS strains and its wider applications. Thus, these microbial strains are promising cell factories for the commercial production of nutraceuticals.

  11. 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.

  12. 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.

  13. Thiophene-Fused Nickel Dithiolenes: A Synthetic Scaffold for Highly Delocalized π-Electron Systems.

    PubMed

    Amb, Chad M; Heth, Christopher L; Evenson, Sean J; Pokhodnya, Konstantin I; Rasmussen, Seth C

    2016-11-07

    A series of thiophene-fused nickel dithiolene complexes have been prepared via synthetic methods which allow the addition of peripheral aryl groups to the fused thiophene of the dithiolene ligand, thus providing access to a range of structural and electronic modifications to the dithiolene core. X-ray structural studies of the anionic complexes show that the peripheral aryl rings lie in near-perfect coplanarity to the dithiolene core and can form π-stacked columns with N-methylpyridinium cations. Density functional theory calculations show significant delocalization of the frontier orbital electron density into the peripheral aryl rings. The complexes exhibit tunable, intense near-IR (NIR) absorption in the range of 1076-1160 nm with molar absorptivity as high as 25100 M(-1) cm(-1) in solution. The electronic tunability as well as the desirable solid-state packing arrangements of these systems suggests significant potential as NIR-absorbing materials for optoelectronic applications.

  14. Synthetic Manipulation of Hybrid Perovskite Systems in Search of Novel and Enhanced Functionalities.

    PubMed

    Naphade, Rounak; Nagane, Satyawan; Bansode, Umesh; Tathavadekar, Mukta; Sadhanala, Aditya; Ogale, Satishchandra B

    2017-08-13

    Over the past few years the organic/Inorganic hybrid perovskite systems have emerged as a promising class of materials for photo-voltaic and electroluminescent thin film device applications, in view of their unique set of tunable optoelectronic properties. Importantly, these materials can be easily solution-processed at low temperatures and as such are amenable to facile molecular engineering. Thus, a variety of low dimensional forms and quantum structures of these materials can be obtained through strategic synthetic manipulations via small molecule incorporation or molecular ion doping. In this mini review, we specifically focus on these approaches and outline the possibilities of utilizing these for enhanced functionalities and newer application domains. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. 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

  16. Wavefront alignment research of segmented mirror synthetic aperture optical (SAO) system

    NASA Astrophysics Data System (ADS)

    Deng, Jian; An, Xiaoqiang; Tian, Hao

    2010-05-01

    Wavefront control technology and imaging experiment are introduced for a segmented mirror SAO system with deformable sub-mirrors. This system is a RC style with 300mm aperture, 4.5 F#, +/-0.4°FOV, 0.45~0.75μm wave band, and diffraction-limit design MTF. The primary mirror is composed by three sub-mirrors, with parabolic shape, and each deformable sub-mirror has 19 actuators to control and keep the surface shape, and 5 actuators to align sub-mirrors location in 5 degree of freedom. Interferometer is used to feed back and control exit wavefront error, and base on measurement and finite element analysis, location and quanitity of actuators are optimized, making the surface shape and misadjustment errors interact and compensate each other, and the synthetic system exit pupil wavefront error is controlled. The integrated exit pupil wavefront errors are gotten by ZYGO interferometer, and central FOV is 0.077λRMS, and edge FOV is 0.093λRMS. At the end, an imaging experiment is executed, and good results are obtained, which proves, the deformable sub-mirrors have the ability to meliorate alignment and the latter can retroact the former, and this relationship iterate make system exit pupil wavefront error convergence and improve segmented mirror SAO system imaging ability.

  17. Modeling of bottom-related surface patterns imaged by synthetic aperture radar

    NASA Technical Reports Server (NTRS)

    Lyzenga, D. R.; Shuchman, R. A.; Kasischke, E. S.; Meadows, G. A.

    1983-01-01

    A hydrodynamic electromagnetic model is developed in order to provide a qualitative and quantitative description of the relationship between Seasat synthetic aperture radar (SAR) signatures and the bottom topography of the ocean in the English Channel region of the North Sea. The model is based on environmental data for winds, currents, and depth changes, and the SAR parameters of frequency polarization, incidence angle, and resolution cell size. The data are used as inputs and SAR backscatter changes are predicted for individual topographic changes on the ocean floor. It is found that the model estimates of backscatter values are in good agreement with actual Seasat SAR-observed backscatter values. A comparison of the model and actual data shows agreement to be within 1.5 dB. The model is considered to be valid for only shallow water areas (less than 50 meters in depth). It is suggested that for bottom features to be visible on SAR imagery at greater depths, a moderate-to-high velocity current of at least 0.4 m/s and a moderate wind no more than 7.5 m/sec must be present.

  18. Modeling of bottom-related surface patterns imaged by synthetic aperture radar

    NASA Technical Reports Server (NTRS)

    Lyzenga, D. R.; Shuchman, R. A.; Kasischke, E. S.; Meadows, G. A.

    1983-01-01

    A hydrodynamic electromagnetic model is developed in order to provide a qualitative and quantitative description of the relationship between Seasat synthetic aperture radar (SAR) signatures and the bottom topography of the ocean in the English Channel region of the North Sea. The model is based on environmental data for winds, currents, and depth changes, and the SAR parameters of frequency polarization, incidence angle, and resolution cell size. The data are used as inputs and SAR backscatter changes are predicted for individual topographic changes on the ocean floor. It is found that the model estimates of backscatter values are in good agreement with actual Seasat SAR-observed backscatter values. A comparison of the model and actual data shows agreement to be within 1.5 dB. The model is considered to be valid for only shallow water areas (less than 50 meters in depth). It is suggested that for bottom features to be visible on SAR imagery at greater depths, a moderate-to-high velocity current of at least 0.4 m/s and a moderate wind no more than 7.5 m/sec must be present.

  19. Bose-Hubbard models with synthetic spin-orbit coupling: Mott insulators, spin textures, and superfluidity.

    PubMed

    Cole, William S; Zhang, Shizhong; Paramekanti, Arun; Trivedi, Nandini

    2012-08-24

    Motivated by the experimental realization of synthetic spin-orbit coupling for ultracold atoms, we investigate the phase diagram of the Bose-Hubbard model in a non-Abelian gauge field in two dimensions. Using a strong coupling expansion in the combined presence of spin-orbit coupling and tunable interactions, we find a variety of interesting magnetic Hamiltonians in the Mott insulator (MI), which support magnetic textures such as spin spirals and vortex and Skyrmion crystals. An inhomogeneous mean-field treatment shows that the superfluid (SF) phases inherit these exotic magnetic orders from the MI and display, in addition, unusual modulated current patterns. We present a slave-boson theory which gives insight into such intertwined spin-charge orders in the SF, and discuss signatures of these orders in Bragg scattering, in situ microscopy, and dynamic quench experiments.

  20. Iron-sulfur clusters—new features in enzymes and synthetic models

    NASA Astrophysics Data System (ADS)

    Bill, Eckhard

    2012-03-01

    Mössbauer spectroscopy is very important for the characterization of iron sulfur clusters in biological and synthetic molecules. The electric and magnetic hyperfine parameters obtained for 57Fe provide valuable information about the electronic structure of the different iron sites occurring in Fe:S clusters. Although known since more than four decades, research in this field is very active, revealing unexpected functions, structures and redox states. In this overview, new aspects of double exchange and vibronic coupling in a structurally well-characterized two-iron model compound are discussed, the electronic structure of extremely reduced clusters with all iron in ferrous or even in iron(I) state is elucidated, and an exciting new type of cubane cluster occurring in oxygen-insensitive hydrogenases is presented. The latter cluster involves structural changes during function and it supports more than one redox transition, which may be essential for oxygen protection of the enzymes.

  1. The effect of synthetic ovarian hormones on an in vivo model of thrombosis in the rat.

    PubMed Central

    Emms, H.; Lewis, G. P.

    1985-01-01

    The effects of endogenous and exogenous, synthetic ovarian hormones on thrombus formation have been examined using an in vivo model in the rat. Thrombus formation in female rats was greatest during the di-oestrus stage of the oestrous cycle. Thrombus formation in both male and female rats was reduced following 6 weeks treatment with the oestrogen, ethynyl oestradiol whilst in females the progestogen, norethindrone acetate had no effect. These findings are in contrast to the increased risk of thromboembolic disorders reported in women taking oral contraceptives. The inhibitory effect of ethynyl oestradiol was not due to changes in blood flow but was dependent on the heparin concentration, being greatest at the highest heparin concentration used. Thrombus formation was greater in male rats than in females, a sex difference which is consistent with the higher incidence of cardiovascular disease in men than in women. PMID:4038891

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

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

    This paper discusses modeling, simulations and experimental aspects of active aeroelastic control on aircraft wings by using Synthetic Jet Actuators (SJAs). SJAs, a particular class of zero-net mass-flux actuators, have shown very promising results in numerous aeronautical applications, such as boundary layer control and delay of flow separation. A less recognized effect resulting from the SJAs is a momentum exchange that occurs with the flow, leading to a rearrangement of the streamlines around the airfoil modifying the aerodynamic loads. Discussions pertinent to the use of SJAs for flow and aeroelastic control and how these devices can be exploited for flutter suppression and for aerodynamic performances improvement are presented and conclusions are outlined.

  3. Synthetic Aperture Radar Interferometry for Digital Elevation Model of Kuwait Desert - Analysis of Errors

    NASA Astrophysics Data System (ADS)

    Jassar, H. K. Al; Rao, K. S.

    2012-07-01

    Using different combinations of 29 Advanced Synthetic Aperture Radar (ASAR) images, 43 Digital Elevations Models (DEM) were generated adopting SAR Interferometry (InSAR) technique. Due to sand movement in desert terrain, there is a poor phase correlation between different SAR images. Therefore, suitable methodology for generating DEMs of Kuwait desert terrain using InSAR technique were worked out. Time series analysis was adopted to derive the best DEM out of 43 DEMs. The problems related to phase de-correlation over desert terrain are discussed. Various errors associated with the DEM generation are discussed which include atmospheric effects, penetration into soil medium, sand movement. The DEM of Shuttle Radar Topography Mission (SRTM) is used as a reference. The noise levels of DEM of SRTM are presented.

  4. 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.

  5. Toward Engineering Synthetic Microbial Metabolism

    PubMed Central

    McArthur, George H.; Fong, Stephen S.

    2010-01-01

    The generation of well-characterized parts and the formulation of biological design principles in synthetic biology are laying the foundation for more complex and advanced microbial metabolic engineering. Improvements in de novo DNA synthesis and codon-optimization alone are already contributing to the manufacturing of pathway enzymes with improved or novel function. Further development of analytical and computer-aided design tools should accelerate the forward engineering of precisely regulated synthetic pathways by providing a standard framework for the predictable design of biological systems from well-characterized parts. In this review we discuss the current state of synthetic biology within a four-stage framework (design, modeling, synthesis, analysis) and highlight areas requiring further advancement to facilitate true engineering of synthetic microbial metabolism. PMID:20037734

  6. 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