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At least 307 records · Page 17

On Beyond Star Trek, the Role of Synthetic Biology in Nasa's Missions

The time has come to for NASA to exploit the nascent field of synthetic biology in pursuit of its mission, including aeronautics, earth science, astrobiology and notably, human exploration. Conversely, NASA advances the fundamental technology of synthetic biology as no one else can because of its unique expertise in the origin of life and life in extreme environments, including the potential for alternate life forms. This enables unique, creative "game changing" advances. NASA's requirement for minimizing upmass in flight will also drive the field toward miniaturization and automation. These drivers will greatly increase the utility of synthetic biology solutions for military, health in remote areas and commercial purposes. To this end, we have begun a program at NASA to explore the use of synthetic biology in NASA's missions, particularly space exploration. As part of this program, we began hosting an iGEM team of undergraduates drawn from Brown and Stanford Universities to conduct synthetic biology research at NASA Ames Research Center. The 2011 team (http://2011.igem.org/Team:Brown-Stanford) produced an award-winning project on using synthetic biology as a basis for a human Mars settlement and the 2012 team has expanded the use of synthetic biology to estimate the potential for life in the clouds of other planets (http://2012.igem.org/Team:Stanford-Brown; http://www.calacademy.org/sciencetoday/igem-competition/). More recent projects from the Stanford-Brown team have expanded our ideas of how synthetic biology can aid NASA's missions from "Synthetic BioCommunication" (http://2013.igem.org/Team:Stanford-Brown) to a "Biodegradable UAS (drone)" in collaboration with Spelman College (http://2014.igem.org/Team:StanfordBrownSpelman#SBS%20iGEM) and most recently, "Self-Folding Origami" (http://2015.igem.org/Team:Stanford-Brown), the winner of the 2015 award for Manufacturing.

miniaturization and automation↗

The Role of Synthetic Biology in NASA's Missions

The time has come to for NASA to exploit the nascent field of synthetic biology in pursuit of its mission, including aeronautics, earth science, astrobiology and notably, human exploration. Conversely, NASA advances the fundamental technology of synthetic biology as no one else can because of its unique expertise in the origin of life and life in extreme environments, including the potential for alternate life forms. This enables unique, creative "game changing" advances. NASA's requirement for minimizing upmass in flight will also drive the field toward miniaturization and automation. These drivers will greatly increase the utility of synthetic biology solutions for military, health in remote areas and commercial purposes. To this end, we have begun a program at NASA to explore the use of synthetic biology in NASA's missions, particularly space exploration. As part of this program, we began hosting an iGEM team of undergraduates drawn from Brown and Stanford Universities to conduct synthetic biology research at NASA Ames Research Center. The 2011 team (http://2011.igem.org/Team:Brown-Stanford) produced an award-winning project on using synthetic biology as a basis for a human Mars settlement and the 2012 team has expanded the use of synthetic biology to estimate the potential for life in the clouds of other planets (http://2012.igem.org/Team:Stanford-Brown; http://www.calacademy.org/sciencetoday/igem-competition/). More recent projects from the Stanford-Brown team have expanded our ideas of how synthetic biology can aid NASA's missions from "Synthetic BioCommunication" (http://2013.igem.org/Team:Stanford-Brown) to a "Biodegradable UAS (drone)" in collaboration with Spelman College (http://2014.igem.org/Team:StanfordBrownSpelman#SBS%20iGEM) and most recently, "Self-Folding Origami" (http://2015.igem.org/Team:Stanford-Brown), the winner of the 2015 award for Manufacturing.

Rothschild, Lynn J.↗

Separations Consortium: Lignin Rich Stream Fractionation and Purification

In support of the Bioenergy Technologies Office in converting lignin to fuels and chemicals, this project develops scalable separations based on membranes and Electordeionization (EDI) to recover low molecular weight (LMW) compounds from lignin rich streams. The project addresses three technology barriers in developing the bioeconomy; (1) Cost of production (2) Selective separation of organic acid species, and (3) Advanced bioprocess development. Specifically, membrane cascades using Tangential Flow Filtration (TFF) are investigated for the recovery of LMW lignin compounds from lignin rich streams such as Alkaline Pretreatment Liquor (APL), Reductive Catalytic Fractionation (RCF) oil, and Catalytic Oxidation oil. Process concepts, including dynamic filtration, are investigated to meet specific performance targets indicated by the consortium's Industrial Advisory Board for the membrane filtration including maintaining permeance > 1 LMH/bar and an overall cost target of < $1/kg of LMW lignin. EDI is investigated as an integral part of the membrane cascade to recover LMW aromatic acids and as an alternative to nanofiltration. Economic analysis of the processes is presented with a focus on minimizing energy consumption and capital expenditure. Furthermore, a sensitivity analysis is presented to identify key cost drivers and optimize holistic process operating conditions.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

System and method for member articulation

A system including a robot mean to move a member by using a first camera coupled to the robot, a second camera coupled to the robot, a control device configured to control position of the robot in order to minimize a pixel-wise distance between the member and a target based on alternating input from the first camera and the second camera.

Blakeslee, Brigid A.↗

MPI-FAUN: An MPI-Based Framework for Alternating-Updating Nonnegative Matrix Factorization

Non-negative matrix factorization (NMF) is the problem of determining two non-negative low rank factors W and H, for the given input matrix A, such that A≈WH. NMF is a useful tool for many applications in different domains such as topic modeling in text mining, background separation in video analysis, and community detection in social networks. Despite its popularity in the data mining community, there is a lack of efficient parallel algorithms to solve the problem for big data sets. The main contribution of this work is a new, high-performance parallel computational framework for a broad class of NMF algorithms that iteratively solves alternating non-negative least squares (NLS) subproblems for W and H. It maintains the data and factor matrices in memory (distributed across processors), uses MPI for interprocessor communication, and, in the dense case, provably minimizes communication costs (under mild assumptions). The framework is flexible and able to leverage a variety of NMF and NLS algorithms, including Multiplicative Update, Hierarchical Alternating Least Squares, and Block Principal Pivoting. Our implementation allows us to benchmark and compare different algorithms on massive dense and sparse data matrices of size that spans from few hundreds of millions to billions. We demonstrate the scalability of our algorithm and compare it with baseline implementations, showing significant performance improvements. The code and the datasets used for conducting the experiments are available online.

2D↗

Reducing the low-dose lung radiation for central lung tumors by restricting the IMRT beams and arc arrangement

To compare the extent to which 7 different radiotherapy planning techniques for mediastinal lung targets reduces the lung volume receiving low doses of radiation. Thirteen non-small cell lung cancer patients with targets, including the mediastinal nodes, were identified. Treatment plans were generated to both 60- and 74-Gy prescription doses using 7 different planning techniques: conformal, hybrid conformal/intensity-modulated radiation treatment (IMRT), 7 equidistant IMRT beams, 2 restricted beam IMRT plans, a full (360 Degree-Sign ) modulated arc, and a restricted modulated arc plan. All plans were optimized to reduce total lung V5, V10, and V20 volumes, while meeting normal tissue and target coverage constraints. The mean values for the 13 patients are calculated for V5, V10, V20, V{sub ave}, V0-20, and mean lung dose (MLD) lung parameters. For the 74-Gy prescription dose, the mean lung V10 was 42.7, 43.6, 48.2, 56.6, 57, 55.8, and 54.1% for the restricted {+-}36 Degree-Sign IMRT, restricted modulated arc, restricted {+-}45 Degree-Sign IMRT, full modulated arc, hybrid conformal/IMRT, equidistant IMRT, and conformal plans, respectively. A similar lung sparing hierarchy was found for the 60-Gy prescription dose. For the treatment of central lung targets, the {+-}36 Degree-Sign restricted IMRT and restricted modulated arc planning techniques are superior in lowering the lung volume treated to low dose, as well as in minimizing MLD, followed by the {+-}45 Degree-Sign restricted IMRT plan. All planning techniques that allow the use of lateral or lateral/oblique beams result in spreading the low dose over a higher lung volume. The area under the lung dose-volume histogram curve below 20 Gy, V0-20, is proposed as an alternative to individual V{sub dose} parameters, both as a measure of lung sparing and as a parameter to be minimized during IMRT optimization.

61 RADIATION PROTECTION AND DOSIMETRY↗

Quantification and Minimization of Uncertainties of Internal Target Volume for Stereotactic Body Radiation Therapy of Lung Cancer

Purpose: To quantify uncertainties in delineating an internal target volume (ITV) and to understand how these uncertainties may be individually minimized for stereotactic body radiation therapy (SBRT) of early stage non-small cell lung cancer (NSCLC). Methods and Materials: Twenty patients with NSCLC who were undergoing SBRT were imaged with free-breathing 3-dimensional computed tomography (3DCT) and 10-phase 4-dimensional CT (4DCT) for delineating gross tumor volume (GTV){sub 3D} and ITV{sub 10Phase} (ITV3). The maximum intensity projection (MIP) CT was also calculated from 10-phase 4DCT for contouring ITV{sub MIP} (ITV1). Then, ITV{sub COMB} (ITV2), ITV{sub 10Phase+GTV3D} (ITV4), and ITV{sub 10Phase+ITVCOMB} (ITV5) were generated by combining ITV{sub MIP} and GTV{sub 3D}, ITV{sub 10phase} and GTV{sub 3D}, and ITV{sub 10phase} and ITV{sub COMB}, respectively. All 6 volumes (GTV{sub 3D} and ITV1 to ITV5) were delineated in the same lung window by the same radiation oncologist. The percentage of volume difference (PVD) between any 2 different volumes was determined and was correlated to effective tumor diameter (ETD), tumor motion ranges, R{sub 3D}, and the amplitude variability of the recorded breathing signal (v) to assess their volume variations. Results: The mean (range) tumor motion (R{sub SI}, R{sub AP}, R{sub ML}, and R{sub 3D}) and breathing variability (v) were 7.6 mm (2-18 mm), 4.0 mm (2-8 mm), 3.3 mm (0-7.5 mm), 9.9 mm (4.1-18.7 mm), and 0.17 (0.07-0.37), respectively. The trend of volume variation was GTV{sub 3D} =}0.503, P{<=}.047). The PVDs for pairs of ITV2 vs ITV5 and ITV5 vs ITV4 negatively correlated with ETD (r=0.502, -0.626; P=.047, .010). No other correlation was found. Conclusion: Uncertainties in individualized ITVs for SBRT of early stage NSCLC could effectively be minimized by combining information from 3DCT, 4DCT, and MIP. If these images cannot be efficiently contoured, a combination of ITV{sub MIP} and GTV{sub 3D} could be an effective alternative.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Alternatives to NIST Cf-252 Iirradiations for Transfer Calibration of S-32 Neutron Monitors

Gas-flow proportional counting systems are used by the Radiation Metrology Laboratory (RML) at Sandia National Laboratories for reactor fluence monitoring with the 32 S(n,p) 32 P reaction. Calibration of these systems has traditionally been accomplished by fluence-transfer irradiations at the NIST 252 Cf facility. Such calibrations have become increasingly difficult as the NIST 252 Cf source decayed to unusable levels. To minimize the risk to the testing programs from an inability to properly calibrate these systems, the RML has developed two alternative calibration techniques: 1) development and implementation of certified 32 P sources for activity calibrations and subsequent calculation of neutron fluence, and 2) direct counting of non-certified reactor-irradiated sulfur pellets by liquid scintillation counting to determine 32 P activity for the subsequent calibration of gas-flow proportional counters. Preliminary comparisons show that the several calibration methods are capable of overall uncertainties within about 5 percent.

Vehar, David W.↗

Optimally Controlled Flexible Fuel Powertrain System

A multi phase program was undertaken with the stated goal of using advanced design and development tools to create a unique combination of existing technologies to create a powertrain system specification that allowed minimal increase of volumetric fuel consumption when operating on E85 relative to gasoline. Although on an energy basis gasoline / ethanol blends typically return similar fuel economy to straight gasoline, because of its lower energy density (gasoline ~ 31.8MJ/l and ethanol ~ 21.1MJ/l) the volume based fuel economy of gasoline / ethanol blends are typically considerably worse. This project was able to define an initial engine specification envelope, develop specific hardware for the application, and test that hardware in both single and multi-cylinder test engines to verify the ability of the specified powertrain to deliver reduced E85 fuel consumption. Finally, the results from the engine testing were used in a vehicle drive cycle analysis tool to define a final vehicle level fuel economy result. During the course of the project, it was identified that the technologies utilized to improve fuel economy on E85 also enabled improved fuel economy when operating on gasoline. However, the E85 fueled powertrain provided improved vehicle performance when compared to the gasoline fueled powertrain due to the improved high load performance of the E85 fuel. Relative to the baseline comparator engine and considering current market fuels, the volumetric fuel consumption penalty when running on E85 with the fully optimized project powertrain specification was reduced significantly. This result shows that alternative fuels can be utilized in high percentages while maintaining or improving vehicle performance and with minimal or positive impact on total cost of ownership to the end consumer. The justification for this project was two-fold. In order to reduce the US dependence on crude oil, much of which is imported, the US Environmental Protection Agency (EPA) developed the Renewable Fuels Standard (RFS) under the Energy Policy Act of 2005. The RFS specifies targets for the amount of renewable fuel to be blended into petroleum based transportation fuels. The goal is to blend 36 billion gallons of renewable fuels into transportation fuels by 2022 (9 billion gallons were blended in 2008). The RFS also requires that the renewable fuels emit fewer greenhouse gasses than the petroleum fuels replaced. Thus the goal of the EPA is to have a more fuel efficient national fleet, less dependent on petroleum based fuels. The limit to the implementation of certain technologies employed was the requirement to run the developed powertrain on gasoline with minimal performance degradation. The addition of ethanol to gasoline fuels improves the fuels octane rating and increases the fuels evaporative cooling. Both of these fuel property enhancements make gasoline / ethanol blends more suitable than straight gasoline for use in downsized engines or engines with increased compression ratio. The use of engine downsizing and high compression ratios as well as direct injection (DI), dual independent cam phasing, external EGR, and downspeeding were fundamental to the fuel economy improvements targeted in this project. The developed powertrain specification utilized the MAHLE DI3 gasoline downsizing research engine. It was a turbocharged, intercooled, DI engine with dual independent cam phasing utilizing a compression ratio of 11.25 : 1 and a 15% reduction in final drive ratio. When compared to a gasoline fuelled 2.2L Ecotec engine in a Chevrolet HHR, vehicle drive cycle predictions indicate that the optimized powertrain operating on E85 would result in a reduced volume based drive cycle fuel economy penalty of 6% compared to an approximately 30% penalty for current technology engines.

33 ADVANCED PROPULSION SYSTEMS↗

Adaptive laboratory evolution of methylotrophic Escherichia coli enables synthesis of all amino acids from methanol-derived carbon

Recent attempts to create synthetic Escherichia coli methylotrophs identified that de novo biosynthesis of amino acids, in the presence of methanol, presents significant challenges in achieving autonomous methylotrophic growth. Previously engineered methanol-dependent strains required co-utilization of stoichiometric amounts of co-substrates and methanol. As such, these strains could not be evolved to grow on methanol alone. In this work, we have explored an alternative approach to enable biosynthesis of all amino acids from methanol-derived carbon in minimal media without stoichiometric coupling. First, we identified that biosynthesis of threonine was limiting the growth of our methylotrophic E. coli. To address this, we performed adaptive laboratory evolution to generate a strain that grew efficiently in minimal medium with methanol and threonine. Methanol assimilation and growth of the evolved strain were analyzed and, interestingly, we found that the evolved strain synthesized all amino acids, including threonine, from methanol-derived carbon. Here, the evolved strain was then further engineered through overexpression of an optimized threonine biosynthetic pathway. We show that the resulting methylotrophic E. coli strain has a methanol-dependent growth phenotype with homoserine as co-substrate. In contrast to previous methanol-dependent strains, co-utilization of homoserine is not stoichiometrically linked to methanol assimilation. As such, future engineering of this strain and successive adaptive evolution could enable autonomous growth on methanol as the sole carbon source.

13C-labeling analysis↗

Reverse β-oxidation pathways for efficient chemical production

Abstract Microbial production of fuels, chemicals, and materials has the potential to reduce greenhouse gas emissions and contribute to a sustainable bioeconomy. While synthetic biology allows readjusting of native metabolic pathways for the synthesis of desired products, often these native pathways do not support maximum efficiency and are affected by complex regulatory mechanisms. A synthetic or engineered pathway that allows modular synthesis of versatile bioproducts with minimal enzyme requirement and regulation while achieving high carbon and energy efficiency could be an alternative solution to address these issues. The reverse β-oxidation (rBOX) pathways enable iterative non-decarboxylative elongation of carbon molecules of varying chain lengths and functional groups with only four core enzymes and no ATP requirement. Here, we describe recent developments in rBOX pathway engineering to produce alcohols and carboxylic acids with diverse functional groups, along with other commercially important molecules such as polyketides. We discuss the application of rBOX beyond the pathway itself by its interfacing with various carbon-utilization pathways and deployment in different organisms, which allows feedstock diversification from sugars to glycerol, carbon dioxide, methane, and other substrates.

59 BASIC BIOLOGICAL SCIENCES↗

TU-F-17A-04: Respiratory Phase-Resolved 3D MRI with Isotropic High Spatial Resolution: Determination of the Average Breathing Motion Pattern for Abdominal Radiotherapy Planning

Purpose: To develop a retrospective 4D-MRI technique (respiratory phase-resolved 3D-MRI) for providing an accurate assessment of tumor motion secondary to respiration. Methods: A 3D projection reconstruction (PR) sequence with self-gating (SG) was developed for 4D-MRI on a 3.0T MRI scanner. The respiration-induced shift of the imaging target was recorded by SG signals acquired in the superior-inferior direction every 15 radial projections (i.e. temporal resolution 98 ms). A total of 73000 radial projections obtained in 8-min were retrospectively sorted into 10 time-domain evenly distributed respiratory phases based on the SG information. Ten 3D image sets were then reconstructed offline. The technique was validated on a motion phantom (gadolinium-doped water-filled box, frequency of 10 and 18 cycles/min) and humans (4 healthy and 2 patients with liver tumors). Imaging protocol included 8-min 4D-MRI followed by 1-min 2D-realtime (498 ms/frame) MRI as a reference. Results: The multiphase 3D image sets with isotropic high spatial resolution (1.56 mm) permits flexible image reformatting and visualization. No intra-phase motion-induced blurring was observed. Comparing to 2D-realtime, 4D-MRI yielded similar motion range (phantom: 10.46 vs. 11.27 mm; healthy subject: 25.20 vs. 17.9 mm; patient: 11.38 vs. 9.30 mm), reasonable displacement difference averaged over the 10 phases (0.74mm; 3.63mm; 1.65mm), and excellent cross-correlation (0.98; 0.96; 0.94) between the two displacement series. Conclusion: Our preliminary study has demonstrated that the 4D-MRI technique can provide high-quality respiratory phase-resolved 3D images that feature: a) isotropic high spatial resolution, b) a fixed scan time of 8 minutes, c) an accurate estimate of average motion pattern, and d) minimal intra-phase motion artifact. This approach has the potential to become a viable alternative solution to assess the impact of breathing on tumor motion and determine appropriate treatment margins. Comparison with 4D-CT in a clinical setting is warranted to assess the value of 4D-MRI in radiotherapy planning. This work supported in part by grant 1R03CA173273-01.

60 APPLIED LIFE SCIENCES↗

Optimized Finite-Difference Coefficients for Acoustic Modeling.

Although using standard Taylor series coefficients for finite-difference operators is optimal in the sense that in the limit of infinitesimal space and time discretization, the solution approaches the correct analytic solution to the acousto-dynamic system of differential equations, other finite-difference operators may provide optimal computational run time given certain error bounds or source bandwidth constraints. This report describes the results of investigation of alternative optimal finite-difference coefficients based on several optimization/accuracy scenarios and provides recommendations for minimizing run time while retaining error within given error bounds.

58 GEOSCIENCES↗

Factors that Impact the Redox Kinetics Associated with Sr1-xAxFeO3 (A = Ca, Ba) in Air Separations Technologies

Perovskite oxides, including SrFeO3-δ, have garnered significant interest for their impressive oxygen storage thermodynamics and kinetics. While traditional oxygen production is performed through cryogenic separation methods at the industrial scale, oxygen carrier-based separations have offered an attractive alternative at the modular scale. Perovskites are considered ideal oxygen carriers, with their structural flexibility minimizing both the thermodynamic barrier and the structural strain related to the oxygen uptake/release cycle. Our latest work has identified a few major factors that directly impact the oxygen release thermodynamics and kinetics for Sr1-xAxFeO3-δ (A = Ca, Ba) materials including elemental composition, crystallographic symmetry, surface area, and pretreatment conditions. This presentation will discuss these factors using Sr1¬-xCaxFeO3 and Ba1-xSrxFeO3 to illustrate their individual and collective impacts on the design of high-performance oxygen carriers when operating at 300-700 °C. Additionally, we will discuss how each of these factors can be leveraged for the numerous catalytic applications also dependent on the redox properties of mixed metal oxides.

Popczun, Eric↗

Ultrafine polybenzimidazole (PBI) fibers

Mats were made from ultrafine polybenzimidazole (PBI) fibers to provide an alternate to the use of asbestos as separators in fuel cells and alkaline batteries. To minimize distortion during mat drying, a process to provide a dry fibrid was developed. Two fibrid types were developed: one coarse, making mats for battery separators; the other fine, making low permeability matrices for fuel cells. Eventually, it was demonstrated that suitable mat fabrication techniques yielded fuel cell separators from the coarser alkaline battery fibrids. The stability of PBI mats to 45% KOH at 123 C can be increased by heat treatment at high temperatures. Weight loss data to 1000 hours exposure show the alkali resistance of the mats to be superior to that of asbestos.

Chenevey, E. C.↗

Rendezvous strategy impacts on CTV avionics design, system reliability requirements, and available collision avoidance maneuvers

Rockwell International is conducting an ongoing program to develop avionics architectures that provide high intrinsic value while meeting all mission objectives. Studies are being conducted to determine alternative configurations that have low life-cycle cost and minimum development risk, and that minimize launch delays while providing the reliability level to assure a successful mission. This effort is based on four decades of providing ballistic missile avionics to the United States Air Force and has focused on the requirements of the NASA Cargo Transfer Vehicle (CTV) program in 1991. During the development of architectural concepts it became apparent that rendezvous strategy issues have an impact on the architecture of the avionics system. This is in addition to the expected impact on propulsion and electrical power duration, flight profiles, and trajectory during approach.

Donovan, William J.↗

Color Histogram Diffusion for Image Enhancement

Various color histogram equalization (CHE) methods have been proposed to extend grayscale histogram equalization (GHE) for color images. In this paper a new method called histogram diffusion that extends the GHE method to arbitrary dimensions is proposed. Ranges in a histogram are specified as overlapping bars of uniform heights and variable widths which are proportional to their frequencies. This diagram is called the vistogram. As an alternative approach to GHE, the squared error of the vistogram from the uniform distribution is minimized. Each bar in the vistogram is approximated by a Gaussian function. Gaussian particles in the vistoram diffuse as a nonlinear autonomous system of ordinary differential equations. CHE results of color images showed that the approach is effective.

Kim, Taemin↗