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Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
Significance Here we present an unprecedented multiscale simulation platform that enables modeling, hypothesis generation, and discovery across biologically relevant length and time scales to predict mechanisms that can be tested experimentally. We demonstrate that our predictive simulation-experimental validation loop generates accurate insights into RAS-membrane biology. Evaluating over 100,000 correlated simulations, we show that RAS–lipid interactions are dynamic and evolving, resulting in: 1) a reordering and selection of lipid domains in realistic eight-lipid bilayers, 2) clustering of RAS into multimers correlating with specific lipid fingerprints, 3) changes in the orientation of the RAS G-domain impacting its ability to interact with effectors, and 4) demonstration that RAS–RAS G-domain interfaces are nonspecific in these putative signaling domains.
Identification of Program Signatures from Cloud Computing System Telemetry Data
Malicious cloud computing activity can take many forms, including running unauthorized programs in a virtual environment. Detection of these malicious activities while preserving the privacy of the user is an important research challenge. Prior work has shown the potential viability of using cloud service billing metrics as a mechanism for proxy identification of malicious programs. Previously this novel detection method has been evaluated in a synthetic and isolated computational environment. In this paper we demonstrate the ability of billing metrics to identify programs, in an active cloud computing environment, including multiple virtual machines running on the same hypervisor. The open source cloud computing platform OpenStack, is used for private cloud management at Pacific Northwest National Laboratory. OpenStack provides a billing tool (Ceilometer) to collect system telemetry measurements. We identify four different programs running on four virtual machines under the same cloud user account. Programs were identified with up to 95% accuracy. This accuracy is dependent on the distinctiveness of telemetry measurements for the specific programs we tested. Future work will examine the scalability of this approach for a larger selection of programs to better understand the uniqueness needed to identify a program. Additionally, future work should address the separation of signatures when multiple programs are running on the same virtual machine.
Lipid membrane remodeling and metabolic response during isobutanol and ethanol exposure in Zymomonas mobilis
Abstract Background Recent engineering efforts have targeted the ethanologenic bacterium Zymomonas mobilis for isobutanol production. However, significant hurdles remain due this organism’s vulnerability to isobutanol toxicity, adversely affecting its growth and productivity. The limited understanding of the physiological impacts of isobutanol on Z. mobilis constrains our ability to overcome these production barriers. Results We utilized a systems-level approach comprising LC–MS/MS-based lipidomics, metabolomics, and shotgun proteomics, to investigate how exposure to ethanol and isobutanol impact the lipid membrane composition and overall physiology of Z. mobilis . Our analysis revealed significant and distinct alterations in membrane phospholipid and fatty acid composition resulting from ethanol and isobutanol exposure. Notably, ethanol exposure increased membrane cyclopropane fatty acid content and expression of cyclopropane fatty acid (CFA) synthase. Surprisingly, isobutanol decreased cyclopropane fatty acid content despite robust upregulation of CFA synthase. Overexpression of the native Z. mobilis’ CFA synthase increased cyclopropane fatty acid content in all phospholipid classes and was associated with a significant improvement in growth rates in the presence of added ethanol and isobutanol. Heterologous expression of CFA synthase from Clostridium acetobutylicum resulted in a near complete replacement of unsaturated fatty acids with cyclopropane fatty acids, affecting all lipid classes. However, this did not translate to improved growth rates under isobutanol exposure. Correlating with its greater susceptibility to isobutanol, Z. mobilis exhibited more pronounced alterations in its proteome, metabolome, and overall cell morphology—including cell swelling and formation of intracellular protein aggregates —when exposed to isobutanol compared to ethanol. Isobutanol triggered a broad stress response marked by the upregulation of heat shock proteins, efflux transporters, DNA repair systems, and the downregulation of cell motility proteins. Isobutanol also elicited widespread dysregulation of Z. mobilis ’ primary metabolism evidenced by increased levels of nucleotide degradation intermediates and the depletion of biosynthetic and glycolytic intermediates. Conclusions This study provides a comprehensive, systems-level evaluation of the impact of ethanol and isobutanol exposure on the lipid membrane composition and overall physiology of Z. mobilis . These findings will guide engineering of Z. mobilis towards the creation of isobutanol-tolerant strains that can serve as robust platforms for the industrial production of isobutanol from lignocellulosic sugars.
Electric Power Grid and Natural Gas Network Operations and Coordination
In this report, we present findings from three studies related to the coordination of natural gas and electricity system operations. We first propose and demonstrate a modeling platform for examining the interdependence of natural gas and electricity networks based on a direct current unit-commitment and economic dispatch model for the power system and a transient hydraulic gas model for the gas system. We use this platform to analyze the value of day-ahead coordination of power and natural gas network operations and to show the importance of considering gas system constraints when analyzing power systems operation with high penetration of gas generators and variable renewable energy sources. In the second study, we utilize our modeling platform to consider the U.S. Federal Energy Regulatory Commission (FERC) Order 809, issued in 2015 to improve day-ahead and intraday coordination of power and gas systems. Finally, in the third study we expand our modeling platform to focus on market-based coordination of electricity and natural gas system operations for a real system, namely a subset of the power and gas networks in the Front Range region of Colorado. We use real system data to evaluate the benefits of coordination operations under different conditions, including different levels of renewable penetration and the use of time-variant, shaped flow nominations. Our results indicate that coordination at various timescales can contribute to a reduction in curtailed gas in high-stress periods (such as those with large ramps in gas offtakes) and a reduction in energy consumption of gas compressor stations. We find that intraday coordination can reduce total power system production costs and natural gas deliverability constraints, yielding cost and reliability benefits. We observe these benefits for the test system as well as in the Colorado case study, where we find that coordination and shaped flows may provide additional value for systems with high penetration of variable renewable energy. Together, these three studies demonstrate a pathway for integrated gas and electricity grid modeling and for studying the benefits of coordinated operations of these increasingly interdependent energy systems.
Monitoring of streamflow in the Verde River by ERTS-1 Data Collection System (DCS)
The Verde River watershed in central Arizona furnishes municipal, industrial, and agricultural water to the Salt River Valley --an area that contains more than half of Arizona's population and about one-fourth of the State's irrigated land. Water-management decisions related to the operation of large multiple-use reservoirs require accurate and continuous monitoring of moisture conditions over large remote areas. The U.S. Geological Survey in cooperation with the Salt River Valley Water Users' Association installed a specially designed gaging station on the Verde River near the town of Camp Verde to evaluate near-real time streamflow data furnished by the ERTS-1 Data Collection System (DCS). On Nov. 3, 1972, the installation was equipped with a Stevens digital water-level recorder, modified for telemetry, and an ERTS-1 data collection platform operating in the digital-parallel mode.
Investigation of time-sharing of rebalance electronics for sensors in strapdown navigation platforms
This article reports the results of an investigation on time-sharing of a rebalance electronics among several sensors used in a strapdown navigation platform. Various concepts are given. The merits and demerits of the time-sharing for a typical situation are discussed in detail. A possible hardware realization is proposed. In addition, this study develops a general approach, applicable to other systems, for evaluating the use of time-sharing concept.
Pointing system modeling for performance prediction
The paper considers the modeling and analysis of the JPL Precision Pointing and Tracking System, a gyro stabilized platform pointing system using optical target tracking. Sensor and actuator models are described which realistically represent actual hardware, and a practical controller and state estimator is developed through modern control techniques. The effect of the actuator nonlinearities on the system performance evaluation is discussed along with the modeling of the noise sources in the gyro. Finally, the limitations of implementing the control algorithms on the spacecraft computer, and the resulting tradeoffs are presented.
High capacity demonstration of honeycomb panel heat pipes
High capacity honeycomb panel heat pipes were investigated as heat rejection radiators on future space platforms. Starting with a remnant section of honeycomb panel measuring 3.05-m long by 0.127-m wide that was originally designed and built for high-efficiency radiator fins, features were added to increase thermal transport capacity and thus permit test evaluation as an integral heat transport and rejection radiator. A series of subscale panels were fabricated and reworked to isolate individual enhancement features. Key to the enhancement was the addition of a liquid sideflow that utilizes pressure priming. A prediction model was developed and correlated with measured data, and then used to project performance to large, space-station size radiators. Results show that a honeycomb panel with 5.08-cm sideflow spacing and core modification will meet the design load of a 50 kW space heat rejection system.
S-Band propagation measurements
A geosynchronous satellite system capable of providing many channels of digital audio radio service (DARS) to mobile platforms within the contiguous United States using S-band radio frequencies is being implemented. The system is designed uniquely to mitigate both multipath fading and outages from physical blockage in the transmission path by use of satellite spatial diversity in combination with radio frequency and time diversity. The system also employs a satellite orbital geometry wherein all mobile platforms in the contiguous United States have elevation angles greater than 20 deg to both of the diversity satellites. Since implementation of the satellite system will require three years, an emulation has been performed using terrestrial facilities in order to allow evaluation of DARS capabilities in advance of satellite system operations. The major objective of the emulation was to prove the feasibility of broadcasting from satellites 30 channels of CD quality programming using S-band frequencies to an automobile equipped with a small disk antenna and to obtain quantitative performance data on S-band propagation in a satellite spatial diversity system.
Satellite Broadcast of Graphical Weather Data Flight Tested
NASA Glenn Research Center at Lewis Field's aviation Weather Information Communications (WINCOMM) and NASA Langley Research Center's Aviation Weather Information (AWIN) programs collaborated in a flight test and evaluation of a worldwide weather data-link capability using satellites. This successful flight testing moves NASA closer to its goal of developing advanced communications and information technologies to enable high-quality and timely dissemination of aviation weather information to all relevant users on the aviation information network. Recognized as a major contributing factor in aviation accidents and incidents, weather contributes directly or indirectly to nearly 80 percent of fatal general aviation (small private aircraft) accidents. In 1997, the Aeronautics Safety Investment Strategy Team s weather team produced a prioritized list of investment areas under weather accident prevention. Weather data dissemination is the most critical and highest ranked priority on the list. NASA's Aviation Safety Program founded the Aviation Weather Information initiative to focus efforts on significantly reducing the number of weather-related aviation fatalities. Access to accurate and timely weather data could contribute to a major reduction of weather-related incidents and accidents. However, a cost-effective solution has eluded most general aviation pilots because of the high cost of onboard weather radar equipment. Rockwell Collins, through a contract with NASA and in cooperation with WorldSpace Corporation, successfully completed ground and flight testing of a receiver and antenna in Johannesburg, South Africa. This NASA/Rockwell Collins project is an evaluation of worldwide weather data-link capability using transmissions from the Satellite Digital Audio Radio Services (S DARS) AfriStar satellite. Owned and operated by WorldSpace, AfriStar is a geostationary satellite that broadcasts commercial digital audio services to stationary and mobile platforms. S DARS satellites are the most powerful communications satellites produced to date, allowing users to receive signals using simple, low-cost patch antennas instead of more expensive, beam-steered antenna arrays. Engineers connected an inexpensive, commercially available radio receiver to a laptop computer and an antenna designed and built by Rockwell Collins, enabling them to receive WorldSpace signals from the AfriStar satellite during flight tests. WorldSpace broadcast their composite color graphical weather data files, which were multiplexed with normal audio streams, to the flat patch antenna mounted on a single-engine aircraft. The aircraft was equipped with a modified commercial S-DARS receiver, a Global Positioning Satellite (GPS) receiver, and a laptop computer with color display. Continuous data reception occurred during normal aircraft maneuvers performed throughout takeoff, cruise, and landing operations. In addition, engineers monitored receiver power levels during steep turns and banks. In most instances, the receiver was able to maintain acceptable power levels during all phases of flight and to obtain weather data with little or with the successful completion of ground and flight testing of a receiver and antenna in Johannesburg, South Africa, the team has started to prepare for experiments using highspeed aircraft in areas of the world with limited access to timely weather data. NASA plans to provide a more advanced antenna design and consultation support. This successful test of real-time aviation-related weather data is a positive step toward solving communications-specific issues associated with the dissemination of weather data directly to the cockpit.
Full Scale Advanced Systems Testbed (FAST): Capabilities and Recent Flight Research
At the NASA Armstrong Flight Research Center research is being conducted into flight control technologies that will enable the next generation of air and space vehicles. The Full Scale Advanced Systems Testbed (FAST) aircraft provides a laboratory for flight exploration of these technologies. In recent years novel but simple adaptive architectures for aircraft and rockets have been researched along with control technologies for improving aircraft fuel efficiency and control structural interaction. This presentation outlines the FAST capabilities and provides a snapshot of the research accomplishments to date. Flight experimentation allows a researcher to substantiate or invalidate their assumptions and intuition about a new technology or innovative approach Data early in a development cycle is invaluable for determining which technology barriers are real and which ones are imagined Data for a technology at a low TRL can be used to steer and focus the exploration and fuel rapid advances based on real world lessons learned It is important to identify technologies that are mature enough to benefit from flight research data and not be tempted to wait until we have solved all the potential issues prior to getting some data Sometimes a stagnated technology just needs a little real world data to get it going One trick to getting data for low TRL technologies is finding an environment where it is okay to take risks, where occasional failure is an expected outcome Learning how things fail is often as valuable as showing that they work FAST has been architected to facilitate this type of testing for control system technologies, specifically novel algorithms and sensors Rapid prototyping with a quick turnaround in a fly-fix-fly paradigm Sometimes it's easier and cheaper to just go fly it than to analyze the problem to death The goal is to find and test control technologies that would benefit from flight data and find solutions to the real barriers to innovation. The FAST vehicle is a flexible laboratory for nascent technologies that would benefit from early life cycle flight research data It provides a robust and safe environment where innovative techniques can be explored in a fly-fix-fly rapid prototyping paradigm IRAC Simple adaptive control technologies can provide real benefits without undo complexity Adverse pilot/adaptive system interactions can be mitigated and tools have been developed to evaluate those interactions ICP Substantial fuel savings can be achieved over a broad range of vehicles and configurations with intelligent control solutions LVAC The AAC design is robust and effective for the SLS mission, and promises to provide benefits to other platforms as well OCLA Hopefully will show that structural feedback can be seamlessly integrated with performance and stability objectives All of these control technologies have been implemented into the same baseline control law and could be combined into one control solution that answers many pressing questions for modern vehicle configurations
Simulated ASTER data for Geologic Studies
The Advanced Spaceborne Thermal Emission and Reflectance Radiometer (ASTER) is a high spatial resolution imaging instrument, due to be launched on NASA's Earth Observing System AM-1 satellite platform in 1998. ASTER acquires data in 14 bands, spanning the wavelength region from the visible, near infrared, short wavelength infrared, and thermal infrared, with spatial resolution varying from 15 m to 90 m, depending on wavelength region. In order to evaluate our ability to use ASTER data for geological mapping, we used aircraft data over Cuprite, Nevada to create a simulated 14-band ASTER data set. The study site has sparse vegetation, and exposes a wide range of unaltered and hydrothermally altered volcanic rocks. The wide range of wavelengths covered by ASTER allowed us to recognize or separate iron oxide minerals, clay-bearing minerals, sulfate minerals, ammonia minerals, siliceous rocks, and carbonates. Combined with laboratory spectral measurements, we were able to identify these constituents. Based on both sets of information, we produced an alteration map showing the distribution of argillized rocks, opalized rocks with alunite, silicified rocks, and areas dominated by kaolinite and buddingtonite. The map was as accurate as published maps made by traditional field methods. ASTER promises to be a major improvement over existing satellite systems for geologic mapping.
CubeSat constellations provide enhanced crop phenology and digital agricultural insights using daily leaf area index retrievals
Satellite remote sensing has great potential to deliver on the promise of a data-driven agricultural revolution, with emerging space-based platforms providing spatiotemporal insights into precision-level attributes such as crop water use, vegetation health and condition and crop response to management practices. Using a harmonized collection of high-resolution Planet CubeSat, Sentinel-2, Landsat-8 and additional coarser resolution imagery from MODIS and VIIRS, we exploit a multi-satellite data fusion and machine learning approach to deliver a radiometrically calibrated and gap-filled time-series of daily leaf area index (LAI) at an unprecedented spatial resolution of 3 m. The insights available from such high-resolution CubeSat-based LAI data are demonstrated through tracking the growth cycle of a maize crop and identifying observable within-field spatial and temporal variations across key phenological stages. Daily LAI retrievals peaked at the tasseling stage, demonstrating their value for fertilizer and irrigation scheduling. An evaluation of satellite-based retrievals against field-measured LAI data collected from both rain-fed and irrigated fields shows high correlation and captures the spatiotemporal development of intra- and inter-field variations. Novel agricultural insights related to individual vegetative and reproductive growth stages were obtained, showcasing the capacity for new high-resolution CubeSat platforms to deliver actionable intelligence for precision agricultural and related applications.
Transformational Opacity Platforms on the Z Facility: A Design Study
The goal of this one-year LDRD is to study novel experimental approaches to provide benchmark spectral opacity measurements at the most extreme conditions beyond existing measurements (i.e. 2x temperature, ~5x density). These conditions correspond to those at half the solar radius and would provide a unique and novel test for stellar physics. These conditions are also relevant to advance stockpile stewardship research. The basic idea is to embed a sample inside the z-pinch dynamic hohlraum on the Z facility and obtain its opacity from either 1) its self-emission or 2) its absorption from using a capsule backlighter. This study evaluates the feasibility, limitations to these two approaches from a design approach. We found that emission-based perspective gives, at best, an opacity accuracy of about 20% for the current studied pinch conditions due to the limit of LTE approximation and radiation transport effects. The capsule-backlighter-based approach overcomes this limitation although some specific design questions remain to be answered. Promising designs are proposed for follow-on Z experiments. Future designs would help maintain Z relevancy in relation to ignition-enabled platforms at NIF.
Surface observations for the evaluation of geophysical measurements from Seasat
The surface observations used for direct comparison with Seasat-derived values at fixed locations and as input to analyzed fields of pressure, wind, air and sea temperatures, and surface dew point are discussed. These included measurements made by research vessels participating in the Gulf of Alaska Seasat Experiment (GOASEX) and NOAA research platforms in addition to aircraft observations and reports from the World Weather Watch. The application of these observations in describing the synoptic-scale winds over the ocean is discussed, and the sensitivity of the verification statistics to the type of data (observations from buoys, weather ships, and transient vessels with or without anemometers) is considered. Results of a preliminary comparison of wind fields derived from Seasat-A scatterometer observation with winds specified by several types of platforms are presented.
Generation of Electrical Power from Stimulated Muscle Contractions Evaluated
This project is a collaborative effort between NASA Glenn Research Center's Revolutionary Aeropropulsion Concepts (RAC) Project, part of the NASA Aerospace Propulsion and Power Program of the Aerospace Technology Enterprise, and Case Western Reserve University's Cleveland Functional Electrical Stimulation (FES) Center. The RAC Project foresees implantable power requirements for future applications such as organically based sensor platforms and robotics that can interface with the human senses. One of the goals of the FES Center is to develop a totally implantable neural prosthesis. This goal is based on feedback from patients who would prefer a system with an internal power source over the currently used system with an external power source. The conversion system under investigation would transform the energy produced from a stimulated muscle contraction into electrical energy. We hypothesize that the output power of the system will be greater than the input power necessary to initiate, sustain, and control the electrical conversion system because of the stored potential energy of the muscle. If the system can be made biocompatible, durable, and with the potential for sustained use, then the biological power source will be a viable solution.
Developing and Deploying Universal Diagnostic Platforms for One-Health Biosurveillance
ObjectiveOur goal is to develop deployable strategies for infectious disease diagnosis at the point-of-care that are applicable to multiple hosts of infection - conforming to the global One Health Strategy for diagnostics. We aim to develop methods that do not require prior knowledge of the pathogen in question, and can facilitate rapid and effective decision-making and situational awareness.IntroductionThere is an urgent need for diagnostic strategies for infections which are host-independent, so as to effectively track zoonotic spread, monitor animal carriers of pathogens, and evaluate transmission dynamics. Infection of a host - pathogen or human- by an animal results in recognition by the immune response, which consequently causes release of inflammatory mediators. Many scientists have explored the use of cytokines as diagnostic indicators of disease, but the conserved nature of the immune response in humans and animals results in cross-reactivity among many pathogens, making evaluation of the results difficult, especially in high disease burden populations. Measuring the pathogen-specific signature, however, is advantageous - as it offers discrete identification of active infection, and discrimination from exposure. It also offers a universal strategy that can be applied to human and animal hosts of infection - allowing for One Health Biosurveillance. Achieving this, however, requires the development of a) tailored strategies for the measurement of biochemically disparate pathogen signatures in clinical samples and b) ultra-sensitive detection of such signatures in the host. The sensor team at Los Alamos National Laboratory is working on both of these aspects, and the development of One Health Diagnostic platforms, the focus of the work presented here.MethodsMany of the biomarkers secreted by bacterial pathogens and recognized by innate immune receptors elicit host cytokine responses that are amphiphilic (largely glycolipids, lipoproteins or lipoglycans). Based on such, our team has developed tailored methods – membrane insertion and lipoprotein capture for the capture and detection of these greasy and stealthy molecules in infected blood. Sensitivity and specificity, assay optimization, alinearity associated with lipidic molecules and assay parameter development for biomarkers associated with bacterial pathogens will be presented. Considerations for clinical sampling for amphiphile detection in blood, and clinical study design will be demonstrated. Our team has developed an ultra-sensitive biosensor for detection of biomarkers in complex matrices based on the evanescent field properties of single mode planar optical waveguides. Detection of amphiphilic biomarkers in clinical samples, using the waveguide-based biosensor and tailored methods for the detection of such molecules has allowed for the diagnosis of infection in both human and animals hosts. Herein, we present two examples of the same; 1) diagnosis of tuberculosis in humans, cattle and badgers using pathogen-based diagnostic strategies; and 2) detection of Gram-negative Lipopolysacharides in beef and in patients with Salmonella-induced sepsis.ResultsWe have developed tailored ultra-sensitive waveguide-biosensor assays for the detection of Lipoarabinomannan (and other biomarkers) from Mycobacteria and demonstrated feasibility in blinded clinical studies in humans and cattle, demonstrating one -health compatibility.We have also demonstrated detection of lipopolysacharides from eight different serotypes of Shiga-toxin carrying E. coli in beef, and Salmonella Typhimurium in pediatric patients using the same approach.ConclusionsWe have demonstrated clinical feasibility of a One Health Strategy for point-of-care diagnostics of bacterial infections in blood for tuberculosis and Gram-negative pathogens in clinical samples. The results will be demonstrated with several discussion points on the consideration of unconventional biochemistry of pathogens for diagnostics, factors influencing point-of-care deployment and integration of diagnostic platforms for biosurveillance. One Health Considerations and challenges therein will also merit discussion.ReferencesSakamuri, R; et al. Accurate Tracking of Bovine Tuberculosis Biomarkers in Infected Cattle using a Novel Biomarker Capture Strategy, Analytical Sciences, 33(4): 457-460, 2017.Noormohammed A et al. Detection of Salmonella LPS in Patient blood by Lipoprotein Capture. Proc. SPIE 10072, Optical Diagnostics and Sensing XVII: Toward Point-of-Care Diagnostics, 100720A , 2017. doi:10.1117/12.2253506Stromberg L et al. Membrane Insertion for the Detection of Lipopolysaccharides: Exploring the Dynamics of Amphiphile-in-Lipid Assays, PloS One, April 2016.Sakamuri RM et al. Association of lipoarabinomannan with high density lipoprotein in blood: implications for diagnostics.Tuberculosis (Edinb). 2013 May;93(3):301-7. doi: 10.1016/j.tube.2013.02.015. Epub 2013 Mar 16Mukundan H et al. Understanding the interaction of Lipoarabinomannan with membrane mimetic architectures. Tuberculosis, 92(1) 32-47, 2012.Mukundan H et al., Waveguide-based Sensors for Pathogen Detection, Invited Review, Sensors, 9(7), 5783-5809.