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At least 1,009 records · Page 56

Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles

Genome-wide expression profiles contain global patterns that evade visual detection in current gene clustering analysis. Here, a Gene Expression Dynamics Inspector (GEDI) is described that uses self-organizing maps to translate high-dimensional expression profiles of time courses or sample classes into animated, coherent and robust mosaics images. GEDI facilitates identification of interesting patterns of molecular activity simultaneously across gene, time and sample space without prior assumption of any structure in the data, and then permits the user to retrieve genes of interest. Important changes in genome-wide activities may be quickly identified based on 'Gestalt' recognition and hence, GEDI may be especially useful for non-specialist end users, such as physicians. AVAILABILITY: GEDI v1.0 is written in Matlab, and binary Matlab.dll files which require Matlab to run can be downloaded for free by academic institutions at http://www.chip.org/~ge/gedihome.html Supplementary information: http://www.chip.org/~ge/gedihome.html.

Database Management Systems↗

Sensitivity analysis of automatic flight control systems using singular value concepts

A sensitivity analysis is presented that can be used to judge the impact of vehicle dynamic model variations on the relative stability of multivariable continuous closed-loop control systems. The sensitivity analysis uses and extends the singular-value concept by developing expressions for the gradients of the singular value with respect to variations in the vehicle dynamic model and the controller design. Combined with a priori estimates of the accuracy of the model, the gradients are used to identify the elements in the vehicle dynamic model and controller that could severely impact the system's relative stability. The technique is demonstrated for a yaw/roll damper stability augmentation designed for a business jet.

Herrera-Vaillard, A.↗

Quantified Event Automata: Towards Expressive and Efficient Runtime Monitors

Runtime verification is the process of checking a property on a trace of events produced by the execution of a computational system. Runtime verification techniques have recently focused on parametric specifications where events take data values as parameters. These techniques exist on a spectrum inhabited by both efficient and expressive techniques. These characteristics are usually shown to be conflicting - in state-of-the-art solutions, efficiency is obtained at the cost of loss of expressiveness and vice-versa. To seek a solution to this conflict we explore a new point on the spectrum by defining an alternative runtime verification approach.We introduce a new formalism for concisely capturing expressive specifications with parameters. Our technique is more expressive than the currently most efficient techniques while at the same time allowing for optimizations.

state machines↗

A Multifaceted Approach to Modernizing NASA's Advanced Multi-Mission Operations System (AMMOS) System Architecture

The Advanced Multi-Mission Operations Systems (AMMOS) is NASA's premier space mission operations product line offering for use in deep-space robotic and astrophysics missions. The general approach to AMMOS modernization over the course of its 29-year history exemplifies a continual, evolutionary approach with periods of sponsor investment peaks and valleys in between. Today, the Multimission Ground Systems and Services (MGSS) office-the program office that manages the AMMOS for NASA-actively pursues modernization initiatives and continues to evolve the AMMOS by incorporating enhanced capabilities and newer technologies into its end-user tool and service offerings. Despite the myriad of modernization investments that have been made over the evolutionary course of the AMMOS, pain points remain. These pain points, based on interviews with numerous flight project mission operations personnel, can be classified principally into two major categories: 1) information-related issues, and 2) process-related issues. By information-related issues, we mean pain points associated with the management and flow of MOS data across the various system interfaces. By process-related issues, we mean pain points associated with the MOS activities performed by mission operators (i.e., humans) and supporting software infrastructure used in support of those activities. In this paper, three foundational concepts-Timeline, Closed Loop Control, and Separation of Concerns-collectively form the basis for expressing a set of core architectural tenets that provides a multifaceted approach to AMMOS system architecture modernization intended to address the information- and process-related issues. Each of these architectural tenets will be further explored in this paper. Ultimately, we envision the application of these core tenets resulting in a unified vision of a future-state architecture for the AMMOS-one that is intended to result in a highly adaptable, highly efficient, and highly cost-effective set of multimission MOS products and services.

Estefan, Jeff A.↗

Automated Rendezvous and Capture System Development and Simulation for NASA

The United States does not have an Automated Rendezvous and Capture/Docking (AR and C) capability and is reliant on manned control for rendezvous and docking of orbiting spacecraft. This reliance on the labor intensive manned interface for control of rendezvous and docking vehicles has a significant impact on the cost of the operation of the International Space Station (ISS) and precludes the use of any U.S. expendable launch capabilities for Space Station resupply. The Soviets have the capability to autonomously dock in space, but their system produces a hard docking with excessive force and contact velocity. Automated Rendezvous and Capture/Docking has been identified as a key enabling technology for the Space Launch Initiative (SLI) Program, DARPA Orbital Express and other DOD Programs. The development and implementation of an AR&C capability can significantly enhance system flexibility, improve safety, and lower the cost of maintaining, supplying, and operating the International Space Station. The Marshall Space Flight Center (MSFC) has conducted pioneering research in the development of an automated rendezvous and capture (or docking) (AR and C) system for U.S. space vehicles. This AR&C system was tested extensively using hardware-in-the-loop simulations in the Flight Robotics Laboratory, and a rendezvous sensor, the Video Guidance Sensor was developed and successfully flown on the Space Shuttle on flights STS-87 and STS-95, proving the concept of a video- based sensor. Further developments in sensor technology and vehicle and target configuration have lead to continued improvements and changes in AR&C system development and simulation. A new Advanced Video Guidance Sensor (AVGS) with target will be utilized on the Demonstration of Autonomous Rendezvous Technologies (DART) flight experiment in 2004.

Roe, Fred D.↗

Real-Time Seismic System for Monitoring, Imaging, and Characterization (RT-SEISMIC)

The goal of this Laboratory Directed Research and Development (LDRD) project was to develop a borehole seismic source and sensor array to enable real-time seismic imaging at scales and conditions relevant to the energy industry including both fossil-energy and geothermal. In FY21 and FY22, we designed, built, and tested both a prototype impulse source module for generating seismic energy and a sensing module for recording ground motions generated by the source module array. A pneumatically driven vibratory source was also designed. The source modules were fabricated with all high temperature components and the team has worked to incorporate the current RT-SEISMIC electronics design into a commercially available, high temperature silicon-on-insulator chip integrated circuit. Several issues were identified during fabrication and lab testing that led to redesign of several system components and subsequent retesting. The final round of testing showed that while metal/graphite-based seals worked quite well for static seals, they were unable to provide an adequate gas seal for dynamic, reciprocating part movements which necessitated a final redesign using Kalrez. This change will result in a continuous temperature rating of approximately 275 degrees C for the system. While a field test of the RT-SEISMIC system was targeted in FY22, due to the extended lab testing and redesign efforts, field testing was not achieved. As a result of this LDRD investment, several sponsors have expressed interest in RT-SEISMIC and we expect to continue towards a field demonstration of the full system in the future.

58 GEOSCIENCES↗

Thermal analysis of the vertical bridgman semiconductor crystal growth technique

The quality of semiconductor crystals grown by the vertical Bridgman technique is strongly influenced by the axial and radial variations of temperature within the charge. The relationship between the thermal parameters of the vertical Bridgman system and the thermal behavior of the charge are examined. Thermal models are developed which are capable of producing results expressable in analytical form and which can be used without recourse to extensive computer work for the preliminary thermal design of vertical Bridgman crystal growth systems. These models include the effects of thermal coupling between the furnace and the charge, charge translation rate, charge diameter, thickness and thermal conductivity of the confining crucible, thermal conductivity change and liberation of latent heat at the growth interface, and infinite charge length. The hot and cold zone regions, considered to be at spatially uniform temperatures, are separated by a gradient control region which provides added thermal design flexibility for controlling the temperature variations near the growth interface.

Jasinski, T. J.↗

Expansion-driven Weibel instability in magnetohydrodynamics: Linear theory for static systems

The Weibel dispersion relation is obtained in the magnetohydrodynamic (MHD) approximation by including a tensor expression for temperature. MHD gives an upper cutoff wavenumber for Weibel growth identical to kinetic theory if the electron drift velocity is included in the evolution of the electron temperature. MHD overestimates growth rates compared to kinetic theory and gives maximum growth at larger wavenumbers, but it only leads to divergent results as temperature anisotropy tends to infinity. Thermal conduction in MHD lowers the growth rates and shifts maximum growth to smaller wavenumbers, but flux-limited or nonlocal thermal conduction is found to significantly limit these effects. The results are used as a first step in evaluating the potential of MHD to simulate expansion-driven Weibel instability, which occurs due to the temperature tensor only cooling in the direction of expansion. Finally, the small temperature anisotropy found in expansion-driven Weibel instability means that MHD could be an adequate model because growth rates are much less than the electron plasma frequency, and wavelengths are much greater than the Debye length.

Davies, J. R. [Univ. of Rochester, NY (United Stat↗

Express Testing Makes for More Effective Vet Visit

This paper presents a discussion on Vetscan, a system designed to provide veterinarians with instant diagnostic information needed for rapid treatment decisions. VetScan is designed for point-of-care testing in any treatment setting, including mobile environments, where veterinarians can operate the analyzer from a car-lighter adapter. A full range of tests is available for almost every species normally treated by veterinarians, including cats, dogs, birds, reptiles, and large animals, such as those in the equine and bovine families.

Source record↗

The Fiber Optic Subsystem Components on Express Logistics Carrier for International Space Station

ISS SSP 50184 HRDL optical fiber communication subsystem, has system level requirements that were changed to accommodate large loss optical fiber links previously installed. SSQ22680 design is difficult to implement, no metal shell over socket/pin combination to protect the weak part of the pin. Additions to ISS are planned for the future. AVIM still used for interconnection in space flight applications without incident. Thermal cycling resulted in less than 0.25 dB max change in Insertion Loss for all types during cycling, nominal as compared to the AVIM. Vibration testing results conclusion; no significant changes, nominal as compared to AVIM.

Ott, Melanie N.↗

Analytic Expressions for Derivatives from Series Solutions to the Three Body Problem

This paper presents a notation system to facilitate to solution of differential equations via Taylor series expansions and applies it to solve the circular restricted three body problem. Unlike previous Taylor series methods in the astrodynamics literature, computer algebra solvers are not used. Instead the notation system allows one to solve a system of differential equations analytically “by hand” without resorting to computer algebra software. This method produces recurrence relations explicitly in terms of a sequence of derivatives of the state with respect to time for the coefficients of Taylor Series solutions that can be evaluated numerically or manipulated further to investigate properties of the solution. For example, additional derivatives with respect to other parameters may also be found, including those that describe the dependence of the solution on initial conditions.

Strange, Nathan↗

Transcription initiation as a control point in plastid gene expression

The extensive processing and protein-assisted stabilization of transcripts have been taken as evidence for a viewpoint that the control of gene expression had shifted entirely in evolution from transcriptional in the bacterial endosymbiont to posttranscriptional in the plastid. This suggestion is however at odds with many observations on plastid gene transcription. Chloroplasts of flowering plants and mosses contain two or more RNA polymerases with distinct promoter preference and division of labor for the coordinated synthesis of plastid RNAs. Plant and algal plastids further possess multiple nonredundant sigma factors that function as transcription initiation factors. The controlled accumulation of plastid sigma factors and modification of their activity by sigma-binding proteins and phosphorylation constitute additional transcriptional regulatory strategies. Plant and algal plastids also contain dedicated one- or two-component transcriptional regulators. Finally, transcription initiation thus continues to form a critical control point at which varied developmental and environmental signals intersect with plastid gene expression.

59 BASIC BIOLOGICAL SCIENCES↗

Cell-Free-Based Thermophilic Biocatalyst for the Synthesis of Amino Acids from One-Carbon Feedstocks

Bioproduction from one-carbon compounds, such as formate, is an attractive prospect due to reduced energy requirements and the possibility for using CO 2 as a sustainable feedstock. Formate-fixing pathways engineered using Escherichia coli lysate-based cell-free expression (CFE) biocatalysts have the potential to route 100% of feedstock carbon toward chemical synthesis but are undermined by siphoning of in-pathway metabolites and cofactors by the CFE background metabolism. To address this limitation, we engineer a CFE-based thermophilic multienzyme biocatalyst for the synthesis of serine and glycine from formate, bicarbonate, and ammonia. After expression of the thermophilic formate-to-serine pathway in a one-pot reaction, the mesophilic E. coli CFE background machinery is removed by simple heat denaturation, eliminating the siphoning of cofactors, inpathway metabolites, and products. After bioprocess optimization, including pathway gene expression duration and chemical synthesis temperature, we achieve near stoichiometric conversion of formate and bicarbonate to serine and glycine, reaching 97% of stoichiometric yield. The use of a moderately thermophilic biocatalyst allowed chemical synthesis to take place at mesophilic temperatures, enabling the balance of optimal enzyme activity with minimal metabolite/cofactor thermal degradation. In a fed-batch experiment, the biocatalyst shows sustained chemical synthesis rates for 8 h, paving the way toward a continuous bioprocess. Finally, a sensitivity analysis of cofactor usage revealed that the most expensive cofactors, THF and NADPH, can be reduced by 5-fold without significantly lowering product yields. To the best of our knowledge, this is the first instance of expressing a thermophilic pathway in an E. coli lysate-based CFE system to generate a thermophilic biocatalyst for use at mesophilic temperatures. The CFEbased thermophilic formate-to-serine biocatalyst triples the combined serine and glycine yield previously obtained by a CFE-based mesophilic formate-to-serine biocatalyst (30%), and quadruple the yield obtained by a purified enzyme system (22%). Ultimately, this work opens the door to using E. coli lysate-based CFE for thermophilic biocatalyst generation to achieve high chemical synthesis yields.

bacteria↗

N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon

Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and bacterial responses are unpredictable across environments. We hypothesized that cereal responses to N-fixing bacteria are dynamic, depending on N supply and time. To quantify the dynamics, a gnotobiotic, fabricated ecosystem (EcoFAB) was adapted to analyse N mass balance, to image shoot and root growth, and to measure gene expression of Brachypodium distachyon inoculated with the N-fixing bacterium Herbaspirillum seropedicae. Phenotyping throughput of EcoFAB-N was 25–30 plants h -1 with open software and imaging systems. Herbaspirillum seropedicae inoculation of B. distachyon shifted root and shoot growth, nitrate versus ammonium uptake, and gene expression with time; directions and magnitude depended on N availability. Primary roots were longer and root hairs shorter regardless of N, with stronger changes at low N. At higher N, H. seropedicae provided 11% of the total plant N that came from sources other than the seed or the nutrient solution. The time-resolved phenotypic and molecular data point to distinct modes of action: at 5 mM NH 4 NO 3 the benefit appears through N fixation, while at 0.5 mM NH 4 NO 3 the mechanism appears to be plant physiological, with H. seropedicae promoting uptake of N from the root medium.Future work could fine-tune plant and root-associated microorganisms to growth and nutrient dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Hydrocarbon Rocket Technology Impact Forecasting

Ever since the Apollo program ended, the development of launch propulsion systems in the US has fallen drastically, with only two new booster engine developments, the SSME and the RS-68, occurring in the past few decades.1 In recent years, however, there has been an increased interest in pursuing more effective launch propulsion technologies in the U.S., exemplified by the NASA Office of the Chief Technologist s inclusion of Launch Propulsion Systems as the first technological area in the Space Technology Roadmaps2. One area of particular interest to both government agencies and commercial entities has been the development of hydrocarbon engines; NASA and the Air Force Research Lab3 have expressed interest in the use of hydrocarbon fuels for their respective SLS Booster and Reusable Booster System concepts, and two major commercially-developed launch vehicles SpaceX s Falcon 9 and Orbital Sciences Antares feature engines that use RP-1 kerosene fuel. Compared to engines powered by liquid hydrogen, hydrocarbon-fueled engines have a greater propellant density (usually resulting in a lighter overall engine), produce greater propulsive force, possess easier fuel handling and loading, and for reusable vehicle concepts can provide a shorter turnaround time between launches. These benefits suggest that a hydrocarbon-fueled launch vehicle would allow for a cheap and frequent means of access to space.1 However, the time and money required for the development of a new engine still presents a major challenge. Long and costly design, development, testing and evaluation (DDT&E) programs underscore the importance of identifying critical technologies and prioritizing investment efforts. Trade studies must be performed on engine concepts examining the affordability, operability, and reliability of each concept, and quantifying the impacts of proposed technologies. These studies can be performed through use of the Technology Impact Forecasting (TIF) method. The Technology Impact Forecasting method is a normative forecasting technique that allows the designer to quantify the effects of adding new technologies on a given design. This method can be used to assess and identify the necessary technological improvements needed to close the gap that exists between the current design and one that satisfies all constraints imposed on the design. The TIF methodology allows for more design knowledge to be brought to the earlier phases of the design process, making use of tools such as Quality Function Deployments, Morphological Matrices, Response Surface Methodology, and Monte Carlo Simulations.2 This increased knowledge allows for more informed decisions to be made earlier in the design process, resulting in shortened design cycle time. This paper will investigate applying the TIF method, which has been widely used in aircraft applications, to the conceptual design of a hydrocarbon rocket engine. In order to reinstate a manned presence in space, the U.S. must develop an affordable and sustainable launch capability. Hydrocarbon-fueled rockets have drawn interest from numerous major government and commercial entities because they offer a low-cost heavy-lift option that would allow for frequent launches1. However, the development of effective new hydrocarbon rockets would likely require new technologies in order to overcome certain design constraints. The use of advanced design methods, such as the TIF method, enables the designer to identify key areas in need of improvement, allowing one to dial in a proposed technology and assess its impact on the system. Through analyses such as this one, a conceptual design for a hydrocarbon-fueled vehicle that meets all imposed requirements can be achieved.

Stuber, Eric↗

Systemic Microgravity Response: Utilizing GeneLab to Develop Hypotheses for Spaceflight Risks

Biological risks associated with microgravity is a major concern for space travel. Although determination of risk has been a focus for NASA research, data examining systemic (i.e., multi- or pan-tissue) responses to space flight are sparse. The overall goal of our work is to identify potential master regulators responsible for such responses to microgravity conditions. To do this we utilized the NASA GeneLab database which contains a wide array of omics experiments, including data from: 1) different flight conditions (space shuttle (STS) missions vs. International Space Station (ISS); 2) different tissues; and 3) different types of assays that measure epigenetic, transcriptional, and protein expression changes. We have performed meta-analysis identifying potential master regulators involved with systemic responses to microgravity. The analysis used 7 different murine and rat data sets, examining the following tissues: liver, kidney, adrenal gland, thymus, mammary gland, skin, and skeletal muscle (soleus, extensor digitorum longus, tibialis anterior, quadriceps, and gastrocnemius). Using a systems biology approach, we were able to determine that p53 and immune related pathways appear central to pan-tissue microgravity responses. Evidence for a universal response in the form of consistency of change across tissues in regulatory pathways was observed in both STS and ISS experiments with varying durations; while degree of change in expression of these master regulators varied across species and strain, some change in these master regulators was universally observed. Interestingly, certain skeletal muscle (gastrocnemius and soleus) show an overall down-regulation in these genes, while in other types (extensor digitorum longus, tibialis anterior and quadriceps) they are up-regulated, suggesting certain muscle tissues may be compensating for atrophy responses caused by microgravity. Studying these organtissue-specific perturbations in molecular signaling networks, we demonstrate the value of GeneLab in characterizing potential master regulators associated with biological risks for spaceflight.

Microgravity↗

Stochastic availability analysis of operational data systems in the Deep Space Network

Existing availability models of standby redundant systems consider only an operator's performance and its interaction with the hardware performance. In the case of operational data systems in the Deep Space Network (DSN), in addition to an operator system interface, a controller reconfigures the system and links a standby unit into the network data path upon failure of the operating unit. A stochastic (Markovian) process technique is used to model and analyze the availability performance and occurrence of degradation due to partial failures are quantitatively incorporated into the model. Exact expressions of the steady state availability and proportion degraded performance measures are derived for the systems under study. The interaction among the hardware, operator, and controller performance parameters and that interaction's effect on data availability are evaluated and illustrated for an operational data processing system.

Issa, T. N.↗

Imaging of Fibroblast Activation Protein Alpha Expression in a Preclinical Mouse Model of Glioma Using Positron Emission Tomography

Glioblastoma multiforme (GBM) is the most aggressive glioma of the primary central nervous system. Due to the lack of effective treatment options, the prognosis for patients remains bleak. Fibroblast activation protein alpha (FAP), a 170 kDa type II transmembrane serine protease was observed to be expressed on glioma cells and within the glioma tumor microenvironment. To understand the utility of targeting FAP in this tumor type, the immuno-PET radiopharmaceutical [ 89 Zr]Zr-Df-Bz-F19 mAb was prepared and Lindmo analysis was used for its in vitro evaluation using the U87MG cell line, which expresses FAP endogenously. Lindmo analysis revealed an association constant (K a ) of 10 -8 M -1 and an immunoreactivity of 52%. Biodistribution studies in U87MG tumor-bearing mice revealed increasing radiotracer retention in tumors over time, leading to average tumor-to-muscle ratios of 3.1, 7.3, 7.2, and 8.3 at 2, 24, 48 and 72 h, respectively. Small animal PET corroborated the biodistribution studies; tumor-to-muscle ratios at 2, 24, 48, and 72 h were 2.0, 5.0, 6.1 and 7.8, respectively. Autoradiography demonstrated accumulated activity throughout the interior of FAP + tumors, while sequential tumor sections stained positively for FAP expression. Conversely, FAP - tissues retained minimal radioactivity and were negative for FAP expression by immunohistochemistry. These results demonstrate FAP as a promising biomarker that may be exploited to diagnose and potentially treat GBM and other neuroepithelial cancers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗