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NASA NTRS2003

An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof

The Arabidopsis genome sequencing in 2000 gave to science the first blueprint of a vascular plant. Its successful completion also prompted the US National Science Foundation to launch the Arabidopsis 2010 initiative, the goal of which is to identify the function of each gene by 2010. In this study, an exhaustive analysis of The Institute for Genomic Research (TIGR) and The Arabidopsis Information Resource (TAIR) databases, together with all currently compiled EST sequence data, was carried out in order to determine to what extent the various metabolic networks from phenylalanine ammonia lyase (PAL) to the monolignols were organized and/or could be predicted. In these databases, there are some 65 genes which have been annotated as encoding putative enzymatic steps in monolignol biosynthesis, although many of them have only very low homology to monolignol pathway genes of known function in other plant systems. Our detailed analysis revealed that presently only 13 genes (two PALs, a cinnamate-4-hydroxylase, a p-coumarate-3-hydroxylase, a ferulate-5-hydroxylase, three 4-coumarate-CoA ligases, a cinnamic acid O-methyl transferase, two cinnamoyl-CoA reductases) and two cinnamyl alcohol dehydrogenases can be classified as having a bona fide (definitive) function; the remaining 52 genes currently have undetermined physiological roles. The EST database entries for this particular set of genes also provided little new insight into how the monolignol pathway was organized in the different tissues and organs, this being perhaps a consequence of both limitations in how tissue samples were collected and in the incomplete nature of the EST collections. This analysis thus underscores the fact that even with genomic sequencing, presumed to provide the entire suite of putative genes in the monolignol-forming pathway, a very large effort needs to be conducted to establish actual catalytic roles (including enzyme versatility), as well as the physiological function(s) for each member of the (multi)gene families present and the metabolic networks that are operative. Additionally, one key to identifying physiological functions for many of these (and other) unknown genes, and their corresponding metabolic networks, awaits the development of technologies to comprehensively study molecular processes at the single cell level in particular tissues and organs, in order to establish the actual metabolic context.

NASA Program Fundamental Space Biology↗
NASA NTRS2002

Monolignol radical-radical coupling networks in western red cedar and Arabidopsis and their evolutionary implications

The discovery of a nine-member multigene dirigent family involved in control of monolignol radical-radical coupling in the ancient gymnosperm, western red cedar, suggested that a complex multidimensional network had evolved to regulate such processes in vascular plants. Accordingly, in this study, the corresponding promoter regions for each dirigent multigene member were obtained by genome-walking, with Arabidopsis being subsequently transformed to express each promoter fused to the beta-glucuronidase (GUS) reporter gene. It was found that each component gene of the proposed network is apparently differentially expressed in individual tissues, organs and cells at all stages of plant growth and development. The data so obtained thus further support the hypothesis that a sophisticated monolignol radical-radical coupling network exists in plants which has been highly conserved throughout vascular plant evolution.

NASA Discipline Plant Biology↗
NASA NTRS2004

A Subsonic Aircraft Design Optimization With Neural Network and Regression Approximators

The Flight-Optimization-System (FLOPS) code encountered difficulty in analyzing a subsonic aircraft. The limitation made the design optimization problematic. The deficiencies have been alleviated through use of neural network and regression approximations. The insight gained from using the approximators is discussed in this paper. The FLOPS code is reviewed. Analysis models are developed and validated for each approximator. The regression method appears to hug the data points, while the neural network approximation follows a mean path. For an analysis cycle, the approximate model required milliseconds of central processing unit (CPU) time versus seconds by the FLOPS code. Performance of the approximators was satisfactory for aircraft analysis. A design optimization capability has been created by coupling the derived analyzers to the optimization test bed CometBoards. The approximators were efficient reanalysis tools in the aircraft design optimization. Instability encountered in the FLOPS analyzer was eliminated. The convergence characteristics were improved for the design optimization. The CPU time required to calculate the optimum solution, measured in hours with the FLOPS code was reduced to minutes with the neural network approximation and to seconds with the regression method. Generation of the approximators required the manipulation of a very large quantity of data. Design sensitivity with respect to the bounds of aircraft constraints is easily generated.

Patnaik, Surya N.↗
NASA NTRS2000

Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks

Development of characteristic tissue patterns requires that individual cells be switched locally between different phenotypes or "fates;" while one cell may proliferate, its neighbors may differentiate or die. Recent studies have revealed that local switching between these different gene programs is controlled through interplay between soluble growth factors, insoluble extracellular matrix molecules, and mechanical forces which produce cell shape distortion. Although the precise molecular basis remains unknown, shape-dependent control of cell growth and function appears to be mediated by tension-dependent changes in the actin cytoskeleton. However, the question remains: how can a generalized physical stimulus, such as cell distortion, activate the same set of genes and signaling proteins that are triggered by molecules which bind to specific cell surface receptors. In this article, we use computer simulations based on dynamic Boolean networks to show that the different cell fates that a particular cell can exhibit may represent a preprogrammed set of common end programs or "attractors" which self-organize within the cell's regulatory networks. In this type of dynamic network model of information processing, generalized stimuli (e.g., mechanical forces) and specific molecular cues elicit signals which follow different trajectories, but eventually converge onto one of a small set of common end programs (growth, quiescence, differentiation, apoptosis, etc.). In other words, if cells use this type of information processing system, then control of cell function would involve selection of preexisting (latent) behavioral modes of the cell, rather than instruction by specific binding molecules. Importantly, the results of the computer simulation closely mimic experimental data obtained with living endothelial cells. The major implication of this finding is that current methods used for analysis of cell function that rely on characterization of linear signaling pathways or clusters of genes with common activity profiles may overlook the most critical features of cellular information processing which normally determine how signal specificity is established and maintained in living cells. Copyright 2000 Academic Press.

Review↗
NASA NTRS2004

Proposed Development of NASA Glenn Research Center's Aeronautical Network Research Simulator

Accurate knowledge and understanding of data link traffic loads that will have an impact on the underlying communications infrastructure within the National Airspace System (NAS) is of paramount importance for planning, development and fielding of future airborne and ground-based communications systems. Attempting to better understand this impact, NASA Glenn Research Center (GRC), through its contractor Computer Networks & Software, Inc. (CNS, Inc.), has developed an emulation and test facility known as the Virtual Aircraft and Controller (VAC) to study data link interactions and the capacity of the NAS to support Controller Pilot Data Link Communications (CPDLC) traffic. The drawback of the current VAC test bed is that it does not allow the test personnel and researchers to present a real world RF environment to a complex airborne or ground system. Fortunately, the United States Air Force and Navy Avionics Test Commands, through its contractor ViaSat, Inc., have developed the Joint Communications Simulator (JCS) to provide communications band test and simulation capability for the RF spectrum through 18 GHz including Communications, Navigation, and Identification and Surveillance functions. In this paper, we are proposing the development of a new and robust test bed that will leverage on the existing NASA GRC's VAC and the Air Force and Navy Commands JCS systems capabilities and functionalities. The proposed NASA Glenn Research Center's Aeronautical Networks Research Simulator (ANRS) will combine current Air Traffic Control applications and physical RF stimulation into an integrated system capable of emulating data transmission behaviors including propagation delay, physical protocol delay, transmission failure and channel interference. The ANRS will provide a simulation/stimulation tool and test bed environment that allow the researcher to predict the performance of various aeronautical network protocol standards and their associated waveforms under varying density conditions. The system allows the user to define human-interactive and scripted aircraft and controller models of various standards, such as (but not limited to) Very High Frequency Digital Link (VDL) of various modes.

Nguyen, Thanh C.↗
NASA NTRS2004

Network Performance Measurements for NASA's Earth Observation System

NASA's Earth Observation System (EOS) Project studies all aspects of planet Earth from space, including climate change, and ocean, ice, land, and vegetation characteristics. It consists of about 20 satellite missions over a period of about a decade. Extensive collaboration is used, both with other US. agencies (e.g., National Oceanic and Atmospheric Administration (NOA), United States Geological Survey (USGS), Department of Defense (DoD), and international agencies (e.g., European Space Agency (ESA), Japan Aerospace Exploration Agency (JAXA)), to improve cost effectiveness and obtain otherwise unavailable data. Scientific researchers are located at research institutions worldwide, primarily government research facilities and research universities. The EOS project makes extensive use of networks to support data acquisition, data production, and data distribution. Many of these functions impose requirements on the networks, including throughput and availability. In order to verify that these requirements are being met, and be pro-active in recognizing problems, NASA conducts on-going performance measurements. The purpose of this paper is to examine techniques used by NASA to measure the performance of the networks used by EOSDIS (EOS Data and Information System) and to indicate how this performance information is used.

Loiacono, Joe↗
NASA NTRS2004

An Aerosol Extinction-to-Backscatter Ratio Database Derived from the NASA Micro-Pulse Lidar Network: Applications for Space-based Lidar Observations

Backscatter lidar signals are a function of both backscatter and extinction. Hence, these lidar observations alone cannot separate the two quantities. The aerosol extinction-to-backscatter ratio, S, is the key parameter required to accurately retrieve extinction and optical depth from backscatter lidar observations of aerosol layers. S is commonly defined as 4*pi divided by the product of the single scatter albedo and the phase function at 180-degree scattering angle. Values of S for different aerosol types are not well known, and are even more difficult to determine when aerosols become mixed. Here we present a new lidar-sunphotometer S database derived from Observations of the NASA Micro-Pulse Lidar Network (MPLNET). MPLNET is a growing worldwide network of eye-safe backscatter lidars co-located with sunphotometers in the NASA Aerosol Robotic Network (AERONET). Values of S for different aerosol species and geographic regions will be presented. A framework for constructing an S look-up table will be shown. Look-up tables of S are needed to calculate aerosol extinction and optical depth from space-based lidar observations in the absence of co-located AOD data. Applications for using the new S look-up table to reprocess aerosol products from NASA's Geoscience Laser Altimeter System (GLAS) will be discussed.

Welton, Ellsworth J.↗
NASA NTRS2001

QoS for Real Time Applications over Next Generation Data Networks

Viewgraphs on Qualtity of Service (QOS) for real time applications over next generation data networks are presented. The progress to date include: Task 1: QoS in Integrated Services over DiffServ networks (UD); Task 2: Interconnecting ATN with the next generation Internet (UD); Task 3: QoS in DiffServ over ATM (UD); Task 4: Improving Explicit Congestion Notification with the Mark-Front Strategy (OSU); Task 5: Multiplexing VBR over VBR (OSU); and Task 6: Achieving QoS for TCP traffic in Satellite Networks with Differentiated Services (OSU).

Ivancic, William↗
NASA NTRS2001

Achieving QoS for TCP Traffic in Satellite Networks with Differentiated Services

Satellite networks play an indispensable role in providing global Internet access and electronic connectivity. To achieve such a global communications, provisioning of quality of service (QoS) within the advanced satellite systems is the main requirement. One of the key mechanisms of implementing the quality of service is traffic management. Traffic management becomes a crucial factor in the case of satellite network because of the limited availability of their resources. Currently, Internet Protocol (IP) only has minimal traffic management capabilities and provides best effort services. In this paper, we presented a broadband satellite network QoS model and simulated performance results. In particular, we discussed the TCP flow aggregates performance for their good behavior in the presence of competing UDP flow aggregates in the same assured forwarding. We identified several factors that affect the performance in the mixed environments and quantified their effects using a full factorial design of experiment methodology.

Durresi, Arjan↗
NASA NTRS2004

High Speed Networking and Large-scale Simulation in Geodynamics

Large-scale numerical simulation has been one of the most important approaches for understanding global geodynamical processes. In this approach, peta-scale floating point operations (pflops) are often required to carry out a single physically-meaningful numerical experiment. For example, to model convective flow in the Earth's core and generation of the geomagnetic field (geodynamo), simulation for one magnetic free-decay time (approximately 15000 years) with a modest resolution of 150 in three spatial dimensions would require approximately 0.2 pflops. If such a numerical model is used to predict geomagnetic secular variation over decades and longer, with e.g. an ensemble Kalman filter assimilation approach, approximately 30 (and perhaps more) independent simulations of similar scales would be needed for one data assimilation analysis. Obviously, such a simulation would require an enormous computing resource that exceeds the capacity of a single facility currently available at our disposal. One solution is to utilize a very fast network (e.g. 10Gb optical networks) and available middleware (e.g. Globus Toolkit) to allocate available but often heterogeneous resources for such large-scale computing efforts. At NASA GSFC, we are experimenting with such an approach by networking several clusters for geomagnetic data assimilation research. We shall present our initial testing results in the meeting.

Kuang, Weijia↗
NASA NTRS2004

Insights into Tropospheric Ozone from the INTEX Ozonesonde Network Study (IONS)

Ozone profile data from soundings integrate models, aircraft and other ground-based measurements for better interpretation of atmospheric chemistry and dynamics. A well-designed network of ozonesonde stations, with consistent sampling, can answer questions not possible with short campaigns or current satellite technology. The SHADOZ (Southern Hemisphere Additional Ozonesondes) project, for example, has led to these findings about tropical ozone: definition of the zonal tropospheric wave-one pattern in equatorial ozone, characterization of the "Atlantic ozone paradox" and establishment of a link between tropical Atlantic and Indian Ocean pollution. Building on the SHADOZ concept, a short-term ozone network was formed in July-August 2004 to coordinate ozonesonde launches during the ICARTT/INTEX/NEAQS (International Consortium on Atmospheric Research on Transport and Transformation)/Intercontinental Transport Experiment/New England Air Quality Study. In IONS (INTEX Ozonesonde Network Study), more than 250 soundings, with daily frequency at half the sites, were launched from eleven North American stations and an oceanographic ship in the Gulf of Maine. Although the goal was to examine pollution influences under stable high-pressure systems and transport associated with "warm conveyor belt" flows, the INTEX study region was dominated by a series of weak frontal system that mixed aged pollution with stratospheric ozone in the middle troposphere. Deconvoluting ozone sources provides new insights into ozone in the transition between mid-latitude and polar air.

Thompson, Anne M.↗
NASA NTRS2005

The North Alabama Lightning Mapping Array (LMA): A Network Overview

The North Alabama Lightning Mapping Array (LMA) is s a 3-D VHF regional lightning detection system that provides on-orbit algorithm validation and instrument performance assessments for the NASA Lightning Imaging Sensor, as well as information on storm kinematics and updraft evolution that offers the potential to improve severe storm warning lead time by up t o 50% and decrease te false alarm r a t e ( for non-tornado producing storms). In support of this latter function, the LMA serves as a principal component of a severe weather test bed to infuse new science and technology into the short-term forecasting of severe and hazardous weather, principally within nearby National Weather Service forecast offices. The LMA, which became operational i n November 2001, consists of VHF receivers deployed across northern Alabama and a base station located at the National Space Science and Technology Center (NSSTC), which is on t h e campus of the University of Alabama in Huntsville. The LMA system locates the sources of impulsive VHF radio signals s from lightning by accurately measuring the time that the signals aririve at the different receiving stations. Each station's records the magnitude and time of the peak lightning radiation signal in successive 80 ms intervals within a local unused television channel (channel 5, 76-82 MHz in our case ) . Typically hundreds of sources per flash can be reconstructed, which i n t u r n produces accurate 3-dimensional lightning image maps (nominally <50 m error within 150 la. range). The data are transmitted back t o a base station using 2.4 GHz wireless Ethernet data links and directional parabolic grid antennas. There are four repeaters in the network topology and the links have an effective data throughput rate ranging from 600 kbits s -1 t o 1.5 %its s -1. This presentation provides an overview of t h e North Alabama network, the data processing (both real-time and post processing) and network statistics.

Blakeslee, R. J.↗
NASA NTRS2005

A Noachian/Hesperian Hiatus and Erosive Reactivation of Martian Valley Networks

Despite new evidence for persistent flow and sedimentation on early Mars, it remains unclear whether valley networks were active over long geologic timescales (10(exp 5)-10(exp 8) yr), or if flows were persistent only during multiple discrete episodes of moderate (approx. 10(exp 4) yr) to short (<10 yr) duration. Understanding the long-term stability/variability of valley network hydrology would provide an important control on paleoclimate and groundwater models. Here we describe geologic evidence for a hiatus in highland valley network activity while the fretted terrain formed, followed by a discrete reactivation of persistent (but possibly variable) erosive flows. Additional information is included in the original extended abstract.

Irwin, R. P., III.↗
NASA NTRS1998

Real-Time, Interactive Echocardiography Over High-Speed Networks: Feasibility and Functional Requirements

Real-time, Interactive Echocardiography Over High Speed Networks: Feasibility and Functional Requirements is an experiment in advanced telemedicine being conducted jointly by the NASA Lewis Research Center, the NASA Ames Research Center, and the Cleveland Clinic Foundation. In this project, a patient undergoes an echocardiographic examination in Cleveland while being diagnosed remotely by a cardiologist in California viewing a real-time display of echocardiographic video images transmitted over the broadband NASA Research and Education Network (NREN). The remote cardiologist interactively guides the sonographer administering the procedure through a two-way voice link between the two sites. Echocardiography is a noninvasive medical technique that applies ultrasound imaging to the heart, providing a "motion picture" of the heart in action. Normally, echocardiographic examinations are performed by a sonographer and cardiologist who are located in the same medical facility as the patient. The goal of telemedicine is to allow medical specialists to examine patients located elsewhere, typically in remote or medically underserved geographic areas. For example, a small, rural clinic might have access to an echocardiograph machine but not a cardiologist. By connecting this clinic to a major metropolitan medical facility through a communications network, a minimally trained technician would be able to carry out the procedure under the supervision and guidance of a qualified cardiologist.

Bobinsky, Eric A.↗
NASA NTRS1998

Satellite-Terrestrial Network Interoperability

The developing national and global information infrastructures (NII/GII) are being built upon the asynchronous transfer mode (ATM) telecommunications protocol and associated protocol standards. These protocols are themselves under development through the telecommunications standards process defined by the International Telecommunications Union (ITU), which as a body is sanctioned by the United Nations. All telecommunications manufacturers use these standards to create products that can interoperate. The ITU has recognized the ATM Forum as the instrument for the development of ATM protocols. This forum is a consortium of industry, academia, and government entities formed to quickly develop standards for the ATM infrastructure. However, because the participants represent a predominately terrestrial network viewpoint, the use of satellites in the national and global information infrastructures could be severely compromised. Consequently, through an ongoing task order, the NASA Lewis Research Center asked Sterling Software, Inc., to communicate with the ATM Forum in support of the interoperability of satellite-terrestrial networks. This year, Dr. Raj Jain of the Ohio State University, under contract to Sterling, authored or coauthored 32 explanatory documents delivered to the ATM Forum in the areas of Guaranteed Frame Rate for Transmission Control Protocol/Internet Protocol (TCP/IP), Available Bit Rate, performance testing, Variable Bit Rate voice over ATM, TCP over Unspecified Bit Rate+, Virtual Source/Virtual Destination, and network management. These contributions have had a significant impact on the content of the standards that the ATM Forum is developing. Some of the more significant accomplishments have been: (1) The adoption by the ATM Forum of a new definition for Message-In, Message-Out latency; and (2) Improved text (clearer wording and newly defined terms) for measurement procedures, foreground and background traffic, and scalable configuration in the latency and throughput sections of the Performance Testing Baseline Text.

vonDeak, Thomas C.↗
NASA NTRS2005

Wireless Local Area Network Performance Inside Aircraft Passenger Cabins

An examination of IEEE 802.11 wireless network performance within an aircraft fuselage is performed. This examination measured the propagated RF power along the length of the fuselage, and the associated network performance: the link speed, total throughput, and packet losses and errors. A total of four airplanes: one single-aisle and three twin-aisle airplanes were tested with 802.11a, 802.11b, and 802.11g networks.

Whetten, Frank L.↗
NASA NTRS2004

Development of the On-board Aircraft Network

Phase II will focus on the development of the on-board aircraft networking portion of the testbed which includes the subnet and router configuration and investigation of QoS issues. This implementation of the testbed will consist of a workstation, which functions as the end system, connected to a router. The router will service two subnets that provide data to the cockpit and the passenger cabin. During the testing, data will be transferred between the end systems and those on both subnets. QoS issues will be identified and a preliminary scheme will be developed. The router will be configured for the testbed network and initial security studies will be initiated. In addition, architecture studies of both the SITA and Immarsat networks will be conducted.

Green, Bryan D. W.↗
NASA NTRS1999

Neural Networks Used to Compare Designed and Measured Time-Average Patterns

Electronic time-average holograms are convenient for comparing the measured vibration modes of fan blades with those calculated by finite-element models. At the NASA Lewis Research Center, neural networks recently were trained to perform what had been a simple visual comparison of the predictions of the design models with the measurements. Finite-element models were used to train neural networks to recognize damage and strain information encoded in subtle changes in the time-average patterns of cantilevers. But the design-grade finite element models were unable to train the neural networks to detect damage in complex blade shapes. The design-model-generated patterns simply did not agree well enough with the measured patterns. Instead, hybrid-training records, with measured time-average patterns as the input and model-generated strain information as the output, were used to effect successful training.

Decker, Arthur J.↗