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The Ribosomal Database Project (RDP) complies ribosomal sequences and related data, and redistributes them in aligned and phylogenetically ordered form to its user community. It also offers various software packages for handling, analyzing and displaying sequences. In addition, the RDP offers (or will offer) certain analytic services. At present the project is in an intermediate stage of development.
The preliminary results are reported of a survey of every EINSTEIN image which overlaps any high-latitude molecular cloud in a search for X-ray emitting pre-main sequence stars. This survey, together with complementary KPNO and IRAS data, will allow the determination of how prevalent low mass star formation is in these clouds in general and, particularly, in the translucent molecular clouds.
The Orion Crew Exploration Vehicle (CET) is being designed to include significantly more automation capability than either the Space Shuttle or the International Space Station (ISS). In particular, the vehicle flight software has requirements to accommodate increasingly automated missions throughout all phases of flight. A data-driven flight software architecture will provide an evolvable automation capability to sequence through Guidance, Navigation & Control (GN&C) flight software modes and configurations while maintaining the required flexibility and human control over the automation. This flexibility is a key aspect needed to address the maturation of operational concepts, to permit ground and crew operators to gain trust in the system and mitigate unpredictability in human spaceflight. To allow for mission flexibility and reconfrgurability, a data driven approach is being taken to load the mission event plan as well cis the flight software artifacts associated with the GN&C subsystem. A database of GN&C level sequencing data is presented which manages and tracks the mission specific and algorithm parameters to provide a capability to schedule GN&C events within mission segments. The flight software data schema for performing automated mission sequencing is presented with a concept of operations for interactions with ground and onboard crew members. A prototype architecture for fault identification, isolation and recovery interactions with the automation software is presented and discussed as a forward work item.
The Robot Sequencing and Visualization Program (RSVP) is being used in the Mars Science Laboratory (MSL) mission for downlink data visualization and command sequence generation. RSVP reads and writes downlink data products from the operations data server (ODS) and writes uplink data products to the ODS. The primary users of RSVP are members of the Rover Planner team (part of the Integrated Planning and Execution Team (IPE)), who use it to perform traversability/articulation analyses, take activity plan input from the Science and Mission Planning teams, and create a set of rover sequences to be sent to the rover every sol. The primary inputs to RSVP are downlink data products and activity plans in the ODS database. The primary outputs are command sequences to be placed in the ODS for further processing prior to uplink to each rover. RSVP is composed of two main subsystems. The first, called the Robot Sequence Editor (RoSE), understands the MSL activity and command dictionaries and takes care of converting incoming activity level inputs into command sequences. The Rover Planners use the RoSE component of RSVP to put together command sequences and to view and manage command level resources like time, power, temperature, etc. (via a transparent realtime connection to SEQGEN). The second component of RSVP is called HyperDrive, a set of high-fidelity computer graphics displays of the Martian surface in 3D and in stereo. The Rover Planners can explore the environment around the rover, create commands related to motion of all kinds, and see the simulated result of those commands via its underlying tight coupling with flight navigation, motor, and arm software. This software is the evolutionary replacement for the Rover Sequencing and Visualization software used to create command sequences (and visualize the Martian surface) for the Mars Exploration Rover mission.
The Orion Crew Exploration Vehicle is being designed with greater automation capabilities than any other crewed spacecraft in NASA s history. The Guidance, Navigation, and Control (GN&C) flight software architecture is designed to provide a flexible and evolvable framework that accommodates increasing levels of automation over time. Within the GN&C flight software, a data-driven approach is used to configure software. This approach allows data reconfiguration and updates to automated sequences without requiring recompilation of the software. Because of the great dependency of the automation and the flight software on the configuration data, the data management is a vital component of the processes for software certification, mission design, and flight operations. To enable the automated sequencing and data configuration of the GN&C subsystem on Orion, a desktop database configuration tool has been developed. The database tool allows the specification of the GN&C activity sequences, the automated transitions in the software, and the corresponding parameter reconfigurations. These aspects of the GN&C automation on Orion are all coordinated via data management, and the database tool provides the ability to test the automation capabilities during the development of the GN&C software. In addition to providing the infrastructure to manage the GN&C automation, the database tool has been designed with capabilities to import and export artifacts for simulation analysis and documentation purposes. Furthermore, the database configuration tool, currently used to manage simulation data, is envisioned to evolve into a mission planning tool for generating and testing GN&C software sequences and configurations. A key enabler of the GN&C automation design, the database tool allows both the creation and maintenance of the data artifacts, as well as serving the critical role of helping to manage, visualize, and understand the data-driven parameters both during software development and throughout the life of the Orion project.
We are developing a system for synthesizing image sequences the simulate the facial motion of a speaker. To perform this synthesis, we are pursuing two major areas of effort. We are developing the necessary computer graphics technology to synthesize a realistic image sequence of a person speaking selected speech sequences. Next, we are developing a model that expresses the relation between spoken phonemes and face/mouth shape. A subject is video taped speaking an arbitrary text that contains expression of the full list of desired database phonemes. The subject is video taped from the front speaking normally, recording both audio and video detail simultaneously. Using the audio track, we identify the specific video frames on the tape relating to each spoken phoneme. From this range we digitize the video frame which represents the extreme of mouth motion/shape. Thus, we construct a database of images of face/mouth shape related to spoken phonemes. A selected audio speech sequence is recorded which is the basis for synthesizing a matching video sequence; the speaker need not be the same as used for constructing the database. The audio sequence is analyzed to determine the spoken phoneme sequence and the relative timing of the enunciation of those phonemes. Synthesizing an image sequence corresponding to the spoken phoneme sequence is accomplished using a graphics technique known as morphing. Image sequence keyframes necessary for this processing are based on the spoken phoneme sequence and timing. We have been successful in synthesizing the facial motion of a native English speaker for a small set of arbitrary speech segments. Our future work will focus on advancement of the face shape/phoneme model and independent control of facial features.
The recent genome sequencing of a non-vertebrate deuterostome, the ascidian tunicate Ciona intestinalis, makes a substantial contribution to the fields of evolutionary and developmental biology.1 Tunicates have some of the smallest bilaterian genomes, embryos with relatively few cells, fixed lineages and early determination of cell fates. Initial analyses of the C. intestinalis genome indicate that it has been evolving rapidly. Comparisons with other bilaterians show that C. intestinalis has lost a number of genes, and that many genes linked together in most other bilaterians have become uncoupled. In addition, a number of independent, lineage-specific gene duplications have been detected. These new results, although interesting in themselves, will take on a deeper significance once the genomes of additional invertebrate deuterostomes (e.g. echinoderms, hemichordates and amphioxus) have been sequenced. With such a broadened database, comparative genomics can begin to ask pointed questions about the relationship between the evolution of genomes and the evolution of body plans. Copyright 2003 Wiley Periodicals, Inc.
In order to discern whether the high-latitude molecular clouds are regions of ongoing star formation, we have used X-ray emission as a tracer of youthful stars. The entire Einstein database yields 18 images which overlap 10 of the clouds mapped partially or completely in the CO (1-0) transition, providing a total of approximately 6 deg squared of overlap. Five previously unidentified X-ray sources were detected: one has an optical counterpart which is a pre-main-sequence (PMS) star, and two have normal main-sequence stellar counterparts, while the other two are probably extragalactic sources. The PMS star is located in a high Galactic latitude Lynds dark cloud, so this result is not too suprising. The translucent clouds, though, have yet to reveal any evidence of star formation.
We present a representative sample of near-infrared (1-2 mu m) images spanning the Hubble galaxy morphology classification sequence. The images come from the Two Micron All Sky Survey, with a range in brightness of 7 mag , K-s , 13.5 mag, and the morphological classifications from the NASA/IPAC Extragalactic Database.
Cumulative fatigue under axial and torsional loading conditions can include both load-order (higMow and low/high) as well as load-type sequence (axial/torsional and torsional/axial) effects. Previously reported experimental studies on a cobalt-base superalloy, Haynes 188 at 538 C, addressed these effects. These studies characterized the cumulative axial and torsional fatigue behavior under high amplitude followed by low amplitude (Kalluri, S. and Bonacuse, P. J., "Cumulative Axial and Torsional Fatigue: An Investigation of Load-Type Sequance Effects," in Multiaxial Fatigue and Deformation: Testing and Prediction, ASTM STP 1387, S. Kalluri, and P. J. Bonacuse, Eds., American Society for Testing and Materials, West Conshohocken, PA, 2000, pp. 281-301) and low amplitude followed by high amplitude (Bonacuse, P. and Kalluri, S. "Sequenced Axial and Torsional Cumulative Fatigue: Low Amplitude Followed by High Amplitude Loading," Biaxial/Multiaxial Fatigue and Fracture, ESIS Publication 31, A. Carpinteri, M. De Freitas, and A. Spagnoli, Eds., Elsevier, New York, 2003, pp. 165-182) conditions. In both studies, experiments with the following four load-type sequences were performed: (a) axial/axial, (b) torsional/torsional, (c) axial/torsional, and (d) torsional/axial. In this paper, the cumulative axial and torsional fatigue data generated in the two previous studies are combined to generate a comprehensive cumulative fatigue database on both the load-order and load-type sequence effects. This comprehensive database is used to examine applicability of the Palmgren-langer-Miner linear damage rule and a nonlinear damage curve approach for Haynes 188 subjected to the load-order and load-type sequencing described above. Summations of life fractions from the experiments are compared to the predictions from both the linear and nonlinear cumulative fatigue damage approaches. The significance of load-order versus load-type sequence effects for axial and torsional loading conditions is discussed. Possible reasons for the observed differences between the computed and observed summations of cycle fractions are rationalized in terms of the observed ever lutions of cyclic axial and shear stress ranges in the cumulative fatigue tests.
A method of analyzing 16S rRNA catalog data has been developed in which groupings at various taxonomic levels can be characterized in terms of specific "signature" oligonucleotides. This approach provides an alternative means for evaluating higher order branching possibilities and can be used to assess the phylogenetic position of isolates that are poorly placed by the usual clustering procedures. This signature approach has been applied to forty archaebacterial catalogs and every oligonucleotide with significant signature value has been identified. Sets of specific oligonucleotides were identified for every major group on a dendrogram produced by cluster analysis procedures. Signatures that would establish between group relationships were also sought and found. In the case of the Methanobacteriaceae the clustering methods suggest a specific relationship to the Methanococcaceae. This inclusion is in fact supported by six strong signature oligonucleotides. However there are also significant numbers of signature oligonucleotides supporting a specific relationship of the Methanobacteriaceae to either the Halobacteriaceae or the Methanomicrobiaceae. Thus the placement of the Methanobacteriaceae is less certain than the usual dendrograms imply. The signature approach also was used to assess the phylogenetic position of Thermoplasma acidophilum which is found to be more closely related to the methanogen/halophile Division than to the sulfur dependent Division of the archaebacteria. This does not imply however that Thermoplasma acidophilum is properly regarded as being in the methanogen/halophile Division.
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.
Computer-based statistical techniques used to determine homologies between proteins occurring in different species are reviewed. The technique is based on comparison of two protein sequences, either by relating all segments of a given length in one sequence to all segments of the second or by finding the best alignment of the two sequences. Approaches discussed include selection using printed tabulations, identification of very similar sequences, and computer searches of a database. The use of the SEARCH, RELATE, and ALIGN programs (Dayhoff, 1979) is explained; sample data are presented in graphs, diagrams, and tables and the construction of scoring matrices is considered.
In certain kinds of geophysical surveys, the fields are continua, but measured at discrete points referenced by their position or time of measurement. Systems of this kind are better modelled by databases built from basic data structures attuned to representing traverses across continua that are not of pre-defined fixed length. The general Array DataBase is built on arrays (ordered sequencies of data) with each array holding data elements of one type. The arrays each occupy their own physical data set, in turn inter-related by a hierarchy to other arrays over the same space/time reference points. The GADB illustrates the principle that a data facility should reflect the fundamental properties of its data, and support retrieval based on the application's view. The GADB is being tested by its use in NASA's project MAGSAT.
An IRAF package to assist in SPP code development and debugging is described. SPP is the machine-independent programming language used by virtually all IRAF tasks. Tools have been written to aide both novice and advanced SPP programmers with development and debugging by providing tasks to check the code for the number and type of arguments in all calls to IRAF VOS library procedures, list the calling sequences of IRAF tasks, create a database of identifiers for quick access, check for memory which is not freed, and a source code formatter. Debugging is simplified since the programmer is able to get a better understanding of the structure of his/her code, and IRAF library procedure calls (probably the most common source of errors) are automatically checked for correctness.
Purpose: Knowledge management for space exploration is part of a multi-generational effort. Each mission builds on knowledge from prior missions, and learning is the first step in knowledge production. This paper uses the Mars Exploration Rover mission as a site to explore this process. Approach: Observational study and analysis of the work of the MER science and engineering team during rover operations, to investigate how learning occurs, how it is recorded, and how these representations might be made available for subsequent missions. Findings: Learning occurred in many areas: planning science strategy, using instrumen?s within the constraints of the martian environment, the Deep Space Network, and the mission requirements; using software tools effectively; and running two teams on Mars time for three months. This learning is preserved in many ways. Primarily it resides in individual s memories. It is also encoded in stories, procedures, programming sequences, published reports, and lessons learned databases. Research implications: Shows the earliest stages of knowledge creation in a scientific mission, and demonstrates that knowledge management must begin with an understanding of knowledge creation. Practical implications: Shows that studying learning and knowledge creation suggests proactive ways to capture and use knowledge across multiple missions and generations. Value: This paper provides a unique analysis of the learning process of a scientific space mission, relevant for knowledge management researchers and designers, as well as demonstrating in detail how new learning occurs in a learning organization.
We review evidence supporting the idea that the DNA sequence in genes containing non-coding regions is correlated, and that the correlation is remarkably long range--indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationarity" feature of the sequence of base pairs by applying a new algorithm called detrended fluctuation analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and non-coding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33301 coding and 29453 non-coding) in the entire GenBank database. Finally, we describe briefly some recent work showing that the non-coding sequences have certain statistical features in common with natural and artificial languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts. These statistical properties of non-coding sequences support the possibility that non-coding regions of DNA may carry biological information.
The Operations Engineering Lab (OEL) at JPL has developed the multimission command system as part of JPL's Advanced Multimission Operations System. The command system provides an advanced multimission environment for secure, concurrent commanding of multiple spacecraft. The command functions include real-time command generation, command translation and radiation, status reporting, some remote control of Deep Space Network antenna functions, and command file management. The mission-independent architecture has allowed easy adaptation to new flight projects and the system currently supports all JPL planetary missions (Voyager, Galileo, Magellan, Ulysses, Mars Pathfinder, and CASSINI). This paper will discuss the design and implementation of the command software, especially trade-offs and lessons learned from practical operational use. The lessons learned have resulted in a re-engineering of the command system, especially in its user interface and new automation capabilities. The redesign has allowed streamlining of command operations with significant improvements in productivity and ease of use. In addition, the new system has provided a command capability that works equally well for real-time operations and within a spacecraft testbed. This paper will also discuss new development work including a multimission command database toolkit, a universal command translator for sequencing and real-time commands, and incorporation of telecommand capabilities for new missions.