SEARCH · Search NASA
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
The 16S rRNA of the bacterion Aquifex pyrophilus, a microaerophilic, oxygen-reducing hyperthermophile, has been sequenced directly from the the PCR amplified gene. Phylogenetic analyses show the Aq. pyrophilus lineage to be probably the deepest (earliest) in the (eu)bacterial tree. The addition of this deep branching to the bacterial tree further supports the argument that the Bacteria are of thermophilic ancestry.
A major and too little recognized source of artifact in phylogenetic analysis of molecular sequence data is compositional difference among sequences. The problem becomes particularly acute when alignments contain ribosomal RNAs from both mesophilic and thermophilic species. Among prokaryotes the latter are considerably higher in G + C content than the former, which often results in artificial clustering of thermophilic lineages and their being placed artificially deep in phylogenetic trees. In this communication we review archaeal phylogeny in the light of this consideration, focusing in particular on the phylogenetic position of the sulfate reducing species Archaeoglobus fulgidus, using both 16S rRNA and 23S rRNA sequences. The analysis shows clearly that the previously reported deep branching of the A. fulgidus lineage (very near the base of the euryarchaeal side of the archaeal tree) is incorrect, and that the lineage actually groups with a previously recognized unit that comprises the Methanomicrobiales and extreme halophiles.
How should the world's living organisms be classified? Into how many kingdoms should they be grouped? Scientists have been grappling with these questions since the time of Aristotle, drawing on a broad base of biological characteristics for clues. The fossil record, visible traits of living organisms and, more recently, results from cell biology have all shaped theories of biological classification. But last year a new and controversial concept emerged: a classification of life based solely on molecular traits. The focal point of the controversy is a tree of life, or "phylogeny", devised by Carl Woese of the University of Illinois, Otto Kandler of the University of Munich and Mark Wheelis of the University of California. The tree is unusual because, unlike all previous schemes, it is constructed solely from biochemical data such as DNA sequences rather than a range of different organism characteristics. But that is not all. The scheme also challenges the idea that life on Earth is best divided into five kingdoms, with the main split being between bacteria and all other organisms. Woese and his colleagues create three main groupings by dividing the bacteria in two and unifying all other organisms.
Features of the physical environment surrounding an ancestral organism can be inferred by reconstructing sequences of ancient proteins made by those organisms, resurrecting these proteins in the laboratory, and measuring their properties. Here, we resurrect candidate sequences for elongation factors of the Tu family (EF-Tu) found at ancient nodes in the bacterial evolutionary tree, and measure their activities as a function of temperature. The ancient EF-Tu proteins have temperature optima of 55-65 degrees C. This value seems to be robust with respect to uncertainties in the ancestral reconstruction. This suggests that the ancient bacteria that hosted these particular genes were thermophiles, and neither hyperthermophiles nor mesophiles. This conclusion can be compared and contrasted with inferences drawn from an analysis of the lengths of branches in trees joining proteins from contemporary bacteria, the distribution of thermophily in derived bacterial lineages, the inferred G + C content of ancient ribosomal RNA, and the geological record combined with assumptions concerning molecular clocks. The study illustrates the use of experimental palaeobiochemistry and assumptions about deep phylogenetic relationships between bacteria to explore the character of ancient life.
Members of the Deinococcaceae (e.g., Thermus, Meiothermus, Deinococcus) contain A/V-ATPases typically found in Archaea or Eukaryotes which were probably acquired by horizontal gene transfer. Two methods were used to quantify the extent to which archaeal or eukaryotic genes have been acquired by this lineage. Screening of a Meiothermus ruber library with probes made against Thermoplasma acidophilum DNA yielded a number of clones which hybridized more strongly than background. One of these contained the prolyl tRNA synthetase (RS) gene. Phylogenetic analysis shows the M. ruber and D. radiodurans prolyl RS to be more closely related to archaeal and eukaryal forms of this gene than to the typical bacterial type. Using a bioinformatics approach, putative open reading frames (ORFs) from the prerelease version of the D. radiodurans genome were screened for genes more closely related to archaeal or eukaryotic genes. Putative ORFs were searched against representative genomes from each of the three domains using automated BLAST. ORFs showing the highest matches against archaeal and eukaryotic genes were collected and ranked. Among the top-ranked hits were the A/V-ATPase catalytic and noncatalytic subunits and the prolyl RS genes. Using phylogenetic methods, ORFs were analyzed and trees assessed for evidence of horizontal gene transfer. Of the 45 genes examined, 20 showed topologies in which D. radiodurans homologues clearly group with eukaryotic or archaeal homologues, and 17 additional trees were found to show probable evidence of horizontal gene transfer. Compared to the total number of ORFs in the genome, those that can be identified as having been acquired from Archaea or Eukaryotes are relatively few (approximately 1%), suggesting that interdomain transfer is rare.
We used molecular genetic methods to test two hypotheses, (i) that host plant specificity among ectomycorrhizal fungi would be common in a closed-canopy, mixed Pinus contorta-Picea engelmannii forest in Yellowstone National Park and (ii) that specificity would be more common in the early successional tree species, P. contorta, than in the invader, P. engelmannii. We identified 28 ectomycorrhizal fungal species collected from 27 soil cores. The proportion of P. engelmannii to P. contorta ectomycorrhizae was nearly equal (52 and 48%, respectively). Of the 28 fungal species, 18 composed greater than 95% of the fungal community. No species was associated exclusively with P. contorta, but four species, each found in only one core, and one species found in two cores were associated exclusively with P. engelmannii. These fungi composed less than 5% of the total ectomycorrhizae. Thus, neither hypothesis was supported, and hypothesized benefits of ectomycorrhizal specificity to both trees and fungi probably do not exist in this system.
To compare the relative contributions of gravity and vascular structure to the distribution of pulmonary blood flow, we flew with pigs on the National Aeronautics and Space Administration KC-135 aircraft. A series of parabolas created alternating weightlessness and 1.8-G conditions. Fluorescent microspheres of varying colors were injected into the pulmonary circulation to mark regional blood flow during different postural and gravitational conditions. The lungs were subsequently removed, air dried, and sectioned into approximately 2 cm(3) pieces. Flow to each piece was determined for the different conditions. Perfusion heterogeneity did not change significantly during weightlessness compared with normal and increased gravitational forces. Regional blood flow to each lung piece changed little despite alterations in posture and gravitational forces. With the use of multiple stepwise linear regression, the contributions of gravity and vascular structure to regional perfusion were separated. We conclude that both gravity and the geometry of the pulmonary vascular tree influence regional pulmonary blood flow. However, the structure of the vascular tree is the primary determinant of regional perfusion in these animals.
A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when "genetic temperatures" were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell "crystallized," i.e., became refractory to lateral gene transfer, at different stages of "cooling," with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.
Many human space exploration mission architecture assessments have been performed over the years by diverse organizations and individuals. Direct comparison of metrics among these studies is extremely difficult due to widely varying assumptions involving projected technology readiness, mission goals, acceptable risk criteria, and socio-political environments. However, constant over the years have been the physical laws of celestial dynamics and rocket propulsion systems. A finite diverse yet finite architecture trade space should exist which captures methods of human exploration - particularly of the Moon and Mars - by delineating technical trades and cataloging the physically realizable options of each. A particular architectural approach should then have a traceable path through this "trade tree". It should be pointed out that not every permutation of paths will result in a physically realizable mission approach, but cataloging options that have been examined by past studies should help guide future analysis. This effort was undertaken in two phases by multi-center NASA working groups in the spring and summer of 2004 using more than thirty years of past studies to "flesh out" the Moon-Mars human exploration trade space. The results are presented, not as a "trade tree", which would be unwieldy, but as a "menu" of potential technical options as a function of mission phases. This is envisioned as a tool to aid future mission designers by offering guidance to relevant past analyses.
In many domains, automated reasoning tools must represent graphs of causally linked events. These include fault-tree analysis, probabilistic risk assessment (PRA), planning, procedures, medical reasoning about disease progression, and functional architectures. Each of these fields has its own requirements for the representation of causation, events, actors and conditions. The representations include ontologies of function and cause, data dictionaries for causal dependency, failure and hazard, and interchange formats between some existing tools. In none of the domains has a generally accepted interchange format emerged. The paper makes progress towards interoperability across the wide range of causal analysis methodologies. We survey existing practice and emerging interchange formats in each of these fields. Setting forth a set of terms and concepts that are broadly shared across the domains, we examine the several ways in which current practice represents them. Some phenomena are difficult to represent or to analyze in several domains. These include mode transitions, reachability analysis, positive and negative feedback loops, conditions correlated but not causally linked and bimodal probability distributions. We work through examples and contrast the differing methods for addressing them. We detail recent work in knowledge interchange formats for causal trees in aerospace analysis applications in early design, safety and reliability. Several examples are discussed, with a particular focus on reachability analysis and mode transitions. We generalize the aerospace analysis work across the several other domains. We also recommend features and capabilities for the next generation of causal knowledge representation standards.
In the Brazilian Amazon, selective logging is second only to forest conversion in its extent. Conversion to pasture or agriculture tends to reduce soil nutrients and site productivity over time unless fertilizers are added. Logging removes nutrients in bole wood, enough that repeated logging could deplete essential nutrients over time. After a single logging event, nutrient losses are likely to be too small to observe in the large soil nutrient pools, but disturbances associated with logging also alter soil properties. Selective logging, particularly reduced-impact logging, results in consistent patterns of disturbance that may be associated with particular changes in soil properties. Soil bulk density, pH, carbon (C), nitrogen (N), phosphorus (P), calcium (Ca), magnesium (Mg), potassium (K), iron (Fe), aluminum (Al), delta(sup 3)C, delta(sup 15)N, and P fractionations were measured on the soils of four different types of loggingrelated disturbances: roads, decks, skids, and treefall gaps. Litter biomass and percent bare ground were also determined in these areas. To evaluate the importance of fresh foliage inputs from downed tree crowns in treefall gaps, foliar nutrients for mature forest trees were also determined and compared to that of fresh litterfall. The immediate impacts of logging on soil properties and how these might link to the longer-term estimated nutrient losses and the observed changes in soils were studied.
When developing a domain model, it seems natural to bring the traditional informal tools of inspection and verification, debuggers and automated test suites, to bear upon the problems that will inevitably arise. Debuggers that allow inspection of registers and memory and stepwise execution have been a staple of software development of all sorts from the very beginning. Automated testing has repeatedly proven its considerable worth, to the extent that an entire design philosophy (Test Driven Development) has been developed around the writing of tests. Unfortunately, while not entirely without their uses, the limitations of these tools and the nature of the complexity of models and the underlying planning systems make the diagnosis of certain classes of problems and the verification of their solutions difficult or impossible. Debuggers provide a good local view of executing code, allowing a fine-grained look at algorithms and data. This view is, however, usually only at the level of the current scope in the implementation language, and the data-inspection capabilities of most debuggers usually consist of on-line print statements. More modem graphical debuggers offer a sort of tree view of data structures, but even this is too low-level and is often inappropriate for the kinds of structures created by planning systems. For instance, god or constraint networks are at best awkward when visualized as trees. Any any non-structural link between data structures, as through a lookup table, isn't captured at all. Further, while debuggers have powerful breakpointing facilities that are suitable for finding specific algorithmic errors, they have little use in the diagnosis of modeling errors.
Many types of hazard and risk analyses are used during the life cycle of complex systems, including Failure Modes and Effects Analysis (FMEA), Hazard Analysis, Fault Tree and Event Tree Analysis, Probabilistic Risk Assessment, Reliability Analysis and analysis of Problem Reporting and Corrective Action (PRACA) databases. The success of these methods depends on the availability of input data and the analysts knowledge. Standard nomenclature can increase the reusability of hazard, risk and problem data. When nomenclature in the source texts is not standard, taxonomies with mapping words (sets of rough synonyms) can be combined with semantic search to identify items and tag them with metadata based on a rich standard nomenclature. Semantic search uses word meanings in the context of parsed phrases to find matches. The NASA taxonomies provide the word meanings. Spacecraft taxonomies and ontologies (generalization hierarchies with attributes and relationships, based on terms meanings) are being developed for types of subsystems, functions, entities, hazards and failures. The ontologies are broad and general, covering hardware, software and human systems. Semantic search of Space Station texts was used to validate and extend the taxonomies. The taxonomies have also been used to extract system connectivity (interaction) models and functions from requirements text. Now the Reconciler semantic search tool and the taxonomies are being applied to improve search in the Space Shuttle PRACA database, to discover recurring patterns of failure. Usual methods of string search and keyword search fall short because the entries are terse and have numerous shortcuts (irregular abbreviations, nonstandard acronyms, cryptic codes) and modifier words cannot be used in sentence context to refine the search. The limited and fixed FMEA categories associated with the entries do not make the fine distinctions needed in the search. The approach assigns PRACA report titles to problem classes in the taxonomy. Each ontology class includes mapping words - near-synonyms naming different manifestations of that problem class. The mapping words for Problems, Entities and Functions are converted to a canonical form plus any of a small set of modifier words (e.g. non-uniformity NOT + UNIFORM.) The report titles are parsed as sentences if possible, or treated as a flat sequence of word tokens if parsing fails. When canonical forms in the title match mapping words, the PRACA entry is associated with the corresponding Problem, Entity or Function in the ontology. The user can search for types of failures associated with types of equipment, clustering by type of problem (e.g., all bearings found with problems of being uneven: rough, irregular, gritty ). The results could also be used for tagging PRACA report entries with rich metadata. This approach could also be applied to searching and tagging failure modes, failure effects and mitigations in FMEAs. In the pilot work, parsing 52K+ truncated titles (the test cases that were available), has resulted in identification of both a type of equipment and type of problem in about 75% of the cases. The results are displayed in a manner analogous to Google search results. The effort has also led to the enrichment of the taxonomy, adding some new categories and many new mapping words. Further work would make enhancements that have been identified for improving the clustering and further reducing the false alarm rate. (In searching for recurring problems, good clustering is more important than reducing false alarms). Searching complete PRACA reports should lead to immediate improvement.
National Aeronautics and Space Administration s (NASA) International Space Station (ISS) Program uses Probabilistic Risk Assessment (PRA) as part of its Continuous Risk Management Process. It is used as a decision and management support tool to not only quantify risk for specific conditions, but more importantly comparing different operational and management options to determine the lowest risk option and provide rationale for management decisions. This paper presents the derivation of the probability distributions used to quantify the failure rates and the probability of failures of the basic events employed in the PRA model of the ISS. The paper will show how a Bayesian approach was used with different sources of data including the actual ISS on orbit failures to enhance the confidence in results of the PRA. As time progresses and more meaningful data is gathered from on orbit failures, an increasingly accurate failure rate probability distribution for the basic events of the ISS PRA model can be obtained. The ISS PRA has been developed by mapping the ISS critical systems such as propulsion, thermal control, or power generation into event sequences diagrams and fault trees. The lowest level of indenture of the fault trees was the orbital replacement units (ORU). The ORU level was chosen consistently with the level of statistically meaningful data that could be obtained from the aerospace industry and from the experts in the field. For example, data was gathered for the solenoid valves present in the propulsion system of the ISS. However valves themselves are composed of parts and the individual failure of these parts was not accounted for in the PRA model. In other words the failure of a spring within a valve was considered a failure of the valve itself.
Typically, data collected by a spacecraft is downlinked to Earth and pre-processed before any analysis is performed. We have developed classifiers that can be used onboard a spacecraft to identify high priority data for downlink to Earth, providing a method for maximizing the use of a potentially bandwidth limited downlink channel. Onboard analysis can also enable rapid reaction to dynamic events, such as flooding, volcanic eruptions or sea ice break-up. Four classifiers were developed to identify cryosphere events using hyperspectral images. These classifiers include a manually constructed classifier, a Support Vector Machine (SVM), a Decision Tree and a classifier derived by searching over combinations of thresholded band ratios. Each of the classifiers was designed to run in the computationally constrained operating environment of the spacecraft. A set of scenes was hand-labeled to provide training and testing data. Performance results on the test data indicate that the SVM and manual classifiers outperformed the Decision Tree and band-ratio classifiers with the SVM yielding slightly better classifications than the manual classifier.
The characterization of forested areas is frequently required in resource management practice. Passive remotely sensed data, which are much more accessible and cost effective than are active data, have rarely, if ever, been used to characterize forest structure directly, but rather they usually focus on the estimation of indirect measurement of biomass or canopy coverage. In this study, some spatial analysis techniques are presented that might be employed with Landsat TM data to analyze forest structure characteristics. A case study is presented wherein fractal dimensions, along with a simple spatial autocorrelation technique (Moran s I), were related to stand density parameters of the Oakmulgee National Forest located in the southeastern United States (Alabama). The results of the case study presented herein have shown that as the percentage of smaller diameter trees becomes greater, and particularly if it exceeds 50%, then the canopy image obtained from Landsat TM data becomes sufficiently homogeneous so that the spatial indices reach their lower limits and thus are no longer determinative. It also appears, at least for the Oakmulgee forest, that the relationships between the spatial indices and forest class percentages within the boundaries can reasonably be considered linear. The linear relationship is much more pronounced in the sawtimber and saplings cases than in samples dominated by medium sized trees (poletimber). In addition, it also appears that, at least for the Oakmulgee forest, the relationships between the spatial indices and forest species groups (Hardwood and Softwood) percentages can reasonably be considered linear. The linear relationship is more pronounced in the forest species groups cases than in the forest classes cases. These results appear to indicate that both fractal dimensions and spatial autocorrelation indices hold promise as means of estimating forest stand characteristics from remotely sensed images. However, additional work is needed to confirm that the boundaries identified for Oakmulgee forest and the linear nature of the relationship between image complexity indices and forest characteristics are generally evident in other forests. In addition, the effects of other parameters such ,as topographic relief and image distortion due to sun angle and cloud cover, for example, need to be examined.
CAPRI is a software building tool-kit that refers to two ideas; (1) A simplified, object-oriented, hierarchical view of a solid part integrating both geometry and topology definitions, and (2) programming access to this part or assembly and any attached data. A complete definition of the geometry and application programming interface can be found in the document CAPRI: Computational Analysis PRogramming Interface appended to this report. In summary the interface is subdivided into the following functional components: 1. Utility routines -- These routines include the initialization of CAPRI, loading CAD parts and querying the operational status as well as closing the system down. 2. Geometry data-base queries -- This group of functions allow all top level applications to figure out and get detailed information on any geometric component in the Volume definition. 3. Point queries -- These calls allow grid generators, or solvers doing node adaptation, to snap points directly onto geometric entities. 4. Calculated or geometrically derived queries -- These entry points calculate data from the geometry to aid in grid generation. 5. Boundary data routines -- This part of CAPRI allows general data to be attached to Boundaries so that the boundary conditions can be specified and stored within CAPRI s data-base. 6. Tag based routines -- This part of the API allows the specification of properties associated with either the Volume (material properties) or Boundary (surface properties) entities. 7. Geometry based interpolation routines -- This part of the API facilitates Multi-disciplinary coupling and allows zooming through Boundary Attachments. 8. Geometric creation and manipulation -- These calls facilitate constructing simple solid entities and perform the Boolean solid operations. Geometry constructed in this manner has the advantage that if the data is kept consistent with the CAD package, therefore a new design can be incorporated directly and is manufacturable. 9. Master Model access This addition to the API allows for the querying of the parameters and dimensions of the model. The feature tree is also exposed so it is easy to see where the parameters are applied. Calls exist to allow for the modification of the parameters and the suppression/unsuppression of nodes in the tree. Part regeneration is performed by a single API call and a new part becomes available within CAPRI (if the regeneration was successful). This is described in a separate document. Components 1-7 are considered the CAPRI base level reader.
This research focuses on testing whether or not the hazardous conditions identified by design-level fault tree analysis will occur in the target implementation. Part 1: Integrate fault tree models into functional specifications so as to identify testable interactions between intended behaviors and hazardous conditions. Part 2: Develop a test generator that produces not only functional tests but also safety tests for a target implementation in a cost-effective way. Part 3: Develop a testing environment for executing generated functional and safety tests and evaluating test results against expected behaviors or hazardous conditions. It includes a test harness as well as an environment simulation of external events and conditions.