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At least 1,369 records · Page 76

Spatial expression of Hox cluster genes in the ontogeny of a sea urchin

The Hox cluster of the sea urchin Strongylocentrous purpuratus contains ten genes in a 500 kb span of the genome. Only two of these genes are expressed during embryogenesis, while all of eight genes tested are expressed during development of the adult body plan in the larval stage. We report the spatial expression during larval development of the five 'posterior' genes of the cluster: SpHox7, SpHox8, SpHox9/10, SpHox11/13a and SpHox11/13b. The five genes exhibit a dynamic, largely mesodermal program of expression. Only SpHox7 displays extensive expression within the pentameral rudiment itself. A spatially sequential and colinear arrangement of expression domains is found in the somatocoels, the paired posterior mesodermal structures that will become the adult perivisceral coeloms. No such sequential expression pattern is observed in endodermal, epidermal or neural tissues of either the larva or the presumptive juvenile sea urchin. The spatial expression patterns of the Hox genes illuminate the evolutionary process by which the pentameral echinoderm body plan emerged from a bilateral ancestor.

Non-NASA Center↗

Study of Cluster Formation and its Effects on Rayleigh and Raman Scattering Measurements in a Mach 6 Wind Tunnel

Using a frequency-doubled Nd-YAG pulsed laser and a single-intensified CCD camera, Rayleigh scattering measurements have been performed to study the cluster formation in a Mach 6 wind tunnel at NASA Langley Research Center. These studies were conducted both in the free stream and in a model flow field for various flow conditions to gain an understanding of the dependence of the Rayleigh scattering (by clusters) on the local pressures and temperatures in the facility. Using the same laser system, we have also performed simultaneous measurements of the local temperature using the rotational Raman scattering of molecular nitrogen and determined the densities of molecular oxygen and nitrogen by using the vibrational Raman scattering from these species. Quantitative results will be presented in detail with emphasis on the applicability of the Rayleigh scattering for obtaining quantitative measurements of molecular densities both in the free stream and in the model flow field.

Shirinzadeh, B.↗

Data Management as a Cluster Middleware Centerpiece

Through earth and space modeling and the ongoing launches of satellites to gather data, NASA has become one of the largest producers of data in the world. These large data sets necessitated the creation of a Data Management System (DMS) to assist both the users and the administrators of the data. Halcyon Systems Inc. was contracted by the NASA Center for Computational Sciences (NCCS) to produce a Data Management System. The prototype of the DMS was produced by Halcyon Systems Inc. (Halcyon) for the Global Modeling and Assimilation Office (GMAO). The system, which was implemented and deployed within a relatively short period of time, has proven to be highly reliable and deployable. Following the prototype deployment, Halcyon was contacted by the NCCS to produce a production DMS version for their user community. The system is composed of several existing open source or government-sponsored components such as the San Diego Supercomputer Center s (SDSC) Storage Resource Broker (SRB), the Distributed Oceanographic Data System (DODS), and other components. Since Data Management is one of the foremost problems in cluster computing, the final package not only extends its capabilities as a Data Management System, but also to a cluster management system. This Cluster/Data Management System (CDMS) can be envisioned as the integration of existing packages.

Zero, Jose↗

Conserved gene clusters in bacterial genomes provide further support for the primacy of RNA

Five complete bacterial genome sequences have been released to the scientific community. These include four (eu)Bacteria, Haemophilus influenzae, Mycoplasma genitalium, M. pneumoniae, and Synechocystis PCC 6803, as well as one Archaeon, Methanococcus jannaschii. Features of organization shared by these genomes are likely to have arisen very early in the history of the bacteria and thus can be expected to provide further insight into the nature of early ancestors. Results of a genome comparison of these five organisms confirm earlier observations that gene order is remarkably unpreserved. There are, nevertheless, at least 16 clusters of two or more genes whose order remains the same among the four (eu)Bacteria and these are presumed to reflect conserved elements of coordinated gene expression that require gene proximity. Eight of these gene orders are essentially conserved in the Archaea as well. Many of these clusters are known to be regulated by RNA-level mechanisms in Escherichia coli, which supports the earlier suggestion that this type of regulation of gene expression may have arisen very early. We conclude that although the last common ancestor may have had a DNA genome, it likely was preceded by progenotes with an RNA genome.

Non-NASA Center↗

Clusters of DNA damage induced by ionizing radiation: formation of short DNA fragments. II. Experimental detection

The basic 30-nm chromatin fiber in the mammalian cell consists of an unknown (possibly helical) arrangement of nucleosomes, with about 1.2 kb of DNA per 10-nm length of fiber. Track-structure considerations suggest that interactions of single delta rays or high-LET particles with the chromatin fiber might result in the formation of multiple lesions spread over a few kilobases of DNA (see the accompanying paper: W.R. Holley and A. Chatterjee, Radiat. Res. 145, 188-199, 1996). In particular, multiple DNA double-strand breaks and single-strand breaks may form. To test this experimentally, primary human fibroblasts were labeled with [3H]thymidine and exposed at 0 degrees C to X rays or accelerated nitrogen or iron ions in the LET range of 97-440 keV/microns. DNA was isolated inside agarose plugs and subjected to agarose gel electrophoresis under conditions that allowed good separation of 0.1-2 kb size DNA. The bulk of DNA remained in the well or migrated only a small distance into the gel. It was found that DNA fragments in the expected size range were formed linearly with dose with an efficiency that increased with LET. A comparison of the yield of such fragments with the yield of total DNA double-strand breaks suggests that for the high-LET ions a substantial proportion (20-90%) of DNA double-strand breaks are accompanied within 0.1-2 kb by at least one additional DNA double-strand break. It is shown that these results are in good agreement with theoretical calculations based on treating the 30-nm chromatin fiber as the target for ionizing particles. Theoretical considerations also predict that the clusters will contain numerous single-strand breaks and base damages. It is proposed that such clusters be designated "regionally multiply damaged sites." Postirradiation incubation at 37 degrees C resulted in a decline in the number of short DNA fragments, suggesting a repair activity. The biological significance of regionally multiply damaged sites is presently unknown.

Non-NASA Center↗

The Effect of Approximating Some Molecular Integrals in Coupled-Cluster Calculations: Fundamental Frequencies and Rovibrational Spectroscopic Constants of Cyclopropenylidene

The singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations, denoted CCSD(T), has been used, in conjunction with approximate integral techniques, to compute highly accurate rovibrational spectroscopic constants of cyclopropenylidene, C3H2. The approximate integral technique was proposed in 1994 by Rendell and Lee in order to avoid disk storage and input/output bottlenecks, and today it will also significantly aid in the development of algorithms for distributed memory, massively parallel computer architectures. It is shown in this study that use of approximate integrals does not impact the accuracy of CCSD(T) calculations. In addition, the most accurate spectroscopic data yet for C3H2 is presented based on a CCSD(T)/cc-pVQZ quartic force field that is modified to include the effects of core-valence electron correlation. Cyclopropenylidene is of great astronomical and astrobiological interest because it is the smallest aromatic ringed compound to be positively identified in the interstellar medium, and is thus involved in the prebiotic processing of carbon and hydrogen. The singles and doubles coupled-cluster method that includes a perturbational estimate of

Lee, Timothy J.↗

Analysis of Aircraft Clusters to Measure Sector-Independent Airspace Congestion

The Distributed Air/Ground Traffic Management (DAG-TM) concept of operations* permits appropriately equipped aircraft to conduct Free Maneuvering operations. These independent aircraft have the freedom to optimize their trajectories in real time according to user preferences; however, they also take on the responsibility to separate themselves from other aircraft while conforming to any local Traffic Flow Management (TFM) constraints imposed by the air traffic service provider (ATSP). Examples of local-TFM constraints include temporal constraints such as a required time of arrival (RTA), as well as spatial constraints such as regions of convective weather, special use airspace, and congested airspace. Under current operations, congested airspace typically refers to a sector(s) that cannot accept additional aircraft due to controller workload limitations; hence Dynamic Density (a metric that is indicative of controller workload) can be used to quantify airspace congestion. However, for Free Maneuvering operations under DAG-TM, an additional metric is needed to quantify the airspace congestion problem from the perspective of independent aircraft. Such a metric would enable the ATSP to prevent independent aircraft from entering any local areas of congestion in which the flight deck based systems and procedures may not be able to ensure separation. This new metric, called Gaggle Density, offers the ATSP a mode of control to regulate normal operations and to ensure safety and stability during rare-normal or off-normal situations (e.g., system failures). It may be difficult to certify Free Maneuvering systems for unrestricted operations, but it may be easier to certify systems and procedures for specified levels of Gaggle Density that could be monitored by the ATSP, and maintained through relatively minor flow-rate (RTA type) restrictions. Since flight deck based separation assurance is airspace independent, the challenge is to measure congestion independent of sector boundaries. Figure 1 , reproduced from Ref. 1, depicts an example traffic situation. When the situation is analyzed by sector boundaries (left side of figure), a Dynamic Density metric would identify excessive congestion in the central sector. When the same traffic situation is analyzed independent of sector boundaries (right side of figure), a Gaggle Density metric would identify congestion in two dynamically defined areas covering portions of several sectors. The first step towards measuring airspace-independent congestion is to identify aircraft clusters, i.e., groups of closely spaced aircraft. The objective of this work is to develop techniques to detect and classify clusters of aircraft.

Bilimoria, Karl D.↗

Development of a Genetic Algorithm to Automate Clustering of a Dependency Structure Matrix

Much technology assessment and organization design data exists in Microsoft Excel spreadsheets. Tools are needed to put this data into a form that can be used by design managers to make design decisions. One need is to cluster data that is highly coupled. Tools such as the Dependency Structure Matrix (DSM) and a Genetic Algorithm (GA) can be of great benefit. However, no tool currently combines the DSM and a GA to solve the clustering problem. This paper describes a new software tool that interfaces a GA written as an Excel macro with a DSM in spreadsheet format. The results of several test cases are included to demonstrate how well this new tool works.

Rogers, James L.↗

Semi-Supervised Data Summarization: Using Spectral Libraries to Improve Hyperspectral Clustering

Hyperspectral imagers produce very large images, with each pixel recorded at hundreds or thousands of different wavelengths. The ability to automatically generate summaries of these data sets enables several important applications, such as quickly browsing through a large image repository or determining the best use of a limited bandwidth link (e.g., determining which images are most critical for full transmission). Clustering algorithms can be used to generate these summaries, but traditional clustering methods make decisions based only on the information contained in the data set. In contrast, we present a new method that additionally leverages existing spectral libraries to identify materials that are likely to be present in the image target area. We find that this approach simultaneously reduces runtime and produces summaries that are more relevant to science goals.

Wagstaff, K. L.↗

Interconnect Performance Evaluation of SGI Altix 3700 BX2, Cray X1, Cray Opteron Cluster, and Dell PowerEdge

We study the performance of inter-process communication on four high-speed multiprocessor systems using a set of communication benchmarks. The goal is to identify certain limiting factors and bottlenecks with the interconnect of these systems as well as to compare these interconnects. We measured network bandwidth using different number of communicating processors and communication patterns, such as point-to-point communication, collective communication, and dense communication patterns. The four platforms are: a 512-processor SGI Altix 3700 BX2 shared-memory machine with 3.2 GB/s links; a 64-processor (single-streaming) Cray XI shared-memory machine with 32 1.6 GB/s links; a 128-processor Cray Opteron cluster using a Myrinet network; and a 1280-node Dell PowerEdge cluster with an InfiniBand network. Our, results show the impact of the network bandwidth and topology on the overall performance of each interconnect.

Fatoohi, Rod↗

Determination of the Cosmic Distance Scale from Sunyaev-Zel'dovich Effect and Chandra X-ray Measurements of High Redshift Galaxy Clusters

We determine the distance to 38 clusters of galaxies in the redshift range 0.14 less than or equal to z less than or equal to 0.89 using X-ray data from Chandra and Sunyaev-Zeldovich Effect data from the Owens Valley Radio Observatory and the Berkeley-Illinois-Maryland Association interferometric arrays. The cluster plasma and dark matter distributions are analyzed using a hydrostatic equilibrium model that accounts for radial variations in density, temperature and abundance, and, the statistical and systematic errors of this method are quantified. The analysis is performed via a Markov chain Monte Carlo technique that provides simultaneous estimation of all model parameters. W

Bonamente, Massimiliano↗

Observations of the Hot Horizontal Branch Stars in the Metal-Rich Bulge Globular Cluster NGC 6388

The metal-rich bulge globular cluster NGC 6388 shows a distinct blue horizontal-branch tail in its colour-magnitude diagram (Rich et al. 1997) and is thus a strong case of the well-known 2nd Parameter Problem. In addition, its horizontal branch (HB) shows an upward tilt toward bluer colours, which cannot be explained by canonical evolutionary models. Several non-canonical scenarios have been proposed to explain these puzzling observations. In order to test the predictions of these scenarios, we have obtained medium resolution spectra to determine the atmospheric parameters of a sample of the blue HB stars in NGC 6388.Using the medium resolution spectra, we determine effective temperatures, surface gravities and helium abundances by fitting the observed Balmer and helium lines with appropriate theoretical stellar spectra. As we know the distance to the cluster, we can verify our results by determining masses for the stars. During the data reduction we took special care to correctly subtract the background, which is dominated by the overlapping spectra of cool stars. The cool blue tail stars in our sample with T(sub eff) approximately 10000 K have lower than canonical surface gravities, suggesting that these stars are, on average, approximately equal to 0.4 mag brighter than canonical HB stars in agreement with the observed upward slope of the HB in NGC 6388. Moreover, the mean mass of these stars agrees well with theoretical predictions. In contrast, the hot blue tail stars in our sample with T(sub eff) greater than or equal to 12000 K show significantly lower surface gravities than predicted by any scenario, which can reproduce the photometric observations. Their masses are also too low by about a factor of 2 compared to theoretical predictions. The physical parameters of the blue HB stars at about 10,000 K support the helium pollution scenario. The low gravities and masses of the hot blue tail stars, however, are probably caused by problems with the data reduction, most likely due to remaining background light in the spectra, which would affect the fainter hot blue tail stars much more strongly than the brighter cool blue tail stars. Our study of the hot blue tail stars in NGC 6388 illustrates the obstacles which are encountered when attempting to determine the atmospheric parameters of hot HB stars in very crowded fields using ground-based observations. We discuss these obstacles and offer possible solutions for future projects.

Moehler, S.↗

Access and visualization using clusters and other parallel computers

JPL's Parallel Applications Technologies Group has been exploring the issues of data access and visualization of very large data sets over the past 10 or so years. this work has used a number of types of parallel computers, and today includes the use of commodity clusters. This talk will highlight some of the applications and tools we have developed, including how they use parallel computing resources, and specifically how we are using modern clusters. Our applications focus on NASA's needs; thus our data sets are usually related to Earth and Space Science, including data delivered from instruments in space, and data produced by telescopes on the ground.

data sets↗

Clustering and Recurring Anomaly Identification: Recurring Anomaly Detection System (ReADS)

This viewgraph presentation reviews the Recurring Anomaly Detection System (ReADS). The Recurring Anomaly Detection System is a tool to analyze text reports, such as aviation reports and maintenance records: (1) Text clustering algorithms group large quantities of reports and documents; Reduces human error and fatigue (2) Identifies interconnected reports; Automates the discovery of possible recurring anomalies; (3) Provides a visualization of the clusters and recurring anomalies We have illustrated our techniques on data from Shuttle and ISS discrepancy reports, as well as ASRS data. ReADS has been integrated with a secure online search

McIntosh, Dawn↗

A 70 Kiloparsec X-Ray Tail in the Cluster A3627

We present the discovery of a 70 kpc X-ray tail behind the small late-type galaxy ESO 137-001, in the nearby, hot (T=6.5 keV) merging cluster A3627, from both Chandra and XMM-Newton observations. The tail has a length-to-width ratio of approx. 10. It is luminous (L(0.5-2keV) approx 1041 ergs/s), with a temperature of approx. 0.7 keV and an X-ray gas mass of approx 10(exp 9) solar masses (approx 10% of the galaxy's stellar mass). We interpret this tail as the stripped interstellar medium of ESO 137-001 mixed with the hot cluster medium, with this blue galaxy being converted into a gas-poor galaxy. Three X-ray point sources are detected in the axis of the tail, which may imply active star formation there. The straightness and narrowness of the tail also imply that the turbulence in the intracluster medium is not strong on scales of 20-70 kpc.

Sun, M.↗

Deep RGS Observations of Clusters

This viewgraph presentation reviews the Reflection Grating Spectrometers (RGS) observations of clusters. It includes charts detailing the resolution difference between the European Photon Imaging Camera (EPIC) and the RGS and a partial review of existing observations, in graphic format, and as a table. Other sources show up in the ROSAT observations. The presentation reviews possible results that could be achieved in the event that 300 ks of time were allocated for the observations of clusters.

Smith, R.↗

Cluster: Mission Overview and End-of-Life Analysis

The Cluster mission is part of the scientific programme of the European Space Agency (ESA) and its purpose is the analysis of the Earth's magnetosphere. The Cluster project consists of four satellites. The selected polar orbit has a shape of 4.0 and 19.2 Re which is required for performing measurements near the cusp and the tail of the magnetosphere. When crossing these regions the satellites form a constellation which in most of the cases so far has been a regular tetrahedron. The satellite operations are carried out by the European Space Operations Centre (ESOC) at Darmstadt, Germany. The paper outlines the future orbit evolution and the envisaged operations from a Flight Dynamics point of view. In addition a brief summary of the LEOP and routine operations is included beforehand.

Pallaschke, S.↗

Using PEACE Data from the four CLUSTER Spacecraft to Measure Compressibility, Vorticity, and the Taylor Microscale in the Magnetosheath and Plasma Sheet

We present determinations of compressibility and vorticity in the magnetosheath and plasma sheet using moments from the four PEACE thermal electron instruments on CLUSTER. The methodology used assumes a linear variation of the moments throughout the volume defined by the four satellites, which allows spatially independent estimates of the divergence, curl, and gradient. Once the vorticity has been computed, it is possible to estimate directly the Taylor microscale. We have shown previously that the technique works well in the solar wind. Because the background flow speed in the magnetosheath and plasma sheet is usually less than the Alfven speed, the Taylor frozen-in-flow approximation cannot be used. Consequently, this four spacecraft approach is the only viable method for obtaining the wave number properties of the ambient fluctuations. Our results using electron velocity moments will be compared with previous work using magnetometer data from the FGM experiment on Cluster.

Goldstein, Melvyn L.↗