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NETMARK: A Schema-less Extension for Relational Databases for Managing Semi-structured Data Dynamically

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

Maluf, David A.↗

Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA

Although mRNA amplification is necessary for microarray analyses from limited amounts of cells and tissues, the accuracy of transcription profiles following amplification has not been well characterized. We tested the fidelity of differential gene expression following linear amplification by T7-mediated transcription in a well-established in vitro model of cytokine [tumor necrosis factor alpha (TNFalpha)]-stimulated human endothelial cells using filter arrays of 13,824 human cDNAs. Transcriptional profiles generated from amplified antisense RNA (aRNA) (from 100 ng total RNA, approximately 1 ng mRNA) were compared with profiles generated from unamplified RNA originating from the same homogeneous pool. Amplification accurately identified TNFalpha-induced differential expression in 94% of the genes detected using unamplified samples. Furthermore, an additional 1,150 genes were identified as putatively differentially expressed using amplified RNA which remained undetected using unamplified RNA. Of genes sampled from this set, 67% were validated by quantitative real-time PCR as truly differentially expressed. Thus, in addition to demonstrating fidelity in gene expression relative to unamplified samples, linear amplification results in improved sensitivity of detection and enhances the discovery potential of high-throughput screening by microarrays.

Evaluation Studies↗

Science with Constellation-X

NASA's upcoming Constellation-X mission, one of two flagship missions in the Beyond Einstein program, will have more than 100 times the collecting area of any previous spectroscopic mission operating in the 0.25-40 keV bandpass and will enable high-throughput, high spectral resolution studies of sources ranging from the most luminous accreting supermassive black holes in the Universe to the disks around young stars where planets form. This booklet, which was assembled during early 2005 using the contributions of a large team of Astrophysicists, outlines the important scientific questions for the decade following this one and describes the areas where Constellation-X is going to have a major impact. These areas include the exploration of the space-time geometry of black holes spanning nine orders of magnitude in mass and the nature of the dark energy and dark matter which govern the expansion and ultimate fate of the Universe. Constellation-X will also explore processes referred to as "cosmic feedback" whereby mechanical energy, radiation, and chemical elements from star formation and black holes are returned to interstellar and intergalactic medium, profoundly affecting the development of structure in the Universe, and will also probe all the important life cycles of matter, from stellar and planetary birth to stellar death via supernova to stellar endpoints in the form of accreting binaries and supernova remnants.

Hornschemeier, Ann↗

Replicated Nickel Optics for the Hard-X-Ray Region

Replicated nickel optics has been used extensively in x-ray astronomy, most notable for the XMM/Newton mission. Thc combination of relative ease of fabrication and the inherent stability of full shell optics, make them FIJI attractive approach for medium-resolution, high-throughput applications. MSFC has been developing these optics for use in the hard-x-ray region. Efforts at improving the resolution of these, particularly the very-thin shells required to meet thc weight budget of future missions, will be described together with the prospects for significant improvements down to the 5-arcsec level.

Ramsey, Brian↗

Studying Host-Pathogen Interactions In 3-D: Organotypic Models For Infectious Disease And Drug Development

Representative, reproducible and high-throughput models of human cells and tissues are critical for a meaningful evaluation of host-pathogen interactions and are an essential component of the research developmental pipeline. The most informative infection models - animals, organ explants and human trials - are not suited for extensive evaluation of pathogenesis mechanisms and screening of candidate drugs. At the other extreme, more cost effective and accessible infection models such as conventional cell culture and static co-culture may not capture physiological and three-dimensional aspects of tissue biology that are important in assessing pathogenesis, and effectiveness and cytotoxicity of therapeutics. Our lab has used innovative bioengineering technology to establish biologically meaningful 3-D models of human tissues that recapitulate many aspects of the differentiated structure and function of the parental tissue in vivo, and we have applied these models to study infectious disease. We have established a variety of different 3-D models that are currently being used in infection studies - including small intestine, colon, lung, placenta, bladder, periodontal ligament, and neuronal models. Published work from our lab has shown that our 3-D models respond to infection with bacterial and viral pathogens in ways that reflect the infection process in vivo. By virtue of their physiological relevance, 3-D cell cultures may also hold significant potential as models to provide insight into the neuropathogenesis of HIV infection. Furthermore, the experimental flexibility, reproducibility, cost-efficiency, and high throughput platform afforded by these 3-D models may have important implications for the design and development of drugs with which to effectively treat neurological complications of HIV infection.

Nickerson, Cheryl A.↗

"The Reflection Grating Spectrometer on Constellation-X"

The Constellation-X Reflection Grating Spectrometer (RGS) is designed to provide high-throughput, high-resolution spectra in the long wavelength band of 6 to 50 angstrom. In the nominal design an array of reflection gratings is mounted at the exit of the Spectroscopy X-ray Telescope (SXT) mirror module. The gratings intercept and disperse light to a designated array of CCD detectors. To achieve the throughput (A_eff > 1000 cm2 below 0.6 keV) and resolution (R > 300 below 0.6 keV) requirements for the instrument we are investigating two possible grating designs. The first design uses in-plane gratings in a classical configuration that is very similar to the XMM-Newton RGS. The second design uses off-plane gratings in a conical configuration. The off-plane design has the advantage of providing higher reflectivity and potentially, a higher spectral resolution than the in-plane configuration. In our presentation we will describe the performance requirements and the current status of the technology development.

Cottam, J.↗

POINTS (Precision Optical INTerferometer in Space)

POINTS is a high-precision, high-throughput interferometer intended for astromomy only. It can perform science compatable with astrophysics (AIM) and planet detection (TOPS-1). The spacecraft will be compact, lightweight, and suitable for high Earth orbit. It will employ the minimal number and complexity of mechanisms or deployable parts and be designed for a 10 year mission life.

interferometer astronomy satellite↗

VLSI design of turbo decoder for integrated communication system on a chip applications

A high-throughput low-power turbo decoder core has been developed for integrated communication system applications such as satellite communications, wireless LAN, digital TV, cable modem, Digital Video Broadcast (DVB), and xDSL systems. The turbo decoder is based on convolutional constituent codes, which outperform all other Forward Error Correction techniques. This turbo decoder core is parameterizable and can be modified easily to fit any size for advanced communication system-on-chip products. The turbo decoder core provides Forward Error Correction of up to 15 Mbits/sec on a 0.13-micron CMOS FPGA prototyping chip at a power of 0.1 watts.

turbo decoder↗

Searching Across the International Space Station Databases

Data access in the enterprise generally requires us to combine data from different sources and different formats. It is advantageous thus to focus on the intersection of the knowledge across sources and domains; keeping irrelevant knowledge around only serves to make the integration more unwieldy and more complicated than necessary. A context search over multiple domain is proposed in this paper to use context sensitive queries to support disciplined manipulation of domain knowledge resources. The objective of a context search is to provide the capability for interrogating many domain knowledge resources, which are largely semantically disjoint. The search supports formally the tasks of selecting, combining, extending, specializing, and modifying components from a diverse set of domains. This paper demonstrates a new paradigm in composition of information for enterprise applications. In particular, it discusses an approach to achieving data integration across multiple sources, in a manner that does not require heavy investment in database and middleware maintenance. This lean approach to integration leads to cost-effectiveness and scalability of data integration with an underlying schemaless object-relational database management system. This highly scalable, information on demand system framework, called NX-Search, which is an implementation of an information system built on NETMARK. NETMARK is a flexible, high-throughput open database integration framework for managing, storing, and searching unstructured or semi-structured arbitrary XML and HTML used widely at the National Aeronautics Space Administration (NASA) and industry.

Maluf, David A.↗

Improved Measurement of B(sub 22) of Macromolecules in a Flow Cell

An improved apparatus has been invented for use in determining the osmotic second virial coefficient of macromolecules in solution. In a typical intended application, the macromolecules would be, more specifically, protein molecules, and the protein solution would be pumped through a flow cell to investigate the physical and chemical conditions that affect crystallization of the protein in question. Some background information is prerequisite to a meaningful description of the novel aspects of this apparatus. A method of determining B22 from simultaneous measurements of the static transmittance (taken as an indication of concentration) and static scattering of light from the same location in a flowing protein solution was published in 2004. The apparatus used to implement the method at that time included a dual-detector flow cell, which had two drawbacks: a) The amount of protein required for analysis of each solution condition was of the order of a milligram - far too large a quantity for a high-throughput analysis system, for which microgram or even nanogram quantities of protein per analysis are desirable. b) The design of flow cell was such that two light sources were used to probe different regions of the flowing solution. Consequently, the apparatus did not afford simultaneous measurements at the same location in the solution and, hence, did not guarantee an accurate determination of B22.

Wilson, Wilbur↗

Catalysts for Efficient Production of Carbon Nanotubes

Several metal alloys have shown promise as improved catalysts for catalytic thermal decomposition of hydrocarbon gases to produce carbon nanotubes (CNTs). Heretofore almost every experiment on the production of carbon nanotubes by this method has involved the use of iron, nickel, or cobalt as the catalyst. However, the catalytic-conversion efficiencies of these metals have been observed to be limited. The identification of better catalysts is part of a continuing program to develop means of mass production of high-quality carbon nanotubes at costs lower than those achieved thus far (as much as $100/g for purified multi-wall CNTs or $1,000/g for single-wall CNTs in year 2002). The main effort thus far in this program has been the design and implementation of a process tailored specifically for high-throughput screening of alloys for catalyzing the growth of CNTs. The process includes an integral combination of (1) formulation of libraries of catalysts, (2) synthesis of CNTs from decomposition of ethylene on powders of the alloys in a pyrolytic chemical-vapor-decomposition reactor, and (3) scanning- electron-microscope screening of the CNTs thus synthesized to evaluate the catalytic efficiencies of the alloys. Information gained in this process is put into a database and analyzed to identify promising alloy compositions, which are to be subjected to further evaluation in a subsequent round of testing. Some of these alloys have been found to catalyze the formation of carbon nano tubes from ethylene at temperatures as low as 350 to 400 C. In contrast, the temperatures typically required for prior catalysts range from 550 to 750 C.

Sun, Ted X.↗

VLSI Design of a Turbo Decoder

A very-large-scale-integrated-circuit (VLSI) turbo decoder has been designed to serve as a compact, high-throughput, low-power, lightweight decoder core of a receiver in a data-communication system. In a typical contemplated application, such a decoder core would be part of a single integrated circuit that would include the rest of the receiver circuitry and possibly some or all of the transmitter circuitry, all designed and fabricated together according to an advanced communication-system-on-a-chip design concept. Turbo codes are forward-error-correction (FEC) codes. Relative to older FEC codes, turbo codes enable communication at lower signal-to-noise ratios and offer greater coding gain. In addition, turbo codes can be implemented by relatively simple hardware. Therefore, turbo codes have been adopted as standard for some advanced broadband communication systems.

Fang, Wai-Chi↗

Life Science Research in Outer Space: New Platform Technologies for Low-Cost, Autonomous Small Satellite Missions

We develop integrated instruments and platforms suitable for economical, frequent space access for autonomous life science experiments and processes in outer space. The technologies represented by three of our recent free-flyer small-satellite missions are the basis of a rapidly growing toolbox of miniaturized biologically/biochemically-oriented instrumentation now enabling a new generation of in-situ space experiments. Autonomous small satellites (~ 1 50 kg) are less expensive to develop and build than fullsize spacecraft and not subject to the comparatively high costs and scheduling challenges of human-tended experimentation on the International Space Station, Space Shuttle, and comparable platforms. A growing number of commercial, government, military, and civilian space launches now carry small secondary science payloads at far lower cost than dedicated missions; the number of opportunities is particularly large for so-called cube-sat and multicube satellites in the 1 10 kg range. The recent explosion in nano-, micro-, and miniature technologies, spanning fields from telecommunications to materials to bio/chemical analysis, enables development of remarkably capable autonomous miniaturized instruments to accomplish remote biological experimentation. High-throughput drug discovery, point-of-care medical diagnostics, and genetic analysis are applications driving rapid progress in autonomous bioanalytical technology. Three of our recent missions exemplify the development of miniaturized analytical payload instrumentation: GeneSat-1 (launched: December 2006), PharmaSat (launched: May 2009), and O/OREOS (organism/organics exposure to orbital stresses; scheduled launch: May 2010). We will highlight the overall architecture and integration of fluidic, optical, sensor, thermal, and electronic technologies and subsystems to support and monitor the growth of microorganisms in culture in these small autonomous space satellites, including real-time tracking of their culture density, gene expression, and metabolic activity while in the space environment. Flight data and results will be presented from GeneSat-1, which tracked gene expression levels of GFP-labeled E. coli and from PharmaSat, which monitored the dose dependency of an antifungal agent against S. cerevisiae. The O/OREOS SESLO instrument, which will study the effects of radiation and microgravity upon the viability and growth characteristics of B. subtilis and the halophile Halorubrum chaoviatoris for periods of 0 - 6 months in space, will be described as well. The ongoing expansion of the small satellite toolbox of biological technologies will be summarized.

Ricco, Antonio J.↗

Adding Hierarchical Objects to Relational Database General-Purpose XML-Based Information Managements

NETMARK is a flexible, high-throughput software system for managing, storing, and rapid searching of unstructured and semi-structured documents. NETMARK transforms such documents from their original highly complex, constantly changing, heterogeneous data formats into well-structured, common data formats in using Hypertext Markup Language (HTML) and/or Extensible Markup Language (XML). The software implements an object-relational database system that combines the best practices of the relational model utilizing Structured Query Language (SQL) with those of the object-oriented, semantic database model for creating complex data. In particular, NETMARK takes advantage of the Oracle 8i object-relational database model using physical-address data types for very efficient keyword searches of records across both context and content. NETMARK also supports multiple international standards such as WEBDAV for drag-and-drop file management and SOAP for integrated information management using Web services. The document-organization and -searching capabilities afforded by NETMARK are likely to make this software attractive for use in disciplines as diverse as science, auditing, and law enforcement.

Lin, Shu-Chun↗

Glass Frit Filters for Collecting Metal Oxide Nanoparticles

Filter disks made of glass frit have been found to be effective as means of high-throughput collection of metal oxide particles, ranging in size from a few to a few hundred nanometers, produced in gas-phase condensation reactors. In a typical application, a filter is placed downstream of the reactor and a valve is used to regulate the flow of reactor exhaust through the filter. The exhaust stream includes a carrier gas, particles, byproducts, and unreacted particle-precursor gas. The filter selectively traps the particles while allowing the carrier gas, the byproducts, and, in some cases, the unreacted precursor, to flow through unaffected. Although the pores in the filters are much larger than the particles, the particles are nevertheless trapped to a high degree: Anecdotal information from an experiment indicates that 6-nm-diameter particles of MnO2 were trapped with greater than 99-percent effectiveness by a filtering device comprising a glass-frit disk having pores 70 to 100 micrometer wide immobilized in an 8-cm-diameter glass tube equipped with a simple twist valve at its downstream end.

Ackerman, John↗

Improved Charge-Transfer Fluorescent Dyes

Improved charge-transfer fluorescent dyes have been developed for use as molecular probes. These dyes are based on benzofuran nuclei with attached phenyl groups substituted with, variously, electron donors, electron acceptors, or combinations of donors and acceptors. Optionally, these dyes could be incorporated as parts of polymer backbones or as pendant groups or attached to certain surfaces via self-assembly-based methods. These dyes exhibit high fluorescence quantum yields -- ranging from 0.2 to 0.98, depending upon solvents and chemical structures. The wavelengths, quantum yields, intensities, and lifetimes of the fluorescence emitted by these dyes vary with (and, hence, can be used as indicators of) the polarities of solvents in which they are dissolved: In solvents of increasing polarity, fluorescence spectra shift to longer wavelengths, fluorescence quantum yields decrease, and fluorescence lifetimes increase. The wavelengths, quantum yields, intensities, and lifetimes are also expected to be sensitive to viscosities and/or glass-transition temperatures. Some chemical species -- especially amines, amino acids, and metal ions -- quench the fluorescence of these dyes, with consequent reductions in intensities, quantum yields, and lifetimes. As a result, the dyes can be used to detect these species. Another useful characteristic of these dyes is a capability for both two-photon and one-photon absorption. Typically, these dyes absorb single photons in the ultraviolet region of the spectrum (wavelengths < 400 nm) and emit photons in the long-wavelength ultraviolet, visible, and, when dissolved in some solvents, near-infrared regions. In addition, these dyes can be excited by two-photon absorption at near-infrared wavelengths (600 to 800 nm) to produce fluorescence spectra identical to those obtained in response to excitation by single photons at half the corresponding wavelengths (300 to 400 nm). While many prior fluorescent dyes exhibit high quantum yields, solvent-polarity- dependent fluorescence behavior, susceptibility to quenching by certain chemical species, and/or two-photon fluorescence, none of them has the combination of all of these attributes. Because the present dyes do have all of these attributes, they have potential utility as molecular probes in a variety of applications. Examples include (1) monitoring curing and deterioration of polymers; (2) monitoring protein expression; (3) high-throughput screening of drugs; (4) monitoring such chemical species as glucose, amines, amino acids, and metal ions; and (5) photodynamic therapy of cancers and other diseases.

Meador, Michael↗

Rapid Chemometric Filtering of Spectral Data

A method of rapid, programmable filtering of spectral transmittance, reflectance, or fluorescence data to measure the concentrations of chemical species has been proposed. By programmable is meant that a variety of spectral analyses can readily be performed and modified in software, firmware, and/or electronic hardware, without need to change optical filters or other optical hardware of the associated spectrometers. The method is intended to enable real-time identification of single or multiple target chemical species in applications that involve high-throughput screening of multiple samples. Examples of such applications include (but are not limited to) combinatorial chemistry, flow cytometry, bead assays, testing drugs, remote sensing, and identification of targets. The basic concept of the proposed method is to perform real-time crosscorrelations of a measured spectrum with one or more analytical function(s) of wavelength that could be, for example, the known spectra of target species. Assuming that measured spectral intensities are proportional to concentrations of target species plus background spectral intensities, then after subtraction of background levels, it should be possible to determine target species concentrations from cross-correlation values. Of course, the problem of determining the concentrations is more complex when spectra of different species overlap, but the problem can be solved by use of multiple analytical functions in combination with computational techniques that have been developed previously for analyses of this type. The method is applicable to the design and operation of a spectrometer in which spectrally dispersed light is measured by means of an active-pixel sensor (APS) array. The row or column dimension of such an array is generally chosen to be aligned along the spectral-dispersion dimension, so that each pixel intercepts light in a narrow spectral band centered on a wavelength that is a known function of the pixel position. The proposed method admits of two hardware implementations for computing cross-correlations in real time.

Beaman, Gregory↗

Delta-Doped Back-Illuminated CMOS Imaging Arrays: Progress and Prospects

In this paper, we report the latest results on our development of delta-doped, thinned, back-illuminated CMOS imaging arrays. As with charge-coupled devices, thinning and back-illumination are essential to the development of high performance CMOS imaging arrays. Problems with back surface passivation have emerged as critical to the prospects for incorporating CMOS imaging arrays into high performance scientific instruments, just as they did for CCDs over twenty years ago. In the early 1990's, JPL developed delta-doped CCDs, in which low temperature molecular beam epitaxy was used to form an ideal passivation layer on the silicon back surface. Comprising only a few nanometers of highly-doped epitaxial silicon, delta-doping achieves the stability and uniformity that are essential for high performance imaging and spectroscopy. Delta-doped CCDs were shown to have high, stable, and uniform quantum efficiency across the entire spectral range from the extreme ultraviolet through the near infrared. JPL has recently bump-bonded thinned, delta-doped CMOS imaging arrays to a CMOS readout, and demonstrated imaging. Delta-doped CMOS devices exhibit the high quantum efficiency that has become the standard for scientific-grade CCDs. Together with new circuit designs for low-noise readout currently under development, delta-doping expands the potential scientific applications of CMOS imaging arrays, and brings within reach important new capabilities, such as fast, high-sensitivity imaging with parallel readout and real-time signal processing. It remains to demonstrate manufacturability of delta-doped CMOS imaging arrays. To that end, JPL has acquired a new silicon MBE and ancillary equipment for delta-doping wafers up to 200mm in diameter, and is now developing processes for high-throughput, high yield delta-doping of fully-processed wafers with CCD and CMOS imaging devices.

imagers↗