Circuit design advances for ultra-low power sensing platforms

NASA Astrophysics Data System (ADS)

Wieckowski, Michael; Dreslinski, Ronald G.; Mudge, Trevor; Blaauw, David; Sylvester, Dennis

2010-04-01

This paper explores the recent advances in circuit structures and design methodologies that have enabled ultra-low power sensing platforms and opened up a host of new applications. Central to this theme is the development of Near Threshold Computing (NTC) as a viable design space for low power sensing platforms. In this paradigm, the system's supply voltage is approximately equal to the threshold voltage of its transistors. Operating in this "near-threshold" region provides much of the energy savings previously demonstrated for subthreshold operation while offering more favorable performance and variability characteristics. This makes NTC applicable to a broad range of power-constrained computing segments including energy constrained sensing platforms. This paper explores the barriers to the adoption of NTC and describes current work aimed at overcoming these obstacles in the circuit design space.

Characterization of Polyimide Foams for Ultra-Lightweight Space Structures

NASA Technical Reports Server (NTRS)

Meador, Michael (Technical Monitor); Hillman, Keithan; Veazie, David R.

2003-01-01

Ultra-lightweight materials have played a significant role in nearly every area of human activity ranging from magnetic tapes and artificial organs to atmospheric balloons and space inflatables. The application range of ultra-lightweight materials in past decades has expanded dramatically due to their unsurpassed efficiency in terms of low weight and high compliance properties. A new generation of ultra-lightweight materials involving advanced polymeric materials, such as TEEK (TM) polyimide foams, is beginning to emerge to produce novel performance from ultra-lightweight systems for space applications. As a result, they require that special conditions be fulfilled to ensure adequate structural performance, shape retention, and thermal stability. It is therefore important and essential to develop methodologies for predicting the complex properties of ultra-lightweight foams. To support NASA programs such as the Reusable Launch Vehicle (RLV), Clark Atlanta University, along with SORDAL, Inc., has initiated projects for commercial process development of polyimide foams for the proposed cryogenic tank integrated structure (see figure 1). Fabrication and characterization of high temperature, advanced aerospace-grade polyimide foams and filled foam sandwich composites for specified lifetimes in NASA space applications, as well as quantifying the lifetime of components, are immensely attractive goals. In order to improve the development, durability, safety, and life cycle performance of ultra-lightweight polymeric foams, test methods for the properties are constant concerns in terms of timeliness, reliability, and cost. A major challenge is to identify the mechanisms of failures (i.e., core failure, interfacial debonding, and crack development) that are reflected in the measured properties. The long-term goal of the this research is to develop the tools and capabilities necessary to successfully engineer ultra-lightweight polymeric foams. The desire is to reduce density

Design Method For Ultra-High Resolution Linear CCD Imagers

NASA Astrophysics Data System (ADS)

Sheu, Larry S.; Truong, Thanh; Yuzuki, Larry; Elhatem, Abdul; Kadekodi, Narayan

1984-11-01

This paper presents the design method to achieve ultra-high resolution linear imagers. This method utilizes advanced design rules and novel staggered bilinear photo sensor arrays with quadrilinear shift registers. Design constraint in the detector arrays and shift registers are analyzed. Imager architecture to achieve ultra-high resolution is presented. The characteristics of MTF, aliasing, speed, transfer efficiency and fine photolithography requirements associated with this architecture are also discussed. A CCD imager with advanced 1.5 um minimum feature size was fabricated. It is intended as a test vehicle for the next generation small sampling pitch ultra-high resolution CCD imager. Standard double-poly, two-phase shift registers were fabricated at an 8 um pitch using the advanced design rules. A special process step that blocked the source-drain implant from the shift register area was invented. This guaranteed excellent performance of the shift registers regardless of the small poly overlaps. A charge transfer efficiency of better than 0.99995 and maximum transfer speed of 8 MHz were achieved. The imager showed excellent performance. The dark current was less than 0.2 mV/ms, saturation 250 mV, adjacent photoresponse non-uniformity ± 4% and responsivity 0.7 V/ μJ/cm2 for the 8 μm x 6 μm photosensor size. The MTF was 0.6 at 62.5 cycles/mm. These results confirm the feasibility of the next generation ultra-high resolution CCD imagers.

Molecule database framework: a framework for creating database applications with chemical structure search capability

PubMed Central

2013-01-01

Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was

Molecule database framework: a framework for creating database applications with chemical structure search capability.

PubMed

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework

Short-focus and ultra-wide-angle lens design in wavefront coding

NASA Astrophysics Data System (ADS)

Zhang, Jiyan; Huang, Yuanqing; Xiong, Feibing

2016-10-01

Wavefront coding (WFC) is a hybrid technology designed to increase depth of field of conventional optics. The goal of our research is to apply this technology to the short-focus and ultra-wide-angle lens which suffers from the aberration related with large field of view (FOV) such as coma and astigmatism. WFC can also be used to compensate for other aberration which is sensitive to the FOV. Ultra-wide-angle lens has a little depth of focus because it has small F number and short-focus. We design a hybrid lens combing WFC with the ultra-wide-angle lens. The full FOV and relative aperture of the final design are up to170° and 1/1.8 respectively. The focal length is 2 mm. We adopt the cubic phase mask (CPM) in the design. The conventional design will have a wide variation of the point spread function (PSF) across the FOV and it is very sensitive with the variation of the FOV. The new design we obtain the PSF is nearly invariant over the whole FOV. But the result of the design also shows the little difference between the horizontal and vertical length of the PSF. We analyze that the CPM is non-symmetric phase mask and the FOV is so large, which will generate variation in the final image quality. For that reason, we apply a new method to avoid that happened. We try to make the rays incident on the CPM with small angle and decrease the deformation of the PSF. The experimental result shows the new method to optimize the CPM is fit for the ultra-wide-angle lens. The research above will be a helpful instruction to design the ultra-wide-angle lens with WFC.

PROFESS: a PROtein Function, Evolution, Structure and Sequence database

PubMed Central

Triplet, Thomas; Shortridge, Matthew D.; Griep, Mark A.; Stark, Jaime L.; Powers, Robert; Revesz, Peter

2010-01-01

The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are ∼1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein–protein interaction networks. Database URL: http://cse.unl.edu/∼profess/ PMID:20624718

GlycomeDB – integration of open-access carbohydrate structure databases

PubMed Central

Ranzinger, René; Herget, Stephan; Wetter, Thomas; von der Lieth, Claus-Wilhelm

2008-01-01

Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource. PMID:18803830

Inorganic Crystal Structure Database (ICSD)

National Institute of Standards and Technology Data Gateway

SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

Object-oriented structures supporting remote sensing databases

NASA Technical Reports Server (NTRS)

Wichmann, Keith; Cromp, Robert F.

1995-01-01

Object-oriented databases show promise for modeling the complex interrelationships pervasive in scientific domains. To examine the utility of this approach, we have developed an Intelligent Information Fusion System based on this technology, and applied it to the problem of managing an active repository of remotely-sensed satellite scenes. The design and implementation of the system is compared and contrasted with conventional relational database techniques, followed by a presentation of the underlying object-oriented data structures used to enable fast indexing into the data holdings.

Building structural similarity database for metric learning

NASA Astrophysics Data System (ADS)

Jin, Guoxin; Pappas, Thrasyvoulos N.

2015-03-01

We propose a new approach for constructing databases for training and testing similarity metrics for structurally lossless image compression. Our focus is on structural texture similarity (STSIM) metrics and the matched-texture compression (MTC) approach. We first discuss the metric requirements for structurally lossless compression, which differ from those of other applications such as image retrieval, classification, and understanding. We identify "interchangeability" as the key requirement for metric performance, and partition the domain of "identical" textures into three regions, of "highest," "high," and "good" similarity. We design two subjective tests for data collection, the first relies on ViSiProG to build a database of "identical" clusters, and the second builds a database of image pairs with the "highest," "high," "good," and "bad" similarity labels. The data for the subjective tests is generated during the MTC encoding process, and consist of pairs of candidate and target image blocks. The context of the surrounding image is critical for training the metrics to detect lighting discontinuities, spatial misalignments, and other border artifacts that have a noticeable effect on perceptual quality. The identical texture clusters are then used for training and testing two STSIM metrics. The labelled image pair database will be used in future research.

The Cambridge Structural Database

PubMed Central

Groom, Colin R.; Bruno, Ian J.; Lightfoot, Matthew P.; Ward, Suzanna C.

2016-01-01

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface. PMID:27048719

The Cambridge Structural Database.

PubMed

Groom, Colin R; Bruno, Ian J; Lightfoot, Matthew P; Ward, Suzanna C

2016-04-01

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

LMSD: LIPID MAPS structure database

PubMed Central

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Brown, Alex; Dennis, Edward A.; Glass, Christopher K.; Merrill, Alfred H.; Murphy, Robert C.; Raetz, Christian R. H.; Russell, David W.; Subramaniam, Shankar

2007-01-01

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available at PMID:17098933

Ultra-Deep Drilling Cost Reduction; Design and Fabrication of an Ultra-Deep Drilling Simulator (UDS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindstrom, Jason

2010-01-31

Ultra-deep drilling, below about 20,000 ft (6,096 m), is extremely expensive and limits the recovery of hydrocarbons at these depths. Unfortunately, rock breakage and cuttings removal under these conditions is not understood. To better understand and thus reduce cost at these conditions an ultra-deep single cutter drilling simulator (UDS) capable of drill cutter and mud tests to sustained pressure and temperature of 30,000 psi (207 MPa) and 482 °F (250 °C), respectively, was designed and manufactured at TerraTek, a Schlumberger company, in cooperation with the Department of Energy’s National Energy Technology Laboratory. UDS testing under ultra-deep drilling conditions offers anmore » economical alternative to high day rates and can prove or disprove the viability of a particular drilling technique or fluid to provide opportunity for future domestic energy needs.« less

Experimental Charging Behavior of Orion UltraFlex Array Designs

NASA Technical Reports Server (NTRS)

Golofaro, Joel T.; Vayner, Boris V.; Hillard, Grover B.

2010-01-01

The present ground based investigations give the first definitive look describing the charging behavior of Orion UltraFlex arrays in both the Low Earth Orbital (LEO) and geosynchronous (GEO) environments. Note the LEO charging environment also applies to the International Space Station (ISS). The GEO charging environment includes the bounding case for all lunar mission environments. The UltraFlex photovoltaic array technology is targeted to become the sole power system for life support and on-orbit power for the manned Orion Crew Exploration Vehicle (CEV). The purpose of the experimental tests is to gain an understanding of the complex charging behavior to answer some of the basic performance and survivability issues to ascertain if a single UltraFlex array design will be able to cope with the projected worst case LEO and GEO charging environments. Stage 1 LEO plasma testing revealed that all four arrays successfully passed arc threshold bias tests down to -240 V. Stage 2 GEO electron gun charging tests revealed that only the front side area of indium tin oxide coated array designs successfully passed the arc frequency tests

Functional and Database Architecture Design.

DTIC Science & Technology

1983-09-26

I AD-At3.N 275 FUNCTIONAL AND D ATABASE ARCHITECTURE DESIGN (U) ALPHA / OMEGA GROUP INC HARVARD MA 26 SEP 83 NODS 4-83-C 0525 UNCLASSIFIED FG52 N EE...0525 REPORT AOO1 FUNCTIONAL AND DATABASE ARCHITECTURE DESIGN Submitted to: Office of Naval Research Department of the Navy 800 N. Quincy Street...ZNTIS GRA& I DTIC TAB Unannounced 0 Justification REPORT ON Distribution/ Availability Codes Avail and/or FUNCTIONAL AND DATABASE ARCHITECTURE DESIGN Dist

Inverse design of an ultra-compact broadband optical diode based on asymmetric spatial mode conversion

PubMed Central

Callewaert, Francois; Butun, Serkan; Li, Zhongyang; Aydin, Koray

2016-01-01

The objective-first inverse-design algorithm is used to design an ultra-compact optical diode. Based on silicon and air only, this optical diode relies on asymmetric spatial mode conversion between the left and right ports. The first even mode incident from the left port is transmitted to the right port after being converted into an odd mode. On the other hand, same mode incident from the right port is reflected back by the optical diode dielectric structure. The convergence and performance of the algorithm are studied, along with a transform method that converts continuous permittivity medium into a binary material design. The optimal device is studied with full-wave electromagnetic simulations to compare its behavior under right and left incidences, in 2D and 3D settings as well. A parametric study is designed to understand the impact of the design space size and initial conditions on the optimized devices performance. A broadband optical diode behavior is observed after optimization, with a large rejection ratio between the two transmission directions. This illustrates the potential of the objective-first inverse-design method to design ultra-compact broadband photonic devices. PMID:27586852

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

PubMed

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

Using the structure-function linkage database to characterize functional domains in enzymes.

PubMed

Brown, Shoshana; Babbitt, Patricia

2014-12-12

The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. The information in this unit is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases. Copyright © 2014 John Wiley & Sons, Inc.

Methodology for Designing and Developing a New Ultra-Wideband Antenna Based on Bio-Inspired Optimization Techniques

DTIC Science & Technology

2017-11-01

ARL-TR-8225 ● NOV 2017 US Army Research Laboratory Methodology for Designing and Developing a New Ultra-Wideband Antenna Based...Research Laboratory Methodology for Designing and Developing a New Ultra-Wideband Antenna Based on Bio-Inspired Optimization Techniques by...SUBTITLE Methodology for Designing and Developing a New Ultra-Wideband Antenna Based on Bio-Inspired Optimization Techniques 5a. CONTRACT NUMBER

SM-TF: A structural database of small molecule-transcription factor complexes.

PubMed

Xu, Xianjin; Ma, Zhiwei; Sun, Hongmin; Zou, Xiaoqin

2016-06-30

Transcription factors (TFs) are the proteins involved in the transcription process, ensuring the correct expression of specific genes. Numerous diseases arise from the dysfunction of specific TFs. In fact, over 30 TFs have been identified as therapeutic targets of about 9% of the approved drugs. In this study, we created a structural database of small molecule-transcription factor (SM-TF) complexes, available online at http://zoulab.dalton.missouri.edu/SM-TF. The 3D structures of the co-bound small molecule and the corresponding binding sites on TFs are provided in the database, serving as a valuable resource to assist structure-based drug design related to TFs. Currently, the SM-TF database contains 934 entries covering 176 TFs from a variety of species. The database is further classified into several subsets by species and organisms. The entries in the SM-TF database are linked to the UniProt database and other sequence-based TF databases. Furthermore, the druggable TFs from human and the corresponding approved drugs are linked to the DrugBank. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Link and Network Layers Design for Ultra-High-Speed Terahertz-Band Communications Networks

DTIC Science & Technology

2017-01-01

throughput, and identify the optimal parameter values for their design (Sec. 6.2.3). Moreover, we validate and test the scheme with experimental data obtained...LINK AND NETWORK LAYERS DESIGN FOR ULTRA-HIGH- SPEED TERAHERTZ-BAND COMMUNICATIONS NETWORKS STATE UNIVERSITY OF NEW YORK (SUNY) AT BUFFALO JANUARY...TYPE FINAL TECHNICAL REPORT 3. DATES COVERED (From - To) FEB 2015 – SEP 2016 4. TITLE AND SUBTITLE LINK AND NETWORK LAYERS DESIGN FOR ULTRA-HIGH

Design and demonstration of ultra-wide bandgap AlGaN tunnel junctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yuewei; Krishnamoorthy, Sriram; Akyol, Fatih

Ultra violet light emitting diodes (UV LEDs) face critical limitations in both the injection efficiency and the light extraction efficiency due to the resistive and absorbing p-type contact layers. In this work, we investigate the design and application of polarization engineered tunnel junctions for ultra-wide bandgap AlGaN (Al mole fraction >50%) materials towards highly efficient UV LEDs. We demonstrate that polarization-induced three dimensional charge is beneficial in reducing tunneling barriers especially for high composition AlGaN tunnel junctions. In addition, the design of graded tunnel junction structures could lead to low tunneling resistance below 10 –3 Ω cm 2 and lowmore » voltage consumption below 1 V (at 1 kA/cm 2) for high composition AlGaN tunnel junctions. Experimental demonstration of 292 nm emission was achieved through non-equilibrium hole injection into wide bandgap materials with bandgap energy larger than 4.7 eV, and detailed modeling of tunnel junctions shows that they can be engineered to have low resistance and can enable efficient emitters in the UV-C wavelength range.« less

Design and demonstration of ultra-wide bandgap AlGaN tunnel junctions

DOE PAGES

Zhang, Yuewei; Krishnamoorthy, Sriram; Akyol, Fatih; ...

2016-09-19

Ultra violet light emitting diodes (UV LEDs) face critical limitations in both the injection efficiency and the light extraction efficiency due to the resistive and absorbing p-type contact layers. In this work, we investigate the design and application of polarization engineered tunnel junctions for ultra-wide bandgap AlGaN (Al mole fraction >50%) materials towards highly efficient UV LEDs. We demonstrate that polarization-induced three dimensional charge is beneficial in reducing tunneling barriers especially for high composition AlGaN tunnel junctions. In addition, the design of graded tunnel junction structures could lead to low tunneling resistance below 10 –3 Ω cm 2 and lowmore » voltage consumption below 1 V (at 1 kA/cm 2) for high composition AlGaN tunnel junctions. Experimental demonstration of 292 nm emission was achieved through non-equilibrium hole injection into wide bandgap materials with bandgap energy larger than 4.7 eV, and detailed modeling of tunnel junctions shows that they can be engineered to have low resistance and can enable efficient emitters in the UV-C wavelength range.« less

Constructing Repairable Meta-Structures of Ultra-Broad-Band Electromagnetic Absorption from Three-Dimensional Printed Patterned Shells.

PubMed

Song, Wei-Li; Zhou, Zhili; Wang, Li-Chen; Cheng, Xiao-Dong; Chen, Mingji; He, Rujie; Chen, Haosen; Yang, Yazheng; Fang, Daining

2017-12-13

Ultra-broad-band electromagnetic absorption materials and structures are increasingly attractive for their critical role in competing with the advanced broad-band electromagnetic detection systems. Mechanically soft and weak wax-based materials composites are known to be insufficient to serve in practical electromagnetic absorption applications. To break through such barriers, here we developed an innovative strategy to enable the wax-based composites to be robust and repairable meta-structures by employing a three-dimensional (3D) printed polymeric patterned shell. Because of the integrated merits from both the dielectric loss wax-based composites and mechanically robust 3D printed shells, the as-fabricated meta-structures enable bear mechanical collision and compression, coupled with ultra-broad-band absorption (7-40 and 75-110 GHz, reflection loss  smaller than -10 dB) approaching state-of-the-art electromagnetic absorption materials. With the assistance of experiment and simulation methods, the design advantages and mechanism of employing such 3D printed shells for substantially promoting the electromagnetic absorption performance have been demonstrated. Therefore, such universal strategy that could be widely extended to other categories of wax-based composites highlights a smart stage on which high-performance practical multifunction meta-structures with ultra-broad-band electromagnetic absorption could be envisaged.

Development and ultra-structure of an ultra-thin silicone epidermis of bioengineered alternative tissue.

PubMed

Wessels, Quenton; Pretorius, Etheresia

2015-08-01

Burn wound care today has a primary objective of temporary or permanent wound closure. Commercially available engineered alternative tissues have become a valuable adjunct to the treatment of burn injuries. Their constituents can be biological, alloplastic or a combination of both. Here the authors describe the aspects of the development of a siloxane epidermis for a collagen-glycosaminoglycan and for nylon-based artificial skin replacement products. A method to fabricate an ultra-thin epidermal equivalent is described. Pores, to allow the escape of wound exudate, were punched and a tri-filament nylon mesh or collagen scaffold was imbedded and silicone polymerisation followed at 120°C for 5 minutes. The ultra-structure of these bilaminates was assessed through scanning electron microscopy. An ultra-thin biomedical grade siloxane film was reliably created through precision coating on a pre-treated polyethylene terephthalate carrier. © 2013 The Authors. International Wound Journal © 2013 Medicalhelplines.com Inc and John Wiley & Sons Ltd.

Automating Relational Database Design for Microcomputer Users.

ERIC Educational Resources Information Center

Pu, Hao-Che

1991-01-01

Discusses issues involved in automating the relational database design process for microcomputer users and presents a prototype of a microcomputer-based system (RA, Relation Assistant) that is based on expert systems technology and helps avoid database maintenance problems. Relational database design is explained and the importance of easy input…

PathwayAccess: CellDesigner plugins for pathway databases.

PubMed

Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

Quasi-static Design of Electrically Small Ultra-Wideband Antennas

DTIC Science & Technology

2017-02-01

this design reduces the width of the antenna, which implies that the bulb shape can be non -spherical at high frequencies. The stored energy in an...conclusion. The Quasi-static Antenna Design Algorithm generates three UWB non -spherical bulb shapes. The non -spherical bulb shape performs as well...TECHNICAL REPORT 3056 February 2017 Quasi-static Design of Electrically Small Ultra-Wideband Antennas Thomas O. Jones III Approved for public

Single-mode optical fiber design with wide-band ultra low bending-loss for FTTH application.

PubMed

Watekar, Pramod R; Ju, Seongmin; Han, Won-Taek

2008-01-21

We propose a new design of a single-mode optical fiber (SMF) which exhibits ultra low bend sensitivity over a wide communication band (1.3 microm to 1.65 microm). A five-cladding fiber structure has been proposed to minimize the bending loss, estimated to be as low as 4.4x10(-10) dB/turn for the bend radius of 10 mm.

Advanced germanium layer transfer for ultra thin body on insulator structure

NASA Astrophysics Data System (ADS)

Maeda, Tatsuro; Chang, Wen-Hsin; Irisawa, Toshifumi; Ishii, Hiroyuki; Hattori, Hiroyuki; Poborchii, Vladimir; Kurashima, Yuuichi; Takagi, Hideki; Uchida, Noriyuki

2016-12-01

We present the HEtero-Layer Lift-Off (HELLO) technique to obtain ultra thin body (UTB) Ge on insulator (GeOI) substrates. The transferred ultra thin Ge layers are characterized by the Raman spectroscopy measurements down to the thickness of ˜1 nm, observing a strong Raman intensity enhancement for high quality GeOI structure in ultra thin regime due to quantum size effect. This advanced Ge layer transfer technique enabled us to demonstrate UTB-GeOI nMOSFETs with the body thickness of only 4 nm.

DESIGNING ENVIRONMENTAL MONITORING DATABASES FOR STATISTIC ASSESSMENT

EPA Science Inventory

Databases designed for statistical analyses have characteristics that distinguish them from databases intended for general use. EMAP uses a probabilistic sampling design to collect data to produce statistical assessments of environmental conditions. In addition to supporting the ...

The UltraLightweight Technology for Research in Astronomy (ULTRA) Project

NASA Astrophysics Data System (ADS)

Twarog, B. A.; Anthony-Twarog, B. J.; Shawl, S. J.; Hale, R.; Taghavi, R.; Fesen, R.; Etzel, P. B.; Martin, R.; Romeo, R.

2004-12-01

The collaborative focus of four academic departments (Univ. of Kansas Aerospace Engineering, Univ. of Kansas Physics & Astronomy, San Diego State University Astronomy and Dartmouth College Astronomy) and a private industry partner (Composite Mirror Applications, Inc.-CMA, Inc.) is a three-year plan to develop and test UltraLightweight Technology for Research in Astronomy (ULTRA). The ULTRA technology, using graphite fiber composites to fabricate mirrors and telescope structures, offers a versatile and cost-effective tool for optical astronomy, including the economical fabrication and operation of telescopes ranging from small (1m or smaller) aperture for education and research to extremely large (30m+) segmented telescopes (ELTs). The specific goal of this NSF-funded three-year Major Research Instrumentation project is to design, build, and test a 1m-class optical tube assembly (OTA) and mirrors constructed entirely from composites. In the first year of the project, the team has built and is field-testing two 0.4m prototypes to validate the optical surfaces and figures of the mirrors and to test and refine the structural dynamics of the OTA. Preparation for design and construction of the 1m telescope is underway. When completed in late 2005, the ULTRA telescope will be operated remotely from Mt. Laguna Observatory east of San Diego, where it will undergo a period of intensive optical and imaging tests. A 0.4m prototype OTA with mirrors (12 kg total weight) will be on display at the meeting. Support of this work by NSF through grants AST-0320784 and AST-0321247, NASA grant NCC5-600, the University of Kansas, and San Diego State University is gratefully acknowledged.

MMDB: Entrez’s 3D-structure database

PubMed Central

Wang, Yanli; Anderson, John B.; Chen, Jie; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Liebert, Cynthia A.; Madej, Thomas; Marchler, Gabriele H.; Marchler-Bauer, Aron; Panchenko, Anna R.; Shoemaker, Benjamin A.; Song, James S.; Thiessen, Paul A.; Yamashita, Roxanne A.; Bryant, Stephen H.

2002-01-01

Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez’s 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez’s search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez’s Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure. PMID:11752307

Design of ultra-broadband terahertz polymer waveguide emitters for telecom wavelengths using coupled mode theory.

PubMed

Vallejo, Felipe A; Hayden, L Michael

2013-03-11

We use coupled mode theory, adequately incorporating optical losses, to model ultra-broadband terahertz (THz) waveguide emitters (0.1-20 THz) based on difference frequency generation of femtosecond infrared (IR) optical pulses. We apply the model to a generic, symmetric, five-layer, metal/cladding/core waveguide structure using transfer matrix theory. We provide a design strategy for an efficient ultra-broadband THz emitter and apply it to polymer waveguides with a nonlinear core composed of a poled guest-host electro-optic polymer composite and pumped by a pulsed fiber laser system operating at 1567 nm. The predicted bandwidths are greater than 15 THz and we find a high conversion efficiency of 1.2 × 10(-4) W(-1) by balancing both the modal phase-matching and effective mode attenuation.

Analysis and Design of Rotors at Ultra-Low Reynolds Numbers

NASA Technical Reports Server (NTRS)

Kunz, Peter J.; Strawn, Roger C.

2003-01-01

Design tools have been developed for ultra-low Reynolds number rotors, combining enhanced actuator-ring / blade-element theory with airfoil section data based on two-dimensional Navier-Stokes calculations. This performance prediction method is coupled with an optimizer for both design and analysis applications. Performance predictions from these tools have been compared with three-dimensional Navier Stokes analyses and experimental data for a 2.5 cm diameter rotor with chord Reynolds numbers below 10,000. Comparisons among the analyses and experimental data show reasonable agreement both in the global thrust and power required, but the spanwise distributions of these quantities exhibit significant deviations. The study also reveals that three-dimensional and rotational effects significantly change local airfoil section performance. The magnitude of this issue, unique to this operating regime, may limit the applicability of blade-element type methods for detailed rotor design at ultra-low Reynolds numbers, but these methods are still useful for evaluating concept feasibility and rapidly generating initial designs for further analysis and optimization using more advanced tools.

"TPSX: Thermal Protection System Expert and Material Property Database"

NASA Technical Reports Server (NTRS)

Squire, Thomas H.; Milos, Frank S.; Rasky, Daniel J. (Technical Monitor)

1997-01-01

The Thermal Protection Branch at NASA Ames Research Center has developed a computer program for storing, organizing, and accessing information about thermal protection materials. The program, called Thermal Protection Systems Expert and Material Property Database, or TPSX, is available for the Microsoft Windows operating system. An "on-line" version is also accessible on the World Wide Web. TPSX is designed to be a high-quality source for TPS material properties presented in a convenient, easily accessible form for use by engineers and researchers in the field of high-speed vehicle design. Data can be displayed and printed in several formats. An information window displays a brief description of the material with properties at standard pressure and temperature. A spread sheet window displays complete, detailed property information. Properties which are a function of temperature and/or pressure can be displayed as graphs. In any display the data can be converted from English to SI units with the click of a button. Two material databases included with TPSX are: 1) materials used and/or developed by the Thermal Protection Branch at NASA Ames Research Center, and 2) a database compiled by NASA Johnson Space Center 9JSC). The Ames database contains over 60 advanced TPS materials including flexible blankets, rigid ceramic tiles, and ultra-high temperature ceramics. The JSC database contains over 130 insulative and structural materials. The Ames database is periodically updated and expanded as required to include newly developed materials and material property refinements.

Relational Database Design in Information Science Education.

ERIC Educational Resources Information Center

Brooks, Terrence A.

1985-01-01

Reports on database management system (dbms) applications designed by library school students for university community at University of Iowa. Three dbms design issues are examined: synthesis of relations, analysis of relations (normalization procedure), and data dictionary usage. Database planning prior to automation using data dictionary approach…

SAbDab: the structural antibody database

PubMed Central

Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo; Baker, Terry; Fuchs, Angelika; Georges, Guy; Shi, Jiye; Deane, Charlotte M.

2014-01-01

Structural antibody database (SAbDab; http://opig.stats.ox.ac.uk/webapps/sabdab) is an online resource containing all the publicly available antibody structures annotated and presented in a consistent fashion. The data are annotated with several properties including experimental information, gene details, correct heavy and light chain pairings, antigen details and, where available, antibody–antigen binding affinity. The user can select structures, according to these attributes as well as structural properties such as complementarity determining region loop conformation and variable domain orientation. Individual structures, datasets and the complete database can be downloaded. PMID:24214988

Ultra-wideband filtering of spoof surface plasmon polaritons using deep subwavelength planar structures

PubMed Central

Hu, Ming Zhe; Zhang, Hao Chi; Yin, Jia Yuan; Ding, Zhao; Liu, Jun Feng; Tang, Wen Xuan; Cui, Tie Jun

2016-01-01

Novel ultra-wideband filtering of spoof surface plasmon polaritons (SPPs) is proposed in the microwave frequency using deep subwavelength planar structures printed on thin and flexible dielectric substrate. The proposed planar SPPs waveguide is composed of two mirror-oriented metallic corrugated strips, which are further decorated with parallel-arranged slots in the main corrugated strips. This compound structure provides deep subwavelength field confinement as well as flexible parameters when employed as a plasmonic waveguide, which is potential to construct miniaturization. Using momentum and impedance matching technology, we achieve a smooth conversion between the proposed SPPs waveguide and the conventional transmission line. To verify the validity of the design, we fabricate a spoof SPPs filter, and the measured results illustrate excellent performance, in which the reflection coefficient is less than −10 dB within the −3 dB passband from 1.21 GHz to 7.21 GHz with the smallest insertion loss of 1.23 dB at 2.21 GHz, having very good agreements with numerical simulations. The ultra-wideband filter with low insertion loss and high transmission efficiency possesses great potential in modern communication systems. PMID:27883028

Ultra-wideband filtering of spoof surface plasmon polaritons using deep subwavelength planar structures.

PubMed

Hu, Ming Zhe; Zhang, Hao Chi; Yin, Jia Yuan; Ding, Zhao; Liu, Jun Feng; Tang, Wen Xuan; Cui, Tie Jun

2016-11-24

Novel ultra-wideband filtering of spoof surface plasmon polaritons (SPPs) is proposed in the microwave frequency using deep subwavelength planar structures printed on thin and flexible dielectric substrate. The proposed planar SPPs waveguide is composed of two mirror-oriented metallic corrugated strips, which are further decorated with parallel-arranged slots in the main corrugated strips. This compound structure provides deep subwavelength field confinement as well as flexible parameters when employed as a plasmonic waveguide, which is potential to construct miniaturization. Using momentum and impedance matching technology, we achieve a smooth conversion between the proposed SPPs waveguide and the conventional transmission line. To verify the validity of the design, we fabricate a spoof SPPs filter, and the measured results illustrate excellent performance, in which the reflection coefficient is less than -10 dB within the -3 dB passband from 1.21 GHz to 7.21 GHz with the smallest insertion loss of 1.23 dB at 2.21 GHz, having very good agreements with numerical simulations. The ultra-wideband filter with low insertion loss and high transmission efficiency possesses great potential in modern communication systems.

PathCase-SB architecture and database design

PubMed Central

2011-01-01

Background Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. Description PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database. Conclusions PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. PMID:22070889

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 4. Examples of Discovery-Based Learning Using the Complete Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Comparison of the NCI open database with seven large chemical structural databases.

PubMed

Voigt, J H; Bienfait, B; Wang, S; Nicklaus, M C

2001-01-01

Eight large chemical databases have been analyzed and compared to each other. Central to this comparison is the open National Cancer Institute (NCI) database, consisting of approximately 250 000 structures. The other databases analyzed are the Available Chemicals Directory ("ACD," from MDL, release 1.99, 3D-version); the ChemACX ("ACX," from CamSoft, Version 4.5); the Maybridge Catalog and the Asinex database (both as distributed by CamSoft as part of ChemInfo 4.5); the Sigma-Aldrich Catalog (CD-ROM, 1999 Version); the World Drug Index ("WDI," Derwent, version 1999.03); and the organic part of the Cambridge Crystallographic Database ("CSD," from Cambridge Crystallographic Data Center, 1999 Version 5.18). The database properties analyzed are internal duplication rates; compounds unique to each database; cumulative occurrence of compounds in an increasing number of databases; overlap of identical compounds between two databases; similarity overlap; diversity; and others. The crystallographic database CSD and the WDI show somewhat less overlap with the other databases than those with each other. In particular the collections of commercial compounds and compilations of vendor catalogs have a substantial degree of overlap among each other. Still, no database is completely a subset of any other, and each appears to have its own niche and thus "raison d'être". The NCI database has by far the highest number of compounds that are unique to it. Approximately 200 000 of the NCI structures were not found in any of the other analyzed databases.

A case study for a digital seabed database: Bohai Sea engineering geology database

NASA Astrophysics Data System (ADS)

Tianyun, Su; Shikui, Zhai; Baohua, Liu; Ruicai, Liang; Yanpeng, Zheng; Yong, Wang

2006-07-01

This paper discusses the designing plan of ORACLE-based Bohai Sea engineering geology database structure from requisition analysis, conceptual structure analysis, logical structure analysis, physical structure analysis and security designing. In the study, we used the object-oriented Unified Modeling Language (UML) to model the conceptual structure of the database and used the powerful function of data management which the object-oriented and relational database ORACLE provides to organize and manage the storage space and improve its security performance. By this means, the database can provide rapid and highly effective performance in data storage, maintenance and query to satisfy the application requisition of the Bohai Sea Oilfield Paradigm Area Information System.

Design and Implementation of the CEBAF Element Database

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theodore Larrieu, Christopher Slominski, Michele Joyce

2011-10-01

With inauguration of the CEBAF Element Database (CED) in Fall 2010, Jefferson Lab computer scientists have taken a first step toward the eventual goal of a model-driven accelerator. Once fully populated, the database will be the primary repository of information used for everything from generating lattice decks to booting front-end computers to building controls screens. A particular requirement influencing the CED design is that it must provide consistent access to not only present, but also future, and eventually past, configurations of the CEBAF accelerator. To accomplish this, an introspective database schema was designed that allows new elements, element types, andmore » element properties to be defined on-the-fly without changing table structure. When used in conjunction with the Oracle Workspace Manager, it allows users to seamlessly query data from any time in the database history with the exact same tools as they use for querying the present configuration. Users can also check-out workspaces and use them as staging areas for upcoming machine configurations. All Access to the CED is through a well-documented API that is translated automatically from original C++ into native libraries for script languages such as perl, php, and TCL making access to the CED easy and ubiquitous. Notice: Authored by Jefferson Science Associates, LLC under U.S. DOE Contract No. DE-AC05-06OR23177. The U.S. Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce this manuscript for U.S. Government purposes.« less

microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations.

PubMed

Singh, Nagendra Kumar

2017-09-01

microRNA (miRNA) is an endogenous and evolutionary conserved non-coding RNA, involved in post-transcriptional process as gene repressor and mRNA cleavage through RNA-induced silencing complex (RISC) formation. In RISC, miRNA binds in complementary base pair with targeted mRNA along with Argonaut proteins complex, causes gene repression or endonucleolytic cleavage of mRNAs and results in many diseases and syndromes. After the discovery of miRNA lin-4 and let-7, subsequently large numbers of miRNAs were discovered by low-throughput and high-throughput experimental techniques along with computational process in various biological and metabolic processes. The miRNAs are important non-coding RNA for understanding the complex biological phenomena of organism because it controls the gene regulation. This paper reviews miRNA databases with structural and functional annotations developed by various researchers. These databases contain structural and functional information of animal, plant and virus miRNAs including miRNAs-associated diseases, stress resistance in plant, miRNAs take part in various biological processes, effect of miRNAs interaction on drugs and environment, effect of variance on miRNAs, miRNAs gene expression analysis, sequence of miRNAs, structure of miRNAs. This review focuses on the developmental methodology of miRNA databases such as computational tools and methods used for extraction of miRNAs annotation from different resources or through experiment. This study also discusses the efficiency of user interface design of every database along with current entry and annotations of miRNA (pathways, gene ontology, disease ontology, etc.). Here, an integrated schematic diagram of construction process for databases is also drawn along with tabular and graphical comparison of various types of entries in different databases. Aim of this paper is to present the importance of miRNAs-related resources at a single place.

The Binding Database: data management and interface design.

PubMed

Chen, Xi; Lin, Yuhmei; Liu, Ming; Gilson, Michael K

2002-01-01

The large and growing body of experimental data on biomolecular binding is of enormous value in developing a deeper understanding of molecular biology, in developing new therapeutics, and in various molecular design applications. However, most of these data are found only in the published literature and are therefore difficult to access and use. No existing public database has focused on measured binding affinities and has provided query capabilities that include chemical structure and sequence homology searches. We have created Binding DataBase (BindingDB), a public, web-accessible database of measured binding affinities. BindingDB is based upon a relational data specification for describing binding measurements via Isothermal Titration Calorimetry (ITC) and enzyme inhibition. A corresponding XML Document Type Definition (DTD) is used to create and parse intermediate files during the on-line deposition process and will also be used for data interchange, including collection of data from other sources. The on-line query interface, which is constructed with Java Servlet technology, supports standard SQL queries as well as searches for molecules by chemical structure and sequence homology. The on-line deposition interface uses Java Server Pages and JavaBean objects to generate dynamic HTML and to store intermediate results. The resulting data resource provides a range of functionality with brisk response-times, and lends itself well to continued development and enhancement.

Common hyperspectral image database design

NASA Astrophysics Data System (ADS)

Tian, Lixun; Liao, Ningfang; Chai, Ali

2009-11-01

This paper is to introduce Common hyperspectral image database with a demand-oriented Database design method (CHIDB), which comprehensively set ground-based spectra, standardized hyperspectral cube, spectral analysis together to meet some applications. The paper presents an integrated approach to retrieving spectral and spatial patterns from remotely sensed imagery using state-of-the-art data mining and advanced database technologies, some data mining ideas and functions were associated into CHIDB to make it more suitable to serve in agriculture, geological and environmental areas. A broad range of data from multiple regions of the electromagnetic spectrum is supported, including ultraviolet, visible, near-infrared, thermal infrared, and fluorescence. CHIDB is based on dotnet framework and designed by MVC architecture including five main functional modules: Data importer/exporter, Image/spectrum Viewer, Data Processor, Parameter Extractor, and On-line Analyzer. The original data were all stored in SQL server2008 for efficient search, query and update, and some advance Spectral image data Processing technology are used such as Parallel processing in C#; Finally an application case is presented in agricultural disease detecting area.

Adaptive Constrained Optimal Control Design for Data-Based Nonlinear Discrete-Time Systems With Critic-Only Structure.

PubMed

Luo, Biao; Liu, Derong; Wu, Huai-Ning

2018-06-01

Reinforcement learning has proved to be a powerful tool to solve optimal control problems over the past few years. However, the data-based constrained optimal control problem of nonaffine nonlinear discrete-time systems has rarely been studied yet. To solve this problem, an adaptive optimal control approach is developed by using the value iteration-based Q-learning (VIQL) with the critic-only structure. Most of the existing constrained control methods require the use of a certain performance index and only suit for linear or affine nonlinear systems, which is unreasonable in practice. To overcome this problem, the system transformation is first introduced with the general performance index. Then, the constrained optimal control problem is converted to an unconstrained optimal control problem. By introducing the action-state value function, i.e., Q-function, the VIQL algorithm is proposed to learn the optimal Q-function of the data-based unconstrained optimal control problem. The convergence results of the VIQL algorithm are established with an easy-to-realize initial condition . To implement the VIQL algorithm, the critic-only structure is developed, where only one neural network is required to approximate the Q-function. The converged Q-function obtained from the critic-only VIQL method is employed to design the adaptive constrained optimal controller based on the gradient descent scheme. Finally, the effectiveness of the developed adaptive control method is tested on three examples with computer simulation.

Structural performance of ultra-thin whitetopping on Illinois roadways and parking lots.

DOT National Transportation Integrated Search

2014-08-01

A performance evaluation of ultra-thin whitetopping (UTW) pavements in Illinois was undertaken in 20122014 : to evaluate current design procedures and to determine design life criteria for future projects. The two main : components of this evaluat...

Ultra-wideband design of waveguide magneto-optical isolator operating in 1.31mum and 1.55mum band.

PubMed

Shoji, Yuya; Mizumoto, Tetsuya

2007-01-22

The design of an ultra-wideband waveguide magneto-optical isolator is described. The isolator is based on a Mach-Zehnder interferometer employing nonreciprocal phase shift. The ultra-wideband design is realized by adjusting the wavelength dependence of reciprocal phase difference to compensate for that of nonreciprocal phase difference in the backward direction. We obtained the ultra-wideband design that provides isolation > 35dB from 1.25mum to >1.65mum. This is the proposal of magneto-optical isolator that operates both in 1.31mum band and 1.55mum band.

Ultra-Thin Dual-Band Polarization-Insensitive and Wide-Angle Perfect Metamaterial Absorber Based on a Single Circular Sector Resonator Structure

NASA Astrophysics Data System (ADS)

Luo, Hao; Cheng, Yong Zhi

2018-01-01

We present a simple design for an ultra-thin dual-band polarization-insensitive and wide-angle perfect metamaterial absorber (PMMA) based on a single circular sector resonator structure (CSRS). Both simulation and experimental results reveal that two resonance peaks with average absorption above 99% can be achieved. The dual-band PMMA is ultra-thin with total thickness of 0.5 mm, which is structure reveal the physical picture of the dual-band absorption. Numerical simulations demonstrate that the PMMA could retain high absorption level at large angles of polarization and incidence for both transverse electric (TE) and transverse magnetic (TM) modes. Furthermore, the absorption properties of the PMMA can be adjusted by varying the geometric parameters of the unit-cell structure.

A dynamic clinical dental relational database.

PubMed

Taylor, D; Naguib, R N G; Boulton, S

2004-09-01

The traditional approach to relational database design is based on the logical organization of data into a number of related normalized tables. One assumption is that the nature and structure of the data is known at the design stage. In the case of designing a relational database to store historical dental epidemiological data from individual clinical surveys, the structure of the data is not known until the data is presented for inclusion into the database. This paper addresses the issues concerned with the theoretical design of a clinical dynamic database capable of adapting the internal table structure to accommodate clinical survey data, and presents a prototype database application capable of processing, displaying, and querying the dental data.

Ultra Small Aperture Terminal: System Design and Test Results

NASA Technical Reports Server (NTRS)

Sohn, Philip Y.; Reinhart, Richard C.

1996-01-01

The Ultra Small Aperture Terminal (USAT) has been developed to test and demonstrate remote and broadcast satcom applications via the Advanced Communications Technology Satellite (ACTS). The design of these ground stations emphasize small size, low power consumption, portable and rugged terminals. Each ground station includes several custom design parts such as 35 cm diameter antenna, 1/4 Watt transmitter with built-in upconverter, and 4.0 dB Noise Figure (NF) receiver with built-in downconverter. In addition, state-of-the-art commercial parts such as highly stable ovenized crystal oscillators and dielectric resonator oscillators are used in the ground station design. Presented in this paper are system level design description, performance, and sample applications.

Construction of crystal structure prototype database: methods and applications.

PubMed

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-26

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Construction of crystal structure prototype database: methods and applications

NASA Astrophysics Data System (ADS)

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-01

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Searching the Cambridge Structural Database for polymorphs.

PubMed

van de Streek, Jacco; Motherwell, Sam

2005-10-01

In order to identify all pairs of polymorphs in the Cambridge Structural Database (CSD), a method was devised to automatically compare two crystal structures. The comparison is based on simulated powder diffraction patterns, but with special provisions to deal with differences in unit-cell volumes caused by temperature or pressure. Among the 325,000 crystal structures in the Cambridge Structural Database, 35,000 pairs of crystal structures of the same chemical compound were identified and compared. A total of 7300 pairs of polymorphs were identified, of which 154 previously were unknown.

Design of a broadband ultra-large area acoustic cloak based on a fluid medium

NASA Astrophysics Data System (ADS)

Zhu, Jian; Chen, Tianning; Liang, Qingxuan; Wang, Xiaopeng; Jiang, Ping

2014-10-01

A broadband ultra-large area acoustic cloak based on fluid medium was designed and numerically implemented with homogeneous metamaterials according to the transformation acoustics. In the present work, fluid medium as the body of the inclusion could be tuned by changing the fluid to satisfy the variant acoustic parameters instead of redesign the whole cloak. The effective density and bulk modulus of the composite materials were designed to agree with the parameters calculated from the coordinate transformation methodology by using the effective medium theory. Numerical simulation results showed that the sound propagation and scattering signature could be controlled in the broadband ultra-large area acoustic invisibility cloak, and good cloaking performance has been achieved and physically realized with homogeneous materials. The broadband ultra-large area acoustic cloaking properties have demonstrated great potentials in the promotion of the practical applications of acoustic cloak.

Ab Initio Design of Potent Anti-MRSA Peptides based on Database Filtering Technology

PubMed Central

Mishra, Biswajit; Wang, Guangshun

2012-01-01

To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed.1 This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g. amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database2 by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 minutes. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. A combination of our ab initio design with database screening3 led to yet another peptide with enhanced potency. Because of simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well. PMID:22803960

Ab initio design of potent anti-MRSA peptides based on database filtering technology.

PubMed

Mishra, Biswajit; Wang, Guangshun

2012-08-01

To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed. This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when the most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g., amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 min. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. Our ab initio design combined with database screening led to yet another peptide with enhanced potency. Because of the simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well.

Centralized database for interconnection system design. [for spacecraft

NASA Technical Reports Server (NTRS)

Billitti, Joseph W.

1989-01-01

A database application called DFACS (Database, Forms and Applications for Cabling and Systems) is described. The objective of DFACS is to improve the speed and accuracy of interconnection system information flow during the design and fabrication stages of a project, while simultaneously supporting both the horizontal (end-to-end wiring) and the vertical (wiring by connector) design stratagems used by the Jet Propulsion Laboratory (JPL) project engineering community. The DFACS architecture is centered around a centralized database and program methodology which emulates the manual design process hitherto used at JPL. DFACS has been tested and successfully applied to existing JPL hardware tasks with a resulting reduction in schedule time and costs.

Protein structure database search and evolutionary classification.

PubMed

Yang, Jinn-Moon; Tung, Chi-Hua

2006-01-01

As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

The methodology of database design in organization management systems

NASA Astrophysics Data System (ADS)

Chudinov, I. L.; Osipova, V. V.; Bobrova, Y. V.

2017-01-01

The paper describes the unified methodology of database design for management information systems. Designing the conceptual information model for the domain area is the most important and labor-intensive stage in database design. Basing on the proposed integrated approach to design, the conceptual information model, the main principles of developing the relation databases are provided and user’s information needs are considered. According to the methodology, the process of designing the conceptual information model includes three basic stages, which are defined in detail. Finally, the article describes the process of performing the results of analyzing user’s information needs and the rationale for use of classifiers.

Ultra-thin enhanced-absorption long-wave infrared detectors

NASA Astrophysics Data System (ADS)

Wang, Shaohua; Yoon, Narae; Kamboj, Abhilasha; Petluru, Priyanka; Zheng, Wanhua; Wasserman, Daniel

2018-02-01

We propose an architecture for enhanced absorption in ultra-thin strained layer superlattice detectors utilizing a hybrid optical cavity design. Our detector architecture utilizes a designer-metal doped semiconductor ground plane beneath the ultra-subwavelength thickness long-wavelength infrared absorber material, upon which we pattern metallic antenna structures. We demonstrate the potential for near 50% detector absorption in absorber layers with thicknesses of approximately λ0/50, using realistic material parameters. We investigate detector absorption as a function of wavelength and incidence angle, as well as detector geometry. The proposed device architecture offers the potential for high efficiency detectors with minimal growth costs and relaxed design parameters.

Optimizing Parameters of Axial Pressure-Compounded Ultra-Low Power Impulse Turbines at Preliminary Design

NASA Astrophysics Data System (ADS)

Kalabukhov, D. S.; Radko, V. M.; Grigoriev, V. A.

2018-01-01

Ultra-low power turbine drives are used as energy sources in auxiliary power systems, energy units, terrestrial, marine, air and space transport within the confines of shaft power N td = 0.01…10 kW. In this paper we propose a new approach to the development of surrogate models for evaluating the integrated efficiency of multistage ultra-low power impulse turbine with pressure stages. This method is based on the use of existing mathematical models of ultra-low power turbine stage efficiency and mass. It has been used in a method for selecting the rational parameters of two-stage axial ultra-low power turbine. The article describes the basic features of an algorithm for two-stage turbine parameters optimization and for efficiency criteria evaluating. Pledged mathematical models are intended for use at the preliminary design of turbine drive. The optimization method was tested at preliminary design of an air starter turbine. Validation was carried out by comparing the results of optimization calculations and numerical gas-dynamic simulation in the Ansys CFX package. The results indicate a sufficient accuracy of used surrogate models for axial two-stage turbine parameters selection

Structural and Aerodynamic Optimization of UltraLightweight Technology for Research in Astronomy (ULTRA)

NASA Astrophysics Data System (ADS)

Etzel, P. B.; Martin, R.; Romeo, R.; Fesen, R.; Hale, R.; Taghavi, R.; Anthony-Twarog, B. J.; Shawl, S. J.; Twarog, B. A.

2004-12-01

The focus of ULTRA (see poster by Twarog et al.) is a three-year plan to develop and test ultralightweight technology for research applications in astronomy. The goal is to demonstrate that a viable alternative exists to traditional glass-mirror technology by designing, fabricating, and testing a research telescope prototype comprising fiber reinforced plastic (CFRP) materials. To date, several mirror designs have been tested. The main goal in the first year has been to develop a 0.4m diameter mirror and OTA that serve as prototypes for the 1m telescope design. Mirrors of 0.4m diameter have been successfully fabricated which yield diffraction limited images. This poster will include a display of the complete OTA (including optics), optics test results, and astronomical images taken with prototype mirrors. Finite element analysis has been used to evaluate the OTA and mirror designs. Preliminary design details were incorporated in a knowledge-based system. Adaptive Modeling Language (AML), an object oriented programming language developed by Technosoft, Inc., was used to develop a parameterized geometric model of the preliminary design. The system can generate mirrors with radials/circumferentials, tube core substructures, as well as modeling the support structure. Computational fluid dynamics analyses were performed for sweep, inclination and ambient wind speed. Finite element analyses were performed for core density and arrangement, skin thickness, back-surface curvature, spider configuration and arrangement of the OTA, while the loading conditions considered thus far are thermal, inertial, and aerodynamic pressure loads. Experimental tests, including ultrasonic nondestructive evaluations, infrared imaging, modal testing, and wind tunnel tests, have been performed on the first prototype mirror, with the primary goal of validating analytical models and identifying potential manufacturing induced variations to be expected among "like" mirrors. Support of this work by

Design of special purpose database for credit cooperation bank business processing network system

NASA Astrophysics Data System (ADS)

Yu, Yongling; Zong, Sisheng; Shi, Jinfa

2011-12-01

With the popularization of e-finance in the city, the construction of e-finance is transfering to the vast rural market, and quickly to develop in depth. Developing the business processing network system suitable for the rural credit cooperative Banks can make business processing conveniently, and have a good application prospect. In this paper, We analyse the necessity of adopting special purpose distributed database in Credit Cooperation Band System, give corresponding distributed database system structure , design the specical purpose database and interface technology . The application in Tongbai Rural Credit Cooperatives has shown that system has better performance and higher efficiency.

Ultra-low power wireless sensing for long-term structural health monitoring

NASA Astrophysics Data System (ADS)

Bilbao, Argenis; Hoover, Davis; Rice, Jennifer; Chapman, Jamie

2011-04-01

Researchers have made significant progress in recent years towards realizing long-term structural health monitoring (SHM) utilizing wireless smart sensor networks (WSSNs). These efforts have focused on improving the performance and robustness of such networks to achieve high quality data acquisition and in-network processing. One of the primary challenges still facing the use of smart sensors for long-term monitoring deployments is their limited power resources. Periodically accessing the sensor nodes to change batteries is not feasible or economical in many deployment cases. While energy harvesting techniques show promise for prolonging unattended network life, low-power design and operation are still critically important. This research presents a new, fully integrated ultra-low power wireless smart sensor node and a flexible base station, both designed for long-term SHM applications. The power consumption of the sensor nodes and base station has been minimized through careful hardware selection and the implementation of power-aware network software, without sacrificing flexibility and functionality.

Design of Integrated Database on Mobile Information System: A Study of Yogyakarta Smart City App

NASA Astrophysics Data System (ADS)

Nurnawati, E. K.; Ermawati, E.

2018-02-01

An integration database is a database which acts as the data store for multiple applications and thus integrates data across these applications (in contrast to an Application Database). An integration database needs a schema that takes all its client applications into account. The benefit of the schema that sharing data among applications does not require an extra layer of integration services on the applications. Any changes to data made in a single application are made available to all applications at the time of database commit - thus keeping the applications’ data use better synchronized. This study aims to design and build an integrated database that can be used by various applications in a mobile device based system platforms with the based on smart city system. The built-in database can be used by various applications, whether used together or separately. The design and development of the database are emphasized on the flexibility, security, and completeness of attributes that can be used together by various applications to be built. The method used in this study is to choice of the appropriate database logical structure (patterns of data) and to build the relational-database models (Design Databases). Test the resulting design with some prototype apps and analyze system performance with test data. The integrated database can be utilized both of the admin and the user in an integral and comprehensive platform. This system can help admin, manager, and operator in managing the application easily and efficiently. This Android-based app is built based on a dynamic clientserver where data is extracted from an external database MySQL. So if there is a change of data in the database, then the data on Android applications will also change. This Android app assists users in searching of Yogyakarta (as smart city) related information, especially in culture, government, hotels, and transportation.

SATPdb: a database of structurally annotated therapeutic peptides

PubMed Central

Singh, Sandeep; Chaudhary, Kumardeep; Dhanda, Sandeep Kumar; Bhalla, Sherry; Usmani, Salman Sadullah; Gautam, Ankur; Tuknait, Abhishek; Agrawal, Piyush; Mathur, Deepika; Raghava, Gajendra P.S.

2016-01-01

SATPdb (http://crdd.osdd.net/raghava/satpdb/) is a database of structurally annotated therapeutic peptides, curated from 22 public domain peptide databases/datasets including 9 of our own. The current version holds 19192 unique experimentally validated therapeutic peptide sequences having length between 2 and 50 amino acids. It covers peptides having natural, non-natural and modified residues. These peptides were systematically grouped into 10 categories based on their major function or therapeutic property like 1099 anticancer, 10585 antimicrobial, 1642 drug delivery and 1698 antihypertensive peptides. We assigned or annotated structure of these therapeutic peptides using structural databases (Protein Data Bank) and state-of-the-art structure prediction methods like I-TASSER, HHsearch and PEPstrMOD. In addition, SATPdb facilitates users in performing various tasks that include: (i) structure and sequence similarity search, (ii) peptide browsing based on their function and properties, (iii) identification of moonlighting peptides and (iv) searching of peptides having desired structure and therapeutic activities. We hope this database will be useful for researchers working in the field of peptide-based therapeutics. PMID:26527728

MPD3: a useful medicinal plants database for drug designing.

PubMed

Mumtaz, Arooj; Ashfaq, Usman Ali; Ul Qamar, Muhammad Tahir; Anwar, Farooq; Gulzar, Faisal; Ali, Muhammad Amjad; Saari, Nazamid; Pervez, Muhammad Tariq

2017-06-01

Medicinal plants are the main natural pools for the discovery and development of new drugs. In the modern era of computer-aided drug designing (CADD), there is need of prompt efforts to design and construct useful database management system that allows proper data storage, retrieval and management with user-friendly interface. An inclusive database having information about classification, activity and ready-to-dock library of medicinal plant's phytochemicals is therefore required to assist the researchers in the field of CADD. The present work was designed to merge activities of phytochemicals from medicinal plants, their targets and literature references into a single comprehensive database named as Medicinal Plants Database for Drug Designing (MPD3). The newly designed online and downloadable MPD3 contains information about more than 5000 phytochemicals from around 1000 medicinal plants with 80 different activities, more than 900 literature references and 200 plus targets. The designed database is deemed to be very useful for the researchers who are engaged in medicinal plants research, CADD and drug discovery/development with ease of operation and increased efficiency. The designed MPD3 is a comprehensive database which provides most of the information related to the medicinal plants at a single platform. MPD3 is freely available at: http://bioinform.info .

A new Volcanic managEment Risk Database desIgn (VERDI): Application to El Hierro Island (Canary Islands)

NASA Astrophysics Data System (ADS)

Bartolini, S.; Becerril, L.; Martí, J.

2014-11-01

One of the most important issues in modern volcanology is the assessment of volcanic risk, which will depend - among other factors - on both the quantity and quality of the available data and an optimum storage mechanism. This will require the design of purpose-built databases that take into account data format and availability and afford easy data storage and sharing, and will provide for a more complete risk assessment that combines different analyses but avoids any duplication of information. Data contained in any such database should facilitate spatial and temporal analysis that will (1) produce probabilistic hazard models for future vent opening, (2) simulate volcanic hazards and (3) assess their socio-economic impact. We describe the design of a new spatial database structure, VERDI (Volcanic managEment Risk Database desIgn), which allows different types of data, including geological, volcanological, meteorological, monitoring and socio-economic information, to be manipulated, organized and managed. The root of the question is to ensure that VERDI will serve as a tool for connecting different kinds of data sources, GIS platforms and modeling applications. We present an overview of the database design, its components and the attributes that play an important role in the database model. The potential of the VERDI structure and the possibilities it offers in regard to data organization are here shown through its application on El Hierro (Canary Islands). The VERDI database will provide scientists and decision makers with a useful tool that will assist to conduct volcanic risk assessment and management.

Food Composition Database Format and Structure: A User Focused Approach

PubMed Central

Clancy, Annabel K.; Woods, Kaitlyn; McMahon, Anne; Probst, Yasmine

2015-01-01

This study aimed to investigate the needs of Australian food composition database user’s regarding database format and relate this to the format of databases available globally. Three semi structured synchronous online focus groups (M = 3, F = 11) and n = 6 female key informant interviews were recorded. Beliefs surrounding the use, training, understanding, benefits and limitations of food composition data and databases were explored. Verbatim transcriptions underwent preliminary coding followed by thematic analysis with NVivo qualitative analysis software to extract the final themes. Schematic analysis was applied to the final themes related to database format. Desktop analysis also examined the format of six key globally available databases. 24 dominant themes were established, of which five related to format; database use, food classification, framework, accessibility and availability, and data derivation. Desktop analysis revealed that food classification systems varied considerably between databases. Microsoft Excel was a common file format used in all databases, and available software varied between countries. User’s also recognised that food composition databases format should ideally be designed specifically for the intended use, have a user-friendly food classification system, incorporate accurate data with clear explanation of data derivation and feature user input. However, such databases are limited by data availability and resources. Further exploration of data sharing options should be considered. Furthermore, user’s understanding of food composition data and databases limitations is inherent to the correct application of non-specific databases. Therefore, further exploration of user FCDB training should also be considered. PMID:26554836

Designing Corporate Databases to Support Technology Innovation

ERIC Educational Resources Information Center

Gultz, Michael Jarett

2012-01-01

Based on a review of the existing literature on database design, this study proposed a unified database model to support corporate technology innovation. This study assessed potential support for the model based on the opinions of 200 technology industry executives, including Chief Information Officers, Chief Knowledge Officers and Chief Learning…

Columba: an integrated database of proteins, structures, and annotations.

PubMed

Trissl, Silke; Rother, Kristian; Müller, Heiko; Steinke, Thomas; Koch, Ina; Preissner, Robert; Frömmel, Cornelius; Leser, Ulf

2005-03-31

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web. The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de.

URS DataBase: universe of RNA structures and their motifs.

PubMed

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA-protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/. © The Author(s) 2016. Published by Oxford University Press.

URS DataBase: universe of RNA structures and their motifs

PubMed Central

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA–protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification. Database URL: http://server3.lpm.org.ru/urs/ PMID:27242032

Computerized Design Synthesis (CDS), A database-driven multidisciplinary design tool

NASA Technical Reports Server (NTRS)

Anderson, D. M.; Bolukbasi, A. O.

1989-01-01

The Computerized Design Synthesis (CDS) system under development at McDonnell Douglas Helicopter Company (MDHC) is targeted to make revolutionary improvements in both response time and resource efficiency in the conceptual and preliminary design of rotorcraft systems. It makes the accumulated design database and supporting technology analysis results readily available to designers and analysts of technology, systems, and production, and makes powerful design synthesis software available in a user friendly format.

CREDO: a structural interactomics database for drug discovery

PubMed Central

Schreyer, Adrian M.; Blundell, Tom L.

2013-01-01

CREDO is a unique relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small molecules and macromolecules found in experimentally determined structures from the Protein Data Bank. These interactions are integrated with further chemical and biological data. The database implements useful data structures and algorithms such as cheminformatics routines to create a comprehensive analysis platform for drug discovery. The database can be accessed through a web-based interface, downloads of data sets and web services at http://www-cryst.bioc.cam.ac.uk/credo. Database URL: http://www-cryst.bioc.cam.ac.uk/credo PMID:23868908

Challenges in Database Design with Microsoft Access

ERIC Educational Resources Information Center

Letkowski, Jerzy

2014-01-01

Design, development and explorations of databases are popular topics covered in introductory courses taught at business schools. Microsoft Access is the most popular software used in those courses. Despite quite high complexity of Access, it is considered to be one of the most friendly database programs for beginners. A typical Access textbook…

Structural Analysis of Titan's Tholins by Ultra-High Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Vuitton, V.; Frisari, M.; Thissen, R.; Dutuit, O.; Bonnet, J.-Y.; Quirico, E.; Sciamma O'Brien, E.; Szopa, C.; Carrasco, N.; Somogyi, A.; Smith, M.; Hörst, S. M.; Yelle, R.

2010-04-01

We propose here a systematic ultra-high resolution mass spectrometry and MS/MS study in order to provide a more coherent and complete characterization of the structure of the molecules making up the soluble fraction of the Titan tholins.

Design of Ultra-High-Power-Density Machine Optimized for Future Aircraft

NASA Technical Reports Server (NTRS)

Choi, Benjamin B.

2004-01-01

The NASA Glenn Research Center's Structural Mechanics and Dynamics Branch is developing a compact, nonpolluting, bearingless electric machine with electric power supplied by fuel cells for future "more-electric" aircraft with specific power in the projected range of 50 hp/lb, whereas conventional electric machines generate usually 0.2 hp/lb. The use of such electric drives for propulsive fans or propellers depends on the successful development of ultra-high-power-density machines. One possible candidate for such ultra-high-power-density machines, a round-rotor synchronous machine with an engineering current density as high as 20,000 A/sq cm, was selected to investigate how much torque and power can be produced.

Design of Student Information Management Database Application System for Office and Departmental Target Responsibility System

NASA Astrophysics Data System (ADS)

Zhou, Hui

It is the inevitable outcome of higher education reform to carry out office and departmental target responsibility system, in which statistical processing of student's information is an important part of student's performance review. On the basis of the analysis of the student's evaluation, the student information management database application system is designed by using relational database management system software in this paper. In order to implement the function of student information management, the functional requirement, overall structure, data sheets and fields, data sheet Association and software codes are designed in details.

A Database Design and Development Case: NanoTEK Networks

ERIC Educational Resources Information Center

Ballenger, Robert M.

2010-01-01

This case provides a real-world project-oriented case study for students enrolled in a management information systems, database management, or systems analysis and design course in which database design and development are taught. The case consists of a business scenario to provide background information and details of the unique operating…

LIPS database with LIPService: a microscopic image database of intracellular structures in Arabidopsis guard cells.

PubMed

Higaki, Takumi; Kutsuna, Natsumaro; Hasezawa, Seiichiro

2013-05-16

Intracellular configuration is an important feature of cell status. Recent advances in microscopic imaging techniques allow us to easily obtain a large number of microscopic images of intracellular structures. In this circumstance, automated microscopic image recognition techniques are of extreme importance to future phenomics/visible screening approaches. However, there was no benchmark microscopic image dataset for intracellular organelles in a specified plant cell type. We previously established the Live Images of Plant Stomata (LIPS) database, a publicly available collection of optical-section images of various intracellular structures of plant guard cells, as a model system of environmental signal perception and transduction. Here we report recent updates to the LIPS database and the establishment of a database table, LIPService. We updated the LIPS dataset and established a new interface named LIPService to promote efficient inspection of intracellular structure configurations. Cell nuclei, microtubules, actin microfilaments, mitochondria, chloroplasts, endoplasmic reticulum, peroxisomes, endosomes, Golgi bodies, and vacuoles can be filtered using probe names or morphometric parameters such as stomatal aperture. In addition to the serial optical sectional images of the original LIPS database, new volume-rendering data for easy web browsing of three-dimensional intracellular structures have been released to allow easy inspection of their configurations or relationships with cell status/morphology. We also demonstrated the utility of the new LIPS image database for automated organelle recognition of images from another plant cell image database with image clustering analyses. The updated LIPS database provides a benchmark image dataset for representative intracellular structures in Arabidopsis guard cells. The newly released LIPService allows users to inspect the relationship between organellar three-dimensional configurations and morphometrical parameters.

[Study on ultra-structural pathological changes of rats poisoned by tetramine].

PubMed

Zhi, Chuan-hong; Liu, Liang; Liu, Yan

2005-05-01

To observe ultra-structural pathological changes of materiality viscera of rats poisoned by different dose of tetramine and to study the toxic mechanism. Acute and subacute tetramine toxicity models were made by oral administration with different dose of tetramine. Brain, heart, liver, spleen and kidney were extracted and observed by electromicroscopic examination. The injuries of brain cells, cardiocytes and liver cells were induced by different dose of tetramine. These were not obviously different of the injuries of the kindy cells and spleen cells of rats poisoned by different dose of tetramine. Ultra-structural pathological changes were abserved including mitochondria slight swelling and neurolemma's array turbulence in the brain cells, mitochondria swelling or abolish and rupture of muscle fiber in the heart cells, mitochondria swelling and the glycogen decreased in the liver cells. The toxic target organs of tetramine are the heart, brain and liver.

Ultra-structural hair alterations in Friedreich's ataxia: A scanning electron microscopic investigation.

PubMed

Turkmenoglu, F Pinar; Kasirga, U Baran; Celik, H Hamdi

2015-08-01

Friedreich's ataxia (FRDA) is an autosomal recessive inherited disorder involving progressive damage to the central and peripheral nervous systems and cardiomyopathy. FRDA is caused by the silencing of the FXN gene and reduced levels of the encoded protein, frataxin. Frataxin is a mitochondrial protein that functions primarily in iron-sulfur cluster synthesis. Skin disorders including hair abnormalities have previously been reported in patients with mitochondrial disorders. However, to our knowledge, ultra-structural hair alterations in FRDA were not demonstrated. The purpose of this study was to determine ultra-structural alterations in the hairs of FRDA patients as well as carriers. Hair specimen from four patients, who are in different stages of the disease, and two carriers were examined by scanning electron microscope. Thin and weak hair follicles with absence of homogeneities on the cuticular surface, local damages of the cuticular layer, cuticular fractures were detected in both carriers and patients, but these alterations were much more prominent in the hair follicles of patients. In addition, erosions on the surface of the cuticle and local deep cavities just under the cuticular level were observed only in patients. Indistinct cuticular pattern, pores on the cuticular surface, and presence of concavities on the hair follicle were also detected in patients in later stages of the disease. According to our results, progression of the disease increased the alterations on hair structure. We suggest that ultra-structural alterations observed in hair samples might be due to oxidative stress caused by deficient frataxin expression in mitochondria. © 2015 Wiley Periodicals, Inc.

Pattern database applications from design to manufacturing

NASA Astrophysics Data System (ADS)

Zhuang, Linda; Zhu, Annie; Zhang, Yifan; Sweis, Jason; Lai, Ya-Chieh

2017-03-01

Pattern-based approaches are becoming more common and popular as the industry moves to advanced technology nodes. At the beginning of a new technology node, a library of process weak point patterns for physical and electrical verification are starting to build up and used to prevent known hotspots from re-occurring on new designs. Then the pattern set is expanded to create test keys for process development in order to verify the manufacturing capability and precheck new tape-out designs for any potential yield detractors. With the database growing, the adoption of pattern-based approaches has expanded from design flows to technology development and then needed for mass-production purposes. This paper will present the complete downstream working flows of a design pattern database(PDB). This pattern-based data analysis flow covers different applications across different functional teams from generating enhancement kits to improving design manufacturability, populating new testing design data based on previous-learning, generating analysis data to improve mass-production efficiency and manufacturing equipment in-line control to check machine status consistency across different fab sites.

Key features for ATA / ATR database design in missile systems

NASA Astrophysics Data System (ADS)

Özertem, Kemal Arda

2017-05-01

Automatic target acquisition (ATA) and automatic target recognition (ATR) are two vital tasks for missile systems, and having a robust detection and recognition algorithm is crucial for overall system performance. In order to have a robust target detection and recognition algorithm, an extensive image database is required. Automatic target recognition algorithms use the database of images in training and testing steps of algorithm. This directly affects the recognition performance, since the training accuracy is driven by the quality of the image database. In addition, the performance of an automatic target detection algorithm can be measured effectively by using an image database. There are two main ways for designing an ATA / ATR database. The first and easy way is by using a scene generator. A scene generator can model the objects by considering its material information, the atmospheric conditions, detector type and the territory. Designing image database by using a scene generator is inexpensive and it allows creating many different scenarios quickly and easily. However the major drawback of using a scene generator is its low fidelity, since the images are created virtually. The second and difficult way is designing it using real-world images. Designing image database with real-world images is a lot more costly and time consuming; however it offers high fidelity, which is critical for missile algorithms. In this paper, critical concepts in ATA / ATR database design with real-world images are discussed. Each concept is discussed in the perspective of ATA and ATR separately. For the implementation stage, some possible solutions and trade-offs for creating the database are proposed, and all proposed approaches are compared to each other with regards to their pros and cons.

STCRDab: the structural T-cell receptor database

PubMed Central

de Oliveira, Saulo H P; Krawczyk, Konrad

2018-01-01

Abstract The Structural T–cell Receptor Database (STCRDab; http://opig.stats.ox.ac.uk/webapps/stcrdab) is an online resource that automatically collects and curates TCR structural data from the Protein Data Bank. For each entry, the database provides annotations, such as the α/β or γ/δ chain pairings, major histocompatibility complex details, and where available, antigen binding affinities. In addition, the orientation between the variable domains and the canonical forms of the complementarity-determining region loops are also provided. Users can select, view, and download individual or bulk sets of structures based on these criteria. Where available, STCRDab also finds antibody structures that are similar to TCRs, helping users explore the relationship between TCRs and antibodies. PMID:29087479

Design of a digital, ultra-broadband electro-optic switch for reconfigurable optical networks-on-chip.

PubMed

Van Campenhout, Joris; Green, William M J; Vlasov, Yurii A

2009-12-21

We present a novel design for a noise-tolerant, ultra-broadband electro-optic switch, based on a Mach-Zehnder lattice (MZL) interferometer. We analyze the switch performance through rigorous optical simulations, for devices implemented in silicon-on-insulator with carrier-injection-based phase shifters. We show that such a MZL switch can be designed to have a step-like switching response, resulting in improved tolerance to drive-voltage noise and temperature variations as compared to a single-stage Mach-Zehnder switch. Furthermore, we show that degradation in switching crosstalk and insertion loss due to free-carrier absorption can be largely overcome by a MZL switch design. Finally, MZL switches can be designed for having an ultra-wide, temperature-insensitive optical bandwidth of more than 250 nm. The proposed device shows good potential as a broadband optical switch in reconfigurable optical networks-on-chip.

BtoxDB: a comprehensive database of protein structural data on toxin-antitoxin systems.

PubMed

Barbosa, Luiz Carlos Bertucci; Garrido, Saulo Santesso; Marchetto, Reinaldo

2015-03-01

Toxin-antitoxin (TA) systems are diverse and abundant genetic modules in prokaryotic cells that are typically formed by two genes encoding a stable toxin and a labile antitoxin. Because TA systems are able to repress growth or kill cells and are considered to be important actors in cell persistence (multidrug resistance without genetic change), these modules are considered potential targets for alternative drug design. In this scenario, structural information for the proteins in these systems is highly valuable. In this report, we describe the development of a web-based system, named BtoxDB, that stores all protein structural data on TA systems. The BtoxDB database was implemented as a MySQL relational database using PHP scripting language. Web interfaces were developed using HTML, CSS and JavaScript. The data were collected from the PDB, UniProt and Entrez databases. These data were appropriately filtered using specialized literature and our previous knowledge about toxin-antitoxin systems. The database provides three modules ("Search", "Browse" and "Statistics") that enable searches, acquisition of contents and access to statistical data. Direct links to matching external databases are also available. The compilation of all protein structural data on TA systems in one platform is highly useful for researchers interested in this content. BtoxDB is publicly available at http://www.gurupi.uft.edu.br/btoxdb. Copyright © 2015 Elsevier Ltd. All rights reserved.

Design and evaluation of a single-span bridge using ultra-high performance concrete.

DOT National Transportation Integrated Search

2009-09-01

"Research presented herein describes an application of a newly developed material called Ultra-High Performance Concrete (UHPC) to a : single-span bridge. The two primary objectives of this research were to develop a shear design procedure for possib...

Design and evaluation of a single-span bridge using ultra-high performance concrete.

DOT National Transportation Integrated Search

2009-09-01

Research presented herein describes an application of a newly developed material called Ultra-High Performance Concrete (UHPC) to a : single-span bridge. The two primary objectives of this research were to develop a shear design procedure for possibl...

LAND-deFeND - An innovative database structure for landslides and floods and their consequences.

PubMed

Napolitano, Elisabetta; Marchesini, Ivan; Salvati, Paola; Donnini, Marco; Bianchi, Cinzia; Guzzetti, Fausto

2018-02-01

Information on historical landslides and floods - collectively called "geo-hydrological hazards - is key to understand the complex dynamics of the events, to estimate the temporal and spatial frequency of damaging events, and to quantify their impact. A number of databases on geo-hydrological hazards and their consequences have been developed worldwide at different geographical and temporal scales. Of the few available database structures that can handle information on both landslides and floods some are outdated and others were not designed to store, organize, and manage information on single phenomena or on the type and monetary value of the damages and the remediation actions. Here, we present the LANDslides and Floods National Database (LAND-deFeND), a new database structure able to store, organize, and manage in a single digital structure spatial information collected from various sources with different accuracy. In designing LAND-deFeND, we defined four groups of entities, namely: nature-related, human-related, geospatial-related, and information-source-related entities that collectively can describe fully the geo-hydrological hazards and their consequences. In LAND-deFeND, the main entities are the nature-related entities, encompassing: (i) the "phenomenon", a single landslide or local inundation, (ii) the "event", which represent the ensemble of the inundations and/or landslides occurred in a conventional geographical area in a limited period, and (iii) the "trigger", which is the meteo-climatic or seismic cause (trigger) of the geo-hydrological hazards. LAND-deFeND maintains the relations between the nature-related entities and the human-related entities even where the information is missing partially. The physical model of the LAND-deFeND contains 32 tables, including nine input tables, 21 dictionary tables, and two association tables, and ten views, including specific views that make the database structure compliant with the EC INSPIRE and the Floods

The Animal Genetic Resource Information Network (AnimalGRIN) Database: A Database Design & Implementation Case

ERIC Educational Resources Information Center

Irwin, Gretchen; Wessel, Lark; Blackman, Harvey

2012-01-01

This case describes a database redesign project for the United States Department of Agriculture's National Animal Germplasm Program (NAGP). The case provides a valuable context for teaching and practicing database analysis, design, and implementation skills, and can be used as the basis for a semester-long team project. The case demonstrates the…

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

One approach to design of speech emotion database

NASA Astrophysics Data System (ADS)

Uhrin, Dominik; Chmelikova, Zdenka; Tovarek, Jaromir; Partila, Pavol; Voznak, Miroslav

2016-05-01

This article describes a system for evaluating the credibility of recordings with emotional character. Sound recordings form Czech language database for training and testing systems of speech emotion recognition. These systems are designed to detect human emotions in his voice. The emotional state of man is useful in the security forces and emergency call service. Man in action (soldier, police officer and firefighter) is often exposed to stress. Information about the emotional state (his voice) will help to dispatch to adapt control commands for procedure intervention. Call agents of emergency call service must recognize the mental state of the caller to adjust the mood of the conversation. In this case, the evaluation of the psychological state is the key factor for successful intervention. A quality database of sound recordings is essential for the creation of the mentioned systems. There are quality databases such as Berlin Database of Emotional Speech or Humaine. The actors have created these databases in an audio studio. It means that the recordings contain simulated emotions, not real. Our research aims at creating a database of the Czech emotional recordings of real human speech. Collecting sound samples to the database is only one of the tasks. Another one, no less important, is to evaluate the significance of recordings from the perspective of emotional states. The design of a methodology for evaluating emotional recordings credibility is described in this article. The results describe the advantages and applicability of the developed method.

Ultra-low-mass flexible planar solar arrays using 50-micron-thick solar cells

NASA Technical Reports Server (NTRS)

Costogue, E. N.; Rayl, G.

1978-01-01

A conceptual design study has been completed which has shown the feasibility of ultra-low-mass planar solar arrays with specific power of 200 watts/kilogram. The beginning of life (BOL) power output of the array designs would be 10 kW at 1 astronomical unit (AU) and a 55C deg operating temperature. Two designs were studied: a retractable rollout design and a non-retractable fold-out. The designs employed a flexible low-mass blanket and low-mass structures. The blanket utilized 2 x 2 cm high-efficiency (13.5% at 28C deg AM0), ultra-thin (50 micron), silicon solar cells protected by thin (75 micron) plastic encapsulants. The structural design utilized the 'V'-stiffened approach which allows a lower mass boom to be used. In conjunction with the conceptual design, modules using the thin cells and plastic encapsulant were designed and fabricated.

Design of compact and ultra efficient aspherical lenses for extended Lambertian sources in two-dimensional geometry

PubMed Central

Wu, Rengmao; Hua, Hong; Benítez, Pablo; Miñano, Juan C.; Liang, Rongguang

2016-01-01

The energy efficiency and compactness of an illumination system are two main concerns in illumination design for extended sources. In this paper, we present two methods to design compact, ultra efficient aspherical lenses for extended Lambertian sources in two-dimensional geometry. The light rays are directed by using two aspherical surfaces in the first method and one aspherical surface along with an optimized parabola in the second method. The principles and procedures of each design method are introduced in detail. Three examples are presented to demonstrate the effectiveness of these two methods in terms of performance and capacity in designing compact, ultra efficient aspherical lenses. The comparisons made between the two proposed methods indicate that the second method is much simpler and easier to be implemented, and has an excellent extensibility to three-dimensional designs. PMID:29092336

Ultra-wideband surface plasmonic Y-splitter.

PubMed

Gao, Xi; Zhou, Liang; Yu, Xing Yang; Cao, Wei Ping; Li, Hai Ou; Ma, Hui Feng; Cui, Tie Jun

2015-09-07

We present an ultra-wideband Y-splitter based on planar THz plasmonic metamaterials, which consists of a straight waveguide with composite H-shaped structure and two branch waveguides with H-shaped structure. The spoof surface plasmonic polaritons (SSPPs) supported by the straight waveguide occupy the similar dispersion relation and mode characteristic to the ones confined by the branch waveguides. Attributing to these features, the two branch waveguides can equally separate the SSPPs wave propagating along the straight plasmonic waveguide to form a 3dB power divider in an ultra-wideband frequency range. To verify the functionality and performance of the proposed Y-splitter, we scaled down the working frequency to microwave and implemented microwave experiments. The tested device performances have clearly validated the functionality of our designs. It is believed to be applicable for future plasmonic circuit in microwave and THz ranges.

A sextuple-band ultra-thin metamaterial absorber with perfect absorption

NASA Astrophysics Data System (ADS)

Yu, Dingwang; Liu, Peiguo; Dong, Yanfei; Zhou, Dongming; Zhou, Qihui

2017-08-01

This paper presents the design, simulation and measurement of a sextuple-band ultra-thin metamaterial absorber (MA). The unit cell of this proposed structure is composed of triangular spiral-shaped complementary structures imprinted on the dielectric substrate backed by a metal ground. The measured results are in good agreement with simulations with high absorptivities of more than 90% at all six absorption frequencies. In addition, this proposed absorber has good performances of ultra-thin, polarization insensitivity and a wide-angle oblique incidence, which can easily be used in many potential applications such as detection, imaging and sensing.

MODBASE, a database of annotated comparative protein structure models

PubMed Central

Pieper, Ursula; Eswar, Narayanan; Stuart, Ashley C.; Ilyin, Valentin A.; Sali, Andrej

2002-01-01

MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10–4) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server. PMID:11752309

Teaching Database Design with Constraint-Based Tutors

ERIC Educational Resources Information Center

Mitrovic, Antonija; Suraweera, Pramuditha

2016-01-01

Design tasks are difficult to teach, due to large, unstructured solution spaces, underspecified problems, non-existent problem solving algorithms and stopping criteria. In this paper, we comment on our approach to develop KERMIT, a constraint-based tutor that taught database design. In later work, we re-implemented KERMIT as EER-Tutor, and…

Ultra-wide-field imaging in diabetic retinopathy; an overview.

PubMed

Ghasemi Falavarjani, Khalil; Wang, Kang; Khadamy, Joobin; Sadda, Srinivas R

2016-06-01

To present an overview on ultra-wide-field imaging in diabetic retinopathy. A comprehensive search of the pubmed database was performed using the search terms of "ultra-wide-field imaging", "ultra-wide-field fluorescein angiography" and "diabetic retinopathy". The relevant original articles were reviewed. New advances in ultra-wide-field imaging allow for precise measurements of the peripheral retinal lesions. A consistent finding amongst these articles was that ultra-wide-field imaging improved detection of peripheral lesion. There was discordance among the studies, however, on the correlation between peripheral diabetic lesions and diabetic macular edema. Visualization of the peripheral retina using ultra-wide-field imaging improves diagnosis and classification of diabetic retinopathy. Additional studies are needed to better define the association of peripheral diabetic lesions with diabetic macular edema.

Design and implementation of a database for Brucella melitensis genome annotation.

PubMed

De Hertogh, Benoît; Lahlimi, Leïla; Lambert, Christophe; Letesson, Jean-Jacques; Depiereux, Eric

2008-03-18

The genome sequences of three Brucella biovars and of some species close to Brucella sp. have become available, leading to new relationship analysis. Moreover, the automatic genome annotation of the pathogenic bacteria Brucella melitensis has been manually corrected by a consortium of experts, leading to 899 modifications of start sites predictions among the 3198 open reading frames (ORFs) examined. This new annotation, coupled with the results of automatic annotation tools of the complete genome sequences of the B. melitensis genome (including BLASTs to 9 genomes close to Brucella), provides numerous data sets related to predicted functions, biochemical properties and phylogenic comparisons. To made these results available, alphaPAGe, a functional auto-updatable database of the corrected sequence genome of B. melitensis, has been built, using the entity-relationship (ER) approach and a multi-purpose database structure. A friendly graphical user interface has been designed, and users can carry out different kinds of information by three levels of queries: (1) the basic search use the classical keywords or sequence identifiers; (2) the original advanced search engine allows to combine (by using logical operators) numerous criteria: (a) keywords (textual comparison) related to the pCDS's function, family domains and cellular localization; (b) physico-chemical characteristics (numerical comparison) such as isoelectric point or molecular weight and structural criteria such as the nucleic length or the number of transmembrane helix (TMH); (c) similarity scores with Escherichia coli and 10 species phylogenetically close to B. melitensis; (3) complex queries can be performed by using a SQL field, which allows all queries respecting the database's structure. The database is publicly available through a Web server at the following url: http://www.fundp.ac.be/urbm/bioinfo/aPAGe.

Design and Establishment of Quality Model of Fundamental Geographic Information Database

NASA Astrophysics Data System (ADS)

Ma, W.; Zhang, J.; Zhao, Y.; Zhang, P.; Dang, Y.; Zhao, T.

2018-04-01

In order to make the quality evaluation for the Fundamental Geographic Information Databases(FGIDB) more comprehensive, objective and accurate, this paper studies and establishes a quality model of FGIDB, which formed by the standardization of database construction and quality control, the conformity of data set quality and the functionality of database management system, and also designs the overall principles, contents and methods of the quality evaluation for FGIDB, providing the basis and reference for carry out quality control and quality evaluation for FGIDB. This paper designs the quality elements, evaluation items and properties of the Fundamental Geographic Information Database gradually based on the quality model framework. Connected organically, these quality elements and evaluation items constitute the quality model of the Fundamental Geographic Information Database. This model is the foundation for the quality demand stipulation and quality evaluation of the Fundamental Geographic Information Database, and is of great significance on the quality assurance in the design and development stage, the demand formulation in the testing evaluation stage, and the standard system construction for quality evaluation technology of the Fundamental Geographic Information Database.

Interactive and Versatile Navigation of Structural Databases.

PubMed

Korb, Oliver; Kuhn, Bernd; Hert, Jérôme; Taylor, Neil; Cole, Jason; Groom, Colin; Stahl, Martin

2016-05-12

We present CSD-CrossMiner, a novel tool for pharmacophore-based searches in crystal structure databases. Intuitive pharmacophore queries describing, among others, protein-ligand interaction patterns, ligand scaffolds, or protein environments can be built and modified interactively. Matching crystal structures are overlaid onto the query and visualized as soon as they are available, enabling the researcher to quickly modify a hypothesis on the fly. We exemplify the utility of the approach by showing applications relevant to real-world drug discovery projects, including the identification of novel fragments for a specific protein environment or scaffold hopping. The ability to concurrently search protein-ligand binding sites extracted from the Protein Data Bank (PDB) and small organic molecules from the Cambridge Structural Database (CSD) using the same pharmacophore query further emphasizes the flexibility of CSD-CrossMiner. We believe that CSD-CrossMiner closes an important gap in mining structural data and will allow users to extract more value from the growing number of available crystal structures.

High-performance radial AMTEC cell design for ultra-high-power solar AMTEC systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hendricks, T.J.; Huang, C.

1999-07-01

Alkali Metal Thermal to Electric Conversion (AMTEC) technology is rapidly maturing for potential application in ultra-high-power solar AMTEC systems required by potential future US Air Force (USAF) spacecraft missions in medium-earth and geosynchronous orbits (MEO and GEO). Solar thermal AMTEC power systems potentially have several important advantages over current solar photovoltaic power systems in ultra-high-power spacecraft applications for USAF MEO and GEO missions. This work presents key aspects of radial AMTEC cell design to achieve high cell performance in solar AMTEC systems delivering larger than 50 kW(e) to support high power USAF missions. These missions typically require AMTEC cell conversionmore » efficiency larger than 25%. A sophisticated design parameter methodology is described and demonstrated which establishes optimum design parameters in any radial cell design to satisfy high-power mission requirements. Specific relationships, which are distinct functions of cell temperatures and pressures, define critical dependencies between key cell design parameters, particularly the impact of parasitic thermal losses on Beta Alumina Solid Electrolyte (BASE) area requirements, voltage, number of BASE tubes, and system power production for both maximum power-per-BASE-area and optimum efficiency conditions. Finally, some high-level system tradeoffs are demonstrated using the design parameter methodology to establish high-power radial cell design requirements and philosophy. The discussion highlights how to incorporate this methodology with sophisticated SINDA/FLUINT AMTEC cell modeling capabilities to determine optimum radial AMTEC cell designs.« less

Design of nodes for embedded and ultra low-power wireless sensor networks

NASA Astrophysics Data System (ADS)

Xu, Jun; You, Bo; Cui, Juan; Ma, Jing; Li, Xin

2008-10-01

Sensor network integrates sensor technology, MEMS (Micro-Electro-Mechanical system) technology, embedded computing, wireless communication technology and distributed information management technology. It is of great value to use it where human is quite difficult to reach. Power consumption and size are the most important consideration when nodes are designed for distributed WSN (wireless sensor networks). Consequently, it is of great importance to decrease the size of a node, reduce its power consumption and extend its life in network. WSN nodes have been designed using JN5121-Z01-M01 module produced by jennic company and IEEE 802.15.4/ZigBee technology. Its new features include support for CPU sleep modes and a long-term ultra low power sleep mode for the entire node. In low power configuration the node resembles existing small low power nodes. An embedded temperature sensor node has been developed to verify and explore our architecture. The experiment results indicate that the WSN has the characteristic of high reliability, good stability and ultra low power consumption.

Earlinet database: new design and new products for a wider use of aerosol lidar data

NASA Astrophysics Data System (ADS)

Mona, Lucia; D'Amico, Giuseppe; Amato, Francesco; Linné, Holger; Baars, Holger; Wandinger, Ulla; Pappalardo, Gelsomina

2018-04-01

The EARLINET database is facing a complete reshaping to meet the wide request for more intuitive products and to face the even wider request related to the new initiatives such as Copernicus, the European Earth observation programme. The new design has been carried out in continuity with the past, to take advantage from long-term database. In particular, the new structure will provide information suitable for synergy with other instruments, near real time (NRT) applications, validation and process studies and climate applications.

UbSRD: The Ubiquitin Structural Relational Database.

PubMed

Harrison, Joseph S; Jacobs, Tim M; Houlihan, Kevin; Van Doorslaer, Koenraad; Kuhlman, Brian

2016-02-22

The structurally defined ubiquitin-like homology fold (UBL) can engage in several unique protein-protein interactions and many of these complexes have been characterized with high-resolution techniques. Using Rosetta's structural classification tools, we have created the Ubiquitin Structural Relational Database (UbSRD), an SQL database of features for all 509 UBL-containing structures in the PDB, allowing users to browse these structures by protein-protein interaction and providing a platform for quantitative analysis of structural features. We used UbSRD to define the recognition features of ubiquitin (UBQ) and SUMO observed in the PDB and the orientation of the UBQ tail while interacting with certain types of proteins. While some of the interaction surfaces on UBQ and SUMO overlap, each molecule has distinct features that aid in molecular discrimination. Additionally, we find that the UBQ tail is malleable and can adopt a variety of conformations upon binding. UbSRD is accessible as an online resource at rosettadesign.med.unc.edu/ubsrd. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Computational chemistry in structure-based drug design].

PubMed

Cao, Ran; Li, Wei; Sun, Han-Zi; Zhou, Yu; Huang, Niu

2013-07-01

Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. However, it remains challenging to rationally design small molecular ligands with desired biological characteristics based on the structural information of the drug targets, which demands more accurate calculation of ligand binding free-energy. With the rapid advances in computer power and extensive efforts in algorithm development, physics-based computational chemistry approaches have played more important roles in structure-based drug design. Here we reviewed the newly developed computational chemistry methods in structure-based drug design as well as the elegant applications, including binding-site druggability assessment, large scale virtual screening of chemical database, and lead compound optimization. Importantly, here we address the current bottlenecks and propose practical solutions.

CFRP composite optical telescope assembly for the 1 m ULTRA project

NASA Astrophysics Data System (ADS)

Martin, Robert N.; Romeo, Robert C.

2006-06-01

The focus of the ULTRA Project is to develop and test Ultra-Lightweight Technology for Research applications in Astronomy. The ULTRA project is a collaborative effort involving the private firm Composite Mirror Applications, Inc (CMA) and 3 universities: University of Kansas, San Diego State University, and Dartmouth College. Funding for ULTRA is predominately from a NSF three year MRI program grant to CMA and KU with additional support from CMA, KU and SDSU. The goal of the ULTRA program is to demonstrate that a viable alternative exists to traditional glass mirror and steel telescope technology by designing, fabricating and testing a research telescope constructed from carbon fiber reinforced plastic (CFRP) materials. In particular, a 1m diameter, Cassegrain telescope optics set and optical tube assembly (OTA) are being designed and fabricated by CMA. The completed telescope will be deployed at SDSU's Mt Laguna Observatory in a refurbished structure (new dome and mount provided via KU and SDSU). We expect that a successful completion and testing of this project will lead to future use of CFRP technology in larger telescopes and segmented telescopes. This paper describes the OTA (optical tube assembly) that has been developed for the ULTRA project. The mirror technology is described in another paper in this conference. A poster describes the ULTRA project overview in more detail.

Design optimization of ultra-high concentrator photovoltaic system using two-stage non-imaging solar concentrator

NASA Astrophysics Data System (ADS)

Wong, C.-W.; Yew, T.-K.; Chong, K.-K.; Tan, W.-C.; Tan, M.-H.; Lim, B.-H.

2017-11-01

This paper presents a systematic approach for optimizing the design of ultra-high concentrator photovoltaic (UHCPV) system comprised of non-imaging dish concentrator (primary optical element) and crossed compound parabolic concentrator (secondary optical element). The optimization process includes the design of primary and secondary optics by considering the focal distance, spillage losses and rim angle of the dish concentrator. The imperfection factors, i.e. mirror reflectivity of 93%, lens’ optical efficiency of 85%, circumsolar ratio of 0.2 and mirror surface slope error of 2 mrad, were considered in the simulation to avoid the overestimation of output power. The proposed UHCPV system is capable of attaining effective ultra-high solar concentration ratio of 1475 suns and DC system efficiency of 31.8%.

Compact electromagnetic bandgap structures for notch band in ultra-wideband applications.

PubMed

Rotaru, Mihai; Sykulski, Jan

2010-01-01

This paper introduces a novel approach to create notch band filters in the front-end of ultra-wideband (UWB) communication systems based on electromagnetic bandgap (EBG) structures. The concept presented here can be implemented in any structure that has a microstrip in its configuration. The EBG structure is first analyzed using a full wave electromagnetic solver and then optimized to work at WLAN band (5.15-5.825 GHz). Two UWB passband filters are used to demonstrate the applicability and effectiveness of the novel EBG notch band feature. Simulation results are provided for two cases studied.

Compact Electromagnetic Bandgap Structures for Notch Band in Ultra-Wideband Applications

PubMed Central

Rotaru, Mihai; Sykulski, Jan

2010-01-01

This paper introduces a novel approach to create notch band filters in the front-end of ultra-wideband (UWB) communication systems based on electromagnetic bandgap (EBG) structures. The concept presented here can be implemented in any structure that has a microstrip in its configuration. The EBG structure is first analyzed using a full wave electromagnetic solver and then optimized to work at WLAN band (5.15–5.825 GHz). Two UWB passband filters are used to demonstrate the applicability and effectiveness of the novel EBG notch band feature. Simulation results are provided for two cases studied. PMID:22163430

A new relational database structure and online interface for the HITRAN database

NASA Astrophysics Data System (ADS)

Hill, Christian; Gordon, Iouli E.; Rothman, Laurence S.; Tennyson, Jonathan

2013-11-01

A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

Glycan fragment database: a database of PDB-based glycan 3D structures.

PubMed

Jo, Sunhwan; Im, Wonpil

2013-01-01

The glycan fragment database (GFDB), freely available at http://www.glycanstructure.org, is a database of the glycosidic torsion angles derived from the glycan structures in the Protein Data Bank (PDB). Analogous to protein structure, the structure of an oligosaccharide chain in a glycoprotein, referred to as a glycan, can be characterized by the torsion angles of glycosidic linkages between relatively rigid carbohydrate monomeric units. Knowledge of accessible conformations of biologically relevant glycans is essential in understanding their biological roles. The GFDB provides an intuitive glycan sequence search tool that allows the user to search complex glycan structures. After a glycan search is complete, each glycosidic torsion angle distribution is displayed in terms of the exact match and the fragment match. The exact match results are from the PDB entries that contain the glycan sequence identical to the query sequence. The fragment match results are from the entries with the glycan sequence whose substructure (fragment) or entire sequence is matched to the query sequence, such that the fragment results implicitly include the influences from the nearby carbohydrate residues. In addition, clustering analysis based on the torsion angle distribution can be performed to obtain the representative structures among the searched glycan structures.

A Framework for Mapping User-Designed Forms to Relational Databases

ERIC Educational Resources Information Center

Khare, Ritu

2011-01-01

In the quest for database usability, several applications enable users to design custom forms using a graphical interface, and forward engineer the forms into new databases. The path-breaking aspect of such applications is that users are completely shielded from the technicalities of database creation. Despite this innovation, the process of…

Effects of the ultra-high pressure on structure and α-glucosidase inhibition of polysaccharide from Astragalus.

PubMed

Zhu, Zhen-Yuan; Luo, You; Dong, Guo-Ling; Ren, Yuan-Yuan; Chen, Li-Jing; Guo, Ming-Zhu; Wang, Xiao-Ting; Yang, Xue-Ying; Zhang, Yongmin

2016-06-01

A novel homogeneous polysaccharide fraction (APS) was extracted from Astragalus by hot water and purified by Sephadex G-100 and G-75 column. Its molecular weight was 693kDa. APS and APS with ultra-high pressure treatment exhibited significant inhibitory abilities on a-glucosidase, inhibition rate from high to low in order was 400MPa-APS, 300MPa-APS, 500MPa-APS and APS. The inhibition ​percentage of 400MPa-APS (1.5mg/mL) was 49% (max.). This suggested that the inhibitory activity of APS on a-glucosidase was improved by ultra-high pressure treatment. FT-IR, SEM, CD spectra, atomic force microscope and Congo red test analysis of APS and 400MPa-APS showed ultra-high pressure treatment didn't change the preliminary structure but had an effect on its advanced structure. Copyright © 2016 Elsevier B.V. All rights reserved.

Probabilistic design of fibre concrete structures

NASA Astrophysics Data System (ADS)

Pukl, R.; Novák, D.; Sajdlová, T.; Lehký, D.; Červenka, J.; Červenka, V.

2017-09-01

Advanced computer simulation is recently well-established methodology for evaluation of resistance of concrete engineering structures. The nonlinear finite element analysis enables to realistically predict structural damage, peak load, failure, post-peak response, development of cracks in concrete, yielding of reinforcement, concrete crushing or shear failure. The nonlinear material models can cover various types of concrete and reinforced concrete: ordinary concrete, plain or reinforced, without or with prestressing, fibre concrete, (ultra) high performance concrete, lightweight concrete, etc. Advanced material models taking into account fibre concrete properties such as shape of tensile softening branch, high toughness and ductility are described in the paper. Since the variability of the fibre concrete material properties is rather high, the probabilistic analysis seems to be the most appropriate format for structural design and evaluation of structural performance, reliability and safety. The presented combination of the nonlinear analysis with advanced probabilistic methods allows evaluation of structural safety characterized by failure probability or by reliability index respectively. Authors offer a methodology and computer tools for realistic safety assessment of concrete structures; the utilized approach is based on randomization of the nonlinear finite element analysis of the structural model. Uncertainty of the material properties or their randomness obtained from material tests are accounted in the random distribution. Furthermore, degradation of the reinforced concrete materials such as carbonation of concrete, corrosion of reinforcement, etc. can be accounted in order to analyze life-cycle structural performance and to enable prediction of the structural reliability and safety in time development. The results can serve as a rational basis for design of fibre concrete engineering structures based on advanced nonlinear computer analysis. The presented

Database System Design and Implementation for Marine Air-Traffic-Controller Training

DTIC Science & Technology

2017-06-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. DATABASE SYSTEM DESIGN AND...thesis 4. TITLE AND SUBTITLE DATABASE SYSTEM DESIGN AND IMPLEMENTATION FOR MARINE AIR-TRAFFIC-CONTROLLER TRAINING 5. FUNDING NUMBERS 6. AUTHOR(S...12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) This project focused on the design , development, and implementation of a centralized

Automated Database Schema Design Using Mined Data Dependencies.

ERIC Educational Resources Information Center

Wong, S. K. M.; Butz, C. J.; Xiang, Y.

1998-01-01

Describes a bottom-up procedure for discovering multivalued dependencies in observed data without knowing a priori the relationships among the attributes. The proposed algorithm is an application of technique designed for learning conditional independencies in probabilistic reasoning; a prototype system for automated database schema design has…

Ultra-Wideband Tracking System Design for Relative Navigation

NASA Technical Reports Server (NTRS)

Ni, Jianjun David; Arndt, Dickey; Bgo, Phong; Dekome, Kent; Dusl, John

2011-01-01

This presentation briefly discusses a design effort for a prototype ultra-wideband (UWB) time-difference-of-arrival (TDOA) tracking system that is currently under development at NASA Johnson Space Center (JSC). The system is being designed for use in localization and navigation of a rover in a GPS deprived environment for surface missions. In one application enabled by the UWB tracking, a robotic vehicle carrying equipments can autonomously follow a crewed rover from work site to work site such that resources can be carried from one landing mission to the next thereby saving up-mass. The UWB Systems Group at JSC has developed a UWB TDOA High Resolution Proximity Tracking System which can achieve sub-inch tracking accuracy of a target within the radius of the tracking baseline [1]. By extending the tracking capability beyond the radius of the tracking baseline, a tracking system is being designed to enable relative navigation between two vehicles for surface missions. A prototype UWB TDOA tracking system has been designed, implemented, tested, and proven feasible for relative navigation of robotic vehicles. Future work includes testing the system with the application code to increase the tracking update rate and evaluating the linear tracking baseline to improve the flexibility of antenna mounting on the following vehicle.

Optics Toolbox: An Intelligent Relational Database System For Optical Designers

NASA Astrophysics Data System (ADS)

Weller, Scott W.; Hopkins, Robert E.

1986-12-01

Optical designers were among the first to use the computer as an engineering tool. Powerful programs have been written to do ray-trace analysis, third-order layout, and optimization. However, newer computing techniques such as database management and expert systems have not been adopted by the optical design community. For the purpose of this discussion we will define a relational database system as a database which allows the user to specify his requirements using logical relations. For example, to search for all lenses in a lens database with a F/number less than two, and a half field of view near 28 degrees, you might enter the following: FNO < 2.0 and FOV of 28 degrees ± 5% Again for the purpose of this discussion, we will define an expert system as a program which contains expert knowledge, can ask intelligent questions, and can form conclusions based on the answers given and the knowledge which it contains. Most expert systems store this knowledge in the form of rules-of-thumb, which are written in an English-like language, and which are easily modified by the user. An example rule is: IF require microscope objective in air and require NA > 0.9 THEN suggest the use of an oil immersion objective The heart of the expert system is the rule interpreter, sometimes called an inference engine, which reads the rules and forms conclusions based on them. The use of a relational database system containing lens prototypes seems to be a viable prospect. However, it is not clear that expert systems have a place in optical design. In domains such as medical diagnosis and petrology, expert systems are flourishing. These domains are quite different from optical design, however, because optical design is a creative process, and the rules are difficult to write down. We do think that an expert system is feasible in the area of first order layout, which is sufficiently diagnostic in nature to permit useful rules to be written. This first-order expert would emulate an expert

DB Dehydrogenase: an online integrated structural database on enzyme dehydrogenase.

PubMed

Nandy, Suman Kumar; Bhuyan, Rajabrata; Seal, Alpana

2012-01-01

Dehydrogenase enzymes are almost inevitable for metabolic processes. Shortage or malfunctioning of dehydrogenases often leads to several acute diseases like cancers, retinal diseases, diabetes mellitus, Alzheimer, hepatitis B & C etc. With advancement in modern-day research, huge amount of sequential, structural and functional data are generated everyday and widens the gap between structural attributes and its functional understanding. DB Dehydrogenase is an effort to relate the functionalities of dehydrogenase with its structures. It is a completely web-based structural database, covering almost all dehydrogenases [~150 enzyme classes, ~1200 entries from ~160 organisms] whose structures are known. It is created by extracting and integrating various online resources to provide the true and reliable data and implemented by MySQL relational database through user friendly web interfaces using CGI Perl. Flexible search options are there for data extraction and exploration. To summarize, sequence, structure, function of all dehydrogenases in one place along with the necessary option of cross-referencing; this database will be utile for researchers to carry out further work in this field. The database is available for free at http://www.bifku.in/DBD/

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 2. Teaching Units that Utilize an Interactive Web-Accessible Subset of the Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2010-01-01

A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…

Consumption of ultra-processed foods and body fat during childhood and adolescence: a systematic review.

PubMed

Costa, Caroline Santos; Del-Ponte, Bianca; Assunção, Maria Cecília Formoso; Santos, Iná Silva

2018-01-01

To review the available literature on the association between consumption of ultra-processed foods and body fat during childhood and adolescence. A systematic review was conducted in the PubMed, Web of Science and LILACS databases. Studies that evaluated the association between consumption of ultra-processed food (exposure) and body fat (outcome) during childhood and adolescence were eligible. Healthy children and adolescents. Twenty-six studies that evaluated groups of ultra-processed foods (such as snacks, fast foods, junk foods and convenience foods) or specific ultra-processed foods (soft drinks/sweetened beverages, sweets, chocolate and ready-to-eat cereals) were selected. Most of the studies (n 15) had a cohort design. Consumption was generally evaluated by means of FFQ or food records; and body composition, by means of double indirect methods (bioelectrical impedance analysis and skinfolds). Most of the studies that evaluated consumption of groups of ultra-processed foods and soft drinks/sweetened beverages found positive associations with body fat. Our review showed that most studies have found positive associations between consumption of ultra-processed food and body fat during childhood and adolescence. There is a need to use a standardized classification that considers the level of food processing to promote comparability between studies.

The database design of LAMOST based on MYSQL/LINUX

NASA Astrophysics Data System (ADS)

Li, Hui-Xian, Sang, Jian; Wang, Sha; Luo, A.-Li

2006-03-01

The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) will be set up in the coming years. A fully automated software system for reducing and analyzing the spectra has to be developed with the telescope. This database system is an important part of the software system. The requirements for the database of the LAMOST, the design of the LAMOST database system based on MYSQL/LINUX and performance tests of this system are described in this paper.

The FP4026 Research Database on the fundamental period of RC infilled frame structures.

PubMed

Asteris, Panagiotis G

2016-12-01

The fundamental period of vibration appears to be one of the most critical parameters for the seismic design of buildings because it strongly affects the destructive impact of the seismic forces. In this article, important research data (entitled FP4026 Research Database (Fundamental Period-4026 cases of infilled frames) based on a detailed and in-depth analytical research on the fundamental period of reinforced concrete structures is presented. In particular, the values of the fundamental period which have been analytically determined are presented, taking into account the majority of the involved parameters. This database can be extremely valuable for the development of new code proposals for the estimation of the fundamental period of reinforced concrete structures fully or partially infilled with masonry walls.

Database systems for knowledge-based discovery.

PubMed

Jagarlapudi, Sarma A R P; Kishan, K V Radha

2009-01-01

Several database systems have been developed to provide valuable information from the bench chemist to biologist, medical practitioner to pharmaceutical scientist in a structured format. The advent of information technology and computational power enhanced the ability to access large volumes of data in the form of a database where one could do compilation, searching, archiving, analysis, and finally knowledge derivation. Although, data are of variable types the tools used for database creation, searching and retrieval are similar. GVK BIO has been developing databases from publicly available scientific literature in specific areas like medicinal chemistry, clinical research, and mechanism-based toxicity so that the structured databases containing vast data could be used in several areas of research. These databases were classified as reference centric or compound centric depending on the way the database systems were designed. Integration of these databases with knowledge derivation tools would enhance the value of these systems toward better drug design and discovery.

Ultra-high resolution crystal structure of recombinant caprine β-lactoglobulin.

PubMed

Crowther, Jennifer M; Lassé, Moritz; Suzuki, Hironori; Kessans, Sarah A; Loo, Trevor S; Norris, Gillian E; Hodgkinson, Alison J; Jameson, Geoffrey B; Dobson, Renwick C J

2014-11-03

β-Lactoglobulin (βlg) is the most abundant whey protein in the milks of ruminant animals. While bovine βlg has been subjected to a vast array of studies, little is known about the caprine ortholog. We present an ultra-high resolution crystal structure of caprine βlg complemented by analytical ultracentrifugation and small-angle X-ray scattering data. In both solution and crystalline states caprine βlg is dimeric (K(D)<5 μM); however, our data suggest a flexible quaternary arrangement of subunits within the dimer. These structural findings will provide insight into relationships among structural, processing, nutritional and immunological characteristics that distinguish cow's and goat's milk. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Ultra-High Gradient S-band Linac for Laboratory and Industrial Applications

NASA Astrophysics Data System (ADS)

Faillace, L.; Agustsson, R.; Dolgashev, V.; Frigola, P.; Murokh, A.; Rosenzweig, J.; Yakimenko, V.

2010-11-01

A strong demand for high gradient structures arises from the limited real estate available for linear accelerators. RadiaBeam Technologies is developing a Doubled Energy Compact Accelerator (DECA) structure: an S-band standing wave electron linac designed to operate at accelerating gradients of up to 50 MV/m. In this paper, we present the radio-frequency design of the DECA S-band accelerating structure, operating at 2.856 GHz in the π-mode. The structure design is heavily influenced by NLC collaboration experience with ultra high gradient X-band structures; S-band, however, is chosen to take advantage of commonly available high power S-band klystrons.

Design study of an ultra-compact superconducting cyclotron for isotope production

NASA Astrophysics Data System (ADS)

Smirnov, V.; Vorozhtsov, S.; Vincent, J.

2014-11-01

A 12.5 MeV, 25 μA, proton compact superconducting cyclotron for medical isotope production has been designed and is currently in fabrication. The machine is initially aimed at producing 13N ammonia for Positron Emission Tomography (PET) cardiology applications. With an ultra-compact size and cost-effective price point, this system will offer clinicians unprecedented access to the preferred radiopharmaceutical isotope for cardiac PET imaging. A systems approach that carefully balanced the subsystem requirements coupled to precise beam dynamics calculations was followed. The system is designed to irradiate a liquid target internal to the cyclotron and to minimize the need for radiation shielding. The main parameters of the cyclotron, its design, and principal steps of the development work are presented here.

Design of optical metamaterial waveguide structures (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ortega-Moñux, Alejandro; Halir, Robert; Sánchez-Postigo, Alejandro; Soler-Penadés, Jordi; Ctyroký, Jirí; Luque-González, José Manuel; Sarmiento-Merenguel, José Darío.; Wangüemert-Pérez, Juan Gonzalo; Schmid, Jens H.; Xu, Dan-Xia; Janz, Sigfried; Lapointe, Jean; Molina-Fernández, Iñigo; Nedeljkovic, Milos; Mashanovich, Goran Z.; Cheben, Pavel

2017-05-01

Subwavelength gratings (SWGs) are periodic structures with a pitch (Λ) smaller than the wavelength of the propagating wave (λ), so that diffraction effects are suppressed. These structures thus behave as artificial metamaterials where the refractive index and the dispersion profile can be controlled with a proper design of the geometry of the structure. SWG waveguides have found extensive applications in the field of integrated optics, such as efficient fiber-chip couplers, broadband multimode interference (MMI) couplers, polarization beam splitters or evanescent field sensors, among others. From the point of view of nano-fabrication, the subwavelength condition (Λ << λ) is much easier to meet for long, mid-infrared wavelengths than for the comparatively short near-infrared wavelengths. Since most of the integrated devices based on SWGs have been proposed for the near-infrared, the true potential of subwavelength structures has not yet been completely exploited. In this talk we summarize some valuable guidelines for the design of high performance SWG integrated devices. We will start describing some practical aspects of the design, such as the range of application of semi-analytical methods, the rigorous electromagnetic simulation of Floquet modes, the relevance of substrate leakage losses and the effects of the random jitter, inherent to any fabrication process, on the performance of SWG structures. Finally, we will show the possibilities of the design of SWG structures with two different state-of-the-art applications: i) ultra-broadband MMI beam splitters with an operation bandwidth greater than 300nm for telecom wavelengths and ii) a set of suspended waveguides with SWG lateral cladding for mid-infrared applications, including low loss waveguides, MMI couplers and Mach-Zehnder interferometers.

The challenge of designing a database for auditing surgical in-patients.

PubMed

Branday, J M; Crandon, I; Carpenter, R; Rhoden, A; Meeks-Aitken, N

1999-12-01

Surgical audit is imperative in modern practice, particularly in the developing world where resources are limited and efficient allocation important. The structure, process and outcome of surgical care can be determined for quality assurance or for research. Improved efficiency and reduction of morbidity and mortality are additional goals which may be accomplished. However, computerization, medical staff cooperation and the availability of dedicated staff are among the hurdles which may be encountered. We report the challenge of designing and establishing a database for auditing surgical inpatients in a developing country and the difficulties which were encountered.

Ultra-broadband unidirectional launching of surface plasmon polaritons by a double-slit structure beyond the diffraction limit.

PubMed

Chen, Jianjun; Sun, Chengwei; Li, Hongyun; Gong, Qihuang

2014-11-21

Surface-plasmon-polariton (SPP) launchers, which can couple the free space light to the SPPs on the metal surface, are among the key elements for the plasmonic devices and nano-photonic systems. Downscaling the SPP launchers below the diffraction limit and directly delivering the SPPs to the desired subwavelength plasmonic waveguides are of importance for high-integration plasmonic circuits. By designing a submicron double-slit structure with different slit widths, an ultra-broadband (>330 nm) unidirectional SPP launcher is realized theoretically and experimentally based on the different phase delays of SPPs propagating along the metal surface and the near-field interfering effect. More importantly, the broadband and unidirectional properties of the SPP launcher are still maintained when the slit length is reduced to a subwavelength scale. This can make the launcher occupy only a very small area of <λ(2)/10 on the metal surface. Such a robust unidirectional SPP launcher beyond the diffraction limit can be directly coupled to a subwavelength plasmonic waveguide efficiently, leading to an ultra-tight SPP source, especially as a subwavelength localized guided SPP source.

Discovery of novel aldose reductase inhibitors using a protein structure-based approach: 3D-database search followed by design and synthesis.

PubMed

Iwata, Y; Arisawa, M; Hamada, R; Kita, Y; Mizutani, M Y; Tomioka, N; Itai, A; Miyamoto, S

2001-05-24

Aldose reductase (AR) has been implicated in the etiology of diabetic complications. Due to the limited number of currently available drugs for the treatment of diabetic complications, we have carried out structure-based drug design and synthesis in an attempt to find new types of AR inhibitors. With the ADAM&EVE program, a three-dimensional database (ACD3D) was searched using the ligand binding site of the AR crystal structure. Out of 179 compounds selected through this search followed by visual inspection, 36 compounds were purchased and subjected to a biological assay. Ten compounds showed more than 40% inhibition of AR at a 15 microg/mL concentration. In a subsequent lead optimization, a series of analogues of the most active compound were synthesized based on the docking mode derived by ADAM&EVE. Many of these congeners exhibited higher activities compared to the mother compound. Indeed, the most potent, synthesized compound showed an approximately 20-fold increase in inhibitory activity (IC(50) = 0.21 vs 4.3 microM). Furthermore, a hydrophobic subsite was newly inferred, which would be useful for the design of inhibitors with improved affinity for AR.

Design of an ultra-thin dual band infrared system

NASA Astrophysics Data System (ADS)

Du, Ke; Cheng, Xuemin; Lv, Qichao; Hu, YiFei

2014-11-01

The ultra-thin imaging system using reflective multiple-fold structure has smaller volume and less weight while maintaining high resolution compared with conventional optical systems. The multi-folded approach can significantly extend focal distance within wide spectral range without incurring chromatic aberrations. In this paper, we present a dual infrared imaging system of four-folded reflection with two air-spaced concentric reflective surfaces. The dual brand IR system has 107mm effective focal length, 0.7NA, +/-4° FOV, and 50mm effective aperture with 80mm outer diameter into a 25mm total thickness, which spectral response is 3~12μm.

An Introduction to Database Structure and Database Machines.

ERIC Educational Resources Information Center

Detweiler, Karen

1984-01-01

Enumerates principal management objectives of database management systems (data independence, quality, security, multiuser access, central control) and criteria for comparison (response time, size, flexibility, other features). Conventional database management systems, relational databases, and database machines used for backend processing are…

Structure of a zinc oxide ultra-thin film on Rh(100)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuhara, J.; Kato, D.; Matsui, T.

The structural parameters of ultra-thin zinc oxide films on Rh(100) are investigated using low-energy electron diffraction intensity (LEED I–V) curves, scanning tunneling microscopy (STM), and first-principles density functional theory (DFT) calculations. From the analysis of LEED I–V curves and DFT calculations, two optimized models A and B are determined. Their structures are basically similar to the planer h-BN ZnO(0001) structure, although some oxygen atoms protrude from the surface, associated with an in-plane shift of Zn atoms. From a comparison of experimental STM images and simulated STM images, majority and minority structures observed in the STM images represent the two optimizedmore » models A and B, respectively.« less

Optimal waveforms design for ultra-wideband impulse radio sensors.

PubMed

Li, Bin; Zhou, Zheng; Zou, Weixia; Li, Dejian; Zhao, Chong

2010-01-01

Ultra-wideband impulse radio (UWB-IR) sensors should comply entirely with the regulatory spectral limits for elegant coexistence. Under this premise, it is desirable for UWB pulses to improve frequency utilization to guarantee the transmission reliability. Meanwhile, orthogonal waveform division multiple-access (WDMA) is significant to mitigate mutual interferences in UWB sensor networks. Motivated by the considerations, we suggest in this paper a low complexity pulse forming technique, and its efficient implementation on DSP is investigated. The UWB pulse is derived preliminarily with the objective of minimizing the mean square error (MSE) between designed power spectrum density (PSD) and the emission mask. Subsequently, this pulse is iteratively modified until its PSD completely conforms to spectral constraints. The orthogonal restriction is then analyzed and different algorithms have been presented. Simulation demonstrates that our technique can produce UWB waveforms with frequency utilization far surpassing the other existing signals under arbitrary spectral mask conditions. Compared to other orthogonality design schemes, the designed pulses can maintain mutual orthogonality without any penalty on frequency utilization, and hence, are much superior in a WDMA network, especially with synchronization deviations.

Study of plasma-based stable and ultra-wideband electromagnetic wave absorption for stealth application

NASA Astrophysics Data System (ADS)

Xuyang, CHEN; Fangfang, SHEN; Yanming, LIU; Wei, AI; Xiaoping, LI

2018-06-01

A plasma-based stable, ultra-wideband electromagnetic (EM) wave absorber structure is studied in this paper for stealth applications. The stability is maintained by a multi-layer structure with several plasma layers and dielectric layers distributed alternately. The plasma in each plasma layer is designed to be uniform, whereas it has a discrete nonuniform distribution from the overall view of the structure. The nonuniform distribution of the plasma is the key to obtaining ultra-wideband wave absorption. A discrete Epstein distribution model is put forward to constrain the nonuniform electron density of the plasma layers, by which the wave absorption range is extended to the ultra-wideband. Then, the scattering matrix method (SMM) is employed to analyze the electromagnetic reflection and absorption of the absorber structure. In the simulation, the validation of the proposed structure and model in ultra-wideband EM wave absorption is first illustrated by comparing the nonuniform plasma model with the uniform case. Then, the influence of various parameters on the EM wave reflection of the plasma are simulated and analyzed in detail, verifying the EM wave absorption performance of the absorber. The proposed structure and model are expected to be superior in some realistic applications, such as supersonic aircraft.

LigandBox: A database for 3D structures of chemical compounds

PubMed Central

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

LigandBox: A database for 3D structures of chemical compounds.

PubMed

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

Animal models for treatment of unresectable liver tumours: a histopathologic and ultra-structural study of cellular toxic changes after electrochemical treatment in rat and dog liver.

PubMed

von Euler, Henrik; Olsson, Jerker M; Hultenby, Kjell; Thörne, Anders; Lagerstedt, Anne-Sofie

2003-04-01

Electrochemical treatment (EChT) has been taken under serious consideration as being one of several techniques for local treatment of malignancies. The advantage of EChT is the minimal invasive approach and the absence of serious side effects. Macroscopic, histopathological and ultra-structural findings in liver following a four-electrode configuration (dog) and a two-electrode EChT design (dog and rat) were studied. 30 female Sprague-Dawley rats and four female beagle dogs were studied with EChT using Platinum:Iridium electrodes and the delivered dose was 5, 10 or 90 C (As). After EChT, the animals were euthanized. The distribution of the lesions was predictable, irrespective of dose and electrode configuration. Destruction volumes were found to fit into a logarithmic curve (dose-response). Histopathological examination confirmed a spherical (rat) and cylindrical/ellipsoidal (dog) lesion. The type of necrosis differed due to electrode polarity. Ultra-structural analysis showed distinct features of cell damage depending on the distance from the electrode. Histopathological and ultra-structural examination demonstrated that the liver tissue close to the border of the lesion displayed a normal morphology. The in vivo dose-planning model is reliable, even in species with larger tissue mass such as dogs. A multi-electrode EChT-design could obtain predictable lesions. The cellular toxicity following EChT is clearly identified and varies with the distance from the electrode and polarity. The distinct border between the lesion and normal tissue suggests that EChT in a clinical setting for the treatment of liver tumours can give a reliable destruction margin.

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

PubMed

Hayashi, Takanori; Matsuzaki, Yuri; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

2018-05-08

Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on

Long range ultra-high frequency (UHF) radio frequency identification (RFID) antenna design

NASA Astrophysics Data System (ADS)

Reynolds, Nathan D.

There is an ever-increasing demand for radio frequency identification (RFID) tags that are passive, long range, and mountable on multiple surfaces. Currently, RFID technology is utilized in numerous applications such as supply chain management, access control, and public transportation. With the combination of sensory systems in recent years, the applications of RFID technology have been extended beyond tracking and identifying. This extension includes applications such as environmental monitoring and healthcare applications. The available sensory systems usually operate in the medium or high frequency bands and have a low read range. However, the range limitations of these systems are being overcome by the development of RFID sensors focused on utilizing tags in the ultra-high frequency (UHF) band. Generally, RFID tags have to be mounted to the object that is being identified. Often the objects requiring identification are metallic. The inherent properties of metallic objects have substantial effects on nearby electromagnetic radiation; therefore, the operation of the tag antenna is affected when mounted on a metallic surface. This outlines one of the most challenging problems for RFID systems today: the optimization of tag antenna performance in a complex environment. In this research, a novel UHF RFID tag antenna, which has a low profile, long range, and is mountable on metallic surfaces, is designed analytically and simulated using a 3-D electromagnetic simulator, ANSYS HFSS. A microstrip patch antenna is selected as the antenna structure, as patch antennas are low profile and suitable for mounting on metallic surfaces. Matching and theoretical models of the microstrip patch antenna are investigated. Once matching and theory of a microstrip patch antenna is thoroughly understood, a unique design technique using electromagnetic band gap (EBG) structures is explored. This research shows that the utilization of an EBG structure in the patch antenna design yields

Instability analysis of charges trapped in the oxide of metal-ultra thin oxide-semiconductor structures

NASA Astrophysics Data System (ADS)

Aziz, A.; Kassmi, K.; Maimouni, R.; Olivié, F.; Sarrabayrouse, G.; Martinez, A.

2005-09-01

In this paper, we present the theoretical and experimental results of the influence of a charge trapped in ultra-thin oxide of metal/ultra-thin oxide/semiconductor structures (MOS) on the I(Vg) current-voltage characteristics when the conduction is of the Fowler-Nordheim (FN) tunneling type. The charge, which is negative, is trapped near the cathode (metal/oxide interface) after constant current injection by the metal (Vg<0). Of particular interest is the influence on the Δ Vg(Vg) shift over the whole I(Vg) characteristic at high field (greater than the injection field (>12.5 MV/cm)). It is shown that the charge centroid varies linearly with respect to the voltage Vg. The behavior at low field (<12.5 MV/cm) is analyzed in référence A. Aziz, K. Kassmi, Ka. Kassmi, F. Olivié, Semicond. Sci. Technol. 19, 877 (2004) and considers that the trapped charge centroid is fixed. The results obtained make it possible to analyze the influence of the injected charge and the applied field on the centroid position of the trapped charge, and to highlight the charge instability in the ultra-thin oxide of MOS structures.

Ultra-low-frequency vertical vibration isolator based on a two-stage beam structure for absolute gravimetry.

PubMed

Wang, G; Wu, K; Hu, H; Li, G; Wang, L J

2016-10-01

To reduce seismic and environmental vibration noise, ultra-low-frequency vertical vibration isolation systems play an important role in absolute gravimetry. For this purpose, an isolator based on a two-stage beam structure is proposed and demonstrated. The isolator has a simpler and more robust structure than the present ultra-low-frequency vertical active vibration isolators. In the system, two beams are connected to a frame using flexural pivots. The upper beam is suspended from the frame with a normal hex spring and the lower beam is suspended from the upper one using a zero-length spring. The pivot of the upper beam is not vertically above the pivot of the lower beam. With this special design, the attachment points of the zero-length spring to the beams can be moved to adjust the effective stiffness. A photoelectric detector is used to detect the angle between the two beams, and a voice coil actuator attached to the upper beam is controlled by a feedback circuit to keep the angle at a fixed value. The system can achieve a natural period of 100 s by carefully moving the attachment points of the zero-length spring to the beams and tuning the feedback parameters. The system has been used as an inertial reference in the T-1 absolute gravimeter. The experiment results demonstrate that the system has significant vibration isolation performance that holds promise in applications such as absolute gravimeters.

Ultra-low-frequency vertical vibration isolator based on a two-stage beam structure for absolute gravimetry

NASA Astrophysics Data System (ADS)

Wang, G.; Wu, K.; Hu, H.; Li, G.; Wang, L. J.

2016-10-01

To reduce seismic and environmental vibration noise, ultra-low-frequency vertical vibration isolation systems play an important role in absolute gravimetry. For this purpose, an isolator based on a two-stage beam structure is proposed and demonstrated. The isolator has a simpler and more robust structure than the present ultra-low-frequency vertical active vibration isolators. In the system, two beams are connected to a frame using flexural pivots. The upper beam is suspended from the frame with a normal hex spring and the lower beam is suspended from the upper one using a zero-length spring. The pivot of the upper beam is not vertically above the pivot of the lower beam. With this special design, the attachment points of the zero-length spring to the beams can be moved to adjust the effective stiffness. A photoelectric detector is used to detect the angle between the two beams, and a voice coil actuator attached to the upper beam is controlled by a feedback circuit to keep the angle at a fixed value. The system can achieve a natural period of 100 s by carefully moving the attachment points of the zero-length spring to the beams and tuning the feedback parameters. The system has been used as an inertial reference in the T-1 absolute gravimeter. The experiment results demonstrate that the system has significant vibration isolation performance that holds promise in applications such as absolute gravimeters.

Ultra-Thin Multi-Band Polarization-Insensitive Microwave Metamaterial Absorber Based on Multiple-Order Responses Using a Single Resonator Structure

PubMed Central

Cheng, Zheng Ze; Mao, Xue Song; Gong, Rong Zhou

2017-01-01

We design an ultra-thin multi-band polarization-insensitive metamaterial absorber (MMA) using a single circular sector resonator (CSR) structure in the microwave region. Simulated results show that the proposed MMA has three distinctive absorption peaks at 3.35 GHz, 8.65 GHz, and 12.44 GHz, with absorbance of 98.8%, 99.7%, and 98.3%, respectively, which agree well with an experiment. Simulated surface current distributions of the unit-cell structure reveal that the triple-band absorption mainly originates from multiple-harmonic magnetic resonance. The proposed triple-band MMA can remain at a high absorption level for all polarization of both transverse-electric (TE) and transverse-magnetic (TM) modes under normal incidence. Moreover, by further optimizing the geometric parameters of the CSRs, four-band and five-band MMAs can also be obtained. Thus, our design will have potential application in detection, sensing, and stealth technology. PMID:29077036

Probing Photoinduced Structural Phase Transitions by Fast or Ultra-Fast Time-Resolved X-Ray Diffraction

NASA Astrophysics Data System (ADS)

Cailleau, Hervé Collet, Eric; Buron-Le Cointe, Marylise; Lemée-Cailleau, Marie-Hélène Koshihara, Shin-Ya

A new frontier in the field of structural science is the emergence of the fast and ultra-fast X-ray science. Recent developments in time-resolved X-ray diffraction promise direct access to the dynamics of electronic, atomic and molecular motions in condensed matter triggered by a pulsed laser irradiation, i.e. to record "molecular movies" during the transformation of matter initiated by light pulse. These laser pump and X-ray probe techniques now provide an outstanding opportunity for the direct observation of a photoinduced structural phase transition as it takes place. The use of X-ray short-pulse of about 100ps around third-generation synchrotron sources allows structural investigations of fast photoinduced processes. Other new X-ray sources, such as laser-produced plasma ones, generate ultra-short pulses down to 100 fs. This opens the way to femtosecond X-ray crystallography, but with rather low X-ray intensities and more limited experimental possibilities at present. However this new ultra-fast science rapidly progresses around these sources and new large-scale projects exist. It is the aim of this contribution to overview the state of art and the perspectives of fast and ultra-fast X-ray scattering techniques to study photoinduced phase transitions (here, the word ultra-fast is used for sub-picosecond time resolution). In particular we would like to largely present the contribution of crystallographic methods in comparison with optical methods, such as pump-probe reflectivity measurements, the reader being not necessary familiar with X-ray scattering. Thus we want to present which type of physical information can be obtained from the positions of the Bragg peaks, their intensity and their shape, as well as from the diffuse scattering beyond Bragg peaks. An important physical feature is to take into consideration the difference in nature between a photoinduced phase transition and conventional homogeneous photoinduced chemical or biochemical processes where

Cavity resonance absorption in ultra-high bandwidth CRT deflection structure by a resistive load

DOEpatents

Dunham, M.E.; Hudson, C.L.

1993-05-11

An improved ultra-high bandwidth helical coil deflection structure for a cathode ray tube is described comprising a first metal member having a bore therein, the metal walls of which form a first ground plane; a second metal member coaxially mounted in the bore of the first metal member and forming a second ground plane; a helical deflection coil coaxially mounted within the bore between the two ground planes; and a resistive load disposed in one end of the bore and electrically connected to the first and second ground planes, the resistive load having an impedance substantially equal to the characteristic impedance of the coaxial line formed by the two coaxial ground planes to inhibit cavity resonance in the structure within the ultra-high bandwidth of operation. Preferably, the resistive load comprises a carbon film on a surface of an end plug in one end of the bore.

Cavity resonance absorption in ultra-high bandwidth CRT deflection structure by a resistive load

DOEpatents

Dunham, Mark E.; Hudson, Charles L.

1993-01-01

An improved ultra-high bandwidth helical coil deflection structure for a hode ray tube is described comprising a first metal member having a bore therein, the metal walls of which form a first ground plane; a second metal member coaxially mounted in the bore of the first metal member and forming a second ground plane; a helical deflection coil coaxially mounted within the bore between the two ground planes; and a resistive load disposed in one end of the bore and electrically connected to the first and second ground planes, the resistive load having an impedance substantially equal to the characteristic impedance of the coaxial line formed by the two coaxial ground planes to inhibit cavity resonance in the structure within the ultra-high bandwidth of operation. Preferably, the resistive load comprises a carbon film on a surface of an end plug in one end of the bore.

[Construction of chemical information database based on optical structure recognition technique].

PubMed

Lv, C Y; Li, M N; Zhang, L R; Liu, Z M

2018-04-18

To create a protocol that could be used to construct chemical information database from scientific literature quickly and automatically. Scientific literature, patents and technical reports from different chemical disciplines were collected and stored in PDF format as fundamental datasets. Chemical structures were transformed from published documents and images to machine-readable data by using the name conversion technology and optical structure recognition tool CLiDE. In the process of molecular structure information extraction, Markush structures were enumerated into well-defined monomer molecules by means of QueryTools in molecule editor ChemDraw. Document management software EndNote X8 was applied to acquire bibliographical references involving title, author, journal and year of publication. Text mining toolkit ChemDataExtractor was adopted to retrieve information that could be used to populate structured chemical database from figures, tables, and textual paragraphs. After this step, detailed manual revision and annotation were conducted in order to ensure the accuracy and completeness of the data. In addition to the literature data, computing simulation platform Pipeline Pilot 7.5 was utilized to calculate the physical and chemical properties and predict molecular attributes. Furthermore, open database ChEMBL was linked to fetch known bioactivities, such as indications and targets. After information extraction and data expansion, five separate metadata files were generated, including molecular structure data file, molecular information, bibliographical references, predictable attributes and known bioactivities. Canonical simplified molecular input line entry specification as primary key, metadata files were associated through common key nodes including molecular number and PDF number to construct an integrated chemical information database. A reasonable construction protocol of chemical information database was created successfully. A total of 174 research

Database Design Methodology and Database Management System for Computer-Aided Structural Design Optimization.

DTIC Science & Technology

1984-12-01

52242 Prepared for the AIR FORCE OFFICE OF SCIENTIFIC RESEARCH Under Grant No. AFOSR 82-0322 December 1984 ~ " ’w Unclassified SECURITY CLASSIFICATION4...OF THIS PAGE REPORT DOCUMENTATION PAGE is REPORT SECURITY CLASSIFICATION lb. RESTRICTIVE MARKINGS Unclassified None 20 SECURITY CLASSIFICATION...designer .and computer- are 20 DIiRIBUTION/AVAILABI LIT Y 0P ABSTR4ACT 21 ABSTRACT SECURITY CLASSIFICA1ONr UNCLASSIFIED/UNLIMITED SAME AS APT OTIC USERS

GaN-based metamaterial terahertz bandpass filter design: tunability and ultra-broad passband attainment.

PubMed

Khodaee, M; Banakermani, M; Baghban, H

2015-10-10

Engineering metamaterial-based devices such as terahertz bandpass filters (BPFs) play a definitive role in advancement of terahertz technology. In this article, we propose a design procedure to obtain a considerably broadband terahertz BPF at a normal incidence; it shows promising filtering characteristics, including a wide passband of ∼1.34  THz at a central frequency of 1.17 THz, a flat top in a broad band, and high transmission, compared to previous reports. Then, exploiting the voltage-dependent carrier density control in an AlGaN/GaN heterostructure with a Schottky gate configuration, we investigate the tuning of the transmission properties in a narrow-band terahertz filter. A combination of the ultra-wide, flat-top BPF in series with the tunable, narrow band filter designed in the current study offers the ability to tune the desired resonance frequency along with high out-of-band rejection and the suppression of unwanted resonances in a large spectral range. The proposed structure exhibits a frequency tunability of 103 GHz for a voltage change between -8 and 2 V, and a transmission amplitude change of ∼0.51. This scheme may open up a route for the improved design of terahertz filters and modulators.

Design and implementation of a twin-family database for behavior genetics and genomics studies.

PubMed

Boomsma, Dorret I; Willemsen, Gonneke; Vink, Jacqueline M; Bartels, Meike; Groot, Paul; Hottenga, Jouke Jan; van Beijsterveldt, C E M Toos; Stroet, Therese; van Dijk, Rob; Wertheim, Rien; Visser, Marco; van der Kleij, Frank

2008-06-01

In this article we describe the design and implementation of a database for extended twin families. The database does not focus on probands or on index twins, as this approach becomes problematic when larger multigenerational families are included, when more than one set of multiples is present within a family, or when families turn out to be part of a larger pedigree. Instead, we present an alternative approach that uses a highly flexible notion of persons and relations. The relations among the subjects in the database have a one-to-many structure, are user-definable and extendible and support arbitrarily complicated pedigrees. Some additional characteristics of the database are highlighted, such as the storage of historical data, predefined expressions for advanced queries, output facilities for individuals and relations among individuals and an easy-to-use multi-step wizard for contacting participants. This solution presents a flexible approach to accommodate pedigrees of arbitrary size, multiple biological and nonbiological relationships among participants and dynamic changes in these relations that occur over time, which can be implemented for any type of multigenerational family study.

Flexible ultra-wideband antenna incorporated with metamaterial structures: multiple notches for chipless RFID application

NASA Astrophysics Data System (ADS)

Jalil, M. E.; Rahim, M. K. A.; Samsuri, N. A.; Dewan, R.; Kamardin, K.

2017-01-01

A coplanar waveguide (CPW) ultra-wideband (UWB) antenna incorporated with metamaterial—split ring resonator structure—that operates from 3.0 to 12.0 GHz is proposed for chipless RFID tag. The 30 mm × 40 mm flexible chipless RFID tag is designed on the fleece substrate ( ɛ r = 1.35, thickness = 1 mm and tan δ = 0.025). A six-slotted modified complementary split ring resonator (MCSRR) is introduced into the ultra-wideband antenna to produce multiple band notches at 3.0, 4.0, 5.0, 6.0 and 7.0 GHz. The frequency shifting technique is introduced for designing a high-capacity chipless RFID tag with compact size. Each MCSRR is able to code in four different allocations (00, 01, 10 and 11). To achieve encoding of 10-bits data (10,234 number), six MCSRRs are proposed with three-slotted MCSRR in the radiator and three-slotted MCSRR in the ground plane.

Influence of hydrogen on the structure and stability of ultra-thin ZnO on metal substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bieniek, Bjoern; Hofmann, Oliver T.; Institut für Festkörperphysik, TU Graz, 8010 Graz

2015-03-30

We investigate the atomic and electronic structure of ultra-thin ZnO films (1 to 4 layers) on the (111) surfaces of Ag, Cu, Pd, Pt, Ni, and Rh by means of density-functional theory. The ZnO monolayer is found to adopt an α-BN structure on the metal substrates with coincidence structures in good agreement with experiment. Thicker ZnO layers change into a wurtzite structure. The films exhibit a strong corrugation, which can be smoothed by hydrogen (H) adsorption. An H over-layer with 50% coverage is formed at chemical potentials that range from low to ultra-high vacuum H{sub 2} pressures. For the Agmore » substrate, both α-BN and wurtzite ZnO films are accessible in this pressure range, while for Cu, Pd, Pt, Rh, and Ni wurtzite films are favored. The surface structure and the density of states of these H passivated ZnO thin films agree well with those of the bulk ZnO(0001{sup ¯})-2×1-H surface.« less

Optimal Waveforms Design for Ultra-Wideband Impulse Radio Sensors

PubMed Central

Li, Bin; Zhou, Zheng; Zou, Weixia; Li, Dejian; Zhao, Chong

2010-01-01

Ultra-wideband impulse radio (UWB-IR) sensors should comply entirely with the regulatory spectral limits for elegant coexistence. Under this premise, it is desirable for UWB pulses to improve frequency utilization to guarantee the transmission reliability. Meanwhile, orthogonal waveform division multiple-access (WDMA) is significant to mitigate mutual interferences in UWB sensor networks. Motivated by the considerations, we suggest in this paper a low complexity pulse forming technique, and its efficient implementation on DSP is investigated. The UWB pulse is derived preliminarily with the objective of minimizing the mean square error (MSE) between designed power spectrum density (PSD) and the emission mask. Subsequently, this pulse is iteratively modified until its PSD completely conforms to spectral constraints. The orthogonal restriction is then analyzed and different algorithms have been presented. Simulation demonstrates that our technique can produce UWB waveforms with frequency utilization far surpassing the other existing signals under arbitrary spectral mask conditions. Compared to other orthogonality design schemes, the designed pulses can maintain mutual orthogonality without any penalty on frequency utilization, and hence, are much superior in a WDMA network, especially with synchronization deviations. PMID:22163511

Utilization of Minor Actinides as a Fuel Component for Ultra-Long Life Bhr Configurations: Designs, Advantages and Limitations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dr. Pavel V. Tsvetkov

2009-05-20

This project assessed the advantages and limitations of using minor actinides as a fuel component to achieve ultra-long life Very High Temperature Reactor (VHTR) configurations. Researchers considered and compared the capabilities of pebble-bed and prismatic core designs with advanced actinide fuels to achieve ultra-long operation without refueling. Since both core designs permit flexibility in component configuration, fuel utilization, and fuel management, it is possible to improve fissile properties of minor actinides by neutron spectrum shifting through configuration adjustments. The project studied advanced actinide fuels, which could reduce the long-term radio-toxicity and heat load of high-level waste sent to a geologicmore » repository and enable recovery of the energy contained in spent fuel. The ultra-long core life autonomous approach may reduce the technical need for additional repositories and is capable to improve marketability of the Generation IV VHTR by allowing worldwide deployment, including remote regions and regions with limited industrial resources. Utilization of minor actinides in nuclear reactors facilitates developments of new fuel cycles towards sustainable nuclear energy scenarios.« less

The effect of ultra-violet light curing on the molecular structure and fracture properties of an ultra low-k material

NASA Astrophysics Data System (ADS)

Smith, Ryan Scott

As the gate density increases in microelectronic devices, the interconnect delay or RC response also increases and has become the limiting delay to faster devices. In order to decrease the RC time delay, a new metallization scheme has been chosen by the semiconductor industry. Copper has replaced aluminum as the metal lines and new low-k dielectric materials are being developed to replace silicon dioxide. A promising low-k material is porous organosilicate glass or p-OSG. The p-OSG film is a hybrid material where the silicon dioxide backbone is terminated with methyl or hydrogen, reducing the dielectric constant and creating mechanically weak films that are prone to fracture. A few methods of improving the mechanical properties of p-OSG films have been attempted-- exposing the film to hydrogen plasma, electron beam curing, and ultra-violet light curing. Hydrogen plasma and electron-beam curing suffer from a lack of specificity and can cause charging damage to the gates. Therefore, ultra-violet light curing (UV curing) is preferable. The effect of UV curing on an ultra-low-k, k~2.5, p-OSG film is studied in this dissertation. Changes in the molecular structure were measured with Fourier Transform Infrared Spectroscopy and X-ray Photoelectron Spectroscopy. The evolution of the molecular structure with UV curing was correlated with material and fracture properties. The material properties were film shrinkage, densification, and an increase in dielectric constant. From the changes in molecular structure and material properties, a set of condensation reactions with UV light are predicted. The connectivity of the film increases with the condensation reactions and, therefore, the fracture toughness should also increase. The effect of UV curing on the critical and sub-critical fracture toughness was also studied. The critical fracture toughness was measured at four different mode-mixes-- zero, 15°, 32°, and 42°. It was found that the critical fracture toughness

Potential Energy Surface Database of Group II Dimer

National Institute of Standards and Technology Data Gateway

SRD 143 NIST Potential Energy Surface Database of Group II Dimer (Web, free access)   This database provides critical atomic and molecular data needed in order to evaluate the feasibility of using laser cooled and trapped Group II atomic species (Mg, Ca, Sr, and Ba) for ultra-precise optical clocks or quantum information processing devices.

Designing a User Manual to Support an In-House Database.

ERIC Educational Resources Information Center

Kraft, Melissa A.; Pugh, W. Jean

1988-01-01

Describes the steps involved in designing a user manual for an in-house database. Topics covered include goal definition, target audience identification, production scheduling, design and production choices, testing and review, and updating of the manual. (CLB)

DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides.

PubMed

Pirtskhalava, Malak; Gabrielian, Andrei; Cruz, Phillip; Griggs, Hannah L; Squires, R Burke; Hurt, Darrell E; Grigolava, Maia; Chubinidze, Mindia; Gogoladze, George; Vishnepolsky, Boris; Alekseyev, Vsevolod; Rosenthal, Alex; Tartakovsky, Michael

2016-01-04

Antimicrobial peptides (AMPs) are anti-infectives that may represent a novel and untapped class of biotherapeutics. Increasing interest in AMPs means that new peptides (natural and synthetic) are discovered faster than ever before. We describe herein a new version of the Database of Antimicrobial Activity and Structure of Peptides (DBAASPv.2, which is freely accessible at http://dbaasp.org). This iteration of the database reports chemical structures and empirically-determined activities (MICs, IC50, etc.) against more than 4200 specific target microbes for more than 2000 ribosomal, 80 non-ribosomal and 5700 synthetic peptides. Of these, the vast majority are monomeric, but nearly 200 of these peptides are found as homo- or heterodimers. More than 6100 of the peptides are linear, but about 515 are cyclic and more than 1300 have other intra-chain covalent bonds. More than half of the entries in the database were added after the resource was initially described, which reflects the recent sharp uptick of interest in AMPs. New features of DBAASPv.2 include: (i) user-friendly utilities and reporting functions, (ii) a 'Ranking Search' function to query the database by target species and return a ranked list of peptides with activity against that target and (iii) structural descriptions of the peptides derived from empirical data or calculated by molecular dynamics (MD) simulations. The three-dimensional structural data are critical components for understanding structure-activity relationships and for design of new antimicrobial drugs. We created more than 300 high-throughput MD simulations specifically for inclusion in DBAASP. The resulting structures are described in the database by novel trajectory analysis plots and movies. Another 200+ DBAASP entries have links to the Protein DataBank. All of the structures are easily visualized directly in the web browser. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Design and deployment of a large brain-image database for clinical and nonclinical research

NASA Astrophysics Data System (ADS)

Yang, Guo Liang; Lim, Choie Cheio Tchoyoson; Banukumar, Narayanaswami; Aziz, Aamer; Hui, Francis; Nowinski, Wieslaw L.

2004-04-01

An efficient database is an essential component of organizing diverse information on image metadata and patient information for research in medical imaging. This paper describes the design, development and deployment of a large database system serving as a brain image repository that can be used across different platforms in various medical researches. It forms the infrastructure that links hospitals and institutions together and shares data among them. The database contains patient-, pathology-, image-, research- and management-specific data. The functionalities of the database system include image uploading, storage, indexing, downloading and sharing as well as database querying and management with security and data anonymization concerns well taken care of. The structure of database is multi-tier client-server architecture with Relational Database Management System, Security Layer, Application Layer and User Interface. Image source adapter has been developed to handle most of the popular image formats. The database has a user interface based on web browsers and is easy to handle. We have used Java programming language for its platform independency and vast function libraries. The brain image database can sort data according to clinically relevant information. This can be effectively used in research from the clinicians" points of view. The database is suitable for validation of algorithms on large population of cases. Medical images for processing could be identified and organized based on information in image metadata. Clinical research in various pathologies can thus be performed with greater efficiency and large image repositories can be managed more effectively. The prototype of the system has been installed in a few hospitals and is working to the satisfaction of the clinicians.

Design and implementation of the cacao genome database

USDA-ARS?s Scientific Manuscript database

The Cacao Genome Database (CGD, www.cacaogenomedb.org) is being developed to provide a comprehensive data mining resource of genomic, genetic and breeding data for Theobroma cacao. Designed using Chado and a collection of Drupal modules, known as Tripal, CGD currently contains the genetically anchor...

A manufacturing database of advanced materials used in spacecraft structures

NASA Technical Reports Server (NTRS)

Bao, Han P.

1994-01-01

Cost savings opportunities over the life cycle of a product are highest in the early exploratory phase when different design alternatives are evaluated not only for their performance characteristics but also their methods of fabrication which really control the ultimate manufacturing costs of the product. In the past, Design-To-Cost methodologies for spacecraft design concentrated on the sizing and weight issues more than anything else at the early so-called 'Vehicle Level' (Ref: DOD/NASA Advanced Composites Design Guide). Given the impact of manufacturing cost, the objective of this study is to identify the principal cost drivers for each materials technology and propose a quantitative approach to incorporating these cost drivers into the family of optimization tools used by the Vehicle Analysis Branch of NASA LaRC to assess various conceptual vehicle designs. The advanced materials being considered include aluminum-lithium alloys, thermoplastic graphite-polyether etherketone composites, graphite-bismaleimide composites, graphite- polyimide composites, and carbon-carbon composites. Two conventional materials are added to the study to serve as baseline materials against which the other materials are compared. These two conventional materials are aircraft aluminum alloys series 2000 and series 7000, and graphite-epoxy composites T-300/934. The following information is available in the database. For each material type, the mechanical, physical, thermal, and environmental properties are first listed. Next the principal manufacturing processes are described. Whenever possible, guidelines for optimum processing conditions for specific applications are provided. Finally, six categories of cost drivers are discussed. They include, design features affecting processing, tooling, materials, fabrication, joining/assembly, and quality assurance issues. It should be emphasized that this database is not an exhaustive database. Its primary use is to make the vehicle designer

A manufacturing database of advanced materials used in spacecraft structures

NASA Astrophysics Data System (ADS)

Bao, Han P.

1994-12-01

Cost savings opportunities over the life cycle of a product are highest in the early exploratory phase when different design alternatives are evaluated not only for their performance characteristics but also their methods of fabrication which really control the ultimate manufacturing costs of the product. In the past, Design-To-Cost methodologies for spacecraft design concentrated on the sizing and weight issues more than anything else at the early so-called 'Vehicle Level' (Ref: DOD/NASA Advanced Composites Design Guide). Given the impact of manufacturing cost, the objective of this study is to identify the principal cost drivers for each materials technology and propose a quantitative approach to incorporating these cost drivers into the family of optimization tools used by the Vehicle Analysis Branch of NASA LaRC to assess various conceptual vehicle designs. The advanced materials being considered include aluminum-lithium alloys, thermoplastic graphite-polyether etherketone composites, graphite-bismaleimide composites, graphite- polyimide composites, and carbon-carbon composites. Two conventional materials are added to the study to serve as baseline materials against which the other materials are compared. These two conventional materials are aircraft aluminum alloys series 2000 and series 7000, and graphite-epoxy composites T-300/934. The following information is available in the database. For each material type, the mechanical, physical, thermal, and environmental properties are first listed. Next the principal manufacturing processes are described. Whenever possible, guidelines for optimum processing conditions for specific applications are provided. Finally, six categories of cost drivers are discussed. They include, design features affecting processing, tooling, materials, fabrication, joining/assembly, and quality assurance issues. It should be emphasized that this database is not an exhaustive database. Its primary use is to make the vehicle designer

The EPMI Malay Basin petroleum geology database: Design philosophy and keys to success

DOE Office of Scientific and Technical Information (OSTI.GOV)

Low, H.E.; Creaney, S.; Fairchild, L.H.

1994-07-01

Esso Production Malaysia Inc. (EPMI) developed and populated a database containing information collected in the areas of basic well data: stratigraphy, lithology, facies; pressure, temperature, column/contacts; geochemistry, shows and stains, migration, fluid properties; maturation; seal; structure. Paradox was used as the database engine and query language, with links to ZYCOR ZMAP+ for mapping and SAS for data analysis. Paradox has a query language that is simple enough for users. The ability to link to good analytical packages was deemed more important than having the capability in the package. Important elements of design philosophy were included: (1) information on data qualitymore » had to be rigorously recorded; (2) raw and interpreted data were kept separate and clearly identified; (3) correlations between rock and chronostratigraphic surfaces were recorded; and (4) queries across technical boundaries had to be seamless.« less

An expert system for integrated structural analysis and design optimization for aerospace structures

NASA Technical Reports Server (NTRS)

1992-01-01

The results of a research study on the development of an expert system for integrated structural analysis and design optimization is presented. An Object Representation Language (ORL) was developed first in conjunction with a rule-based system. This ORL/AI shell was then used to develop expert systems to provide assistance with a variety of structural analysis and design optimization tasks, in conjunction with procedural modules for finite element structural analysis and design optimization. The main goal of the research study was to provide expertise, judgment, and reasoning capabilities in the aerospace structural design process. This will allow engineers performing structural analysis and design, even without extensive experience in the field, to develop error-free, efficient and reliable structural designs very rapidly and cost-effectively. This would not only improve the productivity of design engineers and analysts, but also significantly reduce time to completion of structural design. An extensive literature survey in the field of structural analysis, design optimization, artificial intelligence, and database management systems and their application to the structural design process was first performed. A feasibility study was then performed, and the architecture and the conceptual design for the integrated 'intelligent' structural analysis and design optimization software was then developed. An Object Representation Language (ORL), in conjunction with a rule-based system, was then developed using C++. Such an approach would improve the expressiveness for knowledge representation (especially for structural analysis and design applications), provide ability to build very large and practical expert systems, and provide an efficient way for storing knowledge. Functional specifications for the expert systems were then developed. The ORL/AI shell was then used to develop a variety of modules of expert systems for a variety of modeling, finite element analysis, and

An expert system for integrated structural analysis and design optimization for aerospace structures

NASA Astrophysics Data System (ADS)

1992-04-01

The results of a research study on the development of an expert system for integrated structural analysis and design optimization is presented. An Object Representation Language (ORL) was developed first in conjunction with a rule-based system. This ORL/AI shell was then used to develop expert systems to provide assistance with a variety of structural analysis and design optimization tasks, in conjunction with procedural modules for finite element structural analysis and design optimization. The main goal of the research study was to provide expertise, judgment, and reasoning capabilities in the aerospace structural design process. This will allow engineers performing structural analysis and design, even without extensive experience in the field, to develop error-free, efficient and reliable structural designs very rapidly and cost-effectively. This would not only improve the productivity of design engineers and analysts, but also significantly reduce time to completion of structural design. An extensive literature survey in the field of structural analysis, design optimization, artificial intelligence, and database management systems and their application to the structural design process was first performed. A feasibility study was then performed, and the architecture and the conceptual design for the integrated 'intelligent' structural analysis and design optimization software was then developed. An Object Representation Language (ORL), in conjunction with a rule-based system, was then developed using C++. Such an approach would improve the expressiveness for knowledge representation (especially for structural analysis and design applications), provide ability to build very large and practical expert systems, and provide an efficient way for storing knowledge. Functional specifications for the expert systems were then developed. The ORL/AI shell was then used to develop a variety of modules of expert systems for a variety of modeling, finite element analysis, and

Ultra-structural hair alterations of drug abusers: a scanning electron microscopic investigation

PubMed Central

Turkmenoglu, Fatma Pinar; Kasirga, Ugur Baran; Celik, Hakan Hamdi

2015-01-01

As drug abuse carries a societal stigma, patients do not often report their history of drug abuse to the healthcare providers. However, drug abuse is highly co-morbid with a host of other health problems such as psychiatric disorders and skin diseases, and majority of individuals with drug use disorders seek treatment in the first place for other problems. Therefore, it is very important for physicians to be aware of clinical signs and symptoms of drug use. Recently diagnostic value of dermatologic tissue alterations associated with drug abuse has become a very particular interest because skin changes were reported to be the earliest noticeable consequence of drug abuse prompting earlier intervention and treatment. Although hair is an annex of skin, alterations on hair structure due to drug use have not been demonstrated. This study represents the first report on ultra-structural hair alterations of drug abusers. We have investigated ultra-structure of the hair samples obtained from 6 cocaine, 6 heroin, 7 cannabis and 4 lysergic acid diethylamide (LSD) abusers by scanning electron microscope (SEM). SEM analysis of hair samples gave us drug-specific discriminating alterations. We suggest that results of this study will make a noteworthy contribution to cutaneous alterations associated with drug abuse which are regarded as the earliest clinical manifestations, and this SEM approach is a very specific and effective tool in the detection of abuse of respective drugs, leading early treatment. PMID:26309532

Data Model and Relational Database Design for Highway Runoff Water-Quality Metadata

USGS Publications Warehouse

Granato, Gregory E.; Tessler, Steven

2001-01-01

A National highway and urban runoff waterquality metadatabase was developed by the U.S. Geological Survey in cooperation with the Federal Highway Administration as part of the National Highway Runoff Water-Quality Data and Methodology Synthesis (NDAMS). The database was designed to catalog available literature and to document results of the synthesis in a format that would facilitate current and future research on highway and urban runoff. This report documents the design and implementation of the NDAMS relational database, which was designed to provide a catalog of available information and the results of an assessment of the available data. All the citations and the metadata collected during the review process are presented in a stratified metadatabase that contains citations for relevant publications, abstracts (or previa), and reportreview metadata for a sample of selected reports that document results of runoff quality investigations. The database is referred to as a metadatabase because it contains information about available data sets rather than a record of the original data. The database contains the metadata needed to evaluate and characterize how valid, current, complete, comparable, and technically defensible published and available information may be when evaluated for application to the different dataquality objectives as defined by decision makers. This database is a relational database, in that all information is ultimately linked to a given citation in the catalog of available reports. The main database file contains 86 tables consisting of 29 data tables, 11 association tables, and 46 domain tables. The data tables all link to a particular citation, and each data table is focused on one aspect of the information collected in the literature search and the evaluation of available information. This database is implemented in the Microsoft (MS) Access database software because it is widely used within and outside of government and is familiar to many

Collection, processing, and reporting of damage tolerant design data for non-aerospace structural materials

NASA Technical Reports Server (NTRS)

Huber, P. D.; Gallagher, J. P.

1994-01-01

This report describes the organization, format and content of the NASA Johnson damage tolerant database which was created to store damage tolerant property data for non aerospace structural materials. The database is designed to store fracture toughness data (K(sub IC), K(sub c), J(sub IC) and CTOD(sub IC)), resistance curve data (K(sub R) VS. delta a (sub eff) and JR VS. delta a (sub eff)), as well as subcritical crack growth data (a vs. N and da/dN vs. delta K). The database contains complementary material property data for both stainless and alloy steels, as well as for aluminum, nickel, and titanium alloys which were not incorporated into the Damage Tolerant Design Handbook database.

GALT protein database: querying structural and functional features of GALT enzyme.

PubMed

d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

2014-09-01

Knowledge of the impact of variations on protein structure can enhance the comprehension of the mechanisms of genetic diseases related to that protein. Here, we present a new version of GALT Protein Database, a Web-accessible data repository for the storage and interrogation of structural effects of variations of the enzyme galactose-1-phosphate uridylyltransferase (GALT), the impairment of which leads to classic Galactosemia, a rare genetic disease. This new version of this database now contains the models of 201 missense variants of GALT enzyme, including heterozygous variants, and it allows users not only to retrieve information about the missense variations affecting this protein, but also to investigate their impact on substrate binding, intersubunit interactions, stability, and other structural features. In addition, it allows the interactive visualization of the models of variants collected into the database. We have developed additional tools to improve the use of the database by nonspecialized users. This Web-accessible database (http://bioinformatica.isa.cnr.it/GALT/GALT2.0) represents a model of tools potentially suitable for application to other proteins that are involved in human pathologies and that are subjected to genetic variations. © 2014 WILEY PERIODICALS, INC.

Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

PubMed

Allen, Frank H; Motherwell, W D Samuel

2002-06-01

The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

SMUVS: Spitzer Matching survey of the UltraVISTA ultra-deep Stripes

NASA Astrophysics Data System (ADS)

Caputi, Karina; Ashby, Matthew; Fazio, Giovanni; Huang, Jiasheng; Dunlop, James; Franx, Marijn; Le Fevre, Olivier; Fynbo, Johan; McCracken, Henry; Milvang-Jensen, Bo; Muzzin, Adam; Ilbert, Olivier; Somerville, Rachel; Wechsler, Risa; Behroozi, Peter; Lu, Yu

2014-12-01

We request 2026.5 hours to homogenize the matching ultra-deep IRAC data of the UltraVISTA ultra-deep stripes, producing a final area of ~0.6 square degrees with the deepest near- and mid-IR coverage existing in any such large area of the sky (H, Ks, [3.6], [4.5] ~ 25.3-26.1 AB mag; 5 sigma). The UltraVISTA ultra-deep stripes are contained within the larger COSMOS field, which has a rich collection of multi-wavelength, ancillary data, making it ideal to study different aspects of galaxy evolution with high statistical significance and excellent redshift accuracy. The UltraVISTA ultra-deep stripes are the region of the COSMOS field where these studies can be pushed to the highest redshifts, but securely identifying high-z galaxies, and determining their stellar masses, will only be possible if ultra-deep mid-IR data are available. Our IRAC observations will allow us to: 1) extend the galaxy stellar mass function at redshifts z=3 to z=5 to the intermediate mass regime (M~5x10^9-10^10 Msun), which is critical to constrain galaxy formation models; 2) gain a factor of six in the area where it is possible to effectively search for z>=6 galaxies and study their properties; 3) measure, for the first time, the large-scale structure traced by an unbiased galaxy sample at z=5 to z=7, and make the link to their host dark matter haloes. This cannot be done in any other field of the sky, as the UltraVISTA ultra-deep stripes form a quasi-contiguous, regular-shape field, which has a unique combination of large area and photometric depth. 4) provide a unique resource for the selection of secure z>5 targets for JWST and ALMA follow up. Our observations will have an enormous legacy value which amply justifies this new observing-time investment in the COSMOS field. Spitzer cannot miss this unique opportunity to open up a large 0.6 square-degree window to the early Universe.

Research and development of a digital design system for hull structures

NASA Astrophysics Data System (ADS)

Zhan, Yi-Ting; Ji, Zhuo-Shang; Liu, Yin-Dong

2007-06-01

Methods used for digital ship design were studied and formed the basis of a proposed frame model suitable for ship construction modeling. Based on 3-D modeling software, a digital design system for hull structures was developed. Basic software systems for modeling, modifying, and assembly simulation were developed. The system has good compatibility, and models created by it can be saved in different 3-D file formats, and 2D engineering drawings can be output directly. The model can be modified dynamically, overcoming the necessity of repeated modifications during hull structural design. Through operations such as model construction, intervention inspection, and collision detection, problems can be identified and modified during the hull structural design stage. Technologies for centralized control of the system, database management, and 3-D digital design are integrated into this digital model in the preliminary design stage of shipbuilding.

[Design and establishment of modern literature database about acupuncture Deqi].

PubMed

Guo, Zheng-rong; Qian, Gui-feng; Pan, Qiu-yin; Wang, Yang; Xin, Si-yuan; Li, Jing; Hao, Jie; Hu, Ni-juan; Zhu, Jiang; Ma, Liang-xiao

2015-02-01

A search on acupuncture Deqi was conducted using four Chinese-language biomedical databases (CNKI, Wan-Fang, VIP and CBM) and PubMed database and using keywords "Deqi" or "needle sensation" "needling feeling" "needle feel" "obtaining qi", etc. Then, a "Modern Literature Database for Acupuncture Deqi" was established by employing Microsoft SQL Server 2005 Express Edition, introducing the contents, data types, information structure and logic constraint of the system table fields. From this Database, detailed inquiries about general information of clinical trials, acupuncturists' experience, ancient medical works, comprehensive literature, etc. can be obtained. The present databank lays a foundation for subsequent evaluation of literature quality about Deqi and data mining of undetected Deqi knowledge.

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

PubMed

Holliday, Gemma L; Brown, Shoshana D; Akiva, Eyal; Mischel, David; Hicks, Michael A; Morris, John H; Huang, Conrad C; Meng, Elaine C; Pegg, Scott C-H; Ferrin, Thomas E; Babbitt, Patricia C

2017-01-01

With ever-increasing amounts of sequence data available in both the primary literature and sequence repositories, there is a bottleneck in annotating molecular function to a sequence. This article describes the biocuration process and methods used in the structure-function linkage database (SFLD) to help address some of the challenges. We discuss how the hierarchy within the SFLD allows us to infer detailed functional properties for functionally diverse enzyme superfamilies in which all members are homologous, conserve an aspect of their chemical function and have associated conserved structural features that enable the chemistry. Also presented is the Enzyme Structure-Function Ontology (ESFO), which has been designed to capture the relationships between enzyme sequence, structure and function that underlie the SFLD and is used to guide the biocuration processes within the SFLD. http://sfld.rbvi.ucsf.edu/. © The Author 2017. Published by Oxford University Press.

DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides

PubMed Central

Pirtskhalava, Malak; Gabrielian, Andrei; Cruz, Phillip; Griggs, Hannah L.; Squires, R. Burke; Hurt, Darrell E.; Grigolava, Maia; Chubinidze, Mindia; Gogoladze, George; Vishnepolsky, Boris; Alekseev, Vsevolod; Rosenthal, Alex; Tartakovsky, Michael

2016-01-01

Antimicrobial peptides (AMPs) are anti-infectives that may represent a novel and untapped class of biotherapeutics. Increasing interest in AMPs means that new peptides (natural and synthetic) are discovered faster than ever before. We describe herein a new version of the Database of Antimicrobial Activity and Structure of Peptides (DBAASPv.2, which is freely accessible at http://dbaasp.org). This iteration of the database reports chemical structures and empirically-determined activities (MICs, IC50, etc.) against more than 4200 specific target microbes for more than 2000 ribosomal, 80 non-ribosomal and 5700 synthetic peptides. Of these, the vast majority are monomeric, but nearly 200 of these peptides are found as homo- or heterodimers. More than 6100 of the peptides are linear, but about 515 are cyclic and more than 1300 have other intra-chain covalent bonds. More than half of the entries in the database were added after the resource was initially described, which reflects the recent sharp uptick of interest in AMPs. New features of DBAASPv.2 include: (i) user-friendly utilities and reporting functions, (ii) a ‘Ranking Search’ function to query the database by target species and return a ranked list of peptides with activity against that target and (iii) structural descriptions of the peptides derived from empirical data or calculated by molecular dynamics (MD) simulations. The three-dimensional structural data are critical components for understanding structure–activity relationships and for design of new antimicrobial drugs. We created more than 300 high-throughput MD simulations specifically for inclusion in DBAASP. The resulting structures are described in the database by novel trajectory analysis plots and movies. Another 200+ DBAASP entries have links to the Protein DataBank. All of the structures are easily visualized directly in the web browser. PMID:26578581

Engineering ultra-flattened normal dispersion photonic crystal fiber with silica material

NASA Astrophysics Data System (ADS)

Ferhat, Mohamed Lamine; Cherbi, Lynda; Bahloul, Lies; Hariz, Abdelhafid

2017-05-01

The tailoring of the group velocity dispersion (GVD) of an optical fiber is critical in many applications, influence on the bandwidth of information transmission in optical communication systems, successful utilization of nonlinear optical properties in applications such as supercontinuum generation, wavelength conversion and harmonic generation via stimulated Raman scattering ...In this work, we propose a design of ultra-flattened photonic crystal fiber by changing the diameter of the air holes of the cladding rings. The geometry is composed of only four rings, hexagonal structure of air holes and silica as background of the solid core. As a result, we present structures with broadband flat normal dispersion on many wavelengths bands useful for several applications. We obtain flat normal dispersion over 1000 nm broadband flat normal dispersion below -7 [ps/nm.km], and ultra-flat near zero normal dispersion below -0.2 [ps/nm.km] over 150 nm. The modeled photonic crystal fiber would be valuable for the fabrication of ultra-flattened-dispersion fibers, and have potential applications in wide-band high-speed optical communication systems, supercontinuum generation and many other applications.

7 CFR 58.144 - Pasteurization or ultra-pasteurization.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Pasteurization or ultra-pasteurization. 58.144 Section... Service 1 Operations and Operating Procedures § 58.144 Pasteurization or ultra-pasteurization. When pasteurization or ultra-pasteurization is intended or required, or when a product is designated “pasteurized” or...

AbDb: antibody structure database—a database of PDB-derived antibody structures

PubMed Central

Ferdous, Saba

2018-01-01

Abstract In order to analyse structures of proteins of a particular class, these need to be extracted from Protein Data Bank (PDB) files. In the case of antibodies, there are a number of special considerations: (i) identifying antibodies in the PDB is not trivial, (ii) they may be crystallized with or without antigen, (iii) for analysis purposes, one is normally only interested in the Fv region of the antibody, (iv) structural analysis of epitopes, in particular, requires individual antibody–antigen complexes from a PDB file which may contain multiple copies of the same, or different, antibodies and (v) standard numbering schemes should be applied. Consequently, there is a need for a specialist resource containing pre-numbered non-redundant antibody Fv structures with their cognate antigens. We have created an automatically updated resource, AbDb, which collects the Fv regions from antibody structures using information from our SACS database which summarizes antibody structures from the PDB. PDB files containing multiple structures are split and numbered and each antibody structure is associated with its antigen where available. Antibody structures with only light or heavy chains have also been processed and sequences of antibodies are compared to identify multiple structures of the same antibody. The data may be queried on the basis of PDB code, or the name or species of the antibody or antigen, and the complete datasets may be downloaded. Database URL: www.bioinf.org.uk/abs/abdb/ PMID:29718130

Effects of fuel-injector design on ultra-lean combustion performance

NASA Technical Reports Server (NTRS)

Anderson, D. N.

1981-01-01

Emissions data were obtained for six fuel injector configurations tested with ultra lean combustion. Fuel injectors included three multiple source designs and three configurations using a single air assist injector. Only the multiple source fuel injectors provided acceptable emissions. Values of 16g CO/kg fuel, 1.9g HC/kg fuel, and 19.g NO2/kg fuel were obtained for the combustion temperature range of 1450 to 1700 K for both a high blockage 19 source injector and a low blockage 41 source injector. It was shown that high fuel injector pressure drop may not be required to achieve low emissions performance at high inlet air temperature when the fuel is well dispersed in the airstream.

Emission Database for Global Atmospheric Research (EDGAR).

ERIC Educational Resources Information Center

Olivier, J. G. J.; And Others

1994-01-01

Presents the objective and methodology chosen for the construction of a global emissions source database called EDGAR and the structural design of the database system. The database estimates on a regional and grid basis, 1990 annual emissions of greenhouse gases, and of ozone depleting compounds from all known sources. (LZ)

ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.

PubMed

Konc, Janez; Cesnik, Tomo; Konc, Joanna Trykowska; Penca, Matej; Janežič, Dušanka

2012-02-27

ProBiS-Database is a searchable repository of precalculated local structural alignments in proteins detected by the ProBiS algorithm in the Protein Data Bank. Identification of functionally important binding regions of the protein is facilitated by structural similarity scores mapped to the query protein structure. PDB structures that have been aligned with a query protein may be rapidly retrieved from the ProBiS-Database, which is thus able to generate hypotheses concerning the roles of uncharacterized proteins. Presented with uncharacterized protein structure, ProBiS-Database can discern relationships between such a query protein and other better known proteins in the PDB. Fast access and a user-friendly graphical interface promote easy exploration of this database of over 420 million local structural alignments. The ProBiS-Database is updated weekly and is freely available online at http://probis.cmm.ki.si/database.

Ultra-peripheral collisions and hadronic structure

NASA Astrophysics Data System (ADS)

Klein, Spencer R.

2017-11-01

Ultra-peripheral collisions are the energy frontier for photon-mediated interactions, reaching, at the Large Hadron Collider (LHC), γ - p center of mass energies five to ten times higher than at HERA and reaching γγ energies higher than at LEP. Photoproduction of heavy quarkonium and dijets in pp and pA collisions probes the gluon distribution in protons at Bjorken-x values down to 3 ×10-6, far smaller than can be otherwise studied. In AA collisions, these reactions probe the gluon distributions in heavy ions, down to x values of a few 10-5. Although more theoretical work is needed to nail down all of the uncertainties, inclusion of these data in current parton distribution function fits would greatly improve the accuracy of the gluon distributions at low Bjorken-x and low/moderate Q2. High-statistics ρ0 data probe the spatial distribution of the interaction sites; the site distribution is given by the Fourier transform of dσ / dt. After introducing UPCs, this review presents recent measurements of dilepton production and light-by-light scattering and recent data on proton and heavy nuclei structure, emphasizing results presented at Quark Matter 2017 (QM2017).

Structural phase diagram for ultra-thin epitaxial Fe 3O 4 / MgO(0 01) films: thickness and oxygen pressure dependence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alraddadi, S.; Hines, W.; Yilmaz, T.

2016-02-19

A systematic investigation of the thickness and oxygen pressure dependence for the structural properties of ultra-thin epitaxial magnetite (Fe 3O 4) films has been carried out; for such films, the structural properties generally differ from those for the bulk when the thickness ≤10 nm. Iron oxide ultra-thin films with thicknesses varying from 3 nm to 20 nm were grown on MgO (001) substrates using molecular beam epitaxy under different oxygen pressures ranging from 1 × 10 -7 torr to 1 × 10 -5 torr. The crystallographic and electronic structures of the films were characterized using low energy electron diffraction (LEED)more » and x-ray photoemission spectroscopy (XPS), respectively. Moreover, the quality of the epitaxial Fe 3O 4 ultra-thin films was judged by magnetic measurements of the Verwey transition, along with complementary XPS spectra. We observed that under the same growth conditions the stoichiometry of ultra-thin films under 10 nm transforms from the Fe 3O 4 phase to the FeO phase. In this work, a phase diagram based on thickness and oxygen pressure has been constructed to explain the structural phase transformation. It was found that high-quality magnetite films with thicknesses ≤20 nm formed within a narrow range of oxygen pressure. An optimal and controlled growth process is a crucial requirement for the accurate study of the magnetic and electronic properties for ultra-thin Fe 3O 4 films. Furthermore, these results are significant because they may indicate a general trend in the growth of other oxide films, which has not been previously observed or considered.« less

Design & Performance of Wearable Ultra Wide Band Textile Antenna for Medical Applications

NASA Astrophysics Data System (ADS)

Singh, Nikhil; Singh, Ashutosh Kumar; Singh, Vinod Kumar

2015-02-01

The concept of wearable products such as textile antenna are being developed which are capable of monitoring, alerting and demanding attention whenever hospital emergency is needed, hence minimizing labour and resource. In the proposed work by using textile material as a substrate the ultra wideband antenna is designed especially for medical applications.Simulated and measured results here shows that the proposed antenna design meets the requirements of wide working bandwidth and provides 13.08 GHz bandwidth with very small size, washable (if using conductive thread for conductive parts) and flexible materials. Results in terms of bandwidth, radiation pattern, return loss as well as gain and efficiency are presented to validate the usefulness of the current proposed design. The work done here has many implications for future research and it could help patients with such flexible and comfortable medical monitoring techniques.

Development of an Ultra-Wideband Circularly Polarized Multiple Layer Dielectric Rod Antenna Design

NASA Astrophysics Data System (ADS)

Wainwright, Gregory D.

This dissertations focuses on the development of a novel Ultra-Wideband (UWB) circularly polarized dielectric rod antenna (CPDRA) which yields a constant gain, pattern, and phase center. These properties are important in many applications. Within radar systems a constant phase center is desirable to avoid errors within downrange and crossrange measurements. In a reflector antenna the illumination, spillover, and phase efficiencies will remain the same over an ultra-wideband. Lastly, near field probes require smooth amplitude and phase patterns over frequency to avoid errors during the calibration process of the antenna under test. In this dissertation a novel CP feeding network has been developed for an ultra-wideband dielectric rod antenna. Circularly-polarized antennas have a major advantage over its linearly-polarized counterpart in that the polarization mismatch loss caused by misalignment between the polarizations of the incident fields and antenna can be avoided. This is important in satellite communications and broadcasts where signal propagation through the ionosphere can experience Faraday Rotation. A circularly polarized antenna is also helpful in mobile radar and communication systems where the receiving antennas orientation is not fixed. Previous research on UWB dielectric rod antenna designs has focused on Dual linear feeds. Each polarization within the dual linear feed is excited by a pair of linear launcher arms fed with a 0°-180° hybrid balun. The proposed CPDRA design does not require the 0°-180° hybrid baluns or 0°-90° hybrid for achieving CP operation. These hybrids will increase the antennas size, weight, cost, and reduce operational bandwidth. A design technique has been developed for an UWB multilayer dielectric waveguide used in a CPDRA antenna. This design technique uses near-field Electric field data from inside the waveguide, in conjunction with a genetic algorithm optimization to yield a wideband waveguide with a near field

Structural design and analysis for an ultra low CTE optical bench for the Hubble Space Telescope corrective optics

NASA Technical Reports Server (NTRS)

Neam, Douglas C.; Gerber, John D.

1992-01-01

The stringent stability requirements of the Corrective Optics Space Telescope Axial Replacement (COSTAR) necessitates a Deployable Optical Bench (DOB) with both a low CTE and high resonant frequency. The DOB design consists of a monocoque thin shell structure which marries metallic machined parts with graphite epoxy formed structure. Structural analysis of the DOB has been integrated into the laminate design and optimization process. Also, the structural analytical results are compared with vibration and thermal test data to assess the reliability of the analysis.

EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

PubMed

Montes-Grajales, Diana; Olivero-Verbel, Jesus

2015-01-02

Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co. Copyright © 2014. Published by Elsevier Ireland Ltd.

HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors

National Institute of Standards and Technology Data Gateway

SRD 155 HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors (Web, free access)   The HIV structural database (HIVSDB) is a comprehensive collection of the structures of HIV protease, both of unliganded enzyme and of its inhibitor complexes. It contains abstracts and crystallographic data such as inhibitor and protein coordinates for 248 data sets, of which only 141 are from the Protein Data Bank (PDB).

Grouted pile to sleeves connections: Design provisions for the new ISO Standard for offshore structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harwood, R.G.; Billington, C.J.; Buitrago, J.

1996-12-01

A Technical Core Group (TCG) was set up in March 1994 to review the design practice provisions for grouted pile to sleeve connections, mechanical connections and repairs as part of the international harmonization process for the new ISO Standard, ISO 13819-2, Petroleum and Natural Gas Industries--Offshore Structures, Part 2: Fixed Steel Structures. This paper provides an overview of the development of the proposed new design provisions for grouted connections including, the gathering and screening of the data, the evolution of the design formulae, and the evaluation of the resistance factor. Detailed comparisons of the new formulae with current design practicemore » (API, HSE and DnV) are also included. In the development of the new provisions the TCG has been given access to the largest database ever assembled on this topic. This database includes all the major testing programs performed over the last 20 years, and recent UK and Norwegian research projects not previously reported. The limitations in the database are discussed and the areas where future research would be of benefit are highlighted.« less

RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation

PubMed Central

2009-01-01

Background Polymerase chain reaction (PCR) is very useful in many areas of molecular biology research. It is commonly observed that PCR success is critically dependent on design of an effective primer pair. Current tools for primer design do not adequately address the problem of PCR failure due to mis-priming on target-related sequences and structural variations in the genome. Methods We have developed an integrated graphical web-based application for primer design, called RExPrimer, which was written in Python language. The software uses Primer3 as the primer designing core algorithm. Locally stored sequence information and genomic variant information were hosted on MySQLv5.0 and were incorporated into RExPrimer. Results RExPrimer provides many functionalities for improved PCR primer design. Several databases, namely annotated human SNP databases, insertion/deletion (indel) polymorphisms database, pseudogene database, and structural genomic variation databases were integrated into RExPrimer, enabling an effective without-leaving-the-website validation of the resulting primers. By incorporating these databases, the primers reported by RExPrimer avoid mis-priming to related sequences (e.g. pseudogene, segmental duplication) as well as possible PCR failure because of structural polymorphisms (SNP, indel, and copy number variation (CNV)). To prevent mismatching caused by unexpected SNPs in the designed primers, in particular the 3' end (SNP-in-Primer), several SNP databases covering the broad range of population-specific SNP information are utilized to report SNPs present in the primer sequences. Population-specific SNP information also helps customize primer design for a specific population. Furthermore, RExPrimer offers a graphical user-friendly interface through the use of scalable vector graphic image that intuitively presents resulting primers along with the corresponding gene structure. In this study, we demonstrated the program effectiveness in successfully

Design and evaluation of an ultra-slim objective for in-vivo deep optical biopsy

PubMed Central

Landau, Sara M.; Liang, Chen; Kester, Robert T.; Tkaczyk, Tomasz S.; Descour, Michael R.

2010-01-01

An estimated 1.6 million breast biopsies are performed in the US each year. In order to provide real-time, in-vivo imaging with sub-cellular resolution for optical biopsies, we have designed an ultra-slim objective to fit inside the 1-mm-diameter hypodermic needles currently used for breast biopsies to image tissue stained by the fluorescent probe proflavine. To ensure high-quality imaging performance, experimental tests were performed to characterize fiber bundle’s light-coupling efficiency and simulations were performed to evaluate the impact of candidate lens materials’ autofluorescence. A prototype of NA = 0.4, 250-µm field of view, ultra-slim objective optics was built and tested, yielding diffraction-limited performance and estimated resolution of 0.9 µm. When used in conjunction with a commercial coherent fiber bundle to relay the image formed by the objective, the measured resolution was 2.5 µm. PMID:20389489

Design and implementation of the NPOI database and website

NASA Astrophysics Data System (ADS)

Newman, K.; Jorgensen, A. M.; Landavazo, M.; Sun, B.; Hutter, D. J.; Armstrong, J. T.; Mozurkewich, David; Elias, N.; van Belle, G. T.; Schmitt, H. R.; Baines, E. K.

2014-07-01

The Navy Precision Optical Interferometer (NPOI) has been recording astronomical observations for nearly two decades, at this point with hundreds of thousands of individual observations recorded to date for a total data volume of many terabytes. To make maximum use of the NPOI data it is necessary to organize them in an easily searchable manner and be able to extract essential diagnostic information from the data to allow users to quickly gauge data quality and suitability for a specific science investigation. This sets the motivation for creating a comprehensive database of observation metadata as well as, at least, reduced data products. The NPOI database is implemented in MySQL using standard database tools and interfaces. The use of standard database tools allows us to focus on top-level database and interface implementation and take advantage of standard features such as backup, remote access, mirroring, and complex queries which would otherwise be time-consuming to implement. A website was created in order to give scientists a user friendly interface for searching the database. It allows the user to select various metadata to search for and also allows them to decide how and what results are displayed. This streamlines the searches, making it easier and quicker for scientists to find the information they are looking for. The website has multiple browser and device support. In this paper we present the design of the NPOI database and website, and give examples of its use.

Teaching Database Modeling and Design: Areas of Confusion and Helpful Hints

ERIC Educational Resources Information Center

Philip, George C.

2007-01-01

This paper identifies several areas of database modeling and design that have been problematic for students and even are likely to confuse faculty. Major contributing factors are the lack of clarity and inaccuracies that persist in the presentation of some basic database concepts in textbooks. The paper analyzes the problems and discusses ways to…

Exploratory visualization of astronomical data on ultra-high-resolution wall displays

NASA Astrophysics Data System (ADS)

Pietriga, Emmanuel; del Campo, Fernando; Ibsen, Amanda; Primet, Romain; Appert, Caroline; Chapuis, Olivier; Hempel, Maren; Muñoz, Roberto; Eyheramendy, Susana; Jordan, Andres; Dole, Hervé

2016-07-01

Ultra-high-resolution wall displays feature a very high pixel density over a large physical surface, which makes them well-suited to the collaborative, exploratory visualization of large datasets. We introduce FITS-OW, an application designed for such wall displays, that enables astronomers to navigate in large collections of FITS images, query astronomical databases, and display detailed, complementary data and documents about multiple sources simultaneously. We describe how astronomers interact with their data using both the wall's touchsensitive surface and handheld devices. We also report on the technical challenges we addressed in terms of distributed graphics rendering and data sharing over the computer clusters that drive wall displays.

Design of a Multi Dimensional Database for the Archimed DataWarehouse.

PubMed

Bréant, Claudine; Thurler, Gérald; Borst, François; Geissbuhler, Antoine

2005-01-01

The Archimed data warehouse project started in 1993 at the Geneva University Hospital. It has progressively integrated seven data marts (or domains of activity) archiving medical data such as Admission/Discharge/Transfer (ADT) data, laboratory results, radiology exams, diagnoses, and procedure codes. The objective of the Archimed data warehouse is to facilitate the access to an integrated and coherent view of patient medical in order to support analytical activities such as medical statistics, clinical studies, retrieval of similar cases and data mining processes. This paper discusses three principal design aspects relative to the conception of the database of the data warehouse: 1) the granularity of the database, which refers to the level of detail or summarization of data, 2) the database model and architecture, describing how data will be presented to end users and how new data is integrated, 3) the life cycle of the database, in order to ensure long term scalability of the environment. Both, the organization of patient medical data using a standardized elementary fact representation and the use of the multi dimensional model have proved to be powerful design tools to integrate data coming from the multiple heterogeneous database systems part of the transactional Hospital Information System (HIS). Concurrently, the building of the data warehouse in an incremental way has helped to control the evolution of the data content. These three design aspects bring clarity and performance regarding data access. They also provide long term scalability to the system and resilience to further changes that may occur in source systems feeding the data warehouse.

Strabo: An App and Database for Structural Geology and Tectonics Data

NASA Astrophysics Data System (ADS)

Newman, J.; Williams, R. T.; Tikoff, B.; Walker, J. D.; Good, J.; Michels, Z. D.; Ash, J.

2016-12-01

Strabo is a data system designed to facilitate digital storage and sharing of structural geology and tectonics data. The data system allows researchers to store and share field and laboratory data as well as construct new multi-disciplinary data sets. Strabo is built on graph database technology, as opposed to a relational database, which provides the flexibility to define relationships between objects of any type. This framework allows observations to be linked in a complex and hierarchical manner that is not possible in traditional database topologies. Thus, the advantage of the Strabo data structure is the ability of graph databases to link objects in both numerous and complex ways, in a manner that more accurately reflects the realities of the collecting and organizing of geological data sets. The data system is accessible via a mobile interface (iOS and Android devices) that allows these data to be stored, visualized, and shared during primary collection in the field or the laboratory. The Strabo Data System is underlain by the concept of a "Spot," which we define as any observation that characterizes a specific area. This can be anything from a strike and dip measurement of bedding to cross-cutting relationships between faults in complex dissected terrains. Each of these spots can then contain other Spots and/or measurements (e.g., lithology, slickenlines, displacement magnitude.) Hence, the Spot concept is applicable to all relationships and observation sets. Strabo is therefore capable of quantifying and digitally storing large spatial variations and complex geometries of naturally deformed rocks within hierarchically related maps and images. These approaches provide an observational fidelity comparable to a traditional field book, but with the added benefits of digital data storage, processing, and ease of sharing. This approach allows Strabo to integrate seamlessly into the workflow of most geologists. Future efforts will focus on extending Strabo to

A phenome database (NEAUHLFPD) designed and constructed for broiler lines divergently selected for abdominal fat content.

PubMed

Li, Min; Dong, Xiang-yu; Liang, Hao; Leng, Li; Zhang, Hui; Wang, Shou-zhi; Li, Hui; Du, Zhi-Qiang

2017-05-20

Effective management and analysis of precisely recorded phenotypic traits are important components of the selection and breeding of superior livestocks. Over two decades, we divergently selected chicken lines for abdominal fat content at Northeast Agricultural University (Northeast Agricultural University High and Low Fat, NEAUHLF), and collected large volume of phenotypic data related to the investigation on molecular genetic basis of adipose tissue deposition in broilers. To effectively and systematically store, manage and analyze phenotypic data, we built the NEAUHLF Phenome Database (NEAUHLFPD). NEAUHLFPD included the following phenotypic records: pedigree (generations 1-19) and 29 phenotypes, such as body sizes and weights, carcass traits and their corresponding rates. The design and construction strategy of NEAUHLFPD were executed as follows: (1) Framework design. We used Apache as our web server, MySQL and Navicat as database management tools, and PHP as the HTML-embedded language to create dynamic interactive website. (2) Structural components. On the main interface, detailed introduction on the composition, function, and the index buttons of the basic structure of the database could be found. The functional modules of NEAUHLFPD had two main components: the first module referred to the physical storage space for phenotypic data, in which functional manipulation on data can be realized, such as data indexing, filtering, range-setting, searching, etc.; the second module related to the calculation of basic descriptive statistics, where data filtered from the database can be used for the computation of basic statistical parameters and the simultaneous conditional sorting. NEAUHLFPD could be used to effectively store and manage not only phenotypic, but also genotypic and genomics data, which can facilitate further investigation on the molecular genetic basis of chicken adipose tissue growth and development, and expedite the selection and breeding of broilers

Compliance of Ultra-Orthodox and secular pedestrians with traffic lights in Ultra-Orthodox and secular locations.

PubMed

Rosenbloom, Tova; Shahar, Amit; Perlman, Amotz

2008-11-01

Following a previous study that revealed the disobedience of Ultra-Orthodox citizens, as compared to secular citizens, of traffic lights at crosswalks, the present study examined the road habits of 995 Ultra-Orthodox and secular pedestrians in neighboring Ultra-Orthodox and secular cities. Using an observation grid designed specially for this study, the pedestrians were observed at two crosswalks--one in an Ultra-Orthodox city and one in a secular city--as far as similar traffic parameters, using a logistic regression. The tendency to cross on a red light was assessed as a function of estimated age, gender, religiosity, location (religious/secular), the duration of the red light, the number of vehicles crossing and the number of pedestrians waiting at the curb. Ultra-Orthodox pedestrians committed more violations than secular pedestrians did, and there were more road violations in the Ultra-Orthodox location than there were in the secular location. Fewer traffic violations were committed by "local" pedestrians (Ultra-Orthodox pedestrians in the Ultra-Orthodox location and secular pedestrians in the secular location) than by "foreigners" (Ultra-Orthodox pedestrians in the secular location and secular pedestrians in the Ultra-Orthodox location). The odds of crossing on a red light decreased as a function of both the number of people waiting at the curb and the number of vehicles. Consistent with previous research, males crossed on red much more than females did, regardless of religiosity and location. Our discussion focuses on theoretical and practical explanations of the findings.

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan

PubMed Central

Kinjo, Akira R.; Yamashita, Reiko; Nakamura, Haruki

2010-01-01

This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB. Database URL: http://www.pdbj.org/ PMID:20798081

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.

PubMed

Kinjo, Akira R; Yamashita, Reiko; Nakamura, Haruki

2010-08-25

This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB. Database URL: http://www.pdbj.org/

Ultra-long fiber Raman lasers: design considerations

NASA Astrophysics Data System (ADS)

Koltchanov, I.; Kroushkov, D. I.; Richter, A.

2015-03-01

In frame of the European Marie Currie project GRIFFON [http://astonishgriffon.net/] the usage of a green approach in terms of reduced power consumption and maintenance costs is envisioned for long-span fiber networks. This shall be accomplished by coherent transmission in unrepeatered links (100 km - 350 km) utilizing ultra-long Raman fiber laser (URFL)-based distributed amplification, multi-level modulation formats, and adapted Digital Signal Processing (DSP) algorithms. The URFL uses a cascaded 2-order pumping scheme where two (co- and counter-) ˜ 1365 nm pumps illuminate the fiber. The URFL oscillates at ˜ 1450 nm whereas amplification is provided by stimulated Raman scattering (SRS) of the ˜ 1365 nm pumps and the optical feedback is realized by two Fiber Bragg gratings (FBGs) at the fiber ends reflecting at 1450 nm. The light field at 1450 nm provides amplification for signal waves in the 1550 nm range due to SRS. In this work we present URFL design studies intended to characterize and optimize the power and noise characteristics of the fiber links. We use a bidirectional fiber model describing propagation of the signal, pump and noise powers along the fiber length. From the numerical solution we evaluate the on/off Raman gain and its bandwidth, the signal excursion over the fiber length, OSNR spectra, and the accumulated nonlinearities. To achieve best performance for these characteristics the laser design is optimized with respect to the forward/backward pump powers and wavelengths, input/output signal powers, reflectivity profile of the FBGs and other parameters.

3D visualization of molecular structures in the MOGADOC database

NASA Astrophysics Data System (ADS)

Vogt, Natalja; Popov, Evgeny; Rudert, Rainer; Kramer, Rüdiger; Vogt, Jürgen

2010-08-01

The MOGADOC database (Molecular Gas-Phase Documentation) is a powerful tool to retrieve information about compounds which have been studied in the gas-phase by electron diffraction, microwave spectroscopy and molecular radio astronomy. Presently the database contains over 34,500 bibliographic references (from the beginning of each method) for about 10,000 inorganic, organic and organometallic compounds and structural data (bond lengths, bond angles, dihedral angles, etc.) for about 7800 compounds. Most of the implemented molecular structures are given in a three-dimensional (3D) presentation. To create or edit and visualize the 3D images of molecules, new tools (special editor and Java-based 3D applet) were developed. Molecular structures in internal coordinates were converted to those in Cartesian coordinates.

Crystallography Open Database – an open-access collection of crystal structures

PubMed Central

Gražulis, Saulius; Chateigner, Daniel; Downs, Robert T.; Yokochi, A. F. T.; Quirós, Miguel; Lutterotti, Luca; Manakova, Elena; Butkus, Justas; Moeck, Peter; Le Bail, Armel

2009-01-01

The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality. PMID:22477773

PASS2: an automated database of protein alignments organised as structural superfamilies.

PubMed

Bhaduri, Anirban; Pugalenthi, Ganesan; Sowdhamini, Ramanathan

2004-04-02

The functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The Protein Alignment organised as Structural Superfamily (PASS2) database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. An automated and updated version of PASS2 is, in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains have been grouped into 628 multi-member superfamilies and 566 single member superfamilies. Structure-based sequence alignments for the superfamilies have been obtained using COMPARER, while initial equivalencies have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aid annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 presents the phylogeny of its members both based on sequence and structural dissimilarities. Clustering of members allows us to understand diversification of the family members. The search engine has been

Visualization and manipulating the image of a formal data structure (FDS)-based database

NASA Astrophysics Data System (ADS)

Verdiesen, Franc; de Hoop, Sylvia; Molenaar, Martien

1994-08-01

A vector map is a terrain representation with a vector-structured geometry. Molenaar formulated an object-oriented formal data structure for 3D single valued vector maps. This FDS is implemented in a database (Oracle). In this study we describe a methodology for visualizing a FDS-based database and manipulating the image. A data set retrieved by querying the database is converted into an import file for a drawing application. An objective of this study is that an end-user can alter and add terrain objects in the image. The drawing application creates an export file, that is compared with the import file. Differences between these files result in updating the database which involves checks on consistency. In this study Autocad is used for visualizing and manipulating the image of the data set. A computer program has been written for the data exchange and conversion between Oracle and Autocad. The data structure of the FDS is compared to the data structure of Autocad and the data of the FDS is converted into the structure of Autocad equal to the FDS.

Naval Ship Database: Database Design, Implementation, and Schema

DTIC Science & Technology

2013-09-01

incoming data. The solution allows database users to store and analyze data collected by navy ships in the Royal Canadian Navy ( RCN ). The data...understanding RCN jargon and common practices on a typical RCN vessel. This experience led to the development of several error detection methods to...data to be stored in the database. Mr. Massel has also collected data pertaining to day to day activities on RCN vessels that has been imported into

PACSY, a relational database management system for protein structure and chemical shift analysis.

PubMed

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

PACSY, a relational database management system for protein structure and chemical shift analysis

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

Experimental Tests of UltraFlex Array Designs in Low Earth Orbital and Geosynchronous Charging Environments

NASA Technical Reports Server (NTRS)

Galofaro, Joel T.; Vayner, Boris V.; Hillard, Grover B.

2011-01-01

The present ground based investigations give the first definitive look describing the expected on-orbit charging behavior of Orion UltraFlex array coupons in the Low Earth Orbital and Geosynchronous Environments. Furthermore, it is important to note that the LEO charging environment also applies to the International Space Station as well as to the lunar mission charging environments. The GEO charging environment includes the bounding case for all lunar orbital and lunar surface mission environments. The UltraFlex thin film photovoltaic array technology has been targeted to become the sole power system for life support and on-orbit power for the manned Aires Crew Exploration Vehicle. It is therefore, crucial to gain an understanding of the complex charging behavior to answer some of the basic performance and survivability issues in an attempt to ascertain that a single UltraFlex array design will be able to cope with the projected worst case LEO and GEO charging environments. Testing was limited to four array coupons, two coupons each from two different array manufactures, Emcore and Spectrolab. The layout of each array design is identical and varies only in the actual cell technology used. The individual array cells from each manufacturer have an antireflection layered coating and come in two different varieties either uncoated (only AR coating) or coated with a thin conducting ITO layer. The LEO Plasma tests revealed that all four coupons passed the arc threshold -120 V bias tests. GEO electron gun charging tests revealed that only front side area of ITO coated coupons passed tests. Only the Emcore AR array passed backside Stage 2 GEO Tests.

Gene composer: database software for protein construct design, codon engineering, and gene synthesis.

PubMed

Lorimer, Don; Raymond, Amy; Walchli, John; Mixon, Mark; Barrow, Adrienne; Wallace, Ellen; Grice, Rena; Burgin, Alex; Stewart, Lance

2009-04-21

To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease

Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

PubMed Central

Lorimer, Don; Raymond, Amy; Walchli, John; Mixon, Mark; Barrow, Adrienne; Wallace, Ellen; Grice, Rena; Burgin, Alex; Stewart, Lance

2009-01-01

Background To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. Results An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. Conclusion We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis

Retraction Note to: Ultra-High Strength and Ductile Lamellar-Structured Powder Metallurgy Binary Ti-Ta Alloys

NASA Astrophysics Data System (ADS)

Liu, Yong; Xu, Shenghang; Wang, Xin; Li, Kaiyang; Liu, Bin; Wu, Hong; Tang, Huiping

2018-05-01

The editors and authors have retracted the article, "Ultra-High Strength and Ductile Lamellar-Structured Powder Metallurgy Binary Ti-Ta Alloys" by Yong Liu, Shenghang Xu, Xin Wang, Kaiyang Li, Bin Liu, Hong Wu, and Huiping Tang (https://doi.org/10.1007/s11837-015-1801-1).

Ontology-based coupled optimisation design method using state-space analysis for the spindle box system of large ultra-precision optical grinding machine

NASA Astrophysics Data System (ADS)

Wang, Qianren; Chen, Xing; Yin, Yuehong; Lu, Jian

2017-08-01

With the increasing complexity of mechatronic products, traditional empirical or step-by-step design methods are facing great challenges with various factors and different stages having become inevitably coupled during the design process. Management of massive information or big data, as well as the efficient operation of information flow, is deeply involved in the process of coupled design. Designers have to address increased sophisticated situations when coupled optimisation is also engaged. Aiming at overcoming these difficulties involved in conducting the design of the spindle box system of ultra-precision optical grinding machine, this paper proposed a coupled optimisation design method based on state-space analysis, with the design knowledge represented by ontologies and their semantic networks. An electromechanical coupled model integrating mechanical structure, control system and driving system of the motor is established, mainly concerning the stiffness matrix of hydrostatic bearings, ball screw nut and rolling guide sliders. The effectiveness and precision of the method are validated by the simulation results of the natural frequency and deformation of the spindle box when applying an impact force to the grinding wheel.

Distributed structure-searchable toxicity (DSSTox) public database network: a proposal.

PubMed

Richard, Ann M; Williams, ClarLynda R

2002-01-29

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, Structure-Activity Relationship (SAR) model development, or building of chemical relational databases (CRD). The distributed structure-searchable toxicity (DSSTox) public database network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: (1) to adopt and encourage the use of a common standard file format (structure data file (SDF)) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; (2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data sources with potential users of these data from other disciplines (such as chemistry, modeling, and computer science); and (3) to engage public/commercial/academic/industry groups in contributing to and expanding this community-wide, public data sharing and distribution effort. The DSSTox project's overall aims are to effect the closer association of chemical structure information with existing toxicity data, and to promote and facilitate structure

TOPSAN: a dynamic web database for structural genomics.

PubMed

Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John

2011-01-01

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.

SwePep, a database designed for endogenous peptides and mass spectrometry.

PubMed

Fälth, Maria; Sköld, Karl; Norrman, Mathias; Svensson, Marcus; Fenyö, David; Andren, Per E

2006-06-01

A new database, SwePep, specifically designed for endogenous peptides, has been constructed to significantly speed up the identification process from complex tissue samples utilizing mass spectrometry. In the identification process the experimental peptide masses are compared with the peptide masses stored in the database both with and without possible post-translational modifications. This intermediate identification step is fast and singles out peptides that are potential endogenous peptides and can later be confirmed with tandem mass spectrometry data. Successful applications of this methodology are presented. The SwePep database is a relational database developed using MySql and Java. The database contains 4180 annotated endogenous peptides from different tissues originating from 394 different species as well as 50 novel peptides from brain tissue identified in our laboratory. Information about the peptides, including mass, isoelectric point, sequence, and precursor protein, is also stored in the database. This new approach holds great potential for removing the bottleneck that occurs during the identification process in the field of peptidomics. The SwePep database is available to the public.

Preliminary Analysis of the 30-m UltraBoom Flight Test

NASA Technical Reports Server (NTRS)

Agnes, Gregory S.; Abelson, Robert D.; Miyake, Robert; Lin, John K. H.; Welsh, Joe; Watson, Judith J.

2005-01-01

Future NASA missions require long, ultra-lightweight booms to enable solar sails, large sunshields, and other gossamer-type spacecraft structures. The space experiment discussed in this paper will flight validate the non-traditional ultra lightweight rigidizable, inflatable, isogrid structure utilizing graphite shape memory polymer (GR/SMP) called UltraBoom(TradeMark). The focus of this paper is the analysis of the 3-m ground test article. The primary objective of the mission is to show that a combination of ground testing and analysis can predict the on-orbit performance of an ultra lightweight boom that is scalable, predictable, and thermomechanically stable.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE Office of Scientific and Technical Information (OSTI.GOV)

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE PAGES

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the

High-efficiency, broad-band and wide-angle optical absorption in ultra-thin organic photovoltaic devices.

PubMed

Wang, Wenyan; Hao, Yuying; Cui, Yanxia; Tian, Ximin; Zhang, Ye; Wang, Hua; Shi, Fang; Wei, Bin; Huang, Wei

2014-03-10

Metal nanogratings as one of the promising architectures for effective light trapping in organic photovoltaics (OPVs) have been actively studied over the past decade. Here we designed a novel metal nanowall grating with ultra-small period and ultra-high aspect-ratio as the back electrode of the OPV device. Such grating results in the strong hot spot effect in-between the neighboring nanowalls and the localized surface plasmon effect at the corners of nanowalls. These combined effects make the integrated absorption efficiency of light over the wavelength range from 400 to 650 nm in the active layer for the proposed structure, with respect to the equivalent planar structure, increases by 102% at TM polarization and by 36.5% at the TM/TE hybrid polarization, respectively. Moreover, it is noted that the hot spot effect in the proposed structure is more effective for ultra-thin active layers, which is very favorable for the exciton dissociation and charge collection. Therefore such a nanowall grating is expected to improve the overall performance of OPV devices.

Designing Semiconductor Heterostructures Using Digitally Accessible Electronic-Structure Data

NASA Astrophysics Data System (ADS)

Shapera, Ethan; Schleife, Andre

Semiconductor sandwich structures, so-called heterojunctions, are at the heart of modern applications with tremendous societal impact: Light-emitting diodes shape the future of lighting and solar cells are promising for renewable energy. However, their computer-based design is hampered by the high cost of electronic structure techniques used to select materials based on alignment of valence and conduction bands and to evaluate excited state properties. We describe, validate, and demonstrate an open source Python framework which rapidly screens existing online databases and user-provided data to find combinations of suitable, previously fabricated materials for optoelectronic applications. The branch point energy aligns valence and conduction bands of different materials, requiring only the bulk density functional theory band structure. We train machine learning algorithms to predict the dielectric constant, electron mobility, and hole mobility with material descriptors available in online databases. Using CdSe and InP as emitting layers for LEDs and CH3NH3PbI3 and nanoparticle PbS as absorbers for solar cells, we demonstrate our broadly applicable, automated method.

Retinal Structure of Birds of Prey Revealed by Ultra-High Resolution Spectral-Domain Optical Coherence Tomography

PubMed Central

Ruggeri, Marco; Major, James C.; McKeown, Craig; Knighton, Robert W.; Puliafito, Carmen A.

2010-01-01

Purpose. To reveal three-dimensional (3-D) information about the retinal structures of birds of prey in vivo. Methods. An ultra-high resolution spectral-domain optical coherence tomography (SD-OCT) system was built for in vivo imaging of retinas of birds of prey. The calibrated imaging depth and axial resolution of the system were 3.1 mm and 2.8 μm (in tissue), respectively. 3-D segmentation was performed for calculation of the retinal nerve fiber layer (RNFL) map. Results. High-resolution OCT images were obtained of the retinas of four species of birds of prey: two diurnal hawks (Buteo platypterus and Buteo brachyurus) and two nocturnal owls (Bubo virginianus and Strix varia). These images showed the detailed retinal anatomy, including the retinal layers and the structure of the deep and shallow foveae. The calculated thickness map showed the RNFL distribution. Traumatic injury to one bird's retina was also successfully imaged. Conclusions. Ultra-high resolution SD-OCT provides unprecedented high-quality 2-D and 3-D in vivo visualization of the retinal structures of birds of prey. SD-OCT is a powerful imaging tool for vision research in birds of prey. PMID:20554605

Ultra High Bypass Integrated System Test

NASA Image and Video Library

2015-09-14

NASA’s Environmentally Responsible Aviation Project, in collaboration with the Federal Aviation Administration (FAA) and Pratt & Whitney, completed testing of an Ultra High Bypass Ratio Turbofan Model in the 9’ x 15’ Low Speed Wind Tunnel at NASA Glenn Research Center. The fan model is representative of the next generation of efficient and quiet Ultra High Bypass Ratio Turbofan Engine designs.

An ultra-low-power filtering technique for biomedical applications.

PubMed

Zhang, Tan-Tan; Mak, Pui-In; Vai, Mang-I; Mak, Peng-Un; Wan, Feng; Martins, R P

2011-01-01

This paper describes an ultra-low-power filtering technique for biomedical applications designated as T-wave sensing in heart-activities detection systems. The topology is based on a source-follower-based Biquad operating in the sub-threshold region. With the intrinsic advantages of simplicity and high linearity of the source-follower, ultra-low-cutoff filtering can be achieved, simultaneously with ultra low power and good linearity. An 8(th)-order 2.4-Hz lowpass filter design example optimized in a 0.35-μm CMOS process was designed achieving over 85-dB dynamic range, 74-dB stopband attenuation and consuming only 0.36 nW at a 3-V supply.

Profiling modifications for glioblastoma proteome using ultra-tolerant database search: Are the peptide mass shifts biologically relevant or chemically induced?

PubMed

Tarasova, Irina A; Chumakov, Peter M; Moshkovskii, Sergei A; Gorshkov, Mikhail V

2018-05-17

Peptide mass shifts were profiled using ultra-tolerant database search strategy for shotgun proteomics data sets of human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The main objective of this profiling was revealing the cell response to IFN treatment at the level of protein modifications. To achieve this objective, statistically significant changes in peptide mass shift profiles between IFN treated and untreated glioblastoma samples were analyzed. Detailed analysis of MS/MS spectra allowed further interpretation of the observed mass shifts and differentiation between post-translational and artifact modifications. Malignant cells typically acquire increased sensitivity to viruses due to the deregulated antiviral mechanisms. Therefore, a viral therapy is considered as one of the promising approaches to treat cancer. However, recent studies have demonstrated that malignant cells can preserve intact antiviral mechanisms, e.g. interferon signaling, and develop resistance to virus infection in response to interferon treatment. Post translational modifications, e.g. tyrosine phosphorylation, are the interferon signaling drivers. Thus, comprehensive characterization of modifications is crucially important, yet, most challenging problem in cancer proteomics. Here, we report on the application of the recently introduced ultra-tolerant search strategy for profiling peptide modifications in the human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The specific aim of the study was identification of statistically significant changes in peptide mass shift profiles between IFN treated and untreated glioblastoma samples, as well as determination of whether these shifts represent the biologically relevant modification. Copyright © 2018 Elsevier B.V. All rights reserved.

Use of Software Tools in Teaching Relational Database Design.

ERIC Educational Resources Information Center

McIntyre, D. R.; And Others

1995-01-01

Discusses the use of state-of-the-art software tools in teaching a graduate, advanced, relational database design course. Results indicated a positive student response to the prototype of expert systems software and a willingness to utilize this new technology both in their studies and in future work applications. (JKP)

A Database Design and Development Case: Home Theater Video

ERIC Educational Resources Information Center

Ballenger, Robert; Pratt, Renee

2012-01-01

This case consists of a business scenario of a small video rental store, Home Theater Video, which provides background information, a description of the functional business requirements, and sample data. The case provides sufficient information to design and develop a moderately complex database to assist Home Theater Video in solving their…

Current Modulation of a Heterojunction Structure by an Ultra-Thin Graphene Base Electrode.

PubMed

Alvarado Chavarin, Carlos; Strobel, Carsten; Kitzmann, Julia; Di Bartolomeo, Antonio; Lukosius, Mindaugas; Albert, Matthias; Bartha, Johann Wolfgang; Wenger, Christian

2018-02-27

Graphene has been proposed as the current controlling element of vertical transport in heterojunction transistors, as it could potentially achieve high operation frequencies due to its metallic character and 2D nature. Simulations of graphene acting as a thermionic barrier between the transport of two semiconductor layers have shown cut-off frequencies larger than 1 THz. Furthermore, the use of n-doped amorphous silicon, (n)-a-Si:H, as the semiconductor for this approach could enable flexible electronics with high cutoff frequencies. In this work, we fabricated a vertical structure on a rigid substrate where graphene is embedded between two differently doped (n)-a-Si:H layers deposited by very high frequency (140 MHz) plasma-enhanced chemical vapor deposition. The operation of this heterojunction structure is investigated by the two diode-like interfaces by means of temperature dependent current-voltage characterization, followed by the electrical characterization in a three-terminal configuration. We demonstrate that the vertical current between the (n)-a-Si:H layers is successfully controlled by the ultra-thin graphene base voltage. While current saturation is yet to be achieved, a transconductance of ~230 μ S was obtained, demonstrating a moderate modulation of the collector-emitter current by the ultra-thin graphene base voltage. These results show promising progress towards the application of graphene base heterojunction transistors.

Designing for Peta-Scale in the LSST Database

NASA Astrophysics Data System (ADS)

Kantor, J.; Axelrod, T.; Becla, J.; Cook, K.; Nikolaev, S.; Gray, J.; Plante, R.; Nieto-Santisteban, M.; Szalay, A.; Thakar, A.

2007-10-01

The Large Synoptic Survey Telescope (LSST), a proposed ground-based 8.4 m telescope with a 10 deg^2 field of view, will generate 15 TB of raw images every observing night. When calibration and processed data are added, the image archive, catalogs, and meta-data will grow 15 PB yr^{-1} on average. The LSST Data Management System (DMS) must capture, process, store, index, replicate, and provide open access to this data. Alerts must be triggered within 30 s of data acquisition. To do this in real-time at these data volumes will require advances in data management, database, and file system techniques. This paper describes the design of the LSST DMS and emphasizes features for peta-scale data. The LSST DMS will employ a combination of distributed database and file systems, with schema, partitioning, and indexing oriented for parallel operations. Image files are stored in a distributed file system with references to, and meta-data from, each file stored in the databases. The schema design supports pipeline processing, rapid ingest, and efficient query. Vertical partitioning reduces disk input/output requirements, horizontal partitioning allows parallel data access using arrays of servers and disks. Indexing is extensive, utilizing both conventional RAM-resident indexes and column-narrow, row-deep tag tables/covering indices that are extracted from tables that contain many more attributes. The DMS Data Access Framework is encapsulated in a middleware framework to provide a uniform service interface to all framework capabilities. This framework will provide the automated work-flow, replication, and data analysis capabilities necessary to make data processing and data quality analysis feasible at this scale.

CamMedNP: building the Cameroonian 3D structural natural products database for virtual screening.

PubMed

Ntie-Kang, Fidele; Mbah, James A; Mbaze, Luc Meva'a; Lifongo, Lydia L; Scharfe, Michael; Hanna, Joelle Ngo; Cho-Ngwa, Fidelis; Onguéné, Pascal Amoa; Owono Owono, Luc C; Megnassan, Eugene; Sippl, Wolfgang; Efange, Simon M N

2013-04-16

Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We present CamMedNP - a new database beginning with more than 2,500 compounds of natural origin, along with some of their derivatives which were obtained through hemisynthesis. These are pure compounds which have been previously isolated and characterized using modern spectroscopic methods and published by several research teams spread across Cameroon. In the present study, 224 distinct medicinal plant species belonging to 55 plant families from the Cameroonian flora have been considered. About 80 % of these have been previously published and/or referenced in internationally recognized journals. For each compound, the optimized 3D structure, drug-like properties, plant source, collection site and currently known biological activities are given, as well as literature references. We have evaluated the "drug-likeness" of this database using Lipinski's "Rule of Five". A diversity analysis has been carried out in comparison with the ChemBridge diverse database. CamMedNP could be highly useful for database screening and natural product lead generation programs.

The method of abstraction in the design of databases and the interoperability

NASA Astrophysics Data System (ADS)

Yakovlev, Nikolay

2018-03-01

When designing the database structure oriented to the contents of indicators presented in the documents and communications subject area. First, the method of abstraction is applied by expansion of the indices of new, artificially constructed abstract concepts. The use of abstract concepts allows to avoid registration of relations many-to-many. For this reason, when built using abstract concepts, demonstrate greater stability in the processes. The example abstract concepts to address structure - a unique house number. Second, the method of abstraction can be used in the transformation of concepts by omitting some attributes that are unnecessary for solving certain classes of problems. Data processing associated with the amended concepts is more simple without losing the possibility of solving the considered classes of problems. For example, the concept "street" loses the binding to the land. The content of the modified concept of "street" are only the relations of the houses to the declared name. For most accounting tasks and ensure communication is enough.

Ultra-large nonlinear parameter in graphene-silicon waveguide structures.

PubMed

Donnelly, Christine; Tan, Dawn T H

2014-09-22

Mono-layer graphene integrated with optical waveguides is studied for the purpose of maximizing E-field interaction with the graphene layer, for the generation of ultra-large nonlinear parameters. It is shown that the common approach used to minimize the waveguide effective modal area does not accurately predict the configuration with the maximum nonlinear parameter. Both photonic and plasmonic waveguide configurations and graphene integration techniques realizable with today's fabrication tools are studied. Importantly, nonlinear parameters exceeding 10(4) W(-1)/m, two orders of magnitude larger than that in silicon on insulator waveguides without graphene, are obtained for the quasi-TE mode in silicon waveguides incorporating mono-layer graphene in the evanescent part of the optical field. Dielectric loaded surface plasmon polariton waveguides incorporating mono-layer graphene are observed to generate nonlinear parameters as large as 10(5) W(-1)/m, three orders of magnitude larger than that in silicon on insulator waveguides without graphene. The ultra-large nonlinear parameters make such waveguides promising platforms for nonlinear integrated optics at ultra-low powers, and for previously unobserved nonlinear optical effects to be studied in a waveguide platform.

Agricultural Conservation Planning Framework: 3. Land Use and Field Boundary Database Development and Structure.

PubMed

Tomer, Mark D; James, David E; Sandoval-Green, Claudette M J

2017-05-01

Conservation planning information is important for identifying options for watershed water quality improvement and can be developed for use at field, farm, and watershed scales. Translation across scales is a key issue impeding progress at watershed scales because watershed improvement goals must be connected with implementation of farm- and field-level conservation practices to demonstrate success. This is particularly true when examining alternatives for "trap and treat" practices implemented at agricultural-field edges to control (or influence) water flows through fields, landscapes, and riparian corridors within agricultural watersheds. We propose that database structures used in developing conservation planning information can achieve translation across conservation-planning scales, and we developed the Agricultural Conservation Planning Framework (ACPF) to enable practical planning applications. The ACPF comprises a planning concept, a database to facilitate field-level and watershed-scale analyses, and an ArcGIS toolbox with Python scripts to identify specific options for placement of conservation practices. This paper appends two prior publications and describes the structure of the ACPF database, which contains land use, crop history, and soils information and is available for download for 6091 HUC12 watersheds located across Iowa, Illinois, Minnesota, and parts of Kansas, Missouri, Nebraska, and Wisconsin and comprises information on 2.74 × 10 agricultural fields (available through /). Sample results examining land use trends across Iowa and Illinois are presented here to demonstrate potential uses of the database. While designed for use with the ACPF toolbox, users are welcome to use the ACPF watershed data in a variety of planning and modeling approaches. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Practical controller design for ultra-precision positioning of stages with a pneumatic artificial muscle actuator

NASA Astrophysics Data System (ADS)

Tang, T. F.; Chong, S. H.

2017-06-01

This paper presents a practical controller design method for ultra-precision positioning of pneumatic artificial muscle actuator stages. Pneumatic artificial muscle (PAM) actuators are safe to use and have numerous advantages which have brought these actuators to wide applications. However, PAM exhibits strong non-linear characteristics, and these limitations lead to low controllability and limit its application. In practice, the non-linear characteristics of PAM mechanism are difficult to be precisely modeled, and time consuming to model them accurately. The purpose of the present study is to clarify a practical controller design method that emphasizes a simple design procedure that does not acquire plants parameters modeling, and yet is able to demonstrate ultra-precision positioning performance for a PAM driven stage. The practical control approach adopts continuous motion nominal characteristic trajectory following (CM NCTF) control as the feedback controller. The constructed PAM driven stage is in low damping characteristic and causes severe residual vibration that deteriorates motion accuracy of the system. Therefore, the idea to increase the damping characteristic by having an acceleration feedback compensation to the plant has been proposed. The effectiveness of the proposed controller was verified experimentally and compared with a classical PI controller in point-to-point motion. The experiment results proved that the CM NCTF controller demonstrates better positioning performance in smaller motion error than the PI controller. Overall, the CM NCTF controller has successfully to reduce motion error to 3µm, which is 88.7% smaller than the PI controller.

Ultra-Slow Dielectric Relaxation Process in Polyols

NASA Astrophysics Data System (ADS)

Yomogida, Yoshiki; Minoguchi, Ayumi; Nozaki, Ryusuke

2004-04-01

Dielectric relaxation processes with relaxation times larger than that for the structural α process are reported for glycerol, xylitol, sorbitol and their mixtures for the first time. Appearance of this ultra-slow process depends on cooling rate. More rapid cooling gives larger dielectric relaxation strength. However, relaxation time is not affected by cooling rate and shows non-Arrhenius temperature dependence with correlation to the α process. It can be considered that non-equilibrium dynamic structure causes the ultra-slow process. Scale of such structure would be much larger than that of the region for the cooperative molecular orientations for the α process.

The HITRAN 2008 Molecular Spectroscopic Database

NASA Technical Reports Server (NTRS)

Rothman, Laurence S.; Gordon, Iouli E.; Barbe, Alain; Benner, D. Chris; Bernath, Peter F.; Birk, Manfred; Boudon, V.; Brown, Linda R.; Campargue, Alain; Champion, J.-P.;

Ultra-small and broadband polarization splitters based on double-slit interference

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Chengwei; Li, Hongyun; Gong, Qihuang

2016-03-07

An ultra-small and broadband polarization splitter is numerically and experimentally demonstrated based on the double-slit interference in a polymer-film-coated double-slit structure. The hybrid slab waveguide (air-polymer-Au) supports both the transverse-magnetic and transverse-electric modes. The incident beam from the back side can excite these two guided modes of orthogonally polarized states in the hybrid structure. By exploiting the difference slit widths and the large mode birefringence, these two guided modes propagate to the opposite directions along the front metal surface. Moreover, the short interference length broadens the operation bandwidth. Experimentally, a polarization splitter with a lateral dimension of only about 1.6 μmmore » and an operation bandwidth of 50 nm is realized. By designing the double-slit structure in a hybrid strip waveguide, the device dimension can be significant downscaled to about 0.3 × 1.3 μm{sup 2}. Such an ultra-small and broadband polarization splitter may find important applications in the integrated photonic circuits.« less

Wide-Field-of-View Millimeter-Wave Telescope Design with Ultra-Low Cross-Polarization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernacki, Bruce E.; Kelly, James F.; Sheen, David M.

2012-05-01

As millimeter-wave arrays become available, off-axis imaging performance of the fore optics increases in importance due to the relatively large physical extent of the arrays. Typically, simple optical telescope designs are adapted to millimeter-wave imaging but single-mirror spherical or classic conic designs cannot deliver adequate image quality except near the optical axis. Since most millimeter-wave designs are quasi-optical, optical ray tracing and commercial design software can be used to optimize designs to improve off-axis imaging as well as minimize cross-polarization. Methods that obey the Dragone-Mizuguchi condition for the design of reflective millimeter-wave telescopes with low cross-polarization also provide additional degreesmore » of freedom that offer larger fields of view than possible with single-reflector designs. Dragone’s graphical design method does not lend itself readily to computer-based optical design approaches, but subsequent authors expanded on Dragone’s geometric design approach with analytic expressions that describe the location, shape, off-axis height and tilt of the telescope elements that satisfy Dragone’s design rules and can be used as a first-order design for subsequent computer-based design and optimization. We investigate two design variants that obey the Dragone-Mizuguchi conditions that exhibit ultra-low polarization crosstalk and a large diffraction-limited field of view well suited to millimeter-wave imaging arrays.« less

Wide-field-of-view millimeter-wave telescope design with ultra-low cross-polarization

NASA Astrophysics Data System (ADS)

Bernacki, Bruce E.; Kelly, James F.; Sheen, David; Hatchell, Brian; Valdez, Patrick; Tedeschi, Jonathan; Hall, Thomas; McMakin, Douglas

2012-06-01

As millimeter-wave arrays become available, off-axis imaging performance of the fore optics increases in importance due to the relatively large physical extent of the arrays. Typically, simple optical telescope designs are adapted to millimeter-wave imaging but single-mirror spherical or classic conic designs cannot deliver adequate image quality except near the optical axis. Since millimeter-wave designs are quasi-optical, optical ray tracing and commercial design software can be used to optimize designs to improve off-axis imaging as well as minimize cross-polarization. Methods that obey the Dragone-Mizuguchi condition for the design of reflective millimeter-wave telescopes with low cross-polarization also provide additional degrees of freedom that offer larger fields of view than possible with single-reflector designs. Dragone's graphical design method does not lend itself readily to computer-based optical design approaches, but subsequent authors expanded on Dragone's geometric design approach with analytic expressions that describe the location, shape, off-axis height and tilt of the telescope elements that satisfy Dragone's design rules and can be used as a first-order design for subsequent computer-based design and optimization. We investigate two design variants that obey the Dragone-Mizuguchi conditions that exhibit ultra-low cross-polarization and a large diffraction-limited field of view well suited to millimeter-wave imaging arrays.

Feasibility demonstration for electroplating ultra-thin polyimide film. [fabricating film for space erectable structures

NASA Technical Reports Server (NTRS)

Schneier, R.; Braswell, T. V.; Vaughn, R. W.

1978-01-01

The effect of electrodeposition variables on film thickness was investigated using a dilute polyimide solution as a bath into which aluminum (as foil or as a vapor deposited coating) was immersed. The electrodeposited film was dried for 2 hours at 93 C (primarily to remove solvent) and cured for 18 hours at 186 C. Infrared studies indicate that imide formation (curing) occurs at 149 C under vacuum. From a conceptual viewpoint, satisfactory film metallized on one side can be obtained by this method. The cured ultra thin polyimide film exhibits properties equivalent to those of commercial film, and the surface appearance of the strippable polyimide film compares favorably with that of a sample of commercial film of thicker gauge. The feasibility of manufacturing approximately one million sq m of ultra thin film capable of being joined to fabricate an 800 m by 9 800 m square from starting material 0.5 to 1 m wide for space erectable structures was demonstrated.

Applications of GIS and database technologies to manage a Karst Feature Database

USGS Publications Warehouse

Gao, Y.; Tipping, R.G.; Alexander, E.C.

2006-01-01

This paper describes the management of a Karst Feature Database (KFD) in Minnesota. Two sets of applications in both GIS and Database Management System (DBMS) have been developed for the KFD of Minnesota. These applications were used to manage and to enhance the usability of the KFD. Structured Query Language (SQL) was used to manipulate transactions of the database and to facilitate the functionality of the user interfaces. The Database Administrator (DBA) authorized users with different access permissions to enhance the security of the database. Database consistency and recovery are accomplished by creating data logs and maintaining backups on a regular basis. The working database provides guidelines and management tools for future studies of karst features in Minnesota. The methodology of designing this DBMS is applicable to develop GIS-based databases to analyze and manage geomorphic and hydrologic datasets at both regional and local scales. The short-term goal of this research is to develop a regional KFD for the Upper Mississippi Valley Karst and the long-term goal is to expand this database to manage and study karst features at national and global scales.

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures.

PubMed

Khan, Javed Mohammed; Cheruku, Harish Reddy; Tong, Joo Chuan; Ranganathan, Shoba

2011-04-15

Sequence-structure-function information is critical in understanding the mechanism of pMHC and TR/pMHC binding and recognition. A database for sequence-structure-function information on pMHC and TR/pMHC interactions, MHC-Peptide Interaction Database-TR version 2 (MPID-T2), is now available augmented with the latest PDB and IMGT/3Dstructure-DB data, advanced features and new parameters for the analysis of pMHC and TR/pMHC structures. http://biolinfo.org/mpid-t2. shoba.ranganathan@mq.edu.au Supplementary data are available at Bioinformatics online.

Data model and relational database design for the New England Water-Use Data System (NEWUDS)

USGS Publications Warehouse

Tessler, Steven

2001-01-01

The New England Water-Use Data System (NEWUDS) is a database for the storage and retrieval of water-use data. NEWUDS can handle data covering many facets of water use, including (1) tracking various types of water-use activities (withdrawals, returns, transfers, distributions, consumptive-use, wastewater collection, and treatment); (2) the description, classification and location of places and organizations involved in water-use activities; (3) details about measured or estimated volumes of water associated with water-use activities; and (4) information about data sources and water resources associated with water use. In NEWUDS, each water transaction occurs unidirectionally between two site objects, and the sites and conveyances form a water network. The core entities in the NEWUDS model are site, conveyance, transaction/rate, location, and owner. Other important entities include water resources (used for withdrawals and returns), data sources, and aliases. Multiple water-exchange estimates can be stored for individual transactions based on different methods or data sources. Storage of user-defined details is accommodated for several of the main entities. Numerous tables containing classification terms facilitate detailed descriptions of data items and can be used for routine or custom data summarization. NEWUDS handles single-user and aggregate-user water-use data, can be used for large or small water-network projects, and is available as a stand-alone Microsoft? Access database structure. Users can customize and extend the database, link it to other databases, or implement the design in other relational database applications.

TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants.

PubMed

Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

2014-01-01

The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure-activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein-ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. © The Author(s) 2014. Published by Oxford University Press.

Data model and relational database design for the New Jersey Water-Transfer Data System (NJWaTr)

USGS Publications Warehouse

Tessler, Steven

2003-01-01

The New Jersey Water-Transfer Data System (NJWaTr) is a database design for the storage and retrieval of water-use data. NJWaTr can manage data encompassing many facets of water use, including (1) the tracking of various types of water-use activities (withdrawals, returns, transfers, distributions, consumptive-use, wastewater collection, and treatment); (2) the storage of descriptions, classifications and locations of places and organizations involved in water-use activities; (3) the storage of details about measured or estimated volumes of water associated with water-use activities; and (4) the storage of information about data sources and water resources associated with water use. In NJWaTr, each water transfer occurs unidirectionally between two site objects, and the sites and conveyances form a water network. The core entities in the NJWaTr model are site, conveyance, transfer/volume, location, and owner. Other important entities include water resource (used for withdrawals and returns), data source, permit, and alias. Multiple water-exchange estimates based on different methods or data sources can be stored for individual transfers. Storage of user-defined details is accommodated for several of the main entities. Many tables contain classification terms to facilitate the detailed description of data items and can be used for routine or custom data summarization. NJWaTr accommodates single-user and aggregate-user water-use data, can be used for large or small water-network projects, and is available as a stand-alone Microsoft? Access database. Data stored in the NJWaTr structure can be retrieved in user-defined combinations to serve visualization and analytical applications. Users can customize and extend the database, link it to other databases, or implement the design in other relational database applications.

Design Strategies for Ultra-high Efficiency Photovoltaics

NASA Astrophysics Data System (ADS)

Warmann, Emily Cathryn

While concentrator photovoltaic cells have shown significant improvements in efficiency in the past ten years, once these cells are integrated into concentrating optics, connected to a power conditioning system and deployed in the field, the overall module efficiency drops to only 34 to 36%. This efficiency is impressive compared to conventional flat plate modules, but it is far short of the theoretical limits for solar energy conversion. Designing a system capable of achieving ultra high efficiency of 50% or greater cannot be achieved by refinement and iteration of current design approaches. This thesis takes a systems approach to designing a photovoltaic system capable of 50% efficient performance using conventional diode-based solar cells. The effort began with an exploration of the limiting efficiency of spectrum splitting ensembles with 2 to 20 sub cells in different electrical configurations. Incorporating realistic non-ideal performance with the computationally simple detailed balance approach resulted in practical limits that are useful to identify specific cell performance requirements. This effort quantified the relative benefit of additional cells and concentration for system efficiency, which will help in designing practical optical systems. Efforts to improve the quality of the solar cells themselves focused on the development of tunable lattice constant epitaxial templates. Initially intended to enable lattice matched multijunction solar cells, these templates would enable increased flexibility in band gap selection for spectrum splitting ensembles and enhanced radiative quality relative to metamorphic growth. The III-V material family is commonly used for multijunction solar cells both for its high radiative quality and for the ease of integrating multiple band gaps into one monolithic growth. The band gap flexibility is limited by the lattice constant of available growth templates. The virtual substrate consists of a thin III-V film with the desired

Critical Needs for Robust and Reliable Database for Design and Manufacturing of Ceramic Matrix Composites

NASA Technical Reports Server (NTRS)

Singh, M.

1999-01-01

Ceramic matrix composite (CMC) components are being designed, fabricated, and tested for a number of high temperature, high performance applications in aerospace and ground based systems. The critical need for and the role of reliable and robust databases for the design and manufacturing of ceramic matrix composites are presented. A number of issues related to engineering design, manufacturing technologies, joining, and attachment technologies, are also discussed. Examples of various ongoing activities in the area of composite databases. designing to codes and standards, and design for manufacturing are given.

Design of an ultra-thin absorption layer with magnetic materials based on genetic algorithm at the S band

NASA Astrophysics Data System (ADS)

Wang, Fang; Yang, Xiaoning; Liu, Xiaoning; Niu, Tiaoming; Wang, Jing; Mei, Zhonglei; Jian, Yabin

2018-04-01

In this work, we design an ultra-thin absorption coating at the S band, and the total thickness is less than 2 mm. For incident angle less than 30 degree and the whole S band, the reflection is less than -5 dB. The coating is constructed with 4/3 layers of magnetic material with different thicknesses, which are optimized by using genetic algorithm. Analytic and simulation results confirm the correctness of the design.

An Extensible Schema-less Database Framework for Managing High-throughput Semi-Structured Documents

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.; La, Tracy; Clancy, Daniel (Technical Monitor)

2002-01-01

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 searches of records for 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, XML and HTML.

The designing and implementation of PE teaching information resource database based on broadband network

NASA Astrophysics Data System (ADS)

Wang, Jian

2017-01-01

In order to change traditional PE teaching mode and realize the interconnection, interworking and sharing of PE teaching resources, a distance PE teaching platform based on broadband network is designed and PE teaching information resource database is set up. The designing of PE teaching information resource database takes Windows NT 4/2000Server as operating system platform, Microsoft SQL Server 7.0 as RDBMS, and takes NAS technology for data storage and flow technology for video service. The analysis of system designing and implementation shows that the dynamic PE teaching information resource sharing platform based on Web Service can realize loose coupling collaboration, realize dynamic integration and active integration and has good integration, openness and encapsulation. The distance PE teaching platform based on Web Service and the design scheme of PE teaching information resource database can effectively solve and realize the interconnection, interworking and sharing of PE teaching resources and adapt to the informatization development demands of PE teaching.

Ultra-violet avalanche photodiode based on AlN/GaN periodically-stacked-structure

NASA Astrophysics Data System (ADS)

Wu, Xingzhao; Zheng, Jiyuan; Wang, Lai; Brault, Julien; Matta, Samuel; Hao, Zhibiao; Sun, Changzheng; Xiong, Bing; Luo, Yi; Han, Yianjun; Wang, Jian; Li, Hongtao; Khalfioui, Mohamed A.; Li, Mo; Kang, Jianbin; Li, Qian

2018-02-01

The high-gain photomultiplier tube (PMT) is the most popular method to detect weak ultra-violet signals which attenuate quickly in atmosphere, although the vacuum tube makes it fragile and difficult to integrate. To overcome the disadvantage of PMT, an AlN/GaN periodically-stacked-structure (PSS) avalanche photodiode (APD) has been proposed, finally achieving good quality of high gain and low excessive noise. As there is a deep g valley only in the conduction band of both GaN and AlN, the electron transfers suffering less scattering and thus becomes easier to obtain the threshold of ionization impact. Because of unipolar ionization in the PSS APD, it works in linear mode. Four prototype devices of 5-period, 10-period, 15-period, and 20-period were fabricated to verify that the gain of APD increases exponentially with period number. And in 20-period device, a recorded high and stable gain of 104 was achieved under constant bias. In addition, it is proved both experimentally and theoretically, that temperature stability on gain is significantly improved in PSS APD. And it is found that the resonant enhancement in interfacial ionization may bring significant enhancement of electron ionization performance. To make further progress in PSS APD, the device structure is investigated by simulation. Both the gain and temperature stability are optimized alternatively by a proper design of periodical thickness and AlN layer occupancy.

Designing optimized ultra-lightweighted mirror structures made of Cesic for space and ground based applications

NASA Astrophysics Data System (ADS)

Hofbauer, Peter; Krödel, Matthias R.

2010-07-01

Today's space applications increasingly utilize lightweighted construction concepts, motivated by the demands of manufacturing and functionality, and by economics. Particularly for space optics, mirror stability and stiffness need to be maximized, while mass needs to be minimized. Therefore, mirror materials must possess, besides high material strength and manufacturing versatility, high thermal conductivity combined with low heat capacity and long-term stability against varying thermal loads. Additionally, optical surfaces need to be compatible with reflective coating materials. In order to achieve these requirements, the interplay between material properties and mirror design on one hand, and budgetary constraints on the other must be considered. In this paper, we address these issues by presenting an FEM design study of open and closed-back mirror structures with extremely thin reinforcing ribs, with the goal of obtaining optimal physical and optical characteristics. Furthermore, we show that ECM's carbon-fiber reinforced SiC composite, Cesic®, and its newly developed, HB-Cesic® , with their low CTE, low density, and high stiffness, are not only excellent mirror materials, but allow the rapid manufacturing of complex monolithic optical structures at reasonable cost.

Intelligent Access to Sequence and Structure Databases (IASSD) - an interface for accessing information from major web databases.

PubMed

Ganguli, Sayak; Gupta, Manoj Kumar; Basu, Protip; Banik, Rahul; Singh, Pankaj Kumar; Vishal, Vineet; Bera, Abhisek Ranjan; Chakraborty, Hirak Jyoti; Das, Sasti Gopal

2014-01-01

With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. The Jar file is freely available through e-mail from the corresponding author.

TRANSFORMATION OF DEVELOPMENTAL NEUROTOXICITY DATA INTO STRUCTURE-SEARCHABLE TOXML DATABASE IN SUPPORT OF STRUCTURE-ACTIVITY RELATIONSHIP (SAR) WORKFLOW.

EPA Science Inventory

Early hazard identification of new chemicals is often difficult due to lack of data on the novel material for toxicity endpoints, including neurotoxicity. At present, there are no structure searchable neurotoxicity databases. A working group was formed to construct a database to...

Ultra-wideband, Wide Angle and Polarization-insensitive Specular Reflection Reduction by Metasurface based on Parameter-adjustable Meta-Atoms.

PubMed

Su, Jianxun; Lu, Yao; Zhang, Hui; Li, Zengrui; Lamar Yang, Yaoqing; Che, Yongxing; Qi, Kainan

2017-02-09

In this paper, an ultra-wideband, wide angle and polarization-insensitive metasurface is designed, fabricated, and characterized for suppressing the specular electromagnetic wave reflection or backward radar cross section (RCS). Square ring structure is chosen as the basic meta-atoms. A new physical mechanism based on size adjustment of the basic meta-atoms is proposed for ultra-wideband manipulation of electromagnetic (EM) waves. Based on hybrid array pattern synthesis (APS) and particle swarm optimization (PSO) algorithm, the selection and distribution of the basic meta-atoms are optimized simultaneously to obtain the ultra-wideband diffusion scattering patterns. The metasurface can achieve an excellent RCS reduction in an ultra-wide frequency range under x- and y-polarized normal incidences. The new proposed mechanism greatly extends the bandwidth of RCS reduction. The simulation and experiment results show the metasurface can achieve ultra-wideband and polarization-insensitive specular reflection reduction for both normal and wide-angle incidences. The proposed methodology opens up a new route for realizing ultra-wideband diffusion scattering of EM wave, which is important for stealth and other microwave applications in the future.

Use of designed sequences in protein structure recognition.

PubMed

Kumar, Gayatri; Mudgal, Richa; Srinivasan, Narayanaswamy; Sandhya, Sankaran

2018-05-09

Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold. These strategically designed sequences enable detection of distant relationships and here, we have employed them for the purpose of structure recognition of protein families of yet unknown structure. We first measured the success rate of our approach using a dataset of protein families of known fold and achieved a success rate of 88%. Next, for 1392 families of yet unknown structure, we made structural assignments for part/full length of the proteins. Fold association for 423 domains of unknown function (DUFs) are provided as a step towards functional annotation. The results indicate that knowledge-based filling of gaps in protein sequence space is a lucrative approach for structure recognition. Such sequences assist in traversal through protein sequence space and effectively function as 'linkers', where natural linkers between distant proteins are unavailable. This article was reviewed by Oliviero Carugo, Christine Orengo and Srikrishna Subramanian.

TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants

PubMed Central

Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

2014-01-01

The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure–activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein–ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. PMID:24930145

Ultra-stiff metallic glasses through bond energy density design.

PubMed

Schnabel, Volker; Köhler, Mathias; Music, Denis; Bednarcik, Jozef; Clegg, William J; Raabe, Dierk; Schneider, Jochen M

2017-07-05

The elastic properties of crystalline metals scale with their valence electron density. Similar observations have been made for metallic glasses. However, for metallic glasses where covalent bonding predominates, such as metalloid metallic glasses, this relationship appears to break down. At present, the reasons for this are not understood. Using high energy x-ray diffraction analysis of melt spun and thin film metallic glasses combined with density functional theory based molecular dynamics simulations, we show that the physical origin of the ultrahigh stiffness in both metalloid and non-metalloid metallic glasses is best understood in terms of the bond energy density. Using the bond energy density as novel materials design criterion for ultra-stiff metallic glasses, we are able to predict a Co 33.0 Ta 3.5 B 63.5 short range ordered material by density functional theory based molecular dynamics simulations with a high bond energy density of 0.94 eV Å -3 and a bulk modulus of 263 GPa, which is 17% greater than the stiffest Co-B based metallic glasses reported in literature.

Design, fabrication and space suitability tests of wide field of view, ultra-compact, and high resolution telescope for space application.

PubMed

Tumarina, M; Ryazanskiy, M; Jeong, S; Hong, G; Vedenkin, N; Park, I H; Milov, A

2018-02-05

We report on the design, manufacture, and testing of an ultra-compact telescope for 16 unit (16U) CubeSats for Earth and space observation. This telescope provides 1 arcsec resolution at a 2.9 degree field of view. Dimensions are optimized to 230 × 230 × 330mm 3 with a mass of less than 6kg including support structure. Our catadioptric 5-element design consists of a full-aperture corrector, a Mangin primary mirror (PM), a secondary mirror (SM), and a 2-lens field corrector. The focal length is 745mm, and squared-circular aperture has an equivalent diameter of 241mm. The designed modulation transfer function (MTF) is 0.275 for the entire unit including baffles at a Nyquist frequency of 161 cycles/mm for the 450-800nm band. As one of the distinguishing features of our state-of-the-art design, all optical surfaces are spherical to simplify adjustment. For the best thermal stability, all optical elements are produced from fused silica. We describe the details of design, adjustment, and laboratory performance tests for space environments in accordance with the requirements for in-orbit operation onboard Earth-observation micro-satellites to be launched in 2018.

OsB 2 and RuB 2, ultra-incompressible, hard materials: First-principles electronic structure calculations

NASA Astrophysics Data System (ADS)

Chiodo, S.; Gotsis, H. J.; Russo, N.; Sicilia, E.

2006-07-01

Recently it has been reported that osmium diboride has an unusually large bulk modulus combined with high hardness, and consequently is a most interesting candidate as an ultra-incompressible and hard material. The electronic and structural properties of the transition metal diborides OsB 2 and RuB 2 have been calculated within the local density approximation (LDA). It is shown that the high hardness is the result of covalent bonding between transition metal d states and boron p states in the orthorhombic structure.

Ultra-high-speed graphene optical modulator design based on tight field confinement in a slot waveguide

NASA Astrophysics Data System (ADS)

Kovacevic, Goran; Phare, Christopher; Set, Sze Y.; Lipson, Michal; Yamashita, Shinji

2018-06-01

We present a design of an ultra-fast in-line graphene optical modulator on a silicon waveguide with a bandwidth exceeding 100 GHz, very small power consumption below 15 fJ/bit, and insertion loss of 1.5 dB. This is achieved by utilizing the transverse-electric-mode silicon slot to tailor the overlap of graphene electrodes, thus significantly reducing the capacitance of the device while maintaining a low insertion loss and using conservative estimates of the graphene resistance. Our design is substantiated by comprehensive finite-element-method simulations and RC circuit characterization, as well as fabrication feasibility discussion.

Databases of Conformations and NMR Structures of Glycan Determinants.

PubMed

Sarkar, Anita; Drouillard, Sophie; Rivet, Alain; Perez, Serge

2015-12-01

The present study reports a comprehensive nuclear magnetic resonance (NMR) characterization and a systematic conformational sampling of the conformational preferences of 170 glycan moieties of glycosphingolipids as produced in large-scale quantities by bacterial fermentation. These glycans span across a variety of families including the blood group antigens (A, B and O), core structures (Types 1, 2 and 4), fucosylated oligosaccharides (core and lacto-series), sialylated oligosaccharides (Types 1 and 2), Lewis antigens, GPI-anchors and globosides. A complementary set of about 100 glycan determinants occurring in glycoproteins and glycosaminoglycans has also been structurally characterized using molecular mechanics-based computation. The experimental and computational data generated are organized in two relational databases that can be queried by the user through a user-friendly search engine. The NMR ((1)H and (13)C, COSY, TOCSY, HMQC, HMBC correlation) spectra and 3D structures are available for visualization and download in commonly used structure formats. Emphasis has been given to the use of a common nomenclature for the structural encoding of the carbohydrates and each glycan molecule is described by four different types of representations in order to cope with the different usages in chemistry and biology. These web-based databases were developed with non-proprietary software and are open access for the scientific community available at http://glyco3d.cermav.cnrs.fr. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Front-End and Back-End Database Design and Development: Scholar's Academy Case Study

ERIC Educational Resources Information Center

Parks, Rachida F.; Hall, Chelsea A.

2016-01-01

This case study consists of a real database project for a charter school--Scholar's Academy--and provides background information on the school and its cafeteria processing system. Also included are functional requirements and some illustrative data. Students are tasked with the design and development of a database for the purpose of improving the…

Design of ultra-compact composite plasmonic Mach-Zehnder interferometer for chemical vapor sensing

NASA Astrophysics Data System (ADS)

Ghosh, Souvik; Rahman, B. M. A.

2018-02-01

Following the Industrial advancements in the last few decades, highly flammable chemicals, such as ethanol (CH3CH2OH) and methanol (CH3OH) are widely being used in daily life. Ethanol have some degrees of carcinogenic effects in human whereas acute and chronic exposer of methanol results blurred vision and nausea. Therefore, accurate and efficient sensing of these two vapors in industrial environment are of high priorities. We have designed a novel, ultra-compact chemical vapor sensor based on composite plasmonic horizontal slot waveguide (CPHSW) where a low-index porous-ZnO (P-ZnO) layer is sandwiched in between top silver metal and lower silicon layers. Different P-ZnO templates, such as nano-spheres, nano-sheets and nanoplates could be used for high-selectivity of ethanol and methanol at different temperatures. The Lorentz-Lorenz model is used to determine the variation of P-ZnO refractive index (RI) with porosity and equivalent RI of P-ZnO layer for capillary condensation of different percentage of absorbed vapor. An in-house, new divergence modified finite element method is used to calculate effective index and attenuation sensitivity. Plasmonic modal analyses of dominant quasi-TM mode shows a high 42% power confinement in the slot. Next, an ultra-compact MZI incorporating a few micrometres long CPHSW is designed and analysed as a transducer device for accurate detection of effective index change. The device performance has been studied for different percentage of ethanol into P-ZnO with different porosity and a maximum phase sensitivity of >0.35 a.u. is achieved for both the chemical vapors at a mid-IR operating wavelength of 1550 nm.

Ultra-Large Solar Sail

NASA Technical Reports Server (NTRS)

Burton, Rodney; Coverstone, Victoria

2009-01-01

UltraSail is a next-generation ultra-large (km2 class) sail system. Analysis of the launch, deployment, stabilization, and control of these sails shows that high-payload-mass fractions for interplanetary and deep-space missions are possible. UltraSail combines propulsion and control systems developed for formation-flying microsatellites with a solar sail architecture to achieve controllable sail areas approaching 1 km2. Electrically conductive CP-1 polyimide film results in sail subsystem area densities as low as 5 g/m2. UltraSail produces thrust levels many times those of ion thrusters used for comparable deep-space missions. The primary innovation involves the near-elimination of sail-supporting structures by attaching each blade tip to a formation- flying microsatellite, which deploys the sail and then articulates the sail to provide attitude control, including spin stabilization and precession of the spin axis. These microsatellite tips are controlled by microthrusters for sail-film deployment and mission operations. UltraSail also avoids the problems inherent in folded sail film, namely stressing, yielding, or perforating, by storing the film in a roll for launch and deployment. A 5-km long by 2 micrometer thick film roll on a mandrel with a 1 m circumference (32 cm diameter) has a stored thickness of 5 cm. A 5 m-long mandrel can store a film area of 25,000 m2, and a four-blade system has an area of 0.1 sq km.

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions

PubMed Central

Jefferson, Emily R.; Walsh, Thomas P.; Roberts, Timothy J.; Barton, Geoffrey J.

2007-01-01

SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Java Application Programming Interface (API) is described. SNAPPI-DB contains structural data, down to the level of atom co-ordinates, for each structure in the Protein Data Bank (PDB) together with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary Structures (PQS) and secondary structure information. Domain–domain interactions are stored for multiple domain definitions and are classified by their Superfamily/Family pair and interaction interface. Each set of classified domain–domain interactions has an associated multiple structure alignment for each partner. The API facilitates data access via PDB entries, domains and domain–domain interactions. Rapid development, fast database access and the ability to perform advanced queries without the requirement for complex SQL statements are provided via an object oriented database and the Java Data Objects (JDO) API. SNAPPI-DB contains many features which are not available in other databases of structural protein–protein interactions. It has been applied in three studies on the properties of protein–protein interactions and is currently being employed to train a protein–protein interaction predictor and a functional residue predictor. The database, API and manual are available for download at: . PMID:17202171

Development of a Dependency Theory Toolbox for Database Design.

DTIC Science & Technology

1987-12-01

published algorithms and theorems , and hand simulating these algorithms can be a tedious and error prone chore. Additionally, since the process of...to design and study relational databases exists in the form of published algorithms and theorems . However, hand simulating these algorithms can be a...published algorithms and theorems . Hand simulating these algorithms can be a tedious and error prone chore. Therefore, a toolbox of algorithms and

Querying databases of trajectories of differential equations: Data structures for trajectories

NASA Technical Reports Server (NTRS)

Grossman, Robert

1989-01-01

One approach to qualitative reasoning about dynamical systems is to extract qualitative information by searching or making queries on databases containing very large numbers of trajectories. The efficiency of such queries depends crucially upon finding an appropriate data structure for trajectories of dynamical systems. Suppose that a large number of parameterized trajectories gamma of a dynamical system evolving in R sup N are stored in a database. Let Eta is contained in set R sup N denote a parameterized path in Euclidean Space, and let the Euclidean Norm denote a norm on the space of paths. A data structure is defined to represent trajectories of dynamical systems, and an algorithm is sketched which answers queries.

In-Memory Graph Databases for Web-Scale Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castellana, Vito G.; Morari, Alessandro; Weaver, Jesse R.

RDF databases have emerged as one of the most relevant way for organizing, integrating, and managing expo- nentially growing, often heterogeneous, and not rigidly structured data for a variety of scientific and commercial fields. In this paper we discuss the solutions integrated in GEMS (Graph database Engine for Multithreaded Systems), a software framework for implementing RDF databases on commodity, distributed-memory high-performance clusters. Unlike the majority of current RDF databases, GEMS has been designed from the ground up to primarily employ graph-based methods. This is reflected in all the layers of its stack. The GEMS framework is composed of: a SPARQL-to-C++more » compiler, a library of data structures and related methods to access and modify them, and a custom runtime providing lightweight software multithreading, network messages aggregation and a partitioned global address space. We provide an overview of the framework, detailing its component and how they have been closely designed and customized to address issues of graph methods applied to large-scale datasets on clusters. We discuss in details the principles that enable automatic translation of the queries (expressed in SPARQL, the query language of choice for RDF databases) to graph methods, and identify differences with respect to other RDF databases.« less

Enzyme-triggered self-assembly of a small molecule: a supramolecular hydrogel with leaf-like structures and an ultra-low minimum gelation concentration

NASA Astrophysics Data System (ADS)

Wang, Huaimin; Ren, Chunhua; Song, Zhijian; Wang, Ling; Chen, Xuemei; Yang, Zhimou

2010-06-01

We report on the use of a phosphatase to assist the formation of leaf-like structures and a supramolecular hydrogel with an ultra-low minimum gelation concentration. The compound can gel water at a minimum gelation concentration of 0.01 wt%, which is the lowest gelation concentration reported up to now. The images obtained by transmission electron microscopy (TEM) reveal the existence of leaf-like structures serving as the matrix of the hydrogels. The stability of the hydrogels was studied and emission spectra were used to get information about the molecular packing in the leaf-like structures. Since lowering the concentration of the gelator decreases the toxicity of the resulting hydrogels, ultra-low concentration gels have potential uses as biocompatible biomaterials for, e.g., cell cultures, tissue engineering, and drug delivery.

New Multijunction Design Leads to Ultra-Efficient Solar Cell; Highlights in Research & Development, NREL (National Renewable Energy Laboratory)

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2015-09-01

NREL has demonstrated a 45.7% conversion efficiency for a four-junction solar cell at 234 suns concentration. This achievement represents one of the highest photovoltaic research cell efficiencies ever achieved across all types of solar cells. NREL's new solar cell, which is designed for operation in a concentrator photovoltaic (CPV) system where it can receive more than 1,000 suns of concentrated sunlight, greatly improves earlier designs by adding an additional high quality absorber layer to achieve an ultra-high efficiency.

SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database.

PubMed

Chandonia, John-Marc; Fox, Naomi K; Brenner, Steven E

2017-02-03

SCOPe (Structural Classification of Proteins-extended, http://scop.berkeley.edu) is a database of relationships between protein structures that extends the Structural Classification of Proteins (SCOP) database. SCOP is an expert-curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. SCOPe classifies the majority of protein structures released since SCOP development concluded in 2009, using a combination of manual curation and highly precise automated tools, aiming to have the same accuracy as fully hand-curated SCOP releases. SCOPe also incorporates and updates the ASTRAL compendium, which provides several databases and tools to aid in the analysis of the sequences and structures of proteins classified in SCOPe. SCOPe continues high-quality manual classification of new superfamilies, a key feature of SCOP. Artifacts such as expression tags are now separated into their own class, in order to distinguish them from the homology-based annotations in the remainder of the SCOPe hierarchy. SCOPe 2.06 contains 77,439 Protein Data Bank entries, double the 38,221 structures classified in SCOP. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.

PubMed

Hsing, Michael; Cherkasov, Artem

2008-06-25

Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of protein essentiality and their role in protein interaction networks. Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown. We have created a web-based resource, Indel PDB, representing a structural database of insertions/deletions identified from the sequence alignments of highly similar proteins found in the Protein Data Bank (PDB). Indel PDB utilized large amounts of available structural information to characterize 1-, 2- and 3-dimensional features of indel sites. Indel PDB contains 117,266 non-redundant indel sites extracted from 11,294 indel-containing proteins. Unlike loop databases, Indel PDB features more indel sequences with secondary structures including alpha-helices and beta-sheets in addition to loops. The insertion fragments have been characterized by their sequences, lengths, locations, secondary structure composition, solvent accessibility, protein domain association and three dimensional structures. By utilizing the data available in Indel PDB, we have studied and presented here several sequence and structural features of indels. We anticipate that Indel PDB will not only enable future functional studies of indels, but will also assist protein modeling efforts and identification of indel-directed drug binding sites.

Design sensitivity analysis using EAL. Part 1: Conventional design parameters

NASA Technical Reports Server (NTRS)

Dopker, B.; Choi, Kyung K.; Lee, J.

1986-01-01

A numerical implementation of design sensitivity analysis of builtup structures is presented, using the versatility and convenience of an existing finite element structural analysis code and its database management system. The finite element code used in the implemenatation presented is the Engineering Analysis Language (EAL), which is based on a hybrid method of analysis. It was shown that design sensitivity computations can be carried out using the database management system of EAL, without writing a separate program and a separate database. Conventional (sizing) design parameters such as cross-sectional area of beams or thickness of plates and plane elastic solid components are considered. Compliance, displacement, and stress functionals are considered as performance criteria. The method presented is being extended to implement shape design sensitivity analysis using a domain method and a design component method.

Structure and needs of global loss databases about natural disaster

NASA Astrophysics Data System (ADS)

Steuer, Markus

2010-05-01

Global loss databases are used for trend analyses and statistics in scientific projects, studies for governmental and nongovernmental organizations and for the insurance and finance industry as well. At the moment three global data sets are established: EM-DAT (CRED), Sigma (Swiss Re) and NatCatSERVICE (Munich Re). Together with the Asian Disaster Reduction Center (ADRC) and United Nations Development Program (UNDP) started a collaborative initiative in 2007 with the aim to agreed on and implemented a common "Disaster Category Classification and Peril Terminology for Operational Databases". This common classification has been established through several technical meetings and working groups and represents a first and important step in the development of a standardized international classification of disasters and terminology of perils. This means concrete to set up a common hierarchy and terminology for all global and regional databases on natural disasters and establish a common and agreed definition of disaster groups, main types and sub-types of events. Also the theme of georeferencing, temporal aspects, methodology and sourcing were other issues that have been identified and will be discussed. The implementation of the new and defined structure for global loss databases is already set up for Munich Re NatCatSERVICE. In the following oral session we will show the structure of the global databases as defined and in addition to give more transparency of the data sets behind published statistics and analyses. The special focus will be on the catastrophe classification from a moderate loss event up to a great natural catastrophe, also to show the quality of sources and give inside information about the assessment of overall and insured losses. Keywords: disaster category classification, peril terminology, overall and insured losses, definition

An integrated photogrammetric and spatial database management system for producing fully structured data using aerial and remote sensing images.

PubMed

Ahmadi, Farshid Farnood; Ebadi, Hamid

2009-01-01

3D spatial data acquired from aerial and remote sensing images by photogrammetric techniques is one of the most accurate and economic data sources for GIS, map production, and spatial data updating. However, there are still many problems concerning storage, structuring and appropriate management of spatial data obtained using these techniques. According to the capabilities of spatial database management systems (SDBMSs); direct integration of photogrammetric and spatial database management systems can save time and cost of producing and updating digital maps. This integration is accomplished by replacing digital maps with a single spatial database. Applying spatial databases overcomes the problem of managing spatial and attributes data in a coupled approach. This management approach is one of the main problems in GISs for using map products of photogrammetric workstations. Also by the means of these integrated systems, providing structured spatial data, based on OGC (Open GIS Consortium) standards and topological relations between different feature classes, is possible at the time of feature digitizing process. In this paper, the integration of photogrammetric systems and SDBMSs is evaluated. Then, different levels of integration are described. Finally design, implementation and test of a software package called Integrated Photogrammetric and Oracle Spatial Systems (IPOSS) is presented.

Structural health monitoring feature design by genetic programming

NASA Astrophysics Data System (ADS)

Harvey, Dustin Y.; Todd, Michael D.

2014-09-01

Structural health monitoring (SHM) systems provide real-time damage and performance information for civil, aerospace, and other high-capital or life-safety critical structures. Conventional data processing involves pre-processing and extraction of low-dimensional features from in situ time series measurements. The features are then input to a statistical pattern recognition algorithm to perform the relevant classification or regression task necessary to facilitate decisions by the SHM system. Traditional design of signal processing and feature extraction algorithms can be an expensive and time-consuming process requiring extensive system knowledge and domain expertise. Genetic programming, a heuristic program search method from evolutionary computation, was recently adapted by the authors to perform automated, data-driven design of signal processing and feature extraction algorithms for statistical pattern recognition applications. The proposed method, called Autofead, is particularly suitable to handle the challenges inherent in algorithm design for SHM problems where the manifestation of damage in structural response measurements is often unclear or unknown. Autofead mines a training database of response measurements to discover information-rich features specific to the problem at hand. This study provides experimental validation on three SHM applications including ultrasonic damage detection, bearing damage classification for rotating machinery, and vibration-based structural health monitoring. Performance comparisons with common feature choices for each problem area are provided demonstrating the versatility of Autofead to produce significant algorithm improvements on a wide range of problems.

TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.

PubMed Central

Wallace, A. C.; Borkakoti, N.; Thornton, J. M.

1997-01-01

It is well established that sequence templates such as those in the PROSITE and PRINTS databases are powerful tools for predicting the biological function and tertiary structure for newly derived protein sequences. The number of X-ray and NMR protein structures is increasing rapidly and it is apparent that a 3D equivalent of the sequence templates is needed. Here, we describe an algorithm called TESS that automatically derives 3D templates from structures deposited in the Brookhaven Protein Data Bank. While a new sequence can be searched for sequence patterns, a new structure can be scanned against these 3D templates to identify functional sites. As examples, 3D templates are derived for enzymes with an O-His-O "catalytic triad" and for the ribonucleases and lysozymes. When these 3D templates are applied to a large data set of nonidentical proteins, several interesting hits are located. This suggests that the development of a 3D template database may help to identify the function of new protein structures, if unknown, as well as to design proteins with specific functions. PMID:9385633

Ultra-low field nuclear magnetic resonance and magnetic resonance imaging to discriminate and identify materials

DOEpatents

Kraus, Robert H.; Matlashov, Andrei N.; Espy, Michelle A.; Volegov, Petr L.

2010-03-30

An ultra-low magnetic field NMR system can non-invasively examine containers. Database matching techniques can then identify hazardous materials within the containers. Ultra-low field NMR systems are ideal for this purpose because they do not require large powerful magnets and because they can examine materials enclosed in conductive shells such as lead shells. The NMR examination technique can be combined with ultra-low field NMR imaging, where an NMR image is obtained and analyzed to identify target volumes. Spatial sensitivity encoding can also be used to identify target volumes. After the target volumes are identified the NMR measurement technique can be used to identify their contents.

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

PubMed Central

Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

2015-01-01

Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin. PMID:26392543

Signal Design for Improved Ranging Among Multiple Transceivers

NASA Technical Reports Server (NTRS)

Young, Lawrence; Tien, Jeffrey; Srinivasan, Jeffrey

2004-01-01

"Ultra-BOC" (where "BOC" signifies "binary offset carrier") is the name of an improved generic design of microwave signals to be used by a group of spacecraft flying in formation to measure ranges and bearings among themselves and to exchange telemetry needed for these measurements. Ultra-BOC could also be applied on Earth for diverse purposes -- for example, measuring relative positions of vehicles on highways for traffic-control purposes and determining the relative alignments of machines operating in mines and of construction machines and structures at construction sites. Ultra-BOC provides for rapid and robust acquisition of signals, even when signal-to-noise ratios are low. The design further provides that each spacecraft or other platform constantly strives to acquire and track the signals from the other platforms while simultaneously transmitting signals that provide full range, bearing, and telemetry service to the other platforms. In Ultra-BOC, unlike in other signal designs that have been considered for the same purposes, it is not necessary to maneuver the spacecraft or other platforms to obtain the data needed for resolving integer-carrier-cycle phase ambiguities.

76 FR 53912 - FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-30

...] FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code Names... replaced non- informative code names with descriptive identifiers on its public database of products that... on our public database with non-informative code names. After careful consideration of this matter...

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

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

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.

2003-01-01

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.

Data Structures in Natural Computing: Databases as Weak or Strong Anticipatory Systems

NASA Astrophysics Data System (ADS)

Rossiter, B. N.; Heather, M. A.

2004-08-01

Information systems anticipate the real world. Classical databases store, organise and search collections of data of that real world but only as weak anticipatory information systems. This is because of the reductionism and normalisation needed to map the structuralism of natural data on to idealised machines with von Neumann architectures consisting of fixed instructions. Category theory developed as a formalism to explore the theoretical concept of naturality shows that methods like sketches arising from graph theory as only non-natural models of naturality cannot capture real-world structures for strong anticipatory information systems. Databases need a schema of the natural world. Natural computing databases need the schema itself to be also natural. Natural computing methods including neural computers, evolutionary automata, molecular and nanocomputing and quantum computation have the potential to be strong. At present they are mainly at the stage of weak anticipatory systems.

The effect of wild card designations and rare alleles in forensic DNA database searches.

PubMed

Tvedebrink, Torben; Bright, Jo-Anne; Buckleton, John S; Curran, James M; Morling, Niels

2015-05-01

Forensic DNA databases are powerful tools used for the identification of persons of interest in criminal investigations. Typically, they consist of two parts: (1) a database containing DNA profiles of known individuals and (2) a database of DNA profiles associated with crime scenes. The risk of adventitious or chance matches between crimes and innocent people increases as the number of profiles within a database grows and more data is shared between various forensic DNA databases, e.g. from different jurisdictions. The DNA profiles obtained from crime scenes are often partial because crime samples may be compromised in quantity or quality. When an individual's profile cannot be resolved from a DNA mixture, ambiguity is introduced. A wild card, F, may be used in place of an allele that has dropped out or when an ambiguous profile is resolved from a DNA mixture. Variant alleles that do not correspond to any marker in the allelic ladder or appear above or below the extent of the allelic ladder range are assigned the allele designation R for rare allele. R alleles are position specific with respect to the observed/unambiguous allele. The F and R designations are made when the exact genotype has not been determined. The F and R designation are treated as wild cards for searching, which results in increased chance of adventitious matches. We investigated the probability of adventitious matches given these two types of wild cards. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Development of a database of instruments for resource-use measurement: purpose, feasibility, and design.

PubMed

Ridyard, Colin H; Hughes, Dyfrig A

2012-01-01

Health economists frequently rely on methods based on patient recall to estimate resource utilization. Access to questionnaires and diaries, however, is often limited. This study examined the feasibility of establishing an open-access Database of Instruments for Resource-Use Measurement, identified relevant fields for data extraction, and outlined its design. An electronic survey was sent to authors of full UK economic evaluations listed in the National Health Service Economic Evaluation Database (2008-2010), authors of monographs of Health Technology Assessments (1998-2010), and subscribers to the JISCMail health economics e-mailing list. The survey included questions on piloting, validation, recall period, and data capture method. Responses were analyzed and data extracted to generate relevant fields for the database. A total of 143 responses to the survey provided data on 54 resource-use instruments for inclusion in the database. All were reliant on patient or carer recall, and a majority (47) were questionnaires. Thirty-seven were designed for self-completion by the patient, carer, or guardian, and the remainder were designed for completion by researchers or health care professionals while interviewing patients. Methods of development were diverse, particularly in areas such as the planning of resource itemization (evident in 25 instruments), piloting (25), and validation (29). On the basis of the present analysis, we developed a Web-enabled Database of Instruments for Resource-Use Measurement, accessible via www.DIRUM.org. This database may serve as a practical resource for health economists, as well as a means to facilitate further research in the area of resource-use data collection. Copyright © 2012 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Integrated control-structure design

NASA Technical Reports Server (NTRS)

Hunziker, K. Scott; Kraft, Raymond H.; Bossi, Joseph A.

1991-01-01

A new approach for the design and control of flexible space structures is described. The approach integrates the structure and controller design processes thereby providing extra opportunities for avoiding some of the disastrous effects of control-structures interaction and for discovering new, unexpected avenues of future structural design. A control formulation based on Boyd's implementation of Youla parameterization is employed. Control design parameters are coupled with structural design variables to produce a set of integrated-design variables which are selected through optimization-based methodology. A performance index reflecting spacecraft mission goals and constraints is formulated and optimized with respect to the integrated design variables. Initial studies have been concerned with achieving mission requirements with a lighter, more flexible space structure. Details of the formulation of the integrated-design approach are presented and results are given from a study involving the integrated redesign of a flexible geostationary platform.

Ultra-wideband, Wide Angle and Polarization-insensitive Specular Reflection Reduction by Metasurface based on Parameter-adjustable Meta-Atoms

PubMed Central

Su, Jianxun; Lu, Yao; Zhang, Hui; Li, Zengrui; (Lamar) Yang, Yaoqing; Che, Yongxing; Qi, Kainan

2017-01-01

In this paper, an ultra-wideband, wide angle and polarization-insensitive metasurface is designed, fabricated, and characterized for suppressing the specular electromagnetic wave reflection or backward radar cross section (RCS). Square ring structure is chosen as the basic meta-atoms. A new physical mechanism based on size adjustment of the basic meta-atoms is proposed for ultra-wideband manipulation of electromagnetic (EM) waves. Based on hybrid array pattern synthesis (APS) and particle swarm optimization (PSO) algorithm, the selection and distribution of the basic meta-atoms are optimized simultaneously to obtain the ultra-wideband diffusion scattering patterns. The metasurface can achieve an excellent RCS reduction in an ultra-wide frequency range under x- and y-polarized normal incidences. The new proposed mechanism greatly extends the bandwidth of RCS reduction. The simulation and experiment results show the metasurface can achieve ultra-wideband and polarization-insensitive specular reflection reduction for both normal and wide-angle incidences. The proposed methodology opens up a new route for realizing ultra-wideband diffusion scattering of EM wave, which is important for stealth and other microwave applications in the future. PMID:28181593

A Simple Ultra-Wideband Magneto-Electric Dipole Antenna With High Gain

NASA Astrophysics Data System (ADS)

Shuai, Chen-yang; Wang, Guang-ming

2017-12-01

A simple ultra-wideband magneto-electric dipole antenna utilizing a differential-fed structure is designed. The antenna mainly comprises three parts, including a novel circular horned reflector, two vertical semicircular shorted patches as a magnetic dipole, and a horizontal U-shaped semicircular electric dipole. A differential feeding structure working as a perfect balun excites the designed antenna. The results of simulation have a good match with the ones of measurement. Results indicate that the designed antenna achieves a wide frequency bandwidth of 107 % which is 3.19 10.61 GHz, when VSWR is below 2. Via introducing the circular horned reflector, the designed antenna attains a steady and high gain of 12±1.5dBi. Moreover, settled broadside direction main beam, high front-to-back ratio, low cross polarization, and the symmetrical and relatively stable radiation patterns in the E-and H-plane are gotten in the impedance bandwidth range. In the practical applications, the proposed antenna that is dc grounded and has a simple structure satisfies the requirement of many outdoor antennas.

Practical computational toolkits for dendrimers and dendrons structure design.

PubMed

Martinho, Nuno; Silva, Liana C; Florindo, Helena F; Brocchini, Steve; Barata, Teresa; Zloh, Mire

2017-09-01

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

Practical computational toolkits for dendrimers and dendrons structure design

NASA Astrophysics Data System (ADS)

Martinho, Nuno; Silva, Liana C.; Florindo, Helena F.; Brocchini, Steve; Barata, Teresa; Zloh, Mire

2017-09-01

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

The Cambridge Structural Database: a quarter of a million crystal structures and rising.

PubMed

Allen, Frank H

2002-06-01

The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73,000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.

Design of UWB Monopole Antenna with Dual Notched Bands Using One Modified Electromagnetic-Bandgap Structure

PubMed Central

Xu, Ziqiang

2013-01-01

A modified electromagnetic-bandgap (M-EBG) structure and its application to planar monopole ultra-wideband (UWB) antenna are presented. The proposed M-EBG which comprises two strip patch and an edge-located via can perform dual notched bands. By properly designing and placing strip patch near the feedline, the proposed M-EBG not only possesses a simple structure and compact size but also exhibits good band rejection. Moreover, it is easy to tune the dual notched bands by altering the dimensions of the M-EBG. A demonstration antenna with dual band-notched characteristics is designed and fabricated to validate the proposed method. The results show that the proposed antenna can satisfy the requirements of VSWR < 2 over UWB 3.1–10.6 GHz, except for the rejected bands of the world interoperability for microwave access (WiMAX) and the wireless local area network (WLAN) at 3.5 GHz and 5.5 GHz, respectively. PMID:24170984

Ultra-wideband WDM VCSEL arrays by lateral heterogeneous integration

NASA Astrophysics Data System (ADS)

Geske, Jon

Advancements in heterogeneous integration are a driving factor in the development of evermore sophisticated and functional electronic and photonic devices. Such advancements will merge the optical and electronic capabilities of different material systems onto a common integrated device platform. This thesis presents a new lateral heterogeneous integration technology called nonplanar wafer bonding. The technique is capable of integrating multiple dissimilar semiconductor device structures on the surface of a substrate in a single wafer bond step, leaving different integrated device structures adjacent to each other on the wafer surface. Material characterization and numerical simulations confirm that the material quality is not compromised during the process. Nonplanar wafer bonding is used to fabricate ultra-wideband wavelength division multiplexed (WDM) vertical-cavity surface-emitting laser (VCSEL) arrays. The optically-pumped VCSEL arrays span 140 nm from 1470 to 1610 nm, a record wavelength span for devices operating in this wavelength range. The array uses eight wavelength channels to span the 140 nm with all channels separated by precisely 20 nm. All channels in the array operate single mode to at least 65°C with output power uniformity of +/- 1 dB. The ultra-wideband WDM VCSEL arrays are a significant first step toward the development of a single-chip source for optical networks based on coarse WDM (CWDM), a low-cost alternative to traditional dense WDM. The CWDM VCSEL arrays make use of fully-oxidized distributed Bragg reflectors (DBRs) to provide the wideband reflectivity required for optical feedback and lasing across 140 rim. In addition, a novel optically-pumped active region design is presented. It is demonstrated, with an analytical model and experimental results, that the new active-region design significantly improves the carrier uniformity in the quantum wells and results in a 50% lasing threshold reduction and a 20°C improvement in the peak

Ontological modelling of knowledge management for human-machine integrated design of ultra-precision grinding machine

NASA Astrophysics Data System (ADS)

Hong, Haibo; Yin, Yuehong; Chen, Xing

2016-11-01

Despite the rapid development of computer science and information technology, an efficient human-machine integrated enterprise information system for designing complex mechatronic products is still not fully accomplished, partly because of the inharmonious communication among collaborators. Therefore, one challenge in human-machine integration is how to establish an appropriate knowledge management (KM) model to support integration and sharing of heterogeneous product knowledge. Aiming at the diversity of design knowledge, this article proposes an ontology-based model to reach an unambiguous and normative representation of knowledge. First, an ontology-based human-machine integrated design framework is described, then corresponding ontologies and sub-ontologies are established according to different purposes and scopes. Second, a similarity calculation-based ontology integration method composed of ontology mapping and ontology merging is introduced. The ontology searching-based knowledge sharing method is then developed. Finally, a case of human-machine integrated design of a large ultra-precision grinding machine is used to demonstrate the effectiveness of the method.

A low-cost, ultra-fast and ultra-low noise preamplifier for silicon avalanche photodiodes

NASA Astrophysics Data System (ADS)

Gasmi, Khaled

2018-02-01

An ultra-fast and ultra-low noise preamplifier for amplifying the fast and weak electrical signals generated by silicon avalanche photodiodes has been designed and developed. It is characterized by its simplicity, compactness, reliability and low cost of construction. A very wide bandwidth of 300 MHz, a very good linearity from 1 kHz to 280 MHz, an ultra-low noise level at the input of only 1.7 nV Hz-1/2 and a very good stability are its key features. The compact size (70 mm  ×  90 mm) and light weight (45 g), as well as its excellent characteristics, make this preamplifier very competitive compared to any commercial preamplifier. The preamplifier, which is a main part of the detection system of a homemade laser remote sensing system, has been successfully tested. In addition, it is versatile and can be used in any optical detection system requiring high speed and very low noise electronics.

Ultra Reliable Closed Loop Life Support for Long Space Missions

NASA Technical Reports Server (NTRS)

Jones, Harry W.; Ewert, Michael K.

2010-01-01

Spacecraft human life support systems can achieve ultra reliability by providing sufficient spares to replace all failed components. The additional mass of spares for ultra reliability is approximately equal to the original system mass, provided that the original system reliability is not too low. Acceptable reliability can be achieved for the Space Shuttle and Space Station by preventive maintenance and by replacing failed units. However, on-demand maintenance and repair requires a logistics supply chain in place to provide the needed spares. In contrast, a Mars or other long space mission must take along all the needed spares, since resupply is not possible. Long missions must achieve ultra reliability, a very low failure rate per hour, since they will take years rather than weeks and cannot be cut short if a failure occurs. Also, distant missions have a much higher mass launch cost per kilogram than near-Earth missions. Achieving ultra reliable spacecraft life support systems with acceptable mass will require a well-planned and extensive development effort. Analysis must determine the reliability requirement and allocate it to subsystems and components. Ultra reliability requires reducing the intrinsic failure causes, providing spares to replace failed components and having "graceful" failure modes. Technologies, components, and materials must be selected and designed for high reliability. Long duration testing is needed to confirm very low failure rates. Systems design should segregate the failure causes in the smallest, most easily replaceable parts. The system must be designed, developed, integrated, and tested with system reliability in mind. Maintenance and reparability of failed units must not add to the probability of failure. The overall system must be tested sufficiently to identify any design errors. A program to develop ultra reliable space life support systems with acceptable mass should start soon since it must be a long term effort.

UWB Bandpass Filter with Ultra-wide Stopband based on Ring Resonator

NASA Astrophysics Data System (ADS)

Kazemi, Maryam; Lotfi, Saeedeh; Siahkamari, Hesam; Mohammadpanah, Mahmood

2018-04-01

An ultra-wideband (UWB) bandpass filter with ultra-wide stopband based on a rectangular ring resonator is presented. The filter is designed for the operational frequency band from 4.10 GHz to 10.80 GHz with an ultra-wide stopband from 11.23 GHz to 40 GHz. The even and odd equivalent circuits are used to achieve a suitable analysis of the proposed filter performance. To verify the design and analysis, the proposed bandpass filter is simulated using full-wave EM simulator Advanced Design System and fabricated on a 20mil thick Rogers_RO4003 substrate with relative permittivity of 3.38 and a loss tangent of 0.0021. The proposed filter behavior is investigated and simulation results are in good agreement with measurement results.

Broadband enhancement of dielectric light trapping nanostructure used in ultra-thin solar cells

NASA Astrophysics Data System (ADS)

Yang, Dong; Xu, Zhaopeng; Bian, Fei; Wang, Haiyan; Wang, Jiazhuang; Sun, Lu

2018-03-01

A dielectric fishnet nanostructure is designed to increase the light trapping capability of ultra-thin solar cells. The complex performance of ultra-thin cells such as the optical response and electrical response are fully quantified in simulation through a complete optoelectronic investigation. The results show that the optimized light trapping nanostructure can enhances the electromagnetic resonance in active layer then lead to extraordinary enhancement of both absorption and light-conversion capabilities in the solar cell. The short-circuit current density increases by 49.46% from 9.40 mA/cm2 to 14.05 mA/cm2 and light-conversion efficiency increases by 51.84% from 9.51% to 14.44% compared to the benchmark, a solar cell with an ITO-GaAs-Ag structure.

DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS TO DATABASES FOR BUILDING STRUCTURE-TOXICITY PREDICTION MODELS

EPA Science Inventory

DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction Models
Ann M. Richard
US Environmental Protection Agency, Research Triangle Park, NC, USA

Distributed: Decentralized set of standardized, field-delimited databases,...

Rhabdomyolysis and exercise-associated hyponatremia in ultra-bikers and ultra-runners.

PubMed

Chlíbková, Daniela; Knechtle, Beat; Rosemann, Thomas; Tomášková, Ivana; Novotný, Jan; Žákovská, Alena; Uher, Tomáš

2015-01-01

Exercise-associated hyponatremia (EAH), rhabdomyolysis and renal failure appear to be a unique problem in ultra-endurance racers. We investigated the combined occurrence of EAH and rhabdomyolysis in seven different ultra-endurance races and disciplines (i.e. multi-stage mountain biking, 24-h mountain biking, 24-h ultra-running and 100-km ultra-running). Two (15.4%) ultra-runners (man and woman) from hyponatremic ultra-athletes (n = 13) and four (4%) ultra-runners (four men) from the normonatremic group (n = 100) showed rhabdomyolysis following elevated blood creatine kinase (CK) levels > 10,000 U/L without the development of renal failure and the necessity of a medical treatment. Post-race creatine kinase, plasma and urine creatinine significantly increased, while plasma [Na(+)] and creatine clearance decreased in hyponatremic and normonatremic athletes, respectively. The percentage increase of CK was higher in the hyponatremic compared to the normonatremic group (P < 0.05). Post-race CK levels were higher in ultra-runners compared to mountain bikers (P < 0.01), in faster normonatremic (P < 0.05) and older and more experienced hyponatremic ultra-athletes (P < 0.05). In all finishers, pre-race plasma [K(+)] was related to post-race CK (P < 0.05). Hyponatremic ultra-athletes tended to develop exercise-induced rhabdomyolysis more frequently than normonatremic ultra-athletes. Ultra-runners tended to develop rhabdomyolysis more frequently than mountain bikers. We found no association between post-race plasma [Na(+)] and CK concentration in both hypo- and normonatremic ultra-athletes.

Controlled nanostructrures formation by ultra fast laser pulses for color marking.

PubMed

Dusser, B; Sagan, Z; Soder, H; Faure, N; Colombier, J P; Jourlin, M; Audouard, E

2010-02-01

Precise nanostructuration of surface and the subsequent upgrades in material properties is a strong outcome of ultra fast laser irradiations. Material characteristics can be designed on mesoscopic scales, carrying new optical properties. We demonstrate in this work, the possibility of achieving material modifications using ultra short pulses, via polarization dependent structures generation, that can generate specific color patterns. These oriented nanostructures created on the metal surface, called ripples, are typically smaller than the laser wavelength and in the range of visible spectrum. In this way, a complex colorization process of the material, involving imprinting, calibration and reading, has been performed to associate a priori defined colors. This new method based on the control of the laser-driven nanostructure orientation allows cumulating high quantity of information in a minimal surface, proposing new applications for laser marking and new types of identifying codes.

Applying AN Object-Oriented Database Model to a Scientific Database Problem: Managing Experimental Data at Cebaf.

NASA Astrophysics Data System (ADS)

Ehlmann, Bryon K.

Current scientific experiments are often characterized by massive amounts of very complex data and the need for complex data analysis software. Object-oriented database (OODB) systems have the potential of improving the description of the structure and semantics of this data and of integrating the analysis software with the data. This dissertation results from research to enhance OODB functionality and methodology to support scientific databases (SDBs) and, more specifically, to support a nuclear physics experiments database for the Continuous Electron Beam Accelerator Facility (CEBAF). This research to date has identified a number of problems related to the practical application of OODB technology to the conceptual design of the CEBAF experiments database and other SDBs: the lack of a generally accepted OODB design methodology, the lack of a standard OODB model, the lack of a clear conceptual level in existing OODB models, and the limited support in existing OODB systems for many common object relationships inherent in SDBs. To address these problems, the dissertation describes an Object-Relationship Diagram (ORD) and an Object-oriented Database Definition Language (ODDL) that provide tools that allow SDB design and development to proceed systematically and independently of existing OODB systems. These tools define multi-level, conceptual data models for SDB design, which incorporate a simple notation for describing common types of relationships that occur in SDBs. ODDL allows these relationships and other desirable SDB capabilities to be supported by an extended OODB system. A conceptual model of the CEBAF experiments database is presented in terms of ORDs and the ODDL to demonstrate their functionality and use and provide a foundation for future development of experimental nuclear physics software using an OODB approach.

The Xeno-glycomics database (XDB): a relational database of qualitative and quantitative pig glycome repertoire.

PubMed

Park, Hae-Min; Park, Ju-Hyeong; Kim, Yoon-Woo; Kim, Kyoung-Jin; Jeong, Hee-Jin; Jang, Kyoung-Soon; Kim, Byung-Gee; Kim, Yun-Gon

2013-11-15

In recent years, the improvement of mass spectrometry-based glycomics techniques (i.e. highly sensitive, quantitative and high-throughput analytical tools) has enabled us to obtain a large dataset of glycans. Here we present a database named Xeno-glycomics database (XDB) that contains cell- or tissue-specific pig glycomes analyzed with mass spectrometry-based techniques, including a comprehensive pig glycan information on chemical structures, mass values, types and relative quantities. It was designed as a user-friendly web-based interface that allows users to query the database according to pig tissue/cell types or glycan masses. This database will contribute in providing qualitative and quantitative information on glycomes characterized from various pig cells/organs in xenotransplantation and might eventually provide new targets in the α1,3-galactosyltransferase gene-knock out pigs era. The database can be accessed on the web at http://bioinformatics.snu.ac.kr/xdb.

The CEBAF Element Database

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theodore Larrieu, Christopher Slominski, Michele Joyce

2011-03-01

With the inauguration of the CEBAF Element Database (CED) in Fall 2010, Jefferson Lab computer scientists have taken a step toward the eventual goal of a model-driven accelerator. Once fully populated, the database will be the primary repository of information used for everything from generating lattice decks to booting control computers to building controls screens. A requirement influencing the CED design is that it provide access to not only present, but also future and past configurations of the accelerator. To accomplish this, an introspective database schema was designed that allows new elements, types, and properties to be defined on-the-fly withmore » no changes to table structure. Used in conjunction with Oracle Workspace Manager, it allows users to query data from any time in the database history with the same tools used to query the present configuration. Users can also check-out workspaces to use as staging areas for upcoming machine configurations. All Access to the CED is through a well-documented Application Programming Interface (API) that is translated automatically from original C++ source code into native libraries for scripting languages such as perl, php, and TCL making access to the CED easy and ubiquitous.« less

The Cambridge Structural Database in retrospect and prospect.

PubMed

Groom, Colin R; Allen, Frank H

2014-01-13

The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal-organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700,000 structures and is a comprehensive and fully retrospective historical archive of small-molecule crystallography. Nearly 40,000 new structures are added each year. As X-ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self-financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC's funding model in relation to open access and open data paradigms. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

De novo design and synthesis of ultra-short peptidomimetic antibiotics having dual antimicrobial and anti-inflammatory activities.

PubMed

Murugan, Ravichandran N; Jacob, Binu; Ahn, Mija; Hwang, Eunha; Sohn, Hoik; Park, Hyo-Nam; Lee, Eunjung; Seo, Ji-Hyung; Cheong, Chaejoon; Nam, Ky-Youb; Hyun, Jae-Kyung; Jeong, Ki-Woong; Kim, Yangmee; Shin, Song Yub; Bang, Jeong Kyu

2013-01-01

Much attention has been focused on the design and synthesis of potent, cationic antimicrobial peptides (AMPs) that possess both antimicrobial and anti-inflammatory activities. However, their development into therapeutic agents has been limited mainly due to their large size (12 to 50 residues in length) and poor protease stability. In an attempt to overcome the issues described above, a set of ultra-short, His-derived antimicrobial peptides (HDAMPs) has been developed for the first time. Through systematic tuning of pendant hydrophobic alkyl tails at the N(π)- and N(τ)-positions on His, and the positive charge of Arg, much higher prokaryotic selectivity was achieved, compared to human AMP LL-37. Additionally, the most potent HDAMPs showed promising dual antimicrobial and anti-inflammatory activities, as well as anti-methicillin-resistant Staphylococcus aureus (MRSA) activity and proteolytic resistance. Our results from transmission electron microscopy, membrane depolarization, confocal laser-scanning microscopy, and calcein-dye leakage experiments propose that HDAMP-1 kills microbial cells via dissipation of the membrane potential by forming pore/ion channels on bacterial cell membranes. The combination of the ultra-short size, high-prokaryotic selectivity, potent anti-MRSA activity, anti-inflammatory activity, and proteolytic resistance of the designed HDAMP-1, -3, -5, and -6 makes these molecules promising candidates for future antimicrobial therapeutics.

Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database.

PubMed

Akune, Yukie; Lin, Chi-Hung; Abrahams, Jodie L; Zhang, Jingyu; Packer, Nicolle H; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P

2016-08-05

Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database. Copyright © 2016 Elsevier Ltd. All rights reserved.

First year progress report on the development of the Texas flexible pavement database.

DOT National Transportation Integrated Search

2008-01-01

Comprehensive and reliable databases are essential for the development, validation, and calibration of any pavement : design and rehabilitation system. These databases should include material properties, pavement structural : characteristics, highway...

Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.

PubMed

Naghdi, Mohammad Reza; Smail, Katia; Wang, Joy X; Wade, Fallou; Breaker, Ronald R; Perreault, Jonathan

2017-03-15

The discovery of noncoding RNAs (ncRNAs) and their importance for gene regulation led us to develop bioinformatics tools to pursue the discovery of novel ncRNAs. Finding ncRNAs de novo is challenging, first due to the difficulty of retrieving large numbers of sequences for given gene activities, and second due to exponential demands on calculation needed for comparative genomics on a large scale. Recently, several tools for the prediction of conserved RNA secondary structure were developed, but many of them are not designed to uncover new ncRNAs, or are too slow for conducting analyses on a large scale. Here we present various approaches using the database RiboGap as a primary tool for finding known ncRNAs and for uncovering simple sequence motifs with regulatory roles. This database also can be used to easily extract intergenic sequences of eubacteria and archaea to find conserved RNA structures upstream of given genes. We also show how to extend analysis further to choose the best candidate ncRNAs for experimental validation. Copyright © 2017 Elsevier Inc. All rights reserved.

Ultra-wideband high-speed Mach-Zehnder switch based on hybrid plasmonic waveguides.

PubMed

Janjan, Babak; Fathi, Davood; Miri, Mehdi; Ghaffari-Miab, Mohsen

2017-02-20

In this paper, the distinctive dispersion characteristic of hybrid plasmonic waveguides is exploited for designing ultra-wideband directional couplers. It is shown that by using optimized geometrical dimensions for hybrid plasmonic waveguides, nearly wavelength-independent directional couplers can be achieved. These broadband directional couplers are then used to design Mach-Zehnder-interferometer-based switches. Our simulation results show the ultra-wide bandwidth of ∼260  nm for the proposed hybrid plasmonic-waveguide-based switch. Further investigation of the proposed Mach-Zehnder switch confirms that because of the strong light confinement in the hybrid plasmonic waveguide structure, the switching time, power consumption, and overall footprint of the device can be significantly improved compared to silicon-ridge-waveguide-based Mach-Zehnder switches. For the Mach-Zehnder switch designed by using the optimized directional coupler, the switching time is found to be less than one picosecond, while the power consumption, V_πL_π figure of merit, and active length of the device are ∼61  fJ/bit, 85  V×μm, and 30 μm, respectively.

Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces.

PubMed

Ezra Tsur, Elishai

2017-01-01

Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed. The framework supports user-designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c.dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3-dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http://nbel-lab.com.

An improved ultra-wideband bandpass filter design using split ring resonator with coupled microstrip line

NASA Astrophysics Data System (ADS)

Umeshkumar, Dubey Suhmita; Kumar, Manish

2018-04-01

This paper incorporates an improved design of Ultra Wideband Bandpass filter by using split ring resonators (SRR) along with the coupled microstrip lines. The use of split ring resonators and shunt step impedance open circuit stub enhances the stability due to transmission zeroes at the ends. The designing of filter and simulation of parameters is carried out using Ansoft's HFSS 13.0 software on RT/Duroid 6002 as a substrate with dielectric constant of 2.94. The design utilizes a frequency band from 22GHz to 29GHz. This band is reserved for Automotive Radar system and sensors as per FCC specifications. The proposed design demonstrates insertion loss less than 0.6dB and return loss better than 12dB at mid frequency i.e. 24.4GHz. The reflection coefficient shows high stability of about 12.47dB at mid frequency. The fractional bandwidth of the proposed filter is about 28.7% and size of filter design is small due to thickness of 0.127mm.

Ultra-spatial synchrotron radiation for imaging molecular chemical structure: Applications in plant and animal studies

DOE PAGES

Yu, Peiqiang

2007-01-01

Synchrotron-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical features and make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced synchrotron technique to the study of plant and animal tissues' inherent structure at a cellular or subcellular level. In this article, a novel approach was introduced to show the potential of themore » newly developed, advanced synchrotron-based analytical technology, which can be used to reveal molecular structural-chemical features of various plant and animal tissues.« less

The MAJORANA Parts Tracking Database

NASA Astrophysics Data System (ADS)

Abgrall, N.; Aguayo, E.; Avignone, F. T.; Barabash, A. S.; Bertrand, F. E.; Brudanin, V.; Busch, M.; Byram, D.; Caldwell, A. S.; Chan, Y.-D.; Christofferson, C. D.; Combs, D. C.; Cuesta, C.; Detwiler, J. A.; Doe, P. J.; Efremenko, Yu.; Egorov, V.; Ejiri, H.; Elliott, S. R.; Esterline, J.; Fast, J. E.; Finnerty, P.; Fraenkle, F. M.; Galindo-Uribarri, A.; Giovanetti, G. K.; Goett, J.; Green, M. P.; Gruszko, J.; Guiseppe, V. E.; Gusev, K.; Hallin, A. L.; Hazama, R.; Hegai, A.; Henning, R.; Hoppe, E. W.; Howard, S.; Howe, M. A.; Keeter, K. J.; Kidd, M. F.; Kochetov, O.; Konovalov, S. I.; Kouzes, R. T.; LaFerriere, B. D.; Leon, J. Diaz; Leviner, L. E.; Loach, J. C.; MacMullin, J.; Martin, R. D.; Meijer, S. J.; Mertens, S.; Miller, M. L.; Mizouni, L.; Nomachi, M.; Orrell, J. L.; O`Shaughnessy, C.; Overman, N. R.; Petersburg, R.; Phillips, D. G.; Poon, A. W. P.; Pushkin, K.; Radford, D. C.; Rager, J.; Rielage, K.; Robertson, R. G. H.; Romero-Romero, E.; Ronquest, M. C.; Shanks, B.; Shima, T.; Shirchenko, M.; Snavely, K. J.; Snyder, N.; Soin, A.; Suriano, A. M.; Tedeschi, D.; Thompson, J.; Timkin, V.; Tornow, W.; Trimble, J. E.; Varner, R. L.; Vasilyev, S.; Vetter, K.; Vorren, K.; White, B. R.; Wilkerson, J. F.; Wiseman, C.; Xu, W.; Yakushev, E.; Young, A. R.; Yu, C.-H.; Yumatov, V.; Zhitnikov, I.

2015-04-01

The MAJORANA DEMONSTRATOR is an ultra-low background physics experiment searching for the neutrinoless double beta decay of 76Ge. The MAJORANA Parts Tracking Database is used to record the history of components used in the construction of the DEMONSTRATOR. The tracking implementation takes a novel approach based on the schema-free database technology CouchDB. Transportation, storage, and processes undergone by parts such as machining or cleaning are linked to part records. Tracking parts provide a great logistics benefit and an important quality assurance reference during construction. In addition, the location history of parts provides an estimate of their exposure to cosmic radiation. A web application for data entry and a radiation exposure calculator have been developed as tools for achieving the extreme radio-purity required for this rare decay search.

Reliability-based econometrics of aerospace structural systems: Design criteria and test options. Ph.D. Thesis - Georgia Inst. of Tech.

NASA Technical Reports Server (NTRS)

Thomas, J. M.; Hanagud, S.

1974-01-01

The design criteria and test options for aerospace structural reliability were investigated. A decision methodology was developed for selecting a combination of structural tests and structural design factors. The decision method involves the use of Bayesian statistics and statistical decision theory. Procedures are discussed for obtaining and updating data-based probabilistic strength distributions for aerospace structures when test information is available and for obtaining subjective distributions when data are not available. The techniques used in developing the distributions are explained.

Design of an Ultra-wide Band Waveguide Transition for the Ex-vessel Transmission Line of ITER Plasma Position Reflectometry

NASA Astrophysics Data System (ADS)

Simonetto, A.; Platania, P.; Garavaglia, S.; Gittini, G.; Granucci, G.; Pallotta, F.

2018-02-01

Plasma position reflectometry for ITER requires interfaces between in-vessel and ex-vessel waveguides. An ultra broadband interface (15-75 GHz) was designed between moderately oversized rectangular waveguide (20 × 12 mm), operated in TE01 (i.e., tall waveguide mode), and circular corrugated waveguide, with 88.9-mm internal diameter, propagating HE11. The interface was designed both as a sequence of waveguide components and as a quasi-optical confocal telescope. The design and the simulated performance are described for both concepts. The latter one requires more space but has better performance, and shall be prototyped.

Induced radioactivity of LDEF materials and structural components

NASA Technical Reports Server (NTRS)

Harmon, B. A.; Laird, C. E.; Fishman, G. J.; Parnell, T. A.; Camp, D. C.; Frederick, C. E.; Hurley, D. L.; Lindstrom, D. J.; Moss, C. E.; Reedy, R. C.;

Structural and Machine Design Using Piezoceramic Materials: A Guide for Structural Design Engineers

NASA Technical Reports Server (NTRS)

Inman, Daniel J.; Cudney, Harley H.

2000-01-01

Using piezoceramic materials is one way the design engineer can create structures which have an ability to both sense and respond to their environment. Piezoceramic materials can be used to create structural sensors and structural actuators. Because piezoceramic materials have transduction as a material property, their sensing or actuation functions are a result of what happens to the material. This is different than discrete devices we might attach to the structure. For example, attaching an accelerometer to a structure will yield an electrical signal proportional to the acceleration at the attachment point on the structure. Using a electromagnetic shaker as an actuator will create an applied force at the attachment point. Active material elements in a structural design are not easily modeled as providing transduction at a point, but rather they change the physics of the structure in the areas where they are used. Hence, a designer must not think of adding discrete devices to a structure to obtain an effect, but rather must design a structural system which accounts for the physical principles of all the elements in the structure. The purpose of this manual is to provide practicing engineers the information necessary to incorporate piezoelectric materials in structural design and machine design. First, we will review the solid-state physics of piezoelectric materials. Then we will discuss the physical characteristics of the electrical-active material-structural system. We will present the elements of this system which must be considered as part of the design task for a structural engineer. We will cover simple modeling techniques and review the features and capabilities of commercial design tools that are available. We will then cover practical how-to elements of working with piezoceramic materials. We will review sources of piezoceramic materials and built-up devices, and their characteristics. Finally, we will provide two design examples using piezoceramic

EVALUATING AND DESIGNING ULTRA-LOW-COST SOLAR WATER HEATING SYSTEMS

EPA Science Inventory

This project will have three key outputs:

1. an evaluation of the thermal performance of ultra-low-cost solar components, with components being characterized by their absorbed solar energy per cost;
2. a built demonstration prototype of...

3. Ultra-sensitive probe of spectral line structure and detection of isotopic oxygen

   NASA Astrophysics Data System (ADS)

   Garner, Richard M.; Dharamsi, A. N.; Khan, M. Amir

   2018-01-01

   We discuss a new method of investigating and obtaining quantitative behavior of higher harmonic (> 2f) wavelength modulation spectroscopy (WMS) based on the signal structure. It is shown that the spectral structure of higher harmonic WMS signals, quantified by the number of zero crossings and turnings points, can have increased sensitivity to ambient conditions or line-broadening effects from changes in temperature, pressure, or optical depth. The structure of WMS signals, characterized by combinations of signal magnitude and spectral locations of turning points and zero crossings, provides a unique scale that quantifies lineshape parameters and, thus, useful in optimization of measurements obtained from multi-harmonic WMS signals. We demonstrate this by detecting weaker rotational-vibrational transitions of isotopic atmospheric oxygen (16O18O) in the near-infrared region where higher harmonic WMS signals are more sensitive contrary to their signal-to-noise ratio considerations. The proposed approach based on spectral structure provides the ability to investigate and quantify signals not only at linecenter but also in the wing region of the absorption profile. This formulation is particularly useful in tunable diode laser spectroscopy and ultra-precision laser-based sensors where absorption signal profile carries information of quantities of interest, e.g., concentration, velocity, or gas collision dynamics, etc.

4. Analysing and Rationalising Molecular and Materials Databases Using Machine-Learning

   NASA Astrophysics Data System (ADS)

   de, Sandip; Ceriotti, Michele

   Computational materials design promises to greatly accelerate the process of discovering new or more performant materials. Several collaborative efforts are contributing to this goal by building databases of structures, containing between thousands and millions of distinct hypothetical compounds, whose properties are computed by high-throughput electronic-structure calculations. The complexity and sheer amount of information has made manual exploration, interpretation and maintenance of these databases a formidable challenge, making it necessary to resort to automatic analysis tools. Here we will demonstrate how, starting from a measure of (dis)similarity between database items built from a combination of local environment descriptors, it is possible to apply hierarchical clustering algorithms, as well as dimensionality reduction methods such as sketchmap, to analyse, classify and interpret trends in molecular and materials databases, as well as to detect inconsistencies and errors. Thanks to the agnostic and flexible nature of the underlying metric, we will show how our framework can be applied transparently to different kinds of systems ranging from organic molecules and oligopeptides to inorganic crystal structures as well as molecular crystals. Funded by National Center for Computational Design and Discovery of Novel Materials (MARVEL) and Swiss National Science Foundation.

5. Sentence-Based Metadata: An Approach and Tool for Viewing Database Designs.

   ERIC Educational Resources Information Center

   Boyle, John M.; Gunge, Jakob; Bryden, John; Librowski, Kaz; Hanna, Hsin-Yi

   2002-01-01

   Describes MARS (Museum Archive Retrieval System), a research tool which enables organizations to exchange digital images and documents by means of a common thesaurus structure, and merge the descriptive data and metadata of their collections. Highlights include theoretical basis; searching the MARS database; and examples in European museums.…

6. [Design of computerised database for clinical and basic management of uveal melanoma].

   PubMed

   Bande Rodríguez, M F; Santiago Varela, M; Blanco Teijeiro, M J; Mera Yañez, P; Pardo Perez, M; Capeans Tome, C; Piñeiro Ces, A

   2012-09-01

   The uveal melanoma is the most common primary intraocular tumour in adults. The objective of this work is to show how a computerised database has been formed with specific applications, for clinical and research use, to an extensive group of patients diagnosed with uveal melanoma. For the design of the database a selection of categories, attributes and values was created based on the classifications and parameters given by various authors of articles which have had great relevance in the field of uveal melanoma in recent years. The database has over 250 patient entries with specific information on their clinical history, diagnosis, treatment and progress. It enables us to search any parameter of the entry and make quick and simple statistical studies of them. The database models have been transformed into a basic tool for clinical practice, as they are an efficient way of storing, compiling and selective searching of information. When creating a database it is very important to define a common strategy and the use of a standard language. Copyright © 2011 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

7. Heterogeneous Biomedical Database Integration Using a Hybrid Strategy: A p53 Cantcer Research Database

   PubMed Central

   Bichutskiy, Vadim Y.; Colman, Richard; Brachmann, Rainer K.; Lathrop, Richard H.

   2006-01-01

   Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.) PMID:19458771

Designing an Integrated System of Databases: A Workstation for Information Seekers.

ERIC Educational Resources Information Center

Micco, Mary; Smith, Irma

1987-01-01

Proposes a framework for the design of a full function workstation for information retrieval based on study of information seeking behavior. A large amount of local storage of the CD-ROM jukebox variety and full networking capability to both local and external databases are identified as requirements of the prototype. (MES)

A new design of photonic crystal fiber with ultra-flattened dispersion to simultaneously minimize the dispersion and confinement loss

NASA Astrophysics Data System (ADS)

Olyaee, Saeed; Taghipour, Fahimeh

2011-02-01

Photonic crystal fibers (PCFs) are highly suitable transmission media for wavelength-division-multiplexing (WDM) systems, in which low and ultra-flattened dispersion of PCFs is extremely desirable. It is also required to concurrently achieve both a low confinement loss as well as a large effective area in a wide range of wavelengths. Relatively low dispersion with negligible variation has become feasible in the wavelength range of 1.1 to 1.8μm through the proposed design in this paper. According to a new structure of PCF presented in this study, the dispersion slope is 6.8×10-4ps/km.nm2 and the confinement loss reaches below 10-6 dB/km in this range, while at the same time an effective area of more than 50μm2 has been attained. For the analysis of this PCF, finite-difference time-domain (FDTD) method with the perfectly matched layers (PML) boundary conditions has been used.

Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.

PubMed Central

Billoud, B; Kontic, M; Viari, A

1996-01-01

At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usually dedicated to particular structures and are written using general purpose programming languages through a complex and time consuming process where the biological problem of defining the structure and the computer engineering problem of looking for it are intimately intertwined. In this paper, we describe a general representation of structures, suitable for database scanning, together with a programming language, Palingol, designed to manipulate it. Palingol has specific data types, corresponding to structural elements-basically helices-that can be arranged in any way to form a complex structure. As a consequence of the declarative approach used in Palingol, the user should only focus on 'what to search for' while the language engine takes care of 'how to look for it'. Therefore, it becomes simpler to write a scanning program and the structural constraints that define the required structure are more clearly identified. PMID:8628670

Ultra-high Temperature Emittance Measurements for Space and Missile Applications

NASA Technical Reports Server (NTRS)

Rogers, Jan; Crandall, David

2009-01-01

Advanced modeling and design efforts for many aerospace components require high temperature emittance data. Applications requiring emittance data include propulsion systems, radiators, aeroshells, heatshields/thermal protection systems, and leading edge surfaces. The objective of this work is to provide emittance data at ultra-high temperatures. MSFC has a new instrument for the measurement of emittance at ultra-high temperatures, the Ultra-High Temperature Emissometer System (Ultra-HITEMS). AZ Technology Inc. developed the instrument, designed to provide emittance measurements over the temperature range 700-3500K. The Ultra-HITEMS instrument measures the emittance of samples, heated by lasers, in vacuum, using a blackbody source and a Fourier Transform Spectrometer. Detectors in a Nicolet 6700 FT-IR spectrometer measure emittance over the spectral range of 0.4-25 microns. Emitted energy from the specimen and output from a Mikron M390S blackbody source at the same temperature with matched collection geometry are measured. Integrating emittance over the spectral range yields the total emittance. The ratio provides a direct measure of total hemispherical emittance. Samples are heated using lasers. Optical pyrometry provides temperature data. Optical filters prevent interference from the heating lasers. Data for Inconel 718 show excellent agreement with results from literature and ASTM 835. Measurements taken from levitated spherical specimens provide total hemispherical emittance data; measurements taken from flat specimens mounted in the chamber provide near-normal emittance data. Data from selected characterization studies will be presented. The Ultra-HITEMS technique could advance space and missile technologies by advancing the knowledge base and the technology readiness level for ultra-high temperature materials.

Mobile-bearing knee systems: ultra-high molecular weight polyethylene wear and design issues.

PubMed

Greenwald, A Seth; Heim, Christine S

2005-01-01

In June 2004, the U.S. Food and Drug Administration Orthopaedic Advisory Panel recommended the reclassification of mobile-bearing knee systems for general use. This reflects the increasing use of mobile-bearing knee systems internationally, which is currently limited in the United States by regulatory requirement. Mobile-bearing knee systems are distinguished from conventional, fixed-plateau systems in that they allow dual-surface articulation between an ultra-high molecular weight polyethylene insert and metallic femoral and tibial tray components. Their in vivo success is dependent on patient selection, design, and material choice, as well as surgical precision during implantation. Laboratory and clinical experience extending over 25 years with individual systems suggests that mobile-bearing knee systems represent a viable treatment option for patients with knee arthrosis.

Bias Selectable Dual Band AlGaN Ultra-violet Detectors

NASA Technical Reports Server (NTRS)

Yan, Feng; Miko, Laddawan; Franz, David; Guan, Bing; Stahle, Carl M.

2007-01-01

Bias selectable dual band AlGaN ultra-violet (UV) detectors, which can separate UV-A and UV-B using one detector in the same pixel by bias switching, have been designed, fabricated and characterized. A two-terminal n-p-n photo-transistor-like structure was used. When a forward bias is applied between the top electrode and the bottom electrode, the detectors can successfully detect W-A and reject UV-B. Under reverse bias, they can detect UV-B and reject UV-A. The proof of concept design shows that it is feasible to fabricate high performance dual-band UV detectors based on the current AlGaN material growth and fabrication technologies.

Template-free synthesis of porous ZnO/Ag microspheres as recyclable and ultra-sensitive SERS substrates

NASA Astrophysics Data System (ADS)

Liu, Yanjun; Xu, Chunxiang; Lu, Junfeng; Zhu, Zhu; Zhu, Qiuxiang; Manohari, A. Gowri; Shi, Zengliang

2018-01-01

The porous structured zinc oxide (ZnO) microspheres decorated with silver nanoparticles (Ag NPs) have been fabricated as surface-enhanced Raman scattering (SERS) substrate for ultra-sensitive, highly reproducible and stable biological/chemical sensing of various organic molecules. The ZnO microspheres were hydrothermally synthesized without any template, and the Ag NPs decorated on microspheres via photochemical reaction in situ, which provided stable Ag/ZnO contact to achieve a sensitive SERS response. It demonstrates a higher enhancement factor (EF) of 2.44 × 1011 and a lower detection limit of 10-11 M-10-12 M. This porous SERS substrate could also be self-cleaned through a photocatalytic process and then further recycled for the detection of same or different molecules, such as phenol red (PhR), dopamine (DA) and glucose (GLU) with ultra-low concentration and it possessed a sensitive response. The excellent performances are attributed to morphology of porous microspheres, hybrid structure of semiconductor/metal and corresponding localized field enhancement of surface plasmons. Therefore, it is expected to design the recyclable ultra-sensitive SERS sensors for the detection of biological molecules and organic pollutant monitoring.

Structural Transitions in Elemental Tin at Ultra High Pressures up to 230 GPa

NASA Astrophysics Data System (ADS)

Gavriliuk, A. G.; Troyan, I. A.; Ivanova, A. G.; Aksenov, S. N.; Starchikov, S. S.; Lyubutin, I. S.; Morgenroth, W.; Glazyrin, K. V.; Mezouar, M.

2017-12-01

The crystal structure of elemental Sn was investigated by synchrotron X-ray diffraction at ultra high pressures up to ˜230 GPa creating in diamond anvil cells. Above 70 GPa, a pure bcc structure of Sn was observed, which is stable up to 160GPa, until an occurrence of the hcp phase was revealed. At the onset of the bcc- hcp transition at pressure of about 160GPa, the drop of the unit cell volume is about 1%. A mixture of the bcc- hcp states was observed at least up to 230GPa, and it seems that this state could exist even up to higher pressures. The fractions of the bcc and hcp phases were evaluated in the pressure range of the phase coexistence 160-230 GPa. The difference between static and dynamic compression and its effect on the V- P phase diagram of Sn are discussed.

The Protein-DNA Interface database

PubMed Central

2010-01-01

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 Å or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface. We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes. PMID:20482798

The Protein-DNA Interface database.

PubMed

Norambuena, Tomás; Melo, Francisco

2010-05-18

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 A or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface.We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes.

Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration

PubMed Central

Gražulis, Saulius; Daškevič, Adriana; Merkys, Andrius; Chateigner, Daniel; Lutterotti, Luca; Quirós, Miguel; Serebryanaya, Nadezhda R.; Moeck, Peter; Downs, Robert T.; Le Bail, Armel

2012-01-01

Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge. PMID:22070882

Solar assisted alkali pretreatment of garden biomass: Effects on lignocellulose degradation, enzymatic hydrolysis, crystallinity and ultra-structural changes in lignocellulose.

PubMed

Gabhane, Jagdish; William, S P M Prince; Vaidya, Atul N; Das, Sera; Wate, Satish R

2015-06-01

A comprehensive study was carried out to assess the effectiveness of solar assisted alkali pretreatment (SAAP) on garden biomass (GB). The pretreatment efficiency was assessed based on lignocellulose degradation, conversion of cellulose into reducing sugars, changes in the ultra-structure and functional groups of lignocellulose and impact on the crystallinity of cellulose, etc. SAAP was found to be efficient for the removal of lignin and hemicellulose that facilitated enzymatic hydrolysis of cellulose. FTIR and XRD studies provided details on the effectiveness of SAAP on lignocellulosic moiety and crystallinity of cellulose. Scanning electron microscopic analysis showed ultra-structural disturbances in the microfibrils of GB as a result of pretreatment. The mass balance closer of 97.87% after pretreatment confirmed the reliability of SAAP pretreatment. Based on the results, it is concluded that SAAP is not only an efficient means of pretreatment but also economical as it involved no energy expenditure for heat generation during pretreatment. Copyright © 2015 Elsevier Ltd. All rights reserved.

An approach in building a chemical compound search engine in oracle database.

PubMed

Wang, H; Volarath, P; Harrison, R

2005-01-01

A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

De Novo Design and Synthesis of Ultra-Short Peptidomimetic Antibiotics Having Dual Antimicrobial and Anti-Inflammatory Activities

PubMed Central

Ahn, Mija; Hwang, Eunha; Sohn, Hoik; Park, Hyo-Nam; Lee, Eunjung; Seo, Ji-Hyung; Cheong, Chaejoon; Nam, Ky-Youb; Hyun, Jae-Kyung; Jeong, Ki-Woong; Kim, Yangmee; Shin, Song Yub; Bang, Jeong Kyu

2013-01-01

Background Much attention has been focused on the design and synthesis of potent, cationic antimicrobial peptides (AMPs) that possess both antimicrobial and anti-inflammatory activities. However, their development into therapeutic agents has been limited mainly due to their large size (12 to 50 residues in length) and poor protease stability. Methodology/Principal Findings In an attempt to overcome the issues described above, a set of ultra-short, His-derived antimicrobial peptides (HDAMPs) has been developed for the first time. Through systematic tuning of pendant hydrophobic alkyl tails at the N(π)- and N(τ)-positions on His, and the positive charge of Arg, much higher prokaryotic selectivity was achieved, compared to human AMP LL-37. Additionally, the most potent HDAMPs showed promising dual antimicrobial and anti-inflammatory activities, as well as anti–methicillin-resistant Staphylococcus aureus (MRSA) activity and proteolytic resistance. Our results from transmission electron microscopy, membrane depolarization, confocal laser-scanning microscopy, and calcein-dye leakage experiments propose that HDAMP-1 kills microbial cells via dissipation of the membrane potential by forming pore/ion channels on bacterial cell membranes. Conclusion/Significance The combination of the ultra-short size, high-prokaryotic selectivity, potent anti-MRSA activity, anti-inflammatory activity, and proteolytic resistance of the designed HDAMP-1, -3, -5, and -6 makes these molecules promising candidates for future antimicrobial therapeutics. PMID:24302996

Performance Investigation on an Ultra-compact Interstage Turbine Burner with Trapped-vortex Slot Inlet

NASA Astrophysics Data System (ADS)

Zhang, Hongtao; Luo, Guangqi; Guan, Lei; Zeng, Jianchen

2017-10-01

Ultra-Compact Combustor (UCC), which is one of mainstream design concepts of Interstage Turbine Burner (ITB), has the advantages of compact structure and high combustion efficiency. A design concept of an UCC with trapped-vortex slot inlet was proposed and numerical simulation of the stability, emissions, internal flow velocity and temperature distribution was carried out. The results indicated that the UCC with trapped-vortex slot inlet could enhance the mixing of combustion mixture and the mainstream airflow, improve the combustion efficiency, outlet temperature and the uniformity of outlet temperature field.

The Majorana Parts Tracking Database

DOE PAGES

Abgrall, N.; Aguayo, E.; Avignone, F. T.; ...

2015-01-16

The Majorana Demonstrator is an ultra-low background physics experiment searching for the neutrinoless double beta decay of 76Ge. The Majorana Parts Tracking Database is used to record the history of components used in the construction of the Demonstrator. The tracking implementation takes a novel approach based on the schema-free database technology CouchDB. Transportation, storage, and processes undergone by parts such as machining or cleaning are linked to part records. Tracking parts provides a great logistics benefit and an important quality assurance reference during construction. In addition, the location history of parts provides an estimate of their exposure to cosmic radiation.more » In summary, a web application for data entry and a radiation exposure calculator have been developed as tools for achieving the extreme radio-purity required for this rare decay search.« less

Ultra-short beam expander with segmented curvature control: the emergence of a semi-lens

DOE PAGES

Abbaslou, Siamak; Gatdula, Robert; Lu, Ming; ...

2017-01-01

We introduce direct curvature control in designing a segmented beam expander, and explore novel design possibilities for ultra-compact beam expanders. Assisted by the particle swarm optimization algorithm, we search for an optimal curvature-controlled multi-segment taper that maintains width continuity. Counterintuitively, the optimization yields a structure with abrupt width discontinuity and width compression features. Through spatial phase and parameterized analysis, a semi-lens feature is revealed that helps to flatten the wavefront at the output end for higher coupling efficiency. Such functionality cannot be achieved by normal tapers in a short distance. The structure is fabricated and characterized experimentally. By a figuremore » of merit that accounts for expansion ratio, length, and efficiency, this structure outperforms an adiabatic taper by 9 times.« less

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.

PubMed

Wu, Gang; Zheng, Yuanpu; Qureshi, Imran; Zin, Htar Thant; Beck, Tyler; Bulka, Blazej; Freeland, Stephen J

2007-01-01

Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index.php, or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at http://www.evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27.

Establishment of Kansei Database and Application to Design for Consensus Building

NASA Astrophysics Data System (ADS)

Yasuda, Keiichi; Shiraki, Wataru

Reflecting the recent social background where the importance of bridge landscape design is recognized and the new business style of citizen-involved infrastructure development has started, there has been a growing need of design where aesthetic feeling of actual users is reflected. In this research, a focus has been placed on the Kansei engineering technique where users' needs are reflected on product development. A questionnaire survey has been conducted for bridge engineers who are most intensively involved in design work and students as actual users. The result was analyzed by factor analysis and the Hayashi's quantification methods (category I). A tool required at consensus-building occasions has been created to change design elements and display accompanying evaluation difference while using the Kansei database.

Structural Design of Ares V Interstage Composite Structure

NASA Technical Reports Server (NTRS)

Sleigh, David W.; Sreekantamurthy, Thammaiah; Kosareo, Daniel N.; Martin, Robert A.; Johnson, Theodore F.

2011-01-01

Preliminary and detailed design studies were performed to mature composite structural design concepts for the Ares V Interstage structure as a part of NASA s Advanced Composite Technologies Project. Aluminum honeycomb sandwich and hat-stiffened composite panel structural concepts were considered. The structural design and analysis studies were performed using HyperSizer design sizing software and MSC Nastran finite element analysis software. System-level design trade studies were carried out to predict weight and margins of safety for composite honeycomb-core sandwich and composite hat-stiffened skin design concepts. Details of both preliminary and detailed design studies are presented in the paper. For the range of loads and geometry considered in this work, the hat-stiffened designs were found to be approximately 11-16 percent lighter than the sandwich designs. A down-select process was used to choose the most favorable structural concept based on a set of figures of merit, and the honeycomb sandwich design was selected as the best concept based on advantages in manufacturing cost.

Large Scale Screening of Low Cost Ferritic Steel Designs For Advanced Ultra Supercritical Boiler Using First Principles Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ouyang, Lizhi

Advanced Ultra Supercritical Boiler (AUSC) requires materials that can operate in corrosive environment at temperature and pressure as high as 760°C (or 1400°F) and 5000psi, respectively, while at the same time maintain good ductility at low temperature. We develop automated simulation software tools to enable fast large scale screening studies of candidate designs. While direct evaluation of creep rupture strength and ductility are currently not feasible, properties such as energy, elastic constants, surface energy, interface energy, and stack fault energy can be used to assess their relative ductility and creeping strength. We implemented software to automate the complex calculations tomore » minimize human inputs in the tedious screening studies which involve model structures generation, settings for first principles calculations, results analysis and reporting. The software developed in the project and library of computed mechanical properties of phases found in ferritic steels, many are complex solid solutions estimated for the first time, will certainly help the development of low cost ferritic steel for AUSC.« less

Pulsed 86Sr-labeling and NanoSIMS imaging to study coral biomineralization at ultra-structural length scales

NASA Astrophysics Data System (ADS)

Brahmi, C.; Domart-Coulon, I.; Rougée, L.; Pyle, D. G.; Stolarski, J.; Mahoney, J. J.; Richmond, R. H.; Ostrander, G. K.; Meibom, A.

2012-09-01

A method to label marine biocarbonates is developed based on a concentration enrichment of a minor stable isotope of a trace element that is a natural component of seawater, resulting in the formation of biocarbonate with corresponding isotopic enrichments. This biocarbonate is subsequently imaged with a NanoSIMS ion microprobe to visualize the locations of the isotopic marker on sub-micrometric length scales, permitting resolution of all ultra-structural details. In this study, a scleractinian coral, Pocillopora damicornis, was labeled 3 times with 86Sr-enhanced seawater for a period of 48 h with 5 days under normal seawater conditions separating each labeling event. Two non-specific cellular stress biomarkers, glutathione-S-transferase activity and porphyrin concentration plus carbonic anhydrase, an enzymatic marker involved in the physiology of carbonate biomineralization, as well as unchanged levels of zooxanthellae photosynthesis efficiency indicate that coral physiological processes are not affected by the 86Sr-enhancement. NanoSIMS images of the 86Sr/44Ca ratio in skeleton formed during the experiment allow for a determination of the average extension rate of the two major ultra-structural components of the coral skeleton: Rapid Accretion Deposits are found to form on average about 4.5 times faster than Thickening Deposits. The method opens up new horizons in the study of biocarbonate formation because it holds the potential to observe growth of calcareous structures such as skeletons, shells, tests, spines formed by a wide range of organisms under essentially unperturbed physiological conditions.

Design, Development, and Maintenance of the GLOBE Program Website and Database

NASA Technical Reports Server (NTRS)

Brummer, Renate; Matsumoto, Clifford

2004-01-01

This is a 1-year (Fy 03) proposal to design and develop enhancements, implement improved efficiency and reliability, and provide responsive maintenance for the operational GLOBE (Global Learning and Observations to Benefit the Environment) Program website and database. This proposal is renewable, with a 5% annual inflation factor providing an approximate cost for the out years.

Fine-Scale Structure Design for 3D Printing

NASA Astrophysics Data System (ADS)

Panetta, Francis Julian

Modern additive fabrication technologies can manufacture shapes whose geometric complexities far exceed what existing computational design tools can analyze or optimize. At the same time, falling costs have placed these fabrication technologies within the average consumer's reach. Especially for inexpert designers, new software tools are needed to take full advantage of 3D printing technology. This thesis develops such tools and demonstrates the exciting possibilities enabled by fine-tuning objects at the small scales achievable by 3D printing. The thesis applies two high-level ideas to invent these tools: two-scale design and worst-case analysis. The two-scale design approach addresses the problem that accurately simulating--let alone optimizing--the full-resolution geometry sent to the printer requires orders of magnitude more computational power than currently available. However, we can decompose the design problem into a small-scale problem (designing tileable structures achieving a particular deformation behavior) and a macro-scale problem (deciding where to place these structures in the larger object). This separation is particularly effective, since structures for every useful behavior can be designed once, stored in a database, then reused for many different macroscale problems. Worst-case analysis refers to determining how likely an object is to fracture by studying the worst possible scenario: the forces most efficiently breaking it. This analysis is needed when the designer has insufficient knowledge or experience to predict what forces an object will undergo, or when the design is intended for use in many different scenarios unknown a priori. The thesis begins by summarizing the physics and mathematics necessary to rigorously approach these design and analysis problems. Specifically, the second chapter introduces linear elasticity and periodic homogenization. The third chapter presents a pipeline to design microstructures achieving a wide range of

Study of ultra-low emittance design for SPEAR3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, M. -H.; Huang, X.; Safranek, J.

2015-09-17

Since its 2003 construction, the SPEAR3 synchrotron light source at SLAC has continuously improved its performance by raising beam current, top-off injection, and smaller emittance. This makes SPEAR3 one of the most productive light sources in the world. Now, to further enhance the performance of SPEAR3, we are looking into the possibility of converting SPEAR3 to an ultra-low emittance storage ring within its site constraint.

Coordinated control system modelling of ultra-supercritical unit based on a new T-S fuzzy structure.

PubMed

Hou, Guolian; Du, Huan; Yang, Yu; Huang, Congzhi; Zhang, Jianhua

2018-03-01

The thermal power plant, especially the ultra-supercritical unit is featured with severe nonlinearity, strong multivariable coupling. In order to deal with these difficulties, it is of great importance to build an accurate and simple model of the coordinated control system (CCS) in the ultra-supercritical unit. In this paper, an improved T-S fuzzy model identification approach is proposed. First of all, the k-means++ algorithm is employed to identify the premise parameters so as to guarantee the number of fuzzy rules. Then, the local linearized models are determined by using the incremental historical data around the cluster centers, which are obtained via the stochastic gradient descent algorithm with momentum and variable learning rate. Finally, with the proposed method, the CCS model of a 1000 MW USC unit in Tai Zhou power plant is developed. The effectiveness of the proposed approach is validated by the given extensive simulation results, and it can be further employed to design the overall advanced controllers for the CCS in an USC unit. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.

PubMed

Kadumuri, Rajashekar Varma; Vadrevu, Ramakrishna

2017-10-01

Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.

3DSDSCAR--a three dimensional structural database for sialic acid-containing carbohydrates through molecular dynamics simulation.

PubMed

Veluraja, Kasinadar; Selvin, Jeyasigamani F A; Venkateshwari, Selvakumar; Priyadarzini, Thanu R K

2010-09-23

The inherent flexibility and lack of strong intramolecular interactions of oligosaccharides demand the use of theoretical methods for their structural elucidation. In spite of the developments of theoretical methods, not much research on glycoinformatics is done so far when compared to bioinformatics research on proteins and nucleic acids. We have developed three dimensional structural database for a sialic acid-containing carbohydrates (3DSDSCAR). This is an open-access database that provides 3D structural models of a given sialic acid-containing carbohydrate. At present, 3DSDSCAR contains 60 conformational models, belonging to 14 different sialic acid-containing carbohydrates, deduced through 10 ns molecular dynamics (MD) simulations. The database is available at the URL: http://www.3dsdscar.org. Copyright 2010 Elsevier Ltd. All rights reserved.

Study on Ultra-deep Azimuthal Electromagnetic Resistivity LWD Tool by Influence Quantification on Azimuthal Depth of Investigation and Real Signal

NASA Astrophysics Data System (ADS)

Li, Kesai; Gao, Jie; Ju, Xiaodong; Zhu, Jun; Xiong, Yanchun; Liu, Shuai

2018-05-01

This paper proposes a new tool design of ultra-deep azimuthal electromagnetic (EM) resistivity logging while drilling (LWD) for deeper geosteering and formation evaluation, which can benefit hydrocarbon exploration and development. First, a forward numerical simulation of azimuthal EM resistivity LWD is created based on the fast Hankel transform (FHT) method, and its accuracy is confirmed under classic formation conditions. Then, a reasonable range of tool parameters is designed by analyzing the logging response. However, modern technological limitations pose challenges to selecting appropriate tool parameters for ultra-deep azimuthal detection under detectable signal conditions. Therefore, this paper uses grey relational analysis (GRA) to quantify the influence of tool parameters on voltage and azimuthal investigation depth. After analyzing thousands of simulation data under different environmental conditions, the random forest is used to fit data and identify an optimal combination of tool parameters due to its high efficiency and accuracy. Finally, the structure of the ultra-deep azimuthal EM resistivity LWD tool is designed with a theoretical azimuthal investigation depth of 27.42-29.89 m in classic different isotropic and anisotropic formations. This design serves as a reliable theoretical foundation for efficient geosteering and formation evaluation in high-angle and horizontal (HA/HZ) wells in the future.

Seeing Diversity in Difference: Experiences in an Ultra-Orthodox Jewish College.

ERIC Educational Resources Information Center

Starr-Glass, David; Schwartzbaum, Avraham

2002-01-01

Reviews organizational and administrative history of Ultra-Orthodox Jewish College in Jerusalem, Israel, that leads to an institutional structure that supports distinctiveness. Examines influence of ultra-Orthodox communities in Jerusalem on the academic quality and distinctiveness of the college. Uses perspective of social construct theory to…

Database-Guided Discovery of Potent Peptides to Combat HIV-1 or Superbugs

PubMed Central

Wang, Guangshun

2013-01-01

Antimicrobial peptides (AMPs), small host defense proteins, are indispensable for the protection of multicellular organisms such as plants and animals from infection. The number of AMPs discovered per year increased steadily since the 1980s. Over 2,000 natural AMPs from bacteria, protozoa, fungi, plants, and animals have been registered into the antimicrobial peptide database (APD). The majority of these AMPs (>86%) possess 11–50 amino acids with a net charge from 0 to +7 and hydrophobic percentages between 31–70%. This article summarizes peptide discovery on the basis of the APD. The major methods are the linguistic model, database screening, de novo design, and template-based design. Using these methods, we identified various potent peptides against human immunodeficiency virus type 1 (HIV-1) or methicillin-resistant Staphylococcus aureus (MRSA). While the stepwise designed anti-HIV peptide is disulfide-linked and rich in arginines, the ab initio designed anti-MRSA peptide is linear and rich in leucines. Thus, there are different requirements for antiviral and antibacterial peptides, which could kill pathogens via different molecular targets. The biased amino acid composition in the database-designed peptides, or natural peptides such as θ-defensins, requires the use of the improved two-dimensional NMR method for structural determination to avoid the publication of misleading structure and dynamics. In the case of human cathelicidin LL-37, structural determination requires 3D NMR techniques. The high-quality structure of LL-37 provides a solid basis for understanding its interactions with membranes of bacteria and other pathogens. In conclusion, the APD database is a comprehensive platform for storing, classifying, searching, predicting, and designing potent peptides against pathogenic bacteria, viruses, fungi, parasites, and cancer cells. PMID:24276259

Gas/vapour separation using ultra-microporous metal-organic frameworks: insights into the structure/separation relationship.

PubMed

Adil, Karim; Belmabkhout, Youssef; Pillai, Renjith S; Cadiau, Amandine; Bhatt, Prashant M; Assen, Ayalew H; Maurin, Guillaume; Eddaoudi, Mohamed

2017-06-06

The separation of related molecules with similar physical/chemical properties is of prime industrial importance and practically entails a substantial energy penalty, typically necessitating the operation of energy-demanding low temperature fractional distillation techniques. Certainly research efforts, in academia and industry alike, are ongoing with the main aim to develop advanced functional porous materials to be adopted as adsorbents for the effective and energy-efficient separation of various important commodities. Of special interest is the subclass of metal-organic frameworks (MOFs) with pore aperture sizes below 5-7 Å, namely ultra-microporous MOFs, which in contrast to conventional zeolites and activated carbons show great prospects for addressing key challenges in separations pertaining to energy and environmental sustainability, specifically materials for carbon capture and separation of olefin/paraffin, acetylene/ethylene, linear/branched alkanes, xenon/krypton, etc. In this tutorial review we discuss the latest developments in ultra-microporous MOF adsorbents and their use as separating agents via thermodynamics and/or kinetics and molecular sieving. Appreciably, we provide insights into the distinct microscopic mechanisms governing the resultant separation performances, and suggest a plausible correlation between the inherent structural features/topology of MOFs and the associated gas/vapour separation performance.

UltraSail CubeSat Solar Sail Flight Experiment

NASA Technical Reports Server (NTRS)

Carroll, David; Burton, Rodney; Coverstone, Victoria; Swenson, Gary

2013-01-01

UltraSail is a next-generation, highrisk, high-payoff sail system for the launch, deployment, stabilization, and control of very large (km2 class) solar sails enabling high payload mass fractions for interplanetary and deep space spacecraft. UltraSail is a non-traditional approach to propulsion technology achieved by combining propulsion and control systems developed for formation- flying microsatellites with an innovative solar sail architecture to achieve controllable sail areas approaching 1 km2, sail subsystem area densities approaching 1 g/m2, and thrust levels many times those of ion thrusters used for comparable deep space missions. UltraSail can achieve outer planetary rendezvous, a deep-space capability now reserved for high-mass nuclear and chemical systems. There is a twofold rationale behind the UltraSail concept for advanced solar sail systems. The first is that sail-andboom systems are inherently size-limited. The boom mass must be kept small, and column buckling limits the boom length to a few hundred meters. By eliminating the boom, UltraSail not only offers larger sail area, but also lower areal density, allowing larger payloads and shorter mission transit times. The second rationale for UltraSail is that sail films present deployment handling difficulties as the film thickness approaches one micrometer. The square sail requires that the film be folded in two directions for launch, and similarly unfolded for deployment. The film is stressed at the intersection of two folds, and this stress varies inversely with the film thickness. This stress can cause the film to yield, forming a permanent crease, or worse, to perforate. By rolling the film as UltraSail does, creases are prevented. Because the film is so thin, the roll thickness is small. Dynamic structural analysis of UltraSail coupled with dynamic control analysis shows that the system can be designed to eliminate longitudinal torsional waves created while controlling the pitch of the blades

Design of Vivaldi Microstrip Antenna for Ultra-Wideband Radar Applications

NASA Astrophysics Data System (ADS)

Perdana, M. Y.; Hariyadi, T.; Wahyu, Y.

2017-03-01

The development of radar technology has an important role in several fields such as aviation, civil engineering, geology, and medicine. One of the essential components of the radar system is the antenna. The bandwidth can specify the resolution of the radar. The wider the bandwidth, the higher the resolution of radar. For Ground penetrating radar (GPR) or medical applications need with a high-resolution radar so it needs an antenna with a wide bandwidth. In addition, for the radar application is required antenna with directional radiation pattern. So, we need an antenna with wide bandwidth and directional radiation pattern. One of antenna that has meet with these characteristics is vivaldi antenna. In previous research, has designed several vivaldi microstrip antenna for ultra-wideband radar applications which has a working frequency of 3.1 to 10.7 GHz. However, these studies there is still a shortage of one of them is the radiation pattern from lowest to highest frequency radiation pattern is not uniform in the sense that not all directional. Besides the antenna material used is also not easily available and the price is not cheap. This paper will discuss the design of a vivaldi microstrip antenna which has a wide bandwidth with directional radiation pattern works on 3.1 to 10.7 GHz and using cheaper substrate. Substrates used for vivaldi microstrip antenna vivaldi is FR4 with a dielectric constant of 4.3 and a thickness of 1.6 mm. Based on the simulation results we obtained that the antenna design has frequency range 3.1-10.7 GHz for return loss less than -10 dB with a directional radiation pattern. This antenna gain is 4.8 to 8 dBi with the largest dimension is 50 mm x 40 mm.

Recent Developments in Cultural Heritage Image Databases: Directions for User-Centered Design.

ERIC Educational Resources Information Center

Stephenson, Christie

1999-01-01

Examines the Museum Educational Site Licensing (MESL) Project--a cooperative project between seven cultural heritage repositories and seven universities--as well as other developments of cultural heritage image databases for academic use. Reviews recent literature on image indexing and retrieval, interface design, and tool development, urging a…

A structured vocabulary for indexing dietary supplements in databases in the United States

PubMed Central

Saldanha, Leila G; Dwyer, Johanna T; Holden, Joanne M; Ireland, Jayne D.; Andrews, Karen W; Bailey, Regan L; Gahche, Jaime J.; Hardy, Constance J; Møller, Anders; Pilch, Susan M.; Roseland, Janet M

2011-01-01

Food composition databases are critical to assess and plan dietary intakes. Dietary supplement databases are also needed because dietary supplements make significant contributions to total nutrient intakes. However, no uniform system exists for classifying dietary supplement products and indexing their ingredients in such databases. Differing approaches to classifying these products make it difficult to retrieve or link information effectively. A consistent approach to classifying information within food composition databases led to the development of LanguaL™, a structured vocabulary. LanguaL™ is being adapted as an interface tool for classifying and retrieving product information in dietary supplement databases. This paper outlines proposed changes to the LanguaL™ thesaurus for indexing dietary supplement products and ingredients in databases. The choice of 12 of the original 14 LanguaL™ facets pertinent to dietary supplements, modifications to their scopes, and applications are described. The 12 chosen facets are: Product Type; Source; Part of Source; Physical State, Shape or Form; Ingredients; Preservation Method, Packing Medium, Container or Wrapping; Contact Surface; Consumer Group/Dietary Use/Label Claim; Geographic Places and Regions; and Adjunct Characteristics of food. PMID:22611303

IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data

PubMed Central

Kaas, Quentin; Ruiz, Manuel; Lefranc, Marie-Paule

2004-01-01

IMGT/3Dstructure-DB and IMGT/Structural-Query are a novel 3D structure database and a new tool for immunological proteins. They are part of IMGT, the international ImMunoGenetics information system®, a high-quality integrated knowledge resource specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrate species, which consists of databases, Web resources and interactive on-line tools. IMGT/3Dstructure-DB data are described according to the IMGT Scientific chart rules based on the IMGT-ONTOLOGY concepts. IMGT/3Dstructure-DB provides IMGT gene and allele identification of IG, TR and MHC proteins with known 3D structures, domain delimitations, amino acid positions according to the IMGT unique numbering and renumbered coordinate flat files. Moreover IMGT/3Dstructure-DB provides 2D graphical representations (or Collier de Perles) and results of contact analysis. The IMGT/StructuralQuery tool allows search of this database based on specific structural characteristics. IMGT/3Dstructure-DB and IMGT/StructuralQuery are freely available at http://imgt.cines.fr. PMID:14681396