Databases for LDEF results

NASA Technical Reports Server (NTRS)

Bohnhoff-Hlavacek, Gail

1992-01-01

One of the objectives of the team supporting the LDEF Systems and Materials Special Investigative Groups is to develop databases of experimental findings. These databases identify the hardware flown, summarize results and conclusions, and provide a system for acknowledging investigators, tracing sources of data, and future design suggestions. To date, databases covering the optical experiments, and thermal control materials (chromic acid anodized aluminum, silverized Teflon blankets, and paints) have been developed at Boeing. We used the Filemaker Pro software, the database manager for the Macintosh computer produced by the Claris Corporation. It is a flat, text-retrievable database that provides access to the data via an intuitive user interface, without tedious programming. Though this software is available only for the Macintosh computer at this time, copies of the databases can be saved to a format that is readable on a personal computer as well. Further, the data can be exported to more powerful relational databases, capabilities, and use of the LDEF databases and describe how to get copies of the database for your own research.

Cold Climate Foundation Retrofit Experimental Hygrothermal Performance. Cloquet Residential Research Facility Laboratory Results

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

Goldberg, Louise F.; Harmon, Anna C.

2015-04-09

This project was funded jointly by the National Renewable Energy Laboratory (NREL) and Oak Ridge National Laboratory (ORNL). ORNL focused on developing a full basement wall system experimental database to enable others to validate hygrothermal simulation codes. NREL focused on testing the moisture durability of practical basement wall interior insulation retrofit solutions for cold climates. The project has produced a physically credible and reliable long-term hygrothermal performance database for retrofit foundation wall insulation systems in zone 6 and 7 climates that are fully compliant with the performance criteria in the 2009 Minnesota Energy Code. These data currently span the periodmore » from November 10, 2012 through May 31, 2014 and are anticipated to be extended through November 2014. The experimental data were configured into a standard format that can be published online and that is compatible with standard commercially available spreadsheet and database software.« less

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments.

PubMed

Zhou, Bailing; Zhao, Huiying; Yu, Jiafeng; Guo, Chengang; Dou, Xianghua; Song, Feng; Hu, Guodong; Cao, Zanxia; Qu, Yuanxu; Yang, Yuedong; Zhou, Yaoqi; Wang, Jihua

2018-01-04

Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs. However, these databases are small in scale (with a few hundreds of lncRNAs only) and specific in their focuses (plants, diseases or interactions). Thus, it is highly desirable to have a comprehensive dataset for experimentally validated lncRNAs as a central repository for all of their structures, functions and phenotypes. Here, we established EVLncRNAs by curating lncRNAs validated by low-throughput experiments (up to 1 May 2016) and integrating specific databases (lncRNAdb, LncRANDisease, Lnc2Cancer and PLNIncRBase) with additional functional and disease-specific information not covered previously. The current version of EVLncRNAs contains 1543 lncRNAs from 77 species that is 2.9 times larger than the current largest database for experimentally validated lncRNAs. Seventy-four percent lncRNA entries are partially or completely new, comparing to all existing experimentally validated databases. The established database allows users to browse, search and download as well as to submit experimentally validated lncRNAs. The database is available at http://biophy.dzu.edu.cn/EVLncRNAs. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments

PubMed Central

Zhao, Huiying; Yu, Jiafeng; Guo, Chengang; Dou, Xianghua; Song, Feng; Hu, Guodong; Cao, Zanxia; Qu, Yuanxu

2018-01-01

Abstract Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs. However, these databases are small in scale (with a few hundreds of lncRNAs only) and specific in their focuses (plants, diseases or interactions). Thus, it is highly desirable to have a comprehensive dataset for experimentally validated lncRNAs as a central repository for all of their structures, functions and phenotypes. Here, we established EVLncRNAs by curating lncRNAs validated by low-throughput experiments (up to 1 May 2016) and integrating specific databases (lncRNAdb, LncRANDisease, Lnc2Cancer and PLNIncRBase) with additional functional and disease-specific information not covered previously. The current version of EVLncRNAs contains 1543 lncRNAs from 77 species that is 2.9 times larger than the current largest database for experimentally validated lncRNAs. Seventy-four percent lncRNA entries are partially or completely new, comparing to all existing experimentally validated databases. The established database allows users to browse, search and download as well as to submit experimentally validated lncRNAs. The database is available at http://biophy.dzu.edu.cn/EVLncRNAs. PMID:28985416

WMC Database Evaluation. Case Study Report

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

Palounek, Andrea P. T

The WMC Database is ultimately envisioned to hold a collection of experimental data, design information, and information from computational models. This project was a first attempt at using the Database to access experimental data and extract information from it. This evaluation shows that the Database concept is sound and robust, and that the Database, once fully populated, should remain eminently usable for future researchers.

EMEN2: An Object Oriented Database and Electronic Lab Notebook

PubMed Central

Rees, Ian; Langley, Ed; Chiu, Wah; Ludtke, Steven J.

2013-01-01

Transmission electron microscopy and associated methods such as single particle analysis, 2-D crystallography, helical reconstruction and tomography, are highly data-intensive experimental sciences, which also have substantial variability in experimental technique. Object-oriented databases present an attractive alternative to traditional relational databases for situations where the experiments themselves are continually evolving. We present EMEN2, an easy to use object-oriented database with a highly flexible infrastructure originally targeted for transmission electron microscopy and tomography, which has been extended to be adaptable for use in virtually any experimental science. It is a pure object-oriented database designed for easy adoption in diverse laboratory environments, and does not require professional database administration. It includes a full featured, dynamic web interface in addition to APIs for programmatic access. EMEN2 installations currently support roughly 800 scientists worldwide with over 1/2 million experimental records and over 20 TB of experimental data. The software is freely available with complete source. PMID:23360752

Appropriateness of the food-pics image database for experimental eating and appetite research with adolescents.

PubMed

Jensen, Chad D; Duraccio, Kara M; Barnett, Kimberly A; Stevens, Kimberly S

2016-12-01

Research examining effects of visual food cues on appetite-related brain processes and eating behavior has proliferated. Recently investigators have developed food image databases for use across experimental studies examining appetite and eating behavior. The food-pics image database represents a standardized, freely available image library originally validated in a large sample primarily comprised of adults. The suitability of the images for use with adolescents has not been investigated. The aim of the present study was to evaluate the appropriateness of the food-pics image library for appetite and eating research with adolescents. Three hundred and seven adolescents (ages 12-17) provided ratings of recognizability, palatability, and desire to eat, for images from the food-pics database. Moreover, participants rated the caloric content (high vs. low) and healthiness (healthy vs. unhealthy) of each image. Adolescents rated approximately 75% of the food images as recognizable. Approximately 65% of recognizable images were correctly categorized as high vs. low calorie and 63% were correctly classified as healthy vs. unhealthy in 80% or more of image ratings. These results suggest that a smaller subset of the food-pics image database is appropriate for use with adolescents. With some modifications to included images, the food-pics image database appears to be appropriate for use in experimental appetite and eating-related research conducted with adolescents. Copyright © 2016 Elsevier Ltd. All rights reserved.

A database to enable discovery and design of piezoelectric materials

PubMed Central

de Jong, Maarten; Chen, Wei; Geerlings, Henry; Asta, Mark; Persson, Kristin Aslaug

2015-01-01

Piezoelectric materials are used in numerous applications requiring a coupling between electrical fields and mechanical strain. Despite the technological importance of this class of materials, for only a small fraction of all inorganic compounds which display compatible crystallographic symmetry, has piezoelectricity been characterized experimentally or computationally. In this work we employ first-principles calculations based on density functional perturbation theory to compute the piezoelectric tensors for nearly a thousand compounds, thereby increasing the available data for this property by more than an order of magnitude. The results are compared to select experimental data to establish the accuracy of the calculated properties. The details of the calculations are also presented, along with a description of the format of the database developed to make these computational results publicly available. In addition, the ways in which the database can be accessed and applied in materials development efforts are described. PMID:26451252

Fusion of Dependent and Independent Biometric Information Sources

DTIC Science & Technology

2005-03-01

palmprint , DNA, ECG, signature, etc. The comparison of various biometric techniques is given in [13] and is presented in Table 1. Since, each...theory. Experimental studies on the M2VTS database [32] showed that a reduction in error rates is up to about 40%. Four combination strategies are...taken from the CEDAR benchmark database . The word recognition results were the highest (91%) among published results for handwritten words (before 2001

Automated detection of discourse segment and experimental types from the text of cancer pathway results sections.

PubMed

Burns, Gully A P C; Dasigi, Pradeep; de Waard, Anita; Hovy, Eduard H

2016-01-01

Automated machine-reading biocuration systems typically use sentence-by-sentence information extraction to construct meaning representations for use by curators. This does not directly reflect the typical discourse structure used by scientists to construct an argument from the experimental data available within a article, and is therefore less likely to correspond to representations typically used in biomedical informatics systems (let alone to the mental models that scientists have). In this study, we develop Natural Language Processing methods to locate, extract, and classify the individual passages of text from articles' Results sections that refer to experimental data. In our domain of interest (molecular biology studies of cancer signal transduction pathways), individual articles may contain as many as 30 small-scale individual experiments describing a variety of findings, upon which authors base their overall research conclusions. Our system automatically classifies discourse segments in these texts into seven categories (fact, hypothesis, problem, goal, method, result, implication) with an F-score of 0.68. These segments describe the essential building blocks of scientific discourse to (i) provide context for each experiment, (ii) report experimental details and (iii) explain the data's meaning in context. We evaluate our system on text passages from articles that were curated in molecular biology databases (the Pathway Logic Datum repository, the Molecular Interaction MINT and INTACT databases) linking individual experiments in articles to the type of assay used (coprecipitation, phosphorylation, translocation etc.). We use supervised machine learning techniques on text passages containing unambiguous references to experiments to obtain baseline F1 scores of 0.59 for MINT, 0.71 for INTACT and 0.63 for Pathway Logic. Although preliminary, these results support the notion that targeting information extraction methods to experimental results could provide accurate, automated methods for biocuration. We also suggest the need for finer-grained curation of experimental methods used when constructing molecular biology databases. © The Author(s) 2016. Published by Oxford University Press.

Rapid Prototyping-Unmanned Combat Air Vehicle (UCAV)/Sensorcraft

DTIC Science & Technology

2008-01-01

model. RP may prove to be the fastest means to create a bridge between these CFD and experimental ground testing databases . In the past, it took...UCAV X-45A wind tunnel model within the /RB) ment FD results provide a database of global surface and off-body measurements. It is imperative t...extend the knowledge database for a given aircraft configuration beyond the ground test envelope and into the fligh regime. Working in tandem, in an

Analysis of a virtual memory model for maintaining database views

NASA Technical Reports Server (NTRS)

Kinsley, Kathryn C.; Hughes, Charles E.

1992-01-01

This paper presents an analytical model for predicting the performance of a new support strategy for database views. This strategy, called the virtual method, is compared with traditional methods for supporting views. The analytical model's predictions of improved performance by the virtual method are then validated by comparing these results with those achieved in an experimental implementation.

Aerodynamic Database Development for Mars Smart Lander Vehicle Configurations

NASA Technical Reports Server (NTRS)

Bobskill, Glenn J.; Parikh, Paresh C.; Prabhu, Ramadas K.; Tyler, Erik D.

2002-01-01

An aerodynamic database has been generated for the Mars Smart Lander Shelf-All configuration using computational fluid dynamics (CFD) simulations. Three different CFD codes, USM3D and FELISA, based on unstructured grid technology and LAURA, an established and validated structured CFD code, were used. As part of this database development, the results for the Mars continuum were validated with experimental data and comparisons made where applicable. The validation of USM3D and LAURA with the Unitary experimental data, the use of intermediate LAURA check analyses, as well as the validation of FELISA with the Mach 6 CF(sub 4) experimental data provided a higher confidence in the ability for CFD to provide aerodynamic data in order to determine the static trim characteristics for longitudinal stability. The analyses of the noncontinuum regime showed the existence of multiple trim angles of attack that can be unstable or stable trim points. This information is needed to design guidance controller throughout the trajectory.

Constitutive equations for the cyclic behaviour of short carbon fibre-reinforced thermoplastics and identification on a uniaxial database

NASA Astrophysics Data System (ADS)

Leveuf, Louis; Navrátil, Libor; Le Saux, Vincent; Marco, Yann; Olhagaray, Jérôme; Leclercq, Sylvain

2018-01-01

A constitutive model for the cyclic behaviour of short carbon fibre-reinforced thermoplastics for aeronautical applications is proposed. First, an extended experimental database is generated in order to highlight the specificities of the studied material. This database is composed of complex tests and is used to design a relevant constitutive model able to capture the cyclic behaviour of the material. A general 3D formulation of the model is then proposed, and an identification strategy is defined to identify its parameters. Finally, a validation of the identification is performed by challenging the prediction of the model to the tests that were not used for the identification. An excellent agreement between the numerical results and the experimental data is observed revealing the capabilities of the model.

Shuttle Return To Flight Experimental Results: Protuberance Effects on Boundary Layer Transition

NASA Technical Reports Server (NTRS)

Liechty, Derek S.; Berry, Scott A.; Horvath, Thomas J.

2006-01-01

The effect of isolated roughness elements on the windward boundary layer of the Shuttle Orbiter has been experimentally examined in the Langley Aerothermodynamic Laboratory in support of an agency-wide effort to prepare the Shuttle Orbiter for return to flight. This experimental effort was initiated to provide a roughness effects database for developing transition criteria to support on-orbit decisions to repair damage to the thermal protection system. Boundary layer transition results were obtained using trips of varying heights and locations along the centerline and attachment lines of 0.0075-scale models. Global heat transfer images using phosphor thermography of the Orbiter windward surface and the corresponding heating distributions were used to infer the state of the boundary layer (laminar, transitional, or turbulent). The database contained within this report will be used to formulate protuberance-induced transition correlations using predicted boundary layer edge parameters.

Palm-Vein Classification Based on Principal Orientation Features

PubMed Central

Zhou, Yujia; Liu, Yaqin; Feng, Qianjin; Yang, Feng; Huang, Jing; Nie, Yixiao

2014-01-01

Personal recognition using palm–vein patterns has emerged as a promising alternative for human recognition because of its uniqueness, stability, live body identification, flexibility, and difficulty to cheat. With the expanding application of palm–vein pattern recognition, the corresponding growth of the database has resulted in a long response time. To shorten the response time of identification, this paper proposes a simple and useful classification for palm–vein identification based on principal direction features. In the registration process, the Gaussian-Radon transform is adopted to extract the orientation matrix and then compute the principal direction of a palm–vein image based on the orientation matrix. The database can be classified into six bins based on the value of the principal direction. In the identification process, the principal direction of the test sample is first extracted to ascertain the corresponding bin. One-by-one matching with the training samples is then performed in the bin. To improve recognition efficiency while maintaining better recognition accuracy, two neighborhood bins of the corresponding bin are continuously searched to identify the input palm–vein image. Evaluation experiments are conducted on three different databases, namely, PolyU, CASIA, and the database of this study. Experimental results show that the searching range of one test sample in PolyU, CASIA and our database by the proposed method for palm–vein identification can be reduced to 14.29%, 14.50%, and 14.28%, with retrieval accuracy of 96.67%, 96.00%, and 97.71%, respectively. With 10,000 training samples in the database, the execution time of the identification process by the traditional method is 18.56 s, while that by the proposed approach is 3.16 s. The experimental results confirm that the proposed approach is more efficient than the traditional method, especially for a large database. PMID:25383715

NIST Gas Hydrate Research Database and Web Dissemination Channel.

PubMed

Kroenlein, K; Muzny, C D; Kazakov, A; Diky, V V; Chirico, R D; Frenkel, M; Sloan, E D

2010-01-01

To facilitate advances in application of technologies pertaining to gas hydrates, a freely available data resource containing experimentally derived information about those materials was developed. This work was performed by the Thermodynamic Research Center (TRC) paralleling a highly successful database of thermodynamic and transport properties of molecular pure compounds and their mixtures. Population of the gas-hydrates database required development of guided data capture (GDC) software designed to convert experimental data and metadata into a well organized electronic format, as well as a relational database schema to accommodate all types of numerical and metadata within the scope of the project. To guarantee utility for the broad gas hydrate research community, TRC worked closely with the Committee on Data for Science and Technology (CODATA) task group for Data on Natural Gas Hydrates, an international data sharing effort, in developing a gas hydrate markup language (GHML). The fruits of these efforts are disseminated through the NIST Sandard Reference Data Program [1] as the Clathrate Hydrate Physical Property Database (SRD #156). A web-based interface for this database, as well as scientific results from the Mallik 2002 Gas Hydrate Production Research Well Program [2], is deployed at http://gashydrates.nist.gov.

Hydroacoustic forcing function modeling using DNS database

NASA Technical Reports Server (NTRS)

Zawadzki, I.; Gershfield, J. L.; Na, Y.; Wang, M.

1996-01-01

A wall pressure frequency spectrum model (Blake 1971 ) has been evaluated using databases from Direct Numerical Simulations (DNS) of a turbulent boundary layer (Na & Moin 1996). Good agreement is found for moderate to strong adverse pressure gradient flows in the absence of separation. In the separated flow region, the model underpredicts the directly calculated spectra by an order of magnitude. The discrepancy is attributed to the violation of the model assumptions in that part of the flow domain. DNS computed coherence length scales and the normalized wall pressure cross-spectra are compared with experimental data. The DNS results are consistent with experimental observations.

The IVTANTHERMO-Online database for thermodynamic properties of individual substances with web interface

NASA Astrophysics Data System (ADS)

Belov, G. V.; Dyachkov, S. A.; Levashov, P. R.; Lomonosov, I. V.; Minakov, D. V.; Morozov, I. V.; Sineva, M. A.; Smirnov, V. N.

2018-01-01

The database structure, main features and user interface of an IVTANTHERMO-Online system are reviewed. This system continues the series of the IVTANTHERMO packages developed in JIHT RAS. It includes the database for thermodynamic properties of individual substances and related software for analysis of experimental results, data fitting, calculation and estimation of thermodynamical functions and thermochemistry quantities. In contrast to the previous IVTANTHERMO versions it has a new extensible database design, the client-server architecture, a user-friendly web interface with a number of new features for online and offline data processing.

Workstation Analytics in Distributed Warfighting Experimentation: Results from Coalition Attack Guidance Experiment 3A

DTIC Science & Technology

2014-06-01

central location. Each of the SQLite databases are converted and stored in one MySQL database and the pcap files are parsed to extract call information...from the specific communications applications used during the experiment. This extracted data is then stored in the same MySQL database. With all...rhythm of the event. Figure 3 demonstrates the application usage over the course of the experiment for the EXDIR. As seen, the EXDIR spent the majority

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo.

PubMed

Uhlirova, Hana; Tian, Peifang; Kılıç, Kıvılcım; Thunemann, Martin; Sridhar, Vishnu B; Chmelik, Radim; Bartsch, Hauke; Dale, Anders M; Devor, Anna; Saisan, Payam A

2018-05-04

The importance of sharing experimental data in neuroscience grows with the amount and complexity of data acquired and various techniques used to obtain and process these data. However, the majority of experimental data, especially from individual studies of regular-sized laboratories never reach wider research community. A graphical user interface (GUI) engine called Neurovascular Network Explorer 2.0 (NNE 2.0) has been created as a tool for simple and low-cost sharing and exploring of vascular imaging data. NNE 2.0 interacts with a database containing optogenetically-evoked dilation/constriction time-courses of individual vessels measured in mice somatosensory cortex in vivo by 2-photon microscopy. NNE 2.0 enables selection and display of the time-courses based on different criteria (subject, branching order, cortical depth, vessel diameter, arteriolar tree) as well as simple mathematical manipulation (e.g. averaging, peak-normalization) and data export. It supports visualization of the vascular network in 3D and enables localization of the individual functional vessel diameter measurements within vascular trees. NNE 2.0, its source code, and the corresponding database are freely downloadable from UCSD Neurovascular Imaging Laboratory website 1 . The source code can be utilized by the users to explore the associated database or as a template for databasing and sharing their own experimental results provided the appropriate format.

Database of Novel and Emerging Adsorbent Materials

National Institute of Standards and Technology Data Gateway

SRD 205 NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials (Web, free access)   The NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials is a free, web-based catalog of adsorbent materials and measured adsorption properties of numerous materials obtained from article entries from the scientific literature. Search fields for the database include adsorbent material, adsorbate gas, experimental conditions (pressure, temperature), and bibliographic information (author, title, journal), and results from queries are provided as a list of articles matching the search parameters. The database also contains adsorption isotherms digitized from the cataloged articles, which can be compared visually online in the web application or exported for offline analysis.

A carcinogenic potency database of the standardized results of animal bioassays

PubMed Central

Gold, Lois Swirsky; Sawyer, Charles B.; Magaw, Renae; Backman, Georganne M.; De Veciana, Margarita; Levinson, Robert; Hooper, N. Kim; Havender, William R.; Bernstein, Leslie; Peto, Richard; Pike, Malcolm C.; Ames, Bruce N.

1984-01-01

The preceding paper described our numerical index of carcinogenic potency, the TD50 and the statistical procedures adopted for estimating it from experimental data. This paper presents the Carcinogenic Potency Database, which includes results of about 3000 long-term, chronic experiments of 770 test compounds. Part II is a discussion of the sources of our data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. Part III is a guide to the plot of results presented in Part IV. A number of appendices are provided to facilitate use of the database. The plot includes information about chronic cancer tests in mammals, such as dose and other aspects of experimental protocol, histopathology and tumor incidence, TD50 and its statistical significance, dose response, author's opinion and literature reference. The plot readily permits comparisons of carcinogenic potency and many other aspects of cancer tests; it also provides quantitative information about negative tests. The range of carcinogenic potency is over 10 million-fold. PMID:6525996

On the Reporting of Experimental and Control Therapies in Stroke Rehabilitation Trials: A Systematic Review.

PubMed

Lohse, Keith R; Pathania, Anupriya; Wegman, Rebecca; Boyd, Lara A; Lang, Catherine E

2018-03-01

To use the Centralized Open-Access Rehabilitation database for Stroke to explore reporting of both experimental and control interventions in randomized controlled trials for stroke rehabilitation (including upper and lower extremity therapies). The Centralized Open-Access Rehabilitation database for Stroke was created from a search of MEDLINE, Embase, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and Cumulative Index of Nursing and Allied Health from the earliest available date to May 31, 2014. A total of 2892 titles were reduced to 514 that were screened by full text. This screening left 215 randomized controlled trials in the database (489 independent groups representing 12,847 patients). Using a mixture of qualitative and quantitative methods, we performed a text-based analysis of how the procedures of experimental and control therapies were described. Experimental and control groups were rated by 2 independent coders according to the Template for Intervention Description and Replication criteria. Linear mixed-effects regression with a random effect of study (groups nested within studies) showed that experimental groups had statistically more words in their procedures (mean, 271.8 words) than did control groups (mean, 154.8 words) (P<.001). Experimental groups had statistically more references in their procedures (mean, 1.60 references) than did control groups (mean, .82 references) (P<.001). Experimental groups also scored significantly higher on the total Template for Intervention Description and Replication checklist (mean score, 7.43 points) than did control groups (mean score, 5.23 points) (P<.001). Control treatments in stroke motor rehabilitation trials are underdescribed relative to experimental treatments. These poor descriptions are especially problematic for "conventional" therapy control groups. Poor reporting is a threat to the internal validity and generalizability of clinical trial results. We recommend authors use preregistered protocols and established reporting criteria to improve transparency. Copyright © 2018 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Expediting topology data gathering for the TOPDB database.

PubMed

Dobson, László; Langó, Tamás; Reményi, István; Tusnády, Gábor E

2015-01-01

The Topology Data Bank of Transmembrane Proteins (TOPDB, http://topdb.enzim.ttk.mta.hu) contains experimentally determined topology data of transmembrane proteins. Recently, we have updated TOPDB from several sources and utilized a newly developed topology prediction algorithm to determine the most reliable topology using the results of experiments as constraints. In addition to collecting the experimentally determined topology data published in the last couple of years, we gathered topographies defined by the TMDET algorithm using 3D structures from the PDBTM. Results of global topology analysis of various organisms as well as topology data generated by high throughput techniques, like the sequential positions of N- or O-glycosylations were incorporated into the TOPDB database. Moreover, a new algorithm was developed to integrate scattered topology data from various publicly available databases and a new method was introduced to measure the reliability of predicted topologies. We show that reliability values highly correlate with the per protein topology accuracy of the utilized prediction method. Altogether, more than 52,000 new topology data and more than 2600 new transmembrane proteins have been collected since the last public release of the TOPDB database. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

PubMed

Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian P; Kasif, Simon; Roberts, Richard J; Steffen, Martin

2016-01-04

The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼ 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Comprehensive Validation Methodology for Sparse Experimental Data

NASA Technical Reports Server (NTRS)

Norman, Ryan B.; Blattnig, Steve R.

2010-01-01

A comprehensive program of verification and validation has been undertaken to assess the applicability of models to space radiation shielding applications and to track progress as models are developed over time. The models are placed under configuration control, and automated validation tests are used so that comparisons can readily be made as models are improved. Though direct comparisons between theoretical results and experimental data are desired for validation purposes, such comparisons are not always possible due to lack of data. In this work, two uncertainty metrics are introduced that are suitable for validating theoretical models against sparse experimental databases. The nuclear physics models, NUCFRG2 and QMSFRG, are compared to an experimental database consisting of over 3600 experimental cross sections to demonstrate the applicability of the metrics. A cumulative uncertainty metric is applied to the question of overall model accuracy, while a metric based on the median uncertainty is used to analyze the models from the perspective of model development by analyzing subsets of the model parameter space.

Comparison of LEWICE and GlennICE in the SLD Regime

NASA Technical Reports Server (NTRS)

Wright, William B.; Potapczuk, Mark G.; Levinson, Laurie H.

2008-01-01

A research project is underway at the NASA Glenn Research Center (GRC) to produce computer software that can accurately predict ice growth under any meteorological conditions for any aircraft surface. This report will present results from two different computer programs. The first program, LEWICE version 3.2.2, has been reported on previously. The second program is GlennICE version 0.1. An extensive comparison of the results in a quantifiable manner against the database of ice shapes that have been generated in the GRC Icing Research Tunnel (IRT) has also been performed, including additional data taken to extend the database in the Super-cooled Large Drop (SLD) regime. This paper will show the differences in ice shape between LEWICE 3.2.2, GlennICE, and experimental data. This report will also provide a description of both programs. Comparisons are then made to recent additions to the SLD database and selected previous cases. Quantitative comparisons are shown for horn height, horn angle, icing limit, area, and leading edge thickness. The results show that the predicted results for both programs are within the accuracy limits of the experimental data for the majority of cases.

High Throughput Experimental Materials Database

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

Zakutayev, Andriy; Perkins, John; Schwarting, Marcus

The mission of the High Throughput Experimental Materials Database (HTEM DB) is to enable discovery of new materials with useful properties by releasing large amounts of high-quality experimental data to public. The HTEM DB contains information about materials obtained from high-throughput experiments at the National Renewable Energy Laboratory (NREL).

Experimental Database with Baseline CFD Solutions: 2-D and Axisymmetric Hypersonic Shock-Wave/Turbulent-Boundary-Layer Interactions

NASA Technical Reports Server (NTRS)

Marvin, Joseph G.; Brown, James L.; Gnoffo, Peter A.

2013-01-01

A database compilation of hypersonic shock-wave/turbulent boundary layer experiments is provided. The experiments selected for the database are either 2D or axisymmetric, and include both compression corner and impinging type SWTBL interactions. The strength of the interactions range from attached to incipient separation to fully separated flows. The experiments were chosen based on criterion to ensure quality of the datasets, to be relevant to NASA's missions and to be useful for validation and uncertainty assessment of CFD Navier-Stokes predictive methods, both now and in the future. An emphasis on datasets selected was on surface pressures and surface heating throughout the interaction, but include some wall shear stress distributions and flowfield profiles. Included, for selected cases, are example CFD grids and setup information, along with surface pressure and wall heating results from simulations using current NASA real-gas Navier-Stokes codes by which future CFD investigators can compare and evaluate physics modeling improvements and validation and uncertainty assessments of future CFD code developments. The experimental database is presented tabulated in the Appendices describing each experiment. The database is also provided in computer-readable ASCII files located on a companion DVD.

A Benchmark and Comparative Study of Video-Based Face Recognition on COX Face Database.

PubMed

Huang, Zhiwu; Shan, Shiguang; Wang, Ruiping; Zhang, Haihong; Lao, Shihong; Kuerban, Alifu; Chen, Xilin

2015-12-01

Face recognition with still face images has been widely studied, while the research on video-based face recognition is inadequate relatively, especially in terms of benchmark datasets and comparisons. Real-world video-based face recognition applications require techniques for three distinct scenarios: 1) Videoto-Still (V2S); 2) Still-to-Video (S2V); and 3) Video-to-Video (V2V), respectively, taking video or still image as query or target. To the best of our knowledge, few datasets and evaluation protocols have benchmarked for all the three scenarios. In order to facilitate the study of this specific topic, this paper contributes a benchmarking and comparative study based on a newly collected still/video face database, named COX(1) Face DB. Specifically, we make three contributions. First, we collect and release a largescale still/video face database to simulate video surveillance with three different video-based face recognition scenarios (i.e., V2S, S2V, and V2V). Second, for benchmarking the three scenarios designed on our database, we review and experimentally compare a number of existing set-based methods. Third, we further propose a novel Point-to-Set Correlation Learning (PSCL) method, and experimentally show that it can be used as a promising baseline method for V2S/S2V face recognition on COX Face DB. Extensive experimental results clearly demonstrate that video-based face recognition needs more efforts, and our COX Face DB is a good benchmark database for evaluation.

A fragile zero watermarking scheme to detect and characterize malicious modifications in database relations.

PubMed

Khan, Aihab; Husain, Syed Afaq

2013-01-01

We put forward a fragile zero watermarking scheme to detect and characterize malicious modifications made to a database relation. Most of the existing watermarking schemes for relational databases introduce intentional errors or permanent distortions as marks into the database original content. These distortions inevitably degrade the data quality and data usability as the integrity of a relational database is violated. Moreover, these fragile schemes can detect malicious data modifications but do not characterize the tempering attack, that is, the nature of tempering. The proposed fragile scheme is based on zero watermarking approach to detect malicious modifications made to a database relation. In zero watermarking, the watermark is generated (constructed) from the contents of the original data rather than introduction of permanent distortions as marks into the data. As a result, the proposed scheme is distortion-free; thus, it also resolves the inherent conflict between security and imperceptibility. The proposed scheme also characterizes the malicious data modifications to quantify the nature of tempering attacks. Experimental results show that even minor malicious modifications made to a database relation can be detected and characterized successfully.

LEPER: Library of Experimental PhasE Relations

NASA Astrophysics Data System (ADS)

Davis, F.; Gordon, S.; Mukherjee, S.; Hirschmann, M.; Ghiorso, M.

2006-12-01

The Library of Experimental PhasE Relations (LEPER) seeks to compile published experimental determinations of magmatic phase equilibria and provide those data on the web with a searchable and downloadable interface. Compiled experimental data include the conditions and durations of experiments, the bulk compositions of experimental charges, and the identity, compositions and proportions of phases observed, and, where available, estimates of experimental and analytical uncertainties. Also included are metadata such as the type of experimental device, capsule material, and method(s) of quantitative analysis. The database may be of use to practicing experimentalists as well as the wider Earth science community. Experimentalists may find the data useful for planning new experiments and will easily be able to compare their results to the full body of previous experimentnal data. Geologists may use LEPER to compare rocks sampled in the field with experiments performed on similar bulk composition or with experiments that produced similar-composition product phases. Modelers may use LEPER to parameterize partial melting of various lithologies. One motivation for compiling LEPER is for calibration of updated and revised versions of MELTS, however, it is hoped that the availability of LEPER will facilitate formulation and calibration of additional thermodynamic or empirical models of magmatic phase relations and phase equilibria, geothermometers and more. Data entry for LEPER is occuring presently: As of August, 2006, >6200 experiments have been entered, chiefly from work published between 1997 and 2005. A prototype web interface has been written and beta release on the web is anticipated in Fall, 2006. Eventually, experimentalists will be able to submit their new experimental data to the database via the web. At present, the database contains only data pertaining to the phase equilibria of silicate melts, but extension to other experimental data involving other fluids or sub-solidus phase equilibria may be contemplated. Also, the data are at present limited to natural or near-natural systems, but in the future, extension to synthetic (i.e., CMAS, etc.) systems is also possible. Each would depend in part on whether there is community demand for such databases. A trace element adjunct to LEPER is presently in planning stages.

Analysis of mesenchymal stem cell differentiation in vitro using classification association rule mining.

PubMed

Wang, Weiqi; Wang, Yanbo Justin; Bañares-Alcántara, René; Coenen, Frans; Cui, Zhanfeng

2009-12-01

In this paper, data mining is used to analyze the data on the differentiation of mammalian Mesenchymal Stem Cells (MSCs), aiming at discovering known and hidden rules governing MSC differentiation, following the establishment of a web-based public database containing experimental data on the MSC proliferation and differentiation. To this effect, a web-based public interactive database comprising the key parameters which influence the fate and destiny of mammalian MSCs has been constructed and analyzed using Classification Association Rule Mining (CARM) as a data-mining technique. The results show that the proposed approach is technically feasible and performs well with respect to the accuracy of (classification) prediction. Key rules mined from the constructed MSC database are consistent with experimental observations, indicating the validity of the method developed and the first step in the application of data mining to the study of MSCs.

A Practical Engineering Approach to Predicting Fatigue Crack Growth in Riveted Lap Joints

NASA Technical Reports Server (NTRS)

Harris, Charles E.; Piascik, Robert S.; Newman, James C., Jr.

1999-01-01

An extensive experimental database has been assembled from very detailed teardown examinations of fatigue cracks found in rivet holes of fuselage structural components. Based on this experimental database, a comprehensive analysis methodology was developed to predict the onset of widespread fatigue damage in lap joints of fuselage structure. Several computer codes were developed with specialized capabilities to conduct the various analyses that make up the comprehensive methodology. Over the past several years, the authors have interrogated various aspects of the analysis methods to determine the degree of computational rigor required to produce numerical predictions with acceptable engineering accuracy. This study led to the formulation of a practical engineering approach to predicting fatigue crack growth in riveted lap joints. This paper describes the practical engineering approach and compares predictions with the results from several experimental studies.

A Practical Engineering Approach to Predicting Fatigue Crack Growth in Riveted Lap Joints

NASA Technical Reports Server (NTRS)

Harris, C. E.; Piascik, R. S.; Newman, J. C., Jr.

2000-01-01

An extensive experimental database has been assembled from very detailed teardown examinations of fatigue cracks found in rivet holes of fuselage structural components. Based on this experimental database, a comprehensive analysis methodology was developed to predict the onset of widespread fatigue damage in lap joints of fuselage structure. Several computer codes were developed with specialized capabilities to conduct the various analyses that make up the comprehensive methodology. Over the past several years, the authors have interrogated various aspects of the analysis methods to determine the degree of computational rigor required to produce numerical predictions with acceptable engineering accuracy. This study led to the formulation of a practical engineering approach to predicting fatigue crack growth in riveted lap joints. This paper describes the practical engineering approach and compares predictions with the results from several experimental studies.

Recovery Act: An Integrated Experimental and Numerical Study: Developing a Reaction Transport Model that Couples Chemical Reactions of Mineral Dissolution/Precipitation with Spatial and Temporal Flow Variations.

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

Saar, Martin O.; Seyfried, Jr., William E.; Longmire, Ellen K.

2016-06-24

A total of 12 publications and 23 abstracts were produced as a result of this study. In particular, the compilation of a thermodynamic database utilizing consistent, current thermodynamic data is a major step toward accurately modeling multi-phase fluid interactions with solids. Existing databases designed for aqueous fluids did not mesh well with existing solid phase databases. Addition of a second liquid phase (CO2) magnifies the inconsistencies between aqueous and solid thermodynamic databases. Overall, the combination of high temperature and pressure lab studies (task 1), using a purpose built apparatus, and solid characterization (task 2), using XRCT and more developed technologies,more » allowed observation of dissolution and precipitation processes under CO2 reservoir conditions. These observations were combined with results from PIV experiments on multi-phase fluids (task 3) in typical flow path geometries. The results of the tasks 1, 2, and 3 were compiled and integrated into numerical models utilizing Lattice-Boltzmann simulations (task 4) to realistically model the physical processes and were ultimately folded into TOUGH2 code for reservoir scale modeling (task 5). Compilation of the thermodynamic database assisted comparisons to PIV experiments (Task 3) and greatly improved Lattice Boltzmann (Task 4) and TOUGH2 simulations (Task 5). PIV (Task 3) and experimental apparatus (Task 1) have identified problem areas in TOUGHREACT code. Additional lab experiments and coding work has been integrated into an improved numerical modeling code.« less

Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases

PubMed Central

2011-01-01

Background Although many biological databases are applying semantic web technologies, meaningful biological hypothesis testing cannot be easily achieved. Database-driven high throughput genomic hypothesis testing requires both of the capabilities of obtaining semantically relevant experimental data and of performing relevant statistical testing for the retrieved data. Tissue Microarray (TMA) data are semantically rich and contains many biologically important hypotheses waiting for high throughput conclusions. Methods An application-specific ontology was developed for managing TMA and DNA microarray databases by semantic web technologies. Data were represented as Resource Description Framework (RDF) according to the framework of the ontology. Applications for hypothesis testing (Xperanto-RDF) for TMA data were designed and implemented by (1) formulating the syntactic and semantic structures of the hypotheses derived from TMA experiments, (2) formulating SPARQLs to reflect the semantic structures of the hypotheses, and (3) performing statistical test with the result sets returned by the SPARQLs. Results When a user designs a hypothesis in Xperanto-RDF and submits it, the hypothesis can be tested against TMA experimental data stored in Xperanto-RDF. When we evaluated four previously validated hypotheses as an illustration, all the hypotheses were supported by Xperanto-RDF. Conclusions We demonstrated the utility of high throughput biological hypothesis testing. We believe that preliminary investigation before performing highly controlled experiment can be benefited. PMID:21342584

Domain fusion analysis by applying relational algebra to protein sequence and domain databases

PubMed Central

Truong, Kevin; Ikura, Mitsuhiko

2003-01-01

Background Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. Results This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at . Conclusion As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time. PMID:12734020

The Brain Database: A Multimedia Neuroscience Database for Research and Teaching

PubMed Central

Wertheim, Steven L.

1989-01-01

The Brain Database is an information tool designed to aid in the integration of clinical and research results in neuroanatomy and regional biochemistry. It can handle a wide range of data types including natural images, 2 and 3-dimensional graphics, video, numeric data and text. It is organized around three main entities: structures, substances and processes. The database will support a wide variety of graphical interfaces. Two sample interfaces have been made. This tool is intended to serve as one component of a system that would allow neuroscientists and clinicians 1) to represent clinical and experimental data within a common framework 2) to compare results precisely between experiments and among laboratories, 3) to use computing tools as an aid in collaborative work and 4) to contribute to a shared and accessible body of knowledge about the nervous system.

BioQ: tracing experimental origins in public genomic databases using a novel data provenance model.

PubMed

Saccone, Scott F; Quan, Jiaxi; Jones, Peter L

2012-04-15

Public genomic databases, which are often used to guide genetic studies of human disease, are now being applied to genomic medicine through in silico integrative genomics. These databases, however, often lack tools for systematically determining the experimental origins of the data. We introduce a new data provenance model that we have implemented in a public web application, BioQ, for assessing the reliability of the data by systematically tracing its experimental origins to the original subjects and biologics. BioQ allows investigators to both visualize data provenance as well as explore individual elements of experimental process flow using precise tools for detailed data exploration and documentation. It includes a number of human genetic variation databases such as the HapMap and 1000 Genomes projects. BioQ is freely available to the public at http://bioq.saclab.net.

2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments.

PubMed

Allmer, Jens; Kuhlgert, Sebastian; Hippler, Michael

2008-07-07

The amount of information stemming from proteomics experiments involving (multi dimensional) separation techniques, mass spectrometric analysis, and computational analysis is ever-increasing. Data from such an experimental workflow needs to be captured, related and analyzed. Biological experiments within this scope produce heterogenic data ranging from pictures of one or two-dimensional protein maps and spectra recorded by tandem mass spectrometry to text-based identifications made by algorithms which analyze these spectra. Additionally, peptide and corresponding protein information needs to be displayed. In order to handle the large amount of data from computational processing of mass spectrometric experiments, automatic import scripts are available and the necessity for manual input to the database has been minimized. Information is in a generic format which abstracts from specific software tools typically used in such an experimental workflow. The software is therefore capable of storing and cross analysing results from many algorithms. A novel feature and a focus of this database is to facilitate protein identification by using peptides identified from mass spectrometry and link this information directly to respective protein maps. Additionally, our application employs spectral counting for quantitative presentation of the data. All information can be linked to hot spots on images to place the results into an experimental context. A summary of identified proteins, containing all relevant information per hot spot, is automatically generated, usually upon either a change in the underlying protein models or due to newly imported identifications. The supporting information for this report can be accessed in multiple ways using the user interface provided by the application. We present a proteomics database which aims to greatly reduce evaluation time of results from mass spectrometric experiments and enhance result quality by allowing consistent data handling. Import functionality, automatic protein detection, and summary creation act together to facilitate data analysis. In addition, supporting information for these findings is readily accessible via the graphical user interface provided. The database schema and the implementation, which can easily be installed on virtually any server, can be downloaded in the form of a compressed file from our project webpage.

Compartmental and Data-Based Modeling of Cerebral Hemodynamics: Linear Analysis.

PubMed

Henley, B C; Shin, D C; Zhang, R; Marmarelis, V Z

Compartmental and data-based modeling of cerebral hemodynamics are alternative approaches that utilize distinct model forms and have been employed in the quantitative study of cerebral hemodynamics. This paper examines the relation between a compartmental equivalent-circuit and a data-based input-output model of dynamic cerebral autoregulation (DCA) and CO2-vasomotor reactivity (DVR). The compartmental model is constructed as an equivalent-circuit utilizing putative first principles and previously proposed hypothesis-based models. The linear input-output dynamics of this compartmental model are compared with data-based estimates of the DCA-DVR process. This comparative study indicates that there are some qualitative similarities between the two-input compartmental model and experimental results.

LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system

PubMed Central

Bannasch, Detlev; Mehrle, Alexander; Glatting, Karl-Heinz; Pepperkok, Rainer; Poustka, Annemarie; Wiemann, Stefan

2004-01-01

We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on the encoded proteins produced in functional genomics and proteomics approaches. The database also serves as a sample-tracking system to manage the process from cDNA to experimental read-out and data interpretation. A web interface enables the scientific community to explore and visualize features of the annotated cDNAs and ORFs combined with experimental results, and thus helps to unravel new features of proteins with as yet unknown functions. PMID:14681468

Databases and Associated Tools for Glycomics and Glycoproteomics.

PubMed

Lisacek, Frederique; Mariethoz, Julien; Alocci, Davide; Rudd, Pauline M; Abrahams, Jodie L; Campbell, Matthew P; Packer, Nicolle H; Ståhle, Jonas; Widmalm, Göran; Mullen, Elaine; Adamczyk, Barbara; Rojas-Macias, Miguel A; Jin, Chunsheng; Karlsson, Niclas G

2017-01-01

The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (SugarBind).

An open experimental database for exploring inorganic materials

DOE PAGES

Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus; ...

2018-04-03

The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half ofmore » these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.« less

An open experimental database for exploring inorganic materials.

PubMed

Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus; Perkins, John D; White, Robert; Munch, Kristin; Tumas, William; Phillips, Caleb

2018-04-03

The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half of these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.

An open experimental database for exploring inorganic materials

PubMed Central

Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus; Perkins, John D.; White, Robert; Munch, Kristin; Tumas, William; Phillips, Caleb

2018-01-01

The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half of these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource. PMID:29611842

An open experimental database for exploring inorganic materials

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

Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus

The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half ofmore » these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.« less

Molecular formula and METLIN Personal Metabolite Database matching applied to the identification of compounds generated by LC/TOF-MS.

PubMed

Sana, Theodore R; Roark, Joseph C; Li, Xiangdong; Waddell, Keith; Fischer, Steven M

2008-09-01

In an effort to simplify and streamline compound identification from metabolomics data generated by liquid chromatography time-of-flight mass spectrometry, we have created software for constructing Personalized Metabolite Databases with content from over 15,000 compounds pulled from the public METLIN database (http://metlin.scripps.edu/). Moreover, we have added extra functionalities to the database that (a) permit the addition of user-defined retention times as an orthogonal searchable parameter to complement accurate mass data; and (b) allow interfacing to separate software, a Molecular Formula Generator (MFG), that facilitates reliable interpretation of any database matches from the accurate mass spectral data. To test the utility of this identification strategy, we added retention times to a subset of masses in this database, representing a mixture of 78 synthetic urine standards. The synthetic mixture was analyzed and screened against this METLIN urine database, resulting in 46 accurate mass and retention time matches. Human urine samples were subsequently analyzed under the same analytical conditions and screened against this database. A total of 1387 ions were detected in human urine; 16 of these ions matched both accurate mass and retention time parameters for the 78 urine standards in the database. Another 374 had only an accurate mass match to the database, with 163 of those masses also having the highest MFG score. Furthermore, MFG calculated a formula for a further 849 ions that had no match to the database. Taken together, these results suggest that the METLIN Personal Metabolite database and MFG software offer a robust strategy for confirming the formula of database matches. In the event of no database match, it also suggests possible formulas that may be helpful in interpreting the experimental results.

NASA Airframe Icing Research Overview Past and Current

NASA Technical Reports Server (NTRS)

Potapczuk, Mark

2009-01-01

This slide presentation reviews the past and current research that NASA has done in the area of airframe icing. Both the history experimental efforts and model development to understand the process and problem of ice formation are reviewed. This has resulted in the development of new experimental methods, advanced icing simulation software, flight dynamics and experimental databases that have an impact on design, testing, construction and certification and qualification of the aircraft and its sub-systems.

HIPdb: a database of experimentally validated HIV inhibiting peptides.

PubMed

Qureshi, Abid; Thakur, Nishant; Kumar, Manoj

2013-01-01

Besides antiretroviral drugs, peptides have also demonstrated potential to inhibit the Human immunodeficiency virus (HIV). For example, T20 has been discovered to effectively block the HIV entry and was approved by the FDA as a novel anti-HIV peptide (AHP). We have collated all experimental information on AHPs at a single platform. HIPdb is a manually curated database of experimentally verified HIV inhibiting peptides targeting various steps or proteins involved in the life cycle of HIV e.g. fusion, integration, reverse transcription etc. This database provides experimental information of 981 peptides. These are of varying length obtained from natural as well as synthetic sources and tested on different cell lines. Important fields included are peptide sequence, length, source, target, cell line, inhibition/IC(50), assay and reference. The database provides user friendly browse, search, sort and filter options. It also contains useful services like BLAST and 'Map' for alignment with user provided sequences. In addition, predicted structure and physicochemical properties of the peptides are also included. HIPdb database is freely available at http://crdd.osdd.net/servers/hipdb. Comprehensive information of this database will be helpful in selecting/designing effective anti-HIV peptides. Thus it may prove a useful resource to researchers for peptide based therapeutics development.

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 programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification.

PubMed

Kalyanaraman, Ananth; Cannon, William R; Latt, Benjamin; Baxter, Douglas J

2011-11-01

A MapReduce-based implementation called MR-MSPolygraph for parallelizing peptide identification from mass spectrometry data is presented. The underlying serial method, MSPolygraph, uses a novel hybrid approach to match an experimental spectrum against a combination of a protein sequence database and a spectral library. Our MapReduce implementation can run on any Hadoop cluster environment. Experimental results demonstrate that, relative to the serial version, MR-MSPolygraph reduces the time to solution from weeks to hours, for processing tens of thousands of experimental spectra. Speedup and other related performance studies are also reported on a 400-core Hadoop cluster using spectral datasets from environmental microbial communities as inputs. The source code along with user documentation are available on http://compbio.eecs.wsu.edu/MR-MSPolygraph. ananth@eecs.wsu.edu; william.cannon@pnnl.gov. Supplementary data are available at Bioinformatics online.

PlantDB – a versatile database for managing plant research

PubMed Central

Exner, Vivien; Hirsch-Hoffmann, Matthias; Gruissem, Wilhelm; Hennig, Lars

2008-01-01

Background Research in plant science laboratories often involves usage of many different species, cultivars, ecotypes, mutants, alleles or transgenic lines. This creates a great challenge to keep track of the identity of experimental plants and stored samples or seeds. Results Here, we describe PlantDB – a Microsoft® Office Access database – with a user-friendly front-end for managing information relevant for experimental plants. PlantDB can hold information about plants of different species, cultivars or genetic composition. Introduction of a concise identifier system allows easy generation of pedigree trees. In addition, all information about any experimental plant – from growth conditions and dates over extracted samples such as RNA to files containing images of the plants – can be linked unequivocally. Conclusion We have been using PlantDB for several years in our laboratory and found that it greatly facilitates access to relevant information. PMID:18182106

Cold Climate Foundation Retrofit Experimental Hygrothermal Performance: Cloquet Residential Research Facility Laboratory Results

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

Goldberg, Louise F.; Harmon, Anna C.

2015-04-01

Thermal and moisture problems in existing basements create a unique challenge because the exterior face of the wall is not easily or inexpensively accessible. This approach addresses thermal and moisture management from the interior face of the wall without disturbing the exterior soil and landscaping. the interior and exterior environments. This approach has the potential for improving durability, comfort, and indoor air quality. This project was funded jointly by the National Renewable Energy Laboratory (NREL) and Oak Ridge National Laboratory (ORNL). ORNL focused on developing a full basement wall system experimental database to enable others to validate hygrothermal simulation codes.more » NREL focused on testing the moisture durability of practical basement wall interior insulation retrofit solutions for cold climates. The project has produced a physically credible and reliable long-term hygrothermal performance database for retrofit foundation wall insulation systems in zone 6 and 7 climates that are fully compliant with the performance criteria in the 2009 Minnesota Energy Code. The experimental data were configured into a standard format that can be published online and that is compatible with standard commercially available spreadsheet and database software.« less

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

Lam, Hugo Y.K.; Marenco, Luis; Shepherd, Gordon M.; Miller, Perry L.; Cheung, Kei-Hoi

2006-01-01

Integrative neuroscience involves the integration and analysis of diverse types of neuroscience data involving many different experimental techniques. This data will increasingly be distributed across many heterogeneous databases that are web-accessible. Currently, these databases do not expose their schemas (database structures) and their contents to web applications/agents in a standardized, machine-friendly way. This limits database interoperation. To address this problem, we describe a pilot project that illustrates how neuroscience databases can be expressed using the Web Ontology Language, which is a semantically-rich ontological language, as a common data representation language to facilitate complex cross-database queries. In this pilot project, an existing tool called “D2RQ” was used to translate two neuroscience databases (NeuronDB and CoCoDat) into OWL, and the resulting OWL ontologies were then merged. An OWL-based reasoner (Racer) was then used to provide a sophisticated query language (nRQL) to perform integrated queries across the two databases based on the merged ontology. This pilot project is one step toward exploring the use of semantic web technologies in the neurosciences. PMID:17238384

Graph Databases for Large-Scale Healthcare Systems: A Framework for Efficient Data Management and Data Services

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

Park, Yubin; Shankar, Mallikarjun; Park, Byung H.

Designing a database system for both efficient data management and data services has been one of the enduring challenges in the healthcare domain. In many healthcare systems, data services and data management are often viewed as two orthogonal tasks; data services refer to retrieval and analytic queries such as search, joins, statistical data extraction, and simple data mining algorithms, while data management refers to building error-tolerant and non-redundant database systems. The gap between service and management has resulted in rigid database systems and schemas that do not support effective analytics. We compose a rich graph structure from an abstracted healthcaremore » RDBMS to illustrate how we can fill this gap in practice. We show how a healthcare graph can be automatically constructed from a normalized relational database using the proposed 3NF Equivalent Graph (3EG) transformation.We discuss a set of real world graph queries such as finding self-referrals, shared providers, and collaborative filtering, and evaluate their performance over a relational database and its 3EG-transformed graph. Experimental results show that the graph representation serves as multiple de-normalized tables, thus reducing complexity in a database and enhancing data accessibility of users. Based on this finding, we propose an ensemble framework of databases for healthcare applications.« less

ARMOUR - A Rice miRNA: mRNA Interaction Resource.

PubMed

Sanan-Mishra, Neeti; Tripathi, Anita; Goswami, Kavita; Shukla, Rohit N; Vasudevan, Madavan; Goswami, Hitesh

2018-01-01

ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.

Perspective: Interactive material property databases through aggregation of literature data

NASA Astrophysics Data System (ADS)

Seshadri, Ram; Sparks, Taylor D.

2016-05-01

Searchable, interactive, databases of material properties, particularly those relating to functional materials (magnetics, thermoelectrics, photovoltaics, etc.) are curiously missing from discussions of machine-learning and other data-driven methods for advancing new materials discovery. Here we discuss the manual aggregation of experimental data from the published literature for the creation of interactive databases that allow the original experimental data as well additional metadata to be visualized in an interactive manner. The databases described involve materials for thermoelectric energy conversion, and for the electrodes of Li-ion batteries. The data can be subject to machine-learning, accelerating the discovery of new materials.

Joint Experimentation on Scalable Parallel Processors (JESPP)

DTIC Science & Technology

2006-04-01

made use of local embedded relational databases, implemented using sqlite on each node of an SPP to execute queries and return results via an ad hoc ...rl.af.mil 12a. DISTRIBUTION / AVAILABILITY STATEENT APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED. 12b. DISTRIBUTION CODE 13. ABSTRACT...Experimentation Directorate (J9) required expansion of its joint semi-automated forces (JSAF) code capabilities; including number of entities, behavior complexity

Comparison of Aircraft Icing Growth Assessment Software

NASA Technical Reports Server (NTRS)

Wright, William; Potapczuk, Mark G.; Levinson, Laurie H.

2011-01-01

A research project is underway to produce computer software that can accurately predict ice growth under any meteorological conditions for any aircraft surface. An extensive comparison of the results in a quantifiable manner against the database of ice shapes that have been generated in the NASA Glenn Icing Research Tunnel (IRT) has been performed, including additional data taken to extend the database in the Super-cooled Large Drop (SLD) regime. The project shows the differences in ice shape between LEWICE 3.2.2, GlennICE, and experimental data. The project addresses the validation of the software against a recent set of ice-shape data in the SLD regime. This validation effort mirrors a similar effort undertaken for previous validations of LEWICE. Those reports quantified the ice accretion prediction capabilities of the LEWICE software. Several ice geometry features were proposed for comparing ice shapes in a quantitative manner. The resulting analysis showed that LEWICE compared well to the available experimental data.

The Novel Object and Unusual Name (NOUN) Database: A collection of novel images for use in experimental research.

PubMed

Horst, Jessica S; Hout, Michael C

2016-12-01

Many experimental research designs require images of novel objects. Here we introduce the Novel Object and Unusual Name (NOUN) Database. This database contains 64 primary novel object images and additional novel exemplars for ten basic- and nine global-level object categories. The objects' novelty was confirmed by both self-report and a lack of consensus on questions that required participants to name and identify the objects. We also found that object novelty correlated with qualifying naming responses pertaining to the objects' colors. The results from a similarity sorting task (and a subsequent multidimensional scaling analysis on the similarity ratings) demonstrated that the objects are complex and distinct entities that vary along several featural dimensions beyond simply shape and color. A final experiment confirmed that additional item exemplars comprised both sub- and superordinate categories. These images may be useful in a variety of settings, particularly for developmental psychology and other research in the language, categorization, perception, visual memory, and related domains.

PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature.

PubMed

Yoo, Danny; Xu, Iris; Berardini, Tanya Z; Rhee, Seung Yon; Narayanasamy, Vijay; Twigger, Simon

2006-03-01

For most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results. Manual review of this literature to extract targeted information into biological databases is difficult and time consuming. To address this problem, we developed PubSearch and PubFetch, which store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature. A set of protocols is provided in this unit for installing, populating, running, and using PubSearch and PubFetch. In addition, we provide support protocols for performing controlled vocabulary annotations. Intended users of PubSearch and PubFetch are database curators and biology researchers interested in tracking the literature and capturing information about genes of interest in a more effective way than with conventional spreadsheets and lab notebooks.

HoPaCI-DB: host-Pseudomonas and Coxiella interaction database

PubMed Central

Bleves, Sophie; Dunger, Irmtraud; Walter, Mathias C.; Frangoulidis, Dimitrios; Kastenmüller, Gabi; Voulhoux, Romé; Ruepp, Andreas

2014-01-01

Bacterial infectious diseases are the result of multifactorial processes affected by the interplay between virulence factors and host targets. The host-Pseudomonas and Coxiella interaction database (HoPaCI-DB) is a publicly available manually curated integrative database (http://mips.helmholtz-muenchen.de/HoPaCI/) of host–pathogen interaction data from Pseudomonas aeruginosa and Coxiella burnetii. The resource provides structured information on 3585 experimentally validated interactions between molecules, bioprocesses and cellular structures extracted from the scientific literature. Systematic annotation and interactive graphical representation of disease networks make HoPaCI-DB a versatile knowledge base for biologists and network biology approaches. PMID:24137008

miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs.

PubMed

Wang, Peng; Zhi, Hui; Zhang, Yunpeng; Liu, Yue; Zhang, Jizhou; Gao, Yue; Guo, Maoni; Ning, Shangwei; Li, Xia

2015-01-01

In this study, we describe miRSponge, a manually curated database, which aims at providing an experimentally supported resource for microRNA (miRNA) sponges. Recent evidence suggests that miRNAs are themselves regulated by competing endogenous RNAs (ceRNAs) or 'miRNA sponges' that contain miRNA binding sites. These competitive molecules can sequester miRNAs to prevent them interacting with their natural targets to play critical roles in various biological and pathological processes. It has become increasingly important to develop a high quality database to record and store ceRNA data to support future studies. To this end, we have established the experimentally supported miRSponge database that contains data on 599 miRNA-sponge interactions and 463 ceRNA relationships from 11 species following manual curating from nearly 1200 published articles. Database classes include endogenously generated molecules including coding genes, pseudogenes, long non-coding RNAs and circular RNAs, along with exogenously introduced molecules including viral RNAs and artificial engineered sponges. Approximately 70% of the interactions were identified experimentally in disease states. miRSponge provides a user-friendly interface for convenient browsing, retrieval and downloading of dataset. A submission page is also included to allow researchers to submit newly validated miRNA sponge data. Database URL: http://www.bio-bigdata.net/miRSponge. © The Author(s) 2015. Published by Oxford University Press.

miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs

PubMed Central

Wang, Peng; Zhi, Hui; Zhang, Yunpeng; Liu, Yue; Zhang, Jizhou; Gao, Yue; Guo, Maoni; Ning, Shangwei; Li, Xia

2015-01-01

In this study, we describe miRSponge, a manually curated database, which aims at providing an experimentally supported resource for microRNA (miRNA) sponges. Recent evidence suggests that miRNAs are themselves regulated by competing endogenous RNAs (ceRNAs) or ‘miRNA sponges’ that contain miRNA binding sites. These competitive molecules can sequester miRNAs to prevent them interacting with their natural targets to play critical roles in various biological and pathological processes. It has become increasingly important to develop a high quality database to record and store ceRNA data to support future studies. To this end, we have established the experimentally supported miRSponge database that contains data on 599 miRNA-sponge interactions and 463 ceRNA relationships from 11 species following manual curating from nearly 1200 published articles. Database classes include endogenously generated molecules including coding genes, pseudogenes, long non-coding RNAs and circular RNAs, along with exogenously introduced molecules including viral RNAs and artificial engineered sponges. Approximately 70% of the interactions were identified experimentally in disease states. miRSponge provides a user-friendly interface for convenient browsing, retrieval and downloading of dataset. A submission page is also included to allow researchers to submit newly validated miRNA sponge data. Database URL: http://www.bio-bigdata.net/miRSponge. PMID:26424084

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

PubMed Central

Liu, Zhi-Ping; Wu, Canglin; Miao, Hongyu; Wu, Hulin

2015-01-01

Transcriptional and post-transcriptional regulation of gene expression is of fundamental importance to numerous biological processes. Nowadays, an increasing amount of gene regulatory relationships have been documented in various databases and literature. However, to more efficiently exploit such knowledge for biomedical research and applications, it is necessary to construct a genome-wide regulatory network database to integrate the information on gene regulatory relationships that are widely scattered in many different places. Therefore, in this work, we build a knowledge-based database, named ‘RegNetwork’, of gene regulatory networks for human and mouse by collecting and integrating the documented regulatory interactions among transcription factors (TFs), microRNAs (miRNAs) and target genes from 25 selected databases. Moreover, we also inferred and incorporated potential regulatory relationships based on transcription factor binding site (TFBS) motifs into RegNetwork. As a result, RegNetwork contains a comprehensive set of experimentally observed or predicted transcriptional and post-transcriptional regulatory relationships, and the database framework is flexibly designed for potential extensions to include gene regulatory networks for other organisms in the future. Based on RegNetwork, we characterized the statistical and topological properties of genome-wide regulatory networks for human and mouse, we also extracted and interpreted simple yet important network motifs that involve the interplays between TF-miRNA and their targets. In summary, RegNetwork provides an integrated resource on the prior information for gene regulatory relationships, and it enables us to further investigate context-specific transcriptional and post-transcriptional regulatory interactions based on domain-specific experimental data. Database URL: http://www.regnetworkweb.org PMID:26424082

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.

Determination of absorption coefficient based on laser beam thermal blooming in gas-filled tube.

PubMed

Hafizi, B; Peñano, J; Fischer, R; DiComo, G; Ting, A

2014-08-01

Thermal blooming of a laser beam propagating in a gas-filled tube is investigated both analytically and experimentally. A self-consistent formulation taking into account heating of the gas and the resultant laser beam spreading (including diffraction) is presented. The heat equation is used to determine the temperature variation while the paraxial wave equation is solved in the eikonal approximation to determine the temporal and spatial variation of the Gaussian laser spot radius, Gouy phase (longitudinal phase delay), and wavefront curvature. The analysis is benchmarked against a thermal blooming experiment in the literature using a CO₂ laser beam propagating in a tube filled with air and propane. New experimental results are presented in which a CW fiber laser (1 μm) propagates in a tube filled with nitrogen and water vapor. By matching laboratory and theoretical results, the absorption coefficient of water vapor is found to agree with calculations using MODTRAN (the MODerate-resolution atmospheric TRANsmission molecular absorption database) and HITRAN (the HIgh-resolution atmospheric TRANsmission molecular absorption database).

Data to knowledge: how to get meaning from your result.

PubMed

Berman, Helen M; Gabanyi, Margaret J; Groom, Colin R; Johnson, John E; Murshudov, Garib N; Nicholls, Robert A; Reddy, Vijay; Schwede, Torsten; Zimmerman, Matthew D; Westbrook, John; Minor, Wladek

2015-01-01

Structural and functional studies require the development of sophisticated 'Big Data' technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB 'super' laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results.

The International Experimental Thermal Hydraulic Systems database – TIETHYS: A new NEA validation tool

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

Rohatgi, Upendra S.

Nuclear reactor codes require validation with appropriate data representing the plant for specific scenarios. The thermal-hydraulic data is scattered in different locations and in different formats. Some of the data is in danger of being lost. A relational database is being developed to organize the international thermal hydraulic test data for various reactor concepts and different scenarios. At the reactor system level, that data is organized to include separate effect tests and integral effect tests for specific scenarios and corresponding phenomena. The database relies on the phenomena identification sections of expert developed PIRTs. The database will provide a summary ofmore » appropriate data, review of facility information, test description, instrumentation, references for the experimental data and some examples of application of the data for validation. The current database platform includes scenarios for PWR, BWR, VVER, and specific benchmarks for CFD modelling data and is to be expanded to include references for molten salt reactors. There are place holders for high temperature gas cooled reactors, CANDU and liquid metal reactors. This relational database is called The International Experimental Thermal Hydraulic Systems (TIETHYS) database and currently resides at Nuclear Energy Agency (NEA) of the OECD and is freely open to public access. Going forward the database will be extended to include additional links and data as they become available. https://www.oecd-nea.org/tiethysweb/« less

Analysis of the vibration environment induced on spacecraft components by hypervelocity impact

NASA Astrophysics Data System (ADS)

Pavarin, Daniele

2009-06-01

This paper reports the result achieved within the study ``Spacecraft Disturbances from Hypervelocity Impact'', performed by CISAS and Thales-Alenia Space Italia under European Space Agency contract. The research project investigated the perturbations produced on spacecraft internal components as a consequence of hypervelocity impacts of micrometeoroids and orbital debris on the external walls of the vehicle. Objective of the study was: (i) to set-up a general numerical /experimental procedure to investigate the vibration induced by hypervelocity impact, (ii) to analyze the GOCE mission in order to asses whether the vibration environment induce by the impact of orbital debris and micrometeoroids could jeopardize the mission. The research project was conducted both experimentally and numerically, performing a large number of impact tests on GOCE-like structural configurations and extrapolating the experimental results via numerical simulations based on hydrocode calculations, finite element and statistical energy analysis. As a result, a database was established which correlates the impact conditions in the experimental range (0.6 to 2.3 mm projectiles at 2.5 to 5 km/s) with the shock spectra on selected locations on various types of structural models.The main out coming of the study are: (i) a wide database reporting acceleration values on a wide range of impact condition, (ii) a general numerical methodology to investigate disturbances induced by space debris and micrometeoroids on general satellite structures.

A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

PubMed Central

2014-01-01

Background Constraint-based models of Escherichia coli metabolic flux have played a key role in computational studies of cellular metabolism at the genome scale. We sought to develop a next-generation constraint-based E. coli model that achieved improved phenotypic prediction accuracy while being frequently updated and easy to use. We also sought to compare model predictions with experimental data to highlight open questions in E. coli biology. Results We present EcoCyc–18.0–GEM, a genome-scale model of the E. coli K–12 MG1655 metabolic network. The model is automatically generated from the current state of EcoCyc using the MetaFlux software, enabling the release of multiple model updates per year. EcoCyc–18.0–GEM encompasses 1445 genes, 2286 unique metabolic reactions, and 1453 unique metabolites. We demonstrate a three-part validation of the model that breaks new ground in breadth and accuracy: (i) Comparison of simulated growth in aerobic and anaerobic glucose culture with experimental results from chemostat culture and simulation results from the E. coli modeling literature. (ii) Essentiality prediction for the 1445 genes represented in the model, in which EcoCyc–18.0–GEM achieves an improved accuracy of 95.2% in predicting the growth phenotype of experimental gene knockouts. (iii) Nutrient utilization predictions under 431 different media conditions, for which the model achieves an overall accuracy of 80.7%. The model’s derivation from EcoCyc enables query and visualization via the EcoCyc website, facilitating model reuse and validation by inspection. We present an extensive investigation of disagreements between EcoCyc–18.0–GEM predictions and experimental data to highlight areas of interest to E. coli modelers and experimentalists, including 70 incorrect predictions of gene essentiality on glucose, 80 incorrect predictions of gene essentiality on glycerol, and 83 incorrect predictions of nutrient utilization. Conclusion Significant advantages can be derived from the combination of model organism databases and flux balance modeling represented by MetaFlux. Interpretation of the EcoCyc database as a flux balance model results in a highly accurate metabolic model and provides a rigorous consistency check for information stored in the database. PMID:24974895

A new feature constituting approach to detection of vocal fold pathology

NASA Astrophysics Data System (ADS)

Hariharan, M.; Polat, Kemal; Yaacob, Sazali

2014-08-01

In the last two decades, non-invasive methods through acoustic analysis of voice signal have been proved to be excellent and reliable tool to diagnose vocal fold pathologies. This paper proposes a new feature vector based on the wavelet packet transform and singular value decomposition for the detection of vocal fold pathology. k-means clustering based feature weighting is proposed to increase the distinguishing performance of the proposed features. In this work, two databases Massachusetts Eye and Ear Infirmary (MEEI) voice disorders database and MAPACI speech pathology database are used. Four different supervised classifiers such as k-nearest neighbour (k-NN), least-square support vector machine, probabilistic neural network and general regression neural network are employed for testing the proposed features. The experimental results uncover that the proposed features give very promising classification accuracy of 100% for both MEEI database and MAPACI speech pathology database.

Parallel database search and prime factorization with magnonic holographic memory devices

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

Khitun, Alexander

In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploitmore » wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.« less

Parallel database search and prime factorization with magnonic holographic memory devices

NASA Astrophysics Data System (ADS)

Khitun, Alexander

2015-12-01

In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.

Person identification in irregular cardiac conditions using electrocardiogram signals.

PubMed

Sidek, Khairul Azami; Khalil, Ibrahim

2011-01-01

This paper presents a person identification mechanism in irregular cardiac conditions using ECG signals. A total of 30 subjects were used in the study from three different public ECG databases containing various abnormal heart conditions from the Paroxysmal Atrial Fibrillation Predicition Challenge database (AFPDB), MIT-BIH Supraventricular Arrthymia database (SVDB) and T-Wave Alternans Challenge database (TWADB). Cross correlation (CC) was used as the biometric matching algorithm with defined threshold values to evaluate the performance. In order to measure the efficiency of this simple yet effective matching algorithm, two biometric performance metrics were used which are false acceptance rate (FAR) and false reject rate (FRR). Our experimentation results suggest that ECG based biometric identification with irregular cardiac condition gives a higher recognition rate of different ECG signals when tested for three different abnormal cardiac databases yielding false acceptance rate (FAR) of 2%, 3% and 2% and false reject rate (FRR) of 1%, 2% and 0% for AFPDB, SVDB and TWADB respectively. These results also indicate the existence of salient biometric characteristics in the ECG morphology within the QRS complex that tends to differentiate individuals.

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 development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

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 development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

Term Dependence: Truncating the Bahadur Lazarsfeld Expansion.

ERIC Educational Resources Information Center

Losee, Robert M., Jr.

1994-01-01

Studies the performance of probabilistic information retrieval systems using differing statistical dependence assumptions when estimating the probabilities inherent in the retrieval model. Experimental results using the Bahadur Lazarsfeld expansion on the Cystic Fibrosis database are discussed that suggest that incorporating term dependence…

miRwayDB: a database for experimentally validated microRNA-pathway associations in pathophysiological conditions

PubMed Central

Das, Sankha Subhra; Saha, Pritam

2018-01-01

Abstract MicroRNAs (miRNAs) are well-known as key regulators of diverse biological pathways. A series of experimental evidences have shown that abnormal miRNA expression profiles are responsible for various pathophysiological conditions by modulating genes in disease associated pathways. In spite of the rapid increase in research data confirming such associations, scientists still do not have access to a consolidated database offering these miRNA-pathway association details for critical diseases. We have developed miRwayDB, a database providing comprehensive information of experimentally validated miRNA-pathway associations in various pathophysiological conditions utilizing data collected from published literature. To the best of our knowledge, it is the first database that provides information about experimentally validated miRNA mediated pathway dysregulation as seen specifically in critical human diseases and hence indicative of a cause-and-effect relationship in most cases. The current version of miRwayDB collects an exhaustive list of miRNA-pathway association entries for 76 critical disease conditions by reviewing 663 published articles. Each database entry contains complete information on the name of the pathophysiological condition, associated miRNA(s), experimental sample type(s), regulation pattern (up/down) of miRNA, pathway association(s), targeted member of dysregulated pathway(s) and a brief description. In addition, miRwayDB provides miRNA, gene and pathway score to evaluate the role of a miRNA regulated pathways in various pathophysiological conditions. The database can also be used for other biomedical approaches such as validation of computational analysis, integrated analysis and prediction of computational model. It also offers a submission page to submit novel data from recently published studies. We believe that miRwayDB will be a useful tool for miRNA research community. Database URL: http://www.mirway.iitkgp.ac.in PMID:29688364

SNPdbe: constructing an nsSNP functional impacts database.

PubMed

Schaefer, Christian; Meier, Alice; Rost, Burkhard; Bromberg, Yana

2012-02-15

Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe-SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from >2600 organisms; 'human' being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The database is available as an MySQL dump and via a web front end that allows searches with any combination of organism names, sequences and mutation IDs. http://www.rostlab.org/services/snpdbe.

Relation between experimental and non-experimental study designs. HB vaccines: a case study

PubMed Central

Jefferson, T.; Demicheli, V.

1999-01-01

STUDY OBJECTIVE: To examine the relation between experimental and non- experimental study design in vaccinology. DESIGN: Assessment of each study design's capability of testing four aspects of vaccine performance, namely immunogenicity (the capacity to stimulate the immune system), duration of immunity conferred, incidence and seriousness of side effects, and number of infections prevented by vaccination. SETTING: Experimental and non-experimental studies on hepatitis B (HB) vaccines in the Cochrane Vaccines Field Database. RESULTS: Experimental and non-experimental vaccine study designs are frequently complementary but some aspects of vaccine quality can only be assessed by one of the types of study. More work needs to be done on the relation between study quality and its significance in terms of effect size.   PMID:10326054

RNAimmuno: A database of the nonspecific immunological effects of RNA interference and microRNA reagents

PubMed Central

Olejniczak, Marta; Galka-Marciniak, Paulina; Polak, Katarzyna; Fligier, Andrzej; Krzyzosiak, Wlodzimierz J.

2012-01-01

The RNAimmuno database was created to provide easy access to information regarding the nonspecific effects generated in cells by RNA interference triggers and microRNA regulators. Various RNAi and microRNA reagents, which differ in length and structure, often cause non-sequence-specific immune responses, in addition to triggering the intended sequence-specific effects. The activation of the cellular sensors of foreign RNA or DNA may lead to the induction of type I interferon and proinflammatory cytokine release. Subsequent changes in the cellular transcriptome and proteome may result in adverse effects, including cell death during therapeutic treatments or the misinterpretation of experimental results in research applications. The manually curated RNAimmuno database gathers the majority of the published data regarding the immunological side effects that are caused in investigated cell lines, tissues, and model organisms by different reagents. The database is accessible at http://rnaimmuno.ibch.poznan.pl and may be helpful in the further application and development of RNAi- and microRNA-based technologies. PMID:22411954

RNAimmuno: a database of the nonspecific immunological effects of RNA interference and microRNA reagents.

PubMed

Olejniczak, Marta; Galka-Marciniak, Paulina; Polak, Katarzyna; Fligier, Andrzej; Krzyzosiak, Wlodzimierz J

2012-05-01

The RNAimmuno database was created to provide easy access to information regarding the nonspecific effects generated in cells by RNA interference triggers and microRNA regulators. Various RNAi and microRNA reagents, which differ in length and structure, often cause non-sequence-specific immune responses, in addition to triggering the intended sequence-specific effects. The activation of the cellular sensors of foreign RNA or DNA may lead to the induction of type I interferon and proinflammatory cytokine release. Subsequent changes in the cellular transcriptome and proteome may result in adverse effects, including cell death during therapeutic treatments or the misinterpretation of experimental results in research applications. The manually curated RNAimmuno database gathers the majority of the published data regarding the immunological side effects that are caused in investigated cell lines, tissues, and model organisms by different reagents. The database is accessible at http://rnaimmuno.ibch.poznan.pl and may be helpful in the further application and development of RNAi- and microRNA-based technologies.

Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments

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

Gaponov, Yu.A.; Igarashi, N.; Hiraki, M.

2004-05-12

An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view,more » create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments.« less

Cross-sections of residual nuclei from deuteron irradiation of thin thorium target at energy 7 GeV

NASA Astrophysics Data System (ADS)

Vespalec, Radek; Adam, Jindrich; Baldin, Anton Alexandrovich; Khushvaktov, Jurabek; Solnyshkin, Alexander Alexandrovich; Tsoupko-Sitnikov, Vsevolod Mikhailovich; Tyutyunikov, Sergey Ivanovich; Vrzalova, Jitka; Zavorka, Lukas; Zeman, Miroslav

2017-09-01

The residual nuclei yields are of great importance for the estimation of basic radiation-technology characteristics (like a total target activity, production of long-lived nuclides etc.) of accelerator driven systems planned for transmutation of spent nuclear fuel and for a design of radioisotopes production facilities. Experimental data are also essential for validation of nuclear codes describing various stages of a spallation reaction. Therefore, the main aim of this work is to add new experimental data in energy region of relativistic deuterons, as similar data are missing in nuclear databases. The sample made of thin natural thorium foil was irradiated at JINR Nuclotron accelerator with a deuteron beam of the total kinetic energy 7 GeV. Integral number of deuterons was determined with the use of aluminum activation detectors. Products of deuteron induced spallation reaction were qualified and quantified by means of gamma-ray spectroscopy method. Several important spectroscopic corrections were applied to obtain results of high accuracy. Experimental cumulative and independent cross-sections were determined for more than 80 isotopes including meta-stable isomers. The total uncertainty of results rarely exceeded 9%. Experimental results were compared with MCNP6.1 Monte-Carlo code predictions. Generally, experimental and calculated cross-sections are in a reasonably good agreement, with the exception of a few light isotopes in a fragmentation region, where the calculations are highly under-estimated. Measured data will be useful for future development of high-energy nuclear codes. After completion, final data will be added into the EXFOR database.

hPDI: a database of experimental human protein-DNA interactions.

PubMed

Xie, Zhi; Hu, Shaohui; Blackshaw, Seth; Zhu, Heng; Qian, Jiang

2010-01-15

The human protein DNA Interactome (hPDI) database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The unique characteristics of hPDI are that it contains consensus DNA-binding sequences not only for nearly 500 human transcription factors but also for >500 unconventional DNA-binding proteins, which are completely uncharacterized previously. Users can browse, search and download a subset or the entire data via a web interface. This database is freely accessible for any academic purposes. http://bioinfo.wilmer.jhu.edu/PDI/.

ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding.

PubMed

Guhlin, Joseph; Silverstein, Kevin A T; Zhou, Peng; Tiffin, Peter; Young, Nevin D

2017-08-10

Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data. The Omics Database Generator (ODG) allows users to create customized databases that utilize published genomics data integrated with experimental data which can be queried using a flexible graph database. When provided with omics and experimental data, ODG will create a comparative, multi-dimensional graph database. ODG can import definitions and annotations from other sources such as InterProScan, the Gene Ontology, ENZYME, UniPathway, and others. This annotation data can be especially useful for studying new or understudied species for which transcripts have only been predicted, and rapidly give additional layers of annotation to predicted genes. In better studied species, ODG can perform syntenic annotation translations or rapidly identify characteristics of a set of genes or nucleotide locations, such as hits from an association study. ODG provides a web-based user-interface for configuring the data import and for querying the database. Queries can also be run from the command-line and the database can be queried directly through programming language hooks available for most languages. ODG supports most common genomic formats as well as generic, easy to use tab-separated value format for user-provided annotations. ODG is a user-friendly database generation and query tool that adapts to the supplied data to produce a comparative genomic database or multi-layered annotation database. ODG provides rapid comparative genomic annotation and is therefore particularly useful for non-model or understudied species. For species for which more data are available, ODG can be used to conduct complex multi-omics, pattern-matching queries.

Data to knowledge: how to get meaning from your result

PubMed Central

Berman, Helen M.; Gabanyi, Margaret J.; Groom, Colin R.; Johnson, John E.; Murshudov, Garib N.; Nicholls, Robert A.; Reddy, Vijay; Schwede, Torsten; Zimmerman, Matthew D.; Westbrook, John; Minor, Wladek

2015-01-01

Structural and functional studies require the development of sophisticated ‘Big Data’ technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB ‘super’ laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results. PMID:25610627

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions.

PubMed

Vlachos, Ioannis S; Paraskevopoulou, Maria D; Karagkouni, Dimitra; Georgakilas, Georgios; Vergoulis, Thanasis; Kanellos, Ilias; Anastasopoulos, Ioannis-Laertis; Maniou, Sofia; Karathanou, Konstantina; Kalfakakou, Despina; Fevgas, Athanasios; Dalamagas, Theodore; Hatzigeorgiou, Artemis G

2015-01-01

microRNAs (miRNAs) are short non-coding RNA species, which act as potent gene expression regulators. Accurate identification of miRNA targets is crucial to understanding their function. Currently, hundreds of thousands of miRNA:gene interactions have been experimentally identified. However, this wealth of information is fragmented and hidden in thousands of manuscripts and raw next-generation sequencing data sets. DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalog published experimentally validated miRNA:gene interactions. DIANA-TarBase v7.0 (http://www.microrna.gr/tarbase) aims to provide for the first time hundreds of thousands of high-quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. DIANA-TarBase v7.0 enables users to easily identify positive or negative experimental results, the utilized experimental methodology, experimental conditions including cell/tissue type and treatment. The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments. More than half a million miRNA:gene interactions have been curated from published experiments on 356 different cell types from 24 species, corresponding to 9- to 250-fold more entries than any other relevant database. DIANA-TarBase v7.0 is freely available. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Face liveness detection using shearlet-based feature descriptors

NASA Astrophysics Data System (ADS)

Feng, Litong; Po, Lai-Man; Li, Yuming; Yuan, Fang

2016-07-01

Face recognition is a widely used biometric technology due to its convenience but it is vulnerable to spoofing attacks made by nonreal faces such as photographs or videos of valid users. The antispoof problem must be well resolved before widely applying face recognition in our daily life. Face liveness detection is a core technology to make sure that the input face is a live person. However, this is still very challenging using conventional liveness detection approaches of texture analysis and motion detection. The aim of this paper is to propose a feature descriptor and an efficient framework that can be used to effectively deal with the face liveness detection problem. In this framework, new feature descriptors are defined using a multiscale directional transform (shearlet transform). Then, stacked autoencoders and a softmax classifier are concatenated to detect face liveness. We evaluated this approach using the CASIA Face antispoofing database and replay-attack database. The experimental results show that our approach performs better than the state-of-the-art techniques following the provided protocols of these databases, and it is possible to significantly enhance the security of the face recognition biometric system. In addition, the experimental results also demonstrate that this framework can be easily extended to classify different spoofing attacks.

Multivariate analysis of toxicity experimental results of environmental endpoints. (FutureToxII)

EPA Science Inventory

The toxicity of hundreds of chemicals have been assessed in laboratory animal studies through EPA chemical regulation and toxicological research. Currently, over 5000 laboratory animal toxicity studies have been collected in the Toxicity Reference Database (ToxRefDB). In addition...

Evolving landscape of low-energy nuclear physics publications

DOE PAGES

Pritychenko, B.

2016-10-01

Evolution of low-energy nuclear physics publications over the last 120 years has been analyzed using nuclear physics databases. An extensive study of Nuclear Science References, Experimental Nuclear Reaction Data (EXFOR), and Evaluated Nuclear Structure Data File (ENSDF) contents provides a unique picture of refereed and non-refereed nuclear physics references. Significant fractional contributions of non-refereed reports, private communications and conference proceedings in EXFOR and ENSDF databases in the 1970’s reflect extensive experimental campaigns and an insufficient number of research journals. This trend has been reversed in recent years because the number of measurements is much lower, while number of journals ismore » higher. In addition, nuclear physics results are mainly published in a limited number of journals, such as Physical Review C and Nuclear Physics A. In the present work, historic publication trends and averages have been extracted and analyzed using nuclear data mining techniques. Lastly, the results of this study and implications are discussed and conclusions presented.« less

Assessment of NASA's Aircraft Noise Prediction Capability

NASA Technical Reports Server (NTRS)

Dahl, Milo D. (Editor)

2012-01-01

A goal of NASA s Fundamental Aeronautics Program is the improvement of aircraft noise prediction. This document provides an assessment, conducted from 2006 to 2009, on the current state of the art for aircraft noise prediction by carefully analyzing the results from prediction tools and from the experimental databases to determine errors and uncertainties and compare results to validate the predictions. The error analysis is included for both the predictions and the experimental data and helps identify where improvements are required. This study is restricted to prediction methods and databases developed or sponsored by NASA, although in many cases they represent the current state of the art for industry. The present document begins with an introduction giving a general background for and a discussion on the process of this assessment followed by eight chapters covering topics at both the system and the component levels. The topic areas, each with multiple contributors, are aircraft system noise, engine system noise, airframe noise, fan noise, liner physics, duct acoustics, jet noise, and propulsion airframe aeroacoustics.

Evolving landscape of low-energy nuclear physics publications

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

Pritychenko, B.

Evolution of low-energy nuclear physics publications over the last 120 years has been analyzed using nuclear physics databases. An extensive study of Nuclear Science References, Experimental Nuclear Reaction Data (EXFOR), and Evaluated Nuclear Structure Data File (ENSDF) contents provides a unique picture of refereed and non-refereed nuclear physics references. Significant fractional contributions of non-refereed reports, private communications and conference proceedings in EXFOR and ENSDF databases in the 1970’s reflect extensive experimental campaigns and an insufficient number of research journals. This trend has been reversed in recent years because the number of measurements is much lower, while number of journals ismore » higher. In addition, nuclear physics results are mainly published in a limited number of journals, such as Physical Review C and Nuclear Physics A. In the present work, historic publication trends and averages have been extracted and analyzed using nuclear data mining techniques. Lastly, the results of this study and implications are discussed and conclusions presented.« less

Comparative study of multimodal biometric recognition by fusion of iris and fingerprint.

PubMed

Benaliouche, Houda; Touahria, Mohamed

2014-01-01

This research investigates the comparative performance from three different approaches for multimodal recognition of combined iris and fingerprints: classical sum rule, weighted sum rule, and fuzzy logic method. The scores from the different biometric traits of iris and fingerprint are fused at the matching score and the decision levels. The scores combination approach is used after normalization of both scores using the min-max rule. Our experimental results suggest that the fuzzy logic method for the matching scores combinations at the decision level is the best followed by the classical weighted sum rule and the classical sum rule in order. The performance evaluation of each method is reported in terms of matching time, error rates, and accuracy after doing exhaustive tests on the public CASIA-Iris databases V1 and V2 and the FVC 2004 fingerprint database. Experimental results prior to fusion and after fusion are presented followed by their comparison with related works in the current literature. The fusion by fuzzy logic decision mimics the human reasoning in a soft and simple way and gives enhanced results.

Comparative Study of Multimodal Biometric Recognition by Fusion of Iris and Fingerprint

PubMed Central

Benaliouche, Houda; Touahria, Mohamed

2014-01-01

This research investigates the comparative performance from three different approaches for multimodal recognition of combined iris and fingerprints: classical sum rule, weighted sum rule, and fuzzy logic method. The scores from the different biometric traits of iris and fingerprint are fused at the matching score and the decision levels. The scores combination approach is used after normalization of both scores using the min-max rule. Our experimental results suggest that the fuzzy logic method for the matching scores combinations at the decision level is the best followed by the classical weighted sum rule and the classical sum rule in order. The performance evaluation of each method is reported in terms of matching time, error rates, and accuracy after doing exhaustive tests on the public CASIA-Iris databases V1 and V2 and the FVC 2004 fingerprint database. Experimental results prior to fusion and after fusion are presented followed by their comparison with related works in the current literature. The fusion by fuzzy logic decision mimics the human reasoning in a soft and simple way and gives enhanced results. PMID:24605065

PhosphoBase: a database of phosphorylation sites.

PubMed Central

Blom, N; Kreegipuu, A; Brunak, S

1998-01-01

PhosphoBase is a database of experimentally verified phosphorylation sites. Version 1.0 contains 156 entries and 398 experimentally determined phosphorylation sites. Entries are compiled and revised from the literature and from major protein sequence databases such as SwissProt and PIR. The entries provide information about the phosphoprotein and the exact position of its phosphorylation sites. Furthermore, part of the entries contain information about kinetic data obtained from enzyme assays on specific peptides. To illustrate the use of data extracted from PhosphoBase we present a sequence logo displaying the overall conservation of positions around serines phosphorylated by protein kinase A (PKA). PhosphoBase is available on the WWW at http://www.cbs.dtu.dk/databases/PhosphoBase/ PMID:9399879

Analyzing a multimodal biometric system using real and virtual users

NASA Astrophysics Data System (ADS)

Scheidat, Tobias; Vielhauer, Claus

2007-02-01

Three main topics of recent research on multimodal biometric systems are addressed in this article: The lack of sufficiently large multimodal test data sets, the influence of cultural aspects and data protection issues of multimodal biometric data. In this contribution, different possibilities are presented to extend multimodal databases by generating so-called virtual users, which are created by combining single biometric modality data of different users. Comparative tests on databases containing real and virtual users based on a multimodal system using handwriting and speech are presented, to study to which degree the use of virtual multimodal databases allows conclusions with respect to recognition accuracy in comparison to real multimodal data. All tests have been carried out on databases created from donations from three different nationality groups. This allows to review the experimental results both in general and in context of cultural origin. The results show that in most cases the usage of virtual persons leads to lower accuracy than the usage of real users in terms of the measurement applied: the Equal Error Rate. Finally, this article will address the general question how the concept of virtual users may influence the data protection requirements for multimodal evaluation databases in the future.

Integrating RFID technique to design mobile handheld inventory management system

NASA Astrophysics Data System (ADS)

Huang, Yo-Ping; Yen, Wei; Chen, Shih-Chung

2008-04-01

An RFID-based mobile handheld inventory management system is proposed in this paper. Differing from the manual inventory management method, the proposed system works on the personal digital assistant (PDA) with an RFID reader. The system identifies electronic tags on the properties and checks the property information in the back-end database server through a ubiquitous wireless network. The system also provides a set of functions to manage the back-end inventory database and assigns different levels of access privilege according to various user categories. In the back-end database server, to prevent improper or illegal accesses, the server not only stores the inventory database and user privilege information, but also keeps track of the user activities in the server including the login and logout time and location, the records of database accessing, and every modification of the tables. Some experimental results are presented to verify the applicability of the integrated RFID-based mobile handheld inventory management system.

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore.

PubMed

Ren, Jian; Liu, Zexian; Gao, Xinjiao; Jin, Changjiang; Ye, Mingliang; Zou, Hanfa; Wen, Longping; Zhang, Zhaolei; Xue, Yu; Yao, Xuebiao

2010-01-01

During cell division/mitosis, a specific subset of proteins is spatially and temporally assembled into protein super complexes in three distinct regions, i.e. centrosome/spindle pole, kinetochore/centromere and midbody/cleavage furrow/phragmoplast/bud neck, and modulates cell division process faithfully. Although many experimental efforts have been carried out to investigate the characteristics of these proteins, no integrated database was available. Here, we present the MiCroKit database (http://microkit.biocuckoo.org) of proteins that localize in midbody, centrosome and/or kinetochore. We collected into the MiCroKit database experimentally verified microkit proteins from the scientific literature that have unambiguous supportive evidence for subcellular localization under fluorescent microscope. The current version of MiCroKit 3.0 provides detailed information for 1489 microkit proteins from seven model organisms, including Saccharomyces cerevisiae, Schizasaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, Mus musculus and Homo sapiens. Moreover, the orthologous information was provided for these microkit proteins, and could be a useful resource for further experimental identification. The online service of MiCroKit database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0).

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore

PubMed Central

Liu, Zexian; Gao, Xinjiao; Jin, Changjiang; Ye, Mingliang; Zou, Hanfa; Wen, Longping; Zhang, Zhaolei; Xue, Yu; Yao, Xuebiao

2010-01-01

During cell division/mitosis, a specific subset of proteins is spatially and temporally assembled into protein super complexes in three distinct regions, i.e. centrosome/spindle pole, kinetochore/centromere and midbody/cleavage furrow/phragmoplast/bud neck, and modulates cell division process faithfully. Although many experimental efforts have been carried out to investigate the characteristics of these proteins, no integrated database was available. Here, we present the MiCroKit database (http://microkit.biocuckoo.org) of proteins that localize in midbody, centrosome and/or kinetochore. We collected into the MiCroKit database experimentally verified microkit proteins from the scientific literature that have unambiguous supportive evidence for subcellular localization under fluorescent microscope. The current version of MiCroKit 3.0 provides detailed information for 1489 microkit proteins from seven model organisms, including Saccharomyces cerevisiae, Schizasaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, Mus musculus and Homo sapiens. Moreover, the orthologous information was provided for these microkit proteins, and could be a useful resource for further experimental identification. The online service of MiCroKit database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0). PMID:19783819

An Adaptive and Time-Efficient ECG R-Peak Detection Algorithm.

PubMed

Qin, Qin; Li, Jianqing; Yue, Yinggao; Liu, Chengyu

2017-01-01

R-peak detection is crucial in electrocardiogram (ECG) signal analysis. This study proposed an adaptive and time-efficient R-peak detection algorithm for ECG processing. First, wavelet multiresolution analysis was applied to enhance the ECG signal representation. Then, ECG was mirrored to convert large negative R-peaks to positive ones. After that, local maximums were calculated by the first-order forward differential approach and were truncated by the amplitude and time interval thresholds to locate the R-peaks. The algorithm performances, including detection accuracy and time consumption, were tested on the MIT-BIH arrhythmia database and the QT database. Experimental results showed that the proposed algorithm achieved mean sensitivity of 99.39%, positive predictivity of 99.49%, and accuracy of 98.89% on the MIT-BIH arrhythmia database and 99.83%, 99.90%, and 99.73%, respectively, on the QT database. By processing one ECG record, the mean time consumptions were 0.872 s and 0.763 s for the MIT-BIH arrhythmia database and QT database, respectively, yielding 30.6% and 32.9% of time reduction compared to the traditional Pan-Tompkins method.

An Adaptive and Time-Efficient ECG R-Peak Detection Algorithm

PubMed Central

Qin, Qin

2017-01-01

R-peak detection is crucial in electrocardiogram (ECG) signal analysis. This study proposed an adaptive and time-efficient R-peak detection algorithm for ECG processing. First, wavelet multiresolution analysis was applied to enhance the ECG signal representation. Then, ECG was mirrored to convert large negative R-peaks to positive ones. After that, local maximums were calculated by the first-order forward differential approach and were truncated by the amplitude and time interval thresholds to locate the R-peaks. The algorithm performances, including detection accuracy and time consumption, were tested on the MIT-BIH arrhythmia database and the QT database. Experimental results showed that the proposed algorithm achieved mean sensitivity of 99.39%, positive predictivity of 99.49%, and accuracy of 98.89% on the MIT-BIH arrhythmia database and 99.83%, 99.90%, and 99.73%, respectively, on the QT database. By processing one ECG record, the mean time consumptions were 0.872 s and 0.763 s for the MIT-BIH arrhythmia database and QT database, respectively, yielding 30.6% and 32.9% of time reduction compared to the traditional Pan-Tompkins method. PMID:29104745

Generation of the Ares I-X Flight Test Vehicle Aerodynamic Data Book and Comparison To Flight

NASA Technical Reports Server (NTRS)

Bauer, Steven X.; Krist, Steven E.; Compton, William B.

2011-01-01

A 3.5-year effort to characterize the aerodynamic behavior of the Ares I-X Flight Test Vehicle (AIX FTV) is described in this paper. The AIX FTV was designed to be representative of the Ares I Crew Launch Vehicle (CLV). While there are several differences in the outer mold line from the current revision of the CLV, the overall length, mass distribution, and flight systems of the two vehicles are very similar. This paper briefly touches on each of the aerodynamic databases developed in the program, describing the methodology employed, experimental and computational contributions to the generation of the databases, and how well the databases and underlying computations compare to actual flight test results.

Analysis and Exchange of Multimedia Laboratory Data Using the Brain Database

PubMed Central

Wertheim, Steven L.

1990-01-01

Two principal goals of the Brain Database are: 1) to support laboratory data collection and analysis of multimedia information about the nervous system and 2) to support exchange of these data among researchers and clinicians who may be physically distant. This has been achieved by an implementation of experimental and clinical records within a relational database. An Image Series Editor has been created that provides a graphical interface to these data for the purposes of annotation, quantification and other analyses. Cooperating laboratories each maintain their own copies of the Brain Database to which they may add private data. Although the data in a given experimental or patient record will be distributed among many tables and external image files, the user can treat each record as a unit that can be extracted from the local database and sent to a distant colleague.

A Blind Reversible Robust Watermarking Scheme for Relational Databases

PubMed Central

Chang, Chin-Chen; Nguyen, Thai-Son; Lin, Chia-Chen

2013-01-01

Protecting the ownership and controlling the copies of digital data have become very important issues in Internet-based applications. Reversible watermark technology allows the distortion-free recovery of relational databases after the embedded watermark data are detected or verified. In this paper, we propose a new, blind, reversible, robust watermarking scheme that can be used to provide proof of ownership for the owner of a relational database. In the proposed scheme, a reversible data-embedding algorithm, which is referred to as “histogram shifting of adjacent pixel difference” (APD), is used to obtain reversibility. The proposed scheme can detect successfully 100% of the embedded watermark data, even if as much as 80% of the watermarked relational database is altered. Our extensive analysis and experimental results show that the proposed scheme is robust against a variety of data attacks, for example, alteration attacks, deletion attacks, mix-match attacks, and sorting attacks. PMID:24223033

A blind reversible robust watermarking scheme for relational databases.

PubMed

Chang, Chin-Chen; Nguyen, Thai-Son; Lin, Chia-Chen

2013-01-01

Protecting the ownership and controlling the copies of digital data have become very important issues in Internet-based applications. Reversible watermark technology allows the distortion-free recovery of relational databases after the embedded watermark data are detected or verified. In this paper, we propose a new, blind, reversible, robust watermarking scheme that can be used to provide proof of ownership for the owner of a relational database. In the proposed scheme, a reversible data-embedding algorithm, which is referred to as "histogram shifting of adjacent pixel difference" (APD), is used to obtain reversibility. The proposed scheme can detect successfully 100% of the embedded watermark data, even if as much as 80% of the watermarked relational database is altered. Our extensive analysis and experimental results show that the proposed scheme is robust against a variety of data attacks, for example, alteration attacks, deletion attacks, mix-match attacks, and sorting attacks.

Software aspects of the Geant4 validation repository

NASA Astrophysics Data System (ADS)

Dotti, Andrea; Wenzel, Hans; Elvira, Daniel; Genser, Krzysztof; Yarba, Julia; Carminati, Federico; Folger, Gunter; Konstantinov, Dmitri; Pokorski, Witold; Ribon, Alberto

2017-10-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER is easily accessible via a web application. In addition, a web service allows for programmatic access to the repository to extract records in JSON or XML exchange formats. In this article, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

Software Aspects of the Geant4 Validation Repository

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

Dotti, Andrea; Wenzel, Hans; Elvira, Daniel

2016-01-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientic Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER is easily accessible via a web application. In addition, a web service allows for programmatic access to the repository to extract records in JSON or XML exchange formats. In this article, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

Automatic categorization of diverse experimental information in the bioscience literature

PubMed Central

2012-01-01

Background Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. Results We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort. PMID:22280404

The Effect of Impurities on the Processing of Aluminum Alloys

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

Zi-Kui Liu; Shengjun Zhang; Qingyou Han

2007-04-23

For this Aluminum Industry of the Future (IOF) project, the effect of impurities on the processing of aluminum alloys was systematically investigated. The work was carried out as a collaborative effort between the Pennsylvania State University and Oak Ridge National Laboratory. Industrial support was provided by ALCOA and ThermoCalc, Inc. The achievements described below were made. A method that combines first-principles calculation and calculation of phase diagrams (CALPHAD) was used to develop the multicomponent database Al-Ca-K-Li-Mg-Na. This method was extensively used in this project for the development of a thermodynamic database. The first-principles approach provided some thermodynamic property data thatmore » are not available in the open literature. These calculated results were used in the thermodynamic modeling as experimental data. Some of the thermodynamic property data are difficult, if not impossible, to measure. The method developed and used in this project allows the estimation of these data for thermodynamic database development. The multicomponent database Al-Ca-K-Li-Mg-Na was developed. Elements such as Ca, Li, Na, and K are impurities that strongly affect the formability and corrosion behavior of aluminum alloys. However, these impurity elements are not included in the commercial aluminum alloy database. The process of thermodynamic modeling began from Al-Na, Ca-Li, Li-Na, K-Na, and Li-K sub-binary systems. Then ternary and higher systems were extrapolated because of the lack of experimental information. Databases for five binary alloy systems and two ternary systems were developed. Along with other existing binary and ternary databases, the full database of the multicomponent Al-Ca-K-Li-Mg-Na system was completed in this project. The methodology in integrating with commercial or other aluminum alloy databases can be developed. The mechanism of sodium-induced high-temperature embrittlement (HTE) of Al-Mg is now understood. Using the thermodynamic database developed in this project, thermodynamic simulations were carried out to investigate the effect of sodium on the HTE of Al-Mg alloys. The simulation results indicated that the liquid miscibility gap resulting from the dissolved sodium in the molten material plays an important role in HTE. A liquid phase forms from the solid face-centered cubic (fcc) phase (most likely at grain boundaries) during cooling, resulting in the occurrence of HTE. Comparison of the thermodynamic simulation results with experimental measurements on the high-temperature ductility of an Al-5Mg-Na alloy shows that HTE occurs in the temperature range at which the liquid phase exists. Based on this fundamental understanding of the HTE mechanism during processing of aluminum alloy, an HTE sensitive zone and a hot-rolling safe zone of the Al-Mg-Na alloys are defined as functions of processing temperature and alloy composition. The tendency of HTE was evaluated based on thermodynamic simulations of the fraction of the intergranular sodium-rich liquid phase. Methods of avoiding HTE during rolling/extrusion of Al-Mg-based alloys were suggested. Energy and environmental benefits from the results of this project could occur through a number of avenues: (1) energy benefits accruing from reduced rejection rates of the aluminum sheet and bar, (2) reduced dross formation during the remelting of the aluminum rejects, and (3) reduced CO2 emission related to the energy savings. The sheet and extruded bar quantities produced in the United States during 2000 were 10,822 and 4,546 million pounds, respectively. It is assumed that 50% of the sheet and 10% of the bar will be affected by implementing the results of this project. With the current process, the rejection rate of sheet and bar is estimated at 5%. Assuming that at least half of the 5% rejection of sheet and bar will be eliminated by using the results of this project and that 4% of the aluminum will be lost through dross (Al2O3) during remelting of the rejects, the full-scale industrial implementation of the project results would lead to energy savings in excess of 6.2 trillion Btu/year and cost savings of $42.7 million by 2020.« less

Curation accuracy of model organism databases

PubMed Central

Keseler, Ingrid M.; Skrzypek, Marek; Weerasinghe, Deepika; Chen, Albert Y.; Fulcher, Carol; Li, Gene-Wei; Lemmer, Kimberly C.; Mladinich, Katherine M.; Chow, Edmond D.; Sherlock, Gavin; Karp, Peter D.

2014-01-01

Manual extraction of information from the biomedical literature—or biocuration—is the central methodology used to construct many biological databases. For example, the UniProt protein database, the EcoCyc Escherichia coli database and the Candida Genome Database (CGD) are all based on biocuration. Biological databases are used extensively by life science researchers, as online encyclopedias, as aids in the interpretation of new experimental data and as golden standards for the development of new bioinformatics algorithms. Although manual curation has been assumed to be highly accurate, we are aware of only one previous study of biocuration accuracy. We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions. A database assertion is considered to be in error if that assertion could not be found in the publication cited for that assertion. We identified 10 errors in the 633 facts that we validated across the two databases, for an overall error rate of 1.58%, and individual error rates of 1.82% for CGD and 1.40% for EcoCyc. These data suggest that manual curation of the experimental literature by Ph.D-level scientists is highly accurate. Database URL: http://ecocyc.org/, http://www.candidagenome.org// PMID:24923819

Projections for fast protein structure retrieval

PubMed Central

Bhattacharya, Sourangshu; Bhattacharyya, Chiranjib; Chandra, Nagasuma R

2006-01-01

Background In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching techniques, for retrieving protein structures similar to a query structure from a large protein structure database. Each protein structure is specified by the 3D coordinates of residues of the protein. The algorithm is based on a novel characterization of the residues, called projections, leading to a similarity measure between the residues of the two proteins. This measure is exploited to efficiently compute the optimal equivalences. Results Experimental results show that, the current algorithm outperforms the state of the art on benchmark datasets in terms of speed without losing accuracy. Search results on SCOP 95% nonredundant database, for fold similarity with 5 proteins from different SCOP classes show that the current method performs competitively with the standard algorithm CE. The algorithm is also capable of detecting non-topological similarities between two proteins which is not possible with most of the state of the art tools like Dali. PMID:17254310

Field Experiments in Manpower Issues.

ERIC Educational Resources Information Center

Mobilization for Youth, Inc., New York, NY. Experimental Manpower Lab.

The first three reports in this series describe the data-based results of systematic experimentation and survey research concerned with the following timely manpower issues: (1) The Effects of Monetary Incentives on the Learning of Remedial English by Disadvantaged Trainees, (2) The Reward Preferences of Neighborhood Youth Corps Trainees, and (3)…

Efficient Single-Pass Index Construction for Text Databases.

ERIC Educational Resources Information Center

Heinz, Steffen; Zobel, Justin

2003-01-01

Discusses index construction for text collections, reviews principal approaches to inverted indexes, analyzes their theoretical cost, and presents experimental results of the use of a single-pass inversion method on Web document collections. Shows that the single-pass approach is faster and does not require the complete vocabulary of the indexed…

Variogram-based feature extraction for neural network recognition of logos

NASA Astrophysics Data System (ADS)

Pham, Tuan D.

2003-03-01

This paper presents a new approach for extracting spatial features of images based on the theory of regionalized variables. These features can be effectively used for automatic recognition of logo images using neural networks. Experimental results on a public-domain logo database show the effectiveness of the proposed approach.

A humming retrieval system based on music fingerprint

NASA Astrophysics Data System (ADS)

Han, Xingkai; Cao, Baiyu

2011-10-01

In this paper, we proposed an improved music information retrieval method utilizing the music fingerprint. The goal of this method is to represent the music with compressed musical information. Based on the selected MIDI files, which are generated automatically as our music target database, we evaluate the accuracy, effectiveness, and efficiency of this method. In this research we not only extract the feature sequence, which can represent the file effectively, from the query and melody database, but also make it possible for retrieving the results in an innovative way. We investigate on the influence of noise to the performance of our system. As experimental result shows, the retrieval accuracy arriving at up to91% without noise is pretty well

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

Jorgensen, S.

Testing the behavior of metals in extreme environments is not always feasible, so material scientists use models to try and predict the behavior. To achieve accurate results it is necessary to use the appropriate model and material-specific parameters. This research evaluated the performance of six material models available in the MIDAS database [1] to determine at which temperatures and strain-rates they perform best, and to determine to which experimental data their parameters were optimized. Additionally, parameters were optimized for the Johnson-Cook model using experimental data from Lassila et al [2].

Long Duration Exposure Facility (LDEF) optical systems SIG summary and database

NASA Astrophysics Data System (ADS)

Bohnhoff-Hlavacek, Gail

1992-09-01

The main objectives of the Long Duration Exposure Facility (LDEF) Optical Systems Special Investigative Group (SIG) Discipline are to develop a database of experimental findings on LDEF optical systems and elements hardware, and provide an optical system overview. Unlike the electrical and mechanical disciplines, the optics effort relies primarily on the testing of hardware at the various principal investigator's laboratories, since minimal testing of optical hardware was done at Boeing. This is because all space-exposed optics hardware are part of other individual experiments. At this time, all optical systems and elements testing by experiment investigator teams is not complete, and in some cases has hardly begun. Most experiment results to date, document observations and measurements that 'show what happened'. Still to come from many principal investigators is a critical analysis to explain 'why it happened' and future design implications. The original optical system related concerns and the lessons learned at a preliminary stage in the Optical Systems Investigations are summarized. The design of the Optical Experiments Database and how to acquire and use the database to review the LDEF results are described.

Long Duration Exposure Facility (LDEF) optical systems SIG summary and database

NASA Technical Reports Server (NTRS)

Bohnhoff-Hlavacek, Gail

1992-01-01

The main objectives of the Long Duration Exposure Facility (LDEF) Optical Systems Special Investigative Group (SIG) Discipline are to develop a database of experimental findings on LDEF optical systems and elements hardware, and provide an optical system overview. Unlike the electrical and mechanical disciplines, the optics effort relies primarily on the testing of hardware at the various principal investigator's laboratories, since minimal testing of optical hardware was done at Boeing. This is because all space-exposed optics hardware are part of other individual experiments. At this time, all optical systems and elements testing by experiment investigator teams is not complete, and in some cases has hardly begun. Most experiment results to date, document observations and measurements that 'show what happened'. Still to come from many principal investigators is a critical analysis to explain 'why it happened' and future design implications. The original optical system related concerns and the lessons learned at a preliminary stage in the Optical Systems Investigations are summarized. The design of the Optical Experiments Database and how to acquire and use the database to review the LDEF results are described.

HIV Structural Database

National Institute of Standards and Technology Data Gateway

SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

Validation Results for LEWICE 2.0

NASA Technical Reports Server (NTRS)

Wright, William B.; Rutkowski, Adam

1999-01-01

A research project is underway at NASA Lewis to produce a computer code which can accurately predict ice growth under any meteorological conditions for any aircraft surface. This report will present results from version 2.0 of this code, which is called LEWICE. This version differs from previous releases due to its robustness and its ability to reproduce results accurately for different spacing and time step criteria across computing platform. It also differs in the extensive amount of effort undertaken to compare the results in a quantified manner against the database of ice shapes which have been generated in the NASA Lewis Icing Research Tunnel (IRT). The results of the shape comparisons are analyzed to determine the range of meteorological conditions under which LEWICE 2.0 is within the experimental repeatability. This comparison shows that the average variation of LEWICE 2.0 from the experimental data is 7.2% while the overall variability of the experimental data is 2.5%.

Development of a database system for mapping insertional mutations onto the mouse genome with large-scale experimental data

PubMed Central

2009-01-01

Background Insertional mutagenesis is an effective method for functional genomic studies in various organisms. It can rapidly generate easily tractable mutations. A large-scale insertional mutagenesis with the piggyBac (PB) transposon is currently performed in mice at the Institute of Developmental Biology and Molecular Medicine (IDM), Fudan University in Shanghai, China. This project is carried out via collaborations among multiple groups overseeing interconnected experimental steps and generates a large volume of experimental data continuously. Therefore, the project calls for an efficient database system for recording, management, statistical analysis, and information exchange. Results This paper presents a database application called MP-PBmice (insertional mutation mapping system of PB Mutagenesis Information Center), which is developed to serve the on-going large-scale PB insertional mutagenesis project. A lightweight enterprise-level development framework Struts-Spring-Hibernate is used here to ensure constructive and flexible support to the application. The MP-PBmice database system has three major features: strict access-control, efficient workflow control, and good expandability. It supports the collaboration among different groups that enter data and exchange information on daily basis, and is capable of providing real time progress reports for the whole project. MP-PBmice can be easily adapted for other large-scale insertional mutation mapping projects and the source code of this software is freely available at http://www.idmshanghai.cn/PBmice. Conclusion MP-PBmice is a web-based application for large-scale insertional mutation mapping onto the mouse genome, implemented with the widely used framework Struts-Spring-Hibernate. This system is already in use by the on-going genome-wide PB insertional mutation mapping project at IDM, Fudan University. PMID:19958505

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…

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…

Domain fusion analysis by applying relational algebra to protein sequence and domain databases.

PubMed

Truong, Kevin; Ikura, Mitsuhiko

2003-05-06

Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnres.utoronto.ca/pi. As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.

High accuracy experimental determination of copper and zinc mass attenuation coefficients in the 100 eV to 30 keV photon energy range

NASA Astrophysics Data System (ADS)

Ménesguen, Y.; Gerlach, M.; Pollakowski, B.; Unterumsberger, R.; Haschke, M.; Beckhoff, B.; Lépy, M.-C.

2016-02-01

The knowledge of atomic fundamental parameters such as mass attenuation coefficients with low uncertainties, is of decisive importance in elemental quantification using x-ray fluorescence analysis techniques. Several databases are accessible and frequently used within a large community of users. These compilations are most often in good agreement for photon energies in the hard x-ray ranges. However, they significantly differ for low photon energies and around the absorption edges of any element. In a joint cooperation of the metrology institutes of France and Germany, mass attenuation coefficients of copper and zinc were determined experimentally in the photon energy range from 100 eV to 30 keV by independent approaches using monochromatized synchrotron radiation at SOLEIL (France) and BESSY II (Germany), respectively. The application of high-accuracy experimental techniques resulted in mass attenuation coefficient datasets determined with low uncertainties that are directly compared to existing databases. The novel datasets are expected to enhance the reliability of mass attenuation coefficients.

SFCOMPO-2.0: An OECD NEA database of spent nuclear fuel isotopic assays, reactor design specifications, and operating data

DOE PAGES

Michel-Sendis, F.; Gauld, I.; Martinez, J. S.; ...

2017-08-02

SFCOMPO-2.0 is the new release of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) database of experimental assay measurements. These measurements are isotopic concentrations from destructive radiochemical analyses of spent nuclear fuel (SNF) samples. We supplement the measurements with design information for the fuel assembly and fuel rod from which each sample was taken, as well as with relevant information on operating conditions and characteristics of the host reactors. These data are necessary for modeling and simulation of the isotopic evolution of the fuel during irradiation. SFCOMPO-2.0 has been developed and is maintained by the OECDmore » NEA under the guidance of the Expert Group on Assay Data of Spent Nuclear Fuel (EGADSNF), which is part of the NEA Working Party on Nuclear Criticality Safety (WPNCS). Significant efforts aimed at establishing a thorough, reliable, publicly available resource for code validation and safety applications have led to the capture and standardization of experimental data from 750 SNF samples from more than 40 reactors. These efforts have resulted in the creation of the SFCOMPO-2.0 database, which is publicly available from the NEA Data Bank. Our paper describes the new database, and applications of SFCOMPO-2.0 for computer code validation, integral nuclear data benchmarking, and uncertainty analysis in nuclear waste package analysis are briefly illustrated.« less

SFCOMPO-2.0: An OECD NEA database of spent nuclear fuel isotopic assays, reactor design specifications, and operating data

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

Michel-Sendis, F.; Gauld, I.; Martinez, J. S.

SFCOMPO-2.0 is the new release of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) database of experimental assay measurements. These measurements are isotopic concentrations from destructive radiochemical analyses of spent nuclear fuel (SNF) samples. We supplement the measurements with design information for the fuel assembly and fuel rod from which each sample was taken, as well as with relevant information on operating conditions and characteristics of the host reactors. These data are necessary for modeling and simulation of the isotopic evolution of the fuel during irradiation. SFCOMPO-2.0 has been developed and is maintained by the OECDmore » NEA under the guidance of the Expert Group on Assay Data of Spent Nuclear Fuel (EGADSNF), which is part of the NEA Working Party on Nuclear Criticality Safety (WPNCS). Significant efforts aimed at establishing a thorough, reliable, publicly available resource for code validation and safety applications have led to the capture and standardization of experimental data from 750 SNF samples from more than 40 reactors. These efforts have resulted in the creation of the SFCOMPO-2.0 database, which is publicly available from the NEA Data Bank. Our paper describes the new database, and applications of SFCOMPO-2.0 for computer code validation, integral nuclear data benchmarking, and uncertainty analysis in nuclear waste package analysis are briefly illustrated.« less

Summary Report of the Workshop on The Experimental Nuclear Reaction Data Database

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

Semkova, V.; Pritychenko, B.

2014-12-01

The Workshop on the Experimental Nuclear Reaction Data Database (EXFOR) was held at IAEA Headquarters in Vienna from 6 to 10 October 2014. The workshop was organized to discuss various aspects of the EXFOR compilation process including compilation rules, different techniques for nuclear reaction data measurements, software developments, etc. A summary of the presentations and discussions that took place during the workshop is reported here.

An Experimental Database for Conventional and Alternate Control Concepts on the HSR 1.675% Reference H Model

NASA Technical Reports Server (NTRS)

McMillin, Naomi; Allen, Jerry; Erickson, Gary; Campbell, Jim; Mann, Mike; Kubiatko, Paul; Yingling, David; Mason, Charlie

1999-01-01

The objective was to experimentally evaluate the longitudinal and lateral-directional stability and control characteristics of the Reference H configuration at supersonic and transonic speeds. A series of conventional and alternate control devices were also evaluated at supersonic and transonic speeds. A database on the conventional and alternate control devices was to be created for use in the HSR program.

A new online database of nuclear electromagnetic moments

NASA Astrophysics Data System (ADS)

Mertzimekis, Theo J.

2017-09-01

Nuclear electromagnetic (EM) moments, i.e., the magnetic dipole and the electric quadrupole moments, provide important information of nuclear structure. As in other types of experimental data available to the community, measurements of nuclear EM moments have been organized systematically in compilations since the dawn of nuclear science. However, the wealth of recent moments measurements with radioactive beams, as well as earlier existing measurements, lack an online, easy-to-access, systematically organized presence to disseminate information to researchers. In addition, available printed compilations suffer a rather long life cycle, being left behind experimental measurements published in journals or elsewhere. A new, online database (http://magneticmoments.info) focusing on nuclear EM moments has been recently developed to disseminate experimental data to the community. The database includes non-evaluated experimental data of nuclear EM moments, giving strong emphasis on frequent updates (life cycle is 3 months) and direct connection to the sources via DOI and NSR hyperlinks. It has been recently integrated in IAEA LiveChart [1], but can also be found as a standalone webapp [2]. A detailed review of the database features, as well as plans for further development and expansion in the near future is discussed.

Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1

PubMed Central

Syed, Mustafa H; Karpinets, Tatiana V; Leuze, Michael R; Kora, Guruprasad H; Romine, Margaret R; Uberbacher, Edward C

2009-01-01

Shewanella oneidensis MR-1 is an important model organism for environmental research as it has an exceptional metabolic and respiratory versatility regulated by a complex regulatory network. We have developed a database to collect experimental and computational data relating to regulation of gene and protein expression, and, a visualization environment that enables integration of these data types. The regulatory information in the database includes predictions of DNA regulator binding sites, sigma factor binding sites, transcription units, operons, promoters, and RNA regulators including non-coding RNAs, riboswitches, and different types of terminators. Availability http://shewanella-knowledgebase.org:8080/Shewanella/gbrowserLanding.jsp PMID:20198195

High-throughput ab-initio dilute solute diffusion database.

PubMed

Wu, Henry; Mayeshiba, Tam; Morgan, Dane

2016-07-19

We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.

Measurements and predictions of the 6s6p{sup 1,3}P{sub 1} lifetimes in the Hg isoelectronic sequence

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

Curtis, L. J.; Irving, R. E.; Henderson, M.

2001-04-01

Experimental and theoretical values for the lifetimes of the 6s6p{sup 1}P{sub 1} and {sup 3}P{sub 1} levels in the Hg isoelectronic sequence are examined in the context of a data-based isoelectronic systematization. New beam-foil measurements for lifetimes in Pb III and Bi IV are reported and included in a critical evaluation of the available database. These results are combined with ab initio theoretical calculations and linearizing parametrizations to make predictive extrapolations for ions with 84{<=}Z{le}92.

Genomics Portals: integrative web-platform for mining genomics data

PubMed Central

2010-01-01

Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org. PMID:20070909

Quantification of the Uncertainties for the Space Launch System Liftoff/Transition and Ascent Databases

NASA Technical Reports Server (NTRS)

Favaregh, Amber L.; Houlden, Heather P.; Pinier, Jeremy T.

2016-01-01

A detailed description of the uncertainty quantification process for the Space Launch System Block 1 vehicle configuration liftoff/transition and ascent 6-Degree-of-Freedom (DOF) aerodynamic databases is presented. These databases were constructed from wind tunnel test data acquired in the NASA Langley Research Center 14- by 22-Foot Subsonic Wind Tunnel and the Boeing Polysonic Wind Tunnel in St. Louis, MO, respectively. The major sources of error for these databases were experimental error and database modeling errors.

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.

PubMed

Chamrad, Daniel C; Körting, Gerhard; Schäfer, Heike; Stephan, Christian; Thiele, Herbert; Apweiler, Rolf; Meyer, Helmut E; Marcus, Katrin; Blüggel, Martin

2006-09-01

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.

Tempest: Accelerated MS/MS database search software for heterogeneous computing platforms

PubMed Central

Adamo, Mark E.; Gerber, Scott A.

2017-01-01

MS/MS database search algorithms derive a set of candidate peptide sequences from in-silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU generates peptide candidates that are asynchronously sent to a discrete GPU to be scored against experimental spectra in parallel (Milloy et al., 2012). The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. PMID:27603022

Ionic Liquids Database- (ILThermo)

National Institute of Standards and Technology Data Gateway

SRD 147 NIST Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

An Experimental Investigation of Complexity in Database Query Formulation Tasks

ERIC Educational Resources Information Center

Casterella, Gretchen Irwin; Vijayasarathy, Leo

2013-01-01

Information Technology professionals and other knowledge workers rely on their ability to extract data from organizational databases to respond to business questions and support decision making. Structured query language (SQL) is the standard programming language for querying data in relational databases, and SQL skills are in high demand and are…

Content Is King: Databases Preserve the Collective Information of Science.

PubMed

Yates, John R

2018-04-01

Databases store sequence information experimentally gathered to create resources that further science. In the last 20 years databases have become critical components of fields like proteomics where they provide the basis for large-scale and high-throughput proteomic informatics. Amos Bairoch, winner of the Association of Biomolecular Resource Facilities Frederick Sanger Award, has created some of the important databases proteomic research depends upon for accurate interpretation of data.

ATtRACT-a database of RNA-binding proteins and associated motifs.

PubMed

Giudice, Girolamo; Sánchez-Cabo, Fátima; Torroja, Carlos; Lara-Pezzi, Enrique

2016-01-01

RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non-redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available athttp://attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid-F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discoveringde novomotifs enriched in a set of related sequences and compare them with the motifs included in the database.Database URL:http:// attract. cnic. es. © The Author(s) 2016. Published by Oxford University Press.

Teaching Science to Students with Learning and Other Disabilities: A Review of Topics and Subtopics Appearing in Experimental Research 1991-2015

ERIC Educational Resources Information Center

Vavougios, Dionisios; Verevi, Alkistis; Papalexopoulos, Panagiotis F.; Verevi, Crystallia-Ioanna; Panagopoulou, Athanasia

2016-01-01

This article reviews 24 years of research focused on science education for students with learning and other disabilities. Our results are based on 53 articles from 2 relevant databases. We hereby present and discuss the results of the most popular topics investigated, which include: constructivism, exploratory learning, hands-on activities,…

NNDC Databases

Science.gov Websites

radiation. It includes an interactive chart of nuclides and a level plotting tool. XUNDL Experimental Unevaluated Nuclear Data List Experimental nuclear structure and decay data, covering more than 2,500 recent parameters* Retrieved information CSISRS alias EXFOR Nuclear reaction experimental data Experimental nuclear

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

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

Liu, Ling; Xiong, Yi; Gao, Hongyun

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

DOE PAGES

Liu, Ling; Xiong, Yi; Gao, Hongyun; ...

2018-04-02

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

Physiology-based face recognition in the thermal infrared spectrum.

PubMed

Buddharaju, Pradeep; Pavlidis, Ioannis T; Tsiamyrtzis, Panagiotis; Bazakos, Mike

2007-04-01

The current dominant approaches to face recognition rely on facial characteristics that are on or over the skin. Some of these characteristics have low permanency can be altered, and their phenomenology varies significantly with environmental factors (e.g., lighting). Many methodologies have been developed to address these problems to various degrees. However, the current framework of face recognition research has a potential weakness due to its very nature. We present a novel framework for face recognition based on physiological information. The motivation behind this effort is to capitalize on the permanency of innate characteristics that are under the skin. To establish feasibility, we propose a specific methodology to capture facial physiological patterns using the bioheat information contained in thermal imagery. First, the algorithm delineates the human face from the background using the Bayesian framework. Then, it localizes the superficial blood vessel network using image morphology. The extracted vascular network produces contour shapes that are characteristic to each individual. The branching points of the skeletonized vascular network are referred to as Thermal Minutia Points (TMPs) and constitute the feature database. To render the method robust to facial pose variations, we collect for each subject to be stored in the database five different pose images (center, midleft profile, left profile, midright profile, and right profile). During the classification stage, the algorithm first estimates the pose of the test image. Then, it matches the local and global TMP structures extracted from the test image with those of the corresponding pose images in the database. We have conducted experiments on a multipose database of thermal facial images collected in our laboratory, as well as on the time-gap database of the University of Notre Dame. The good experimental results show that the proposed methodology has merit, especially with respect to the problem of low permanence over time. More importantly, the results demonstrate the feasibility of the physiological framework in face recognition and open the way for further methodological and experimental research in the area.

ThermoFit: A Set of Software Tools, Protocols and Schema for the Organization of Thermodynamic Data and for the Development, Maintenance, and Distribution of Internally Consistent Thermodynamic Data/Model Collections

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2013-12-01

Internally consistent thermodynamic databases are critical resources that facilitate the calculation of heterogeneous phase equilibria and thereby support geochemical, petrological, and geodynamical modeling. These 'databases' are actually derived data/model systems that depend on a diverse suite of physical property measurements, calorimetric data, and experimental phase equilibrium brackets. In addition, such databases are calibrated with the adoption of various models for extrapolation of heat capacities and volumetric equations of state to elevated temperature and pressure conditions. Finally, these databases require specification of thermochemical models for the mixing properties of solid, liquid, and fluid solutions, which are often rooted in physical theory and, in turn, depend on additional experimental observations. The process of 'calibrating' a thermochemical database involves considerable effort and an extensive computational infrastructure. Because of these complexities, the community tends to rely on a small number of thermochemical databases, generated by a few researchers; these databases often have limited longevity and are universally difficult to maintain. ThermoFit is a software framework and user interface whose aim is to provide a modeling environment that facilitates creation, maintenance and distribution of thermodynamic data/model collections. Underlying ThermoFit are data archives of fundamental physical property, calorimetric, crystallographic, and phase equilibrium constraints that provide the essential experimental information from which thermodynamic databases are traditionally calibrated. ThermoFit standardizes schema for accessing these data archives and provides web services for data mining these collections. Beyond simple data management and interoperability, ThermoFit provides a collection of visualization and software modeling tools that streamline the model/database generation process. Most notably, ThermoFit facilitates the rapid visualization of predicted model outcomes and permits the user to modify these outcomes using tactile- or mouse-based GUI interaction, permitting real-time updates that reflect users choices, preferences, and priorities involving derived model results. This ability permits some resolution of the problem of correlated model parameters in the common situation where thermodynamic models must be calibrated from inadequate data resources. The ability also allows modeling constraints to be imposed using natural data and observations (i.e. petrologic or geochemical intuition). Once formulated, ThermoFit facilitates deployment of data/model collections by automated creation of web services. Users consume these services via web-, excel-, or desktop-clients. ThermoFit is currently under active development and not yet generally available; a limited capability prototype system has been coded for Macintosh computers and utilized to construct thermochemical models for H2O-CO2 mixed fluid saturation in silicate liquids. The longer term goal is to release ThermoFit as a web portal application client with server-based cloud computations supporting the modeling environment.

MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases

PubMed Central

Yue, Ming; Zhou, Dianshuang; Zhi, Hui; Wang, Peng; Zhang, Yan; Gao, Yue; Guo, Maoni; Li, Xin; Wang, Yanxia

2018-01-01

Abstract The MiRNA SNP Disease Database (MSDD, http://www.bio-bigdata.com/msdd/) is a manually curated database that provides comprehensive experimentally supported associations among microRNAs (miRNAs), single nucleotide polymorphisms (SNPs) and human diseases. SNPs in miRNA-related functional regions such as mature miRNAs, promoter regions, pri-miRNAs, pre-miRNAs and target gene 3′-UTRs, collectively called ‘miRSNPs’, represent a novel category of functional molecules. miRSNPs can lead to miRNA and its target gene dysregulation, and resulting in susceptibility to or onset of human diseases. A curated collection and summary of miRSNP-associated diseases is essential for a thorough understanding of the mechanisms and functions of miRSNPs. Here, we describe MSDD, which currently documents 525 associations among 182 human miRNAs, 197 SNPs, 153 genes and 164 human diseases through a review of more than 2000 published papers. Each association incorporates information on the miRNAs, SNPs, miRNA target genes and disease names, SNP locations and alleles, the miRNA dysfunctional pattern, experimental techniques, a brief functional description, the original reference and additional annotation. MSDD provides a user-friendly interface to conveniently browse, retrieve, download and submit novel data. MSDD will significantly improve our understanding of miRNA dysfunction in disease, and thus, MSDD has the potential to serve as a timely and valuable resource. PMID:29106642

MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases.

PubMed

Yue, Ming; Zhou, Dianshuang; Zhi, Hui; Wang, Peng; Zhang, Yan; Gao, Yue; Guo, Maoni; Li, Xin; Wang, Yanxia; Zhang, Yunpeng; Ning, Shangwei; Li, Xia

2018-01-04

The MiRNA SNP Disease Database (MSDD, http://www.bio-bigdata.com/msdd/) is a manually curated database that provides comprehensive experimentally supported associations among microRNAs (miRNAs), single nucleotide polymorphisms (SNPs) and human diseases. SNPs in miRNA-related functional regions such as mature miRNAs, promoter regions, pri-miRNAs, pre-miRNAs and target gene 3'-UTRs, collectively called 'miRSNPs', represent a novel category of functional molecules. miRSNPs can lead to miRNA and its target gene dysregulation, and resulting in susceptibility to or onset of human diseases. A curated collection and summary of miRSNP-associated diseases is essential for a thorough understanding of the mechanisms and functions of miRSNPs. Here, we describe MSDD, which currently documents 525 associations among 182 human miRNAs, 197 SNPs, 153 genes and 164 human diseases through a review of more than 2000 published papers. Each association incorporates information on the miRNAs, SNPs, miRNA target genes and disease names, SNP locations and alleles, the miRNA dysfunctional pattern, experimental techniques, a brief functional description, the original reference and additional annotation. MSDD provides a user-friendly interface to conveniently browse, retrieve, download and submit novel data. MSDD will significantly improve our understanding of miRNA dysfunction in disease, and thus, MSDD has the potential to serve as a timely and valuable resource. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

An Investigation of Multidimensional Voice Program Parameters in Three Different Databases for Voice Pathology Detection and Classification.

PubMed

Al-Nasheri, Ahmed; Muhammad, Ghulam; Alsulaiman, Mansour; Ali, Zulfiqar; Mesallam, Tamer A; Farahat, Mohamed; Malki, Khalid H; Bencherif, Mohamed A

2017-01-01

Automatic voice-pathology detection and classification systems may help clinicians to detect the existence of any voice pathologies and the type of pathology from which patients suffer in the early stages. The main aim of this paper is to investigate Multidimensional Voice Program (MDVP) parameters to automatically detect and classify the voice pathologies in multiple databases, and then to find out which parameters performed well in these two processes. Samples of the sustained vowel /a/ of normal and pathological voices were extracted from three different databases, which have three voice pathologies in common. The selected databases in this study represent three distinct languages: (1) the Arabic voice pathology database; (2) the Massachusetts Eye and Ear Infirmary database (English database); and (3) the Saarbruecken Voice Database (German database). A computerized speech lab program was used to extract MDVP parameters as features, and an acoustical analysis was performed. The Fisher discrimination ratio was applied to rank the parameters. A t test was performed to highlight any significant differences in the means of the normal and pathological samples. The experimental results demonstrate a clear difference in the performance of the MDVP parameters using these databases. The highly ranked parameters also differed from one database to another. The best accuracies were obtained by using the three highest ranked MDVP parameters arranged according to the Fisher discrimination ratio: these accuracies were 99.68%, 88.21%, and 72.53% for the Saarbruecken Voice Database, the Massachusetts Eye and Ear Infirmary database, and the Arabic voice pathology database, respectively. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.

PubMed

Gattiker, Alexandre; Niederhauser-Wiederkehr, Christa; Moore, James; Hermida, Leandro; Primig, Michael

2007-01-01

We report a novel release of the GermOnline knowledgebase covering genes relevant for the cell cycle, gametogenesis and fertility. GermOnline was extended into a cross-species systems browser including information on DNA sequence annotation, gene expression and the function of gene products. The database covers eight model organisms and Homo sapiens, for which complete genome annotation data are available. The database is now built around a sophisticated genome browser (Ensembl), our own microarray information management and annotation system (MIMAS) used to extensively describe experimental data obtained with high-density oligonucleotide microarrays (GeneChips) and a comprehensive system for online editing of database entries (MediaWiki). The RNA data include results from classical microarrays as well as tiling arrays that yield information on RNA expression levels, transcript start sites and lengths as well as exon composition. Members of the research community are solicited to help GermOnline curators keep database entries on genes and gene products complete and accurate. The database is accessible at http://www.germonline.org/.

Multiple Representations-Based Face Sketch-Photo Synthesis.

PubMed

Peng, Chunlei; Gao, Xinbo; Wang, Nannan; Tao, Dacheng; Li, Xuelong; Li, Jie

2016-11-01

Face sketch-photo synthesis plays an important role in law enforcement and digital entertainment. Most of the existing methods only use pixel intensities as the feature. Since face images can be described using features from multiple aspects, this paper presents a novel multiple representations-based face sketch-photo-synthesis method that adaptively combines multiple representations to represent an image patch. In particular, it combines multiple features from face images processed using multiple filters and deploys Markov networks to exploit the interacting relationships between the neighboring image patches. The proposed framework could be solved using an alternating optimization strategy and it normally converges in only five outer iterations in the experiments. Our experimental results on the Chinese University of Hong Kong (CUHK) face sketch database, celebrity photos, CUHK Face Sketch FERET Database, IIIT-D Viewed Sketch Database, and forensic sketches demonstrate the effectiveness of our method for face sketch-photo synthesis. In addition, cross-database and database-dependent style-synthesis evaluations demonstrate the generalizability of this novel method and suggest promising solutions for face identification in forensic science.

Authentication Based on Pole-zero Models of Signature Velocity

PubMed Central

Rashidi, Saeid; Fallah, Ali; Towhidkhah, Farzad

2013-01-01

With the increase of communication and financial transaction through internet, on-line signature verification is an accepted biometric technology for access control and plays a significant role in authenticity and authorization in modernized society. Therefore, fast and precise algorithms for the signature verification are very attractive. The goal of this paper is modeling of velocity signal that pattern and properties is stable for persons. With using pole-zero models based on discrete cosine transform, precise method is proposed for modeling and then features is founded from strokes. With using linear, parzen window and support vector machine classifiers, the signature verification technique was tested with a large number of authentic and forgery signatures and has demonstrated the good potential of this technique. The signatures are collected from three different database include a proprietary database, the SVC2004 and the Sabanci University signature database benchmark databases. Experimental results based on Persian, SVC2004 and SUSIG databases show that our method achieves an equal error rate of 5.91%, 5.62% and 3.91% in the skilled forgeries, respectively. PMID:24696797

Biomine: predicting links between biological entities using network models of heterogeneous databases.

PubMed

Eronen, Lauri; Toivonen, Hannu

2012-06-06

Biological databases contain large amounts of data concerning the functions and associations of genes and proteins. Integration of data from several such databases into a single repository can aid the discovery of previously unknown connections spanning multiple types of relationships and databases. Biomine is a system that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. We present Biomine and evaluate its performance in link prediction, where the goal is to predict pairs of nodes that will be connected in the future, based on current data. In particular, we formulate protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph. We consider and experiment with several such measures, and perform a parameter optimization procedure where different edge types are weighted to optimize link prediction accuracy. We also propose a novel method for disease-gene prioritization, defined as finding a subset of candidate genes that cluster together in the graph. We experimentally evaluate Biomine by predicting future annotations in the source databases and prioritizing lists of putative disease genes. The experimental results show that Biomine has strong potential for predicting links when a set of selected candidate links is available. The predictions obtained using the entire Biomine dataset are shown to clearly outperform ones obtained using any single source of data alone, when different types of links are suitably weighted. In the gene prioritization task, an established reference set of disease-associated genes is useful, but the results show that under favorable conditions, Biomine can also perform well when no such information is available.The Biomine system is a proof of concept. Its current version contains 1.1 million entities and 8.1 million relations between them, with focus on human genetics. Some of its functionalities are available in a public query interface at http://biomine.cs.helsinki.fi, allowing searching for and visualizing connections between given biological entities.

Optimal Embedding for Shape Indexing in Medical Image Databases

PubMed Central

Qian, Xiaoning; Tagare, Hemant D.; Fulbright, Robert K.; Long, Rodney; Antani, Sameer

2010-01-01

This paper addresses the problem of indexing shapes in medical image databases. Shapes of organs are often indicative of disease, making shape similarity queries important in medical image databases. Mathematically, shapes with landmarks belong to shape spaces which are curved manifolds with a well defined metric. The challenge in shape indexing is to index data in such curved spaces. One natural indexing scheme is to use metric trees, but metric trees are prone to inefficiency. This paper proposes a more efficient alternative. We show that it is possible to optimally embed finite sets of shapes in shape space into a Euclidean space. After embedding, classical coordinate-based trees can be used for efficient shape retrieval. The embedding proposed in the paper is optimal in the sense that it least distorts the partial Procrustes shape distance. The proposed indexing technique is used to retrieve images by vertebral shape from the NHANES II database of cervical and lumbar spine x-ray images maintained at the National Library of Medicine. Vertebral shape strongly correlates with the presence of osteophytes, and shape similarity retrieval is proposed as a tool for retrieval by osteophyte presence and severity. Experimental results included in the paper evaluate (1) the usefulness of shape-similarity as a proxy for osteophytes, (2) the computational and disk access efficiency of the new indexing scheme, (3) the relative performance of indexing with embedding to the performance of indexing without embedding, and (4) the computational cost of indexing using the proposed embedding versus the cost of an alternate embedding. The experimental results clearly show the relevance of shape indexing and the advantage of using the proposed embedding. PMID:20163981

Optimal embedding for shape indexing in medical image databases.

PubMed

Qian, Xiaoning; Tagare, Hemant D; Fulbright, Robert K; Long, Rodney; Antani, Sameer

2010-06-01

This paper addresses the problem of indexing shapes in medical image databases. Shapes of organs are often indicative of disease, making shape similarity queries important in medical image databases. Mathematically, shapes with landmarks belong to shape spaces which are curved manifolds with a well defined metric. The challenge in shape indexing is to index data in such curved spaces. One natural indexing scheme is to use metric trees, but metric trees are prone to inefficiency. This paper proposes a more efficient alternative. We show that it is possible to optimally embed finite sets of shapes in shape space into a Euclidean space. After embedding, classical coordinate-based trees can be used for efficient shape retrieval. The embedding proposed in the paper is optimal in the sense that it least distorts the partial Procrustes shape distance. The proposed indexing technique is used to retrieve images by vertebral shape from the NHANES II database of cervical and lumbar spine X-ray images maintained at the National Library of Medicine. Vertebral shape strongly correlates with the presence of osteophytes, and shape similarity retrieval is proposed as a tool for retrieval by osteophyte presence and severity. Experimental results included in the paper evaluate (1) the usefulness of shape similarity as a proxy for osteophytes, (2) the computational and disk access efficiency of the new indexing scheme, (3) the relative performance of indexing with embedding to the performance of indexing without embedding, and (4) the computational cost of indexing using the proposed embedding versus the cost of an alternate embedding. The experimental results clearly show the relevance of shape indexing and the advantage of using the proposed embedding. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Improved Bond Equations for Fiber-Reinforced Polymer Bars in Concrete.

PubMed

Pour, Sadaf Moallemi; Alam, M Shahria; Milani, Abbas S

2016-08-30

This paper explores a set of new equations to predict the bond strength between fiber reinforced polymer (FRP) rebar and concrete. The proposed equations are based on a comprehensive statistical analysis and existing experimental results in the literature. Namely, the most effective parameters on bond behavior of FRP concrete were first identified by applying a factorial analysis on a part of the available database. Then the database that contains 250 pullout tests were divided into four groups based on the concrete compressive strength and the rebar surface. Afterward, nonlinear regression analysis was performed for each study group in order to determine the bond equations. The results show that the proposed equations can predict bond strengths more accurately compared to the other previously reported models.

The NCBI BioSystems database.

PubMed

Geer, Lewis Y; Marchler-Bauer, Aron; Geer, Renata C; Han, Lianyi; He, Jane; He, Siqian; Liu, Chunlei; Shi, Wenyao; Bryant, Stephen H

2010-01-01

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets.

Second chronological supplement to the Carcinogenic Potency Database: standardized results of animal bioassays published through December 1984 and by the National Toxicology Program through May 1986.

PubMed Central

Gold, L S; Slone, T H; Backman, G M; Magaw, R; Da Costa, M; Lopipero, P; Blumenthal, M; Ames, B N

1987-01-01

This paper is the second chronological supplement to the Carcinogenic Potency Database, published earlier in this journal (1,2,4). We report here results of carcinogenesis bioassays published in the general literature between January 1983 and December 1984, and in Technical Reports of the National Cancer Institute/National Toxicology Program between January 1983 and May 1986. This supplement includes results of 525 long-term, chronic experiments of 199 test compounds, and reports the same information about each experiment in the same plot format as the earlier papers: e.g., the species and strain of test animal, the route and duration of compound administration, dose level and other aspects of experimental protocol, histopathology and tumor incidence, TD50 (carcinogenic potency) and its statistical significance, dose response, author's opinion about carcinogenicity, and literature citation. We refer the reader to the 1984 publications for a description of the numerical index of carcinogenic potency (TD50), a guide to the plot of the database, and a discussion of the sources of data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. The three plots of the database are to be used together, since results of experiments published in earlier plots are not repeated. Taken together, the three plots include results for more than 3500 experiments on 975 chemicals. Appendix 14 is an index to all chemicals in the database and indicates which plot(s) each chemical appears in. PMID:3691431

New data sources and derived products for the SRER digital spatial database

Treesearch

Craig Wissler; Deborah Angell

2003-01-01

The Santa Rita Experimental Range (SRER) digital database was developed to automate and preserve ecological data and increase their accessibility. The digital data holdings include a spatial database that is used to integrate ecological data in a known reference system and to support spatial analyses. Recently, the Advanced Resource Technology (ART) facility has added...

High-throughput ab-initio dilute solute diffusion database

PubMed Central

Wu, Henry; Mayeshiba, Tam; Morgan, Dane

2016-01-01

We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308

A Revised Validation Process for Ice Accretion Codes

NASA Technical Reports Server (NTRS)

Wright, William B.; Porter, Christopher E.

2017-01-01

A research project is underway at NASA Glenn to produce computer software that can accurately predict ice growth under any meteorological conditions for any aircraft surface. This report will present results from the latest LEWICE release, version 3.5. This program differs from previous releases in its ability to model mixed phase and ice crystal conditions such as those encountered inside an engine. It also has expanded capability to use structured grids and a new capability to use results from unstructured grid flow solvers. A quantitative comparison of the results against a database of ice shapes that have been generated in the NASA Glenn Icing Research Tunnel (IRT) has also been performed. This paper will extend the comparison of ice shapes between LEWICE 3.5 and experimental data from a previous paper. Comparisons of lift and drag are made between experimentally collected data from experimentally obtained ice shapes and simulated (CFD) data on simulated (LEWICE) ice shapes. Comparisons are also made between experimentally collected and simulated performance data on select experimental ice shapes to ensure the CFD solver, FUN3D, is valid within the flight regime. The results show that the predicted results are within the accuracy limits of the experimental data for the majority of cases.

Validation Process for LEWICE by Use of a Navier-Stokes Solver

NASA Technical Reports Server (NTRS)

Wright, William B.; Porter, Christopher E.

2017-01-01

A research project is underway at NASA Glenn to produce computer software that can accurately predict ice growth under any meteorological conditions for any aircraft surface. This report will present results from the latest LEWICE release, version 3.5. This program differs from previous releases in its ability to model mixed phase and ice crystal conditions such as those encountered inside an engine. It also has expanded capability to use structured grids and a new capability to use results from unstructured grid flow solvers. A quantitative comparison of the results against a database of ice shapes that have been generated in the NASA Glenn Icing Research Tunnel (IRT) has also been performed. This paper will extend the comparison of ice shapes between LEWICE 3.5 and experimental data from a previous paper. Comparisons of lift and drag are made between experimentally collected data from experimentally obtained ice shapes and simulated (CFD) data on simulated (LEWICE) ice shapes. Comparisons are also made between experimentally collected and simulated performance data on select experimental ice shapes to ensure the CFD solver, FUN3D, is valid within the flight regime. The results show that the predicted results are within the accuracy limits of the experimental data for the majority of cases.

Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb).

PubMed

Baldwin, Thomas T; Basenko, Evelina; Harb, Omar; Brown, Neil A; Urban, Martin; Hammond-Kosack, Kim E; Bregitzer, Phil P

2018-06-01

There is no comprehensive storage for generated mutants of Fusarium graminearum or data associated with these mutants. Instead, researchers relied on several independent and non-integrated databases. FgMutantDb was designed as a simple spreadsheet that is accessible globally on the web that will function as a centralized source of information on F. graminearum mutants. FgMutantDb aids in the maintenance and sharing of mutants within a research community. It will serve also as a platform for disseminating prepublication results as well as negative results that often go unreported. Additionally, the highly curated information on mutants in FgMutantDb will be shared with other databases (FungiDB, Ensembl, PhytoPath, and PHI-base) through updating reports. Here we describe the creation and potential usefulness of FgMutantDb to the F. graminearum research community, and provide a tutorial on its use. This type of database could be easily emulated for other fungal species. Published by Elsevier Inc.

Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System.

PubMed

Liu, Yu; Hong, Yang; Lin, Chun-Yuan; Hung, Che-Lun

2015-01-01

The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively.

SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents

PubMed Central

Heifets, Abraham; Jurisica, Igor

2012-01-01

The patent literature is a rich catalog of biologically relevant chemicals; many public and commercial molecular databases contain the structures disclosed in patent claims. However, patents are an equally rich source of metadata about bioactive molecules, including mechanism of action, disease class, homologous experimental series, structural alternatives, or the synthetic pathways used to produce molecules of interest. Unfortunately, this metadata is discarded when chemical structures are deposited separately in databases. SCRIPDB is a chemical structure database designed to make this metadata accessible. SCRIPDB provides the full original patent text, reactions and relationships described within any individual patent, in addition to the molecular files common to structural databases. We discuss how such information is valuable in medical text mining, chemical image analysis, reaction extraction and in silico pharmaceutical lead optimization. SCRIPDB may be searched by exact chemical structure, substructure or molecular similarity and the results may be restricted to patents describing synthetic routes. SCRIPDB is available at http://dcv.uhnres.utoronto.ca/SCRIPDB. PMID:22067445

Exploring Short Linear Motifs Using the ELM Database and Tools.

PubMed

Gouw, Marc; Sámano-Sánchez, Hugo; Van Roey, Kim; Diella, Francesca; Gibson, Toby J; Dinkel, Holger

2017-06-27

The Eukaryotic Linear Motif (ELM) resource is dedicated to the characterization and prediction of short linear motifs (SLiMs). SLiMs are compact, degenerate peptide segments found in many proteins and essential to almost all cellular processes. However, despite their abundance, SLiMs remain largely uncharacterized. The ELM database is a collection of manually annotated SLiM instances curated from experimental literature. In this article we illustrate how to browse and search the database for curated SLiM data, and cover the different types of data integrated in the resource. We also cover how to use this resource in order to predict SLiMs in known as well as novel proteins, and how to interpret the results generated by the ELM prediction pipeline. The ELM database is a very rich resource, and in the following protocols we give helpful examples to demonstrate how this knowledge can be used to improve your own research. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

GlycoRDF: an ontology to standardize glycomics data in RDF

PubMed Central

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F.; Campbell, Matthew P.; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-01-01

Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. Results: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. Availability and implementation: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). Contact: rene@ccrc.uga.edu or kkiyoko@soka.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388145

Providing R-Tree Support for Mongodb

NASA Astrophysics Data System (ADS)

Xiang, Longgang; Shao, Xiaotian; Wang, Dehao

2016-06-01

Supporting large amounts of spatial data is a significant characteristic of modern databases. However, unlike some mature relational databases, such as Oracle and PostgreSQL, most of current burgeoning NoSQL databases are not well designed for storing geospatial data, which is becoming increasingly important in various fields. In this paper, we propose a novel method to provide R-tree index, as well as corresponding spatial range query and nearest neighbour query functions, for MongoDB, one of the most prevalent NoSQL databases. First, after in-depth analysis of MongoDB's features, we devise an efficient tabular document structure which flattens R-tree index into MongoDB collections. Further, relevant mechanisms of R-tree operations are issued, and then we discuss in detail how to integrate R-tree into MongoDB. Finally, we present the experimental results which show that our proposed method out-performs the built-in spatial index of MongoDB. Our research will greatly facilitate big data management issues with MongoDB in a variety of geospatial information applications.

The Geant4 physics validation repository

NASA Astrophysics Data System (ADS)

Wenzel, H.; Yarba, J.; Dotti, A.

2015-12-01

The Geant4 collaboration regularly performs validation and regression tests. The results are stored in a central repository and can be easily accessed via a web application. In this article we describe the Geant4 physics validation repository which consists of a relational database storing experimental data and Geant4 test results, a java API and a web application. The functionality of these components and the technology choices we made are also described.

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

DOE PAGES

Zerkin, V. V.; Pritychenko, B.

2018-02-04

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ~22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented in this paper. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. Finally,more » it is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.« less

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

NASA Astrophysics Data System (ADS)

Zerkin, V. V.; Pritychenko, B.

2018-04-01

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ∼22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. It is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

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

Zerkin, V. V.; Pritychenko, B.

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ~22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented in this paper. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. Finally,more » it is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.« less

An end to end secure CBIR over encrypted medical database.

PubMed

Bellafqira, Reda; Coatrieux, Gouenou; Bouslimi, Dalel; Quellec, Gwenole

2016-08-01

In this paper, we propose a new secure content based image retrieval (SCBIR) system adapted to the cloud framework. This solution allows a physician to retrieve images of similar content within an outsourced and encrypted image database, without decrypting them. Contrarily to actual CBIR approaches in the encrypted domain, the originality of the proposed scheme stands on the fact that the features extracted from the encrypted images are themselves encrypted. This is achieved by means of homomorphic encryption and two non-colluding servers, we however both consider as honest but curious. In that way an end to end secure CBIR process is ensured. Experimental results carried out on a diabetic retinopathy database encrypted with the Paillier cryptosystem indicate that our SCBIR achieves retrieval performance as good as if images were processed in their non-encrypted form.

Texture-based approach to palmprint retrieval for personal identification

NASA Astrophysics Data System (ADS)

Li, Wenxin; Zhang, David; Xu, Z.; You, J.

2000-12-01

This paper presents a new approach to palmprint retrieval for personal identification. Three key issues in image retrieval are considered - feature selection, similarity measures and dynamic search for the best matching of the sample in the image database. We propose a texture-based method for palmprint feature representation. The concept of texture energy is introduced to define a palm print's global and local features, which are characterized with high convergence of inner-palm similarities and good dispersion of inter-palm discrimination. The search is carried out in a layered fashion: first global features are used to guide the fast selection of a small set of similar candidates from the database from the database and then local features are used to decide the final output within the candidate set. The experimental results demonstrate the effectiveness and accuracy of the proposed method.

Texture-based approach to palmprint retrieval for personal identification

NASA Astrophysics Data System (ADS)

Li, Wenxin; Zhang, David; Xu, Z.; You, J.

2001-01-01

This paper presents a new approach to palmprint retrieval for personal identification. Three key issues in image retrieval are considered - feature selection, similarity measures and dynamic search for the best matching of the sample in the image database. We propose a texture-based method for palmprint feature representation. The concept of texture energy is introduced to define a palm print's global and local features, which are characterized with high convergence of inner-palm similarities and good dispersion of inter-palm discrimination. The search is carried out in a layered fashion: first global features are used to guide the fast selection of a small set of similar candidates from the database from the database and then local features are used to decide the final output within the candidate set. The experimental results demonstrate the effectiveness and accuracy of the proposed method.

The NCBI BioSystems database

PubMed Central

Geer, Lewis Y.; Marchler-Bauer, Aron; Geer, Renata C.; Han, Lianyi; He, Jane; He, Siqian; Liu, Chunlei; Shi, Wenyao; Bryant, Stephen H.

2010-01-01

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI’s Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets. PMID:19854944

microPIR2: a comprehensive database for human–mouse comparative study of microRNA–promoter interactions

PubMed Central

Piriyapongsa, Jittima; Bootchai, Chaiwat; Ngamphiw, Chumpol; Tongsima, Sissades

2014-01-01

microRNA (miRNA)–promoter interaction resource (microPIR) is a public database containing over 15 million predicted miRNA target sites located within human promoter sequences. These predicted targets are presented along with their related genomic and experimental data, making the microPIR database the most comprehensive repository of miRNA promoter target sites. Here, we describe major updates of the microPIR database including new target predictions in the mouse genome and revised human target predictions. The updated database (microPIR2) now provides ∼80 million human and 40 million mouse predicted target sites. In addition to being a reference database, microPIR2 is a tool for comparative analysis of target sites on the promoters of human–mouse orthologous genes. In particular, this new feature was designed to identify potential miRNA–promoter interactions conserved between species that could be stronger candidates for further experimental validation. We also incorporated additional supporting information to microPIR2 such as nuclear and cytoplasmic localization of miRNAs and miRNA–disease association. Extra search features were also implemented to enable various investigations of targets of interest. Database URL: http://www4a.biotec.or.th/micropir2 PMID:25425035

Private and Efficient Query Processing on Outsourced Genomic Databases.

PubMed

Ghasemi, Reza; Al Aziz, Md Momin; Mohammed, Noman; Dehkordi, Massoud Hadian; Jiang, Xiaoqian

2017-09-01

Applications of genomic studies are spreading rapidly in many domains of science and technology such as healthcare, biomedical research, direct-to-consumer services, and legal and forensic. However, there are a number of obstacles that make it hard to access and process a big genomic database for these applications. First, sequencing genomic sequence is a time consuming and expensive process. Second, it requires large-scale computation and storage systems to process genomic sequences. Third, genomic databases are often owned by different organizations, and thus, not available for public usage. Cloud computing paradigm can be leveraged to facilitate the creation and sharing of big genomic databases for these applications. Genomic data owners can outsource their databases in a centralized cloud server to ease the access of their databases. However, data owners are reluctant to adopt this model, as it requires outsourcing the data to an untrusted cloud service provider that may cause data breaches. In this paper, we propose a privacy-preserving model for outsourcing genomic data to a cloud. The proposed model enables query processing while providing privacy protection of genomic databases. Privacy of the individuals is guaranteed by permuting and adding fake genomic records in the database. These techniques allow cloud to evaluate count and top-k queries securely and efficiently. Experimental results demonstrate that a count and a top-k query over 40 Single Nucleotide Polymorphisms (SNPs) in a database of 20 000 records takes around 100 and 150 s, respectively.

Private and Efficient Query Processing on Outsourced Genomic Databases

PubMed Central

Ghasemi, Reza; Al Aziz, Momin; Mohammed, Noman; Dehkordi, Massoud Hadian; Jiang, Xiaoqian

2017-01-01

Applications of genomic studies are spreading rapidly in many domains of science and technology such as healthcare, biomedical research, direct-to-consumer services, and legal and forensic. However, there are a number of obstacles that make it hard to access and process a big genomic database for these applications. First, sequencing genomic sequence is a time-consuming and expensive process. Second, it requires large-scale computation and storage systems to processes genomic sequences. Third, genomic databases are often owned by different organizations and thus not available for public usage. Cloud computing paradigm can be leveraged to facilitate the creation and sharing of big genomic databases for these applications. Genomic data owners can outsource their databases in a centralized cloud server to ease the access of their databases. However, data owners are reluctant to adopt this model, as it requires outsourcing the data to an untrusted cloud service provider that may cause data breaches. In this paper, we propose a privacy-preserving model for outsourcing genomic data to a cloud. The proposed model enables query processing while providing privacy protection of genomic databases. Privacy of the individuals is guaranteed by permuting and adding fake genomic records in the database. These techniques allow cloud to evaluate count and top-k queries securely and efficiently. Experimental results demonstrate that a count and a top-k query over 40 SNPs in a database of 20,000 records takes around 100 and 150 seconds, respectively. PMID:27834660

Third chronological supplement to the carcinogenic potency database: standardized results of animal bioassays published through December 1986 and by the National Toxicology Program through June 1987.

PubMed Central

Gold, L S; Slone, T H; Backman, G M; Eisenberg, S; Da Costa, M; Wong, M; Manley, N B; Rohrbach, L; Ames, B N

1990-01-01

This paper is the third chronological supplement to the Carcinogenic Potency Database that first appeared in this journal in 1984. We report here results of carcinogenesis bioassays published in the general literature between January 1985 and December 1986, and in Technical Reports of the National Toxicology Program between June 1986 and June 1987. This supplement includes results of 337 long-term, chronic experiments of 121 compounds, and reports the same information about each experiment in the same plot format as the earlier papers, e.g., the species and strain of animal, the route and duration of compound administration, dose level, and other aspects of experimental protocol, histopathology, and tumor incidence, TD50 (carcinogenic potency) and its statistical significance, dose response, opinion of the author about carcinogenicity, and literature citation. The reader needs to refer to the 1984 publication for a guide to the plot of the database, a complete description of the numerical index of carcinogenic potency, and a discussion of the sources of data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. The four plots of the database are to be used together as results published earlier are not repeated. In all, the four plots include results for approximately 4000 experiments on 1050 chemicals. Appendix 14 of this paper is an alphabetical index to all chemicals in the database and indicates which plot(s) each chemical appears in. A combined plot of all results from the four separate papers, that is ordered alphabetically by chemical, is available from the first author, in printed form or on computer tape or diskette. PMID:2351123

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.

EAB induced tree mortality impacts ecosystem respiration and tree water use in an experimental forest

Treesearch

Charles E. Flower; Douglas J. Lynch; Kathleen S. Knight; Miquel A. Gonzales-Meler

2011-01-01

The invasive emerald ash borer (Agrilus planipennis Fairmaire, EAB) has been spreading across the forest landscape of the Midwest resulting in the rapid decline of ash trees (Fraxinus spp.). Ash trees represent a dominant riparian species in temperate deciduous forests of the Eastern United States (USDA FIA Database). Prior...

NUCFRG2: An evaluation of the semiempirical nuclear fragmentation database

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Tripathi, R. K.; Cucinotta, F. A.; Shinn, J. L.; Badavi, F. F.; Chun, S. Y.; Norbury, J. W.; Zeitlin, C. J.; Heilbronn, L.; Miller, J.

1995-01-01

A semiempirical abrasion-ablation model has been successful in generating a large nuclear database for the study of high charge and energy (HZE) ion beams, radiation physics, and galactic cosmic ray shielding. The cross sections that are generated are compared with measured HZE fragmentation data from various experimental groups. A research program for improvement of the database generator is also discussed.

An infrared spectral database for detection of gases emitted by biomass burning

Treesearch

Timothy J. Johnson; Luisa T. M. Profeta; Robert L. Sams; David W. T. Griffith; Robert L. Yokelson

2010-01-01

We report the construction of a database of infrared spectra aimed at detecting the gases emitted by biomass burning. The project uses many of the methods of the Pacific Northwest National Laboratory (PNNL) infrared database, but the selection of the species and special experimental considerations are optimized. Each spectrum is a weighted average derived from 10 or...

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

PubMed

Kawano, Shin; Watanabe, Tsutomu; Mizuguchi, Sohei; Araki, Norie; Katayama, Toshiaki; Yamaguchi, Atsuko

2014-07-01

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding.

PubMed

Mizutani, Hisashi; Sugawara, Hideaki; Buckle, Ashley M; Sangawa, Takeshi; Miyazono, Ken-Ichi; Ohtsuka, Jun; Nagata, Koji; Shojima, Tomoki; Nosaki, Shohei; Xu, Yuqun; Wang, Delong; Hu, Xiao; Tanokura, Masaru; Yura, Kei

2017-04-24

More than 7000 papers related to "protein refolding" have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource - "REFOLDdb" that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest. We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17 th , 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/ . REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.

PubMed

Huang, Kai-Yao; Su, Min-Gang; Kao, Hui-Ju; Hsieh, Yun-Chung; Jhong, Jhih-Hua; Cheng, Kuang-Hao; Huang, Hsien-Da; Lee, Tzong-Yi

2016-01-04

Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein-protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

High-temperature experimental and thermodynamic modelling research on the pyrometallurgical processing of copper

NASA Astrophysics Data System (ADS)

Hidayat, Taufiq; Shishin, Denis; Decterov, Sergei A.; Hayes, Peter C.; Jak, Evgueni

2017-01-01

Uncertainty in the metal price and competition between producers mean that the daily operation of a smelter needs to target high recovery of valuable elements at low operating cost. Options for the improvement of the plant operation can be examined and decision making can be informed based on accurate information from laboratory experimentation coupled with predictions using advanced thermodynamic models. Integrated high-temperature experimental and thermodynamic modelling research on phase equilibria and thermodynamics of copper-containing systems have been undertaken at the Pyrometallurgy Innovation Centre (PYROSEARCH). The experimental phase equilibria studies involve high-temperature equilibration, rapid quenching and direct measurement of phase compositions using electron probe X-ray microanalysis (EPMA). The thermodynamic modelling deals with the development of accurate thermodynamic database built through critical evaluation of experimental data, selection of solution models, and optimization of models parameters. The database covers the Al-Ca-Cu-Fe-Mg-O-S-Si chemical system. The gas, slag, matte, liquid and solid metal phases, spinel solid solution as well as numerous solid oxide and sulphide phases are included. The database works within the FactSage software environment. Examples of phase equilibria data and thermodynamic models of selected systems, as well as possible implementation of the research outcomes to selected copper making processes are presented.

Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles

PubMed Central

2011-01-01

Background Experimentally verified protein-protein interactions (PPIs) cannot be easily retrieved by researchers unless they are stored in PPI databases. The curation of such databases can be facilitated by employing text-mining systems to identify genes which play the interactor role in PPIs and to map these genes to unique database identifiers (interactor normalization task or INT) and then to return a list of interaction pairs for each article (interaction pair task or IPT). These two tasks are evaluated in terms of the area under curve of the interpolated precision/recall (AUC iP/R) score because the order of identifiers in the output list is important for ease of curation. Results Our INT system developed for the BioCreAtIvE II.5 INT challenge achieved a promising AUC iP/R of 43.5% by using a support vector machine (SVM)-based ranking procedure. Using our new re-ranking algorithm, we have been able to improve system performance (AUC iP/R) by 1.84%. Our experimental results also show that with the re-ranked INT results, our unsupervised IPT system can achieve a competitive AUC iP/R of 23.86%, which outperforms the best BC II.5 INT system by 1.64%. Compared to using only SVM ranked INT results, using re-ranked INT results boosts AUC iP/R by 7.84%. Statistical significance t-test results show that our INT/IPT system with re-ranking outperforms that without re-ranking by a statistically significant difference. Conclusions In this paper, we present a new re-ranking algorithm that considers co-occurrence among identifiers in an article to improve INT and IPT ranking results. Combining the re-ranked INT results with an unsupervised approach to find associations among interactors, the proposed method can boost the IPT performance. We also implement score computation using dynamic programming, which is faster and more efficient than traditional approaches. PMID:21342534

Modeling of boron species in the Falcon 17 and ISP-34 integral tests

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

Lazaridis, M.; Capitao, J.A.; Drossinos, Y.

1996-09-01

The RAFT computer code for aerosol formation and transport was modified to include boron species in its chemical database. The modification was necessary to calculate fission product transport and deposition in the FAL-17 and ISP-34 Falcon tests, where boric acid was injected. The experimental results suggest that the transport of cesium is modified in the presence of boron. The results obtained with the modified RAFT code are presented; they show good agreement with experimental results for cesium and partial agreement for boron deposition in the Falcon silica tube. The new version of the RAFT code predicts the same behavior formore » iodine deposition as the previous version, where boron species were not included.« less

Electron-Impact Ionization Cross Section Database

National Institute of Standards and Technology Data Gateway

SRD 107 Electron-Impact Ionization Cross Section Database (Web, free access)   This is a database primarily of total ionization cross sections of molecules by electron impact. The database also includes cross sections for a small number of atoms and energy distributions of ejected electrons for H, He, and H2. The cross sections were calculated using the Binary-Encounter-Bethe (BEB) model, which combines the Mott cross section with the high-incident energy behavior of the Bethe cross section. Selected experimental data are included.

Lynx: a database and knowledge extraction engine for integrative medicine.

PubMed

Sulakhe, Dinanath; Balasubramanian, Sandhya; Xie, Bingqing; Feng, Bo; Taylor, Andrew; Wang, Sheng; Berrocal, Eduardo; Dave, Utpal; Xu, Jinbo; Börnigen, Daniela; Gilliam, T Conrad; Maltsev, Natalia

2014-01-01

We have developed Lynx (http://lynx.ci.uchicago.edu)--a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from >35 public databases and private collections, as well as manually curated data from our group and collaborators. Lynx provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization to assist the user in extracting meaningful knowledge from LynxKB and experimental data, whereas its service-oriented architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces.

Experimental Validation Plan for the Xolotl Plasma-Facing Component Simulator Using Tokamak Sample Exposures

NASA Astrophysics Data System (ADS)

Chan, V. S.; Wong, C. P. C.; McLean, A. G.; Luo, G. N.; Wirth, B. D.

2013-10-01

The Xolotl code under development by PSI-SciDAC will enhance predictive modeling capability of plasma-facing materials under burning plasma conditions. The availability and application of experimental data to compare to code-calculated observables are key requirements to validate the breadth and content of physics included in the model and ultimately gain confidence in its results. A dedicated effort has been in progress to collect and organize a) a database of relevant experiments and their publications as previously carried out at sample exposure facilities in US and Asian tokamaks (e.g., DIII-D DiMES, and EAST MAPES), b) diagnostic and surface analysis capabilities available at each device, and c) requirements for future experiments with code validation in mind. The content of this evolving database will serve as a significant resource for the plasma-material interaction (PMI) community. Work supported in part by the US Department of Energy under GA-DE-SC0008698, DE-AC52-07NA27344 and DE-AC05-00OR22725.

A framework for interval-valued information system

NASA Astrophysics Data System (ADS)

Yin, Yunfei; Gong, Guanghong; Han, Liang

2012-09-01

Interval-valued information system is used to transform the conventional dataset into the interval-valued form. To conduct the interval-valued data mining, we conduct two investigations: (1) construct the interval-valued information system, and (2) conduct the interval-valued knowledge discovery. In constructing the interval-valued information system, we first make the paired attributes in the database discovered, and then, make them stored in the neighbour locations in a common database and regard them as 'one' new field. In conducting the interval-valued knowledge discovery, we utilise some related priori knowledge and regard the priori knowledge as the control objectives; and design an approximate closed-loop control mining system. On the implemented experimental platform (prototype), we conduct the corresponding experiments and compare the proposed algorithms with several typical algorithms, such as the Apriori algorithm, the FP-growth algorithm and the CLOSE+ algorithm. The experimental results show that the interval-valued information system method is more effective than the conventional algorithms in discovering interval-valued patterns.

Using the Textpresso Site-Specific Recombinases Web server to identify Cre expressing mouse strains and floxed alleles.

PubMed

Condie, Brian G; Urbanski, William M

2014-01-01

Effective tools for searching the biomedical literature are essential for identifying reagents or mouse strains as well as for effective experimental design and informed interpretation of experimental results. We have built the Textpresso Site Specific Recombinases (Textpresso SSR) Web server to enable researchers who use mice to perform in-depth searches of a rapidly growing and complex part of the mouse literature. Our Textpresso Web server provides an interface for searching the full text of most of the peer-reviewed publications that report the characterization or use of mouse strains that express Cre or Flp recombinase. The database also contains most of the publications that describe the characterization or analysis of strains carrying conditional alleles or transgenes that can be inactivated or activated by site-specific recombinases such as Cre or Flp. Textpresso SSR complements the existing online databases that catalog Cre and Flp expression patterns by providing a unique online interface for the in-depth text mining of the site specific recombinase literature.

Prediction of friction factor of pure water flowing inside vertical smooth and microfin tubes by using artificial neural networks

NASA Astrophysics Data System (ADS)

Çebi, A.; Akdoğan, E.; Celen, A.; Dalkilic, A. S.

2017-02-01

An artificial neural network (ANN) model of friction factor in smooth and microfin tubes under heating, cooling and isothermal conditions was developed in this study. Data used in ANN was taken from a vertically positioned heat exchanger experimental setup. Multi-layered feed-forward neural network with backpropagation algorithm, radial basis function networks and hybrid PSO-neural network algorithm were applied to the database. Inputs were the ratio of cross sectional flow area to hydraulic diameter, experimental condition number depending on isothermal, heating, or cooling conditions and mass flow rate while the friction factor was the output of the constructed system. It was observed that such neural network based system could effectively predict the friction factor values of the flows regardless of their tube types. A dependency analysis to determine the strongest parameter that affected the network and database was also performed and tube geometry was found to be the strongest parameter of all as a result of analysis.

Kefir and Cancer: A Systematic Review of Literatures.

PubMed

Rafie, Nahid; Golpour Hamedani, Sahar; Ghiasvand, Reza; Miraghajani, Maryam

2015-12-01

Some studies have suggested chemopreventive effects of kefir, a fermented milk product, on carcinogenesis. The aim of this review study was to evaluate the scientific evidence for effects of kefir on cancer prevention and treatment. We systematically searched for all relevant studies published before June 2015, using PubMed, Google scholar, Cochrane and Science Direct, SID, MedLib and Srlst databases. Relevant studies were reviewed based on systematic review (PRISMA) guidelines. From a total of 2208 papers obtained at the initial database search, 11 publications including 7 in vitro and 4 experimental studies were eligible. In vitro studies on breast, colon, skin and gastric cancers and leukemia cell lines and experimental studies on different sarcomas consistently showed beneficial effects of kefir on cancer prevention and treatment. The results of this systematic review suggest that kefir may be associated with cancer prevention and it also has beneficial effects in cancer treatment. This protection may be associated with kefir bioactive components including peptides, polysaccharides and sphingolipids.

The Microphysiology Systems Database for Analyzing and Modeling Compound Interactions with Human and Animal Organ Models

PubMed Central

Vernetti, Lawrence; Bergenthal, Luke; Shun, Tong Ying; Taylor, D. Lansing

2016-01-01

Abstract Microfluidic human organ models, microphysiology systems (MPS), are currently being developed as predictive models of drug safety and efficacy in humans. To design and validate MPS as predictive of human safety liabilities requires safety data for a reference set of compounds, combined with in vitro data from the human organ models. To address this need, we have developed an internet database, the MPS database (MPS-Db), as a powerful platform for experimental design, data management, and analysis, and to combine experimental data with reference data, to enable computational modeling. The present study demonstrates the capability of the MPS-Db in early safety testing using a human liver MPS to relate the effects of tolcapone and entacapone in the in vitro model to human in vivo effects. These two compounds were chosen to be evaluated as a representative pair of marketed drugs because they are structurally similar, have the same target, and were found safe or had an acceptable risk in preclinical and clinical trials, yet tolcapone induced unacceptable levels of hepatotoxicity while entacapone was found to be safe. Results demonstrate the utility of the MPS-Db as an essential resource for relating in vitro organ model data to the multiple biochemical, preclinical, and clinical data sources on in vivo drug effects. PMID:28781990

The ability of older adults to use customized online medical databases to improve their health-related knowledge.

PubMed

Freund, Ophir; Reychav, Iris; McHaney, Roger; Goland, Ella; Azuri, Joseph

2017-06-01

Patient compliance with medical advice and recommended treatment depends on perception of health condition, medical knowledge, attitude, and self-efficacy. This study investigated how use of customized online medical databases, intended to improve knowledge in a variety of relevant medical topics, influenced senior adults' perceptions. Seventy-nine older adults in residence homes completed a computerized, tablet-based questionnaire, with medical scenarios and related questions. Following an intervention, control group participants answered questions without online help while an experimental group received internet links that directed them to customized, online medical databases. Medical knowledge and test scores among the experimental group significantly improved from pre- to post-intervention (p<0.0001) and was higher in comparison with the control group (p<0.0001). No significant change occurred in the control group. Older adults improved their knowledge in desired medical topic areas using customized online medical databases. The study demonstrated how such databases help solve health-related questions among older adult population members, and that older patients appear willing to consider technology usage in information acquisition. Copyright © 2017 Elsevier B.V. All rights reserved.

CDM analysis

NASA Technical Reports Server (NTRS)

Larson, Robert E.; Mcentire, Paul L.; Oreilly, John G.

1993-01-01

The C Data Manager (CDM) is an advanced tool for creating an object-oriented database and for processing queries related to objects stored in that database. The CDM source code was purchased and will be modified over the course of the Arachnid project. In this report, the modified CDM is referred to as MCDM. Using MCDM, a detailed series of experiments was designed and conducted on a Sun Sparcstation. The primary results and analysis of the CDM experiment are provided in this report. The experiments involved creating the Long-form Faint Source Catalog (LFSC) database and then analyzing it with respect to following: (1) the relationships between the volume of data and the time required to create a database; (2) the storage requirements of the database files; and (3) the properties of query algorithms. The effort focused on defining, implementing, and analyzing seven experimental scenarios: (1) find all sources by right ascension--RA; (2) find all sources by declination--DEC; (3) find all sources in the right ascension interval--RA1, RA2; (4) find all sources in the declination interval--DEC1, DEC2; (5) find all sources in the rectangle defined by--RA1, RA2, DEC1, DEC2; (6) find all sources that meet certain compound conditions; and (7) analyze a variety of query algorithms. Throughout this document, the numerical results obtained from these scenarios are reported; conclusions are presented at the end of the document.

Effects of Solid Solution Strengthening Elements Mo, Re, Ru, and W on Transition Temperatures in Nickel-Based Superalloys with High γ'-Volume Fraction: Comparison of Experiment and CALPHAD Calculations

NASA Astrophysics Data System (ADS)

Ritter, Nils C.; Sowa, Roman; Schauer, Jan C.; Gruber, Daniel; Goehler, Thomas; Rettig, Ralf; Povoden-Karadeniz, Erwin; Koerner, Carolin; Singer, Robert F.

2018-06-01

We prepared 41 different superalloy compositions by an arc melting, casting, and heat treatment process. Alloy solid solution strengthening elements were added in graded amounts, and we measured the solidus, liquidus, and γ'-solvus temperatures of the samples by DSC. The γ'-phase fraction increased as the W, Mo, and Re contents were increased, and W showed the most pronounced effect. Ru decreased the γ'-phase fraction. Melting temperatures (i.e., solidus and liquidus) were increased by addition of Re, W, and Ru (the effect increased in that order). Addition of Mo decreased the melting temperature. W was effective as a strengthening element because it acted as a solid solution strengthener and increased the fraction of fine γ'-precipitates, thus improving precipitation strengthening. Experimentally determined values were compared with calculated values based on the CALPHAD software tools Thermo-Calc (databases: TTNI8 and TCNI6) and MatCalc (database ME-NI). The ME-NI database, which was specially adapted to the present investigation, showed good agreement. TTNI8 also showed good results. The TCNI6 database is suitable for computational design of complex nickel-based superalloys. However, a large deviation remained between the experiment results and calculations based on this database. It also erroneously predicted γ'-phase separations and failed to describe the Ru-effect on transition temperatures.

Improved Bond Equations for Fiber-Reinforced Polymer Bars in Concrete

PubMed Central

Pour, Sadaf Moallemi; Alam, M. Shahria; Milani, Abbas S.

2016-01-01

This paper explores a set of new equations to predict the bond strength between fiber reinforced polymer (FRP) rebar and concrete. The proposed equations are based on a comprehensive statistical analysis and existing experimental results in the literature. Namely, the most effective parameters on bond behavior of FRP concrete were first identified by applying a factorial analysis on a part of the available database. Then the database that contains 250 pullout tests were divided into four groups based on the concrete compressive strength and the rebar surface. Afterward, nonlinear regression analysis was performed for each study group in order to determine the bond equations. The results show that the proposed equations can predict bond strengths more accurately compared to the other previously reported models. PMID:28773859

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

The Geant4 physics validation repository

DOE PAGES

Wenzel, H.; Yarba, J.; Dotti, A.

2015-12-23

The Geant4 collaboration regularly performs validation and regression tests. The results are stored in a central repository and can be easily accessed via a web application. In this article we describe the Geant4 physics validation repository which consists of a relational database storing experimental data and Geant4 test results, a java API and a web application. Lastly, the functionality of these components and the technology choices we made are also described

Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles.

PubMed

Tsai, Richard Tzong-Han; Lai, Po-Ting

2011-02-23

Experimentally verified protein-protein interactions (PPIs) cannot be easily retrieved by researchers unless they are stored in PPI databases. The curation of such databases can be facilitated by employing text-mining systems to identify genes which play the interactor role in PPIs and to map these genes to unique database identifiers (interactor normalization task or INT) and then to return a list of interaction pairs for each article (interaction pair task or IPT). These two tasks are evaluated in terms of the area under curve of the interpolated precision/recall (AUC iP/R) score because the order of identifiers in the output list is important for ease of curation. Our INT system developed for the BioCreAtIvE II.5 INT challenge achieved a promising AUC iP/R of 43.5% by using a support vector machine (SVM)-based ranking procedure. Using our new re-ranking algorithm, we have been able to improve system performance (AUC iP/R) by 1.84%. Our experimental results also show that with the re-ranked INT results, our unsupervised IPT system can achieve a competitive AUC iP/R of 23.86%, which outperforms the best BC II.5 INT system by 1.64%. Compared to using only SVM ranked INT results, using re-ranked INT results boosts AUC iP/R by 7.84%. Statistical significance t-test results show that our INT/IPT system with re-ranking outperforms that without re-ranking by a statistically significant difference. In this paper, we present a new re-ranking algorithm that considers co-occurrence among identifiers in an article to improve INT and IPT ranking results. Combining the re-ranked INT results with an unsupervised approach to find associations among interactors, the proposed method can boost the IPT performance. We also implement score computation using dynamic programming, which is faster and more efficient than traditional approaches.

A novel approach: chemical relational databases, and the role of the ISSCAN database on assessing chemical carcinogenicity.

PubMed

Benigni, Romualdo; Bossa, Cecilia; Richard, Ann M; Yang, Chihae

2008-01-01

Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did not contain chemical structures. Concepts and technologies originated from the structure-activity relationships science have provided powerful tools to create new types of databases, where the effective linkage of chemical toxicity with chemical structure can facilitate and greatly enhance data gathering and hypothesis generation, by permitting: a) exploration across both chemical and biological domains; and b) structure-searchability through the data. This paper reviews the main public databases, together with the progress in the field of chemical relational databases, and presents the ISSCAN database on experimental chemical carcinogens.

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

PubMed Central

2011-01-01

Background Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments. Description MeRy-B, the first platform for plant 1H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues. Conclusion MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php. PMID:21668943

Physical–chemical determinants of coil conformations in globular proteins

PubMed Central

Perskie, Lauren L; Rose, George D

2010-01-01

We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from α-helices and/or β-strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two-, three-, and four-residue turns from X-ray–elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash-free conformers in which no backbone polar group lacks a hydrogen-bond partner. Further, at least 90% of longer coil segments, ranging from 5- to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or ab initio methods. Empirical methods use database-derived information; ab initio methods rely on physical–chemical principles exclusively. Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue. PMID:20512968

Molecular scaffold analysis of natural products databases in the public domain.

PubMed

Yongye, Austin B; Waddell, Jacob; Medina-Franco, José L

2012-11-01

Natural products represent important sources of bioactive compounds in drug discovery efforts. In this work, we compiled five natural products databases available in the public domain and performed a comprehensive chemoinformatic analysis focused on the content and diversity of the scaffolds with an overview of the diversity based on molecular fingerprints. The natural products databases were compared with each other and with a set of molecules obtained from in-house combinatorial libraries, and with a general screening commercial library. It was found that publicly available natural products databases have different scaffold diversity. In contrast to the common concept that larger libraries have the largest scaffold diversity, the largest natural products collection analyzed in this work was not the most diverse. The general screening library showed, overall, the highest scaffold diversity. However, considering the most frequent scaffolds, the general reference library was the least diverse. In general, natural products databases in the public domain showed low molecule overlap. In addition to benzene and acyclic compounds, flavones, coumarins, and flavanones were identified as the most frequent molecular scaffolds across the different natural products collections. The results of this work have direct implications in the computational and experimental screening of natural product databases for drug discovery. © 2012 John Wiley & Sons A/S.

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

PubMed

Li, Feng; Li, Maoyu; Xiao, Zhiqiang; Zhang, Pengfei; Li, Jianling; Chen, Zhuchu

2006-01-11

Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database. The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database. Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.

Validation of the kinetic-turbulent-neoclassical theory for edge intrinsic rotation in DIII-D

NASA Astrophysics Data System (ADS)

Ashourvan, Arash; Grierson, B. A.; Battaglia, D. J.; Haskey, S. R.; Stoltzfus-Dueck, T.

2018-05-01

In a recent kinetic model of edge main-ion (deuterium) toroidal velocity, intrinsic rotation results from neoclassical orbits in an inhomogeneous turbulent field [T. Stoltzfus-Dueck, Phys. Rev. Lett. 108, 065002 (2012)]. This model predicts a value for the toroidal velocity that is co-current for a typical inboard X-point plasma at the core-edge boundary (ρ ˜ 0.9). Using this model, the velocity prediction is tested on the DIII-D tokamak for a database of L-mode and H-mode plasmas with nominally low neutral beam torque, including both signs of plasma current. Values for the flux-surface-averaged main-ion rotation velocity in the database are obtained from the impurity carbon rotation by analytically calculating the main-ion—impurity neoclassical offset. The deuterium rotation obtained in this manner has been validated by direct main-ion measurements for a limited number of cases. Key theoretical parameters of ion temperature and turbulent scale length are varied across a wide range in an experimental database of discharges. Using a characteristic electron temperature scale length as a proxy for a turbulent scale length, the predicted main-ion rotation velocity has a general agreement with the experimental measurements for neutral beam injection (NBI) powers in the range PNBI < 4 MW. At higher NBI power, the experimental rotation is observed to saturate and even degrade compared to theory. TRANSP-NUBEAM simulations performed for the database show that for discharges with nominally balanced—but high powered—NBI, the net injected torque through the edge can exceed 1 Nm in the counter-current direction. The theory model has been extended to compute the rotation degradation from this counter-current NBI torque by solving a reduced momentum evolution equation for the edge and found the revised velocity prediction to be in agreement with experiment. Using the theory modeled—and now tested—velocity to predict the bulk plasma rotation opens up a path to more confidently projecting the confinement and stability in ITER.

Aerodynamic Performance of an Active Flow Control Configuration Using Unstructured-Grid RANS

NASA Technical Reports Server (NTRS)

Joslin, Ronald D.; Viken, Sally A.

2001-01-01

This research is focused on assessing the value of the Reynolds-Averaged Navier-Stokes (RANS) methodology for active flow control applications. An experimental flow control database exists for a TAU0015 airfoil, which is a modification of a NACA0015 airfoil. The airfoil has discontinuities at the leading edge due to the implementation of a fluidic actuator and aft of mid chord on the upper surface. This paper documents two- and three-dimensional computational results for the baseline wing configuration (no control) with tile experimental results. The two-dimensional results suggest that the mid-chord discontinuity does not effect the aerodynamics of the wing and can be ignored for more efficient computations. The leading-edge discontinuity significantly affects tile lift and drag; hence, the integrity of the leading-edge notch discontinuity must be maintained in the computations to achieve a good match with the experimental data. The three-dimensional integrated performance results are in good agreement with the experiments inspite of some convergence and grid resolution issues.

A database of charged cosmic rays

NASA Astrophysics Data System (ADS)

Maurin, D.; Melot, F.; Taillet, R.

2014-09-01

Aims: This paper gives a description of a new online database and associated online tools (data selection, data export, plots, etc.) for charged cosmic-ray measurements. The experimental setups (type, flight dates, techniques) from which the data originate are included in the database, along with the references to all relevant publications. Methods: The database relies on the MySQL5 engine. The web pages and queries are based on PHP, AJAX and the jquery, jquery.cluetip, jquery-ui, and table-sorter third-party libraries. Results: In this first release, we restrict ourselves to Galactic cosmic rays with Z ≤ 30 and a kinetic energy per nucleon up to a few tens of TeV/n. This corresponds to more than 200 different sub-experiments (i.e., different experiments, or data from the same experiment flying at different times) in as many publications. Conclusions: We set up a cosmic-ray database (CRDB) and provide tools to sort and visualise the data. New data can be submitted, providing the community with a collaborative tool to archive past and future cosmic-ray measurements. http://lpsc.in2p3.fr/crdb; Contact: crdatabase@lpsc.in2p3.fr

Image-based query-by-example for big databases of galaxy images

NASA Astrophysics Data System (ADS)

Shamir, Lior; Kuminski, Evan

2017-01-01

Very large astronomical databases containing millions or even billions of galaxy images have been becoming increasingly important tools in astronomy research. However, in many cases the very large size makes it more difficult to analyze these data manually, reinforcing the need for computer algorithms that can automate the data analysis process. An example of such task is the identification of galaxies of a certain morphology of interest. For instance, if a rare galaxy is identified it is reasonable to expect that more galaxies of similar morphology exist in the database, but it is virtually impossible to manually search these databases to identify such galaxies. Here we describe computer vision and pattern recognition methodology that receives a galaxy image as an input, and searches automatically a large dataset of galaxies to return a list of galaxies that are visually similar to the query galaxy. The returned list is not necessarily complete or clean, but it provides a substantial reduction of the original database into a smaller dataset, in which the frequency of objects visually similar to the query galaxy is much higher. Experimental results show that the algorithm can identify rare galaxies such as ring galaxies among datasets of 10,000 astronomical objects.

Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana.

PubMed

Hansen, Bjoern Oest; Meyer, Etienne H; Ferrari, Camilla; Vaid, Neha; Movahedi, Sara; Vandepoele, Klaas; Nikoloski, Zoran; Mutwil, Marek

2018-03-01

Recent advances in gene function prediction rely on ensemble approaches that integrate results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We have explored and compared two methods to integrate 10 gene co-function networks for Arabidopsis thaliana and demonstrate how the integration of these networks produces more accurate gene function predictions for a larger fraction of genes with unknown function. These predictions were used to identify genes involved in mitochondrial complex I formation, and for five of them, we confirmed the predictions experimentally. The ensemble predictions are provided as a user-friendly online database, EnsembleNet. The methods presented here demonstrate that ensemble gene function prediction is a powerful method to boost prediction performance, whereas the EnsembleNet database provides a cutting-edge community tool to guide experimentalists. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Accelerated Leach Testing of GLASS: ALTGLASS Version 3.0

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

Trivelpiece, Cory L.; Jantzen, Carol M.; Crawford, Charles L.

The Accelerated Leach Testing of GLASS (ALTGLASS) database is a collection of data from short- and long-term product consistency tests (PCT, ASTM C1285 A and B) on high level waste (HLW) as well as low activity waste (LAW) glasses. The database provides both U.S. and international researchers with an archive of experimental data for the purpose of studying, modeling, or validating existing models of nuclear waste glass corrosion. The ALTGLASS database is maintained and updated by researchers at the Savannah River National Laboratory (SRNL). This newest version, ALTGLASS Version 3.0, has been updated with an additional 503 rows of datamore » representing PCT results from corrosion experiments conducted in the United States by the Savannah River National Laboratory, Pacific Northwest National Laboratory, Argonne National Laboratory, and the Vitreous State Laboratory (SRNL, PNNL, ANL, VSL, respectively) as well as the National Nuclear Laboratory (NNL) in the United Kingdom.« less

Competitive code-based fast palmprint identification using a set of cover trees

NASA Astrophysics Data System (ADS)

Yue, Feng; Zuo, Wangmeng; Zhang, David; Wang, Kuanquan

2009-06-01

A palmprint identification system recognizes a query palmprint image by searching for its nearest neighbor from among all the templates in a database. When applied on a large-scale identification system, it is often necessary to speed up the nearest-neighbor searching process. We use competitive code, which has very fast feature extraction and matching speed, for palmprint identification. To speed up the identification process, we extend the cover tree method and propose to use a set of cover trees to facilitate the fast and accurate nearest-neighbor searching. We can use the cover tree method because, as we show, the angular distance used in competitive code can be decomposed into a set of metrics. Using the Hong Kong PolyU palmprint database (version 2) and a large-scale palmprint database, our experimental results show that the proposed method searches for nearest neighbors faster than brute force searching.

Tempest: Accelerated MS/MS Database Search Software for Heterogeneous Computing Platforms.

PubMed

Adamo, Mark E; Gerber, Scott A

2016-09-07

MS/MS database search algorithms derive a set of candidate peptide sequences from in silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU (central processing unit) generates peptide candidates that are asynchronously sent to a discrete GPU (graphics processing unit) to be scored against experimental spectra in parallel. The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Human Thermal Model Evaluation Using the JSC Human Thermal Database

NASA Technical Reports Server (NTRS)

Bue, Grant; Makinen, Janice; Cognata, Thomas

2012-01-01

Human thermal modeling has considerable long term utility to human space flight. Such models provide a tool to predict crew survivability in support of vehicle design and to evaluate crew response in untested space environments. It is to the benefit of any such model not only to collect relevant experimental data to correlate it against, but also to maintain an experimental standard or benchmark for future development in a readily and rapidly searchable and software accessible format. The Human thermal database project is intended to do just so; to collect relevant data from literature and experimentation and to store the data in a database structure for immediate and future use as a benchmark to judge human thermal models against, in identifying model strengths and weakness, to support model development and improve correlation, and to statistically quantify a model s predictive quality. The human thermal database developed at the Johnson Space Center (JSC) is intended to evaluate a set of widely used human thermal models. This set includes the Wissler human thermal model, a model that has been widely used to predict the human thermoregulatory response to a variety of cold and hot environments. These models are statistically compared to the current database, which contains experiments of human subjects primarily in air from a literature survey ranging between 1953 and 2004 and from a suited experiment recently performed by the authors, for a quantitative study of relative strength and predictive quality of the models.

A joint numerical and experimental study of the jet of an aircraft engine installation with advanced techniques

NASA Astrophysics Data System (ADS)

Brunet, V.; Molton, P.; Bézard, H.; Deck, S.; Jacquin, L.

2012-01-01

This paper describes the results obtained during the European Union JEDI (JEt Development Investigations) project carried out in cooperation between ONERA and Airbus. The aim of these studies was first to acquire a complete database of a modern-type engine jet installation set under a wall-to-wall swept wing in various transonic flow conditions. Interactions between the engine jet, the pylon, and the wing were studied thanks to ¤advanced¥ measurement techniques. In parallel, accurate Reynolds-averaged Navier Stokes (RANS) simulations were carried out from simple ones with the Spalart Allmaras model to more complex ones like the DRSM-SSG (Differential Reynolds Stress Modef of Speziale Sarkar Gatski) turbulence model. In the end, Zonal-Detached Eddy Simulations (Z-DES) were also performed to compare different simulation techniques. All numerical results are accurately validated thanks to the experimental database acquired in parallel. This complete and complex study of modern civil aircraft engine installation allowed many upgrades in understanding and simulation methods to be obtained. Furthermore, a setup for engine jet installation studies has been validated for possible future works in the S3Ch transonic research wind-tunnel. The main conclusions are summed up in this paper.

Human Thermal Model Evaluation Using the JSC Human Thermal Database

NASA Technical Reports Server (NTRS)

Cognata, T.; Bue, G.; Makinen, J.

2011-01-01

The human thermal database developed at the Johnson Space Center (JSC) is used to evaluate a set of widely used human thermal models. This database will facilitate a more accurate evaluation of human thermoregulatory response using in a variety of situations, including those situations that might otherwise prove too dangerous for actual testing--such as extreme hot or cold splashdown conditions. This set includes the Wissler human thermal model, a model that has been widely used to predict the human thermoregulatory response to a variety of cold and hot environments. These models are statistically compared to the current database, which contains experiments of human subjects primarily in air from a literature survey ranging between 1953 and 2004 and from a suited experiment recently performed by the authors, for a quantitative study of relative strength and predictive quality of the models. Human thermal modeling has considerable long term utility to human space flight. Such models provide a tool to predict crew survivability in support of vehicle design and to evaluate crew response in untested environments. It is to the benefit of any such model not only to collect relevant experimental data to correlate it against, but also to maintain an experimental standard or benchmark for future development in a readily and rapidly searchable and software accessible format. The Human thermal database project is intended to do just so; to collect relevant data from literature and experimentation and to store the data in a database structure for immediate and future use as a benchmark to judge human thermal models against, in identifying model strengths and weakness, to support model development and improve correlation, and to statistically quantify a model s predictive quality.

Intra- and Inter-database Study for Arabic, English, and German Databases: Do Conventional Speech Features Detect Voice Pathology?

PubMed

Ali, Zulfiqar; Alsulaiman, Mansour; Muhammad, Ghulam; Elamvazuthi, Irraivan; Al-Nasheri, Ahmed; Mesallam, Tamer A; Farahat, Mohamed; Malki, Khalid H

2017-05-01

A large population around the world has voice complications. Various approaches for subjective and objective evaluations have been suggested in the literature. The subjective approach strongly depends on the experience and area of expertise of a clinician, and human error cannot be neglected. On the other hand, the objective or automatic approach is noninvasive. Automatic developed systems can provide complementary information that may be helpful for a clinician in the early screening of a voice disorder. At the same time, automatic systems can be deployed in remote areas where a general practitioner can use them and may refer the patient to a specialist to avoid complications that may be life threatening. Many automatic systems for disorder detection have been developed by applying different types of conventional speech features such as the linear prediction coefficients, linear prediction cepstral coefficients, and Mel-frequency cepstral coefficients (MFCCs). This study aims to ascertain whether conventional speech features detect voice pathology reliably, and whether they can be correlated with voice quality. To investigate this, an automatic detection system based on MFCC was developed, and three different voice disorder databases were used in this study. The experimental results suggest that the accuracy of the MFCC-based system varies from database to database. The detection rate for the intra-database ranges from 72% to 95%, and that for the inter-database is from 47% to 82%. The results conclude that conventional speech features are not correlated with voice, and hence are not reliable in pathology detection. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Development of a Knowledge Base of Ti-Alloys From First-Principles and Thermodynamic Modeling

NASA Astrophysics Data System (ADS)

Marker, Cassie

An aging population with an active lifestyle requires the development of better load-bearing implants, which have high levels of biocompatibility and a low elastic modulus. Titanium alloys, in the body centered cubic phase, are great implant candidates, due to their mechanical properties and biocompatibility. The present work aims at investigating the thermodynamic and elastic properties of bcc Tialloys, using the integrated first-principles based on Density Functional Theory (DFT) and the CALculation of PHAse Diagrams (CALPHAD) method. The use of integrated first-principles calculations based on DFT and CALPHAD modeling has greatly reduced the need for trial and error metallurgy, which is ineffective and costly. The phase stability of Ti-alloys has been shown to greatly affect their elastic properties. Traditionally, CALPHAD modeling has been used to predict the equilibrium phase formation, but in the case of Ti-alloys, predicting the formation of two metastable phases o and alpha" is of great importance as these phases also drastically effect the elastic properties. To build a knowledge base of Ti-alloys, for biomedical load-bearing implants, the Ti-Mo-Nb-Sn-Ta-Zr system was studied because of the biocompatibility and the bcc stabilizing effects of some of the elements. With the focus on bcc Ti-rich alloys, a database of thermodynamic descriptions of each phase for the pure elements, binary and Ti-rich ternary alloys was developed in the present work. Previous thermodynamic descriptions for the pure elements were adopted from the widely used SGTE database for global compatibility. The previous binary and ternary models from the literature were evaluated for accuracy and new thermodynamic descriptions were developed when necessary. The models were evaluated using available experimental data, as well as the enthalpy of formation of the bcc phase obtained from first-principles calculations based on DFT. The thermodynamic descriptions were combined into a database ensuring that the sublattice models are compatible with each other. For subsystems, such as the Sn-Ta system, where no thermodynamic description had been evaluated and minimal experimental data was available, first-principles calculations based on DFT were used. The Sn-Ta system has two intermetallic phases, TaSn2 and Ta3Sn, with three solution phases: bcc, body centered tetragonal (bct) and diamond. First-principles calculations were completed on the intermetallic and solution phases. Special quasirandom structures (SQS) were used to obtain information about the solution phases across the entire composition range. The Debye-Gruneisen approach, as well as the quasiharmonic phonon method, were used to obtain the finite-temperature data. Results from the first-principles calculations and experiments were used to complete the thermodynamic description. The resulting phase diagram reproduced the first-principles calculations and experimental data accurately. In order to determine the effect of alloying on the elastic properties, first-principles calculations based on DFT were systematically done on the pure elements, five Ti-X binary systems and Ti-X-Y ternary systems (X ≠ Y = Mo, Nb, Sn, Ta Zr) in the bcc phase. The first-principles calculations predicted the single crystal elastic stiffness constants cij 's. Correspondingly, the polycrystalline aggregate properties were also estimated from the cij's, including bulk modulus B, shear modulus G and Young's modulus E. The calculated results showed good agreement with experimental results. The CALPHAD method was then adapted to assist in the database development of the elastic properties as a function of composition. On average, the database predicted the elastic properties of higher order Ti-alloys within 5 GPa of the experimental results. Finally, the formation of the metastable phases, o and alpha" was studied in the Ti-Ta and Ti-Nb systems. The formation energy of these phases, calculated from first-principles at 0 K, showed that the phases have similar formation energies to the bcc and hcp phases. Inelastic neutron scattering was completed on four different Ti-Nb compositions to study the entropy of the phases as well as the transformations occurring when the phases form and the phase fractions. Ongoing work is being done to use the experimental information to introduce thermodynamic descriptions for these two phases in the Ti-Nb system in order to be able to predict the formation and phase fractions. DFT based first-principles were used to predict the effect these phases have on the elastic properties and a rule of mixtures was used to determine the elastic properties of multi-phase alloys. The results were compared with experiments and showed that if the ongoing modeling can predict the phase fraction, the elastic database can accurately predict the elastic properties of the o and alpha" phases. This thesis provides a knowledge base of the thermodynamic and elastic properties of Ti-alloys from computational thermodynamics. The databases created will impact research activities on Ti-alloys and specifically efforts focused on Ti-alloys for biomedical applications.

Automatic categorization of diverse experimental information in the bioscience literature.

PubMed

Fang, Ruihua; Schindelman, Gary; Van Auken, Kimberly; Fernandes, Jolene; Chen, Wen; Wang, Xiaodong; Davis, Paul; Tuli, Mary Ann; Marygold, Steven J; Millburn, Gillian; Matthews, Beverley; Zhang, Haiyan; Brown, Nick; Gelbart, William M; Sternberg, Paul W

2012-01-26

Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort.

Sixth plot of the carcinogenic potency database: results of animal bioassays published in the General Literature 1989 to 1990 and by the National Toxicology Program 1990 to 1993.

PubMed Central

Gold, L S; Manley, N B; Slone, T H; Garfinkel, G B; Ames, B N; Rohrbach, L; Stern, B R; Chow, K

1995-01-01

This paper presents two types of information from the Carcinogenic Potency Database (CPDB): (a) the sixth chronological plot of analyses of long-term carcinogenesis bioassays, and (b) an index to chemicals in all six plots, including a summary compendium of positivity and potency for each chemical (Appendix 14). The five earlier plots of the CPDB have appeared in this journal, beginning in 1984 (1-5). Including the plot in this paper, the CPDB reports results of 5002 experiments on 1230 chemicals. This paper includes bioassay results published in the general literature between January 1989 and December 1990, and in Technical Reports of the National Toxicology Program between January 1990 and June 1993. Analyses are included on 17 chemicals tested in nonhuman primates by the Laboratory of Chemical Pharmacology, National Cancer Institute. This plot presents results of 531 long-term, chronic experiments of 182 test compounds and includes the same information about each experiment in the same plot format as the earlier papers: the species and strain of test animal, the route and duration of compound administration, dose level and other aspects of experimental protocol, histopathology and tumor incidence, TD50 (carcinogenic potency) and its statistical significance, dose response, author's opinion about carcinogenicity, and literature citation. We refer the reader to the 1984 publications (1,6,7) for a detailed guide to the plot of the database, a complete description of the numerical index of carcinogenic potency, and a discussion of the sources of data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. The six plots of the CPDB are to be used together since results of individual experiments that were published earlier are not repeated. Appendix 14 is designed to facilitate access to results on all chemicals. References to the published papers that are the source of experimental data are reported in each of the published plots. For readers using the CPDB extensively, a combined plot is available of all results from the six separate plot papers, ordered alphabetically by chemical; the combined plot in printed form or on computer tape or diskette is available from the first author. A SAS database is also available. PMID:8741772

An ensemble rank learning approach for gene prioritization.

PubMed

Lee, Po-Feng; Soo, Von-Wun

2013-01-01

Several different computational approaches have been developed to solve the gene prioritization problem. We intend to use the ensemble boosting learning techniques to combine variant computational approaches for gene prioritization in order to improve the overall performance. In particular we add a heuristic weighting function to the Rankboost algorithm according to: 1) the absolute ranks generated by the adopted methods for a certain gene, and 2) the ranking relationship between all gene-pairs from each prioritization result. We select 13 known prostate cancer genes in OMIM database as training set and protein coding gene data in HGNC database as test set. We adopt the leave-one-out strategy for the ensemble rank boosting learning. The experimental results show that our ensemble learning approach outperforms the four gene-prioritization methods in ToppGene suite in the ranking results of the 13 known genes in terms of mean average precision, ROC and AUC measures.

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…

Verification of the databases EXFOR and ENDF

NASA Astrophysics Data System (ADS)

Berton, Gottfried; Damart, Guillaume; Cabellos, Oscar; Beauzamy, Bernard; Soppera, Nicolas; Bossant, Manuel

2017-09-01

The objective of this work is for the verification of large experimental (EXFOR) and evaluated nuclear reaction databases (JEFF, ENDF, JENDL, TENDL…). The work is applied to neutron reactions in EXFOR data, including threshold reactions, isomeric transitions, angular distributions and data in the resonance region of both isotopes and natural elements. Finally, a comparison of the resonance integrals compiled in EXFOR database with those derived from the evaluated libraries is also performed.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

Mining moving object trajectories in location-based services for spatio-temporal database update

NASA Astrophysics Data System (ADS)

Guo, Danhuai; Cui, Weihong

2008-10-01

Advances in wireless transmission and mobile technology applied to LBS (Location-based Services) flood us with amounts of moving objects data. Vast amounts of gathered data from position sensors of mobile phones, PDAs, or vehicles hide interesting and valuable knowledge and describe the behavior of moving objects. The correlation between temporal moving patterns of moving objects and geo-feature spatio-temporal attribute was ignored, and the value of spatio-temporal trajectory data was not fully exploited too. Urban expanding or frequent town plan change bring about a large amount of outdated or imprecise data in spatial database of LBS, and they cannot be updated timely and efficiently by manual processing. In this paper we introduce a data mining approach to movement pattern extraction of moving objects, build a model to describe the relationship between movement patterns of LBS mobile objects and their environment, and put up with a spatio-temporal database update strategy in LBS database based on trajectories spatiotemporal mining. Experimental evaluation reveals excellent performance of the proposed model and strategy. Our original contribution include formulation of model of interaction between trajectory and its environment, design of spatio-temporal database update strategy based on moving objects data mining, and the experimental application of spatio-temporal database update by mining moving objects trajectories.

Experimental quantum private queries with linear optics

NASA Astrophysics Data System (ADS)

de Martini, Francesco; Giovannetti, Vittorio; Lloyd, Seth; Maccone, Lorenzo; Nagali, Eleonora; Sansoni, Linda; Sciarrino, Fabio

2009-07-01

The quantum private query is a quantum cryptographic protocol to recover information from a database, preserving both user and data privacy: the user can test whether someone has retained information on which query was asked and the database provider can test the amount of information released. Here we discuss a variant of the quantum private query algorithm that admits a simple linear optical implementation: it employs the photon’s momentum (or time slot) as address qubits and its polarization as bus qubit. A proof-of-principle experimental realization is implemented.

Lynx: a database and knowledge extraction engine for integrative medicine

PubMed Central

Sulakhe, Dinanath; Balasubramanian, Sandhya; Xie, Bingqing; Feng, Bo; Taylor, Andrew; Wang, Sheng; Berrocal, Eduardo; Dave, Utpal; Xu, Jinbo; Börnigen, Daniela; Gilliam, T. Conrad; Maltsev, Natalia

2014-01-01

We have developed Lynx (http://lynx.ci.uchicago.edu)—a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from >35 public databases and private collections, as well as manually curated data from our group and collaborators. Lynx provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization to assist the user in extracting meaningful knowledge from LynxKB and experimental data, whereas its service-oriented architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces. PMID:24270788

Internet-based profiler system as integrative framework to support translational research

PubMed Central

Kim, Robert; Demichelis, Francesca; Tang, Jeffery; Riva, Alberto; Shen, Ronglai; Gibbs, Doug F; Mahavishno, Vasudeva; Chinnaiyan, Arul M; Rubin, Mark A

2005-01-01

Background Translational research requires taking basic science observations and developing them into clinically useful tests and therapeutics. We have developed a process to develop molecular biomarkers for diagnosis and prognosis by integrating tissue microarray (TMA) technology and an internet-database tool, Profiler. TMA technology allows investigators to study hundreds of patient samples on a single glass slide resulting in the conservation of tissue and the reduction in inter-experimental variability. The Profiler system allows investigator to reliably track, store, and evaluate TMA experiments. Here within we describe the process that has evolved through an empirical basis over the past 5 years at two academic institutions. Results The generic design of this system makes it compatible with multiple organ system (e.g., prostate, breast, lung, renal, and hematopoietic system,). Studies and folders are restricted to authorized users as required. Over the past 5 years, investigators at 2 academic institutions have scanned 656 TMA experiments and collected 63,311 digital images of these tissue samples. 68 pathologists from 12 major user groups have accessed the system. Two groups directly link clinical data from over 500 patients for immediate access and the remaining groups choose to maintain clinical and pathology data on separate systems. Profiler currently has 170 K data points such as staining intensity, tumor grade, and nuclear size. Due to the relational database structure, analysis can be easily performed on single or multiple TMA experimental results. The TMA module of Profiler can maintain images acquired from multiple systems. Conclusion We have developed a robust process to develop molecular biomarkers using TMA technology and an internet-based database system to track all steps of this process. This system is extendable to other types of molecular data as separate modules and is freely available to academic institutions for licensing. PMID:16364175

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets

PubMed Central

2012-01-01

Background To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. Results We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. Conclusions SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery. PMID:23281852

Immunoinformatics: an integrated scenario

PubMed Central

Tomar, Namrata; De, Rajat K

2010-01-01

Genome sequencing of humans and other organisms has led to the accumulation of huge amounts of data, which include immunologically relevant data. A large volume of clinical data has been deposited in several immunological databases and as a result immunoinformatics has emerged as an important field which acts as an intersection between experimental immunology and computational approaches. It not only helps in dealing with the huge amount of data but also plays a role in defining new hypotheses related to immune responses. This article reviews classical immunology, different databases and prediction tools. It also describes applications of immunoinformatics in designing in silico vaccination and immune system modelling. All these efforts save time and reduce cost. PMID:20722763

Androgen-responsive gene database: integrated knowledge on androgen-responsive genes.

PubMed

Jiang, Mei; Ma, Yunsheng; Chen, Congcong; Fu, Xuping; Yang, Shu; Li, Xia; Yu, Guohua; Mao, Yumin; Xie, Yi; Li, Yao

2009-11-01

Androgen signaling plays an important role in many biological processes. Androgen Responsive Gene Database (ARGDB) is devoted to providing integrated knowledge on androgen-controlled genes. Gene records were collected on the basis of PubMed literature collections. More than 6000 abstracts and 950 original publications were manually screened, leading to 1785 human genes, 993 mouse genes, and 583 rat genes finally included in the database. All the collected genes were experimentally proved to be regulated by androgen at the expression level or to contain androgen-responsive regions. For each gene important details of the androgen regulation experiments were collected from references, such as expression change, androgen-responsive sequence, response time, tissue/cell type, experimental method, ligand identity, and androgen amount, which will facilitate further evaluation by researchers. Furthermore, the database was integrated with multiple annotation resources, including National Center for Biotechnology Information, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway, to reveal the biological characteristics and significance of androgen-regulated genes. The ARGDB web site is mainly composed of the Browse, Search, Element Scan, and Submission modules. It is user friendly and freely accessible at http://argdb.fudan.edu.cn. Preliminary analysis of the collected data was performed. Many disease pathways, such as prostate carcinogenesis, were found to be enriched in androgen-regulated genes. The discovered androgen-response motifs were similar to those in previous reports. The analysis results are displayed in the web site. In conclusion, ARGDB provides a unified gateway to storage, retrieval, and update of information on androgen-regulated genes.

Perspectives in biological physics: the nDDB project for a neutron Dynamics Data Bank for biological macromolecules.

PubMed

Rusevich, Leonid; García Sakai, Victoria; Franzetti, Bruno; Johnson, Mark; Natali, Francesca; Pellegrini, Eric; Peters, Judith; Pieper, Jörg; Weik, Martin; Zaccai, Giuseppe

2013-07-01

Neutron spectroscopy provides experimental data on time-dependent trajectories, which can be directly compared to molecular dynamics simulations. Its importance in helping us to understand biological macromolecules at a molecular level is demonstrated by the results of a literature survey over the last two to three decades. Around 300 articles in refereed journals relate to neutron scattering studies of biological macromolecular dynamics, and the results of the survey are presented here. The scope of the publications ranges from the general physics of protein and solvent dynamics, to the biologically relevant dynamics-function relationships in live cells. As a result of the survey we are currently setting up a neutron Dynamics Data Bank (nDDB) with the aim to make the neutron data on biological systems widely available. This will benefit, in particular, the MD simulation community to validate and improve their force fields. The aim of the database is to expose and give easy access to a body of experimental data to the scientific community. The database will be populated with as much of the existing data as possible. In the future it will give value, as part of a bigger whole, to high throughput data, as well as more detailed studies. A range and volume of experimental data will be of interest in determining how quantitatively MD simulations can reproduce trends across a range of systems and to what extent such trends may depend on sample preparation and data reduction and analysis methods. In this context, we strongly encourage researchers in the field to deposit their data in the nDDB.

Application of kernel functions for accurate similarity search in large chemical databases.

PubMed

Wang, Xiaohong; Huan, Jun; Smalter, Aaron; Lushington, Gerald H

2010-04-29

Similarity search in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions can not be applied to large chemical compound database due to the high computational complexity and the difficulties in indexing similarity search for large databases. To bridge graph kernel function and similarity search in chemical databases, we applied a novel kernel-based similarity measurement, developed in our team, to measure similarity of graph represented chemicals. In our method, we utilize a hash table to support new graph kernel function definition, efficient storage and fast search. We have applied our method, named G-hash, to large chemical databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Moreover, the similarity measurement and the index structure is scalable to large chemical databases with smaller indexing size, and faster query processing time as compared to state-of-the-art indexing methods such as Daylight fingerprints, C-tree and GraphGrep. Efficient similarity query processing method for large chemical databases is challenging since we need to balance running time efficiency and similarity search accuracy. Our previous similarity search method, G-hash, provides a new way to perform similarity search in chemical databases. Experimental study validates the utility of G-hash in chemical databases.

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.

Integration and management of massive remote-sensing data based on GeoSOT subdivision model

NASA Astrophysics Data System (ADS)

Li, Shuang; Cheng, Chengqi; Chen, Bo; Meng, Li

2016-07-01

Owing to the rapid development of earth observation technology, the volume of spatial information is growing rapidly; therefore, improving query retrieval speed from large, rich data sources for remote-sensing data management systems is quite urgent. A global subdivision model, geographic coordinate subdivision grid with one-dimension integer coding on 2n-tree, which we propose as a solution, has been used in data management organizations. However, because a spatial object may cover several grids, ample data redundancy will occur when data are stored in relational databases. To solve this redundancy problem, we first combined the subdivision model with the spatial array database containing the inverted index. We proposed an improved approach for integrating and managing massive remote-sensing data. By adding a spatial code column in an array format in a database, spatial information in remote-sensing metadata can be stored and logically subdivided. We implemented our method in a Kingbase Enterprise Server database system and compared the results with the Oracle platform by simulating worldwide image data. Experimental results showed that our approach performed better than Oracle in terms of data integration and time and space efficiency. Our approach also offers an efficient storage management system for existing storage centers and management systems.

WormQTLHD—a web database for linking human disease to natural variation data in C. elegans

PubMed Central

van der Velde, K. Joeri; de Haan, Mark; Zych, Konrad; Arends, Danny; Snoek, L. Basten; Kammenga, Jan E.; Jansen, Ritsert C.; Swertz, Morris A.; Li, Yang

2014-01-01

Interactions between proteins are highly conserved across species. As a result, the molecular basis of multiple diseases affecting humans can be studied in model organisms that offer many alternative experimental opportunities. One such organism—Caenorhabditis elegans—has been used to produce much molecular quantitative genetics and systems biology data over the past decade. We present WormQTLHD (Human Disease), a database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene–disease associations in man. WormQTLHD, available online at http://www.wormqtl-hd.org, is a user-friendly set of tools to reveal functionally coherent, evolutionary conserved gene networks. These can be used to predict novel gene-to-gene associations and the functions of genes underlying the disease of interest. We created a new database that links C. elegans eQTL data sets to human diseases (34 337 gene–disease associations from OMIM, DGA, GWAS Central and NHGRI GWAS Catalogue) based on overlapping sets of orthologous genes associated to phenotypes in these two species. We utilized QTL results, high-throughput molecular phenotypes, classical phenotypes and genotype data covering different developmental stages and environments from WormQTL database. All software is available as open source, built on MOLGENIS and xQTL workbench. PMID:24217915

WormQTLHD--a web database for linking human disease to natural variation data in C. elegans.

PubMed

van der Velde, K Joeri; de Haan, Mark; Zych, Konrad; Arends, Danny; Snoek, L Basten; Kammenga, Jan E; Jansen, Ritsert C; Swertz, Morris A; Li, Yang

2014-01-01

Interactions between proteins are highly conserved across species. As a result, the molecular basis of multiple diseases affecting humans can be studied in model organisms that offer many alternative experimental opportunities. One such organism-Caenorhabditis elegans-has been used to produce much molecular quantitative genetics and systems biology data over the past decade. We present WormQTL(HD) (Human Disease), a database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene-disease associations in man. WormQTL(HD), available online at http://www.wormqtl-hd.org, is a user-friendly set of tools to reveal functionally coherent, evolutionary conserved gene networks. These can be used to predict novel gene-to-gene associations and the functions of genes underlying the disease of interest. We created a new database that links C. elegans eQTL data sets to human diseases (34 337 gene-disease associations from OMIM, DGA, GWAS Central and NHGRI GWAS Catalogue) based on overlapping sets of orthologous genes associated to phenotypes in these two species. We utilized QTL results, high-throughput molecular phenotypes, classical phenotypes and genotype data covering different developmental stages and environments from WormQTL database. All software is available as open source, built on MOLGENIS and xQTL workbench.

Public perceptions of animal experimentation across Europe.

PubMed

von Roten, Fabienne Crettaz

2013-08-01

The goal of this article is to map out public perceptions of animal experimentation in 28 European countries. Postulating cross-cultural differences, this study mixes country-level variables (from the Eurostat database) and individual-level variables (from Eurobarometer Science and Technology 2010). It is shown that experimentation on animals such as mice is generally accepted in European countries, but perceptions are divided on dogs and monkeys. Between 2005 and 2010, we observe globally a change of approval on dogs and monkeys, with a significant decrease in nine countries. Multilevel analysis results show differences at country level (related to a post-industrialism model) and at individual level (related to gender, age, education, proximity and perceptions of science and the environment). These results may have consequences for public perceptions of science and we call for more cross-cultural research on press coverage of animal research and on the level of public engagement of scientists doing animal research.

Design Evolution and Performance Characterization of the GTX Air-Breathing Launch Vehicle Inlet

NASA Technical Reports Server (NTRS)

DeBonis, J. R.; Steffen, C. J., Jr.; Rice, T.; Trefny, C. J.

2002-01-01

The design and analysis of a second version of the inlet for the GTX rocket-based combine-cycle launch vehicle is discussed. The previous design did not achieve its predicted performance levels due to excessive turning of low-momentum comer flows and local over-contraction due to asymmetric end-walls. This design attempts to remove these problems by reducing the spike half-angle to 10- from 12-degrees and by implementing true plane of symmetry end-walls. Axisymmetric Reynolds-Averaged Navier-Stokes simulations using both perfect gas and real gas, finite rate chemistry, assumptions were performed to aid in the design process and to create a comprehensive database of inlet performance. The inlet design, which operates over the entire air-breathing Mach number range from 0 to 12, and the performance database are presented. The performance database, for use in cycle analysis, includes predictions of mass capture, pressure recovery, throat Mach number, drag force, and heat load, for the entire Mach range. Results of the computations are compared with experimental data to validate the performance database.

Novel dynamic Bayesian networks for facial action element recognition and understanding

NASA Astrophysics Data System (ADS)

Zhao, Wei; Park, Jeong-Seon; Choi, Dong-You; Lee, Sang-Woong

2011-12-01

In daily life, language is an important tool of communication between people. Besides language, facial action can also provide a great amount of information. Therefore, facial action recognition has become a popular research topic in the field of human-computer interaction (HCI). However, facial action recognition is quite a challenging task due to its complexity. In a literal sense, there are thousands of facial muscular movements, many of which have very subtle differences. Moreover, muscular movements always occur simultaneously when the pose is changed. To address this problem, we first build a fully automatic facial points detection system based on a local Gabor filter bank and principal component analysis. Then, novel dynamic Bayesian networks are proposed to perform facial action recognition using the junction tree algorithm over a limited number of feature points. In order to evaluate the proposed method, we have used the Korean face database for model training. For testing, we used the CUbiC FacePix, facial expressions and emotion database, Japanese female facial expression database, and our own database. Our experimental results clearly demonstrate the feasibility of the proposed approach.

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

Webb-Robertson, Bobbie-Jo M.

Accurate identification of peptides is a current challenge in mass spectrometry (MS) based proteomics. The standard approach uses a search routine to compare tandem mass spectra to a database of peptides associated with the target organism. These database search routines yield multiple metrics associated with the quality of the mapping of the experimental spectrum to the theoretical spectrum of a peptide. The structure of these results make separating correct from false identifications difficult and has created a false identification problem. Statistical confidence scores are an approach to battle this false positive problem that has led to significant improvements in peptidemore » identification. We have shown that machine learning, specifically support vector machine (SVM), is an effective approach to separating true peptide identifications from false ones. The SVM-based peptide statistical scoring method transforms a peptide into a vector representation based on database search metrics to train and validate the SVM. In practice, following the database search routine, a peptides is denoted in its vector representation and the SVM generates a single statistical score that is then used to classify presence or absence in the sample« less

SparCLeS: dynamic l₁ sparse classifiers with level sets for robust beard/moustache detection and segmentation.

PubMed

Le, T Hoang Ngan; Luu, Khoa; Savvides, Marios

2013-08-01

Robust facial hair detection and segmentation is a highly valued soft biometric attribute for carrying out forensic facial analysis. In this paper, we propose a novel and fully automatic system, called SparCLeS, for beard/moustache detection and segmentation in challenging facial images. SparCLeS uses the multiscale self-quotient (MSQ) algorithm to preprocess facial images and deal with illumination variation. Histogram of oriented gradients (HOG) features are extracted from the preprocessed images and a dynamic sparse classifier is built using these features to classify a facial region as either containing skin or facial hair. A level set based approach, which makes use of the advantages of both global and local information, is then used to segment the regions of a face containing facial hair. Experimental results demonstrate the effectiveness of our proposed system in detecting and segmenting facial hair regions in images drawn from three databases, i.e., the NIST Multiple Biometric Grand Challenge (MBGC) still face database, the NIST Color Facial Recognition Technology FERET database, and the Labeled Faces in the Wild (LFW) database.

Visual Attention Modeling for Stereoscopic Video: A Benchmark and Computational Model.

PubMed

Fang, Yuming; Zhang, Chi; Li, Jing; Lei, Jianjun; Perreira Da Silva, Matthieu; Le Callet, Patrick

2017-10-01

In this paper, we investigate the visual attention modeling for stereoscopic video from the following two aspects. First, we build one large-scale eye tracking database as the benchmark of visual attention modeling for stereoscopic video. The database includes 47 video sequences and their corresponding eye fixation data. Second, we propose a novel computational model of visual attention for stereoscopic video based on Gestalt theory. In the proposed model, we extract the low-level features, including luminance, color, texture, and depth, from discrete cosine transform coefficients, which are used to calculate feature contrast for the spatial saliency computation. The temporal saliency is calculated by the motion contrast from the planar and depth motion features in the stereoscopic video sequences. The final saliency is estimated by fusing the spatial and temporal saliency with uncertainty weighting, which is estimated by the laws of proximity, continuity, and common fate in Gestalt theory. Experimental results show that the proposed method outperforms the state-of-the-art stereoscopic video saliency detection models on our built large-scale eye tracking database and one other database (DML-ITRACK-3D).

Unique identification code for medical fundus images using blood vessel pattern for tele-ophthalmology applications.

PubMed

Singh, Anushikha; Dutta, Malay Kishore; Sharma, Dilip Kumar

2016-10-01

Identification of fundus images during transmission and storage in database for tele-ophthalmology applications is an important issue in modern era. The proposed work presents a novel accurate method for generation of unique identification code for identification of fundus images for tele-ophthalmology applications and storage in databases. Unlike existing methods of steganography and watermarking, this method does not tamper the medical image as nothing is embedded in this approach and there is no loss of medical information. Strategic combination of unique blood vessel pattern and patient ID is considered for generation of unique identification code for the digital fundus images. Segmented blood vessel pattern near the optic disc is strategically combined with patient ID for generation of a unique identification code for the image. The proposed method of medical image identification is tested on the publically available DRIVE and MESSIDOR database of fundus image and results are encouraging. Experimental results indicate the uniqueness of identification code and lossless recovery of patient identity from unique identification code for integrity verification of fundus images. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

LocSigDB: a database of protein localization signals

PubMed Central

Negi, Simarjeet; Pandey, Sanjit; Srinivasan, Satish M.; Mohammed, Akram; Guda, Chittibabu

2015-01-01

LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will help support many important areas of biomedical research. By performing an extensive literature study, we compiled a collection of 533 experimentally determined localization signals, along with the proteins that harbor such signals. Each signal in the LocSigDB is annotated with its localization, source, PubMed references and is linked to the proteins in UniProt database along with the organism information that contain the same amino acid pattern as the given signal. From LocSigDB webserver, users can download the whole database or browse/search for data using an intuitive query interface. To date, LocSigDB is the most comprehensive compendium of protein localization signals for eight distinct subcellular locations. Database URL: http://genome.unmc.edu/LocSigDB/ PMID:25725059

A database of aerothermal measurements in hypersonic flow for CFD validation

NASA Technical Reports Server (NTRS)

Holden, M. S.; Moselle, J. R.

1992-01-01

This paper presents an experimental database selected and compiled from aerothermal measurements obtained on basic model configurations on which fundamental flow phenomena could be most easily examined. The experimental studies were conducted in hypersonic flows in 48-inch, 96-inch, and 6-foot shock tunnels. A special computer program was constructed to provide easy access to the measurements in the database as well as the means to plot the measurements and compare them with imported data. The database contains tabulations of model configurations, freestream conditions, and measurements of heat transfer, pressure, and skin friction for each of the studies selected for inclusion. The first segment contains measurements in laminar flow emphasizing shock-wave boundary-layer interaction. In the second segment, measurements in transitional flows over flat plates and cones are given. The third segment comprises measurements in regions of shock-wave/turbulent-boundary-layer interactions. Studies of the effects of surface roughness of nosetips and conical afterbodies are presented in the fourth segment of the database. Detailed measurements in regions of shock/shock boundary layer interaction are contained in the fifth segment. Measurements in regions of wall jet and transpiration cooling are presented in the final two segments.

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

PubMed Central

Chowdhury, Saikat; Sarkar, Ram Rup

2015-01-01

Elucidating the complexities of cell signaling pathways is of immense importance to gain understanding about various biological phenomenon, such as dynamics of gene/protein expression regulation, cell fate determination, embryogenesis and disease progression. The successful completion of human genome project has also helped experimental and theoretical biologists to analyze various important pathways. To advance this study, during the past two decades, systematic collections of pathway data from experimental studies have been compiled and distributed freely by several databases, which also integrate various computational tools for further analysis. Despite significant advancements, there exist several drawbacks and challenges, such as pathway data heterogeneity, annotation, regular update and automated image reconstructions, which motivated us to perform a thorough review on popular and actively functioning 24 cell signaling databases. Based on two major characteristics, pathway information and technical details, freely accessible data from commercial and academic databases are examined to understand their evolution and enrichment. This review not only helps to identify some novel and useful features, which are not yet included in any of the databases but also highlights their current limitations and subsequently propose the reasonable solutions for future database development, which could be useful to the whole scientific community. PMID:25632107

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.

PubMed

May, Patrick; Christian, Jan-Ole; Kempa, Stefan; Walther, Dirk

2009-05-04

The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

Valence, arousal, familiarity, concreteness, and imageability ratings for 292 two-character Chinese nouns in Cantonese speakers in Hong Kong.

PubMed

Yee, Lydia T S

2017-01-01

Words are frequently used as stimuli in cognitive psychology experiments, for example, in recognition memory studies. In these experiments, it is often desirable to control for the words' psycholinguistic properties because differences in such properties across experimental conditions might introduce undesirable confounds. In order to avoid confounds, studies typically check to see if various affective and lexico-semantic properties are matched across experimental conditions, and so databases that contain values for these properties are needed. While word ratings for these variables exist in English and other European languages, ratings for Chinese words are not comprehensive. In particular, while ratings for single characters exist, ratings for two-character words-which often have different meanings than their constituent characters, are scarce. In this study, ratings for 292 two-character Chinese nouns were obtained from Cantonese speakers in Hong Kong. Affective variables, including valence and arousal, and lexico-semantic variables, including familiarity, concreteness, and imageability, were rated in the study. The words were selected from a film subtitle database containing word frequency information that could be extracted and listed alongside the resulting ratings. Overall, the subjective ratings showed good reliability across all rated dimensions, as well as good reliability within and between the different groups of participants who each rated a subset of the words. Moreover, several well-established relationships between the variables found consistently in other languages were also observed in this study, demonstrating that the ratings are valid. The resulting word database can be used in studies where control for the above psycholinguistic variables is critical to the research design.

Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances.

PubMed

Merkley, Eric D; Rysavy, Steven; Kahraman, Abdullah; Hafen, Ryan P; Daggett, Valerie; Adkins, Joshua N

2014-06-01

Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS(3) ) have a linker arm that is 11.4 Å long when fully extended, allowing Cα (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ∼24 Å apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ∼3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine-lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS(3), a distance constraint of 26-30 Å between Cα atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods. © 2014 The Protein Society.

Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances

PubMed Central

Merkley, Eric D; Rysavy, Steven; Kahraman, Abdullah; Hafen, Ryan P; Daggett, Valerie; Adkins, Joshua N

2014-01-01

Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS3) have a linker arm that is 11.4 Å long when fully extended, allowing Cα (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ∼24 Å apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ∼3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine–lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS3, a distance constraint of 26–30 Å between Cα atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods. PMID:24639379

EMQIT: a machine learning approach for energy based PWM matrix quality improvement.

PubMed

Smolinska, Karolina; Pacholczyk, Marcin

2017-08-01

Transcription factor binding affinities to DNA play a key role for the gene regulation. Learning the specificity of the mechanisms of binding TFs to DNA is important both to experimentalists and theoreticians. With the development of high-throughput methods such as, e.g., ChiP-seq the need to provide unbiased models of binding events has been made apparent. We present EMQIT a modification to the approach introduced by Alamanova et al. and later implemented as 3DTF server. We observed that tuning of Boltzmann factor weights, used for conversion of calculated energies to nucleotide probabilities, has a significant impact on the quality of the associated PWM matrix. Consequently, we proposed to use receiver operator characteristics curves and the 10-fold cross-validation to learn best weights using experimentally verified data from TRANSFAC database. We applied our method to data available for various TFs. We verified the efficiency of detecting TF binding sites by the 3DTF matrices improved with our technique using experimental data from the TRANSFAC database. The comparison showed a significant similarity and comparable performance between the improved and the experimental matrices (TRANSFAC). Improved 3DTF matrices achieved significantly higher AUC values than the original 3DTF matrices (at least by 0.1) and, at the same time, detected notably more experimentally verified TFBSs. The resulting new improved PWM matrices for analyzed factors show similarity to TRANSFAC matrices. Matrices had comparable predictive capabilities. Moreover, improved PWMs achieve better results than matrices downloaded from 3DTF server. Presented approach is general and applicable to any energy-based matrices. EMQIT is available online at http://biosolvers.polsl.pl:3838/emqit . This article was reviewed by Oliviero Carugo, Marek Kimmel and István Simon.

Review and assessment of turbulence models for hypersonic flows

NASA Astrophysics Data System (ADS)

Roy, Christopher J.; Blottner, Frederick G.

2006-10-01

Accurate aerodynamic prediction is critical for the design and optimization of hypersonic vehicles. Turbulence modeling remains a major source of uncertainty in the computational prediction of aerodynamic forces and heating for these systems. The first goal of this article is to update the previous comprehensive review of hypersonic shock/turbulent boundary-layer interaction experiments published in 1991 by Settles and Dodson (Hypersonic shock/boundary-layer interaction database. NASA CR 177577, 1991). In their review, Settles and Dodson developed a methodology for assessing experiments appropriate for turbulence model validation and critically surveyed the existing hypersonic experiments. We limit the scope of our current effort by considering only two-dimensional (2D)/axisymmetric flows in the hypersonic flow regime where calorically perfect gas models are appropriate. We extend the prior database of recommended hypersonic experiments (on four 2D and two 3D shock-interaction geometries) by adding three new geometries. The first two geometries, the flat plate/cylinder and the sharp cone, are canonical, zero-pressure gradient flows which are amenable to theory-based correlations, and these correlations are discussed in detail. The third geometry added is the 2D shock impinging on a turbulent flat plate boundary layer. The current 2D hypersonic database for shock-interaction flows thus consists of nine experiments on five different geometries. The second goal of this study is to review and assess the validation usage of various turbulence models on the existing experimental database. Here we limit the scope to one- and two-equation turbulence models where integration to the wall is used (i.e., we omit studies involving wall functions). A methodology for validating turbulence models is given, followed by an extensive evaluation of the turbulence models on the current hypersonic experimental database. A total of 18 one- and two-equation turbulence models are reviewed, and results of turbulence model assessments for the six models that have been extensively applied to the hypersonic validation database are compiled and presented in graphical form. While some of the turbulence models do provide reasonable predictions for the surface pressure, the predictions for surface heat flux are generally poor, and often in error by a factor of four or more. In the vast majority of the turbulence model validation studies we review, the authors fail to adequately address the numerical accuracy of the simulations (i.e., discretization and iterative error) and the sensitivities of the model predictions to freestream turbulence quantities or near-wall y+ mesh spacing. We recommend new hypersonic experiments be conducted which (1) measure not only surface quantities but also mean and fluctuating quantities in the interaction region and (2) provide careful estimates of both random experimental uncertainties and correlated bias errors for the measured quantities and freestream conditions. For the turbulence models, we recommend that a wide-range of turbulence models (including newer models) be re-examined on the current hypersonic experimental database, including the more recent experiments. Any future turbulence model validation efforts should carefully assess the numerical accuracy and model sensitivities. In addition, model corrections (e.g., compressibility corrections) should be carefully examined for their effects on a standard, low-speed validation database. Finally, as new experiments or direct numerical simulation data become available with information on mean and fluctuating quantities, they should be used to improve the turbulence models and thus increase their predictive capability.

Role of Nigella sativa and Its Constituent Thymoquinone on Chemotherapy-Induced Nephrotoxicity: Evidences from Experimental Animal Studies

PubMed Central

Cascella, Marco; Palma, Giuseppe; Barbieri, Antonio; Bimonte, Sabrina; Amruthraj, Nagoth Joseph; Muzio, Maria Rosaria; del Vecchio, Vitale; Rea, Domenica; Falco, Michela; Luciano, Antonio; Arra, Claudio; Cuomo, Arturo

2017-01-01

Background: Most chemotherapeutic drugs are known to cause nephrotoxicity. Therefore, new strategies have been considered to prevent chemotherapy-induced nephrotoxicity. It is of note that Nigella sativa (NS), or its isolated compound Thymoquinone (TQ), has a potential role in combating chemotherapy-induced nephrotoxicity. AIM: To analyze and report the outcome of experimental animal studies on the protective effects of NS/TQ on chemotherapy-associated kidney complications. Design: Standard systematic review and narrative synthesis. Data Sources: MEDLINE, EMBASE databases were searched for relevant articles published up to March 2017. Additionally, a manual search was performed. Criteria for a study’s inclusion were: conducted in animals, systematic reviews and meta-analysis, containing data on nephroprotective effects of NS/TQ compared to a placebo or other substance. All strains and genders were included. Results: The database search yielded 71 studies, of which 12 (cisplatin-induced nephrotoxicity 8; methotrexate-induced nephrotoxicity 1; doxorubicin-induced nephrotoxicity 2; ifosfamide-induced nephrotoxicity 1) were included in this review. Conclusions: Experimental animal studies showed the protective effect of NS, or TQ, on chemotherapy-induced nephrotoxicity. These effects are caused by decreasing lipid peroxidation and increasing activity of antioxidant enzymes in renal tissue of chemotherapy-treated animals. PMID:28629150

DOMe: A deduplication optimization method for the NewSQL database backups

PubMed Central

Wang, Longxiang; Zhu, Zhengdong; Zhang, Xingjun; Wang, Yinfeng

2017-01-01

Reducing duplicated data of database backups is an important application scenario for data deduplication technology. NewSQL is an emerging database system and is now being used more and more widely. NewSQL systems need to improve data reliability by periodically backing up in-memory data, resulting in a lot of duplicated data. The traditional deduplication method is not optimized for the NewSQL server system and cannot take full advantage of hardware resources to optimize deduplication performance. A recent research pointed out that the future NewSQL server will have thousands of CPU cores, large DRAM and huge NVRAM. Therefore, how to utilize these hardware resources to optimize the performance of data deduplication is an important issue. To solve this problem, we propose a deduplication optimization method (DOMe) for NewSQL system backup. To take advantage of the large number of CPU cores in the NewSQL server to optimize deduplication performance, DOMe parallelizes the deduplication method based on the fork-join framework. The fingerprint index, which is the key data structure in the deduplication process, is implemented as pure in-memory hash table, which makes full use of the large DRAM in NewSQL system, eliminating the performance bottleneck problem of fingerprint index existing in traditional deduplication method. The H-store is used as a typical NewSQL database system to implement DOMe method. DOMe is experimentally analyzed by two representative backup data. The experimental results show that: 1) DOMe can reduce the duplicated NewSQL backup data. 2) DOMe significantly improves deduplication performance by parallelizing CDC algorithms. In the case of the theoretical speedup ratio of the server is 20.8, the speedup ratio of DOMe can achieve up to 18; 3) DOMe improved the deduplication throughput by 1.5 times through the pure in-memory index optimization method. PMID:29049307

EDDIX--a database of ionisation double differential cross sections.

PubMed

MacGibbon, J H; Emerson, S; Liamsuwan, T; Nikjoo, H

2011-02-01

The use of Monte Carlo track structure is a choice method in biophysical modelling and calculations. To precisely model 3D and 4D tracks, the cross section for the ionisation by an incoming ion, double differential in the outgoing electron energy and angle, is required. However, the double differential cross section cannot be theoretically modelled over the full range of parameters. To address this issue, a database of all available experimental data has been constructed. Currently, the database of Experimental Double Differential Ionisation Cross sections (EDDIX) contains over 1200 digitalised experimentally measured datasets from the 1960s to present date, covering all available ion species (hydrogen to uranium) and all available target species. Double differential cross sections are also presented with the aid of an eight parameter functions fitted to the cross sections. The parameters include projectile species and charge, target nuclear charge and atomic mass, projectile atomic mass and energy, electron energy and deflection angle. It is planned to freely distribute EDDIX and make it available to the radiation research community for use in the analytical and numerical modelling of track structure.

The dye-sensitized solar cell database.

PubMed

Venkatraman, Vishwesh; Raju, Rajesh; Oikonomopoulos, Solon P; Alsberg, Bjørn K

2018-04-03

Dye-sensitized solar cells (DSSCs) have garnered a lot of attention in recent years. The solar energy to power conversion efficiency of a DSSC is influenced by various components of the cell such as the dye, electrolyte, electrodes and additives among others leading to varying experimental configurations. A large number of metal-based and metal-free dye sensitizers have now been reported and tools using such data to indicate new directions for design and development are on the rise. DSSCDB, the first of its kind dye-sensitized solar cell database, aims to provide users with up-to-date information from publications on the molecular structures of the dyes, experimental details and reported measurements (efficiencies and spectral properties) and thereby facilitate a comprehensive and critical evaluation of the data. Currently, the DSSCDB contains over 4000 experimental observations spanning multiple dye classes such as triphenylamines, carbazoles, coumarins, phenothiazines, ruthenium and porphyrins. The DSSCDB offers a web-based, comprehensive source of property data for dye sensitized solar cells. Access to the database is available through the following URL: www.dyedb.com .

75 FR 53371 - Liquefied Natural Gas Facilities: Obtaining Approval of Alternative Vapor-Gas Dispersion Models

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-31

... factors as the approved models, are validated by experimental test data, and receive the Administrator's... stage of the MEP involves applying the model against a database of experimental test cases including..., particularly the requirement for validation by experimental test data. That guidance is based on the MEP's...

Expanding Academic Vocabulary with an Interactive On-Line Database

ERIC Educational Resources Information Center

Horst, Marlise; Cobb, Tom; Nicolae, Ioana

2005-01-01

University students used a set of existing and purpose-built on-line tools for vocabulary learning in an experimental ESL course. The resources included concordance, dictionary, cloze-builder, hypertext, and a database with interactive self-quizzing feature (all freely available at www.lextutor.ca). The vocabulary targeted for learning consisted…

A comprehensive and scalable database search system for metaproteomics.

PubMed

Chatterjee, Sandip; Stupp, Gregory S; Park, Sung Kyu Robin; Ducom, Jean-Christophe; Yates, John R; Su, Andrew I; Wolan, Dennis W

2016-08-16

Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations. Our approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed "Blazmass") to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy and allowing for a more in-depth characterization of the functional landscape of the samples. The combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomic search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis.

Analysis of the ecotoxicity data submitted within the framework of the REACH Regulation. Part 3. Experimental sediment toxicity assays.

PubMed

Cesnaitis, Romanas; Sobanska, Marta A; Versonnen, Bram; Sobanski, Tomasz; Bonnomet, Vincent; Tarazona, Jose V; De Coen, Wim

2014-03-15

For the first REACH registration deadline, companies have submitted registrations with relevant hazard and exposure information for substances at the highest tonnage level (above 1000 tonnes per year). At this tonnage level, information on the long-term toxicity of a substance to sediment organisms is required. There are a number of available test guidelines developed and accepted by various national/international organisations, which can be used to investigate long-term toxicity to sediment organisms. However instead of testing, registrants may also use other options to address toxicity to sediment organisms, e.g. weight of evidence approach, grouping of substances and read-across approaches, as well as substance-tailored exposure-driven testing. The current analysis of the data provided in ECHA database focuses on the test methods applied and the test organisms used in the experimental studies to assess long-term toxicity to sediment organisms. The main guidelines used for the testing of substances registered under REACH are the OECD guidelines and OSPAR Protocols on Methods for the Testing of Chemicals used in the Offshore Oil Industry: "Part A: A Sediment Bioassay using an Amphipod Corophium sp." explaining why one of the mostly used test organisms is the marine amphipod Corophium sp. In total, testing results with at least 40 species from seven phyla are provided in the database. However, it can be concluded that the ECHA database does not contain a high enough number of available experimental data on toxicity to sediment organisms for it to be used extensively by the scientific community (e.g. for development of non-testing methods to predict hazards to sediment organisms). © 2013.

Detection of co-eluted peptides using database search methods

PubMed Central

Alves, Gelio; Ogurtsov, Aleksey Y; Kwok, Siwei; Wu, Wells W; Wang, Guanghui; Shen, Rong-Fong; Yu, Yi-Kuo

2008-01-01

Background Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS2) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost. Results We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS2 spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods – SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS – in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides. Open peer review Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section. PMID:18597684

Genomics Portals: integrative web-platform for mining genomics data.

PubMed

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Quantitative x-ray photoelectron spectroscopy: Quadrupole effects, shake-up, Shirley background, and relative sensitivity factors from a database of true x-ray photoelectron spectra

NASA Astrophysics Data System (ADS)

Seah, M. P.; Gilmore, I. S.

2006-05-01

An analysis is provided of the x-ray photoelectron spectroscopy (XPS) intensities measured in the National Physical Laboratory (NPL) XPS database for 46 solid elements. This present analysis does not change our previous conclusions concerning the excellent correlation between experimental intensities, following deconvolving the spectra with angle-averaged reflection electron energy loss data, and the theoretical intensities involving the dipole approximation using Scofield’s cross sections. Here, more recent calculations for cross sections by Trzhaskovskaya involving quadrupole terms are evaluated and it is shown that their cross sections diverge from the experimental database results by up to a factor of 5. The quadrupole angular terms lead to small corrections that are close to our measurement limit but do appear to be supported in the present analysis. Measurements of the extent of shake-up for the 46 elements broadly agree with the calculations of Yarzhemsky but not in detail. The predicted constancy in the shake-up contribution by Yarzhemsky implies that the use of the Shirley background will lead to a peak area that is a constant fraction of the true peak area including the shake-up intensities. However, the measured variability of the shake-up contribution makes the Shirley background invalid for quantification except for situations where the sensitivity factors are from reference samples similar to those being analyzed.

Conformational flexibility of two RNA trimers explored by computational tools and database search.

PubMed

Fadrná, Eva; Koca, Jaroslav

2003-04-01

Two RNA sequences, AAA and AUG, were studied by the conformational search program CICADA and by molecular dynamics (MD) in the framework of the AMBER force field, and also via thorough PDB database search. CICADA was used to provide detailed information about conformers and conformational interconversions on the energy surfaces of the above molecules. Several conformational families were found for both sequences. Analysis of the results shows differences, especially between the energy of the single families, and also in flexibility and concerted conformational movement. Therefore, several MD trajectories (altogether 16 ns) were run to obtain more details about both the stability of conformers belonging to different conformational families and about the dynamics of the two systems. Results show that the trajectories strongly depend on the starting structure. When the MD start from the global minimum found by CICADA, they provide a stable run, while MD starting from another conformational family generates a trajectory where several different conformational families are visited. The results obtained by theoretical methods are compared with the thorough database search data. It is concluded that all except for the highest energy conformational families found in theoretical result also appear in experimental data. Registry numbers: adenylyl-(3' --> 5')-adenylyl-(3' --> 5')-adenosine [917-44-2] adenylyl-(3' --> 5')-uridylyl-(3' --> 5')-guanosine [3494-35-7].

The fifth plot of the Carcinogenic Potency Database: results of animal bioassays published in the general literature through 1988 and by the National Toxicology Program through 1989.

PubMed Central

Gold, L S; Manley, N B; Slone, T H; Garfinkel, G B; Rohrbach, L; Ames, B N

1993-01-01

This paper is the fifth plot of the Carcinogenic Potency Database (CPDB) that first appeared in this journal in 1984 (1-5). We report here results of carcinogenesis bioassays published in the general literature between January 1987 and December 1988, and in technical reports of the National Toxicology Program between July 1987 and December 1989. This supplement includes results of 412 long-term, chronic experiments of 147 test compounds and reports the same information about each experiment in the same plot format as the earlier papers: the species and strain of test animal, the route and duration of compound administration, dose level and other aspects of experimental protocol, histopathology and tumor incidence, TD50 (carcinogenic potency) and its statistical significance, dose response, author's opinion about carcinogenicity, and literature citation. We refer the reader to the 1984 publications (1,5,6) for a guide to the plot of the database, a complete description of the numerical index of carcinogenic potency, and a discussion of the sources of data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. The five plots of the database are to be used together, as results of individual experiments that were published earlier are not repeated. In all, the five plots include results of 4487 experiments on 1136 chemicals. Several analyses based on the CPDB that were published earlier are described briefly, and updated results based on all five plots are given for the following earlier analyses: the most potent TD50 value by species, reproducibility of bioassay results, positivity rates, and prediction between species.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8354183

TAMEE: data management and analysis for tissue microarrays.

PubMed

Thallinger, Gerhard G; Baumgartner, Kerstin; Pirklbauer, Martin; Uray, Martina; Pauritsch, Elke; Mehes, Gabor; Buck, Charles R; Zatloukal, Kurt; Trajanoski, Zlatko

2007-03-07

With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories. TAMEE (Tissue Array Management and Evaluation Environment) is a web-based database application for the management and analysis of data resulting from the production and application of TMAs. It facilitates storage of production and experimental parameters, of images generated throughout the TMA workflow, and of results from core evaluation. Database content consistency is achieved using structured classifications of parameters. This allows the extraction of high quality results for subsequent biologically-relevant data analyses. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be evaluated using a set of predefined analysis algorithms. Additional evaluation algorithms can be easily integrated into the application via a plug-in interface. Downstream analysis of results is facilitated via a flexible query generator. We have developed an integrated system tailored to the specific needs of research projects using high density TMAs. It covers the complete workflow of TMA production, experimental use and subsequent analysis. The system is freely available for academic and non-profit institutions from http://genome.tugraz.at/Software/TAMEE.

Development of the Orion Crew Module Static Aerodynamic Database. Part 1; Hypersonic

NASA Technical Reports Server (NTRS)

Bibb, Karen L.; Walker, Eric L.; Robinson, Philip E.

2011-01-01

The Orion aerodynamic database provides force and moment coefficients given the velocity, attitude, configuration, etc. of the Crew Exploration Vehicle (CEV). The database is developed and maintained by the NASA CEV Aerosciences Project team from computational and experimental aerodynamic simulations. The database is used primarily by the Guidance, Navigation, and Control (GNC) team to design vehicle trajectories and assess flight performance. The initial hypersonic re-entry portion of the Crew Module (CM) database was developed in 2006. Updates incorporating additional data and improvements to the database formulation and uncertainty methodologies have been made since then. This paper details the process used to develop the CM database, including nominal values and uncertainties, for Mach numbers greater than 8 and angles of attack between 140deg and 180deg. The primary available data are more than 1000 viscous, reacting gas chemistry computational simulations using both the Laura and Dplr codes, over a range of Mach numbers from 2 to 37 and a range of angles of attack from 147deg to 172deg. Uncertainties were based on grid convergence, laminar-turbulent solution variations, combined altitude and code-to-code variations, and expected heatshield asymmetry. A radial basis function response surface tool, NEAR-RS, was used to fit the coefficient data smoothly in a velocity-angle-of-attack space. The resulting database is presented and includes some data comparisons and a discussion of the predicted variation of trim angle of attack and lift-to-drag ratio. The database provides a variation in trim angle of attack on the order of +/-2deg, and a range in lift-to-drag ratio of +/-0.035 for typical vehicle flight conditions.

Validation of Shielding Analysis Capability of SuperMC with SINBAD

NASA Astrophysics Data System (ADS)

Chen, Chaobin; Yang, Qi; Wu, Bin; Han, Yuncheng; Song, Jing

2017-09-01

Abstract: The shielding analysis capability of SuperMC was validated with the Shielding Integral Benchmark Archive Database (SINBAD). The SINBAD was compiled by RSICC and NEA, it includes numerous benchmark experiments performed with the D-T fusion neutron source facilities of OKTAVIAN, FNS, IPPE, etc. The results from SuperMC simulation were compared with experimental data and MCNP results. Very good agreement with deviation lower than 1% was achieved and it suggests that SuperMC is reliable in shielding calculation.

The NUBASE2016 evaluation of nuclear properties

NASA Astrophysics Data System (ADS)

Audi, G.; Kondev, F. G.; Wang, Meng; Huang, W. J.; Naimi, S.

2017-03-01

This paper presents the NUBASE2016 evaluation that contains the recommended values for nuclear and decay properties of 3437 nuclides in their ground and excited isomeric (T1/2 >= 100 ns) states. All nuclides for which any experimental information is known were considered. NUBASE2016 covers all data published by October 2016 in primary (journal articles) and secondary (mainly laboratory reports and conference proceedings) references, together with the corresponding bibliographical information. During the development of NUBASE2016, the data available in the 'Evaluated Nuclear Structure Data File' (ENSDF) database were consulted and critically assessed for their validity and completeness. Furthermore, a large amount of new data and some older experimental results that were missing from ENSDF were compiled, evaluated and included in NUBASE2016. The atomic mass values were taken from the 'Atomic Mass Evaluation' (AME2016, second and third parts of the present issue). In cases where no experimental data were available for a particular nuclide, trends in the behavior of specific properties in neighboring nuclides (TNN) were examined. This approach allowed to estimate values for a range of properties that are labeled in NUBASE2016 as 'non-experimental' (flagged '#'). Evaluation procedures and policies used during the development of this database are presented, together with a detailed table of recommended values and their uncertainties. AMDC: http://amdc.impcas.ac.cn/ Contents The NUBASE2016 evaluation of nuclear propertiesAcrobat PDF (1.1 MB) Table I. The NUBASE2016 table of nuclear and decay propertiesAcrobat PDF (706 KB)

Temperature Dependence of Mineral Solubility in Water. Part 3. Alkaline and Alkaline Earth Sulfates

NASA Astrophysics Data System (ADS)

Krumgalz, B. S.

2018-06-01

The databases of alkaline and alkaline earth sulfate solubilities in water at various temperatures were created using experimental data from the publications over about the last two centuries. Statistical critical evaluation of the created databases was produced since there were enough independent data sources to justify such evaluation. The reliable experimental data were adequately described by polynomial expressions over various temperature ranges. Using the Pitzer approach for ionic activity and osmotic coefficients, the thermodynamic solubility products for the discussed minerals have been calculated at various temperatures and represented by polynomial expressions.

Temperature Dependence of Mineral Solubility in Water. Part 2. Alkaline and Alkaline Earth Bromides

NASA Astrophysics Data System (ADS)

Krumgalz, B. S.

2018-03-01

Databases of alkaline and alkaline earth bromide solubilities in water at various temperatures were created using experimental data from publications over about the last two centuries. Statistical critical evaluation of the created databases was produced since there were enough independent data sources to justify such evaluation. The reliable experimental data were adequately described by polynomial expressions over various temperature ranges. Using the Pitzer approach for ionic activity and osmotic coefficients, the thermodynamic solubility products for the discussed bromide minerals have been calculated at various temperature intervals and also represented by polynomial expressions.

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.

PubMed

Hitz, Benjamin C; Rowe, Laurence D; Podduturi, Nikhil R; Glick, David I; Baymuradov, Ulugbek K; Malladi, Venkat S; Chan, Esther T; Davidson, Jean M; Gabdank, Idan; Narayana, Aditi K; Onate, Kathrina C; Hilton, Jason; Ho, Marcus C; Lee, Brian T; Miyasato, Stuart R; Dreszer, Timothy R; Sloan, Cricket A; Strattan, J Seth; Tanaka, Forrest Y; Hong, Eurie L; Cherry, J Michael

2017-01-01

The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, unified processing, and distribution to community resources and the scientific community. As the volume of data increases, the identification and organization of experimental details becomes increasingly intricate and demands careful curation. The ENCODE DCC has created a general purpose software system, known as SnoVault, that supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata. The software is fully open-source, code and installation instructions can be found at: http://github.com/ENCODE-DCC/snovault/ (for the generic database) and http://github.com/ENCODE-DCC/encoded/ to store genomic data in the manner of ENCODE. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data) has been released as a separate Python package.

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

PubMed Central

Podduturi, Nikhil R.; Glick, David I.; Baymuradov, Ulugbek K.; Malladi, Venkat S.; Chan, Esther T.; Davidson, Jean M.; Gabdank, Idan; Narayana, Aditi K.; Onate, Kathrina C.; Hilton, Jason; Ho, Marcus C.; Lee, Brian T.; Miyasato, Stuart R.; Dreszer, Timothy R.; Sloan, Cricket A.; Strattan, J. Seth; Tanaka, Forrest Y.; Hong, Eurie L.; Cherry, J. Michael

2017-01-01

The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, unified processing, and distribution to community resources and the scientific community. As the volume of data increases, the identification and organization of experimental details becomes increasingly intricate and demands careful curation. The ENCODE DCC has created a general purpose software system, known as SnoVault, that supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata. The software is fully open-source, code and installation instructions can be found at: http://github.com/ENCODE-DCC/snovault/ (for the generic database) and http://github.com/ENCODE-DCC/encoded/ to store genomic data in the manner of ENCODE. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data) has been released as a separate Python package. PMID:28403240

Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants.

PubMed

Gromiha, M Michael; Anoosha, P; Huang, Liang-Tsung

2016-01-01

Protein stability is the free energy difference between unfolded and folded states of a protein, which lies in the range of 5-25 kcal/mol. Experimentally, protein stability is measured with circular dichroism, differential scanning calorimetry, and fluorescence spectroscopy using thermal and denaturant denaturation methods. These experimental data have been accumulated in the form of a database, ProTherm, thermodynamic database for proteins and mutants. It also contains sequence and structure information of a protein, experimental methods and conditions, and literature information. Different features such as search, display, and sorting options and visualization tools have been incorporated in the database. ProTherm is a valuable resource for understanding/predicting the stability of proteins and it can be accessed at http://www.abren.net/protherm/ . ProTherm has been effectively used to examine the relationship among thermodynamics, structure, and function of proteins. We describe the recent progress on the development of methods for understanding/predicting protein stability, such as (1) general trends on mutational effects on stability, (2) relationship between the stability of protein mutants and amino acid properties, (3) applications of protein three-dimensional structures for predicting their stability upon point mutations, (4) prediction of protein stability upon single mutations from amino acid sequence, and (5) prediction methods for addressing double mutants. A list of online resources for predicting has also been provided.

A review and experimental study on the application of classifiers and evolutionary algorithms in EEG-based brain-machine interface systems

NASA Astrophysics Data System (ADS)

Tahernezhad-Javazm, Farajollah; Azimirad, Vahid; Shoaran, Maryam

2018-04-01

Objective. Considering the importance and the near-future development of noninvasive brain-machine interface (BMI) systems, this paper presents a comprehensive theoretical-experimental survey on the classification and evolutionary methods for BMI-based systems in which EEG signals are used. Approach. The paper is divided into two main parts. In the first part, a wide range of different types of the base and combinatorial classifiers including boosting and bagging classifiers and evolutionary algorithms are reviewed and investigated. In the second part, these classifiers and evolutionary algorithms are assessed and compared based on two types of relatively widely used BMI systems, sensory motor rhythm-BMI and event-related potentials-BMI. Moreover, in the second part, some of the improved evolutionary algorithms as well as bi-objective algorithms are experimentally assessed and compared. Main results. In this study two databases are used, and cross-validation accuracy (CVA) and stability to data volume (SDV) are considered as the evaluation criteria for the classifiers. According to the experimental results on both databases, regarding the base classifiers, linear discriminant analysis and support vector machines with respect to CVA evaluation metric, and naive Bayes with respect to SDV demonstrated the best performances. Among the combinatorial classifiers, four classifiers, Bagg-DT (bagging decision tree), LogitBoost, and GentleBoost with respect to CVA, and Bagging-LR (bagging logistic regression) and AdaBoost (adaptive boosting) with respect to SDV had the best performances. Finally, regarding the evolutionary algorithms, single-objective invasive weed optimization (IWO) and bi-objective nondominated sorting IWO algorithms demonstrated the best performances. Significance. We present a general survey on the base and the combinatorial classification methods for EEG signals (sensory motor rhythm and event-related potentials) as well as their optimization methods through the evolutionary algorithms. In addition, experimental and statistical significance tests are carried out to study the applicability and effectiveness of the reviewed methods.

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

PubMed

Slenter, Denise N; Kutmon, Martina; Hanspers, Kristina; Riutta, Anders; Windsor, Jacob; Nunes, Nuno; Mélius, Jonathan; Cirillo, Elisa; Coort, Susan L; Digles, Daniela; Ehrhart, Friederike; Giesbertz, Pieter; Kalafati, Marianthi; Martens, Marvin; Miller, Ryan; Nishida, Kozo; Rieswijk, Linda; Waagmeester, Andra; Eijssen, Lars M T; Evelo, Chris T; Pico, Alexander R; Willighagen, Egon L

2018-01-04

WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

High-performance Negative Database for Massive Data Management System of The Mingantu Spectral Radioheliograph

NASA Astrophysics Data System (ADS)

Shi, Congming; Wang, Feng; Deng, Hui; Liu, Yingbo; Liu, Cuiyin; Wei, Shoulin

2017-08-01

As a dedicated synthetic aperture radio interferometer in China, the MingantU SpEctral Radioheliograph (MUSER), initially known as the Chinese Spectral RadioHeliograph (CSRH), has entered the stage of routine observation. More than 23 million data records per day need to be effectively managed to provide high-performance data query and retrieval for scientific data reduction. In light of these massive amounts of data generated by the MUSER, in this paper, a novel data management technique called the negative database (ND) is proposed and used to implement a data management system for the MUSER. Based on the key-value database, the ND technique makes complete utilization of the complement set of observational data to derive the requisite information. Experimental results showed that the proposed ND can significantly reduce storage volume in comparison with a relational database management system (RDBMS). Even when considering the time needed to derive records that were absent, its overall performance, including querying and deriving the data of the ND, is comparable with that of a relational database management system (RDBMS). The ND technique effectively solves the problem of massive data storage for the MUSER and is a valuable reference for the massive data management required in next-generation telescopes.

Gaze-fixation to happy faces predicts mood repair after a negative mood induction.

PubMed

Sanchez, Alvaro; Vazquez, Carmelo; Gomez, Diego; Joormann, Jutta

2014-02-01

The present study tested the interplay between mood and attentional deployment by examining attention to positive (i.e., happy faces) and negative (i.e., angry and sad faces) stimuli in response to experimental inductions of sad and happy mood. Participants underwent a negative, neutral, or positive mood induction procedure (MIP) which was followed by an assessment of their attentional deployment to emotional faces using eye-tracking technology. Faces were selected from the Karolinska Directed Emotional Faces (KDEF) database (Lundqvist, Flykt, & Öhman, 1998). In the positive MIP condition, analyses revealed a mood-congruent relation between positive mood and greater attentional deployment to happy faces. In the negative MIP condition, however, analyses revealed a mood-incongruent relation between increased negative mood and greater attentional deployment to happy faces. Furthermore, attentional deployment to happy faces after the negative MIP predicted participants' mood recovery at the end of the experimental session. These results suggest that attentional processing of positive information may play a role in mood repair, which may have important clinical implications. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Effect of digluconate chlorhexidine on bond strength between dental adhesive systems and dentin: A systematic review.

PubMed

Dionysopoulos, Dimitrios

2016-01-01

This study aimed to systematically review the literature for the effect of digluconate chlorhexidine (CHX) on bond strength between dental adhesive systems and dentin of composite restorations. The electronic databases that were searched to identify manuscripts for inclusion were Medline via PubMed and Google search engine. The search strategies were computer search of the database and review of reference lists of the related articles. Search words/terms were as follows: (digluconate chlorhexidine*) AND (dentin* OR adhesive system* OR bond strength*). Bond strength reduction after CHX treatments varied among the studies, ranging 0-84.9%. In most of the studies, pretreatment CHX exhibited lower bond strength reduction than the control experimental groups. Researchers who previously investigated the effect of CHX on the bond strength of dental adhesive systems on dentin have reported contrary results, which may be attributed to different experimental methods, different designs of the experiments, and different materials investigated. Further investigations, in particular clinical studies, would be necessary to clarify the effect of CHX on the longevity of dentin bonds.

Nuclear astrophysics in the laboratory and in the universe

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

Champagne, A. E., E-mail: artc@physics.unc.edu; Iliadis, C.; Longland, R.

Nuclear processes drive stellar evolution and so nuclear physics, stellar models and observations together allow us to describe the inner workings of stars and their life stories. This Information on nuclear reaction rates and nuclear properties are critical ingredients in addressing most questions in astrophysics and often the nuclear database is incomplete or lacking the needed precision. Direct measurements of astrophysically-interesting reactions are necessary and the experimental focus is on improving both sensitivity and precision. In the following, we review recent results and approaches taken at the Laboratory for Experimental Nuclear Astrophysics (LENA, http://research.physics.unc.edu/project/nuclearastro/Welcome.html )

Word-addressable holographic memory using symbolic substitution and SLRs

NASA Astrophysics Data System (ADS)

McAulay, Alastair D.; Wang, Junqing

1990-12-01

A heteroassociative memory is proposed that allows a key word in a dictionary of key words to be used to recall an associated holographic image in a database of images. Symbolic substitution search finds the word sought in a dictionary of key words and generates a beam that selects the corresponding holographic image from a directory of images. In this case, symbolic substitution is used to orthogonalize the key words. Spatial light rebroadcasters are proposed for the key word database. Experimental results demonstrate that symbolic substitution will enable a holographic image to be selected and reconstructed. In the case considered, a holographic image having over 40,000-bits is selected out of eight by using a key word from a dictionary of eight words.

The improved Apriori algorithm based on matrix pruning and weight analysis

NASA Astrophysics Data System (ADS)

Lang, Zhenhong

2018-04-01

This paper uses the matrix compression algorithm and weight analysis algorithm for reference and proposes an improved matrix pruning and weight analysis Apriori algorithm. After the transactional database is scanned for only once, the algorithm will construct the boolean transaction matrix. Through the calculation of one figure in the rows and columns of the matrix, the infrequent item set is pruned, and a new candidate item set is formed. Then, the item's weight and the transaction's weight as well as the weight support for items are calculated, thus the frequent item sets are gained. The experimental result shows that the improved Apriori algorithm not only reduces the number of repeated scans of the database, but also improves the efficiency of data correlation mining.

Nuclear Data Matters - The obvious case of a bad mixing ratio for 58Co

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

Hoffman, R. D.; Nesaraja, Caroline D.; Mattoon, Caleb

We present results of modeled cross sections for neutron- and proton-induced reactions leading to the final product nucleus 58Co. In each case the gamma-cascade branching ratios given in the ENSDF database circa 2014 predict modeled nuclear cross sections leading to the ground and first excited metastable state that are incompatible with measured cross sections found in the NNDC experimental cross section database EXFOR. We show that exploring the uncertainty in the mixing ratio used to calculate the gamma-cascade branching ratios for the 53.15 keV 2 nd excited state leads to changes in the predicted partial cross sections by amounts thatmore » give good agreement with measured data.« less

An Integrated In Silico Method to Discover Novel Rock1 Inhibitors: Multi- Complex-Based Pharmacophore, Molecular Dynamics Simulation and Hybrid Protocol Virtual Screening.

PubMed

Chen, Haining; Li, Sijia; Hu, Yajiao; Chen, Guo; Jiang, Qinglin; Tong, Rongsheng; Zang, Zhihe; Cai, Lulu

2016-01-01

Rho-associated, coiled-coil containing protein kinase 1 (ROCK1) is an important regulator of focal adhesion, actomyosin contraction and cell motility. In this manuscript, a combination of the multi-complex-based pharmacophore (MCBP), molecular dynamics simulation and a hybrid protocol of a virtual screening method, comprised of multipharmacophore- based virtual screening (PBVS) and ensemble docking-based virtual screening (DBVS) methods were used for retrieving novel ROCK1 inhibitors from the natural products database embedded in the ZINC database. Ten hit compounds were selected from the hit compounds, and five compounds were tested experimentally. Thus, these results may provide valuable information for further discovery of more novel ROCK1 inhibitors.

Mini-DIAL system measurements coupled with multivariate data analysis to identify TIC and TIM simulants: preliminary absorption database analysis.

NASA Astrophysics Data System (ADS)

Gaudio, P.; Malizia, A.; Gelfusa, M.; Martinelli, E.; Di Natale, C.; Poggi, L. A.; Bellecci, C.

2017-01-01

Nowadays Toxic Industrial Components (TICs) and Toxic Industrial Materials (TIMs) are one of the most dangerous and diffuse vehicle of contamination in urban and industrial areas. The academic world together with the industrial and military one are working on innovative solutions to monitor the diffusion in atmosphere of such pollutants. In this phase the most common commercial sensors are based on “point detection” technology but it is clear that such instruments cannot satisfy the needs of the smart cities. The new challenge is developing stand-off systems to continuously monitor the atmosphere. Quantum Electronics and Plasma Physics (QEP) research group has a long experience in laser system development and has built two demonstrators based on DIAL (Differential Absorption of Light) technology could be able to identify chemical agents in atmosphere. In this work the authors will present one of those DIAL system, the miniaturized one, together with the preliminary results of an experimental campaign conducted on TICs and TIMs simulants in cell with aim of use the absorption database for the further atmospheric an analysis using the same DIAL system. The experimental results are analysed with standard multivariate data analysis technique as Principal Component Analysis (PCA) to develop a classification model aimed at identifying organic chemical compound in atmosphere. The preliminary results of absorption coefficients of some chemical compound are shown together pre PCA analysis.

Age 60 Study. Part 1. Bibliographic Database

DTIC Science & Technology

1994-10-01

seven of these aircraft types participated in a spectacle design study. Experimental spectacles were designed for each pilot and evaluated for...observation flight administered by observers who were uninformed of the details of the experimental design . Students and instructors also completed a critique...intraindividual lability in field-dependence-field independence, and (4) various measurement, sampling, and experimental design concerns associated

Upper Washita River experimental watersheds: Sediment Database

USDA-ARS?s Scientific Manuscript database

Improving the scientific understanding of the effectiveness of watershed conservation practices and floodwater-retardation structures to control floods and soil erosion is one of the primary objectives for sediment studies in the upper Washita River Experimental Watersheds. This paper summarizes se...

Monitoring of small laboratory animal experiments by a designated web-based database.

PubMed

Frenzel, T; Grohmann, C; Schumacher, U; Krüll, A

2015-10-01

Multiple-parametric small animal experiments require, by their very nature, a sufficient number of animals which may need to be large to obtain statistically significant results.(1) For this reason database-related systems are required to collect the experimental data as well as to support the later (re-) analysis of the information gained during the experiments. In particular, the monitoring of animal welfare is simplified by the inclusion of warning signals (for instance, loss in body weight >20%). Digital patient charts have been developed for human patients but are usually not able to fulfill the specific needs of animal experimentation. To address this problem a unique web-based monitoring system using standard MySQL, PHP, and nginx has been created. PHP was used to create the HTML-based user interface and outputs in a variety of proprietary file formats, namely portable document format (PDF) or spreadsheet files. This article demonstrates its fundamental features and the easy and secure access it offers to the data from any place using a web browser. This information will help other researchers create their own individual databases in a similar way. The use of QR-codes plays an important role for stress-free use of the database. We demonstrate a way to easily identify all animals and samples and data collected during the experiments. Specific ways to record animal irradiations and chemotherapy applications are shown. This new analysis tool allows the effective and detailed analysis of huge amounts of data collected through small animal experiments. It supports proper statistical evaluation of the data and provides excellent retrievable data storage. © The Author(s) 2015.

Integral nuclear data validation using experimental spent nuclear fuel compositions

DOE PAGES

Gauld, Ian C.; Williams, Mark L.; Michel-Sendis, Franco; ...

2017-07-19

Measurements of the isotopic contents of spent nuclear fuel provide experimental data that are a prerequisite for validating computer codes and nuclear data for many spent fuel applications. Under the auspices of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) and guidance of the Expert Group on Assay Data of Spent Nuclear Fuel of the NEA Working Party on Nuclear Criticality Safety, a new database of expanded spent fuel isotopic compositions has been compiled. The database, Spent Fuel Compositions (SFCOMPO) 2.0, includes measured data for more than 750 fuel samples acquired from 44 different reactors andmore » representing eight different reactor technologies. Measurements for more than 90 isotopes are included. This new database provides data essential for establishing the reliability of code systems for inventory predictions, but it also has broader potential application to nuclear data evaluation. Furthermore, the database, together with adjoint based sensitivity and uncertainty tools for transmutation systems developed to quantify the importance of nuclear data on nuclide concentrations, are described.« less

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

Integral nuclear data validation using experimental spent nuclear fuel compositions

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

Gauld, Ian C.; Williams, Mark L.; Michel-Sendis, Franco

Measurements of the isotopic contents of spent nuclear fuel provide experimental data that are a prerequisite for validating computer codes and nuclear data for many spent fuel applications. Under the auspices of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) and guidance of the Expert Group on Assay Data of Spent Nuclear Fuel of the NEA Working Party on Nuclear Criticality Safety, a new database of expanded spent fuel isotopic compositions has been compiled. The database, Spent Fuel Compositions (SFCOMPO) 2.0, includes measured data for more than 750 fuel samples acquired from 44 different reactors andmore » representing eight different reactor technologies. Measurements for more than 90 isotopes are included. This new database provides data essential for establishing the reliability of code systems for inventory predictions, but it also has broader potential application to nuclear data evaluation. Furthermore, the database, together with adjoint based sensitivity and uncertainty tools for transmutation systems developed to quantify the importance of nuclear data on nuclide concentrations, are described.« less

A comparative cellular and molecular biology of longevity database.

PubMed

Stuart, Jeffrey A; Liang, Ping; Luo, Xuemei; Page, Melissa M; Gallagher, Emily J; Christoff, Casey A; Robb, Ellen L

2013-10-01

Discovering key cellular and molecular traits that promote longevity is a major goal of aging and longevity research. One experimental strategy is to determine which traits have been selected during the evolution of longevity in naturally long-lived animal species. This comparative approach has been applied to lifespan research for nearly four decades, yielding hundreds of datasets describing aspects of cell and molecular biology hypothesized to relate to animal longevity. Here, we introduce a Comparative Cellular and Molecular Biology of Longevity Database, available at ( http://genomics.brocku.ca/ccmbl/ ), as a compendium of comparative cell and molecular data presented in the context of longevity. This open access database will facilitate the meta-analysis of amalgamated datasets using standardized maximum lifespan (MLSP) data (from AnAge). The first edition contains over 800 data records describing experimental measurements of cellular stress resistance, reactive oxygen species metabolism, membrane composition, protein homeostasis, and genome homeostasis as they relate to vertebrate species MLSP. The purpose of this review is to introduce the database and briefly demonstrate its use in the meta-analysis of combined datasets.

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.

Asteroid surface processes: Experimental studies of the solar wind on reflectance and optical properties of asteroids

NASA Technical Reports Server (NTRS)

Mcfadden, Lucy-Ann

1991-01-01

The effect of the solar wind on the optical properties of meteorites was studied to determine whether the solar wind can alter the properties of ordinary chondrite parent bodies resulting in the spectral properties of S-type asteroids. The existing database of optical properties of asteroids was analyzed to determine the effect of solar wind in altering asteroid surface properties.

Offline signature verification using convolution Siamese network

NASA Astrophysics Data System (ADS)

Xing, Zi-Jian; Yin, Fei; Wu, Yi-Chao; Liu, Cheng-Lin

2018-04-01

This paper presents an offline signature verification approach using convolutional Siamese neural network. Unlike the existing methods which consider feature extraction and metric learning as two independent stages, we adopt a deepleaning based framework which combines the two stages together and can be trained end-to-end. The experimental results on two offline public databases (GPDSsynthetic and CEDAR) demonstrate the superiority of our method on the offline signature verification problem.

Modelling Precipitation Kinetics During Aging of Al-Mg-Si Alloys

NASA Astrophysics Data System (ADS)

Du, Qiang; Friis, Jepser

A classical Kaufmann-Wagner numerical model is employed to predict the evolution of precipitate size distribution during the aging treatment of Al-Mg-Si alloys. One feature of the model is its fully coupling with CALPHAD database, and with the input of interfacial energy from ab-initial calculation, it is able to capture the morphological change of the precipitates. The simulation results will be compared with the experimental measurements.

An Automated Ab Initio Framework for Identifying New Ferroelectrics

NASA Astrophysics Data System (ADS)

Smidt, Tess; Reyes-Lillo, Sebastian E.; Jain, Anubhav; Neaton, Jeffrey B.

Ferroelectric materials have a wide-range of technological applications including non-volatile RAM and optoelectronics. In this work, we present an automated first-principles search for ferroelectrics. We integrate density functional theory, crystal structure databases, symmetry tools, workflow software, and a custom analysis toolkit to build a library of known and proposed ferroelectrics. We screen thousands of candidates using symmetry relations between nonpolar and polar structure pairs. We use two search strategies 1) polar-nonpolar pairs with the same composition and 2) polar-nonpolar structure type pairs. Results are automatically parsed, stored in a database, and accessible via a web interface showing distortion animations and plots of polarization and total energy as a function of distortion. We benchmark our results against experimental data, present new ferroelectric candidates found through our search, and discuss future work on expanding this search methodology to other material classes such as anti-ferroelectrics and multiferroics.

A High Temperature Cyclic Oxidation Data Base for Selected Materials Tested at NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Barrett, Charles A.

2003-01-01

The cyclic oxidation test results for some 1000 high temperature commercial and experimental alloys have been collected in an EXCEL database. This database represents over thirty years of research at NASA Glenn Research Center in Cleveland, Ohio. The data is in the form of a series of runs of specific weight change versus time values for a set of samples tested at a given temperature, cycle time, and exposure time. Included on each run is a set of embedded plots of the critical data. The nature of the data is discussed along with analysis of the cyclic oxidation process. In addition examples are given as to how a set of results can be analyzed. The data is assembled on a read-only compact disk which is available on request from Materials Durability Branch, NASA Glenn Research Center, Cleveland, Ohio.

Towards the Truly Predictive 3D Modeling of Recrystallization and Grain Growth in Advanced Technical Alloys

DTIC Science & Technology

2010-06-11

MODELING WITH IMPLEMENTED GBI AND MD DATA (STEADY STATE GB MIGRATION) PAGE 48 5. FORMATION AND ANALYSIS OF GB PROPERTIES DATABASE PAGE 53 5.1...Relative GB energy for specified GBM averaged on possible GBIs PAGE 53 5.2. Database validation on available experimental data PAGE 56 5.3. Comparison...PAGE 70 Fig. 6.11. MC Potts Rex. and GG software: (a) modeling volume analysis; (b) searching for GB energy value within included database . PAGE

The Web-Based DNA Vaccine Database DNAVaxDB and Its Usage for Rational DNA Vaccine Design.

PubMed

Racz, Rebecca; He, Yongqun

2016-01-01

A DNA vaccine is a vaccine that uses a mammalian expression vector to express one or more protein antigens and is administered in vivo to induce an adaptive immune response. Since the 1990s, a significant amount of research has been performed on DNA vaccines and the mechanisms behind them. To meet the needs of the DNA vaccine research community, we created DNAVaxDB ( http://www.violinet.org/dnavaxdb ), the first Web-based database and analysis resource of experimentally verified DNA vaccines. All the data in DNAVaxDB, which includes plasmids, antigens, vaccines, and sources, is manually curated and experimentally verified. This chapter goes over the detail of DNAVaxDB system and shows how the DNA vaccine database, combined with the Vaxign vaccine design tool, can be used for rational design of a DNA vaccine against a pathogen, such as Mycobacterium bovis.

RAIN: RNA–protein Association and Interaction Networks

PubMed Central

Junge, Alexander; Refsgaard, Jan C.; Garde, Christian; Pan, Xiaoyong; Santos, Alberto; Alkan, Ferhat; Anthon, Christian; von Mering, Christian; Workman, Christopher T.; Jensen, Lars Juhl; Gorodkin, Jan

2017-01-01

Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA–RNA and ncRNA–protein interactions and its integration with the STRING database of protein–protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessible web interface and all interaction data can be downloaded. Database URL: http://rth.dk/resources/rain PMID:28077569

Novel Hybrid Virtual Screening Protocol Based on Molecular Docking and Structure-Based Pharmacophore for Discovery of Methionyl-tRNA Synthetase Inhibitors as Antibacterial Agents

PubMed Central

Liu, Chi; He, Gu; Jiang, Qinglin; Han, Bo; Peng, Cheng

2013-01-01

Methione tRNA synthetase (MetRS) is an essential enzyme involved in protein biosynthesis in all living organisms and is a potential antibacterial target. In the current study, the structure-based pharmacophore (SBP)-guided method has been suggested to generate a comprehensive pharmacophore of MetRS based on fourteen crystal structures of MetRS-inhibitor complexes. In this investigation, a hybrid protocol of a virtual screening method, comprised of pharmacophore model-based virtual screening (PBVS), rigid and flexible docking-based virtual screenings (DBVS), is used for retrieving new MetRS inhibitors from commercially available chemical databases. This hybrid virtual screening approach was then applied to screen the Specs (202,408 compounds) database, a structurally diverse chemical database. Fifteen hit compounds were selected from the final hits and shifted to experimental studies. These results may provide important information for further research of novel MetRS inhibitors as antibacterial agents. PMID:23839093

PDB-wide collection of binding data: current status of the PDBbind database.

PubMed

Liu, Zhihai; Li, Yan; Han, Li; Li, Jie; Liu, Jie; Zhao, Zhixiong; Nie, Wei; Liu, Yuchen; Wang, Renxiao

2015-02-01

Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank (PDB). It thus provides the linkage between structural information and energetic properties of biomolecular complexes, which is especially desirable for computational studies or statistical analyses. Since its first public release in 2004, the PDBbind database has been updated on an annual basis. The latest release (version 2013) provides experimental binding affinity data for 10,776 biomolecular complexes in PDB, including 8302 protein-ligand complexes and 2474 other types of complexes. In this article, we will describe the current methods used for compiling PDBbind and the updated status of this database. We will also review some typical applications of PDBbind published in the scientific literature. All contents of this database are freely accessible at the PDBbind-CN Web server at http://www.pdbbind-cn.org/. wangrx@mail.sioc.ac.cn. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

BμG@Sbase—a microbial gene expression and comparative genomic database

PubMed Central

Witney, Adam A.; Waldron, Denise E.; Brooks, Lucy A.; Tyler, Richard H.; Withers, Michael; Stoker, Neil G.; Wren, Brendan W.; Butcher, Philip D.; Hinds, Jason

2012-01-01

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future. PMID:21948792

BμG@Sbase--a microbial gene expression and comparative genomic database.

PubMed

Witney, Adam A; Waldron, Denise E; Brooks, Lucy A; Tyler, Richard H; Withers, Michael; Stoker, Neil G; Wren, Brendan W; Butcher, Philip D; Hinds, Jason

2012-01-01

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future.

Cyclotron production of 48V via natTi(d,x)48V nuclear reaction; a promising radionuclide

NASA Astrophysics Data System (ADS)

Usman, A. R.; Khandaker, M. U.; Haba, H.

2017-06-01

In this experimental work, we studied the excitation function of natTi(d,x)48V nuclear reactions from 24 MeV down to threshold energy. Natural titanium foils were arranged in the popular stacked-foil method and activated with deuteron beam generated from an AVF cyclotron at RIKEN, Wako, Japan. The emitted γ activities from the activated foils were measured using an offline γ-ray spectrometry. The present results were analyzed, compared with earlier published experimental data and also with the evaluated data of Talys code. Our new measured data agree with some of the earlier reported experimental data while a partial agreement is found with the evaluated theoretical data. In addition to the use of 48V as a beam intensity monitor, recent studies indicate its potentials as calibrating source in PET cameras and also as a (radioactive) label for medical applications. The results are also expected to further enrich the experimental database and also to play an important role in nuclear reactions model codes design.

RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary.

PubMed

Akiyama, Kenji; Kurotani, Atsushi; Iida, Kei; Kuromori, Takashi; Shinozaki, Kazuo; Sakurai, Tetsuya

2014-01-01

Arabidopsis thaliana is one of the most popular experimental plants. However, only 40% of its genes have at least one experimental Gene Ontology (GO) annotation assigned. Systematic observation of mutant phenotypes is an important technique for elucidating gene functions. Indeed, several large-scale phenotypic analyses have been performed and have generated phenotypic data sets from many Arabidopsis mutant lines and overexpressing lines, which are freely available online. Since each Arabidopsis mutant line database uses individual phenotype expression, the differences in the structured term sets used by each database make it difficult to compare data sets and make it impossible to search across databases. Therefore, we obtained publicly available information for a total of 66,209 Arabidopsis mutant lines, including loss-of-function (RATM and TARAPPER) and gain-of-function (AtFOX and OsFOX) lines, and integrated the phenotype data by mapping the descriptions onto Plant Ontology (PO) and Phenotypic Quality Ontology (PATO) terms. This approach made it possible to manage the four different phenotype databases as one large data set. Here, we report a publicly accessible web-based database, the RIKEN Arabidopsis Genome Encyclopedia II (RARGE II; http://rarge-v2.psc.riken.jp/), in which all of the data described in this study are included. Using the database, we demonstrated consistency (in terms of protein function) with a previous study and identified the presumed function of an unknown gene. We provide examples of AT1G21600, which is a subunit in the plastid-encoded RNA polymerase complex, and AT5G56980, which is related to the jasmonic acid signaling pathway.

Follicle Online: an integrated database of follicle assembly, development and ovulation.

PubMed

Hua, Juan; Xu, Bo; Yang, Yifan; Ban, Rongjun; Iqbal, Furhan; Cooke, Howard J; Zhang, Yuanwei; Shi, Qinghua

2015-01-01

Folliculogenesis is an important part of ovarian function as it provides the oocytes for female reproductive life. Characterizing genes/proteins involved in folliculogenesis is fundamental for understanding the mechanisms associated with this biological function and to cure the diseases associated with folliculogenesis. A large number of genes/proteins associated with folliculogenesis have been identified from different species. However, no dedicated public resource is currently available for folliculogenesis-related genes/proteins that are validated by experiments. Here, we are reporting a database 'Follicle Online' that provides the experimentally validated gene/protein map of the folliculogenesis in a number of species. Follicle Online is a web-based database system for storing and retrieving folliculogenesis-related experimental data. It provides detailed information for 580 genes/proteins (from 23 model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Mesocricetus auratus, Bos Taurus, Drosophila and Xenopus laevis) that have been reported to be involved in folliculogenesis, POF (premature ovarian failure) and PCOS (polycystic ovary syndrome). The literature was manually curated from more than 43,000 published articles (till 1 March 2014). The Follicle Online database is implemented in PHP + MySQL + JavaScript and this user-friendly web application provides access to the stored data. In summary, we have developed a centralized database that provides users with comprehensive information about genes/proteins involved in folliculogenesis. This database can be accessed freely and all the stored data can be viewed without any registration. Database URL: http://mcg.ustc.edu.cn/sdap1/follicle/index.php © The Author(s) 2015. Published by Oxford University Press.

Follicle Online: an integrated database of follicle assembly, development and ovulation

PubMed Central

Hua, Juan; Xu, Bo; Yang, Yifan; Ban, Rongjun; Iqbal, Furhan; Zhang, Yuanwei; Shi, Qinghua

2015-01-01

Folliculogenesis is an important part of ovarian function as it provides the oocytes for female reproductive life. Characterizing genes/proteins involved in folliculogenesis is fundamental for understanding the mechanisms associated with this biological function and to cure the diseases associated with folliculogenesis. A large number of genes/proteins associated with folliculogenesis have been identified from different species. However, no dedicated public resource is currently available for folliculogenesis-related genes/proteins that are validated by experiments. Here, we are reporting a database ‘Follicle Online’ that provides the experimentally validated gene/protein map of the folliculogenesis in a number of species. Follicle Online is a web-based database system for storing and retrieving folliculogenesis-related experimental data. It provides detailed information for 580 genes/proteins (from 23 model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Mesocricetus auratus, Bos Taurus, Drosophila and Xenopus laevis) that have been reported to be involved in folliculogenesis, POF (premature ovarian failure) and PCOS (polycystic ovary syndrome). The literature was manually curated from more than 43 000 published articles (till 1 March 2014). The Follicle Online database is implemented in PHP + MySQL + JavaScript and this user-friendly web application provides access to the stored data. In summary, we have developed a centralized database that provides users with comprehensive information about genes/proteins involved in folliculogenesis. This database can be accessed freely and all the stored data can be viewed without any registration. Database URL: http://mcg.ustc.edu.cn/sdap1/follicle/index.php PMID:25931457

Systematic approach to verification and validation: High explosive burn models

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

Menikoff, Ralph; Scovel, Christina A.

2012-04-16

Most material models used in numerical simulations are based on heuristics and empirically calibrated to experimental data. For a specific model, key questions are determining its domain of applicability and assessing its relative merits compared to other models. Answering these questions should be a part of model verification and validation (V and V). Here, we focus on V and V of high explosive models. Typically, model developers implemented their model in their own hydro code and use different sets of experiments to calibrate model parameters. Rarely can one find in the literature simulation results for different models of the samemore » experiment. Consequently, it is difficult to assess objectively the relative merits of different models. This situation results in part from the fact that experimental data is scattered through the literature (articles in journals and conference proceedings) and that the printed literature does not allow the reader to obtain data from a figure in electronic form needed to make detailed comparisons among experiments and simulations. In addition, it is very time consuming to set up and run simulations to compare different models over sufficiently many experiments to cover the range of phenomena of interest. The first difficulty could be overcome if the research community were to support an online web based database. The second difficulty can be greatly reduced by automating procedures to set up and run simulations of similar types of experiments. Moreover, automated testing would be greatly facilitated if the data files obtained from a database were in a standard format that contained key experimental parameters as meta-data in a header to the data file. To illustrate our approach to V and V, we have developed a high explosive database (HED) at LANL. It now contains a large number of shock initiation experiments. Utilizing the header information in a data file from HED, we have written scripts to generate an input file for a hydro code, run a simulation, and generate a comparison plot showing simulated and experimental velocity gauge data. These scripts are then applied to several series of experiments and to several HE burn models. The same systematic approach is applicable to other types of material models; for example, equations of state models and material strength models.« less

T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System.

PubMed

Tay, Daniel Ming Ming; Govindarajan, Kunde Ramamoorthy; Khan, Asif M; Ong, Terenze Yao Rui; Samad, Hanif M; Soh, Wei Wei; Tong, Minyan; Zhang, Fan; Tan, Tin Wee

2010-10-15

Effectors of Type III Secretion System (T3SS) play a pivotal role in establishing and maintaining pathogenicity in the host and therefore the identification of these effectors is important in understanding virulence. However, the effectors display high level of sequence diversity, therefore making the identification a difficult process. There is a need to collate and annotate existing effector sequences in public databases to enable systematic analyses of these sequences for development of models for screening and selection of putative novel effectors from bacterial genomes that can be validated by a smaller number of key experiments. Herein, we present T3SEdb http://effectors.bic.nus.edu.sg/T3SEdb, a specialized database of annotated T3SS effector (T3SE) sequences containing 1089 records from 46 bacterial species compiled from the literature and public protein databases. Procedures have been defined for i) comprehensive annotation of experimental status of effectors, ii) submission and curation review of records by users of the database, and iii) the regular update of T3SEdb existing and new records. Keyword fielded and sequence searches (BLAST, regular expression) are supported for both experimentally verified and hypothetical T3SEs. More than 171 clusters of T3SEs were detected based on sequence identity comparisons (intra-cluster difference up to ~60%). Owing to this high level of sequence diversity of T3SEs, the T3SEdb provides a large number of experimentally known effector sequences with wide species representation for creation of effector predictors. We created a reliable effector prediction tool, integrated into the database, to demonstrate the application of the database for such endeavours. T3SEdb is the first specialised database reported for T3SS effectors, enriched with manual annotations that facilitated systematic construction of a reliable prediction model for identification of novel effectors. The T3SEdb represents a platform for inclusion of additional annotations of metadata for future developments of sophisticated effector prediction models for screening and selection of putative novel effectors from bacterial genomes/proteomes that can be validated by a small number of key experiments.

The PMDB Protein Model Database

PubMed Central

Castrignanò, Tiziana; De Meo, Paolo D'Onorio; Cozzetto, Domenico; Talamo, Ivano Giuseppe; Tramontano, Anna

2006-01-01

The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. It is a relational database and it currently contains >74 000 models for ∼240 proteins. The system is accessible at and allows predictors to submit models along with related supporting evidence and users to download them through a simple and intuitive interface. Users can navigate in the database and retrieve models referring to the same target protein or to different regions of the same protein. Each model is assigned a unique identifier that allows interested users to directly access the data. PMID:16381873

Internet-based Profiler system as integrative framework to support translational research.

PubMed

Kim, Robert; Demichelis, Francesca; Tang, Jeffery; Riva, Alberto; Shen, Ronglai; Gibbs, Doug F; Mahavishno, Vasudeva; Chinnaiyan, Arul M; Rubin, Mark A

2005-12-19

Translational research requires taking basic science observations and developing them into clinically useful tests and therapeutics. We have developed a process to develop molecular biomarkers for diagnosis and prognosis by integrating tissue microarray (TMA) technology and an internet-database tool, Profiler. TMA technology allows investigators to study hundreds of patient samples on a single glass slide resulting in the conservation of tissue and the reduction in inter-experimental variability. The Profiler system allows investigator to reliably track, store, and evaluate TMA experiments. Here within we describe the process that has evolved through an empirical basis over the past 5 years at two academic institutions. The generic design of this system makes it compatible with multiple organ system (e.g., prostate, breast, lung, renal, and hematopoietic system,). Studies and folders are restricted to authorized users as required. Over the past 5 years, investigators at 2 academic institutions have scanned 656 TMA experiments and collected 63,311 digital images of these tissue samples. 68 pathologists from 12 major user groups have accessed the system. Two groups directly link clinical data from over 500 patients for immediate access and the remaining groups choose to maintain clinical and pathology data on separate systems. Profiler currently has 170 K data points such as staining intensity, tumor grade, and nuclear size. Due to the relational database structure, analysis can be easily performed on single or multiple TMA experimental results. The TMA module of Profiler can maintain images acquired from multiple systems. We have developed a robust process to develop molecular biomarkers using TMA technology and an internet-based database system to track all steps of this process. This system is extendable to other types of molecular data as separate modules and is freely available to academic institutions for licensing.

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

PubMed

Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

2012-01-01

To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

White Paper on Nuclear Data Needs and Capabilities for Basic Science

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

Batchelder, J.; Kawano, T.; Kelley, J.

Reliable nuclear structure and reaction data represent the fundamental building blocks of nuclear physics and astrophysics research, and are also of importance in many applications. There is a continuous demand for high-quality updates of the main nuclear physics databases via the prompt compilation and evaluation of the latest experimental and theoretical results. The nuclear physics research community benefits greatly from comprehensive, systematic and up-to-date reviews of the experimentally determined nuclear properties and observables, as well as from the ability to rapidly access these data in user-friendly forms. Such credible databases also act as a bridge between science, technology, and societymore » by making the results of basic nuclear physics research available to a broad audience of users, and hence expand the societal utilization of nuclear science. Compilation and evaluation of nuclear data has deep roots in the history of nuclear science research, as outlined in Appendix 1. They have an enormous impact on many areas of science and applications, as illustrated in Figure 2 for the Evaluated Nuclear Structure Data File (ENSDF) database. The present workshop concentrated on the needs of the basic nuclear science community for data and capabilities. The main role of this community is to generate and use data in order to understand the basic nuclear forces and interactions that are responsible for the existence and the properties of all nuclides and, as a consequence, to gain knowledge about the origins, evolution and structure of the universe. Thus, the experiments designed to measure a wealth of nuclear properties towards these fundamental scientific goals are typically performed from within this community.« less

MortalityPredictors.org: a manually-curated database of published biomarkers of human all-cause mortality

PubMed Central

Winslow, Ksenia; Ho, Andrew; Fortney, Kristen; Morgen, Eric

2017-01-01

Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers have resulted in numerous associations documented across hundreds of publications. Here, we present MortalityPredictors.org, a manually-curated, publicly accessible database, housing published, statistically-significant relationships between biomarkers and all-cause mortality in population-based or generally healthy samples. To gather the information for this database, we searched PubMed for appropriate research papers and then manually curated relevant data from each paper. We manually curated 1,576 biomarker associations, involving 471 distinct biomarkers. Biomarkers ranged in type from hematologic (red blood cell distribution width) to molecular (DNA methylation changes) to physical (grip strength). Via the web interface, the resulting data can be easily browsed, searched, and downloaded for further analysis. MortalityPredictors.org provides comprehensive results on published biomarkers of human all-cause mortality that can be used to compare biomarkers, facilitate meta-analysis, assist with the experimental design of aging studies, and serve as a central resource for analysis. We hope that it will facilitate future research into human mortality and aging. PMID:28858850

MortalityPredictors.org: a manually-curated database of published biomarkers of human all-cause mortality.

PubMed

Peto, Maximus V; De la Guardia, Carlos; Winslow, Ksenia; Ho, Andrew; Fortney, Kristen; Morgen, Eric

2017-08-31

Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers have resulted in numerous associations documented across hundreds of publications. Here, we present MortalityPredictors.org , a manually-curated, publicly accessible database, housing published, statistically-significant relationships between biomarkers and all-cause mortality in population-based or generally healthy samples. To gather the information for this database, we searched PubMed for appropriate research papers and then manually curated relevant data from each paper. We manually curated 1,576 biomarker associations, involving 471 distinct biomarkers. Biomarkers ranged in type from hematologic (red blood cell distribution width) to molecular (DNA methylation changes) to physical (grip strength). Via the web interface, the resulting data can be easily browsed, searched, and downloaded for further analysis. MortalityPredictors.org provides comprehensive results on published biomarkers of human all-cause mortality that can be used to compare biomarkers, facilitate meta-analysis, assist with the experimental design of aging studies, and serve as a central resource for analysis. We hope that it will facilitate future research into human mortality and aging.

Toward More Accurate Iris Recognition Using Cross-Spectral Matching.

PubMed

Nalla, Pattabhi Ramaiah; Kumar, Ajay

2017-01-01

Iris recognition systems are increasingly deployed for large-scale applications such as national ID programs, which continue to acquire millions of iris images to establish identity among billions. However, with the availability of variety of iris sensors that are deployed for the iris imaging under different illumination/environment, significant performance degradation is expected while matching such iris images acquired under two different domains (either sensor-specific or wavelength-specific). This paper develops a domain adaptation framework to address this problem and introduces a new algorithm using Markov random fields model to significantly improve cross-domain iris recognition. The proposed domain adaptation framework based on the naive Bayes nearest neighbor classification uses a real-valued feature representation, which is capable of learning domain knowledge. Our approach to estimate corresponding visible iris patterns from the synthesis of iris patches in the near infrared iris images achieves outperforming results for the cross-spectral iris recognition. In this paper, a new class of bi-spectral iris recognition system that can simultaneously acquire visible and near infra-red images with pixel-to-pixel correspondences is proposed and evaluated. This paper presents experimental results from three publicly available databases; PolyU cross-spectral iris image database, IIITD CLI and UND database, and achieve outperforming results for the cross-sensor and cross-spectral iris matching.

Creating and virtually screening databases of fluorescently-labelled compounds for the discovery of target-specific molecular probes

NASA Astrophysics Data System (ADS)

Kamstra, Rhiannon L.; Dadgar, Saedeh; Wigg, John; Chowdhury, Morshed A.; Phenix, Christopher P.; Floriano, Wely B.

2014-11-01

Our group has recently demonstrated that virtual screening is a useful technique for the identification of target-specific molecular probes. In this paper, we discuss some of our proof-of-concept results involving two biologically relevant target proteins, and report the development of a computational script to generate large databases of fluorescence-labelled compounds for computer-assisted molecular design. The virtual screening of a small library of 1,153 fluorescently-labelled compounds against two targets, and the experimental testing of selected hits reveal that this approach is efficient at identifying molecular probes, and that the screening of a labelled library is preferred over the screening of base compounds followed by conjugation of confirmed hits. The automated script for library generation explores the known reactivity of commercially available dyes, such as NHS-esters, to create large virtual databases of fluorescence-tagged small molecules that can be easily synthesized in a laboratory. A database of 14,862 compounds, each tagged with the ATTO680 fluorophore was generated with the automated script reported here. This library is available for downloading and it is suitable for virtual ligand screening aiming at the identification of target-specific fluorescent molecular probes.

GPU-based cloud service for Smith-Waterman algorithm using frequency distance filtration scheme.

PubMed

Lee, Sheng-Ta; Lin, Chun-Yuan; Hung, Che Lun

2013-01-01

As the conventional means of analyzing the similarity between a query sequence and database sequences, the Smith-Waterman algorithm is feasible for a database search owing to its high sensitivity. However, this algorithm is still quite time consuming. CUDA programming can improve computations efficiently by using the computational power of massive computing hardware as graphics processing units (GPUs). This work presents a novel Smith-Waterman algorithm with a frequency-based filtration method on GPUs rather than merely accelerating the comparisons yet expending computational resources to handle such unnecessary comparisons. A user friendly interface is also designed for potential cloud server applications with GPUs. Additionally, two data sets, H1N1 protein sequences (query sequence set) and human protein database (database set), are selected, followed by a comparison of CUDA-SW and CUDA-SW with the filtration method, referred to herein as CUDA-SWf. Experimental results indicate that reducing unnecessary sequence alignments can improve the computational time by up to 41%. Importantly, by using CUDA-SWf as a cloud service, this application can be accessed from any computing environment of a device with an Internet connection without time constraints.

SPINS: standardized protein NMR storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra.

PubMed

Baran, Michael C; Moseley, Hunter N B; Sahota, Gurmukh; Montelione, Gaetano T

2002-10-01

Modern protein NMR spectroscopy laboratories have a rapidly growing need for an easily queried local archival system of raw experimental NMR datasets. SPINS (Standardized ProteIn Nmr Storage) is an object-oriented relational database that provides facilities for high-volume NMR data archival, organization of analyses, and dissemination of results to the public domain by automatic preparation of the header files required for submission of data to the BioMagResBank (BMRB). The current version of SPINS coordinates the process from data collection to BMRB deposition of raw NMR data by standardizing and integrating the storage and retrieval of these data in a local laboratory file system. Additional facilities include a data mining query tool, graphical database administration tools, and a NMRStar v2. 1.1 file generator. SPINS also includes a user-friendly internet-based graphical user interface, which is optionally integrated with Varian VNMR NMR data collection software. This paper provides an overview of the data model underlying the SPINS database system, a description of its implementation in Oracle, and an outline of future plans for the SPINS project.

Peptide Identification by Database Search of Mixture Tandem Mass Spectra*

PubMed Central

Wang, Jian; Bourne, Philip E.; Bandeira, Nuno

2011-01-01

In high-throughput proteomics the development of computational methods and novel experimental strategies often rely on each other. In certain areas, mass spectrometry methods for data acquisition are ahead of computational methods to interpret the resulting tandem mass spectra. Particularly, although there are numerous situations in which a mixture tandem mass spectrum can contain fragment ions from two or more peptides, nearly all database search tools still make the assumption that each tandem mass spectrum comes from one peptide. Common examples include mixture spectra from co-eluting peptides in complex samples, spectra generated from data-independent acquisition methods, and spectra from peptides with complex post-translational modifications. We propose a new database search tool (MixDB) that is able to identify mixture tandem mass spectra from more than one peptide. We show that peptides can be reliably identified with up to 95% accuracy from mixture spectra while considering only a 0.01% of all possible peptide pairs (four orders of magnitude speedup). Comparison with current database search methods indicates that our approach has better or comparable sensitivity and precision at identifying single-peptide spectra while simultaneously being able to identify 38% more peptides from mixture spectra at significantly higher precision. PMID:21862760

Image ratio features for facial expression recognition application.

PubMed

Song, Mingli; Tao, Dacheng; Liu, Zicheng; Li, Xuelong; Zhou, Mengchu

2010-06-01

Video-based facial expression recognition is a challenging problem in computer vision and human-computer interaction. To target this problem, texture features have been extracted and widely used, because they can capture image intensity changes raised by skin deformation. However, existing texture features encounter problems with albedo and lighting variations. To solve both problems, we propose a new texture feature called image ratio features. Compared with previously proposed texture features, e.g., high gradient component features, image ratio features are more robust to albedo and lighting variations. In addition, to further improve facial expression recognition accuracy based on image ratio features, we combine image ratio features with facial animation parameters (FAPs), which describe the geometric motions of facial feature points. The performance evaluation is based on the Carnegie Mellon University Cohn-Kanade database, our own database, and the Japanese Female Facial Expression database. Experimental results show that the proposed image ratio feature is more robust to albedo and lighting variations, and the combination of image ratio features and FAPs outperforms each feature alone. In addition, we study asymmetric facial expressions based on our own facial expression database and demonstrate the superior performance of our combined expression recognition system.

Vehicle-triggered video compression/decompression for fast and efficient searching in large video databases

NASA Astrophysics Data System (ADS)

Bulan, Orhan; Bernal, Edgar A.; Loce, Robert P.; Wu, Wencheng

2013-03-01

Video cameras are widely deployed along city streets, interstate highways, traffic lights, stop signs and toll booths by entities that perform traffic monitoring and law enforcement. The videos captured by these cameras are typically compressed and stored in large databases. Performing a rapid search for a specific vehicle within a large database of compressed videos is often required and can be a time-critical life or death situation. In this paper, we propose video compression and decompression algorithms that enable fast and efficient vehicle or, more generally, event searches in large video databases. The proposed algorithm selects reference frames (i.e., I-frames) based on a vehicle having been detected at a specified position within the scene being monitored while compressing a video sequence. A search for a specific vehicle in the compressed video stream is performed across the reference frames only, which does not require decompression of the full video sequence as in traditional search algorithms. Our experimental results on videos captured in a local road show that the proposed algorithm significantly reduces the search space (thus reducing time and computational resources) in vehicle search tasks within compressed video streams, particularly those captured in light traffic volume conditions.

Estimation of Solvation Quantities from Experimental Thermodynamic Data: Development of the Comprehensive CompSol Databank for Pure and Mixed Solutes

NASA Astrophysics Data System (ADS)

Moine, Edouard; Privat, Romain; Sirjean, Baptiste; Jaubert, Jean-Noël

2017-09-01

The Gibbs energy of solvation measures the affinity of a solute for its solvent and is thus a key property for the selection of an appropriate solvent for a chemical synthesis or a separation process. More fundamentally, Gibbs energies of solvation are choice data for developing and benchmarking molecular models predicting solvation effects. The Comprehensive Solvation—CompSol—database was developed with the ambition to propose very large sets of new experimental solvation chemical-potential, solvation entropy, and solvation enthalpy data of pure and mixed components, covering extended temperature ranges. For mixed compounds, the solvation quantities were generated in infinite-dilution conditions by combining experimental values of pure-component and binary-mixture thermodynamic properties. Three types of binary-mixture properties were considered: partition coefficients, activity coefficients at infinite dilution, and Henry's-law constants. A rigorous methodology was implemented with the aim to select data at appropriate conditions of temperature, pressure, and concentration for the estimation of solvation data. Finally, our comprehensive CompSol database contains 21 671 data associated with 1969 pure species and 70 062 data associated with 14 102 binary mixtures (including 760 solvation data related to the ionic-liquid class of solvents). On the basis of the very large amount of experimental data contained in the CompSol database, it is finally discussed how solvation energies are influenced by hydrogen-bonding association effects.

Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database

PubMed Central

Keator, David B.; Wei, Dingying; Fennema-Notestine, Christine; Pease, Karen R.; Bockholt, Jeremy; Grethe, Jeffrey S.

2010-01-01

Managing vast datasets collected throughout multiple clinical imaging communities has become critical with the ever increasing and diverse nature of datasets. Development of data management infrastructure is further complicated by technical and experimental advances that drive modifications to existing protocols and acquisition of new types of research data to be incorporated into existing data management systems. In this paper, an extensible data management system for clinical neuroimaging studies is introduced: The Human Clinical Imaging Database (HID) and Toolkit. The database schema is constructed to support the storage of new data types without changes to the underlying schema. The complex infrastructure allows management of experiment data, such as image protocol and behavioral task parameters, as well as subject-specific data, including demographics, clinical assessments, and behavioral task performance metrics. Of significant interest, embedded clinical data entry and management tools enhance both consistency of data reporting and automatic entry of data into the database. The Clinical Assessment Layout Manager (CALM) allows users to create on-line data entry forms for use within and across sites, through which data is pulled into the underlying database via the generic clinical assessment management engine (GAME). Importantly, the system is designed to operate in a distributed environment, serving both human users and client applications in a service-oriented manner. Querying capabilities use a built-in multi-database parallel query builder/result combiner, allowing web-accessible queries within and across multiple federated databases. The system along with its documentation is open-source and available from the Neuroimaging Informatics Tools and Resource Clearinghouse (NITRC) site. PMID:20567938

S2RSLDB: a comprehensive manually curated, internet-accessible database of the sigma-2 receptor selective ligands.

PubMed

Nastasi, Giovanni; Miceli, Carla; Pittalà, Valeria; Modica, Maria N; Prezzavento, Orazio; Romeo, Giuseppe; Rescifina, Antonio; Marrazzo, Agostino; Amata, Emanuele

2017-01-01

Sigma (σ) receptors are accepted as a particular receptor class consisting of two subtypes: sigma-1 (σ 1 ) and sigma-2 (σ 2 ). The two receptor subtypes have specific drug actions, pharmacological profiles and molecular characteristics. The σ 2 receptor is overexpressed in several tumor cell lines, and its ligands are currently under investigation for their role in tumor diagnosis and treatment. The σ 2 receptor structure has not been disclosed, and researchers rely on σ 2 receptor radioligand binding assay to understand the receptor's pharmacological behavior and design new lead compounds. Here we present the sigma-2 Receptor Selective Ligands Database (S2RSLDB) a manually curated database of the σ 2 receptor selective ligands containing more than 650 compounds. The database is built with chemical structure information, radioligand binding affinity data, computed physicochemical properties, and experimental radioligand binding procedures. The S2RSLDB is freely available online without account login and having a powerful search engine the user may build complex queries, sort tabulated results, generate color coded 2D and 3D graphs and download the data for additional screening. The collection here reported is extremely useful for the development of new ligands endowed of σ 2 receptor affinity, selectivity, and appropriate physicochemical properties. The database will be updated yearly and in the near future, an online submission form will be available to help with keeping the database widely spread in the research community and continually updated. The database is available at http://www.researchdsf.unict.it/S2RSLDB.

Federated web-accessible clinical data management within an extensible neuroimaging database.

PubMed

Ozyurt, I Burak; Keator, David B; Wei, Dingying; Fennema-Notestine, Christine; Pease, Karen R; Bockholt, Jeremy; Grethe, Jeffrey S

2010-12-01

Managing vast datasets collected throughout multiple clinical imaging communities has become critical with the ever increasing and diverse nature of datasets. Development of data management infrastructure is further complicated by technical and experimental advances that drive modifications to existing protocols and acquisition of new types of research data to be incorporated into existing data management systems. In this paper, an extensible data management system for clinical neuroimaging studies is introduced: The Human Clinical Imaging Database (HID) and Toolkit. The database schema is constructed to support the storage of new data types without changes to the underlying schema. The complex infrastructure allows management of experiment data, such as image protocol and behavioral task parameters, as well as subject-specific data, including demographics, clinical assessments, and behavioral task performance metrics. Of significant interest, embedded clinical data entry and management tools enhance both consistency of data reporting and automatic entry of data into the database. The Clinical Assessment Layout Manager (CALM) allows users to create on-line data entry forms for use within and across sites, through which data is pulled into the underlying database via the generic clinical assessment management engine (GAME). Importantly, the system is designed to operate in a distributed environment, serving both human users and client applications in a service-oriented manner. Querying capabilities use a built-in multi-database parallel query builder/result combiner, allowing web-accessible queries within and across multiple federated databases. The system along with its documentation is open-source and available from the Neuroimaging Informatics Tools and Resource Clearinghouse (NITRC) site.

A lightweight approach for biometric template protection

NASA Astrophysics Data System (ADS)

Al-Assam, Hisham; Sellahewa, Harin; Jassim, Sabah

2009-05-01

Privacy and security are vital concerns for practical biometric systems. The concept of cancelable or revocable biometrics has been proposed as a solution for biometric template security. Revocable biometric means that biometric templates are no longer fixed over time and could be revoked in the same way as lost or stolen credit cards are. In this paper, we describe a novel and an efficient approach to biometric template protection that meets the revocability property. This scheme can be incorporated into any biometric verification scheme while maintaining, if not improving, the accuracy of the original biometric system. However, we shall demonstrate the result of applying such transforms on face biometric templates and compare the efficiency of our approach with that of the well-known random projection techniques. We shall also present the results of experimental work on recognition accuracy before and after applying the proposed transform on feature vectors that are generated by wavelet transforms. These results are based on experiments conducted on a number of well-known face image databases, e.g. Yale and ORL databases.

SFCOMPO 2.0 - A relational database of spent fuel isotopic measurements, reactor operational histories, and design data

NASA Astrophysics Data System (ADS)

Michel-Sendis, Franco; Martinez-González, Jesus; Gauld, Ian

2017-09-01

SFCOMPO-2.0 is a database of experimental isotopic concentrations measured in destructive radiochemical analysis of spent nuclear fuel (SNF) samples. The database includes corresponding design description of the fuel rods and assemblies, relevant operating conditions and characteristics of the host reactors necessary for modelling and simulation. Aimed at establishing a thorough, reliable, and publicly available resource for code and data validation of safety-related applications, SFCOMPO-2.0 is developed and maintained by the OECD Nuclear Energy Agency (NEA). The SFCOMPO-2.0 database is a Java application which is downloadable from the NEA website.

Exploring Genetic, Genomic, and Phenotypic Data at the Rat Genome Database

PubMed Central

Laulederkind, Stanley J. F.; Hayman, G. Thomas; Wang, Shur-Jen; Lowry, Timothy F.; Nigam, Rajni; Petri, Victoria; Smith, Jennifer R.; Dwinell, Melinda R.; Jacob, Howard J.; Shimoyama, Mary

2013-01-01

The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.edu) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components for genes, quantitative trait loci, and strains. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat. PMID:23255149

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.

PubMed

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-09-01

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.

Revisiting the Canadian English vowel space

NASA Astrophysics Data System (ADS)

Hagiwara, Robert

2005-04-01

In order to fill a need for experimental-acoustic baseline measurements of Canadian English vowels, a database is currently being constructed in Winnipeg, Manitoba. The database derives from multiple repetitions of fifteen English vowels (eleven standard monophthongs, syllabic /r/ and three standard diphthongs) in /hVd/ and /hVt/ contexts, as spoken by multiple speakers. Frequencies of the first four formants are taken from three timepoints in every vowel token (25, 50, and 75% of vowel duration). Preliminary results (from five men and five women) confirm some features characteristic of Canadian English, but call others into question. For instance the merger of low back vowels appears to be complete for these speakers, but the result is a lower-mid and probably rounded vowel rather than the low back unround vowel often described. With these data Canadian Raising can be quantified as an average 200 Hz or 1.5 Bark downward shift in the frequency of F1 before voiceless /t/. Analysis of the database will lead to a more accurate picture of the Canadian English vowel system, as well as provide a practical and up-to-date point of reference for further phonetic and sociophonetic comparisons.

Biometric sample extraction using Mahalanobis distance in Cardioid based graph using electrocardiogram signals.

PubMed

Sidek, Khairul; Khali, Ibrahim

2012-01-01

In this paper, a person identification mechanism implemented with Cardioid based graph using electrocardiogram (ECG) is presented. Cardioid based graph has given a reasonably good classification accuracy in terms of differentiating between individuals. However, the current feature extraction method using Euclidean distance could be further improved by using Mahalanobis distance measurement producing extracted coefficients which takes into account the correlations of the data set. Identification is then done by applying these extracted features to Radial Basis Function Network. A total of 30 ECG data from MITBIH Normal Sinus Rhythm database (NSRDB) and MITBIH Arrhythmia database (MITDB) were used for development and evaluation purposes. Our experimentation results suggest that the proposed feature extraction method has significantly increased the classification performance of subjects in both databases with accuracy from 97.50% to 99.80% in NSRDB and 96.50% to 99.40% in MITDB. High sensitivity, specificity and positive predictive value of 99.17%, 99.91% and 99.23% for NSRDB and 99.30%, 99.90% and 99.40% for MITDB also validates the proposed method. This result also indicates that the right feature extraction technique plays a vital role in determining the persistency of the classification accuracy for Cardioid based person identification mechanism.

Reassessment of Atomic Mobilities in fcc Cu-Ag-Sn System Aiming at Establishment of an Atomic Mobility Database in Sn-Ag-Cu-In-Sb-Bi-Pb Solder Alloys

NASA Astrophysics Data System (ADS)

Xu, Huixia; Zhang, Lijun; Cheng, Kaiming; Chen, Weimin; Du, Yong

2017-04-01

To establish an accurate atomic mobility database in solder alloys, a reassessment of atomic mobilities in the fcc (face centered cubic) Cu-Ag-Sn system was performed as reported in the present work. The work entailed initial preparation of three fcc Cu-Sn diffusion couples, which were used to determine the composition-dependent interdiffusivities at 873 K, 923 K, and 973 K, to validate the literature data and provide new experimental data at low temperatures. Then, atomic mobilities in three boundary binaries, fcc Cu-Sn, fcc Ag-Sn, and fcc Cu-Ag, were updated based on the data for various experimental diffusivities obtained from the literature and the present work, together with the available thermodynamic database for solder alloys. Finally, based on the large number of interdiffusivities recently measured from the present authors, atomic mobilities in the fcc Cu-Ag-Sn ternary system were carefully evaluated. A comprehensive comparison between various calculated/model-predicted diffusion properties and the experimental data was used to validate the reliability of the obtained atomic mobilities in ternary fcc Cu-Ag-Sn alloys.

The importance of molecular structures, endpoints' values, and predictivity parameters in QSAR research: QSAR analysis of a series of estrogen receptor binders.

PubMed

Li, Jiazhong; Gramatica, Paola

2010-11-01

Quantitative structure-activity relationship (QSAR) methodology aims to explore the relationship between molecular structures and experimental endpoints, producing a model for the prediction of new data; the predictive performance of the model must be checked by external validation. Clearly, the qualities of chemical structure information and experimental endpoints, as well as the statistical parameters used to verify the external predictivity have a strong influence on QSAR model reliability. Here, we emphasize the importance of these three aspects by analyzing our models on estrogen receptor binders (Endocrine disruptor knowledge base (EDKB) database). Endocrine disrupting chemicals, which mimic or antagonize the endogenous hormones such as estrogens, are a hot topic in environmental and toxicological sciences. QSAR shows great values in predicting the estrogenic activity and exploring the interactions between the estrogen receptor and ligands. We have verified our previously published model for additional external validation on new EDKB chemicals. Having found some errors in the used 3D molecular conformations, we redevelop a new model using the same data set with corrected structures, the same method (ordinary least-square regression, OLS) and DRAGON descriptors. The new model, based on some different descriptors, is more predictive on external prediction sets. Three different formulas to calculate correlation coefficient for the external prediction set (Q2 EXT) were compared, and the results indicated that the new proposal of Consonni et al. had more reasonable results, consistent with the conclusions from regression line, Williams plot and root mean square error (RMSE) values. Finally, the importance of reliable endpoints values has been highlighted by comparing the classification assignments of EDKB with those of another estrogen receptor binders database (METI): we found that 16.1% assignments of the common compounds were opposite (20 among 124 common compounds). In order to verify the real assignments for these inconsistent compounds, we predicted these samples, as a blind external set, by our regression models and compared the results with the two databases. The results indicated that most of the predictions were consistent with METI. Furthermore, we built a kNN classification model using the 104 consistent compounds to predict those inconsistent ones, and most of the predictions were also in agreement with METI database.

Using the Cambridge Structural Database to Teach Molecular Geometry Concepts in Organic Chemistry

ERIC Educational Resources Information Center

Wackerly, Jay Wm.; Janowicz, Philip A.; Ritchey, Joshua A.; Caruso, Mary M.; Elliott, Erin L.; Moore, Jeffrey S.

2009-01-01

This article reports a set of two homework assignments that can be used in a second-year undergraduate organic chemistry class. These assignments were designed to help reinforce concepts of molecular geometry and to give students the opportunity to use a technological database and data mining to analyze experimentally determined chemical…

The NUBASE2016 evaluation of nuclear properties

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

Audi, G.; Kondev, F. G.; Wang, Meng

This paper presents the NUBASE2016 evaluation that contains the recommended values for nuclear and decay properties of 3437 nuclides in their ground and excited isomeric (T1/2≥100 ns) states. All nuclides for which any experimental information is known were considered. NUBASE2016 covers all data published by October 2016 in primary (journal articles) and secondary (mainly laboratory reports and conference proceedings) references, together with the corresponding bibliographical information. During the development of NUBASE2016, the data available in the “Evaluated Nuclear Structure Data File” (ENSDF) database were consulted and critically assessed for their validity and completeness. Furthermore, a large amount of new datamore » and some older experimental results that were missing from ENSDF were compiled, evaluated and included in NUBASE2016. The atomic mass values were taken from the “Atomic Mass Evaluation” (AME2016, second and third parts of the present issue). In cases where no experimental data were available for a particular nuclide, trends in the behavior of specific properties in neighboring nuclides (TNN) were examined. This approach allowed to estimate values for a range of properties that are labeled in NUBASE2016 as “non-experimental” (flagged “#”). Evaluation procedures and policies used during the development of this database are presented, together with a detailed table of recommended values and their uncertainties. AMDC: http://amdc.impcas.ac.cn/« less

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

PubMed

Moriya, Yuki; Yamada, Takuji; Okuda, Shujiro; Nakagawa, Zenichi; Kotera, Masaaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

2016-03-28

Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes.

X-38 Experimental Aeroheating at Mach 10

NASA Technical Reports Server (NTRS)

Berry, Scott A.; Horvath, Thomas J.; Weilmuenster, K. James; Alter, Stephan J.; Merski, N. Ronald

2001-01-01

This report provides an update of the hypersonic aerothermodynamic wind tunnel test program conducted at the NASA Langley Research Center in support of the X-38 program. Global surface heat transfer distributions were measured on 0.0177 and 0.0236 scale models of the proposed X-38 configuration at Mach 10 in air. The parametrics that were investigated primarily include freestream unit Reynolds numbers of 0.6 to 2.2 million per foot and body flap deflections of 15, 20, and 25 deg for an angle-of-attack of 40 deg. The model-scale variance was tested to obtain laminar, transitional, and turbulent heating levels on the defected bodyflaps. In addition, a limited investigation of forced boundary layer transition through the use of discrete roughness elements was performed. Comparisons of the present experimental results to computational predictions and previous experimental data were conducted Laminar, transitional, and turbulent heating levels were observed on the deflected body flap, which compared favorably to the computational results and to the predicted heating based on the flight aerothermodynamic database.

Benchmarking comparison and validation of MCNP photon interaction data

NASA Astrophysics Data System (ADS)

Colling, Bethany; Kodeli, I.; Lilley, S.; Packer, L. W.

2017-09-01

The objective of the research was to test available photoatomic data libraries for fusion relevant applications, comparing against experimental and computational neutronics benchmarks. Photon flux and heating was compared using the photon interaction data libraries (mcplib 04p, 05t, 84p and 12p). Suitable benchmark experiments (iron and water) were selected from the SINBAD database and analysed to compare experimental values with MCNP calculations using mcplib 04p, 84p and 12p. In both the computational and experimental comparisons, the majority of results with the 04p, 84p and 12p photon data libraries were within 1σ of the mean MCNP statistical uncertainty. Larger differences were observed when comparing computational results with the 05t test photon library. The Doppler broadening sampling bug in MCNP-5 is shown to be corrected for fusion relevant problems through use of the 84p photon data library. The recommended libraries for fusion neutronics are 84p (or 04p) with MCNP6 and 84p if using MCNP-5.

Palmprint identification using FRIT

NASA Astrophysics Data System (ADS)

Kisku, D. R.; Rattani, A.; Gupta, P.; Hwang, C. J.; Sing, J. K.

2011-06-01

This paper proposes a palmprint identification system using Finite Ridgelet Transform (FRIT) and Bayesian classifier. FRIT is applied on the ROI (region of interest), which is extracted from palmprint image, to extract a set of distinctive features from palmprint image. These features are used to classify with the help of Bayesian classifier. The proposed system has been tested on CASIA and IIT Kanpur palmprint databases. The experimental results reveal better performance compared to all well known systems.

Multi-stream face recognition for crime-fighting

NASA Astrophysics Data System (ADS)

Jassim, Sabah A.; Sellahewa, Harin

2007-04-01

Automatic face recognition (AFR) is a challenging task that is increasingly becoming the preferred biometric trait for identification and has the potential of becoming an essential tool in the fight against crime and terrorism. Closed-circuit television (CCTV) cameras have increasingly been used over the last few years for surveillance in public places such as airports, train stations and shopping centers. They are used to detect and prevent crime, shoplifting, public disorder and terrorism. The work of law-enforcing and intelligence agencies is becoming more reliant on the use of databases of biometric data for large section of the population. Face is one of the most natural biometric traits that can be used for identification and surveillance. However, variations in lighting conditions, facial expressions, face size and pose are a great obstacle to AFR. This paper is concerned with using waveletbased face recognition schemes in the presence of variations of expressions and illumination. In particular, we will investigate the use of a combination of wavelet frequency channels for a multi-stream face recognition using various wavelet subbands as different face signal streams. The proposed schemes extend our recently developed face veri.cation scheme for implementation on mobile devices. We shall present experimental results on the performance of our proposed schemes for a number of face databases including a new AV database recorded on a PDA. By analyzing the various experimental data, we shall demonstrate that the multi-stream approach is robust against variations in illumination and facial expressions than the previous single-stream approach.

Experimental study of operation performance for hydrocarbon fuel pump with low specific speed

NASA Astrophysics Data System (ADS)

Wu, Xianyu; Yang, Jun; Jin, Xuan

2017-10-01

In this paper, a small flow rate hydrocarbon turbine pump was used to pressurize the fuel supply system of scramjet engine. Some experiments were carried out to investigate the characteristics of turbine pump driven by nitrogen or combustion gas under different operating conditions. A experimental database with regard to the curves of the rotational speed, mass flow rate and net head with regard to centrifugal pump were plotted. These curves were represented as functions of the pressure and temperature at turbine inlet/outlet and the throttle diameter at downstream of centrifugal pump. A sensitivity study has been carried out based on design of experiments. The experimental was employed to analyze net head of centrifugal and throttle characteristics. The research results can accumulate foundations for the close loop control system of turbine pump.

Research on Improved Depth Belief Network-Based Prediction of Cardiovascular Diseases

PubMed Central

Zhang, Hongpo

2018-01-01

Quantitative analysis and prediction can help to reduce the risk of cardiovascular disease. Quantitative prediction based on traditional model has low accuracy. The variance of model prediction based on shallow neural network is larger. In this paper, cardiovascular disease prediction model based on improved deep belief network (DBN) is proposed. Using the reconstruction error, the network depth is determined independently, and unsupervised training and supervised optimization are combined. It ensures the accuracy of model prediction while guaranteeing stability. Thirty experiments were performed independently on the Statlog (Heart) and Heart Disease Database data sets in the UCI database. Experimental results showed that the mean of prediction accuracy was 91.26% and 89.78%, respectively. The variance of prediction accuracy was 5.78 and 4.46, respectively. PMID:29854369

Calculation of Phase Equilibria in the Y2O3-Yb2O3-ZrO2 System

NASA Technical Reports Server (NTRS)

Jacobson, Nathan S.; Liu, Zi-Kui; Kaufman, Larry; Zhang, Fan

2001-01-01

Rare earth oxide stabilized zirconias find a wide range of applications. An understanding of phase equilibria is essential to all applications. In this study, the available phase boundary data and thermodynamic data is collected and assessed. Calphad-type databases are developed to completely describe the Y2O3-ZrO2, Yb2O3-ZrO2, and Y2O3-Yb2O3 systems. The oxide units are treated as components and regular and subregular solution models are used. The resultant calculated phase diagrams show good agreement with the experimental data. Then the binaries are combined to form the database for the Y2O3-Yb2O3-ZrO2 psuedo-ternary.

Space Weather Studies Using Ground-based Experimental Complex in Kazakhstan

NASA Astrophysics Data System (ADS)

Kryakunova, O.; Yakovets, A.; Monstein, C.; Nikolayevskiy, N.; Zhumabayev, B.; Gordienko, G.; Andreyev, A.; Malimbayev, A.; Levin, Yu.; Salikhov, N.; Sokolova, O.; Tsepakina, I.

2015-12-01

Kazakhstan ground-based experimental complex for space weather study is situated near Almaty. Results of space environment monitoring are accessible via Internet on the web-site of the Institute of Ionosphere (http://www.ionos.kz/?q=en/node/21) in real time. There is a complex database with hourly data of cosmic ray intensity, geomagnetic field intensity, and solar radio flux at 10.7 cm and 27.8 cm wavelengths. Several studies using those data are reported. They are an estimation of speed of a coronal mass ejection, a study of large scale traveling distrubances, an analysis of geomagnetically induced currents using the geomagnetic field data, and a solar energetic proton event on 27 January 2012.

Transport modeling of L- and H-mode discharges with LHCD on EAST

NASA Astrophysics Data System (ADS)

Li, M. H.; Ding, B. J.; Imbeaux, F.; Decker, J.; Zhang, X. J.; Kong, E. H.; Zhang, L.; Wei, W.; Shan, J. F.; Liu, F. K.; Wang, M.; Xu, H. D.; Yang, Y.; Peysson, Y.; Basiuk, V.; Artaud, J.-F.; Yuynh, P.; Wan, B. N.

2013-04-01

High-confinement (H-mode) discharges with lower hybrid current drive (LHCD) as the only heating source are obtained on EAST. In this paper, an empirical transport model of mixed Bohm/gyro-Bohm for electron and ion heat transport was first calibrated against a database of 3 L-mode shots on EAST. The electron and ion temperature profiles are well reproduced in the predictive modeling with the calibrated model coupled to the suite of codes CRONOS. CRONOS calculations with experimental profiles are also performed for electron power balance analysis. In addition, the time evolutions of LHCD are calculated by the C3PO/LUKE code involving current diffusion, and the results are compared with experimental observations.

Automated identification of retinal vessels using a multiscale directional contrast quantification (MDCQ) strategy

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

Zhen, Yi; Zhang, Xinyuan; Wang, Ningli, E-mail: wningli@vip.163.com, E-mail: puj@upmc.edu

2014-09-15

Purpose: A novel algorithm is presented to automatically identify the retinal vessels depicted in color fundus photographs. Methods: The proposed algorithm quantifies the contrast of each pixel in retinal images at multiple scales and fuses the resulting consequent contrast images in a progressive manner by leveraging their spatial difference and continuity. The multiscale strategy is to deal with the variety of retinal vessels in width, intensity, resolution, and orientation; and the progressive fusion is to combine consequent images and meanwhile avoid a sudden fusion of image noise and/or artifacts in space. To quantitatively assess the performance of the algorithm, wemore » tested it on three publicly available databases, namely, DRIVE, STARE, and HRF. The agreement between the computer results and the manual delineation in these databases were quantified by computing their overlapping in both area and length (centerline). The measures include sensitivity, specificity, and accuracy. Results: For the DRIVE database, the sensitivities in identifying vessels in area and length were around 90% and 70%, respectively, the accuracy in pixel classification was around 99%, and the precisions in terms of both area and length were around 94%. For the STARE database, the sensitivities in identifying vessels were around 90% in area and 70% in length, and the accuracy in pixel classification was around 97%. For the HRF database, the sensitivities in identifying vessels were around 92% in area and 83% in length for the healthy subgroup, around 92% in area and 75% in length for the glaucomatous subgroup, around 91% in area and 73% in length for the diabetic retinopathy subgroup. For all three subgroups, the accuracy was around 98%. Conclusions: The experimental results demonstrate that the developed algorithm is capable of identifying retinal vessels depicted in color fundus photographs in a relatively reliable manner.« less

Extension of the sasCIF format and its applications for data processing and deposition

DOE PAGES

Kachala, Michael; Westbrook, John; Svergun, Dmitri

2016-02-01

Recent advances in small-angle scattering (SAS) experimental facilities and data analysis methods have prompted a dramatic increase in the number of users and of projects conducted, causing an upsurge in the number of objects studied, experimental data available and structural models generated. To organize the data and models and make them accessible to the community, the Task Forces on SAS and hybrid methods for the International Union of Crystallography and the Worldwide Protein Data Bank envisage developing a federated approach to SAS data and model archiving. Within the framework of this approach, the existing databases may exchange information and providemore » independent but synchronized entries to users. At present, ways of exchanging information between the various SAS databases are not established, leading to possible duplication and incompatibility of entries, and limiting the opportunities for data-driven research for SAS users. In this work, a solution is developed to resolve these issues and provide a universal exchange format for the community, based on the use of the widely adopted crystallographic information framework (CIF). The previous version of the sasCIF format, implemented as an extension of the core CIF dictionary, has been available since 2000 to facilitate SAS data exchange between laboratories. The sasCIF format has now been extended to describe comprehensively the necessary experimental information, results and models, including relevant metadata for SAS data analysis and for deposition into a database. Processing tools for these files (sasCIFtools) have been developed, and these are available both as standalone open-source programs and integrated into the SAS Biological Data Bank, allowing the export and import of data entries as sasCIF files. Software modules to save the relevant information directly from beamline data-processing pipelines in sasCIF format are also developed. Lastly, this update of sasCIF and the relevant tools are an important step in the standardization of the way SAS data are presented and exchanged, to make the results easily accessible to users and to promote further the application of SAS in the structural biology community.« less

The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases.

PubMed

Mostaguir, Khaled; Hoogland, Christine; Binz, Pierre-Alain; Appel, Ron D

2003-08-01

The Make 2D-DB tool has been previously developed to help build federated two-dimensional gel electrophoresis (2-DE) databases on one's own web site. The purpose of our work is to extend the strength of the first package and to build a more efficient environment. Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data.

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

Further Refinement of the LEWICE SLD Model

NASA Technical Reports Server (NTRS)

Wright, William B.

2006-01-01

A research project is underway at NASA Glenn Research Center to produce computer software that can accurately predict ice growth for any meteorological conditions for any aircraft surface. This report will present results from version 3.2 of this software, which is called LEWICE. This version differs from previous releases in that it incorporates additional thermal analysis capabilities, a pneumatic boot model, interfaces to external computational fluid dynamics (CFD) flow solvers and has an empirical model for the supercooled large droplet (SLD) regime. An extensive comparison against the database of ice shapes and collection efficiencies that have been generated in the NASA Glenn Icing Research Tunnel (IRT) has also been performed. The complete set of data used for this comparison will eventually be available in a contractor report. This paper will show the differences in collection efficiency and ice shape between LEWICE 3.2 and experimental data. This report will first describe the LEWICE 3.2 SLD model. A semi-empirical approach was used to incorporate first order physical effects of large droplet phenomena into icing software. Comparisons are then made to every two-dimensional case in the water collection database and the ice shape database. Each collection efficiency condition was run using the following four assumptions: 1) potential flow, no splashing; 2) potential flow, with splashing; 3) Navior-Stokes, no splashing; 4) Navi r-Stokes, with splashing. All cases were run with 21 bin drop size distributions and a lift correction (angle of attack adjustment). Quantitative comparisons are shown for impingement limit, maximum water catch, and total collection efficiency. Due to the large number of ice shape cases, comprehensive comparisons were limited to potential flow cases with and without splashing. Quantitative comparisons are shown for horn height, horn angle, icing limit, area, and leading edge thickness. The results show that the predicted results for both ice shape and water collection are within the accuracy limits of the experimental data for the majority of cases.

Automatic anatomy partitioning of the torso region on CT images by using multiple organ localizations with a group-wise calibration technique

NASA Astrophysics Data System (ADS)

Zhou, Xiangrong; Morita, Syoichi; Zhou, Xinxin; Chen, Huayue; Hara, Takeshi; Yokoyama, Ryujiro; Kanematsu, Masayuki; Hoshi, Hiroaki; Fujita, Hiroshi

2015-03-01

This paper describes an automatic approach for anatomy partitioning on three-dimensional (3D) computedtomography (CT) images that divide the human torso into several volume-of-interesting (VOI) images based on anatomical definition. The proposed approach combines several individual detections of organ-location with a groupwise organ-location calibration and correction to achieve an automatic and robust multiple-organ localization task. The essence of the proposed method is to jointly detect the 3D minimum bounding box for each type of organ shown on CT images based on intra-organ-image-textures and inter-organ-spatial-relationship in the anatomy. Machine-learning-based template matching and generalized Hough transform-based point-distribution estimation are used in the detection and calibration processes. We apply this approach to the automatic partitioning of a torso region on CT images, which are divided into 35 VOIs presenting major organ regions and tissues required by routine diagnosis in clinical medicine. A database containing 4,300 patient cases of high-resolution 3D torso CT images is used for training and performance evaluations. We confirmed that the proposed method was successful in target organ localization on more than 95% of CT cases. Only two organs (gallbladder and pancreas) showed a lower success rate: 71 and 78% respectively. In addition, we applied this approach to another database that included 287 patient cases of whole-body CT images scanned for positron emission tomography (PET) studies and used for additional performance evaluation. The experimental results showed that no significant difference between the anatomy partitioning results from those two databases except regarding the spleen. All experimental results showed that the proposed approach was efficient and useful in accomplishing localization tasks for major organs and tissues on CT images scanned using different protocols.

NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases

PubMed Central

Wang, Jianjian; Cao, Yuze; Zhang, Huixue; Wang, Tianfeng; Tian, Qinghua; Lu, Xiaoyu; Lu, Xiaoyan; Kong, Xiaotong; Liu, Zhaojun; Wang, Ning; Zhang, Shuai; Ma, Heping; Ning, Shangwei; Wang, Lihua

2017-01-01

The Nervous System Disease NcRNAome Atlas (NSDNA) (http://www.bio-bigdata.net/nsdna/) is a manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDs represent a common group of disorders, some of which are characterized by high morbidity and disabilities. The pathogenesis of NSDs at the molecular level remains poorly understood. ncRNAs are a large family of functionally important RNA molecules. Increasing evidence shows that diverse ncRNAs play a critical role in various NSDs. Mining and summarizing NSD–ncRNA association data can help researchers discover useful information. Hence, we developed an NSDNA database that documents 24 713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD–ncRNA associations. It represents an extremely useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs. PMID:27899613

A Summary of Validation Results for LEWICE 2.0

NASA Technical Reports Server (NTRS)

Wright, William B.

1998-01-01

A research project is underway at NASA Lewis to produce a computer code which can accurately predict ice growth under any meteorological conditions for any aircraft surface. This report will present results from version 2.0 of this code, which is called LEWICE. This version differs from previous releases due to its robustness and its ability to reproduce results accurately for different point spacing, and time step criteria across general computing platforms. It also differs in the extensive amount of effort undertaken to compare the results in a quantifiable manner against the database of ice shapes which have been generated in the NASA Lewis Icing, Research Tunnel (IRT), The complete set of data used for this comparison is available in a recent contractor report . The result of this comparison shows that the difference between the predicted ice shape from LEWICE 2.0 and the average of the experimental data is 7.2% while the variability of the experimental data is 2.5%.

Introduction to December 2013 issue.

PubMed

Rogers, Wendy A

2013-12-01

In this introduction to the December 2013 issue of the Journal of Experimental Psychology: Applied, the editor discusses her goals to get the Journal back on track. She gives thanks for the research that continues to advance both science and practice in experimental psychology. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Predictions of nuclear charge radii

NASA Astrophysics Data System (ADS)

Bao, M.; Lu, Y.; Zhao, Y. M.; Arima, A.

2016-12-01

The nuclear charge radius is a fundamental property of an atomic nucleus. In this article we study the predictive power of empirical relations for experimental nuclear charge radii of neighboring nuclei and predict the unknown charge radii of 1085 nuclei based on the experimental CR2013 database within an uncertainty of 0.03 fm.

MIPS: analysis and annotation of proteins from whole genomes

PubMed Central

Mewes, H. W.; Amid, C.; Arnold, R.; Frishman, D.; Güldener, U.; Mannhaupt, G.; Münsterkötter, M.; Pagel, P.; Strack, N.; Stümpflen, V.; Warfsmann, J.; Ruepp, A.

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein–protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de). PMID:14681354

MIPS: analysis and annotation of proteins from whole genomes.

PubMed

Mewes, H W; Amid, C; Arnold, R; Frishman, D; Güldener, U; Mannhaupt, G; Münsterkötter, M; Pagel, P; Strack, N; Stümpflen, V; Warfsmann, J; Ruepp, A

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein-protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).

Data mining the EXFOR database

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

Brown, David A.; Hirdt, John; Herman, Michal

2013-12-13

The EXFOR database contains the largest collection of experimental nuclear reaction data available as well as this data's bibliographic information and experimental details. We created an undirected graph from the EXFOR datasets with graph nodes representing single observables and graph links representing the connections of various types between these observables. This graph is an abstract representation of the connections in EXFOR, similar to graphs of social networks, authorship networks, etc. Analysing this abstract graph, we are able to address very specific questions such as 1) what observables are being used as reference measurements by the experimental community? 2) are thesemore » observables given the attention needed by various standards organisations? 3) are there classes of observables that are not connected to these reference measurements? In addressing these questions, we propose several (mostly cross section) observables that should be evaluated and made into reaction reference standards.« less

ENFIN--A European network for integrative systems biology.

PubMed

Kahlem, Pascal; Clegg, Andrew; Reisinger, Florian; Xenarios, Ioannis; Hermjakob, Henning; Orengo, Christine; Birney, Ewan

2009-11-01

Integration of biological data of various types and the development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both the generation of new bioinformatics tools and the experimental validation of computational predictions. With the aim of bridging the gap existing between standard wet laboratories and bioinformatics, the ENFIN Network runs integrative research projects to bring the latest computational techniques to bear directly on questions dedicated to systems biology in the wet laboratory environment. The Network maintains internally close collaboration between experimental and computational research, enabling a permanent cycling of experimental validation and improvement of computational prediction methods. The computational work includes the development of a database infrastructure (EnCORE), bioinformatics analysis methods and a novel platform for protein function analysis FuncNet.

Mixing characterization of highly underexpanded fluid jets with real gas expansion

NASA Astrophysics Data System (ADS)

Förster, Felix J.; Baab, Steffen; Steinhausen, Christoph; Lamanna, Grazia; Ewart, Paul; Weigand, Bernhard

2018-03-01

We report a comprehensive speed of sound database for multi-component mixing of underexpanded fuel jets with real gas expansion. The paper presents several reference test cases with well-defined experimental conditions providing quantitative data for validation of computational simulations. Two injectant fluids, fundamentally different with respect to their critical properties, are brought to supercritical state and discharged into cold nitrogen at different pressures. The database features a wide range of nozzle pressure ratios covering the regimes that are generally classified as highly and extremely highly underexpanded jets. Further variation is introduced by investigating different injection temperatures. Measurements are obtained along the centerline at different axial positions. In addition, an adiabatic mixing model based on non-ideal thermodynamic mixture properties is used to extract mixture compositions from the experimental speed of sound data. The concentration data obtained are complemented by existing experimental data and represented by an empirical fit.

Characterizing the Response of Composite Panels to a Pyroshock Induced Environment Using Design of Experiments Methodology

NASA Technical Reports Server (NTRS)

Parsons, David S.; Ordway, David; Johnson, Kenneth

2013-01-01

This experimental study seeks to quantify the impact various composite parameters have on the structural response of a composite structure in a pyroshock environment. The prediction of an aerospace structure's response to pyroshock induced loading is largely dependent on empirical databases created from collections of development and flight test data. While there is significant structural response data due to pyroshock induced loading for metallic structures, there is much less data available for composite structures. One challenge of developing a composite pyroshock response database as well as empirical prediction methods for composite structures is the large number of parameters associated with composite materials. This experimental study uses data from a test series planned using design of experiments (DOE) methods. Statistical analysis methods are then used to identify which composite material parameters most greatly influence a flat composite panel's structural response to pyroshock induced loading. The parameters considered are panel thickness, type of ply, ply orientation, and pyroshock level induced into the panel. The results of this test will aid in future large scale testing by eliminating insignificant parameters as well as aid in the development of empirical scaling methods for composite structures' response to pyroshock induced loading.

Characterizing the Response of Composite Panels to a Pyroshock Induced Environment using Design of Experiments Methodology

NASA Technical Reports Server (NTRS)

Parsons, David S.; Ordway, David O.; Johnson, Kenneth L.

2013-01-01

This experimental study seeks to quantify the impact various composite parameters have on the structural response of a composite structure in a pyroshock environment. The prediction of an aerospace structure's response to pyroshock induced loading is largely dependent on empirical databases created from collections of development and flight test data. While there is significant structural response data due to pyroshock induced loading for metallic structures, there is much less data available for composite structures. One challenge of developing a composite pyroshock response database as well as empirical prediction methods for composite structures is the large number of parameters associated with composite materials. This experimental study uses data from a test series planned using design of experiments (DOE) methods. Statistical analysis methods are then used to identify which composite material parameters most greatly influence a flat composite panel's structural response to pyroshock induced loading. The parameters considered are panel thickness, type of ply, ply orientation, and pyroshock level induced into the panel. The results of this test will aid in future large scale testing by eliminating insignificant parameters as well as aid in the development of empirical scaling methods for composite structures' response to pyroshock induced loading.

Robust Optical Recognition of Cursive Pashto Script Using Scale, Rotation and Location Invariant Approach

PubMed Central

Ahmad, Riaz; Naz, Saeeda; Afzal, Muhammad Zeshan; Amin, Sayed Hassan; Breuel, Thomas

2015-01-01

The presence of a large number of unique shapes called ligatures in cursive languages, along with variations due to scaling, orientation and location provides one of the most challenging pattern recognition problems. Recognition of the large number of ligatures is often a complicated task in oriental languages such as Pashto, Urdu, Persian and Arabic. Research on cursive script recognition often ignores the fact that scaling, orientation, location and font variations are common in printed cursive text. Therefore, these variations are not included in image databases and in experimental evaluations. This research uncovers challenges faced by Arabic cursive script recognition in a holistic framework by considering Pashto as a test case, because Pashto language has larger alphabet set than Arabic, Persian and Urdu. A database containing 8000 images of 1000 unique ligatures having scaling, orientation and location variations is introduced. In this article, a feature space based on scale invariant feature transform (SIFT) along with a segmentation framework has been proposed for overcoming the above mentioned challenges. The experimental results show a significantly improved performance of proposed scheme over traditional feature extraction techniques such as principal component analysis (PCA). PMID:26368566

Metabolic pathway reconstruction of eugenol to vanillin bioconversion in Aspergillus niger

PubMed Central

Srivastava, Suchita; Luqman, Suaib; Khan, Feroz; Chanotiya, Chandan S; Darokar, Mahendra P

2010-01-01

Identification of missing genes or proteins participating in the metabolic pathways as enzymes are of great interest. One such class of pathway is involved in the eugenol to vanillin bioconversion. Our goal is to develop an integral approach for identifying the topology of a reference or known pathway in other organism. We successfully identify the missing enzymes and then reconstruct the vanillin biosynthetic pathway in Aspergillus niger. The procedure combines enzyme sequence similarity searched through BLAST homology search and orthologs detection through COG & KEGG databases. Conservation of protein domains and motifs was searched through CDD, PFAM & PROSITE databases. Predictions regarding how proteins act in pathway were validated experimentally and also compared with reported data. The bioconversion of vanillin was screened on UV-TLC plates and later confirmed through GC and GC-MS techniques. We applied a procedure for identifying missing enzymes on the basis of conserved functional motifs and later reconstruct the metabolic pathway in target organism. Using the vanillin biosynthetic pathway of Pseudomonas fluorescens as a case study, we indicate how this approach can be used to reconstruct the reference pathway in A. niger and later results were experimentally validated through chromatography and spectroscopy techniques. PMID:20978605

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.

PubMed

Keseler, Ingrid M; Mackie, Amanda; Santos-Zavaleta, Alberto; Billington, Richard; Bonavides-Martínez, César; Caspi, Ron; Fulcher, Carol; Gama-Castro, Socorro; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Muñiz-Rascado, Luis; Ong, Quang; Paley, Suzanne; Peralta-Gil, Martin; Subhraveti, Pallavi; Velázquez-Ramírez, David A; Weaver, Daniel; Collado-Vides, Julio; Paulsen, Ian; Karp, Peter D

2017-01-04

EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. New SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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 diversity of experimental organisms in biomedical research may be influenced by biomedical funding.

PubMed

Erick Peirson, B R; Kropp, Heather; Damerow, Julia; Laubichler, Manfred D

2017-05-01

Contrary to concerns of some critics, we present evidence that biomedical research is not dominated by a small handful of model organisms. An exhaustive analysis of research literature suggests that the diversity of experimental organisms in biomedical research has increased substantially since 1975. There has been a longstanding worry that organism-centric funding policies can lead to biases in experimental organism choice, and thus negatively impact the direction of research and the interpretation of results. Critics have argued that a focus on model organisms has unduly constrained the diversity of experimental organisms. The availability of large electronic databases of scientific literature, combined with interest in quantitative methods among philosophers of science, presents new opportunities for data-driven investigations into organism choice in biomedical research. The diversity of organisms used in NIH-funded research may be considerably lower than in the broader biomedical sciences, and may be subject to greater constraints on organism choice. © 2017 WILEY Periodicals, Inc.

CFD Validation Experiment of a Mach 2.5 Axisymmetric Shock-Wave/Boundary-Layer Interaction

NASA Technical Reports Server (NTRS)

Davis, David O.

2015-01-01

Experimental investigations of specific flow phenomena, e.g., Shock Wave Boundary-Layer Interactions (SWBLI), provide great insight to the flow behavior but often lack the necessary details to be useful as CFD validation experiments. Reasons include: 1.Undefined boundary conditions Inconsistent results 2.Undocumented 3D effects (CL only measurements) 3.Lack of uncertainty analysis While there are a number of good subsonic experimental investigations that are sufficiently documented to be considered test cases for CFD and turbulence model validation, the number of supersonic and hypersonic cases is much less. This was highlighted by Settles and Dodsons [1] comprehensive review of available supersonic and hypersonic experimental studies. In all, several hundred studies were considered for their database.Of these, over a hundred were subjected to rigorous acceptance criteria. Based on their criteria, only 19 (12 supersonic, 7 hypersonic) were considered of sufficient quality to be used for validation purposes. Aeschliman and Oberkampf [2] recognized the need to develop a specific methodology for experimental studies intended specifically for validation purposes.

Ascent Aerodynamic Pressure Distributions on WB001

NASA Technical Reports Server (NTRS)

Vu, B.; Ruf, J.; Canabal, F.; Brunty, J.

1996-01-01

To support the reusable launch vehicle concept study, the aerodynamic data and surface pressure for WB001 were predicted using three computational fluid dynamic (CFD) codes at several flow conditions between code to code and code to aerodynamic database as well as available experimental data. A set of particular solutions have been selected and recommended for use in preliminary conceptual designs. These computational fluid dynamic (CFD) results have also been provided to the structure group for wing loading analysis.

Experiments in the EXFOR library for evaluation of thermal neutron constants

NASA Astrophysics Data System (ADS)

Otuka, Naohiko; Capote, Roberto; Semkova, Valentina; Kawai, Takuma; Noguere, Gilles

2017-09-01

E.J. Axton's experimental database adopted in evaluation of thermal neutron constants by himself and also by a recent project to update the IAEA Neutron Standard was checked against the experimental literature and EXFOR library. We discovered that many data are found neither in the EXFOR library nor in the articles quoted by Axton due to various reasons. This paper summarizes the status of the experimental data cited by Axton in the experimental literature as well as in the EXFOR library.

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.

MetaboLights: An Open-Access Database Repository for Metabolomics Data.

PubMed

Kale, Namrata S; Haug, Kenneth; Conesa, Pablo; Jayseelan, Kalaivani; Moreno, Pablo; Rocca-Serra, Philippe; Nainala, Venkata Chandrasekhar; Spicer, Rachel A; Williams, Mark; Li, Xuefei; Salek, Reza M; Griffin, Julian L; Steinbeck, Christoph

2016-03-24

MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools. Copyright © 2016 John Wiley & Sons, Inc.

Development of a Searchable Database of Cryoablation Simulations for Use in Treatment Planning

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

Boas, F. Edward, E-mail: boasf@mskcc.org; Srimathveeravalli, Govindarajan, E-mail: srimaths@mskcc.org; Durack, Jeremy C., E-mail: durackj@mskcc.org

PurposeTo create and validate a planning tool for multiple-probe cryoablation, using simulations of ice ball size and shape for various ablation probe configurations, ablation times, and types of tissue ablated.Materials and MethodsIce ball size and shape was simulated using the Pennes bioheat equation. Five thousand six hundred and seventy different cryoablation procedures were simulated, using 1–6 cryoablation probes and 1–2 cm spacing between probes. The resulting ice ball was measured along three perpendicular axes and recorded in a database. Simulated ice ball sizes were compared to gel experiments (26 measurements) and clinical cryoablation cases (42 measurements). The clinical cryoablation measurements weremore » obtained from a HIPAA-compliant retrospective review of kidney and liver cryoablation procedures between January 2015 and February 2016. Finally, we created a web-based cryoablation planning tool, which uses the cryoablation simulation database to look up the probe spacing and ablation time that produces the desired ice ball shape and dimensions.ResultsAverage absolute error between the simulated and experimentally measured ice balls was 1 mm in gel experiments and 4 mm in clinical cryoablation cases. The simulations accurately predicted the degree of synergy in multiple-probe ablations. The cryoablation simulation database covers a wide range of ice ball sizes and shapes up to 9.8 cm.ConclusionCryoablation simulations accurately predict the ice ball size in multiple-probe ablations. The cryoablation database can be used to plan ablation procedures: given the desired ice ball size and shape, it will find the number and type of probes, probe configuration and spacing, and ablation time required.« less

Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data.

PubMed

Su, Xiaoquan; Xu, Jian; Ning, Kang

2012-10-01

It has long been intriguing scientists to effectively compare different microbial communities (also referred as 'metagenomic samples' here) in a large scale: given a set of unknown samples, find similar metagenomic samples from a large repository and examine how similar these samples are. With the current metagenomic samples accumulated, it is possible to build a database of metagenomic samples of interests. Any metagenomic samples could then be searched against this database to find the most similar metagenomic sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure the similarity of metagenomic data work well only for small set of samples by pairwise comparison. It is not yet clear, how to efficiently search for metagenomic samples against a large metagenomic database. In this study, we have proposed a novel method, Meta-Storms, that could systematically and efficiently organize and search metagenomic data. It includes the following components: (i) creating a database of metagenomic samples based on their taxonomical annotations, (ii) efficient indexing of samples in the database based on a hierarchical taxonomy indexing strategy, (iii) searching for a metagenomic sample against the database by a fast scoring function based on quantitative phylogeny and (iv) managing database by index export, index import, data insertion, data deletion and database merging. We have collected more than 1300 metagenomic data from the public domain and in-house facilities, and tested the Meta-Storms method on these datasets. Our experimental results show that Meta-Storms is capable of database creation and effective searching for a large number of metagenomic samples, and it could achieve similar accuracies compared with the current popular significance testing-based methods. Meta-Storms method would serve as a suitable database management and search system to quickly identify similar metagenomic samples from a large pool of samples. ningkang@qibebt.ac.cn Supplementary data are available at Bioinformatics online.

High-Throughput Combinatorial Development of High-Entropy Alloys For Light-Weight Structural Applications

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

Van Duren, Jeroen K; Koch, Carl; Luo, Alan

The primary limitation of today’s lightweight structural alloys is that specific yield strengths (SYS) higher than 200MPa x cc/g (typical value for titanium alloys) are extremely difficult to achieve. This holds true especially at a cost lower than 5dollars/kg (typical value for magnesium alloys). Recently, high-entropy alloys (HEA) have shown promising SYS, yet the large composition space of HEA makes screening compositions complex and time-consuming. Over the course of this 2-year project we started from 150 billion compositions and reduced the number of potential low-density (<5g/cc), low-cost (<5dollars/kg) high-entropy alloy (LDHEA) candidates that are single-phase, disordered, solid-solution (SPSS) to amore » few thousand compositions. This was accomplished by means of machine learning to guide design for SPSS LDHEA based on a combination of recursive partitioning, an extensive, experimental HEA database compiled from 24 literature sources, and 91 calculated parameters serving as phenomenological selection rules. Machine learning shows an accuracy of 82% in identifying which compositions of a separate, smaller, experimental HEA database are SPSS HEA. Calculation of Phase Diagrams (CALPHAD) shows an accuracy of 71-77% for the alloys supported by the CALPHAD database, where 30% of the compiled HEA database is not supported by CALPHAD. In addition to machine learning, and CALPHAD, a third tool was developed to aid design of SPSS LDHEA. Phase diagrams were calculated by constructing the Gibbs-free energy convex hull based on easily accessible enthalpy and entropy terms. Surprisingly, accuracy was 78%. Pursuing these LDHEA candidates by high-throughput experimental methods resulted in SPSS LDHEA composed of transition metals (e.g. Cr, Mn, Fe, Ni, Cu) alloyed with Al, yet the high concentration of Al, necessary to bring the mass density below 5.0g/cc, makes these materials hard and brittle, body-centered-cubic (BCC) alloys. A related, yet multi-phase BCC alloy, based on Al-Cr-Fe-Ni, shows compressive strain >10% and specific compressive yield strength of 229 MPa x cc/g, yet does not show ductility in tensile tests due to cleavage. When replacing Cr in Al-Cr-Fe-based 4- and 5-element LDHEA with Mn, hardness drops 2x. Combined with compression test results, including those on the ternaries Al-Cr-Fe and Al-Mn-Fe suggest that Al-Mn-Fe-based LDHEA are still worth pursuing. These initial results only represent one compressive stress-strain curve per composition without any property optimization. As such, reproducibility needs to be followed by optimization to show their full potential. When including Li, Mg, and Zn, single-phase Li-Mg-Al-Ti-Zn LDHEA has been found with a specific ultimate compressive strength of 289MPa x cc/g. Al-Ti-Mn-Zn showed a specific ultimate compressive strength of 73MPa x cc/g. These initial results after hot isostatic pressing (HIP) of the ball-milled powders represent the lower end of what is possible, since no secondary processing (e.g. extrusion) has been performed to optimize strength and ductility. Compositions for multi-phase (e.g. dual-phase) LDHEA were identified largely by automated searches through CALPHAD databases, while screening for large face-centered-cubic (FCC) volume fractions, followed by experimental verification. This resulted in several new alloys. Li-Mg-Al-Mn-Fe and Mg-Mn-Fe-Co ball-milled powders upon HIP show specific ultimate compressive strengths of 198MPa x cc/g and 45MPa x cc/g, respectively. Several malleable quarternary Al-Zn-based alloys have been found upon arc/induction melting, yet with limited specific compressive yield strength (<75 MPa x cc/g). These initial results are all without any optimization for strength and/or ductility. High-throughput experimentation allowed us to triple the existing experimental HEA database as published in the past 10 years in less than 2 years which happened at a rate 10x higher than previous methods. Furthermore, we showed that high-throughput thin-film combinatorial methods can be used to get insight in isothermal phase diagram slices. Although it is straightforward to map hardness as a function of composition for sputtered, thin-film, compositional gradients by nano-indentation and compare the results to micro-indentation on bulk samples, the simultaneous impact of composition, roughness, film density, and microstructure on hardness requires monitoring all these properties as a function of location on the compositional gradient, including dissecting the impact of these 4 factors on the hardness map. These additional efforts impact throughput significantly. This work shows that a lot of progress has been made over the years in predicting phase formation that aids the discovery of new alloys, yet that a lot of work needs to be done to predict phases more accurately for LDHEA, whether done by CALPHAD or by other means. More importantly, more work needs to be done to predict mechanical properties of novel alloys, like yield strength, and ductility. Furthermore, this work shows that there is a need for the generation of an empirical alloy database covering strategic points in a multi-dimensional composition space to allow for faster and more accurate predictive interpolations to identify the oasis in the dessert more quickly. Finally, this work suggests that it is worth pursuing a ductile alloy with a SYS > 300 MPa x cc/g in a mass density range of 6-7 g/cc, since the chances for a single-phase or majority-phase FCC increase significantly. Today’s lightweight steels are in this density range.« less

Experimental Investigation of Gas/Slag/Matte/Tridymite Equilibria in the Cu-Fe-O-S-Si System in Controlled Gas Atmospheres: Experimental Results at 1473 K (1200 °C) and P(SO2) = 0.25 atm

NASA Astrophysics Data System (ADS)

Fallah-Mehrjardi, Ata; Hidayat, Taufiq; Hayes, Peter C.; Jak, Evgueni

2017-12-01

Experimental studies were undertaken to determine the gas/slag/matte/tridymite equilibria in the Cu-Fe-O-S-Si system at 1473 K (1200 °C), P(SO2) = 0.25 atm, and a range of P(O2)'s. The experimental methodology involved high-temperature equilibration using a substrate support technique in controlled gas atmospheres (CO/CO2/SO2/Ar), rapid quenching of equilibrium phases, followed by direct measurement of the chemical compositions of the phases with Electron Probe X-ray Microanalysis (EPMA). The experimental data for slag and matte were presented as a function of copper concentration in matte (matte grade). The data provided are essential for the evaluation of the effect of oxygen potential under controlled atmosphere on the matte grade, liquidus composition of slag and chemically dissolved copper in slag. The new data provide important accurate and reliable quantitative foundation for improvement of the thermodynamic databases for copper-containing systems.

An experimental investigation of referential looking in free-ranging Barbary macaques (Macaca sylvanus).

PubMed

Roberts, Sam G B; McComb, Karen; Ruffman, Ted

2008-02-01

The authors examined looking behavior between 15 Barbary macaque (Macaca sylvanus) infants and their mothers in the presence of a rubber snake (experimental period) and in the absence of the snake (control period). Two of the 15 infants looked referentially at their mother in the experimental period. Including both referential and nonreferential looks, the six older infants (aged 5 to 12 months) displayed a higher frequency of looks to mother than nine younger infants (aged 3 to 4.5 months) in the experimental period, but not in the control period. Older infants looked more to the mother in the experimental condition, whereas the younger infants looked more to the mother in the control condition, or looked equally in the two conditions. These results suggest that age is an important factor in determining looking behavior to mother in situations of uncertainty. Compared to hand-reared chimpanzees or human infants tested in standard social referencing paradigms, the infant macaques displayed a low rate of referential looking. Possible explanations for this are discussed. (PsycINFO Database Record (c) 2008 APA, all rights reserved).

Counterbalancing for serial order carryover effects in experimental condition orders.

PubMed

Brooks, Joseph L

2012-12-01

Reactions of neural, psychological, and social systems are rarely, if ever, independent of previous inputs and states. The potential for serial order carryover effects from one condition to the next in a sequence of experimental trials makes counterbalancing of condition order an essential part of experimental design. Here, a method is proposed for generating counterbalanced sequences for repeated-measures designs including those with multiple observations of each condition on one participant and self-adjacencies of conditions. Condition ordering is reframed as a graph theory problem. Experimental conditions are represented as vertices in a graph and directed edges between them represent temporal relationships between conditions. A counterbalanced trial order results from traversing an Euler circuit through such a graph in which each edge is traversed exactly once. This method can be generalized to counterbalance for higher order serial order carryover effects as well as to create intentional serial order biases. Modern graph theory provides tools for finding other types of paths through such graph representations, providing a tool for generating experimental condition sequences with useful properties. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Quasi-experimental study designs series-paper 8: identifying quasi-experimental studies to inform systematic reviews.

PubMed

Glanville, Julie; Eyers, John; Jones, Andrew M; Shemilt, Ian; Wang, Grace; Johansen, Marit; Fiander, Michelle; Rothstein, Hannah

2017-09-01

This article reviews the available evidence and guidance on methods to identify reports of quasi-experimental (QE) studies to inform systematic reviews of health care, public health, international development, education, crime and justice, and social welfare. Research, guidance, and examples of search strategies were identified by searching a range of databases, key guidance documents, selected reviews, conference proceedings, and personal communication. Current practice and research evidence were summarized. Four thousand nine hundred twenty-four records were retrieved by database searches, and additional documents were obtained by other searches. QE studies are challenging to identify efficiently because they have no standardized nomenclature and may be indexed in various ways. Reliable search filters are not available. There is a lack of specific resources devoted to collecting QE studies and little evidence on where best to search. Searches to identify QE studies should search a range of resources and, until indexing improves, use strategies that focus on the topic rather than the study design. Better definitions, better indexing in databases, prospective registers, and reporting guidance are required to improve the retrieval of QE studies and promote systematic reviews of what works based on the evidence from such studies. Copyright © 2017 Elsevier Inc. All rights reserved.

G4RNA: an RNA G-quadruplex database

PubMed Central

Garant, Jean-Michel; Luce, Mikael J.; Scott, Michelle S.

2015-01-01

Abstract G-quadruplexes (G4) are tetrahelical structures formed from planar arrangement of guanines in nucleic acids. A simple, regular motif was originally proposed to describe G4-forming sequences. More recently, however, formation of G4 was discovered to depend, at least in part, on the contextual backdrop of neighboring sequences. Prediction of G4 folding is thus becoming more challenging as G4 outlier structures, not described by the originally proposed motif, are increasingly reported. Recent observations thus call for a comprehensive tool, capable of consolidating the expanding information on tested G4s, in order to conduct systematic comparative analyses of G4-promoting sequences. The G4RNA Database we propose was designed to help meet the need for easily-retrievable data on known RNA G4s. A user-friendly, flexible query system allows for data retrieval on experimentally tested sequences, from many separate genes, to assess G4-folding potential. Query output sorts data according to sequence position, G4 likelihood, experimental outcomes and associated bibliographical references. G4RNA also provides an ideal foundation to collect and store additional sequence and experimental data, considering the growing interest G4s currently generate. Database URL: scottgroup.med.usherbrooke.ca/G4RNA PMID:26200754

Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers

PubMed Central

Ning, Shangwei; Zhang, Jizhou; Wang, Peng; Zhi, Hui; Wang, Jianjian; Liu, Yue; Gao, Yue; Guo, Maoni; Yue, Ming; Wang, Lihua; Li, Xia

2016-01-01

Lnc2Cancer (http://www.bio-bigdata.net/lnc2cancer) is a manually curated database of cancer-associated long non-coding RNAs (lncRNAs) with experimental support that aims to provide a high-quality and integrated resource for exploring lncRNA deregulation in various human cancers. LncRNAs represent a large category of functional RNA molecules that play a significant role in human cancers. A curated collection and summary of deregulated lncRNAs in cancer is essential to thoroughly understand the mechanisms and functions of lncRNAs. Here, we developed the Lnc2Cancer database, which contains 1057 manually curated associations between 531 lncRNAs and 86 human cancers. Each association includes lncRNA and cancer name, the lncRNA expression pattern, experimental techniques, a brief functional description, the original reference and additional annotation information. Lnc2Cancer provides a user-friendly interface to conveniently browse, retrieve and download data. Lnc2Cancer also offers a submission page for researchers to submit newly validated lncRNA-cancer associations. With the rapidly increasing interest in lncRNAs, Lnc2Cancer will significantly improve our understanding of lncRNA deregulation in cancer and has the potential to be a timely and valuable resource. PMID:26481356

An NMR database for simulations of membrane dynamics.

PubMed

Leftin, Avigdor; Brown, Michael F

2011-03-01

Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations. Copyright © 2010 Elsevier B.V. All rights reserved.

Development and Experimental Verification of a High Resolution, Tunable LIDAR Computer Simulation Model for Atmospheric Laser Remote Sensing

NASA Astrophysics Data System (ADS)

Wilcox, William Edward, Jr.

1995-01-01

A computer program (LIDAR-PC) and associated atmospheric spectral databases have been developed which accurately simulate the laser remote sensing of the atmosphere and the system performance of a direct-detection Lidar or tunable Differential Absorption Lidar (DIAL) system. This simulation program allows, for the first time, the use of several different large atmospheric spectral databases to be coupled with Lidar parameter simulations on the same computer platform to provide a real-time, interactive, and easy to use design tool for atmospheric Lidar simulation and modeling. LIDAR -PC has been used for a range of different Lidar simulations and compared to experimental Lidar data. In general, the simulations agreed very well with the experimental measurements. In addition, the simulation offered, for the first time, the analysis and comparison of experimental Lidar data to easily determine the range-resolved attenuation coefficient of the atmosphere and the effect of telescope overlap factor. The software and databases operate on an IBM-PC or compatible computer platform, and thus are very useful to the research community for Lidar analysis. The complete Lidar and atmospheric spectral transmission modeling program uses the HITRAN database for high-resolution molecular absorption lines of the atmosphere, the BACKSCAT/LOWTRAN computer databases and models for the effects of aerosol and cloud backscatter and attenuation, and the range-resolved Lidar equation. The program can calculate the Lidar backscattered signal-to-noise for a slant path geometry from space and simulate the effect of high resolution, tunable, single frequency, and moderate line width lasers on the Lidar/DIAL signal. The program was used to model and analyze the experimental Lidar data obtained from several measurements. A fixed wavelength, Ho:YSGG aerosol Lidar (Sugimoto, 1990) developed at USF and a tunable Ho:YSGG DIAL system (Cha, 1991) for measuring atmospheric water vapor at 2.1 μm were analyzed. The simulations agreed very well with the measurements, and also yielded, for the first time, the ability to easily deduce the atmospheric attentuation coefficient, alpha, from the Lidar data. Simulations and analysis of other Lidar measurements included that of a 1.57 mu m OPO aerosol Lidar system developed at USF (Harrell, 1995) and of the NASA LITE (Laser-in-Space Technology Experiment) Lidar recently flown in the Space shuttle. Finally, an extensive series of laboratory experiments were made with the 1.57 μm OPO Lidar system to test calculations of the telescope/laser overlap and the effect of different telescope sizes and designs. The simulations agreed well with the experimental data for the telescope diameter and central obscuration test cases. The LIDAR-PC programs are available on the Internet from the USAF Lidar Home Page Web site, http://www.cas.usf.edu/physics/lidar.html/.

The Starlite Project - Prototyping Real-Time Software.

DTIC Science & Technology

1992-11-01

by ONR under contract ledge of transactions and a temporal data model. A N00014-91-J-l 102, by DOE, and by NOSC. multiversion data object is one...environment. Section 4 presents experimentations of priority-based synchronization algorithms and multiversion data objects using the prototyping environment...priority-based .yn- chronization algorithms and between a multiversion database and its corresponding single- version database, through the sensitivity

Experimental Verification of the Individual Energy Dependencies of the Partial L-Shell Photoionization Cross Sections of Pd and Mo

NASA Astrophysics Data System (ADS)

Hönicke, Philipp; Kolbe, Michael; Müller, Matthias; Mantler, Michael; Krämer, Markus; Beckhoff, Burkhard

2014-10-01

An experimental method for the verification of the individually different energy dependencies of L1-, L2-, and L3- subshell photoionization cross sections is described. The results obtained for Pd and Mo are well in line with theory regarding both energy dependency and absolute values, and confirm the theoretically calculated cross sections by Scofield from the early 1970 s and, partially, more recent data by Trzhaskovskaya, Nefedov, and Yarzhemsky. The data also demonstrate the questionability of quantitative x-ray spectroscopical results based on the widely used fixed jump ratio approximated cross sections with energy independent ratios. The experiments are carried out by employing the radiometrically calibrated instrumentation of the Physikalisch-Technische Bundesanstalt at the electron storage ring BESSY II in Berlin; the obtained fluorescent intensities are thereby calibrated at an absolute level in reference to the International System of Units. Experimentally determined fixed fluorescence line ratios for each subshell are used for a reliable deconvolution of overlapping fluorescence lines. The relevant fundamental parameters of Mo and Pd are also determined experimentally in order to calculate the subshell photoionization cross sections independently of any database.

Enhancement of real-time EPICS IOC PV management for the data archiving system

NASA Astrophysics Data System (ADS)

Kim, Jae-Ha

2015-10-01

The operation of a 100-MeV linear proton accelerator, the major driving values and experimental data need to be archived. According to the experimental conditions, different data are required. Functions that can add new data and delete data in real time need to be implemented. In an experimental physics and industrial control system (EPICS) input output controller (IOC), the value of process variables (PVs) are matched with the driving values and data. The PV values are archived in text file format by using the channel archiver. There is no need to create a database (DB) server, just a need for large hard disk. Through the web, the archived data can be loaded, and new PV values can be archived without stopping the archive engine. The details of the implementation of a data archiving system with channel archiver are presented, and some preliminary results are reported.

Charge optimized many-body potential for aluminum.

PubMed

Choudhary, Kamal; Liang, Tao; Chernatynskiy, Aleksandr; Lu, Zizhe; Goyal, Anuj; Phillpot, Simon R; Sinnott, Susan B

2015-01-14

An interatomic potential for Al is developed within the third generation of the charge optimized many-body (COMB3) formalism. The database used for the parameterization of the potential consists of experimental data and the results of first-principles and quantum chemical calculations. The potential exhibits reasonable agreement with cohesive energy, lattice parameters, elastic constants, bulk and shear modulus, surface energies, stacking fault energies, point defect formation energies, and the phase order of metallic Al from experiments and density functional theory. In addition, the predicted phonon dispersion is in good agreement with the experimental data and first-principles calculations. Importantly for the prediction of the mechanical behavior, the unstable stacking fault energetics along the [Formula: see text] direction on the (1 1 1) plane are similar to those obtained from first-principles calculations. The polycrsytal when strained shows responses that are physical and the overall behavior is consistent with experimental observations.

Detection and quantification of creep strain using process compensated resonance testing (PCRT) sorting modules trained with modeled resonance spectra

NASA Astrophysics Data System (ADS)

Heffernan, Julieanne; Biedermann, Eric; Mayes, Alexander; Livings, Richard; Jauriqui, Leanne; Goodlet, Brent; Aldrin, John C.; Mazdiyasni, Siamack

2018-04-01

Process Compensated Resonant Testing (PCRT) is a full-body nondestructive testing (NDT) method that measures the resonance frequencies of a part and correlates them to the part's material and/or damage state. PCRT testing is used in the automotive, aerospace, and power generation industries via automated PASS/FAIL inspections to distinguish parts with nominal process variation from those with the defect(s) of interest. Traditional PCRT tests are created through the statistical analysis of populations of "good" and "bad" parts. However, gathering a statistically significant number of parts can be costly and time-consuming, and the availability of defective parts may be limited. This work uses virtual databases of good and bad parts to create two targeted PCRT inspections for single crystal (SX) nickel-based superalloy turbine blades. Using finite element (FE) models, populations were modeled to include variations in geometric dimensions, material properties, crystallographic orientation, and creep damage. Model results were verified by comparing the frequency variation in the modeled populations with the measured frequency variations of several physical blade populations. Additionally, creep modeling results were verified through the experimental evaluation of coupon geometries. A virtual database of resonance spectra was created from the model data. The virtual database was used to create PCRT inspections to detect crystallographic defects and creep strain. Quantification of creep strain values using the PCRT inspection results was also demonstrated.

Combining Evidence of Preferential Gene-Tissue Relationships from Multiple Sources

PubMed Central

Guo, Jing; Hammar, Mårten; Öberg, Lisa; Padmanabhuni, Shanmukha S.; Bjäreland, Marcus; Dalevi, Daniel

2013-01-01

An important challenge in drug discovery and disease prognosis is to predict genes that are preferentially expressed in one or a few tissues, i.e. showing a considerably higher expression in one tissue(s) compared to the others. Although several data sources and methods have been published explicitly for this purpose, they often disagree and it is not evident how to retrieve these genes and how to distinguish true biological findings from those that are due to choice-of-method and/or experimental settings. In this work we have developed a computational approach that combines results from multiple methods and datasets with the aim to eliminate method/study-specific biases and to improve the predictability of preferentially expressed human genes. A rule-based score is used to merge and assign support to the results. Five sets of genes with known tissue specificity were used for parameter pruning and cross-validation. In total we identify 3434 tissue-specific genes. We compare the genes of highest scores with the public databases: PaGenBase (microarray), TiGER (EST) and HPA (protein expression data). The results have 85% overlap to PaGenBase, 71% to TiGER and only 28% to HPA. 99% of our predictions have support from at least one of these databases. Our approach also performs better than any of the databases on identifying drug targets and biomarkers with known tissue-specificity. PMID:23950964

GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms

PubMed Central

David, Fabrice P.A.; Rougemont, Jacques; Deplancke, Bart

2017-01-01

GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing gene- and transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification of one or several splice variants of most known genes. To ease selection, primers have also been ranked according to defined criteria such as genome-wide specificity (with BLAST), amplicon size, and isoform coverage. Here, we report a major upgrade (2.0) of the database: eight new species (yeast, chicken, macaque, chimpanzee, rat, platypus, pufferfish, and Anolis carolinensis) now complement the five already included in the previous version (human, mouse, zebrafish, fly, and worm). Furthermore, the genomic reference has been updated to Ensembl v81 (while keeping earlier versions for backward compatibility) as a result of re-designing the back-end database and automating the import of relevant sections of the Ensembl database in species-independent fashion. This also allowed us to map known polymorphisms to the primers (on average three per primer for human), with the aim of reducing experimental error when targeting specific strains or individuals. Another consequence is that the inclusion of future Ensembl releases and other species has now become a relatively straightforward task. PMID:28053161

Latent fingerprint matching.

PubMed

Jain, Anil K; Feng, Jianjiang

2011-01-01

Latent fingerprint identification is of critical importance to law enforcement agencies in identifying suspects: Latent fingerprints are inadvertent impressions left by fingers on surfaces of objects. While tremendous progress has been made in plain and rolled fingerprint matching, latent fingerprint matching continues to be a difficult problem. Poor quality of ridge impressions, small finger area, and large nonlinear distortion are the main difficulties in latent fingerprint matching compared to plain or rolled fingerprint matching. We propose a system for matching latent fingerprints found at crime scenes to rolled fingerprints enrolled in law enforcement databases. In addition to minutiae, we also use extended features, including singularity, ridge quality map, ridge flow map, ridge wavelength map, and skeleton. We tested our system by matching 258 latents in the NIST SD27 database against a background database of 29,257 rolled fingerprints obtained by combining the NIST SD4, SD14, and SD27 databases. The minutiae-based baseline rank-1 identification rate of 34.9 percent was improved to 74 percent when extended features were used. In order to evaluate the relative importance of each extended feature, these features were incrementally used in the order of their cost in marking by latent experts. The experimental results indicate that singularity, ridge quality map, and ridge flow map are the most effective features in improving the matching accuracy.

A privacy-preserved analytical method for ehealth database with minimized information loss.

PubMed

Chen, Ya-Ling; Cheng, Bo-Chao; Chen, Hsueh-Lin; Lin, Chia-I; Liao, Guo-Tan; Hou, Bo-Yu; Hsu, Shih-Chun

2012-01-01

Digitizing medical information is an emerging trend that employs information and communication technology (ICT) to manage health records, diagnostic reports, and other medical data more effectively, in order to improve the overall quality of medical services. However, medical information is highly confidential and involves private information, even legitimate access to data raises privacy concerns. Medical records provide health information on an as-needed basis for diagnosis and treatment, and the information is also important for medical research and other health management applications. Traditional privacy risk management systems have focused on reducing reidentification risk, and they do not consider information loss. In addition, such systems cannot identify and isolate data that carries high risk of privacy violations. This paper proposes the Hiatus Tailor (HT) system, which ensures low re-identification risk for medical records, while providing more authenticated information to database users and identifying high-risk data in the database for better system management. The experimental results demonstrate that the HT system achieves much lower information loss than traditional risk management methods, with the same risk of re-identification.

On Applicability of Tunable Filter Bank Based Feature for Ear Biometrics: A Study from Constrained to Unconstrained.

PubMed

Chowdhury, Debbrota Paul; Bakshi, Sambit; Guo, Guodong; Sa, Pankaj Kumar

2017-11-27

In this paper, an overall framework has been presented for person verification using ear biometric which uses tunable filter bank as local feature extractor. The tunable filter bank, based on a half-band polynomial of 14th order, extracts distinct features from ear images maintaining its frequency selectivity property. To advocate the applicability of tunable filter bank on ear biometrics, recognition test has been performed on available constrained databases like AMI, WPUT, IITD and unconstrained database like UERC. Experiments have been conducted applying tunable filter based feature extractor on subparts of the ear. Empirical experiments have been conducted with four and six subdivisions of the ear image. Analyzing the experimental results, it has been found that tunable filter moderately succeeds to distinguish ear features at par with the state-of-the-art features used for ear recognition. Accuracies of 70.58%, 67.01%, 81.98%, and 57.75% have been achieved on AMI, WPUT, IITD, and UERC databases through considering Canberra Distance as underlying measure of separation. The performances indicate that tunable filter is a candidate for recognizing human from ear images.

Molecular Oxygen in the Thermosphere: Issues and Measurement Strategies

NASA Astrophysics Data System (ADS)

Picone, J. M.; Hedin, A. E.; Drob, D. P.; Meier, R. R.; Bishop, J.; Budzien, S. A.

2002-05-01

We review the state of empirical knowledge regarding the distribution of molecular oxygen in the lower thermosphere (100-200 km), as embodied by the new NRLMSISE-00 empirical atmospheric model, its predecessors, and the underlying databases. For altitudes above 120 km, the two major classes of data (mass spectrometer and solar ultraviolet [UV] absorption) disagree significantly regarding the magnitude of the O2 density and the dependence on solar activity. As a result, the addition of the Solar Maximum Mission (SMM) data set (based on solar UV absorption) to the NRLMSIS database has directly impacted the new model, increasing the complexity of the model's formulation and generally reducing the thermospheric O2 density relative to MSISE-90. Beyond interest in the thermosphere itself, this issue materially affects detailed models of ionospheric chemistry and dynamics as well as modeling of the upper atmospheric airglow. Because these are key elements of both experimental and operational systems which measure and forecast the near-Earth space environment, we present strategies for augmenting the database through analysis of existing data and through future measurements in order to resolve this issue.

Freely Accessible Chemical Database Resources of Compounds for in Silico Drug Discovery.

PubMed

Yang, JingFang; Wang, Di; Jia, Chenyang; Wang, Mengyao; Hao, GeFei; Yang, GuangFu

2018-05-07

In silico drug discovery has been proved to be a solidly established key component in early drug discovery. However, this task is hampered by the limitation of quantity and quality of compound databases for screening. In order to overcome these obstacles, freely accessible database resources of compounds have bloomed in recent years. Nevertheless, how to choose appropriate tools to treat these freely accessible databases are crucial. To the best of our knowledge, this is the first systematic review on this issue. The existed advantages and drawbacks of chemical databases were analyzed and summarized based on the collected six categories of freely accessible chemical databases from literature in this review. Suggestions on how and in which conditions the usage of these databases could be reasonable were provided. Tools and procedures for building 3D structure chemical libraries were also introduced. In this review, we described the freely accessible chemical database resources for in silico drug discovery. In particular, the chemical information for building chemical database appears as attractive resources for drug design to alleviate experimental pressure. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Protein Information Resource: a community resource for expert annotation of protein data

PubMed Central

Barker, Winona C.; Garavelli, John S.; Hou, Zhenglin; Huang, Hongzhan; Ledley, Robert S.; McGarvey, Peter B.; Mewes, Hans-Werner; Orcutt, Bruce C.; Pfeiffer, Friedhelm; Tsugita, Akira; Vinayaka, C. R.; Xiao, Chunlin; Yeh, Lai-Su L.; Wu, Cathy

2001-01-01

The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database. To provide timely and high quality annotation and promote database interoperability, the PIR-International employs rule-based and classification-driven procedures based on controlled vocabulary and standard nomenclature and includes status tags to distinguish experimentally determined from predicted protein features. The database contains about 200 000 non-redundant protein sequences, which are classified into families and superfamilies and their domains and motifs identified. Entries are extensively cross-referenced to other sequence, classification, genome, structure and activity databases. The PIR web site features search engines that use sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. The PIR-Inter­national databases and search tools are accessible on the PIR web site at http://pir.georgetown.edu/ and at the MIPS web site at http://www.mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP. PMID:11125041

In silico design and screening of hypothetical MOF-74 analogs and their experimental synthesis

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

Witman, Matthew; Ling, Sanliang; Anderson, Samantha

2016-01-01

We present thein silico designof MOFs exhibiting 1-dimensional rod topologies by enumerating MOF-74-type analogs based on the PubChem Compounds database. We simulate the adsorption behavior of CO 2in the generated analogs and experimentally validate a novel MOF-74 analog, Mg 2(olsalazine).

Free online access to experimental and predicted chemical properties through the EPA’s CompTox Chemistry Dashboard (ACS Spring meeting)

EPA Science Inventory

The increasing number and size of public databases is facilitating the collection of chemical structures and associated experimental data for QSAR modeling. However, the performance of QSAR models is highly dependent not only on the modeling methodology, but also on the quality o...

Development plan for the External Hazards Experimental Group. Light Water Reactor Sustainability Program

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

Coleman, Justin Leigh; Smith, Curtis Lee; Burns, Douglas Edward

This report describes the development plan for a new multi-partner External Hazards Experimental Group (EHEG) coordinated by Idaho National Laboratory (INL) within the Risk-Informed Safety Margin Characterization (RISMC) technical pathway of the Light Water Reactor Sustainability Program. Currently, there is limited data available for development and validation of the tools and methods being developed in the RISMC Toolkit. The EHEG is being developed to obtain high-quality, small- and large-scale experimental data validation of RISMC tools and methods in a timely and cost-effective way. The group of universities and national laboratories that will eventually form the EHEG (which is ultimately expectedmore » to include both the initial participants and other universities and national laboratories that have been identified) have the expertise and experimental capabilities needed to both obtain and compile existing data archives and perform additional seismic and flooding experiments. The data developed by EHEG will be stored in databases for use within RISMC. These databases will be used to validate the advanced external hazard tools and methods.« less

Application of new type of distributed multimedia databases to networked electronic museum

NASA Astrophysics Data System (ADS)

Kuroda, Kazuhide; Komatsu, Naohisa; Komiya, Kazumi; Ikeda, Hiroaki

1999-01-01

Recently, various kinds of multimedia application systems have actively been developed based on the achievement of advanced high sped communication networks, computer processing technologies, and digital contents-handling technologies. Under this background, this paper proposed a new distributed multimedia database system which can effectively perform a new function of cooperative retrieval among distributed databases. The proposed system introduces a new concept of 'Retrieval manager' which functions as an intelligent controller so that the user can recognize a set of distributed databases as one logical database. The logical database dynamically generates and performs a preferred combination of retrieving parameters on the basis of both directory data and the system environment. Moreover, a concept of 'domain' is defined in the system as a managing unit of retrieval. The retrieval can effectively be performed by cooperation of processing among multiple domains. Communication language and protocols are also defined in the system. These are used in every action for communications in the system. A language interpreter in each machine translates a communication language into an internal language used in each machine. Using the language interpreter, internal processing, such internal modules as DBMS and user interface modules can freely be selected. A concept of 'content-set' is also introduced. A content-set is defined as a package of contents. Contents in the content-set are related to each other. The system handles a content-set as one object. The user terminal can effectively control the displaying of retrieved contents, referring to data indicating the relation of the contents in the content- set. In order to verify the function of the proposed system, a networked electronic museum was experimentally built. The results of this experiment indicate that the proposed system can effectively retrieve the objective contents under the control to a number of distributed domains. The result also indicate that the system can effectively work even if the system becomes large.

Pulmonary Nodule Classification with Deep Convolutional Neural Networks on Computed Tomography Images.

PubMed

Li, Wei; Cao, Peng; Zhao, Dazhe; Wang, Junbo

2016-01-01

Computer aided detection (CAD) systems can assist radiologists by offering a second opinion on early diagnosis of lung cancer. Classification and feature representation play critical roles in false-positive reduction (FPR) in lung nodule CAD. We design a deep convolutional neural networks method for nodule classification, which has an advantage of autolearning representation and strong generalization ability. A specified network structure for nodule images is proposed to solve the recognition of three types of nodules, that is, solid, semisolid, and ground glass opacity (GGO). Deep convolutional neural networks are trained by 62,492 regions-of-interest (ROIs) samples including 40,772 nodules and 21,720 nonnodules from the Lung Image Database Consortium (LIDC) database. Experimental results demonstrate the effectiveness of the proposed method in terms of sensitivity and overall accuracy and that it consistently outperforms the competing methods.

Novel face-detection method under various environments

NASA Astrophysics Data System (ADS)

Jing, Min-Quan; Chen, Ling-Hwei

2009-06-01

We propose a method to detect a face with different poses under various environments. On the basis of skin color information, skin regions are first extracted from an input image. Next, the shoulder part is cut out by using shape information and the head part is then identified as a face candidate. For a face candidate, a set of geometric features is applied to determine if it is a profile face. If not, then a set of eyelike rectangles extracted from the face candidate and the lighting distribution are used to determine if the face candidate is a nonprofile face. Experimental results show that the proposed method is robust under a wide range of lighting conditions, different poses, and races. The detection rate for the HHI face database is 93.68%. For the Champion face database, the detection rate is 95.15%.

The path to enlightenment: making sense of genomic and proteomic information.

PubMed

Maurer, Martin H

2004-05-01

Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.

Matching CCD images to a stellar catalog using locality-sensitive hashing

NASA Astrophysics Data System (ADS)

Liu, Bo; Yu, Jia-Zong; Peng, Qing-Yu

2018-02-01

The usage of a subset of observed stars in a CCD image to find their corresponding matched stars in a stellar catalog is an important issue in astronomical research. Subgraph isomorphic-based algorithms are the most widely used methods in star catalog matching. When more subgraph features are provided, the CCD images are recognized better. However, when the navigation feature database is large, the method requires more time to match the observing model. To solve this problem, this study investigates further and improves subgraph isomorphic matching algorithms. We present an algorithm based on a locality-sensitive hashing technique, which allocates quadrilateral models in the navigation feature database into different hash buckets and reduces the search range to the bucket in which the observed quadrilateral model is located. Experimental results indicate the effectivity of our method.

Constructing compact and effective graphs for recommender systems via node and edge aggregations

DOE PAGES

Lee, Sangkeun; Kahng, Minsuk; Lee, Sang-goo

2014-12-10

Exploiting graphs for recommender systems has great potential to flexibly incorporate heterogeneous information for producing better recommendation results. As our baseline approach, we first introduce a naive graph-based recommendation method, which operates with a heterogeneous log-metadata graph constructed from user log and content metadata databases. Although the na ve graph-based recommendation method is simple, it allows us to take advantages of heterogeneous information and shows promising flexibility and recommendation accuracy. However, it often leads to extensive processing time due to the sheer size of the graphs constructed from entire user log and content metadata databases. In this paper, we proposemore » node and edge aggregation approaches to constructing compact and e ective graphs called Factor-Item bipartite graphs by aggregating nodes and edges of a log-metadata graph. Furthermore, experimental results using real world datasets indicate that our approach can significantly reduce the size of graphs exploited for recommender systems without sacrificing the recommendation quality.« less

Noise Radiation From a Leading-Edge Slat

NASA Technical Reports Server (NTRS)

Lockard, David P.; Choudhari, Meelan M.

2009-01-01

This paper extends our previous computations of unsteady flow within the slat cove region of a multi-element high-lift airfoil configuration, which showed that both statistical and structural aspects of the experimentally observed unsteady flow behavior can be captured via 3D simulations over a computational domain of narrow spanwise extent. Although such narrow domain simulation can account for the spanwise decorrelation of the slat cove fluctuations, the resulting database cannot be applied towards acoustic predictions of the slat without invoking additional approximations to synthesize the fluctuation field over the rest of the span. This deficiency is partially alleviated in the present work by increasing the spanwise extent of the computational domain from 37.3% of the slat chord to nearly 226% (i.e., 15% of the model span). The simulation database is used to verify consistency with previous computational results and, then, to develop predictions of the far-field noise radiation in conjunction with a frequency-domain Ffowcs-Williams Hawkings solver.

High-throughput determination of structural phase diagram and constituent phases using GRENDEL

NASA Astrophysics Data System (ADS)

Kusne, A. G.; Keller, D.; Anderson, A.; Zaban, A.; Takeuchi, I.

2015-11-01

Advances in high-throughput materials fabrication and characterization techniques have resulted in faster rates of data collection and rapidly growing volumes of experimental data. To convert this mass of information into actionable knowledge of material process-structure-property relationships requires high-throughput data analysis techniques. This work explores the use of the Graph-based endmember extraction and labeling (GRENDEL) algorithm as a high-throughput method for analyzing structural data from combinatorial libraries, specifically, to determine phase diagrams and constituent phases from both x-ray diffraction and Raman spectral data. The GRENDEL algorithm utilizes a set of physical constraints to optimize results and provides a framework by which additional physics-based constraints can be easily incorporated. GRENDEL also permits the integration of database data as shown by the use of critically evaluated data from the Inorganic Crystal Structure Database in the x-ray diffraction data analysis. Also the Sunburst radial tree map is demonstrated as a tool to visualize material structure-property relationships found through graph based analysis.

Molecular signatures database (MSigDB) 3.0.

PubMed

Liberzon, Arthur; Subramanian, Aravind; Pinchback, Reid; Thorvaldsdóttir, Helga; Tamayo, Pablo; Mesirov, Jill P

2011-06-15

Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets. We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site. MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.

Design and Development of a Technology Platform for DNA-Encoded Library Production and Affinity Selection.

PubMed

Castañón, Jesús; Román, José Pablo; Jessop, Theodore C; de Blas, Jesús; Haro, Rubén

2018-06-01

DNA-encoded libraries (DELs) have emerged as an efficient and cost-effective drug discovery tool for the exploration and screening of very large chemical space using small-molecule collections of unprecedented size. Herein, we report an integrated automation and informatics system designed to enhance the quality, efficiency, and throughput of the production and affinity selection of these libraries. The platform is governed by software developed according to a database-centric architecture to ensure data consistency, integrity, and availability. Through its versatile protocol management functionalities, this application captures the wide diversity of experimental processes involved with DEL technology, keeps track of working protocols in the database, and uses them to command robotic liquid handlers for the synthesis of libraries. This approach provides full traceability of building-blocks and DNA tags in each split-and-pool cycle. Affinity selection experiments and high-throughput sequencing reads are also captured in the database, and the results are automatically deconvoluted and visualized in customizable representations. Researchers can compare results of different experiments and use machine learning methods to discover patterns in data. As of this writing, the platform has been validated through the generation and affinity selection of various libraries, and it has become the cornerstone of the DEL production effort at Lilly.

A framework of multitemplate ensemble for fingerprint verification

NASA Astrophysics Data System (ADS)

Yin, Yilong; Ning, Yanbin; Ren, Chunxiao; Liu, Li

2012-12-01

How to improve performance of an automatic fingerprint verification system (AFVS) is always a big challenge in biometric verification field. Recently, it becomes popular to improve the performance of AFVS using ensemble learning approach to fuse related information of fingerprints. In this article, we propose a novel framework of fingerprint verification which is based on the multitemplate ensemble method. This framework is consisted of three stages. In the first stage, enrollment stage, we adopt an effective template selection method to select those fingerprints which best represent a finger, and then, a polyhedron is created by the matching results of multiple template fingerprints and a virtual centroid of the polyhedron is given. In the second stage, verification stage, we measure the distance between the centroid of the polyhedron and a query image. In the final stage, a fusion rule is used to choose a proper distance from a distance set. The experimental results on the FVC2004 database prove the improvement on the effectiveness of the new framework in fingerprint verification. With a minutiae-based matching method, the average EER of four databases in FVC2004 drops from 10.85 to 0.88, and with a ridge-based matching method, the average EER of these four databases also decreases from 14.58 to 2.51.

Towards online iris and periocular recognition under relaxed imaging constraints.

PubMed

Tan, Chun-Wei; Kumar, Ajay

2013-10-01

Online iris recognition using distantly acquired images in a less imaging constrained environment requires the development of a efficient iris segmentation approach and recognition strategy that can exploit multiple features available for the potential identification. This paper presents an effective solution toward addressing such a problem. The developed iris segmentation approach exploits a random walker algorithm to efficiently estimate coarsely segmented iris images. These coarsely segmented iris images are postprocessed using a sequence of operations that can effectively improve the segmentation accuracy. The robustness of the proposed iris segmentation approach is ascertained by providing comparison with other state-of-the-art algorithms using publicly available UBIRIS.v2, FRGC, and CASIA.v4-distance databases. Our experimental results achieve improvement of 9.5%, 4.3%, and 25.7% in the average segmentation accuracy, respectively, for the UBIRIS.v2, FRGC, and CASIA.v4-distance databases, as compared with most competing approaches. We also exploit the simultaneously extracted periocular features to achieve significant performance improvement. The joint segmentation and combination strategy suggest promising results and achieve average improvement of 132.3%, 7.45%, and 17.5% in the recognition performance, respectively, from the UBIRIS.v2, FRGC, and CASIA.v4-distance databases, as compared with the related competing approaches.

Multiple electron processes of He and Ne by proton impact

NASA Astrophysics Data System (ADS)

Terekhin, Pavel Nikolaevich; Montenegro, Pablo; Quinto, Michele; Monti, Juan; Fojon, Omar; Rivarola, Roberto

2016-05-01

A detailed investigation of multiple electron processes (single and multiple ionization, single capture, transfer-ionization) of He and Ne is presented for proton impact at intermediate and high collision energies. Exclusive absolute cross sections for these processes have been obtained by calculation of transition probabilities in the independent electron and independent event models as a function of impact parameter in the framework of the continuum distorted wave-eikonal initial state theory. A binomial analysis is employed to calculate exclusive probabilities. The comparison with available theoretical and experimental results shows that exclusive probabilities are needed for a reliable description of the experimental data. The developed approach can be used for obtaining the input database for modeling multiple electron processes of charged particles passing through the matter.

Integrative Systems Biology for Data Driven Knowledge Discovery

PubMed Central

Greene, Casey S.; Troyanskaya, Olga G.

2015-01-01

Integrative systems biology is an approach that brings together diverse high throughput experiments and databases to gain new insights into biological processes or systems at molecular through physiological levels. These approaches rely on diverse high-throughput experimental techniques that generate heterogeneous data by assaying varying aspects of complex biological processes. Computational approaches are necessary to provide an integrative view of these experimental results and enable data-driven knowledge discovery. Hypotheses generated from these approaches can direct definitive molecular experiments in a cost effective manner. Using integrative systems biology approaches, we can leverage existing biological knowledge and large-scale data to improve our understanding of yet unknown components of a system of interest and how its malfunction leads to disease. PMID:21044756

High-throughput density-functional perturbation theory phonons for inorganic materials

NASA Astrophysics Data System (ADS)

Petretto, Guido; Dwaraknath, Shyam; P. C. Miranda, Henrique; Winston, Donald; Giantomassi, Matteo; van Setten, Michiel J.; Gonze, Xavier; Persson, Kristin A.; Hautier, Geoffroy; Rignanese, Gian-Marco

2018-05-01

The knowledge of the vibrational properties of a material is of key importance to understand physical phenomena such as thermal conductivity, superconductivity, and ferroelectricity among others. However, detailed experimental phonon spectra are available only for a limited number of materials, which hinders the large-scale analysis of vibrational properties and their derived quantities. In this work, we perform ab initio calculations of the full phonon dispersion and vibrational density of states for 1521 semiconductor compounds in the harmonic approximation based on density functional perturbation theory. The data is collected along with derived dielectric and thermodynamic properties. We present the procedure used to obtain the results, the details of the provided database and a validation based on the comparison with experimental data.

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

Ginsz, M.; Duchene, G.; Didierjean, F.

The state-of-the art gamma-ray spectrometers such as AGATA and GRETA are using position sensitive multi-segmented HPGe crystals. Pulse-shape analysis (PSA) allows to retrieve the localisation of the gamma interactions and to perform gamma-ray tracking within germanium. The precision of the localisation depends on the quality of the pulse-shape database used for comparison. The IPHC laboratory developed a new fast scanning table allowing to measure experimental pulse shapes in the whole volume of any crystal. The results of the scan of an AGATA 36-fold segmented tapered coaxial detector are shown here, 48580 experimental pulse shapes are extracted within 2 weeks ofmore » scanning. These data will contribute to AGATA PSA performances, but have also applications for gamma cameras or Compton-suppressed detectors. (authors)« less

TAP score: torsion angle propensity normalization applied to local protein structure evaluation

PubMed Central

Tosatto, Silvio CE; Battistutta, Roberto

2007-01-01

Background Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish between distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging. Results A new criterion, called TAP score, measuring local sequence to structure fitness based on torsion angle propensities normalized against the global minimum and maximum is introduced. It is shown to be more accurate than previous methods at estimating the validity of a protein model in terms of commonly used experimental quality parameters on two test sets representing the full PDB database and a subset of obsolete PDB structures. Highly selective TAP thresholds are derived to recognize over 90% of the top experimental structures in the absence of experimental information. Both a web server and an executable version of the TAP score are available at . Conclusion A novel procedure for energy normalization (TAP) has significantly improved the possibility to recognize the best experimental structures. It will allow the user to more reliably isolate problematic structures in the context of automated experimental structure determination. PMID:17504537

Development of a critically evaluated thermodynamic database for the systems containing alkaline-earth oxides

NASA Astrophysics Data System (ADS)

Shukla, Adarsh

In a thermodynamic system which contains several elements, the phase relationships among the components are usually very complex. Especially, systems containing oxides are generally very difficult to investigate owing to the very high experimental temperatures and corrosive action of slags. Due to such difficulties, large inconsistencies are often observed among the available experimental data. In order to investigate and understand the complex phase relationships effectively, it is very useful to develop thermodynamic databases containing optimized model parameters giving the thermodynamic properties of all phases as functions of temperature and composition. In a thermodynamic optimization, adjustable model parameters are calculated using, simultaneously, all available thermodynamic and phase-equilibrium data in order to obtain one set of model equations as functions of temperature and composition. Thermodynamic data, such as activities, can aid in the evaluation of the phase diagrams, and information on phase equilibria can be used to deduce thermodynamic properties. Thus, it is frequently possible to resolve discrepancies in the available data. From the model equations, all the thermodynamic properties and phase diagrams can be back-calculated, and interpolations and extrapolations can be made in a thermodynamically correct manner. The data are thereby rendered self-consistent and consistent with thermodynamic principles, and the available data are distilled into a small set of model parameters, ideal for computer storage. As part of a broader research project at the Centre de Recherche en Calcul Thermochimique (CRCT), Ecole Polytechnique to develop a thermodynamic database for multicomponent oxide systems, this thesis deals with the addition of components SrO and BaO to the existing multicomponent database of the SiO2-B2O3-Al2O 3-CaO-MgO system. Over the years, in collaboration with many industrial companies, a thermodynamic database for the SiO2-B2O 3-Al2O3-CaO-MgO system has been built quite satisfactorily. The aim of the present work was to improve the applicability of this five component database by adding SrO and BaO to it. The databases prepared in this work will be of special importance to the glass and steel industries. In the SiO2-B2O3-Al2O 3-CaO-MgO-BaO-SrO system there are 11 binary systems and 25 ternary systems which contain either BaO or SrO or both. For most of these binary systems, and for none of these ternary systems, is there a previous thermodynamic optimization available in the literature. In this thesis, thermodynamic evaluation and optimization for the 11 binary, 17 ternary and 5 quaternary BaO- and SrO- containing systems in the SiO2-B2O3-Al 2O3-CaO-MgO-BaO-SrO system is presented. All these thermodynamic optimizations were performed based on the experimental data available in the literature, except for the SrO-B2O3-SiO2 system. This latter system was optimized on the basis of a few experimental data points generated in the present work together with the data from the literature. In the present work, all the calculations were performed using the FactSage™ thermochemical software. The Modified Quasichemical Model (MQM), which is capable of taking short-range ordering into account, was used for the liquid phase. All the binary systems were critically evaluated and optimized using available phase equilibrium and thermodynamic data. The model parameters obtained as a result of this simultaneous optimization were used to represent the Gibbs energies of all phases as functions of temperature and composition. Optimized binary model parameters were used to estimate the thermodynamic properties of phases in the ternary systems. Proper “geometric” models were used for these estimations. Ternary phase diagram were calculated and compared with available experimental data. Wherever required, ternary interaction parameters were also added. The first part of this thesis comprises a general literature review on the subject of thermodynamic modeling and experimental techniques for phase diagram determination. The next chapters include the literature review and the thermodynamic optimizations of the various systems. The last part of the thesis is the presentation of experiments performed in the present work, by quenching and EPMA, in the SrO-B2O3-SiO2 system. The experiments were designed to generate the maximum amount of information with the minimum number of experiments using the thermodynamic optimization, based only on the data available in the literature, as a guide. These newly-obtained data improved the (preceding) thermodynamic optimization, based on the experimental data in the literature, of this ternary system.

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

PubMed Central

Cserhati, Matyas F.; Pandey, Sanjit; Beaudoin, James J.; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S.

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33 017 407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. Database URL: http://nntc-dcc.unmc.edu PMID:26228431

Generating Modeling Data From Repeat-Dose Toxicity Reports

PubMed Central

López-Massaguer, Oriol; Pinto-Gil, Kevin; Sanz, Ferran; Amberg, Alexander; Anger, Lennart T; Stolte, Manuela; Ravagli, Carlo

2018-01-01

Abstract Over the past decades, pharmaceutical companies have conducted a large number of high-quality in vivo repeat-dose toxicity (RDT) studies for regulatory purposes. As part of the eTOX project, a high number of these studies have been compiled and integrated into a database. This valuable resource can be queried directly, but it can be further exploited to build predictive models. As the studies were originally conducted to investigate the properties of individual compounds, the experimental conditions across the studies are highly heterogeneous. Consequently, the original data required normalization/standardization, filtering, categorization and integration to make possible any data analysis (such as building predictive models). Additionally, the primary objectives of the RDT studies were to identify toxicological findings, most of which do not directly translate to in vivo endpoints. This article describes a method to extract datasets containing comparable toxicological properties for a series of compounds amenable for building predictive models. The proposed strategy starts with the normalization of the terms used within the original reports. Then, comparable datasets are extracted from the database by applying filters based on the experimental conditions. Finally, carefully selected profiles of toxicological findings are mapped to endpoints of interest, generating QSAR-like tables. In this work, we describe in detail the strategy and tools used for carrying out these transformations and illustrate its application in a data sample extracted from the eTOX database. The suitability of the resulting tables for developing hazard-predicting models was investigated by building proof-of-concept models for in vivo liver endpoints. PMID:29155963

In silico database screening of potential targets and pathways of compounds contained in plants used for psoriasis vulgaris.

PubMed

May, Brian H; Deng, Shiqiang; Zhang, Anthony L; Lu, Chuanjian; Xue, Charlie C L

2015-09-01

Reviews and meta-analyses of clinical trials identified plants used as traditional medicines (TMs) that show promise for psoriasis. These include Rehmannia glutinosa, Camptotheca acuminata, Indigo naturalis and Salvia miltiorrhiza. Compounds contained in these TMs have shown activities of relevance to psoriasis in experimental models. To further investigate the likely mechanisms of action of the multiple compounds in these TMs, we undertook a computer-based in silico investigation of the proteins known to be regulated by these compounds and their associated biological pathways. The proteins reportedly regulated by compounds in these four TMs were identified using the HIT (Herbal Ingredients' Targets) database. The resultant data were entered into the PANTHER (Protein ANnotation THrough Evolutionary Relationship) database to identify the pathways in which the proteins could be involved. The study identified 237 compounds in the TMs and these retrieved 287 proteins from HIT. These proteins identified 59 pathways in PANTHER with most proteins being located in the Apoptosis, Angiogenesis, Inflammation mediated by chemokine and cytokine, Gonadotropin releasing hormone receptor, and/or Interleukin signaling pathways. All four TMs contained compounds that had regulating effects on Apoptosis regulator BAX, Apoptosis regulator Bcl-2, Caspase-3, Tumor necrosis factor (TNF) or Prostaglandin G/H synthase 2 (COX2). The main proteins and pathways are primarily related to inflammation, proliferation and angiogenesis which are all processes involved in psoriasis. Experimental studies have reported that certain compounds from these TMs can regulate the expression of proteins involved in each of these pathways.

Comprehensive analysis of orthologous protein domains using the HOPS database.

PubMed

Storm, Christian E V; Sonnhammer, Erik L L

2003-10-01

One of the most reliable methods for protein function annotation is to transfer experimentally known functions from orthologous proteins in other organisms. Most methods for identifying orthologs operate on a subset of organisms with a completely sequenced genome, and treat proteins as single-domain units. However, it is well known that proteins are often made up of several independent domains, and there is a wealth of protein sequences from genomes that are not completely sequenced. A comprehensive set of protein domain families is found in the Pfam database. We wanted to apply orthology detection to Pfam families, but first some issues needed to be addressed. First, orthology detection becomes impractical and unreliable when too many species are included. Second, shorter domains contain less information. It is therefore important to assess the quality of the orthology assignment and avoid very short domains altogether. We present a database of orthologous protein domains in Pfam called HOPS: Hierarchical grouping of Orthologous and Paralogous Sequences. Orthology is inferred in a hierarchic system of phylogenetic subgroups using ortholog bootstrapping. To avoid the frequent errors stemming from horizontally transferred genes in bacteria, the analysis is presently limited to eukaryotic genes. The results are accessible in the graphical browser NIFAS, a Java tool originally developed for analyzing phylogenetic relations within Pfam families. The method was tested on a set of curated orthologs with experimentally verified function. In comparison to tree reconciliation with a complete species tree, our approach finds significantly more orthologs in the test set. Examples for investigating gene fusions and domain recombination using HOPS are given.

Experimental validation of a new heterogeneous mechanical test design

NASA Astrophysics Data System (ADS)

Aquino, J.; Campos, A. Andrade; Souto, N.; Thuillier, S.

2018-05-01

Standard material parameters identification strategies generally use an extensive number of classical tests for collecting the required experimental data. However, a great effort has been made recently by the scientific and industrial communities to support this experimental database on heterogeneous tests. These tests can provide richer information on the material behavior allowing the identification of a more complete set of material parameters. This is a result of the recent development of full-field measurements techniques, like digital image correlation (DIC), that can capture the heterogeneous deformation fields on the specimen surface during the test. Recently, new specimen geometries were designed to enhance the richness of the strain field and capture supplementary strain states. The butterfly specimen is an example of these new geometries, designed through a numerical optimization procedure where an indicator capable of evaluating the heterogeneity and the richness of strain information. However, no experimental validation was yet performed. The aim of this work is to experimentally validate the heterogeneous butterfly mechanical test in the parameter identification framework. For this aim, DIC technique and a Finite Element Model Up-date inverse strategy are used together for the parameter identification of a DC04 steel, as well as the calculation of the indicator. The experimental tests are carried out in a universal testing machine with the ARAMIS measuring system to provide the strain states on the specimen surface. The identification strategy is accomplished with the data obtained from the experimental tests and the results are compared to a reference numerical solution.

Boundary Layer Transition Experiments in Support of the Hypersonics Program

NASA Technical Reports Server (NTRS)

Berry, Scott A.; Chen, Fang-Jenq; Wilder, Michael C.; Reda, Daniel C.

2007-01-01

Two experimental boundary layer transition studies in support of fundamental hypersonics research are reviewed. The two studies are the HyBoLT flight experiment and a new ballistic range effort. Details are provided of the objectives and approach associated with each experimental program. The establishment of experimental databases from ground and flight are to provide better understanding of high-speed flows and data to validate and guide the development of simulation tools.

Flight testing and frequency domain analysis for rotorcraft handling qualities characteristics

NASA Technical Reports Server (NTRS)

Ham, Johnnie A.; Gardner, Charles K.; Tischler, Mark B.

1993-01-01

A demonstration of frequency domain flight testing techniques and analyses was performed on a U.S. Army OH-58D helicopter in support of the OH-58D Airworthiness and Flight Characteristics Evaluation and the Army's development and ongoing review of Aeronautical Design Standard 33C, Handling Qualities Requirements for Military Rotorcraft. Hover and forward flight (60 knots) tests were conducted in 1 flight hour by Army experimental test pilots. Further processing of the hover data generated a complete database of velocity, angular rate, and acceleration frequency responses to control inputs. A joint effort was then undertaken by the Airworthiness Qualification Test Directorate (AQTD) and the U.S. Army Aeroflightdynamics Directorate (AFDD) to derive handling qualities information from the frequency response database. A significant amount of information could be extracted from the frequency domain database using a variety of approaches. This report documents numerous results that have been obtained from the simple frequency domain tests; in many areas, these results provide more insight into the aircraft dynamics that affect handling qualities than to traditional flight tests. The handling qualities results include ADS-33C bandwidth and phase delay calculations, vibration spectral determinations, transfer function models to examine single axis results, and a six degree of freedom fully coupled state space model. The ability of this model to accurately predict aircraft responses was verified using data from pulse inputs. This report also documents the frequency-sweep flight test technique and data analysis used to support the tests.

Validation Results for LEWICE 3.0

NASA Technical Reports Server (NTRS)

Wright, William B.

2005-01-01

A research project is underway at NASA Glenn to produce computer software that can accurately predict ice growth under any meteorological conditions for any aircraft surface. This report will present results from version 3.0 of this software, which is called LEWICE. This version differs from previous releases in that it incorporates additional thermal analysis capabilities, a pneumatic boot model, interfaces to computational fluid dynamics (CFD) flow solvers and has an empirical model for the supercooled large droplet (SLD) regime. An extensive comparison of the results in a quantifiable manner against the database of ice shapes and collection efficiency that have been generated in the NASA Glenn Icing Research Tunnel (IRT) has also been performed. The complete set of data used for this comparison will eventually be available in a contractor report. This paper will show the differences in collection efficiency between LEWICE 3.0 and experimental data. Due to the large amount of validation data available, a separate report is planned for ice shape comparison. This report will first describe the LEWICE 3.0 model for water collection. A semi-empirical approach was used to incorporate first order physical effects of large droplet phenomena into icing software. Comparisons are then made to every single element two-dimensional case in the water collection database. Each condition was run using the following five assumptions: 1) potential flow, no splashing; 2) potential flow, no splashing with 21 bin drop size distributions and a lift correction (angle of attack adjustment); 3) potential flow, with splashing; 4) Navier-Stokes, no splashing; and 5) Navier-Stokes, with splashing. Quantitative comparisons are shown for impingement limit, maximum water catch, and total collection efficiency. The results show that the predicted results are within the accuracy limits of the experimental data for the majority of cases.

Interactive, Automated Management of Icing Data

NASA Technical Reports Server (NTRS)

Levinson, Laurie H.

2009-01-01

IceVal DatAssistant is software (see figure) that provides an automated, interactive solution for the management of data from research on aircraft icing. This software consists primarily of (1) a relational database component used to store ice shape and airfoil coordinates and associated data on operational and environmental test conditions and (2) a graphically oriented database access utility, used to upload, download, process, and/or display data selected by the user. The relational database component consists of a Microsoft Access 2003 database file with nine tables containing data of different types. Included in the database are the data for all publicly releasable ice tracings with complete and verifiable test conditions from experiments conducted to date in the Glenn Research Center Icing Research Tunnel. Ice shapes from computational simulations with the correspond ing conditions performed utilizing the latest version of the LEWICE ice shape prediction code are likewise included, and are linked to the equivalent experimental runs. The database access component includes ten Microsoft Visual Basic 6.0 (VB) form modules and three VB support modules. Together, these modules enable uploading, downloading, processing, and display of all data contained in the database. This component also affords the capability to perform various database maintenance functions for example, compacting the database or creating a new, fully initialized but empty database file.

SAR target recognition and posture estimation using spatial pyramid pooling within CNN

NASA Astrophysics Data System (ADS)

Peng, Lijiang; Liu, Xiaohua; Liu, Ming; Dong, Liquan; Hui, Mei; Zhao, Yuejin

2018-01-01

Many convolution neural networks(CNN) architectures have been proposed to strengthen the performance on synthetic aperture radar automatic target recognition (SAR-ATR) and obtained state-of-art results on targets classification on MSTAR database, but few methods concern about the estimation of depression angle and azimuth angle of targets. To get better effect on learning representation of hierarchies of features on both 10-class target classification task and target posture estimation tasks, we propose a new CNN architecture with spatial pyramid pooling(SPP) which can build high hierarchy of features map by dividing the convolved feature maps from finer to coarser levels to aggregate local features of SAR images. Experimental results on MSTAR database show that the proposed architecture can get high recognition accuracy as 99.57% on 10-class target classification task as the most current state-of-art methods, and also get excellent performance on target posture estimation tasks which pays attention to depression angle variety and azimuth angle variety. What's more, the results inspire us the application of deep learning on SAR target posture description.

ECG Sensor Card with Evolving RBP Algorithms for Human Verification.

PubMed

Tseng, Kuo-Kun; Huang, Huang-Nan; Zeng, Fufu; Tu, Shu-Yi

2015-08-21

It is known that cardiac and respiratory rhythms in electrocardiograms (ECGs) are highly nonlinear and non-stationary. As a result, most traditional time-domain algorithms are inadequate for characterizing the complex dynamics of the ECG. This paper proposes a new ECG sensor card and a statistical-based ECG algorithm, with the aid of a reduced binary pattern (RBP), with the aim of achieving faster ECG human identity recognition with high accuracy. The proposed algorithm has one advantage that previous ECG algorithms lack-the waveform complex information and de-noising preprocessing can be bypassed; therefore, it is more suitable for non-stationary ECG signals. Experimental results tested on two public ECG databases (MIT-BIH) from MIT University confirm that the proposed scheme is feasible with excellent accuracy, low complexity, and speedy processing. To be more specific, the advanced RBP algorithm achieves high accuracy in human identity recognition and is executed at least nine times faster than previous algorithms. Moreover, based on the test results from a long-term ECG database, the evolving RBP algorithm also demonstrates superior capability in handling long-term and non-stationary ECG signals.

A knowledge-based approach for identification of drugs against vivapain-2 protein of Plasmodium vivax through pharmacophore-based virtual screening with comparative modelling.

PubMed

Yadav, Manoj Kumar; Singh, Amisha; Swati, D

2014-08-01

Malaria is one of the most infectious diseases in the world. Plasmodium vivax, the pathogen causing endemic malaria in humans worldwide, is responsible for extensive disease morbidity. Due to the emergence of resistance to common anti-malarial drugs, there is a continuous need to develop a new class of drugs for this pathogen. P. vivax cysteine protease, also known as vivapain-2, plays an important role in haemoglobin hydrolysis and is considered essential for the survival of the parasite. The three-dimensional (3D) structure of vivapain-2 is not predicted experimentally, so its structure is modelled by using comparative modelling approach and further validated by Qualitative Model Energy Analysis (QMEAN) and RAMPAGE tools. The potential binding site of selected vivapain-2 structure has been detected by grid-based function prediction method. Drug targets and their respective drugs similar to vivapain-2 have been identified using three publicly available databases: STITCH 3.1, DrugBank and Therapeutic Target Database (TTD). The second approach of this work focuses on docking study of selected drug E-64 against vivapain-2 protein. Docking reveals crucial information about key residues (Asn281, Cys283, Val396 and Asp398) that are responsible for holding the ligand in the active site. The similarity-search criterion is used for the preparation of our in-house database of drugs, obtained from filtering the drugs from the DrugBank database. A five-point 3D pharmacophore model is generated for the docked complex of vivapain-2 with E-64. This study of 3D pharmacophore-based virtual screening results in identifying three new drugs, amongst which one is approved and the other two are experimentally proved. The ADMET properties of these drugs are found to be in the desired range. These drugs with novel scaffolds may act as potent drugs for treating malaria caused by P. vivax.

A PC-controlled microwave tomographic scanner for breast imaging

NASA Astrophysics Data System (ADS)

Padhi, Shantanu; Howard, John; Fhager, A.; Bengtsson, Sebastian

2011-01-01

This article presents the design and development of a personal computer based controller for a microwave tomographic system for breast cancer detection. The system uses motorized, dual-polarized antennas and a custom-made GUI interface to control stepper motors, a wideband vector network analyzer (VNA) and to coordinate data acquisition and archival in a local MDSPlus database. Both copolar and cross-polar scattered field components can be measured directly. Experimental results are presented to validate the various functionalities of the scanner.

A Study of the Behavior and Micromechanical Modelling of Granular Soil. Volume 2. An Experimental Investigation of the Behavior of Granular Media Under Load

DTIC Science & Technology

1991-05-22

infinite number of possi’le crystal orientations is assumed, this infinitely sided polyhedron becomes a curved yield surface. Plastic strain in the...families, each surface of yield polyhedron mentioned above expands and shifts differently. These slip directions are all more or less parallel to the...result, only the monotonic portion of test D29 was corrected for membrane compliance and used as part of the monotonic proportional test database

Global Binary Continuity for Color Face Detection With Complex Background

NASA Astrophysics Data System (ADS)

Belavadi, Bhaskar; Mahendra Prashanth, K. V.; Joshi, Sujay S.; Suprathik, N.

2017-08-01

In this paper, we propose a method to detect human faces in color images, with complex background. The proposed algorithm makes use of basically two color space models, specifically HSV and YCgCr. The color segmented image is filled uniformly with a single color (binary) and then all unwanted discontinuous lines are removed to get the final image. Experimental results on Caltech database manifests that the purported model is able to accomplish far better segmentation for faces of varying orientations, skin color and background environment.

Creating an Electronic Reference and Information Database for Computer-aided ECM Design

NASA Astrophysics Data System (ADS)

Nekhoroshev, M. V.; Pronichev, N. D.; Smirnov, G. V.

2018-01-01

The paper presents a review on electrochemical shaping. An algorithm has been developed to implement a computer shaping model applicable to pulse electrochemical machining. For that purpose, the characteristics of pulse current occurring in electrochemical machining of aviation materials have been studied. Based on integrating the experimental results and comprehensive electrochemical machining process data modeling, a subsystem for computer-aided design of electrochemical machining for gas turbine engine blades has been developed; the subsystem was implemented in the Teamcenter PLM system.

Face recognition using slow feature analysis and contourlet transform

NASA Astrophysics Data System (ADS)

Wang, Yuehao; Peng, Lingling; Zhe, Fuchuan

2018-04-01

In this paper we propose a novel face recognition approach based on slow feature analysis (SFA) in contourlet transform domain. This method firstly use contourlet transform to decompose the face image into low frequency and high frequency part, and then takes technological advantages of slow feature analysis for facial feature extraction. We named the new method combining the slow feature analysis and contourlet transform as CT-SFA. The experimental results on international standard face database demonstrate that the new face recognition method is effective and competitive.

Multielectron spectroscopy: energy levels of K n+ and Rb n+ ions (n = 2, 3, 4)

NASA Astrophysics Data System (ADS)

Khalal, M. A.; Soronen, J.; Jänkälä, K.; Huttula, S.-M.; Huttula, M.; Bizau, J.-M.; Cubaynes, D.; Guilbaud, S.; Ito, K.; Andric, L.; Feng, J.; Lablanquie, P.; Palaudoux, J.; Penent, F.

2017-11-01

A magnetic bottle time-of-flight spectrometer has been used to perform spectroscopy of K n+ and Rb n+ states with ionization degrees n of 2, 3 and 4. Energy levels are directly measured by detecting in coincidence the n electrons that are emitted as a result of single photon absorption. Experimental results are compared with the energies from the NIST atomic database and ab initio multiconfiguration Dirac-Fock calculations. Previously unidentified 3p 4(3P)3d 1 4D energy levels of K2+ are assigned.

The NASA Hyper-X Program

NASA Technical Reports Server (NTRS)

Freeman, Delman C., Jr.; Reubush, Daivd E.; McClinton, Charles R.; Rausch, Vincent L.; Crawford, J. Larry

1997-01-01

This paper provides an overview of NASA's Hyper-X Program; a focused hypersonic technology effort designed to move hypersonic, airbreathing vehicle technology from the laboratory environment to the flight environment. This paper presents an overview of the flight test program, research objectives, approach, schedule and status. Substantial experimental database and concept validation have been completed. The program is currently concentrating on the first, Mach 7, vehicle development, verification and validation in preparation for wind-tunnel testing in 1998 and flight testing in 1999. Parallel to this effort the Mach 5 and 10 vehicle designs are being finalized. Detailed analytical and experimental evaluation of the Mach 7 vehicle at the flight conditions is nearing completion, and will provide a database for validation of design methods once flight test data are available.

Ant-App-DB: a smart solution for monitoring arthropods activities, experimental data management and solar calculations without GPS in behavioral field studies.

PubMed

Ahmed, Zeeshan; Zeeshan, Saman; Fleischmann, Pauline; Rössler, Wolfgang; Dandekar, Thomas

2014-01-01

Field studies on arthropod ecology and behaviour require simple and robust monitoring tools, preferably with direct access to an integrated database. We have developed and here present a database tool allowing smart-phone based monitoring of arthropods. This smart phone application provides an easy solution to collect, manage and process the data in the field which has been a very difficult task for field biologists using traditional methods. To monitor our example species, the desert ant Cataglyphis fortis, we considered behavior, nest search runs, feeding habits and path segmentations including detailed information on solar position and azimuth calculation, ant orientation and time of day. For this we established a user friendly database system integrating the Ant-App-DB with a smart phone and tablet application, combining experimental data manipulation with data management and providing solar position and timing estimations without any GPS or GIS system. Moreover, the new desktop application Dataplus allows efficient data extraction and conversion from smart phone application to personal computers, for further ecological data analysis and sharing. All features, software code and database as well as Dataplus application are made available completely free of charge and sufficiently generic to be easily adapted to other field monitoring studies on arthropods or other migratory organisms. The software applications Ant-App-DB and Dataplus described here are developed using the Android SDK, Java, XML, C# and SQLite Database.

Ant-App-DB: a smart solution for monitoring arthropods activities, experimental data management and solar calculations without GPS in behavioral field studies

PubMed Central

Ahmed, Zeeshan; Zeeshan, Saman; Fleischmann, Pauline; Rössler, Wolfgang; Dandekar, Thomas

2015-01-01

Field studies on arthropod ecology and behaviour require simple and robust monitoring tools, preferably with direct access to an integrated database. We have developed and here present a database tool allowing smart-phone based monitoring of arthropods. This smart phone application provides an easy solution to collect, manage and process the data in the field which has been a very difficult task for field biologists using traditional methods. To monitor our example species, the desert ant Cataglyphis fortis, we considered behavior, nest search runs, feeding habits and path segmentations including detailed information on solar position and azimuth calculation, ant orientation and time of day. For this we established a user friendly database system integrating the Ant-App-DB with a smart phone and tablet application, combining experimental data manipulation with data management and providing solar position and timing estimations without any GPS or GIS system. Moreover, the new desktop application Dataplus allows efficient data extraction and conversion from smart phone application to personal computers, for further ecological data analysis and sharing. All features, software code and database as well as Dataplus application are made available completely free of charge and sufficiently generic to be easily adapted to other field monitoring studies on arthropods or other migratory organisms. The software applications Ant-App-DB and Dataplus described here are developed using the Android SDK, Java, XML, C# and SQLite Database. PMID:25977753

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

PubMed Central

Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth E

2012-01-01

Taxonomic classification of the thousands–millions of 16S rRNA gene sequences generated in microbiome studies is often achieved using a naïve Bayesian classifier (for example, the Ribosomal Database Project II (RDP) classifier), due to favorable trade-offs among automation, speed and accuracy. The resulting classification depends on the reference sequences and taxonomic hierarchy used to train the model; although the influence of primer sets and classification algorithms have been explored in detail, the influence of training set has not been characterized. We compared classification results obtained using three different publicly available databases as training sets, applied to five different bacterial 16S rRNA gene pyrosequencing data sets generated (from human body, mouse gut, python gut, soil and anaerobic digester samples). We observed numerous advantages to using the largest, most diverse training set available, that we constructed from the Greengenes (GG) bacterial/archaeal 16S rRNA gene sequence database and the latest GG taxonomy. Phylogenetic clusters of previously unclassified experimental sequences were identified with notable improvements (for example, 50% reduction in reads unclassified at the phylum level in mouse gut, soil and anaerobic digester samples), especially for phylotypes belonging to specific phyla (Tenericutes, Chloroflexi, Synergistetes and Candidate phyla TM6, TM7). Trimming the reference sequences to the primer region resulted in systematic improvements in classification depth, and greatest gains at higher confidence thresholds. Phylotypes unclassified at the genus level represented a greater proportion of the total community variation than classified operational taxonomic units in mouse gut and anaerobic digester samples, underscoring the need for greater diversity in existing reference databases. PMID:21716311

Joint Sparse Representation for Robust Multimodal Biometrics Recognition

DTIC Science & Technology

2012-01-01

described in III. Experimental evaluations on a comprehensive multimodal dataset and a face database have been described in section V. Finally, in...WVU Multimodal Dataset The WVU multimodal dataset is a comprehensive collection of different biometric modalities such as fingerprint, iris, palmprint ...Martnez and R. Benavente, “The AR face database ,” CVC Technical Report, June 1998. [29] U. Park and A. Jain, “Face matching and retrieval using soft

Measurements and Experimental Database Review for Laminar Flame Speed Premixed Ch4/Air Flames

NASA Astrophysics Data System (ADS)

Zubrilin, I. A.; Matveev, S. S.; Matveev, S. G.; Idrisov, D. V.

2018-01-01

Laminar flame speed (SL ) of CH4 was determined at atmospheric pressure and initial gas temperatures in range from 298 to 358 K. The heat flux method was employed to measure the flame speed in non-stretched flames. The kinetic mechanism GRI 3.0 [1] were used to simulate SL . The measurements were compared with available literature results. The data determined with the heat flux method agree with some previous burner measurements and disagree with the data from some vessel closed method and counterflow method. The GRI 3.0 mechanism was able to reproduce the present experiments. Laminar flame speed was determined at pressures range from of 1 to 20 atmospheres through mechanism GRI 3.0. Based on experimental data and calculations was obtained SL dependence on pressure and temperature. The resulting of dependence recommended use during the numerical simulation of methane combustion.

Lysine acetylation sites prediction using an ensemble of support vector machine classifiers.

PubMed

Xu, Yan; Wang, Xiao-Bo; Ding, Jun; Wu, Ling-Yun; Deng, Nai-Yang

2010-05-07

Lysine acetylation is an essentially reversible and high regulated post-translational modification which regulates diverse protein properties. Experimental identification of acetylation sites is laborious and expensive. Hence, there is significant interest in the development of computational methods for reliable prediction of acetylation sites from amino acid sequences. In this paper we use an ensemble of support vector machine classifiers to perform this work. The experimentally determined acetylation lysine sites are extracted from Swiss-Prot database and scientific literatures. Experiment results show that an ensemble of support vector machine classifiers outperforms single support vector machine classifier and other computational methods such as PAIL and LysAcet on the problem of predicting acetylation lysine sites. The resulting method has been implemented in EnsemblePail, a web server for lysine acetylation sites prediction available at http://www.aporc.org/EnsemblePail/. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

An Object-Relational Ifc Storage Model Based on Oracle Database

NASA Astrophysics Data System (ADS)

Li, Hang; Liu, Hua; Liu, Yong; Wang, Yuan

2016-06-01

With the building models are getting increasingly complicated, the levels of collaboration across professionals attract more attention in the architecture, engineering and construction (AEC) industry. In order to adapt the change, buildingSMART developed Industry Foundation Classes (IFC) to facilitate the interoperability between software platforms. However, IFC data are currently shared in the form of text file, which is defective. In this paper, considering the object-based inheritance hierarchy of IFC and the storage features of different database management systems (DBMS), we propose a novel object-relational storage model that uses Oracle database to store IFC data. Firstly, establish the mapping rules between data types in IFC specification and Oracle database. Secondly, design the IFC database according to the relationships among IFC entities. Thirdly, parse the IFC file and extract IFC data. And lastly, store IFC data into corresponding tables in IFC database. In experiment, three different building models are selected to demonstrate the effectiveness of our storage model. The comparison of experimental statistics proves that IFC data are lossless during data exchange.

Similar compounds searching system by using the gene expression microarray database.

PubMed

Toyoshiba, Hiroyoshi; Sawada, Hiroshi; Naeshiro, Ichiro; Horinouchi, Akira

2009-04-10

Numbers of microarrays have been examined and several public and commercial databases have been developed. However, it is not easy to compare in-house microarray data with those in a database because of insufficient reproducibility due to differences in the experimental conditions. As one of the approach to use these databases, we developed the similar compounds searching system (SCSS) on a toxicogenomics database. The datasets of 55 compounds administered to rats in the Toxicogenomics Project (TGP) database in Japan were used in this study. Using the fold-change ranking method developed by Lamb et al. [Lamb, J., Crawford, E.D., Peck, D., Modell, J.W., Blat, I.C., Wrobel, M.J., Lerner, J., Brunet, J.P., Subramanian, A., Ross, K.N., Reich, M., Hieronymus, H., Wei, G., Armstrong, S.A., Haggarty, S.J., Clemons, P.A., Wei, R., Carr, S.A., Lander, E.S., Golub, T.R., 2006. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313, 1929-1935] and criteria called hit ratio, the system let us compare in-house microarray data and those in the database. In-house generated data for clofibrate, phenobarbital, and a proprietary compound were tested to evaluate the performance of the SCSS method. Phenobarbital and clofibrate, which were included in the TGP database, scored highest by the SCSS method. Other high scoring compounds had effects similar to either phenobarbital (a cytochrome P450s inducer) or clofibrate (a peroxisome proliferator). Some of high scoring compounds identified using the proprietary compound-administered rats have been known to cause similar toxicological changes in different species. Our results suggest that the SCSS method could be used in drug discovery and development. Moreover, this method may be a powerful tool to understand the mechanisms by which biological systems respond to various chemical compounds and may also predict adverse effects of new compounds.

CPLA 1.0: an integrated database of protein lysine acetylation.

PubMed

Liu, Zexian; Cao, Jun; Gao, Xinjiao; Zhou, Yanhong; Wen, Longping; Yang, Xiangjiao; Yao, Xuebiao; Ren, Jian; Xue, Yu

2011-01-01

As a reversible post-translational modification (PTM) discovered decades ago, protein lysine acetylation was known for its regulation of transcription through the modification of histones. Recent studies discovered that lysine acetylation targets broad substrates and especially plays an essential role in cellular metabolic regulation. Although acetylation is comparable with other major PTMs such as phosphorylation, an integrated resource still remains to be developed. In this work, we presented the compendium of protein lysine acetylation (CPLA) database for lysine acetylated substrates with their sites. From the scientific literature, we manually collected 7151 experimentally identified acetylation sites in 3311 targets. We statistically studied the regulatory roles of lysine acetylation by analyzing the Gene Ontology (GO) and InterPro annotations. Combined with protein-protein interaction information, we systematically discovered a potential human lysine acetylation network (HLAN) among histone acetyltransferases (HATs), substrates and histone deacetylases (HDACs). In particular, there are 1862 triplet relationships of HAT-substrate-HDAC retrieved from the HLAN, at least 13 of which were previously experimentally verified. The online services of CPLA database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0). The CPLA database is freely available for all users at: http://cpla.biocuckoo.org.

NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases.

PubMed

Wang, Jianjian; Cao, Yuze; Zhang, Huixue; Wang, Tianfeng; Tian, Qinghua; Lu, Xiaoyu; Lu, Xiaoyan; Kong, Xiaotong; Liu, Zhaojun; Wang, Ning; Zhang, Shuai; Ma, Heping; Ning, Shangwei; Wang, Lihua

2017-01-04

The Nervous System Disease NcRNAome Atlas (NSDNA) (http://www.bio-bigdata.net/nsdna/) is a manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDs represent a common group of disorders, some of which are characterized by high morbidity and disabilities. The pathogenesis of NSDs at the molecular level remains poorly understood. ncRNAs are a large family of functionally important RNA molecules. Increasing evidence shows that diverse ncRNAs play a critical role in various NSDs. Mining and summarizing NSD-ncRNA association data can help researchers discover useful information. Hence, we developed an NSDNA database that documents 24 713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents an extremely useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

CPLA 1.0: an integrated database of protein lysine acetylation

PubMed Central

Liu, Zexian; Cao, Jun; Gao, Xinjiao; Zhou, Yanhong; Wen, Longping; Yang, Xiangjiao; Yao, Xuebiao; Ren, Jian; Xue, Yu

2011-01-01

As a reversible post-translational modification (PTM) discovered decades ago, protein lysine acetylation was known for its regulation of transcription through the modification of histones. Recent studies discovered that lysine acetylation targets broad substrates and especially plays an essential role in cellular metabolic regulation. Although acetylation is comparable with other major PTMs such as phosphorylation, an integrated resource still remains to be developed. In this work, we presented the compendium of protein lysine acetylation (CPLA) database for lysine acetylated substrates with their sites. From the scientific literature, we manually collected 7151 experimentally identified acetylation sites in 3311 targets. We statistically studied the regulatory roles of lysine acetylation by analyzing the Gene Ontology (GO) and InterPro annotations. Combined with protein–protein interaction information, we systematically discovered a potential human lysine acetylation network (HLAN) among histone acetyltransferases (HATs), substrates and histone deacetylases (HDACs). In particular, there are 1862 triplet relationships of HAT-substrate-HDAC retrieved from the HLAN, at least 13 of which were previously experimentally verified. The online services of CPLA database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0). The CPLA database is freely available for all users at: http://cpla.biocuckoo.org. PMID:21059677

Convolutional Neural Network-Based Finger-Vein Recognition Using NIR Image Sensors

PubMed Central

Hong, Hyung Gil; Lee, Min Beom; Park, Kang Ryoung

2017-01-01

Conventional finger-vein recognition systems perform recognition based on the finger-vein lines extracted from the input images or image enhancement, and texture feature extraction from the finger-vein images. In these cases, however, the inaccurate detection of finger-vein lines lowers the recognition accuracy. In the case of texture feature extraction, the developer must experimentally decide on a form of the optimal filter for extraction considering the characteristics of the image database. To address this problem, this research proposes a finger-vein recognition method that is robust to various database types and environmental changes based on the convolutional neural network (CNN). In the experiments using the two finger-vein databases constructed in this research and the SDUMLA-HMT finger-vein database, which is an open database, the method proposed in this research showed a better performance compared to the conventional methods. PMID:28587269

Convolutional Neural Network-Based Finger-Vein Recognition Using NIR Image Sensors.

PubMed

Hong, Hyung Gil; Lee, Min Beom; Park, Kang Ryoung

2017-06-06

Conventional finger-vein recognition systems perform recognition based on the finger-vein lines extracted from the input images or image enhancement, and texture feature extraction from the finger-vein images. In these cases, however, the inaccurate detection of finger-vein lines lowers the recognition accuracy. In the case of texture feature extraction, the developer must experimentally decide on a form of the optimal filter for extraction considering the characteristics of the image database. To address this problem, this research proposes a finger-vein recognition method that is robust to various database types and environmental changes based on the convolutional neural network (CNN). In the experiments using the two finger-vein databases constructed in this research and the SDUMLA-HMT finger-vein database, which is an open database, the method proposed in this research showed a better performance compared to the conventional methods.

[Discussion of the implementation of MIMIC database in emergency medical study].

PubMed

Li, Kaiyuan; Feng, Cong; Jia, Lijing; Chen, Li; Pan, Fei; Li, Tanshi

2018-05-01

To introduce Medical Information Mart for Intensive Care (MIMIC) database and elaborate the approach of critically emergent research with big data based on the feature of MIMIC and updated studies both domestic and overseas, we put forward the feasibility and necessity of introducing medical big data to research in emergency. Then we discuss the role of MIMIC database in emergency clinical study, as well as the principles and key notes of experimental design and implementation under the medical big data circumstance. The implementation of MIMIC database in emergency medical research provides a brand new field for the early diagnosis, risk warning and prognosis of critical illness, however there are also limitations. To meet the era of big data, emergency medical database which is in accordance with our national condition is needed, which will provide new energy to the development of emergency medicine.

Caracterisation et modelisation de la degradation des proprietes fonctionnelles des AMF soumis a un chargement cyclique

NASA Astrophysics Data System (ADS)

Paradis, Alexandre

The principal objective of the present thesis is to elaborate a computational model describing the mechanical properties of NiTi under different loading conditions. Secondary objectives are to build an experimental database of NiTi under stress, strain and temperature in order to validate the versatility of the new model proposed herewith. The simulation model used presently at Laboratoire sur les Alliage a Memoire et les Systemes Intelligents (LAMSI) of ETS is showing good behaviour in quasi-static loading. However, dynamic loading with the same model do not allows one to include degradation. The goal of the present thesis is to build a model capable of describing such degradation in a relatively accurate manner. Some experimental testing and results will be presented. In particular, new results on the behaviour of NiTi being paused during cycling are presented in chapter 2. A model is developed in chapter 3 based on Likhachev's micromechanical model. Good agreement is found with experimental data. Finally, an adaptation of the model is presented in chapter 4, allowing it to be eventually implemented into a finite-element commercial software.

InverPep: A database of invertebrate antimicrobial peptides.

PubMed

Gómez, Esteban A; Giraldo, Paula; Orduz, Sergio

2017-03-01

The aim of this work was to construct InverPep, a database specialised in experimentally validated antimicrobial peptides (AMPs) from invertebrates. AMP data contained in InverPep were manually curated from other databases and the scientific literature. MySQL was integrated with the development platform Laravel; this framework allows to integrate programming in PHP with HTML and was used to design the InverPep web page's interface. InverPep contains 18 separated fields, including InverPep code, phylum and species source, peptide name, sequence, peptide length, secondary structure, molar mass, charge, isoelectric point, hydrophobicity, Boman index, aliphatic index and percentage of hydrophobic amino acids. CALCAMPI, an algorithm to calculate the physicochemical properties of multiple peptides simultaneously, was programmed in PERL language. To date, InverPep contains 702 experimentally validated AMPs from invertebrate species. All of the peptides contain information associated with their source, physicochemical properties, secondary structure, biological activity and links to external literature. Most AMPs in InverPep have a length between 10 and 50 amino acids, a positive charge, a Boman index between 0 and 2 kcal/mol, and 30-50% hydrophobic amino acids. InverPep includes 33 AMPs not reported in other databases. Besides, CALCAMPI and statistical analysis of InverPep data is presented. The InverPep database is available in English and Spanish. InverPep is a useful database to study invertebrate AMPs and its information could be used for the design of new peptides. The user-friendly interface of InverPep and its information can be freely accessed via a web-based browser at http://ciencias.medellin.unal.edu.co/gruposdeinvestigacion/prospeccionydisenobiomoleculas/InverPep/public/home_en. Copyright © 2016 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Long-term research at the USDA Forest Service's experimental forests and ranges.

Treesearch

Ariel D. Lugo; Frederick J. Swanson; Olga Ramos González; Mary Beth Adams; Brian Palik; Ronald E. Thill; Dale G. Brockway; Christel Kern; Richard Woodsmith; Robert Musselman

2006-01-01

The network of experimental forests and ranges administered by the U.S. Department of Agriculture Forest Service consists of 77 properties that are representative of most forest cover types and many ecological regions in the Nation. Established as early as 1908, these sites maintain exceptional, long-term databases on environmental dynamics and biotic responses. Early...

Web-Based Search and Plot System for Nuclear Reaction Data

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

Otuka, N.; Nakagawa, T.; Fukahori, T.

2005-05-24

A web-based search and plot system for nuclear reaction data has been developed, covering experimental data in EXFOR format and evaluated data in ENDF format. The system is implemented for Linux OS, with Perl and MySQL used for CGI scripts and the database manager, respectively. Two prototypes for experimental and evaluated data are presented.

Santa Rita Experimental Range digital database: user's guide

Treesearch

Mitchel P. McClaran; Deborah L. Angell; Craig Wissler

2002-01-01

Long-term measurements and repeat photograph collections have been collected in a systematic manner on the approximately 21,000 ha Santa Rita Experimental Range (SRER) since its establishment in 1903. This research facility, located in the Desert Grassland vegetation of southern Arizona, was administered by the U.S. Department of Agriculture until 1988, when it was...

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.

PubMed

Cserhati, Matyas F; Pandey, Sanjit; Beaudoin, James J; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33,017,407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. © The Author(s) 2015. Published by Oxford University Press.

Rapid Structural Design Change Evaluation with AN Experiment Based FEM

NASA Astrophysics Data System (ADS)

Chu, C.-H.; Trethewey, M. W.

1998-04-01

The work in this paper proposes a dynamic structural design model that can be developed in a rapid fashion. The approach endeavours to produce a simplified FEM developed in conjunction with an experimental modal database. The FEM is formulated directly from the geometry and connectivity used in an experimental modal test using beam/frame elements. The model sacrifices fine detail for a rapid development time. The FEM is updated at the element level so the dynamic response replicates the experimental results closely. The physical attributes of the model are retained, making it well suited to evaluate the effect of potential design changes. The capabilities are evaluated in a series of computational and laboratory tests. First, a study is performed with a simulated cantilever beam with a variable mass and stiffness distribution. The modal characteristics serve as the updating target with random noise added to simulate experimental uncertainty. A uniformly distributed FEM is developed and updated. The results show excellent results, all natural frequencies are within 0·001% with MAC values above 0·99. Next, the method is applied to predict the dynamic changes of a hardware portal frame structure for a radical design change. Natural frequency predictions from the original FEM differ by as much as almost 18% with reasonable MAC values. The results predicted from the updated model produce excellent results when compared to the actual hardware changes, the first five modal natural frequency difference is around 5% and the corresponding mode shapes producing MAC values above 0·98.

Big Data Mining and Adverse Event Pattern Analysis in Clinical Drug Trials

PubMed Central

Federer, Callie; Yoo, Minjae

2016-01-01

Abstract Drug adverse events (AEs) are a major health threat to patients seeking medical treatment and a significant barrier in drug discovery and development. AEs are now required to be submitted during clinical trials and can be extracted from ClinicalTrials.gov (https://clinicaltrials.gov/), a database of clinical studies around the world. By extracting drug and AE information from ClinicalTrials.gov and structuring it into a database, drug-AEs could be established for future drug development and repositioning. To our knowledge, current AE databases contain mainly U.S. Food and Drug Administration (FDA)-approved drugs. However, our database contains both FDA-approved and experimental compounds extracted from ClinicalTrials.gov. Our database contains 8,161 clinical trials of 3,102,675 patients and 713,103 reported AEs. We extracted the information from ClinicalTrials.gov using a set of python scripts, and then used regular expressions and a drug dictionary to process and structure relevant information into a relational database. We performed data mining and pattern analysis of drug-AEs in our database. Our database can serve as a tool to assist researchers to discover drug-AE relationships for developing, repositioning, and repurposing drugs. PMID:27631620

Big Data Mining and Adverse Event Pattern Analysis in Clinical Drug Trials.

PubMed

Federer, Callie; Yoo, Minjae; Tan, Aik Choon

2016-12-01

Drug adverse events (AEs) are a major health threat to patients seeking medical treatment and a significant barrier in drug discovery and development. AEs are now required to be submitted during clinical trials and can be extracted from ClinicalTrials.gov ( https://clinicaltrials.gov/ ), a database of clinical studies around the world. By extracting drug and AE information from ClinicalTrials.gov and structuring it into a database, drug-AEs could be established for future drug development and repositioning. To our knowledge, current AE databases contain mainly U.S. Food and Drug Administration (FDA)-approved drugs. However, our database contains both FDA-approved and experimental compounds extracted from ClinicalTrials.gov . Our database contains 8,161 clinical trials of 3,102,675 patients and 713,103 reported AEs. We extracted the information from ClinicalTrials.gov using a set of python scripts, and then used regular expressions and a drug dictionary to process and structure relevant information into a relational database. We performed data mining and pattern analysis of drug-AEs in our database. Our database can serve as a tool to assist researchers to discover drug-AE relationships for developing, repositioning, and repurposing drugs.

Detailed Uncertainty Analysis of the Ares I A106 Liftoff/Transition Database

NASA Technical Reports Server (NTRS)

Hanke, Jeremy L.

2011-01-01

The Ares I A106 Liftoff/Transition Force and Moment Aerodynamics Database describes the aerodynamics of the Ares I Crew Launch Vehicle (CLV) from the moment of liftoff through the transition from high to low total angles of attack at low subsonic Mach numbers. The database includes uncertainty estimates that were developed using a detailed uncertainty quantification procedure. The Ares I Aerodynamics Panel developed both the database and the uncertainties from wind tunnel test data acquired in the NASA Langley Research Center s 14- by 22-Foot Subsonic Wind Tunnel Test 591 using a 1.75 percent scale model of the Ares I and the tower assembly. The uncertainty modeling contains three primary uncertainty sources: experimental uncertainty, database modeling uncertainty, and database query interpolation uncertainty. The final database and uncertainty model represent a significant improvement in the quality of the aerodynamic predictions for this regime of flight over the estimates previously used by the Ares Project. The maximum possible aerodynamic force pushing the vehicle towards the launch tower assembly in a dispersed case using this database saw a 40 percent reduction from the worst-case scenario in previously released data for Ares I.

cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila

PubMed Central

2014-01-01

Background Cis-regulatory modules (CRMs), or the DNA sequences required for regulating gene expression, play the central role in biological researches on transcriptional regulation in metazoan species. Nowadays, the systematic understanding of CRMs still mainly resorts to computational methods due to the time-consuming and small-scale nature of experimental methods. But the accuracy and reliability of different CRM prediction tools are still unclear. Without comparative cross-analysis of the results and combinatorial consideration with extra experimental information, there is no easy way to assess the confidence of the predicted CRMs. This limits the genome-wide understanding of CRMs. Description It is known that transcription factor binding and epigenetic profiles tend to determine functions of CRMs in gene transcriptional regulation. Thus integration of the genome-wide epigenetic profiles with systematically predicted CRMs can greatly help researchers evaluate and decipher the prediction confidence and possible transcriptional regulatory functions of these potential CRMs. However, these data are still fragmentary in the literatures. Here we performed the computational genome-wide screening for potential CRMs using different prediction tools and constructed the pioneer database, cisMEP (cis-regulatory module epigenetic profile database), to integrate these computationally identified CRMs with genomic epigenetic profile data. cisMEP collects the literature-curated TFBS location data and nine genres of epigenetic data for assessing the confidence of these potential CRMs and deciphering the possible CRM functionality. Conclusions cisMEP aims to provide a user-friendly interface for researchers to assess the confidence of different potential CRMs and to understand the functions of CRMs through experimentally-identified epigenetic profiles. The deposited potential CRMs and experimental epigenetic profiles for confidence assessment provide experimentally testable hypotheses for the molecular mechanisms of metazoan gene regulation. We believe that the information deposited in cisMEP will greatly facilitate the comparative usage of different CRM prediction tools and will help biologists to study the modular regulatory mechanisms between different TFs and their target genes. PMID:25521507

Relation between experimental and non-experimental study designs. HB vaccines: a case study.

PubMed

Jefferson, T; Demicheli, V

1999-01-01

To examine the relation between experimental and non-experimental study design in vaccinology. Assessment of each study design's capability of testing four aspects of vaccine performance, namely immunogenicity (the capacity to stimulate the immune system), duration of immunity conferred, incidence and seriousness of side effects, and number of infections prevented by vaccination. Experimental and non-experimental studies on hepatitis B (HB) vaccines in the Cochrane Vaccines Field Database. Experimental and non-experimental vaccine study designs are frequently complementary but some aspects of vaccine quality can only be assessed by one of the types of study. More work needs to be done on the relation between study quality and its significance in terms of effect size.

Recent Efforts in Data Compilations for Nuclear Astrophysics

NASA Astrophysics Data System (ADS)

Dillmann, Iris

2008-05-01

Some recent efforts in compiling data for astrophysical purposes are introduced, which were discussed during a JINA-CARINA Collaboration meeting on ``Nuclear Physics Data Compilation for Nucleosynthesis Modeling'' held at the ECT* in Trento/Italy from May 29th-June 3rd, 2007. The main goal of this collaboration is to develop an updated and unified nuclear reaction database for modeling a wide variety of stellar nucleosynthesis scenarios. Presently a large number of different reaction libraries (REACLIB) are used by the astrophysics community. The ``JINA Reaclib Database'' on http://www.nscl.msu.edu/~nero/db/ aims to merge and fit the latest experimental stellar cross sections and reaction rate data of various compilations, e.g. NACRE and its extension for Big Bang nucleosynthesis, Caughlan and Fowler, Iliadis et al., and KADoNiS. The KADoNiS (Karlsruhe Astrophysical Database of Nucleosynthesis in Stars, http://nuclear-astrophysics.fzk.de/kadonis) project is an online database for neutron capture cross sections relevant to the s process. The present version v0.2 is already included in a REACLIB file from Basel university (http://download.nucastro.org/astro/reaclib). The present status of experimental stellar (n,γ) cross sections in KADoNiS is shown. It contains recommended cross sections for 355 isotopes between 1H and 210Bi, over 80% of them deduced from experimental data. A ``high priority list'' for measurements and evaluations for light charged-particle reactions set up by the JINA-CARINA collaboration is presented. The central web access point to submit and evaluate new data is provided by the Oak Ridge group via the http://www.nucastrodata.org homepage. ``Workflow tools'' aim to make the evaluation process transparent and allow users to follow the progress.

The Proximal Effects of Acute Alcohol Consumption on Male-to-Female Aggression: A Meta-Analytic Review of the Experimental Literature.

PubMed

Crane, Cory A; Godleski, Stephanie A; Przybyla, Sarahmona M; Schlauch, Robert C; Testa, Maria

2016-12-01

The current meta-analytic review examined the experimental literature to quantify the causal effect of acute alcohol consumption on self-reported and observed indicators of male-to-female general, sexual, and intimate partner aggression. Database and reference list searches yielded 22 studies conducted between 1981 and 2014 that met all criteria for inclusion and that were subjected to full text coding for analysis. Results detected a significant overall effect (d = .36), indicating that male participants who consumed alcohol evidenced greater aggressive behavior toward females while completing a subsequent laboratory aggression paradigm than male participants who received no alcohol. We found homogeneity across all categories of potential moderator variables. Results further indicated that alcohol resulted in comparable increases of male-to-female sexual (d = .32) and intimate partner (d = .45) aggression. Further research is required to draw meaningful conclusions about individual and situational factors that may interact with acute alcohol consumption to produce the highest levels of risk. © The Author(s) 2015.

The Proximal Effects of Acute Alcohol Consumption on Male-to-Female Aggression: A Meta-Analytic Review of the Experimental Literature

PubMed Central

Crane, Cory A.; Godleski, Stephanie A.; Przybyla, Sarahmona M.; Schlauch, Robert C.; Testa, Maria

2015-01-01

The current meta-analytic review examined the experimental literature to quantify the causal effect of acute alcohol consumption on self-reported and observed indicators of male-to-female general, sexual, and intimate partner aggression. Database and reference list searches yielded 22 studies conducted between 1981 and 2014 that met all criteria for inclusion and that were subjected to full text coding for analysis. Results detected a significant overall effect (d = .36), indicating that male participants who consumed alcohol evidenced greater aggressive behavior toward females while completing a subsequent laboratory aggression paradigm than male participants who received no alcohol. We found homogeneity across all categories of potential moderator variables. Results further indicated that alcohol resulted in comparable increases of male-to-female sexual (d = .32) and intimate partner (d = .45) aggression. Further research is required to draw meaningful conclusions about individual and situational factors that may interact with acute alcohol consumption to produce the highest levels of risk. PMID:26009568