Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees.

Science.gov (United States)

Wang, Qinghua; Arighi, Cecilia N; King, Benjamin L; Polson, Shawn W; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F; Page, Shallee T; Rendino, Marc Farnum; Thomas, William Kelley; Udwary, Daniel W; Wu, Cathy H

2012-01-01

Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.

Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees

Science.gov (United States)

Wang, Qinghua; Arighi, Cecilia N.; King, Benjamin L.; Polson, Shawn W.; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F.; Page, Shallee T.; Farnum Rendino, Marc; Thomas, William Kelley; Udwary, Daniel W.; Wu, Cathy H.

2012-01-01

Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome. PMID:22434832

Low-gravity homogenization and solidification of aluminum antimonide. [Apollo-Soyuz test project

Science.gov (United States)

Ang, C.-Y.; Lacy, L. L.

1976-01-01

The III-V semiconducting compound AlSb shows promise as a highly efficient solar cell material, but it has not been commercially exploited because of difficulties in compound synthesis. Liquid state homogenization and solidification of AlSb were carried out in the Apollo-Soyuz Test Project Experiment MA-044 in the hope that compositional homogeneity would be improved by negating the large density difference between the two constituents. Post-flight analysis and comparative characterization of the space-processed and ground-processed samples indicate that there are major homogeneity improvements in the low-gravity solidified material.

annot8r: GO, EC and KEGG annotation of EST datasets

Directory of Open Access Journals (Sweden)

Schmid Ralf

2008-04-01

Full Text Available Abstract Background The expressed sequence tag (EST methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways. Results annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO, Enzyme Commission (EC and Kyoto Encyclopaedia of Genes and Genomes (KEGG annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools. Conclusion annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non

Annotating abstract pronominal anaphora in the DAD project

DEFF Research Database (Denmark)

Navarretta, Costanza; Olsen, Sussi Anni

2008-01-01

n this paper we present an extension of the MATE/GNOME annotation scheme for anaphora (Poesio 2004) which accounts for abstract anaphora in Danish and Italian. By abstract anaphora it is here meant pronouns whose linguistic antecedents are verbal phrases, clauses and discourse segments. The exten......n this paper we present an extension of the MATE/GNOME annotation scheme for anaphora (Poesio 2004) which accounts for abstract anaphora in Danish and Italian. By abstract anaphora it is here meant pronouns whose linguistic antecedents are verbal phrases, clauses and discourse segments....... The extended scheme, which we call the DAD annotation scheme, allows to annotate information about abstract anaphora which is important to investigate their use, see Webber (1988), Gundel et al. (2003), Navarretta (2004) and which can influence their automatic treatment. Intercoder agreement scores obtained...... by applying the DAD annotation scheme on texts and dialogues in the two languages are given and show that th information proposed in the scheme can be recognised in a reliable way....

Apollo 13 emblem

Science.gov (United States)

1969-01-01

This is the insignia of the Apollo 13 lunar landing mission. Represented in the Apollo 13 emblem is Apollo, the sun god of Greek mythology, symbolizing how the Apollo flights have extended the light of knowledge to all mankind. The Latin phrase Ex Luna, Scientia means 'From the Moon, Knowledge'.

Combined evidence annotation of transposable elements in genome sequences.

Directory of Open Access Journals (Sweden)

Hadi Quesneville

2005-07-01

Full Text Available Transposable elements (TEs are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated "TE models" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1, and we found a substantially higher number of TEs (n = 6,013 than previously identified (n = 1,572. Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1. We also estimated that 518 TE copies (8.6% are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other

Women, Islam, and Pakistan: A Selected Annotated Bibliography. Fulbright-Hays Summer Seminar Abroad Project.

Science.gov (United States)

Phillips, Brenda

This bibliography features selected books, book chapters, research projects, and journal articles, published between 1953 and 1994, about the social, legal, economic, educational political, and professional position of Muslim Pakistani women. Sixteen of the references are annotated. An additional 41 bibliographic references to other materials, not…

Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

Science.gov (United States)

Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

2014-01-01

Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.

Apollo 16 astronauts in Apollo Command Module Mission Simulator

Science.gov (United States)

1972-01-01

Astronaut Thomas K. Mattingly II, command module pilot of the Apollo 16 lunar landing mission, participates in extravehicular activity (EVA) training in bldg 5 at the Manned Spacecraft Center (MSC). In the right background is Astronaut Charles M. Duke Jr., lunar module pilot. They are inside the Apollo Command Module Mission Simulator (31046); Mattingly (right foreground) and Duke (right backgroung) in the Apollo Command Module Mission Simulator for EVA simulation and training. Astronaut John W. Young, commander, can be seen in the left background (31047).

Restoration of Apollo Data by the Lunar Data Project/PDS Lunar Data Node: An Update

Science.gov (United States)

Williams, David R.; Hills, H. Kent; Taylor, Patrick T.; Grayzeck, Edwin J.; Guinness, Edward A.

2016-01-01

The Apollo 11, 12, and 14 through 17 missions orbited and landed on the Moon, carrying scientific instruments that returned data from all phases of the missions, included long-lived Apollo Lunar Surface Experiments Packages (ALSEPs) deployed by the astronauts on the lunar surface. Much of these data were never archived, and some of the archived data were on media and in formats that are outmoded, or were deposited with little or no useful documentation to aid outside users. This is particularly true of the ALSEP data returned autonomously for many years after the Apollo missions ended. The purpose of the Lunar Data Project and the Planetary Data System (PDS) Lunar Data Node is to take data collections already archived at the NASA Space Science Data Coordinated Archive (NSSDCA) and prepare them for archiving through PDS, and to locate lunar data that were never archived, bring them into NSSDCA, and then archive them through PDS. Preparing these data for archiving involves reading the data from the original media, be it magnetic tape, microfilm, microfiche, or hard-copy document, converting the outmoded, often binary, formats when necessary, putting them into a standard digital form accepted by PDS, collecting the necessary ancillary data and documentation (metadata) to ensure that the data are usable and well-described, summarizing the metadata in documentation to be included in the data set, adding other information such as references, mission and instrument descriptions, contact information, and related documentation, and packaging the results in a PDS-compliant data set. The data set is then validated and reviewed by a group of external scientists as part of the PDS final archive process. We present a status report on some of the data sets that we are processing.

Workflow and web application for annotating NCBI BioProject transcriptome data.

Science.gov (United States)

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A; Barrero, Luz S; Landsman, David; Mariño-Ramírez, Leonardo

2017-01-01

The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. URL: http://www.ncbi.nlm.nih.gov/projects/physalis/. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Apollo Image Atlas

Data.gov (United States)

National Aeronautics and Space Administration — The Apollo Image Atlas is a comprehensive collection of Apollo-Saturn mission photography. Included are almost 25,000 lunar images, both from orbit and from the...

Annotating temporal information in clinical narratives.

Science.gov (United States)

Sun, Weiyi; Rumshisky, Anna; Uzuner, Ozlem

2013-12-01

Temporal information in clinical narratives plays an important role in patients' diagnosis, treatment and prognosis. In order to represent narrative information accurately, medical natural language processing (MLP) systems need to correctly identify and interpret temporal information. To promote research in this area, the Informatics for Integrating Biology and the Bedside (i2b2) project developed a temporally annotated corpus of clinical narratives. This corpus contains 310 de-identified discharge summaries, with annotations of clinical events, temporal expressions and temporal relations. This paper describes the process followed for the development of this corpus and discusses annotation guideline development, annotation methodology, and corpus quality. Copyright © 2013 Elsevier Inc. All rights reserved.

LeARN: a platform for detecting, clustering and annotating non-coding RNAs

Directory of Open Access Journals (Sweden)

Schiex Thomas

2008-01-01

Full Text Available Abstract Background In the last decade, sequencing projects have led to the development of a number of annotation systems dedicated to the structural and functional annotation of protein-coding genes. These annotation systems manage the annotation of the non-protein coding genes (ncRNAs in a very crude way, allowing neither the edition of the secondary structures nor the clustering of ncRNA genes into families which are crucial for appropriate annotation of these molecules. Results LeARN is a flexible software package which handles the complete process of ncRNA annotation by integrating the layers of automatic detection and human curation. Conclusion This software provides the infrastructure to deal properly with ncRNAs in the framework of any annotation project. It fills the gap between existing prediction software, that detect independent ncRNA occurrences, and public ncRNA repositories, that do not offer the flexibility and interactivity required for annotation projects. The software is freely available from the download section of the website http://bioinfo.genopole-toulouse.prd.fr/LeARN

The Apollo experiment for document delivery via satellite communication

Science.gov (United States)

1985-03-01

Dutch participation possibilities in the Apollo document delivery project, wishes and idea's of potential user and tender groups, and plans and activities of Dutch institutes and companies, are surveyed. The Apollo storage and transport system, demand and administration network, potential markets, and subject areas of the documents are investigated. Utilization areas (scientific, technical, administration, and business information) are listed. High tariffs and the lack of necessary provision make a direct participation strategy impossible. However, in the experimental phase, Dutch companies must be allowed to contribute in technical developments and availability of organizational and technical facilities must be stimulated.

Displaying Annotations for Digitised Globes

Science.gov (United States)

Gede, Mátyás; Farbinger, Anna

2018-05-01

Thanks to the efforts of the various globe digitising projects, nowadays there are plenty of old globes that can be examined as 3D models on the computer screen. These globes usually contain a lot of interesting details that an average observer would not entirely discover for the first time. The authors developed a website that can display annotations for such digitised globes. These annotations help observers of the globe to discover all the important, interesting details. Annotations consist of a plain text title, a HTML formatted descriptive text and a corresponding polygon and are stored in KML format. The website is powered by the Cesium virtual globe engine.

Annotated bibliography

International Nuclear Information System (INIS)

1997-08-01

Under a cooperative agreement with the U.S. Department of Energy's Office of Science and Technology, Waste Policy Institute (WPI) is conducting a five-year research project to develop a research-based approach for integrating communication products in stakeholder involvement related to innovative technology. As part of the research, WPI developed this annotated bibliography which contains almost 100 citations of articles/books/resources involving topics related to communication and public involvement aspects of deploying innovative cleanup technology. To compile the bibliography, WPI performed on-line literature searches (e.g., Dialog, International Association of Business Communicators Public Relations Society of America, Chemical Manufacturers Association, etc.), consulted past years proceedings of major environmental waste cleanup conferences (e.g., Waste Management), networked with professional colleagues and DOE sites to gather reports or case studies, and received input during the August 1996 Research Design Team meeting held to discuss the project's research methodology. Articles were selected for annotation based upon their perceived usefulness to the broad range of public involvement and communication practitioners

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project : open letter

NARCIS (Netherlands)

Archibald, A.L.; Bottema, C.D.; Brauning, R.; Burgess, S.C.; Burt, D.W.; Casas, E.; Cheng, H.H.; Clarke, L.; Couldrey, C.; Dalrymple, B.P.; Elsik, C.G.; Foissac, S.; Giuffra, E.; Groenen, M.A.M.; Hayes, B.J.; Huang, L.S.; Khatib, H.; Kijas, J.W.; Kim, H.; Lunney, J.K.; McCarthy, F.M.; McEwan, J.; Moore, S.; Nanduri, B.; Notredame, C.; Palti, Y.; Plastow, G.S.; Reecy, J.M.; Rohrer, G.; Sarropoulou, E.; Schmidt, C.J.; Silverstein, J.; Tellam, R.L.; Tixier-Boichard, M.; Tosser-klopp, G.; Tuggle, C.K.; Vilkki, J.; White, S.N.; Zhao, S.; Zhou, H.

2015-01-01

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

Directory of Open Access Journals (Sweden)

Doran Anthony G

2013-02-01

Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.

The APOLLO assembly spectrum code

International Nuclear Information System (INIS)

Kavenoky, A.; Sanchez, R.

1987-04-01

The APOLLO code was originally developed as a design tool for HTR's, later it was aimed at the calculation of PWR lattices. APOLLO is a general purpose assembly spectrum code based on the multigroup integral transport equation; refined collision probability modules allow the computation of 1D geometries with linearly anisotropic scattering and two term flux expansion. In 2D geometries modules based on the substructure method provide fast and accurate design calculations and a module based on a direct discretization is devoted to reference calculations. The SPH homogenization technique provides corrected cross sections performing an equivalence between coarse and refined calculations. The post processing module of APOLLO generate either APOLLIB to be used by APOLLO or NEPLIB for reactor diffusion calculation. The cross section library of APOLLO contains data and self-shielding data for more than 400 isotopes. APOLLO is able to compute the depletion of any medium accounting for any heavy isotope or fission product chain. 21 refs

GSV Annotated Bibliography

Energy Technology Data Exchange (ETDEWEB)

Roberts, Randy S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pope, Paul A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jiang, Ming [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Trucano, Timothy G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aragon, Cecilia R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ni, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wei, Thomas [Argonne National Lab. (ANL), Argonne, IL (United States); Chilton, Lawrence K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bakel, Alan [Argonne National Lab. (ANL), Argonne, IL (United States)

2010-09-14

The following annotated bibliography was developed as part of the geospatial algorithm verification and validation (GSV) project for the Simulation, Algorithms and Modeling program of NA-22. Verification and Validation of geospatial image analysis algorithms covers a wide range of technologies. Papers in the bibliography are thus organized into the following five topic areas: Image processing and analysis, usability and validation of geospatial image analysis algorithms, image distance measures, scene modeling and image rendering, and transportation simulation models. Many other papers were studied during the course of the investigation including. The annotations for these articles can be found in the paper "On the verification and validation of geospatial image analysis algorithms".

WormBase: Annotating many nematode genomes.

Science.gov (United States)

Howe, Kevin; Davis, Paul; Paulini, Michael; Tuli, Mary Ann; Williams, Gary; Yook, Karen; Durbin, Richard; Kersey, Paul; Sternberg, Paul W

2012-01-01

WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.

Solar Tutorial and Annotation Resource (STAR)

Science.gov (United States)

Showalter, C.; Rex, R.; Hurlburt, N. E.; Zita, E. J.

2009-12-01

We have written a software suite designed to facilitate solar data analysis by scientists, students, and the public, anticipating enormous datasets from future instruments. Our “STAR" suite includes an interactive learning section explaining 15 classes of solar events. Users learn software tools that exploit humans’ superior ability (over computers) to identify many events. Annotation tools include time slice generation to quantify loop oscillations, the interpolation of event shapes using natural cubic splines (for loops, sigmoids, and filaments) and closed cubic splines (for coronal holes). Learning these tools in an environment where examples are provided prepares new users to comfortably utilize annotation software with new data. Upon completion of our tutorial, users are presented with media of various solar events and asked to identify and annotate the images, to test their mastery of the system. Goals of the project include public input into the data analysis of very large datasets from future solar satellites, and increased public interest and knowledge about the Sun. In 2010, the Solar Dynamics Observatory (SDO) will be launched into orbit. SDO’s advancements in solar telescope technology will generate a terabyte per day of high-quality data, requiring innovation in data management. While major projects develop automated feature recognition software, so that computers can complete much of the initial event tagging and analysis, still, that software cannot annotate features such as sigmoids, coronal magnetic loops, coronal dimming, etc., due to large amounts of data concentrated in relatively small areas. Previously, solar physicists manually annotated these features, but with the imminent influx of data it is unrealistic to expect specialized researchers to examine every image that computers cannot fully process. A new approach is needed to efficiently process these data. Providing analysis tools and data access to students and the public have proven

Apollo for Adobe Flex Developers Pocket Guide A Developer's Reference for Apollo's Alpha Release

CERN Document Server

Chambers, Mike; Swartz, Jeff

2009-01-01

Now you can build and deploy Flash-based Rich Internet Applications (RIAs) to the desktop using Adobe's Flex framework. Written by members of the Apollo product team, this is the official guide to the Alpha release of Adobe Apollo, the new cross platform desktop runtime from Adobe Labs. Numerous examples illustrate how Apollo works so you can start building RIAs for the desktop right away.

Apollo food technology

Science.gov (United States)

Smith, M. C., Jr.; Heidelbaugh, N. D.; Rambaut, P. C.; Rapp, R. M.; Wheeler, H. O.; Huber, C. S.; Bourland, C. T.

1975-01-01

Large improvements and advances in space food systems achieved during the Apollo food program are discussed. Modifications of the Apollo food system were directed primarily toward improving delivery of adequate nutrition to the astronaut. Individual food items and flight menus were modified as nutritional countermeasures to the effects of weightlessness. Unique food items were developed, including some that provided nutritional completeness, high acceptability, and ready-to-eat, shelf-stable convenience. Specialized food packages were also developed. The Apollo program experience clearly showed that future space food systems will require well-directed efforts to achieve the optimum potential of food systems in support of the physiological and psychological well-being of astronauts and crews.

Annotating individual human genomes.

Science.gov (United States)

Torkamani, Ali; Scott-Van Zeeland, Ashley A; Topol, Eric J; Schork, Nicholas J

2011-10-01

Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. Copyright © 2011 Elsevier Inc. All rights reserved.

ANNOTATING INDIVIDUAL HUMAN GENOMES*

Science.gov (United States)

Torkamani, Ali; Scott-Van Zeeland, Ashley A.; Topol, Eric J.; Schork, Nicholas J.

2014-01-01

Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. PMID:21839162

The Impact of Apollo-Era Microbiology on Human Space Flight

Science.gov (United States)

Elliott, T. F; Castro, V. A.; Bruce, R. J.; Pierson, D. L.

2014-01-01

The microbiota of crewmembers and the spacecraft environment contributes significant risk to crew health during space flight missions. NASA reduces microbial risk with various mitigation methods that originated during the Apollo Program and continued to evolve through subsequent programs: Skylab, Shuttle, and International Space Station (ISS). A quarantine of the crew and lunar surface samples, within the Lunar Receiving Laboratory following return from the Moon, was used to prevent contamination with unknown extraterrestrial organisms. The quarantine durations for the crew and lunar samples were 21 days and 50 days, respectively. A series of infections among Apollo crewmembers resulted in a quarantine before launch to limit exposure to infectious organisms. This Health Stabilization Program isolated the crew for 21 days before flight and was effective in reducing crew illness. After the program developed water recovery hardware for Apollo spacecraft, the 1967 National Academy of Science Space Science Board recommended the monitoring of potable water. NASA implemented acceptability limits of 10 colony forming units (CFU) per mL and the absence of viable E. coli, anaerobes, yeasts, and molds in three separate 150 mL aliquots. Microbiological investigations of the crew and spacecraft environment were conducted during the Apollo program, including the Apollo-Soyuz Test Project and Skylab. Subsequent space programs implemented microbial screening of the crew for pathogens and acceptability limits on spacecraft surfaces and air. Microbiology risk mitigation methods have evolved since the Apollo program. NASA cancelled the quarantine of the crew after return from the lunar surface, reduced the duration of the Health Stabilization Program; and implemented acceptability limits for spacecraft surfaces and air. While microbial risks were not a main focus of the early Mercury and Gemini programs, the extended duration of Apollo flights resulted in the increased scrutiny of

Vertical view Apollo 16 Descartes landing sites as photographed by Apollo 14

Science.gov (United States)

1972-01-01

An almost vertical view of the Apollo 16 Descartes landing sites as photographed from the Apollo 14 spacecraft. Overlays are provided to point out extravehicular activity (EVA), Lunar Roving Vehicle (LRV) travers routes and the nicknames of features. The Roman numerals indicate the EVA numbers and the Arabic numbers point out stations or traverse stops.

Apollo rocks, fines and soil cores

Science.gov (United States)

Allton, J.; Bevill, T.

Apollo rocks and soils not only established basic lunar properties and ground truth for global remote sensing, they also provided important lessons for planetary protection (Adv. Space Res ., 1998, v. 22, no. 3 pp. 373-382). The six Apollo missions returned 2196 samples weighing 381.7 kg, comprised of rocks, fines, soil cores and 2 gas samples. By examining which samples were allocated for scientific investigations, information was obtained on usefulness of sampling strategy, sampling devices and containers, sample types and diversity, and on size of sample needed by various disciplines. Diversity was increased by using rakes to gather small rocks on the Moon and by removing fragments >1 mm from soils by sieving in the laboratory. Breccias and soil cores are diverse internally. Per unit weight these samples were more often allocated for research. Apollo investigators became adept at wringing information from very small sample sizes. By pushing the analytical limits, the main concern was adequate size for representative sampling. Typical allocations for trace element analyses were 750 mg for rocks, 300 mg for fines and 70 mg for core subsamples. Age-dating and isotope systematics allocations were typically 1 g for rocks and fines, but only 10% of that amount for core depth subsamples. Historically, allocations for organics and microbiology were 4 g (10% for cores). Modern allocations for biomarker detection are 100mg. Other disciplines supported have been cosmogenic nuclides, rock and soil petrology, sedimentary volatiles, reflectance, magnetics, and biohazard studies . Highly applicable to future sample return missions was the Apollo experience with organic contamination, estimated to be from 1 to 5 ng/g sample for Apollo 11 (Simonheit &Flory, 1970; Apollo 11, 12 &13 Organic contamination Monitoring History, U.C. Berkeley; Burlingame et al., 1970, Apollo 11 LSC , pp. 1779-1792). Eleven sources of contaminants, of which 7 are applicable to robotic missions, were

How to find the Apollo landing sites

CERN Document Server

Chen, James L

2014-01-01

This book is for anyone who wants to be able to connect the history of lunar exploration to the Moon visible above. It addresses what Apollo equipment and experiments were left behind and what the Apollo landings sites look like now. Each Apollo mission is examined in detail, with photos that progressively zoom-in to guide the reader in locating the Apollo landing sites. Guided by official NASA photographs from the Lunar Reconnaissance Orbiter and the original Apollo missions, the reader can view the Moon with a new appreciation of the accomplishment of landing astronauts on its surface.  Countless people have gazed at the Moon in the night sky knowing the successes of the Apollo Program in landing men on the Moon. After the information in this guide, casual and serious observers can actually point out where the Apollo landings occurred as well as knowing why those sites were chosen.

Individualization and Modularization of Vocational Education Instructional Materials. An Annotated Bibliography of Publications and Projects. Bibliography Series No. 32.

Science.gov (United States)

Magisos, Joel H., Comp.; Stakelon, Anne E., Comp.

This annotated bibliography is designed to assist applicants for research grants under part C (section 131a) of the amendments to the Vocational Education Act of 1963 by providing access to documents, journal articles, and current projects related to the individualization and modularization of vocational education instructional materials. The…

Evaluation of three automated genome annotations for Halorhabdus utahensis.

Directory of Open Access Journals (Sweden)

Peter Bakke

2009-07-01

Full Text Available Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited in databases such as NCBI and used to validate subsequent annotation errors. We submitted the genome sequence of halophilic archaeon Halorhabdus utahensis to be analyzed by three genome annotation services. We have examined the output from each service in a variety of ways in order to compare the methodology and effectiveness of the annotations, as well as to explore the genes, pathways, and physiology of the previously unannotated genome. The annotation services differ considerably in gene calls, features, and ease of use. We had to manually identify the origin of replication and the species-specific consensus ribosome-binding site. Additionally, we conducted laboratory experiments to test H. utahensis growth and enzyme activity. Current annotation practices need to improve in order to more accurately reflect a genome's biological potential. We make specific recommendations that could improve the quality of microbial annotation projects.

PDS Archive Release of Apollo 11, Apollo 12, and Apollo 17 Lunar Rock Sample Images

Science.gov (United States)

Garcia, P. A.; Stefanov, W. L.; Lofgren, G. E.; Todd, N. S.; Gaddis, L. R.

2013-01-01

Scientists at the Johnson Space Center (JSC) Lunar Sample Laboratory, Information Resources Directorate, and Image Science & Analysis Laboratory have been working to digitize (scan) the original film negatives of Apollo Lunar Rock Sample photographs [1, 2]. The rock samples, and associated regolith and lunar core samples, were obtained during the Apollo 11, 12, 14, 15, 16 and 17 missions. The images allow scientists to view the individual rock samples in their original or subdivided state prior to requesting physical samples for their research. In cases where access to the actual physical samples is not practical, the images provide an alternate mechanism for study of the subject samples. As the negatives are being scanned, they have been formatted and documented for permanent archive in the NASA Planetary Data System (PDS). The Astromaterials Research and Exploration Science Directorate (which includes the Lunar Sample Laboratory and Image Science & Analysis Laboratory) at JSC is working collaboratively with the Imaging Node of the PDS on the archiving of these valuable data. The PDS Imaging Node is now pleased to announce the release of the image archives for Apollo missions 11, 12, and 17.

Apollo in the North

DEFF Research Database (Denmark)

Østermark-Johansen, Lene

2015-01-01

Walter Pater’s fascination with the Hyperborean Apollo, who according to myth resided north of the home of the northern wind, is explored in two of his pieces of short fiction, ‘Duke Carl of Rosenmold’ (1887) and ‘Apollo in Picardy’ (1893). The essay discusses some of Pater’s complex dialogue wit...

Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.

Science.gov (United States)

Apweiler, R; Gateau, A; Contrino, S; Martin, M J; Junker, V; O'Donovan, C; Lang, F; Mitaritonna, N; Kappus, S; Bairoch, A

1997-01-01

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases. Ongoing genome sequencing projects have dramatically increased the number of protein sequences to be incorporated into SWISS-PROT. Since we do not want to dilute the quality standards of SWISS-PROT by incorporating sequences without proper sequence analysis and annotation, we cannot speed up the incorporation of new incoming data indefinitely. However, as we also want to make the sequences available as fast as possible, we introduced TREMBL (TRanslation of EMBL nucleotide sequence database), a supplement to SWISS-PROT. TREMBL consists of computer-annotated entries in SWISS-PROT format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except for CDS already included in SWISS-PROT. While TREMBL is already of immense value, its computer-generated annotation does not match the quality of SWISS-PROTs. The main difference is in the protein functional information attached to sequences. With this in mind, we are dedicating substantial effort to develop and apply computer methods to enhance the functional information attached to TREMBL entries.

Apollo The Definitive Sourcebook

CERN Document Server

Orloff, Richard W

2006-01-01

On 25 May 1961, John F Kennedy announced the goal of landing an American man on the Moon by the end of the decade. This challenge forced NASA to review the planned lunar landing of a three-man spaceship named Apollo in the mid-1970s. In 1962, it was decided that a specialized vehicle would accompany the main spacecraft, to make the lunar landing while the mothership remained in lunar orbit. To send these vehicles to the Moon would require the development of an enormous rocket. Development was protracted, but in December 1968 Apollo 8 was launched on a pioneering mission to perform an initial reconnaissance in lunar orbit. When Apollo 17 lifted off from the Moon in December 1972, the program was concluded. Now, at long last, there is a real prospect of a resumption of human exploration of the Moon. This book provides an overview of the origins of the Apollo program and descriptions of the ground facilities, launch vehicles and spacecraft that will serve as an invaluable single-volume sourcebook for space enthu...

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

Science.gov (United States)

Lewis, Tony E; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L; Buchan, Daniel W A; Chothia, Cyrus; Cuff, Alison; Dana, Jose M; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T; Kelley, Lawrence A; Kleywegt, Gerard J; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G; Ochoa-Montaño, Bernardo; Rackham, Owen J L; Smith, James; Sternberg, Michael J E; Velankar, Sameer; Yeats, Corin; Orengo, Christine

2013-01-01

Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence-structure-function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker's yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs).

The GATO gene annotation tool for research laboratories

Directory of Open Access Journals (Sweden)

A. Fujita

2005-11-01

Full Text Available Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

Roadmap for annotating transposable elements in eukaryote genomes.

Science.gov (United States)

Permal, Emmanuelle; Flutre, Timothée; Quesneville, Hadi

2012-01-01

Current high-throughput techniques have made it feasible to sequence even the genomes of non-model organisms. However, the annotation process now represents a bottleneck to genome analysis, especially when dealing with transposable elements (TE). Combined approaches, using both de novo and knowledge-based methods to detect TEs, are likely to produce reasonably comprehensive and sensitive results. This chapter provides a roadmap for researchers involved in genome projects to address this issue. At each step of the TE annotation process, from the identification of TE families to the annotation of TE copies, we outline the tools and good practices to be used.

Book Reviews, Annotation, and Web Technology.

Science.gov (United States)

Schulze, Patricia

From reading texts to annotating web pages, grade 6-8 students rely on group cooperation and individual reading and writing skills in this research project that spans six 50-minute lessons. Student objectives for this project are that they will: read, discuss, and keep a journal on a book in literature circles; understand the elements of and…

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.

Science.gov (United States)

Cohen, K Bretonnel; Lanfranchi, Arrick; Choi, Miji Joo-Young; Bada, Michael; Baumgartner, William A; Panteleyeva, Natalya; Verspoor, Karin; Palmer, Martha; Hunter, Lawrence E

2017-08-17

Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction from the scientific literature. In order to better understand the nature of the phenomenon of coreference in biomedical publications and to increase performance on the task, we annotated the Colorado Richly Annotated Full Text (CRAFT) corpus with coreference relations. The corpus was manually annotated with coreference relations, including identity and appositives for all coreferring base noun phrases. The OntoNotes annotation guidelines, with minor adaptations, were used. Interannotator agreement ranges from 0.480 (entity-based CEAF) to 0.858 (Class-B3), depending on the metric that is used to assess it. The resulting corpus adds nearly 30,000 annotations to the previous release of the CRAFT corpus. Differences from related projects include a much broader definition of markables, connection to extensive annotation of several domain-relevant semantic classes, and connection to complete syntactic annotation. Tool performance was benchmarked on the data. A publicly available out-of-the-box, general-domain coreference resolution system achieved an F-measure of 0.14 (B3), while a simple domain-adapted rule-based system achieved an F-measure of 0.42. An ensemble of the two reached F of 0.46. Following the IDENTITY chains in the data would add 106,263 additional named entities in the full 97-paper corpus, for an increase of 76% percent in the semantic classes of the eight ontologies that have been annotated in earlier versions of the CRAFT corpus. The project produced a large data set for further investigation of coreference and coreference resolution in the scientific literature. The work raised issues in the phenomenon of reference in this domain and genre, and the paper proposes that many mentions that would be considered generic in the general domain are not

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

Science.gov (United States)

Pilkington, Sarah M; Crowhurst, Ross; Hilario, Elena; Nardozza, Simona; Fraser, Lena; Peng, Yongyan; Gunaseelan, Kularajathevan; Simpson, Robert; Tahir, Jibran; Deroles, Simon C; Templeton, Kerry; Luo, Zhiwei; Davy, Marcus; Cheng, Canhong; McNeilage, Mark; Scaglione, Davide; Liu, Yifei; Zhang, Qiong; Datson, Paul; De Silva, Nihal; Gardiner, Susan E; Bassett, Heather; Chagné, David; McCallum, John; Dzierzon, Helge; Deng, Cecilia; Wang, Yen-Yi; Barron, Lorna; Manako, Kelvina; Bowen, Judith; Foster, Toshi M; Erridge, Zoe A; Tiffin, Heather; Waite, Chethi N; Davies, Kevin M; Grierson, Ella P; Laing, William A; Kirk, Rebecca; Chen, Xiuyin; Wood, Marion; Montefiori, Mirco; Brummell, David A; Schwinn, Kathy E; Catanach, Andrew; Fullerton, Christina; Li, Dawei; Meiyalaghan, Sathiyamoorthy; Nieuwenhuizen, Niels; Read, Nicola; Prakash, Roneel; Hunter, Don; Zhang, Huaibi; McKenzie, Marian; Knäbel, Mareike; Harris, Alastair; Allan, Andrew C; Gleave, Andrew; Chen, Angela; Janssen, Bart J; Plunkett, Blue; Ampomah-Dwamena, Charles; Voogd, Charlotte; Leif, Davin; Lafferty, Declan; Souleyre, Edwige J F; Varkonyi-Gasic, Erika; Gambi, Francesco; Hanley, Jenny; Yao, Jia-Long; Cheung, Joey; David, Karine M; Warren, Ben; Marsh, Ken; Snowden, Kimberley C; Lin-Wang, Kui; Brian, Lara; Martinez-Sanchez, Marcela; Wang, Mindy; Ileperuma, Nadeesha; Macnee, Nikolai; Campin, Robert; McAtee, Peter; Drummond, Revel S M; Espley, Richard V; Ireland, Hilary S; Wu, Rongmei; Atkinson, Ross G; Karunairetnam, Sakuntala; Bulley, Sean; Chunkath, Shayhan; Hanley, Zac; Storey, Roy; Thrimawithana, Amali H; Thomson, Susan; David, Charles; Testolin, Raffaele; Huang, Hongwen; Hellens, Roger P; Schaffer, Robert J

2018-04-16

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and

Designing a Lexical Database for a Combined Use of Corpus Annotation and Dictionary Editing

DEFF Research Database (Denmark)

Kristoffersen, Jette Hedegaard; Troelsgård, Thomas; Langer, Gabriele

2016-01-01

In a combined corpus-dictionary project, you would need one lexical database that could serve as a shared “backbone” for both corpus annotation and dictionary editing, but it is not that easy to define a database structure that applies satisfactorily to both these purposes. In this paper, we...... will exemplify the problem and present ideas on how to model structures in a lexical database that facilitate corpus annotation as well as dictionary editing. The paper is a joint work between the DGS Corpus Project and the DTS Dictionary Project. The two projects come from opposite sides of the spectrum (one...... adjusting a lexical database grown from dictionary making for corpus annotating, one building a lexical database in parallel with corpus annotation and editing a corpus-based dictionary), and we will consider requirements and feasible structures for a database that can serve both corpus and dictionary....

Annotation of the Evaluative Language in a Dependency Treebank

Directory of Open Access Journals (Sweden)

Šindlerová Jana

2017-12-01

Full Text Available In the paper, we present our efforts to annotate evaluative language in the Prague Dependency Treebank 2.0. The project is a follow-up of the series of annotations of small plaintext corpora. It uses automatic identification of potentially evaluative nodes through mapping a Czech subjectivity lexicon to syntactically annotated data. These nodes are then manually checked by an annotator and either dismissed as standing in a non-evaluative context, or confirmed as evaluative. In the latter case, information about the polarity orientation, the source and target of evaluation is added by the annotator. The annotations unveiled several advantages and disadvantages of the chosen framework. The advantages involve more structured and easy-to-handle environment for the annotator, visibility of syntactic patterning of the evaluative state, effective solving of discontinuous structures or a new perspective on the influence of good/bad news. The disadvantages include little capability of treating cases with evaluation spread among more syntactically connected nodes at once, little capability of treating metaphorical expressions, or disregarding the effects of negation and intensification in the current scheme.

Managing and Querying Image Annotation and Markup in XML.

Science.gov (United States)

Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

2010-01-01

Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid.

Managing and Querying Image Annotation and Markup in XML

Science.gov (United States)

Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

2010-01-01

Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid. PMID:21218167

Recovery and Restoration of Apollo Data - An Update

Science.gov (United States)

Williams, D. R.; Taylor, P. T.; Hills, H. K.; Nagihara, S.; Nakamura, Y.; Kiefer, W. S.; Guinness, E. A.

2017-12-01

The effort to restore Apollo lunar data, much of which was stored in obsolete formats and on unwieldy media, typically without sufficient documentation, continues to provide new insights into the workings of the Moon. The endeavor, under the auspices of the NASA Space Science Data Coordinated Archive (NSSDCA) Lunar Data Project and Planetary Data System (PDS) Lunar Data Node, and also funded by LASER and PDART proposals, is designed to take the data from the Apollo orbital instruments, astronaut experiments, and long-lived surface stations and convert them into well-documented, digital formats for archive in the NSSDCA and PDS. The data from the ALSEP (Apollo Lunar Surface Experiment Package) surface stations in particular had not been thoroughly examined. Now in standard digital formats with the aid of modern computers and algorithms, they are yielding long-term information on the lunar environment. We will review the data restoration effort in general, concentrating on data sets we have completed and those we are currently working on, which have resulted in advances in our understanding of the Moon. For example, we have restored the archived ALSEP heat flow data from Apollo 15 and 17 that covered the period from deployment to 1 January 1975 and archived them with PDS. In addition, raw data for a three month period from April to June, 1975 have been discovered and restored, and data from March 1976 through September 1977 have been read from the Apollo Work Tapes. These data confirm the subsurface temperatures at the heat flow site have been warming over many years, even at depth, and have implications for the interpretation of the heat flow coming from the Moon. Examination of the restored Lunar Ejecta And Meteorite (LEAM) data and comparison with the restored ALSEP Housekeeping data indicates that the anomalous signals recorded by LEAM are not due to electrical interference and may be due to charged dust particles. Re-examination of restored Lunar Atmospheric

Current trend of annotating single nucleotide variation in humans--A case study on SNVrap.

Science.gov (United States)

Li, Mulin Jun; Wang, Junwen

2015-06-01

As high throughput methods, such as whole genome genotyping arrays, whole exome sequencing (WES) and whole genome sequencing (WGS), have detected huge amounts of genetic variants associated with human diseases, function annotation of these variants is an indispensable step in understanding disease etiology. Large-scale functional genomics projects, such as The ENCODE Project and Roadmap Epigenomics Project, provide genome-wide profiling of functional elements across different human cell types and tissues. With the urgent demands for identification of disease-causal variants, comprehensive and easy-to-use annotation tool is highly in demand. Here we review and discuss current progress and trend of the variant annotation field. Furthermore, we introduce a comprehensive web portal for annotating human genetic variants. We use gene-based features and the latest functional genomics datasets to annotate single nucleotide variation (SNVs) in human, at whole genome scale. We further apply several function prediction algorithms to annotate SNVs that might affect different biological processes, including transcriptional gene regulation, alternative splicing, post-transcriptional regulation, translation and post-translational modifications. The SNVrap web portal is freely available at http://jjwanglab.org/snvrap. Copyright © 2014 Elsevier Inc. All rights reserved.

A Novel Approach to Semantic and Coreference Annotation at LLNL

Energy Technology Data Exchange (ETDEWEB)

Firpo, M

2005-02-04

A case is made for the importance of high quality semantic and coreference annotation. The challenges of providing such annotation are described. Asperger's Syndrome is introduced, and the connections are drawn between the needs of text annotation and the abilities of persons with Asperger's Syndrome to meet those needs. Finally, a pilot program is recommended wherein semantic annotation is performed by people with Asperger's Syndrome. The primary points embodied in this paper are as follows: (1) Document annotation is essential to the Natural Language Processing (NLP) projects at Lawrence Livermore National Laboratory (LLNL); (2) LLNL does not currently have a system in place to meet its need for text annotation; (3) Text annotation is challenging for a variety of reasons, many related to its very rote nature; (4) Persons with Asperger's Syndrome are particularly skilled at rote verbal tasks, and behavioral experts agree that they would excel at text annotation; and (6) A pilot study is recommend in which two to three people with Asperger's Syndrome annotate documents and then the quality and throughput of their work is evaluated relative to that of their neuro-typical peers.

Estimating the annotation error rate of curated GO database sequence annotations

Directory of Open Access Journals (Sweden)

Brown Alfred L

2007-05-01

Full Text Available Abstract Background Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigation into the data quality of sequence function annotations. Here we have developed a new method of estimating the error rate of curated sequence annotations, and applied this to the Gene Ontology (GO sequence database (GOSeqLite. This method involved artificially adding errors to sequence annotations at known rates, and used regression to model the impact on the precision of annotations based on BLAST matched sequences. Results We estimated the error rate of curated GO sequence annotations in the GOSeqLite database (March 2006 at between 28% and 30%. Annotations made without use of sequence similarity based methods (non-ISS had an estimated error rate of between 13% and 18%. Annotations made with the use of sequence similarity methodology (ISS had an estimated error rate of 49%. Conclusion While the overall error rate is reasonably low, it would be prudent to treat all ISS annotations with caution. Electronic annotators that use ISS annotations as the basis of predictions are likely to have higher false prediction rates, and for this reason designers of these systems should consider avoiding ISS annotations where possible. Electronic annotators that use ISS annotations to make predictions should be viewed sceptically. We recommend that curators thoroughly review ISS annotations before accepting them as valid. Overall, users of curated sequence annotations from the GO database should feel assured that they are using a comparatively high quality source of information.

Integrating UIMA annotators in a web-based text processing framework.

Science.gov (United States)

Chen, Xiang; Arnold, Corey W

2013-01-01

The Unstructured Information Management Architecture (UIMA) [1] framework is a growing platform for natural language processing (NLP) applications. However, such applications may be difficult for non-technical users deploy. This project presents a web-based framework that wraps UIMA-based annotator systems into a graphical user interface for researchers and clinicians, and a web service for developers. An annotator that extracts data elements from lung cancer radiology reports is presented to illustrate the use of the system. Annotation results from the web system can be exported to multiple formats for users to utilize in other aspects of their research and workflow. This project demonstrates the benefits of a lay-user interface for complex NLP applications. Efforts such as this can lead to increased interest and support for NLP work in the clinical domain.

Ten steps to get started in Genome Assembly and Annotation

Science.gov (United States)

Dominguez Del Angel, Victoria; Hjerde, Erik; Sterck, Lieven; Capella-Gutierrez, Salvadors; Notredame, Cederic; Vinnere Pettersson, Olga; Amselem, Joelle; Bouri, Laurent; Bocs, Stephanie; Klopp, Christophe; Gibrat, Jean-Francois; Vlasova, Anna; Leskosek, Brane L.; Soler, Lucile; Binzer-Panchal, Mahesh; Lantz, Henrik

2018-01-01

As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR). PMID:29568489

Sharing Map Annotations in Small Groups: X Marks the Spot

Science.gov (United States)

Congleton, Ben; Cerretani, Jacqueline; Newman, Mark W.; Ackerman, Mark S.

Advances in location-sensing technology, coupled with an increasingly pervasive wireless Internet, have made it possible (and increasingly easy) to access and share information with context of one’s geospatial location. We conducted a four-phase study, with 27 students, to explore the practices surrounding the creation, interpretation and sharing of map annotations in specific social contexts. We found that annotation authors consider multiple factors when deciding how to annotate maps, including the perceived utility to the audience and how their contributions will reflect on the image they project to others. Consumers of annotations value the novelty of information, but must be convinced of the author’s credibility. In this paper we describe our study, present the results, and discuss implications for the design of software for sharing map annotations.

The integration of a metadata generation framework in a music annotation workflow

OpenAIRE

Corthaut, Nik; Lippens, Stefaan; Govaerts, Sten; Duval, Erik; Martens, Jean-Pierre

2009-01-01

In the MuziK project we try to automate the typically hard task of annotating music files manually. This annotation is used for music recommendation and for automated playlist creation. The music experts of Aristo Music (http://www.aristomusic.com) defined the data fields. High quality annotations are required since the results, playlists, are used in commercial live settings and the cost of a wrong selection is high [1].

Apollo Lunar Sample Photographs: Digitizing the Moon Rock Collection

Science.gov (United States)

Lofgren, Gary E.; Todd, Nancy S.; Runco, S. K.; Stefanov, W. L.

2011-01-01

The Acquisition and Curation Office at JSC has undertaken a 4-year data restoration project effort for the lunar science community funded by the LASER program (Lunar Advanced Science and Exploration Research) to digitize photographs of the Apollo lunar rock samples and create high resolution digital images. These sample photographs are not easily accessible outside of JSC, and currently exist only on degradable film in the Curation Data Storage Facility

How Apollo Flew to the Moon

CERN Document Server

Woods, W David

2011-01-01

This new and expanded edition of the bestselling How Apollo Flew to the Moon tells the exciting story of how the Apollo missions were conducted and follows a virtual flight to the Moon and back. New material includes: - the exploration of the lunar surface; - more illustrations; - more technical explanations and anecdotes. From launch to splashdown, hitch a ride in the incredible Apollo spaceships, the most sophisticated machines of their time. Explore each step of the journey and glimpse the enormous range of disciplines, techniques, and procedures the Apollo crews had to master. Although the tremendous technological accomplishments are well documented, the human dimension is not forgotten, and the book calls on the testimony of the people who were there at the time. A wealth of fascinating and accessible material is provided, including: the role of the powerful Saturn V; the reasoning  behind trajectories; the day-to-day concerns of human and spacecraft health; the triumphs and difficulties of working in...

GSV Annotated Bibliography

Energy Technology Data Exchange (ETDEWEB)

Roberts, Randy S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pope, Paul A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jiang, Ming [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Trucano, Timothy G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aragon, Cecilia R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ni, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wei, Thomas [Argonne National Lab. (ANL), Argonne, IL (United States); Chilton, Lawrence K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bakel, Alan [Argonne National Lab. (ANL), Argonne, IL (United States)

2011-06-14

The following annotated bibliography was developed as part of the Geospatial Algorithm Veri cation and Validation (GSV) project for the Simulation, Algorithms and Modeling program of NA-22. Veri cation and Validation of geospatial image analysis algorithms covers a wide range of technologies. Papers in the bibliography are thus organized into the following ve topic areas: Image processing and analysis, usability and validation of geospatial image analysis algorithms, image distance measures, scene modeling and image rendering, and transportation simulation models.

MIPS: analysis and annotation of genome information in 2007.

Science.gov (United States)

Mewes, H W; Dietmann, S; Frishman, D; Gregory, R; Mannhaupt, G; Mayer, K F X; Münsterkötter, M; Ruepp, A; Spannagl, M; Stümpflen, V; Rattei, T

2008-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse. To cope with the task of global in-depth genome annotation has become unfeasible. Therefore, our efforts are dedicated to three levels of annotation: (i) the curation of selected genomes, in particular from fungal and plant taxa (e.g. CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).

Qualification of the APOLLO2 lattice physics code of the NURISP platform for WWER hexagonal lattices

International Nuclear Information System (INIS)

Hegyi, G.; Kereszturi, A.; Tota, A.

2011-01-01

The experiments performed at the ZR-6 zero critical reactor by the Temporary International Collective and a numerical assembly burnup benchmark specified for depletion calculation of a WWER-440 assembly containing gadolinium burnable poison were used to qualify the APOLLO2 (APOLLO2.8-E3) code as a part of its ongoing validation activity. The work is part of the NURISP project, where KFKI Atomic Energy Research Institute undertook to develop and qualify some calculation schemes for hexagonal problems. Concerning the ZR-6 measurements, single cell, macro cell and two-dimensional calculations of selected regular and perturbed experiments are being used for the validation. In the two-dimensional cases the radial leakage is also taken into account in the calculations together with the axial leakage represented by the measured axial buckling. Criticality parameter and reaction rate comparisons are presented. Although various sets of the experiments have been selected for the validation, good agreement of the measured and calculated parameters could be found by using the different options offered by APOLLO2. An additional mathematical benchmark-presented in the paper - also attests for the reliability of APOLLO2. All the test results prove the reliability of APOLLO2 for WWER core calculations. (Authors)

Apollo 11 Commander Armstrong Presents President With Commemorative Plaque

Science.gov (United States)

1974-01-01

On June 4, 1974, 5 years after the successful Apollo 11 lunar landing mission, commander Neil Armstrong (right) presented a plaque to U.S. President Richard Milhous Nixon (left) on behalf of all people who had taken part in the space program. In making the presentation, Armstrong said 'Mr. President, you have proclaimed this week to be United States Space week in conjunction with the fifth anniversary of our first successful landing on the Moon. It is my privilege to represent my colleagues, the crewmen of projects Mercury, Gemini, Apollo, and Skylab, and the men and women of NASA, and the hundreds of thousands of Americans from across the land who contributed so mightily to the success of our efforts in space in presenting this plaque which bears the names of each individual who has had the privilege of representing this country' in a space flight. The presentation was made at the California white house in San Clemente.

Tracking Apollo to the Moon

CERN Document Server

Lindsay, Hamish

2001-01-01

This is perhaps the most complete, detailed and readable story of manned space-flight ever published Beginning with the historical origins of the dream of walking on the Moon, Tracking Apollo to the Moon is the complete story of manned spaceflight, from the earliest Mercury and Gemini flights through to the end of the Apollo era In readable, fascinating detail, Hamish Lindsay - who was directly involved in all three programs - chronicles mankind's greatest adventure with a great narrative, interviews, quotes and masses of photographs, including some previously unpublished As well as bringing the history of these missions to life Tracking Apollo to the Moon serves as a detailed reference for space enthusiasts and students Having seen the manuscript, the Smithsonian requested two copies of the finished book, and Buzz Aldrin asked for five!

Doppler measurements of the ionosphere on the occasion of the Apollo-Soyuz test project. Part 1: Computer simulation of ionospheric-induced Doppler shifts

Science.gov (United States)

Grossi, M. D.; Gay, R. H.

1975-01-01

A computer simulation of the ionospheric experiment of the Apollo-Soyuz Test Project (ASTP) was performed. ASTP is the first example of USA/USSR cooperation in space and is scheduled for summer 1975. The experiment consists of performing dual-frequency Doppler measurements (at 162 and 324 MHz) between the Apollo Command Service Module (CSM) and the ASTP Docking Module (DM), both orbiting at 221-km height and at a relative distance of 300 km. The computer simulation showed that, with the Doppler measurement resolution of approximately 3 mHz provided by the instrumentation (in 10-sec integration time), ionospheric-induced Doppler shifts will be measurable accurately at all times, with some rare exceptions occurring when the radio path crosses regions of minimum ionospheric density. The computer simulation evaluated the ability of the experiment to measure changes of columnar electron content between CSM and DM (from which horizontal gradients of electron density at 221-km height can be obtained) and to measure variations in DM-to-ground columnar content (from which an averaged columnar content and the electron density at the DM can be deduced, under some simplifying assumptions).

Five Apollo astronauts with Lunar Module at ASVC prior to grand opening

Science.gov (United States)

1997-01-01

Some of the former Apollo program astronauts observe a Lunar Module and Moon mockup during a tour the new Apollo/Saturn V Center (ASVC) at KSC prior to the gala grand opening ceremony for the facility that was held Jan. 8, 1997. The astronauts were invited to participate in the event, which also featured NASA Administrator Dan Goldin and KSC Director Jay Honeycutt. Some of the visiting astonauts were (from left): Apollo 10 Lunar Module Pilot and Apollo 17 Commander Eugene A. Cernan; Apollo 9 Lunar Module Pilot Russell L. Schweikart; Apollo 10 Command Module Pilot and Apollo 16 Commander John W. Young; Apollo 10 Commander Thomas P. Stafford; and Apollo 11 Lunar Module Pilot Edwin E. 'Buzz' Aldrin, Jr. The ASVC also features several other Apollo program spacecraft components, multimedia presentations and a simulated Apollo/Saturn V liftoff. The facility will be a part of the KSC bus tour that embarks from the KSC Visitor Center.

APOLLO 10 ASTRONAUT ENTERS LUNAR MODULE SIMULATOR

Science.gov (United States)

1969-01-01

Apollo 10 lunar module pilot Eugene A. Cernan prepares to enter the lunar module simulator at the Flight Crew Training Building at the NASA Spaceport. Cernan, Apollo 10 commander Thomas P. Stafford and John W. Young, command module pilot, are to be launched May 18 on the Apollo 10 mission, a dress rehearsal for a lunar landing later this summer. Cernan and Stafford are to detach the lunar module and drop to within 10 miles of the moon's surface before rejoining Young in the command/service module. Looking on as Cernan puts on his soft helmet is Snoopy, the lovable cartoon mutt whose name will be the lunar module code name during the Apollo 10 flight. The command/service module is to bear the code name Charlie Brown.

Apollo 12 ropy glasses revisited

Science.gov (United States)

Wentworth, S. J.; Mckay, D. S.; Lindstrom, D. J.; Basu, A.; Martinez, R. R.; Bogard, D. D.; Garrison, D. H.

1994-01-01

We analyzed ropy glasses from Apollo 12 soils 12032 and 12033 by a variety of techniques including SEM/EDX, electron microprobe analysis, INAA, and Ar-39-Ar-40 age dating. The ropy glasses have potassium rare earth elements phosphorous (KREEP)-like compositions different from those of local Apollo 12 mare soils; it is likely that the ropy glasses are of exotic origin. Mixing calculations indicate that the ropy glasses formed from a liquid enriched in KREEP and that the ropy glass liquid also contained a significant amount of mare material. The presence of solar Ar and a trace of regolith-derived glass within the ropy glasses are evidence that the ropy glasses contain a small regolith component. Anorthosite and crystalline breccia (KREEP) clasts occur in some ropy glasses. We also found within these glasses clasts of felsite (fine-grained granitic fragments) very similar in texture and composition to the larger Apollo 12 felsites, which have a Ar-39-Ar-40 degassing age of 800 +/- 15 Ma. Measurements of 39-Ar-40-Ar in 12032 ropy glass indicate that it was degassed at the same time as the large felsite although the ropy glass was not completely degassed. The ropy glasses and felsites, therefore, probably came from the same source. Most early investigators suggested that the Apollo 12 ropy glasses were part of the ejecta deposited at the Apollo 12 site from the Copernicus impact. Our new data reinforce this model. If these ropy glasses are from Copernicus, they provide new clues to the nature of the target material at the Copernicus site, a part of the Moon that has not been sampled directly.

A Set of Annotation Interfaces for Alignment of Parallel Corpora

Directory of Open Access Journals (Sweden)

Singh Anil Kumar

2014-09-01

Full Text Available Annotation interfaces for parallel corpora which fit in well with other tools can be very useful. We describe a set of annotation interfaces which fulfill this criterion. This set includes a sentence alignment interface, two different word or word group alignment interfaces and an initial version of a parallel syntactic annotation alignment interface. These tools can be used for manual alignment, or they can be used to correct automatic alignments. Manual alignment can be performed in combination with certain kinds of linguistic annotation. Most of these interfaces use a representation called the Shakti Standard Format that has been found to be very robust and has been used for large and successful projects. It ties together the different interfaces, so that the data created by them is portable across all tools which support this representation. The existence of a query language for data stored in this representation makes it possible to build tools that allow easy search and modification of annotated parallel data.

Apollo's scientific legacy

International Nuclear Information System (INIS)

Meadows, J.

1979-01-01

The scientific value and importance of the Apollo lunar programme is assessed in the light of data obtained both from the lunar surface itself and also from the command modules which orbited above. It is stated that much of the material they returned still awaits a detailed examination and that the cooperative teams set up to handle the lunar material have established new methods and standards of analysis, which are currently revitalising the old science of meteoritics. The new forms of organised research have also been carried over in the rapidly developing subject of planetary science. It is concluded that whatever the motives for launching the Apollo missions, planetary scientists have been in a much better position to understand the Solar System since then. (UK)

Ubiquitous Annotation Systems

DEFF Research Database (Denmark)

Hansen, Frank Allan

2006-01-01

Ubiquitous annotation systems allow users to annotate physical places, objects, and persons with digital information. Especially in the field of location based information systems much work has been done to implement adaptive and context-aware systems, but few efforts have focused on the general...... requirements for linking information to objects in both physical and digital space. This paper surveys annotation techniques from open hypermedia systems, Web based annotation systems, and mobile and augmented reality systems to illustrate different approaches to four central challenges ubiquitous annotation...... systems have to deal with: anchoring, structuring, presentation, and authoring. Through a number of examples each challenge is discussed and HyCon, a context-aware hypermedia framework developed at the University of Aarhus, Denmark, is used to illustrate an integrated approach to ubiquitous annotations...

Restoration of the Apollo Heat Flow Experiments Metadata

Science.gov (United States)

Nagihara, S.; Stephens, M. K.; Taylor, P. T.; Williams, D. R.; Hills, H. K.; Nakamura, Y.

2015-01-01

Geothermal heat flow probes were deployed on the Apollo 15 and 17 missions as part of the Apollo Lunar Surface Experiments Package (ALSEP). At each landing site, the astronauts drilled 2 holes, 10-m apart, and installed a probe in each. The holes were 1- and 1.5-m deep at the Apollo 15 site and 2.5-m deep at the Apollo 17 sites. The probes monitored surface temperature and subsurface temperatures at different depths. At the Apollo 15 site, the monitoring continued from July 1971 to January 1977. At the Apollo 17 site, it did from December 1972 to September 1977. Based on the observations made through December 1974, Marcus Langseth, the principal investigator of the heat flow experiments (HFE), determined the thermal conductivity of the lunar regolith by mathematically modeling how the seasonal temperature fluctuation propagated down through the regolith. He also determined the temperature unaffected by diurnal and seasonal thermal waves of the regolith at different depths, which yielded the geothermal gradient. By multiplying the thermal gradient and the thermal conductivity, Langseth obtained the endogenic heat flow of the Moon as 21 mW/m(exp 2) at Site 15 and 16 mW/m(exp 2) at Site 17.

Neutron radiography of Apollo ordnance

International Nuclear Information System (INIS)

Golliher, K.G.

1983-01-01

Neutron radiography played an important role in the successful Apollo missions. Neutron radiography was used, for the first time, on a production basis to examine the internal details of ordnance devices employed in the Apollo Program. Ordnance devices ranged from charges which separated the massive booster stages to those which triggered the release of re-entry parachutes. Discussed are the early developments in neutron radiography and the conversion of this infant nondestructive technology into production capabilities. (Auth.)

Deterioration of plasticized PVC components in Apollo spacesuits

DEFF Research Database (Denmark)

Shashoua, Yvonne; Schnell, Ulrich; Young, Lisa

2002-01-01

Spacesuits from the Apollo era are unique in their history, materials and construction. This project involved the first detailed examination of the condition of the spacesuits since their acquisition by the National Air and Space Museum in the 1970s. Plasticized polyvinyl chloride (PVC) tubing...... in the Life Support System, used to transport air and water to the astronaut, and in the Liquid Cooling Garment, used to cool the wearer of the spacesuit, exhibited high levels of deterioration. Tubing was unacceptably discoloured, tacky to the touch and surfaces were obscured by crystals. Visual examination...

NASA Administrator Dan Goldin greets Neil Armstrong at Apollo 11 anniversary banquet.

Science.gov (United States)

1999-01-01

During an anniversary banquet honoring the Apollo team, the people who made the entire lunar landing program possible, former Apollo astronaut Neil A. Armstrong (left) shakes the hand of Judy Goldin (center), wife of NASA Administrator Daniel S. Goldin (right). The banquet was held in the Apollo/Saturn V Center, part of the KSC Visitor Complex. This is the 30th anniversary of the Apollo 11 launch and moon landing, July 16 and July 20, 1969. Among the guests at the banquet were former Apollo astronauts are Neil A. Armstrong and Edwin 'Buzz' Aldrin who flew on Apollo 11, the launch of the first moon landing; Gene Cernan, who flew on Apollo 10 and 17 and was the last man to walk on the moon; and Walt Cunningham, who flew on Apollo 7.

AutoFACT: An Automatic Functional Annotation and Classification Tool

Directory of Open Access Journals (Sweden)

Lang B Franz

2005-06-01

Full Text Available Abstract Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1 analyzes nucleotide and protein sequence data; (2 determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3 assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4 generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1–2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. Conclusion AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at http://megasun.bch.umontreal.ca/Software/AutoFACT.htm.

Apollo Missions to the Lunar Surface

Science.gov (United States)

Graff, Paige V.

2018-01-01

Six Apollo missions to the Moon, from 1969-1972, enabled astronauts to collect and bring lunar rocks and materials from the lunar surface to Earth. Apollo lunar samples are curated by NASA Astromaterials at the NASA Johnson Space Center in Houston, TX. Samples continue to be studied and provide clues about our early Solar System. Learn more and view collected samples at: https://curator.jsc.nasa.gov/lunar.

MEETING: Chlamydomonas Annotation Jamboree - October 2003

Energy Technology Data Exchange (ETDEWEB)

Grossman, Arthur R

2007-04-13

Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

AGORA : Organellar genome annotation from the amino acid and nucleotide references.

Science.gov (United States)

Jung, Jaehee; Kim, Jong Im; Jeong, Young-Sik; Yi, Gangman

2018-03-29

Next-generation sequencing (NGS) technologies have led to the accumulation of highthroughput sequence data from various organisms in biology. To apply gene annotation of organellar genomes for various organisms, more optimized tools for functional gene annotation are required. Almost all gene annotation tools are mainly focused on the chloroplast genome of land plants or the mitochondrial genome of animals.We have developed a web application AGORA for the fast, user-friendly, and improved annotations of organellar genomes. AGORA annotates genes based on a BLAST-based homology search and clustering with selected reference sequences from the NCBI database or user-defined uploaded data. AGORA can annotate the functional genes in almost all mitochondrion and plastid genomes of eukaryotes. The gene annotation of a genome with an exon-intron structure within a gene or inverted repeat region is also available. It provides information of start and end positions of each gene, BLAST results compared with the reference sequence, and visualization of gene map by OGDRAW. Users can freely use the software, and the accessible URL is https://bigdata.dongguk.edu/gene_project/AGORA/.The main module of the tool is implemented by the python and php, and the web page is built by the HTML and CSS to support all browsers. gangman@dongguk.edu.

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

Science.gov (United States)

Huntemann, Marcel; Ivanova, Natalia N; Mavromatis, Konstantinos; Tripp, H James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M; Kyrpides, Nikos C

2015-01-01

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.

Photogrammetry using Apollo 16 orbital photography, part B

Science.gov (United States)

Wu, S. S. C.; Schafer, F. J.; Jordan, R.; Nakata, G. M.

1972-01-01

Discussion is made of the Apollo 15 and 16 metric and panoramic cameras which provided photographs for accurate topographic portrayal of the lunar surface using photogrammetric methods. Nine stereoscopic models of Apollo 16 metric photographs and three models of panoramic photographs were evaluated photogrammetrically in support of the Apollo 16 geologic investigations. Four of the models were used to collect profile data for crater morphology studies; three models were used to collect evaluation data for the frequency distributions of lunar slopes; one model was used to prepare a map of the Apollo 16 traverse area; and one model was used to determine elevations of the Cayley Formation. The remaining three models were used to test photogrammetric techniques using oblique metric and panoramic camera photographs. Two preliminary contour maps were compiled and a high-oblique metric photograph was rectified.

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.

Science.gov (United States)

Brister, James Rodney; Bao, Yiming; Kuiken, Carla; Lefkowitz, Elliot J; Le Mercier, Philippe; Leplae, Raphael; Madupu, Ramana; Scheuermann, Richard H; Schobel, Seth; Seto, Donald; Shrivastava, Susmita; Sterk, Peter; Zeng, Qiandong; Klimke, William; Tatusova, Tatiana

2010-10-01

Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world's biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

Directory of Open Access Journals (Sweden)

Qiandong Zeng

2010-10-01

Full Text Available Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.

Extending eScience Provenance with User-Submitted Semantic Annotations

Science.gov (United States)

Michaelis, J.; Zednik, S.; West, P.; Fox, P. A.; McGuinness, D. L.

2010-12-01

eScience based systems generate provenance of their data products, related to such things as: data processing, data collection conditions, expert evaluation, and data product quality. Recent advances in web-based technology offer users the possibility of making annotations to both data products and steps in accompanying provenance traces, thereby expanding the utility of such provenance for others. These contributing users may have varying backgrounds, ranging from system experts to outside domain experts to citizen scientists. Furthermore, such users may wish to make varying types of annotations - ranging from documenting the purpose of a provenance step to raising concerns about the quality of data dependencies. Semantic Web technologies allow for such kinds of rich annotations to be made to provenance through the use of ontology vocabularies for (i) organizing provenance, and (ii) organizing user/annotation classifications. Furthermore, through Linked Data practices, Semantic linkages may be made from provenance steps to external data of interest. A desire for Semantically-annotated provenance has been motivated by data management issues in the Mauna Loa Solar Observatory’s (MLSO) Advanced Coronal Observing System (ACOS). In ACOS, photomoeter-based readings are taken of solar activity and subsequently processed into final data products consumable by end users. At intermediate stages of ACOS processing, factors such as evaluations by human experts and weather conditions are logged, which could impact data product quality. If such factors are linked via user-submitted annotations to provenance, it could be significantly beneficial for other users. Likewise, the background of a user could impact the credibility of their annotations. For example, an annotation made by a citizen scientist describing the purpose of a provenance step may not be as reliable as a similar annotation made by an ACOS project member. For this work, we have developed a software package that

Jannovar: a java library for exome annotation.

Science.gov (United States)

Jäger, Marten; Wang, Kai; Bauer, Sebastian; Smedley, Damian; Krawitz, Peter; Robinson, Peter N

2014-05-01

Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar. © 2014 WILEY PERIODICALS, INC.

Apollo management: A key to the solution of the social-economical dilemma - The transferability of space-travel managerial techniques to the civil sector

Science.gov (United States)

Puttkamer, J. V.

1973-01-01

An analysis has been conducted to find out whether the management techniques developed in connection with the Apollo project could be used for dealing with such urgent problems of modern society as the crisis of the cities, the increasing environmental pollution, and the steadily growing traffic. Basic concepts and definitions of program and system management are discussed together with details regarding the employment of these concepts in connection with the solution of the problems of the Apollo program. Principles and significance of a systems approach are considered, giving attention to planning, system analysis, system integration, and project management. An application of the methods of project management to the problems of the civil sector is possible if the special characteristics of each particular case are taken into account.

Neil Armstrong chats with attendees at Apollo 11 anniversary banquet.

Science.gov (United States)

1999-01-01

Former Apollo 11 astronaut Neil A. Armstrong is the center of attention at the anniversary banquet honoring the Apollo team, the people who made the entire lunar landing program possible. The banquet was held in the Apollo/Saturn V Center, part of the KSC Visitor Complex. This is the 30th anniversary of the Apollo 11 launch and moon landing, July 16 and July 20, 1969. Neil Armstrong was the first man to set foot on the moon. He appeared at the banquet with other former astronauts Edwin 'Buzz' Aldrin, Gene Cernan, Walt Cunningham and others.

A topic modeling approach for web service annotation

Directory of Open Access Journals (Sweden)

Leandro Ordóñez-Ante

2014-06-01

Full Text Available The actual implementation of semantic-based mechanisms for service retrieval has been restricted, given the resource-intensive procedure involved in the formal specification of services, which generally comprises associating semantic annotations to their documentation sources. Typically, developer performs such a procedure by hand, requiring specialized knowledge on models for semantic description of services (e.g. OWL-S, WSMO, SAWSDL, as well as formal specifications of knowledge. Thus, this semantic-based service description procedure turns out to be a cumbersome and error-prone task. This paper introduces a proposal for service annotation, based on processing web service documentation for extracting information regarding its offered capabilities. By uncovering the hidden semantic structure of such information through statistical analysis techniques, we are able to associate meaningful annotations to the services operations/resources, while grouping those operations into non-exclusive semantic related categories. This research paper belongs to the TelComp 2.0 project, which Colciencas and University of Cauca founded in cooperation.

The spectral code Apollo2: from lattice to 2D core calculations

International Nuclear Information System (INIS)

Coste-Delclaux, M.; Santandrea, S.; Damian, F.; Blanc-Tranchant, P.; Zmijarevic, I.; Santamarina, A.

2005-01-01

Apollo2 is a powerful code dedicated to neutron transport, it is a highly qualified tool for a wide range of applications from research and development studies to industrial applications. Today Apollo2 is part of several advanced 3-dimensional nuclear code packages dedicated to reactor physics, fuel cycle, criticality and safety analysis. The presentations have been organized into 7 topics: -) an introduction to Apollo2, -) cross-sections, -) flux calculation, -) advanced applications, -) Apollo2 users, specialized packages, -) qualification program, and -) the future of Apollo2. This document gathers only the slides of the presentations

The spectral code Apollo2: from lattice to 2D core calculations

Energy Technology Data Exchange (ETDEWEB)

Coste-Delclaux, M.; Santandrea, S.; Damian, F.; Blanc-Tranchant, P.; Zmijarevic, I. [CEA Saclay (DEN/DANS/SERMA), 91 - Gif-sur-Yvette (France); Santamarina, A. [CEA Cadarache (CEA/DEN/DER/SPRC), 13 - Saint Paul lez Durance (France)

2005-07-01

Apollo2 is a powerful code dedicated to neutron transport, it is a highly qualified tool for a wide range of applications from research and development studies to industrial applications. Today Apollo2 is part of several advanced 3-dimensional nuclear code packages dedicated to reactor physics, fuel cycle, criticality and safety analysis. The presentations have been organized into 7 topics: -) an introduction to Apollo2, -) cross-sections, -) flux calculation, -) advanced applications, -) Apollo2 users, specialized packages, -) qualification program, and -) the future of Apollo2. This document gathers only the slides of the presentations.

Semi-Semantic Annotation: A guideline for the URDU.KON-TB treebank POS annotation

Directory of Open Access Journals (Sweden)

Qaiser ABBAS

2016-12-01

Full Text Available This work elaborates the semi-semantic part of speech annotation guidelines for the URDU.KON-TB treebank: an annotated corpus. A hierarchical annotation scheme was designed to label the part of speech and then applied on the corpus. This raw corpus was collected from the Urdu Wikipedia and the Jang newspaper and then annotated with the proposed semi-semantic part of speech labels. The corpus contains text of local & international news, social stories, sports, culture, finance, religion, traveling, etc. This exercise finally contributed a part of speech annotation to the URDU.KON-TB treebank. Twenty-two main part of speech categories are divided into subcategories, which conclude the morphological, and semantical information encoded in it. This article reports the annotation guidelines in major; however, it also briefs the development of the URDU.KON-TB treebank, which includes the raw corpus collection, designing & employment of annotation scheme and finally, its statistical evaluation and results. The guidelines presented as follows, will be useful for linguistic community to annotate the sentences not only for the national language Urdu but for the other indigenous languages like Punjab, Sindhi, Pashto, etc., as well.

Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data

Directory of Open Access Journals (Sweden)

Merchant Sabeeha S

2011-07-01

Full Text Available Abstract Background Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. Description The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of

The Apollo lunar samples collection analysis and results

CERN Document Server

Young, Anthony

2017-01-01

This book focuses on the specific mission planning for lunar sample collection, the equipment used, and the analysis and findings concerning the samples at the Lunar Receiving Laboratory in Texas. Anthony Young documents the collection of Apollo samples for the first time for readers of all backgrounds, and includes interviews with many of those involved in planning and analyzing the samples. NASA contracted with the U.S. Geologic Survey to perform classroom and field training of the Apollo astronauts. NASA’s Geology Group within the Manned Spacecraft Center in Houston, Texas, helped to establish the goals of sample collection, as well as the design of sample collection tools, bags, and storage containers. In this book, detailed descriptions are given on the design of the lunar sampling tools, the Modular Experiment Transporter used on Apollo 14, and the specific areas of the Lunar Rover vehicle used for the Apollo 15, 16, and 17 missions, which carried the sampling tools, bags, and other related equipment ...

BioAnnote: a software platform for annotating biomedical documents with application in medical learning environments.

Science.gov (United States)

López-Fernández, H; Reboiro-Jato, M; Glez-Peña, D; Aparicio, F; Gachet, D; Buenaga, M; Fdez-Riverola, F

2013-07-01

Automatic term annotation from biomedical documents and external information linking are becoming a necessary prerequisite in modern computer-aided medical learning systems. In this context, this paper presents BioAnnote, a flexible and extensible open-source platform for automatically annotating biomedical resources. Apart from other valuable features, the software platform includes (i) a rich client enabling users to annotate multiple documents in a user friendly environment, (ii) an extensible and embeddable annotation meta-server allowing for the annotation of documents with local or remote vocabularies and (iii) a simple client/server protocol which facilitates the use of our meta-server from any other third-party application. In addition, BioAnnote implements a powerful scripting engine able to perform advanced batch annotations. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

PDS Lunar Data Node Restoration of Apollo In-Situ Surface Data

Science.gov (United States)

Williams, David R.; Hills, H. Kent; Guinness, Edward A.; Lowman, Paul D.; Taylor, Patrick T.

2010-01-01

The Apollo missions between 1969 and 1972 deployed scientific instruments on the Moon's surface which made in-situ measurements of the lunar environment. Apollo II had the short-term Early Apollo Surface Experiments Package (EASEP) and Apollos 12, 14, 15, 16, and 17 each set up an Apollo Lunar Surface Experiments Package (ALSEP). Each ALSEP package contained a different suite of instruments which took measurements and radioed the results back to Earth over periods from 5 to 7 years until they were turned off on 30 September 1977. To this day the ALSEP data remain the only long-term in-situ information on the Moon's surface environment. The Lunar Data Node (LDN) has been formed under the auspices of the Planetary Data System (PDS) Geosciences Node to put relevant, scientifically important Apollo data into accessible digital form for use by researchers and mission planners. We will report on progress made since last year and plans for future data restorations.

Apollo lugejate lemmikraamatud

Index Scriptorium Estoniae

2006-01-01

Apollo kaupluse koduleheküljel valiti parimaks ilukirjandusteoseks Jan Kausi "Tema", tõlgitud ilukirjanduse osas David Mitchelli "Pilveatlas", luuleraamatutest Ott Arderi "Luule sünnib kus sünnib kui sünnib" ja lasteraamatutest Christopher Paolini "Vanem". Vt. ka SL Õhtuleht, 14. dets., lk. 13

Physics analysis of the Apollo D-3He tokamak reactor

International Nuclear Information System (INIS)

Santarius, J.F.; Emmert, G.A.

1990-01-01

Recent developments in the analysis and conceptual design of Apollo, a D- 3 He Tokamak Reactor are presented. Encouraging experimental results on TEXT motivated a key change in the Apollo concept utilization of an ergodic magnetic limiter for impurity control instead of a divertor. Parameters for the updated Apollo design and an analysis of the ergoidc magnetic limiter are given. The Apollo reference case uses direct conversion of synchrotron radiation to electricity by rectifying antennas (rectennas) for its power conversion system. Previous analyses of this concept are expanded, including further details of the rectennas and of the loss of synchrotron power to the waveguides and walls. Although Apollo will burn D- 3 He fuel, a significant amount of unburned tritium will be generated by D4D reactions. The possibility of operating a short, dedicated, T+ 3 He burn phase to eliminate this tritium will be examined

Comparison between KARBUS and APOLLO 1; Vergleichsrechnungen mit KARBUS und APOLLO 1

Energy Technology Data Exchange (ETDEWEB)

Payer, L.; Broeders, C.

1995-08-01

A comparison is made between benchmark calculations by the French APOLLO 1 code and the Karlsruhe KARBUS procedure. Independently these two codes had been developed for transport computations in infinite reactor configurations and for burnup calculations. (orig.)

Sensor Control And Film Annotation For Long Range, Standoff Reconnaissance

Science.gov (United States)

Schmidt, Thomas G.; Peters, Owen L.; Post, Lawrence H.

1984-12-01

This paper describes a Reconnaissance Data Annotation System that incorporates off-the-shelf technology and system designs providing a high degree of adaptability and interoperability to satisfy future reconnaissance data requirements. The history of data annotation for reconnaissance is reviewed in order to provide the base from which future developments can be assessed and technical risks minimized. The system described will accommodate new developments in recording head assemblies and the incorporation of advanced cameras of both the film and electro-optical type. Use of microprocessor control and digital bus inter-face form the central design philosophy. For long range, high altitude, standoff missions, the Data Annotation System computes the projected latitude and longitude of central target position from aircraft position and attitude. This complements the use of longer ranges and high altitudes for reconnaissance missions.

Apollo 15 mare units and their petrogenesis

International Nuclear Information System (INIS)

Binder, A.A.

1985-01-01

Samples from 12 different mare sites were identified and classified among the Apollo 15 samples. The genesis of the Apollo 15 mare units is summarized given the general model of mare basalt source regions and of more basalt genesis derived from a synthesis of the major oxide/major mineral, compatible siderophile, and incompatible trace element data and isotopic ratios of the Rb/Sr and Sm/Nd systems

MicroScope: a platform for microbial genome annotation and comparative genomics.

Science.gov (United States)

Vallenet, D; Engelen, S; Mornico, D; Cruveiller, S; Fleury, L; Lajus, A; Rouy, Z; Roche, D; Salvignol, G; Scarpelli, C; Médigue, C

2009-01-01

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of

Ten steps to get started in Genome Assembly and Annotation [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Victoria Dominguez Del Angel

2018-02-01

Full Text Available As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR.

Apollo 12 - On the Ocean of Storms

CERN Document Server

Harland, David

2011-01-01

With its two moonwalks, deployment of a geophysical station and geological sampling, Apollo 12 did what many had hoped would be achieved by the first men to land on the Moon. It spectacularly demonstrated the precision landing capability required for the success of future lunar surface explorations. Apollo 12 - On the Ocean of Storms contains over 30 page of color images, including high-resolution scans recently produced by NASA from the original Hasselblad film; covers the mission from its planning through to completion; includes conversations among the crew in the spacecraft that were not transmitted; in the definitive 'popular' account of this mission. This is the first time in 40 years that the story of the Apollo 12 mission to the Moon has bene told in its entirety, using official documents, flight transcripts, and post-mission debriefing to recreate the drama.

Neil Armstrong gets round of applaus at Apollo 11 anniversary banquet.

Science.gov (United States)

1999-01-01

Former Apollo 11 astronaut Neil A. Armstrong stands to a round of applause after being introduced at the anniversary banquet honoring the Apollo team, the people who made the entire lunar landing program possible. The banquet was held in the Apollo/Saturn V Center, part of the KSC Visitor Complex. This is the 30th anniversary of the Apollo 11 launch and moon landing, July 16 and July 20, 1969. Neil Armstrong was the first man to set foot on the moon. He appeared at the banquet with other former astronauts Edwin 'Buzz' Aldrin, Gene Cernan, Walt Cunningham and others.

The link between aerospace industry and NASA during the Apollo years

Science.gov (United States)

Turcat, Nicolas

2008-01-01

Made in the frame of a French master on political history of USA in Paris IV La Sorbonne University, this subject is the third part of " The Economy of Apollo during the 60s". Nicolas Turcat is actually preparing his PhD in History of Innovation (DEA—Paris IV La Sorbonne). Our actual subject is " the link between aerospace industry and NASA during the Apollo years". This speech will highlight on some aspects of the link between NASA and aerospace industry. NASA could achieve the Apollo mission safely and under heavy financial pressure during the sixties due to a new type of organization for a civil agency; the contractor system. In fact, Military used it since the 1950s. And we will see how the development of this type of contract permitted a better interaction between the two parts. NASA would make another type of link with universities and technical institutes; a real brain trust was created, and between 1961 and 1967, 10,000 students worked and more than 200 universities on Apollo program. We will try to study briefly the procurement plan and process during the Apollo years. Without entering the " spin-offs debate", we will try to watch different aspects of the impacts and realities of the contractor and subcontractor system. We will see that would create a political debate inside USA when presidents Johnson and Nixon would decide to reduce Apollo program. Which states will benefit Apollo program? Or questions like how the debate at the end of the 1960s will become more and more political? Actually, almost 60% of the country's R&D was focused on Apollo, economical and moreover, political impacts would be great. We will try to study this under the light of different example: and particularly in California. The industrial and military complex was a part of the Apollo program. Apollo reoriented the aim of this complex for making it the first aerospace industry. Since this time, USA had not only acquired space ambition but real space capabilities. But more than

WORKSHOPS FOR THE HANDICAPPED, AN ANNOTATED BIBLIOGRAPHY--NO. 3.

Science.gov (United States)

PERKINS, DOROTHY C.; AND OTHERS

THESE 126 ANNOTATIONS ARE THE THIRD VOLUME OF A CONTINUING SERIES OF BIBLIOGRAPHIES LISTING ARTICLES APPEARING IN JOURNALS AND CONFERENCE, RESEARCH, AND PROJECT REPORTS. LISTINGS INCLUDE TESTS, TEST RESULTS, STAFF TRAINING PROGRAMS, GUIDES FOR COUNSELORS AND TEACHERS, AND ARCHITECTURAL PLANNING, AND RELATE TO THE MENTALLY RETARDED, EMOTIONALLY…

Biochemical Space: A Framework for Systemic Annotation of Biological Models

Czech Academy of Sciences Publication Activity Database

Klement, M.; Děd, T.; Šafránek, D.; Červený, Jan; Müller, Stefan; Steuer, Ralf

2014-01-01

Roč. 306, JUL (2014), s. 31-44 ISSN 1571-0661 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : biological models * model annotation * systems biology * cyanobacteria Subject RIV: EH - Ecology, Behaviour

Apollo Saturn V Height Comparison to Statue of Liberty

Science.gov (United States)

1967-01-01

This 1967 illustration compares the Apollo Saturn V Spacecraft of the Moon Landing era to the Statue of Liberty located on Ellis Island in New York City. The Apollo Saturn V, at 363 feet towers above Lady Liberty, as the statue is called, standing at 305 feet.

Apollo 14 emblem

Science.gov (United States)

1970-01-01

This is the Apollo 14 crew patch. It features the astronaut lapel pin approaching the Moon and leaving a comet trail from the liftoff point on Earth. The pin design was adopted by the astronaut corps several years ago. Astronauts who have not yet flown in space wear silver pins. Those who have flown wear gold pins.

Apollo 7 prime crew during water egress training in Gulf of Mexico

Science.gov (United States)

1968-01-01

The prime crew of the first manned Apollo space mission, Apollo 7, is seen in Apollo Command Module Boilerplate 1102 during water egress training in the Gulf of Mexico. In foreground is Astronaut Walter M. Schirra Jr., in center is Astronaut Donn F. Eisele, and in background is Astronaut Walter Cunningham.

MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

Directory of Open Access Journals (Sweden)

Shu-Chuan Chen

Full Text Available The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

Emblem of the Apollo 17 lunar landing mission

Science.gov (United States)

1972-01-01

This is the Official emblem of the Apollo 17 lunar landing mission which will be flown by Astronauts Eugene A. Cernan, Ronald E. Evans and Harrison H. Schmitt. The insignia is dominated by the image of Apollo, the Greek sun god. Suspended in space behind the head of Apollo is an American eagle of contemporary design, the red bars of the eagle's wing represent the bars in the U.S. flag; the three white stars symbolize the three astronaut crewmen. The background is deep blue space and within it are the Moon, the planet Saturn and a spiral galaxy or nebula. The Moon is partially overlaid by the eagle's wing suggesting that this is a celestial body that man has visited and in that sense conquered. The thrust of the eagle and the gaze of Apollo to the right and toward Saturn and the galaxy is meant to imply that man's goals in space will someday include the planets and perhaps the stars. The colors of the emblem are red, white and blue, the colors of our flag; with the addition of gold, to

Genome Annotation in a Community College Cell Biology Lab

Science.gov (United States)

Beagley, C. Timothy

2013-01-01

The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning…

Rock and Roll at the Apollo 17 Site

Science.gov (United States)

Martel, L. M. V.

2016-06-01

Astronauts Eugene A. Cernan and Harrison H. (Jack) Schmitt collected 243 pounds (110 kg) of rock and regolith samples during 22 hours working on the lunar surface during the Apollo 17 mission in December 1972, while Astronaut Ronald Evans orbited in the command module. The field observations, audio descriptions, and photographs coupled with orbital data and detailed, laboratory analyses of Apollo samples provided unprecedented information about the Moon and its geologic history. The Apollo samples continue to inspire new questions and answers about the Moon. Debra Hurwitz and David Kring (Lunar and Planetary Institute and NASA Solar System Exploration Research Virtual Institute; Hurwitz now at NASA Goddard Space Flight Center) were particularly interested in solving the mystery of where the boulders came from at the base of the North Massif (station 6) and at the base of the South Massif (station 2) from which Apollo 17 astronauts collected samples of impact melt breccias. The breccias were unequivocally formed by impact processes, but forty years of analyses had not yet determined unambiguously which impact event was responsible. Was it the basin-forming event of the landing site's neighbor Serenitatis (possibly Nectarian age); the larger, nearby Imbrium basin (Imbrian age and one of the last large basins to form); a combination of these impacts or an impact event older or younger than all of the above. Tracking down the origin of the boulders would ideally unravel details of the formation age of the breccias and, ultimately, help with the historical record of basin formation on the Moon. Hurwitz and Kring verified the boulders rolled down from massif walls - Apollo 17 impact melt breccias originated in massif material, not from the Sculptured Hills, an overlying geologic unit. But the relative geologic context is easier to explain than the absolute age, at least until some discrepancies are resolved in existing Ar-Ar and U-Pb radiometric ages of the Apollo 17

Evaluating Hierarchical Structure in Music Annotations.

Science.gov (United States)

McFee, Brian; Nieto, Oriol; Farbood, Morwaread M; Bello, Juan Pablo

2017-01-01

Music exhibits structure at multiple scales, ranging from motifs to large-scale functional components. When inferring the structure of a piece, different listeners may attend to different temporal scales, which can result in disagreements when they describe the same piece. In the field of music informatics research (MIR), it is common to use corpora annotated with structural boundaries at different levels. By quantifying disagreements between multiple annotators, previous research has yielded several insights relevant to the study of music cognition. First, annotators tend to agree when structural boundaries are ambiguous. Second, this ambiguity seems to depend on musical features, time scale, and genre. Furthermore, it is possible to tune current annotation evaluation metrics to better align with these perceptual differences. However, previous work has not directly analyzed the effects of hierarchical structure because the existing methods for comparing structural annotations are designed for "flat" descriptions, and do not readily generalize to hierarchical annotations. In this paper, we extend and generalize previous work on the evaluation of hierarchical descriptions of musical structure. We derive an evaluation metric which can compare hierarchical annotations holistically across multiple levels. sing this metric, we investigate inter-annotator agreement on the multilevel annotations of two different music corpora, investigate the influence of acoustic properties on hierarchical annotations, and evaluate existing hierarchical segmentation algorithms against the distribution of inter-annotator agreement.

Evaluating Hierarchical Structure in Music Annotations

Directory of Open Access Journals (Sweden)

Brian McFee

2017-08-01

Full Text Available Music exhibits structure at multiple scales, ranging from motifs to large-scale functional components. When inferring the structure of a piece, different listeners may attend to different temporal scales, which can result in disagreements when they describe the same piece. In the field of music informatics research (MIR, it is common to use corpora annotated with structural boundaries at different levels. By quantifying disagreements between multiple annotators, previous research has yielded several insights relevant to the study of music cognition. First, annotators tend to agree when structural boundaries are ambiguous. Second, this ambiguity seems to depend on musical features, time scale, and genre. Furthermore, it is possible to tune current annotation evaluation metrics to better align with these perceptual differences. However, previous work has not directly analyzed the effects of hierarchical structure because the existing methods for comparing structural annotations are designed for “flat” descriptions, and do not readily generalize to hierarchical annotations. In this paper, we extend and generalize previous work on the evaluation of hierarchical descriptions of musical structure. We derive an evaluation metric which can compare hierarchical annotations holistically across multiple levels. sing this metric, we investigate inter-annotator agreement on the multilevel annotations of two different music corpora, investigate the influence of acoustic properties on hierarchical annotations, and evaluate existing hierarchical segmentation algorithms against the distribution of inter-annotator agreement.

Apollo 11 Moon Landing

Science.gov (United States)

1969-01-01

The crowning achievement for the Saturn V rocket came when it launched Apollo 11 astronauts, Neil Armstrong, Edwin (Buzz) Aldrin, and Michael Collins, to the Moon in July 1969. In this photograph, astronaut Aldrin takes his first step onto the surface of the Moon.

ONEMercury: Towards Automatic Annotation of Earth Science Metadata

Science.gov (United States)

Tuarob, S.; Pouchard, L. C.; Noy, N.; Horsburgh, J. S.; Palanisamy, G.

2012-12-01

Earth sciences have become more data-intensive, requiring access to heterogeneous data collected from multiple places, times, and thematic scales. For example, research on climate change may involve exploring and analyzing observational data such as the migration of animals and temperature shifts across the earth, as well as various model-observation inter-comparison studies. Recently, DataONE, a federated data network built to facilitate access to and preservation of environmental and ecological data, has come to exist. ONEMercury has recently been implemented as part of the DataONE project to serve as a portal for discovering and accessing environmental and observational data across the globe. ONEMercury harvests metadata from the data hosted by multiple data repositories and makes it searchable via a common search interface built upon cutting edge search engine technology, allowing users to interact with the system, intelligently filter the search results on the fly, and fetch the data from distributed data sources. Linking data from heterogeneous sources always has a cost. A problem that ONEMercury faces is the different levels of annotation in the harvested metadata records. Poorly annotated records tend to be missed during the search process as they lack meaningful keywords. Furthermore, such records would not be compatible with the advanced search functionality offered by ONEMercury as the interface requires a metadata record be semantically annotated. The explosion of the number of metadata records harvested from an increasing number of data repositories makes it impossible to annotate the harvested records manually, urging the need for a tool capable of automatically annotating poorly curated metadata records. In this paper, we propose a topic-model (TM) based approach for automatic metadata annotation. Our approach mines topics in the set of well annotated records and suggests keywords for poorly annotated records based on topic similarity. We utilize the

Compositional characteristics of some Apollo 14 clastic materials.

Science.gov (United States)

Lindstrom, M. M.; Duncan, A. R.; Fruchter, J. S.; Mckay, S. M.; Stoeser, J. W.; Goles, G. G.; Lindstrom, D. J.

1972-01-01

Eighty-two subsamples of Apollo 14 materials have been analyzed by instrumental neutron activation analysis techniques for as many as 25 elements. In many cases, it was necessary to develop new procedures to allow analyses of small specimens. Compositional relationships among Apollo 14 materials indicate that there are small but systematic differences between regolith from the valley terrain and that from Cone Crater ejecta. Fragments from 1-2 mm size fractions of regolith samples may be divided into compositional classes, and the 'soil breccias' among them are very similar to valley soils. Multicomponent linear mixing models have been used as interpretive tools in dealing with data on regolith fractions and subsamples from breccia 14321. These mixing models show systematic compositional variations with inferred age for Apollo 14 clastic materials.

APOLLO 16 COMMANDER JOHN YOUNG ENTERS ALTITUDE CHAMBER FOR TESTS

Science.gov (United States)

1971-01-01

Apollo 16 commander John W. Young prepares to enter the lunar module in an altitude chamber in the Manned Spacecraft Operations Building at the spaceport prior to an altitude run. During the altitude run, in which Apollo 16 lunar module pilot Charles M. Duke also participated, the chamber was pumped down to simulate pressure at an altitude in excess of 200,000 feet. Young, Duke and command module pilot Thomas K. Mattingly II, are training at the Kennedy Space Center for the Apollo 16 mission. Launch is scheduled from Pad 39A, March 17, 1972.

Apollo, Marsyas and Ferdinand I

Czech Academy of Sciences Publication Activity Database

Bažant, Jan

2009-01-01

Roč. 2007, č. 22 (2009), s. 127-136 ISSN 0567-8269 Institutional research plan: CEZ:AV0Z90090514 Keywords : Apollo * Marsyas * Ferdinand I * Prague * Renaissance Subject RIV: AA - Philosophy ; Religion

Review of measurements of dust movements on the Moon during Apollo

Science.gov (United States)

O'Brien, Brian J.

2011-11-01

This is the first review of 3 Apollo experiments, which made the only direct measurements of dust on the lunar surface: (i) minimalist matchbox-sized 270 g Dust Detector Experiments (DDEs) of Apollo 11, 12, 14 and 15, produced 30 million Lunar Day measurements 21 July 1969-30 September, 1977; (ii) Thermal Degradation Samples (TDS) of Apollo 14, sprinkled with dust, photographed, taken back to Earth into quarantine and lost; and (iii) the 7.5 kg Lunar Ejecta and Meteoroids (LEAM) experiment of Apollo 17, whose original tapes and plots are lost. LEAM, designed to measure rare impacts of cosmic dust, registered scores of events each lunation most frequently around sunrise and sunset. LEAM data are accepted as caused by heavily-charged particles of lunar dust at speeds of motivation for returning to the Moon. New analyses here show some raw data are sporadic bursts of 1, 2, 3 or more events within time bubbles smaller than 0.6 s, not predicted by theoretical dust models but consistent with noise bits caused by electromagnetic interference (EMI) from switching of large currents in the Apollo 17 Lunar Surface Experiment Package (ALSEP), as occurred in pre-flight LEAM-acceptance tests. On the Moon switching is most common around sunrise and sunset in a dozen heavy-duty heaters essential for operational survival during 350 h of lunar night temperatures of minus 170 °C. Another four otherwise unexplained features of LEAM data are consistent with the "noise bits" hypothesis. Discoveries with DDE and TDS reported in 1970 and 1971, though overlooked, and extensive DDE discoveries in 2009 revealed strengths of adhesive and cohesive forces of lunar dust. Rocket exhaust gases during Lunar Module (LM) ascent caused dust and debris to (i) contaminate instruments 17 m distant (Apollo 11) as expected, and (ii) unexpectedly cleanse Apollo hardware 130 m (Apollo 12) and 180 m (Apollo 14) from LM. TDS photos uniquely document in situ cohesion of dust particles and their adhesion to 12

Pipeline to upgrade the genome annotations

Directory of Open Access Journals (Sweden)

Lijin K. Gopi

2017-12-01

Full Text Available Current era of functional genomics is enriched with good quality draft genomes and annotations for many thousands of species and varieties with the support of the advancements in the next generation sequencing technologies (NGS. Around 25,250 genomes, of the organisms from various kingdoms, are submitted in the NCBI genome resource till date. Each of these genomes was annotated using various tools and knowledge-bases that were available during the period of the annotation. It is obvious that these annotations will be improved if the same genome is annotated using improved tools and knowledge-bases. Here we present a new genome annotation pipeline, strengthened with various tools and knowledge-bases that are capable of producing better quality annotations from the consensus of the predictions from different tools. This resource also perform various additional annotations, apart from the usual gene predictions and functional annotations, which involve SSRs, novel repeats, paralogs, proteins with transmembrane helices, signal peptides etc. This new annotation resource is trained to evaluate and integrate all the predictions together to resolve the overlaps and ambiguities of the boundaries. One of the important highlights of this resource is the capability of predicting the phylogenetic relations of the repeats using the evolutionary trace analysis and orthologous gene clusters. We also present a case study, of the pipeline, in which we upgrade the genome annotation of Nelumbo nucifera (sacred lotus. It is demonstrated that this resource is capable of producing an improved annotation for a better understanding of the biology of various organisms.

Microtask crowdsourcing for disease mention annotation in PubMed abstracts.

Science.gov (United States)

Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I

2015-01-01

Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon's Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the 'training set' of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation_with_Mechanical_Turk/1126402.

Apollo 11 Earth Training Exercises

Science.gov (United States)

1969-01-01

In preparation of the nation's first lunar landing mission, Apollo 11 crew members underwent training to practice activities they would be performing during the mission. In this photograph, taken at the Manned Spacecraft Center in Houston, Texas, an engineer, Bob Mason, donned in a space suit, goes through some of those training exercises on the mock lunar surface. He performed activites similar to those planned for astronauts Neil Armstrong and Edwin Aldrin during their moon walk. The Apollo 11 mission launched from the Kennedy Space Center (KSC) in Florida via the Marshall Space Flight Center (MSFC) developed Saturn V launch vehicle on July 16, 1969 and safely returned to Earth on July 24, 1969. Aboard the space craft were astronauts Neil A. Armstrong, commander; Michael Collins, Command Module (CM) pilot; and Edwin E. (Buzz) Aldrin Jr., Lunar Module (LM) pilot. The CM, 'Columbia', piloted by Collins, remained in a parking orbit around the Moon while the LM, 'Eagle'', carrying astronauts Armstrong and Aldrin, landed on the Moon. On July 20, 1969, Armstrong was the first human to ever stand on the lunar surface, followed by Aldrin. During 2½ hours of surface exploration, the crew collected 47 pounds of lunar surface material for analysis back on Earth. With the success of Apollo 11, the national objective to land men on the Moon and return them safely to Earth had been accomplished.

Indigenous Carbon Embedded in Apollo 17 Black Volcanic Glass Surface Deposits

Science.gov (United States)

Thomas-Keprta, Kathie L.; Ross, D. K.; Le, L.; Gonzalez, C.; McKay, D. S.; Gibson, E. K.

2012-01-01

The assessment of indigenous organic matter in returned lunar samples was one of the primary scientific goals of the Apollo program. The levels of such organic material were expected to be and found to be small. Previous work on this topic includes Murphy et al. [1] who reported the presence of anthropogenic organics with sub-ppm concentrations in Apollo 11 fines. In Apollo 12 samples, Preti et al. [2] detected low levels, < 10 ppb or below, of more complex organic material that may have been synthesized by abrupt heating during analysis. Kvenvolden et al. [3] detected porphyrin-like pigments at the ng to pg level in an Apollo 11 bulk sample. Hodgson et al. [4] and Ponnamperuma et al. [5] suggested that most if not all porphyrins were synthesized from rocket fuel during module landing. Chang et al. [6] reported indigenous carbon ranging from 5-20 g/g in the form of metal carbides in Apollo 11 fines. Hare et al. [7] reported amino acids at he 50 ng/g level in Apollo 11 samples but suggested the results may be explained as contamination. More recently, Clemett et al. [8] reported simple polycyclic aromatic hydrocarbons at concentrations of < 1ppm in an Apollo 16 soil. Low concentrations of lunar organics may be a consequence not only of its paucity, but also its heterogeneous distribution. If the sample size required for a measurement is large relative to the localization of organics, detection is limited not by ultimate sensitivity but rather by the ability to distinguish an indigenous signature from background contamination [9].

Reasoning with Annotations of Texts

OpenAIRE

Ma , Yue; Lévy , François; Ghimire , Sudeep

2011-01-01

International audience; Linguistic and semantic annotations are important features for text-based applications. However, achieving and maintaining a good quality of a set of annotations is known to be a complex task. Many ad hoc approaches have been developed to produce various types of annotations, while comparing those annotations to improve their quality is still rare. In this paper, we propose a framework in which both linguistic and domain information can cooperate to reason with annotat...

Hawaii Geothermal Project annotated bibliography: Biological resources of the geothermal subzones, the transmission corridors and the Puna District, Island of Hawaii

Energy Technology Data Exchange (ETDEWEB)

Miller, S.E.; Burgett, J.M. [Fish and Wildlife Service, Honolulu, HI (United States). Pacific Islands Office

1993-10-01

Task 1 of the Hawaii Geothermal Project Interagency Agreement between the Fish and Wildlife Service and the Department of Energy-Oak Ridge National Laboratory (DOE) includes an annotated bibliography of published and unpublished documents that cover biological issues related to the lowland rain forest in Puna, adjacent areas, transmission corridors, and in the proposed Hawaii Geothermal Project (HGP). The 51 documents reviewed in this report cover the main body of biological information for these projects. The full table of contents and bibliography for each document is included along with two copies (as requested in the Interagency Agreement) of the biological sections of each document. The documents are reviewed in five main categories: (1) geothermal subzones (29 documents); (2) transmission cable routes (8 documents); (3) commercial satellite launching facility (Spaceport; 1 document); (4) manganese nodule processing facility (2 documents); (5) water resource development (1 document); and (6) ecosystem stability and introduced species (11 documents).

Log of Apollo 11.

Science.gov (United States)

National Aeronautics and Space Administration, Washington, DC.

The major events of the first manned moon landing mission, Apollo 11, are presented in chronological order from launch time until arrival of the astronauts aboard the U.S.S. Hornet. The log is descriptive, non-technical, and includes numerous color photographs of the astronauts on the moon. (PR)

Discoveries from Revisiting Apollo Direct Active Measurements of Lunar Dust

Science.gov (United States)

O'Brien, Brian

2010-05-01

New missions to the moon being developed by China, Japan, India, USA, Russia and Europe and possibilities of human missions about 2020 face the reality that 6 Apollo expeditions did not totally manage or mitigate effects of easily-mobilised and very "sticky" lunar dust on humans and hardware. Laboratory and theoretical modelling cannot reliably simulate the complex lunar environments that affect dynamical movements of lunar dust. The only direct active measurements of lunar dust during Apollo were made by matchbox-sized minimalist Dust Detector Experiments (DDEs) deployed to transmit some 30 million digital measurements from Apollo 11, 12, 14 and 15. These were misplaced or relatively ignored until 2009, when a self-funded suite of discoveries (O'Brien Geophys. Research Letters FIX 6 May 2099) revealed unexpected properties of lunar dust, such as the adhesive force being stronger as illumination increased. We give the first reports of contrasting effects, contamination or cleansing, from rocket exhausts of Apollo 11, 12, 14 and 15 Lunar Modules leaving the moon. We further strengthen the importance of collateral dust inadvertently splashed on Apollo hardware by human activities. Dust management designs and mission plans require optimum use of such in situ measurements, extended by laboratory simulations and theoretical modelling.

Vertical view of Apollo 16 landing site located Descartes area lunar nearside

Science.gov (United States)

1971-01-01

A vertical view of the Apollo 16 landing site located in the Descartes area lunar nearside. The overlay indicates the location of the proposed touchdown point for the Apollo 16 Lunar Module. Descartes is located west of the Sea of Nectar and southwest of the Sea of Tranquility. This photograph was taken with a 500mm lens camera from lunar orbit by the Apollo 14 crew.

Semantic annotation of consumer health questions.

Science.gov (United States)

Kilicoglu, Halil; Ben Abacha, Asma; Mrabet, Yassine; Shooshan, Sonya E; Rodriguez, Laritza; Masterton, Kate; Demner-Fushman, Dina

2018-02-06

Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health information needs are complex and can only fully be expressed in natural language. Consumer health question answering (QA) systems aim to fill this gap. A major challenge in developing consumer health QA systems is extracting relevant semantic content from the natural language questions (question understanding). To develop effective question understanding tools, question corpora semantically annotated for relevant question elements are needed. In this paper, we present a two-part consumer health question corpus annotated with several semantic categories: named entities, question triggers/types, question frames, and question topic. The first part (CHQA-email) consists of relatively long email requests received by the U.S. National Library of Medicine (NLM) customer service, while the second part (CHQA-web) consists of shorter questions posed to MedlinePlus search engine as queries. Each question has been annotated by two annotators. The annotation methodology is largely the same between the two parts of the corpus; however, we also explain and justify the differences between them. Additionally, we provide information about corpus characteristics, inter-annotator agreement, and our attempts to measure annotation confidence in the absence of adjudication of annotations. The resulting corpus consists of 2614 questions (CHQA-email: 1740, CHQA-web: 874). Problems are the most frequent named entities, while treatment and general information questions are the most common question types. Inter-annotator agreement was generally modest: question types and topics yielded highest agreement, while the agreement for more complex frame annotations was lower. Agreement in CHQA-web was consistently higher than that in CHQA-email. Pairwise inter-annotator agreement proved most

Predicting word sense annotation agreement

DEFF Research Database (Denmark)

Martinez Alonso, Hector; Johannsen, Anders Trærup; Lopez de Lacalle, Oier

2015-01-01

High agreement is a common objective when annotating data for word senses. However, a number of factors make perfect agreement impossible, e.g. the limitations of the sense inventories, the difficulty of the examples or the interpretation preferences of the annotations. Estimating potential...... agreement is thus a relevant task to supplement the evaluation of sense annotations. In this article we propose two methods to predict agreement on word-annotation instances. We experiment with a continuous representation and a three-way discretization of observed agreement. In spite of the difficulty...

Alignment-Annotator web server: rendering and annotating sequence alignments.

Science.gov (United States)

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pulmonary function evaluation during the Skylab and Apollo-Soyuz missions

Science.gov (United States)

Sawin, C. F.; Nicogossian, A. E.; Rummel, J. A.; Michel, E. L.

1976-01-01

Previous experience during Apollo postflight exercise testing indicated no major changes in pulmonary function. Pulmonary function has been studied in detail following exposure to hypoxic and hyperoxic normal gravity environments, but no previous study has reported on men exposed to an environment that was both normoxic at 258 torr total pressure and at null gravity as encountered in Skylab. Forced vital capacity (FVC) was measured during the preflight and postflight periods of the Skylab 2 mission. Inflight measurements of vital capacity (VC) were obtained during the last 2 weeks of the second manned mission (Skylab 3). More detailed pulmonary function screening was accomplished during the Skylab 4 mission. The primary measurements made during Skylab 4 testing included residual volume determination (RV), closing volume (CV), VC, FVC and its derivatives. In addition, VC was measured in flight at regular intervals during the Skylab 4 mission. Vital capacity was decreased slightly (-10%) in flight in all Skylab 4 crewmen. No major preflight-to-postflight changes were observed. The Apollo-Soyuz Test Project (ASTP) crewmen were studied using equipment and procedures similar to those employed during Skylab 4. Postflight evaluation of the ASTP crewmen was complicated by their inadvertent exposure to nitrogen tetroxide gas fumes upon reentry.

Astronaut John Young during final suiting operations for Apollo 10 mission

Science.gov (United States)

1969-01-01

A technician attaches hose from test stand to spacesuit of Astronaut John W. Young, Apollo 10 command module pilot, during final suiting operations for the Apollo 10 lunar orbit mission. Another technician makes adjustment behind Young.

Apollo Spacecraft 012 Command/Service Module being moved to Operations bldg

Science.gov (United States)

1967-01-01

Transfer of Apollo Spacecraft 012 Command/Service Module for mating to the Saturn Lunar Module Adapter No. 05 in the Manned Spacecraft Operations bldg. S/C 012 will be flown on the Apollo/Saturn 204 mission.

Neil Armstrong talks of his experiences at Apollo 11 anniversary banquet

Science.gov (United States)

1999-01-01

Neil Armstrong, former Apollo 11 astronaut, and first man to walk on the moon, talks about his experiences for an enthusiastic audience at the Apollo/Saturn V Center, part of the KSC Visitor Complex. The occasion was a banquet celebrating the 30th anniversary of the Apollo 11 launch and moon landing, July 16 and July 20, 1969. Among other guests at the banquet were astronauts Wally Schirra, Edwin 'Buzz' Aldrin and Walt Cunningham. Gene Cernan was the last man to walk on the moon.

Cosmic ray exposure ages of features and events at the Apollo landing sites

International Nuclear Information System (INIS)

Arvidson, R.; Crozaz, G.; Drozd, R.J.; Hohenberg, C.M.; Morgan, C.J.

1975-01-01

Cosmic ray exposure ages of lunar samples have been used to date surface features related to impact cratering and downslope movement of material. Only when multiple samples related to a feature have the same rare gas exposure age, or when a single sample has the same 81 Kr-Kr and track exposure age can a feature be considered reliably dated. Because any single lunar sample is likely to have had a complex history, assignment of ages to features based upon only one determination by any method should be avoided. Based on the above criteria, there are only five well-dated lunar features: Cone Crater (Apollo 14) 26 m.y., North Ray Crater (Apollo 16) 50 m.y., South Ray Crater (Apollo 16) 2 m.y., the emplacement of the Station 6 boulders (Apollo 17) 22 m.y., and the emplacement of the Station 7 boulder (Apollo 17) 28 m.y. Other features are tentatively dated or have limits set on their ages: Bench Crater (Apollo 12) =50 m.y. (Auth.)

Reporters Interview Family of Apollo 11 Astronaut Neil Armstrong

Science.gov (United States)

1969-01-01

Newsmen talked with the wife and sons of Apollo 11 astronaut Neil A. Armstrong after the successful launch of Apollo 11 on its trajectory to the moon. The Apollo 11 mission, the first lunar landing mission, launched from the Kennedy Space Center (KSC) in Florida via the Marshall Space Flight Center (MSFC) developed Saturn V launch vehicle on July 16, 1969 and safely returned to Earth on July 24, 1969. Aboard the space craft were astronauts Neil A. Armstrong, commander; Michael Collins, Command Module (CM) pilot; and Edwin E. (Buzz) Aldrin Jr., Lunar Module (LM) pilot. The CM, 'Columbia', piloted by Collins, remained in a parking orbit around the Moon while the LM, 'Eagle'', carrying astronauts Armstrong and Aldrin, landed on the Moon. On July 20, 1969, Armstrong was the first human to ever stand on the lunar surface, followed by Aldrin. During 2½ hours of surface exploration, the crew collected 47 pounds of lunar surface material for analysis back on Earth. With the success of Apollo 11, the national objective to land men on the Moon and return them safely to Earth had been accomplished.

Objective-guided image annotation.

Science.gov (United States)

Mao, Qi; Tsang, Ivor Wai-Hung; Gao, Shenghua

2013-04-01

Automatic image annotation, which is usually formulated as a multi-label classification problem, is one of the major tools used to enhance the semantic understanding of web images. Many multimedia applications (e.g., tag-based image retrieval) can greatly benefit from image annotation. However, the insufficient performance of image annotation methods prevents these applications from being practical. On the other hand, specific measures are usually designed to evaluate how well one annotation method performs for a specific objective or application, but most image annotation methods do not consider optimization of these measures, so that they are inevitably trapped into suboptimal performance of these objective-specific measures. To address this issue, we first summarize a variety of objective-guided performance measures under a unified representation. Our analysis reveals that macro-averaging measures are very sensitive to infrequent keywords, and hamming measure is easily affected by skewed distributions. We then propose a unified multi-label learning framework, which directly optimizes a variety of objective-specific measures of multi-label learning tasks. Specifically, we first present a multilayer hierarchical structure of learning hypotheses for multi-label problems based on which a variety of loss functions with respect to objective-guided measures are defined. And then, we formulate these loss functions as relaxed surrogate functions and optimize them by structural SVMs. According to the analysis of various measures and the high time complexity of optimizing micro-averaging measures, in this paper, we focus on example-based measures that are tailor-made for image annotation tasks but are seldom explored in the literature. Experiments show consistency with the formal analysis on two widely used multi-label datasets, and demonstrate the superior performance of our proposed method over state-of-the-art baseline methods in terms of example-based measures on four

Giles, Petrone, and Garriott Chat at Apollo 16 Display

Science.gov (United States)

1974-01-01

Huntsville's Jack Giles, Alabama State Senator (left), and Dr. Rocco Petrone, Marshall Space Flight Center Director (Middle), speak with Astronaut Owen Garriott who is inside the Apollo 16 Command Module on display at the Alabama Space and Rocket Center in Huntsville, Alabama. The successful Apollo 16 manned lunar landing mission took place April 16, 1972 through April 27, 1972. (Photograph courtesy of Huntsville/Madison County Public Library)

Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach

Directory of Open Access Journals (Sweden)

Bárcena José A

2008-12-01

Full Text Available Abstract Background Annotation of protein-coding genes is a key step in sequencing projects. Protein functions are mainly assigned on the basis of the amino acid sequence alone by searching of homologous proteins. However, fully automated annotation processes often lead to wrong prediction of protein functions, and therefore time-intensive manual curation is often essential. Here we describe a fast and reliable way to correct function annotation in sequencing projects, focusing on surface proteomes. We use a proteomics approach, previously proven to be very powerful for identifying new vaccine candidates against Gram-positive pathogens. It consists of shaving the surface of intact cells with two proteases, the specific cleavage-site trypsin and the unspecific proteinase K, followed by LC/MS/MS analysis of the resulting peptides. The identified proteins are contrasted by computational analysis and their sequences are inspected to correct possible errors in function prediction. Results When applied to the zoonotic pathogen Streptococcus suis, of which two strains have been recently sequenced and annotated, we identified a set of surface proteins without cytoplasmic contamination: all the proteins identified had exporting or retention signals towards the outside and/or the cell surface, and viability of protease-treated cells was not affected. The combination of both experimental evidences and computational methods allowed us to determine that two of these proteins are putative extracellular new adhesins that had been previously attributed a wrong cytoplasmic function. One of them is a putative component of the pilus of this bacterium. Conclusion We illustrate the complementary nature of laboratory-based and computational methods to examine in concert the localization of a set of proteins in the cell, and demonstrate the utility of this proteomics-based strategy to experimentally correct function annotation errors in sequencing projects. This

Regolith irradiation stratigraphy at the Apollo 16 and 17 landing sites

Science.gov (United States)

Crozaz, G.

1978-01-01

Additional fossil track measurements in the Apollo 17 deep drill stem, as well as detailed track studies in section 3 of the Apollo 16 deep drill core are reported. Although the upper part of the Apollo 17 core seems to have accreted rapidly, no evidence for a rapid accretion of the lower part, as postulated by some authors, is found. Despite the apparent inhomogeneity of section 60003, its track record is unexpectedly homogeneous; all levels are heavily irradiated and emplacement of big slabs of material is not favored.

The Lunar Potential Determination Using Apollo-Era Data and Modern Measurements and Models

Science.gov (United States)

Collier, Michael R.; Farrell, William M.; Espley, Jared; Webb, Phillip; Stubbs, Timothy J.; Webb, Phillip; Hills, H. Kent; Delory, Greg

2008-01-01

Since the Apollo era the electric potential of the Moon has been a subject of interest and debate. Deployed by three Apollo missions, Apollo 12, Apollo 14 and Apollo 15, the Suprathermal Ion Detector Experiment (SIDE) determined the sunlit lunar surface potential to be about +10 Volts using the energy spectra of lunar ionospheric thermal ions accelerated toward the Moon. More recently, the Lunar Prospector (LP) Electron Reflectometer used electron distributions to infer negative lunar surface potentials, primarily in shadow. We will present initial results from a study to combine lunar surface potential measurements from both SIDE and the LP/Electron Reflectometer to calibrate an advanced model of lunar surface charging which includes effects from the plasma environment, photoemission, secondaries ejected by ion impact onto the lunar surface, and the lunar wake created downstream by the solar wind-lunar interaction.

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

Science.gov (United States)

Swain, Martin T; Tsai, Isheng J; Assefa, Samual A; Newbold, Chris; Berriman, Matthew; Otto, Thomas D

2012-06-07

Genome projects now produce draft assemblies within weeks owing to advanced high-throughput sequencing technologies. For milestone projects such as Escherichia coli or Homo sapiens, teams of scientists were employed to manually curate and finish these genomes to a high standard. Nowadays, this is not feasible for most projects, and the quality of genomes is generally of a much lower standard. This protocol describes software (PAGIT) that is used to improve the quality of draft genomes. It offers flexible functionality to close gaps in scaffolds, correct base errors in the consensus sequence and exploit reference genomes (if available) in order to improve scaffolding and generating annotations. The protocol is most accessible for bacterial and small eukaryotic genomes (up to 300 Mb), such as pathogenic bacteria, malaria and parasitic worms. Applying PAGIT to an E. coli assembly takes ∼24 h: it doubles the average contig size and annotates over 4,300 gene models.

Simulator fidelity and training effectiveness: a comprehensive bibliography with selected annotations

International Nuclear Information System (INIS)

Rankin, W.L.; Bolton, P.A.; Shikiar, R.; Saari, L.M.

1984-05-01

This document contains a comprehensive bibliography on the topic of simulator fidelity and training effectiveness, prepared during the preliminary phases of work on an NRC-sponsored project on the Role of Nuclear Power Plant Simulators in Operator Licensing and Training. Section A of the document is an annotated bibliography consisting of articles and reports with relevance to the psychological aspects of simulator fidelity and the effectiveness of training simulators in a variety of settings, including military. The annotated items are drawn from a more comprehensive bibliography, presented in Section B, listing documents treating the role of simulators in operator training both in the nuclear industry and elsewhere

The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines

Directory of Open Access Journals (Sweden)

Gaston K Mazandu

2014-08-01

Full Text Available With the advancement of new high throughput sequencing technologies, there has been an increase in the number of genome sequencing projects worldwide, which has yielded complete genome sequences of human, animals and plants. Subsequently, several labs have focused on genome annotation, consisting of assigning functions to gene products, mostly using Gene Ontology (GO terms. As a consequence, there is an increased heterogeneity in annotations across genomes due to different approaches used by different pipelines to infer these annotations and also due to the nature of the GO structure itself. This makes a curator's task difficult, even if they adhere to the established guidelines for assessing these protein annotations. Here we develop a genome-scale approach for integrating GO annotations from different pipelines using semantic similarity measures. We used this approach to identify inconsistencies and similarities in functional annotations between orthologs of human and Drosophila melanogaster, to assess the quality of GO annotations derived from InterPro2GO mappings compared to manually annotated GO annotations for the Drosophila melanogaster proteome from a FlyBase dataset and human, and to filter GO annotation data for these proteomes. Results obtained indicate that an efficient integration of GO annotations eliminates redundancy up to 27.08 and 22.32% in the Drosophila melanogaster and human GO annotation datasets, respectively. Furthermore, we identified lack of and missing annotations for some orthologs, and annotation mismatches between InterPro2GO and manual pipelines in these two proteomes, thus requiring further curation. This simplifies and facilitates tasks of curators in assessing protein annotations, reduces redundancy and eliminates inconsistencies in large annotation datasets for ease of comparative functional genomics.

An Annotated Checklist of the Mammals of Kuwait

Directory of Open Access Journals (Sweden)

Peter J. Cowan

2013-12-01

Full Text Available An annotated checklist of the mammals of Kuwait is presented, based on the literature, personal communications, a Kuwait website and a blog and the author’s observations. Twenty five species occur, a further four are uncommon or rare visitors, six used to occur whilst another two are of doubtful provenance. This list should assist those planning desert rehabilitation, animal reintroduction and protected area projects in Kuwait.

Apollo premeeris lugejate lemmikautoreid

Index Scriptorium Estoniae

2010-01-01

Raamatupood Apollo kuulutas välja lugejate lemmikraamatud 2010: Mihkel Raua romaan "Sinine on sinu taevas", tõlketeostest Mika Waltari "Sinuhe : egiptlane", aja- ja elulooraamatutest Mart Laari "101 Eesti ajaloo sündmust", lasteraamatutest Andrus Kivirähki "Kaka ja kevad" ning luuleraamatutest Asko Künnapi, Jürgen Rooste ja Karl Martin Sinijärve "Eesti haiku"

Application of Apollo cosmic radiation dosimetry to lunar colonization studies

International Nuclear Information System (INIS)

English, R.A.; Bailey, J.V.; Brown, R.D.

1972-01-01

The radiation data gathered from the lunar landing missions of Apollo 11 through Apollo 15 are presented. These data have been analyzed to provide dosimetry evaluation of the ambient radiation and radiation from potential solar particle events for the planning of safe, long-term stays of relatively large numbers of individuals upon the moon. (U.S.)

Spacecraft Conceptual Design Compared to the Apollo Lunar Lander

Science.gov (United States)

Young, C.; Bowie, J.; Rust, R.; Lenius, J.; Anderson, M.; Connolly, J.

2011-01-01

Future human exploration of the Moon will require an optimized spacecraft design with each sub-system achieving the required minimum capability and maintaining high reliability. The objective of this study was to trade capability with reliability and minimize mass for the lunar lander spacecraft. The NASA parametric concept for a 3-person vehicle to the lunar surface with a 30% mass margin totaled was considerably heavier than the Apollo 15 Lunar Module "as flown" mass of 16.4 metric tons. The additional mass was attributed to mission requirements and system design choices that were made to meet the realities of modern spaceflight. The parametric tool used to size the current concept, Envision, accounts for primary and secondary mass requirements. For example, adding an astronaut increases the mass requirements for suits, water, food, oxygen, as well as, the increase in volume. The environmental control sub-systems becomes heavier with the increased requirements and more structure was needed to support the additional mass. There was also an increase in propellant usage. For comparison, an "Apollo-like" vehicle was created by removing these additional requirements. Utilizing the Envision parametric mass calculation tool and a quantitative reliability estimation tool designed by Valador Inc., it was determined that with today?s current technology a Lunar Module (LM) with Apollo capability could be built with less mass and similar reliability. The reliability of this new lander was compared to Apollo Lunar Module utilizing the same methodology, adjusting for mission timeline changes as well as component differences. Interestingly, the parametric concept's overall estimated risk for loss of mission (LOM) and loss of crew (LOC) did not significantly improve when compared to Apollo.

Concept annotation in the CRAFT corpus.

Science.gov (United States)

Bada, Michael; Eckert, Miriam; Evans, Donald; Garcia, Kristin; Shipley, Krista; Sitnikov, Dmitry; Baumgartner, William A; Cohen, K Bretonnel; Verspoor, Karin; Blake, Judith A; Hunter, Lawrence E

2012-07-09

Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.

Essential Requirements for Digital Annotation Systems

Directory of Open Access Journals (Sweden)

ADRIANO, C. M.

2012-06-01

Full Text Available Digital annotation systems are usually based on partial scenarios and arbitrary requirements. Accidental and essential characteristics are usually mixed in non explicit models. Documents and annotations are linked together accidentally according to the current technology, allowing for the development of disposable prototypes, but not to the support of non-functional requirements such as extensibility, robustness and interactivity. In this paper we perform a careful analysis on the concept of annotation, studying the scenarios supported by digital annotation tools. We also derived essential requirements based on a classification of annotation systems applied to existing tools. The analysis performed and the proposed classification can be applied and extended to other type of collaborative systems.

ArcGIS Digitization of Apollo Surface Traverses

Science.gov (United States)

Petro, N. E.; Bleacher, J. E.; Gladdis, L. R.; Garry, W. B.; Lam, F.; Mest, S. C.

2012-01-01

The Apollo surface activities were documented in extraordinary detail, with every action performed by the astronauts while on the surface recorded either in photo, audio, film, or by written testimony [1]. The samples and in situ measurements the astronauts collected while on the lunar surface have shaped our understanding of the geologic history of the Moon, and the earliest history and evolution of the inner Solar System. As part of an ongoing LASERfunded effort, we are digitizing and georeferencing data from astronaut traverses and spatially associating them to available, co-registered remote sensing data. Here we introduce the products produced so far for Apollo 15, 16, and 17 missions.

Apollo 11 Astronauts In Prayer Within Quarantine Facility

Science.gov (United States)

1969-01-01

The Apollo 11 mission, the first manned lunar mission, launched from the Kennedy Space Center, Florida via a Saturn V launch vehicle on July 16, 1969 and safely returned to Earth on July 24, 1969. The Saturn V vehicle was developed by the Marshall Space Flight Center (MSFC) under the direction of Dr. Wernher von Braun. Aboard were Neil A. Armstrong, commander; Michael Collins, Command Module (CM) pilot; and Edwin E. Aldrin Jr., Lunar Module (LM) pilot. The CM, piloted by Michael Collins remained in a parking orbit around the Moon while the LM, named 'Eagle'', carrying astronauts Neil Armstrong and Edwin Aldrin, landed on the Moon. Armstrong was the first human to ever stand on the lunar surface, followed by Edwin (Buzz) Aldrin. During 2½ hours of surface exploration, the crew collected 47 pounds of lunar surface material for analysis back on Earth. The recovery operation took place in the Pacific Ocean where Navy para-rescue men recovered the capsule housing the 3-man Apollo 11 crew. The crew was taken to safety aboard the USS Hornet, where they were quartered in a mobile quarantine facility. Shown here is the Apollo 11 crew inside the quarantine facility as prayer is offered by Lt. Commander John Pirrto, USS Hornet Chaplain accompanied by U.S. President Richard Nixon (front right). With the success of Apollo 11, the national objective to land men on the Moon and return them safely to Earth had been accomplished.

A methodology to annotate systems biology markup language models with the synthetic biology open language.

Science.gov (United States)

Roehner, Nicholas; Myers, Chris J

2014-02-21

Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application to new projects, a problem exacerbated by a lack of engineering standards that combine descriptions of the structure and function of DNA. To address this need, this paper describes a methodology to connect the systems biology markup language (SBML) to the synthetic biology open language (SBOL), existing standards that describe biochemical models and DNA components, respectively. Our methodology involves first annotating SBML model elements such as species and reactions with SBOL DNA components. A graph is then constructed from the model, with vertices corresponding to elements within the model and edges corresponding to the cause-and-effect relationships between these elements. Lastly, the graph is traversed to assemble the annotating DNA components into a composite DNA component, which is used to annotate the model itself and can be referenced by other composite models and DNA components. In this way, our methodology can be used to build up a hierarchical library of models annotated with DNA components. Such a library is a useful input to any future genetic technology mapping algorithm that would automate the process of composing DNA components to satisfy a behavioral specification. Our methodology for SBML-to-SBOL annotation is implemented in the latest version of our genetic design automation (GDA) software tool, iBioSim.

Making web annotations persistent over time

Energy Technology Data Exchange (ETDEWEB)

Sanderson, Robert [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory

2010-01-01

As Digital Libraries (DL) become more aligned with the web architecture, their functional components need to be fundamentally rethought in terms of URIs and HTTP. Annotation, a core scholarly activity enabled by many DL solutions, exhibits a clearly unacceptable characteristic when existing models are applied to the web: due to the representations of web resources changing over time, an annotation made about a web resource today may no longer be relevant to the representation that is served from that same resource tomorrow. We assume the existence of archived versions of resources, and combine the temporal features of the emerging Open Annotation data model with the capability offered by the Memento framework that allows seamless navigation from the URI of a resource to archived versions of that resource, and arrive at a solution that provides guarantees regarding the persistence of web annotations over time. More specifically, we provide theoretical solutions and proof-of-concept experimental evaluations for two problems: reconstructing an existing annotation so that the correct archived version is displayed for all resources involved in the annotation, and retrieving all annotations that involve a given archived version of a web resource.

Semantic annotation in biomedicine: the current landscape.

Science.gov (United States)

Jovanović, Jelena; Bagheri, Ebrahim

2017-09-22

The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS. As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing. This process is widely known as semantic annotation, and the tools that perform it are known as semantic annotators.Over the last dozen years, the biomedical research community has invested significant efforts in the development of biomedical semantic annotation technology. Aiming to establish grounds for further developments in this area, we review a selected set of state of the art biomedical semantic annotators, focusing particularly on general purpose annotators, that is, semantic annotation tools that can be customized to work with texts from any area of biomedicine. We also examine potential directions for further improvements of today's annotators which could make them even more capable of meeting the needs of real-world applications. To motivate and encourage further developments in this area, along the suggested and/or related directions, we review existing and potential practical applications and benefits of semantic annotators.

Gene coexpression network analysis as a source of functional annotation for rice genes.

Directory of Open Access Journals (Sweden)

Kevin L Childs

Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

A Comparison of Fuzzy and Annotated Logic Programming

Czech Academy of Sciences Publication Activity Database

Krajči, S.; Lencses, R.; Vojtáš, Peter

2004-01-01

Roč. 144, - (2004), s. 173-192 ISSN 0165-0114 R&D Projects: GA ČR GA201/00/1489 Grant - others:VEGA(SK) 1/7557/20; VEGA(SK) 1/7555/20; VEGA(SK) 1/0385/03 Institutional research plan: CEZ:AV0Z1030915 Keywords : fuzzy logic programming * generalized annotated programs * declarative and procedural semantics * continuous semantics and computable fixpoint * soundness and completeness Subject RIV: BA - General Mathematics Impact factor: 0.734, year: 2004

Apollo 16 Lunar Module 'Orion' at the Descartes landing site

Science.gov (United States)

1972-01-01

The Apollo 16 Lunar Module 'Orion' is part of the lunar scene at the Descartes landing site, as seen in the reproduction taken from a color television transmission made by the color TV camera mounted on the Lunar Roving Vehicle. Note the U.S. flag deployed on the left. This picture was made during the second Apollo 16 extravehicular activity (EVA-2).

Virtual Microscope Views of the Apollo 11, 12, and 15 Lunar Samples

Science.gov (United States)

Gibson, E. K.; Tindle, A. G.; Kelley, S. P.; Pillinger, J. M.

2017-01-01

The Apollo virtual microscope is a means of viewing, over the Internet, polished thin sections of every rock in the Apollo lunar sample collections. It uses software that duplicates many of the functions of a petrological microscope.

Restoration and Reexamination of Apollo Lunar Dust Detector Data from Original Telemetry Files

Science.gov (United States)

McBride, M. J.; Williams, David R.; Hills, H. Kent

2012-01-01

We are recovering the original telemetry (Figure I) from the Apollo Dust, Thermal, Radiation Environment Monitor (DTREM) experiment, more commonly known as the Dust Detector, and producing full time resolution (54 second) data sets for release through the Planetary Data System (PDS). The primary objective of the experiment was to evaluate the effect of dust deposition, temperature, and radiation damage on solar cells on the lunar surface. The monitor was a small box consisting of three solar cells and thermistors mounted on the ALSEP (Apollo Lunar Surface Experiments Package) central station. The Dust Detector was carried on Apollo's 11, 12, 14 and 15. The Apollo 11 DTREM was powered by solar cells and only operated for a few months as planned. The Apollo 12, 14, and 15 detectors operated for 5 to 7 years, returning data every 54 seconds, consisting of voltage outputs from the three solar cells and temperatures measured by the three thermistors. The telemetry was received at ground stations and held on the Apollo Housekeeping (known as "Word 33") tapes. made available to the National Space Science Data Center (NSSDC) by Yosio Nakamura (University of Texas Institute for Geophysics). We have converted selected parts of the telemetry into uncalibrated and calibrated output voltages and temperatures.

Apollo-Soyuz Pamphlet No. 2: X-Rays, Gamma-Rays. Apollo-Soyuz Experiments in Space.

Science.gov (United States)

Page, Lou Williams; Page, Thornton

This booklet is the second in a series of nine that describe the Apollo-Soyuz mission and experiments. This set is designed as a curriculum supplement for high school and college teachers, supervisors, curriculum specialists, textbook writers, and the general public. These booklets provide sources of ideas, examples of the scientific method,…

NASA Officials in MCC to decide whether to land Apollo 16 or cancel landing

Science.gov (United States)

1972-01-01

NASA Officials gather around a console in the Mission Operations Control Room (MOCR) in the Mission Control Center (MCC) prior to the making of a decision whether to land Apollo 16 on the moon or to abort the landing. Seated, left to right, are Dr. Christopher C. Kraft Jr., Director of the Manned Spacecraft Center (MSC), and Brig. Gen. James A. McDivitt (USAF), Manager, Apollo Spacecraft Program Office, MSC; and standing, left to right, are Dr. Rocco A. Petrone, Apollo Program Director, Office Manned Space Flight (OMSF), NASA HQ.; Capt. John K. Holcolmb (U.S. Navy, Ret.), Director of Apollo Operations, OMSF; Sigurd A. Sjoberg, Deputy Director, MSC; Capt. Chester M. Lee (U.S. Navy, Ret.), Apollo Mission Director, OMSF; Dale D. Myers, NASA Associate Administrator for Manned Space Flight; and Dr. George M. Low, NASA Deputy Administrator.

Contributions to In Silico Genome Annotation

KAUST Repository

Kalkatawi, Manal M.

2017-11-30

Genome annotation is an important topic since it provides information for the foundation of downstream genomic and biological research. It is considered as a way of summarizing part of existing knowledge about the genomic characteristics of an organism. Annotating different regions of a genome sequence is known as structural annotation, while identifying functions of these regions is considered as a functional annotation. In silico approaches can facilitate both tasks that otherwise would be difficult and timeconsuming. This study contributes to genome annotation by introducing several novel bioinformatics methods, some based on machine learning (ML) approaches. First, we present Dragon PolyA Spotter (DPS), a method for accurate identification of the polyadenylation signals (PAS) within human genomic DNA sequences. For this, we derived a novel feature-set able to characterize properties of the genomic region surrounding the PAS, enabling development of high accuracy optimized ML predictive models. DPS considerably outperformed the state-of-the-art results. The second contribution concerns developing generic models for structural annotation, i.e., the recognition of different genomic signals and regions (GSR) within eukaryotic DNA. We developed DeepGSR, a systematic framework that facilitates generating ML models to predict GSR with high accuracy. To the best of our knowledge, no available generic and automated method exists for such task that could facilitate the studies of newly sequenced organisms. The prediction module of DeepGSR uses deep learning algorithms to derive highly abstract features that depend mainly on proper data representation and hyperparameters calibration. DeepGSR, which was evaluated on recognition of PAS and translation initiation sites (TIS) in different organisms, yields a simpler and more precise representation of the problem under study, compared to some other hand-tailored models, while producing high accuracy prediction results. Finally

Active learning reduces annotation time for clinical concept extraction.

Science.gov (United States)

Kholghi, Mahnoosh; Sitbon, Laurianne; Zuccon, Guido; Nguyen, Anthony

2017-10-01

To investigate: (1) the annotation time savings by various active learning query strategies compared to supervised learning and a random sampling baseline, and (2) the benefits of active learning-assisted pre-annotations in accelerating the manual annotation process compared to de novo annotation. There are 73 and 120 discharge summary reports provided by Beth Israel institute in the train and test sets of the concept extraction task in the i2b2/VA 2010 challenge, respectively. The 73 reports were used in user study experiments for manual annotation. First, all sequences within the 73 reports were manually annotated from scratch. Next, active learning models were built to generate pre-annotations for the sequences selected by a query strategy. The annotation/reviewing time per sequence was recorded. The 120 test reports were used to measure the effectiveness of the active learning models. When annotating from scratch, active learning reduced the annotation time up to 35% and 28% compared to a fully supervised approach and a random sampling baseline, respectively. Reviewing active learning-assisted pre-annotations resulted in 20% further reduction of the annotation time when compared to de novo annotation. The number of concepts that require manual annotation is a good indicator of the annotation time for various active learning approaches as demonstrated by high correlation between time rate and concept annotation rate. Active learning has a key role in reducing the time required to manually annotate domain concepts from clinical free text, either when annotating from scratch or reviewing active learning-assisted pre-annotations. Copyright © 2017 Elsevier B.V. All rights reserved.

Artist's concept of eastward view of Apollo 16 Descartes landing site

Science.gov (United States)

1972-01-01

An artist's concept illustrating an eastward view of the Apollo 16 Descartes landing site. The white overlay indicates the scheduled tranverses by the Apollo 16 astronauts in the Lunar Roving Vehicle. The Roman numerals are the extravehicular activities (EVA's); and the Arabic numbers are the station stops along the traverse.

A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data.

Science.gov (United States)

Lu, Qiongshi; Hu, Yiming; Sun, Jiehuan; Cheng, Yuwei; Cheung, Kei-Hoi; Zhao, Hongyu

2015-05-27

Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://genocanyon.med.yale.edu.

Comparison between KARBUS and APOLLO 1

International Nuclear Information System (INIS)

Payer, L.; Broeders, C.

1995-01-01

A comparison is made between benchmark calculations by the French APOLLO 1 code and the Karlsruhe KARBUS procedure. Independently these two codes had been developed for transport computations in infinite reactor configurations and for burnup calculations. (orig.)

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

Science.gov (United States)

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-04-10

Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

Directory of Open Access Journals (Sweden)

Pardinas Jose R

2008-04-01

Full Text Available Abstract Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

DEFF Research Database (Denmark)

Panitz, Frank; Stengaard, Henrik; Hornshoj, Henrik

2007-01-01

MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data...... manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non...

The 2008 update of the Aspergillus nidulans genome annotation: A community effort

DEFF Research Database (Denmark)

Wortman, Jennifer Russo; Gilsenan, Jane Mabey; Joardar, Vinita

2009-01-01

The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional ap...

The 2008 update of the Aspergillus nidulans genome annotation : a community effort

NARCIS (Netherlands)

Wortman, Jennifer Russo; Gilsenan, Jane Mabey; Joardar, Vinita; Deegan, Jennifer; Clutterbuck, John; Andersen, Mikael R; Archer, David; Bencina, Mojca; Braus, Gerhard; Coutinho, Pedro; von Döhren, Hans; Doonan, John; Driessen, Arnold J M; Durek, Pawel; Espeso, Eduardo; Fekete, Erzsébet; Flipphi, Michel; Estrada, Carlos Garcia; Geysens, Steven; Goldman, Gustavo; de Groot, Piet W J; Hansen, Kim; Harris, Steven D; Heinekamp, Thorsten; Helmstaedt, Kerstin; Henrissat, Bernard; Hofmann, Gerald; Homan, Tim; Horio, Tetsuya; Horiuchi, Hiroyuki; James, Steve; Jones, Meriel; Karaffa, Levente; Karányi, Zsolt; Kato, Masashi; Keller, Nancy; Kelly, Diane E; Kiel, Jan A K W; Kim, Jung-Mi; van der Klei, Ida J; Klis, Frans M; Kovalchuk, Andriy; Krasevec, Nada; Kubicek, Christian P; Liu, Bo; Maccabe, Andrew; Meyer, Vera; Mirabito, Pete; Miskei, Márton; Mos, Magdalena; Mullins, Jonathan; Nelson, David R; Nielsen, Jens; Oakley, Berl R; Osmani, Stephen A; Pakula, Tiina; Paszewski, Andrzej; Paulsen, Ian; Pilsyk, Sebastian; Pócsi, István; Punt, Peter J; Ram, Arthur F J; Ren, Qinghu; Robellet, Xavier; Robson, Geoff; Seiboth, Bernhard; van Solingen, Piet; Specht, Thomas; Sun, Jibin; Taheri-Talesh, Naimeh; Takeshita, Norio; Ussery, Dave; vanKuyk, Patricia A; Visser, Hans; van de Vondervoort, Peter J I; de Vries, Ronald P; Walton, Jonathan; Xiang, Xin; Xiong, Yi; Zeng, An Ping; Brandt, Bernd W; Cornell, Michael J; van den Hondel, Cees A M J J; Visser, Jacob; Oliver, Stephen G; Turner, Geoffrey

The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional

The 2008 update of the Aspergillus nidulans genome annotation : A community effort

NARCIS (Netherlands)

Wortman, Jennifer Russo; Gilsenan, Jane Mabey; Joardar, Vinita; Deegan, Jennifer; Clutterbuck, John; Andersen, Mikael R.; Archer, David; Bencina, Mojca; Braus, Gerhard; Coutinho, Pedro; von Doehren, Hans; Doonan, John; Driessen, Arnold J. M.; Durek, Pawel; Espeso, Eduardo; Fekete, Erzsebet; Flipphi, Michel; Garcia Estrada, Carlos; Geysens, Steven; Goldman, Gustavo; de Groot, Piet W. J.; Hansen, Kim; Harris, Steven D.; Heinekamp, Thorsten; Helmstaedt, Kerstin; Henrissat, Bernard; Hofmann, Gerald; Homan, Tim; Horio, Tetsuya; Horiuchi, Hiroyuki; James, Steve; Jones, Meriel; Karaffa, Levente; Karanyi, Zsolt; Kato, Masashi; Keller, Nancy; Kelly, Diane E.; Kiel, Jan A. K. W.; Kim, Jung-Mi; van der Klei, Ida J.; Klis, Frans M.; Kovalchuk, Andriy; Krasevec, Nada; Kubicek, Christian P.; Liu, Bo; MacCabe, Andrew; Meyer, Vera; Mirabito, Pete; Miskei, Marton; Mos, Magdalena; Mullins, Jonathan; Nelson, David R.; Nielsen, Jens; Oakley, Berl R.; Osmani, Stephen A.; Pakula, Tiina; Paszewski, Andrzej; Paulsen, Ian; Pilsyk, Sebastian; Pocsi, Istvan; Punt, Peter J.; Ram, Arthur F. J.; Ren, Qinghu; Robellet, Xavier; Robson, Geoff; Seiboth, Bernhard; van Solingen, Piet; Specht, Thomas; Sun, Jibin; Taheri-Talesh, Naimeh; Takeshita, Norio; Ussery, Dave; Vankuyk, Patricia A.; Visser, Hans; de Vondervoort, Peter J. I. van; Walton, Jonathan; Xiang, Xin; Xiong, Yi; Zeng, An Ping; Brandt, Bernd W.; Cornell, Michael J.; van den Hondel, Cees A. M. J. J.; Visser, Jacob; Oliver, Stephen G.; Turner, Geoffrey; Kraševec, Nada; Kuyk, Patricia A. van; Döhren, D.H.; van Seilboth, B; de Vries, R.

The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

Energy Technology Data Exchange (ETDEWEB)

Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

2015-02-10

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.

Science.gov (United States)

Brettin, Thomas; Davis, James J; Disz, Terry; Edwards, Robert A; Gerdes, Svetlana; Olsen, Gary J; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D; Shukla, Maulik; Thomason, James A; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R; Xia, Fangfang

2015-02-10

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

Annotated Bibliography for the DEWPOINT project

Energy Technology Data Exchange (ETDEWEB)

Oehmen, Christopher S.

2009-04-21

This bibliography covers aspects of the Detection and Early Warning of Proliferation from Online INdicators of Threat (DEWPOINT) project including 1) data management and querying, 2) baseline and advanced methods for classifying free text, and 3) algorithms to achieve the ultimate goal of inferring intent from free text sources. Metrics for assessing the quality and correctness of classification are addressed in the second group. Data management and querying include methods for efficiently storing, indexing, searching, and organizing the data we expect to operate on within the DEWPOINT project.

Conversion of CATHENA from the VAX to APOLLO computer

International Nuclear Information System (INIS)

Kawa, D.M.

1986-12-01

The thermal-hydraulic computer code developed by Atomic Energy of Canada Limited, CATHENA, has been converted from the VAX computer to operate on a low-cost, high-performance APOLLO 3000 work station. Full functionality of the program has been retained. Three verification cases have been analyzed which indicate accuracy to the sixth decimal place as printed in output listings. The APOLLO 3000 computing times for the 3 cases are approximately 15% faster than achieved on the Wardrop VAX 11 750

76 FR 7853 - Patient Safety Organizations: Voluntary Delisting From Apollo Publishing, Inc.

Science.gov (United States)

2011-02-11

... notification of voluntary relinquishment from Apollo Publishing, Inc., of its status as a Patient Safety... DEPARTMENT OF HEALTH AND HUMAN SERVICES Agency for Healthcare Research and Quality Patient Safety Organizations: Voluntary Delisting From Apollo Publishing, Inc. AGENCY: Agency for Healthcare Research and...

Apollo 16 lunar module 'Orion' photographed from distance during EVA

Science.gov (United States)

1972-01-01

The Apollo 16 Lunar Module 'Orion' is photographed from a distance by Astronaut Chares M. Duke Jr., lunar module pilot, aboard the moving Lunar Roving Vehicle. Astronauts Duke and John W. Young, commander, were returing from the third Apollo 16 extravehicular activity (EVA-2). The RCA color television camera mounted on the LRV is in the foreground. A portion of the LRV's high-gain antenna is at top left.

Computer systems for annotation of single molecule fragments

Science.gov (United States)

Schwartz, David Charles; Severin, Jessica

2016-07-19

There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

Image annotation under X Windows

Science.gov (United States)

Pothier, Steven

1991-08-01

A mechanism for attaching graphic and overlay annotation to multiple bits/pixel imagery while providing levels of performance approaching that of native mode graphics systems is presented. This mechanism isolates programming complexity from the application programmer through software encapsulation under the X Window System. It ensures display accuracy throughout operations on the imagery and annotation including zooms, pans, and modifications of the annotation. Trade-offs that affect speed of display, consumption of memory, and system functionality are explored. The use of resource files to tune the display system is discussed. The mechanism makes use of an abstraction consisting of four parts; a graphics overlay, a dithered overlay, an image overly, and a physical display window. Data structures are maintained that retain the distinction between the four parts so that they can be modified independently, providing system flexibility. A unique technique for associating user color preferences with annotation is introduced. An interface that allows interactive modification of the mapping between image value and color is discussed. A procedure that provides for the colorization of imagery on 8-bit display systems using pixel dithering is explained. Finally, the application of annotation mechanisms to various applications is discussed.

Genome annotation in a community college cell biology lab.

Science.gov (United States)

Beagley, C Timothy

2013-01-01

The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning skills. Additionally, the project strengthens student understanding of the scientific method and contributes to student learning gains in curricular objectives centered around basic molecular biology, specifically, the Central Dogma. Importantly, inclusion of this project in the laboratory course provides students with a positive learning environment and allows for the use of cooperative learning strategies to increase overall student success. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

Directory of Open Access Journals (Sweden)

Pontarotti Pierre

2005-08-01

Full Text Available Abstract Background Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes. Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. Results Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset. The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. Conclusion The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.

SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.

Science.gov (United States)

Sun, Xiaoyong; Zuo, Fenghua; Ru, Yuanbin; Guo, Jiqiang; Yan, Xiaoyan; Sablok, Gaurav

2015-04-01

Alternative splicing plays a key role in the regulation of the central dogma. Four major types of alternative splicing have been classified as intron retention, exon skipping, alternative 5 splice sites or alternative donor sites, and alternative 3 splice sites or alternative acceptor sites. A few algorithms have been developed to detect splice junctions from RNA-Seq reads. However, there are few tools targeting at the major alternative splicing types at the exon/intron level. This type of analysis may reveal subtle, yet important events of alternative splicing, and thus help gain deeper understanding of the mechanism of alternative splicing. This paper describes a user-friendly R package, extracting, annotating and analyzing alternative splicing types for sequence alignment files from RNA-Seq. SplicingTypesAnno can: (1) provide annotation for major alternative splicing at exon/intron level. By comparing the annotation from GTF/GFF file, it identifies the novel alternative splicing sites; (2) offer a convenient two-level analysis: genome-scale annotation for users with high performance computing environment, and gene-scale annotation for users with personal computers; (3) generate a user-friendly web report and additional BED files for IGV visualization. SplicingTypesAnno is a user-friendly R package for extracting, annotating and analyzing alternative splicing types at exon/intron level for sequence alignment files from RNA-Seq. It is publically available at https://sourceforge.net/projects/splicingtypes/files/ or http://genome.sdau.edu.cn/research/software/SplicingTypesAnno.html. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Motion lecture annotation system to learn Naginata performances

Science.gov (United States)

Kobayashi, Daisuke; Sakamoto, Ryota; Nomura, Yoshihiko

2013-12-01

This paper describes a learning assistant system using motion capture data and annotation to teach "Naginata-jutsu" (a skill to practice Japanese halberd) performance. There are some video annotation tools such as YouTube. However these video based tools have only single angle of view. Our approach that uses motion-captured data allows us to view any angle. A lecturer can write annotations related to parts of body. We have made a comparison of effectiveness between the annotation tool of YouTube and the proposed system. The experimental result showed that our system triggered more annotations than the annotation tool of YouTube.

BEACON: automated tool for Bacterial GEnome Annotation ComparisON

KAUST Repository

Kalkatawi, Manal M.

2015-08-18

Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

Science.gov (United States)

Kalkatawi, Manal; Alam, Intikhab; Bajic, Vladimir B

2015-08-18

Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON's utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27%, while the number of genes without any function assignment is reduced. We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

JGI Plant Genomics Gene Annotation Pipeline

Energy Technology Data Exchange (ETDEWEB)

Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

2014-07-14

Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

'Shooting at the sun god Apollo': the Apollonian-Dionysian balance of the TimeSlips Storytelling Project.

Science.gov (United States)

George, Daniel R

2013-09-01

In The Birth of Tragedy, Friedrich Nietzsche celebrated the dueling forces of reason and emotion as personified by the ancient Greek gods Apollo and Dionysus. A subtle Apollonian-Dionysian balance can be observed in TimeSlips, a group-based creative storytelling activity developed in the 1990s and increasingly used in dementia care settings worldwide. This article explains how the Apollonion-Dionysian aspects of TimeSlips are beneficial not only for persons with dementia, but also for their carers. Narrative data from medical students at Penn State College of Medicine who participated in TimeSlips at a local retirement community are shared.

MIPS: analysis and annotation of proteins from whole genomes.

Science.gov (United States)

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).

Apollo 17 'melt sheet': chemistry, age and Rb/Sr systematics

Energy Technology Data Exchange (ETDEWEB)

Winzer, S R [Martin Marietta Labs., Baltimore, Md. (USA); Nava, D F; Schuhmann, S; Philpotts, J A [National Aeronautics and Space Administration, Greenbelt, Md. (USA). Goddard Space Flight Center; Schuhmann, P J; Lum, R K.L.; Lindstrom, M M; Lindstrom, D J [Maryland Univ., College Park (USA)

1977-01-01

Major, minor and trace element compositions, age data and Rb/Sr systematics of Apollo 17 boulders have been compiled, and additional analyses performed on a norite breccia clast (77215) included in the Apollo 17, Station 7 boulder. The Apollo 17 boulders are found to be identical or nearly so in major, minor and trace element composition, suggesting that they all originated as an impact melt analogous to melt sheets found in larger terrestrial craters. The matrix dates (/sup 40/Ar//sup 39/Ar) and Rb/Sr systematics available suggest that this impact melt formed by a single impact about 4 b.y. ago. This impact excavated, shocked, brecciated and melted norites, norite cumulates and possibly anorthositic gabbros and dunites about 4.4 b.y. old. The impact was likely a major one, possibly the Serenitatis basin-forming event.

A method for increasing the accuracy of image annotating in crowd-sourcing

OpenAIRE

Nurmukhametov, O.R.; Baklanov, A.

2016-01-01

Crowdsourcing is a new approach to solve tasks when a group of volunteers replaces experts. Recent results show that crowdsourcing is an efficient tool for annotating large datasets. Geo-Wiki is an example of successful citizen science projects. The goal of Geo-Wiki project is to improve a global land cover map by applying crowdsourcing for image recognition. In our research, we investigate methods for increasing reliability of data collected during The Cropland Capture Game (Geo-Wiki). In th...

Facilitating functional annotation of chicken microarray data

Directory of Open Access Journals (Sweden)

Gresham Cathy R

2009-10-01

Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

Complex Indigenous Organic Matter Embedded in Apollo 17 Volcanic Black Glass Surface Deposits

Science.gov (United States)

Thomas-Keprta, Kathie L.; Clemett, S. J.; Ross, D. K.; Le, L.; Rahman, Z.; Gonzalez, C.; McKay, D. S.; Gibson, E. K.

2013-01-01

Papers presented at the first Lunar Science Conference [1] and those published in the subsequent Science Moon Issue [2] reported the C content of Apollo II soils, breccias, and igneous rocks as rang-ing from approx.50 to 250 parts per million (ppm). Later Fegley & Swindle [3] summarized the C content of bulk soils from all the Apollo missions as ranging from 2.5 (Apollo 15) to 280 ppm (Apollo 16) with an overall average of 124+/- 45 ppm. These values are unexpectedly low given that multiple processes should have contributed (and in some cases continue to contribute) to the lunar C inventory. These include exogenous accretion of cometary and asteroidal dust, solar wind implantation, and synthesis of C-bearing species during early lunar volcanism. We estimate the contribution of C from exogenous sources alone is approx.500 ppm, which is approx.4x greater than the reported average. While the assessm ent of indigenous organic matter (OM) in returned lunar samples was one of the primary scientific goals of the Apollo program, extensive analysis of Apollo samples yielded no evidence of any significant indigenous organic species. Furthermore, with such low concentrations of OM reported, the importance of discriminating indigenous OM from terrestrial contamination (e.g., lunar module exhaust, sample processing and handling) became a formidable task. After more than 40 years, with the exception of CH4 [5-7], the presence of indigenous lunar organics still remains a subject of considerable debate. We report for the first time the identification of arguably indigenous OM present within surface deposits of black glass grains collected on the rim of Shorty crater during the Apollo 17 mission by astronauts Eugene Cernan and Harrison Schmitt.

Dictionary-driven protein annotation.

Science.gov (United States)

Rigoutsos, Isidore; Huynh, Tien; Floratos, Aris; Parida, Laxmi; Platt, Daniel

2002-09-01

Computational methods seeking to automatically determine the properties (functional, structural, physicochemical, etc.) of a protein directly from the sequence have long been the focus of numerous research groups. With the advent of advanced sequencing methods and systems, the number of amino acid sequences that are being deposited in the public databases has been increasing steadily. This has in turn generated a renewed demand for automated approaches that can annotate individual sequences and complete genomes quickly, exhaustively and objectively. In this paper, we present one such approach that is centered around and exploits the Bio-Dictionary, a collection of amino acid patterns that completely covers the natural sequence space and can capture functional and structural signals that have been reused during evolution, within and across protein families. Our annotation approach also makes use of a weighted, position-specific scoring scheme that is unaffected by the over-representation of well-conserved proteins and protein fragments in the databases used. For a given query sequence, the method permits one to determine, in a single pass, the following: local and global similarities between the query and any protein already present in a public database; the likeness of the query to all available archaeal/ bacterial/eukaryotic/viral sequences in the database as a function of amino acid position within the query; the character of secondary structure of the query as a function of amino acid position within the query; the cytoplasmic, transmembrane or extracellular behavior of the query; the nature and position of binding domains, active sites, post-translationally modified sites, signal peptides, etc. In terms of performance, the proposed method is exhaustive, objective and allows for the rapid annotation of individual sequences and full genomes. Annotation examples are presented and discussed in Results, including individual queries and complete genomes that were

Apollo 11 Command Service Module

Science.gov (United States)

1969-01-01

A close-up view of the Apollo 11 command service module ready to be mated with the spacecraft LEM adapter of the third stage. The towering 363-foot Saturn V was a multi-stage, multi-engine launch vehicle standing taller than the Statue of Liberty. Altogether, the Saturn V engines produced as much power as 85 Hoover Dams.

A lack of Wolbachia-specific DNA in samples from apollo butterfly (Parnassius apollo, Lepidoptera: Papilionidae) individuals with deformed or reduced wings.

Science.gov (United States)

Łukasiewicz, Kinga; Sanak, Marek; Węgrzyn, Grzegorz

2016-05-01

Various insects contain maternally inherited endosymbiotic bacteria which can cause reproductive alterations, modulation of some physiological responses (like immunity, heat shock response, and oxidative stress response), and resistance to viral infections. In butterflies, Wolbachia sp. is the most frequent endosymbiont from this group, occurring in about 30 % of species tested to date. In this report, the presence of Wolbachia-specific DNA has been detected in apollo butterfly (Parnassius apollo). In the isolated population of this insect occurring in Pieniny National Park (Poland), malformed individuals with deformed or reduced wings appear with an exceptionally high frequency. Interestingly, while total DNA isolated from most (about 85 %) normal insects contained Wolbachia-specific sequences detected by PCR, such sequences were absent in a large fraction (70 %) of individuals with deformed wings and in all tested individuals with reduced wings. These results indicate for the first time the correlation between malformation of wings and the absence of Wolbachia sp. in insects. Although the lack of the endosymbiotic bacteria cannot be considered as the sole cause of the deformation or reduction of wings, one might suggest that Wolbachia sp. could play a protective role in the ontogenetic development of apollo butterfly.

The effectiveness of annotated (vs. non-annotated) digital pathology slides as a teaching tool during dermatology and pathology residencies.

Science.gov (United States)

Marsch, Amanda F; Espiritu, Baltazar; Groth, John; Hutchens, Kelli A

2014-06-01

With today's technology, paraffin-embedded, hematoxylin & eosin-stained pathology slides can be scanned to generate high quality virtual slides. Using proprietary software, digital images can also be annotated with arrows, circles and boxes to highlight certain diagnostic features. Previous studies assessing digital microscopy as a teaching tool did not involve the annotation of digital images. The objective of this study was to compare the effectiveness of annotated digital pathology slides versus non-annotated digital pathology slides as a teaching tool during dermatology and pathology residencies. A study group composed of 31 dermatology and pathology residents was asked to complete an online pre-quiz consisting of 20 multiple choice style questions, each associated with a static digital pathology image. After completion, participants were given access to an online tutorial composed of digitally annotated pathology slides and subsequently asked to complete a post-quiz. A control group of 12 residents completed a non-annotated version of the tutorial. Nearly all participants in the study group improved their quiz score, with an average improvement of 17%, versus only 3% (P = 0.005) in the control group. These results support the notion that annotated digital pathology slides are superior to non-annotated slides for the purpose of resident education. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Apollo 12 feldspathic basalts 12031, 12038, and 12072; petrology, comparison and interpretations

International Nuclear Information System (INIS)

Beaty, E.W.; Hill, S.M.R.; Albee, A.L.; Baldridge, W.S.

1979-01-01

Modal and chemical data indicate that 12072, 12038, and 12031, the Apollo 12 feldspathic basalts, form a well-defined group which cannot be related to the other Apollo 12 rock types. 12072 contains phenocrysts of olivine and pigeonite and microphenocrysts of Cr-spinel set in a fine-grained, variolitic groundmass. 12038 is a medium-grained, equigranular basalt with a texture indicating it was multiply saturated. 12031 is a coarse-grained rock with granular to graphic intergrowths of pyroxene and plagioclase; it was also multiply saturated. Petrologic observations, as well as the bulk chemistry, are consistent with the interpretation that 12031 could be derived from 12072 through fractionation of Cr-spinel, olivine, and pigeonite, the observed phenocryst assemblage. 12038, however, contains more pigeonite, less olivine, three times as much Ca-phosphate minerals, one-fifth as much troilite, and much more sodic plagioclase than 12072. These differences indicate that 12038 must have come from a separate igneous body. Consideration of the bulk compositions indicates that neither 12072 and 12031 nor 12038 could have been derived from the Apollo 12 olivine, pigeonite, or ilmenite basalts by crystal--liquid fractionation. The general petrologic similarities between 12072, 12031, and the other Apollo 12 basalts suggests that they were produced in either the same or similar source regions. 12038, however, is petrologically and chemically unique, and is probably exotic to the Apollo 12 landing site

Automatic annotation of head velocity and acceleration in Anvil

DEFF Research Database (Denmark)

Jongejan, Bart

2012-01-01

We describe an automatic face tracker plugin for the ANVIL annotation tool. The face tracker produces data for velocity and for acceleration in two dimensions. We compare the annotations generated by the face tracking algorithm with independently made manual annotations for head movements....... The annotations are a useful supplement to manual annotations and may help human annotators to quickly and reliably determine onset of head movements and to suggest which kind of head movement is taking place....

Mesotext. Framing and exploring annotations

NARCIS (Netherlands)

Boot, P.; Boot, P.; Stronks, E.

2007-01-01

From the introduction: Annotation is an important item on the wish list for digital scholarly tools. It is one of John Unsworth’s primitives of scholarship (Unsworth 2000). Especially in linguistics,a number of tools have been developed that facilitate the creation of annotations to source material

Annotating images by mining image search results

NARCIS (Netherlands)

Wang, X.J.; Zhang, L.; Li, X.; Ma, W.Y.

2008-01-01

Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search

Virtual Microscope Views of the Apollo 11 and 12 Lunar Samples

Science.gov (United States)

Gibson, E. K.; Tindle, A. G.; Kelley, S. P.; Pillinger, J. M.

2016-01-01

The Apollo virtual microscope is a means of viewing, over the Internet, polished thin sections of every rock in the Apollo lunar sample collections via software, duplicating many of the functions of a petrological microscope, is described. Images from the Apollo 11 and 12 missions may be viewed at: www.virtualmicroscope.org/content/apollo. Introduction: During the six NASA missions to the Moon from 1969-72 a total of 382 kilograms of rocks and soils, often referred to as "the legacy of Apollo", were collected and returned to Earth. A unique collection of polished thin sections (PTSs) was made from over 400 rocks by the Lunar Sample Curatorial Facility at the Johnson Spacecraft Center (JSC), Houston. These materials have been available for loan to approved PIs but of course they can't be simultaneously investigated by several researchers unless they are co-located or the sample is passed back and forward between them by mail/hand carrying which is inefficient and very risky for irreplaceable material. When The Open University (OU), the world's largest Distance Learning Higher Education Establishment found itself facing a comparable problem (how to supply thousands of undergraduate students with an interactive petrological microscope and a personal set of thin sections), it decided to develop a software tool called the Virtual Microscope (VM). As a result it is now able to make the unique and precious collection of Apollo specimens universally available as a resource for concurrent study by anybody in the world's Earth and Planetary Sciences community. Herein, we describe the first steps of a collaborative project between OU and the Johnson Space Center (JSC) Curatorial Facility to record a PTS for every lunar rock, beginning with those collected by the Apollo 11 and 12 missions. Method: Production of a virtual microscope dedicated to a particular theme divides into four main parts - photography, image processing, building and assembly of virtual microscope

Validation de schemas de calcul APOLLO3 pour assemblages de type RNR

Science.gov (United States)

Berche, Simon

The next generation nuclear reactors are already under construction or under development in the R&D labs around the world. The 3rd and 4th generation nuclear reactors will need a neutronic calculation code able to deal with any kind of technology (FBR or PWR for example). APOLLO3, a new neutronic code developped by the Commissariat a l'Energie Atomique, will receive the heritage of his two predecessors, APOLLO2 (PWR) and ECCO/ERANOS (FBR), and to play a major role in the design of the next nuclear reactors. Validation is an essential step along the development of a deterministic neutronic code. It comes right after implementation and verification and it gives the team in charge of the calculation models in Cadarache the necessary feedbacks on the code's behaviour in various situations. This thesis goal is to suggest a validation (without evolution) of the current APOLLO3 reference calculation route used for FBR. This validation is supposed to be as complete as possible and to cover various configurations. This work will be a preparatory work for the complete validation which will be performed by the APOLLO3 project team in Cadarache. This validation is based on a study of various configurations composed of basic elements like pincells or assemblies. To complete this task, we study different aspects : geometry, sodium void effect, AEMC-RNR-1200 energy mesh, JEFF3.2 nuclear data evaluation for Pu239. We conduct a macroscopical study (multiplication factor, reactivity, neutron flux,...) and an isotopical study (fission and capture rates for Pu239 and U238 for example). We use TRIPOLI4, a Monte-Carlo simulation code, as a reference for all of our APOLLO3 calculations. We consider an infinite lattice (no neutron leakage model keff = kinfinity). This first validation phase led us to several conclusions. First of all, we observed that the geometrical configuration defined for the single pincell used in ASTRID predefinition studies is heterogeneous enough. Indeed, void

Teaching and Learning Communities through Online Annotation

Science.gov (United States)

van der Pluijm, B.

2016-12-01

What do colleagues do with your assigned textbook? What they say or think about the material? Want students to be more engaged in their learning experience? If so, online materials that complement standard lecture format provide new opportunity through managed, online group annotation that leverages the ubiquity of internet access, while personalizing learning. The concept is illustrated with the new online textbook "Processes in Structural Geology and Tectonics", by Ben van der Pluijm and Stephen Marshak, which offers a platform for sharing of experiences, supplementary materials and approaches, including readings, mathematical applications, exercises, challenge questions, quizzes, alternative explanations, and more. The annotation framework used is Hypothes.is, which offers a free, open platform markup environment for annotation of websites and PDF postings. The annotations can be public, grouped or individualized, as desired, including export access and download of annotations. A teacher group, hosted by a moderator/owner, limits access to members of a user group of teachers, so that its members can use, copy or transcribe annotations for their own lesson material. Likewise, an instructor can host a student group that encourages sharing of observations, questions and answers among students and instructor. Also, the instructor can create one or more closed groups that offers study help and hints to students. Options galore, all of which aim to engage students and to promote greater responsibility for their learning experience. Beyond new capacity, the ability to analyze student annotation supports individual learners and their needs. For example, student notes can be analyzed for key phrases and concepts, and identify misunderstandings, omissions and problems. Also, example annotations can be shared to enhance notetaking skills and to help with studying. Lastly, online annotation allows active application to lecture posted slides, supporting real-time notetaking

Update on Apollo Data Restoration by the NSSDC and the PDS Lunar Data Node

Science.gov (United States)

Williams, David R.; Hills, K. Kent; Taylor, Patrick T.; McBride, Marie J.; Guinness, Edward A.

2012-01-01

The Lunar Data Node (LDN) , under the auspices of the Geosciences Node of the Planetary Data System (PDS) and the National Space Science Data Center (NSSDC), is continuing its efforts to recover and restore Apollo science data. The data being restored are in large part archived with NSSDC on older media, but unarchived data are also being recovered from other sources. They are typically on 7- or 9-track magnetic tapes, often in obsolete formats, or held on microfilm, microfiche, or paper documents. The goal of the LDN is to restore these data from their current form, which is difficult for most researchers to access, into common digital formats with all necessary supporting data (metadata) and archive the data sets with PDS. Restoration involves reading the data from the original media, deciphering the data formats to produce readable digital data and converting the data into usable tabular formats. Each set of values in the table must then be understood in terms of the quantity measured and the units used. Information on instrument properties, operational history, and calibrations is gathered and added to the data set, along with pertinent references, contacts, and other ancillary documentation. The data set then undergoes a peer review and the final validated product is archived with PDS. Although much of this effort has concentrated on data archived at NSSDC in the 1970's, we have also recovered data and information that were never sent to NSSDC. These data, retrieved from various outside sources, include raw and reduced Gamma-Ray Spectrometer data from Apollos 15 and 16, information on the Apollo 17 Lunar Ejecta And Meteorites experiment, Dust Detector data from Apollos 11, 12, 14, and I5, raw telemetry tapes from the Apollo ALSEPs, and Weekly Status Reports for all the Apollo missions. These data are currently being read or organized, and supporting data is being gathered. We are still looking for the calibrated heat flow data from Apollos 15 and 17 for the

An Annotated List of New Social Studies Projects.

Science.gov (United States)

Knight, Merle M., Comp.

The curriculum materials developed by 34 projects are described in this directory. The discussions are organized by discipline: Anthropology, Economics, Geography, History, Political Science, Social Psychology, Sociology, and General and Interdisciplinary. Each individual project note includes: project name, director, address, and a summary of the…

THE DIMENSIONS OF COMPOSITION ANNOTATION.

Science.gov (United States)

MCCOLLY, WILLIAM

ENGLISH TEACHER ANNOTATIONS WERE STUDIED TO DETERMINE THE DIMENSIONS AND PROPERTIES OF THE ENTIRE SYSTEM FOR WRITING CORRECTIONS AND CRITICISMS ON COMPOSITIONS. FOUR SETS OF COMPOSITIONS WERE WRITTEN BY STUDENTS IN GRADES 9 THROUGH 13. TYPESCRIPTS OF THE COMPOSITIONS WERE ANNOTATED BY CLASSROOM ENGLISH TEACHERS. THEN, 32 ENGLISH TEACHERS JUDGED…

Paradigm shifts about dust on the Moon: From Apollo 11 to Chang'e-4

Science.gov (United States)

O'Brien, Brian J.

2018-07-01

Strategic purposes of this DAP-2017 report are to update our DAP-2010 report on movements of inescapable fine lunar dust, to summarise key new measurements and to assist rigorous focus. Lunar dust is defined here in two sciences, Apollo dust and Ejecta dust, to end several confusions. The Kuhn Cycle is introduced to stimulate progression of a science about movements of Apollo dust which lacks an agreed paradigm to supply puzzles for scientists to solve and tools for their solution. We populate the cycle with two paradigm shifts. The first was serendipitous invention in 1966 of the Apollo Dust Detector Experiment (DDE), 3 orthogonal solar cells each with a thermometer, which on Apollo 12 measured cause and effect, collective movements of billions to trillions of low-energy Apollo dust particles and changes in temperature they cause. In contrast, Apollo 17 LEAM and LADEE LDEX experiments follow traditions to measure impacts of high-velocity Ejecta dust particles, one by one. In 2015, Apollo 12 DDE discoveries of sunrise-driven storms of Apollo dust stimulated a measurement-based 5-step model of dust transport at astronaut waist height. The discoveries solve (i) 50-year-old mysteries of Horizon Glow, (ii) 30-year-old uncertainties about levitated dust, (iii) processes leading to lunar surfaces being smooth and (iv) immobilisation of the Chang'e-3 lunar rover Yutu in 2014 after its first sunrise. The IAC-2017 Website Abstract of a withdrawn Chang'e-3 presentation may support our views that sunrise-mobilised dust caused immobilisation of Yutu. A precursor to a second paradigm shift was May 2016 announced revision of Chang'e-4 scientific priorities. Using Kuhn terminology of scientific progress, a second shift would follow our "revolution" in 2015 that sunrise-driven dust storms caused the 2014 ″crisis" of immobilisation of Chang'e-3 lunar rover Yutu. No such sequence occurred previously with lunar dust. Measurement-based evidence from Apollo 11 to Chang'e-3 confirms

MimoSA: a system for minimotif annotation

Directory of Open Access Journals (Sweden)

Kundeti Vamsi

2010-06-01

Full Text Available Abstract Background Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature. Results We have built the MimoSA application for minimotif annotation. The application supports management of the Minimotif Miner database, literature tracking, and annotation of new minimotifs. MimoSA enables the visualization, organization, selection and editing functions of minimotifs and their attributes in the MnM database. For the literature components, Mimosa provides paper status tracking and scoring of papers for annotation through a freely available machine learning approach, which is based on word correlation. The paper scoring algorithm is also available as a separate program, TextMine. Form-driven annotation of minimotif attributes enables entry of new minimotifs into the MnM database. Several supporting features increase the efficiency of annotation. The layered architecture of MimoSA allows for extensibility by separating the functions of paper scoring, minimotif visualization, and database management. MimoSA is readily adaptable to other annotation efforts that manually curate literature into a MySQL database. Conclusions MimoSA is an extensible application that facilitates minimotif annotation and integrates with the Minimotif Miner database. We have built MimoSA as an application that integrates dynamic abstract scoring with a high performance relational model of minimotif syntax. MimoSA's TextMine, an efficient paper-scoring algorithm, can be used to

Paving the Way for Apollo 11

CERN Document Server

Harland, David M

2009-01-01

In 'Paving the Way for Apollo 11' David Harland explains the lure of the Moon to classical philosophers, astronomers, and geologists, and how NASA set out to investigate the Moon in preparation for a manned lunar landing mission. It focuses particularly on the Lunar Orbiter and Surveyor missions.

Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease.

Science.gov (United States)

Sifrim, Alejandro; Van Houdt, Jeroen Kj; Tranchevent, Leon-Charles; Nowakowska, Beata; Sakai, Ryo; Pavlopoulos, Georgios A; Devriendt, Koen; Vermeesch, Joris R; Moreau, Yves; Aerts, Jan

2012-01-01

The increasing size and complexity of exome/genome sequencing data requires new tools for clinical geneticists to discover disease-causing variants. Bottlenecks in identifying the causative variation include poor cross-sample querying, constantly changing functional annotation and not considering existing knowledge concerning the phenotype. We describe a methodology that facilitates exploration of patient sequencing data towards identification of causal variants under different genetic hypotheses. Annotate-it facilitates handling, analysis and interpretation of high-throughput single nucleotide variant data. We demonstrate our strategy using three case studies. Annotate-it is freely available and test data are accessible to all users at http://www.annotate-it.org.

Annotated chemical patent corpus: a gold standard for text mining.

Directory of Open Access Journals (Sweden)

Saber A Akhondi

Full Text Available Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.

Apollo 11 Astronaut Neil Armstrong Performs Ladder Practice

Science.gov (United States)

1969-01-01

In preparation of the nation's first Lunar landing mission, Apollo 11 crew members underwent training activities to practice activities they would be performing during the mission. In this photograph, Neil Armstrong, donned in his space suit, practices getting back to the first rung of the ladder on the Lunar Module (LM). The Apollo 11 mission launched from the Kennedy Space Center (KSC) in Florida via the Marshall Space Flight Center (MSFC) developed Saturn V launch vehicle on July 16, 1969 and safely returned to Earth on July 24, 1969. Aboard the space craft were astronauts Neil A. Armstrong, commander; Michael Collins, Command Module (CM) pilot; and Edwin E. (Buzz) Aldrin Jr., Lunar Module (LM) pilot. The CM, 'Columbia', piloted by Collins, remained in a parking orbit around the Moon while the LM, 'Eagle'', carrying astronauts Armstrong and Aldrin, landed on the Moon. On July 20, 1969, Armstrong was the first human to ever stand on the lunar surface, followed by Aldrin. During 2½ hours of surface exploration, the crew collected 47 pounds of lunar surface material for analysis back on Earth. With the success of Apollo 11, the national objective to land men on the Moon and return them safely to Earth had been accomplished.

Apollo 11 Astronaut Neil Armstrong Approaches Practice Helicopter

Science.gov (United States)

1969-01-01

In preparation of the nation's first lunar landing mission, Apollo 11, crew members underwent training to practice activities they would be performing during the mission. In this photograph Neil Armstrong approaches the helicopter he flew to practice landing the Lunar Module (LM) on the Moon. The Apollo 11 mission launched from the Kennedy Space Center (KSC) in Florida via the Marshall Space Flight Center (MSFC) developed Saturn V launch vehicle on July 16, 1969 and safely returned to Earth on July 24, 1969. Aboard the space craft were astronauts Neil A. Armstrong, commander; Michael Collins, Command Module (CM) pilot; and Edwin E. (Buzz) Aldrin Jr., Lunar Module (LM) pilot. The CM, 'Columbia', piloted by Collins, remained in a parking orbit around the Moon while the LM, 'Eagle'', carrying astronauts Armstrong and Aldrin, landed on the Moon. On July 20, 1969, Armstrong was the first human to ever stand on the lunar surface, followed by Aldrin. During 2½ hours of surface exploration, the crew collected 47 pounds of lunar surface material for analysis back on Earth. With the success of Apollo 11, the national objective to land men on the Moon and return them safely to Earth had been accomplished

Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction.

Directory of Open Access Journals (Sweden)

Thomas H A Ederveen

Full Text Available Nowadays, prokaryotic genomes are sequenced faster than the capacity to manually curate gene annotations. Automated genome annotation engines provide users a straight-forward and complete solution for predicting ORF coordinates and function. For many labs, the use of AGEs is therefore essential to decrease the time necessary for annotating a given prokaryotic genome. However, it is not uncommon for AGEs to provide different and sometimes conflicting predictions. Combining multiple AGEs might allow for more accurate predictions. Here we analyzed the ab initio open reading frame (ORF calling performance of different AGEs based on curated genome annotations of eight strains from different bacterial species with GC% ranging from 35-52%. We present a case study which demonstrates a novel way of comparative genome annotation, using combinations of AGEs in a pre-defined order (or path to predict ORF start codons. The order of AGE combinations is from high to low specificity, where the specificity is based on the eight genome annotations. For each AGE combination we are able to derive a so-called projected confidence value, which is the average specificity of ORF start codon prediction based on the eight genomes. The projected confidence enables estimating likeliness of a correct prediction for a particular ORF start codon by a particular AGE combination, pinpointing ORFs notoriously difficult to predict start codons. We correctly predict start codons for 90.5±4.8% of the genes in a genome (based on the eight genomes with an accuracy of 81.1±7.6%. Our consensus-path methodology allows a marked improvement over majority voting (9.7±4.4% and with an optimal path ORF start prediction sensitivity is gained while maintaining a high specificity.

Launch of Apollo 8 lunar orbit mission

Science.gov (United States)

1968-01-01

The Apollo 8 (Spacecraft 103/Saturn 503) space vehicle launched from Pad A, Launch Complex 39, Kennedy Space Center, at 7:51 a.m., December 21, 1968. In this view there is water in the foreground and seagulls.

Diverse Image Annotation

KAUST Repository

Wu, Baoyuan

2017-11-09

In this work we study the task of image annotation, of which the goal is to describe an image using a few tags. Instead of predicting the full list of tags, here we target for providing a short list of tags under a limited number (e.g., 3), to cover as much information as possible of the image. The tags in such a short list should be representative and diverse. It means they are required to be not only corresponding to the contents of the image, but also be different to each other. To this end, we treat the image annotation as a subset selection problem based on the conditional determinantal point process (DPP) model, which formulates the representation and diversity jointly. We further explore the semantic hierarchy and synonyms among the candidate tags, and require that two tags in a semantic hierarchy or in a pair of synonyms should not be selected simultaneously. This requirement is then embedded into the sampling algorithm according to the learned conditional DPP model. Besides, we find that traditional metrics for image annotation (e.g., precision, recall and F1 score) only consider the representation, but ignore the diversity. Thus we propose new metrics to evaluate the quality of the selected subset (i.e., the tag list), based on the semantic hierarchy and synonyms. Human study through Amazon Mechanical Turk verifies that the proposed metrics are more close to the humans judgment than traditional metrics. Experiments on two benchmark datasets show that the proposed method can produce more representative and diverse tags, compared with existing image annotation methods.

Diverse Image Annotation

KAUST Repository

Wu, Baoyuan; Jia, Fan; Liu, Wei; Ghanem, Bernard

2017-01-01

In this work we study the task of image annotation, of which the goal is to describe an image using a few tags. Instead of predicting the full list of tags, here we target for providing a short list of tags under a limited number (e.g., 3), to cover as much information as possible of the image. The tags in such a short list should be representative and diverse. It means they are required to be not only corresponding to the contents of the image, but also be different to each other. To this end, we treat the image annotation as a subset selection problem based on the conditional determinantal point process (DPP) model, which formulates the representation and diversity jointly. We further explore the semantic hierarchy and synonyms among the candidate tags, and require that two tags in a semantic hierarchy or in a pair of synonyms should not be selected simultaneously. This requirement is then embedded into the sampling algorithm according to the learned conditional DPP model. Besides, we find that traditional metrics for image annotation (e.g., precision, recall and F1 score) only consider the representation, but ignore the diversity. Thus we propose new metrics to evaluate the quality of the selected subset (i.e., the tag list), based on the semantic hierarchy and synonyms. Human study through Amazon Mechanical Turk verifies that the proposed metrics are more close to the humans judgment than traditional metrics. Experiments on two benchmark datasets show that the proposed method can produce more representative and diverse tags, compared with existing image annotation methods.

The Apollo 17 'melt sheet': chemistry, age and Rb/Sr systematics

International Nuclear Information System (INIS)

Winzer, S.R.; Nava, D.F.; Schuhmann, S.; Philpotts, J.A.

1977-01-01

Major, minor and trace element compositions, age data and Rb/Sr systematics of Apollo 17 boulders have been compiled, and additional analyses performed on a norite breccia clast (77215) included in the Apollo 17, Station 7 boulder. The Apollo 17 boulders are found to be identical or nearly so in major, minor and trace element composition, suggesting that they all originated as an impact melt analogous to melt sheets found in larger terrestrial craters. The matrix dates ( 40 Ar/ 39 Ar) and Rb/Sr systematics available suggest that this impact melt formed by a single impact about 4 b.y. ago. This impact excavated, shocked, brecciated and melted norites, norite cumulates and possibly anorthositic gabbros and dunites about 4.4 b.y. old. The impact was likely a major one, possibly the Serenitatis basin-forming event. (Auth.)

Parnassiana nova : XLVII. Neue Unterarten von Parnassius apollo L. und Parnassius mnemosyne L.

NARCIS (Netherlands)

Eisner, C.

1974-01-01

1. DREI NEUE PARNASSIUS APOLLO L. UNTERARTEN AUS SPANIEN Die Herren P. Capdeville und P. C. Rougeot haben in den letzten Jahren die verschiedenen Flugplätze von Parnassius apollo L. in Spanien aufgesucht und eine Anzahl neuer Unterarten aufgestellt. Die Kenntnis wird ergänzt durch die Beschreibung

Apollo Lunar Module Electrical Power System Overview

Science.gov (United States)

Interbartolo, Michael

2009-01-01

Objectives include: a) Describe LM Electrical System original specifications; b) Describe the decision to change from fuel cells to batteries and other changes; c) Describe the Electrical system; and d) Describe the Apollo 13 failure from the LM perspective.

MAX: an expert system for running the modular transport code APOLLO II

International Nuclear Information System (INIS)

Loussouarn, O.; Ferraris, C.; Boivineau, A.

1990-01-01

MAX is an expert system built to help users of the APOLLO II code to prepare the input data deck to run a job. APOLLO II is a modular transport-theory code for calculating the neutron flux in various geometries. The associated GIBIANE command language allows the user to specify the physical structure and the computational method to be used in the calculation. The purpose of MAX is to bring into play expertise in both neutronic and computing aspects of the code, as well as various computational schemes, in order to generate automatically a batch data set corresponding to the APOLLO II calculation desired by the user. MAX is implemented on the SUN 3/60 workstation with the S1 tool and graphic interface external functions

Discovering gene annotations in biomedical text databases

Directory of Open Access Journals (Sweden)

Ozsoyoglu Gultekin

2008-03-01

Full Text Available Abstract Background Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data. Results In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products. In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general. Conclusion GEANN is useful for two distinct purposes: (i automating the annotation of genomic entities with Gene Ontology concepts, and (ii providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate

Apollo Video Photogrammetry Estimation Of Plume Impingement Effects

Science.gov (United States)

Immer, Christopher; Lane, John; Metzger, Philip T.; Clements, Sandra

2008-01-01

The Constellation Project's planned return to the moon requires numerous landings at the same site. Since the top few centimeters are loosely packed regolith, plume impingement from the Lander ejects the granular material at high velocities. Much work is needed to understand the physics of plume impingement during landing in order to protect hardware surrounding the landing sites. While mostly qualitative in nature, the Apollo Lunar Module landing videos can provide a wealth of quantitative information using modem photogrammetry techniques. The authors have used the digitized videos to quantify plume impingement effects of the landing exhaust on the lunar surface. The dust ejection angle from the plume is estimated at 1-3 degrees. The lofted particle density is estimated at 10(exp 8)- 10(exp 13) particles per cubic meter. Additionally, evidence for ejection of large 10-15 cm sized objects and a dependence of ejection angle on thrust are presented. Further work is ongoing to continue quantitative analysis of the landing videos.

Annotating the human genome with Disease Ontology

Science.gov (United States)

Osborne, John D; Flatow, Jared; Holko, Michelle; Lin, Simon M; Kibbe, Warren A; Zhu, Lihua (Julie); Danila, Maria I; Feng, Gang; Chisholm, Rex L

2009-01-01

Background The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases. Results We used the Unified Medical Language System (UMLS) MetaMap Transfer tool (MMTx) to discover gene-disease relationships from the GeneRIF database. We utilized a comprehensive subset of UMLS, which is disease-focused and structured as a directed acyclic graph (the Disease Ontology), to filter and interpret results from MMTx. The results were validated against the Homayouni gene collection using recall and precision measurements. We compared our results with the widely used Online Mendelian Inheritance in Man (OMIM) annotations. Conclusion The validation data set suggests a 91% recall rate and 97% precision rate of disease annotation using GeneRIF, in contrast with a 22% recall and 98% precision using OMIM. Our thesaurus-based approach allows for comparisons to be made between disease containing databases and allows for increased accuracy in disease identification through synonym matching. The much higher recall rate of our approach demonstrates that annotating human genome with Disease Ontology and GeneRIF for diseases dramatically increases the coverage of the disease annotation of human genome. PMID:19594883

MIPS bacterial genomes functional annotation benchmark dataset.

Science.gov (United States)

Tetko, Igor V; Brauner, Barbara; Dunger-Kaltenbach, Irmtraud; Frishman, Goar; Montrone, Corinna; Fobo, Gisela; Ruepp, Andreas; Antonov, Alexey V; Surmeli, Dimitrij; Mewes, Hans-Wernen

2005-05-15

Any development of new methods for automatic functional annotation of proteins according to their sequences requires high-quality data (as benchmark) as well as tedious preparatory work to generate sequence parameters required as input data for the machine learning methods. Different program settings and incompatible protocols make a comparison of the analyzed methods difficult. The MIPS Bacterial Functional Annotation Benchmark dataset (MIPS-BFAB) is a new, high-quality resource comprising four bacterial genomes manually annotated according to the MIPS functional catalogue (FunCat). These resources include precalculated sequence parameters, such as sequence similarity scores, InterPro domain composition and other parameters that could be used to develop and benchmark methods for functional annotation of bacterial protein sequences. These data are provided in XML format and can be used by scientists who are not necessarily experts in genome annotation. BFAB is available at http://mips.gsf.de/proj/bfab

Annotating non-coding regions of the genome.

Science.gov (United States)

Alexander, Roger P; Fang, Gang; Rozowsky, Joel; Snyder, Michael; Gerstein, Mark B

2010-08-01

Most of the human genome consists of non-protein-coding DNA. Recently, progress has been made in annotating these non-coding regions through the interpretation of functional genomics experiments and comparative sequence analysis. One can conceptualize functional genomics analysis as involving a sequence of steps: turning the output of an experiment into a 'signal' at each base pair of the genome; smoothing this signal and segmenting it into small blocks of initial annotation; and then clustering these small blocks into larger derived annotations and networks. Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis.

Rocket ranch the nuts and bolts of the Apollo Moon program at Kennedy Space Center

CERN Document Server

Ward, Jonathan H

2015-01-01

Jonathan Ward takes the reader deep into the facilities at Kennedy Space Center to describe NASA’s first computer systems used for spacecraft and rocket checkout and explain how tests and launches proceeded. Descriptions of early operations include a harrowing account of the heroic efforts of pad workers during the Apollo 1 fire. A companion to the author’s book Countdown to a Moon Launch: Preparing Apollo for Its Historic Journey, this explores every facet of the facilities that served as the base for the Apollo/Saturn missions. Hundreds of illustrations complement the firsthand accounts of more than 70 Apollo program managers and engineers. The era of the Apollo/Saturn missions was perhaps the most exciting period in American space exploration history. Cape Canaveral and Kennedy Space Center were buzzing with activity. Thousands of workers came to town to build the facilities and launch the missions needed to put an American on the Moon before the end of the decade. Work at KSC involved much more than j...

Systems Theory and Communication. Annotated Bibliography.

Science.gov (United States)

Covington, William G., Jr.

This annotated bibliography presents annotations of 31 books and journal articles dealing with systems theory and its relation to organizational communication, marketing, information theory, and cybernetics. Materials were published between 1963 and 1992 and are listed alphabetically by author. (RS)

The surplus value of semantic annotations

NARCIS (Netherlands)

Marx, M.

2010-01-01

We compare the costs of semantic annotation of textual documents to its benefits for information processing tasks. Semantic annotation can improve the performance of retrieval tasks and facilitates an improved search experience through faceted search, focused retrieval, better document summaries,

Annotation-based enrichment of Digital Objects using open-source frameworks

Directory of Open Access Journals (Sweden)

Marcus Emmanuel Barnes

2017-07-01

Full Text Available The W3C Web Annotation Data Model, Protocol, and Vocabulary unify approaches to annotations across the web, enabling their aggregation, discovery and persistence over time. In addition, new javascript libraries provide the ability for users to annotate multi-format content. In this paper, we describe how we have leveraged these developments to provide annotation features alongside Islandora’s existing preservation, access, and management capabilities. We also discuss our experience developing with the Web Annotation Model as an open web architecture standard, as well as our approach to integrating mature external annotation libraries. The resulting software (the Web Annotation Utility Module for Islandora accommodates annotation across multiple formats. This solution can be used in various digital scholarship contexts.

Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome.

Science.gov (United States)

Islam, Mohammad T; Garg, Gagan; Hancock, William S; Risk, Brian A; Baker, Mark S; Ranganathan, Shoba

2014-01-03

The chromosome-centric human proteome project (C-HPP) aims to define the complete set of proteins encoded in each human chromosome. The neXtProt database (September 2013) lists 20,128 proteins for the human proteome, of which 3831 human proteins (∼19%) are considered "missing" according to the standard metrics table (released September 27, 2013). In support of the C-HPP initiative, we have extended the annotation strategy developed for human chromosome 7 "missing" proteins into a semiautomated pipeline to functionally annotate the "missing" human proteome. This pipeline integrates a suite of bioinformatics analysis and annotation software tools to identify homologues and map putative functional signatures, gene ontology, and biochemical pathways. From sequential BLAST searches, we have primarily identified homologues from reviewed nonhuman mammalian proteins with protein evidence for 1271 (33.2%) "missing" proteins, followed by 703 (18.4%) homologues from reviewed nonhuman mammalian proteins and subsequently 564 (14.7%) homologues from reviewed human proteins. Functional annotations for 1945 (50.8%) "missing" proteins were also determined. To accelerate the identification of "missing" proteins from proteomics studies, we generated proteotypic peptides in silico. Matching these proteotypic peptides to ENCODE proteogenomic data resulted in proteomic evidence for 107 (2.8%) of the 3831 "missing proteins, while evidence from a recent membrane proteomic study supported the existence for another 15 "missing" proteins. The chromosome-wise functional annotation of all "missing" proteins is freely available to the scientific community through our web server (http://biolinfo.org/protannotator).

Cosmic rays score direct hits with Apollo crew

CERN Multimedia

1971-01-01

Apollo 14 astronauts conduted experiments during the spaceflight to help scientists to understand why previous crews have seen flashes of light during missions, believed to be caused by cosmic rays (1 page).

Inert gas investigations of the Apollo 15 and 17 landing sites

International Nuclear Information System (INIS)

Jordan, J.L.

1975-01-01

The inert gas contents in size fractions of the following fines from the Apollo 15 site: 15071, 15501, 15511, 15421, and 15080 has been determined. In addition, the same for size fractions of fines 79221, 79241, and 79261 from depths of 0 to 2 cm, 2 to 7 cm, and 7 to 17 cm in a trench near Van Serg Crater at the Apollo 17 site was determined. The very low gas contents and lack of anticorrelation with grain diameter of 15421 suggests that these fines are undersaturated with respect to solar wind irradiation. The decrease in slope of the curves for gas concentration vs grain diameter of 15071 for successively heavier gases is interpreted to be the effects of the Rosiwal principle + comminution + agglutinate formation. Evidence for heavily irradiated (with respect to cosmic rays) zones deep within or beneath the regolith exists at both Apollo 15 and 17 landing sites. This may in part explain the ''missing'' cosmic ray record. Scatter between ''young'' and ''old'' age limits in 40 Ar vs 36 Ar plots exists for 15511, and the 3 trench fines from the Apollo 17 landing site. In the case of 15511 the observed ratios suggest that these may be the result of large impacts on the Apennine Front contributing material to the site where 15511 was collected. The observed 40 Ar/ 36 Ar ratios in the trench fines may be the result of excavation of materials with high 40 Ar/ 36 Ar ratios during the Van Serg event. The low apparent 40 K-- 40 Ar ages of the Apollo 15 fines are interpreted to be the result of addition of young 40 K-- 40 Ar age material (less than 1.8 by) from Autolycus and Aristillus, two large craters north of the site, to the older (3.3 by) mare materials

Students' Framing of a Reading Annotation Tool in the Context of Research-Based Teaching

Science.gov (United States)

Dahl, Jan Erik

2016-01-01

In the studied master's course, students participated both as research objects in a digital annotation experiment and as critical investigators of this technology in their semester projects. The students' role paralleled the researcher's role, opening an opportunity for researcher-student co-learning within what is often referred to as…

Current and future trends in marine image annotation software

Science.gov (United States)

Gomes-Pereira, Jose Nuno; Auger, Vincent; Beisiegel, Kolja; Benjamin, Robert; Bergmann, Melanie; Bowden, David; Buhl-Mortensen, Pal; De Leo, Fabio C.; Dionísio, Gisela; Durden, Jennifer M.; Edwards, Luke; Friedman, Ariell; Greinert, Jens; Jacobsen-Stout, Nancy; Lerner, Steve; Leslie, Murray; Nattkemper, Tim W.; Sameoto, Jessica A.; Schoening, Timm; Schouten, Ronald; Seager, James; Singh, Hanumant; Soubigou, Olivier; Tojeira, Inês; van den Beld, Inge; Dias, Frederico; Tempera, Fernando; Santos, Ricardo S.

2016-12-01

Given the need to describe, analyze and index large quantities of marine imagery data for exploration and monitoring activities, a range of specialized image annotation tools have been developed worldwide. Image annotation - the process of transposing objects or events represented in a video or still image to the semantic level, may involve human interactions and computer-assisted solutions. Marine image annotation software (MIAS) have enabled over 500 publications to date. We review the functioning, application trends and developments, by comparing general and advanced features of 23 different tools utilized in underwater image analysis. MIAS requiring human input are basically a graphical user interface, with a video player or image browser that recognizes a specific time code or image code, allowing to log events in a time-stamped (and/or geo-referenced) manner. MIAS differ from similar software by the capability of integrating data associated to video collection, the most simple being the position coordinates of the video recording platform. MIAS have three main characteristics: annotating events in real time, posteriorly to annotation and interact with a database. These range from simple annotation interfaces, to full onboard data management systems, with a variety of toolboxes. Advanced packages allow to input and display data from multiple sensors or multiple annotators via intranet or internet. Posterior human-mediated annotation often include tools for data display and image analysis, e.g. length, area, image segmentation, point count; and in a few cases the possibility of browsing and editing previous dive logs or to analyze the annotations. The interaction with a database allows the automatic integration of annotations from different surveys, repeated annotation and collaborative annotation of shared datasets, browsing and querying of data. Progress in the field of automated annotation is mostly in post processing, for stable platforms or still images

APOLLO 17 PRELAUNCH ASTRONAUT TRAINING

Science.gov (United States)

1972-01-01

Apollo Command Module Pilot Evans, left, and Mission Commander Cernan, right, discuss their flight plans as each prepares to fly a T-38 jet aircraft at Patrick Air Force Base just south of the Spaceport. Astronauts Cernan and Evans flew the T-38 aircraft today on training flights over the Kennedy Space Center area to practice flying skills in preparation for upcoming launch to the Moon scheduled 12/06/72.

Vital analysis: field validation of a framework for annotating biological signals of first responders in action.

Science.gov (United States)

Gomes, P; Lopes, B; Coimbra, M

2012-01-01

First responders are professionals that are exposed to extreme stress and fatigue during extended periods of time. That is why it is necessary to research and develop technological solutions based on wearable sensors that can continuously monitor the health of these professionals in action, namely their stress and fatigue levels. In this paper we present the Vital Analysis smartphone-based framework, integrated into the broader Vital Responder project, that allows the annotation and contextualization of the signals collected during real action. After a contextual study we have implemented and deployed this framework in a firefighter team with 5 elements, from where we have collected over 3300 hours of annotations during 174 days, covering 382 different events. Results are analysed and discussed, validating the framework as a useful and usable tool for annotating biological signals of first responders in action.

PANNZER2: a rapid functional annotation web server.

Science.gov (United States)

Törönen, Petri; Medlar, Alan; Holm, Liisa

2018-05-08

The unprecedented growth of high-throughput sequencing has led to an ever-widening annotation gap in protein databases. While computational prediction methods are available to make up the shortfall, a majority of public web servers are hindered by practical limitations and poor performance. Here, we introduce PANNZER2 (Protein ANNotation with Z-scoRE), a fast functional annotation web server that provides both Gene Ontology (GO) annotations and free text description predictions. PANNZER2 uses SANSparallel to perform high-performance homology searches, making bulk annotation based on sequence similarity practical. PANNZER2 can output GO annotations from multiple scoring functions, enabling users to see which predictions are robust across predictors. Finally, PANNZER2 predictions scored within the top 10 methods for molecular function and biological process in the CAFA2 NK-full benchmark. The PANNZER2 web server is updated on a monthly schedule and is accessible at http://ekhidna2.biocenter.helsinki.fi/sanspanz/. The source code is available under the GNU Public Licence v3.

Evolution of KREEP - Further petrologic evidence. [igneous rocks from Apollo 15 site

Science.gov (United States)

Crawford, M. L.; Hollister, L. S.

1977-01-01

It is hypothesized that KREEP samples from the Apollo 15 site are igneous. To support the hypothesis, comparisons are made with other crystalline KREEP samples, especially 14310. It is noted that the low siderophile element content and lack of high pressure phenocrysts in the Apollo 15 KREEP may be indications of a slower rise of KREEP melt to the surface, when contrasted with sample 14310. Gravitational separation of Fe-Ni metal is proposed as a mechanism to account for the depletion of siderophile elements relative to the Si-rich component. It is further suggested that KREEP may be the parent of Apollo 12 and 15 basalts, as well as of granitic rocks, due to the liquid immiscibility occurring during the KREEP melt crystallization, and the subsequent independent evolution of the components.

Annotating activation/inhibition relationships to protein-protein interactions using gene ontology relations.

Science.gov (United States)

Yim, Soorin; Yu, Hasun; Jang, Dongjin; Lee, Doheon

2018-04-11

Signaling pathways can be reconstructed by identifying 'effect types' (i.e. activation/inhibition) of protein-protein interactions (PPIs). Effect types are composed of 'directions' (i.e. upstream/downstream) and 'signs' (i.e. positive/negative), thereby requiring directions as well as signs of PPIs to predict signaling events from PPI networks. Here, we propose a computational method for systemically annotating effect types to PPIs using relations between functional information of proteins. We used regulates, positively regulates, and negatively regulates relations in Gene Ontology (GO) to predict directions and signs of PPIs. These relations indicate both directions and signs between GO terms so that we can project directions and signs between relevant GO terms to PPIs. Independent test results showed that our method is effective for predicting both directions and signs of PPIs. Moreover, our method outperformed a previous GO-based method that did not consider the relations between GO terms. We annotated effect types to human PPIs and validated several highly confident effect types against literature. The annotated human PPIs are available in Additional file 2 to aid signaling pathway reconstruction and network biology research. We annotated effect types to PPIs by using regulates, positively regulates, and negatively regulates relations in GO. We demonstrated that those relations are effective for predicting not only signs, but also directions of PPIs. The usefulness of those relations suggests their potential applications to other types of interactions such as protein-DNA interactions.

APOLLO 11 COMMANDER NEIL ARMSTRONG IN SIMULATOR

Science.gov (United States)

1969-01-01

Apollo 11 commander Neil Armstrong is going through flight training in the lunar module simulator situated in the flight crew training building at KSC. Armstrong will pilot the lunar module to a moon landing on July 20, following launch from KSC on July 16.

Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation.

Science.gov (United States)

Clark, Alex M; Bunin, Barry A; Litterman, Nadia K; Schürer, Stephan C; Visser, Ubbo

2014-01-01

Bioinformatics and computer aided drug design rely on the curation of a large number of protocols for biological assays that measure the ability of potential drugs to achieve a therapeutic effect. These assay protocols are generally published by scientists in the form of plain text, which needs to be more precisely annotated in order to be useful to software methods. We have developed a pragmatic approach to describing assays according to the semantic definitions of the BioAssay Ontology (BAO) project, using a hybrid of machine learning based on natural language processing, and a simplified user interface designed to help scientists curate their data with minimum effort. We have carried out this work based on the premise that pure machine learning is insufficiently accurate, and that expecting scientists to find the time to annotate their protocols manually is unrealistic. By combining these approaches, we have created an effective prototype for which annotation of bioassay text within the domain of the training set can be accomplished very quickly. Well-trained annotations require single-click user approval, while annotations from outside the training set domain can be identified using the search feature of a well-designed user interface, and subsequently used to improve the underlying models. By drastically reducing the time required for scientists to annotate their assays, we can realistically advocate for semantic annotation to become a standard part of the publication process. Once even a small proportion of the public body of bioassay data is marked up, bioinformatics researchers can begin to construct sophisticated and useful searching and analysis algorithms that will provide a diverse and powerful set of tools for drug discovery researchers.

Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation

Directory of Open Access Journals (Sweden)

Alex M. Clark

2014-08-01

Full Text Available Bioinformatics and computer aided drug design rely on the curation of a large number of protocols for biological assays that measure the ability of potential drugs to achieve a therapeutic effect. These assay protocols are generally published by scientists in the form of plain text, which needs to be more precisely annotated in order to be useful to software methods. We have developed a pragmatic approach to describing assays according to the semantic definitions of the BioAssay Ontology (BAO project, using a hybrid of machine learning based on natural language processing, and a simplified user interface designed to help scientists curate their data with minimum effort. We have carried out this work based on the premise that pure machine learning is insufficiently accurate, and that expecting scientists to find the time to annotate their protocols manually is unrealistic. By combining these approaches, we have created an effective prototype for which annotation of bioassay text within the domain of the training set can be accomplished very quickly. Well-trained annotations require single-click user approval, while annotations from outside the training set domain can be identified using the search feature of a well-designed user interface, and subsequently used to improve the underlying models. By drastically reducing the time required for scientists to annotate their assays, we can realistically advocate for semantic annotation to become a standard part of the publication process. Once even a small proportion of the public body of bioassay data is marked up, bioinformatics researchers can begin to construct sophisticated and useful searching and analysis algorithms that will provide a diverse and powerful set of tools for drug discovery researchers.

Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

Directory of Open Access Journals (Sweden)

Mungall Christopher J

2010-10-01

Full Text Available Abstract Background The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation. Results We have formalized the taxonomic constraints implicit in some GO classes, and specified these at various levels in the ontology. We have also developed an inference system that can be used to check for violations of these constraints in annotations. Using the constraints in conjunction with the inference system, we have detected and removed errors in annotations and improved the structure of the ontology. Conclusions Detection of inconsistencies in taxon-specificity enables gradual improvement of the ontologies, the annotations, and the formalized constraints. This is progressively improving the quality of our data. The full system is available for download, and new constraints or proposed changes to constraints can be submitted online at https://sourceforge.net/tracker/?atid=605890&group_id=36855.

Apollo-12 gift to the Agency

International Nuclear Information System (INIS)

1970-01-01

On March 2 the Agency was host to the three Apollo-12 astronauts who placed the first atomic power generator on the moon. Accompanied by their wives, they were given a warm welcome and received mementos prepared by the Agency. In return they presented the Director General with a model of the SNAP-27 generator. (author)

Conservation Science Fair Projects.

Science.gov (United States)

Soil Conservation Society of America, Ankeny, IA.

Included are ideas, suggestions, and examples for selecting and designing conservation science projects. Over 70 possible conservation subject areas are presented with suggested projects. References are cited with each of these subject areas, and a separate list of annotated references is included. The references pertain to general subject…

Technicians work with Apollo 14 lunar sample material in Lunar Receiving Lab.

Science.gov (United States)

1971-01-01

Glove handlers work with freshly opened Apollo 14 lunar sample material in modularized cabinets in the Lunar Receiving Laboratory at the Manned Spacecraft Center. The glove operator on the right starts to pour fine lunar material which he has just taken from a tote bag. This powdery sample was among the last to be revealed of the 90-odd pounds of material brought back to Earth by the Apollo 14 crewmen.

MitoBamAnnotator: A web-based tool for detecting and annotating heteroplasmy in human mitochondrial DNA sequences.

Science.gov (United States)

Zhidkov, Ilia; Nagar, Tal; Mishmar, Dan; Rubin, Eitan

2011-11-01

The use of Next-Generation Sequencing of mitochondrial DNA is becoming widespread in biological and clinical research. This, in turn, creates a need for a convenient tool that detects and analyzes heteroplasmy. Here we present MitoBamAnnotator, a user friendly web-based tool that allows maximum flexibility and control in heteroplasmy research. MitoBamAnnotator provides the user with a comprehensively annotated overview of mitochondrial genetic variation, allowing for an in-depth analysis with no prior knowledge in programming. Copyright © 2011 Elsevier B.V. and Mitochondria Research Society. All rights reserved. All rights reserved.

Correction of the Caulobacter crescentus NA1000 genome annotation.

Directory of Open Access Journals (Sweden)

Bert Ely

Full Text Available Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading frame of 38 genes that had been incorrectly annotated. Furthermore, our manual method of identifying protein-coding genes allowed us to remove 112 non-coding regions that had been designated as coding regions. The improved NA1000 genome annotation resulted in a reduction in the use of rare codons since noncoding regions with atypical codon usage were removed from the annotation and 49 new coding regions were added to the annotation. Thus, a more accurate codon usage table was generated as well. These results demonstrate that a comparison of the location of peaks third codon position GC content to the location of protein coding regions could be used to verify the annotation of any genome that has a GC content that is greater than 60%.

Quantification of the impact of PSI:Biology according to the annotations of the determined structures.

Science.gov (United States)

DePietro, Paul J; Julfayev, Elchin S; McLaughlin, William A

2013-10-21

Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third phase entailed the formation of PSI:Biology Partnerships which are composed of structural genomics centers and biomedical science laboratories. We present a method to examine the impact of protein structures determined under the auspices of PSI:Biology by measuring their rates of annotations. The mean numbers of annotations per structure and per residue are examined. These are designed to provide measures of the amount of structure to function connections that can be leveraged from each structure. One result is that PSI:Biology structures are found to have a higher rate of annotations than structures determined during the first two phases of PSI. A second result is that the subset of PSI:Biology structures determined through PSI:Biology Partnerships have a higher rate of annotations than those determined exclusive of those partnerships. Both results hold when the annotation rates are examined either at the level of the entire protein or for annotations that are known to fall at specific residues within the portion of the protein that has a determined structure. We conclude that PSI:Biology determines structures that are estimated to have a higher degree of biomedical interest than those determined during the first two phases of PSI based on a broad array of biomedical annotations. For the PSI:Biology Partnerships, we see that there is an associated added value that represents part of the progress toward the goals of PSI:Biology. We interpret the added value to mean that team-based structural biology projects that utilize the expertise and technologies of structural genomics centers together with biological laboratories in the community are conducted in a synergistic manner. We show that the annotation rates can be used in conjunction with established metrics, i

Annotation of regular polysemy and underspecification

DEFF Research Database (Denmark)

Martínez Alonso, Héctor; Pedersen, Bolette Sandford; Bel, Núria

2013-01-01

We present the result of an annotation task on regular polysemy for a series of seman- tic classes or dot types in English, Dan- ish and Spanish. This article describes the annotation process, the results in terms of inter-encoder agreement, and the sense distributions obtained with two methods...

PCAS – a precomputed proteome annotation database resource

Directory of Open Access Journals (Sweden)

Luo Jingchu

2003-11-01

Full Text Available Abstract Background Many model proteomes or "complete" sets of proteins of given organisms are now publicly available. Much effort has been invested in computational annotation of those "draft" proteomes. Motif or domain based algorithms play a pivotal role in functional classification of proteins. Employing most available computational algorithms, mainly motif or domain recognition algorithms, we set up to develop an online proteome annotation system with integrated proteome annotation data to complement existing resources. Results We report here the development of PCAS (ProteinCentric Annotation System as an online resource of pre-computed proteome annotation data. We applied most available motif or domain databases and their analysis methods, including hmmpfam search of HMMs in Pfam, SMART and TIGRFAM, RPS-PSIBLAST search of PSSMs in CDD, pfscan of PROSITE patterns and profiles, as well as PSI-BLAST search of SUPERFAMILY PSSMs. In addition, signal peptide and TM are predicted using SignalP and TMHMM respectively. We mapped SUPERFAMILY and COGs to InterPro, so the motif or domain databases are integrated through InterPro. PCAS displays table summaries of pre-computed data and a graphical presentation of motifs or domains relative to the protein. As of now, PCAS contains human IPI, mouse IPI, and rat IPI, A. thaliana, C. elegans, D. melanogaster, S. cerevisiae, and S. pombe proteome. PCAS is available at http://pak.cbi.pku.edu.cn/proteome/gca.php Conclusion PCAS gives better annotation coverage for model proteomes by employing a wider collection of available algorithms. Besides presenting the most confident annotation data, PCAS also allows customized query so users can inspect statistically less significant boundary information as well. Therefore, besides providing general annotation information, PCAS could be used as a discovery platform. We plan to update PCAS twice a year. We will upgrade PCAS when new proteome annotation algorithms

Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58

Science.gov (United States)

Yu, Jia-Feng; Sui, Tian-Xiang; Wang, Hong-Mei; Wang, Chun-Ling; Jing, Li; Wang, Ji-Hua

2015-12-01

Agrobacterium tumefaciens strain C58 is a type of pathogen that can cause tumors in some dicotyledonous plants. Ever since the genome of A. tumefaciens strain C58 was sequenced, the quality of annotation of its protein-coding genes has been queried continually, because the annotation varies greatly among different databases. In this paper, the questionable hypothetical genes were re-predicted by integrating the TN curve and Z curve methods. As a result, 30 genes originally annotated as “hypothetical” were discriminated as being non-coding sequences. By testing the re-prediction program 10 times on data sets composed of the function-known genes, the mean accuracy of 99.99% and mean Matthews correlation coefficient value of 0.9999 were obtained. Further sequence analysis and COG analysis showed that the re-annotation results were very reliable. This work can provide an efficient tool and data resources for future studies of A. tumefaciens strain C58. Project supported by the National Natural Science Foundation of China (Grant Nos. 61302186 and 61271378) and the Funding from the State Key Laboratory of Bioelectronics of Southeast University.

A semi-automatic annotation tool for cooking video

Science.gov (United States)

Bianco, Simone; Ciocca, Gianluigi; Napoletano, Paolo; Schettini, Raimondo; Margherita, Roberto; Marini, Gianluca; Gianforme, Giorgio; Pantaleo, Giuseppe

2013-03-01

In order to create a cooking assistant application to guide the users in the preparation of the dishes relevant to their profile diets and food preferences, it is necessary to accurately annotate the video recipes, identifying and tracking the foods of the cook. These videos present particular annotation challenges such as frequent occlusions, food appearance changes, etc. Manually annotate the videos is a time-consuming, tedious and error-prone task. Fully automatic tools that integrate computer vision algorithms to extract and identify the elements of interest are not error free, and false positive and false negative detections need to be corrected in a post-processing stage. We present an interactive, semi-automatic tool for the annotation of cooking videos that integrates computer vision techniques under the supervision of the user. The annotation accuracy is increased with respect to completely automatic tools and the human effort is reduced with respect to completely manual ones. The performance and usability of the proposed tool are evaluated on the basis of the time and effort required to annotate the same video sequences.

Experiments with crowdsourced re-annotation of a POS tagging data set

DEFF Research Database (Denmark)

Hovy, Dirk; Plank, Barbara; Søgaard, Anders

2014-01-01

Crowdsourcing lets us collect multiple annotations for an item from several annotators. Typically, these are annotations for non-sequential classification tasks. While there has been some work on crowdsourcing named entity annotations, researchers have assumed that syntactic tasks such as part......-of-speech (POS) tagging cannot be crowdsourced. This paper shows that workers can actually annotate sequential data almost as well as experts. Further, we show that the models learned from crowdsourced annotations fare as well as the models learned from expert annotations in downstream tasks....

Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.

Science.gov (United States)

Standley, Daron M; Toh, Hiroyuki; Nakamura, Haruki

2008-09-01

A method to functionally annotate structural genomics targets, based on a novel structural alignment scoring function, is proposed. In the proposed score, position-specific scoring matrices are used to weight structurally aligned residue pairs to highlight evolutionarily conserved motifs. The functional form of the score is first optimized for discriminating domains belonging to the same Pfam family from domains belonging to different families but the same CATH or SCOP superfamily. In the optimization stage, we consider four standard weighting functions as well as our own, the "maximum substitution probability," and combinations of these functions. The optimized score achieves an area of 0.87 under the receiver-operating characteristic curve with respect to identifying Pfam families within a sequence-unique benchmark set of domain pairs. Confidence measures are then derived from the benchmark distribution of true-positive scores. The alignment method is next applied to the task of functionally annotating 230 query proteins released to the public as part of the Protein 3000 structural genomics project in Japan. Of these queries, 78 were found to align to templates with the same Pfam family as the query or had sequence identities > or = 30%. Another 49 queries were found to match more distantly related templates. Within this group, the template predicted by our method to be the closest functional relative was often not the most structurally similar. Several nontrivial cases are discussed in detail. Finally, 103 queries matched templates at the fold level, but not the family or superfamily level, and remain functionally uncharacterized. 2008 Wiley-Liss, Inc.

MPEG-7 based video annotation and browsing

Science.gov (United States)

Hoeynck, Michael; Auweiler, Thorsten; Wellhausen, Jens

2003-11-01

The huge amount of multimedia data produced worldwide requires annotation in order to enable universal content access and to provide content-based search-and-retrieval functionalities. Since manual video annotation can be time consuming, automatic annotation systems are required. We review recent approaches to content-based indexing and annotation of videos for different kind of sports and describe our approach to automatic annotation of equestrian sports videos. We especially concentrate on MPEG-7 based feature extraction and content description, where we apply different visual descriptors for cut detection. Further, we extract the temporal positions of single obstacles on the course by analyzing MPEG-7 edge information. Having determined single shot positions as well as the visual highlights, the information is jointly stored with meta-textual information in an MPEG-7 description scheme. Based on this information, we generate content summaries which can be utilized in a user-interface in order to provide content-based access to the video stream, but further for media browsing on a streaming server.

Ground Truth Annotation in T Analyst

DEFF Research Database (Denmark)

2015-01-01

This video shows how to annotate the ground truth tracks in the thermal videos. The ground truth tracks are produced to be able to compare them to tracks obtained from a Computer Vision tracking approach. The program used for annotation is T-Analyst, which is developed by Aliaksei Laureshyn, Ph...

The triumph and decline of the "squares": Grumman Aerospace engineers and production workers in the Apollo era, 1957--1973

Science.gov (United States)

Onkst, David Hugh

This dissertation is a social, cultural, and economic history of the men and women of the Grumman Aerospace Company of Bethpage, New York from 1957 through 1973. These "Grummanites" were the engineers and production workers who designed and built the Apollo Lunar Modules that allowed humans to land on the Moon. This study provides unique insights into the impact that the Apollo Program---a large state-initiated and -supported program---had on those "squares," people whom many contemporaries saw as a vital part of mainstream 1960s American society. By the beginning of the Space Age in 1957, Grumman, Long Island's single largest employer, had firmly established a workplace culture of paternalism that Grummanites largely embraced. Company officials believed strongly in worker retention and had established a policy of providing every sort of benefit their employees seemingly desired, including a highly personal and participatory form of management. Many Grummanites had joined the firm during the early years of the Apollo Program because they believed in the promise of permanent employment on exciting projects that would explore the endless frontier of space. But, as many of these mainly self-reliant, individualistic "squares" would bitterly discover, their dedication to Grumman did little to secure their livelihoods during the aerospace industry's early 1970s downsizing; their individual successes were too largely tied to federal spending and declined when Americans grew disenchanted with space exploration. This dissertation demonstrates how the cultural bond of paternalism between aerospace workers and their company unraveled in the 1960s, and then ended in the early 1970s, because of forces within the company, the economy, and the American state. The word "triumph" in this study's title not only applies to Grummanites' triumphs with the Lunar Modules, but also their individual socioeconomic victories. The term "decline" refers to the early 1970s downsizing of more

Apollo 15 mare volcanism: constraints and problems

International Nuclear Information System (INIS)

Delano, J.W.

1985-01-01

The Apollo 15 landing site contains more volcanics in the form of crystalline basalts and pristine glasses, which form the framework for all models dealing with the mantle beneath that site. Major issues on the petrology of the mare source regions beneath that portion of Mare Imbrium are summarized

Remembering the Giants: Apollo Rocket Propulsion Development

Science.gov (United States)

Fisher, Steven C. (Editor); Rahman, Shamim A. (Editor)

2009-01-01

Topics discussed include: Rocketdyne - F-1 Saturn V First Stage Engine; Rocketdyne - J-2 Saturn V 2nd & 3rd Stage Engine; Rocketdyne - SE-7 & SE-8 Engines; Aerojet - AJ10-137 Apollo Service Module Engine; Aerojet - Attitude Control Engines; TRW - Lunar Descent Engine; and Rocketdyne - Lunar Ascent Engine.

Propagating annotations of molecular networks using in silico fragmentation.

Science.gov (United States)

da Silva, Ricardo R; Wang, Mingxun; Nothias, Louis-Félix; van der Hooft, Justin J J; Caraballo-Rodríguez, Andrés Mauricio; Fox, Evan; Balunas, Marcy J; Klassen, Jonathan L; Lopes, Norberto Peporine; Dorrestein, Pieter C

2018-04-18

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.

Gene calling and bacterial genome annotation with BG7.

Science.gov (United States)

Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Kovach, Evdokim; Alekhin, Alexey; Pareja, Eduardo

2015-01-01

New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but a refined annotation of these genomes is crucial for obtaining scientific findings and new knowledge. Thus, bacterial genome annotation has emerged as a key point to investigate in bacteria. Any efficient tool designed specifically to annotate bacterial genomes sequenced with massively parallel technologies has to consider the specific features of bacterial genomes (absence of introns and scarcity of nonprotein-coding sequence) and of next-generation sequencing (NGS) technologies (presence of errors and not perfectly assembled genomes). These features make it convenient to focus on coding regions and, hence, on protein sequences that are the elements directly related with biological functions. In this chapter we describe how to annotate bacterial genomes with BG7, an open-source tool based on a protein-centered gene calling/annotation paradigm. BG7 is specifically designed for the annotation of bacterial genomes sequenced with NGS. This tool is sequence error tolerant maintaining their capabilities for the annotation of highly fragmented genomes or for annotating mixed sequences coming from several genomes (as those obtained through metagenomics samples). BG7 has been designed with scalability as a requirement, with a computing infrastructure completely based on cloud computing (Amazon Web Services).

Annotated bibliography of cultural resources literature for the Nevada Nuclear Waste Storage Investigations

International Nuclear Information System (INIS)

1983-11-01

This annotated bibliography of the cultural resources literature pertinent for the Nevada Nuclear Waste Storage Investigations was assembled in order to (1) identify and evaluate the prehistoric and historic properties previously recorded in the Nevada Nuclear Waste Storage Investigations Project Area of southern Nye County, Nevada, (2) identify and develop research problems that have been and/or could be addressed by the cultural resources of this area, (3) isolate factors that might be important in the selection of a potential locality for a high level nuclear waste repository in the project area, and (4) critically evaluate the adequacy and current status of cultural resources knowledge in the project area. 195 references

A model for calculating expected performance of the Apollo unified S-band (USB) communication system

Science.gov (United States)

Schroeder, N. W.

1971-01-01

A model for calculating the expected performance of the Apollo unified S-band (USB) communication system is presented. The general organization of the Apollo USB is described. The mathematical model is reviewed and the computer program for implementation of the calculations is included.

APOLLO-2: An advanced transport code for LWRs

International Nuclear Information System (INIS)

Mathonniere, G.

1995-01-01

APOLLO-2 is a fully modular code in which each module corresponds to a specific task: access to the cross-sections libraries, creation of isotopes medium or mixtures, geometry definition, self-shielding calculations, computation of multigroup collision probabilities, flux solver, depletion calculations, transport-transport or transport-diffusion equivalence process, SN calculations, etc... Modules communicate exclusively by ''objects'' containing structured data, these objects are identified and handled by user's given names. Among the major improvements offered by APOLLO-2 the modelization of the self-shielding: it is possible now to deal with a great precision, checked versus Montecarlo calculations, a fuel rod divided into several concentric rings. So the total production of Plutonium is quite better estimated than before and its radial distribution may be predicted also with a good accuracy. Thanks to the versatility of the code some reference calculations and routine ones may be compared easily because only one parameter is changed; for example the self-shielding approximations are modified, the libraries or the flux solver being exactly the same. Other interesting features have been introduced in APOLLO-2: the new isotopes JEF.2 are available in 99 and 172 energy groups libraries, the surface leakage model improves the calculation of the control rod efficiency, the flux-current method allows faster calculations, the possibility of an automatic convergence checking during the depletion calculations coupled with fully automatic corrections, heterogeneous diffusion coefficients used for voiding analysis. 17 refs, 1 tab

Interoperable Multimedia Annotation and Retrieval for the Tourism Sector

NARCIS (Netherlands)

Chatzitoulousis, Antonios; Efraimidis, Pavlos S.; Athanasiadis, I.N.

2015-01-01

The Atlas Metadata System (AMS) employs semantic web annotation techniques in order to create an interoperable information annotation and retrieval platform for the tourism sector. AMS adopts state-of-the-art metadata vocabularies, annotation techniques and semantic web technologies.

High performance 3D neutron transport on peta scale and hybrid architectures within APOLLO3 code

International Nuclear Information System (INIS)

Jamelot, E.; Dubois, J.; Lautard, J-J.; Calvin, C.; Baudron, A-M.

2011-01-01

APOLLO3 code is a common project of CEA, AREVA and EDF for the development of a new generation system for core physics analysis. We present here the parallelization of two deterministic transport solvers of APOLLO3: MINOS, a simplified 3D transport solver on structured Cartesian and hexagonal grids, and MINARET, a transport solver based on triangular meshes on 2D and prismatic ones in 3D. We used two different techniques to accelerate MINOS: a domain decomposition method, combined with an accelerated algorithm using GPU. The domain decomposition is based on the Schwarz iterative algorithm, with Robin boundary conditions to exchange information. The Robin parameters influence the convergence and we detail how we optimized the choice of these parameters. MINARET parallelization is based on angular directions calculation using explicit message passing. Fine grain parallelization is also available for each angular direction using shared memory multithreaded acceleration. Many performance results are presented on massively parallel architectures using more than 103 cores and on hybrid architectures using some tens of GPUs. This work contributes to the HPC development in reactor physics at the CEA Nuclear Energy Division. (author)

Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae

Directory of Open Access Journals (Sweden)

Deng Jixin

2009-02-01

Full Text Available Abstract Background Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. Methods A similarity-based (i.e., computational GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. Results In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO. In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57% being annotated with 1,957 distinct and specific GO terms. Unannotated proteins

Image processing and data reduction of Apollo low light level photographs

Science.gov (United States)

Alvord, G. C.

1975-01-01

The removal of the lens induced vignetting from a selected sample of the Apollo low light level photographs is discussed. The methods used were developed earlier. A study of the effect of noise on vignetting removal and the comparability of the Apollo 35mm Nikon lens vignetting was also undertaken. The vignetting removal was successful to about 10% photometry, and noise has a severe effect on the useful photometric output data. Separate vignetting functions must be used for different flights since the vignetting function varies from camera to camera in size and shape.

Apollo 16 time and motion study

Science.gov (United States)

Kubis, J. F.; Elrod, J. T.; Rusnak, R.; Barnes, J. E.; Saxon, S. C.

1972-01-01

A time and motion study is presented of astronaut lunar surface activity on Apollo 16 which consists of five distinct analyses: an evaluation of lunar mobility, a comparison of task performance in 1-g training and lunar EVA, a study of metabolic costs and adaptation, a discussion of falls, and retrieval of fallen objects. Two basic mobility patterns, the hop or canter and the traditional walking gait, were consistently utilized in longer traverses. The metabolic rates associated with these two mobility types, each used by a different astronaut, were relatively equivalent. The time to perform tasks on the lunar surface was significantly longer (on the order of 70%) than the time to perform the same tasks during the last 1-g training session. These results corroborated the findings on Apollo 15 and were not significantly different from them. There was general improvement in lunar EVA performance upon repetition of tasks. Metabolic rate (BTU/hr.) and metabolic cost (BTU) decreased over successive EVAs. Specifically, the metabolic rate associated with riding the lunar roving vehicle (LRV) decreased by approximately 18% from EVA 1 to EVA 2 and by 15% from EVA 2 to EVA 3.

Hadley Rille, lava tubes and mare volcanism at the Apollo 15 site

International Nuclear Information System (INIS)

Greeley, R.; Spudis, P.D.

1985-01-01

Hadley Rille appears to be a collapsed lava tube/channel, whose formation history may be more intimately related to the mare units sampled at 15 than was previously thought. More work is needed relating samples and observations from Apollo 15 to the rille and its geologic evolution. As the only sinuous rille visited during the Apollo missions, Hadley Rille represents a data source that is directly applicable to the deciphering of processes involved in lunar mare volcanism

NoGOA: predicting noisy GO annotations using evidences and sparse representation.

Science.gov (United States)

Yu, Guoxian; Lu, Chang; Wang, Jun

2017-07-21

Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation, only a small portion of annotations are manually checked by curators, and the others are electronically inferred. Although quality control techniques have been applied to ensure the quality of annotations, the community consistently report that there are still considerable noisy (or incorrect) annotations. Given the wide application of annotations, however, how to identify noisy annotations is an important but yet seldom studied open problem. We introduce a novel approach called NoGOA to predict noisy annotations. NoGOA applies sparse representation on the gene-term association matrix to reduce the impact of noisy annotations, and takes advantage of sparse representation coefficients to measure the semantic similarity between genes. Secondly, it preliminarily predicts noisy annotations of a gene based on aggregated votes from semantic neighborhood genes of that gene. Next, NoGOA estimates the ratio of noisy annotations for each evidence code based on direct annotations in GOA files archived on different periods, and then weights entries of the association matrix via estimated ratios and propagates weights to ancestors of direct annotations using GO hierarchy. Finally, it integrates evidence-weighted association matrix and aggregated votes to predict noisy annotations. Experiments on archived GOA files of six model species (H. sapiens, A. thaliana, S. cerevisiae, G. gallus, B. Taurus and M. musculus) demonstrate that NoGOA achieves significantly better results than other related methods and removing noisy annotations improves the performance of gene function prediction. The comparative study justifies the effectiveness of integrating evidence codes with sparse representation for predicting noisy GO annotations. Codes and datasets are available at http://mlda.swu.edu.cn/codes.php?name=NoGOA .

Plann: A command-line application for annotating plastome sequences.

Science.gov (United States)

Huang, Daisie I; Cronk, Quentin C B

2015-08-01

Plann automates the process of annotating a plastome sequence in GenBank format for either downstream processing or for GenBank submission by annotating a new plastome based on a similar, well-annotated plastome. Plann is a Perl script to be executed on the command line. Plann compares a new plastome sequence to the features annotated in a reference plastome and then shifts the intervals of any matching features to the locations in the new plastome. Plann's output can be used in the National Center for Biotechnology Information's tbl2asn to create a Sequin file for GenBank submission. Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastome. Because it executes from the command line, it is ready to use in other software pipelines and can be easily rerun as a draft plastome is improved.

Restoration of APOLLO Data by the NSSDC and PDS Lunar Data Node

Science.gov (United States)

Williams, David R.; Hills, H. Kent; Guinness, Edward A.; Taylor, Patrick T.; McBride, Marie J.

2012-01-01

The Apollo Lunar Surface Experiment Packages (ALSEPs), suites of instruments deployed by the Apollo 12. 14, 15, 16 and 17 astronauts on the lunar surface, still represent the only in-situ measurements of the Moon's environment taken over long time periods, Much of these data are housed at the National Space Science Data Center (NSSDC) at Goddard Space Flight Center but are in forms that are not readily usable, such as microfilm, hardcopy, and magnetic tapes with older, obsolete formats. The Lunar Data Node (LDN) has been formed under the auspices of the Planetary Data System (PDS) Geosciences Node to put relevant, scientifically important Apollo data into accessible digital form for use by researchers and mission planners. The LDN has prioritized the restoration of these data based on their scientific and engineering value and the level of effort required. We will report on progress made and plans for future data restorations.

Semantator: annotating clinical narratives with semantic web ontologies.

Science.gov (United States)

Song, Dezhao; Chute, Christopher G; Tao, Cui

2012-01-01

To facilitate clinical research, clinical data needs to be stored in a machine processable and understandable way. Manual annotating clinical data is time consuming. Automatic approaches (e.g., Natural Language Processing systems) have been adopted to convert such data into structured formats; however, the quality of such automatically extracted data may not always be satisfying. In this paper, we propose Semantator, a semi-automatic tool for document annotation with Semantic Web ontologies. With a loaded free text document and an ontology, Semantator supports the creation/deletion of ontology instances for any document fragment, linking/disconnecting instances with the properties in the ontology, and also enables automatic annotation by connecting to the NCBO annotator and cTAKES. By representing annotations in Semantic Web standards, Semantator supports reasoning based upon the underlying semantics of the owl:disjointWith and owl:equivalentClass predicates. We present discussions based on user experiences of using Semantator.

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.

Science.gov (United States)

Letunic, Ivica; Bork, Peer

2011-07-01

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.

Ontology modularization to improve semantic medical image annotation.

Science.gov (United States)

Wennerberg, Pinar; Schulz, Klaus; Buitelaar, Paul

2011-02-01

Searching for medical images and patient reports is a significant challenge in a clinical setting. The contents of such documents are often not described in sufficient detail thus making it difficult to utilize the inherent wealth of information contained within them. Semantic image annotation addresses this problem by describing the contents of images and reports using medical ontologies. Medical images and patient reports are then linked to each other through common annotations. Subsequently, search algorithms can more effectively find related sets of documents on the basis of these semantic descriptions. A prerequisite to realizing such a semantic search engine is that the data contained within should have been previously annotated with concepts from medical ontologies. One major challenge in this regard is the size and complexity of medical ontologies as annotation sources. Manual annotation is particularly time consuming labor intensive in a clinical environment. In this article we propose an approach to reducing the size of clinical ontologies for more efficient manual image and text annotation. More precisely, our goal is to identify smaller fragments of a large anatomy ontology that are relevant for annotating medical images from patients suffering from lymphoma. Our work is in the area of ontology modularization, which is a recent and active field of research. We describe our approach, methods and data set in detail and we discuss our results. Copyright © 2010 Elsevier Inc. All rights reserved.

Code-Name: Spider, Flight of Apollo 9.

Science.gov (United States)

National Aeronautics and Space Administration, Washington, DC.

Apollo 9, an earth orbiting mission during which the Lunar Module was first tested in space flight in preparation for the eventual moon landing missions, is the subject of this pamphlet. Many color photographs and diagrams of the Lunar Module and flight activities are included with a brief description of the mission. (PR)

[Prescription annotations in Welfare Pharmacy].

Science.gov (United States)

Han, Yi

2018-03-01

Welfare Pharmacy contains medical formulas documented by the government and official prescriptions used by the official pharmacy in the pharmaceutical process. In the last years of Southern Song Dynasty, anonyms gave a lot of prescription annotations, made textual researches for the name, source, composition and origin of the prescriptions, and supplemented important historical data of medical cases and researched historical facts. The annotations of Welfare Pharmacy gathered the essence of medical theory, and can be used as precious materials to correctly understand the syndrome differentiation, compatibility regularity and clinical application of prescriptions. This article deeply investigated the style and form of the prescription annotations in Welfare Pharmacy, the name of prescriptions and the evolution of terminology, the major functions of the prescriptions, processing methods, instructions for taking medicine and taboos of prescriptions, the medical cases and clinical efficacy of prescriptions, the backgrounds, sources, composition and cultural meanings of prescriptions, proposed that the prescription annotations played an active role in the textual dissemination, patent medicine production and clinical diagnosis and treatment of Welfare Pharmacy. This not only helps understand the changes in the names and terms of traditional Chinese medicines in Welfare Pharmacy, but also provides the basis for understanding the knowledge sources, compatibility regularity, important drug innovations and clinical medications of prescriptions in Welfare Pharmacy. Copyright© by the Chinese Pharmaceutical Association.

A framework for annotating human genome in disease context.

Science.gov (United States)

Xu, Wei; Wang, Huisong; Cheng, Wenqing; Fu, Dong; Xia, Tian; Kibbe, Warren A; Lin, Simon M

2012-01-01

Identification of gene-disease association is crucial to understanding disease mechanism. A rapid increase in biomedical literatures, led by advances of genome-scale technologies, poses challenge for manually-curated-based annotation databases to characterize gene-disease associations effectively and timely. We propose an automatic method-The Disease Ontology Annotation Framework (DOAF) to provide a comprehensive annotation of the human genome using the computable Disease Ontology (DO), the NCBO Annotator service and NCBI Gene Reference Into Function (GeneRIF). DOAF can keep the resulting knowledgebase current by periodically executing automatic pipeline to re-annotate the human genome using the latest DO and GeneRIF releases at any frequency such as daily or monthly. Further, DOAF provides a computable and programmable environment which enables large-scale and integrative analysis by working with external analytic software or online service platforms. A user-friendly web interface (doa.nubic.northwestern.edu) is implemented to allow users to efficiently query, download, and view disease annotations and the underlying evidences.

wANNOVAR: annotating genetic variants for personal genomes via the web.

Science.gov (United States)

Chang, Xiao; Wang, Kai

2012-07-01

High-throughput DNA sequencing platforms have become widely available. As a result, personal genomes are increasingly being sequenced in research and clinical settings. However, the resulting massive amounts of variants data pose significant challenges to the average biologists and clinicians without bioinformatics skills. We developed a web server called wANNOVAR to address the critical needs for functional annotation of genetic variants from personal genomes. The server provides simple and intuitive interface to help users determine the functional significance of variants. These include annotating single nucleotide variants and insertions/deletions for their effects on genes, reporting their conservation levels (such as PhyloP and GERP++ scores), calculating their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieving allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 5400 exomes), and implementing a 'variants reduction' protocol to identify a subset of potentially deleterious variants/genes. We illustrated how wANNOVAR can help draw biological insights from sequencing data, by analysing genetic variants generated on two Mendelian diseases. We conclude that wANNOVAR will help biologists and clinicians take advantage of the personal genome information to expedite scientific discoveries. The wANNOVAR server is available at http://wannovar.usc.edu, and will be continuously updated to reflect the latest annotation information.

Countdown to a Moon launch preparing Apollo for its historic journey

CERN Document Server

Ward, Jonathan H

2015-01-01

Thousands of workers labored at Kennedy Space Center around the clock, seven days a week, for half a year to prepare a mission for the liftoff of Apollo 11. This is the story of what went on during those hectic six months. Countdown to a Moon Launch provides an in-depth look at the carefully choreographed workflow for an Apollo mission at KSC. Using the Apollo 11 mission as an example, readers will learn what went on day by day to transform partially completed stages and crates of parts into a ready-to-fly Saturn V. Firsthand accounts of launch pad accidents, near misses, suspected sabotage, and last-minute changes to hardware are told by more than 70 NASA employees and its contractors. A companion to Rocket Ranch, it includes many diagrams and photographs, some never before published, to illustrate all aspects of the process. NASA’s groundbreaking use of computers for testing and advanced management techniques are also covered in detail. This book will demystify the question of how NASA could build and lau...

Apollo 11 Astronaut Armstrong Arrives at the Flight Crew Training Building

Science.gov (United States)

1969-01-01

In this photograph, Apollo 11 astronaut Neil Armstrong walks to the flight crew training building at the NASA Kennedy Space Center (KSC) in Florida, one week before the nation's first lunar landing mission. The Apollo 11 mission launched from KSC via the Marshall Space Flight Center (MSFC) developed Saturn V launch vehicle on July 16, 1969 and safely returned to Earth on July 24, 1969. Aboard the space craft were astronauts Neil A. Armstrong, commander; Michael Collins, Command Module (CM) pilot; and Edwin E. (Buzz) Aldrin Jr., Lunar Module (LM) pilot. The CM, 'Columbia', piloted by Collins, remained in a parking orbit around the Moon while the LM, 'Eagle'', carrying astronauts Armstrong and Aldrin, landed on the Moon. On July 20, 1969, Armstrong was the first human to ever stand on the lunar surface, followed by Aldrin. During 2½ hours of surface exploration, the crew collected 47 pounds of lunar surface material for analysis back on Earth. With the success of Apollo 11, the national objective to land men on the Moon and return them safely to Earth had been accomplished.

Apollo 11 crew on ship during water egress training in Gulf of Mexico

Science.gov (United States)

1969-01-01

The prime crew of the Apollo 11 lunar landing mission relaxes on the deck of the NASA Motor Vessel Retriever prior to participating in water egress training in the Gulf of Mexico. Left to right, are Astronauts Edwin A. Aldrin Jr., lunar module pilot; Neil A. Armstrong, commander; and Michael Collins, command module pilot. In the background is Apollo Boilerplate 1102 which was used in the training exercise.

Supporting Keyword Search for Image Retrieval with Integration of Probabilistic Annotation

Directory of Open Access Journals (Sweden)

Tie Hua Zhou

2015-05-01

Full Text Available The ever-increasing quantities of digital photo resources are annotated with enriching vocabularies to form semantic annotations. Photo-sharing social networks have boosted the need for efficient and intuitive querying to respond to user requirements in large-scale image collections. In order to help users formulate efficient and effective image retrieval, we present a novel integration of a probabilistic model based on keyword query architecture that models the probability distribution of image annotations: allowing users to obtain satisfactory results from image retrieval via the integration of multiple annotations. We focus on the annotation integration step in order to specify the meaning of each image annotation, thus leading to the most representative annotations of the intent of a keyword search. For this demonstration, we show how a probabilistic model has been integrated to semantic annotations to allow users to intuitively define explicit and precise keyword queries in order to retrieve satisfactory image results distributed in heterogeneous large data sources. Our experiments on SBU (collected by Stony Brook University database show that (i our integrated annotation contains higher quality representatives and semantic matches; and (ii the results indicating annotation integration can indeed improve image search result quality.

Odysseus and the Cult of Apollo at Delos

Directory of Open Access Journals (Sweden)

Jim Marks

2016-03-01

Full Text Available This paper explores literary representations of the cult of Apollo on Delos. This island is, to be sure, mentioned only occasionally in early Greek poetry, but details specific to the cult do appear. Thus, for example, Odysseus describes a palm tree he saw at an altar of Apollo on Delos (Od. 6.162-3, and a third-century inscription from the island mentions just such a feature. References to a palm, altar, and temple at Delos in later classical authors, including Callimachus, Pliny, Cicero, and Plutarch, demonstrate that the Archaic period traditions represented by the Homeric passages continued to shape how successive generations of visitors understood Delos. The material record makes clear that the Greek epic tradition documents a time when Delos was already a well attended sanctuary, and that later constructions at the site attempted to remain consistent with the details preserved in the epics.

Lesions in the wingless gene of the Apollo butterfly (Parnassius apollo, Lepidoptera: Papilionidae) individuals with deformed or reduced wings, coming from the isolated population in Pieniny (Poland).

Science.gov (United States)

Łukasiewicz, Kinga; Sanak, Marek; Węgrzyn, Grzegorz

2016-02-01

Parnassius apollo (Lepidoptera: Papilionidae) is a butterfly species which was common in Europe in 19th century, but now it is considered as near threatened. Various programs devoted to protect and save P. apollo have been established, between others the one in Pieniny National Park (Poland). An isolated population of this butterfly has been restored there from a small group of 20-30 individuals in early 1990s. However, deformations or reductions of wings occur in this population in a relatively large number of insects, and the cause of this phenomenon is not known. In this report, the occurrence of lesions in the wingless (wg) gene is demonstrated in most of tested butterflies with deformed or reduced wings, but not in normal insects. Although the analyses indicated that wg lesion(s) cannot be the sole cause of the deformed or reduced wings in the population of P. apollo from Pieniny, the discovery that this genetic defect occurs in most of malformed individuals, can be considered as an important step in understanding this phenomenon. Copyright © 2015 Elsevier B.V. All rights reserved.

Annotated bibliography of selected reports relating to the isolation of nuclear waste in crystalline rock

International Nuclear Information System (INIS)

1988-06-01

BMI/OCRD-29 is an annotated bibliography of published reports that have been produced for the US Department of Energy Crystalline Repository Project Office or the Swedish-American Cooperative Program on Radioactive Waste Storage in Mined Caverns. This document consists of a main report listing of citations and abstracts and a topical index

Quick Pad Tagger : An Efficient Graphical User Interface for Building Annotated Corpora with Multiple Annotation Layers

OpenAIRE

Marc Schreiber; Kai Barkschat; Bodo Kraft; Albert Zundorf

2015-01-01

More and more domain specific applications in the internet make use of Natural Language Processing (NLP) tools (e. g. Information Extraction systems). The output quality of these applications relies on the output quality of the used NLP tools. Often, the quality can be increased by annotating a domain specific corpus. However, annotating a corpus is a time consuming and exhaustive task. To reduce the annota tion time we present...

Benchmark calculation of APOLLO-2 and SLAROM-UF in a fast reactor lattice

International Nuclear Information System (INIS)

Hazama, T.

2009-07-01

A lattice cell benchmark calculation is carried out for APOLLO2 and SLAROM-UF on the infinite lattice of a simple pin cell featuring a fast reactor. The accuracy in k-infinity and reaction rates is investigated in their reference and standard level calculations. In the 1. reference level calculation, APOLLO2 and SLAROM-UF agree with the reference value of k-infinity obtained by a continuous energy Monte Carlo calculation within 50 pcm. However, larger errors are observed in a particular reaction rate and energy range. The major problem common to both codes is in the cross section library of 239 Pu in the unresolved energy range. In the 2. reference level calculation, which is based on the ECCO 1968 group structure, both results of k-infinity agree with the reference value within 100 pcm. The resonance overlap effect is observed by several percents in cross sections of heavy nuclides. In the standard level calculation based on the APOLLO2 library creation methodology, a discrepancy appears by more than 300 pcm. A restriction is revealed in APOLLO2. Its standard cross section library does not have a sufficiently small background cross section to evaluate the self shielding effect on 56 Fe cross sections. The restriction can be removed by introducing the mixture self-shielding treatment recently introduced to APOLLO2. SLAROM-UF original standard level calculation based on the JFS-3 library creation methodology is the best among the standard level calculations. Improvement from the SLAROM-UF standard level calculation is achieved mainly by use of a proper weight function for light or intermediate nuclides. (author)

Supplementary Material for: BEACON: automated tool for Bacterial GEnome Annotation ComparisON

KAUST Repository

Kalkatawi, Manal M.; Alam, Intikhab; Bajic, Vladimir B.

2015-01-01

Abstract Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACONâ s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

Stratigraphy of the Descartes region /Apollo 16/ - Implications for the origin of samples

Science.gov (United States)

Head, J. W.

1974-01-01

Analysis of terrain in the Apollo 16 Descartes landing region shows a series of features that form a stratigraphic sequence which dominates the history and petrogenesis at the site. An ancient 150-km diam crater centered on the Apollo 16 site is one of the earliest recognizable major structures. Nectaris ejecta was concentrated in a regional low at the base of the back slope of the Nectaris basin to form the Descartes Mountains. Subsequently, a 60-km diam crater formed in the Descartes Mountains centered about 25 km to the west of the site. This crater dominates the geology and petrogenetic history of the site. Stone and Smoky Mountains represent the degraded terraced crater walls, and the dark matrix breccias and metaclastic rocks derived from North and South Ray craters represent floor fallback breccias from this cratering event. The interpretation is developed that the stratigraphy of the Cayley and Descartes, and thus the historical record of the Apollo 16 region, documents the complex interaction of deposits and morphology of local and regional impact cratering events. Large local 60- to 150-km diam craters have had a dramatic and previously unrecognized effect on the history and petrology of the Apollo 16 site.

Chemical differences between small subsamples of Apollo 15 olivine-normative basalts

Science.gov (United States)

Shervais, J. W.; Vetter, S. K.; Lindstrom, M. M.

1990-01-01

Results are presented on the chemical and petrological characterization of nine samples of an Apollo 15 mare basalt suite. The results show that all nine samples are low-silica olivine normative basalts (ONBs) similar to those described earlier for low-silica ONBs from Apollo 15 site. The samples were found to vary in texture and grain size, from fine-grained intergranular or subophitic basalts to coarse-grained granular 'microgabbros'. Several displayed macroscopic heterogeneity. Variation diagrams show that the overall trend of the data is consistent with the fractionation of olivine (plus minor Cr-spinel) from a high-MgO parent magma.

Harnessing Collaborative Annotations on Online Formative Assessments

Science.gov (United States)

Lin, Jian-Wei; Lai, Yuan-Cheng

2013-01-01

This paper harnesses collaborative annotations by students as learning feedback on online formative assessments to improve the learning achievements of students. Through the developed Web platform, students can conduct formative assessments, collaboratively annotate, and review historical records in a convenient way, while teachers can generate…

Crowdsourcing and annotating NER for Twitter #drift

DEFF Research Database (Denmark)

Fromreide, Hege; Hovy, Dirk; Søgaard, Anders

2014-01-01

We present two new NER datasets for Twitter; a manually annotated set of 1,467 tweets (kappa=0.942) and a set of 2,975 expert-corrected, crowdsourced NER annotated tweets from the dataset described in Finin et al. (2010). In our experiments with these datasets, we observe two important points: (a......) language drift on Twitter is significant, and while off-the-shelf systems have been reported to perform well on in-sample data, they often perform poorly on new samples of tweets, (b) state-of-the-art performance across various datasets can beobtained from crowdsourced annotations, making it more feasible...

SNAD: sequence name annotation-based designer

Directory of Open Access Journals (Sweden)

Gorbalenya Alexander E

2009-08-01

Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

An open annotation ontology for science on web 3.0.

Science.gov (United States)

Ciccarese, Paolo; Ocana, Marco; Garcia Castro, Leyla Jael; Das, Sudeshna; Clark, Tim

2011-05-17

There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables "stand-off" or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO's Google Code page: http://code.google.com/p/annotation-ontology/ . The Annotation Ontology meets critical requirements for

ACID: annotation of cassette and integron data

Directory of Open Access Journals (Sweden)

Stokes Harold W

2009-04-01

Full Text Available Abstract Background Although integrons and their associated gene cassettes are present in ~10% of bacteria and can represent up to 3% of the genome in which they are found, very few have been properly identified and annotated in public databases. These genetic elements have been overlooked in comparison to other vectors that facilitate lateral gene transfer between microorganisms. Description By automating the identification of integron integrase genes and of the non-coding cassette-associated attC recombination sites, we were able to assemble a database containing all publicly available sequence information regarding these genetic elements. Specialists manually curated the database and this information was used to improve the automated detection and annotation of integrons and their encoded gene cassettes. ACID (annotation of cassette and integron data can be searched using a range of queries and the data can be downloaded in a number of formats. Users can readily annotate their own data and integrate it into ACID using the tools provided. Conclusion ACID is a community resource providing easy access to annotations of integrons and making tools available to detect them in novel sequence data. ACID also hosts a forum to prompt integron-related discussion, which can hopefully lead to a more universal definition of this genetic element.

First massively parallel algorithm to be implemented in Apollo-II code

International Nuclear Information System (INIS)

Stankovski, Z.

1994-01-01

The collision probability (CP) method in neutron transport, as applied to arbitrary 2D XY geometries, like the TDT module in APOLLO-II, is very time consuming. Consequently RZ or 3D extensions became prohibitive. Fortunately, this method is very suitable for parallelization. Massively parallel computer architectures, especially MIMD machines, bring a new breath to this method. In this paper we present a CM5 implementation of the CP method. Parallelization is applied to the energy groups, using the CMMD message passing library. In our case we use 32 processors for the standard 99-group APOLLIB-II library. The real advantage of this algorithm will appear in the calculation of the future fine multigroup library (about 8000 groups) of the SAPHYR project with a massively parallel computer (to the order of hundreds of processors). (author). 3 tabs., 4 figs., 4 refs

First massively parallel algorithm to be implemented in APOLLO-II code

International Nuclear Information System (INIS)

Stankovski, Z.

1994-01-01

The collision probability method in neutron transport, as applied to arbitrary 2-dimensional geometries, like the two dimensional transport module in APOLLO-II is very time consuming. Consequently 3-dimensional extension became prohibitive. Fortunately, this method is very suitable for parallelization. Massively parallel computer architectures, especially MIMD machines, bring a new breath to this method. In this paper we present a CM5 implementation of the collision probability method. Parallelization is applied to the energy groups, using the CMMD massage passing library. In our case we used 32 processors for the standard 99-group APOLLIB-II library. The real advantage of this algorithm will appear in the calculation of the future multigroup library (about 8000 groups) of the SAPHYR project with a massively parallel computer (to the order of hundreds of processors). (author). 4 refs., 4 figs., 3 tabs

Use of Annotations for Component and Framework Interoperability

Science.gov (United States)

David, O.; Lloyd, W.; Carlson, J.; Leavesley, G. H.; Geter, F.

2009-12-01

The popular programming languages Java and C# provide annotations, a form of meta-data construct. Software frameworks for web integration, web services, database access, and unit testing now take advantage of annotations to reduce the complexity of APIs and the quantity of integration code between the application and framework infrastructure. Adopting annotation features in frameworks has been observed to lead to cleaner and leaner application code. The USDA Object Modeling System (OMS) version 3.0 fully embraces the annotation approach and additionally defines a meta-data standard for components and models. In version 3.0 framework/model integration previously accomplished using API calls is now achieved using descriptive annotations. This enables the framework to provide additional functionality non-invasively such as implicit multithreading, and auto-documenting capabilities while achieving a significant reduction in the size of the model source code. Using a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework. Since models and modeling components are not directly bound to framework by the use of specific APIs and/or data types they can more easily be reused both within the framework as well as outside of it. To study the effectiveness of an annotation based framework approach with other modeling frameworks, a framework-invasiveness study was conducted to evaluate the effects of framework design on model code quality. A monthly water balance model was implemented across several modeling frameworks and several software metrics were collected. The metrics selected were measures of non-invasive design methods for modeling frameworks from a software engineering perspective. It appears that the use of annotations positively impacts several software quality measures. In a next step, the PRMS model was implemented in OMS 3.0 and is currently being implemented for water supply forecasting in the

SoFIA: a data integration framework for annotating high-throughput datasets.

Science.gov (United States)

Childs, Liam Harold; Mamlouk, Soulafa; Brandt, Jörgen; Sers, Christine; Leser, Ulf

2016-09-01

Integrating heterogeneous datasets from several sources is a common bioinformatics task that often requires implementing a complex workflow intermixing database access, data filtering, format conversions, identifier mapping, among further diverse operations. Data integration is especially important when annotating next generation sequencing data, where a multitude of diverse tools and heterogeneous databases can be used to provide a large variety of annotation for genomic locations, such a single nucleotide variants or genes. Each tool and data source is potentially useful for a given project and often more than one are used in parallel for the same purpose. However, software that always produces all available data is difficult to maintain and quickly leads to an excess of data, creating an information overload rather than the desired goal-oriented and integrated result. We present SoFIA, a framework for workflow-driven data integration with a focus on genomic annotation. SoFIA conceptualizes workflow templates as comprehensive workflows that cover as many data integration operations as possible in a given domain. However, these templates are not intended to be executed as a whole; instead, when given an integration task consisting of a set of input data and a set of desired output data, SoFIA derives a minimal workflow that completes the task. These workflows are typically fast and create exactly the information a user wants without requiring them to do any implementation work. Using a comprehensive genome annotation template, we highlight the flexibility, extensibility and power of the framework using real-life case studies. https://github.com/childsish/sofia/releases/latest under the GNU General Public License liam.childs@hu-berlin.de Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Ensembl genome database project.

Science.gov (United States)

Hubbard, T; Barker, D; Birney, E; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Huminiecki, L; Kasprzyk, A; Lehvaslaiho, H; Lijnzaad, P; Melsopp, C; Mongin, E; Pettett, R; Pocock, M; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Clamp, M

2002-01-01

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

Creating Gaze Annotations in Head Mounted Displays

DEFF Research Database (Denmark)

Mardanbeigi, Diako; Qvarfordt, Pernilla

2015-01-01

To facilitate distributed communication in mobile settings, we developed GazeNote for creating and sharing gaze annotations in head mounted displays (HMDs). With gaze annotations it possible to point out objects of interest within an image and add a verbal description. To create an annota- tion...

Three astronauts inside Command Module Simulator during Apollo Simulation

Science.gov (United States)

1968-01-01

Three astronauts inside the Command Module Simulator in bldg 5 during an Apollo Simulation. Left to right are Astronauts Thomas P. Stafford, commander; John W. Young, command module pilot; and Eugene A. Cernan, lunar module pilot.

Ontological Annotation with WordNet

Energy Technology Data Exchange (ETDEWEB)

Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

2006-06-06

Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

Energy Technology Data Exchange (ETDEWEB)

Kuo, Alan; Grigoriev, Igor

2009-04-17

Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

Changes is genes coding for laccases 1 and 2 may contribute to deformation and reduction of wings in apollo butterfly (Parnassius apollo, Lepidoptera: Papilionidae) from the isolated population in Pieniny National Park (Poland).

Science.gov (United States)

Łukasiewicz, Kinga; Węgrzyn, Grzegorz

2016-01-01

An isolated population of apollo butterfly (Parnassius apollo, Lepidoptera: Papilionidae) occurs in Pieniny National Park (Poland). Deformations and reductions of wings in a relatively large number of individuals from this population is found, yet the reasons for these defects are unknown. During studies devoted to identify cause(s) of this phenomenon, we found that specific regions of genes coding of enzymes laccases 1 and 2 could not be amplified from DNA samples isolated from large fractions of malformed insects while expected PCR products were detected in almost all (with one exception) normal butterflies. Laccases (p-diphenol:dioxygen oxidoreductases) are oxidases containing several copper atoms. They catalyse single-electron oxidations of phenolic or other compounds with concomitant reduction of oxygen to water. In insects, their enzymatic activities were found previously in epidermis, midgut, Malpighian tubules, salivary glands, and reproductive tissues. Therefore, we suggest that defects in genes coding for laccases might contribute to deformation and reduction of wings in apollo butterflies, though it seems obvious that deficiency in these enzymes could not be the sole cause of these developmental improperties in P. apollo from Pieniny National Park.

On the Moon with Apollo 15, A Guidebook to Hadley Rille and the Apennine Mountains.

Science.gov (United States)

Simmons, Gene

The booklet, published before the Apollo 15 mission, gives a timeline for the mission; describes and illustrates the physiography of the landing site; and describes and illustrates each lunar surface scientific experiment. Separate timelines are included for all traverses (the traverses are the Moon walks and, for Apollo 15, the Moon rides in the…

Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services.

Science.gov (United States)

Wagner, Michael M; Levander, John D; Brown, Shawn; Hogan, William R; Millett, Nicholas; Hanna, Josh

2013-01-01

This paper describes the Apollo Web Services and Apollo-SV, its related ontology. The Apollo Web Services give an end-user application a single point of access to multiple epidemic simulators. An end user can specify an analytic problem-which we define as a configuration and a query of results-exactly once and submit it to multiple epidemic simulators. The end user represents the analytic problem using a standard syntax and vocabulary, not the native languages of the simulators. We have demonstrated the feasibility of this design by implementing a set of Apollo services that provide access to two epidemic simulators and two visualizer services.

Functional annotation of hierarchical modularity.

Directory of Open Access Journals (Sweden)

Kanchana Padmanabhan

Full Text Available In biological networks of molecular interactions in a cell, network motifs that are biologically relevant are also functionally coherent, or form functional modules. These functionally coherent modules combine in a hierarchical manner into larger, less cohesive subsystems, thus revealing one of the essential design principles of system-level cellular organization and function-hierarchical modularity. Arguably, hierarchical modularity has not been explicitly taken into consideration by most, if not all, functional annotation systems. As a result, the existing methods would often fail to assign a statistically significant functional coherence score to biologically relevant molecular machines. We developed a methodology for hierarchical functional annotation. Given the hierarchical taxonomy of functional concepts (e.g., Gene Ontology and the association of individual genes or proteins with these concepts (e.g., GO terms, our method will assign a Hierarchical Modularity Score (HMS to each node in the hierarchy of functional modules; the HMS score and its p-value measure functional coherence of each module in the hierarchy. While existing methods annotate each module with a set of "enriched" functional terms in a bag of genes, our complementary method provides the hierarchical functional annotation of the modules and their hierarchically organized components. A hierarchical organization of functional modules often comes as a bi-product of cluster analysis of gene expression data or protein interaction data. Otherwise, our method will automatically build such a hierarchy by directly incorporating the functional taxonomy information into the hierarchy search process and by allowing multi-functional genes to be part of more than one component in the hierarchy. In addition, its underlying HMS scoring metric ensures that functional specificity of the terms across different levels of the hierarchical taxonomy is properly treated. We have evaluated our

Fluid Annotations in a Open World

DEFF Research Database (Denmark)

Zellweger, Polle Trescott; Bouvin, Niels Olof; Jehøj, Henning

2001-01-01

Fluid Documents use animated typographical changes to provide a novel and appealing user experience for hypertext browsing and for viewing document annotations in context. This paper describes an effort to broaden the utility of Fluid Documents by using the open hypermedia Arakne Environment to l...... to layer fluid annotations and links on top of abitrary HTML pages on the World Wide Web. Changes to both Fluid Documents and Arakne are required....

Pratiques d'annotations à l'ère des médias numériques : étude de cas de l'architexte Diigo.

OpenAIRE

Kerneis , Jacques; Thiault , Florence

2014-01-01

International audience; The integration of technology in higher education raises questions about the potential of digital university teaching. In this article, we approach the influence of environments (hardware or platforms) on the practice of digital annotation. Our project is to analyze the types of use produced by the architext of an online management tool of bookmarks Diigo. We rely on two case studies to identify annotation practices. A first study relates to the practices which student...

Apollo Anniversary: Moon Landing "Inspired World"

Institute of Scientific and Technical Information of China (English)

John Roach; 李然

2004-01-01

@@ On July 20, 1969, at 10:56 p.m. ET, Apollo 11 astronaut Neil Armstrong stepped onto the surface of the moon and said, "That' s one small step for man,one giant leap for mankind." Thirty-five years later, Steven Dick, NASA's chief historian at the space agency's headquarters in Washington, D.C. , said that a thousand years from now, that step may be considered the crowning① achievement of the 20th century.

Apollo experience report: Earth landing system

Science.gov (United States)

West, R. B.

1973-01-01

A brief discussion of the development of the Apollo earth landing system and a functional description of the system are presented in this report. The more significant problems that were encountered during the program, the solutions, and, in general, the knowledge that was gained are discussed in detail. Two appendixes presenting a detailed description of the various system components and a summary of the development and the qualification test programs are included.

Annotations to quantum statistical mechanics

CERN Document Server

Kim, In-Gee

2018-01-01

This book is a rewritten and annotated version of Leo P. Kadanoff and Gordon Baym’s lectures that were presented in the book Quantum Statistical Mechanics: Green’s Function Methods in Equilibrium and Nonequilibrium Problems. The lectures were devoted to a discussion on the use of thermodynamic Green’s functions in describing the properties of many-particle systems. The functions provided a method for discussing finite-temperature problems with no more conceptual difficulty than ground-state problems, and the method was equally applicable to boson and fermion systems and equilibrium and nonequilibrium problems. The lectures also explained nonequilibrium statistical physics in a systematic way and contained essential concepts on statistical physics in terms of Green’s functions with sufficient and rigorous details. In-Gee Kim thoroughly studied the lectures during one of his research projects but found that the unspecialized method used to present them in the form of a book reduced their readability. He st...

Model and Interoperability using Meta Data Annotations

Science.gov (United States)

David, O.

2011-12-01

Software frameworks and architectures are in need for meta data to efficiently support model integration. Modelers have to know the context of a model, often stepping into modeling semantics and auxiliary information usually not provided in a concise structure and universal format, consumable by a range of (modeling) tools. XML often seems the obvious solution for capturing meta data, but its wide adoption to facilitate model interoperability is limited by XML schema fragmentation, complexity, and verbosity outside of a data-automation process. Ontologies seem to overcome those shortcomings, however the practical significance of their use remains to be demonstrated. OMS version 3 took a different approach for meta data representation. The fundamental building block of a modular model in OMS is a software component representing a single physical process, calibration method, or data access approach. Here, programing language features known as Annotations or Attributes were adopted. Within other (non-modeling) frameworks it has been observed that annotations lead to cleaner and leaner application code. Framework-supported model integration, traditionally accomplished using Application Programming Interfaces (API) calls is now achieved using descriptive code annotations. Fully annotated components for various hydrological and Ag-system models now provide information directly for (i) model assembly and building, (ii) data flow analysis for implicit multi-threading or visualization, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, calibration, and optimization, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Such a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework but a strong reference to its originating code. Since models and

Black English Annotations for Elementary Reading Programs.

Science.gov (United States)

Prasad, Sandre

This report describes a program that uses annotations in the teacher's editions of existing reading programs to indicate the characteristics of black English that may interfere with the reading process of black children. The first part of the report provides a rationale for the annotation approach, explaining that the discrepancy between written…

Bibliography. Computer-Oriented Projects, 1987.

Science.gov (United States)

Smith, Richard L., Comp.

1988-01-01

Provides an annotated list of references on computer-oriented projects. Includes information on computers; hands-on versus simulations; games; instruction; students' attitudes and learning styles; artificial intelligence; tutoring; and application of spreadsheets. (RT)

Special Issue: Annotated Bibliography for Volumes XIX-XXXII.

Science.gov (United States)

Pullin, Richard A.

1998-01-01

This annotated bibliography lists 310 articles from the "Journal of Cooperative Education" from Volumes XIX-XXXII, 1983-1997. Annotations are presented in the order they appear in the journal; author and subject indexes are provided. (JOW)

Apollo experience report: Guidance and control systems. Engineering simulation program

Science.gov (United States)

Gilbert, D. W.

1973-01-01

The Apollo Program experience from early 1962 to July 1969 with respect to the engineering-simulation support and the problems encountered is summarized in this report. Engineering simulation in support of the Apollo guidance and control system is discussed in terms of design analysis and verification, certification of hardware in closed-loop operation, verification of hardware/software compatibility, and verification of both software and procedures for each mission. The magnitude, time, and cost of the engineering simulations are described with respect to hardware availability, NASA and contractor facilities (for verification of the command module, the lunar module, and the primary guidance, navigation, and control system), and scheduling and planning considerations. Recommendations are made regarding implementation of similar, large-scale simulations for future programs.

MetaStorm: A Public Resource for Customizable Metagenomics Annotation.

Directory of Open Access Journals (Sweden)

Gustavo Arango-Argoty

Full Text Available Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/, which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution.

MetaStorm: A Public Resource for Customizable Metagenomics Annotation.

Science.gov (United States)

Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

2016-01-01

Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution.

MetaStorm: A Public Resource for Customizable Metagenomics Annotation

Science.gov (United States)

Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S.; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

2016-01-01

Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution. PMID:27632579

Improving Microbial Genome Annotations in an Integrated Database Context

Science.gov (United States)

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Anderson, Iain; Mavromatis, Konstantinos; Kyrpides, Nikos C.; Ivanova, Natalia N.

2013-01-01

Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/. PMID:23424620

Improving microbial genome annotations in an integrated database context.

Directory of Open Access Journals (Sweden)

I-Min A Chen

Full Text Available Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

Science.gov (United States)

Profiti, Giuseppe; Martelli, Pier Luigi; Casadio, Rita

2017-07-03

BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

BAT: An open-source, web-based audio events annotation tool

OpenAIRE

Blai Meléndez-Catalan, Emilio Molina, Emilia Gómez

2017-01-01

In this paper we present BAT (BMAT Annotation Tool), an open-source, web-based tool for the manual annotation of events in audio recordings developed at BMAT (Barcelona Music and Audio Technologies). The main feature of the tool is that it provides an easy way to annotate the salience of simultaneous sound sources. Additionally, it allows to define multiple ontologies to adapt to multiple tasks and offers the possibility to cross-annotate audio data. Moreover, it is easy to install and deploy...

Age Distribution of Lunar Impact-Melt Rocks in Apollo Drive-Tube 68001/2

Science.gov (United States)

Curran, N. M.; Bower, D. M.; Frasl, B.; Cohen, B. A.

2018-01-01

Apollo 16 double-drive tube 68001 /68002 provides impact and volcanic materials along a depth of approximately 60 cm in five compositional distinct units. 68001 /2 offers the potential to study distinct populations of impact melts with depth to understand how 'gardening' affects these samples. We will use unbiased major-element chemistry, mineralogy, and age to understand the impact history of Apollo 16 landing site. The study demonstrates the techniques that landed missions require to identify lithologies of interest (e.g., impact melts).

Apollo 8 prime crew seen during water egress training in Gulf of Mexico

Science.gov (United States)

1968-01-01

The prime crew of the Apollo 8 mission in life raft awaiting pickup by U.S. Coast Guard helicopter during water egress training in the Gulf of Mexico. They had just egressed Apollo Boilerplate 1102A, at left. Inflated bags were used to upright the boilerplate. Left to right, are Astronauts William A. Anders, lunar module pilot; James A. Lovell Jr., command module pilot; and Frank Borman, commander. A team of Manned Spacecraft Center (MSC) swimmers assisted with the training exercise.

Annotating images by mining image search results.

Science.gov (United States)

Wang, Xin-Jing; Zhang, Lei; Li, Xirong; Ma, Wei-Ying

2008-11-01

Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search results. Some 2.4 million images with their surrounding text are collected from a few photo forums to support this approach. The entire process is formulated in a divide-and-conquer framework where a query keyword is provided along with the uncaptioned image to improve both the effectiveness and efficiency. This is helpful when the collected data set is not dense everywhere. In this sense, our approach contains three steps: 1) the search process to discover visually and semantically similar search results, 2) the mining process to identify salient terms from textual descriptions of the search results, and 3) the annotation rejection process to filter out noisy terms yielded by Step 2. To ensure real-time annotation, two key techniques are leveraged-one is to map the high-dimensional image visual features into hash codes, the other is to implement it as a distributed system, of which the search and mining processes are provided as Web services. As a typical result, the entire process finishes in less than 1 second. Since no training data set is required, our approach enables annotating with unlimited vocabulary and is highly scalable and robust to outliers. Experimental results on both real Web images and a benchmark image data set show the effectiveness and efficiency of the proposed algorithm. It is also worth noting that, although the entire approach is illustrated within the divide-and conquer framework, a query keyword is not crucial to our current implementation. We provide experimental results to prove this.

Collaborative Paper-Based Annotation of Lecture Slides

Science.gov (United States)

Steimle, Jurgen; Brdiczka, Oliver; Muhlhauser, Max

2009-01-01

In a study of notetaking in university courses, we found that the large majority of students prefer paper to computer-based media like Tablet PCs for taking notes and making annotations. Based on this finding, we developed CoScribe, a concept and system which supports students in making collaborative handwritten annotations on printed lecture…

Music journals in South Africa 1854-2010: an annotated bibliography

African Journals Online (AJOL)

Music journals in South Africa 1854-2010: an annotated bibliography. ... The article focuses on presenting an annotated bibliography of music journalism in South Africa from as early as 1854 until 2010. Most of ... Key words: annotated bibliography, electronic journals, music journals, periodicals, South African music history ...

An annotated corpus with nanomedicine and pharmacokinetic parameters.

Science.gov (United States)

Lewinski, Nastassja A; Jimenez, Ivan; McInnes, Bridget T

2017-01-01

A vast amount of data on nanomedicines is being generated and published, and natural language processing (NLP) approaches can automate the extraction of unstructured text-based data. Annotated corpora are a key resource for NLP and information extraction methods which employ machine learning. Although corpora are available for pharmaceuticals, resources for nanomedicines and nanotechnology are still limited. To foster nanotechnology text mining (NanoNLP) efforts, we have constructed a corpus of annotated drug product inserts taken from the US Food and Drug Administration's Drugs@FDA online database. In this work, we present the development of the Engineered Nanomedicine Database corpus to support the evaluation of nanomedicine entity extraction. The data were manually annotated for 21 entity mentions consisting of nanomedicine physicochemical characterization, exposure, and biologic response information of 41 Food and Drug Administration-approved nanomedicines. We evaluate the reliability of the manual annotations and demonstrate the use of the corpus by evaluating two state-of-the-art named entity extraction systems, OpenNLP and Stanford NER. The annotated corpus is available open source and, based on these results, guidelines and suggestions for future development of additional nanomedicine corpora are provided.

Plann: A command-line application for annotating plastome sequences1

Science.gov (United States)

Huang, Daisie I.; Cronk, Quentin C. B.

2015-01-01

Premise of the study: Plann automates the process of annotating a plastome sequence in GenBank format for either downstream processing or for GenBank submission by annotating a new plastome based on a similar, well-annotated plastome. Methods and Results: Plann is a Perl script to be executed on the command line. Plann compares a new plastome sequence to the features annotated in a reference plastome and then shifts the intervals of any matching features to the locations in the new plastome. Plann’s output can be used in the National Center for Biotechnology Information’s tbl2asn to create a Sequin file for GenBank submission. Conclusions: Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastome. Because it executes from the command line, it is ready to use in other software pipelines and can be easily rerun as a draft plastome is improved. PMID:26312193

A Virtual Petrological Microscope for All Apollo 11 Lunar Samples

Science.gov (United States)

Pillnger, C. T.; Tindle, A. G.; Kelley, S. P.; Quick, K.; Scott, P.; Gibson, E. K.; Zeigler, R. A.

2014-01-01

A means of viewing, over the Internet, polished thin sections of every rock in the Apollo lunar sample collections via software, duplicaing many of the functions of a petrological microscope, is described.

Evaluation of web-based annotation of ophthalmic images for multicentric clinical trials.

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Chalam, K V; Jain, P; Shah, V A; Shah, Gaurav Y

2006-06-01

An Internet browser-based annotation system can be used to identify and describe features in digitalized retinal images, in multicentric clinical trials, in real time. In this web-based annotation system, the user employs a mouse to draw and create annotations on a transparent layer, that encapsulates the observations and interpretations of a specific image. Multiple annotation layers may be overlaid on a single image. These layers may correspond to annotations by different users on the same image or annotations of a temporal sequence of images of a disease process, over a period of time. In addition, geometrical properties of annotated figures may be computed and measured. The annotations are stored in a central repository database on a server, which can be retrieved by multiple users in real time. This system facilitates objective evaluation of digital images and comparison of double-blind readings of digital photographs, with an identifiable audit trail. Annotation of ophthalmic images allowed clinically feasible and useful interpretation to track properties of an area of fundus pathology. This provided an objective method to monitor properties of pathologies over time, an essential component of multicentric clinical trials. The annotation system also allowed users to view stereoscopic images that are stereo pairs. This web-based annotation system is useful and valuable in monitoring patient care, in multicentric clinical trials, telemedicine, teaching and routine clinical settings.

Essential Annotation Schema for Ecology (EASE)-A framework supporting the efficient data annotation and faceted navigation in ecology.

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Pfaff, Claas-Thido; Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian

2017-01-01

Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.

Essential Annotation Schema for Ecology (EASE-A framework supporting the efficient data annotation and faceted navigation in ecology.

Directory of Open Access Journals (Sweden)

Claas-Thido Pfaff

Full Text Available Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.

Annotating Logical Forms for EHR Questions.

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Roberts, Kirk; Demner-Fushman, Dina

2016-05-01

This paper discusses the creation of a semantically annotated corpus of questions about patient data in electronic health records (EHRs). The goal is to provide the training data necessary for semantic parsers to automatically convert EHR questions into a structured query. A layered annotation strategy is used which mirrors a typical natural language processing (NLP) pipeline. First, questions are syntactically analyzed to identify multi-part questions. Second, medical concepts are recognized and normalized to a clinical ontology. Finally, logical forms are created using a lambda calculus representation. We use a corpus of 446 questions asking for patient-specific information. From these, 468 specific questions are found containing 259 unique medical concepts and requiring 53 unique predicates to represent the logical forms. We further present detailed characteristics of the corpus, including inter-annotator agreement results, and describe the challenges automatic NLP systems will face on this task.

ASTP crewmen in Apollo Command Module Trainer during training session at JSC

Science.gov (United States)

1975-01-01

The three members of the American ASTP prime crew are photographed inside the Apollo Command Module (CM) trainer in a water tank in bldg 260 during water egress training at JSC. They are, left to right, Astronauts Thomas P. Stafford, commander; Vance D. Brand, command module pilot; and Donald K. Slayton, docking module pilot (23430); Slayton attaches his life preserver as he egresses an Apollo Command Module trainer in a water tank in bldg 260 during water egresss training at JSC. Astronauts Brand (on left) and Stafford have already egressed the trainer and are seated in a three-man life raft.

Apollo 11 crewmembers participate in water egress training in Gulf of Mexico

Science.gov (United States)

1969-01-01

The third member of the prime crew of the Apollo 11 lunar landing mission egresses Apollo Boilerplate 1102 during water egress training in the Gulf of Mexico. The other two crewmen are in raft. Taking part in the training were Astronauts Neil A. Armstrong, commander; Michael Collins, command module pilot; and Edwin E. Aldrin Jr., lunar module pilot. The three crewmen practiced donning and wearing biological isolation garments (B.I.G.) as a part of the exercise. The Manned Spacecraft Center (MSC) swimmer standing up, who assisted in the training, is also wearing a B.I.G.

Expressed Peptide Tags: An additional layer of data for genome annotation

Energy Technology Data Exchange (ETDEWEB)

Savidor, Alon [ORNL; Donahoo, Ryan S [ORNL; Hurtado-Gonzales, Oscar [University of Tennessee, Knoxville (UTK); Verberkmoes, Nathan C [ORNL; Shah, Manesh B [ORNL; Lamour, Kurt H [ORNL; McDonald, W Hayes [ORNL

2006-01-01

While genome sequencing is becoming ever more routine, genome annotation remains a challenging process. Identification of the coding sequences within the genomic milieu presents a tremendous challenge, especially for eukaryotes with their complex gene architectures. Here we present a method to assist the annotation process through the use of proteomic data and bioinformatics. Mass spectra of digested protein preparations of the organism of interest were acquired and searched against a protein database created by a six frame translation of the genome. The identified peptides were mapped back to the genome, compared to the current annotation, and then categorized as supporting or extending the current genome annotation. We named the classified peptides Expressed Peptide Tags (EPTs). The well annotated bacterium Rhodopseudomonas palustris was used as a control for the method and showed high degree of correlation between EPT mapping and the current annotation, with 86% of the EPTs confirming existing gene calls and less than 1% of the EPTs expanding on the current annotation. The eukaryotic plant pathogens Phytophthora ramorum and Phytophthora sojae, whose genomes have been recently sequenced and are much less well annotated, were also subjected to this method. A series of algorithmic steps were taken to increase the confidence of EPT identification for these organisms, including generation of smaller sub-databases to be searched against, and definition of EPT criteria that accommodates the more complex eukaryotic gene architecture. As expected, the analysis of the Phytophthora species showed less correlation between EPT mapping and their current annotation. While ~77% of Phytophthora EPTs supported the current annotation, a portion of them (7.2% and 12.6% for P. ramorum and P. sojae, respectively) suggested modification to current gene calls or identified novel genes that were missed by the current genome annotation of these organisms.

Fuzzy Emotional Semantic Analysis and Automated Annotation of Scene Images

Directory of Open Access Journals (Sweden)

Jianfang Cao

2015-01-01

Full Text Available With the advances in electronic and imaging techniques, the production of digital images has rapidly increased, and the extraction and automated annotation of emotional semantics implied by images have become issues that must be urgently addressed. To better simulate human subjectivity and ambiguity for understanding scene images, the current study proposes an emotional semantic annotation method for scene images based on fuzzy set theory. A fuzzy membership degree was calculated to describe the emotional degree of a scene image and was implemented using the Adaboost algorithm and a back-propagation (BP neural network. The automated annotation method was trained and tested using scene images from the SUN Database. The annotation results were then compared with those based on artificial annotation. Our method showed an annotation accuracy rate of 91.2% for basic emotional values and 82.4% after extended emotional values were added, which correspond to increases of 5.5% and 8.9%, respectively, compared with the results from using a single BP neural network algorithm. Furthermore, the retrieval accuracy rate based on our method reached approximately 89%. This study attempts to lay a solid foundation for the automated emotional semantic annotation of more types of images and therefore is of practical significance.

The Apollo peak-ring impact basin: Insights into the structure and evolution of the South Pole-Aitken basin

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Potter, Ross W. K.; Head, James W.; Guo, Dijun; Liu, Jianzhong; Xiao, Long

2018-05-01

The 492 km-diameter Apollo impact basin post-dates, and is located at the inner edge of, the ∼2240 km-diameter South Pole-Aitken (SPA) basin, providing an opportunity to assess the SPA substructure and lateral heterogeneity. Gravity Recovery and Interior Laboratory gravity data suggest an average crustal thickness on the floor of SPA of ∼20 km and within the Apollo basin of ∼5 km, yet remote sensing data reveal no conclusive evidence for the presence of exposed mantle material. We use the iSALE shock physics code to model the formation of the Apollo basin and find that the observational data are best fit by the impact of a 40 km diameter body traveling at 15 km/s into 20-40 km thick crustal material. These results strongly suggest that the Apollo impact occurred on ejecta deposits and collapsed crustal material of the SPA basin and could help place constraints on the location, size and geometry of the SPA transient cavity. The peak ring in the interior of Apollo basin is plausibly interpreted to be composed of inwardly collapsed lower crustal material that experienced peak shock pressures in excess of 35 GPa, consistent with remote sensing observations that suggest shocked plagioclase. Proposed robotic and/or human missions to SPA and Apollo would present an excellent opportunity to test the predictions of this work and address many scientific questions about SPA basin evolution and structure.

Multiview Hessian regularization for image annotation.

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Liu, Weifeng; Tao, Dacheng

2013-07-01

The rapid development of computer hardware and Internet technology makes large scale data dependent models computationally tractable, and opens a bright avenue for annotating images through innovative machine learning algorithms. Semisupervised learning (SSL) therefore received intensive attention in recent years and was successfully deployed in image annotation. One representative work in SSL is Laplacian regularization (LR), which smoothes the conditional distribution for classification along the manifold encoded in the graph Laplacian, however, it is observed that LR biases the classification function toward a constant function that possibly results in poor generalization. In addition, LR is developed to handle uniformly distributed data (or single-view data), although instances or objects, such as images and videos, are usually represented by multiview features, such as color, shape, and texture. In this paper, we present multiview Hessian regularization (mHR) to address the above two problems in LR-based image annotation. In particular, mHR optimally combines multiple HR, each of which is obtained from a particular view of instances, and steers the classification function that varies linearly along the data manifold. We apply mHR to kernel least squares and support vector machines as two examples for image annotation. Extensive experiments on the PASCAL VOC'07 dataset validate the effectiveness of mHR by comparing it with baseline algorithms, including LR and HR.

Flight feeding systems design and evaluation. Supplement 1: Production guides. [for the Apollo food system

Science.gov (United States)

1973-01-01

The requirements for processing, packaging, testing, and shipment of foods selected for use in the Apollo food system are presented. Specific foodstuffs chosen from the following categories are discussed: (1) soups; (2) juices; (3) breads; (4) meat and poultry products; (5) fruits and nuts; (6) desserts; and (7) beverages. Food procurement for the mobile quarantine facility and for Apollo preflight and postflight activities is also discussed.

Annotation-based feature extraction from sets of SBML models.

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Alm, Rebekka; Waltemath, Dagmar; Wolfien, Markus; Wolkenhauer, Olaf; Henkel, Ron

2015-01-01

Model repositories such as BioModels Database provide computational models of biological systems for the scientific community. These models contain rich semantic annotations that link model entities to concepts in well-established bio-ontologies such as Gene Ontology. Consequently, thematically similar models are likely to share similar annotations. Based on this assumption, we argue that semantic annotations are a suitable tool to characterize sets of models. These characteristics improve model classification, allow to identify additional features for model retrieval tasks, and enable the comparison of sets of models. In this paper we discuss four methods for annotation-based feature extraction from model sets. We tested all methods on sets of models in SBML format which were composed from BioModels Database. To characterize each of these sets, we analyzed and extracted concepts from three frequently used ontologies, namely Gene Ontology, ChEBI and SBO. We find that three out of the methods are suitable to determine characteristic features for arbitrary sets of models: The selected features vary depending on the underlying model set, and they are also specific to the chosen model set. We show that the identified features map on concepts that are higher up in the hierarchy of the ontologies than the concepts used for model annotations. Our analysis also reveals that the information content of concepts in ontologies and their usage for model annotation do not correlate. Annotation-based feature extraction enables the comparison of model sets, as opposed to existing methods for model-to-keyword comparison, or model-to-model comparison.

DaMold: A data-mining platform for variant annotation and visualization in molecular diagnostics research.

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Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2017-07-01

Next-generation sequencing (NGS) has become a powerful and efficient tool for routine mutation screening in clinical research. As each NGS test yields hundreds of variants, the current challenge is to meaningfully interpret the data and select potential candidates. Analyzing each variant while manually investigating several relevant databases to collect specific information is a cumbersome and time-consuming process, and it requires expertise and familiarity with these databases. Thus, a tool that can seamlessly annotate variants with clinically relevant databases under one common interface would be of great help for variant annotation, cross-referencing, and visualization. This tool would allow variants to be processed in an automated and high-throughput manner and facilitate the investigation of variants in several genome browsers. Several analysis tools are available for raw sequencing-read processing and variant identification, but an automated variant filtering, annotation, cross-referencing, and visualization tool is still lacking. To fulfill these requirements, we developed DaMold, a Web-based, user-friendly tool that can filter and annotate variants and can access and compile information from 37 resources. It is easy to use, provides flexible input options, and accepts variants from NGS and Sanger sequencing as well as hotspots in VCF and BED formats. DaMold is available as an online application at http://damold.platomics.com/index.html, and as a Docker container and virtual machine at https://sourceforge.net/projects/damold/. © 2017 Wiley Periodicals, Inc.

ePIANNO: ePIgenomics ANNOtation tool.

Directory of Open Access Journals (Sweden)

Chia-Hsin Liu

Full Text Available Recently, with the development of next generation sequencing (NGS, the combination of chromatin immunoprecipitation (ChIP and NGS, namely ChIP-seq, has become a powerful technique to capture potential genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions. For most researchers, additional information including genomic variations on the TF binding site, allele frequency of variation between different populations, variation associated disease, and other neighbour TF binding sites are essential to generate a proper hypothesis or a meaningful conclusion. Many ChIP-seq datasets had been deposited on the public domain to help researchers make new discoveries. However, researches are often intimidated by the complexity of data structure and largeness of data volume. Such information would be more useful if they could be combined or downloaded with ChIP-seq data. To meet such demands, we built a webtool: ePIgenomic ANNOtation tool (ePIANNO, http://epianno.stat.sinica.edu.tw/index.html. ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project and gene-disease association information of GWAS (NHGRI with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly. We use two examples to demonstrate how users could use functions of ePIANNO webserver to explore useful information about TF related genomic variants. Users could use our query functions to search target regions, transcription factors, or annotations. ePIANNO may help users to generate hypothesis or explore potential biological functions for their studies.

Apollo 12, A New Vista for Lunar Science.

Science.gov (United States)

National Aeronautics and Space Administration, Washington, DC.

Man's second lunar landing, Apollo 12, provided a wealth of scientific information about the moon. The deployment of the magnetometer, seismometer, and ionosphere detector, and other activities on the lunar surface are described. A number of color photographs show the astronauts setting up equipment on the moon as well as close-ups of the lunar…

DOE Hydropower Program biennial report 1990--1991 (with updated annotated bibliography)

Energy Technology Data Exchange (ETDEWEB)

Chappell, J.R.; Rinehart, B.N.; Sommers, G.L. (Idaho National Engineering Lab., Idaho Falls, ID (United States)); Sale, M.J. (Oak Ridge National Lab., TN (United States))

1991-07-01

This report summarizes the activities of the US Department of Energy's (DOE) Hydropower Program for fiscal years 1990 and 1991, and provides an annotated bibliography of research, engineering, operations, regulations, and costs of projects pertinent to hydropower development. The Hydropower Program is organized as follows: background (including Technology Development and Engineering Research and Development); Resource Assessment; National Energy Strategy; Technology Transfer; Environmental Research; and, the bibliography discusses reports written by both private and non-Federal Government sectors. Most reports are available from the National Technical Information Service. 5 figs., 2 tabs.

Automatic annotation of protein motif function with Gene Ontology terms

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Gopalakrishnan Vanathi

2004-09-01

Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

The Effects of Multimedia Annotations on Iranian EFL Learners’ L2 Vocabulary Learning

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Saeideh Ahangari

2010-05-01

Full Text Available In our modern technological world, Computer-Assisted Language learning (CALL is a new realm towards learning a language in general, and learning L2 vocabulary in particular. It is assumed that the use of multimedia annotations promotes language learners’ vocabulary acquisition. Therefore, this study set out to investigate the effects of different multimedia annotations (still picture annotations, dynamic picture annotations, and written annotations on L2 vocabulary learning. To fulfill this objective, the researchers selected sixty four EFL learners as the participants of this study. The participants were randomly assigned to one of the four groups: a control group that received no annotations and three experimental groups that received:  still picture annotations, dynamic picture annotations, and written annotations. Each participant was required to take a pre-test. A vocabulary post- test was also designed and administered to the participants in order to assess the efficacy of each annotation. First for each group a paired t-test was conducted between their pre and post test scores in order to observe their improvement; then through an ANCOVA test the performance of four groups was compared. The results showed that using multimedia annotations resulted in a significant difference in the participants’ vocabulary learning. Based on the results of the present study, multimedia annotations are suggested as a vocabulary teaching strategy.

Astronaut John Young in Command Module Simulator during Apollo Simulation

Science.gov (United States)

1968-01-01

Astronaut John W. Young, command module pilot, inside the Command Module Simulator in bldg 5 during an Apollo Simulation. Astronauts Thomas P. Stafford, commander and Eugene A. Cernan, lunar module pilot are out of the view.

Evaluating Functional Annotations of Enzymes Using the Gene Ontology.

Science.gov (United States)

Holliday, Gemma L; Davidson, Rebecca; Akiva, Eyal; Babbitt, Patricia C

2017-01-01

The Gene Ontology (GO) (Ashburner et al., Nat Genet 25(1):25-29, 2000) is a powerful tool in the informatics arsenal of methods for evaluating annotations in a protein dataset. From identifying the nearest well annotated homologue of a protein of interest to predicting where misannotation has occurred to knowing how confident you can be in the annotations assigned to those proteins is critical. In this chapter we explore what makes an enzyme unique and how we can use GO to infer aspects of protein function based on sequence similarity. These can range from identification of misannotation or other errors in a predicted function to accurate function prediction for an enzyme of entirely unknown function. Although GO annotation applies to any gene products, we focus here a describing our approach for hierarchical classification of enzymes in the Structure-Function Linkage Database (SFLD) (Akiva et al., Nucleic Acids Res 42(Database issue):D521-530, 2014) as a guide for informed utilisation of annotation transfer based on GO terms.

Photogrammetry of Apollo 15 photography, part C

Science.gov (United States)

Wu, S. S. C.; Schafer, F. J.; Jordan, R.; Nakata, G. M.; Derick, J. L.

1972-01-01

In the Apollo 15 mission, a mapping camera system and a 61 cm optical bar, high resolution panoramic camera, as well as a laser altimeter were used. The panoramic camera is described, having several distortion sources, such as cylindrical shape of the negative film surface, the scanning action of the lens, the image motion compensator, and the spacecraft motion. Film products were processed on a specifically designed analytical plotter.

IntelliGO: a new vector-based semantic similarity measure including annotation origin

Directory of Open Access Journals (Sweden)

Devignes Marie-Dominique

2010-12-01

previously published measures. Conclusions The IntelliGO similarity measure provides a customizable and comprehensive method for quantifying gene similarity based on GO annotations. It also displays a robust set-discriminating power which suggests it will be useful for functional clustering. Availability An on-line version of the IntelliGO similarity measure is available at: http://bioinfo.loria.fr/Members/benabdsi/intelligo_project/

Essential Annotation Schema for Ecology (EASE)—A framework supporting the efficient data annotation and faceted navigation in ecology

Science.gov (United States)

Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian

2017-01-01

Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines. PMID:29023519

An absolute calibration system for millimeter-accuracy APOLLO measurements

Science.gov (United States)

Adelberger, E. G.; Battat, J. B. R.; Birkmeier, K. J.; Colmenares, N. R.; Davis, R.; Hoyle, C. D.; Huang, L. R.; McMillan, R. J.; Murphy, T. W., Jr.; Schlerman, E.; Skrobol, C.; Stubbs, C. W.; Zach, A.

2017-12-01

Lunar laser ranging provides a number of leading experimental tests of gravitation—important in our quest to unify general relativity and the standard model of physics. The apache point observatory lunar laser-ranging operation (APOLLO) has for years achieved median range precision at the  ∼2 mm level. Yet residuals in model-measurement comparisons are an order-of-magnitude larger, raising the question of whether the ranging data are not nearly as accurate as they are precise, or if the models are incomplete or ill-conditioned. This paper describes a new absolute calibration system (ACS) intended both as a tool for exposing and eliminating sources of systematic error, and also as a means to directly calibrate ranging data in situ. The system consists of a high-repetition-rate (80 MHz) laser emitting short (motivating continued work on model capabilities. The ACS provides the means to deliver APOLLO data both accurate and precise below the 2 mm level.

Phoebus volentem proelia me loqui: The Apollo of Callimachus in Horace

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Kristina Tomc

2010-07-01

Full Text Available The Augustan poets often modelled their recusationes on Callimachus’ portrayal of Apollo in theAetiaPrologue. The paper discusses parallel passages in Horace’s oeuvre, illustrating some typical characteristics of Horace’s poetry and of his attitude to his poetic models. After a brief introduction, the paper first touches on three poems by Horace where the role of Callimachus’ Apollo is taken over by another deity: the Muse in C. 1.6.10-12, Venus in C. 1.19.9-12, and adeus (presumably Cupid in Epod. 14.6-8. The three examples display similarities to, rather than identity with, the Callimachean situation: instead of supplying a direct quote, Horace merely reports the words of a ῾higher power’ which allegedly prevented him from writing what he wanted or what was expected of him. In the two Odes Horace thus refuses to compose an epic, while Epode 14 is not a typical recusatio: Horace’s polished iambics paradoxically profess his inability to compose iambic poetry, and his preference for erotic lyric poetry. The next section focuses on Satire 1.10.31-35, which portrays the Roman god Quirinus warning the young poet in a dream that writing Greek verse is pointless. An analysis of this complex programmatic satire reveals continual departures from, and approximations to, Callimachean poetic, as Horace interweaves several, at times clearly irreconcilable, traditions. Indeed, Callimachean poetic itself is not unequivocal or monolithic but contains many tensions.  The short fourth section discusses Horace’s prayer to Mercury in Satire 2.6.13-15. Although superficially lacking a ῾programmatic’ dimension, the satire in fact contains several allusions to Callimachus. It serves to show that Horace’s images function at several levels at once, and that his satires closely interweave ethics with aesthetics. The final and longest section focuses on Horace’s last poem, C. 4.15. In the first strophe, Horace is finally given

Automating Ontological Annotation with WordNet

Energy Technology Data Exchange (ETDEWEB)

Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

2006-01-22

Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

Apollo 15 clastic materials and their relationship to local geologic features

Science.gov (United States)

Fruchter, J. S.; Stoeser, J. W.; Lindstrom, M. M.; Goles, G. G.

1973-01-01

Ninety sub-samples of Apollo 15 materials have been analyzed by instrumental neutron activation analysis techniques for as many as 21 elements. Soil and soil breccia compositions show considerable variation from station to station although at any given station the soils and soil breccias were compositionally very similar to one another. Mixing model calculations show that the station-to-station variations can be related to important local geologic features. These features include the Apennine Front, Hadley Rille and the ray from the craters Aristillus or Autolycus. Compositional similarities between soils and soil breccias at the Apollo 15 site indicate that the breccias and soils are related in some fundamental way, although the exact nature of this relationship is not yet fully understood.

A Selected Annotated Bibliography on Work Time Options.

Science.gov (United States)

Ivantcho, Barbara

This annotated bibliography is divided into three sections. Section I contains annotations of general publications on work time options. Section II presents resources on flexitime and the compressed work week. In Section III are found resources related to these reduced work time options: permanent part-time employment, job sharing, voluntary…

Prepare-Participate-Connect: Active Learning with Video Annotation

Science.gov (United States)

Colasante, Meg; Douglas, Kathy

2016-01-01

Annotation of video provides students with the opportunity to view and engage with audiovisual content in an interactive and participatory way rather than in passive-receptive mode. This article discusses research into the use of video annotation in four vocational programs at RMIT University in Melbourne, which allowed students to interact with…

Developing Annotation Solutions for Online Data Driven Learning

Science.gov (United States)

Perez-Paredes, Pascual; Alcaraz-Calero, Jose M.

2009-01-01

Although "annotation" is a widely-researched topic in Corpus Linguistics (CL), its potential role in Data Driven Learning (DDL) has not been addressed in depth by Foreign Language Teaching (FLT) practitioners. Furthermore, most of the research in the use of DDL methods pays little attention to annotation in the design and implementation…

Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence

Directory of Open Access Journals (Sweden)

Dorrell Nick

2007-06-01

Full Text Available Abstract Background Campylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and published in 2000. The original annotation was a milestone in Campylobacter research, but is outdated. We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation. Results Re-annotation was carried out using sequence database searches such as FASTA, along with programs such as TMHMM for additional support. The re-annotation also utilises sequence data from additional Campylobacter strains and species not available during the original annotation. Re-annotation was accompanied by a full literature search that was incorporated into the updated EMBL file [EMBL: AL111168]. The C. jejuni NCTC11168 re-annotation reduced the total number of coding sequences from 1654 to 1643, of which 90.0% have additional information regarding the identification of new motifs and/or relevant literature. Re-annotation has led to 18.2% of coding sequence product functions being revised. Conclusions Major updates were made to genes involved in the biosynthesis of important surface structures such as lipooligosaccharide, capsule and both O- and N-linked glycosylation. This re-annotation will be a key resource for Campylobacter research and will also provide a prototype for the re-annotation and re-interpretation of other bacterial genomes.

Comparison of concept recognizers for building the Open Biomedical Annotator

Directory of Open Access Journals (Sweden)

Rubin Daniel

2009-09-01

Full Text Available Abstract The National Center for Biomedical Ontology (NCBO is developing a system for automated, ontology-based access to online biomedical resources (Shah NH, et al.: Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics 2009, 10(Suppl 2:S1. The system's indexing workflow processes the text metadata of diverse resources such as datasets from GEO and ArrayExpress to annotate and index them with concepts from appropriate ontologies. This indexing requires the use of a concept-recognition tool to identify ontology concepts in the resource's textual metadata. In this paper, we present a comparison of two concept recognizers – NLM's MetaMap and the University of Michigan's Mgrep. We utilize a number of data sources and dictionaries to evaluate the concept recognizers in terms of precision, recall, speed of execution, scalability and customizability. Our evaluations demonstrate that Mgrep has a clear edge over MetaMap for large-scale service oriented applications. Based on our analysis we also suggest areas of potential improvements for Mgrep. We have subsequently used Mgrep to build the Open Biomedical Annotator service. The Annotator service has access to a large dictionary of biomedical terms derived from the United Medical Language System (UMLS and NCBO ontologies. The Annotator also leverages the hierarchical structure of the ontologies and their mappings to expand annotations. The Annotator service is available to the community as a REST Web service for creating ontology-based annotations of their data.

Effects of Reviewing Annotations and Homework Solutions on Math Learning Achievement

Science.gov (United States)

Hwang, Wu-Yuin; Chen, Nian-Shing; Shadiev, Rustam; Li, Jin-Sing

2011-01-01

Previous studies have demonstrated that making annotations can be a meaningful and useful learning method that promote metacognition and enhance learning achievement. A web-based annotation system, Virtual Pen (VPEN), which provides for the creation and review of annotations and homework solutions, has been developed to foster learning process…

Searchlights Illuminate Apollo 8 on Pad 39-A

Science.gov (United States)

1968-01-01

Searchlights penetrate the darkness surrounding Apollo 8 on Pad 39-A at Kennedy Space Center. This mission was the first manned flight using the Saturn V. The towering 363-foot Saturn V was a multi-stage, multi-engine launch vehicle standing taller than the Statue of Liberty. Altogether, the Saturn V engines produced as much power as 85 Hoover Dams.

Apollo 6 Transported to Launch Pad at KSC

Science.gov (United States)

1968-01-01

Apollo 6, the second and last of the unmarned Saturn V test flights, is slowly transported past the Vehicle Assembly Building on the way to launch pad 39-A. The towering 363-foot Saturn V was a multi-stage, multi-engine launch vehicle standing taller than the Statue of Liberty. Altogether, the Saturn V engines produced as much power as 85 Hoover Dams.

First-Time Analysis of Completely Restored DTREM Instrument Data from Apollo 14 and 15

Science.gov (United States)

McBride, Marie J.; Williams, David R.; Hills, H. Kent; Turner, Niescja

2013-01-01

The Dust, Thermal and Radiation Engineering Measurement (DTREM) packages (figure 1) mounted on the central stations of the Apollo 11, 12, 14, and 15 ALSEPs (Apollo Lunar Surface Experiments Packages) measured the outputs of exposed solar cells and thermistors over time. The goal of the experiment, also commonly known as the dust detector, was to study the long-term effects of dust, radiation, and temperature at the lunar surface on solar cells. The monitors returned data for up to almost 8 years from the lunar surface.

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.

Science.gov (United States)

Habegger, Lukas; Balasubramanian, Suganthi; Chen, David Z; Khurana, Ekta; Sboner, Andrea; Harmanci, Arif; Rozowsky, Joel; Clarke, Declan; Snyder, Michael; Gerstein, Mark

2012-09-01

The functional annotation of variants obtained through sequencing projects is generally assumed to be a simple intersection of genomic coordinates with genomic features. However, complexities arise for several reasons, including the differential effects of a variant on alternatively spliced transcripts, as well as the difficulty in assessing the impact of small insertions/deletions and large structural variants. Taking these factors into consideration, we developed the Variant Annotation Tool (VAT) to functionally annotate variants from multiple personal genomes at the transcript level as well as obtain summary statistics across genes and individuals. VAT also allows visualization of the effects of different variants, integrates allele frequencies and genotype data from the underlying individuals and facilitates comparative analysis between different groups of individuals. VAT can either be run through a command-line interface or as a web application. Finally, in order to enable on-demand access and to minimize unnecessary transfers of large data files, VAT can be run as a virtual machine in a cloud-computing environment. VAT is implemented in C and PHP. The VAT web service, Amazon Machine Image, source code and detailed documentation are available at vat.gersteinlab.org.

Indigenous Carbonaceous Phases Embedded Within Surface Deposits on Apollo 17 Volcanic Glass Beads

Science.gov (United States)

Thomas-Keprta, K. L.; Clemett, S. J.; Ross, D. K.; Le, L.; McKay, D. S.; Gibson, E. K.; Gonzalez, C.

2012-01-01

The assessment of indigenous organic matter in returned lunar samples was one of the primary scientific goals of the Apollo program. Prior studies of Apollo samples have shown the total amount of organic matter to be in the range of approx 50 to 250 ppm. Low concentrations of lunar organics may be a consequence not only of its paucity but also its heterogeneous distribution. Several processes should have contributed to the lunar organic inventory including exogenous carbonaceous accretion from meteoroids and interplanetary dust particles, and endogenous synthesis driven by early planetary volcanism and cosmic and solar radiation.

LocusTrack: Integrated visualization of GWAS results and genomic annotation.

Science.gov (United States)

Cuellar-Partida, Gabriel; Renteria, Miguel E; MacGregor, Stuart

2015-01-01

Genome-wide association studies (GWAS) are an important tool for the mapping of complex traits and diseases. Visual inspection of genomic annotations may be used to generate insights into the biological mechanisms underlying GWAS-identified loci. We developed LocusTrack, a web-based application that annotates and creates plots of regional GWAS results and incorporates user-specified tracks that display annotations such as linkage disequilibrium (LD), phylogenetic conservation, chromatin state, and other genomic and regulatory elements. Currently, LocusTrack can integrate annotation tracks from the UCSC genome-browser as well as from any tracks provided by the user. LocusTrack is an easy-to-use application and can be accessed at the following URL: http://gump.qimr.edu.au/general/gabrieC/LocusTrack/. Users can upload and manage GWAS results and select from and/or provide annotation tracks using simple and intuitive menus. LocusTrack scripts and associated data can be downloaded from the website and run locally.

"Annotated Lectures": Student-Instructor Interaction in Large-Scale Global Education

Directory of Open Access Journals (Sweden)

Roger Diehl

2009-10-01

Full Text Available We describe an "Annotated Lectures" system, which will be used in a global virtual teaching and student collaboration event on embodied intelligence presented by the University of Zurich. The lectures will be broadcasted via video-conference to lecture halls of different universities around the globe. Among other collaboration features, an "Annotated Lectures" system will be implemented in a 3D collaborative virtual environment and used by the participating students to make annotations to the video-recorded lectures, which will be sent to and answered by their supervisors, and forwarded to the lecturers in an aggregated way. The "Annotated Lectures" system aims to overcome the issues of limited studentinstructor interaction in large-scale education, and to foster an intercultural and multidisciplinary discourse among students who review the lectures in a group. After presenting the concept of the "Annotated Lectures" system, we discuss a prototype version including a description of the technical components and its expected benefit for large-scale global education.

Annotation an effective device for student feedback: a critical review of the literature.

Science.gov (United States)

Ball, Elaine C

2010-05-01

The paper examines hand-written annotation, its many features, difficulties and strengths as a feedback tool. It extends and clarifies what modest evidence is in the public domain and offers an evaluation of how to use annotation effectively in the support of student feedback [Marshall, C.M., 1998a. The Future of Annotation in a Digital (paper) World. Presented at the 35th Annual GLSLIS Clinic: Successes and Failures of Digital Libraries, June 20-24, University of Illinois at Urbana-Champaign, March 24, pp. 1-20; Marshall, C.M., 1998b. Toward an ecology of hypertext annotation. Hypertext. In: Proceedings of the Ninth ACM Conference on Hypertext and Hypermedia, June 20-24, Pittsburgh Pennsylvania, US, pp. 40-49; Wolfe, J.L., Nuewirth, C.M., 2001. From the margins to the centre: the future of annotation. Journal of Business and Technical Communication, 15(3), 333-371; Diyanni, R., 2002. One Hundred Great Essays. Addison-Wesley, New York; Wolfe, J.L., 2002. Marginal pedagogy: how annotated texts affect writing-from-source texts. Written Communication, 19(2), 297-333; Liu, K., 2006. Annotation as an index to critical writing. Urban Education, 41, 192-207; Feito, A., Donahue, P., 2008. Minding the gap annotation as preparation for discussion. Arts and Humanities in Higher Education, 7(3), 295-307; Ball, E., 2009. A participatory action research study on handwritten annotation feedback and its impact on staff and students. Systemic Practice and Action Research, 22(2), 111-124; Ball, E., Franks, H., McGrath, M., Leigh, J., 2009. Annotation is a valuable tool to enhance learning and assessment in student essays. Nurse Education Today, 29(3), 284-291]. Although a significant number of studies examine annotation, this is largely related to on-line tools and computer mediated communication and not hand-written annotation as comment, phrase or sign written on the student essay to provide critique. Little systematic research has been conducted to consider how this latter form

BioCause: Annotating and analysing causality in the biomedical domain.

Science.gov (United States)

Mihăilă, Claudiu; Ohta, Tomoko; Pyysalo, Sampo; Ananiadou, Sophia

2013-01-16

Biomedical corpora annotated with event-level information represent an important resource for domain-specific information extraction (IE) systems. However, bio-event annotation alone cannot cater for all the needs of biologists. Unlike work on relation and event extraction, most of which focusses on specific events and named entities, we aim to build a comprehensive resource, covering all statements of causal association present in discourse. Causality lies at the heart of biomedical knowledge, such as diagnosis, pathology or systems biology, and, thus, automatic causality recognition can greatly reduce the human workload by suggesting possible causal connections and aiding in the curation of pathway models. A biomedical text corpus annotated with such relations is, hence, crucial for developing and evaluating biomedical text mining. We have defined an annotation scheme for enriching biomedical domain corpora with causality relations. This schema has subsequently been used to annotate 851 causal relations to form BioCause, a collection of 19 open-access full-text biomedical journal articles belonging to the subdomain of infectious diseases. These documents have been pre-annotated with named entity and event information in the context of previous shared tasks. We report an inter-annotator agreement rate of over 60% for triggers and of over 80% for arguments using an exact match constraint. These increase significantly using a relaxed match setting. Moreover, we analyse and describe the causality relations in BioCause from various points of view. This information can then be leveraged for the training of automatic causality detection systems. Augmenting named entity and event annotations with information about causal discourse relations could benefit the development of more sophisticated IE systems. These will further influence the development of multiple tasks, such as enabling textual inference to detect entailments, discovering new facts and providing new

Automatic Function Annotations for Hoare Logic

Directory of Open Access Journals (Sweden)

Daniel Matichuk

2012-11-01

Full Text Available In systems verification we are often concerned with multiple, inter-dependent properties that a program must satisfy. To prove that a program satisfies a given property, the correctness of intermediate states of the program must be characterized. However, this intermediate reasoning is not always phrased such that it can be easily re-used in the proofs of subsequent properties. We introduce a function annotation logic that extends Hoare logic in two important ways: (1 when proving that a function satisfies a Hoare triple, intermediate reasoning is automatically stored as function annotations, and (2 these function annotations can be exploited in future Hoare logic proofs. This reduces duplication of reasoning between the proofs of different properties, whilst serving as a drop-in replacement for traditional Hoare logic to avoid the costly process of proof refactoring. We explain how this was implemented in Isabelle/HOL and applied to an experimental branch of the seL4 microkernel to significantly reduce the size and complexity of existing proofs.

Automatically Annotated Mapping for Indoor Mobile Robot Applications

DEFF Research Database (Denmark)

Özkil, Ali Gürcan; Howard, Thomas J.

2012-01-01

This paper presents a new and practical method for mapping and annotating indoor environments for mobile robot use. The method makes use of 2D occupancy grid maps for metric representation, and topology maps to indicate the connectivity of the ‘places-of-interests’ in the environment. Novel use...... localization and mapping in topology space, and fuses camera and robot pose estimations to build an automatically annotated global topo-metric map. It is developed as a framework for a hospital service robot and tested in a real hospital. Experiments show that the method is capable of producing globally...... consistent, automatically annotated hybrid metric-topological maps that is needed by mobile service robots....

Reference calculations on critical assemblies with Apollo2 code working with a fine multigroup mesh; Calculs de reference avec un maillage multigroupe fin sur des assemblages critiques par Apollo2

Energy Technology Data Exchange (ETDEWEB)

Aggery, A

1999-12-01

The objective of this thesis is to add to the multigroup transport code APOLLO2 the capability to perform deterministic reference calculations, for any type of reactor, using a very fine energy mesh of several thousand groups. This new reference tool allows us to validate the self-shielding model used in industrial applications, to perform depletion calculations, differential effects calculations, critical buckling calculations or to evaluate precisely data required by the self shielding model. At its origin, APOLLO2 was designed to perform routine calculations with energy meshes around one hundred groups. That is why, in the current format of cross sections libraries, almost each value of the multigroup energy transfer matrix is stored. As this format is not convenient for a high number of groups (concerning memory size), we had to search out a new format for removal matrices and consequently to modify the code. In the new format we found, only some values of removal matrices are kept (these values depend on a reconstruction precision choice), the other ones being reconstructed by a linear interpolation, what reduces the size of these matrices. Then we had to show that APOLLO2 working with a fine multigroup mesh had the capability to perform reference calculations on any assembly geometry. For that, we successfully carried out the validation with several calculations for which we compared APOLLO2 results (obtained with the universal mesh of 11276 groups) to results obtained with Monte Carlo codes (MCNP, TRIPOLI4). Physical analysis led with this new tool have been very fruitful and show a great potential for such an R and D tool. (author)

Assessment of Scheduling and Plan Execution of Apollo 14 Lunar Surface Operations

Science.gov (United States)

Marquez, Jessica J.

2010-01-01

Although over forty years have passed since first landing on the Moon, there is not yet a comprehensive, quantitative assessment of Apollo extravehicular activities (EVAs). Quantitatively evaluating lunar EVAs will provide a better understanding of the challenges involved with surface operations. This first evaluation of a surface EVA centers on comparing the planned and the as-ran timeline, specifically collecting data on discrepancies between durations that were estimated versus executed. Differences were summarized by task categories in order to gain insight as to the type of surface operation activities that were most challenging. One Apollo 14 EVA was assessed utilizing the described methodology. Selected metrics and task categorizations were effective, and limitations to this process were identified.

APOLLO 15 HEAT FLOW THERMAL CONDUCTIVITY RDR SUBSAMPLED V1.0

Data.gov (United States)

National Aeronautics and Space Administration — This data set comprises a reduced, subsampled set of the data returned from the Apollo 15 Heat Flow Experiment from 31 July 1971 through 31 December 1974. The...

APOLLO 17 HEAT FLOW THERMAL CONDUCTIVITY RDR SUBSAMPLED V1.0

Data.gov (United States)

National Aeronautics and Space Administration — This data set comprises a reduced, subsampled set of the data returned from the Apollo 17 Heat Flow Experiment from 12 December 1972 through 31 December 1974. The...

Apollo 10 astronauts in space suits in front of Command Module

Science.gov (United States)

1968-01-01

Three astronauts named as the prime crew of the Apollo 10 space mission. Left to right, are Eugene A. Cernan, lunar module pilot; John W. Young, command module pilot; and Thomas P. Stafford, commander.

Students' annotated drawings of Sun, Moon and Earth mediating teachers' professional development

DEFF Research Database (Denmark)

Nielsen, Birgitte Lund

A case study of a teacher examining her 4th graders’ conceptual understanding of factors causing day and night, seasons, and the phases of the Moon is presented. The teaching example and the data-collection are sourced from the Danish continuous professional development (CPD) project QUEST......-making model. The pre-teaching annotated drawings reveal several alternative conceptions, but based on the post-teaching drawings the teaching must be seen as rather efficient in most areas concerning challenging students’ alternative conceptions; however not in relation to the phases of the Moon. The teacher...

Mosaic of Apollo 16 Descartes landing site taken from TV transmission

Science.gov (United States)

1972-01-01

A 360 degree field of view of the Apollo 16 Descartes landing site area composed of individual scenes taken from a color transmission made by the color RCA TV camera mounted on the Lunar Roving Vehicle. This panorama was made while the LRV was parked at the rim of North Ray crater (Stations 11 and 12) during the third Apollo 16 lunar surface extravehicular activity (EVA-3) by Astronauts John W. Young and Charles M. Duke Jr. The overlay identifies the directions and the key lunar terrain features. The camera panned across the rear portion of the LRV in its 360 degree sweep. Note Young and Duke walking along the edge of the crater in one of the scenes. The TV camera was remotely controlled from a console in the Mission Control Center.

An annotated corpus with nanomedicine and pharmacokinetic parameters

Directory of Open Access Journals (Sweden)

Lewinski NA

2017-10-01

Full Text Available Nastassja A Lewinski,1 Ivan Jimenez,1 Bridget T McInnes2 1Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, 2Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA Abstract: A vast amount of data on nanomedicines is being generated and published, and natural language processing (NLP approaches can automate the extraction of unstructured text-based data. Annotated corpora are a key resource for NLP and information extraction methods which employ machine learning. Although corpora are available for pharmaceuticals, resources for nanomedicines and nanotechnology are still limited. To foster nanotechnology text mining (NanoNLP efforts, we have constructed a corpus of annotated drug product inserts taken from the US Food and Drug Administration’s Drugs@FDA online database. In this work, we present the development of the Engineered Nanomedicine Database corpus to support the evaluation of nanomedicine entity extraction. The data were manually annotated for 21 entity mentions consisting of nanomedicine physicochemical characterization, exposure, and biologic response information of 41 Food and Drug Administration-approved nanomedicines. We evaluate the reliability of the manual annotations and demonstrate the use of the corpus by evaluating two state-of-the-art named entity extraction systems, OpenNLP and Stanford NER. The annotated corpus is available open source and, based on these results, guidelines and suggestions for future development of additional nanomedicine corpora are provided. Keywords: nanotechnology, informatics, natural language processing, text mining, corpora

Annotated Tsunami bibliography: 1962-1976

International Nuclear Information System (INIS)

Pararas-Carayannis, G.; Dong, B.; Farmer, R.

1982-08-01

This compilation contains annotated citations to nearly 3000 tsunami-related publications from 1962 to 1976 in English and several other languages. The foreign-language citations have English titles and abstracts

Assessment of community-submitted ontology annotations from a novel database-journal partnership.

Science.gov (United States)

Berardini, Tanya Z; Li, Donghui; Muller, Robert; Chetty, Raymond; Ploetz, Larry; Singh, Shanker; Wensel, April; Huala, Eva

2012-01-01

As the scientific literature grows, leading to an increasing volume of published experimental data, so does the need to access and analyze this data using computational tools. The most commonly used method to convert published experimental data on gene function into controlled vocabulary annotations relies on a professional curator, employed by a model organism database or a more general resource such as UniProt, to read published articles and compose annotation statements based on the articles' contents. A more cost-effective and scalable approach capable of capturing gene function data across the whole range of biological research organisms in computable form is urgently needed. We have analyzed a set of ontology annotations generated through collaborations between the Arabidopsis Information Resource and several plant science journals. Analysis of the submissions entered using the online submission tool shows that most community annotations were well supported and the ontology terms chosen were at an appropriate level of specificity. Of the 503 individual annotations that were submitted, 97% were approved and community submissions captured 72% of all possible annotations. This new method for capturing experimental results in a computable form provides a cost-effective way to greatly increase the available body of annotations without sacrificing annotation quality. Database URL: www.arabidopsis.org.

Annotation-Based Whole Genomic Prediction and Selection

DEFF Research Database (Denmark)

Kadarmideen, Haja; Do, Duy Ngoc; Janss, Luc

Genomic selection is widely used in both animal and plant species, however, it is performed with no input from known genomic or biological role of genetic variants and therefore is a black box approach in a genomic era. This study investigated the role of different genomic regions and detected QTLs...... in their contribution to estimated genomic variances and in prediction of genomic breeding values by applying SNP annotation approaches to feed efficiency. Ensembl Variant Predictor (EVP) and Pig QTL database were used as the source of genomic annotation for 60K chip. Genomic prediction was performed using the Bayes...... classes. Predictive accuracy was 0.531, 0.532, 0.302, and 0.344 for DFI, RFI, ADG and BF, respectively. The contribution per SNP to total genomic variance was similar among annotated classes across different traits. Predictive performance of SNP classes did not significantly differ from randomized SNP...

Expanded microbial genome coverage and improved protein family annotation in the COG database.

Science.gov (United States)

Galperin, Michael Y; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2015-01-01

Microbial genome sequencing projects produce numerous sequences of deduced proteins, only a small fraction of which have been or will ever be studied experimentally. This leaves sequence analysis as the only feasible way to annotate these proteins and assign to them tentative functions. The Clusters of Orthologous Groups of proteins (COGs) database (http://www.ncbi.nlm.nih.gov/COG/), first created in 1997, has been a popular tool for functional annotation. Its success was largely based on (i) its reliance on complete microbial genomes, which allowed reliable assignment of orthologs and paralogs for most genes; (ii) orthology-based approach, which used the function(s) of the characterized member(s) of the protein family (COG) to assign function(s) to the entire set of carefully identified orthologs and describe the range of potential functions when there were more than one; and (iii) careful manual curation of the annotation of the COGs, aimed at detailed prediction of the biological function(s) for each COG while avoiding annotation errors and overprediction. Here we present an update of the COGs, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level. This re-analysis of the COGs shows that the original COG assignments had an error rate below 0.5% and allows an assessment of the progress in functional genomics in the past 12 years. During this time, functions of many previously uncharacterized COGs have been elucidated and tentative functional assignments of many COGs have been validated, either by targeted experiments or through the use of high-throughput methods. A particularly important development is the assignment of functions to several widespread, conserved proteins many of which turned out to participate in translation, in particular rRNA maturation and tRNA modification. The new version of the

Connecting Returned Apollo Soils and Remote Sensing: Application to the Diviner Lunar Radiometer

Science.gov (United States)

Greenhagen, B. T.; DonaldsonHanna, K. L.; Thomas, I. R.; Bowles, N. E.; Allen, Carlton C.; Pieters, C. M.; Paige, D. A.

2014-01-01

The Diviner Lunar Radiometer, onboard NASA's Lunar Reconnaissance Orbiter, has produced the first global, high resolution, thermal infrared observations of an airless body. The Moon, which is the most accessible member of this most abundant class of solar system objects, is also the only body for which we have extraterrestrial samples with known spatial context, returned Apollo samples. Here we present the results of a comprehensive study to reproduce an accurate simulated lunar environment, evaluate the most appropriate sample and measurement conditions, collect thermal infrared spectra of a representative suite of Apollo soils, and correlate them with Diviner observations of the lunar surface. It has been established previously that thermal infrared spectra measured in simulated lunar environment (SLE) are significantly altered from spectra measured under terrestrial or martian conditions. The data presented here were collected at the University of Oxford Simulated Lunar Environment Chamber (SLEC). In SLEC, we simulate the lunar environment by: (1) pumping the chamber to vacuum pressures (less than 10-4 mbar) sufficient to simulate lunar heat transport processes within the sample, (2) cooling the chamber with liquid nitrogen to simulate radiation to the cold space environment, and (3) heating the samples with heaters and lamp to set-up thermal gradients similar to those experienced in the upper hundreds of microns of the lunar surface. We then conducted a comprehensive suite of experiments using different sample preparation and heating conditions on Apollo soils 15071 (maria) and 67701 (highland) and compared the results to Diviner noontime data to select the optimal experimental conditions. This study includes thermal infrared SLE measurements of 10084 (A11 - LM), 12001 (A12 - LM), 14259 (A14 - LM), 15071 (A15 - S1), 15601 (A15 - S9a), 61141 (A16 - S1), 66031 (A16 - S6), 67701 (A16 - S11), and 70181 (A17 - LM). The Diviner dataset includes all six Apollo sites

Creating New Medical Ontologies for Image Annotation A Case Study

CERN Document Server

Stanescu, Liana; Brezovan, Marius; Mihai, Cristian Gabriel

2012-01-01

Creating New Medical Ontologies for Image Annotation focuses on the problem of the medical images automatic annotation process, which is solved in an original manner by the authors. All the steps of this process are described in detail with algorithms, experiments and results. The original algorithms proposed by authors are compared with other efficient similar algorithms. In addition, the authors treat the problem of creating ontologies in an automatic way, starting from Medical Subject Headings (MESH). They have presented some efficient and relevant annotation models and also the basics of the annotation model used by the proposed system: Cross Media Relevance Models. Based on a text query the system will retrieve the images that contain objects described by the keywords.

Restoration of Apollo Data by the NSSDC and the PDS Lunar Data Node

Science.gov (United States)

Williams, David R.; Hills, H. Kent; Lowman, Paul D.; Taylor, Patrick T.; Guinness, Edward A.

2011-01-01

The Lunar Data Node (LDN), under the auspices of the Geosciences Node of the Planetary Data System (PDS), is restoring Apollo data archived at the National Space Science Data Center. The Apollo data were arch ived on older media (7 -track tapes. microfilm, microfiche) and in ob solete digital formats, which limits use of the data. The LDN is maki ng these data accessible by restoring them to standard formats and archiving them through PDS. The restoration involves reading the older m edia, collecting supporting data (metadata), deciphering and understa nding the data, and organizing into a data set. The data undergo a pe er review before archive at PDS. We will give an update on last year' s work. We have scanned notebooks from Otto Berg, P.1. for the Lunar Ejecta and Meteorites Experiment. These notebooks contain information on the data and calibration coefficients which we hope to be able to use to restore the raw data into a usable archive. We have scanned Ap ollo 14 and 15 Dust Detector data from microfilm and are in the proce ss of archiving thc scans with PDS. We are also restoring raw dust de tector data from magnetic tape supplied by Yosio Nakamura (UT Austin) . Seiichi Nagihara (Texas Tech Univ.) and others in cooperation with NSSDC are recovering ARCSAV tapes (tapes containing raw data streams from all the ALSEP instruments). We will be preparing these data for archive with PDS. We are also in the process of recovering and archivi ng data not previously archived, from the Apollo 16 Gamma Ray Spectro meter and the Apollo 17 Infrared Spectrometer.

Elucidating high-dimensional cancer hallmark annotation via enriched ontology.

Science.gov (United States)

Yan, Shankai; Wong, Ka-Chun

2017-09-01

Cancer hallmark annotation is a promising technique that could discover novel knowledge about cancer from the biomedical literature. The automated annotation of cancer hallmarks could reveal relevant cancer transformation processes in the literature or extract the articles that correspond to the cancer hallmark of interest. It acts as a complementary approach that can retrieve knowledge from massive text information, advancing numerous focused studies in cancer research. Nonetheless, the high-dimensional nature of cancer hallmark annotation imposes a unique challenge. To address the curse of dimensionality, we compared multiple cancer hallmark annotation methods on 1580 PubMed abstracts. Based on the insights, a novel approach, UDT-RF, which makes use of ontological features is proposed. It expands the feature space via the Medical Subject Headings (MeSH) ontology graph and utilizes novel feature selections for elucidating the high-dimensional cancer hallmark annotation space. To demonstrate its effectiveness, state-of-the-art methods are compared and evaluated by a multitude of performance metrics, revealing the full performance spectrum on the full set of cancer hallmarks. Several case studies are conducted, demonstrating how the proposed approach could reveal novel insights into cancers. https://github.com/cskyan/chmannot. Copyright © 2017 Elsevier Inc. All rights reserved.

Report of Apollo 204 Review Board to the Administrator, National Aeronautics and Space Administration . Appendix F ; Schedule of Physical Evidence

Science.gov (United States)

1967-01-01

Immediately following the Apollo 204 accident of January 27, 1961. all associated equipment and material were impounded. Release of this equipment and material for normal use was under the close control of the Apollo 204 Review Board. Apollo Review Board Administrative Procedure No. 11, February 11, 1961, established the Apollo 204 Review Board Material Release Record (MRR). This MRR was the official form used to release material from full impoundment and was valid only after being approved by the Board and signed by a Member. The form was used as the authority to place any impounded item into one of the three Categories defined in Administrative Procedure No. 11. This appendix contains all of the authorized MRR's. Each item submitted on an MRR was given a control number; a description, including the part number and serial number; the relevance and location to the accident; any constraints before release; and the control category. The categories placed on the equipment were as follows: Category A - Items which may have a significant influence or bearing on the results or findings of the Apollo 204 Review Board; Category B - All material other than Category A which is considered relevant to the Apollo 204 Review Board investigation; Category C - Material released from Board jurisdiction. Several classes of equipment were released by special Board action prior to the establishment of the MRR system. The operating procedure for release of these classes is Enclosure F-l to this appendix.

Rescue and Preservation of Sample Data from the Apollo Missions to the Moon

Science.gov (United States)

Todd, Nancy S.; Zeigler, Ryan A.; Evans, Cindy A.; Lehnert, Kerstin

2016-01-01

Six Apollo missions landed on the Moon from 1969-72, returning to Earth 382 kg of lunar rock, soil, and core samples. These samples are among the best documented and preserved samples on Earth that have supported a robust research program for 45 years. From mission planning through sample collection, preliminary examination, and subsequent research, strict protocols and procedures are followed for handling and allocating Apollo subsamples, resulting in the production of vast amounts of documentation. Even today, hundreds of samples are allocated for research each year, building on the science foundation laid down by the early Apollo sample studies and combining new data from today's instrumentation, lunar remote sensing missions and lunar meteorites. Much sample information is available to researchers at curator.jsc.nasa.gov. Decades of analyses on lunar samples are published in LPSC proceedings volumes and other peer-reviewed journals, and tabulated in lunar sample compendia entries. However, for much of the 1969-1995 period, the processing documentation, individual and consortia analyses, and unpublished results exist only in analog forms or primitive digital formats that are either inaccessible or at risk of being lost forever because critical data from early investigators remain unpublished.

Rfam: annotating families of non-coding RNA sequences.

Science.gov (United States)

Daub, Jennifer; Eberhardt, Ruth Y; Tate, John G; Burge, Sarah W

2015-01-01

The primary task of the Rfam database is to collate experimentally validated noncoding RNA (ncRNA) sequences from the published literature and facilitate the prediction and annotation of new homologues in novel nucleotide sequences. We group homologous ncRNA sequences into "families" and related families are further grouped into "clans." We collate and manually curate data cross-references for these families from other databases and external resources. Our Web site offers researchers a simple interface to Rfam and provides tools with which to annotate their own sequences using our covariance models (CMs), through our tools for searching, browsing, and downloading information on Rfam families. In this chapter, we will work through examples of annotating a query sequence, collating family information, and searching for data.

A computational genomics pipeline for prokaryotic sequencing projects.

Science.gov (United States)

Kislyuk, Andrey O; Katz, Lee S; Agrawal, Sonia; Hagen, Matthew S; Conley, Andrew B; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C; Sammons, Scott A; Govil, Dhwani; Mair, Raydel D; Tatti, Kathleen M; Tondella, Maria L; Harcourt, Brian H; Mayer, Leonard W; Jordan, I King

2010-08-01

New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.

Intra-species sequence comparisons for annotating genomes

Energy Technology Data Exchange (ETDEWEB)

Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

2004-07-15

Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome

Directory of Open Access Journals (Sweden)

McCarthy Fiona M

2007-11-01

Full Text Available Abstract Background The chicken genome was sequenced because of its phylogenetic position as a non-mammalian vertebrate, its use as a biomedical model especially to study embryology and development, its role as a source of human disease organisms and its importance as the major source of animal derived food protein. However, genomic sequence data is, in itself, of limited value; generally it is not equivalent to understanding biological function. The benefit of having a genome sequence is that it provides a basis for functional genomics. However, the sequence data currently available is poorly structurally and functionally annotated and many genes do not have standard nomenclature assigned. Results We analysed eight chicken tissues and improved the chicken genome structural annotation by providing experimental support for the in vivo expression of 7,809 computationally predicted proteins, including 30 chicken proteins that were only electronically predicted or hypothetical translations in human. To improve functional annotation (based on Gene Ontology, we mapped these identified proteins to their human and mouse orthologs and used this orthology to transfer Gene Ontology (GO functional annotations to the chicken proteins. The 8,213 orthology-based GO annotations that we produced represent an 8% increase in currently available chicken GO annotations. Orthologous chicken products were also assigned standardized nomenclature based on current chicken nomenclature guidelines. Conclusion We demonstrate the utility of high-throughput expression proteomics for rapid experimental structural annotation of a newly sequenced eukaryote genome. These experimentally-supported predicted proteins were further annotated by assigning the proteins with standardized nomenclature and functional annotation. This method is widely applicable to a diverse range of species. Moreover, information from one genome can be used to improve the annotation of other genomes and

Automatically annotating topics in transcripts of patient-provider interactions via machine learning.

Science.gov (United States)

Wallace, Byron C; Laws, M Barton; Small, Kevin; Wilson, Ira B; Trikalinos, Thomas A

2014-05-01

Annotated patient-provider encounters can provide important insights into clinical communication, ultimately suggesting how it might be improved to effect better health outcomes. But annotating outpatient transcripts with Roter or General Medical Interaction Analysis System (GMIAS) codes is expensive, limiting the scope of such analyses. We propose automatically annotating transcripts of patient-provider interactions with topic codes via machine learning. We use a conditional random field (CRF) to model utterance topic probabilities. The model accounts for the sequential structure of conversations and the words comprising utterances. We assess predictive performance via 10-fold cross-validation over GMIAS-annotated transcripts of 360 outpatient visits (>230,000 utterances). We then use automated in place of manual annotations to reproduce an analysis of 116 additional visits from a randomized trial that used GMIAS to assess the efficacy of an intervention aimed at improving communication around antiretroviral (ARV) adherence. With respect to 6 topic codes, the CRF achieved a mean pairwise kappa compared with human annotators of 0.49 (range: 0.47-0.53) and a mean overall accuracy of 0.64 (range: 0.62-0.66). With respect to the RCT reanalysis, results using automated annotations agreed with those obtained using manual ones. According to the manual annotations, the median number of ARV-related utterances without and with the intervention was 49.5 versus 76, respectively (paired sign test P = 0.07). When automated annotations were used, the respective numbers were 39 versus 55 (P = 0.04). While moderately accurate, the predicted annotations are far from perfect. Conversational topics are intermediate outcomes, and their utility is still being researched. This foray into automated topic inference suggests that machine learning methods can classify utterances comprising patient-provider interactions into clinically relevant topics with reasonable accuracy.

Basin Contributions to the Stratigraphy of the Apollo 16 Landing Site

Science.gov (United States)

Haskin, Larry A.

2001-01-01

Ejecta deposit modeling suggests that the megaregolith at the Apollo 16 landing site is dominated by Imbrium and Serenitatis ejecta, and Nectaris ejecta are a minor componen Additional information is contained in the original extended abstract.t.

Annotating risk factors for heart disease in clinical narratives for diabetic patients.

Science.gov (United States)

Stubbs, Amber; Uzuner, Özlem

2015-12-01

The 2014 i2b2/UTHealth natural language processing shared task featured a track focused on identifying risk factors for heart disease (specifically, Cardiac Artery Disease) in clinical narratives. For this track, we used a "light" annotation paradigm to annotate a set of 1304 longitudinal medical records describing 296 patients for risk factors and the times they were present. We designed the annotation task for this track with the goal of balancing annotation load and time with quality, so as to generate a gold standard corpus that can benefit a clinically-relevant task. We applied light annotation procedures and determined the gold standard using majority voting. On average, the agreement of annotators with the gold standard was above 0.95, indicating high reliability. The resulting document-level annotations generated for each record in each longitudinal EMR in this corpus provide information that can support studies of progression of heart disease risk factors in the included patients over time. These annotations were used in the Risk Factor track of the 2014 i2b2/UTHealth shared task. Participating systems achieved a mean micro-averaged F1 measure of 0.815 and a maximum F1 measure of 0.928 for identifying these risk factors in patient records. Copyright © 2015 Elsevier Inc. All rights reserved.

Annotating Emotions in Meetings

NARCIS (Netherlands)

Reidsma, Dennis; Heylen, Dirk K.J.; Ordelman, Roeland J.F.

We present the results of two trials testing procedures for the annotation of emotion and mental state of the AMI corpus. The first procedure is an adaptation of the FeelTrace method, focusing on a continuous labelling of emotion dimensions. The second method is centered around more discrete

Stratigraphy and depositional history of the Apollo 17 drill core

Science.gov (United States)

Taylor, G. J.; Warner, R. D.; Keil, K.

1979-01-01

Lithologic abundances obtained from modal analyses of a continuous string of polished thin sections indicate that the Apollo 17 deep drill core can be divided into three main zones: An upper zone (0-19 cm depth) characterized by high abundances of agglutinates (30%) and a high ratio of mare to non-mare lithic fragments (less than 0.8); a coarse-grained layer (24-56 cm) rich in fragments of high-Ti mare basalts and mineral fragments derived from them, and poor in agglutinates (6%); and a lower zone (56-285 cm) characterized by variable but generally high agglutinate abundances (25%) and a low ratio of mare to nonmare lithic fragments (0.6). Using observations of the geology of the landing site, the principles of cratering dynamics, and the vast amount of data collected on the core, the following depositional history for the section of regolith sampled by the Apollo 17 drill core: was devised.

Estimation of Apollo Lunar Dust Transport using Optical Extinction Measurements

Science.gov (United States)

Lane, John E.; Metzger, Philip T.

2015-04-01

A technique to estimate mass erosion rate of surface soil during landing of the Apollo Lunar Module (LM) and total mass ejected due to the rocket plume interaction is proposed and tested. The erosion rate is proportional to the product of the second moment of the lofted particle size distribution N(D), and third moment of the normalized soil size distribution S(D), divided by the integral of S(D)ṡD2/v(D), where D is particle diameter and v(D) is the vertical component of particle velocity. The second moment of N(D) is estimated by optical extinction analysis of the Apollo cockpit video. Because of the similarity between mass erosion rate of soil as measured by optical extinction and rainfall rate as measured by radar reflectivity, traditional NWS radar/rainfall correlation methodology can be applied to the lunar soil case where various S(D) models are assumed corresponding to specific lunar sites.

Consumer energy research: an annotated bibliography. Vol. 3

Energy Technology Data Exchange (ETDEWEB)

Anderson, D.C.; McDougall, G.H.G.

1983-04-01

This annotated bibliography attempts to provide a comprehensive package of existing information in consumer related energy research. A concentrated effort was made to collect unpublished material as well as material from journals and other sources, including governments, utilities research institutes and private firms. A deliberate effort was made to include agencies outside North America. For the most part the bibliography is limited to annotations of empiracal studies. However, it includes a number of descriptive reports which appear to make a significant contribution to understanding consumers and energy use. The format of the annotations displays the author, date of publication, title and source of the study. Annotations of empirical studies are divided into four parts: objectives, methods, variables and findings/implications. Care was taken to provide a reasonable amount of detail in the annotations to enable the reader to understand the methodology, the results and the degree to which the implications fo the study can be generalized to other situations. Studies are arranged alphabetically by author. The content of the studies reviewed is classified in a series of tables which are intended to provide a summary of sources, types and foci of the various studies. These tables are intended to aid researchers interested in specific topics to locate those studies most relevant to their work. The studies are categorized using a number of different classification criteria, for example, methodology used, type of energy form, type of policy initiative, and type of consumer activity. A general overview of the studies is also presented. 17 tabs.

Portrait of Astronaut Neil A. Armstrong, commander of Apollo 11 mission

Science.gov (United States)

1969-01-01

Portrait of Astronaut Neil A. Armstrong, commander of the Apollo 11 Lunar Landing mission in his space suit, with his helmet on the table in front of him. Behind him is a large photograph of the lunar surface.

m6ASNP: a tool for annotating genetic variants by m6A function.

Science.gov (United States)

Jiang, Shuai; Xie, Yubin; He, Zhihao; Zhang, Ya; Zhao, Yuli; Chen, Li; Zheng, Yueyuan; Miao, Yanyan; Zuo, Zhixiang; Ren, Jian

2018-04-02

Large-scale genome sequencing projects have identified many genetic variants for diverse diseases. A major goal of these projects is to characterize these genetic variants to provide insight into their function and roles in diseases. N6-methyladenosine (m6A) is one of the most abundant RNA modifications in eukaryotes. Recent studies have revealed that aberrant m6A modifications are involved in many diseases. In this study, we present a user-friendly web server called "m6ASNP" that is dedicated to the identification of genetic variants targeting m6A modification sites. A random forest model was implemented in m6ASNP to predict whether the methylation status of a m6A site is altered by the variants surrounding the site. In m6ASNP, genetic variants in a standard VCF format are accepted as the input data, and the output includes an interactive table containing the genetic variants annotated by m6A function. In addition, statistical diagrams and a genome browser are provided to visualize the characteristics and annotate the genetic variants. We believe that m6ASNP is a highly convenient tool that can be used to boost further functional studies investigating genetic variants. The web server "m6ASNP" is implemented in JAVA and PHP and is freely available at http://m6asnp.renlab.org.

APOLLO: a quality assessment service for single and multiple protein models.

Science.gov (United States)

Wang, Zheng; Eickholt, Jesse; Cheng, Jianlin

2011-06-15

We built a web server named APOLLO, which can evaluate the absolute global and local qualities of a single protein model using machine learning methods or the global and local qualities of a pool of models using a pair-wise comparison approach. Based on our evaluations on 107 CASP9 (Critical Assessment of Techniques for Protein Structure Prediction) targets, the predicted quality scores generated from our machine learning and pair-wise methods have an average per-target correlation of 0.671 and 0.917, respectively, with the true model quality scores. Based on our test on 92 CASP9 targets, our predicted absolute local qualities have an average difference of 2.60 Å with the actual distances to native structure. http://sysbio.rnet.missouri.edu/apollo/. Single and pair-wise global quality assessment software is also available at the site.

Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.

Science.gov (United States)

Xiang, Zuoshuang; Zheng, Jie; Lin, Yu; He, Yongqun

2015-01-01

It is time-consuming to build an ontology with many terms and axioms. Thus it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a recurrent modeling problem in the context of ontology engineering. Because ontology terms often follow specific ODPs, the Ontology for Biomedical Investigations (OBI) developers proposed a Quick Term Templates (QTTs) process targeted at generating new ontology classes following the same pattern, using term templates in a spreadsheet format. Inspired by the ODPs and QTTs, the Ontorat web application is developed to automatically generate new ontology terms, annotations of terms, and logical axioms based on a specific ODP(s). The inputs of an Ontorat execution include axiom expression settings, an input data file, ID generation settings, and a target ontology (optional). The axiom expression settings can be saved as a predesigned Ontorat setting format text file for reuse. The input data file is generated based on a template file created by a specific ODP (text or Excel format). Ontorat is an efficient tool for ontology expansion. Different use cases are described. For example, Ontorat was applied to automatically generate over 1,000 Japan RIKEN cell line cell terms with both logical axioms and rich annotation axioms in the Cell Line Ontology (CLO). Approximately 800 licensed animal vaccines were represented and annotated in the Vaccine Ontology (VO) by Ontorat. The OBI team used Ontorat to add assay and device terms required by ENCODE project. Ontorat was also used to add missing annotations to all existing Biobank specific terms in the Biobank Ontology. A collection of ODPs and templates with examples are provided on the Ontorat website and can be reused to facilitate ontology development. With ever increasing ontology development and applications, Ontorat provides a timely platform for generating and annotating a large number of ontology terms by following

Image annotation based on positive-negative instances learning

Science.gov (United States)

Zhang, Kai; Hu, Jiwei; Liu, Quan; Lou, Ping

2017-07-01

Automatic image annotation is now a tough task in computer vision, the main sense of this tech is to deal with managing the massive image on the Internet and assisting intelligent retrieval. This paper designs a new image annotation model based on visual bag of words, using the low level features like color and texture information as well as mid-level feature as SIFT, and mixture the pic2pic, label2pic and label2label correlation to measure the correlation degree of labels and images. We aim to prune the specific features for each single label and formalize the annotation task as a learning process base on Positive-Negative Instances Learning. Experiments are performed using the Corel5K Dataset, and provide a quite promising result when comparing with other existing methods.

Design development of the Apollo command and service module thrust vector attitude control systems

Science.gov (United States)

Peters, W. H.

1978-01-01

Development of the Apollo thrust vector control digital autopilot (TVC DAP) was summarized. This is the control system that provided pitch and yaw attitude control during velocity change maneuvers using the main rocket engine on the Apollo service module. A list of ten primary functional requirements for this control system are presented, each being subordinate to a more general requirement appearing earlier on the list. Development process functions were then identified and the essential information flow paths were explored. This provided some visibility into the particular NASA/contractor interface, as well as relationships between the many individual activities.

An Annotated Dataset of 14 Meat Images

DEFF Research Database (Denmark)

Stegmann, Mikkel Bille

2002-01-01

This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given.......This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given....

Graph-based sequence annotation using a data integration approach

Directory of Open Access Journals (Sweden)

Pesch Robert

2008-06-01

Full Text Available The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara- Cyc which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation.

The Dust Management Project: Final Report

Science.gov (United States)

Hyatt, Mark J.; Straka, Sharon

2011-01-01

A return to the Moon to extend human presence, pursue scientific activities, use the Moon to prepare for future human missions to Mars, and expand Earth s economic sphere, will require investment in developing new technologies and capabilities to achieve affordable and sustainable human exploration. From the operational experience gained and lessons learned during the Apollo missions, conducting longterm operations in the lunar environment will be a particular challenge, given the difficulties presented by the unique physical properties and other characteristics of lunar regolith, including dust. The Apollo missions and other lunar explorations have identified significant lunar dust-related problems that will challenge future mission success. Comprised of regolith particles ranging in size from tens of nanometers to microns, lunar dust is a manifestation of the complex interaction of the lunar soil with multiple mechanical, electrical, and gravitational effects. The environmental and anthropogenic factors effecting the perturbation, transport, and deposition of lunar dust must be studied in order to mitigate it s potentially harmful effects on exploration systems and human explorers. The Dust Management Project (DMP) is tasked with the evaluation of lunar dust effects, assessment of the resulting risks, and development of mitigation and management strategies and technologies related to Exploration Systems architectures. To this end, the DMP supports the overall goal of the Exploration Technology Development Program (ETDP) of addressing the relevant high priority technology needs of multiple elements within the Constellation Program (CxP) and sister ETDP projects. Project scope, approach, accomplishments, summary of deliverables, and lessons learned are presented.

Engineering aspects of the experiment and results of animal tests. [Apollo 17 Biological Cosmic Ray Experiment

Science.gov (United States)

Look, B. C.; Tremor, J. W.; Barrows, W. F.; Zabower, H. R.; Suri, K.; Park, E. G., Jr.; Durso, J. A.; Leon, H. A.; Haymaker, W.; Lindberg, R. G.

1975-01-01

A closed passive system independent of support from the spacecraft or its crew was developed to house five pocket mice for their flight on Apollo XVII. The reaction of potassium superoxide with carbon dioxide and water vapor to produce oxygen provided a habitable atmosphere within the experiment package. The performance of the system and the ability of the mice to survive the key preflight tests gave reasonable assurance that the mice would also withstand the Apollo flight.-

Lunar heat flow: Regional prospective of the Apollo landing sites

Science.gov (United States)

Siegler, M. A.; Smrekar, S. E.

2014-01-01

reexamine the Apollo Heat Flow Experiment in light of new orbital data. Using three-dimensional thermal conduction models, we examine effects of crustal thickness, density, and radiogenic abundance on measured heat flow values at the Apollo 15 and 17 sites. These models show the importance of regional context on heat flux measurements. We find that measured heat flux can be greatly altered by deep subsurface radiogenic content and crustal density. However, total crustal thickness and the presence of a near-surface radiogenic-rich ejecta provide less leverage, representing only minor (<1.5 mW m-2) perturbations on surface heat flux. Using models of the crust implied by Gravity Recovery and Interior Laboratory results, we found that a roughly 9-13 mW m-2 mantle heat flux best approximate the observed heat flux. This equates to a total mantle heat production of 2.8-4.1 × 1011 W. These heat flow values could imply that the lunar interior is slightly less radiogenic than the Earth's mantle, perhaps implying that a considerable fraction of terrestrial mantle material was incorporated at the time of formation. These results may also imply that heat flux at the crust-mantle boundary beneath the Procellarum potassium, rare earth element, and phosphorus (KREEP) Terrane (PKT) is anomalously elevated compared to the rest of the Moon. These results also suggest that a limited KREEP-rich layer exists beneath the PKT crust. If a subcrustal KREEP-rich layer extends below the Apollo 17 landing site, required mantle heat flux can drop to roughly 7 mW m-2, underlining the need for future heat flux measurements outside of the radiogenic-rich PKT region.

EST-PAC a web package for EST annotation and protein sequence prediction

Directory of Open Access Journals (Sweden)

Strahm Yvan

2006-10-01

Full Text Available Abstract With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1 searching local or remote biological databases for sequence similarities using Blast services, 2 predicting protein coding sequence from EST data and, 3 annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.

An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets.

Science.gov (United States)

Hosseini, Parsa; Tremblay, Arianne; Matthews, Benjamin F; Alkharouf, Nadim W

2010-07-02

The data produced by an Illumina flow cell with all eight lanes occupied, produces well over a terabyte worth of images with gigabytes of reads following sequence alignment. The ability to translate such reads into meaningful annotation is therefore of great concern and importance. Very easily, one can get flooded with such a great volume of textual, unannotated data irrespective of read quality or size. CASAVA, a optional analysis tool for Illumina sequencing experiments, enables the ability to understand INDEL detection, SNP information, and allele calling. To not only extract from such analysis, a measure of gene expression in the form of tag-counts, but furthermore to annotate such reads is therefore of significant value. We developed TASE (Tag counting and Analysis of Solexa Experiments), a rapid tag-counting and annotation software tool specifically designed for Illumina CASAVA sequencing datasets. Developed in Java and deployed using jTDS JDBC driver and a SQL Server backend, TASE provides an extremely fast means of calculating gene expression through tag-counts while annotating sequenced reads with the gene's presumed function, from any given CASAVA-build. Such a build is generated for both DNA and RNA sequencing. Analysis is broken into two distinct components: DNA sequence or read concatenation, followed by tag-counting and annotation. The end result produces output containing the homology-based functional annotation and respective gene expression measure signifying how many times sequenced reads were found within the genomic ranges of functional annotations. TASE is a powerful tool to facilitate the process of annotating a given Illumina Solexa sequencing dataset. Our results indicate that both homology-based annotation and tag-count analysis are achieved in very efficient times, providing researchers to delve deep in a given CASAVA-build and maximize information extraction from a sequencing dataset. TASE is specially designed to translate sequence data

BEACON: automated tool for Bacterial GEnome Annotation ComparisON

KAUST Repository

Kalkatawi, Manal M.; Alam, Intikhab; Bajic, Vladimir B.

2015-01-01

We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project

Directory of Open Access Journals (Sweden)

McDonagh Paul D

2003-06-01

Full Text Available Abstract Background Seattle Biomedical Research Institute (SBRI as part of the Leishmania Genome Network (LGN is sequencing chromosomes of the trypanosomatid protozoan species Leishmania major. At SBRI, chromosomal sequence is annotated using a combination of trained and untrained non-consensus gene-prediction algorithms with ARTEMIS, an annotation platform with rich and user-friendly interfaces. Results Here we describe a methodology used to import results from three different protein-coding gene-prediction algorithms (GLIMMER, TESTCODE and GENESCAN into the ARTEMIS sequence viewer and annotation tool. Comparison of these methods, along with the CODONUSAGE algorithm built into ARTEMIS, shows the importance of combining methods to more accurately annotate the L. major genomic sequence. Conclusion An improvised and powerful tool for gene prediction has been developed by importing data from widely-used algorithms into an existing annotation platform. This approach is especially fruitful in the Leishmania genome project where there is large proportion of novel genes requiring manual annotation.

The 1000 bull genome project

Science.gov (United States)

To meet growing global demands for high value protein from milk and meat, rates of genetic gain in domestic cattle must be accelerated. At the same time, animal health and welfare must be considered. The 1000 bull genomes project supports these goals by providing annotated sequence variants and ge...

PUBLIC AFFAIRS DIRECTOR HUGH HARRIS SPEAKS AT THE APOLLO/SATURN V CENTER RIBBON-CUTTING CEREMONY

Science.gov (United States)

1996-01-01

NASA/KSC Public Affairs Director Hugh W. Harris gives the welcome and introductions at the ribbon-cutting ceremony to officially open the new Apollo/Saturn V Center, part of the Kennedy Space Center Visitor Center. The 100,000- square-foot facility includes two theaters, various exhibits and an Apollo-era Saturn V rocket, which formerly was on display outside the Vehicle Assembly Building and is one of only three moon rockets remaining in existence. The new center is located off the Kennedy Parkway at the Banana Creek launch viewing site.

The Apollo Number: space suits, self-support, and the walk-run transition.

Directory of Open Access Journals (Sweden)

Christopher E Carr

Full Text Available BACKGROUND: How space suits affect the preferred walk-run transition is an open question with relevance to human biomechanics and planetary extravehicular activity. Walking and running energetics differ; in reduced gravity (<0.5 g, running, unlike on Earth, uses less energy per distance than walking. METHODOLOGY/PRINCIPAL FINDINGS: The walk-run transition (denoted * correlates with the Froude Number (Fr = v(2/gL, velocity v, gravitational acceleration g, leg length L. Human unsuited Fr* is relatively constant (approximately 0.5 with gravity but increases substantially with decreasing gravity below approximately 0.4 g, rising to 0.9 in 1/6 g; space suits appear to lower Fr*. Because of pressure forces, space suits partially (1 g or completely (lunar-g support their own weight. We define the Apollo Number (Ap = Fr/M as an expected invariant of locomotion under manipulations of M, the ratio of human-supported to total transported mass. We hypothesize that for lunar suited conditions Ap* but not Fr* will be near 0.9, because the Apollo Number captures the effect of space suit self-support. We used the Apollo Lunar Surface Journal and other sources to identify 38 gait events during lunar exploration for which we could determine gait type (walk/lope/run and calculate Ap. We estimated the binary transition between walk/lope (0 and run (1, yielding Fr* (0.36+/-0.11, mean+/-95% CI and Ap* (0.68+/-0.20. CONCLUSIONS/SIGNIFICANCE: The Apollo Number explains 60% of the difference between suited and unsuited Fr*, appears to capture in large part the effects of space suits on the walk-run transition, and provides several testable predictions for space suit locomotion and, of increasing relevance here on Earth, exoskeleton locomotion. The knowledge of how space suits affect gait transitions can be used to optimize space suits for use on the Moon and Mars.

Automatic medical image annotation and keyword-based image retrieval using relevance feedback.

Science.gov (United States)

Ko, Byoung Chul; Lee, JiHyeon; Nam, Jae-Yeal

2012-08-01

This paper presents novel multiple keywords annotation for medical images, keyword-based medical image retrieval, and relevance feedback method for image retrieval for enhancing image retrieval performance. For semantic keyword annotation, this study proposes a novel medical image classification method combining local wavelet-based center symmetric-local binary patterns with random forests. For keyword-based image retrieval, our retrieval system use the confidence score that is assigned to each annotated keyword by combining probabilities of random forests with predefined body relation graph. To overcome the limitation of keyword-based image retrieval, we combine our image retrieval system with relevance feedback mechanism based on visual feature and pattern classifier. Compared with other annotation and relevance feedback algorithms, the proposed method shows both improved annotation performance and accurate retrieval results.

Annotated bibliography National Environmental Policy Act (NEPA) documents for Sandia National Laboratories

International Nuclear Information System (INIS)

Harris, J.M.

1995-04-01

The following annotated bibliography lists documents prepared by the Department of Energy (DOE), and predecessor agencies, to meet the requirements of the National Environmental Policy Act (NEPA) for activities and facilities at Sandia National Laboratories sites. For each NEPA document summary information and a brief discussion of content is provided. This information may be used to reduce the amount of time or cost associated with NEPA compliance for future Sandia National Laboratories projects. This summary may be used to identify model documents, documents to use as sources of information, or documents from which to tier additional NEPA documents

Annotated bibliography National Environmental Policy Act (NEPA) documents for Sandia National Laboratories

Energy Technology Data Exchange (ETDEWEB)

Harris, J.M.

1995-04-01

The following annotated bibliography lists documents prepared by the Department of Energy (DOE), and predecessor agencies, to meet the requirements of the National Environmental Policy Act (NEPA) for activities and facilities at Sandia National Laboratories sites. For each NEPA document summary information and a brief discussion of content is provided. This information may be used to reduce the amount of time or cost associated with NEPA compliance for future Sandia National Laboratories projects. This summary may be used to identify model documents, documents to use as sources of information, or documents from which to tier additional NEPA documents.

Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology.

Science.gov (United States)

Hu, Yang; Zhou, Wenyang; Ren, Jun; Dong, Lixiang; Wang, Yadong; Jin, Shuilin; Cheng, Liang

2016-01-01

Increasing evidences indicated that function annotation of human genome in molecular level and phenotype level is very important for systematic analysis of genes. In this study, we presented a framework named Gene2Function to annotate Gene Reference into Functions (GeneRIFs), in which each functional description of GeneRIFs could be annotated by a text mining tool Open Biomedical Annotator (OBA), and each Entrez gene could be mapped to Human Genome Organisation Gene Nomenclature Committee (HGNC) gene symbol. After annotating all the records about human genes of GeneRIFs, 288,869 associations between 13,148 mRNAs and 7,182 terms, 9,496 associations between 948 microRNAs and 533 terms, and 901 associations between 139 long noncoding RNAs (lncRNAs) and 297 terms were obtained as a comprehensive annotation resource of human genome. High consistency of term frequency of individual gene (Pearson correlation = 0.6401, p = 2.2e - 16) and gene frequency of individual term (Pearson correlation = 0.1298, p = 3.686e - 14) in GeneRIFs and GOA shows our annotation resource is very reliable.

Visibility of lunar surface features - Apollo 14 orbital observations and lunar landing.

Science.gov (United States)

Ziedman, K.

1972-01-01

Description of an in-flight visibility test conducted during the Apollo 14 mission for the purpose of validating and extending the mathematical visibility models used previously in the course of the Apollo program to examine the constraints on descent operations imposed by lunar visibility limitations. Following a background review of the effects on mission planning of the visibility limitations due to downsun lunar surface detail 'washout' and a discussion of the visibility prediction techniques previously used for studying lunar visibility problems, the visibility test rationale and procedures are defined and the test results presented. The results appear to confirm the validity of the visibility prediction techniques employed in lunar visibility problem studies. These results provide also a basis for improving the accuracy of the prediction techniques by appropriate modifications.

Vesicles in Apollo 15 Green Glasses: The Nature of Ancient Lunar Gases

Science.gov (United States)

Thomas-Keprta, K. L.; Clemett, S. J.; Berger, E. L.; Rahman, Z.; McKay, D. S.; Gibson, E. K.; Wentworth, S. J.

2014-01-01

Detailed studies of Apollo 15 green glass and related beads have shown they were formed in gas-rich fire fountains.. As the magmatic fluid became super-saturated in volatile gas, bubbles or vesicles formed within the magma. These exsolved gases became trapped within vesicles as the glasses were ejected from the fire-fountain and subsequently quenched. One of the keys to understanding formation processes on the ancient moon includes determining the composition of volatile species and elements, including metals, dissolved in magmatic gases. Here we report the nature of mineral phases spatially associated with vesicles in a green glass bead from Apollo sample 15411,42. The phases reflect the composition of the cooling/degassing magmatic vapors and fluids present at the time of bead formation approx, 3 Ga ago

Apollo - An advanced fuel fusion power reactor for the 21st century

International Nuclear Information System (INIS)

Kulcinski, G.L.; Emmert, G.A.; Blanchard, J.P.

1989-01-01

A preconceptual design of a tokamak reactor fueled by a D-He-3 plasma is presented. A low aspect ratio (A=2-4) device is studied here but high aspect ratio devices (A > 6) may also be quite attractive. The Apollo D-He-3 tokamak capitalizes on recent advances in high field magnets (20 T) and utilizes rectennas to convert the synchrotron radiation directly to electricity. The overall efficiency ranges from 37 to 52% depending on whether the bremsstrahlung energy is utilized. The low neutron wall loading (0.1 MW/m/sup 2/) allows a permanent first wall to be designed and the low nuclear decay heat enables the reactor to be classed as inherently safe. The cost of electricity from Apollo is > 40% lower than electricity from a similar sized DT reactor

Effects of Apollo 12 lunar material on lipid levels of tobacco tissue and slash pine cultures

Science.gov (United States)

Weete, J. D.

1972-01-01

Investigations of the lipid components of pine tissues (Pinus elloitii) are discussed, emphasizing fatty acids and steroids. The response by slash pine tissue cultures to growth in contact with Apollo lunar soil, earth basalt, and Iowa soil is studied. Tissue cultures of tobacco grown for 12 weeks in contact with lunar material from Apollo 12 flight contained 21 to 35 percent more total pigment than control tissues. No differences were noted in the fresh or dry weight of the experimental and control samples.

Annotation: The Savant Syndrome

Science.gov (United States)

Heaton, Pamela; Wallace, Gregory L.

2004-01-01

Background: Whilst interest has focused on the origin and nature of the savant syndrome for over a century, it is only within the past two decades that empirical group studies have been carried out. Methods: The following annotation briefly reviews relevant research and also attempts to address outstanding issues in this research area.…

Annotation and Curation of Uncharacterized proteins- Challenges

Directory of Open Access Journals (Sweden)

Johny eIjaq

2015-03-01

Full Text Available Hypothetical Proteins are the proteins that are predicted to be expressed from an open reading frame (ORF, constituting a substantial fraction of proteomes in both prokaryotes and eukaryotes. Genome projects have led to the identification of many therapeutic targets, the putative function of the protein and their interactions. In this review we have enlisted various methods. Annotation linked to structural and functional prediction of hypothetical proteins assist in the discovery of new structures and functions serving as markers and pharmacological targets for drug designing, discovery and screening. Mass spectrometry is an analytical technique for validating protein characterisation. Matrix-assisted laser desorption ionization–mass spectrometry (MALDI-MS is an efficient analytical method. Microarrays and Protein expression profiles help understanding the biological systems through a systems-wide study of proteins and their interactions with other proteins and non-proteinaceous molecules to control complex processes in cells and tissues and even whole organism. Next generation sequencing technology accelerates multiple areas of genomics research.

Analysis of LYSA-calculus with explicit confidentiality annotations

DEFF Research Database (Denmark)

Gao, Han; Nielson, Hanne Riis

2006-01-01

Recently there has been an increased research interest in applying process calculi in the verification of cryptographic protocols due to their ability to formally model protocols. This work presents LYSA with explicit confidentiality annotations for indicating the expected behavior of target...... malicious activities performed by attackers as specified by the confidentiality annotations. The proposed analysis approach is fully automatic without the need of human intervention and has been applied successfully to a number of protocols....

First generation annotations for the fathead minnow (Pimephales promelas) genome

Science.gov (United States)

Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minno...

Apollo 15 yellow-brown volcanic glass: Chemistry and petrogenetic relations to green volcanic glass and olivine-normative mare basalts

Energy Technology Data Exchange (ETDEWEB)

Hughes, S.S.; Schmitt, R.A.; (Oregon State Univ., Corvallis (USA)); Delano, J.W. (State Univ. of New York, Albany (USA))

1988-10-01

Apollo 15 yellow-brown glass is one of twenty-five, high Mg, primary magmas emplaced on the lunar surface in pyroclastic eruptions. Forty spherules of this glass were individually analyzed by electron microprobe and INAA for major- and trace-elements. The abundances demonstrate that this primary magma was produced by partial melting of differentiated cumulates in the lunar mantle. Models are developed to explain the possible source-regions of several Apollo 15 and Apollo 12 low-Ti mare magmas as being products of hybridization involving three ancient differentiated components of a primordial lunar magma ocean: (a) early olivine {plus minus} orthopyroxene cumulates; (b) late-stage clinopyroxene + pigeonite + ilmenite + plagioclase cumulates; and (c) late-stage inter-cumulus liquid.

Extracting Cross-Ontology Weighted Association Rules from Gene Ontology Annotations.

Science.gov (United States)

Agapito, Giuseppe; Milano, Marianna; Guzzi, Pietro Hiram; Cannataro, Mario

2016-01-01

Gene Ontology (GO) is a structured repository of concepts (GO Terms) that are associated to one or more gene products through a process referred to as annotation. The analysis of annotated data is an important opportunity for bioinformatics. There are different approaches of analysis, among those, the use of association rules (AR) which provides useful knowledge, discovering biologically relevant associations between terms of GO, not previously known. In a previous work, we introduced GO-WAR (Gene Ontology-based Weighted Association Rules), a methodology for extracting weighted association rules from ontology-based annotated datasets. We here adapt the GO-WAR algorithm to mine cross-ontology association rules, i.e., rules that involve GO terms present in the three sub-ontologies of GO. We conduct a deep performance evaluation of GO-WAR by mining publicly available GO annotated datasets, showing how GO-WAR outperforms current state of the art approaches.

FE-SEM, FIB and TEM Study of Surface Deposits of Apollo 15 Green Glass Volcanic Spherules

Science.gov (United States)

Ross, Daniel K.; Thomas-Keprta, K. L.; Rahman, Z.; Wentworth, S. J.; McKay, D. S.

2011-01-01

Surface deposits on lunar pyroclastic green (Apollo 15) and orange (Apollo 17) glass spherules have been attributed to condensation from the gas clouds that accompanied fire-fountain eruptions. The fire fountains cast molten lava high above the lunar surface and the silicate melt droplets quenched before landing producing the glass beads. Early investigations showed that these deposits are rich in sulfur and zinc. The deposits are extremely fine-grained and thin, so that it was never possible to determine their chemical compositions cleanly by SEM/EDX or electron probe x-ray analysis because most of the excited volume was in the under-lying silicate glass. We are investigating the surface deposits by TEM, using focused ion beam (FIB) microscopy to extract and thin the surface deposits. Here we report on chemical mapping of a FIB section of surface deposits of an Apollo green glass bead 15401using the ultra-high resolution JEOL 2500 STEM located at NASA Johnson Space Center.

Graph-based sequence annotation using a data integration approach.

Science.gov (United States)

Pesch, Robert; Lysenko, Artem; Hindle, Matthew; Hassani-Pak, Keywan; Thiele, Ralf; Rawlings, Christopher; Köhler, Jacob; Taubert, Jan

2008-08-25

The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara-Cyc) which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation. The methods and algorithms presented in this publication are an integral part of the ONDEX system which is freely available from http://ondex.sf.net/.

Linking Disparate Datasets of the Earth Sciences with the SemantEco Annotator

Science.gov (United States)

Seyed, P.; Chastain, K.; McGuinness, D. L.

2013-12-01

Use of Semantic Web technologies for data management in the Earth sciences (and beyond) has great potential but is still in its early stages, since the challenges of translating data into a more explicit or semantic form for immediate use within applications has not been fully addressed. In this abstract we help address this challenge by introducing the SemantEco Annotator, which enables anyone, regardless of expertise, to semantically annotate tabular Earth Science data and translate it into linked data format, while applying the logic inherent in community-standard vocabularies to guide the process. The Annotator was conceived under a desire to unify dataset content from a variety of sources under common vocabularies, for use in semantically-enabled web applications. Our current use case employs linked data generated by the Annotator for use in the SemantEco environment, which utilizes semantics to help users explore, search, and visualize water or air quality measurement and species occurrence data through a map-based interface. The generated data can also be used immediately to facilitate discovery and search capabilities within 'big data' environments. The Annotator provides a method for taking information about a dataset, that may only be known to its maintainers, and making it explicit, in a uniform and machine-readable fashion, such that a person or information system can more easily interpret the underlying structure and meaning. Its primary mechanism is to enable a user to formally describe how columns of a tabular dataset relate and/or describe entities. For example, if a user identifies columns for latitude and longitude coordinates, we can infer the data refers to a point that can be plotted on a map. Further, it can be made explicit that measurements of 'nitrate' and 'NO3-' are of the same entity through vocabulary assignments, thus more easily utilizing data sets that use different nomenclatures. The Annotator provides an extensive and searchable

X-Ray Micro-Computed Tomography of Apollo Samples as a Curation Technique Enabling Better Research

Science.gov (United States)

Ziegler, R. A.; Almeida, N. V.; Sykes, D.; Smith, C. L.

2014-01-01

X-ray micro-computed tomography (micro-CT) is a technique that has been used to research meteorites for some time and many others], and recently it is becoming a more common tool for the curation of meteorites and Apollo samples. Micro-CT is ideally suited to the characterization of astromaterials in the curation process as it can provide textural and compositional information at a small spatial resolution rapidly, nondestructively, and without compromising the cleanliness of the samples (e.g., samples can be scanned sealed in Teflon bags). This data can then inform scientists and curators when making and processing future sample requests for meteorites and Apollo samples. Here we present some preliminary results on micro-CT scans of four Apollo regolith breccias. Methods: Portions of four Apollo samples were used in this study: 14321, 15205, 15405, and 60639. All samples were 8-10 cm in their longest dimension and approximately equant. These samples were micro-CT scanned on the Nikon HMXST 225 System at the Natural History Museum in London. Scans were made at 205-220 kV, 135-160 microamps beam current, with an effective voxel size of 21-44 microns. Results: Initial examination of the data identify a variety of mineral clasts (including sub-voxel FeNi metal grains) and lithic clasts within the regolith breccias. Textural information within some of the lithic clasts was also discernable. Of particular interest was a large basalt clast (approx.1.3 cc) found within sample 60639, which appears to have a sub-ophitic texture. Additionally, internal void space, e.g., fractures and voids, is readily identifiable. Discussion: It is clear from the preliminary data that micro-CT analyses are able to identify important "new" clasts within the Apollo breccias, and better characterize previously described clasts or igneous samples. For example, the 60639 basalt clast was previously believed to be quite small based on its approx.0.5 sq cm exposure on the surface of the main mass

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.

Science.gov (United States)

Balhoff, James P; Dahdul, Wasila M; Dececchi, T Alexander; Lapp, Hilmar; Mabee, Paula M; Vision, Todd J

2014-01-01

Phenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology. Since its initial publication, we have added new features that address several major bottlenecks in the efficiency of the phenotype curation process: allowing curators during the data curation phase to provisionally request terms that are not yet available from a relevant ontology; supporting quality control against annotation guidelines to reduce later manual review and revision; and enabling the sharing of files for collaboration among curators. We decoupled data annotation from ontology development by creating an Ontology Request Broker (ORB) within Phenex. Curators can use the ORB to request a provisional term for use in data annotation; the provisional term can be automatically replaced with a permanent identifier once the term is added to an ontology. We added a set of annotation consistency checks to prevent common curation errors, reducing the need for later correction. We facilitated collaborative editing by improving the reliability of Phenex when used with online folder sharing services, via file change monitoring and continual autosave. With the addition of these new features, and in particular the Ontology Request Broker, Phenex users have been able to focus more effectively on data annotation. Phenoscape curators using Phenex have reported a smoother annotation workflow, with much reduced interruptions from ontology maintenance and file management issues.

Automated evaluation of annotators for museum collections using subjective login

NARCIS (Netherlands)

Ceolin, D.; Nottamkandath, A.; Fokkink, W.J.; Dimitrakos, Th.; Moona, R.; Patel, Dh.; Harrison McKnight, D.

2012-01-01

Museums are rapidly digitizing their collections, and face a huge challenge to annotate every digitized artifact in store. Therefore they are opening up their archives for receiving annotations from experts world-wide. This paper presents an architecture for choosing the most eligible set of

Annotation of the protein coding regions of the equine genome

DEFF Research Database (Denmark)

Hestand, Matthew S.; Kalbfleisch, Theodore S.; Coleman, Stephen J.

2015-01-01

Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced m...... and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross...

Genome Annotation and Transcriptomics of Oil-Producing Algae

Science.gov (United States)

2015-03-16

AFRL-OSR-VA-TR-2015-0103 GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE Sabeeha Merchant UNIVERSITY OF CALIFORNIA LOS ANGELES Final...2010 To 12-31-2014 4. TITLE AND SUBTITLE GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE 5a. CONTRACT NUMBER FA9550-10-1-0095 5b...NOTES 14. ABSTRACT Most algae accumulate triacylglycerols (TAGs) when they are starved for essential nutrients like N, S, P (or Si in the case of some

Annotating smart environment sensor data for activity learning.

Science.gov (United States)

Szewcyzk, S; Dwan, K; Minor, B; Swedlove, B; Cook, D

2009-01-01

The pervasive sensing technologies found in smart homes offer unprecedented opportunities for providing health monitoring and assistance to individuals experiencing difficulties living independently at home. In order to monitor the functional health of smart home residents, we need to design technologies that recognize and track the activities that people perform at home. Machine learning techniques can perform this task, but the software algorithms rely upon large amounts of sample data that is correctly labeled with the corresponding activity. Labeling, or annotating, sensor data with the corresponding activity can be time consuming, may require input from the smart home resident, and is often inaccurate. Therefore, in this paper we investigate four alternative mechanisms for annotating sensor data with a corresponding activity label. We evaluate the alternative methods along the dimensions of annotation time, resident burden, and accuracy using sensor data collected in a real smart apartment.

Apollo 11 Cmdr Neil Armstrong watches STS-83 launch

Science.gov (United States)

1997-01-01

Apollo 11 Commander Neil A. Armstrong and his wife, Carol, were among the many special NASA STS-83 launch guests who witnessed the liftoff of the Space Shuttle Columbia April 4 at the Banana Creek VIP Viewing Site at KSC. Columbia took off from Launch Pad 39A at 2:20:32 p.m. EST to begin the 16-day Microgravity Science Laboratory-1 (MSL-1) mission.

Annotation Method (AM): SE7_AM1 [Metabolonote[Archive

Lifescience Database Archive (English)