Literature and History--A Focus on the Era of the Great Depression and World War II (1929-1945).

ERIC Educational Resources Information Center

Ahern, John; Sandmann, Alexa

1997-01-01

Provides an annotated bibliography and suggested teaching activities for units on the Great Depression and World War II. The materials support inquiry into the causes of the Great Depression and World War II and how these events transformed U.S. society. The annotated bibliography includes novels, memoirs, biographies, and political studies. (MJP)

A Selected Annotated Bibliography on Work Time Options.

ERIC Educational Resources Information Center

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…

CASTp 3.0: computed atlas of surface topography of proteins.

PubMed

Tian, Wei; Chen, Chang; Lei, Xue; Zhao, Jieling; Liang, Jie

2018-06-01

Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.

Universities of the Caribbean Region--Struggles to Democratize. An Annotated Bibliography.

ERIC Educational Resources Information Center

Waggoner, Barbara Ashton; Waggoner, George R.

An annotated bibliography on universities in the Caribbean region for the period since World War II is presented. The focus is on access to universities. For book citations, each annotation contains the author's name, publication title, place of publication, publisher, date, and number of pages. Journal references consist of author, title of…

A Selected Annotated Bibliography of Material Relating to Racism, Blacks, Chicanos, Native Americans and Multi-Ethnicity. Vol. 4.

ERIC Educational Resources Information Center

Michigan Education Association, East Lansing. Div. of Minority Affairs.

Volume Four of this selected annotated bibliography is composed of the most recently discovered materials, pertaining to blacks, Latinos, Native Americans, multi-ethnicity and racism. Like the three previous annotated bibliographies, it is considered to reflect only that material which is held to be most representative and most relevant in terms…

ANALYTiC: An Active Learning System for Trajectory Classification.

PubMed

Soares Junior, Amilcar; Renso, Chiara; Matwin, Stan

2017-01-01

The increasing availability and use of positioning devices has resulted in large volumes of trajectory data. However, semantic annotations for such data are typically added by domain experts, which is a time-consuming task. Machine-learning algorithms can help infer semantic annotations from trajectory data by learning from sets of labeled data. Specifically, active learning approaches can minimize the set of trajectories to be annotated while preserving good performance measures. The ANALYTiC web-based interactive tool visually guides users through this annotation process.

Social networks to biological networks: systems biology of Mycobacterium tuberculosis.

PubMed

Vashisht, Rohit; Bhardwaj, Anshu; Osdd Consortium; Brahmachari, Samir K

2013-07-01

Contextualizing relevant information to construct a network that represents a given biological process presents a fundamental challenge in the network science of biology. The quality of network for the organism of interest is critically dependent on the extent of functional annotation of its genome. Mostly the automated annotation pipelines do not account for unstructured information present in volumes of literature and hence large fraction of genome remains poorly annotated. However, if used, this information could substantially enhance the functional annotation of a genome, aiding the development of a more comprehensive network. Mining unstructured information buried in volumes of literature often requires manual intervention to a great extent and thus becomes a bottleneck for most of the automated pipelines. In this review, we discuss the potential of scientific social networking as a solution for systematic manual mining of data. Focusing on Mycobacterium tuberculosis, as a case study, we discuss our open innovative approach for the functional annotation of its genome. Furthermore, we highlight the strength of such collated structured data in the context of drug target prediction based on systems level analysis of pathogen.

Plant genome and transcriptome annotations: from misconceptions to simple solutions

PubMed Central

Bolger, Marie E; Arsova, Borjana; Usadel, Björn

2018-01-01

Abstract Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome and transcriptome sequencing has become orders of magnitudes cheaper and more efficient, often the functional annotation process is lagging behind. This might be hampered by the lack of a comprehensive enumeration of simple-to-use tools available to the plant researcher. In this comprehensive review, we present (i) typical ontologies to be used in the plant sciences, (ii) useful databases and resources used for functional annotation, (iii) what to expect from an annotated plant genome, (iv) an automated annotation pipeline and (v) a recipe and reference chart outlining typical steps used to annotate plant genomes/transcriptomes using publicly available resources. PMID:28062412

Educating about Social Issues in the 20th and 21st Centuries: A Critical Annotated Bibliography. Research in Curriculum and Instruction. Volume 1

ERIC Educational Resources Information Center

Totten, Samuel, Ed.; Pedersen, Jon, Ed.

2012-01-01

Educating About Social Issues in the 20th and 21st Centuries: A Critical Annotated Bibliography, is comprised of critical essays accompanied by annotated bibliographies on a host of programs, models, strategies and concerns vis-a-vis teaching and learning about social issues facing society. The primary goal of the book is to provide undergraduate…

Peaceful Peoples: An Annotated Bibliography.

ERIC Educational Resources Information Center

Bonta, Bruce D.

This annotated bibliography includes 438 selected references to books, journal articles, essays within edited volumes, and dissertations that provide significant information about peaceful societies. Peaceful societies are groups that have developed harmonious social structures that allow them to get along with each other, and with outsiders,…

The Viking viewer for connectomics: scalable multi-user annotation and summarization of large volume data sets

PubMed Central

ANDERSON, JR; MOHAMMED, S; GRIMM, B; JONES, BW; KOSHEVOY, P; TASDIZEN, T; WHITAKER, R; MARC, RE

2011-01-01

Modern microscope automation permits the collection of vast amounts of continuous anatomical imagery in both two and three dimensions. These large data sets present significant challenges for data storage, access, viewing, annotation and analysis. The cost and overhead of collecting and storing the data can be extremely high. Large data sets quickly exceed an individual's capability for timely analysis and present challenges in efficiently applying transforms, if needed. Finally annotated anatomical data sets can represent a significant investment of resources and should be easily accessible to the scientific community. The Viking application was our solution created to view and annotate a 16.5 TB ultrastructural retinal connectome volume and we demonstrate its utility in reconstructing neural networks for a distinctive retinal amacrine cell class. Viking has several key features. (1) It works over the internet using HTTP and supports many concurrent users limited only by hardware. (2) It supports a multi-user, collaborative annotation strategy. (3) It cleanly demarcates viewing and analysis from data collection and hosting. (4) It is capable of applying transformations in real-time. (5) It has an easily extensible user interface, allowing addition of specialized modules without rewriting the viewer. PMID:21118201

An annotation system for 3D fluid flow visualization

NASA Technical Reports Server (NTRS)

Loughlin, Maria M.; Hughes, John F.

1995-01-01

Annotation is a key activity of data analysis. However, current systems for data analysis focus almost exclusively on visualization. We propose a system which integrates annotations into a visualization system. Annotations are embedded in 3D data space, using the Post-it metaphor. This embedding allows contextual-based information storage and retrieval, and facilitates information sharing in collaborative environments. We provide a traditional database filter and a Magic Lens filter to create specialized views of the data. The system has been customized for fluid flow applications, with features which allow users to store parameters of visualization tools and sketch 3D volumes.

Program Evaluation in Alternative Education: An Annotated Bibliography. Teacher Education Forum; Volume 4, Number 17.

ERIC Educational Resources Information Center

Esp, Barbara

The Forum Series is a collection of papers dealing with all phases of teacher education including inservice training and graduate study. This selection is an annotated bibliography in two parts: (1) Evaluation Issues and Methods; and (2) Studies of Alternative Environments. (DMT)

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

ERIC Educational Resources Information Center

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…

Whole-genome sequence of Cupriavidus sp. strain BIS7, a heavy-metal-resistant bacterium.

PubMed

Hong, Kar Wai; Thinagaran, Dinaiz al; Gan, Han Ming; Yin, Wai-Fong; Chan, Kok-Gan

2012-11-01

Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits broad heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate, Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III), and Zn(II). Here we present the assembly and annotation of its genome.

A Bibliography of Recreational Mathematics, Volume 1. Fourth Edition.

ERIC Educational Resources Information Center

Schaaf, William L.

This book is a partially annotated bibliography of books, articles, and periodicals concerned with mathematical games, puzzles, and amusements. It is a reprinting of Volume 1 of a three-volume series. This volume, originally published in 1955, treats problems and recreations which have been important in the history of mathematics as well as some…

Whole-Genome Sequence of Cupriavidus sp. Strain BIS7, a Heavy-Metal-Resistant Bacterium

PubMed Central

Hong, Kar Wai; Thinagaran, Dinaiz a/l; Gan, Han Ming; Yin, Wai-Fong

2012-01-01

Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits broad heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate, Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III), and Zn(II). Here we present the assembly and annotation of its genome. PMID:23115161

Teleconferencing, an annotated bibliography, volume 3

NASA Technical Reports Server (NTRS)

Shervis, K.

1971-01-01

In this annotated and indexed listing of works on teleconferencing, emphasis has been placed upon teleconferencing as real-time, two way audio communication with or without visual aids. However, works on the use of television in two-way or multiway nets, data transmission, regional communications networks and on telecommunications in general are also included.

Irrigation in the Rio Grande Valley, New Mexico: A study and annotated bibliography of the development of irrigation systems

Treesearch

Frank E. Wozniak

1998-01-01

This publication reviews both published and unpublished sources on Puebloan, Hispanic, and AngloAmerican irrigation systems in the Rio Grande Valley. Settlement patterns and Spanish and Mexican land grants in the valley are also discussed. The volume includes an annotated bibliography.

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 7, Number 4, 1973.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

This annotated bibliography contains 108 English language annotations of newspapers and government publications covering educational materials of interest to North Africans. The materials relate a clear trend toward increased awareness of Arab and Islamic heritage and the adaptation of education to a multilingual population. Citations are…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 8, Number 1, 1974.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

This annotated bibliography contains 100 English-language annotations of newspapers and government publications covering educational topics of interest to North Africans. The majority of the items cited were published in 1974. Citations are categorized by country: Algeria, Libya, Morocco, and Tunisia. Within these major categories are subtopics…

College Students in Transition: An Annotated Bibliography

ERIC Educational Resources Information Center

Foote, Stephanie M., Ed.; Hinkle, Sara M., Ed.; Kranzow, Jeannine, Ed.; Pistilli, Matthew D., Ed.; Miles, LaTonya Rease, Ed.; Simmons, Jannell G., Ed.

2013-01-01

The transition from high school to college is an important milestone, but it is only one of many steps in the journey through higher education. This volume is an annotated bibliography of the emerging literature examining the many other transitions students make beyond the first year, including the sophomore year, the transfer experience, and the…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 8, Number 2, 1974.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

This bibliography contains 100 English-language annotations of newspaper articles and government publications from four North African nations. Most of the items were published in 1974. Annotations are categorized by topic: philosophy and theory of education, educational level, adult education, teacher training, teaching methods and aids, artistic…

A Selected Annotated Bibliography on the Analysis of Water Resources System, Volume 2.

ERIC Educational Resources Information Center

Kriss, Carol; And Others

Presented is an annotated bibliography of some recent selected publications pertaining to the application of systems analysis techniques for defining and evaluating alternative solutions to water resource problems. Both subject and author indices are provided. Keywords are listed at the end of each abstract. The abstracted material emphasizes the…

Banned Books; 387 B.C. to 1978 A.D.

ERIC Educational Resources Information Center

Haight, Anne Lyon; Grannis, Chandler B.

The first half of this volume presents an introductory essay defining the First Amendment and the legal aspects of censorship, and offers an annotated list of books that have been banned at various times throughout history. The annotations, arranged according to the birth dates of the authors, include a chronological account of the censorship…

Counselor's Information Service. A Quarterly Annotated Bibliography of Current Literature on Educational and Vocational Guidance. Volume 32, Number 1.

ERIC Educational Resources Information Center

B'nai B'rith, Washington, DC. Career and Counseling Services.

This quarterly annotated bibliography of current literature on educational and vocational guidance describes various pamphlets, guides and brochures which provide occupational information, educational, vocational and personal guidance, guidance administration and procedures, information on student aids and aids for the teacher. Additional guidance…

The Viking viewer for connectomics: scalable multi-user annotation and summarization of large volume data sets.

PubMed

Anderson, J R; Mohammed, S; Grimm, B; Jones, B W; Koshevoy, P; Tasdizen, T; Whitaker, R; Marc, R E

2011-01-01

Modern microscope automation permits the collection of vast amounts of continuous anatomical imagery in both two and three dimensions. These large data sets present significant challenges for data storage, access, viewing, annotation and analysis. The cost and overhead of collecting and storing the data can be extremely high. Large data sets quickly exceed an individual's capability for timely analysis and present challenges in efficiently applying transforms, if needed. Finally annotated anatomical data sets can represent a significant investment of resources and should be easily accessible to the scientific community. The Viking application was our solution created to view and annotate a 16.5 TB ultrastructural retinal connectome volume and we demonstrate its utility in reconstructing neural networks for a distinctive retinal amacrine cell class. Viking has several key features. (1) It works over the internet using HTTP and supports many concurrent users limited only by hardware. (2) It supports a multi-user, collaborative annotation strategy. (3) It cleanly demarcates viewing and analysis from data collection and hosting. (4) It is capable of applying transformations in real-time. (5) It has an easily extensible user interface, allowing addition of specialized modules without rewriting the viewer. © 2010 The Authors Journal of Microscopy © 2010 The Royal Microscopical Society.

Recovery of Navy distillate fuel from reclaimed product. Volume I. Technical discussion

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

Brinkman, D.W.; Whisman, M.L.

1984-11-01

In an effort to assist the Navy to better utilize its waste hydrocarbons, NIPER, with support from the US Department of Energy, is conducting research designed to ultimately develop a practical technique for converting Reclaimed Product (RP) into specification Naval Distillate Fuel (F-76). The first phase of the project was focused on reviewing the literature and available information from equipment manufacturers. The literature survey has been carefully culled for methodology applicable to the conversion of RP into diesel fuel suitable for Navy use. Based upon the results of this study, a second phase has been developed and outlined in whichmore » experiments will be performed to determine the most practical recycling technologies. It is realized that the final selection of one particular technology may be site-specific due to vast differences in RP volume and available facilities. A final phase, if funded, would involve full-scale testing of one of the recommended techniques at a refueling depot. The Phase I investigations are published in two volumes. Volume 1, Technical Discussion, includes the narrative and Appendices I and II. Appendix III, a detailed Literature Review, includes both a narrative portion and an annotated bibliography containing about 800 referenvces and abstracts. This appendix, because of its volume, has been published separately as Volume 2. 18 figures, 4 tables.« less

Modeling multiple time series annotations as noisy distortions of the ground truth: An Expectation-Maximization approach.

PubMed

Gupta, Rahul; Audhkhasi, Kartik; Jacokes, Zach; Rozga, Agata; Narayanan, Shrikanth

2018-01-01

Studies of time-continuous human behavioral phenomena often rely on ratings from multiple annotators. Since the ground truth of the target construct is often latent, the standard practice is to use ad-hoc metrics (such as averaging annotator ratings). Despite being easy to compute, such metrics may not provide accurate representations of the underlying construct. In this paper, we present a novel method for modeling multiple time series annotations over a continuous variable that computes the ground truth by modeling annotator specific distortions. We condition the ground truth on a set of features extracted from the data and further assume that the annotators provide their ratings as modification of the ground truth, with each annotator having specific distortion tendencies. We train the model using an Expectation-Maximization based algorithm and evaluate it on a study involving natural interaction between a child and a psychologist, to predict confidence ratings of the children's smiles. We compare and analyze the model against two baselines where: (i) the ground truth in considered to be framewise mean of ratings from various annotators and, (ii) each annotator is assumed to bear a distinct time delay in annotation and their annotations are aligned before computing the framewise mean.

Measures Pertaining to Health Education: II. Drugs. An Annotated Bibliography.

ERIC Educational Resources Information Center

Guthrie, P. D.

An annotated bibliography of instruments designed to assess attitudes, behaviors, practices, knowledge, and correlations in the area of drugs (other than nicotine and alcohol) are described. Some of the instruments described are for use with general populations of students or adults and others are appropriate only for use with drug addicted or…

The One-Parent Family: Perspectives and Annotated Bibliography. Fourth Edition.

ERIC Educational Resources Information Center

Schlesinger, Benjamin

This source-book on the one parent family contains two sections. The first section includes six papers dealing with motherless families, fatherless separated families, divorce and children, the crisis of widowhood in the family cycle, the unmarried mother who keeps her child, and single parent adoptions. Section II includes 750 annotations of…

Acceleration Tolerance: Effect of Exercise, Acceleration Training; Bed Rest and Weightlessness Deconditioning. A Compendium of Research (1950-1996)

NASA Technical Reports Server (NTRS)

Chou, J. L.; McKenzie, M. A.; Stad, N. J.; Barnes, P. R.; Jackson, C. G. R.; Ghiasvand, F.; Greenleaf, J. E.

1997-01-01

This compendium includes abstracts and annotations of clinical observations and of more basic studies involving physiological mechanisms concerning interaction of acceleration, training and deconditioning. If the author's abstract or summary was appropriate, it was included. In other cases a more detailed annotation of the paper was prepared under the subheadings Purpose, Methods, Results, and Conclusions. Author and keyword indices are provided, plus an additional selected bibliography of related work and of those papers received after the volume was prepared for publication. This volume includes material published from 1950-1996.

3D annotation and manipulation of medical anatomical structures

NASA Astrophysics Data System (ADS)

Vitanovski, Dime; Schaller, Christian; Hahn, Dieter; Daum, Volker; Hornegger, Joachim

2009-02-01

Although the medical scanners are rapidly moving towards a three-dimensional paradigm, the manipulation and annotation/labeling of the acquired data is still performed in a standard 2D environment. Editing and annotation of three-dimensional medical structures is currently a complex task and rather time-consuming, as it is carried out in 2D projections of the original object. A major problem in 2D annotation is the depth ambiguity, which requires 3D landmarks to be identified and localized in at least two of the cutting planes. Operating directly in a three-dimensional space enables the implicit consideration of the full 3D local context, which significantly increases accuracy and speed. A three-dimensional environment is as well more natural optimizing the user's comfort and acceptance. The 3D annotation environment requires the three-dimensional manipulation device and display. By means of two novel and advanced technologies, Wii Nintendo Controller and Philips 3D WoWvx display, we define an appropriate 3D annotation tool and a suitable 3D visualization monitor. We define non-coplanar setting of four Infrared LEDs with a known and exact position, which are tracked by the Wii and from which we compute the pose of the device by applying a standard pose estimation algorithm. The novel 3D renderer developed by Philips uses either the Z-value of a 3D volume, or it computes the depth information out of a 2D image, to provide a real 3D experience without having some special glasses. Within this paper we present a new framework for manipulation and annotation of medical landmarks directly in three-dimensional volume.

Scripps Genome ADVISER: Annotation and Distributed Variant Interpretation SERver

PubMed Central

Pham, Phillip H.; Shipman, William J.; Erikson, Galina A.; Schork, Nicholas J.; Torkamani, Ali

2015-01-01

Interpretation of human genomes is a major challenge. We present the Scripps Genome ADVISER (SG-ADVISER) suite, which aims to fill the gap between data generation and genome interpretation by performing holistic, in-depth, annotations and functional predictions on all variant types and effects. The SG-ADVISER suite includes a de-identification tool, a variant annotation web-server, and a user interface for inheritance and annotation-based filtration. SG-ADVISER allows users with no bioinformatics expertise to manipulate large volumes of variant data with ease – without the need to download large reference databases, install software, or use a command line interface. SG-ADVISER is freely available at genomics.scripps.edu/ADVISER. PMID:25706643

A Bibliography of Recreational Mathematics, Volume 3.

ERIC Educational Resources Information Center

Schaaf, William L.

This book is a partially annotated bibliography of books, articles and periodicals concerned with mathematical games, puzzles, tricks, amusements, and paradoxes. Because the literature in recreational mathematics has proliferated to amazing proportions since Volume 2 of this series (ED 040 874), Volume 3 is more than just an updating of the…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 6, Number 2, 1972.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

Annotations of articles, written in English, provide the content for an annotated bibliography of educational materials written in French useful to those with an interest in North Africa. Sections on Algeria, Libya, Morocco, and Tunisia cover topics such as the philosophy and theory of education, educational organization, adult education, teacher…

Counselor's Information Service, Volume 33, Number 1, February 1978. A Quarterly Annotated Bibliography of Current Literature on Educational and Vocational Guidance.

ERIC Educational Resources Information Center

B'nai B'rith, Washington, DC. Career and Counseling Services.

This annotated bibliography of current literature on educational and vocational guidance is divided into the following sections: occupational information; educational, vocational, and personal guidance; guidance administration and procedures; student aids; teacher aids; free or inexpensive guidance material; adult education and the aging;…

Counselors' Information Service: A Quarterly Annotated Bibliography of Current Literature on Educational and Vocational Guidance. Volume 32, Number 2, May 1977.

ERIC Educational Resources Information Center

B'nai B'rith, Washington, DC. Career and Counseling Services.

This quarterly annotated bibliography lists current literature on educational and vocational guidance. It is divided into the following sections: (1) Occupational Information; (2) Educational, Vocational and Personal Guidance; (3) Guidance Administration and Procedures; (4) Student Aids; (5) Aids for the Teacher; (6) Guidance Material--Free or…

Menominee Indian Tribe of Wisconsin. Part I: Inventory of Resources; Part II: Annotated Bibliography. Report No. 230.

ERIC Educational Resources Information Center

Stephens, Wayne E.; And Others

Designed to provide data and resource materials needed by the Menominee Restoration Committee and others involved in reservation organizational and development planning, this report covers the present status of the Menominee tribal resources and presents an annotated bibliography. The resource inventory includes maps, tables, and charts and is…

Counselor's Information Service: A Quarterly Annotated Bibliography of Current Literature on Educational and Vocational Guidance. Volume 30, Number 4, December 1975.

ERIC Educational Resources Information Center

B'nai B'rith, Washington, DC. Career and Counseling Services.

This publication is a quarterly annotated bibliography of current literature on educational and vocational guidance, and is developed by the B'nai B'rith Career and Counseling Services, Washington, D.C. The topics covered are occupational information, educational, vocational and personal guidance; guidance administration and procedures; student…

A World Full of Stories. An Annotated Bibliography of Folk Literature. Traditional Literature and Folklore in Library and Storytelling Programs.

ERIC Educational Resources Information Center

Johnson, Paul Anthony, Ed.

The first volume of a projected series entitled "Traditional Literature and Folklore in Library and Storytelling Programs," this annotated bibliography was produced by graduate students in the Traditional Literature and Oral Narration class at the University of Hawaii at Manoa. The bibliography is designed to provide librarians and…

Northeastern Gulf of Mexico coastal and marine ecosystem program: Data search and synthesis, annotated bibliography. Appendix A: Physical oceanography. Final report

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

NONE

This study summarizes environmental and socioeconomic information related to the Florida Panhandle Outer Continental Shelf (OCS). It contains a conceptual model of active processes and identification of information gaps that will be useful in the design of future environmental studies in the geographic area. The annotated bibliography for this study is printer in six volumes, each pertaining to a specific topic. They are as follows: Appendix A--Physical Oceanography; Appendix B--Meteorology; Appendix C--Geology; Appendix D--Chemistry; Appendix E--Biology; and Appendix F--Socioeconomics. This volume contains bibliographic references pertaining to physical oceanography.

Sma3s: a three-step modular annotator for large sequence datasets.

PubMed

Muñoz-Mérida, Antonio; Viguera, Enrique; Claros, M Gonzalo; Trelles, Oswaldo; Pérez-Pulido, Antonio J

2014-08-01

Automatic sequence annotation is an essential component of modern 'omics' studies, which aim to extract information from large collections of sequence data. Most existing tools use sequence homology to establish evolutionary relationships and assign putative functions to sequences. However, it can be difficult to define a similarity threshold that achieves sufficient coverage without sacrificing annotation quality. Defining the correct configuration is critical and can be challenging for non-specialist users. Thus, the development of robust automatic annotation techniques that generate high-quality annotations without needing expert knowledge would be very valuable for the research community. We present Sma3s, a tool for automatically annotating very large collections of biological sequences from any kind of gene library or genome. Sma3s is composed of three modules that progressively annotate query sequences using either: (i) very similar homologues, (ii) orthologous sequences or (iii) terms enriched in groups of homologous sequences. We trained the system using several random sets of known sequences, demonstrating average sensitivity and specificity values of ~85%. In conclusion, Sma3s is a versatile tool for high-throughput annotation of a wide variety of sequence datasets that outperforms the accuracy of other well-established annotation algorithms, and it can enrich existing database annotations and uncover previously hidden features. Importantly, Sma3s has already been used in the functional annotation of two published transcriptomes. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Counselor's Information Service; a Quarterly Annotated Bibliography of Current Literature on Educational and Vocational Guidance. Volume 30, Number 1, February 1975.

ERIC Educational Resources Information Center

B'nai B'rith, Washington, DC. Career and Counseling Services.

The Counselor's Information Service is a quarterly publication of the B'nai B'rith Career and Counseling Services. This annotated bibliography of current literature on educational and vocational guidance provides the names and addresses of the publishers of the material reviewed and the cost of each publication. The reviews are organized according…

Counselor's Information Service; a Quarterly Annotated Bibliography of Current Literature on Educational and Vocational Guidance. Volume 30, Number 2, May 1975.

ERIC Educational Resources Information Center

B'nai B'rith, Washington, DC. Career and Counseling Services.

The Counselor's Information Service is a quarterly publication of the B'nai B'rith Career and Counseling Services. This annotated bibliography of current literature on educational and vocational guidance provides the names and addresses of the publishers of the material reviewed and the cost of each publication. The reviews are organized according…

Smoking: The Health Consequences of Tobacco Use. An Annotated Bibliography with Analytical Introduction. Science and Social Responsibility Series, No. 2.

ERIC Educational Resources Information Center

Schmitz, Cecilia M.; Gray, Richard A.

This volume contains an extensive introduction to the health consequences of tobacco use and extended annotations of the most important English-language monographs and articles to appear on the subject in the 1980s and 1990s arranged in classified order under select headings. The introductory analytical essay by Richard A. Gray covers: early and…

Linking wilderness research and management-volume 3. Recreation fees in wilderness and other public lands: an annotated reading list

Treesearch

Annette Puttkammer; Vita Wright

2001-01-01

This annotated reading list provides an introduction to the issue of recreation fees on public lands. With an emphasis on wilderness recreation fees, this compilation of historical and recent publications is divided into the following sections: historical context, arguments for and against fees, pricing mechanisms and the effects of price, public attitudes toward fees...

Folktale Themes and Activities for Children. Volume 2: Trickster and Transformation Tales. Learning through Folklore Series.

ERIC Educational Resources Information Center

Kraus, Anne Marie

This companion volume to "Folktale Themes Volume 1: Pourquoi Tales," shows educators how to use folktales to provide meaningful, educational experiences for children. This book provides a complete package using folktales in the classroom--activity pages, teaching ideas, story themes, and an annotated bibliography of further reading for a…

A National State of the Art Study of Curriculum Instructional Materials for Distributive Education. Volume 1.

ERIC Educational Resources Information Center

Hirshfeld, Marvin; Leventhal, Jerome I.

Volume 1 of the two-volume annotated bibliography provides a partial listing of available materials for curriculum and instructional enrichment in distributive education. The grouping of all materials was made according to the U. S. Office of Education Classification of Instructional Programs for Distributive Education. Alphabetized by title under…

A National State of the Art Study of Curriculum Instructional Materials for Distributive Education. Volume 2.

ERIC Educational Resources Information Center

Hirshfeld, Marvin; Leventhal, Jerome I.

Volume 2 of the two-volume annotated bibliography provides a partial listing of available materials for curriculum and instructional enrichment in distributive education. The grouping of all materials was made according to the U. S. Office of Education Classification of Instructional Programs for Distributive Education. Alphabetized by title under…

Selected Bibliographies for Pharmaceutical Supply Systems. Volume 5: Pharmaceutical Supply Systems Bibliographies. International Health Planning Reference Series.

ERIC Educational Resources Information Center

Schaumann, Leif

Intended as a companion piece to volume 7 in the Method Series, Pharmaceutical Supply System Planning (CE 024 234), this fifth of six volumes in the International Health Planning Reference Series is a combined literature review and annotated bibliography dealing with alternative methodologies for planning and analyzing pharmaceutical supply…

MIPS: analysis and annotation of genome information in 2007

PubMed Central

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). PMID:18158298

MIPS: analysis and annotation of genome information in 2007.

PubMed

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).

The Battle of Okinawa, 1945: Final Turning Point in the Pacific.

ERIC Educational Resources Information Center

Tzeng, Megan

2000-01-01

Reviews the last major battle of World War II that occurred at Okinawa (Japan) in 1945. Explains why the Battle of Okinawa was the turning point in World War II. Includes two maps in the appendix and an annotated bibliography. (CMK)

Review of the physical oceanography of the Cape Hatteras, North Carolina Region. Volume 1. Literature synthesis. Appendix A. Annotated bibliography

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

Adams, C.E.; Berger, T.J.; Boicourt, W.C.

The report, second in a three set series, is an annotated bibliography of the pertinent literature, primarily from 1970 to the present. The literature discusses the physical oceanography of the complex region offshore of Cape Hatteras, North Carolina as it relates to the ocean circulation and fate of any discharges resulting from offshore oil and gas activity.

Counselor's Information Service; a Quarterly Annotated Bibliography of Current Literature on Educational and Vocational Guidance (with Special Supplement). Volume 30, Number 3, September 1975.

ERIC Educational Resources Information Center

B'nai B'rith, Washington, DC. Career and Counseling Services.

The Counselor's Information Service is a quarterly publication of the B'nai B'rith Career and Counseling Services. This annotated bibliography of current literature on educational and vocational guidance provides the names and addresses of the publishers of the material reviewed and the cost of each publication. The reviews are organized according…

ODMedit: uniform semantic annotation for data integration in medicine based on a public metadata repository.

PubMed

Dugas, Martin; Meidt, Alexandra; Neuhaus, Philipp; Storck, Michael; Varghese, Julian

2016-06-01

The volume and complexity of patient data - especially in personalised medicine - is steadily increasing, both regarding clinical data and genomic profiles: Typically more than 1,000 items (e.g., laboratory values, vital signs, diagnostic tests etc.) are collected per patient in clinical trials. In oncology hundreds of mutations can potentially be detected for each patient by genomic profiling. Therefore data integration from multiple sources constitutes a key challenge for medical research and healthcare. Semantic annotation of data elements can facilitate to identify matching data elements in different sources and thereby supports data integration. Millions of different annotations are required due to the semantic richness of patient data. These annotations should be uniform, i.e., two matching data elements shall contain the same annotations. However, large terminologies like SNOMED CT or UMLS don't provide uniform coding. It is proposed to develop semantic annotations of medical data elements based on a large-scale public metadata repository. To achieve uniform codes, semantic annotations shall be re-used if a matching data element is available in the metadata repository. A web-based tool called ODMedit ( https://odmeditor.uni-muenster.de/ ) was developed to create data models with uniform semantic annotations. It contains ~800,000 terms with semantic annotations which were derived from ~5,800 models from the portal of medical data models (MDM). The tool was successfully applied to manually annotate 22 forms with 292 data items from CDISC and to update 1,495 data models of the MDM portal. Uniform manual semantic annotation of data models is feasible in principle, but requires a large-scale collaborative effort due to the semantic richness of patient data. A web-based tool for these annotations is available, which is linked to a public metadata repository.

Current challenges in genome annotation through structural biology and bioinformatics.

PubMed

Furnham, Nicholas; de Beer, Tjaart A P; Thornton, Janet M

2012-10-01

With the huge volume in genomic sequences being generated from high-throughout sequencing projects the requirement for providing accurate and detailed annotations of gene products has never been greater. It is proving to be a huge challenge for computational biologists to use as much information as possible from experimental data to provide annotations for genome data of unknown function. A central component to this process is to use experimentally determined structures, which provide a means to detect homology that is not discernable from just the sequence and permit the consequences of genomic variation to be realized at the molecular level. In particular, structures also form the basis of many bioinformatics methods for improving the detailed functional annotations of enzymes in combination with similarities in sequence and chemistry. Copyright © 2012. Published by Elsevier Ltd.

Deburring: an annotated bibliography. Volume VI

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

Gillespie, L.K.

1980-07-01

An annotated summary of 138 articles and publications on burrs, burr prevention and deburring is presented. Thirty-seven deburring processes are listed. Entries cited include English, Russian, French, Japanese, and German language articles. Entries are indexed by deburring processes, author, and language. Indexes also indicate which references discuss equipment and tooling, how to use a proces economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred.

Deburring: an annotated bibliography. Volume V

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

Gillespie, L.K.

1978-01-01

An annotated summary of 204 articles and publications on burrs, burr prevention and deburring is presented. Thirty-seven deburring processes are listed. Entries cited include English, Russian, French, Japanese and German language articles. Entries are indexed by deburring processes, author, and language. Indexes also indicate which references discuss equipment and tooling, how to use a process, economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred.

PlantCAZyme: a database for plant carbohydrate-active enzymes

PubMed Central

Ekstrom, Alexander; Taujale, Rahil; McGinn, Nathan; Yin, Yanbin

2014-01-01

PlantCAZyme is a database built upon dbCAN (database for automated carbohydrate active enzyme annotation), aiming to provide pre-computed sequence and annotation data of carbohydrate active enzymes (CAZymes) to plant carbohydrate and bioenergy research communities. The current version contains data of 43 790 CAZymes of 159 protein families from 35 plants (including angiosperms, gymnosperms, lycophyte and bryophyte mosses) and chlorophyte algae with fully sequenced genomes. Useful features of the database include: (i) a BLAST server and a HMMER server that allow users to search against our pre-computed sequence data for annotation purpose, (ii) a download page to allow batch downloading data of a specific CAZyme family or species and (iii) protein browse pages to provide an easy access to the most comprehensive sequence and annotation data. Database URL: http://cys.bios.niu.edu/plantcazyme/ PMID:25125445

Selected Bibliographies and State-of-the-Art Review for Environmental Health. Volume 2: Environmental Health References. International Health Planning Reference Series.

ERIC Educational Resources Information Center

Fraser, Renee White; Shani, Hadasa

Intended as a companion piece to volume 2 in the Method Series, Environmental Health Planning (CE 024 230), this second of six volumes in the International Health Planning Reference Series is a combined literature review and annotated bibliography dealing with environmental factors in health planning for developing countries. The review identifies…

A Factor Graph Approach to Automated GO Annotation

PubMed Central

Spetale, Flavio E.; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

2016-01-01

As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum. PMID:26771463

A Factor Graph Approach to Automated GO Annotation.

PubMed

Spetale, Flavio E; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

2016-01-01

As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.

Accessing the SEED genome databases via Web services API: tools for programmers.

PubMed

Disz, Terry; Akhter, Sajia; Cuevas, Daniel; Olson, Robert; Overbeek, Ross; Vonstein, Veronika; Stevens, Rick; Edwards, Robert A

2010-06-14

The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.

Toward autonomous driving: The CMU Navlab. II - Architecture and systems

NASA Technical Reports Server (NTRS)

Thorpe, Charles; Hebert, Martial; Kanade, Takeo; Shafer, Steven

1991-01-01

A description is given of EDDIE, the architecture for the Navlab mobile robot which provides a toolkit for building specific systems quickly and easily. Included in the discussion are the annotated maps used by EDDIE and the Navlab's road-following system, called the Autonomous Mail Vehicle, which was built using EDDIE and its annotated maps as a basis. The contributions of the Navlab project and the lessons learned from it are examined.

An Aspect of the History of Medicine in Ancient Korea as Examined through Silla Buddhist Monks'Annotations on the "Chapter on Eliminating Disease"in the Sutra of Golden Light (Suvarnabhāsa-sūtra).

PubMed

Oh, Chaekun; Jeon, Jongwook; Shin, Dongwon

2016-12-01

Nearly nothing is known of medicine in ancient Korea due to insufficient materials. With several extant prescriptions and esoteric methods of treating diseases alone, it is impossible to gauge in depth the management of medicine during this period. If one exception were to be cited, that would be the fact that the annotations for understanding the contents on Indian medicine in the "Chapter on Eliminating Disease" in the Sutra of Golden Light, a Buddhist sutra originating from India, reflected the medical knowledge of Buddhist monks from Silla (57 BC-935 AD) who were active immediately after the nation's unification of the two other kingdoms on the Korean Peninsula (668 AD) such as Wonhyo (617-686 AD), Gyeongheung (620?-700? AD), and Seungjang (684-? AD). Along with those by other monks, these annotations are collected in the Mysterious Pivot of the Sutra of Golden Light, which was compiled by Gangyō(835-871 AD), a Japanese monk from the Heian era (794-1185 AD). Representative versions of the "Chapter on Eliminating Disease" in the Sutra of Golden Light include: a classical Chinese translation by the Indian monk Dharmakṣema (385-433 AD); the eight-volume edition by Chinese monk Baogui, which differs little from the preceding work in terms of the contents of the "Chapter on Eliminating Disease"; and the ten-volume edition by Yijing (635-713 AD), who had full-fledged knowledge of Indian medicine. When the contents of the annotations thus collected are examined, it seems that Wonhyo had not been aware of the existence of the ten-volume edition, and Gyeongheung and Seungjang most certainly used the ten-volume edition in their annotations as well. Especially noteworthy are Wonhyo's annotations on the Indian medical knowledge found in the "Chapter on Eliminating Disease" in the Sutra of Golden Light. Here, he made a bold attempt to link and understand consistently even discussions on Indian and Buddhist medicine on the basis of the traditional East Asian medical theory centering on the yin-yang and five phases (wuxing). In accordance with East Asia's theory of the seasonal five phases, Wonhyo sought to explain aspects of Indian medicine, e.g., changes in the four great elements (catvāri mahā-bhūtāni) of earth, water, fire, and wind according to seasonal factors and their effect on the internal organs; patterns of diseases such as wind (vāta)-induced disease, bile (pitta)-induced disease, phlegm (śleṣman)-induced disease, and a combination (saṃnipāta) of these three types of diseases; pathogenesis due to the indigestion of food, as pathological mechanisms centering on the theory of the mutual overcoming (xiangke) of the five phases including the five viscera (wuzang), five flavors (wuwei), and five colors (wuse). They existed in the text contents on Indian medicine, which could not be explicated well with the existing medical knowledge based on the theory of the five phases. Consequently, he boldly modified the theory of the five phases in his own way for such passages, thus attempting a reconciliation, or harmonization of disputes (hwajaeng), of the two medical systems. Such an attempt was even bolder than those by earlier annotators, and Wonhyo's annotations came to be accepted by later annotators as one persuasive explanation as well. In the case of Gyeongheung and Seungjang, who obtained and examined the ten-volume edition, a new classical Chinese translation produced following Wonhyo's death, annotated the "Chapter on Eliminating Disease" based on their outstanding proficiency in Sanskrit and knowledge of new Indian and Buddhist medicine. This fact signifies that knowledge of the eight arts of Ayurvedic medicine in India was introduced into Silla around the early 8th century. The medical knowledge of Wonhyo, Gyeongheung, and Seungjang demonstrates that intellectual circles in contemporary Silla were arenas in which not only traditional East Asian medicine as represented by works such as the Inner Canon of the Yellow Emperor (Huangdi Neijing) but also Indian medicine of Buddhism coexisted in almost real time.

Automated linking of suspicious findings between automated 3D breast ultrasound volumes

NASA Astrophysics Data System (ADS)

Gubern-Mérida, Albert; Tan, Tao; van Zelst, Jan; Mann, Ritse M.; Karssemeijer, Nico

2016-03-01

Automated breast ultrasound (ABUS) is a 3D imaging technique which is rapidly emerging as a safe and relatively inexpensive modality for screening of women with dense breasts. However, reading ABUS examinations is very time consuming task since radiologists need to manually identify suspicious findings in all the different ABUS volumes available for each patient. Image analysis techniques to automatically link findings across volumes are required to speed up clinical workflow and make ABUS screening more efficient. In this study, we propose an automated system to, given the location in the ABUS volume being inspected (source), find the corresponding location in a target volume. The target volume can be a different view of the same study or the same view from a prior examination. The algorithm was evaluated using 118 linkages between suspicious abnormalities annotated in a dataset of ABUS images of 27 patients participating in a high risk screening program. The distance between the predicted location and the center of the annotated lesion in the target volume was computed for evaluation. The mean ± stdev and median distance error achieved by the presented algorithm for linkages between volumes of the same study was 7.75±6.71 mm and 5.16 mm, respectively. The performance was 9.54±7.87 and 8.00 mm (mean ± stdev and median) for linkages between volumes from current and prior examinations. The proposed approach has the potential to minimize user interaction for finding correspondences among ABUS volumes.

A DDC Bibliography on Computers in Information Sciences. Volume I. Information Sciences Series.

ERIC Educational Resources Information Center

Defense Documentation Center, Alexandria, VA.

The unclassified and unlimited bibliography compiles references dealing specifically with the role of computers in information sciences. The volume contains 249 annotated references grouped under two major headings: Time Shared, On-Line, and Real Time Systems, and Computer Components. The references are arranged in accesion number (AD-number)…

Population Education Interchange. Volume 17, Numbers 1-4, 1988.

ERIC Educational Resources Information Center

Crews, Kimberly A.

1988-01-01

The four issues of this volume are each concerned with a specific topic in population studies. Issue number 1 , "Demographic Illiteracy," indicates that U.S. students are not aware of world population growth patterns. The information is taken from the Second International Science Study, 1983. An annotated list of 16 population studies resources is…

An Annotated Bibliography of MANPRINT-Related Assessments and Evaluations Conducted by the U.S. Army, 2nd Edition: 1953 to 2009. Volume 2 - MANPRINT Assessment and Evaluations

DTIC Science & Technology

2010-02-01

Research Laboratory Aberdeen Proving Ground, MD 21005-5425 ARL-SR-189 February 2010 An Annotated Bibliography of MANPRINT-Related...Middlebrooks, Ph.D. Human Research and Engineering Directorate, ARL Approved for public release; distribution...7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) U.S. Army Research Laboratory ATTN: RDRL-HRM-AV Fort Hood, TX 76544-5073 8. PERFORMING

Annotation: a computational solution for streamlining metabolomics analysis

PubMed Central

Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Benton, H. Paul; Siuzdak, Gary

2017-01-01

Metabolite identification is still considered an imposing bottleneck in liquid chromatography mass spectrometry (LC/MS) untargeted metabolomics. The identification workflow usually begins with detecting relevant LC/MS peaks via peak-picking algorithms and retrieving putative identities based on accurate mass searching. However, accurate mass search alone provides poor evidence for metabolite identification. For this reason, computational annotation is used to reveal the underlying metabolites monoisotopic masses, improving putative identification in addition to confirmation with tandem mass spectrometry. This review examines LC/MS data from a computational and analytical perspective, focusing on the occurrence of neutral losses and in-source fragments, to understand the challenges in computational annotation methodologies. Herein, we examine the state-of-the-art strategies for computational annotation including: (i) peak grouping or full scan (MS1) pseudo-spectra extraction, i.e., clustering all mass spectral signals stemming from each metabolite; (ii) annotation using ion adduction and mass distance among ion peaks; (iii) incorporation of biological knowledge such as biotransformations or pathways; (iv) tandem MS data; and (v) metabolite retention time calibration, usually achieved by prediction from molecular descriptors. Advantages and pitfalls of each of these strategies are discussed, as well as expected future trends in computational annotation. PMID:29039932

Comprehensive phylogenetic analysis of bacterial reverse transcriptases.

PubMed

Toro, Nicolás; Nisa-Martínez, Rafael

2014-01-01

Much less is known about reverse transcriptases (RTs) in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center) platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity) per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs), Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L), and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology.

Comprehensive Phylogenetic Analysis of Bacterial Reverse Transcriptases

PubMed Central

Toro, Nicolás; Nisa-Martínez, Rafael

2014-01-01

Much less is known about reverse transcriptases (RTs) in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center) platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity) per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs), Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L), and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology. PMID:25423096

Optimizing high performance computing workflow for protein functional annotation.

PubMed

Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

2014-09-10

Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data.

Optimizing high performance computing workflow for protein functional annotation

PubMed Central

Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

2014-01-01

Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data. PMID:25313296

Camping and Backpacking. A Guide to Information Sources. Volume 2 in the Sports, Games and Pastimes Information Guide Series.

ERIC Educational Resources Information Center

Clotfelter, Cecil F.; Clotfelter, Mary L.

Sources of information regarding camping, backpacking, and related activities are annotated in a comprehensive listing of books, films and other non-print media, pamphlets, and periodicals largely dating from 1960. The volume contains chapters pertaining to: general directories, general camping, organized camping, camp related activities,…

Environmental Toxicology: A Guide to Information Sources. Volume 7 in the "Man and the Environment Information Guide" Series.

ERIC Educational Resources Information Center

Rudd, Robert L.

This annotated bibliography on environmental toxicology brings together a diverse set of information sources from the physical, social, and natural sciences. These sources include periodical literature, government documents, scientific journals, and teaching materials. The volume is divided into sixteen sections organized into four parts: (1)…

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

PubMed Central

Rocca-Serra, Philippe; Brandizi, Marco; Maguire, Eamonn; Sklyar, Nataliya; Taylor, Chris; Begley, Kimberly; Field, Dawn; Harris, Stephen; Hide, Winston; Hofmann, Oliver; Neumann, Steffen; Sterk, Peter; Tong, Weida; Sansone, Susanna-Assunta

2010-01-01

Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories. Availability and Implementation: Software, documentation, case studies and implementations at http://www.isa-tools.org Contact: isatools@googlegroups.com PMID:20679334

SG-ADVISER CNV: copy-number variant annotation and interpretation.

PubMed

Erikson, Galina A; Deshpande, Neha; Kesavan, Balachandar G; Torkamani, Ali

2015-09-01

Copy-number variants have been associated with a variety of diseases, especially cancer, autism, schizophrenia, and developmental delay. The majority of clinically relevant events occur de novo, necessitating the interpretation of novel events. In this light, we present the Scripps Genome ADVISER CNV annotation pipeline and Web server, which aims to fill the gap between copy number variant detection and interpretation by performing in-depth annotations and functional predictions for copy number variants. The Scripps Genome ADVISER CNV suite includes a Web server interface to a high-performance computing environment for calculations of annotations and a table-based user interface that allows for the execution of numerous annotation-based variant filtration strategies and statistics. The annotation results include details regarding location, impact on the coding portion of genes, allele frequency information (including allele frequencies from the Scripps Wellderly cohort), and overlap information with other reference data sets (including ClinVar, DGV, DECIPHER). A summary variant classification is produced (ADVISER score) based on the American College of Medical Genetics and Genomics scoring guidelines. We demonstrate >90% sensitivity/specificity for detection of pathogenic events. Scripps Genome ADVISER CNV is designed to allow users with no prior bioinformatics expertise to manipulate large volumes of copy-number variant data. Scripps Genome ADVISER CNV is available at http://genomics.scripps.edu/ADVISER/.

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

PubMed

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.

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

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

2014-01-01

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. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

Haptic exploratory behavior during object discrimination: a novel automatic annotation method.

PubMed

Jansen, Sander E M; Bergmann Tiest, Wouter M; Kappers, Astrid M L

2015-01-01

In order to acquire information concerning the geometry and material of handheld objects, people tend to execute stereotypical hand movement patterns called haptic Exploratory Procedures (EPs). Manual annotation of haptic exploration trials with these EPs is a laborious task that is affected by subjectivity, attentional lapses, and viewing angle limitations. In this paper we propose an automatic EP annotation method based on position and orientation data from motion tracking sensors placed on both hands and inside a stimulus. A set of kinematic variables is computed from these data and compared to sets of predefined criteria for each of four EPs. Whenever all criteria for a specific EP are met, it is assumed that that particular hand movement pattern was performed. This method is applied to data from an experiment where blindfolded participants haptically discriminated between objects differing in hardness, roughness, volume, and weight. In order to validate the method, its output is compared to manual annotation based on video recordings of the same trials. Although mean pairwise agreement is less between human-automatic pairs than between human-human pairs (55.7% vs 74.5%), the proposed method performs much better than random annotation (2.4%). Furthermore, each EP is linked to a specific object property for which it is optimal (e.g., Lateral Motion for roughness). We found that the percentage of trials where the expected EP was found does not differ between manual and automatic annotation. For now, this method cannot yet completely replace a manual annotation procedure. However, it could be used as a starting point that can be supplemented by manual annotation.

Low-Cost Rural Health Care and Health Manpower Training. An Annotated Bibliography with Special Emphasis on Developing Countries. Volume 4.

ERIC Educational Resources Information Center

Delaney, Frances M., Comp.

This fourth volume in a bibliography series on low-cost rural health care contains 700 entries covering the 1960's-1970's and focusing on developing countries. The bibliography is organized under five major subject headings: reference works, organization and planning, implementation of primary health care, training and utilization of primary…

Energy Education Materials Inventory, Volume 1: An Annotated Bibliography of Currently Available Materials, K-12, Published Prior to May, 1976.

ERIC Educational Resources Information Center

Houston Univ., TX. Energy Inst.

This publication is a systematic listing of energy education materials and reference sources suitable for use in elementary and secondary schools. Items in this volume, located through computer searches, were still available in May, 1978. This inventory of energy resource materials consists of three indexes: media, grade level, and subject. Each…

Religious Higher Education in the United States: A Source Book. Source Books on Education Volume 46. Garland Reference Library of Social Science Volume 950.

ERIC Educational Resources Information Center

Hunt, Thomas C., Ed.; Carper, James C., Ed.

This book presents 24 chapters on religious denomination affiliated institutions of higher education. Most chapters begin with an historical essay followed by annotated bibliographic entries covering primary and secondary sources dating back to 1986 on various denomination-connected institutions. Chapters have the following titles and authors:…

Validating automatic semantic annotation of anatomy in DICOM CT images

NASA Astrophysics Data System (ADS)

Pathak, Sayan D.; Criminisi, Antonio; Shotton, Jamie; White, Steve; Robertson, Duncan; Sparks, Bobbi; Munasinghe, Indeera; Siddiqui, Khan

2011-03-01

In the current health-care environment, the time available for physicians to browse patients' scans is shrinking due to the rapid increase in the sheer number of images. This is further aggravated by mounting pressure to become more productive in the face of decreasing reimbursement. Hence, there is an urgent need to deliver technology which enables faster and effortless navigation through sub-volume image visualizations. Annotating image regions with semantic labels such as those derived from the RADLEX ontology can vastly enhance image navigation and sub-volume visualization. This paper uses random regression forests for efficient, automatic detection and localization of anatomical structures within DICOM 3D CT scans. A regression forest is a collection of decision trees which are trained to achieve direct mapping from voxels to organ location and size in a single pass. This paper focuses on comparing automated labeling with expert-annotated ground-truth results on a database of 50 highly variable CT scans. Initial investigations show that regression forest derived localization errors are smaller and more robust than those achieved by state-of-the-art global registration approaches. The simplicity of the algorithm's context-rich visual features yield typical runtimes of less than 10 seconds for a 5123 voxel DICOM CT series on a single-threaded, single-core machine running multiple trees; each tree taking less than a second. Furthermore, qualitative evaluation demonstrates that using the detected organs' locations as index into the image volume improves the efficiency of the navigational workflow in all the CT studies.

Annotation analysis for testing drug safety signals using unstructured clinical notes

PubMed Central

2012-01-01

Background The electronic surveillance for adverse drug events is largely based upon the analysis of coded data from reporting systems. Yet, the vast majority of electronic health data lies embedded within the free text of clinical notes and is not gathered into centralized repositories. With the increasing access to large volumes of electronic medical data—in particular the clinical notes—it may be possible to computationally encode and to test drug safety signals in an active manner. Results We describe the application of simple annotation tools on clinical text and the mining of the resulting annotations to compute the risk of getting a myocardial infarction for patients with rheumatoid arthritis that take Vioxx. Our analysis clearly reveals elevated risks for myocardial infarction in rheumatoid arthritis patients taking Vioxx (odds ratio 2.06) before 2005. Conclusions Our results show that it is possible to apply annotation analysis methods for testing hypotheses about drug safety using electronic medical records. PMID:22541596

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

PubMed

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 in a CASAVA-build into functional annotations while producing corresponding gene expression measurements. Achieving such analysis is executed in an ultrafast and highly efficient manner, whether the analysis be a single-read or paired-end sequencing experiment. TASE is a user-friendly and freely available application, allowing rapid analysis and annotation of any given Illumina Solexa sequencing dataset with ease.

20 CFR 408.1225 - What happens if you receive an overpayment?

Code of Federal Regulations, 2013 CFR

2013-04-01

... CERTAIN WORLD WAR II VETERANS Federal Administration of State Recognition Payments § 408.1225 What happens... to State recognition payments ends before you have repaid the overpayment, we will annotate your...

20 CFR 408.1225 - What happens if you receive an overpayment?

Code of Federal Regulations, 2014 CFR

2014-04-01

... CERTAIN WORLD WAR II VETERANS Federal Administration of State Recognition Payments § 408.1225 What happens... to State recognition payments ends before you have repaid the overpayment, we will annotate your...

20 CFR 408.1225 - What happens if you receive an overpayment?

Code of Federal Regulations, 2010 CFR

2010-04-01

... CERTAIN WORLD WAR II VETERANS Federal Administration of State Recognition Payments § 408.1225 What happens... to State recognition payments ends before you have repaid the overpayment, we will annotate your...

20 CFR 408.1225 - What happens if you receive an overpayment?

Code of Federal Regulations, 2012 CFR

2012-04-01

... CERTAIN WORLD WAR II VETERANS Federal Administration of State Recognition Payments § 408.1225 What happens... to State recognition payments ends before you have repaid the overpayment, we will annotate your...

20 CFR 408.1225 - What happens if you receive an overpayment?

Code of Federal Regulations, 2011 CFR

2011-04-01

... CERTAIN WORLD WAR II VETERANS Federal Administration of State Recognition Payments § 408.1225 What happens... to State recognition payments ends before you have repaid the overpayment, we will annotate your...

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA

PubMed Central

Djebali, Sarah; Delaplace, Franck; Crollius, Hugues Roest

2006-01-01

Background Accurate and automatic gene identification in eukaryotic genomic DNA is more than ever of crucial importance to efficiently exploit the large volume of assembled genome sequences available to the community. Automatic methods have always been considered less reliable than human expertise. This is illustrated in the EGASP project, where reference annotations against which all automatic methods are measured are generated by human annotators and experimentally verified. We hypothesized that replicating the accuracy of human annotators in an automatic method could be achieved by formalizing the rules and decisions that they use, in a mathematical formalism. Results We have developed Exogean, a flexible framework based on directed acyclic colored multigraphs (DACMs) that can represent biological objects (for example, mRNA, ESTs, protein alignments, exons) and relationships between them. Graphs are analyzed to process the information according to rules that replicate those used by human annotators. Simple individual starting objects given as input to Exogean are thus combined and synthesized into complex objects such as protein coding transcripts. Conclusion We show here, in the context of the EGASP project, that Exogean is currently the method that best reproduces protein coding gene annotations from human experts, in terms of identifying at least one exact coding sequence per gene. We discuss current limitations of the method and several avenues for improvement. PMID:16925841

Incorporating Feature-Based Annotations into Automatically Generated Knowledge Representations

NASA Astrophysics Data System (ADS)

Lumb, L. I.; Lederman, J. I.; Aldridge, K. D.

2006-12-01

Earth Science Markup Language (ESML) is efficient and effective in representing scientific data in an XML- based formalism. However, features of the data being represented are not accounted for in ESML. Such features might derive from events (e.g., a gap in data collection due to instrument servicing), identifications (e.g., a scientifically interesting area/volume in an image), or some other source. In order to account for features in an ESML context, we consider them from the perspective of annotation, i.e., the addition of information to existing documents without changing the originals. Although it is possible to extend ESML to incorporate feature-based annotations internally (e.g., by extending the XML schema for ESML), there are a number of complicating factors that we identify. Rather than pursuing the ESML-extension approach, we focus on an external representation for feature-based annotations via XML Pointer Language (XPointer). In previous work (Lumb &Aldridge, HPCS 2006, IEEE, doi:10.1109/HPCS.2006.26), we have shown that it is possible to extract relationships from ESML-based representations, and capture the results in the Resource Description Format (RDF). Thus we explore and report on this same requirement for XPointer-based annotations of ESML representations. As in our past efforts, the Global Geodynamics Project (GGP) allows us to illustrate with a real-world example this approach for introducing annotations into automatically generated knowledge representations.

Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking

PubMed Central

Soh, Jung; Gordon, Paul MK; Taschuk, Morgan L; Dong, Anguo; Ah-Seng, Andrew C; Turinsky, Andrei L; Sensen, Christoph W

2008-01-01

Background The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research. Beginning with a browser capable of rendering views of XML-based genomic information and providing scalable vector graphics output, we have now completed version 1.0 of the system with many additional features. Our development efforts were guided by our observation that biologists who use both gene expression profiling and comparative genomics gain functional insights above and beyond those provided by traditional per-gene analyses. Results Bluejay 1.0 is a genome viewer integrating genome annotation with: (i) gene expression information; and (ii) comparative analysis with an unlimited number of other genomes in the same view. This allows the biologist to see a gene not just in the context of its genome, but also its regulation and its evolution. Bluejay now has rich provision for personalization by users: (i) numerous display customization features; (ii) the availability of waypoints for marking multiple points of interest on a genome and subsequently utilizing them; and (iii) the ability to take user relevance feedback of annotated genes or textual items to offer personalized recommendations. Bluejay 1.0 also embeds the Seahawk browser for the Moby protocol, enabling users to seamlessly invoke hundreds of Web Services on genomic data of interest without any hard-coding. Conclusion Bluejay offers a unique set of customizable genome-browsing features, with the goal of allowing biologists to quickly focus on, analyze, compare, and retrieve related information on the parts of the genomic data they are most interested in. We expect these capabilities of Bluejay to benefit the many biologists who want to answer complex questions using the information available from completely sequenced genomes. PMID:18940007

Eastern gas shales bibliography selected annotations: gas, oil, uranium, etc. Citations in bituminous shales worldwide

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

Hall, V.S.

1980-06-01

This bibliography contains 2702 citations, most of which are annotated. They are arranged by author in numerical order with a geographical index following the listing. The work is international in scope and covers the early geological literature, continuing through 1979 with a few 1980 citations in Addendum II. Addendum I contains a listing of the reports, well logs and symposiums of the Unconventional Gas Recovery Program (UGR) through August 1979. There is an author-subject index for these publications following the listing. The second part of Addendum I is a listing of the UGR maps which also has a subject-author indexmore » following the map listing. Addendum II includes several important new titles on the Devonian shale as well as a few older citations which were not found until after the bibliography had been numbered and essentially completed. A geographic index for these citations follows this listing.« less

Discovering gene annotations in biomedical text databases

PubMed Central

Cakmak, Ali; Ozsoyoglu, Gultekin

2008-01-01

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 pattern occurrences with similar semantics. Relatively low recall performance of our pattern-based approach may be enhanced either by employing a probabilistic annotation framework based on the annotation neighbourhoods in textual data, or, alternatively, the statistical enrichment threshold may be adjusted to lower values for applications that put more value on achieving higher recall values. PMID:18325104

Discovering gene annotations in biomedical text databases.

PubMed

Cakmak, Ali; Ozsoyoglu, Gultekin

2008-03-06

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. 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. 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 pattern occurrences with similar semantics. Relatively low recall performance of our pattern-based approach may be enhanced either by employing a probabilistic annotation framework based on the annotation neighbourhoods in textual data, or, alternatively, the statistical enrichment threshold may be adjusted to lower values for applications that put more value on achieving higher recall values.

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.

PubMed

Wimalaratne, Sarala M; Grenon, Pierre; Hoehndorf, Robert; Gkoutos, Georgios V; de Bono, Bernard

2012-02-01

The article presents an infrastructure for supporting the semantic interoperability of biomedical resources based on the management (storing and inference-based querying) of their ontology-based annotations. This infrastructure consists of: (i) a repository to store and query ontology-based annotations; (ii) a knowledge base server with an inference engine to support the storage of and reasoning over ontologies used in the annotation of resources; (iii) a set of applications and services allowing interaction with the integrated repository and knowledge base. The infrastructure is being prototyped and developed and evaluated by the RICORDO project in support of the knowledge management of biomedical resources, including physiology and pharmacology models and associated clinical data. The RICORDO toolkit and its source code are freely available from http://ricordo.eu/relevant-resources. sarala@ebi.ac.uk.

A large-scale evaluation of computational protein function prediction

PubMed Central

Radivojac, Predrag; Clark, Wyatt T; Ronnen Oron, Tal; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kassner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Böhm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

2013-01-01

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based Critical Assessment of protein Function Annotation (CAFA) experiment. Fifty-four methods representing the state-of-the-art for protein function prediction were evaluated on a target set of 866 proteins from eleven organisms. Two findings stand out: (i) today’s best protein function prediction algorithms significantly outperformed widely-used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is significant need for improvement of currently available tools. PMID:23353650

Datalingvistik, 2000.

ERIC Educational Resources Information Center

Kjaersgaard, Poul Soren, Ed.

2002-01-01

Papers from the conference in this volume include the following: "Towards Corpus Annotation Standards--The MATE Workbench" (Laila Dybkjaer and Niels Ole Bernsen); "Danish Text-to-Speech Synthesis Based on Stored Acoustic Segments" (Charles Hoequist); "Toward a Method for the Automated Design of Semantic…

A Teacher's Bookshelf: The Historical Geography of the United States.

ERIC Educational Resources Information Center

Danzer, Gerald A.

1993-01-01

Contends that historical geography helps teachers understand the link between history and geography. Presents an annotated bibliography of recommended geography books for teachers. Asserts that the most essential volume is an atlas of U.S. history. (CFR)

Drugs and driving : a selected bibliography. Supplement 3

DOT National Transportation Integrated Search

1980-06-01

This report presents a bibliography of literature dealing primarily with the relationship of drug use (other than alcohol alone) and highway safety. This volume is the fourth of a series of annotated bibliographies designed to provide ready access to...

dictyBase 2015: Expanding data and annotations in a new software environment.

PubMed

Basu, Siddhartha; Fey, Petra; Jimenez-Morales, David; Dodson, Robert J; Chisholm, Rex L

2015-08-01

dictyBase is the model organism database for the social amoeba Dictyostelium discoideum and related species. The primary mission of dictyBase is to provide the biomedical research community with well-integrated high quality data, and tools that enable original research. Data presented at dictyBase is obtained from sequencing centers, groups performing high throughput experiments such as large-scale mutagenesis studies, and RNAseq data, as well as a growing number of manually added functional gene annotations from the published literature, including Gene Ontology, strain, and phenotype annotations. Through the Dicty Stock Center we provide the community with an impressive amount of annotated strains and plasmids. Recently, dictyBase accomplished a major overhaul to adapt an outdated infrastructure to the current technological advances, thus facilitating the implementation of innovative tools and comparative genomics. It also provides new strategies for high quality annotations that enable bench researchers to benefit from the rapidly increasing volume of available data. dictyBase is highly responsive to its users needs, building a successful relationship that capitalizes on the vast efforts of the Dictyostelium research community. dictyBase has become the trusted data resource for Dictyostelium investigators, other investigators or organizations seeking information about Dictyostelium, as well as educators who use this model system. © 2015 Wiley Periodicals, Inc.

Tests in Print II: An Index to Tests, Test Reviews, and the Literature on Specific Tests.

ERIC Educational Resources Information Center

Buros, Oscar K., Ed.

Tests in Print II is a comprehensive, annotated bibliography of all in-print tests published as separates for use with English-speaking subjects. The 1,155 two-column pages list 2,467 tests in print as of early 1974; 16,574 references through 1971 on specific tests; a reprinting of the 1974 APA-AERA-NCME Standards for Educational andPsychological…

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

PubMed Central

2010-01-01

Background 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. Findings 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. Conclusions 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 in a CASAVA-build into functional annotations while producing corresponding gene expression measurements. Achieving such analysis is executed in an ultrafast and highly efficient manner, whether the analysis be a single-read or paired-end sequencing experiment. TASE is a user-friendly and freely available application, allowing rapid analysis and annotation of any given Illumina Solexa sequencing dataset with ease. PMID:20598141

Tower Shielding Reactor II design and operation report: Vol. 2. Safety Analysis

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

Holland, L. B.; Kolb, J. O.

1970-01-01

Information on the Tower Shielding Reactor II is contained in the TSR-II Design and Operation Report and in the Tower Shielding Facility Manual. The TSR-II Design and Operating Report consists of three volumes. Volume 1 is Descriptions of the Tower Shielding Reactor II and Facility; Volume 2 is Safety analysis of the Tower Shielding Reactor II; and Volume 3 is the Assembly and Testing of the Tower Shielding Reactor II Control Mechanism Housing.

Drugs and driving : a selected bibliography. Supplement 2

DOT National Transportation Integrated Search

1980-06-01

The report presents a bibliography of literature dealing primarily with the relationship of drug use (other than alcohol alone) and highway safety. This volume is the third of a series of annotated bibliographies designed to provide ready access to a...

Arms Control and Disarmament, Volume 8, Number 2, Spring 1972. A Quarterly Bibliography with Abstracts and Annotations

DTIC Science & Technology

Contents: Preface; The international political environment; The strategic environment; Institutions and means for the maintenance of peace; Arms control--general discussion; Arms control--specific problems and measures; Author index ; Subject index.

GAP Final Technical Report 12-14-04

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

Andrew J. Bordner, PhD, Senior Research Scientist

2004-12-14

The Genomics Annotation Platform (GAP) was designed to develop new tools for high throughput functional annotation and characterization of protein sequences and structures resulting from genomics and structural proteomics, benchmarking and application of those tools. Furthermore, this platform integrated the genomic scale sequence and structural analysis and prediction tools with the advanced structure prediction and bioinformatics environment of ICM. The development of GAP was primarily oriented towards the annotation of new biomolecular structures using both structural and sequence data. Even though the amount of protein X-ray crystal data is growing exponentially, the volume of sequence data is growing even moremore » rapidly. This trend was exploited by leveraging the wealth of sequence data to provide functional annotation for protein structures. The additional information provided by GAP is expected to assist the majority of the commercial users of ICM, who are involved in drug discovery, in identifying promising drug targets as well in devising strategies for the rational design of therapeutics directed at the protein of interest. The GAP also provided valuable tools for biochemistry education, and structural genomics centers. In addition, GAP incorporates many novel prediction and analysis methods not available in other molecular modeling packages. This development led to signing the first Molsoft agreement in the structural genomics annotation area with the University of oxford Structural Genomics Center. This commercial agreement validated the Molsoft efforts under the GAP project and provided the basis for further development of the large scale functional annotation platform.« less

Astronomy Books of 1984: Part II--The Technical List.

ERIC Educational Resources Information Center

Fraknoi, Andrew

1985-01-01

An annotated bibliography of astronomy books is presented. These books (most of which are designed for research astronomers and graduate students) demand substantial background in astronomy and physics. Nontechnical books are reviewed in part I (SE 537 910). (JN)

Learning Supervised Topic Models for Classification and Regression from Crowds.

PubMed

Rodrigues, Filipe; Lourenco, Mariana; Ribeiro, Bernardete; Pereira, Francisco C

2017-12-01

The growing need to analyze large collections of documents has led to great developments in topic modeling. Since documents are frequently associated with other related variables, such as labels or ratings, much interest has been placed on supervised topic models. However, the nature of most annotation tasks, prone to ambiguity and noise, often with high volumes of documents, deem learning under a single-annotator assumption unrealistic or unpractical for most real-world applications. In this article, we propose two supervised topic models, one for classification and another for regression problems, which account for the heterogeneity and biases among different annotators that are encountered in practice when learning from crowds. We develop an efficient stochastic variational inference algorithm that is able to scale to very large datasets, and we empirically demonstrate the advantages of the proposed model over state-of-the-art approaches.

Assessing computerized eye tracking technology for gaining insight into expert interpretation of the 12-lead electrocardiogram: an objective quantitative approach.

PubMed

Bond, R R; Zhu, T; Finlay, D D; Drew, B; Kligfield, P D; Guldenring, D; Breen, C; Gallagher, A G; Daly, M J; Clifford, G D

2014-01-01

It is well known that accurate interpretation of the 12-lead electrocardiogram (ECG) requires a high degree of skill. There is also a moderate degree of variability among those who interpret the ECG. While this is the case, there are no best practice guidelines for the actual ECG interpretation process. Hence, this study adopts computerized eye tracking technology to investigate whether eye-gaze can be used to gain a deeper insight into how expert annotators interpret the ECG. Annotators were recruited in San Jose, California at the 2013 International Society of Computerised Electrocardiology (ISCE). Each annotator was recruited to interpret a number of 12-lead ECGs (N=12) while their eye gaze was recorded using a Tobii X60 eye tracker. The device is based on corneal reflection and is non-intrusive. With a sampling rate of 60Hz, eye gaze coordinates were acquired every 16.7ms. Fixations were determined using a predefined computerized classification algorithm, which was then used to generate heat maps of where the annotators looked. The ECGs used in this study form four groups (3=ST elevation myocardial infarction [STEMI], 3=hypertrophy, 3=arrhythmias and 3=exhibiting unique artefacts). There was also an equal distribution of difficulty levels (3=easy to interpret, 3=average and 3=difficult). ECGs were displayed using the 4x3+1 display format and computerized annotations were concealed. Precisely 252 expert ECG interpretations (21 annotators×12 ECGs) were recorded. Average duration for ECG interpretation was 58s (SD=23). Fleiss' generalized kappa coefficient (Pa=0.56) indicated a moderate inter-rater reliability among the annotators. There was a 79% inter-rater agreement for STEMI cases, 71% agreement for arrhythmia cases, 65% for the lead misplacement and dextrocardia cases and only 37% agreement for the hypertrophy cases. In analyzing the total fixation duration, it was found that on average annotators study lead V1 the most (4.29s), followed by leads V2 (3.83s), the rhythm strip (3.47s), II (2.74s), V3 (2.63s), I (2.53s), aVL (2.45s), V5 (2.27s), aVF (1.74s), aVR (1.63s), V6 (1.39s), III (1.32s) and V4 (1.19s). It was also found that on average the annotator spends an equal amount of time studying leads in the frontal plane (15.89s) when compared to leads in the transverse plane (15.70s). It was found that on average the annotators fixated on lead I first followed by leads V2, aVL, V1, II, aVR, V3, rhythm strip, III, aVF, V5, V4 and V6. We found a strong correlation (r=0.67) between time to first fixation on a lead and the total fixation duration on each lead. This indicates that leads studied first are studied the longest. There was a weak negative correlation between duration and accuracy (r=-0.2) and a strong correlation between age and accuracy (r=0.67). Eye tracking facilitated a deeper insight into how expert annotators interpret the 12-lead ECG. As a result, the authors recommend ECG annotators to adopt an initial first impression/pattern recognition approach followed by a conventional systematic protocol to ECG interpretation. This recommendation is based on observing misdiagnoses given due to first impression only. In summary, this research presents eye gaze results from expert ECG annotators and provides scope for future work that involves exploiting computerized eye tracking technology to further the science of ECG interpretation. Copyright © 2014 Elsevier Inc. All rights reserved.

Images of the Universe, Part II: The Decade in Astronomical Photographs.

ERIC Educational Resources Information Center

Mercury, 1982

1982-01-01

Provides an annotated list of technical and nontechnical astronomy books (reviewer's remarks, cost, publisher's name/address). Topics include general astronomy, general astronomy textbooks, solar system, amateur astronomy, astronomy history, archeoastronomy, space exploration, related physics books, pseudoscience, and others. (JN)

Resources for Performance-Based Education.

ERIC Educational Resources Information Center

Houston, W. Robert; And Others

This volume presents annotations of resources on performance-based teacher education. The materials, produced after 1967, include films, slide/tapes, modules, programmed texts, and multimedia kits for training pre- and in-service educational personnel. The materials are indexed according to both competency categories and key words, descriptions,…

Counselor's Information Service, Volume 34, Number 3, September 1979.

ERIC Educational Resources Information Center

Feingold, S. Norman, Ed.

1979-01-01

This annotated bibliography provides information on current literature on educational and vocational guidance. Major subject headings are: (1) occupational information; (2) educational, vocational and personal guidance; (3) guidance administration and procedures; (4) student and teacher aids; (5) free or inexpensive guidance material; (6) adult…

Gas Detectors, Volume 1.

ERIC Educational Resources Information Center

Defense Documentation Center, Alexandria, VA.

The report contains annotated references on gas detectors compiled from the Defense Documentation Center's data bank. The range of the topics deals with detection of toxic propellants, odors, gas leaks, oxygen, etc. Included with the bibliographic reference are the corporate author-monitoring agency, subject, and title indexes. (Author/JR)

PathJam: a new service for integrating biological pathway information.

PubMed

Glez-Peña, Daniel; Reboiro-Jato, Miguel; Domínguez, Rubén; Gómez-López, Gonzalo; Pisano, David G; Fdez-Riverola, Florentino

2010-10-28

Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i) being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii) giving support to the development of new integrative pathway applications. PathJam’s unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized RESTful API.

Cross-Cultural Psychology Newsletter. Volume 7, Number 2.

ERIC Educational Resources Information Center

Dawson, John, Ed.

The Cross-Cultural Psychology Newsletter, an official publication of the International Association for Cross-Cultural Psychology, reports on recent publications and research in cross-cultural psychology. Notes on international conferences in the field are followed by annotations of new publications. In addition, recent research projects are…

An Agent Based Collaborative Simplification of 3D Mesh Model

NASA Astrophysics Data System (ADS)

Wang, Li-Rong; Yu, Bo; Hagiwara, Ichiro

Large-volume mesh model faces the challenge in fast rendering and transmission by Internet. The current mesh models obtained by using three-dimensional (3D) scanning technology are usually very large in data volume. This paper develops a mobile agent based collaborative environment on the development platform of mobile-C. Communication among distributed agents includes grasping image of visualized mesh model, annotation to grasped image and instant message. Remote and collaborative simplification can be efficiently conducted by Internet.

Project Basic Instructional Guide. Instructional Resources. Volume IV. World of Work.

ERIC Educational Resources Information Center

Maryland State Dept. of Education, Baltimore.

Designed to provide a listing of suggested resources to support the Project Basic instructional guide on the world of work, this bibliography consists of annotated listings of student-use materials (library books, films, filmstrips, kits, records, games, audio and videotapes, filmloops, transparencies, periodicals, and pamphlets) arranged…

Science Books: A Quarterly Review, Volume 5 Number 3.

ERIC Educational Resources Information Center

Deason, Hilary J.

This publication reviews tradebooks, textbooks, and reference works in the pure and applied sciences for students in the elementary schools, secondary schools, and in the first two years of college. Included are selected advanced and professional books useful for reference by students and faculty members. Evaluations and annotations of books…

Science Books: A Quarterly Review, Volume 8, Number 4.

ERIC Educational Resources Information Center

American Association for the Advancement of Science, Washington, DC.

This quarterly journal reviews trade books, textbooks, and reference works in the pure and applied sciences for students in kindergartens, elementary schools, secondary schools, and in the first two years of college. Also included are selected advanced and professional books useful for reference by students and faculty members. Annotations are…

Science Policy Reviews, Volume 5 Number 1.

ERIC Educational Resources Information Center

Simons, Eugene M.

Presented in this quarterly publication are reviews, highlights, and 391 annotated bibliographic references from current and international literature in the area of science and public policy. The term "science" is used here to denote both engineering and technology as well as science. The literature reviewed includes books, reports, and periodical…

Multicultural Prism: Voices from the Field. [Volume 1.

ERIC Educational Resources Information Center

Adams, J. Q., Ed.; Welsch, Janice R., Ed.

This book weaves together original essays with several that have been published earlier to address establishing the context for multicultural education, implementing multicultural perspectives in the classroom, and assessing the impact of multicultural education. The book also presents two annotated bibliographies. Following a foreword by J. Q.…

Books in School; Volume 1, Number 1, March 1977.

ERIC Educational Resources Information Center

Moyle, Donald, Ed.

The 59 books annotated in this issue are arranged under five headings: infant schools; junior schools; secondary schools; adult literacy work; and apparatus, games, and kits. The books for school-age children are further subdivided into reading and language development, fiction, and nonfiction. Each entry contains a subjective readability rating…

ELECTROSTATIC EFFECTS IN FABRIC FILTRATION: VOLUME I. FIELDS, FABRICS, AND PARTICLES. (ANNOTATED DATA)

EPA Science Inventory

The report examines the effect of particle charge and electric fields on the filtration of dust by fabrics. Both frictional charging and charging by corona are studied. Charged particles and an electric field driving particles toward the fabric can greatly reduce the initial pres...

Intermodal Freight Transportation, Volume 1: Overview Of Impediments, Data Sources For Intermodal Transportation Planning, And Annotated Bibliography

DOT National Transportation Integrated Search

1997-08-01

This is the first Federal Highway Cost Allocation Study (HCAS) since 1982. There are two key reasons for conducting this study. The first is to determine how changes in the Federal highway program and user fees which support that program have affecte...

Science Policy Reviews, Volume 4 Number 4.

ERIC Educational Resources Information Center

Simons, Eugene M., Ed.

Presented in this quarterly publication are reviews, highlights, and 402 annotated bibliographic references from current and international literature in the area of science and public policy. The term "science" is used here to denote both engineering and technology as well as science. The literature reviewed includes books, reports, and periodical…

Selected Bibliography of Polish Educational Materials. Volume 11, Number 4, 1972.

ERIC Educational Resources Information Center

Wieczorek, Barbara, Ed.; Krajewska, Korolina, Ed.

The publication is an annotated bibliography of books, papers, and articles on Polish education which were published from September to November, 1972. Entries are arranged alphabetically by author under the following subjects: History of Education, Laws and Legislation, General Information on Education, Social and Educational Sciences, Teacher's…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia, Volume 1 Number 4 1967.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

This is an annotated bibliography with abstracts of 110 entries including materials in English, French, and Arabic on educational organization, philosophy and theory, school administration, higher education, adult education, special problems, and structure of North Africa's educational organization. Vocational, religious, fine arts, and special…

Science Policy Reviews, Volume 5 Number 4.

ERIC Educational Resources Information Center

Simons, Eugene M., Ed.

Presented in this final issue of a quarterly publication are reviews, highlights, and 391 annotated bibliographic references from current and international literature in the area of science and public policy. The literature reviewed includes books, reports, and periodical articles and focuses on matters of broad public policy. In addition to the…

Forcible Rape: The Criminal Justice System Response.

ERIC Educational Resources Information Center

Battelle Memorial Inst., Seattle, WA. Law and Justice Study Center.

This annotated bibliography contains 11 documents that describe, analyze and recommend procedures for investigating and prosecuting rape cases. The documents are grouped according to intended audience; there are four volumes for police, three for prosecutors, and one for victims. Also listed are a book analyzing legal issues; a literature review…

American Indian Literature. A Selected Bibliography for Iowa Schools.

ERIC Educational Resources Information Center

Bataille, Gretchen Mueller

Avoidance of stereotypes and realistic portrayal of American Indian life are among the criteria used for the references included in this annotated bibliography. The volume is intended to assist Iowa teachers, particularly of language arts and social studies, in correcting misconceptions about American Indians by identifying materials and resources…

Water Pollution: Part I, Municipal Wastewaters; Part II, Industrial Wastewaters.

ERIC Educational Resources Information Center

Fowler, K. E. M.

This publication is an annotated bibliography of municipal and industrial wastewater literature. This publication consists of two parts plus appendices. Part one is entitled Municipal Wastewaters and includes publications in such areas as health effects of polluted waters, federal policy and legislation, biology and chemistry of polluted water,…

FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets

PubMed Central

2013-01-01

Background Characterising genetic diversity through the analysis of massively parallel sequencing (MPS) data offers enormous potential to significantly improve our understanding of the genetic basis for observed phenotypes, including predisposition to and progression of complex human disease. Great challenges remain in resolving genetic variants that are genuine from the millions of artefactual signals. Results FAVR is a suite of new methods designed to work with commonly used MPS analysis pipelines to assist in the resolution of some of the issues related to the analysis of the vast amount of resulting data, with a focus on relatively rare genetic variants. To the best of our knowledge, no equivalent method has previously been described. The most important and novel aspect of FAVR is the use of signatures in comparator sequence alignment files during variant filtering, and annotation of variants potentially shared between individuals. The FAVR methods use these signatures to facilitate filtering of (i) platform and/or mapping-specific artefacts, (ii) common genetic variants, and, where relevant, (iii) artefacts derived from imbalanced paired-end sequencing, as well as annotation of genetic variants based on evidence of co-occurrence in individuals. We applied conventional variant calling applied to whole-exome sequencing datasets, produced using both SOLiD and TruSeq chemistries, with or without downstream processing by FAVR methods. We demonstrate a 3-fold smaller rare single nucleotide variant shortlist with no detected reduction in sensitivity. This analysis included Sanger sequencing of rare variant signals not evident in dbSNP131, assessment of known variant signal preservation, and comparison of observed and expected rare variant numbers across a range of first cousin pairs. The principles described herein were applied in our recent publication identifying XRCC2 as a new breast cancer risk gene and have been made publically available as a suite of software tools. Conclusions FAVR is a platform-agnostic suite of methods that significantly enhances the analysis of large volumes of sequencing data for the study of rare genetic variants and their influence on phenotypes. PMID:23441864

Design Criteria for Microbiological Facilities at Fort Detrick. Volume II: Design Criteria

ERIC Educational Resources Information Center

Army Biological Labs., Fort Detrick, MD. Industrial Health and Safety Div.

Volume II of a two-volume manual of design criteria, based primarily on biological safety considerations. It is prepared for the use of architect-engineers in designing new or modified microbiological facilities for Fort Detrick, Maryland. Volume II is divided into the following sections: (1) architectural, (2) heating, ventilating, and air…

A-MADMAN: Annotation-based microarray data meta-analysis tool

PubMed Central

Bisognin, Andrea; Coppe, Alessandro; Ferrari, Francesco; Risso, Davide; Romualdi, Chiara; Bicciato, Silvio; Bortoluzzi, Stefania

2009-01-01

Background Publicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitation of this exceptionally rich mine of information is still hampered by the lack of appropriate computational tools, able to overcome the critical issues raised by meta-analysis. Results This work presents A-MADMAN, an open source web application which allows the retrieval, annotation, organization and meta-analysis of gene expression datasets obtained from Gene Expression Omnibus. A-MADMAN addresses and resolves several open issues in the meta-analysis of gene expression data. Conclusion A-MADMAN allows i) the batch retrieval from Gene Expression Omnibus and the local organization of raw data files and of any related meta-information, ii) the re-annotation of samples to fix incomplete, or otherwise inadequate, metadata and to create user-defined batches of data, iii) the integrative analysis of data obtained from different Affymetrix platforms through custom chip definition files and meta-normalization. Software and documentation are available on-line at . PMID:19563634

Microbial genome analysis: the COG approach.

PubMed

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

2017-09-14

For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

COMP Superscalar, an interoperable programming framework

NASA Astrophysics Data System (ADS)

Badia, Rosa M.; Conejero, Javier; Diaz, Carlos; Ejarque, Jorge; Lezzi, Daniele; Lordan, Francesc; Ramon-Cortes, Cristian; Sirvent, Raul

2015-12-01

COMPSs is a programming framework that aims to facilitate the parallelization of existing applications written in Java, C/C++ and Python scripts. For that purpose, it offers a simple programming model based on sequential development in which the user is mainly responsible for (i) identifying the functions to be executed as asynchronous parallel tasks and (ii) annotating them with annotations or standard Python decorators. A runtime system is in charge of exploiting the inherent concurrency of the code, automatically detecting and enforcing the data dependencies between tasks and spawning these tasks to the available resources, which can be nodes in a cluster, clouds or grids. In cloud environments, COMPSs provides scalability and elasticity features allowing the dynamic provision of resources.

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

PubMed Central

Casadio, Rita

2017-01-01

Abstract 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. PMID:28453653

An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry.

PubMed

Dhanyalakshmi, K H; Naika, Mahantesha B N; Sajeevan, R S; Mathew, Oommen K; Shafi, K Mohamed; Sowdhamini, Ramanathan; N Nataraja, Karaba

2016-01-01

The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs). Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools. Here, we report an approach to assign putative functions to PUFs, identified in the transcriptome of mulberry, a perennial tree commonly cultivated as host of silkworm. We utilized the mulberry PUFs generated from leaf tissues exposed to drought stress at whole plant level. A sequence and structure based computational analysis predicted the probable function of the PUFs. For rapid and easy annotation of PUFs, we developed an automated pipeline by integrating diverse bioinformatics tools, designated as PUFs Annotation Server (PUFAS), which also provides a web service API (Application Programming Interface) for a large-scale analysis up to a genome. The expression analysis of three selected PUFs annotated by the pipeline revealed abiotic stress responsiveness of the genes, and hence their potential role in stress acclimation pathways. The automated pipeline developed here could be extended to assign functions to PUFs from any organism in general. PUFAS web server is available at http://caps.ncbs.res.in/pufas/ and the web service is accessible at http://capservices.ncbs.res.in/help/pufas.

DynGO: a tool for visualizing and mining of Gene Ontology and its associations

PubMed Central

Liu, Hongfang; Hu, Zhang-Zhi; Wu, Cathy H

2005-01-01

Background A large volume of data and information about genes and gene products has been stored in various molecular biology databases. A major challenge for knowledge discovery using these databases is to identify related genes and gene products in disparate databases. The development of Gene Ontology (GO) as a common vocabulary for annotation allows integrated queries across multiple databases and identification of semantically related genes and gene products (i.e., genes and gene products that have similar GO annotations). Meanwhile, dozens of tools have been developed for browsing, mining or editing GO terms, their hierarchical relationships, or their "associated" genes and gene products (i.e., genes and gene products annotated with GO terms). Tools that allow users to directly search and inspect relations among all GO terms and their associated genes and gene products from multiple databases are needed. Results We present a standalone package called DynGO, which provides several advanced functionalities in addition to the standard browsing capability of the official GO browsing tool (AmiGO). DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations. The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. Conclusion We have presented a standalone package DynGO that provides functionalities to search and browse GO and its association databases as well as several additional functions such as batch retrieval and semantic retrieval. The complete documentation and software are freely available for download from the website . PMID:16091147

Genome improvement of the acarbose producer Actinoplanes sp. SE50/110 and annotation refinement based on RNA-seq analysis.

PubMed

Wolf, Timo; Schneiker-Bekel, Susanne; Neshat, Armin; Ortseifen, Vera; Wibberg, Daniel; Zemke, Till; Pühler, Alfred; Kalinowski, Jörn

2017-06-10

Actinoplanes sp. SE50/110 is the natural producer of acarbose, which is used in the treatment of diabetes mellitus type II. However, until now the transcriptional organization and regulation of the acarbose biosynthesis are only understood rudimentarily. The genome sequence of Actinoplanes sp. SE50/110 was known before, but was resequenced in this study to remove assembly artifacts and incorrect base callings. The annotation of the genome was refined in a multi-step approach, including modern bioinformatic pipelines, transcriptome and proteome data. A whole transcriptome RNA-seq library as well as an RNA-seq library enriched for primary 5'-ends were used for the detection of transcription start sites, to correct tRNA predictions, to identify novel transcripts like small RNAs and to improve the annotation through the correction of falsely annotated translation start sites. The transcriptome data sets were also applied to identify 31 cis-regulatory RNA structures, such as riboswitches or RNA thermometers as well as three leaderless transcribed short peptides found in putative attenuators upstream of genes for amino acid biosynthesis. The transcriptional organization of the acarbose biosynthetic gene cluster was elucidated in detail and fourteen novel biosynthetic gene clusters were suggested. The accurate genome sequence and precise annotation of the Actinoplanes sp. SE50/110 genome will be the foundation for future genetic engineering and systems biology studies. Copyright © 2017 Elsevier B.V. All rights reserved.

The Listeria monocytogenes strain 10403S BioCyc database

PubMed Central

Orsi, Renato H.; Bergholz, Teresa M.; Wiedmann, Martin; Boor, Kathryn J.

2015-01-01

Listeria monocytogenes is a food-borne pathogen of humans and other animals. The striking ability to survive several stresses usually used for food preservation makes L. monocytogenes one of the biggest concerns to the food industry, while the high mortality of listeriosis in specific groups of humans makes it a great concern for public health. Previous studies have shown that a regulatory network involving alternative sigma (σ) factors and transcription factors is pivotal to stress survival. However, few studies have evaluated at the metabolic networks controlled by these regulatory mechanisms. The L. monocytogenes BioCyc database uses the strain 10403S as a model. Computer-generated initial annotation for all genes also allowed for identification, annotation and display of predicted reactions and pathways carried out by a single cell. Further ongoing manual curation based on published data as well as database mining for selected genes allowed the more refined annotation of functions, which, in turn, allowed for annotation of new pathways and fine-tuning of previously defined pathways to more L. monocytogenes-specific pathways. Using RNA-Seq data, several transcription start sites and promoter regions were mapped to the 10403S genome and annotated within the database. Additionally, the identification of promoter regions and a comprehensive review of available literature allowed the annotation of several regulatory interactions involving σ factors and transcription factors. The L. monocytogenes 10403S BioCyc database is a new resource for researchers studying Listeria and related organisms. It allows users to (i) have a comprehensive view of all reactions and pathways predicted to take place within the cell in the cellular overview, as well as to (ii) upload their own data, such as differential expression data, to visualize the data in the scope of predicted pathways and regulatory networks and to carry on enrichment analyses using several different annotations available within the database. Database URL: http://biocyc.org/organism-summary?object=10403S_RAST PMID:25819074

The Listeria monocytogenes strain 10403S BioCyc database.

PubMed

Orsi, Renato H; Bergholz, Teresa M; Wiedmann, Martin; Boor, Kathryn J

2015-01-01

Listeria monocytogenes is a food-borne pathogen of humans and other animals. The striking ability to survive several stresses usually used for food preservation makes L. monocytogenes one of the biggest concerns to the food industry, while the high mortality of listeriosis in specific groups of humans makes it a great concern for public health. Previous studies have shown that a regulatory network involving alternative sigma (σ) factors and transcription factors is pivotal to stress survival. However, few studies have evaluated at the metabolic networks controlled by these regulatory mechanisms. The L. monocytogenes BioCyc database uses the strain 10403S as a model. Computer-generated initial annotation for all genes also allowed for identification, annotation and display of predicted reactions and pathways carried out by a single cell. Further ongoing manual curation based on published data as well as database mining for selected genes allowed the more refined annotation of functions, which, in turn, allowed for annotation of new pathways and fine-tuning of previously defined pathways to more L. monocytogenes-specific pathways. Using RNA-Seq data, several transcription start sites and promoter regions were mapped to the 10403S genome and annotated within the database. Additionally, the identification of promoter regions and a comprehensive review of available literature allowed the annotation of several regulatory interactions involving σ factors and transcription factors. The L. monocytogenes 10403S BioCyc database is a new resource for researchers studying Listeria and related organisms. It allows users to (i) have a comprehensive view of all reactions and pathways predicted to take place within the cell in the cellular overview, as well as to (ii) upload their own data, such as differential expression data, to visualize the data in the scope of predicted pathways and regulatory networks and to carry on enrichment analyses using several different annotations available within the database. © The Author(s) 2015. Published by Oxford University Press.

Smoking Gun or Circumstantial Evidence? Comparison of Statistical Learning Methods using Functional Annotations for Prioritizing Risk Variants.

PubMed

Gagliano, Sarah A; Ravji, Reena; Barnes, Michael R; Weale, Michael E; Knight, Jo

2015-08-24

Although technology has triumphed in facilitating routine genome sequencing, new challenges have been created for the data-analyst. Genome-scale surveys of human variation generate volumes of data that far exceed capabilities for laboratory characterization. By incorporating functional annotations as predictors, statistical learning has been widely investigated for prioritizing genetic variants likely to be associated with complex disease. We compared three published prioritization procedures, which use different statistical learning algorithms and different predictors with regard to the quantity, type and coding. We also explored different combinations of algorithm and annotation set. As an application, we tested which methodology performed best for prioritizing variants using data from a large schizophrenia meta-analysis by the Psychiatric Genomics Consortium. Results suggest that all methods have considerable (and similar) predictive accuracies (AUCs 0.64-0.71) in test set data, but there is more variability in the application to the schizophrenia GWAS. In conclusion, a variety of algorithms and annotations seem to have a similar potential to effectively enrich true risk variants in genome-scale datasets, however none offer more than incremental improvement in prediction. We discuss how methods might be evolved for risk variant prediction to address the impending bottleneck of the new generation of genome re-sequencing studies.

Newspaper Indexes, Guides, Directories, and Union Lists. No. 4.

ERIC Educational Resources Information Center

Fikes, Robert, Jr.

This annotated bibliography lists 52 citations for U.S. and foreign newspaper indexes, summaries, guides and directories, and union lists held by San Diego State University Libraries. Entries are arranged alphabetically in the above categories by main entry, followed by imprint, frequency and/or date of publication, volumes held by the library,…

Reports 6. The Yugoslav Serbo-Croatian-English Contrastive Project.

ERIC Educational Resources Information Center

Filipovic, Rudolf, Ed.

The first part of the sixth volume in this series consists of a 116-item annotated bibliography of American doctoral dissertations in contrastive linguistics. The second part consists of six articles dealing with various aspects of Serbo-Croatian-English contrastive analysis. They are: "A Contrastive Analysis Evaluation of Conversion in English…

Science Books, A Quarterly Review, Volume 6 Number 4.

ERIC Educational Resources Information Center

Deason, Hilary J.

1971-01-01

For the improvement of science education and to facilitate the public understanding of science, the American Association for the Advancement of Science publishes this quarterly review of science books. Evaluations and annotations are given for trade books, textbooks, and reference works in the pure and applied sciences. Books are for students in…

Science Books, Volume 10 Number 4.

ERIC Educational Resources Information Center

Wolff, Kathryn, Ed.

This quarterly journal reviews trade books, textbooks, and reference works in the pure and applied sciences for students in elementary and secondary schools and in the first two years of college. Included are selected advanced and professional books useful for reference by students and teachers. Each book is reviewed and annotated by a qualified…

Science Books, A Quarterly Review, Volume 8 Number 1.

ERIC Educational Resources Information Center

American Association for the Advancement of Science, Washington, DC.

This quarterly journal reviews trade books, textbooks, and reference works in the pure and applied sciences for students in the elementary schools, in secondary school and in the first two years of college. Included are selected advanced and professional books useful for reference by students and faculty members. Annotations are listed in order of…

The New Religions: An Annotated Introductory Bibliography.

ERIC Educational Resources Information Center

Center for the Study of New Religious Movements, Berkeley, CA.

This bibliography is a collection of approximately 100 citations of articles, books, and edited volumes on various aspects of new religious teachings and religious cults. Most of the entries were published between 1970 and 1977, although a few date back to the mid 1960s. Entries are divided into three major sections. Section I, New Religious…

Selected Bibliography and Abstracts of Educational Materials in Pakistan. Volume 14, No. 4, Period Covered October - December, 1980.

ERIC Educational Resources Information Center

Saad, Geti, Comp.

This annotated listing cites newspaper articles, government publications, and monographs dealing with education in Pakistan. Items cited were published between October and December 1980. The listing is organized by subject area. Subjects include: administration, organization, and financing of education; adult education; agricultural education;…

Selected Bibliography and Abstracts of Educational Materials in Pakistan. Volume 4, Number 4.

ERIC Educational Resources Information Center

Saad, Ismail, Ed.

This selected list of 121 citations on the public education system of Pakistan is annotated to give the description and appropriate level of each document. Entries are arranged according to 33 major topics: 1) education administration, organization, and finance; 2) educational history, educational philosophy; 3) educational development,…

Selected Bibliography and Abstracts of Educational Materials in Pakistan. Volume 14, No. 2, 1980. Period Covered April-June 1980.

ERIC Educational Resources Information Center

Saad, Geti, Comp.

This annotated listing cites newspaper articles, government publications, journal articles, and monographs dealing with education in Pakistan. Items cited were published between April and June 1980. The listing is organized by subject area. Subjects include administration, organization, and financing of education; curriculum; development of…

Selected Bibliography and Abstracts of Educational Materials in Pakistan, Volume 9, Number 4: Period Covered, October-December 1975.

ERIC Educational Resources Information Center

Saad, Geti, Comp.

Contained in this annotated bibliography are 100 references to selected educational materials published in Pakistan during the period October through December, 1975. Pakistani journals, newspapers, and government publications provide the source of the materials. They are organized into 26 categories: administration, organization and financing of…

Selected Bibliography and Abstracts of Educational Materials in Pakistan. Volume 14, Number 1, 1980. Period Covered January-March 1980.

ERIC Educational Resources Information Center

Saad, Geti, Comp.

This annotated bibliography cites newspaper articles, government publications, and journal articles dealing with education in Pakistan. Items listed were published between January and March 1980. Topics covered include the following: educational administration, organization and financing; childhood education; curriculum; educational goals,…

Education in Asia and the Pacific: Reviews, Reports, and Notes. Number 25.

ERIC Educational Resources Information Center

United Nations Educational, Scientific and Cultural Organization, Bangkok (Thailand). Principal Regional Office for Asia and the Pacific.

This volume consists of report summaries, literature reviews, and document annotations on the subject of education in Asia and the Pacific. The reviewed literature includes the following: "Reorientation and Reform of Secondary Education in the Asian and Pacific Region: A Status Report," edited by R.S. Adams; Unesco's "Primary…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 7, Number 3, 1973.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

This bibliography includes English language annotations of newspapers and government publications covering educational materials of interest to North Africans (1) to raise the consciousness of their Islamic and Arabic heritages and (2) to adapt education to the problems of the multilingual population. Citations are categorized by country. Within…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 6, Number 4, 1972.

ERIC Educational Resources Information Center

Azzouz, Azzedine

English language annotations of newspapers and government publications covering educational materials of interest to North Africans to (1) raise the consciousness of their Islamic and Arabic heritages (Arabization) and (2) to adapt education to the problems of the multilingual population are included in this bibliography. Citations are categorized…

Global Journal of Computer Science and Technology. Volume 1.2

ERIC Educational Resources Information Center

Dixit, R. K.

2009-01-01

Articles in this issue of "Global Journal of Computer Science and Technology" include: (1) Input Data Processing Techniques in Intrusion Detection Systems--Short Review (Suhair H. Amer and John A. Hamilton, Jr.); (2) Semantic Annotation of Stock Photography for CBIR Using MPEG-7 standards (R. Balasubramani and V. Kannan); (3) An Experimental Study…

Textbooks in German 1942-1973: A Descriptive Bibliography.

ERIC Educational Resources Information Center

Buck, Kathryn, Comp.; Haase, Arthur, Comp.

This annotated bibliography lists German textbooks published in the United States for use in junior high, high school, and college by students whose first language is English. Intended for those interested in researching old and writing new texts, as well as for those searching for an extant volume for classroom use, the bibliography consists of…

Children and Television. Current Issues in Education: A Bibliographic Series. Volume 5, No. 1, July 1988.

ERIC Educational Resources Information Center

Christo, Doris Hedlund

Focused on research concerning children and television, this annotated bibliography lists 44 articles selected from the Educational Resources Information Center (ERIC) database from 1983 to 1988. Topics include: (1) the effects of television violence on children; (2) television viewing patterns; (3) children's television programs; and (4)…

Construction of ontology augmented networks for protein complex prediction.

PubMed

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian

2013-01-01

Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational methods for protein complex prediction. Most existing methods focus mainly on the topological structure of protein-protein interaction networks, and largely ignore the gene ontology annotation information. In this article, we constructed ontology augmented networks with protein-protein interaction data and gene ontology, which effectively unified the topological structure of protein-protein interaction networks and the similarity of gene ontology annotations into unified distance measures. After constructing ontology augmented networks, a novel method (clustering based on ontology augmented networks) was proposed to predict protein complexes, which was capable of taking into account the topological structure of the protein-protein interaction network, as well as the similarity of gene ontology annotations. Our method was applied to two different yeast protein-protein interaction datasets and predicted many well-known complexes. The experimental results showed that (i) ontology augmented networks and the unified distance measure can effectively combine the structure closeness and gene ontology annotation similarity; (ii) our method is valuable in predicting protein complexes and has higher F1 and accuracy compared to other competing methods.

Deliberate Social Change in the City: List of Suggested Readings.

ERIC Educational Resources Information Center

Duhl, Leonard; Schon, Donald A.

The suggested readings in this occasionally annotated bibliography concerning deliberate socialchange in the city are listed under five subject areas. These subject areas are as follows: I. The Scope of "Social Change"; II. Toward a Theory of Social Change; III. A. The Rational Problem Solving Process, B. Behavioral Approaches to Social Change;…

Rural Health Abstracts and Citations 1980-1987. Part II: Indian Health Care.

ERIC Educational Resources Information Center

North Dakota Univ., Grand Forks. Center for Rural Health.

Over 300 articles concerning rural health as it pertains to American Indians and Alaska Natives are cited in this bibliography. Most of the articles were published between 1980 and 1988. Abstracts are reprinted verbatim and the bibliography is organized into sections by subject matter. Within each section, annotated citations are listed…

Manufacturing Math Classes: An Instructional Program Guide for Manufacturing Workers.

ERIC Educational Resources Information Center

McBride, Pamela G.; And Others

This program guide documents a manufacturing job family curriculum that develops competence in generic work force education skills through three courses: Reading Rulers, Charts, and Gauges and Math for Manufacturing Workers I and II. An annotated table of contents lists a brief description of the questions answered in each section. An introduction…

Use of Annotations for Component and Framework Interoperability

NASA Astrophysics Data System (ADS)

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 western United States at the USDA NRCS National Water and Climate Center. PRMS is a component based modular precipitation-runoff model developed to evaluate the impacts of various combinations of precipitation, climate, and land use on streamflow and general basin hydrology. The new OMS 3.0 PRMS model source code is more concise and flexible as a result of using the new framework’s annotation based approach. The fully annotated components are now providing information directly for (i) model assembly and building, (ii) dataflow analysis for implicit multithreading, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Experience to date has demonstrated the multi-purpose value of using annotations. Annotations are also a feasible and practical method to enable interoperability among models and modeling frameworks. As a prototype example, model code annotations were used to generate binding and mediation code to allow the use of OMS 3.0 model components within the OpenMI context.

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

None

Volume II of the Site Environmental Report for 2006 is provided by Ernest Orlando Lawrence Berkeley National Laboratory as a supplemental appendix to Volume I, which contains the body of the report. Volume II contains the environmental monitoring and sampling data used to generate summary results of routine and nonroutine activities at the Laboratory (except for groundwater sampling data, which may be found in the reports referred to in Chapter 4). Volume I summarizes the results from analyses of the data. The results from sample collections are more comprehensive in Volume II than in Volume I: For completeness, all resultsmore » from sample collections that began or ended in calendar year (CY) 2006 are included in this volume. However, the samples representing CY 2005 data have not been used in the summary results that are reported in Volume I. (For example, although ambient air samples collected on January 2, 2006, are presented in Volume II, they represent December 2005 data and are not included in Table 4-2 in Volume I.)« less

Reinforced soil structures. Volume II, Summary of research and systems information

DOT National Transportation Integrated Search

1989-11-01

Volume II was essentially prepared as an Appendix of supporting information for Volume I. This volume contains much of the supporting theory and a summary of the research used to verify the design approach contained in Volume I, as well as general in...

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

PubMed

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.

Savannah River Site Approved Site Treatment Plan, 2001 Annual Update (Volumes I and II)

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

Lawrence, B.

2001-04-30

The Compliance Plan Volume (Volume I) identifies project activity scheduled milestones for achieving compliance with Land Disposal Restrictions. Information regarding the technical evaluation of treatment options for SRS mixed wastes is contained in the Background Volume (Volume II) and is provided for information.

BACIE Register of Programmed Instruction in the Field of Education and Training in Commerce and Industry. Volume 2, 1968.

ERIC Educational Resources Information Center

British Association for Commercial and Industrial Education, London (England).

The British Association for Commercial and Industrial Education has included in its register of annotated programed instructional materials: programs available in the United Kingdom; programs dealing with industrial and commercial training and related further education; and information as supplied by the authors or producers of programs. The areas…

Science Books, A Quarterly Review, Volume 8 Number 2.

ERIC Educational Resources Information Center

American Association for the Advancement of Science, Washington, DC.

This quarterly journal reviews books in different science fields which could be used by teachers in elementary school, secondary school, and in the first two years of college. Not only are the textbooks reviewed, but trade books and reference works in pure and applied sciences are included. Annotations are listed in order of Dewey Decimal…

Outstanding Women Athletes: Who They Are and How They Influenced Sports in America.

ERIC Educational Resources Information Center

Woolum, Janet

This book highlights the stories of 60 of this century's female athletes who pioneered, participated in, or continue to compete in women's sports. Following forewords by Billie Jean King, Anita DeFrantz, and Deborah Slaner Anderson, the volume contains biography, history, an annotated bibliography, and statistics on women athletes from the late…

Selected Bibliography and Abstracts of Educational Materials in Pakistan. Volume 6, Number 1, 1972. Period Covered January-March 1972.

ERIC Educational Resources Information Center

Saad, Geti, Comp.

The annotated bibliography lists 111 entries of selected educational materials from Pakistan covering the period from January through March 1972. Entries are listed alphabetically by author under the following thirty-one categories; 1) administrative, organization and financing of education; 2) agricultural education; 3) childhood education; 4)…

Sourcebook for English Teachers: Directed Reading/Teaching Guides for Selected Literacy Works. Volume 2.

ERIC Educational Resources Information Center

Ley, Terry C., Ed.

This sourcebook presents reading guides for 27 literary works frequently used by secondary school English teachers. The guides contain an overview of the work, a pool of instructional objectives for each work, a variety of activities, a series of discussion options, suggestions for evaluation, and annotated lists of related works. Included are:…

Sourcebook for English Teachers: Directed Reading/Teaching Guides for Selected Literary Works. Volume 1.

ERIC Educational Resources Information Center

Ley, Terry C., Ed.

This sourcebook presents reading guides for 22 literary works frequently used by secondary school English teachers. The guides contain an overview of the work, a pool of instructional objectives for each work, a variety of activities, a series of discussion options, suggestions for evaluation, and annotated lists of related works. Included are:…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 6, Number 1, 1972.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

Annotations of articles, written in English, provide the content for a bibliography of educational materials written in French useful to those with an interest in North Africa. Sections on Algeria, Libya, Morocco, and Tunisia are preceded by a section on the Maghreb which deals with the special problems of illiteracy, multilingualism, and rapid…

Sourcebook for English Teachers: Directed Reading/Teaching Guides for Selected Literacy Works. Volume 3.

ERIC Educational Resources Information Center

Ley, Terry C., Ed.

This sourcebook presents reading guides for 39 literary works frequently used by scondary school English teachers. The guides contain an overview of the work, a pool of instructional objectives for each work, a variety of activities, a series of discussion options, suggestions for evaluation, and annotated lists of related works. Included are:…

Film Research; A Critical Bibliography With Annotations and Essay.

ERIC Educational Resources Information Center

Bukalski, Peter J.

The quantity of research into film has grown tremendously in the last 15 years, presenting various viewpoints ranging from a literary to a reality-perception approach. This volume was created to provide a research tool for investigators so that the state of film knowledge could be advance. An introductory section discusses some aspects of film…

Sequence alignment visualization in HTML5 without Java.

PubMed

Gille, Christoph; Birgit, Weyand; Gille, Andreas

2014-01-01

Java has been extensively used for the visualization of biological data in the web. However, the Java runtime environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for some tasks may render Java unnecessary. Alignment-To-HTML is the first HTML-based interactive visualization for annotated multiple sequence alignments. The server side script interpreter can perform all tasks like (i) sequence retrieval, (ii) alignment computation, (iii) rendering, (iv) identification of a homologous structural models and (v) communication with BioDAS-servers. The rendered alignment can be included in web pages and is displayed in all browsers on all platforms including touch screen tablets. The functionality of the user interface is similar to legacy Java applets and includes color schemes, highlighting of conserved and variable alignment positions, row reordering by drag and drop, interlinked 3D visualization and sequence groups. Novel features are (i) support for multiple overlapping residue annotations, such as chemical modifications, single nucleotide polymorphisms and mutations, (ii) mechanisms to quickly hide residue annotations, (iii) export to MS-Word and (iv) sequence icons. Alignment-To-HTML, the first interactive alignment visualization that runs in web browsers without additional software, confirms that to some extend HTML5 is already sufficient to display complex biological data. The low speed at which programs are executed in browsers is still the main obstacle. Nevertheless, we envision an increased use of HTML and JavaScript for interactive biological software. Under GPL at: http://www.bioinformatics.org/strap/toHTML/.

South Carolina Voices: Lessons from the Holocaust.

ERIC Educational Resources Information Center

South Carolina State Dept. of Education, Columbia. Council on the Holocaust.

This resource guide is based on interviews with survivors of the Holocaust and those who took part in liberating them from the concentration camps in World War II. The guide is divided into three main parts: (1) overviews, (2) lesson plans, and (3) student handouts. A Holocaust time line, a glossary of key terms, and an annotated bibliography are…

A Reader's Guide for Parents of Children with Mental, Physical, or Emotional Disabilities. An Update.

ERIC Educational Resources Information Center

Moore, Cory; And Others

Intended for parents of children with disabilities, the guide lists and provides information on helpful books. Part I presents annotations on books relevant to all disabilities. Topics covered include personal accounts, early intervention at home, special education rights, and disabled adults. Part II focuses on specific disabilities: autism,…

Special Project Grants Awarded for Improvement in Nurse Training. A Listing.

ERIC Educational Resources Information Center

National Institutes of Health (DHEW), Bethesda, MD. Div. of Nursing.

This current directory lists alphabetically by state, special projects funded by the Title II Nurse Training Act of the Health Manpower Act of 1968, which are awarded for improvement programs in nurse training. Projects funded through June 1971 are listed and briefly annotated, including planning grants awarded for the first time during the fiscal…

41 CFR 101-27.207-3 - Marking material to show extended shelf life.

Code of Federal Regulations, 2013 CFR

2013-07-01

... extended shelf life. 101-27.207-3 Section 101-27.207-3 Public Contracts and Property Management Federal... extended shelf life. When the shelf-life period of Type II material (except for critical end-use items as described below) is extended, only the exterior containers of bulk stocks need be annotated or labeled to...

41 CFR 101-27.207-3 - Marking material to show extended shelf life.

Code of Federal Regulations, 2012 CFR

2012-07-01

... extended shelf life. 101-27.207-3 Section 101-27.207-3 Public Contracts and Property Management Federal... extended shelf life. When the shelf-life period of Type II material (except for critical end-use items as described below) is extended, only the exterior containers of bulk stocks need be annotated or labeled to...

41 CFR 101-27.207-3 - Marking material to show extended shelf life.

Code of Federal Regulations, 2011 CFR

2011-07-01

... extended shelf life. 101-27.207-3 Section 101-27.207-3 Public Contracts and Property Management Federal... extended shelf life. When the shelf-life period of Type II material (except for critical end-use items as described below) is extended, only the exterior containers of bulk stocks need be annotated or labeled to...

41 CFR 101-27.207-3 - Marking material to show extended shelf life.

Code of Federal Regulations, 2010 CFR

2010-07-01

... extended shelf life. 101-27.207-3 Section 101-27.207-3 Public Contracts and Property Management Federal... extended shelf life. When the shelf-life period of Type II material (except for critical end-use items as described below) is extended, only the exterior containers of bulk stocks need be annotated or labeled to...

41 CFR 101-27.207-3 - Marking material to show extended shelf life.

Code of Federal Regulations, 2014 CFR

2014-07-01

... extended shelf life. 101-27.207-3 Section 101-27.207-3 Public Contracts and Property Management Federal... extended shelf life. When the shelf-life period of Type II material (except for critical end-use items as described below) is extended, only the exterior containers of bulk stocks need be annotated or labeled to...

Citizenship Education Software: A Selective, Annotated Bibliography of Microcomputer Programs for the Social Studies.

ERIC Educational Resources Information Center

White, Charles S.

1983-01-01

Software listed was evaluated on the basis of content relevance, variety of instructional strategies, exemplary use of computer for instruction, factual accuracy, evidence of skillful programing, and general "user friendliness." Compatibility with an Apple II+, 48K, was required. Materials for use in grades three through the college level are…

United States History. Annotated Bibliography of Tests.

ERIC Educational Resources Information Center

Educational Testing Service, Princeton, NJ. Test Collection.

The 33 tests in this bibliography cover United States History from the period of exploration of the continent through the Civil War to Post World War II. One test measures knowledge of African American history. Types of measures include credit by examination, item banks, and end-of-course tests. All ages are represented but the majority of tests…

SATPdb: a database of structurally annotated therapeutic peptides

PubMed Central

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

2016-01-01

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

Computer Program (HEVSIM) for Heavy Duty Vehicle Fuel Economy and Performance Simulation. Volume II: Users' Manual.

DOT National Transportation Integrated Search

1981-09-01

Volume II is the second volume of a three volume document describing the computer program HEVSIM for use with buses and heavy duty trucks. This volume is a user's manual describing how to prepare data input and execute the program. A strong effort ha...

An Independent Scientific Assessment of Well Stimulation in California Volume II

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

Jane C.S. Long; Laura C. Feinstein; Corinne E. Bachmann

This study is issued in three volumes. Volume I, issued in January 2015, describes how well stimulation technologies work, how and where operators deploy these technologies for oil and gas production in California, and where they might enable production in the future. Volume II, the present volume, discusses how well stimulation could affect water, atmosphere, seismic activity, wildlife and vegetation, and human health. Volume II reviews available data, and identifies knowledge gaps and alternative practices that could avoid or mitigate these possible impacts. Volume III, also issued in July 2015, presents case studies that assess environmental issues and qualitative risksmore » for specific geographic regions. A final Summary Report summarizes key findings, conclusions and recommendations of all three volumes.« less

Microcomputer Applications for Health Care Professionals. Volume II. Curriculum Improvement Project. Region II.

ERIC Educational Resources Information Center

Bruce, Lucy

This volume is one of three in a self-paced computer literacy course that gives allied health students a firm base of knowledge concerning computer usage in the hospital environment. It also develops skill in several applications software packages. Volume II contains materials for three one-hour courses on word processing applications, spreadsheet…

New York State Educational Information System (NYSEIS) Systems Design. Volume I, Phase II. Final Report.

ERIC Educational Resources Information Center

Price Waterhouse and Co., New York, NY.

This volume on Phase II of the New York State Educational Information System (NYSEIS) describes the Gross Systems Analysis and Design, which includes the general flow diagram and processing chart for each of the student, personnel, and financial subsystems. Volume II, Functional Specifications, includes input/output requirements and file…

Computer Program User’s Manual for FIREFINDER Digital Topographic Data Verification Library Dubbing System. Volume II. Dubbing.

DTIC Science & Technology

1982-01-29

N - Nw .VA COMPUTER PROGRAM USER’S MANUAL FOR . 0FIREFINDER DIGITAL TOPOGRAPHIC DATA VERIFICATION LIBRARY DUBBING SYSTEM VOLUME II DUBBING 29 JANUARY...Digital Topographic Data Verification Library Dubbing System, Volume II, Dubbing 6. PERFORMING ORG. REPORT NUMER 7. AUTHOR(q) S. CONTRACT OR GRANT...Software Library FIREFINDER Dubbing 20. ABSTRACT (Continue an revWee *Ide II necessary end identify by leek mauber) PThis manual describes the computer

History of the United States Atomic Energy Commission. Volume II. 1947 / 1952, Atomic Shield

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

Hewlett, Richard G.; Duncan, Francis

1972-01-01

Sponsored by the Historical Advisory Committee of the Atomic Energy Commission (AEC), this 2-volume series provides an unclassified history of the AEC. Volume I is subtitled ''The New World'' and covers the AEC from 1939 through 1946. This volume, Volume II, is subtitled ''Atomic Shield'' and covers the years 1947 through 1952.

Data Acquisition and Linguistic Resources

NASA Astrophysics Data System (ADS)

Strassel, Stephanie; Christianson, Caitlin; McCary, John; Staderman, William; Olive, Joseph

All human language technology demands substantial quantities of data for system training and development, plus stable benchmark data to measure ongoing progress. While creation of high quality linguistic resources is both costly and time consuming, such data has the potential to profoundly impact not just a single evaluation program but language technology research in general. GALE's challenging performance targets demand linguistic data on a scale and complexity never before encountered. Resources cover multiple languages (Arabic, Chinese, and English) and multiple genres -- both structured (newswire and broadcast news) and unstructured (web text, including blogs and newsgroups, and broadcast conversation). These resources include significant volumes of monolingual text and speech, parallel text, and transcribed audio combined with multiple layers of linguistic annotation, ranging from word aligned parallel text and Treebanks to rich semantic annotation.

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

PubMed Central

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 COGs is expected to become an important tool for microbial genomics. PMID:25428365

Railroad Classification Yard Technology Manual: Volume II : Yard Computer Systems

DOT National Transportation Integrated Search

1981-08-01

This volume (Volume II) of the Railroad Classification Yard Technology Manual documents the railroad classification yard computer systems methodology. The subjects covered are: functional description of process control and inventory computer systems,...

Annotated Bibliography for Lake Erie. Volume IV. Physical,

DTIC Science & Technology

1974-10-01

Presque Isle Bay, Erie , Pennsylvania - interim report. Environ- mental Sciences Inc. Pittsburg, Pa. 235 P. The factors... Presque Isle Peninsula, Erie , Pennsylvania , indicates apparent correlation of initial high erosion rates of placed beach fill with sand size character...changes since 1854. (CE) 777. U. S. Army Corps of Engineers. 1960. Presque Isle Peninsula, Erie , Pennsylvania , beach erosion con- trol study.

Linking wilderness research and management-volume 1. Wilderness fire restoration and management: an annotated reading list

Treesearch

Marion Hourdequin; Vita Wright

2001-01-01

The Wilderness Act of 1964 designates wilderness areas as places where natural conditions prevail and humans leave landscapes untrammeled. Managers of wilderness and similarly protected areas have a mandate to maintain wildland fire as a natural ecological process. However, because fire suppression has dominated Federal land management for most of the past century, the...

Counselor's Information Service: A Quarterly Annotated Bibliography of Current Literature on Educational and Vocational Guidance. Volume 31, Number 2, May, 1976.

ERIC Educational Resources Information Center

B'nai B'rith, Washington, DC. Career and Counseling Services.

The materials reviewed are categorized according to the following topics: (1) Occupational Information; (2) Educational, Vocational, and Personal Guidance; (3) Guidance Administration and Procedures; (4) Student Aids; (5) Aids for the Teacher; (6) Guidance Material--Free or Inexpensive; (7) Adult Education and the Aging; (8) Handicapped and…

Geopressured geothermal bibliography. Volume I. Citation extracts. Second edition

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

Sepehrnoori, K.; Carter, F.; Schneider, R.

This annoted bibliography contains 1131 citations. It represents reports, papers, and articles appearing over the past eighteen years covering topics from the scientific and technical aspects of geopressured geothermal reservoirs to the social, environmental, and legal considerations of exploiting those reservoirs for their energy resources. Six indexes include: author, conference title, descriptor, journal title, report number, and sponsor. (MHR)

Linking wilderness research and management-volume 2. Defining, managing, and monitoring wilderness visitor experiences: an annotated reading list

Treesearch

Annette Puttkammer; Vita Wright

2001-01-01

Opportunities for unique visitor experiences are among the defining attributes of wilderness. In order to understand and protect these experiences, natural and social scientists have pursued an ever-expanding program of wildland recreation research. While much of the early research sought to identify simple relationships between setting attributes and visitor...

Research Results of the National Day Care Study. Final Report of the National Day Care Study. Volume II.

ERIC Educational Resources Information Center

Travers, Jeffrey; And Others

This final report of the National Day Care Study (NDCS), Volume II, provides researchers, social scientists and lay readers with information for judging the soundness of the evidence underlying NDCS conclusions about relationships between regulatable center characteristics and the outcome of care for the child. Thus, Volume II makes free use of…

Subseabed disposal program annual report, January-December 1980. Volume II. Appendices (principal investigator progress reports). Part 1

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

Hinga, K.R.

Volume II of the sixth annual report describing the progress and evaluating the status of the Subseabed Disposal Program contains the appendices referred to in Volume I, Summary and Status. Because of the length of Volume II, it has been split into two parts for publication purposes. Part 1 contains Appendices A-Q; Part 2 contains Appendices R-MM. Separate abstracts have been prepared for each appendix for inclusion in the Energy Data Base.

Model and Interoperability using Meta Data Annotations

NASA Astrophysics Data System (ADS)

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 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. While providing all those capabilities, a significant reduction in the size of the model source code was achieved. To support the benefit of annotations for a modeler, studies were conducted to evaluate the effectiveness of an annotation based framework approach with other modeling frameworks and libraries, a framework-invasiveness study was conducted to evaluate the effects of framework design on model code quality. A typical hydrological 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. Experience to date has demonstrated the multi-purpose value of using annotations. Annotations are also a feasible and practical method to enable interoperability among models and modeling frameworks.

Hydrocarbons and Air Pollution: An Annotated Bibliography. Part I., Categories A to E and Part II., Categories F to M and Indexes.

ERIC Educational Resources Information Center

National Air Pollution Control Administration (DHEW), Raleigh, NC.

This two-part bibliography represents an effort to collect, condense, and organize the literature on the hydrocarbons in relation to air pollution. The approximately 2,300 documents abstracted are all included in the information storage and retrieval system of the National Air Pollution Control Administration's (NAPCA) Air Pollution Technical…

India Through Literature: An Annotated Bibliography for Teaching India. Part II: India Through Contemporary Fiction.

ERIC Educational Resources Information Center

Johnson, Donald; Johnson, Jean

The purpose of this bibliography is to suggest interesting and educational Indian novels and short stories which are appropriate for American secondary school student use. The best books written by Indians in their own languages and translated for the English speaking reader are included along with many written in English. There are two lists: 1)…

MalaCards: an integrated compendium for diseases and their annotation

PubMed Central

Rappaport, Noa; Nativ, Noam; Stelzer, Gil; Twik, Michal; Guan-Golan, Yaron; Iny Stein, Tsippi; Bahir, Iris; Belinky, Frida; Morrey, C. Paul; Safran, Marilyn; Lancet, Doron

2013-01-01

Comprehensive disease classification, integration and annotation are crucial for biomedical discovery. At present, disease compilation is incomplete, heterogeneous and often lacking systematic inquiry mechanisms. We introduce MalaCards, an integrated database of human maladies and their annotations, modeled on the architecture and strategy of the GeneCards database of human genes. MalaCards mines and merges 44 data sources to generate a computerized card for each of 16 919 human diseases. Each MalaCard contains disease-specific prioritized annotations, as well as inter-disease connections, empowered by the GeneCards relational database, its searches and GeneDecks set analyses. First, we generate a disease list from 15 ranked sources, using disease-name unification heuristics. Next, we use four schemes to populate MalaCards sections: (i) directly interrogating disease resources, to establish integrated disease names, synonyms, summaries, drugs/therapeutics, clinical features, genetic tests and anatomical context; (ii) searching GeneCards for related publications, and for associated genes with corresponding relevance scores; (iii) analyzing disease-associated gene sets in GeneDecks to yield affiliated pathways, phenotypes, compounds and GO terms, sorted by a composite relevance score and presented with GeneCards links; and (iv) searching within MalaCards itself, e.g. for additional related diseases and anatomical context. The latter forms the basis for the construction of a disease network, based on shared MalaCards annotations, embodying associations based on etiology, clinical features and clinical conditions. This broadly disposed network has a power-law degree distribution, suggesting that this might be an inherent property of such networks. Work in progress includes hierarchical malady classification, ontological mapping and disease set analyses, striving to make MalaCards an even more effective tool for biomedical research. Database URL: http://www.malacards.org/ PMID:23584832

Dentate gyrus-cornu ammonis (CA) 4 volume is decreased and associated with depressive episodes and lipid peroxidation in bipolar II disorder: Longitudinal and cross-sectional analyses.

PubMed

Elvsåshagen, Torbjørn; Zuzarte, Pedro; Westlye, Lars T; Bøen, Erlend; Josefsen, Dag; Boye, Birgitte; Hol, Per K; Malt, Ulrik F; Young, L Trevor; Andreazza, Ana C

2016-12-01

Reduced dentate gyrus volume and increased oxidative stress have emerged as potential pathophysiological mechanisms in bipolar disorder. However, the relationship between dentate gyrus volume and peripheral oxidative stress markers remains unknown. Here, we examined dentate gyrus-cornu ammonis (CA) 4 volume longitudinally in patients with bipolar II disorder (BD-II) and healthy controls and investigated whether BD-II is associated with elevated peripheral levels of oxidative stress. We acquired high-resolution structural 3T-magnetic resonance imaging (MRI) images and quantified hippocampal subfield volumes using an automated segmentation algorithm in individuals with BD-II (n=29) and controls (n=33). The participants were scanned twice, at study inclusion and on average 2.4 years later. In addition, we measured peripheral levels of two lipid peroxidation markers (4-hydroxy-2-nonenal [4-HNE] and lipid hydroperoxides [LPH]). First, we demonstrated that the automated hippocampal subfield segmentation technique employed in this work reliably measured dentate gyrus-CA4 volume. Second, we found a decreased left dentate gyrus-CA4 volume in patients and that a larger number of depressive episodes between T1 and T2 predicted greater volume decline. Finally, we showed that 4-HNE was elevated in BD-II and that 4-HNE was negatively associated with left and right dentate gyrus-CA4 volumes in patients. These results are consistent with a role for the dentate gyrus in the pathophysiology of bipolar disorder and suggest that depressive episodes and elevated oxidative stress might contribute to hippocampal volume decreases. In addition, these findings provide further support for the hypothesis that peripheral lipid peroxidation markers may reflect brain alterations in bipolar disorders. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Forest Soil Disturbance Monitoring Protocol: Volume II: Supplementary methods, statistics, and data collection

Treesearch

Deborah S. Page-Dumroese; Ann M. Abbott; Thomas M. Rice

2009-01-01

Volume I and volume II of the Forest Soil Disturbance Monitoring Protocol (FSDMP) provide information for a wide range of users, including technicians, field crew leaders, private landowners, land managers, forest professionals, and researchers. Volume I: Rapid Assessment includes the basic methods for establishing forest soil monitoring transects and consistently...

Design and Applications of a GeoSemantic Framework for Integration of Data and Model Resources in Hydrologic Systems

NASA Astrophysics Data System (ADS)

Elag, M.; Kumar, P.

2016-12-01

Hydrologists today have to integrate resources such as data and models, which originate and reside in multiple autonomous and heterogeneous repositories over the Web. Several resource management systems have emerged within geoscience communities for sharing long-tail data, which are collected by individual or small research groups, and long-tail models, which are developed by scientists or small modeling communities. While these systems have increased the availability of resources within geoscience domains, deficiencies remain due to the heterogeneity in the methods, which are used to describe, encode, and publish information about resources over the Web. This heterogeneity limits our ability to access the right information in the right context so that it can be efficiently retrieved and understood without the Hydrologist's mediation. A primary challenge of the Web today is the lack of the semantic interoperability among the massive number of resources, which already exist and are continually being generated at rapid rates. To address this challenge, we have developed a decentralized GeoSemantic (GS) framework, which provides three sets of micro-web services to support (i) semantic annotation of resources, (ii) semantic alignment between the metadata of two resources, and (iii) semantic mediation among Standard Names. Here we present the design of the framework and demonstrate its application for semantic integration between data and models used in the IML-CZO. First we show how the IML-CZO data are annotated using the Semantic Annotation Services. Then we illustrate how the Resource Alignment Services and Knowledge Integration Services are used to create a semantic workflow among TopoFlow model, which is a spatially-distributed hydrologic model and the annotated data. Results of this work are (i) a demonstration of how the GS framework advances the integration of heterogeneous data and models of water-related disciplines by seamless handling of their semantic heterogeneity, (ii) an introduction of new paradigm for reusing existing and new standards as well as tools and models without the need of their implementation in the Cyberinfrastructures of water-related disciplines, and (iii) an investigation of a methodology by which distributed models can be coupled in a workflow using the GS services.

An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs.

PubMed

Cuadrat, Rafael R C; da Serra Cruz, Sérgio Manuel; Tschoeke, Diogo Antônio; Silva, Edno; Tosta, Frederico; Jucá, Henrique; Jardim, Rodrigo; Campos, Maria Luiza M; Mattoso, Marta; Dávila, Alberto M R

2014-08-01

A key focus in 21(st) century integrative biology and drug discovery for neglected tropical and other diseases has been the use of BLAST-based computational methods for identification of orthologous groups in pathogenic organisms to discern orthologs, with a view to evaluate similarities and differences among species, and thus allow the transfer of annotation from known/curated proteins to new/non-annotated ones. We used here a profile-based sensitive methodology to identify distant homologs, coupled to the NCBI's COG (Unicellular orthologs) and KOG (Eukaryote orthologs), permitting us to perform comparative genomics analyses on five protozoan genomes. OrthoSearch was used in five protozoan proteomes showing that 3901 and 7473 orthologs can be identified by comparison with COG and KOG proteomes, respectively. The core protozoa proteome inferred was 418 Protozoa-COG orthologous groups and 704 Protozoa-KOG orthologous groups: (i) 31.58% (132/418) belongs to the category J (translation, ribosomal structure, and biogenesis), and 9.81% (41/418) to the category O (post-translational modification, protein turnover, chaperones) using COG; (ii) 21.45% (151/704) belongs to the categories J, and 13.92% (98/704) to the O using KOG. The phylogenomic analysis showed four well-supported clades for Eukarya, discriminating Multicellular [(i) human, fly, plant and worm] and Unicellular [(ii) yeast, (iii) fungi, and (iv) protozoa] species. These encouraging results attest to the usefulness of the profile-based methodology for comparative genomics to accelerate semi-automatic re-annotation, especially of the protozoan proteomes. This approach may also lend itself for applications in global health, for example, in the case of novel drug target discovery against pathogenic organisms previously considered difficult to research with traditional drug discovery tools.

An Orthology-Based Analysis of Pathogenic Protozoa Impacting Global Health: An Improved Comparative Genomics Approach with Prokaryotes and Model Eukaryote Orthologs

PubMed Central

Cuadrat, Rafael R. C.; da Serra Cruz, Sérgio Manuel; Tschoeke, Diogo Antônio; Silva, Edno; Tosta, Frederico; Jucá, Henrique; Jardim, Rodrigo; Campos, Maria Luiza M.; Mattoso, Marta

2014-01-01

Abstract A key focus in 21st century integrative biology and drug discovery for neglected tropical and other diseases has been the use of BLAST-based computational methods for identification of orthologous groups in pathogenic organisms to discern orthologs, with a view to evaluate similarities and differences among species, and thus allow the transfer of annotation from known/curated proteins to new/non-annotated ones. We used here a profile-based sensitive methodology to identify distant homologs, coupled to the NCBI's COG (Unicellular orthologs) and KOG (Eukaryote orthologs), permitting us to perform comparative genomics analyses on five protozoan genomes. OrthoSearch was used in five protozoan proteomes showing that 3901 and 7473 orthologs can be identified by comparison with COG and KOG proteomes, respectively. The core protozoa proteome inferred was 418 Protozoa-COG orthologous groups and 704 Protozoa-KOG orthologous groups: (i) 31.58% (132/418) belongs to the category J (translation, ribosomal structure, and biogenesis), and 9.81% (41/418) to the category O (post-translational modification, protein turnover, chaperones) using COG; (ii) 21.45% (151/704) belongs to the categories J, and 13.92% (98/704) to the O using KOG. The phylogenomic analysis showed four well-supported clades for Eukarya, discriminating Multicellular [(i) human, fly, plant and worm] and Unicellular [(ii) yeast, (iii) fungi, and (iv) protozoa] species. These encouraging results attest to the usefulness of the profile-based methodology for comparative genomics to accelerate semi-automatic re-annotation, especially of the protozoan proteomes. This approach may also lend itself for applications in global health, for example, in the case of novel drug target discovery against pathogenic organisms previously considered difficult to research with traditional drug discovery tools. PMID:24960463

Future Professional Communication in Astronomy II

NASA Astrophysics Data System (ADS)

Accomazzi, Alberto

The present volume gathers together the talks presented at the second colloquium on the Future Professional Communication in Astronomy (FPCAII), held at the Harvard-Smithsonian Center for Astrophysics (Cambridge, MA) on 13-14 April 2010. This meeting provided a forum for editors, publishers, scientists, librarians and officers of learned societies to discuss the future of the field. The program included talks from leading researchers and practitioners and drew a crowd of approximately 50 attendees from 10 countries. These proceedings contain contributions from invited and contributed talks from leaders in the field, touching on a number of topics. Among them: The role of disciplinary repositories such as ADS and arXiv in astronomy and the physical sciences; Current status and future of Open Access Publishing models and their impact on astronomy and astrophysics publishing; Emerging trends in scientific article publishing: semantic annotations, multimedia content, links to data products hosted by astrophysics archives; Novel approaches to the evaluation of facilities and projects based on bibliometric indicators; Impact of Government mandates, Privacy laws, and Intellectual Property Rights on the evolving digital publishing environment in astronomy; Communicating astronomy to the public: the experience of the International Year of Astronomy 2009.

Temperature dependence of polyhedral cage volumes in clathrate hydrates

USGS Publications Warehouse

Chakoumakos, B.C.; Rawn, C.J.; Rondinone, A.J.; Stern, L.A.; Circone, S.; Kirby, S.H.; Ishii, Y.; Jones, C.Y.; Toby, B.H.

2003-01-01

The polyhedral cage volumes of structure I (sI) (carbon dioxide, methane, trimethylene oxide) and structure II (sII) (methane-ethane, propane, tetrahydrofuran, trimethylene oxide) hydrates are computed from atomic positions determined from neutron powder-diffraction data. The ideal structural formulas for sI and sII are, respectively, S2L6 ?? 46H2O and S16L???8 ?? 136H2O, where S denotes a polyhedral cage with 20 vertices, L a 24-cage, and L??? a 28-cage. The space-filling polyhedral cages are defined by the oxygen atoms of the hydrogen-bonded network of water molecules. Collectively, the mean cage volume ratio is 1.91 : 1.43 : 1 for the 28-cage : 24-cage : 20-cage, which correspond to equivalent sphere radii of 4.18, 3.79, and 3.37 A??, respectively. At 100 K, mean polyhedral volumes are 303.8, 227.8, and 158.8 A??3 for the 28-cage, 24-cage, and 20-cage, respectively. In general, the 20-cage volume for a sII is larger than that of a sI, although trimethylene oxide is an exception. The temperature dependence of the cage volumes reveals differences between apparently similar cages with similar occupants. In the case of trimethylene oxide hydrate, which forms both sI and sII, the 20-cages common to both structures contract quite differently. From 220 K, the sII 20-cage exhibits a smooth monotonic reduction in size, whereas the sI 20-cage initially expands upon cooling to 160 K, then contracts more rapidly to 10 K, and overall the sI 20-cage is larger than the sII 20-cage. The volumes of the large cages in both structures contract monotonically with decreasing temperature. These differences reflect reoriented motion of the trimethyelene oxide molecule in the 24-cage of sI, consistent with previous spectroscopic and calorimetric studies. For the 20-cages in methane hydrate (sI) and a mixed methane-ethane hydrate (sII), both containing methane as the guest molecule, the temperature dependence of the 20-cage volume in sII is much less than that in sI, but sII is overall larger in volume.

Historical Characteristics of Combat for Wargames. (Benchmarks)

DTIC Science & Technology

1988-07-01

0 __ ,7_ .. ,ILIUBIN T. O0 .. 0./ /. 7.5 CALCIUM 77- q. 6" CAR8oN DIOXIDE .21 mEQ/, -2i - ;2. CHLORIDE ;ý a n-EQ/1 J06’ CHOLESTEROL )9-/iq...Battle narratives for Volume I, No. 1. (Original source of data on 1967 and 1973 Arab Israeli Wars. Revised by Volume II, No. 1.) Volume I, No. 3, Summer...1975. (Original source of data on 1948 and 1956 Arab -Israeli Wars. Table on World War II tank battles (p 69).) Volume II, No. 1, Winter, 1976

Utilizing Social Media Data for Pharmacovigilance: A Review

PubMed Central

Sarker, Abeed; Ginn, Rachel; Nikfarjam, Azadeh; O’Connor, Karen; Smith, Karen; Jayaraman, Swetha; Upadhaya, Tejaswi; Gonzalez, Graciela

2015-01-01

Objective Automatic monitoring of Adverse Drug Reactions (ADRs), defined as adverse patient outcomes caused by medications, is a challenging research problem that is currently receiving significant attention from the medical informatics community. In recent years, user-posted data on social media, primarily due to its sheer volume, has become a useful resource for ADR monitoring. Research using social media data has progressed using various data sources and techniques, making it difficult to compare distinct systems and their performances. In this paper, we perform a methodical review to characterize the different approaches to ADR detection/extraction from social media, and their applicability to pharmacovigilance. In addition, we present a potential systematic pathway to ADR monitoring from social media. Methods We identified studies, describing approaches for ADR detection from social media from the Medline, Embase, Scopus and Web of Science databases, and the Google Scholar search engine. Studies that met our inclusion criteria were those that attempted to utilize ADR information posted by users on any publicly available social media platform. We categorized the studies into various dimensions such as primary ADR detection approach, size of data, source(s), availability, evaluation criteria, and so on. Results Twenty-two studies met our inclusion criteria, with fifteen (68.2%) published within the last two years. The survey revealed a clear trend towards the usage of annotated data with eleven of the fifteen (73.3%) studies published in the last two years relying on expert annotations. However, publicly available annotated data is still scarce, and we found only six (27.3%) studies that made the annotations used publicly available, making system performance comparisons difficult. In terms of algorithms, supervised classification techniques to detect posts containing ADR mentions, and lexicon-based approaches for extraction of ADR mentions from texts have been the most popular. Conclusion Our review suggests that interest in the utilization of the vast amounts of available social media data for ADR monitoring is increasing with time. In terms of sources, both health-related and general social media data have been used for ADR detection— while health-related sources tend to contain higher proportions of relevant data, the volume of data from general social media websites is significantly higher. There is still very limited publicly available annotated data available, and, as indicated by the promising results obtained by recent supervised learning approaches, there is a strong need to make such data available to the research community. PMID:25720841

An Exploratory Study of Women in the Health Professions Schools. Volume X: Bibliography and Annotated Bibliography.

ERIC Educational Resources Information Center

Urban and Rural Systems Associates, San Francisco, CA.

The bibliography is part of an extensive study of the barriers to women's success in the schools and practice of eight health professions. It divides resources into 14 segments: one covers the health professions in general; one treats women and careers in general; one is devoted to each of eight health professions (medicine, osteopathic medicine,…

Concurrent Engineering Teams. Volume 2: Annotated Bibliography

DTIC Science & Technology

1990-11-01

publishles. They normally embody restilts of major projects which (a) have a direct bearing am decisionse affecting major program , III) addrnss...D., "What Processes do You Own? How are They Doing?," Program Manager, Journal of the Defense Systems Management College, September-October 1989, pp...216. The key ingredient to any successful TQM program is top management commitment and involvement. The early top management involvement reflects

Linking wilderness research and management-volume 5. Understanding and managing backcountry recreation impacts on terrestrial wildlife: an annotated reading list

Treesearch

Douglas Tempel; Vita Wright; Janet Neilson; Tammy Mildenstein

2008-01-01

Increasing levels of recreational use in wilderness, backcountry, and roadless areas has the potential to impact wildlife species, including those that depend on these protected areas for survival. Wildlife and wilderness managers will be more successful at reducing these impacts if they understand the potential impacts, factors affecting the magnitude of impacts, and...

Review of the Scientific Literature and Preparation of an Annotated Bibliography on Effects of Cigarette Smoking and Nicotine on Human Performance. Volume 2

DTIC Science & Technology

1985-01-01

RUSSELL N A H, CARRUTHERS M E, FEYERABEND C 222 EFFECT OF NICOTINE REPLACEMENT ON THE CIGARETTE WITHDRAWAL SYNDROME BRITISH JOURNAL ADDICTION 79:215-219...RUSSELL M A, JARVIS M J, FEYERABEND C 147 DOES SWITCHING TO AN ULTRA LOW NICOTINE CIGARETTE INDUCE NICOTINE WITHDRAWAL EFFECTS? PSYCHOPHARMACOLOGY, 84:120

Selected Bibliography and Abstracts of Educational Materials in Pakistan. Volume 6, Number 4, 1972. Period Covered October-December 1972.

ERIC Educational Resources Information Center

Saad, Geti, Comp.

This annotated bibliography lists 104 entries of selected educational materials in Pakistan covering the period from October to December 1972. The materials are organized into 30 topical categories as listed for related document ED 074 847. A new section is added on nationalization of education. The materials are drawn from a variety of Pakistani…

Selected Bibliography and Abstracts of Educational Materials in Pakistan. Volume 6, Number 3, 1972. Period Covered July-September 1972.

ERIC Educational Resources Information Center

Saad, Geti, Comp.

This annotated bibliography lists 102 entries of selected educational materials in Pakistan covering the period from July to September 1972. The materials are organized into 24 categories as listed for related document ED 074 847. A new section is added on nationalization of education. The materials are drawn from a variety of Pakistani journals,…

A Trainer's Manual for Basic Helping Skills. Counseling Older Persons. Volume III.

ERIC Educational Resources Information Center

Myers, Jane E., Ed.

This manual, the third in a three-volume series on counseling older adults, is designed to accompany and supplement volume II, "Basic Helping Skills for Service Providers," and focuses on training for communication skills. The units and their sections correspond to those in volume II, for easy cross-referencing. The units contain information for…

Vesalius Revised. His Annotations to the 1555 Fabrica1

PubMed Central

Nutton, Vivian

2012-01-01

The De humani corporis fabrica [The Fabric of the Human Body], Basle, 1543, of Andreas Vesalius is deservedly famous as the first modern book of anatomy. A second edition was published in Basle in 1555, but little is known of Vesalius’ activities after that date. This article discusses a recent find: Vesalius’ own copy of the 1555 edition, heavily annotated in preparation for a never published third edition. Vesalius made hundreds of changes to the second edition, the great majority being stylistic, altering the Latin words but not the overall meaning. There are also changes to the plates to give greater clarity or to correct mistakes by the original block-cutter. There is little new anatomical material, although Vesalius continued to meditate about what he had earlier discovered. He shows no sign of being acquainted with the findings of others, like Colombo or Falloppia, that were published after he had moved his residence from Brussels to Spain in summer 1559, perhaps leaving this volume behind. The number of annotations shows Vesalius’ passionate concern not only for accuracy but also for the most effective way of proclaiming his new anatomical message. PMID:23112379

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.

PubMed

Uyar, Bora; Yusuf, Dilmurat; Wurmus, Ricardo; Rajewsky, Nikolaus; Ohler, Uwe; Akalin, Altuna

2017-06-02

In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies. The design of RCAS is modular, which enables flexible usage and convenient integration with other bioinformatics workflows. RCAS is an R/Bioconductor package but we also created graphical user interfaces including a Galaxy wrapper and a stand-alone web service. The application of RCAS on published datasets shows that RCAS is not only able to reproduce published findings but also helps generate novel knowledge and hypotheses. The meta-gene profiles, gene-centric annotation, motif analysis and gene-set analysis provided by RCAS provide contextual knowledge which is necessary for understanding the functional aspects of different biological events that involve RNAs. In addition, the array of different interfaces and deployment options adds the convenience of use for different levels of users. RCAS is available at http://bioconductor.org/packages/release/bioc/html/RCAS.html and http://rcas.mdc-berlin.de. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Rural Schools Prototype Analysis. Volume II: Methodology. An Example Process of Identifying Determinants, Selecting Options, & Developing Schematic Designs.

ERIC Educational Resources Information Center

Construction Systems Management, Inc., Anchorage, AK.

Volume II of a 3-volume report demonstrates the use of Design Determinants and Options (presented in Volume I) in the planning and design of small rural Alaskan secondary schools. Section I, a checklist for gathering site-specific information to be used as a data base for facility design, is organized in the same format as Volume I, which can be…

Secure annotation for medical images based on reversible watermarking in the Integer Fibonacci-Haar transform domain

NASA Astrophysics Data System (ADS)

Battisti, F.; Carli, M.; Neri, A.

2011-03-01

The increasing use of digital image-based applications is resulting in huge databases that are often difficult to use and prone to misuse and privacy concerns. These issues are especially crucial in medical applications. The most commonly adopted solution is the encryption of both the image and the patient data in separate files that are then linked. This practice results to be inefficient since, in order to retrieve patient data or analysis details, it is necessary to decrypt both files. In this contribution, an alternative solution for secure medical image annotation is presented. The proposed framework is based on the joint use of a key-dependent wavelet transform, the Integer Fibonacci-Haar transform, of a secure cryptographic scheme, and of a reversible watermarking scheme. The system allows: i) the insertion of the patient data into the encrypted image without requiring the knowledge of the original image, ii) the encryption of annotated images without causing loss in the embedded information, and iii) due to the complete reversibility of the process, it allows recovering the original image after the mark removal. Experimental results show the effectiveness of the proposed scheme.

Motivations for speeding : Volume II : findings report.

DOT National Transportation Integrated Search

2013-09-01

This is Volume II of a three-volume report. It contains the results of a study that examined the speeding behavior of drivers in their own vehicles over the course of three to four weeks of naturalistic driving in urban (Seattle, WA) and rural (Colle...

The Aerospace Database data element dictionary with issues and recommendations from the meetings of July 24-25, August 13-14, and September 24-25, 1991

NASA Technical Reports Server (NTRS)

1991-01-01

The present volume contains descriptions of the individual fields (data elements) which comprise the bibliographic records of the Aerospace Database. Indexes by field name and field mnemonic are provided. In addition, the issues and recommendations defined by the NASA STI Database Upgrade Working Group are included as annotations to the individual field descriptions and are listed at the end of the volume. The activities of the Working Group were initiated by the NASA STI Program Coordinating Council as part of an effort to improve overall database quality.

Emerging Technologies Program Integration Report. Volume 2. Background, Delphi and Workshop Data. Appendices

DTIC Science & Technology

1987-05-04

FTIILE COP’ AD-A196 840 EMERGING TECHNOLOGIES PROGRAM INTEGRATION REPORT VOLUME II BACKGROUND, DELPHI AND WORKSHOP DATA, APPENDICES . -- PREPARED...Security Classification) Emerging Technologies Program Integration Report Volume II: Background, Delphi and Workshop Data; Appendices (U) 12 PERSONAL...volumes of this integration report assess and synthesize information gathered through a Delphi survey, defense needs prioritization workshops, and

The relation of hippocampal subfield volumes to verbal episodic memory measured by the California Verbal Learning Test II in healthy adults.

PubMed

Aslaksen, Per M; Bystad, Martin K; Ørbo, Marte C; Vangberg, Torgil R

2018-06-08

Total hippocampal volume has previously been shown to correlate with performance on tests for verbal episodic memory. However, there are sparse evidence on how hippocampal subfield volumes are related to verbal episodic memory in healthy adults. The present study investigated the association between volumes of separate hippocampal subfields and verbal episodic memory performance in healthy volunteers. Forty-seven participants (31 females) between 20 to 71 years age underwent testing with the California Verbal Learning Test II (CVLT II), and the Wechsler Abbreviated Scale of Intelligence (WASI) to obtain an estimate of cognitive functioning. T1-weighted MR images were obtained after cognitive testing, and volumetric estimates adjusted for age and estimated total intracranial volume were calculated in the FreeSurfer 6.0 software suite for cerebral -and hippocampal structures. The sample performed within the statistical normal range on both CVLT II and WASI. Significant correlations adjusted for multiple testing were found between CVLT II subtests of total learning, free immediate recall and free delayed recall and volumes of the left Cornu Ammonis (CA) 1-4 subfields. There were no significant correlations between right hippocampal subfields and CVLT II performance, and no significant correlation between WASI results and hippocampal subfields. The present results suggest that better verbal episodic memory measured by the CVLT II is associated with relative larger volumes of specific left CA hippocampal subfields in healthy adults. Due to the small sample size and large age-span of the participants, the present findings are preliminary and should be confirmed in larger samples. Copyright © 2018 Elsevier B.V. All rights reserved.

January 1998 Volume II 1996 Field Investigation Report Ecological Risk Assessment of the Marsh Area of the LCP Chemical Site in Brunswick, Georgia

EPA Pesticide Factsheets

Volume II contains the data tables and quality assurance review summaries cited in Volume I of the Ecological Risk Assessment for the Marsh (Estuarine) Operable Unit of the LCP Chemicals Site in Brunswick, Georgia.

A Curriculum Activities Guide to Water Pollution and Environmental Studies, Volume II - Appendices.

ERIC Educational Resources Information Center

Hershey, John T., Ed.; And Others

This publication, Volume II of a two volume set of water pollution studies, contains seven appendices which support the studies. Appendix 1, Water Quality Parameters, consolidates the technical aspects of water quality including chemical, biological, computer program, and equipment information. Appendix 2, Implementation, outlines techniques…

Enhanced Night Visibility Series, Volume XII : Overview of Phase II and Development of Phase III Experimental Plan

DOT National Transportation Integrated Search

2005-12-01

This volume provides an overview of the six studies that compose Phase II of the Enhanced Night Visibility project and the experimental plan for its third and final portion, Phase III. The Phase II studies evaluated up to 12 vision enhancement system...

Spine segmentation from C-arm CT data sets: application to region-of-interest volumes for spinal interventions

NASA Astrophysics Data System (ADS)

Buerger, C.; Lorenz, C.; Babic, D.; Hoppenbrouwers, J.; Homan, R.; Nachabe, R.; Racadio, J. M.; Grass, M.

2017-03-01

Spinal fusion is a common procedure to stabilize the spinal column by fixating parts of the spine. In such procedures, metal screws are inserted through the patients back into a vertebra, and the screws of adjacent vertebrae are connected by metal rods to generate a fixed bridge. In these procedures, 3D image guidance for intervention planning and outcome control is required. Here, for anatomical guidance, an automated approach for vertebra segmentation from C-arm CT images of the spine is introduced and evaluated. As a prerequisite, 3D C-arm CT images are acquired covering the vertebrae of interest. An automatic model-based segmentation approach is applied to delineate the outline of the vertebrae of interest. The segmentation approach is based on 24 partial models of the cervical, thoracic and lumbar vertebrae which aggregate information about (i) the basic shape itself, (ii) trained features for image based adaptation, and (iii) potential shape variations. Since the volume data sets generated by the C-arm system are limited to a certain region of the spine the target vertebra and hence initial model position is assigned interactively. The approach was trained and tested on 21 human cadaver scans. A 3-fold cross validation to ground truth annotations yields overall mean segmentation errors of 0.5 mm for T1 to 1.1 mm for C6. The results are promising and show potential to support the clinician in pedicle screw path and rod planning to allow accurate and reproducible insertions.

Anthropometric Source Book. Volume 3: Annotated Bibliography of Anthropometry

DTIC Science & Technology

1978-07-01

on Isometric Strength and Endurance, Blood Flow, and the Blood Pressure and Heart Rate Response to Isometric Exercise . TR 75 0086, Air Force Office... somatotype . In this report the subgroup statistics were combined to yield summary statistics arranged into more convenient tabulations for the...devices and tech- niques developed under the auspices of NASA for use in measuring and estim- ating human responses under zero-gravity conditions

Compilation of References and Bibliography. Volume 1. An Annotated Bibliography on Low Intensity Conflict Taken from the Joint Low- Intensity Conflict Project Final Report of 1 August 1986. CLIC PAPERS.

DTIC Science & Technology

1987-08-01

conditions--especially in rural areas. Moreover, the author recognizes a continued dependence upon the army in various matters. Some of these are electoral ...Mau Mau revolt in Kenya in East Africa, and the period of the " violencia " in Colombia. 54. Book, Insurgency, COIN. Wesson, Robert, editor, Communism

Linking wilderness research and management-volume 4. Understanding and managing invasive plants in wilderness and other natural areas: an annotated reading list

Treesearch

Sophie Osborn; Vita Wright; Brett Walker; Amy Cilimburg; Alison Perkins

2002-01-01

Nonnative invasive plants are altering ecosystems around the world with alarming speed. They outcompete native plants and ultimately change the composition and function of the ecosystems they invade. This poses a particular problem in wilderness and other natural areas that are set aside to maintain natural conditions. Wilderness managers are not only faced with the...

An Annotated Bibliography of Patents Related to Coastal Engineering. Volume I. 1967-1970. Appendix.

DTIC Science & Technology

1979-11-01

HYDRAULIC MODEL BASIN PILE, STRUCTURE CONNECTION ICE PROTECTION PILE, WOOD 16 -- mi • . ... -- POLLUTANT ABSORPTION SEISMIC ACOUSTIC TRANSMITTER ARRAY...NT SEABED PIPELINE PLACEMENT WIND MEASUREMENT SEABED PROPERTY MEASUREMENT WOOD PRESERVATIVE SEABED SCOUR PROTECTION SEABED SITE SURVEY SEABED SOIL...concrete, wood , or thin steel piling to aid driving. PILE EXTRACTOR - A means of removing a pile from the earth. PILE FOOTING - A means of increasing a

A Survey and Analysis of Military Computer-Based Training Systems: A Two Part Study. Volume I: A Survey and Annotated Bibliography of Authoring Aids for Instructional Systems Development.

ERIC Educational Resources Information Center

Logan, Robert S.

The authoring process and authoring aids which facilitate development of instructional materials have recently emerged as an area of concern in the field of instructional systems development (ISD). This process includes information gathering, its conversion to learning packages, its revision, and its formal publication. The purpose of this…

Advanced Residual Strength Degradation Rate Modeling for Advanced Composite Structures. Volume II. Tasks II and III.

DTIC Science & Technology

1981-07-01

ADVANCED COMPOSITE STRUCTURES VOLUME II - TASKS Ix AND III K. N. Lauraitis Tl J. T. Ryder ?l4 D. E. Pettit ~ Lockheed-California Company S Burbank...Strength Degradation Rate Final Report Modeling for Advanced Composite Structures 1 July 1979 to 29 May 1981 Vol II - Task II and III S. PERFORMIN ONG...identify by block namber) composites , graphite/epoxy, impact damage, damaged holes, fatigue, damage propagation, residual strength, NDI 20. ABSTRACT

Using video-annotation software to identify interactions in group therapies for schizophrenia: assessing reliability and associations with outcomes.

PubMed

Orfanos, Stavros; Akther, Syeda Ferhana; Abdul-Basit, Muhammad; McCabe, Rosemarie; Priebe, Stefan

2017-02-10

Research has shown that interactions in group therapies for people with schizophrenia are associated with a reduction in negative symptoms. However, it is unclear which specific interactions in groups are linked with these improvements. The aims of this exploratory study were to i) develop and test the reliability of using video-annotation software to measure interactions in group therapies in schizophrenia and ii) explore the relationship between interactions in group therapies for schizophrenia with clinically relevant changes in negative symptoms. Video-annotation software was used to annotate interactions from participants selected across nine video-recorded out-patient therapy groups (N = 81). Using the Individual Group Member Interpersonal Process Scale, interactions were coded from participants who demonstrated either a clinically significant improvement (N = 9) or no change (N = 8) in negative symptoms at the end of therapy. Interactions were measured from the first and last sessions of attendance (>25 h of therapy). Inter-rater reliability between two independent raters was measured. Binary logistic regression analysis was used to explore the association between the frequency of interactive behaviors and changes in negative symptoms, assessed using the Positive and Negative Syndrome Scale. Of the 1275 statements that were annotated using ELAN, 1191 (93%) had sufficient audio and visual quality to be coded using the Individual Group Member Interpersonal Process Scale. Rater-agreement was high across all interaction categories (>95% average agreement). A higher frequency of self-initiated statements measured in the first session was associated with improvements in negative symptoms. The frequency of questions and giving advice measured in the first session of attendance was associated with improvements in negative symptoms; although this was only a trend. Video-annotation software can be used to reliably identify interactive behaviors in groups for schizophrenia. The results suggest that proactive communicative gestures, as assessed by the video-analysis, predict outcomes. Future research should use this novel method in larger and clinically different samples to explore which aspects of therapy facilitate such proactive communication early on in therapy.

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

PubMed

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 COGs is expected to become an important tool for microbial genomics. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by US Government employees and is in the public domain in the US.

Ontological interpretation of biomedical database content.

PubMed

Santana da Silva, Filipe; Jansen, Ludger; Freitas, Fred; Schulz, Stefan

2017-06-26

Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a database record is often ambiguous. We address this problem by grounding implicit and explicit database content in a formal-ontological framework. By using a typical extract from the databases UniProt and Ensembl, annotated with content from GO, PR, ChEBI and NCBI Taxonomy, we created four ontological models (in OWL), which generate explicit, distinct interpretations under the BioTopLite2 (BTL2) upper-level ontology. The first three models interpret database entries as individuals (IND), defined classes (SUBC), and classes with dispositions (DISP), respectively; the fourth model (HYBR) is a combination of SUBC and DISP. For the evaluation of these four models, we consider (i) database content retrieval, using ontologies as query vocabulary; (ii) information completeness; and, (iii) DL complexity and decidability. The models were tested under these criteria against four competency questions (CQs). IND does not raise any ontological claim, besides asserting the existence of sample individuals and relations among them. Modelling patterns have to be created for each type of annotation referent. SUBC is interpreted regarding maximally fine-grained defined subclasses under the classes referred to by the data. DISP attempts to extract truly ontological statements from the database records, claiming the existence of dispositions. HYBR is a hybrid of SUBC and DISP and is more parsimonious regarding expressiveness and query answering complexity. For each of the four models, the four CQs were submitted as DL queries. This shows the ability to retrieve individuals with IND, and classes in SUBC and HYBR. DISP does not retrieve anything because the axioms with disposition are embedded in General Class Inclusion (GCI) statements. Ambiguity of biological database content is addressed by a method that identifies implicit knowledge behind semantic annotations in biological databases and grounds it in an expressive upper-level ontology. The result is a seamless representation of database structure, content and annotations as OWL models.

Annotated Bibliography of Water Optical Properties of Ocean Waters.

DTIC Science & Technology

1982-05-01

24. Barrett, B. B. ( 1971 ). Cooperative Gulf of Mexico Estuarine Inventory and Study, Louisiana, Phase II, Hydrology and Phase III, Sedimentology...Assoc. U.K. (39), 227-238. Ambient light measurements to depths of 400 m. 35. Boulter, Jacques ( 1971 ). Photometric Sous-marine. Measures effectuees...Florida coastal water with a Hydroproducts transmissometer (550 nm). 41. Carder, Kendall L., G. F. Beardsley, Jr., and Hasong Pak ( 1971 ). Particle Size

An Annotated Bibliography on Second Language Acquisition

DTIC Science & Technology

1994-06-01

not assessment purposes. Examples of three ’serious’ rote learning programs are SPRECH, GERAD, and LEX. DEDUCT is a question/answer game where the...interactively create game-trees for context-bound vocabulary drills from scratch without modifications to the program software through CREATE. C 1985...II (pp. 223-294). Stanford, CA: Heuristech Press. The goal of CAI research is to build instructional programs that incorporate well-prepared course

Annotated zoogeography of non-marine Tardigrada. Part II: South America.

PubMed

Kaczmarek, Łukasz; Michalczyk, Łukasz; Mcinnes, Sandra J

2015-02-25

This paper is the second monograph of nine that describes the global records of limno-terrestrial water bears (Tardigrada). Here, we provide a comprehensive list of non-marine tardigrades recorded from South America, providing an updated and revised taxonomy accompanied by geographic co-ordinates, habitat, and biogeographic comments. It is hoped this work will serve as a reference point and background for further zoogeographical and taxonomical studies.

Invertebrates of the H.J. Andrews Experimental Forest, western Cascades, Oregon II. an annotated checklist of caddisflies (Trichoptera)

Treesearch

N.H. Anderson; G.M. Cooper; D.G Denning

1982-01-01

At least 99 species, representing 14 families of Trichoptera, are recorded from the H.J. Andrews Experimental Forest, near Blue River, Oregon. The collecting sites include a wide diversity of environmental conditions in a 6000-hectare watershed of the western Cascade Range (from 400 to 1 630 meters in altitude and from 1st- to 7th-order streams).

Translations on USSR Military Affairs, Number 1303

DTIC Science & Technology

1977-09-27

descendents of the Katyusha launcher of World War II — would be subsequently installed here. At present armament consists of only the two 57mm L/80...Sciences: "It Was the 5th Year of War ..."] [Excerpts] The eighth volume has been published of the history of World War II (Footnote) (The History of... World War II, 1939-1945. In 12 volumes. Chairman of the main editorial commission: D. F. Ustinov. Volume eight: The Collapse of the Fascist Bloc’s

Only One of the Five Ralstonia solanacearum Long-Chain 3-Ketoacyl-Acyl Carrier Protein Synthase Homologues Functions in Fatty Acid Synthesis

PubMed Central

Cheng, Juanli; Ma, Jincheng; Lin, Jinshui; Fan, Zhen-Chuan; Cronan, John E.

2012-01-01

Ralstonia solanacearum, a major phytopathogenic bacterium, causes a bacterial wilt disease in diverse plants. Although fatty acid analyses of total membranes of R. solanacearum showed that they contain primarily palmitic (C16:0), palmitoleic (C16:1) and cis-vaccenic (C18:1) acids, little is known regarding R. solanacearum fatty acid synthesis. The R. solanacearum GMI1000 genome is unusual in that it contains four genes (fabF1, fabF2, fabF3, and fabF4) annotated as encoding 3-ketoacyl-acyl carrier protein synthase II homologues and one gene (fabB) annotated as encoding 3-ketoacyl-acyl carrier protein synthase I. We have analyzed this puzzling apparent redundancy and found that only one of these genes, fabF1, encoded a long-chain 3-ketoacyl-acyl carrier protein synthase, whereas the other homologues did not play roles in R. solanacearum fatty acid synthesis. Mutant strains lacking fabF1 are nonviable, and thus, FabF1 is essential for R. solanacearum fatty acid biosynthesis. Moreover, R. solanacearum FabF1 has the activities of both 3-ketoacyl-acyl carrier protein synthase II and 3-ketoacyl-acyl carrier protein synthase I. PMID:22194290

Site Environmental Report for 2009, Volume 2

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

Xu, Suying

2010-08-19

Volume II of the Site Environmental Report for 2009 is provided by Ernest Orlando Lawrence Berkeley National Laboratory as a supplemental appendix to Volume I, which contains the body of the report. Volume II contains the environmental monitoring and sampling data used to generate summary results of routine and nonroutine sampling at the Laboratory, except for groundwater sampling data, which may be found in the reports referred to in Chapter 4 of Volume I. The results from sample collections are more comprehensive in Volume II than in Volume I: for completeness, all results from sample collections that began or endedmore » in calendar year (CY) 2009 are included in this volume. However, the samples representing CY 2008 data have not been used in the summary results that are reported in Volume I. (For example, although ambient air samples collected on January 6, 2009, are presented in Volume II, they represent December 2008 data and are not included in Table 4-2 in Volume I.) When appropriate, sampling results are reported in both conventional and International System (SI) units. For some results, the rounding procedure used in data reporting may result in apparent differences between the numbers reported in SI and conventional units. (For example, stack air tritium results reported as < 1.5 Bq/m3 are shown variously as < 39 and < 41 pCi/m3. Both of these results are rounded correctly to two significant digits.)« less

In Situ Biological Treatment Test at Kelly Air Force Base. Volume 2. Field Test Results and Cost Model

DTIC Science & Technology

1987-07-01

Groundwater." Developments in Industrial Microbiology, Volume 24, pp. 225-234. Society of Industrial Microbiology, Arlington, Virginia. 18. Product ...ESL-TR-85-52 cv) VOLUME II CN IN SITU BIOLOGICAL TREATMENT TEST AT KELLY AIR FORCE BASE, VOLUME !1: FIELD TEST RESULTS AND COST MODEL R.S. WETZEL...Kelly Air Force Base, Volume II: Field Test Results and Cost Model (UNCLASSIFIED) 12 PERSONAL AUTHOR(S) Roger S. Wetzel, Connie M. Durst, Donald H

Potential means of cost reduction in grade crossing automatic gate systems. volume II : improved gate arm concepts for railroad/highway grade crossings gate systems

DOT National Transportation Integrated Search

1977-02-28

This report, Volume II of a two-volume study, examines the potential for reduction of the cost of installing and maintaining automatic gates at railroad-highway grade crossings. It includes a review of current practices, equipment, and standards; con...

Human Rehabilitation Techniques. Disability Analyses: Behavioral Disabilities. Volume II, Part B.

ERIC Educational Resources Information Center

Sigelman, C.; And Others

Volume II, Section B of a six-volume final report (which covers the findings of a research project on policy and technology related to rehabilitation of disabled individuals) presents a review of literature on three types of behavior disabilities--epilepsy, mental retardation, and schizophrenia. Individual chapters on each disability cover the…

1978-79 Michigan Social Studies Textbook Study, Volume II.

ERIC Educational Resources Information Center

Chapman, John M., Ed.

This document, Volume II of a two-volume report on the extent to which four elementary level social studies programs reflect the multi-racial, multi-cultural nature of American society, contains individual reports of each reviewer. Fifteen reviewers examined textbooks and accompanying instructional materials according to the degree to which they…

Family Finance Education; An Interdisciplinary Approach. Volume II.

ERIC Educational Resources Information Center

Gibbs, Mary S., Ed.; And Others, Eds.

Volume II of a two-part series related to family finance education provides materials for study and discussion in the 1968 workshop. In Part I, members of the advisory council present their viewpoints concerning an interdisciplinary approach to education in family finance. Part II presents basic and current information related to principal areas…

RNA-Seq Analysis Using De Novo Transcriptome Assembly as a Reference for the Salmon Louse Caligus rogercresseyi

PubMed Central

Gallardo-Escárate, Cristian; Valenzuela-Muñoz, Valentina; Nuñez-Acuña, Gustavo

2014-01-01

Despite the economic and environmental impacts that sea lice infestations have on salmon farming worldwide, genomic data generated by high-throughput transcriptome sequencing for different developmental stages, sexes, and strains of sea lice is still limited or unknown. In this study, RNA-seq analysis was performed using de novo transcriptome assembly as a reference for evidenced transcriptional changes from six developmental stages of the salmon louse Caligus rogercresseyi. EST-datasets were generated from the nauplius I, nauplius II, copepodid and chalimus stages and from female and male adults using MiSeq Illumina sequencing. A total of 151,788,682 transcripts were yielded, which were assembled into 83,444 high quality contigs and subsequently annotated into roughly 24,000 genes based on known proteins. To identify differential transcription patterns among salmon louse stages, cluster analyses were performed using normalized gene expression values. Herein, four clusters were differentially expressed between nauplius I–II and copepodid stages (604 transcripts), five clusters between copepodid and chalimus stages (2,426 transcripts), and six clusters between female and male adults (2,478 transcripts). Gene ontology analysis revealed that the nauplius I–II, copepodid and chalimus stages are mainly annotated to aminoacid transfer/repair/breakdown, metabolism, molting cycle, and nervous system development. Additionally, genes showing differential transcription in female and male adults were highly related to cytoskeletal and contractile elements, reproduction, cell development, morphogenesis, and transcription-translation processes. The data presented in this study provides the most comprehensive transcriptome resource available for C. rogercresseyi, which should be used for future genomic studies linked to host-parasite interactions. PMID:24691066

RNA-Seq analysis using de novo transcriptome assembly as a reference for the salmon louse Caligus rogercresseyi.

PubMed

Gallardo-Escárate, Cristian; Valenzuela-Muñoz, Valentina; Nuñez-Acuña, Gustavo

2014-01-01

Despite the economic and environmental impacts that sea lice infestations have on salmon farming worldwide, genomic data generated by high-throughput transcriptome sequencing for different developmental stages, sexes, and strains of sea lice is still limited or unknown. In this study, RNA-seq analysis was performed using de novo transcriptome assembly as a reference for evidenced transcriptional changes from six developmental stages of the salmon louse Caligus rogercresseyi. EST-datasets were generated from the nauplius I, nauplius II, copepodid and chalimus stages and from female and male adults using MiSeq Illumina sequencing. A total of 151,788,682 transcripts were yielded, which were assembled into 83,444 high quality contigs and subsequently annotated into roughly 24,000 genes based on known proteins. To identify differential transcription patterns among salmon louse stages, cluster analyses were performed using normalized gene expression values. Herein, four clusters were differentially expressed between nauplius I-II and copepodid stages (604 transcripts), five clusters between copepodid and chalimus stages (2,426 transcripts), and six clusters between female and male adults (2,478 transcripts). Gene ontology analysis revealed that the nauplius I-II, copepodid and chalimus stages are mainly annotated to aminoacid transfer/repair/breakdown, metabolism, molting cycle, and nervous system development. Additionally, genes showing differential transcription in female and male adults were highly related to cytoskeletal and contractile elements, reproduction, cell development, morphogenesis, and transcription-translation processes. The data presented in this study provides the most comprehensive transcriptome resource available for C. rogercresseyi, which should be used for future genomic studies linked to host-parasite interactions.

High-level waste borosilicate glass: A compendium of corrosion characteristics. Volume 2

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

Cunnane, J.C.; Bates, J.K.; Bradley, C.R.

The objective of this document is to summarize scientific information pertinent to evaluating the extent to which high-level waste borosilicate glass corrosion and the associated radionuclide release processes are understood for the range of environmental conditions to which waste glass may be exposed in service. Alteration processes occurring within the bulk of the glass (e.g., devitrification and radiation-induced changes) are discussed insofar as they affect glass corrosion.This document is organized into three volumes. Volumes I and II represent a tiered set of information intended for somewhat different audiences. Volume I is intended to provide an overview of waste glass corrosion,more » and Volume 11 is intended to provide additional experimental details on experimental factors that influence waste glass corrosion. Volume III contains a bibliography of glass corrosion studies, including studies that are not cited in Volumes I and II. Volume I is intended for managers, decision makers, and modelers, the combined set of Volumes I, II, and III is intended for scientists and engineers working in the field of high-level waste.« less

DeepScope: Nonintrusive Whole Slide Saliency Annotation and Prediction from Pathologists at the Microscope

PubMed Central

Schaumberg, Andrew J.; Sirintrapun, S. Joseph; Al-Ahmadie, Hikmat A.; Schüffler, Peter J.; Fuchs, Thomas J.

2018-01-01

Modern digital pathology departments have grown to produce whole-slide image data at petabyte scale, an unprecedented treasure chest for medical machine learning tasks. Unfortunately, most digital slides are not annotated at the image level, hindering large-scale application of supervised learning. Manual labeling is prohibitive, requiring pathologists with decades of training and outstanding clinical service responsibilities. This problem is further aggravated by the United States Food and Drug Administration’s ruling that primary diagnosis must come from a glass slide rather than a digital image. We present the first end-to-end framework to overcome this problem, gathering annotations in a nonintrusive manner during a pathologist’s routine clinical work: (i) microscope-specific 3D-printed commodity camera mounts are used to video record the glass-slide-based clinical diagnosis process; (ii) after routine scanning of the whole slide, the video frames are registered to the digital slide; (iii) motion and observation time are estimated to generate a spatial and temporal saliency map of the whole slide. Demonstrating the utility of these annotations, we train a convolutional neural network that detects diagnosis-relevant salient regions, then report accuracy of 85.15% in bladder and 91.40% in prostate, with 75.00% accuracy when training on prostate but predicting in bladder, despite different pathologists examining the different tissues. When training on one patient but testing on another, AUROC in bladder is 0.79±0.11 and in prostate is 0.96±0.04. Our tool is available at https://bitbucket.org/aschaumberg/deepscope PMID:29601065

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2012-01-01

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

Eliciting the Functional Taxonomy from protein annotations and taxa

PubMed Central

Falda, Marco; Lavezzo, Enrico; Fontana, Paolo; Bianco, Luca; Berselli, Michele; Formentin, Elide; Toppo, Stefano

2016-01-01

The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules. PMID:27534507

Active shape models incorporating isolated landmarks for medical image annotation

NASA Astrophysics Data System (ADS)

Norajitra, Tobias; Meinzer, Hans-Peter; Stieltjes, Bram; Maier-Hein, Klaus H.

2014-03-01

Apart from their robustness in anatomic surface segmentation, purely surface based 3D Active Shape Models lack the ability to automatically detect and annotate non-surface key points of interest. However, annotation of anatomic landmarks is desirable, as it yields additional anatomic and functional information. Moreover, landmark detection might help to further improve accuracy during ASM segmentation. We present an extension of surface-based 3D Active Shape Models incorporating isolated non-surface landmarks. Positions of isolated and surface landmarks are modeled conjoint within a point distribution model (PDM). Isolated landmark appearance is described by a set of haar-like features, supporting local landmark detection on the PDM estimates using a kNN-Classi er. Landmark detection was evaluated in a leave-one-out cross validation on a reference dataset comprising 45 CT volumes of the human liver after shape space projection. Depending on the anatomical landmark to be detected, our experiments have shown in about 1/4 up to more than 1/2 of all test cases a signi cant improvement in detection accuracy compared to the position estimates delivered by the PDM. Our results encourage further research with regard to the combination of shape priors and machine learning for landmark detection within the Active Shape Model Framework.

Automated Detection of Synapses in Serial Section Transmission Electron Microscopy Image Stacks

PubMed Central

Kreshuk, Anna; Koethe, Ullrich; Pax, Elizabeth; Bock, Davi D.; Hamprecht, Fred A.

2014-01-01

We describe a method for fully automated detection of chemical synapses in serial electron microscopy images with highly anisotropic axial and lateral resolution, such as images taken on transmission electron microscopes. Our pipeline starts from classification of the pixels based on 3D pixel features, which is followed by segmentation with an Ising model MRF and another classification step, based on object-level features. Classifiers are learned on sparse user labels; a fully annotated data subvolume is not required for training. The algorithm was validated on a set of 238 synapses in 20 serial 7197×7351 pixel images (4.5×4.5×45 nm resolution) of mouse visual cortex, manually labeled by three independent human annotators and additionally re-verified by an expert neuroscientist. The error rate of the algorithm (12% false negative, 7% false positive detections) is better than state-of-the-art, even though, unlike the state-of-the-art method, our algorithm does not require a prior segmentation of the image volume into cells. The software is based on the ilastik learning and segmentation toolkit and the vigra image processing library and is freely available on our website, along with the test data and gold standard annotations (http://www.ilastik.org/synapse-detection/sstem). PMID:24516550

Human Rehabilitation Techniques. Disability Analyses: Motor Disabilities. Volume II, Part A.

ERIC Educational Resources Information Center

Sigelman, C.; And Others

Volume II, Section A of a six-volume final report (which covers the findings of a research project on policy and technology related to rehabilitation of disabled individuals) presents a review of literature on three types of motor disabilities--stroke, spinal cord injury, and cerebral palsy. Individual chapters on each disability cover the…

Human Rehabilitation Techniques. Disability Analyses: Chronic Disease Disabilities. Volume II, Part C.

ERIC Educational Resources Information Center

Sigelman, C.; And Others

Volume II, Section C of a six-volume final report (which covers the findings of a research project on policy and technology related to rehabilitation of disabled individuals) presents a review of literature on six types of chronic disease disabilities--rheumatoid arthritis, coronary heart disease, emphysema, carcinoma of the colon/rectum, kidney…

Annotated Bibliography of USAARL Technical and Letter Reports. Volume 2. October 1988 - April 1991

DTIC Science & Technology

1991-05-01

G. Lilienthal, Robert S. Kennedy, Jennifer E. Fowlkes, and Dennis R. Baltzley. As technelogy has been developed to provide improved visual and motion...Gower, Jr., and Jennifer Fowlkes. The U.S. Army Aeromedical Research Laboratory conducted field studies of operational flight simulators to assess the...Daniel W. Gower, Jr., and Jennifer Fowlkes. The U.S. Army Aeromedical Research Laboratory conducted field studies of operational flight simulators to

Annotated Bibliography for Lake Erie. Volume I. Biological,

DTIC Science & Technology

1974-10-01

varieties of naiades from I Lake Erie . Nautilus. 32(l):9-12. Three new varieties of naiades collected at Presque Isle , Pennsylvania are carefully...E. 1909. A botanical survey of Presque Isle , Erie County, Pennsylvania . Annals Carnegie Mus. Pittsburgh, Penn. Pub. 53. 5(l):2 9-421. This study...of vegetation on Presque Isle . (SM) 401. Jennings, Otto E. 1930. A survey of the phytoplankton at Erie , Pennsylvania . Science. 71(1848):560-61. A

PATRAM '80. Proceedings. Volume 2

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

Huebner, H.W.

1980-01-01

Volume 2 contains papers from the following sessions: Safeguards-Related Problems; Neutronics and Criticality; Operations and Systems Experience II; Plutonium Systems; Intermediate Storage in Casks; Operations and Systems Planning; Institutional Issues; Structural and Thermal Evaluation I; Poster Session B; Extended Testing I; Structural and Thermal Evaluation II; Extended Testing II; and Emergency Preparedness and Response. Individual papers were processed. (LM)

Guidelines for Conducting a Training Effectiveness Evaluation (TEE). Volume 2. Data Collector’s Manual

DTIC Science & Technology

1985-02-01

D : ■>■■ ’•.’.’. Research Product 85-15 Guidelines for Conducting a Training Effectiveness Evaluation (TEE) Volume II: Data...CONDUCTING A TRAINING EFFECTIVENESS EVALUATION (TEE) VOLUME II: DATA COLLECTOR’S MANUAL 1 t. TV*CO» READ INSTRUCTIONS BEFORE COMWLETWC FORM I...2Q263739A793 3227 52A M. COMTAOLUMQ O’ttCC RAMC AND ADO* CSS Co—and ant U.S. Army Air Defense School ATTN: ATSA-TDI, Ft. Bliss, TX II. RCRORf OATC

Changes in the transcriptomic profiles of maize roots in response to iron-deficiency stress.

PubMed

Li, Yan; Wang, Nian; Zhao, Fengtao; Song, Xuejiao; Yin, Zhaohua; Huang, Rong; Zhang, Chunqing

2014-07-01

Plants are often subjected to iron (Fe)-deficiency stress because of its low solubility. Plants have evolved two distinct strategies to solubilize and transport Fe to acclimate to this abiotic stress condition. Transcriptomic profiling analysis was performed using Illumina digital gene expression to understand the mechanism underlying resistance responses of roots to Fe starvation in maize, an important Strategy II plant. A total of 3,427, 4,069, 4,881, and 2,610 genes had significantly changed expression levels after Fe-deficiency treatments of 1, 2, 4 or 7 days, respectively. Genes involved in 2'-deoxymugineic acid (DMA) synthesis, secretion, and Fe(III)-DMA uptake were significantly induced. Many genes related to plant hormones, protein kinases, and protein phosphatases responded to Fe-deficiency stress, suggesting their regulatory roles in response to the Fe-deficiency stress. Functional annotation clustering analysis, using the Database for Annotation, Visualization and Integrated Discovery, revealed maize root responses to Fe starvation. This resulted in 38 functional annotation clusters: 25 for up-regulated genes, and 13 for down-regulated ones. These included genes encoding enzymes involved in the metabolism of carboxylic acids, isoprenoids and aromatic compounds, transporters, and stress response proteins. Our work provides integrated information for understanding maize response to Fe-deficiency stress.

IMG/M: integrated genome and metagenome comparative data analysis system

DOE PAGES

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; ...

2016-10-13

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support formore » examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.« less

IMG/M: integrated genome and metagenome comparative data analysis system

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

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support formore » examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.« less

EcoGene 3.0

PubMed Central

Zhou, Jindan; Rudd, Kenneth E.

2013-01-01

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection. PMID:23197660

IMG/M: integrated genome and metagenome comparative data analysis system

PubMed Central

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Palaniappan, Krishna; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Andersen, Evan; Huntemann, Marcel; Varghese, Neha; Hadjithomas, Michalis; Tennessen, Kristin; Nielsen, Torben; Ivanova, Natalia N.; Kyrpides, Nikos C.

2017-01-01

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review (ER) companion system (IMG/M ER: https://img.jgi.doe.gov/mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system. PMID:27738135

EcoGene 3.0.

PubMed

Zhou, Jindan; Rudd, Kenneth E

2013-01-01

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection.

MIPS: analysis and annotation of proteins from whole genomes in 2005

PubMed Central

Mewes, H. W.; Frishman, D.; Mayer, K. F. X.; Münsterkötter, M.; Noubibou, O.; Pagel, P.; Rattei, T.; Oesterheld, M.; Ruepp, A.; Stümpflen, V.

2006-01-01

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein–protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server (). PMID:16381839

MIPS: analysis and annotation of proteins from whole genomes in 2005.

PubMed

Mewes, H W; Frishman, D; Mayer, K F X; Münsterkötter, M; Noubibou, O; Pagel, P; Rattei, T; Oesterheld, M; Ruepp, A; Stümpflen, V

2006-01-01

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein-protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.gsf.de).

Know Before You Do: Anticipating Maneuvers via Learning Temporal Driving Models

DTIC Science & Technology

2015-04-01

features/index.htm. Accessed: 2014-09-30. [3] Google self driving car . http://en.wikipedia.org/wiki/ Google driverless car . Accessed: 2014-10-11. [4...and outside the car , GPS, and speed information, with lane and driving maneuver annotations. II. RELATED WORK Assistive features for vehicles . Recent...made driving safer over the last decade. They prepare vehicles for unsafe road conditions and alert drivers if they perform a dangerous maneuver

Computer Chips and Paper Clips. Technology and Women's Employment. Volume II. Case Studies and Policy Perspectives.

ERIC Educational Resources Information Center

Hartmann, Heidi I., Ed.; And Others

This volume contains 12 papers commissioned by the Panel on Technology and Women's Employment. "Technology, Women, and Work: Policy Perspectives" (Eli Ginzberg) is an overview that provides a context for the volume. The four case studies in Part II describe the impact of information technology in the insurance industry, among bookkeepers, among…

Integration of external metadata into the Earth System Grid Federation (ESGF)

NASA Astrophysics Data System (ADS)

Berger, Katharina; Levavasseur, Guillaume; Stockhause, Martina; Lautenschlager, Michael

2015-04-01

International projects with high volume data usually disseminate their data in a federated data infrastructure, e.g.~the Earth System Grid Federation (ESGF). The ESGF aims to make the geographically distributed data seamlessly discoverable and accessible. Additional data-related information is currently collected and stored in separate repositories by each data provider. This scattered and useful information is not or only partly available for ESGF users. Examples for such additional information systems are ES-DOC/metafor for model and simulation information, IPSL's versioning information, CHARMe for user annotations, DKRZ's quality information and data citation information. The ESGF Quality Control working team (esgf-qcwt) aims to integrate these valuable pieces of additional information into the ESGF in order to make them available to users and data archive managers by (i) integrating external information into ESGF portal, (ii) integrating links to external information objects into the ESGF metadata index, e.g. by the use of PIDs (Persistent IDentifiers), and (iii) automating the collection of external information during the ESGF data publication process. For the sixth phase of CMIP (Coupled Model Intercomparison Project), the ESGF metadata index is to be enriched by additional information on data citation, file version, etc. This information will support users directly and can be automatically exploited by higher level services (human and machine readability).

IVHS Countermeasures for Rear-End Collisions, Task 1; Vol. II: Statistical Analysis

DOT National Transportation Integrated Search

1994-02-25

This report is from the NHTSA sponsored program, "IVHS Countermeasures for Rear-End Collisions". This Volume, Volume II, Statistical Analysis, presents the statistical analysis of rear-end collision accident data that characterizes the accidents with...

Study of Alternate Space Shuttle Concepts. Volume 2, Part 2: Concept Analysis and Definition

NASA Technical Reports Server (NTRS)

1971-01-01

This is the final report of a Phase A Study of Alternate Space Shuttle Concepts by the Lockheed Missiles & Space Company (LMSC) for the National Aeronautics and Space Administration George C. Marshall Space Flight Center (MSFC). The eleven-month study, which began on 30 June 1970, is to examine the stage-and-one-half and other Space Shuttle configurations and to establish feasibility, performance, cost, and schedules for the selected concepts. This final report consists of four volumes as follows: Volume I - Executive Summary, Volume II - Concept Analysis and Definition, Volume III - Program Planning, and Volume IV - Data Cost Data. This document is Volume II, Concept Analysis and Definition.

An Independent Scientific Assessment of Well Stimulation in California Volume III

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

Jane C.S. Long; Laura C. Feinstein; Birkholzer, Jens

This study is issued in three volumes. Volume I, issued in January 2015, describes how well stimulation technologies work, how and where operators deploy these technologies for oil and gas production in California, and where they might enable production in the future. Volume II, issued in July 2015, discusses how well stimulation could affect water, atmosphere, seismic activity, wildlife and vegetation, and human health. Volume II reviews available data, and identifies knowledge gaps and alternative practices that could avoid or mitigate these possible impacts. Volume III, this volume, presents case studies that assess environmental issues and qualitative risks for specificmore » geographic regions. The Summary Report summarizes key findings, conclusions and recommendations of all three volumes.« less

Clinical impact of leak compensation during non-invasive ventilation.

PubMed

Storre, Jan Hendrik; Bohm, Philipp; Dreher, Michael; Windisch, Wolfram

2009-10-01

This study aimed to assess the impact of leak compensation capabilities during pressure- and volume-limited non-invasive positive-pressure ventilation (NPPV) in COPD patients. Fourteen patients with stable hypercapnic COPD who were receiving long-term NPPV were included in the study. For both modes of NPPV, a full face mask and an artificial leak in the ventilatory circuit were used at three different settings, and applied during daytime NPPV, either without leakage (setting I), with leakage during inspiration only (setting II), and with leakage during inspiration and expiration (setting III). Ventilation pattern was pneumotachy-graphically recorded. NPPV was feasible with negligible leak volumes, indicating optimal mask fitting during the daytime (setting I). In the presence of leakage (settings II and III), the attempt to compensate for leak was only evident during pressure-limited NPPV, since inspiratory volumes delivered by the ventilator increased from 726+/-129 (setting I) to 1104+/-164 (setting II), and to 1257+/-166 (setting III) ml during pressure-limited NPPV, respectively (all p<0.001); however, they remained stable during volume-limited NPPV. Leak compensation resulted in a decrease in leakage-induced dyspnea. However, 83%/87% (setting II/III) of the additionally-delivered inspiratory volume during pressure-limited NPPV was also lost via leakage. Expiratory volume was higher in setting II compared to setting III (both p<0.001), indicating the presence of significant expiratory leakage. The attempt at leak compensation largely feeds the leakage itself and only results in a marginal increase of tidal volume. However, pressure-limited--but not volume-limited--NPPV results in a clinically-important leak compensation in vivo. www.uniklinik-freiburg.de/zks/live/uklregister/Oeffentlich.html Identifier: UKF001272.

LCR-initiated rearrangements at the IDS locus, completed with Alu-mediated recombination or non-homologous end joining.

PubMed

Oshima, Junko; Lee, Jennifer A; Breman, Amy M; Fernandes, Priscilla H; Babovic-Vuksanovic, Dusica; Ward, Patricia A; Wolfe, Lynne A; Eng, Christine M; Del Gaudio, Daniela

2011-07-01

Mucopolysaccharidosis type II (MPS II) is caused by mutations in the IDS gene, which encodes the lysosomal enzyme iduronate-2-sulfatase. In ∼20% of MPS II patients the disorder is caused by gross IDS structural rearrangements. We identified two male cases harboring complex rearrangements involving the IDS gene and the nearby pseudogene, IDSP1, which has been annotated as a low-copy repeat (LCR). In both cases the rearrangement included a partial deletion of IDS and an inverted insertion of the neighboring region. In silico analyses revealed the presence of repetitive elements as well as LCRs at the junctions of rearrangements. Our models illustrate two alternative consequences of rearrangements initiated by non-allelic homologous recombination of LCRs: resolution by a second recombination event (that is, Alu-mediated recombination), or resolution by non-homologous end joining repair. These complex rearrangements have the potential to be recurrent and may be present among those MSP II cases with previously uncharacterized aberrations involving IDS.

Semi-automatic semantic annotation of PubMed Queries: a study on quality, efficiency, satisfaction

PubMed Central

Névéol, Aurélie; Islamaj-Doğan, Rezarta; Lu, Zhiyong

2010-01-01

Information processing algorithms require significant amounts of annotated data for training and testing. The availability of such data is often hindered by the complexity and high cost of production. In this paper, we investigate the benefits of a state-of-the-art tool to help with the semantic annotation of a large set of biomedical information queries. Seven annotators were recruited to annotate a set of 10,000 PubMed® queries with 16 biomedical and bibliographic categories. About half of the queries were annotated from scratch, while the other half were automatically pre-annotated and manually corrected. The impact of the automatic pre-annotations was assessed on several aspects of the task: time, number of actions, annotator satisfaction, inter-annotator agreement, quality and number of the resulting annotations. The analysis of annotation results showed that the number of required hand annotations is 28.9% less when using pre-annotated results from automatic tools. As a result, the overall annotation time was substantially lower when pre-annotations were used, while inter-annotator agreement was significantly higher. In addition, there was no statistically significant difference in the semantic distribution or number of annotations produced when pre-annotations were used. The annotated query corpus is freely available to the research community. This study shows that automatic pre-annotations are found helpful by most annotators. Our experience suggests using an automatic tool to assist large-scale manual annotation projects. This helps speed-up the annotation time and improve annotation consistency while maintaining high quality of the final annotations. PMID:21094696

Native Hawaiians Study Commission: Report on the Culture, Needs and Concerns of Native Hawaiians. Final Report. Volume II. Claims of Conscience: A Dissenting Study of the Culture, Needs and Concerns of Native Hawaiians.

ERIC Educational Resources Information Center

Department of the Interior, Washington, DC.

Volume II of the final report of the Native Hawaiians Study Commission (NHSC) on the culture, needs, and concerns of native Hawaiians, this book contains a formal dissent to the conclusions and recommendations presented in Volume I made by three of the NHSC commissioners. Its principal criticism is that Volume I fails to address the underlying…

EFICAz2: enzyme function inference by a combined approach enhanced by machine learning.

PubMed

Arakaki, Adrian K; Huang, Ying; Skolnick, Jeffrey

2009-04-13

We previously developed EFICAz, an enzyme function inference approach that combines predictions from non-completely overlapping component methods. Two of the four components in the original EFICAz are based on the detection of functionally discriminating residues (FDRs). FDRs distinguish between member of an enzyme family that are homofunctional (classified under the EC number of interest) or heterofunctional (annotated with another EC number or lacking enzymatic activity). Each of the two FDR-based components is associated to one of two specific kinds of enzyme families. EFICAz exhibits high precision performance, except when the maximal test to training sequence identity (MTTSI) is lower than 30%. To improve EFICAz's performance in this regime, we: i) increased the number of predictive components and ii) took advantage of consensual information from the different components to make the final EC number assignment. We have developed two new EFICAz components, analogs to the two FDR-based components, where the discrimination between homo and heterofunctional members is based on the evaluation, via Support Vector Machine models, of all the aligned positions between the query sequence and the multiple sequence alignments associated to the enzyme families. Benchmark results indicate that: i) the new SVM-based components outperform their FDR-based counterparts, and ii) both SVM-based and FDR-based components generate unique predictions. We developed classification tree models to optimally combine the results from the six EFICAz components into a final EC number prediction. The new implementation of our approach, EFICAz2, exhibits a highly improved prediction precision at MTTSI < 30% compared to the original EFICAz, with only a slight decrease in prediction recall. A comparative analysis of enzyme function annotation of the human proteome by EFICAz2 and KEGG shows that: i) when both sources make EC number assignments for the same protein sequence, the assignments tend to be consistent and ii) EFICAz2 generates considerably more unique assignments than KEGG. Performance benchmarks and the comparison with KEGG demonstrate that EFICAz2 is a powerful and precise tool for enzyme function annotation, with multiple applications in genome analysis and metabolic pathway reconstruction. The EFICAz2 web service is available at: http://cssb.biology.gatech.edu/skolnick/webservice/EFICAz2/index.html.

Research safety vehicle, Phase II. Volume I. Executive summary. Final report jul 75-dec 76

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

Struble, D.

1976-12-01

Volume I summarizes the results of the Minicars Research Safety Vehicle Phase II program, as detailed in Volumes II and III. Phase I identified trends leading to the desired national social goals of the mid-1980's in vehicle crashworthiness, crash avoidance, damageability, pedestrian safety, fuel economy, emissions and cost, and characterized an RSV to satisfy them. In Phase II an RSV prototype was designed, developed and tested to demonstrate the feasibility of meeting these goals simultaneously. Although further refinement is necessary to assure operational validity, in all categories the results meet or exceed the most advanced performance specified by The Presidentialmore » Task Force on Motor Vehicle Goals beyond 1980.« less

Nuclear Propulsion Technical Interchange Meeting, volume 2

NASA Technical Reports Server (NTRS)

1993-01-01

The purpose of the meeting was to review the work performed in fiscal year 1992 in the areas of nuclear thermal and nuclear electric propulsion technology development. These proceedings are an accumulation of the presentations provided at the meeting along with annotations provided by authors. The proceedings cover system concepts, technology development, and system modeling for nuclear thermal propulsion (NTP) and nuclear electric propulsion (NEP). The test facilities required for the development of the nuclear propulsion systems are also discussed.

Annotated Bibliography of USAARL Technical and Letter Reports. Volume 1. June 1963 - September 1987

DTIC Science & Technology

1991-05-01

continuous information concerning the duration, ampli- tude and slow-phase velocity of each nystagmic beat during experiments involving the vestibular...one lead of EKG for a full work day. Mean heart rates were tabulated from the record during: Administrative work (87.2 beats per minute), automobile...driving (85.5 beats per minute), eating (90.1 beats per minute), and flying (92.0 beats per minute). Using Tukey’s multiple comparison of means

Development and Utility of Automatic Language Processing Technologies. Volume 2

DTIC Science & Technology

2014-04-01

speech for each word using the existing Treetagger program. 3. Stem the word using the revised RevP stemmer, “RussianStemmer2013. java ” (see Section...KBaselineParaphrases2013. java ,” with the paraphrase table and a LM built from the TED training data. Information from the LM was called using the new utility query_interp...GATE/ Java Annotation Patterns Engine (JAPE) interface and on transliteration of Chinese named entities. Available Linguistic Data Consortium (LDC

Genome Wide DNA Methylation Profiles Provide Clues to the Origin and Pathogenesis of Germ Cell Tumors

PubMed Central

Rijlaarsdam, Martin A.; Tax, David M. J.; Gillis, Ad J. M.; Dorssers, Lambert C. J.; Koestler, Devin C.; de Ridder, Jeroen; Looijenga, Leendert H. J.

2015-01-01

The cell of origin of the five subtypes (I-V) of germ cell tumors (GCTs) are assumed to be germ cells from different maturation stages. This is (potentially) reflected in their methylation status as fetal maturing primordial germ cells are globally demethylated during migration from the yolk sac to the gonad. Imprinted regions are erased in the gonad and later become uniparentally imprinted according to fetal sex. Here, 91 GCTs (type I-IV) and four cell lines were profiled (Illumina’s HumanMethylation450BeadChip). Data was pre-processed controlling for cross hybridization, SNPs, detection rate, probe-type bias and batch effects. The annotation was extended, covering snRNAs/microRNAs, repeat elements and imprinted regions. A Hidden Markov Model-based genome segmentation was devised to identify differentially methylated genomic regions. Methylation profiles allowed for separation of clusters of non-seminomas (type II), seminomas/dysgerminomas (type II), spermatocytic seminomas (type III) and teratomas/dermoid cysts (type I/IV). The seminomas, dysgerminomas and spermatocytic seminomas were globally hypomethylated, in line with previous reports and their demethylated precursor. Differential methylation and imprinting status between subtypes reflected their presumed cell of origin. Ovarian type I teratomas and dermoid cysts showed (partial) sex specific uniparental maternal imprinting. The spermatocytic seminomas showed uniparental paternal imprinting while testicular teratomas exhibited partial imprinting erasure. Somatic imprinting in type II GCTs might indicate a cell of origin after global demethylation but before imprinting erasure. This is earlier than previously described, but agrees with the totipotent/embryonic stem cell like potential of type II GCTs and their rare extra-gonadal localization. The results support the common origin of the type I teratomas and show strong similarity between ovarian type I teratomas and dermoid cysts. In conclusion, we identified specific and global methylation differences between GCT subtypes, providing insight into their developmental timing and underlying developmental biology. Data and extended annotation are deposited at GEO (GSE58538 and GPL18809). PMID:25859847

Carbon footprint estimator, phase II : volume I - GASCAP model & volume II - technical appendices [technical brief].

DOT National Transportation Integrated Search

2014-03-01

This study resulted in the development of the GASCAP model (the Greenhouse Gas Assessment : Spreadsheet for Transportation Capital Projects). This spreadsheet model provides a user-friendly interface for determining the greenhouse gas (GHG) emissions...

Assisted annotation of medical free text using RapTAT

PubMed Central

Gobbel, Glenn T; Garvin, Jennifer; Reeves, Ruth; Cronin, Robert M; Heavirland, Julia; Williams, Jenifer; Weaver, Allison; Jayaramaraja, Shrimalini; Giuse, Dario; Speroff, Theodore; Brown, Steven H; Xu, Hua; Matheny, Michael E

2014-01-01

Objective To determine whether assisted annotation using interactive training can reduce the time required to annotate a clinical document corpus without introducing bias. Materials and methods A tool, RapTAT, was designed to assist annotation by iteratively pre-annotating probable phrases of interest within a document, presenting the annotations to a reviewer for correction, and then using the corrected annotations for further machine learning-based training before pre-annotating subsequent documents. Annotators reviewed 404 clinical notes either manually or using RapTAT assistance for concepts related to quality of care during heart failure treatment. Notes were divided into 20 batches of 19–21 documents for iterative annotation and training. Results The number of correct RapTAT pre-annotations increased significantly and annotation time per batch decreased by ∼50% over the course of annotation. Annotation rate increased from batch to batch for assisted but not manual reviewers. Pre-annotation F-measure increased from 0.5 to 0.6 to >0.80 (relative to both assisted reviewer and reference annotations) over the first three batches and more slowly thereafter. Overall inter-annotator agreement was significantly higher between RapTAT-assisted reviewers (0.89) than between manual reviewers (0.85). Discussion The tool reduced workload by decreasing the number of annotations needing to be added and helping reviewers to annotate at an increased rate. Agreement between the pre-annotations and reference standard, and agreement between the pre-annotations and assisted annotations, were similar throughout the annotation process, which suggests that pre-annotation did not introduce bias. Conclusions Pre-annotations generated by a tool capable of interactive training can reduce the time required to create an annotated document corpus by up to 50%. PMID:24431336

Forecasting the Future Food Service World of Work. Final Report. Volume II. Centralized Food Service Systems. Service Management Reports.

ERIC Educational Resources Information Center

Powers, Thomas F., Ed.; Swinton, John R., Ed.

Volume II of a three-volume study on the future of the food service industry considers the effects that centralized food production will have on the future of food production systems. Based on information from the Fair Acres Project and the Michigan State University Vegetable Processing Center, the authors describe the operations of a centralized…

Adolescent Health. Volume II: Background and the Effectiveness of Selected Prevention and Treatment Services [and] Indexes to Volumes I, II, and III.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Office of Technology Assessment.

This document, the second of three volumes in the U.S. Congress Office of Technology Assessment's "Adolescent Health" series, provides background information on aspects of adolescents' lives and examines the effectiveness of prevention and treatment interventions. Chapter 1, an introduction to this two-part document, provides a summary of the…

Keeping the Edge. Air Force Materiel Command Cold War Context (1945-1991). Volume 3: Index

DTIC Science & Technology

2003-08-01

485 The Architects Collaborative (Harvard University) see Gropius , Walter , under Architects and Engineers, across the Department of Defense The...Sons (Newark, New Jersey) Volume II: 250 Graham, Anderson, Probst & White (Chicago) Volume II: 392, 455, 460, 461,475 Gropius , Walter ...models for Air Force research and development centers Gropius , Walter (The Architects Collaborative) see Architects and Engineers, across the

ASTRONAUTICS INFORMATION OPEN LITERATURE SURVEY. VOLUME II. NO. 10 (Entries 22,871-23,094)

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

None

1960-10-01

An open literature survey on astronautics is presented which covers the period of Oct. 1960. The material is organized alphabetically according to subject. A list of periodicals scanned is given in volume II No. 1-2 with addendums in subsequent volumes. Cumulative author and subject indexes are given at the end of the entries. (About 220 references.) (J.R.D.)

Joint Hampton-Michigan Program for Training Minority and Women Researchers. Volume II of II Volumes. Final Report.

ERIC Educational Resources Information Center

Michigan Univ., Ann Arbor. School of Education.

The papers presented in this volume are the team research reports of the Joint Hampton-Michigan Program conducted in 1979-1980 for junior faculty members of the Hampton Institute (Virginia) and graduate students and faculty members of the University of Michigan. The titles of the papers are: (1) Social and Economic Implications of Teacher Training…

Flexible Display and Integrated Communication Devices (FDICD) Technology. Volume 2

DTIC Science & Technology

2008-06-01

AFRL-RH-WP-TR-2008-0072 Flexible Display and Integrated Communication Devices (FDICD) Technology, Volume II David Huffman Keith Tognoni...14 April 2004 – 20 June 2008 4. TITLE AND SUBTITLE Flexible Display and Integrated Communication Devices (FDICD) Technology, Volume II 5a...14. ABSTRACT This flexible display and integrated communication devices (FDICD) technology program sought to create a family of powerful

ASDIR-II. Volume II. Program Description

DTIC Science & Technology

1975-01-01

in ASDIR. INPUT: Engine description, gas properties and case definition (See ASDIR-II, Volume I, User’s Manual). OIWPUT: Primarily the information...conditions Special surface cooling flow conditions Exhaust system surface properties The predictions provided by the progi un for the combination of a...nonattenuated by the atmosphere Optional exhaust system information which can be requested from the program is: Internal fluid flow properties Surface

International Linear Collider Technical Design Report (Volumes 1 through 4)

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

Harrison M.

2013-03-27

The design report consists of four volumes: Volume 1, Executive Summary; Volume 2, Physics; Volume 3, Accelerator (Part I, R and D in the Technical Design Phase, and Part II, Baseline Design); and Volume 4, Detectors.

Introduction to "Global Tsunami Science: Past and Future, Volume II"

NASA Astrophysics Data System (ADS)

Rabinovich, Alexander B.; Fritz, Hermann M.; Tanioka, Yuichiro; Geist, Eric L.

2017-08-01

Twenty-two papers on the study of tsunamis are included in Volume II of the PAGEOPH topical issue "Global Tsunami Science: Past and Future". Volume I of this topical issue was published as PAGEOPH, vol. 173, No. 12, 2016 (Eds., E. L. Geist, H. M. Fritz, A. B. Rabinovich, and Y. Tanioka). Three papers in Volume II focus on details of the 2011 and 2016 tsunami-generating earthquakes offshore of Tohoku, Japan. The next six papers describe important case studies and observations of recent and historical events. Four papers related to tsunami hazard assessment are followed by three papers on tsunami hydrodynamics and numerical modelling. Three papers discuss problems of tsunami warning and real-time forecasting. The final set of three papers importantly investigates tsunamis generated by non-seismic sources: volcanic explosions, landslides, and meteorological disturbances. Collectively, this volume highlights contemporary trends in global tsunami research, both fundamental and applied toward hazard assessment and mitigation.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

PubMed

Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

2013-04-15

In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

PubMed Central

2013-01-01

Background In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. Results We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. Conclusions BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic. PMID:23586394

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

PubMed Central

Arighi, Cecilia N.; Carterette, Ben; Cohen, K. Bretonnel; Krallinger, Martin; Wilbur, W. John; Fey, Petra; Dodson, Robert; Cooper, Laurel; Van Slyke, Ceri E.; Dahdul, Wasila; Mabee, Paula; Li, Donghui; Harris, Bethany; Gillespie, Marc; Jimenez, Silvia; Roberts, Phoebe; Matthews, Lisa; Becker, Kevin; Drabkin, Harold; Bello, Susan; Licata, Luana; Chatr-aryamontri, Andrew; Schaeffer, Mary L.; Park, Julie; Haendel, Melissa; Van Auken, Kimberly; Li, Yuling; Chan, Juancarlos; Muller, Hans-Michael; Cui, Hong; Balhoff, James P.; Chi-Yang Wu, Johnny; Lu, Zhiyong; Wei, Chih-Hsuan; Tudor, Catalina O.; Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar; Cejuela, Juan Miguel; Dubey, Pratibha; Wu, Cathy

2013-01-01

In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature. Some biocuration efforts already make use of a text mining tool, but there have not been many broad-based systematic efforts to study which aspects of a text mining tool contribute to its usefulness for a curation task. Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools. Six text mining systems presenting diverse biocuration tasks participated in a formal evaluation, and appropriate biocurators were recruited for testing. The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly (∼1.7- to 2.5-fold) over manual curation. In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set. In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent difficulty of the curation and attention to annotation guidelines. After the task, annotators were asked to complete a survey to help identify strengths and weaknesses of the various systems. The analysis of this survey highlights how important task completion is to the biocurators’ overall experience of a system, regardless of the system’s high score on design, learnability and usability. In addition, strategies to refine the annotation guidelines and systems documentation, to adapt the tools to the needs and query types the end user might have and to evaluate performance in terms of efficiency, user interface, result export and traditional evaluation metrics have been analyzed during this task. This analysis will help to plan for a more intense study in BioCreative IV. PMID:23327936

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.

PubMed

Arighi, Cecilia N; Carterette, Ben; Cohen, K Bretonnel; Krallinger, Martin; Wilbur, W John; Fey, Petra; Dodson, Robert; Cooper, Laurel; Van Slyke, Ceri E; Dahdul, Wasila; Mabee, Paula; Li, Donghui; Harris, Bethany; Gillespie, Marc; Jimenez, Silvia; Roberts, Phoebe; Matthews, Lisa; Becker, Kevin; Drabkin, Harold; Bello, Susan; Licata, Luana; Chatr-aryamontri, Andrew; Schaeffer, Mary L; Park, Julie; Haendel, Melissa; Van Auken, Kimberly; Li, Yuling; Chan, Juancarlos; Muller, Hans-Michael; Cui, Hong; Balhoff, James P; Chi-Yang Wu, Johnny; Lu, Zhiyong; Wei, Chih-Hsuan; Tudor, Catalina O; Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar; Cejuela, Juan Miguel; Dubey, Pratibha; Wu, Cathy

2013-01-01

In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature. Some biocuration efforts already make use of a text mining tool, but there have not been many broad-based systematic efforts to study which aspects of a text mining tool contribute to its usefulness for a curation task. Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools. Six text mining systems presenting diverse biocuration tasks participated in a formal evaluation, and appropriate biocurators were recruited for testing. The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly (∼1.7- to 2.5-fold) over manual curation. In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set. In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent difficulty of the curation and attention to annotation guidelines. After the task, annotators were asked to complete a survey to help identify strengths and weaknesses of the various systems. The analysis of this survey highlights how important task completion is to the biocurators' overall experience of a system, regardless of the system's high score on design, learnability and usability. In addition, strategies to refine the annotation guidelines and systems documentation, to adapt the tools to the needs and query types the end user might have and to evaluate performance in terms of efficiency, user interface, result export and traditional evaluation metrics have been analyzed during this task. This analysis will help to plan for a more intense study in BioCreative IV.

An Evaluation of Public Preferences for Superfund Site Cleanup, Volume II: Pilot Study (1995)

EPA Pesticide Factsheets

In volume II, the authors present the detailed technical results of a pilot market research study that was conducted to determine preferences for the specific type and level of cleanup desired by the public at Superfund sites.

Seismic Design Considerations : Volume I, Technical Approaches and Results; Volume II, Appendices II-VIII

DOT National Transportation Integrated Search

2012-03-01

NJDOT has adopted AASHTO Guide Specifications for LRFD Seismic Bridge Design approved by the Highway : Subcommittee on Bridges and Structures in 2007. The main objective of research presented in this report has : been to resolve following issue...

Theoretical Studies of Microstrip Antennas : Volume II, Analysis and Synthesis of Multi-Frequency Elements

DOT National Transportation Integrated Search

1979-09-01

Volume II of Theoretical Studies of Microstrip Antennas deals with the analysis and synthesis of several types of novel multi-resonant elements with emphasis on dual-frequency operation of rectangular microstrip patch antennas with or without externa...

Field testing of hand-held infrared thermography, phase II TPF-5(247) : final report.

DOT National Transportation Integrated Search

2016-05-01

This report is the second of two volumes that document results from the pooled fund study TPF-5 (247), Development of : Handheld Infrared Thermography, Phase II. The interim report (volume I) studied the implementation of handheld thermography : by p...

Taxicab Regulation in U.S. Cities. Volume II, Case Studies

DOT National Transportation Integrated Search

1983-10-01

Volume II of the study, Taxicab Regulation in U.S. Cities, contains case study reports. Ten U.S. cities were visited in June and July, 1983, for more in-depth study of their experiences with taxicab regulation. These cities are Fayetteville and Charl...

Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms: VISCERAL Anatomy Benchmarks.

PubMed

Jimenez-Del-Toro, Oscar; Muller, Henning; Krenn, Markus; Gruenberg, Katharina; Taha, Abdel Aziz; Winterstein, Marianne; Eggel, Ivan; Foncubierta-Rodriguez, Antonio; Goksel, Orcun; Jakab, Andras; Kontokotsios, Georgios; Langs, Georg; Menze, Bjoern H; Salas Fernandez, Tomas; Schaer, Roger; Walleyo, Anna; Weber, Marc-Andre; Dicente Cid, Yashin; Gass, Tobias; Heinrich, Mattias; Jia, Fucang; Kahl, Fredrik; Kechichian, Razmig; Mai, Dominic; Spanier, Assaf B; Vincent, Graham; Wang, Chunliang; Wyeth, Daniel; Hanbury, Allan

2016-11-01

Variations in the shape and appearance of anatomical structures in medical images are often relevant radiological signs of disease. Automatic tools can help automate parts of this manual process. A cloud-based evaluation framework is presented in this paper including results of benchmarking current state-of-the-art medical imaging algorithms for anatomical structure segmentation and landmark detection: the VISCERAL Anatomy benchmarks. The algorithms are implemented in virtual machines in the cloud where participants can only access the training data and can be run privately by the benchmark administrators to objectively compare their performance in an unseen common test set. Overall, 120 computed tomography and magnetic resonance patient volumes were manually annotated to create a standard Gold Corpus containing a total of 1295 structures and 1760 landmarks. Ten participants contributed with automatic algorithms for the organ segmentation task, and three for the landmark localization task. Different algorithms obtained the best scores in the four available imaging modalities and for subsets of anatomical structures. The annotation framework, resulting data set, evaluation setup, results and performance analysis from the three VISCERAL Anatomy benchmarks are presented in this article. Both the VISCERAL data set and Silver Corpus generated with the fusion of the participant algorithms on a larger set of non-manually-annotated medical images are available to the research community.

Annotated bibliography of environmentally relevant investigations of uranium mining and milling in the Grants Mineral Belt, northwestern New Mexico

USGS Publications Warehouse

Otton, James K.

2011-01-01

Studies of the natural environment in the Grants Mineral Belt in northwestern New Mexico have been conducted since the 1930s; however, few such investigations predate uranium mining and milling operations, which began in the early 1950s. This report provides an annotated bibliography of reports that describe the hydrology and geochemistry of groundwaters and surface waters and the geochemistry of soils and sediments in the Grants Mineral Belt and contiguous areas. The reports referenced and discussed provide a large volume of information about the environmental conditions in the area after mining started. Data presented in many of these studies, if evaluated carefully, may provide much basic information about the baseline conditions that existed over large parts of the Grants Mineral Belt prior to mining. Other data may provide information that can direct new work in efforts to discriminate between baseline conditions and the effects of the mining and milling on the natural environment.

Physical properties of biological entities: an introduction to the ontology of physics for biology.

PubMed

Cook, Daniel L; Bookstein, Fred L; Gennari, John H

2011-01-01

As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB), a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration. © 2011 Cook et al.

Environmental aspects of the transuranics. A selected, annotated bibliography. Volume 9

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

Ensminger, J.T.; Fore, C.S.; Dailey, N.S.

This ninth published bibliography of 589 references is compiled from the Nevada Applied Ecology Information Center`s Data Base on the Environmental Aspects of the Transuranics. The data base was built to provide information support to the Nevada Applied Ecology Group (NAEG) of DOE`s Nevada Operations Office. The general scope covers environmental aspects of uranium and the transuranic elements, with emphasis on plutonium. This annotated bibliography highlights literature on plutonium 238 and 239 and americium 241 in the critical organs of man and animals. Studies on the migration of plutonium and the transplutonics through the environment are also emphasized. Supporting informationmore » on ecology of the Nevada Test Site and reviews and summarizing literature on other radionuclides have been included at the request of the NAEG. The references are arranged by subject category with leading authors appearing alphabetically within each category. Indexes are provided for author(s), geographic location, keywords, taxonomic name, title, and publication description.« less

HYDRA-II: A hydrothermal analysis computer code: Volume 3, Verification/validation assessments

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

McCann, R.A.; Lowery, P.S.

1987-10-01

HYDRA-II is a hydrothermal computer code capable of three-dimensional analysis of coupled conduction, convection, and thermal radiation problems. This code is especially appropriate for simulating the steady-state performance of spent fuel storage systems. The code has been evaluated for this application for the US Department of Energy's Commercial Spent Fuel Management Program. HYDRA-II provides a finite difference solution in cartesian coordinates to the equations governing the conservation of mass, momentum, and energy. A cylindrical coordinate system may also be used to enclose the cartesian coordinate system. This exterior coordinate system is useful for modeling cylindrical cask bodies. The difference equationsmore » for conservation of momentum are enhanced by the incorporation of directional porosities and permeabilities that aid in modeling solid structures whose dimensions may be smaller than the computational mesh. The equation for conservation of energy permits modeling of orthotropic physical properties and film resistances. Several automated procedures are available to model radiation transfer within enclosures and from fuel rod to fuel rod. The documentation of HYDRA-II is presented in three separate volumes. Volume I - Equations and Numerics describes the basic differential equations, illustrates how the difference equations are formulated, and gives the solution procedures employed. Volume II - User's Manual contains code flow charts, discusses the code structure, provides detailed instructions for preparing an input file, and illustrates the operation of the code by means of a model problem. This volume, Volume III - Verification/Validation Assessments, provides a comparison between the analytical solution and the numerical simulation for problems with a known solution. This volume also documents comparisons between the results of simulations of single- and multiassembly storage systems and actual experimental data. 11 refs., 55 figs., 13 tabs.« less

Fourth - generation languages. Volume 2. Representative 4GLs

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

Martin, J.

1986-01-01

The chapters in Part II each describe one representative product marketed by a vendor other than IBM. (Volume III of this work covers IBM languages.) The chapters in Part II cover the following 4GLs: ADS/ONLINE, APPLICATION FACTORY, DATATRIEVE, FOCUS, IDEAL, INTELLECT, MANTIS, MIMER, NATURAL, NOMAD2, RAMIS II, SYSTEM W, and USE-IT. The Perspective section of Part II presents a general overview of the product and describes its role in the marketplace. The Tutorial section describes how a user employs the language in application development.

Evaluation and Repair of Concrete Structures: Annotated Bibliography 1978 - 1988. Volume 1. (Repair, Evaluation, Maintenance and Rehabilitation Research Program)

DTIC Science & Technology

1991-06-01

32303, "Application of New Technology to Maintenance and Minor Repair," for which Mr. James E. McDonald (CEWES-SC-R) was Principal Investigator. Dr. Tony...materials, shotcrete, and silica-fume concrete. 6. Section -D contains 710 references-on maintenance and repair tech- niques including bonding new concrote to...sys- -tem. The process problems have been resolved-by introduction of new instrumentation, static mixers, elimination of washers and high density

Annotated Bibliography for Lake Erie. Volume V. Physical,

DTIC Science & Technology

1974-10-01

119, 120, 1144, 183, 197, 203, 210, 508, 5148, 577, 580, 660, 682, 687 Regulation - financial capacity - federal - 7, 27, 31, 44, 48 55, 56, 71, 88...656, 657, 658, r 659, 660, 661, 662, 6614, 665, 677, 681, 682, 683, 702, 705, 706, 710, 711, 7314 Regulation - financial capacity - state -25, 27 28 29...17 Regulation - financial capacity - local - 7, 22, 27, 28, 29, 30, 32, 314, 35, 36, 39, 40, 43, 48, 55, 59, 80, 88,91, 102, 113, 1114, 115, 116, 117

Human Performance in Continuous/Sustained Operations and the Demands of Extended Work/Rest Schedules: An Annotated Bibliography. Volume 2

DTIC Science & Technology

1989-06-01

subjective self -report questionnaires and more objective activity measures to estimate the amount of sleep obtained. The aim of the study was to determine...helicopter crews were observed and analyzed. It is concluded that the operational effiency of flight crews can be obtained by adopting four measures...task on simulated truck- driving task performance. Human factors. 27(2): 201-207. A study examined the effects of extra task stimulation and extra

ASTRONAUTICS INFORMATION. OPEN LITERATURE SURVEY, VOLUME III, NO. 2 (ENTRIES 30,202-30,404)

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

None

1961-02-01

<>15:014925. An annotated list of references on temperature control of satellite and space vehicles is presented. Methods and systems for maintaining vehicles within tolerable temperature bounds while operating outside planetary atmospheres are outlined. Discussions of the temperature environment in space and how it might affect vehicle operation are given. Re-entry heating problems are not included. Among the sources used were: Engineering Index, Applied Science and Technology Index, Astronautics Abstracts, PAL uniterm index, ASTIA, and LMSD card catalog. (auth)

Evaluation and Repair of Concrete Structures: Annotated Bibliography 1978 - 1988. Volume 2. (Repair, Evaluation, Maintenance and Rehabilitation Research Program)

DTIC Science & Technology

1991-06-01

steps at the Rugby Football Union Ground in Twickenham, England. The deteriorated steps were cut away from the existing steel support beams. Reinforcing...provided in each vol- ume as a guide for users of this -bibliography. 6 SECTION C MAINTENANCE AND--REPAIR MATERIALS and a matching of these needs to a...calculations were correct). 73 Several types- of repair mediums are available. The medium should match -the quality of the-6riginal concrete but with-greater

Review of the Scientific Literature and Preparation of an Annotated Bibliography on Effects of Cigarette Smoking and Nicotine on Human Performance. Volume 1

DTIC Science & Technology

1986-01-01

physiological changes that contribute to the state of arousal upon which a smoking habit may depend. TheI radial muscle of the iris in the eye contracts...studied the vestibular nystagnus pattern of smokers; amplitude, frequency, speed of slow component, speed of fast component, and angular deviation of eyes ...carbon monoxide was measured before and after treatment in order to estimate the degree of inhalation, and cigarette butts were collected for analysis

An Annotated Bibliography of Patents Related to Coastal Engineering. Volume III. 1974-1976. Appendix.

DTIC Science & Technology

1979-11-01

infrared detectors produce signals which are proportional to the detected reflected radia- tion at the wavelengths k, and A,. A processing channel is con...instrument including an oscillator for sup- T___ plying AC energy to a transducer. The oscillator is keyed on /I by a multvibrator which produces clock pulses... includes dams including such units when installed, and methods of damming water flow. o- 3.786.640 .MEANS AND METHOD FOR PRODUCING STEPPED CONCRETE SLOPE

Occupational Information 1990/91. Volume II.

ERIC Educational Resources Information Center

Nebraska Univ., Lincoln. Nebraska Career Information System.

The Nebraska Occupational Information books (volumes I and II) contain information about 386 different occupations in the state and answer questions about specific occupations in detail. The descriptions are arranged according to a U.S. Department of Labor classification system, with occupational titles clustered in general groups of selected…

User's manual for the BNW-II optimization code for dry/wet-cooled power plants

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

Braun, D.J.; Bamberger, J.A.; Braun, D.J.

1978-05-01

This volume provides a listing of the BNW-II dry/wet ammonia heat rejection optimization code and is an appendix to Volume I which gives a narrative description of the code's algorithms as well as logic, input and output information.

Community annotation experiment for ground truth generation for the i2b2 medication challenge

PubMed Central

Solti, Imre; Xia, Fei; Cadag, Eithon

2010-01-01

Objective Within the context of the Third i2b2 Workshop on Natural Language Processing Challenges for Clinical Records, the authors (also referred to as ‘the i2b2 medication challenge team’ or ‘the i2b2 team’ for short) organized a community annotation experiment. Design For this experiment, the authors released annotation guidelines and a small set of annotated discharge summaries. They asked the participants of the Third i2b2 Workshop to annotate 10 discharge summaries per person; each discharge summary was annotated by two annotators from two different teams, and a third annotator from a third team resolved disagreements. Measurements In order to evaluate the reliability of the annotations thus produced, the authors measured community inter-annotator agreement and compared it with the inter-annotator agreement of expert annotators when both the community and the expert annotators generated ground truth based on pooled system outputs. For this purpose, the pool consisted of the three most densely populated automatic annotations of each record. The authors also compared the community inter-annotator agreement with expert inter-annotator agreement when the experts annotated raw records without using the pool. Finally, they measured the quality of the community ground truth by comparing it with the expert ground truth. Results and conclusions The authors found that the community annotators achieved comparable inter-annotator agreement to expert annotators, regardless of whether the experts annotated from the pool. Furthermore, the ground truth generated by the community obtained F-measures above 0.90 against the ground truth of the experts, indicating the value of the community as a source of high-quality ground truth even on intricate and domain-specific annotation tasks. PMID:20819855

aGEM: an integrative system for analyzing spatial-temporal gene-expression information

PubMed Central

Jiménez-Lozano, Natalia; Segura, Joan; Macías, José Ramón; Vega, Juanjo; Carazo, José María

2009-01-01

Motivation: The work presented here describes the ‘anatomical Gene-Expression Mapping (aGEM)’ Platform, a development conceived to integrate phenotypic information with the spatial and temporal distributions of genes expressed in the mouse. The aGEM Platform has been built by extending the Distributed Annotation System (DAS) protocol, which was originally designed to share genome annotations over the WWW. DAS is a client-server system in which a single client integrates information from multiple distributed servers. Results: The aGEM Platform provides information to answer three main questions. (i) Which genes are expressed in a given mouse anatomical component? (ii) In which mouse anatomical structures are a given gene or set of genes expressed? And (iii) is there any correlation among these findings? Currently, this Platform includes several well-known mouse resources (EMAGE, GXD and GENSAT), hosting gene-expression data mostly obtained from in situ techniques together with a broad set of image-derived annotations. Availability: The Platform is optimized for Firefox 3.0 and it is accessed through a friendly and intuitive display: http://agem.cnb.csic.es Contact: natalia@cnb.csic.es Supplementary information: Supplementary data are available at http://bioweb.cnb.csic.es/VisualOmics/aGEM/home.html and http://bioweb.cnb.csic.es/VisualOmics/index_VO.html and Bioinformatics online. PMID:19592395

Inferring nucleosome positions with their histone mark annotation from ChIP data

PubMed Central

Mammana, Alessandro; Vingron, Martin; Chung, Ho-Ryun

2013-01-01

Motivation: The nucleosome is the basic repeating unit of chromatin. It contains two copies each of the four core histones H2A, H2B, H3 and H4 and about 147 bp of DNA. The residues of the histone proteins are subject to numerous post-translational modifications, such as methylation or acetylation. Chromatin immunoprecipitiation followed by sequencing (ChIP-seq) is a technique that provides genome-wide occupancy data of these modified histone proteins, and it requires appropriate computational methods. Results: We present NucHunter, an algorithm that uses the data from ChIP-seq experiments directed against many histone modifications to infer positioned nucleosomes. NucHunter annotates each of these nucleosomes with the intensities of the histone modifications. We demonstrate that these annotations can be used to infer nucleosomal states with distinct correlations to underlying genomic features and chromatin-related processes, such as transcriptional start sites, enhancers, elongation by RNA polymerase II and chromatin-mediated repression. Thus, NucHunter is a versatile tool that can be used to predict positioned nucleosomes from a panel of histone modification ChIP-seq experiments and infer distinct histone modification patterns associated to different chromatin states. Availability: The software is available at http://epigen.molgen.mpg.de/nuchunter/. Contact: chung@molgen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23981350

Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

PubMed Central

Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

2015-01-01

Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. In particular, our approach effectively identifies multiple independent cis-eQTL signals that are consistent across populations, accounting for population heterogeneity in allele frequencies and linkage disequilibrium patterns. Furthermore, by integrating genomic annotations, our analysis framework enables high-resolution functional analysis of eQTLs. We applied our statistical approach to analyze the GEUVADIS data consisting of samples from five population groups. From this analysis, we concluded that i) jointly analysis across population groups greatly improves the power of eQTL discovery and the resolution of fine mapping of causal eQTL ii) many genes harbor multiple independent eQTLs in their cis regions iii) genetic variants that disrupt transcription factor binding are significantly enriched in eQTLs (p-value = 4.93 × 10-22). PMID:25906321

From Higher Education To Employment. Volume II: Canada, Denmark, Spain, United States = De l'enseignement superieur a l'emploi. Volume II: Canada, Danemark, Expagne, Etats-Unis.

ERIC Educational Resources Information Center

Organisation for Economic Cooperation and Development, Paris (France).

This volume presents reports on the flows of graduates from higher education and on their entry into working life in Canada, Denmark, Spain and the United States. Each paper is written according to detailed guidelines designed to assemble information from many sources, to reflect the state of the art, and to illustrate a variety of approaches,…

Personal, societal, and ecological values of wilderness: Sixth World Wilderness Congress proceedings on research, management, and allocation, Volume II

Treesearch

Alan E. Watson; Greg H. Aplet; John C. Hendee

2000-01-01

The papers contained in Volume II of these Proceedings represent a combination of papers originally scheduled for the delayed 1997 meeting of the World Wilderness Congress and those submitted in response to a second call for papers when the Congress was rescheduled for October 24-29, 1998, in Bangalore, India. Just as in Volume I, the papers are divided into seven...

The Archaeology of Coralville Lake, Iowa. Volume 4. Recreation Area Survey. (Interim Report 2).

DTIC Science & Technology

1985-09-01

THE ARCHAEOLOGY OF CORALVILLE LAKE, IOWA VOLUME IV: RECREATION AREA SURVEY (INTERIM REPORT II) p - [ JAN 1 4 1986 WAUWATOSA. WISCONSIN 86 1.13 117...THE ARCHAEOLOGY OF CORALVILLE LAKE, IOWA ; VOLUME IV: RECREATION AREA SURVEY (INTERIM REPORT II) Submitted To: Rock Island District Corps of Engineers...presents the results of intensive archaeological and geomorphic investigations at 14 special use or recreation areas at Coralville Lake, Iowa . The

Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects.

PubMed

Pérez-Pérez, Martín; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Lourenço, Anália

2015-02-01

Document annotation is a key task in the development of Text Mining methods and applications. High quality annotated corpora are invaluable, but their preparation requires a considerable amount of resources and time. Although the existing annotation tools offer good user interaction interfaces to domain experts, project management and quality control abilities are still limited. Therefore, the current work introduces Marky, a new Web-based document annotation tool equipped to manage multi-user and iterative projects, and to evaluate annotation quality throughout the project life cycle. At the core, Marky is a Web application based on the open source CakePHP framework. User interface relies on HTML5 and CSS3 technologies. Rangy library assists in browser-independent implementation of common DOM range and selection tasks, and Ajax and JQuery technologies are used to enhance user-system interaction. Marky grants solid management of inter- and intra-annotator work. Most notably, its annotation tracking system supports systematic and on-demand agreement analysis and annotation amendment. Each annotator may work over documents as usual, but all the annotations made are saved by the tracking system and may be further compared. So, the project administrator is able to evaluate annotation consistency among annotators and across rounds of annotation, while annotators are able to reject or amend subsets of annotations made in previous rounds. As a side effect, the tracking system minimises resource and time consumption. Marky is a novel environment for managing multi-user and iterative document annotation projects. Compared to other tools, Marky offers a similar visually intuitive annotation experience while providing unique means to minimise annotation effort and enforce annotation quality, and therefore corpus consistency. Marky is freely available for non-commercial use at http://sing.ei.uvigo.es/marky. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Is the Juice Worth the Squeeze? Costs and Benefits of Multiple Human Annotators for Clinical Text De-identification.

PubMed

Carrell, David S; Cronkite, David J; Malin, Bradley A; Aberdeen, John S; Hirschman, Lynette

2016-08-05

Clinical text contains valuable information but must be de-identified before it can be used for secondary purposes. Accurate annotation of personally identifiable information (PII) is essential to the development of automated de-identification systems and to manual redaction of PII. Yet the accuracy of annotations may vary considerably across individual annotators and annotation is costly. As such, the marginal benefit of incorporating additional annotators has not been well characterized. This study models the costs and benefits of incorporating increasing numbers of independent human annotators to identify the instances of PII in a corpus. We used a corpus with gold standard annotations to evaluate the performance of teams of annotators of increasing size. Four annotators independently identified PII in a 100-document corpus consisting of randomly selected clinical notes from Family Practice clinics in a large integrated health care system. These annotations were pooled and validated to generate a gold standard corpus for evaluation. Recall rates for all PII types ranged from 0.90 to 0.98 for individual annotators to 0.998 to 1.0 for teams of three, when meas-ured against the gold standard. Median cost per PII instance discovered during corpus annotation ranged from $ 0.71 for an individual annotator to $ 377 for annotations discovered only by a fourth annotator. Incorporating a second annotator into a PII annotation process reduces unredacted PII and improves the quality of annotations to 0.99 recall, yielding clear benefit at reasonable cost; the cost advantages of annotation teams larger than two diminish rapidly.

Active learning reduces annotation time for clinical concept extraction.

PubMed

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.

Corpus annotation for mining biomedical events from literature

PubMed Central

Kim, Jin-Dong; Ohta, Tomoko; Tsujii, Jun'ichi

2008-01-01

Background Advanced Text Mining (TM) such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attempts to succeed, text annotation from the biological point of view is indispensable. However, due to the complexity of the task, semantic annotation has never been tried on a large scale, apart from relatively simple term annotation. Results We have completed a new type of semantic annotation, event annotation, which is an addition to the existing annotations in the GENIA corpus. The corpus has already been annotated with POS (Parts of Speech), syntactic trees, terms, etc. The new annotation was made on half of the GENIA corpus, consisting of 1,000 Medline abstracts. It contains 9,372 sentences in which 36,114 events are identified. The major challenges during event annotation were (1) to design a scheme of annotation which meets specific requirements of text annotation, (2) to achieve biology-oriented annotation which reflect biologists' interpretation of text, and (3) to ensure the homogeneity of annotation quality across annotators. To meet these challenges, we introduced new concepts such as Single-facet Annotation and Semantic Typing, which have collectively contributed to successful completion of a large scale annotation. Conclusion The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing)-based TM in the bio-medical domain. PMID:18182099

Volume changes and electrostriction in the primary photoreactions of various photosynthetic systems: estimation of dielectric coefficient in bacterial reaction centers and of the observed volume changes with the Drude-Nernst equation.

PubMed

Mauzerall, David; Hou, Jian-Min; Boichenko, Vladimir A

2002-01-01

Photoacoustics (PA) allows the determination of enthalpy and volume changes of photoreactions in photosynthetic reaction centers on the 0.1-10 mus time scale. These include the bacterial centers from Rb. sphaeroides, PS I and PS II centers from Synechocystis and in whole cells. In vitro and in vivo PA data on PS I and PS II revealed that both the volume change (-26 A(3)) and reaction enthalpy (-0.4 eV) in PS I are the same as those in the bacterial centers. However the volume change in PS II is small and the enthalpy far larger, -1 eV. Assigning the volume changes to electrostriction allows a coherent explanation of these observations. One can explain the large volume decrease in the bacterial centers with an effective dielectric coefficient of approximately 4. This is a unique approach to this parameter so important in estimation of protein energetics. The value of the volume contraction for PS I can only be explained if the acceptor is the super- cluster (Fe(4)S(4))(Cys(4)) with charge change from -1 to -2. The small volume change in PS II is explained by sub-mus electron transfer from Y(Z) anion to P(680) cation, in which charge is only moved from the Y(Z) anion to the Q(A) with no charge separation or with rapid proton transfer from oxidized Y(Z) to a polar region and thus very little change in electrostriction. At more acid pH equally rapid proton transfer from a neighboring histidine to a polar region may be caused by the electric field of the P(680) cation.

Fiber, Fabric and Fashion. Environment II.

ERIC Educational Resources Information Center

Arizona State Univ., Tempe.

A competency-based instructional guide for grades 7-14, this volume is one of three parts, each of which focuses on a different environment (psychomotor, cognitive, or affective), and each of which includes competencies and learning activities for each of three instructional levels. The topics for this volume (Environment II--cognitive) are…

Information Processing Techniques Program. Volume II. Communications- Adaptive Internetting

DTIC Science & Technology

1977-09-30

LABORATORY INFORMATION PROCESSING TECHNIQUES PROGRAM VOLUME II: COMMUNICATIONS-ADAPTIVE INTERNETTING I SEMIANNUAL TECHNICAL SUMMARY REPORT TO THE...MASSACHUSETTS ABSTRACT This repori describes work performed on the Communications-Adaptive Internetting program sponsored by the Information ... information processing techniques network speech terminal communicatlons-adaptive internetting 04 links digital voice communications time-varying

40 CFR 52.70 - Identification of plan.

Code of Federal Regulations, 2011 CFR

2011-07-01

... nonattainment areas submitted by the Governor of Alaska on January 18, 1980 as follows: Volume II. Analysis of...: Volume II. Analysis of Problems, Control Actions Section V. Ambient Air Monitoring A. Purpose C. Air Monitoring Network E. Annual Review (9) Provisions of a State Air Quality Control Plan submitted by the...

40 CFR 52.70 - Identification of plan.

Code of Federal Regulations, 2012 CFR

2012-07-01

... nonattainment areas submitted by the Governor of Alaska on January 18, 1980 as follows: Volume II. Analysis of...: Volume II. Analysis of Problems, Control Actions Section V. Ambient Air Monitoring A. Purpose C. Air Monitoring Network E. Annual Review (9) Provisions of a State Air Quality Control Plan submitted by the...

Increased Rail Transit Vehicle Crashworthiness in Head-On Collisions. Volume II. Primary Collision.

DOT National Transportation Integrated Search

1980-06-01

A specific goal of safety is to reduce the number of injuries that may result from the collision of two trains. In Volume II, an analytical model in two dimensions, longitudinal and vertical, of the primary collision of two impacting urban railcar co...

Behavioral Science Elementary Teacher Education Program. Final Report. Volume II.

ERIC Educational Resources Information Center

Michigan State Univ., East Lansing.

Volume II separately details two model components: Scholarly Modes of Knowledge, in which problem-solving techniques and the applicability of subject content to teaching are emphasized, and Professional Use of Knowledge, in which the student translates what he knows about various disciplines and human learning into instructional strategies. Each…

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

PubMed

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

2010-10-15

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

Synthesis and Structural Characterization of New Light Molecular Weight Inorganic Oxidizers and Related Derivatives. Volume: 2

DTIC Science & Technology

1993-02-01

of the strong inductive effect of the five fluorine ligands attached to the tellurium atom. 34 It is prepared under anhydrous conditions according to...MOLECULAR WEIGHT INORGANIC OXIDIZERS AND RELATED DERIVATIVES. VOLUME: II Professor G. J. Schrobilgen McMaster University Department of Chemistry...C: F04611-91-K-0004 Molecular Weight Inorganic Oxidizers and Relative PE: 62302F SDerivatives: Volume II 1PR: 5730 6. AUTHOFR(S) TA: 0*( C

Raman Frequencies Calculated from the Volume Data as a Function of Temperature at High Pressures for the Disordered Phase II of NH4I

NASA Astrophysics Data System (ADS)

Yurtseven, H.; Kavruk, D.

In this study, we calculate the Raman frequencies as a function of temperature for the fixed pressures of 706, 1080 and 6355 bars using the volume data for phase II of ammonium iodide. The Raman frequencies calculated here are for the translational optic ν5 TOM (125 cm-1) lattice mode that is located at the zone boundary (M point) of the Brillouin zone of phase II for NH4I. For this calculation the volume data obtained at zero pressure, is used through the mode Grüneisen parameter for the disordered phase II (β phase) which has the CsCl structure of NH4I. Our predicted frequencies of the ν5 TOM (125 cm-1) mode can be compared when the Raman data for this lattice mode is available at various temperatures for fixed pressures of 706, 1080 and 6355 bars in the disordered phase II of ammonium iodide.

Selective removal of cesium from aqueous solutions with nickel (II) hexacyanoferrate (III) functionalized agricultural residue-walnut shell.

PubMed

Ding, Dahu; Lei, Zhongfang; Yang, Yingnan; Feng, Chuanping; Zhang, Zhenya

2014-04-15

A novel nickel (II) hexacyanoferrate (III) functionalized agricultural residue-walnut shell (Ni(II)HCF(III)-WS) was developed to selectively remove cesium ion (Cs(+)) from aqueous solutions. This paper showed the first integral study on Cs(+) removal behavior and waste reduction analysis by using biomass adsorption material. The results indicated that the removal process was rapid and reached saturation within 2h. As a special characteristic of Ni(II)HCF(III)-WS, acidic condition was preferred for Cs(+) removal, which was useful for extending the application scope of the prepared biomass material in treating acidic radioactive liquid waste. The newly developed Ni(II)HCF(III)-WS could selectively remove Cs(+) though the coexisting ions (Na(+) and K(+) in this study) exhibited negative effects. In addition, approximately 99.8% (in volume) of the liquid waste was reduced by using Ni(II)HCF(III)-WS and furthermore 91.9% (in volume) of the spent biomass material (Cs-Ni(II)HCF(III)-WS) was reduced after incineration (at 500°C for 2h). Due to its relatively high distribution coefficient and significant volume reduction, Ni(II)HCF(III)-WS is expected to be a promising material for Cs(+) removal in practice. Copyright © 2014 Elsevier B.V. All rights reserved.

Infinite dilution partial molar volumes of platinum(II) 2,4-pentanedionate in supercritical carbon dioxide.

PubMed

Kong, Chang Yi; Siratori, Tomoya; Funazukuri, Toshitaka; Wang, Guosheng

2014-10-03

The effects of temperature and density on retention of platinum(II) 2,4-pentanedionate in supercritical fluid chromatography were investigated at temperatures of 308.15-343.15K and pressure range from 8 to 40MPa by the chromatographic impulse response method with curve fitting. The retention factors were utilized to derive the infinite dilution partial molar volumes of platinum(II) 2,4-pentanedionate in supercritical carbon dioxide. The determined partial molar volumes were small and positive at high pressures but exhibited very large and negative values in the highly compressible near critical region of carbon dioxide. Copyright © 2014 Elsevier B.V. All rights reserved.

Modeling loosely annotated images using both given and imagined annotations

NASA Astrophysics Data System (ADS)

Tang, Hong; Boujemaa, Nozha; Chen, Yunhao; Deng, Lei

2011-12-01

In this paper, we present an approach to learn latent semantic analysis models from loosely annotated images for automatic image annotation and indexing. The given annotation in training images is loose due to: 1. ambiguous correspondences between visual features and annotated keywords; 2. incomplete lists of annotated keywords. The second reason motivates us to enrich the incomplete annotation in a simple way before learning a topic model. In particular, some ``imagined'' keywords are poured into the incomplete annotation through measuring similarity between keywords in terms of their co-occurrence. Then, both given and imagined annotations are employed to learn probabilistic topic models for automatically annotating new images. We conduct experiments on two image databases (i.e., Corel and ESP) coupled with their loose annotations, and compare the proposed method with state-of-the-art discrete annotation methods. The proposed method improves word-driven probability latent semantic analysis (PLSA-words) up to a comparable performance with the best discrete annotation method, while a merit of PLSA-words is still kept, i.e., a wider semantic range.

Automatic quantification of mammary glands on non-contrast x-ray CT by using a novel segmentation approach

NASA Astrophysics Data System (ADS)

Zhou, Xiangrong; Kano, Takuya; Cai, Yunliang; Li, Shuo; Zhou, Xinxin; Hara, Takeshi; Yokoyama, Ryujiro; Fujita, Hiroshi

2016-03-01

This paper describes a brand new automatic segmentation method for quantifying volume and density of mammary gland regions on non-contrast CT images. The proposed method uses two processing steps: (1) breast region localization, and (2) breast region decomposition to accomplish a robust mammary gland segmentation task on CT images. The first step detects two minimum bounding boxes of left and right breast regions, respectively, based on a machine-learning approach that adapts to a large variance of the breast appearances on different age levels. The second step divides the whole breast region in each side into mammary gland, fat tissue, and other regions by using spectral clustering technique that focuses on intra-region similarities of each patient and aims to overcome the image variance caused by different scan-parameters. The whole approach is designed as a simple structure with very minimum number of parameters to gain a superior robustness and computational efficiency for real clinical setting. We applied this approach to a dataset of 300 CT scans, which are sampled with the equal number from 30 to 50 years-old-women. Comparing to human annotations, the proposed approach can measure volume and quantify distributions of the CT numbers of mammary gland regions successfully. The experimental results demonstrated that the proposed approach achieves results consistent with manual annotations. Through our proposed framework, an efficient and effective low cost clinical screening scheme may be easily implemented to predict breast cancer risk, especially on those already acquired scans.

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

PubMed Central

Leroy, Philippe; Guilhot, Nicolas; Sakai, Hiroaki; Bernard, Aurélien; Choulet, Frédéric; Theil, Sébastien; Reboux, Sébastien; Amano, Naoki; Flutre, Timothée; Pelegrin, Céline; Ohyanagi, Hajime; Seidel, Michael; Giacomoni, Franck; Reichstadt, Mathieu; Alaux, Michael; Gicquello, Emmanuelle; Legeai, Fabrice; Cerutti, Lorenzo; Numa, Hisataka; Tanaka, Tsuyoshi; Mayer, Klaus; Itoh, Takeshi; Quesneville, Hadi; Feuillet, Catherine

2012-01-01

In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future. PMID:22645565

21 CFR 868.1760 - Volume plethysmograph.

Code of Federal Regulations, 2010 CFR

2010-04-01

...) Identification. A volume plethysmograph is an airtight box, in which a patient sits, that is used to determine the patient's lung volume changes. (b) Classification. Class II (performance standards). ...

The Clinical Teacher for Special Education. Final Report: Volume II; Evaluating the Model.

ERIC Educational Resources Information Center

Schwartz, Louis; Oseroff, Andrew

Effectiveness of the clinical teaching model (CTM) developed at Florida State University is documented in Volume II of the project's final report. Reviewed is literature related to teacher effectiveness and conceptual changes, conceptual models and instructional systems, and evaluation research in education. Research design and procedures are…

National Environmental Policy Act compliance guide. Volume II (reference book)

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

NONE

1994-09-01

This document (Volume II of the National Environmental Policy Act Compliance Guide) contains current copies of regulations and guidance from the Council on Environmental Quality, the Department of Energy, the Department of State, and the Environmental Protection Agency, related to compliance with the National Environmental Policy Act of 1969 (NEPA).

Retrofit of waste-to-energy facilities equipped with electrostatic precipitators. Volume II: Field and laboratory reports, Part 2 of 2

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

Rigo, H.G.; Chandler, A.J.

Volume II (part 2 of 2) of ''Retrofit of Waste-to-energy Facilities Equipped with Electrostatic Precipitators'' contains the field and laboratory reports, including: (1) field reports, (2) analytic laboratory reports, (3) chain of custody forms, and (4) TCLP laboratory reports.

Retrofit of waste-to-energy facilities equipped with electrostatic precipitators. Volume II: Field and Laboratory Reports, Part 1 of 2

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

Rigo, H.G.; Chandler, A.J.

1996-04-01

Volume II (part 1 of 2) of ''Retrofit of Waste-to-energy Facilities Equipped with Electrostatic Precipitators'' contains the documentation and raw data, including: (1) field reports, (2) analytic laboratory reports, (3) chain of custody forms, and (4) TCLP laboratory reports.

40 CFR 52.74 - Original identification of plan section.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Governor of Alaska on January 18, 1980 as follows: Volume II. Analysis of Problems, Control Actions Section... requirements of Air Quality Monitoring, 40 CFR part 58, subpart C, § 58.20, as follows: Volume II. Analysis of Problems, Control Actions Section V. Ambient Air Monitoring A. Purpose C. Air Monitoring Network E. Annual...

40 CFR 52.70 - Identification of plan.

Code of Federal Regulations, 2013 CFR

2013-07-01

... submitted by the Governor of Alaska on January 18, 1980 as follows: Volume II. Analysis of Problems, Control... requirements of Air Quality Monitoring, 40 CFR part 58, subpart C, § 58.20, as follows: Volume II. Analysis of Problems, Control Actions Section V. Ambient Air Monitoring A. Purpose C. Air Monitoring Network E. Annual...

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation

PubMed Central

Kruesi, William S; Core, Leighton J; Waters, Colin T; Lis, John T; Meyer, Barbara J

2013-01-01

The X-chromosome gene regulatory process called dosage compensation ensures that males (1X) and females (2X) express equal levels of X-chromosome transcripts. The mechanism in Caenorhabditis elegans has been elusive due to improperly annotated transcription start sites (TSSs). Here we define TSSs and the distribution of transcriptionally engaged RNA polymerase II (Pol II) genome-wide in wild-type and dosage-compensation-defective animals to dissect this regulatory mechanism. Our TSS-mapping strategy integrates GRO-seq, which tracks nascent transcription, with a new derivative of this method, called GRO-cap, which recovers nascent RNAs with 5′ caps prior to their removal by co-transcriptional processing. Our analyses reveal that promoter-proximal pausing is rare, unlike in other metazoans, and promoters are unexpectedly far upstream from the 5′ ends of mature mRNAs. We find that C. elegans equalizes X-chromosome expression between the sexes, to a level equivalent to autosomes, by reducing Pol II recruitment to promoters of hermaphrodite X-linked genes using a chromosome-restructuring condensin complex. DOI: http://dx.doi.org/10.7554/eLife.00808.001 PMID:23795297

EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

PubMed Central

Thibaud-Nissen, Françoise; Campbell, Matthew; Hamilton, John P; Zhu, Wei; Buell, C Robin

2007-01-01

Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation) is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging knowledge from a dispersed community of scientists is a demonstrated way of improving a genome annotation. This requires tools that facilitate 1) the submission of gene annotation to an annotation project, 2) the review of the submitted models by project annotators, and 3) the incorporation of the submitted models in the ongoing annotation effort. Results We have developed the Eukaryotic Community Annotation Package (EuCAP), an annotation tool, and have applied it to the rice genome. The primary level of curation by community annotators (CA) has been the annotation of gene families. Annotation can be submitted by email or through the EuCAP Web Tool. The CA models are aligned to the rice pseudomolecules and the coordinates of these alignments, along with functional annotation, are stored in the MySQL EuCAP Gene Model database. Web pages displaying the alignments of the CA models to the Osa1 Genome models are automatically generated from the EuCAP Gene Model database. The alignments are reviewed by the project annotators (PAs) in the context of experimental evidence. Upon approval by the PAs, the CA models, along with the corresponding functional annotations, are integrated into the Osa1 Genome Annotation. The CA annotations, grouped by family, are displayed on the Community Annotation pages of the project website , as well as in the Community Annotation track of the Genome Browser. Conclusion We have applied EuCAP to rice. As of July 2007, the structural and/or functional annotation of 1,094 genes representing 57 families have been deposited and integrated into the current gene set. All of the EuCAP components are open-source, thereby allowing the implementation of EuCAP for the annotation of other genomes. EuCAP is available at . PMID:17961238

The Different Volume Effects of Small-Bowel Toxicity During Pelvic Irradiation Between Gynecologic Patients With and Without Abdominal Surgery: A Prospective Study With Computed Tomography-Based Dosimetry

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

Huang, E.-Y.; Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Kaohsiung, Taiwan; School of Traditional Chinese Medicine, Chang Gung University College of Medicine, Kaohsiung, Taiwan

Purpose: To evaluate the effect of abdominal surgery on the volume effects of small-bowel toxicity during whole-pelvic irradiation in patients with gynecologic malignancies. Methods and Materials: From May 2003 through November 2006, 80 gynecologic patients without (Group I) or with (Group II) prior abdominal surgery were analyzed. We used a computed tomography (CT) planning system to measure the small-bowel volume and dosimetry. We acquired the range of small-bowel volume in 10% (V10) to 100% (V100) of dose, at 10% intervals. The onset and grade of diarrhea during whole-pelvic irradiation were recorded as small-bowel toxicity up to 39.6 Gy in 22more » fractions. Results: The volume effect of Grade 2-3 diarrhea existed from V10 to V100 in Group I patients and from V60 to V100 in Group II patients on univariate analyses. The V40 of Group I and the V100 of Group II achieved most statistical significance. The mean V40 was 281 {+-} 27 cm{sup 3} and 489 {+-} 34 cm{sup 3} (p < 0.001) in Group I patients with Grade 0-1 and Grade 2-3 diarrhea, respectively. The corresponding mean V100 of Group II patients was 56 {+-} 14 cm{sup 3} and 132 {+-} 19 cm{sup 3} (p = 0.003). Multivariate analyses revealed that V40 (p = 0.001) and V100 (p = 0.027) were independent factors for the development of Grade 2-3 diarrhea in Groups I and II, respectively. Conclusions: Gynecologic patients without and with abdominal surgery have different volume effects on small-bowel toxicity during whole-pelvic irradiation. Low-dose volume can be used as a predictive index of Grade 2 or greater diarrhea in patients without abdominal surgery. Full-dose volume is more important than low-dose volume for Grade 2 or greater diarrhea in patients with abdominal surgery.« less

Memory performance, global cerebral volumes and hippocampal subfield volumes in long-term survivors of Out-of-Hospital Cardiac Arrest.

PubMed

Ørbo, Marte C; Vangberg, Torgil R; Tande, Pål M; Anke, Audny; Aslaksen, Per M

2018-05-01

We explored the associations between global brain volumes, hippocampal subfield volumes and verbal memory performance in long-term survivors of out-of-hospital cardiac arrest (OHCA). Three months after OHCA, survivors and healthy, age-matched controls were assessed with cerebral MRI and the California Verbal Learning Test-II (CVLT-II). Volumetric brain segmentation was performed automatically by FreeSurfer. Twenty-six OHCA survivors who were living independently in regular homes at the time of assessment and 19 controls participated in the study. Thirteen of the survivors had been conscious upon arrival to the emergency department. The other 13 survivors had 0.5-7 days of inpatient coma before recovery. Memory was poorer in the OHCA group that had been comatose beyond initial hospital admission compared to both other groups. Total cortical volumes, total hippocampus volumes and several hippocampal subfield volumes were significantly smaller in the OHCA group comatose beyond initial hospital admission compared to controls. No significant differences between the OHCA group conscious upon emergency department arrival and the other two groups were found for brain volumes. No significant differences were observed between any groups for white matter or total subcortical volumes. In OHCA survivors with recovery from inpatient coma, the various CVLT-II trials were significantly, but differentially, correlated to total gray matter volume, cortical volume and the hippocampal subfield subiculum. In this small, single-site study, both hippocampal volume and cortical volume were smaller in good outcome OHCA survivors 3 months after resuscitation in comparison to healthy controls. Smaller cerebral volumes were correlated with poorer memory performance. Copyright © 2018 Elsevier B.V. All rights reserved.

Labeled carbon dioxide (C18O2): an indicator gas for phase II in expirograms.

PubMed

Schulz, Holger; Schulz, Anne; Eder, Gunter; Heyder, Joachim

2004-11-01

Carbon dioxide labeled with 18O (C18O2) was used as a tracer gas for single-breath measurements in six anesthetized, mechanically ventilated beagle dogs. C18O2 is taken up quasi-instantaneously in the gas-exchanging region of the lungs but much less so in the conducting airways. Its use allows a clear separation of phase II in an expirogram even from diseased individuals and excludes the influence of alveolar concentration differences. Phase II of a C18O2 expirogram mathematically corresponds to the cumulative distribution of bronchial pathways to be traversed completely in the course of exhalation. The derivative of this cumulative distribution with respect to respired volume was submitted to a power moment analysis to characterize volumetric mean (position), standard deviation (broadness), and skewness (asymmetry) of phase II. Position is an estimate of dead space volume, whereas broadness and skewness are measures of the range and asymmetry of functional airway pathway lengths. The effects of changing ventilatory patterns and of changes in airway size (via carbachol-induced bronchoconstriction) were studied. Increasing inspiratory or expiratory flow rates or tidal volume had only minor influence on position and shape of phase II. With the introduction of a postinspiratory breath hold, phase II was continually shifted toward the airway opening (maximum 45% at 16 s) and became steeper by up to 16%, whereas skewness showed a biphasic response with a moderate decrease at short breath holding and a significant increase at longer breath holds. Stepwise bronchoconstriction decreased position up to 45 +/- 2% and broadness of phase II up to 43 +/- 4%, whereas skewness was increased up to twofold at high-carbachol concentrations. Under all circumstances, position of phase II by power moment analysis and dead space volume by the Fowler technique agreed closely in our healthy dogs. Overall, power moment analysis provides a more comprehensive view on phase II of single-breath expirograms than conventional dead space volume determinations and may be useful for respiratory physiology studies as well as for the study of diseased lungs.

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

PubMed

Akhondi, Saber A; Klenner, Alexander G; Tyrchan, Christian; Manchala, Anil K; Boppana, Kiran; Lowe, Daniel; Zimmermann, Marc; Jagarlapudi, Sarma A R P; Sayle, Roger; Kors, Jan A; Muresan, Sorel

2014-01-01

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.

Annotated Chemical Patent Corpus: A Gold Standard for Text Mining

PubMed Central

Akhondi, Saber A.; Klenner, Alexander G.; Tyrchan, Christian; Manchala, Anil K.; Boppana, Kiran; Lowe, Daniel; Zimmermann, Marc; Jagarlapudi, Sarma A. R. P.; Sayle, Roger; Kors, Jan A.; Muresan, Sorel

2014-01-01

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. PMID:25268232

Guidance, Navigation and Control Digital Emulation Technology Laboratory. Volume 1. Part 2. Task 1: Digital Emulation Technology Laboratory

DTIC Science & Technology

1991-09-27

AD-A241 692 II I] II I11 ANNUAL REPORT VOLUME 1 PART 2 TASK 1: DIGITAL EMULATION TECHNOLOGY LABORATOIRY REPORT NO. AR-0142-91-001 September 27, 1991... DIGITAL EMULATION TECHNOLOGY LABORATORY Contract No. DASG60-89-C-0142 Sponsored By The United States Army ? trategic Defense Command COMPUTER...ANNUAL REPORT VOLUME 1 PART 2 TASK 1: DIGITAL EMULATION TECHNOLOGY LABORATORY September 27, 1991 Authors Thomas R. Collins and Stephen R. Wachtel

Prenatal Testosterone Exposure Decreases Aldosterone Production but Maintains Normal Plasma Volume and Increases Blood Pressure in Adult Female Rats.

PubMed

More, Amar S; Mishra, Jay S; Hankins, Gary D; Kumar, Sathish

2016-08-01

Plasma testosterone levels are elevated in pregnant women with preeclampsia and polycystic ovaries; their offspring are at increased risk for hypertension during adult life. We tested the hypothesis that prenatal testosterone exposure induces dysregulation of the renin-angiotensin-aldosterone system, which is known to play an important role in water and electrolyte balance and blood pressure regulation. Female rats (6 mo old) prenatally exposed to testosterone were examined for adrenal expression of steroidogenic genes, telemetric blood pressure, blood volume and Na(+) and K(+) levels, plasma aldosterone, angiotensin II and vasopressin levels, and vascular responses to angiotensin II and arg(8)-vasopressin. The levels of Cyp11b2 (aldosterone synthase), but not the other adrenal steroidogenic genes, were decreased in testosterone females. Accordingly, plasma aldosterone levels were lower in testosterone females. Plasma volume and serum and urine Na(+) and K(+) levels were not significantly different between control and testosterone females; however, prenatal testosterone exposure significantly increased plasma vasopressin and angiotensin II levels and arterial pressure in adult females. In testosterone females, mesenteric artery contractile responses to angiotensin II were significantly greater, while contractile responses to vasopressin were unaffected. Angiotensin II type-1 receptor expression was increased, while angiotensin II type-2 receptor was decreased in testosterone arteries. These results suggest that prenatal testosterone exposure downregulates adrenal Cyp11b2 expression, leading to decreased plasma aldosterone levels. Elevated angiotensin II and vasopressin levels along with enhanced vascular responsiveness to angiotensin II may serve as an underlying mechanism to maintain plasma volume and Na(+) and K(+) levels and mediate hypertension in adult testosterone females. © 2016 by the Society for the Study of Reproduction, Inc.

Evaluating Computational Gene Ontology Annotations.

PubMed

Škunca, Nives; Roberts, Richard J; Steffen, Martin

2017-01-01

Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computational annotations have broad coverage, but the quality of annotations may be variable, and therefore evaluating the quality of computational annotations is a critical concern.In this chapter, we provide an overview of strategies to evaluate the quality of computational annotations. First, we discuss why evaluating quality in this setting is not trivial. We highlight the various issues that threaten to bias the evaluation of computational annotations, most of which stem from the incompleteness of biological databases. Second, we discuss solutions that address these issues, for example, targeted selection of new experimental annotations and leveraging the existing experimental annotations.

HYDRA-II: A hydrothermal analysis computer code: Volume 2, User's manual

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

McCann, R.A.; Lowery, P.S.; Lessor, D.L.

1987-09-01

HYDRA-II is a hydrothermal computer code capable of three-dimensional analysis of coupled conduction, convection, and thermal radiation problems. This code is especially appropriate for simulating the steady-state performance of spent fuel storage systems. The code has been evaluated for this application for the US Department of Energy's Commercial Spent Fuel Management Program. HYDRA-II provides a finite-difference solution in cartesian coordinates to the equations governing the conservation of mass, momentum, and energy. A cylindrical coordinate system may also be used to enclose the cartesian coordinate system. This exterior coordinate system is useful for modeling cylindrical cask bodies. The difference equations formore » conservation of momentum incorporate directional porosities and permeabilities that are available to model solid structures whose dimensions may be smaller than the computational mesh. The equation for conservation of energy permits modeling of orthotropic physical properties and film resistances. Several automated methods are available to model radiation transfer within enclosures and from fuel rod to fuel rod. The documentation of HYDRA-II is presented in three separate volumes. Volume 1 - Equations and Numerics describes the basic differential equations, illustrates how the difference equations are formulated, and gives the solution procedures employed. This volume, Volume 2 - User's Manual, contains code flow charts, discusses the code structure, provides detailed instructions for preparing an input file, and illustrates the operation of the code by means of a sample problem. The final volume, Volume 3 - Verification/Validation Assessments, provides a comparison between the analytical solution and the numerical simulation for problems with a known solution. 6 refs.« less

BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

PubMed

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/ .

Representing annotation compositionality and provenance for the Semantic Web

PubMed Central

2013-01-01

Background Though the annotation of digital artifacts with metadata has a long history, the bulk of that work focuses on the association of single terms or concepts to single targets. As annotation efforts expand to capture more complex information, annotations will need to be able to refer to knowledge structures formally defined in terms of more atomic knowledge structures. Existing provenance efforts in the Semantic Web domain primarily focus on tracking provenance at the level of whole triples and do not provide enough detail to track how individual triple elements of annotations were derived from triple elements of other annotations. Results We present a task- and domain-independent ontological model for capturing annotations and their linkage to their denoted knowledge representations, which can be singular concepts or more complex sets of assertions. We have implemented this model as an extension of the Information Artifact Ontology in OWL and made it freely available, and we show how it can be integrated with several prominent annotation and provenance models. We present several application areas for the model, ranging from linguistic annotation of text to the annotation of disease-associations in genome sequences. Conclusions With this model, progressively more complex annotations can be composed from other annotations, and the provenance of compositional annotations can be represented at the annotation level or at the level of individual elements of the RDF triples composing the annotations. This in turn allows for progressively richer annotations to be constructed from previous annotation efforts, the precise provenance recording of which facilitates evidence-based inference and error tracking. PMID:24268021

BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models

PubMed Central

Bilgin, Cemal Cagatay; Fontenay, Gerald; Cheng, Qingsu; Chang, Hang; Han, Ju; Parvin, Bahram

2016-01-01

BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation. PMID:26978075

Tri-level study of the causes of traffic accidents, volume 2 : special analyses.

DOT National Transportation Integrated Search

1979-05-01

This final report is comprised of two volumes. Volume I provides causal result tabulations and related analyses. Volume II presents several special analysis reports dealing with driver vision knowledge, psychological make-up, etc. Human, environmenta...

21 CFR 868.1760 - Volume plethysmograph.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the patient's lung volume changes. (b) Classification. Class II (performance standards). ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Volume plethysmograph. 868.1760 Section 868.1760...) MEDICAL DEVICES ANESTHESIOLOGY DEVICES Diagnostic Devices § 868.1760 Volume plethysmograph. (a...

TRIM.FaTE Evaluation Report

EPA Pesticide Factsheets

The TRIM.FaTE Evaluation Report is composed of three volumes. Volume I presents conceptual, mechanistic, and structural complexity evaluations of various aspects of the model. Volumes II and III present performance evaluation.

A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC

PubMed Central

Clematide, Simon; Akhondi, Saber A; van Mulligen, Erik M; Rebholz-Schuhmann, Dietrich

2015-01-01

Objective To create a multilingual gold-standard corpus for biomedical concept recognition. Materials and methods We selected text units from different parallel corpora (Medline abstract titles, drug labels, biomedical patent claims) in English, French, German, Spanish, and Dutch. Three annotators per language independently annotated the biomedical concepts, based on a subset of the Unified Medical Language System and covering a wide range of semantic groups. To reduce the annotation workload, automatically generated preannotations were provided. Individual annotations were automatically harmonized and then adjudicated, and cross-language consistency checks were carried out to arrive at the final annotations. Results The number of final annotations was 5530. Inter-annotator agreement scores indicate good agreement (median F-score 0.79), and are similar to those between individual annotators and the gold standard. The automatically generated harmonized annotation set for each language performed equally well as the best annotator for that language. Discussion The use of automatic preannotations, harmonized annotations, and parallel corpora helped to keep the manual annotation efforts manageable. The inter-annotator agreement scores provide a reference standard for gauging the performance of automatic annotation techniques. Conclusion To our knowledge, this is the first gold-standard corpus for biomedical concept recognition in languages other than English. Other distinguishing features are the wide variety of semantic groups that are being covered, and the diversity of text genres that were annotated. PMID:25948699

World History. Volumes I and II. [Sahuarita High School Career Curriculum Project].

ERIC Educational Resources Information Center

Hoffman, Judy

Volumes I and II of a world history course, part of a high school career curriculum project, are outlined. Objectives are listed by course title. Course titles include: Early Communication - Languages and Writing; World History; Law and Order in Ancient Times; Early Transportation; Women in Ancient Times; Art and Literature in Ancient Times;…

Tokamak experimental power reactor conceptual design. Volume II

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

Not Available

1976-08-01

Volume II contains the following appendices: (1) summary of EPR design parameters, (2) impurity control, (3) plasma computational models, (4) structural support system, (5) materials considerations for the primary energy conversion system, (6) magnetics, (7) neutronics penetration analysis, (8) first wall stress analysis, (9) enrichment of isotopes of hydrogen by cryogenic distillation, and (10) noncircular plasma considerations. (MOW)

Field Operations and Enforcement Manual for Air Pollution Control. Volume II: Control Technology and General Source Inspection.

ERIC Educational Resources Information Center

Weisburd, Melvin I.

The Field Operations and Enforcement Manual for Air Pollution Control, Volume II, explains in detail the following: technology of source control, modification of operations, particulate control equipment, sulfur dioxide removal systems for power plants, and control equipment for gases and vapors; inspection procedures for general sources, fuel…

Rehabilitation Needs Assessment for Vocational Rehabilitation Agencies. Volume II. Needs Assessment Topics Identified in the Rehabilitation Act: Issues and Resources.

ERIC Educational Resources Information Center

Wisconsin Univ.-Stout, Menomonie. Stout Vocational Rehabilitation Inst.

This guide was developed to help Wisconsin agency assessment, evaluation, and planning personnel to develop a perspective on how needs assessment fits into their state's vocational rehabilitation program planning. Volume II provides state agency personnel with tools for conducting rehabilitation needs assessment. The first three chapters consider…

Acheii Bahane': Naaki Gone' Yiltsiligii II = Grandfather Stories: Volume II.

ERIC Educational Resources Information Center

Yellowhair, Marvin

At one time all Navaho stories were handed down from generation to generation by word of mouth. Some stories were recorded and then trnsalated into English. In the process of translation, the stories often times lost their meaning. To avoid this, the second volume of "Grandfather Stories," which were told by elders living in the vicinity…

A useful method for assessing differences of compensatory hypertrophy in the contralateral kidney before and after radical nephrectomy in patients with renal cell carcinoma: ellipsoid formula on computed tomography.

PubMed

Park, Bong Hee; Cho, Kang Jun; Kim, Jung Im; Bae, Sang Rak; Lee, Yong Seok; Kang, Sung Hak; Kim, Joon Chul; Han, Chang Hee

2018-02-01

To investigate the usefulness of the ellipsoid formula for assessing compensatory hypertrophy of the contralateral kidney on pre-operative and post-operative CT in renal cell carcinoma (RCC) patients. We retrospectively identified 389 patients who had radical nephrectomy for RCC between 2011  and 2015. Contrast-enhanced CT was performed within 3 months pre-operative and at 1 year post-operative. The kidney volumes were calculated from CT using the ellipsoid formula. We subdivided patients into three groups based on tumour size (I: ≤4 cm, II: 4-7 cm, III: >7 cm). Volumetric renal parameters were compared and multivariate analyses were performed to determine predictors associated with pre-operative  and post-operative compensatory hypertrophy. Kidney volume calculation using the ellipsoid  method took a median of 51 s. Group III had a significantly larger median pre-operative contralateral renal volume than Groups I and II (I:  140.4, II: 141.6, III: 166.7 ml, p < 0.05). However, the median ratio of post-operative contralateral renal volume change was significantly higher in Groups I and II than Group III (I: 0.36, II: 0.23, III: 0.12, p < 0.001). On multivariate analysis, tumour size revealed the strongest positive association with pre-operative contralateral kidney volume (partial regression coefficient: β = 30.8, >7 cm) and ratio of post-operative contralateral kidney volume change (β  = 0.214, I vs III; β = 0.168, II vs III). Kidney volume calculation for assessing pre- and post-operative compensatory hypertrophy of the contralateral kidney in RCC patients can be easily and rapidly performed from CT images using the ellipsoid formula. Advances in knowledge: The ellipsoid formula allows reliable method for assessing pre-operative and post-operative compensatory hypertrophy of the contralateral kidney in RCC.

Workflow and web application for annotating NCBI BioProject transcriptome data

PubMed Central

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

2017-01-01

Abstract 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. Database URL: http://www.ncbi.nlm.nih.gov/projects/physalis/ PMID:28605765

Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome

PubMed Central

2010-01-01

Background A goal of the Bovine Genome Database (BGD; http://BovineGenome.org) has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC) in the annotation and analysis of the bovine genome. We were faced with several challenges, including the need to maintain consistent quality despite diversity in annotation expertise in the research community, the need to maintain consistent data formats, and the need to minimize the potential duplication of annotation effort. With new sequencing technologies allowing many more eukaryotic genomes to be sequenced, the demand for collaborative annotation is likely to increase. Here we present our approach, challenges and solutions facilitating a large distributed annotation project. Results and Discussion BGD has provided annotation tools that supported 147 members of the BGSAC in contributing 3,871 gene models over a fifteen-week period, and these annotations have been integrated into the bovine Official Gene Set. Our approach has been to provide an annotation system, which includes a BLAST site, multiple genome browsers, an annotation portal, and the Apollo Annotation Editor configured to connect directly to our Chado database. In addition to implementing and integrating components of the annotation system, we have performed computational analyses to create gene evidence tracks and a consensus gene set, which can be viewed on individual gene pages at BGD. Conclusions We have provided annotation tools that alleviate challenges associated with distributed annotation. Our system provides a consistent set of data to all annotators and eliminates the need for annotators to format data. Involving the bovine research community in genome annotation has allowed us to leverage expertise in various areas of bovine biology to provide biological insight into the genome sequence. PMID:21092105

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

PubMed Central

2011-01-01

Background The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Results Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Conclusions Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework. PMID:21806842

Prediction of overall survival in stage II and III colon cancer beyond TNM system: a retrospective, pooled biomarker study.

PubMed

Dienstmann, R; Mason, M J; Sinicrope, F A; Phipps, A I; Tejpar, S; Nesbakken, A; Danielsen, S A; Sveen, A; Buchanan, D D; Clendenning, M; Rosty, C; Bot, B; Alberts, S R; Milburn Jessup, J; Lothe, R A; Delorenzi, M; Newcomb, P A; Sargent, D; Guinney, J

2017-05-01

TNM staging alone does not accurately predict outcome in colon cancer (CC) patients who may be eligible for adjuvant chemotherapy. It is unknown to what extent the molecular markers microsatellite instability (MSI) and mutations in BRAF or KRAS improve prognostic estimation in multivariable models that include detailed clinicopathological annotation. After imputation of missing at random data, a subset of patients accrued in phase 3 trials with adjuvant chemotherapy (n = 3016)-N0147 (NCT00079274) and PETACC3 (NCT00026273)-was aggregated to construct multivariable Cox models for 5-year overall survival that were subsequently validated internally in the remaining clinical trial samples (n = 1499), and also externally in different population cohorts of chemotherapy-treated (n = 949) or -untreated (n = 1080) CC patients, and an additional series without treatment annotation (n = 782). TNM staging, MSI and BRAFV600E mutation status remained independent prognostic factors in multivariable models across clinical trials cohorts and observational studies. Concordance indices increased from 0.61-0.68 in the TNM alone model to 0.63-0.71 in models with added molecular markers, 0.65-0.73 with clinicopathological features and 0.66-0.74 with all covariates. In validation cohorts with complete annotation, the integrated time-dependent AUC rose from 0.64 for the TNM alone model to 0.67 for models that included clinicopathological features, with or without molecular markers. In patient cohorts that received adjuvant chemotherapy, the relative proportion of variance explained (R2) by TNM, clinicopathological features and molecular markers was on an average 65%, 25% and 10%, respectively. Incorporation of MSI, BRAFV600E and KRAS mutation status to overall survival models with TNM staging improves the ability to precisely prognosticate in stage II and III CC patients, but only modestly increases prediction accuracy in multivariable models that include clinicopathological features, particularly in chemotherapy-treated patients. © The Author 2017. Published by Oxford University Press on behalf of the European Society for Medical Oncology.

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

PubMed

Katayama, Toshiaki; Wilkinson, Mark D; Vos, Rutger; Kawashima, Takeshi; Kawashima, Shuichi; Nakao, Mitsuteru; Yamamoto, Yasunori; Chun, Hong-Woo; Yamaguchi, Atsuko; Kawano, Shin; Aerts, Jan; Aoki-Kinoshita, Kiyoko F; Arakawa, Kazuharu; Aranda, Bruno; Bonnal, Raoul Jp; Fernández, José M; Fujisawa, Takatomo; Gordon, Paul Mk; Goto, Naohisa; Haider, Syed; Harris, Todd; Hatakeyama, Takashi; Ho, Isaac; Itoh, Masumi; Kasprzyk, Arek; Kido, Nobuhiro; Kim, Young-Joo; Kinjo, Akira R; Konishi, Fumikazu; Kovarskaya, Yulia; von Kuster, Greg; Labarga, Alberto; Limviphuvadh, Vachiranee; McCarthy, Luke; Nakamura, Yasukazu; Nam, Yunsun; Nishida, Kozo; Nishimura, Kunihiro; Nishizawa, Tatsuya; Ogishima, Soichi; Oinn, Tom; Okamoto, Shinobu; Okuda, Shujiro; Ono, Keiichiro; Oshita, Kazuki; Park, Keun-Joon; Putnam, Nicholas; Senger, Martin; Severin, Jessica; Shigemoto, Yasumasa; Sugawara, Hideaki; Taylor, James; Trelles, Oswaldo; Yamasaki, Chisato; Yamashita, Riu; Satoh, Noriyuki; Takagi, Toshihisa

2011-08-02

The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.

Improving integrative searching of systems chemical biology data using semantic annotation.

PubMed

Chen, Bin; Ding, Ying; Wild, David J

2012-03-08

Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

PubMed

Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

2011-06-20

One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

PubMed Central

2011-01-01

Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins. PMID:21689388

Building a comprehensive syntactic and semantic corpus of Chinese clinical texts.

PubMed

He, Bin; Dong, Bin; Guan, Yi; Yang, Jinfeng; Jiang, Zhipeng; Yu, Qiubin; Cheng, Jianyi; Qu, Chunyan

2017-05-01

To build a comprehensive corpus covering syntactic and semantic annotations of Chinese clinical texts with corresponding annotation guidelines and methods as well as to develop tools trained on the annotated corpus, which supplies baselines for research on Chinese texts in the clinical domain. An iterative annotation method was proposed to train annotators and to develop annotation guidelines. Then, by using annotation quality assurance measures, a comprehensive corpus was built, containing annotations of part-of-speech (POS) tags, syntactic tags, entities, assertions, and relations. Inter-annotator agreement (IAA) was calculated to evaluate the annotation quality and a Chinese clinical text processing and information extraction system (CCTPIES) was developed based on our annotated corpus. The syntactic corpus consists of 138 Chinese clinical documents with 47,426 tokens and 2612 full parsing trees, while the semantic corpus includes 992 documents that annotated 39,511 entities with their assertions and 7693 relations. IAA evaluation shows that this comprehensive corpus is of good quality, and the system modules are effective. The annotated corpus makes a considerable contribution to natural language processing (NLP) research into Chinese texts in the clinical domain. However, this corpus has a number of limitations. Some additional types of clinical text should be introduced to improve corpus coverage and active learning methods should be utilized to promote annotation efficiency. In this study, several annotation guidelines and an annotation method for Chinese clinical texts were proposed, and a comprehensive corpus with its NLP modules were constructed, providing a foundation for further study of applying NLP techniques to Chinese texts in the clinical domain. Copyright © 2017. Published by Elsevier Inc.

An Annotated Bibliography of MANPRINT-Related Assessments and Evaluations Conducted by the U.S. Army, 2nd Edition: 1953 to 2009. Volume 1- Index

DTIC Science & Technology

2010-02-01

System (ACABA) MA 1973 Armored Vest M1955 Body Armor- Armored Vest M1955 USMC M1955 Armored Vest and the Proposed Titanium Nylon Improved... Laser - MILES Multiple Integrated Laser Engagement System in an Operational Environment (MILES) MA 1980 SAW M249 Rifle- 5.56mm- Machine Gun- SAW M249...Weapon System MA 1993 MCF MCF Modular Causeway Ferry (MCF) MA 1993 MDS NBC- Decon- MDS Modular Decontamination System (MDS) MA 1993 MELIOS Laser

Building bridges between cellular and molecular structural biology.

PubMed

Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

2017-07-06

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

White Matter Volume Predicts Language Development in Congenital Heart Disease

PubMed Central

Rollins, Caitlin K.; Asaro, Lisa A.; Akhondi-Asl, Alireza; Kussman, Barry D.; Rivkin, Michael J.; Bellinger, David C.; Warfield, Simon K.; Wypij, David; Newburger, Jane W.; Soul, Janet S.

2016-01-01

Objective To determine whether brain volume is reduced at one year and whether these volumes are associated with neurodevelopment in biventricular congenital heart disease (CHD) repaired in infancy. Study design Infants with biventricular CHD (n = 48) underwent brain magnetic resonance imaging (MRI) and neurodevelopmental testing with the Bayley Scales of Infant Development-II (BSID-II) and the MacArthur-Bates Communicative Development Inventories (CDI) at one year. A multi-template based probabilistic segmentation algorithm was applied to volumetric MRI data. We compared volumes with those of 13 healthy control infants of comparable ages. In the CHD group, we measured Spearman correlations between neurodevelopmental outcomes and the residuals from linear regression of the volumes on corrected chronological age at MRI and sex. Results Compared with controls, CHD infant had reductions of 54 mL in total brain (P = 0.009), 40 mL in cerebral white matter (P < 0.001), and 1.2 mL in brainstem (P = 0.003) volumes. Within the CHD group, brain volumes were not correlated with BSID-II scores but did correlate positively with CDI language development. Conclusion Infants with biventricular CHD show total brain volume reductions at one year of age, driven by differences in cerebral white matter. White matter volume correlates with language development, but not broader developmental indices. These findings suggest that abnormalities in white matter development detected months after corrective heart surgery may contribute to language impairment. Trial registration ClinicalTrials.gov: NCT00006183 PMID:27837950

Hypertext Annotation: Effects of Presentation Formats and Learner Proficiency on Reading Comprehension and Vocabulary Learning in Foreign Languages

ERIC Educational Resources Information Center

Chen, I-Jung; Yen, Jung-Chuan

2013-01-01

This study extends current knowledge by exploring the effect of different annotation formats, namely in-text annotation, glossary annotation, and pop-up annotation, on hypertext reading comprehension in a foreign language and vocabulary acquisition across student proficiencies. User attitudes toward the annotation presentation were also…

An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB.

PubMed

Bell, Michael J; Gillespie, Colin S; Swan, Daniel; Lord, Phillip

2012-09-15

Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires expert knowledge and training. Given these issues and the exponential increase of data, many databases implement automated annotation pipelines in an attempt to avoid un-annotated entries. Both manual and automated annotations vary in quality between databases and annotators, making assessment of annotation reliability problematic for users. The community lacks a generic measure for determining annotation quality and correctness, which we look at addressing within this article. Specifically we investigate word reuse within bulk textual annotations and relate this to Zipf's Principle of Least Effort. We use the UniProt Knowledgebase (UniProtKB) as a case study to demonstrate this approach since it allows us to compare annotation change, both over time and between automated and manually curated annotations. By applying power-law distributions to word reuse in annotation, we show clear trends in UniProtKB over time, which are consistent with existing studies of quality on free text English. Further, we show a clear distinction between manual and automated analysis and investigate cohorts of protein records as they mature. These results suggest that this approach holds distinct promise as a mechanism for judging annotation quality. Source code is available at the authors website: http://homepages.cs.ncl.ac.uk/m.j.bell1/annotation. phillip.lord@newcastle.ac.uk.

A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC.

PubMed

Kors, Jan A; Clematide, Simon; Akhondi, Saber A; van Mulligen, Erik M; Rebholz-Schuhmann, Dietrich

2015-09-01

To create a multilingual gold-standard corpus for biomedical concept recognition. We selected text units from different parallel corpora (Medline abstract titles, drug labels, biomedical patent claims) in English, French, German, Spanish, and Dutch. Three annotators per language independently annotated the biomedical concepts, based on a subset of the Unified Medical Language System and covering a wide range of semantic groups. To reduce the annotation workload, automatically generated preannotations were provided. Individual annotations were automatically harmonized and then adjudicated, and cross-language consistency checks were carried out to arrive at the final annotations. The number of final annotations was 5530. Inter-annotator agreement scores indicate good agreement (median F-score 0.79), and are similar to those between individual annotators and the gold standard. The automatically generated harmonized annotation set for each language performed equally well as the best annotator for that language. The use of automatic preannotations, harmonized annotations, and parallel corpora helped to keep the manual annotation efforts manageable. The inter-annotator agreement scores provide a reference standard for gauging the performance of automatic annotation techniques. To our knowledge, this is the first gold-standard corpus for biomedical concept recognition in languages other than English. Other distinguishing features are the wide variety of semantic groups that are being covered, and the diversity of text genres that were annotated. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Quality of Computationally Inferred Gene Ontology Annotations

PubMed Central

Škunca, Nives; Altenhoff, Adrian; Dessimoz, Christophe

2012-01-01

Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation. PMID:22693439

OceanVideoLab: A Tool for Exploring Underwater Video

NASA Astrophysics Data System (ADS)

Ferrini, V. L.; Morton, J. J.; Wiener, C.

2016-02-01

Video imagery acquired with underwater vehicles is an essential tool for characterizing seafloor ecosystems and seafloor geology. It is a fundamental component of ocean exploration that facilitates real-time operations, augments multidisciplinary scientific research, and holds tremendous potential for public outreach and engagement. Acquiring, documenting, managing, preserving and providing access to large volumes of video acquired with underwater vehicles presents a variety of data stewardship challenges to the oceanographic community. As a result, only a fraction of underwater video content collected with research submersibles is documented, discoverable and/or viewable online. With more than 1 billion users, YouTube offers infrastructure that can be leveraged to help address some of the challenges associated with sharing underwater video with a broad global audience. Anyone can post content to YouTube, and some oceanographic organizations, such as the Schmidt Ocean Institute, have begun live-streaming video directly from underwater vehicles. OceanVideoLab (oceanvideolab.org) was developed to help improve access to underwater video through simple annotation, browse functionality, and integration with related environmental data. Any underwater video that is publicly accessible on YouTube can be registered with OceanVideoLab by simply providing a URL. It is strongly recommended that a navigational file also be supplied to enable geo-referencing of observations. Once a video is registered, it can be viewed and annotated using a simple user interface that integrates observations with vehicle navigation data if provided. This interface includes an interactive map and a list of previous annotations that allows users to jump to times of specific observations in the video. Future enhancements to OceanVideoLab will include the deployment of a search interface, the development of an application program interface (API) that will drive the search and enable querying of content by other systems/tools, the integration of related environmental data from complementary data systems (e.g. temperature, bathymetry), and the expansion of infrastructure to enable broad crowdsourcing of annotations.

OVAS: an open-source variant analysis suite with inheritance modelling.

PubMed

Mozere, Monika; Tekman, Mehmet; Kari, Jameela; Bockenhauer, Detlef; Kleta, Robert; Stanescu, Horia

2018-02-08

The advent of modern high-throughput genetics continually broadens the gap between the rising volume of sequencing data, and the tools required to process them. The need to pinpoint a small subset of functionally important variants has now shifted towards identifying the critical differences between normal variants and disease-causing ones. The ever-increasing reliance on cloud-based services for sequence analysis and the non-transparent methods they utilize has prompted the need for more in-situ services that can provide a safer and more accessible environment to process patient data, especially in circumstances where continuous internet usage is limited. To address these issues, we herein propose our standalone Open-source Variant Analysis Sequencing (OVAS) pipeline; consisting of three key stages of processing that pertain to the separate modes of annotation, filtering, and interpretation. Core annotation performs variant-mapping to gene-isoforms at the exon/intron level, append functional data pertaining the type of variant mutation, and determine hetero/homozygosity. An extensive inheritance-modelling module in conjunction with 11 other filtering components can be used in sequence ranging from single quality control to multi-file penetrance model specifics such as X-linked recessive or mosaicism. Depending on the type of interpretation required, additional annotation is performed to identify organ specificity through gene expression and protein domains. In the course of this paper we analysed an autosomal recessive case study. OVAS made effective use of the filtering modules to recapitulate the results of the study by identifying the prescribed compound-heterozygous disease pattern from exome-capture sequence input samples. OVAS is an offline open-source modular-driven analysis environment designed to annotate and extract useful variants from Variant Call Format (VCF) files, and process them under an inheritance context through a top-down filtering schema of swappable modules, run entirely off a live bootable medium and accessed locally through a web-browser.

Qcorp: an annotated classification corpus of Chinese health questions.

PubMed

Guo, Haihong; Na, Xu; Li, Jiao

2018-03-22

Health question-answering (QA) systems have become a typical application scenario of Artificial Intelligent (AI). An annotated question corpus is prerequisite for training machines to understand health information needs of users. Thus, we aimed to develop an annotated classification corpus of Chinese health questions (Qcorp) and make it openly accessible. We developed a two-layered classification schema and corresponding annotation rules on basis of our previous work. Using the schema, we annotated 5000 questions that were randomly selected from 5 Chinese health websites within 6 broad sections. 8 annotators participated in the annotation task, and the inter-annotator agreement was evaluated to ensure the corpus quality. Furthermore, the distribution and relationship of the annotated tags were measured by descriptive statistics and social network map. The questions were annotated using 7101 tags that covers 29 topic categories in the two-layered schema. In our released corpus, the distribution of questions on the top-layered categories was treatment of 64.22%, diagnosis of 37.14%, epidemiology of 14.96%, healthy lifestyle of 10.38%, and health provider choice of 4.54% respectively. Both the annotated health questions and annotation schema were openly accessible on the Qcorp website. Users can download the annotated Chinese questions in CSV, XML, and HTML format. We developed a Chinese health question corpus including 5000 manually annotated questions. It is openly accessible and would contribute to the intelligent health QA system development.

A novel vaporization-enucleation technique for benign prostate hyperplasia using 120-W HPS GreenLight™ laser: Seoul technique II in comparison with vaporization and previously reported modified vaporization-resection technique.

PubMed

Yoo, Sangjun; Park, Juhyun; Cho, Sung Yong; Cho, Min Chul; Jeong, Hyeon; Son, Hwancheol

2017-12-01

We developed a novel vaporization-enucleation technique (Seoul II), which consists of vaporization-enucleation of the prostate using 120-W HPS GreenLight laser, and enucleated prostate resection using bipolar devices for tissue removal. We compared the outcomes of the Seoul II with vaporization and a previously reported modified vaporization-resection technique (Seoul I). Among patients with benign prostate hyperplasia who underwent transurethral surgery using GreenLight laser at our institute, 347 patients with prostate volume ≥ 40 ml were included. The impact of surgical techniques on efficacy and postoperative functional outcomes was compared. No difference was found in baseline characteristics, although the prostate volume was marginally greater in Seoul II (p = 0.051). Prostate volume reduction per operation time (p < 0.001) and lasing time (p = 0.016) were greater in Seoul II. At postoperative 12 months, the International Prostate Symptom Score (I-PSS) was lower (p = 0.011), and the decrement in I-PSS was greater in Seoul II (p = 0.001) than other techniques. In multivariate analysis, postoperative 12-month I-PSS for Seoul II was significantly superior to vaporization (p < 0.001), although it was similar to Seoul I. The maintenance of immediate postoperative I-PSS decrement, until postoperative 12 months was superior in Seoul II compared with vaporization (p = 0.014) and Seoul I (p = 0.048). Seoul II showed improved efficacy and voiding functional maintenance over postoperative 12 months in patients with prostate volume ≥ 40 ml compared with vaporization and Seoul I. This technique could be easily accepted by clinicians who are familiar with GreenLight lasers and add flexibility to surgery without additional equipment.

Healthy People 2010: Conference Edition, Volume I [and] Volume II.

ERIC Educational Resources Information Center

Department of Health and Human Services, Washington, DC.

This document contains the two volumes of the Conference Edition of Healthy People 2010, a comprehensive, nationwide health promotion and disease prevention agenda. The first section of Volume I, "Healthy People 2010: Understanding and Improving Health," includes "Introduction,""Leading Health Indicators," and…

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

PubMed

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 .

Intrasystem Electromagnetic Compatibility Analysis Program. Volume 2. User’s Manual Usage Section

DTIC Science & Technology

1974-12-01

AD-A008 527 INTRASYSTEM ELECTROMAGNETIC COMPATI- BILITY ANALYSIS PROGRAM. VOLUME II.USER’S MANUAL USAGE SECTION J. L. Bogdanor , et al McDonnell...NUMBERVolume II - User’s Manual Usage Section None 7. AUTHOR(&) 8. CONTRACT OR GRANT NUMBER(s) J.L. Bogdanor F30602-72-C-0277 R.A. Pearlman M.D. Siegel

Annotation Graphs: A Graph-Based Visualization for Meta-Analysis of Data Based on User-Authored Annotations.

PubMed

Zhao, Jian; Glueck, Michael; Breslav, Simon; Chevalier, Fanny; Khan, Azam

2017-01-01

User-authored annotations of data can support analysts in the activity of hypothesis generation and sensemaking, where it is not only critical to document key observations, but also to communicate insights between analysts. We present annotation graphs, a dynamic graph visualization that enables meta-analysis of data based on user-authored annotations. The annotation graph topology encodes annotation semantics, which describe the content of and relations between data selections, comments, and tags. We present a mixed-initiative approach to graph layout that integrates an analyst's manual manipulations with an automatic method based on similarity inferred from the annotation semantics. Various visual graph layout styles reveal different perspectives on the annotation semantics. Annotation graphs are implemented within C8, a system that supports authoring annotations during exploratory analysis of a dataset. We apply principles of Exploratory Sequential Data Analysis (ESDA) in designing C8, and further link these to an existing task typology in the visualization literature. We develop and evaluate the system through an iterative user-centered design process with three experts, situated in the domain of analyzing HCI experiment data. The results suggest that annotation graphs are effective as a method of visually extending user-authored annotations to data meta-analysis for discovery and organization of ideas.

Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts

PubMed Central

Lu, Zhiyong

2012-01-01

Today’s biomedical research has become heavily dependent on access to the biological knowledge encoded in expert curated biological databases. As the volume of biological literature grows rapidly, it becomes increasingly difficult for biocurators to keep up with the literature because manual curation is an expensive and time-consuming endeavour. Past research has suggested that computer-assisted curation can improve efficiency, but few text-mining systems have been formally evaluated in this regard. Through participation in the interactive text-mining track of the BioCreative 2012 workshop, we developed PubTator, a PubMed-like system that assists with two specific human curation tasks: document triage and bioconcept annotation. On the basis of evaluation results from two external user groups, we find that the accuracy of PubTator-assisted curation is comparable with that of manual curation and that PubTator can significantly increase human curatorial speed. These encouraging findings warrant further investigation with a larger number of publications to be annotated. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/ PMID:23160414

Automatic cerebrospinal fluid segmentation in non-contrast CT images using a 3D convolutional network

NASA Astrophysics Data System (ADS)

Patel, Ajay; van de Leemput, Sil C.; Prokop, Mathias; van Ginneken, Bram; Manniesing, Rashindra

2017-03-01

Segmentation of anatomical structures is fundamental in the development of computer aided diagnosis systems for cerebral pathologies. Manual annotations are laborious, time consuming and subject to human error and observer variability. Accurate quantification of cerebrospinal fluid (CSF) can be employed as a morphometric measure for diagnosis and patient outcome prediction. However, segmenting CSF in non-contrast CT images is complicated by low soft tissue contrast and image noise. In this paper we propose a state-of-the-art method using a multi-scale three-dimensional (3D) fully convolutional neural network (CNN) to automatically segment all CSF within the cranial cavity. The method is trained on a small dataset comprised of four manually annotated cerebral CT images. Quantitative evaluation of a separate test dataset of four images shows a mean Dice similarity coefficient of 0.87 +/- 0.01 and mean absolute volume difference of 4.77 +/- 2.70 %. The average prediction time was 68 seconds. Our method allows for fast and fully automated 3D segmentation of cerebral CSF in non-contrast CT, and shows promising results despite a limited amount of training data.

WormBase 2016: expanding to enable helminth genomic research.

PubMed

Howe, Kevin L; Bolt, Bruce J; Cain, Scott; Chan, Juancarlos; Chen, Wen J; Davis, Paul; Done, James; Down, Thomas; Gao, Sibyl; Grove, Christian; Harris, Todd W; Kishore, Ranjana; Lee, Raymond; Lomax, Jane; Li, Yuling; Muller, Hans-Michael; Nakamura, Cecilia; Nuin, Paulo; Paulini, Michael; Raciti, Daniela; Schindelman, Gary; Stanley, Eleanor; Tuli, Mary Ann; Van Auken, Kimberly; Wang, Daniel; Wang, Xiaodong; Williams, Gary; Wright, Adam; Yook, Karen; Berriman, Matthew; Kersey, Paul; Schedl, Tim; Stein, Lincoln; Sternberg, Paul W

2016-01-04

WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

MIPS: a database for genomes and protein sequences.

PubMed Central

Mewes, H W; Heumann, K; Kaps, A; Mayer, K; Pfeiffer, F; Stocker, S; Frishman, D

1999-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried near Munich, Germany, develops and maintains genome oriented databases. It is commonplace that the amount of sequence data available increases rapidly, but not the capacity of qualified manual annotation at the sequence databases. Therefore, our strategy aims to cope with the data stream by the comprehensive application of analysis tools to sequences of complete genomes, the systematic classification of protein sequences and the active support of sequence analysis and functional genomics projects. This report describes the systematic and up-to-date analysis of genomes (PEDANT), a comprehensive database of the yeast genome (MYGD), a database reflecting the progress in sequencing the Arabidopsis thaliana genome (MATD), the database of assembled, annotated human EST clusters (MEST), and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). MIPS provides access through its WWW server (http://www.mips.biochem.mpg.de) to a spectrum of generic databases, including the above mentioned as well as a database of protein families (PROTFAM), the MITOP database, and the all-against-all FASTA database. PMID:9847138

Ensembl BioMarts: a hub for data retrieval across taxonomic space.

PubMed

Kinsella, Rhoda J; Kähäri, Andreas; Haider, Syed; Zamora, Jorge; Proctor, Glenn; Spudich, Giulietta; Almeida-King, Jeff; Staines, Daniel; Derwent, Paul; Kerhornou, Arnaud; Kersey, Paul; Flicek, Paul

2011-01-01

For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/.

Chemical Laser Facility Study. Volume III. Cost Analysis.

DTIC Science & Technology

Chemical Laser Test Facility. The design criteria for the architectural and engineering design of the facility are presented in Volume I and the design requirements for the Laser Test System are presented in Volume II.

The RNA-binding complex ESCRT-II in Xenopus laevis eggs recognizes purine-rich sequences through its subunit Vps25.

PubMed

Emerman, Amy B; Blower, Michael

2018-06-14

RNA-binding proteins (RBPs) are critical regulators of gene expression. Recent studies have uncovered hundreds of mRNA-binding proteins that do not contain annotated RNA-binding domains and have well-established roles in other cellular processes. Investigation of these nonconventional RBPs is critical for revealing novel RNA-binding domains and may disclose connections between RNA regulation and other aspects of cell biology. Endosomal sorting complex required for transport II (ESCRT-II) is a nonconventional RNA-binding complex that has a canonical role in multivesicular body formation. ESCRT-II previously has been identified as an RNA-binding complex in Drosophila oocytes, but whether its RNA-binding properties extend beyond Drosophila is unknown. In this study, we found that the RNA-binding properties of ESCRT-II are conserved in Xenopus eggs, where ESCRT-II interacted with hundreds of mRNAs. Using a UV-crosslinking approach, we demonstrated that ESCRT-II binds directly to RNA through its subunit Vps25. UV-crosslinking and immunoprecipitation (CLIP)-Seq revealed that Vps25 specifically recognizes a polypurine (i.e. GA-rich) motif in RNA. Using purified components, we could reconstitute the selective Vps25-mediated binding of the polypurine motif in vitro. Our results provide insight into the mechanism by which ESCRT-II selectively binds to mRNAs and also suggest an unexpected link between endosome biology and RNA regulation. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Annotation of UAV surveillance video

NASA Astrophysics Data System (ADS)

Howlett, Todd; Robertson, Mark A.; Manthey, Dan; Krol, John

2004-08-01

Significant progress toward the development of a video annotation capability is presented in this paper. Research and development of an object tracking algorithm applicable for UAV video is described. Object tracking is necessary for attaching the annotations to the objects of interest. A methodology and format is defined for encoding video annotations using the SMPTE Key-Length-Value encoding standard. This provides the following benefits: a non-destructive annotation, compliance with existing standards, video playback in systems that are not annotation enabled and support for a real-time implementation. A model real-time video annotation system is also presented, at a high level, using the MPEG-2 Transport Stream as the transmission medium. This work was accomplished to meet the Department of Defense"s (DoD"s) need for a video annotation capability. Current practices for creating annotated products are to capture a still image frame, annotate it using an Electric Light Table application, and then pass the annotated image on as a product. That is not adequate for reporting or downstream cueing. It is too slow and there is a severe loss of information. This paper describes a capability for annotating directly on the video.

compMS2Miner: An Automatable Metabolite Identification, Visualization, and Data-Sharing R Package for High-Resolution LC-MS Data Sets.

PubMed

Edmands, William M B; Petrick, Lauren; Barupal, Dinesh K; Scalbert, Augustin; Wilson, Mark J; Wickliffe, Jeffrey K; Rappaport, Stephen M

2017-04-04

A long-standing challenge of untargeted metabolomic profiling by ultrahigh-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) is efficient transition from unknown mass spectral features to confident metabolite annotations. The compMS 2 Miner (Comprehensive MS 2 Miner) package was developed in the R language to facilitate rapid, comprehensive feature annotation using a peak-picker-output and MS 2 data files as inputs. The number of MS 2 spectra that can be collected during a metabolomic profiling experiment far outweigh the amount of time required for pain-staking manual interpretation; therefore, a degree of software workflow autonomy is required for broad-scale metabolite annotation. CompMS 2 Miner integrates many useful tools in a single workflow for metabolite annotation and also provides a means to overview the MS 2 data with a Web application GUI compMS 2 Explorer (Comprehensive MS 2 Explorer) that also facilitates data-sharing and transparency. The automatable compMS 2 Miner workflow consists of the following steps: (i) matching unknown MS 1 features to precursor MS 2 scans, (ii) filtration of spectral noise (dynamic noise filter), (iii) generation of composite mass spectra by multiple similar spectrum signal summation and redundant/contaminant spectra removal, (iv) interpretation of possible fragment ion substructure using an internal database, (v) annotation of unknowns with chemical and spectral databases with prediction of mammalian biotransformation metabolites, wrapper functions for in silico fragmentation software, nearest neighbor chemical similarity scoring, random forest based retention time prediction, text-mining based false positive removal/true positive ranking, chemical taxonomic prediction and differential evolution based global annotation score optimization, and (vi) network graph visualizations, data curation, and sharing are made possible via the compMS 2 Explorer application. Metabolite identities and comments can also be recorded using an interactive table within compMS 2 Explorer. The utility of the package is illustrated with a data set of blood serum samples from 7 diet induced obese (DIO) and 7 nonobese (NO) C57BL/6J mice, which were also treated with an antibiotic (streptomycin) to knockdown the gut microbiota. The results of fully autonomous and objective usage of compMS 2 Miner are presented here. All automatically annotated spectra output by the workflow are provided in the Supporting Information and can alternatively be explored as publically available compMS 2 Explorer applications for both positive and negative modes ( https://wmbedmands.shinyapps.io/compMS2_mouseSera_POS and https://wmbedmands.shinyapps.io/compMS2_mouseSera_NEG ). The workflow provided rapid annotation of a diversity of endogenous and gut microbially derived metabolites affected by both diet and antibiotic treatment, which conformed to previously published reports. Composite spectra (n = 173) were autonomously matched to entries of the Massbank of North America (MoNA) spectral repository. These experimental and virtual (lipidBlast) spectra corresponded to 29 common endogenous compound classes (e.g., 51 lysophosphatidylcholines spectra) and were then used to calculate the ranking capability of 7 individual scoring metrics. It was found that an average of the 7 individual scoring metrics provided the most effective weighted average ranking ability of 3 for the MoNA matched spectra in spite of potential risk of false positive annotations emerging from automation. Minor structural differences such as relative carbon-carbon double bond positions were found in several cases to affect the correct rank of the MoNA annotated metabolite. The latest release and an example workflow is available in the package vignette ( https://github.com/WMBEdmands/compMS2Miner ) and a version of the published application is available on the shinyapps.io site ( https://wmbedmands.shinyapps.io/compMS2Example ).

BioUSeR: a semantic-based tool for retrieving Life Science web resources driven by text-rich user requirements

PubMed Central

2013-01-01

Background Open metadata registries are a fundamental tool for researchers in the Life Sciences trying to locate resources. While most current registries assume that resources are annotated with well-structured metadata, evidence shows that most of the resource annotations simply consists of informal free text. This reality must be taken into account in order to develop effective techniques for resource discovery in Life Sciences. Results BioUSeR is a semantic-based tool aimed at retrieving Life Sciences resources described in free text. The retrieval process is driven by the user requirements, which consist of a target task and a set of facets of interest, both expressed in free text. BioUSeR is able to effectively exploit the available textual descriptions to find relevant resources by using semantic-aware techniques. Conclusions BioUSeR overcomes the limitations of the current registries thanks to: (i) rich specification of user information needs, (ii) use of semantics to manage textual descriptions, (iii) retrieval and ranking of resources based on user requirements. PMID:23635042

LMSD: LIPID MAPS structure database

PubMed Central

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

2007-01-01

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

Three-dimensional registration of intravascular optical coherence tomography and cryo-image volumes for microscopic-resolution validation.

PubMed

Prabhu, David; Mehanna, Emile; Gargesha, Madhusudhana; Brandt, Eric; Wen, Di; van Ditzhuijzen, Nienke S; Chamie, Daniel; Yamamoto, Hirosada; Fujino, Yusuke; Alian, Ali; Patel, Jaymin; Costa, Marco; Bezerra, Hiram G; Wilson, David L

2016-04-01

Evidence suggests high-resolution, high-contrast, [Formula: see text] intravascular optical coherence tomography (IVOCT) can distinguish plaque types, but further validation is needed, especially for automated plaque characterization. We developed experimental and three-dimensional (3-D) registration methods to provide validation of IVOCT pullback volumes using microscopic, color, and fluorescent cryo-image volumes with optional registered cryo-histology. A specialized registration method matched IVOCT pullback images acquired in the catheter reference frame to a true 3-D cryo-image volume. Briefly, an 11-parameter registration model including a polynomial virtual catheter was initialized within the cryo-image volume, and perpendicular images were extracted, mimicking IVOCT image acquisition. Virtual catheter parameters were optimized to maximize cryo and IVOCT lumen overlap. Multiple assessments suggested that the registration error was better than the [Formula: see text] spacing between IVOCT image frames. Tests on a digital synthetic phantom gave a registration error of only [Formula: see text] (signed distance). Visual assessment of randomly presented nearby frames suggested registration accuracy within 1 IVOCT frame interval ([Formula: see text]). This would eliminate potential misinterpretations confronted by the typical histological approaches to validation, with estimated 1-mm errors. The method can be used to create annotated datasets and automated plaque classification methods and can be extended to other intravascular imaging modalities.

Responsible science: Ensuring the integrity of the research process. Volume 2. Final report, 1989--1992

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

Not Available

In 1989, the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine initiated a major study to examine issues related to the responsible conduct of research. The findings and recommendations were published in March 1992 as: Responsible Science: Ensuring the Integrity of the Research Process, Vol. 1. Volume II of the report, this volume, includes the six commissioned background papers as well as selected institutional guidelines, reports, policies, and procedures. The institutional statements reprinted in Volume II have been selected to convey the diverse approaches for addressing different aspects of misconduct or integrity in sciencemore » within research institutions.« less

High Performance Schools Best Practices Manual. Volume I: Planning [and] Volume II: Design [and] Volume III: Criteria.

ERIC Educational Resources Information Center

Eley, Charles, Ed.

This three-volume manual, focusing on California's K-12 public schools, presents guidelines for establishing schools that are healthy, comfortable, energy efficient, resource efficient, water efficient, secure, adaptable, and easy to operate and maintain. The first volume describes why high performance schools are important, what components are…

'Tumour volume' as a predictor of survival after resection of non-small-cell lung cancer (NSCLC)

PubMed Central

Jefferson, M. F.; Pendleton, N.; Faragher, E. B.; Dixon, G. R.; Myskow, M. W.; Horan, M. A.

1996-01-01

Many factors have been individually related to outcome in populations of non-small-cell lung cancer (NSCLC) patients. Factors responsible for the outcome of an individual after surgical resection are poorly understood. We have examined the importance of 'tumour volume' in determining prognosis of patients following resection of NSCLC in a multivariate model. Cox's proportional hazard analysis was used to determine the relative prognostic significance of stage, patient age, gender, tumour cell-type, nodal score and estimated 'tumour volume' in 669 cases with NSCLC treated with surgical resection, of which 280 had died. All factors (except tumour cell-type, P = 0.33) were individually related to survival (P < 0.05). When examined together, survival time was significantly and independently related to 'tumour volume' and stage (P < 0.001), and other factors ceased to be significant. In cases with stage I or II tumours, risk of death was found to increase significantly with increasing estimated 'tumour volume' (23.8% relative increase in hazard to death per doubling of 'tumour volume', 95% confidence interval 13.2-35.2%, P < 0.001 stage I; P < 0.006 stage II). In cases with stage IIIa tumours this factor alone was the significant prognostic variable. In conclusion, an estimate of 'tumour volume' significantly improves prediction of prognosis for individual NSCLC patients with UICC stage I or II tumours. PMID:8695364

Environmental contaminants in food. Volume II-part a: working papers. I. Priority setting of toxic substances for guiding monitoring programs. II. Five case studies of environmental food contamination

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

Not Available

This volume contains working papers written for Office of Technology Assessment (OTA) to assist in preparation of the report Environmental Contaminants in Food. The contents include: (1) Priority setting of toxic substances for guiding monitoring programs; and (2) Five case studies of environmental food contamination.

TECHNICAL REPORT ON TECHNOLOGICALLY ENHANCED NATURALLY OCCURRING RADIOACTIVE MATERIALS FROM URANIUM MINING, VOLUME II: INVESTIGATION OF POTENTIAL HEALTH, GEOGRAPHIC, AND ENVIRONMENTAL ISSUES OF ABANDONED URANIUM MINES

EPA Science Inventory

Volume II investigates the potential radiogenic risks from abandoned uranium mines and evaluates which may pose the greatest hazards to members of the public and to the environment. The intent of this report is to identify who may be most likely to be exposed to wastes at small a...

FAA Rotorcraft Research, Engineering, and Development Bibliography, 1962-1988. Supplement

DTIC Science & Technology

1989-03-01

fires, the aircraft engine was the major fire origin for twin- and single- engine air - craft. Only in single- engine aircraft was the instrument panel a...Certification Issues. The topics of Operational Requirements, Procedures, Air - worthiness and Engineering Capabilities are discussed. Volume II presents the...Issues. The topics of Operational Requirements, Procedures, Air - worthiness and Engineering Capabilities are discussed. Volume II presents the operator

Gene Ontology annotations at SGD: new data sources and annotation methods

PubMed Central

Hong, Eurie L.; Balakrishnan, Rama; Dong, Qing; Christie, Karen R.; Park, Julie; Binkley, Gail; Costanzo, Maria C.; Dwight, Selina S.; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin C.; Krieger, Cynthia J.; Livstone, Michael S.; Miyasato, Stuart R.; Nash, Robert S.; Oughtred, Rose; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Zhu, Kathy K.; Dolinski, Kara; Botstein, David; Cherry, J. Michael

2008-01-01

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current. PMID:17982175

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

DOE PAGES

Brettin, Thomas; Davis, James J.; Disz, Terry; ...

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 offersmore » 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.« less

40 CFR Appendix II to Subpart E - Sampling Tables

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 25 2011-07-01 2011-07-01 false Sampling Tables II Appendix II to Subpart E Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) NOISE ABATEMENT PROGRAMS... II to Subpart E—Sampling Tables Table 1—Model Year Production Volume of 50-99 Vehicles Cumulative...

40 CFR Appendix II to Subpart E - Sampling Tables

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Sampling Tables II Appendix II to Subpart E Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) NOISE ABATEMENT PROGRAMS... II to Subpart E—Sampling Tables Table 1—Model Year Production Volume of 50-99 Vehicles Cumulative...

Antimicrobial Exposure Assessment Task Force II (AEATF II) Volume 5: Governing Document for a Multi-Year Antimicrobial Chemical Exposure Monitoring Program (interim draft document)

EPA Pesticide Factsheets

Describes the overall scope of the AEATF II program, demonstrates the need for additional human exposure monitoring data and explains the proposed methodology for the exposure monitoring studies proposed for conduct by the AEATF II.

An Annotated and Federated Digital Library of Marine Animal Sounds

DTIC Science & Technology

2005-01-01

of the annotations and the relevant segment delimitation points and linkages to other relevant metadata fields; e) search engines that support the...annotators to add information to the same recording, and search engines that permit either all-annotator or specific-annotator searches. To our knowledge

Relations between brain volumes, neuropsychological assessment and parental questionnaire in prematurely born children.

PubMed

Lind, Annika; Haataja, Leena; Rautava, Liisi; Väliaho, Anniina; Lehtonen, Liisa; Lapinleimu, Helena; Parkkola, Riitta; Korkman, Marit

2010-05-01

The objective of this study is to assess the relationship between brain volumes at term equivalent age and neuropsychological functions at 5 years of age in very low birth weight (VLBW) children, and to compare the results from a neuropsychological assessment and a parental questionnaire at 5 years of age. The study group included a regional cohort of 97 VLBW children and a control group of 161 children born at term. At term equivalent age, brain magnetic resonance imaging (MRI) was performed on the VLBW children, and analysed for total and regional brain volumes. At 5 years of age, a psychologist assessed the neuropsychological performance with NEPSY II, and parents completed the Five to fifteen (FTF) questionnaire on development and behaviour. The results of the control group were used to give the age-specific reference values. No significant associations were found between the brain volumes and the NEPSY II domains. As for the FTF, significant associations were found between a smaller total brain tissue volume and poorer executive functions, between a smaller cerebellar volume and both poorer executive functions and motor skills, and, surprisingly, between a larger volume of brainstem and poorer language functions. Even after adjustment for total brain tissue volume, the two associations between the cerebellar volume and the FTF domains remained borderline significant (P = 0.05). The NEPSY II domains Executive Functioning, Language and Motor Skills were significantly associated with the corresponding FTF domains. In conclusion, altered brain volumes at term equivalent age appear to affect development still at 5 years of age. The FTF seems to be a good instrument when used in combination with other neuropsychological assessment.

Preintervention lesion remodelling affects operative mechanisms of balloon optimised directional coronary atherectomy procedures: a volumetric study with three dimensional intravascular ultrasound

PubMed Central

von Birgelen, C; Mintz, G; de Vrey, E A; Serruys, P; Kimura, T; Nobuyoshi, M; Popma, J; Leon, M; Erbel, R; de Feyter, P J

2000-01-01

AIMS—To classify atherosclerotic coronary lesions on the basis of adequate or inadequate compensatory vascular enlargement, and to examine changes in lumen, plaque, and vessel volumes during balloon optimised directional coronary atherectomy procedures in relation to the state of adaptive remodelling before the intervention.
DESIGN—29 lesion segments in 29 patients were examined with intravascular ultrasound before and after successful balloon optimised directional coronary atherectomy procedures, and a validated volumetric intravascular ultrasound analysis was performed off-line to assess the atherosclerotic lesion remodelling and changes in plaque and vessel volumes that occurred during the intervention. Based on the intravascular ultrasound data, lesions were classified according to whether there was inadequate (group I) or adequate (group II) compensatory enlargement.
RESULTS—There was no significant difference in patient and lesion characteristics between groups I and II (n = 10 and 19), including lesion length and details of the intervention. Quantitative coronary angiographic data were similar for both groups. However, plaque and vessel volumes were significantly smaller in group I than in II. In group I, 9 (4)% (mean (SD)) of the plaque volume was ablated, while in group II 16 (11)% was ablated (p = 0.01). This difference was reflected in a lower lumen volume gain in group I than in group II (46 (18) mm3 v 80 (49) mm3 (p < 0.02)).
CONCLUSIONS—Preintervention lesion remodelling has an impact on the operative mechanisms of balloon optimised directional coronary atherectomy procedures. Plaque ablation was found to be particularly low in lesions with inadequate compensatory vascular enlargement.


Keywords: intravascular ultrasound; ultrasonics; remodelling; coronary artery disease; atherectomy PMID:10648496

Prokaryotic Contig Annotation Pipeline Server: Web Application for a Prokaryotic Genome Annotation Pipeline Based on the Shiny App Package.

PubMed

Park, Byeonghyeok; Baek, Min-Jeong; Min, Byoungnam; Choi, In-Geol

2017-09-01

Genome annotation is a primary step in genomic research. To establish a light and portable prokaryotic genome annotation pipeline for use in individual laboratories, we developed a Shiny app package designated as "P-CAPS" (Prokaryotic Contig Annotation Pipeline Server). The package is composed of R and Python scripts that integrate publicly available annotation programs into a server application. P-CAPS is not only a browser-based interactive application but also a distributable Shiny app package that can be installed on any personal computer. The final annotation is provided in various standard formats and is summarized in an R markdown document. Annotation can be visualized and examined with a public genome browser. A benchmark test showed that the annotation quality and completeness of P-CAPS were reliable and compatible with those of currently available public pipelines.

Computer systems for annotation of single molecule fragments

DOEpatents

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.

A guide to best practices for Gene Ontology (GO) manual annotation

PubMed Central

Balakrishnan, Rama; Harris, Midori A.; Huntley, Rachael; Van Auken, Kimberly; Cherry, J. Michael

2013-01-01

The Gene Ontology Consortium (GOC) is a community-based bioinformatics project that classifies gene product function through the use of structured controlled vocabularies. A fundamental application of the Gene Ontology (GO) is in the creation of gene product annotations, evidence-based associations between GO definitions and experimental or sequence-based analysis. Currently, the GOC disseminates 126 million annotations covering >374 000 species including all the kingdoms of life. This number includes two classes of GO annotations: those created manually by experienced biocurators reviewing the literature or by examination of biological data (1.1 million annotations covering 2226 species) and those generated computationally via automated methods. As manual annotations are often used to propagate functional predictions between related proteins within and between genomes, it is critical to provide accurate consistent manual annotations. Toward this goal, we present here the conventions defined by the GOC for the creation of manual annotation. This guide represents the best practices for manual annotation as established by the GOC project over the past 12 years. We hope this guide will encourage research communities to annotate gene products of their interest to enhance the corpus of GO annotations available to all. Database URL: http://www.geneontology.org PMID:23842463

GARNET--gene set analysis with exploration of annotation relations.

PubMed

Rho, Kyoohyoung; Kim, Bumjin; Jang, Youngjun; Lee, Sanghyun; Bae, Taejeong; Seo, Jihae; Seo, Chaehwa; Lee, Jihyun; Kang, Hyunjung; Yu, Ungsik; Kim, Sunghoon; Lee, Sanghyuk; Kim, Wan Kyu

2011-02-15

Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways or gene ontology (GO) terms. Major difficulties towards biological interpretation are integrating diverse types of annotation categories and exploring the relationships between annotation terms of similar information. GARNET (Gene Annotation Relationship NEtwork Tools) is an integrative platform for gene set analysis with many novel features. It includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, we have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations. GARNET (gene annotation relationship network tools) is an integrative platform for diverse types of gene set analysis, where complex relationships among gene annotations can be easily explored with an intuitive network visualization tool (http://garnet.isysbio.org/ or http://ercsb.ewha.ac.kr/garnet/).

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

Buttler, D J

The Java Metadata Facility is introduced by Java Specification Request (JSR) 175 [1], and incorporated into the Java language specification [2] in version 1.5 of the language. The specification allows annotations on Java program elements: classes, interfaces, methods, and fields. Annotations give programmers a uniform way to add metadata to program elements that can be used by code checkers, code generators, or other compile-time or runtime components. Annotations are defined by annotation types. These are defined the same way as interfaces, but with the symbol {at} preceding the interface keyword. There are additional restrictions on defining annotation types: (1) Theymore » cannot be generic; (2) They cannot extend other annotation types or interfaces; (3) Methods cannot have any parameters; (4) Methods cannot have type parameters; (5) Methods cannot throw exceptions; and (6) The return type of methods of an annotation type must be a primitive, a String, a Class, an annotation type, or an array, where the type of the array is restricted to one of the four allowed types. See [2] for additional restrictions and syntax. The methods of an annotation type define the elements that may be used to parameterize the annotation in code. Annotation types may have default values for any of its elements. For example, an annotation that specifies a defect report could initialize an element defining the defect outcome submitted. Annotations may also have zero elements. This could be used to indicate serializability for a class (as opposed to the current Serializability interface).« less

Smolt Monitoring Program, Part II, Volume II, Migrational Characteristics of Columbia Basin Salmon and Steelhead Trout, 1985 Annual Report.

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

Fish Passage Center

1986-02-01

Volume I of this report describes the results of travel time monitoring and other migrational characteristics of yearling and sub-yearling chinook salmon (Oncorhynchus tshawytscha), sockeye salmon (Oncorhynchus nerka), and steelhead trout (Salmo gairdneri). This volume presents the freeze brand data used in the analysis of travel time for Lower Granite, Rock Island, McNary, and John Day dams. Brand recoveries for Lower Monumental dam also are presented. Summary of data collection procedures and explanation of data listings are presented in conjunction with the mark recapture data.

A recursively formulated first-order semianalytic artificial satellite theory based on the generalized method of averaging. Volume 1: The generalized method of averaging applied to the artificial satellite problem

NASA Technical Reports Server (NTRS)

Mcclain, W. D.

1977-01-01

A recursively formulated, first-order, semianalytic artificial satellite theory, based on the generalized method of averaging is presented in two volumes. Volume I comprehensively discusses the theory of the generalized method of averaging applied to the artificial satellite problem. Volume II presents the explicit development in the nonsingular equinoctial elements of the first-order average equations of motion. The recursive algorithms used to evaluate the first-order averaged equations of motion are also presented in Volume II. This semianalytic theory is, in principle, valid for a term of arbitrary degree in the expansion of the third-body disturbing function (nonresonant cases only) and for a term of arbitrary degree and order in the expansion of the nonspherical gravitational potential function.

Simulation model for wind energy storage systems. Volume II. Operation manual. [SIMWEST code

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

Warren, A.W.; Edsinger, R.W.; Burroughs, J.D.

1977-08-01

The effort developed a comprehensive computer program for the modeling of wind energy/storage systems utilizing any combination of five types of storage (pumped hydro, battery, thermal, flywheel and pneumatic). An acronym for the program is SIMWEST (Simulation Model for Wind Energy Storage). The level of detail of SIMWEST is consistent with a role of evaluating the economic feasibility as well as the general performance of wind energy systems. The software package consists of two basic programs and a library of system, environmental, and load components. Volume II, the SIMWEST operation manual, describes the usage of the SIMWEST program, the designmore » of the library components, and a number of simple example simulations intended to familiarize the user with the program's operation. Volume II also contains a listing of each SIMWEST library subroutine.« less

Military Testing Association (Proceedings of the Annual Conference (27th, San Diego, California, October 21-25, 1985). Volume I and Volume II.

ERIC Educational Resources Information Center

Navy Personnel Research and Development Center, San Diego, CA.

The 169 paper and symposium presentations given during 57 sessions of the conference are provided in these two volumes. The first volume contains the keynote speech, which addressed military entrance processing command and its acquired immune deficiency snydrome testing program. Symposia topics in this volume include: (1) computerized diagnostic…

Learn Japanese--Elementary School Text, Volume III.

ERIC Educational Resources Information Center

Sato, Yaeko; And Others

This volume is the teacher's text for the first semester program on level two (fourth grade). See AL 001 718 for Volume I and ED 019 666 for Volume II. Text materials for the second level continue to introduce new structures systematically, according to the pupils' interest, ability, and rate of learning. Dialogs for level two, Volumes III and IV,…

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

PubMed

Feuermann, Marc; Gaudet, Pascale; Mi, Huaiyu; Lewis, Suzanna E; Thomas, Paul D

2016-01-01

We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This 'GO Phylogenetic Annotation' approach integrates GO annotations from evolutionarily related genes across ∼100 different organisms in the context of a gene family tree, in which curators build an explicit model of the evolution of gene functions. GO Phylogenetic Annotation models the gain and loss of functions in a gene family tree, which is used to infer the functions of uncharacterized (or incompletely characterized) gene products, even for human proteins that are relatively well studied. Here, we report our results from applying this paradigm to two well-characterized cellular processes, apoptosis and autophagy. This revealed several important observations with respect to GO annotations and how they can be used for function inference. Notably, we applied only a small fraction of the experimentally supported GO annotations to infer function in other family members. The majority of other annotations describe indirect effects, phenotypes or results from high throughput experiments. In addition, we show here how feedback from phylogenetic annotation leads to significant improvements in the PANTHER trees, the GO annotations and GO itself. Thus GO phylogenetic annotation both increases the quantity and improves the accuracy of the GO annotations provided to the research community. We expect these phylogenetically based annotations to be of broad use in gene enrichment analysis as well as other applications of GO annotations.Database URL: http://amigo.geneontology.org/amigo. © The Author(s) 2016. Published by Oxford University Press.

Paratransit Vehicle Test and Evaluation : Volume 2. Acceleration and Interior Measurement Tests.

DOT National Transportation Integrated Search

1978-06-01

A series of tests and evaluations of two prototype vehicles for paratransit were conducted. This volume (Volume II) presents the test procedure and results of the acceleration and interior measurement test series. The tests determined the acceleratio...

AnnotateGenomicRegions: a web application.

PubMed

Zammataro, Luca; DeMolfetta, Rita; Bucci, Gabriele; Ceol, Arnaud; Muller, Heiko

2014-01-01

Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software. Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user. The increasing spread of genomic technologies generates the need for a simple-to-use annotation tool for genomic regions that can be used by biologists and bioinformaticians alike. AnnotateGenomicRegions meets this demand. AnnotateGenomicRegions is an open-source web application that can be installed on any personal computer or institute server. AnnotateGenomicRegions is available at: http://cru.genomics.iit.it/AnnotateGenomicRegions.

AnnotateGenomicRegions: a web application

PubMed Central

2014-01-01

Background Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software. Results Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user. Conclusions The increasing spread of genomic technologies generates the need for a simple-to-use annotation tool for genomic regions that can be used by biologists and bioinformaticians alike. AnnotateGenomicRegions meets this demand. AnnotateGenomicRegions is an open-source web application that can be installed on any personal computer or institute server. AnnotateGenomicRegions is available at: http://cru.genomics.iit.it/AnnotateGenomicRegions. PMID:24564446

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

PubMed

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.

Evaluating Hierarchical Structure in Music Annotations

PubMed Central

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. PMID:28824514

ePIANNO: ePIgenomics ANNOtation tool.

PubMed

Liu, Chia-Hsin; Ho, Bing-Ching; Chen, Chun-Ling; Chang, Ya-Hsuan; Hsu, Yi-Chiung; Li, Yu-Cheng; Yuan, Shin-Sheng; Huang, Yi-Huan; Chang, Chi-Sheng; Li, Ker-Chau; Chen, Hsuan-Yu

2016-01-01

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.

BigQ: a NoSQL based framework to handle genomic variants in i2b2.

PubMed

Gabetta, Matteo; Limongelli, Ivan; Rizzo, Ettore; Riva, Alberto; Segagni, Daniele; Bellazzi, Riccardo

2015-12-29

Precision medicine requires the tight integration of clinical and molecular data. To this end, it is mandatory to define proper technological solutions able to manage the overwhelming amount of high throughput genomic data needed to test associations between genomic signatures and human phenotypes. The i2b2 Center (Informatics for Integrating Biology and the Bedside) has developed a widely internationally adopted framework to use existing clinical data for discovery research that can help the definition of precision medicine interventions when coupled with genetic data. i2b2 can be significantly advanced by designing efficient management solutions of Next Generation Sequencing data. We developed BigQ, an extension of the i2b2 framework, which integrates patient clinical phenotypes with genomic variant profiles generated by Next Generation Sequencing. A visual programming i2b2 plugin allows retrieving variants belonging to the patients in a cohort by applying filters on genomic variant annotations. We report an evaluation of the query performance of our system on more than 11 million variants, showing that the implemented solution scales linearly in terms of query time and disk space with the number of variants. In this paper we describe a new i2b2 web service composed of an efficient and scalable document-based database that manages annotations of genomic variants and of a visual programming plug-in designed to dynamically perform queries on clinical and genetic data. The system therefore allows managing the fast growing volume of genomic variants and can be used to integrate heterogeneous genomic annotations.

Workflow and web application for annotating NCBI BioProject transcriptome data.

PubMed

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.

Bilingual Preschools. Volume 2: Best Practices

ERIC Educational Resources Information Center

Kersten, Kristin, Ed.; Rohde, Andreas, Ed.; Schelletter, Christina, Ed.; Steinlen, Anja K., Ed.

2010-01-01

Drawing on data from eleven preschools in four European countries (Germany, Belgium, Sweden, and the UK), this edited volume explores the progress of preschool children learning English over a period of two years. This edited volume (Volume II) gives details on best practices in bilingual preschools as well as background and training on topics…

O*NET Final Technical Report. Volume I [and] Volume II [and] Volume III.

ERIC Educational Resources Information Center

Peterson, Norman G.; Mumford, Michael D.; Borman, Walter C.; Jeanneret, P. Richard; Fleishman, Edwin A.; Levin, Kerry Y.

This document contains the three volumes of the technical report for development of the prototype of the Occupational Information Network (O*NET), which is intended to replace the "Dictionary of Occupational Titles.""General Introduction" (Norman G. Peterson) presents an overview of O*NET's purpose, content, and structure.…

Pre-Employment Laboratory Training. General Agricultural Mechanics Volume II. Instructional Materials.

ERIC Educational Resources Information Center

Texas A and M Univ., College Station. Vocational Instructional Services.

This course outline, the second volume of a two-volume set, consists of lesson plans for pre-employment laboratory training in general agricultural mechanics. Covered in the eight lessons included in this volume are cold metal work, soldering, agricultural safety programs, farm shops, farm structures, farm and ranch electrification, soil and water…

General Revenue Sharing Data Study: Executive Summary. Volume I.

ERIC Educational Resources Information Center

Wilson, Reese C.; Bowditch, E. Francis, Jr.

The results of the General Revenue Sharing Data Study carried out by Stanford Research Institute for the Office of Revenue Sharing are reported in four volumes. This volume, Executive Summary, presents highlights excerpted from Volumes II, III, and IV. Emphasis is placed on those findings, conclusions, and recommendations that deserve special…

Annotations and the Collaborative Digital Library: Effects of an Aligned Annotation Interface on Student Argumentation and Reading Strategies

ERIC Educational Resources Information Center

Wolfe, Joanna

2008-01-01

Recent research on annotation interfaces provides provocative evidence that anchored, annotation-based discussion environments may lead to better conversations about a text. However, annotation interfaces raise complicated tradeoffs regarding screen real estate and positioning. It is argued that solving this screen real estate problem requires…

IMG ER: a system for microbial genome annotation expert review and curation.

PubMed

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

2009-09-01

A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.

HAMAP in 2013, new developments in the protein family classification and annotation system

PubMed Central

Pedruzzi, Ivo; Rivoire, Catherine; Auchincloss, Andrea H.; Coudert, Elisabeth; Keller, Guillaume; de Castro, Edouard; Baratin, Delphine; Cuche, Béatrice A.; Bougueleret, Lydie; Poux, Sylvain; Redaschi, Nicole; Xenarios, Ioannis; Bridge, Alan

2013-01-01

HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. HAMAP was originally developed to support the manual curation of UniProtKB/Swiss-Prot records describing microbial proteins. Here we describe new developments in HAMAP, including the extension of HAMAP to eukaryotic proteins, the use of HAMAP in the automated annotation of UniProtKB/TrEMBL, providing high-quality annotation for millions of protein sequences, and the future integration of HAMAP into a unified system for UniProtKB annotation, UniRule. HAMAP is continuously updated by expert curators with new family profiles and annotation rules as new protein families are characterized. The collection of HAMAP family classification profiles and annotation rules can be browsed and viewed on the HAMAP website, which also provides an interface to scan user sequences against HAMAP profiles. PMID:23193261

Bismuth-Based, Disposable Sensor for the Detection of Hydrogen Sulfide Gas.

PubMed

Rosolina, Samuel M; Carpenter, Thomas S; Xue, Zi-Ling

2016-02-02

A new sensor for the detection of hydrogen sulfide (H2S) gas has been developed to replace commercial lead(II) acetate-based test papers. The new sensor is a wet, porous, paper-like substrate coated with Bi(OH)3 or its alkaline derivatives at pH 11. In contrast to the neurotoxic lead(II) acetate, bismuth is used due to its nontoxic properties, as Bi(III) has been a reagent in medications such as Pepto-Bismol. The reaction between H2S gas and the current sensor produces a visible color change from white to yellow/brown, and the sensor responds to ≥ 30 ppb H2S in a total volume of 1.35 L of gas, a typical volume of human breath. The alkaline, wet coating helps the trapping of acidic H2S gas and its reaction with Bi(III) species, forming colored Bi2S3. The sensor is suitable for testing human bad breath and is at least 2 orders of magnitude more sensitive than a commercial H2S test paper based on Pb(II)(acetate)2. The small volume of 1.35-L H2S is important, as the commercial Pb(II)(acetate)2-based paper requires large volumes of 5 ppm H2S gas. The new sensor reported here is inexpensive, disposable, safe, and user-friendly. A simple, laboratory setup for generating small volumes of ppb-ppm of H2S gas is also reported.

Prediction of Supersonic Store Separation Characteristics Including Fuselage and Stores of Noncircular Cross Section, Volume IV. Appendices C and D, Details of Program II.

DTIC Science & Technology

1980-11-01

act in the sense displayed in Figure 17 of Volume II. All moments are about the store moment center COMMON /ONE/ DELTP(250),FN(250), PNLC (250),SWPPLE...linear loading pressure coefficient of Jth u-velocity panel FN(J) normal force divided by q for Jth u-velocity panel PNLC (J) panel chord through control

Teaching Standard English as a Second Dialect to Primary School Children in Hilo, Hawaii. Appendix B: Teacher's Guide and Lessons. Volume II of II Volumes. Final Report.

ERIC Educational Resources Information Center

Sugai, Elaine E.; Sugano, Miyoko

This document comprises the teacher's guide and lessons for teaching standard English to kindergarten through third grade children in Hilo, Hawaii. Sections are (1) Teacher's Guide, (2) Audio-Visual Aids, (3) Phonemic Symbol List, (4) Phonology Lesson Section, and (5) Structure Lesson Section. Appended are a short glossary of terms,…

Optimization and determination of Cd (II) in different environmental water samples with dispersive liquid-liquid microextraction preconcentration combined with inductively coupled plasma optical emission spectrometry.

PubMed

Salahinejad, Maryam; Aflaki, Fereydoon

2011-06-01

Dispersive liquid-liquid microextraction followed by inductively coupled plasma-optical emission spectrometry has been investigated for determination of Cd(II) ions in water samples. Ammonium pyrrolidine dithiocarbamate was used as chelating agent. Several factors influencing the microextraction efficiency of Cd (II) ions such as extracting and dispersing solvent type and their volumes, pH, sample volume, and salting effect were optimized. The optimization was performed both via one variable at a time, and central composite design methods and the optimum conditions were selected. Both optimization methods showed nearly the same results: sample size 5 mL; dispersive solvent ethanol; dispersive solvent volume 2 mL; extracting solvent chloroform; extracting solvent volume 200 [Formula: see text]L; pH and salt amount do not affect significantly the microextraction efficiency. The limits of detection and quantification were 0.8 and 2.5 ng L( - 1), respectively. The relative standard deviation for five replicate measurements of 0.50 mg L( - 1) of Cd (II) was 4.4%. The recoveries for the spiked real samples from tap, mineral, river, dam, and sea waters samples ranged from 92.2% to 104.5%.

Antimicrobial Exposure Assessment Task Force II (AEATF II) Volume 5: Governing Document for a Multi-Year Antimicrobial Chemical Exposure Monitoring Program (interim draft document with changes)

EPA Pesticide Factsheets

This document describes the overall scope of the AEATF II program, demonstrates the need for additional human exposure monitoring data and explains the proposed methodology for the exposure monitoring studies proposed for conduct by the AEATF II.

Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening.

PubMed

Olvera-García, Myrna; Sanchez-Flores, Alejandro; Quirasco Baruch, Maricarmen

2018-03-01

Enterococcus spp. are present in the native microbiota of many traditional fermented foods. Their ability to produce antibacterial compounds, mainly against Listeria monocytogenes, has raised interest recently. However, there is scarce information about their proteolytic and lipolytic potential, and their biotechnological application is currently limited because enterococcal strains have been related to nosocomial infections. In this work, next-generation sequencing and optimised bioinformatic pipelines were used to annotate the genomes of two Enterococcus strains-one E. faecium and one E. faecalis-isolated from the Mexican artisanal ripened Cotija cheese. A battery of genes involved in their proteolytic system was annotated. Genes coding for lipases, esterases and other enzymes whose final products contribute to cheese aroma and flavour were identified as well. As for the production of antibacterial compounds, several peptidoglycan hydrolase- and bacteriocin-coding genes were identified in both genomes experimentally and by bioinformatic analyses. E. faecalis showed resistance to aminoglycosides and E. faecium to aminoglycosides and macrolides, as predicted by the genome functional annotation. No pathogenicity islands were found in any of the strains, although traits such as the ability of biofilm formation and cell aggregation were observed. Finally, a comparative genomic analysis was able to discriminate between the food strains isolated and nosocomial strains. In summary, pathogenic strains are resistant to a wide range of antibiotics and contain virulence factors that cause host damage; in contrast, food strains display less antibiotic resistance, include genes that encode class II bacteriocins and express virulence factors associated with host colonisation rather than invasion.

Topology-function conservation in protein-protein interaction networks.

PubMed

Davis, Darren; Yaveroğlu, Ömer Nebil; Malod-Dognin, Noël; Stojmirovic, Aleksandar; Pržulj, Nataša

2015-05-15

Proteins underlay the functioning of a cell and the wiring of proteins in protein-protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species. To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms. © The Author 2015. Published by Oxford University Press.

Toward computational cumulative biology by combining models of biological datasets.

PubMed

Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

2014-01-01

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations-for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.