handwritten textual annotations: Topics by WorldWideScience.org

Impact of Basic Computerized Prescribing on Outpatient Medication Errors and Adverse Drug Events

Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale,...Full Text Available

2010-09-01

Incremental learning for recognizing handwritten characters using neural networks

Few data exist about the impact of computerized prescribing systems on outpatient medication errors (MEs) and adverse drug events (ADEs). We compared the rates of MEs and ADEs in handwritten sites versus...Full Text Available

2002-11-01

Problem-centric Organization and Visualization of Patient Imaging and Clinical Data

Artificial Neural Networks (ANNs) are parallel distributed processing machines. The unique characteristics of ANNs are: Fault tolerance, robustness, plasticity and generalization. These offer great potential in many AI applications such as character recognition. Handwritten character recognition is an intrinsically interesting problem, but the difficulties of this task are the many variations in the characters. A robust new incremental learning method, which combines supervised and unsupervised learning paradigms implemented by the Functional Link Net, is illustrated with experimental results. Clustering, based on unsupervised learning, classifies the input data into several categories. The supervised learning paradigm then further classifies the data in the clustered categories.

1989-01-01

Integrating Query of Relational and Textual Data in Clinical Databases: A Case Study

A patient’s electronic medical record contains a large amount of unstructured textual information. As patient records become increasingly dense owing to an aging population and increased occurrence...Full Text Available

2009-03-01

Semantic annotation of biosystematics literature without training examples

Objectives: The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS).Design:...Full Text Available

2003-01-01

British Library Electronic Table of Contents (United Kingdom)

This article presents an unsupervised algorithm for semantic annotation of morphological descriptions of whole organisms. The algorithm is able to annotate plain text descriptions with high accuracy at the clause level by exploiting the corpus itself. In other words, the algorithm does not need lexicons, syntactic parsers, training examples, or annotation templates. The evaluation on two real-life description collections in botany and paleontology shows that the algorithm has the following desirable features: (a) reduces/eliminates manual labor required to compile dictionaries and prepare source documents; (b) improves annotation coverage: the algorithm annotates what appears in documents and is not limited by predefined and often incomplete templates; (c) learns clean and reusable concept...

2010-01-01

The Anopheles gambiae glutathione transferase supergene family: annotation, phylogeny and expression profiles

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

BackgroundTwenty-eight genes putatively encoding cytosolic glutathione transferases have been identified in the Anopheles gambiae genome. We manually annotated these...Full Text Available

Simple high-throughput annotation pipeline (SHAP)

The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...Full Text Available

2003-10-01

British Library Electronic Table of Contents (United Kingdom)

Summary: SHAP (simple high-throughput annotation pipeline) is a lightweight and scalable sequence annotation pipeline capable of supporting research efforts that generate or utilize large volumes of DNA sequence data. The software provides Grid capable analysis, relational storage and Web-based full-text searching of annotation results. Implemented in Java, SHAP recognizes the limited resources of many smaller research groups. Availability: Source code is freely available under GPLv3 at External Link Not Shown. Contact: matt.demaere@unsw.edu.au; r.cavicchioli@unsw.edu.au

2011-01-01

Efficient higher-order derivatives of the hypergeometric function.

Space Shuttle Annotated Bibliography, CH14 - NASA's History Office

Various physics applications involve the computation of the standard hypergeometric function {sub 2}F{sub 1} and its derivatives. Because it is not an intrinsic in the common programming languages, automatic differentiation tools will either differentiate through the code that computes {sub 2}F{sub 1} if that code is available or require the user to provide a hand-written derivative code. We present options for the derivative computation in the context of an ionization problem and compare the approach implemented in the Diamant library to standard methods.

2008-01-01

Some proposed relations among the domains of behavior analysis

"Report of the Ad Hoc Subpanel on Reusable Launch Vehicle Technology. ... The author comments that the United State's space transportation system is ...

AN ANNOTATED BIBLIOGRAPHY OF ADULT LITERACY ...

The present article examines the nature of and relations among the domains of behavior analysis. It first proposes a set of annotated, descriptive criteria to aid in distinguishing the experimental...Full Text Available

2003-01-01

A Bookshelf in Public Health, Medical Care, and Allied Fields

... Stone, CR & Grover, CC Practice Readers ... Tolbert, M., Withers, S. & Watkins, HT, Good Workers All State Department of Education, Columbia, South ...

1954-09-30

Afterlife Conceptions in the Vedas

This bibliography of nonserial publications consists of 610 annotations. It is intended as a guide to the development of a collection for librarians and for health professionals in research and education....Full Text Available

1972-01-01

British Library Electronic Table of Contents (United Kingdom)

Abstract Continuity and change in ancient Indian afterlife conceptions are discussed in a broad overview of the most relevant Vedic texts (the Rig Veda, the Krishna Yajur Veda, the Atharva Veda, the Shatapatha Brahmana, the Jaiminiya Brahmana and the Upanishads). Despite the introduction of (or re-emphasis on) certain ideas, such as reincarnation and moksha (liberation from the cycle of death and rebirth), there is also continuity of a core set of conceptions from the earliest texts to the latest. Return-from-death narratives are also found in each textual strand, and are discussed separately.

2011-01-01

Ixodes scapularis tick serine proteinase inhibitor (serpin) gene family; annotation and transcriptional analysis

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

BackgroundSerine proteinase inhibitors (Serpins) are a large superfamily of structurally related, but functionally diverse proteins that control essential proteolytic pathways in...Full Text Available

Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus

BackgroundThe Gene Ontology (GO) is a well known controlled vocabulary describing the biological process, molecular function and cellular...Full Text Available

Environmental assessment of the Alaskan continental shelf. Final reports of principal investigators, Volume 15. Biological studies

Multiple discrete regions at 8q24 were recently shown to contain alleles that predispose to many cancers including prostate, breast, and colon. These regions are far from any annotated gene and their...Full Text Available

2009-08-01

Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration

The contents of the report include: Identification, documentation and delineation of coastal migratory bird habitat; and an annotated bibliography of literature on Alaska Water Birds.

1981-12-01

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CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

BackgroundThere is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming...Full Text Available

The program HAMILTON for the analytic solution of the equations of motion through fifth order

BackgroundThe implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce...Full Text Available

International Nuclear Information System (INIS)

HAMILTON is a computer code performing all algebraic operations necessary for an analytic determination of the power series of the Hamiltonian equations of motion in the electromagnetic fields with at least one plane of symmetry. It is written entirely in FORTRAN in order to achieve fast machine performance, a requirement which is essential due to the complexity of the equations of motion in higher orders. HAMILTON is considerably faster than common more versatile formula manipulators and uses noticeably less storage. Besides the mere solution of the equations of motion, HAMILTON also produces FORTRAN code compatible with the program COSY 5.0 allowing the computation of matrix elements of individual optical elements and their concatenation. The produced FORTRAN code is highly optimized and on average requires only 30% of the execution time of a handwritten comparable code. (orig.).

Literary Lives and a Literal Death: Yajnavalkya, Sakalya, and an Upaniṣadic Death Sentence

British Library Electronic Table of Contents (United Kingdom)

One of the most popular stories found in the Upani?ads centers around a debate between the ritualist and philosopher, Yajnavalkya, and a series of interlocutors about the nature of sacrifice, the self, and the cosmos. This story, from a textual-historical perspective, is unique in that the last interlocutor, Sakalya, is said to die by having his head shatter because he is unable to answer a question about the fundamental nature of immortality. In this paper, I analyze the interrelationship of these two main characters and argue that this relationship is one key to not only understanding the portrayal of these characters, but also the larger import of this debate about immortality. I provide an intratextual rationale for the head-shattering conclusion and discuss how character and d...

2011-01-01

Flue-gas desulfurization inspection and performance evaluation. Manual

Clustering Unstructured Data (Flat Files) - An Implementation in Text Mining Tool

The intent of this manual is to provide inspectors from Federal and state environmental agencies with information regarding the problems that plague lime/limestone slurry flue-gas desulfurization (FGD) systems that will aid them in their inspections and performance evaluations of these systems with respect to compliance with the emission standards that have evolved since the passage of the 1970 Clean Air Act. A unique feature of the manual is its structure as a tool, or working document, which will accompany the inspector on each plant inspection. Thus, the document is presented in user friendly fashion and tailored to provide practical information for its intended use--to assist in the systematic inspection of an FGD system to determine present and future compliance status. The approach entails the use of nomographs, checklists, matrices, simplified diagrams, cross-referencing, and indexing of textual information, and the presentation of important guidelines and ...

1985-10-01

PDBpaint, a visualization webservice to tag protein structures with sequence annotations

With the advancement of technology and reduced storage costs, individuals and organizations are tending towards the usage of electronic media for storing textual information and documents. It is time consuming for readers to retrieve relevant information from unstructured document collection. It is easier and less time consuming to find documents from a large collection when the collection is ordered or classified by group or category. The problem of finding best such grouping is still there. This paper discusses the implementation of k-Means clustering algorithm for clustering unstructured text documents that we implemented, beginning with the representation of unstructured text and reaching the resulting set of clusters. Based on the analysis of resulting clusters for a sample set of documents, we have also proposed a technique to represent documents that can further improve the clustering result.

2010-01-01

British Library Electronic Table of Contents (United Kingdom)

Summary: Protein features are often displayed along the linear sequence of amino acids that make up that protein, but in reality these features occupy a position in the folded proteins 3D space. Mapping sequence features to known or predicted protein structures is useful when trying to deduce the function of those features and when evaluating sequence or structural predictions. To facilitate this goal, we developed PDBpaint, a simple tool that displays protein sequence features gathered from bioinformatics resources on top of protein structures, which are displayed in an interactive window (using the Jmol Java viewer). PDBpaint can be used either with existing protein structures or with novel structures provided by the user. The current version of PDBpaint allows the visualization of annot...

2011-01-01

Knowledge Encapsulation Framework for Collaborative Social Modeling

Grouping Synonyms by Definitions

This paper describes the Knowledge Encapsulation Framework (KEF), a suite of tools to enable knowledge inputs (relevant, domain-specific facts) to modeling and simulation projects, as well as other domains that require effective collaborative workspaces for knowledge-based task. This framework can be used to capture evidence (e.g., trusted material such as journal articles and government reports), discover new evidence (covering both trusted and social media), enable discussions surrounding domain-specific topics and provide automatically generated semantic annotations for improved corpus investigation. The current KEF implementation is presented within a wiki environment, providing a simple but powerful collaborative space for team members to review, annotate, discuss and align evidence with their modeling frameworks. The novelty in this approach lies in the combination of automatically tagged and user-vetted resources, which increases user ...

2009-03-24

Automating Frame Analysis

We present a method for grouping the synonyms of a lemma according to its dictionary senses. The senses are defined by a large machine readable dictionary for French, the TLFi (Tr\\'esor de la langue fran\\c{c}aise informatis\\'e) and the synonyms are given by 5 synonym dictionaries (also for French). To evaluate the proposed method, we manually constructed a gold standard where for each (word, definition) pair and given the set of synonyms defined for that word by the 5 synonym dictionaries, 4 lexicographers specified the set of synonyms they judge adequate. While inter-annotator agreement ranges on that task from 67% to at best 88% depending on the annotator pair and on the synonym dictionary being considered, the automatic procedure we propose scores a precision of 67% and a recall of 71%. The proposed method is compared with related work namely, word sense disambiguation, synonym lexicon acquisition and WordNet construction.

2009-01-01

Law project adopted by the National Assembly at a first reading, after urgency declaration, of program relative to the sustainable management of radioactive materials and wastes; Projet de Loi adopte par l'assemblee nationale en premiere lecture, apres declaration d'urgence, de programme relatif a la gestion durable des matieres et des dechets radioactifs

Frame Analysis has come to play an increasingly stronger role in the study of social movements in Sociology and Political Science. While significant steps have been made in providing a theory of frames and framing, a systematic characterization of the frame concept is still largely lacking and there are no rec-ognized criteria and methods that can be used to identify and marshal frame evi-dence reliably and in a time and cost effective manner. Consequently, current Frame Analysis work is still too reliant on manual annotation and subjective inter-pretation. The goal of this paper is to present an approach to the representation, acquisition and analysis of frame evidence which leverages Content Analysis, In-formation Extraction and Semantic Search methods to provide a systematic treat-ment of a Frame Analysis and automate frame annotation.

2008-04-01

Draft Genome Sequence of Shewanella sp. Strain HN-41, Which Produces Arsenic-Sulfide Nanotubes.

This text presents the annotations of all different articles of the law text concerning the sustainable development of radioactive materials and wastes. (A.L.B.)

2006-04-15

Annotated bibliography of Accelerator Technology Division research and development, 1978-1985

The dissimilatory metal reducing bacterium Shewanella sp. strain HN-41 was first reported to produce novel photoactive As-S nanotubes via reduction of As(V) and S(2)O(3)(2-) under anaerobic conditions. Here we report the draft genome sequence and annotation of strain HN-41. PMID:21868804

2011-09-01

International Nuclear Information System (INIS)

A bibliography is presented of unclassified published and in-house technical material written by members of the Accelerator Technology Division, Los Alamos National Laboratory, since its inception in January, 1978. The author and subject concordances in this report provide cross-reference to detailed citations kept in a computer database and a microfilm file of the documents. The citations include an abstract and other notes, and can be searched for key words and phrases.

Annotated bibliography covering generation and use of evaluated cross section uncertainty files

Mining associations in text in the presence of background knowledge

Literature references related to definition, generation, and use of evaluated cross section uncertainty (variance-covariance) files are listed with comments intended primarily to guide the reader toward materials of immediate interest. Papers are also cited that cover covariance information for individual experiments and that relate to production and use of multigroup covariance matrices. Titles are divided among several major categories.

1983-03-01

Dynamic User-Defined Similarity Searching in Semi-Structured Text Retrieval

This paper describes the FACT system for knowledge discovery from text. It discovers associations - patterns of co-occurrence - amongst keywords labeling the items in a collection of textual documents. In addition, FACT is able to use background knowledge about the keywords labeling the documents in its discovery process. FACT takes a query-centered view of knowledge discovery, in which a discovery request is viewed as a query over the implicit set of possible results supported by a collection of documents, and where background knowledge is used to specify constraints on the desired results of this query process. Execution of a knowledge-discovery query is structured so that these back-ground-knowledge constraints can be exploited in the search for possible results. Finally, rather than requiring a user to specify an explicit query expression in the knowledge-discovery query language, FACT presents the user with a simple-to-use graphical interface to the query ...

1996-12-31

An evaluation of Flickrs distributed classification system, from the perspective of its members, and as an image retrieval tool in comparison with a controlled vocabulary

Modern text retrieval systems often provide a similarity search utility, that allows the user to find efficiently a fixed number k of documents in the data set that are most similar to a given query (here a query is either a simple sequence of keywords or the identifier of a full document found in previous searches that is considered of interest). We consider the case of a textual database made of semi-structured documents. Each field, in turns, is modelled with a specific vector space. The problem is more complex when we also allow each such vector space to have an associated user-defined dynamic weight that influences its contribution to the overall dynamic aggregated and weighted similarity. This dynamic problem has been tackled in a recent paper by Singitham et al. in in VLDB 2004. Their proposed solution, which we take as baseline, is a variant of the cluster-pruning technique that has the potential for scaling to very large corpora of documents, and is far ...

2007-01-01

Constructing Folksonomies from User-specified Relations on Flickr

The profusion of online digital images presents new challenges for image indexing. Images have always been problematic to describe and catalogue due to lack of inherent textual data and ambiguity of meaning. An alternative to time-consuming professionally-applied metadata has been sought in the form of tags, simple keywords that form a flat structure known as distributed classification, or more popularly as a folksonomy. This research aims to increase understanding of why people tag and how effective they find it for searching, using as the focus. Open-ended questionnaires were sent out to members of the photo-sharing website Flickr, with the opportunity to post comments to an online discussion space. There is also a systematic comparison between a tag-based system and a more traditional controlled vocabulary, to test out the claims made regarding the suitability of tagging for searching and browsing. For this purpose Flickr has been compared with Getty Images ...

2009-01-01

Automatic Annotation of XHTML Pages with Audio Components

Many social Web sites allow users to publish content and annotate with descriptive metadata. In addition to flat tags, some social Web sites have recently began to allow users to organize their content and metadata hierarchically. The social photosharing site Flickr, for example, allows users to group related photos in sets, and related sets in collections. The social bookmarking site Del.icio.us similarly lets users group related tags into bundles. Although the sites themselves don't impose any constraints on how these hierarchies are used, individuals generally use them to capture relationships between concepts, most commonly the broader/narrower relations. Collective annotation of content with hierarchical relations may lead to an emergent classification system, called a folksonomy. While some researchers have explored using tags as evidence for learning folksonomies, we believe that hierarchical relations described above offer a ...

2008-01-01

A novel approach to personal photo album representation and management

In the past ten years, significant research effort was invested in audio browsers, programs able to decode the structure of Web pages and put them into an audio format. Few advanced browsers use machine learning algorithms to classify objects on the Web page and learn browsing behaviors, have multimodal input and outputs and are able to synchronize between the graphical and audio modalities to interact with the Web page. The disadvantages of these audio browsers include the necessity of a high computation power since the user's machine has to decode the structure of the Web page, and, therefore, making impossible the installation of such programs on mobile devices. In this paper, we propose a simpler and more efficient solution for the creation of a multimodal application. We developed a middleware that automatically annotates Web pages with VoiceXML generated from the content of the Web page. Using our system, the user can interact with the Web page, by using ...

2007-01-01

Modeling Resource, Infrastructure, and Policy Cost Layers for Optimizing Renewable Energy Investment and Deployment

In this paper we present a novel approach to personal photo album management allowing the end user to efficiently access the collection without any need for tedious manual annotation or indexing of the photos. The proposed work exploits methods and technology from the field of computer vision and pattern recognition for face detection, face representation and image annotation to automatically create description of images useful for content-based searching and retrieval. In fact, even if most of the used techniques are not reliable enough to address the general problem of content-based image retrieval, we show that, in a limited domain such as the one of personal photo album, it is possible to obtain results that improve the browsing capabilities of current photo album management systems. In particular, starting from the observation that most personal photos depict a usually small number of people in a relatively small number of different ...

2008-01-01

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This paper presents a framework for creating a common spatial canvass that can bring together considerations of resource availability, infrastructure reliability, and development costs while strategizing renewable energy investment. We describe the underlying models and methodologies that annotate an investment plan for potential sites over a time-period with costs and constraints which may be imposed on distance from infrastructure, system impact on infrastructure, and policy incentives. The framework is intended as an enabler for visualization, optimization and decision making across diverse dimensions while searching for lucrative investment-plans.

2010-09-01

Controlling the atom

BUBL LINK: Biblical studies

The authors trace the early history of nuclear power regulation in the US. Focusing on the Atomic Energy Commission, they describe the role of other groups that figured in the development of regulatory policies, including the Congressional Joint Committee on Atomic Energy, other federal agencies, state governments, the nuclear industry, and scientific organizations. They consider changes in public perceptions of and attitudes toward atomic energy and the dangers of radiation exposure. The basic purpose of the book is to provide the Nuclear Regulatory Commission and the general public with information on the historical antecedents and background of regulatory issues so that there will be continuity in policy decisions. The book concludes with an annotated bibliography of selected references. 19 figures.

1984-01-01

Wastenet

...com: Christianity: General All-in-One Biblical Resources Search Anno Domini: Jesus Through the Centuries Bible and Homosexuality Bible Reading Fellowship Bible Society Bible ...of the New Testament Vine's Expository Dictionary of New Testament Words Virtual Christianity: Bibles Whole Bible Comments: bubl@bubl.ac.uk About....com: Christianity: General Offers original articles and features about Christianity in general plus annotated links to selected relevant Internet resources, compiled by ... Also includes a gallery of Christian images such as The Last Supper by Leonardo Da Vinci. Author: About....

BUBL LINK Catalogue of Internet Resources

Wastenet

...O | P | Q | R | S | T | U | V | W | X | Y | Z 230 Christianity: general resources ...com: Christianity: General Anno Domini: Jesus Through the Centuries Bible and Homosexuality Christian Theological Research Fellowship Papers Christianity Links and Resources Directory ...Good Digital Collections Lambert's Web Links MUNDUS New Testament Gateway Omnilist of Christian Starting Points Quartz Hill School of Theology Web Library Theology Online ...com: Christianity: General Offers original articles and features about Christianity in general plus annotated links to selected relevant Internet resources, compiled by ...

A comparison of algorithms for inference and learning in probabilistic graphical models.

Sequences of versatile, broad-host-range vectors of the RK2 family.

Research into methods for reasoning under uncertainty is currently one of the most exciting areas of artificial intelligence, largely because it has recently become possible to record, store, and process large amounts of data. While impressive achievements have been made in pattern classification problems such as handwritten character recognition, face detection, speaker identification, and prediction of gene function, it is even more exciting that researchers are on the verge of introducing systems that can perform large-scale combinatorial analyses of data, decomposing the data into interacting components. For example, computational methods for automatic scene analysis are now emerging in the computer vision community. These methods decompose an input image into its constituent objects, lighting conditions, motion patterns, etc. Two of the main challenges are finding effective representations and models in specific applications and finding efficient algorithms ...

2005-09-01

Searching for immunomodulatory sequences in sea bass (Dicentrarchus labrax L.): Transcripts analysis from thymus

Plasmid pRK404-a smaller derivative of RK2-is a tetracycline-resistant broad-host-range vector that carries a multiple cloning site and the lacZ(alpha) peptide that enables blue/white selection for cloned inserts in Escherichia coli. We present herein the complete and annotated sequence of pRK404 and three related vectors-pRK437, pRK442, and pRK442(H). These derivatives have proven to be valuable tools for genetic manipulation in Gram-negative bacteria. The knowledge of their complete sequences will facilitate efficient future engineering of them and will enhance their general applicability to the design of genetic systems for use in organisms for which new genomic sequence data are becoming available.

2003-07-01

British Library Electronic Table of Contents (United Kingdom)

The thymus is a key organ of the immune system in most vertebrates and, for this reason, it has been used in this paper for the generation of a normalized cDNA library from sea bass (Dicentrarchus labrax), one of the most extensively cultured species in South Mediterranean aquaculture. A total of 1632 ESTs from this library were initially analysed for sequence quality and vector sequences and, after this control, 1264 (77% of total clones sequenced) high-quality ESTs were further processed. The total collection of D. labrax thymus ESTs has been deposited in the EBI-GenBank-DBJ database (GenBank accession numbers from FN565576 to FN566839). The functional classification of ESTs was performed by Gene Ontology and KEGG annotation and, successively, the sequences were analysed using the Immuno...

2010-01-01

Metallization of large silicon wafers. Quarterly technical report No. 1, August 26--December 31, 1977. [45 references

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

A proposed metallization system for large area silicon solar cells with shallow junctions is outlined, and its desirable features are discussed. A baseline process sequence for the nickel palladium metallization system (NPMS) is delineated. This baseline process sequence is serving as the starting point from which process variations are being performed. The eventual goal is optimization of the NPMS process and determination of the control ranges for NPMS process variables. Initial studies of palladium displacement and electroless chemical plating solutions used in the baseline NPMS have begun and progress is reported. In support of this work, an annotated bibliography (45 citations) dealing primarily with palladium plating and palladium-silicon contact formation has been prepared (and will be subject to updating in the future reports).

1977-01-01

British Library Electronic Table of Contents (United Kingdom)

Summary: The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fr...

2011-01-01

ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

Crude oil and finished fuel storage stability: An annotated review

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes entitled ECRbase that is constructed from a collection of pairwise vertebrate genome alignments produced by the ECR Browser database. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a collection of promoters in all vertebrate genomes presented in the database. The database also contains a collection of annotated transcription factor binding sites (TFBS) in all ECRs and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and two pufferfish genomes. It is freely accessible at http://ECRbase.dcode.org.

2006-08-08

British Library Electronic Table of Contents (United Kingdom)

A state-of-the-art review and assessment of storage effects on crude oil and product quality was undertaken through a literature search by computer accessing several data base sources. Pertinent citations from that literature search are tabulated for the years 1980 to the present. This 1990 revision supplements earlier reviews by Brinkman and others which covered stability publications through 1979 and an update in 1983 by Goetzinger and others that covered the period 1952--1982. For purposes of organization, citations are listed in the current revision chronologically starting with the earliest 1980 publications. The citations have also been divided according to primary subject matter. Consequently 11 sections appear including: alternate fuels, gasoline, distillate fuel, jet fuel, residual fuel, crude oil, biodegradation, analyses, reaction mechanisms, containment, and handling and storage. Each section contains a brief narrative followed by all the citations for that category.

1991-01-01

A red basil cell line (T2b) rich in rosmarinic acid (RA) was selected for the stable production of anthocyanins (ACs) in the dark. Cell suspension cultures were subjected to mechanical stress through increased agitation (switch from 90 to 150rpm) to determine the relationship between AC and RA accumulation. Cell extracts were analyzed by HPLC and LC-MS, and the resulting data were processed with multivariate statistical analysis. MS and MS/MS spectra facilitated the putative annotation of several complex cyanidin-based ACs, which were esterified with coumaric acid and, in some cases, also with malonic acid. It was also possible to identify various RA-related molecules, some caffeic and coumaric acid derivatives and some flavanones. Mechanical stress increased the total AC and RA contents, ...

2011-01-01

Analysis of the transcriptome of the root lesion nematode Pratylenchus coffeae generated by 454 sequencing technology

British Library Electronic Table of Contents (United Kingdom)

To study interactions between plants and plant-parasitic nematodes, several omics studies have nowadays become extremely useful. Since most data available so far is derived from sedentary nematodes, we decided to improve the knowledge on migratory nematodes by studying the transcriptome of the nematode Pratylenchus coffeae through generating expressed sequence tags (ESTs) on a 454 sequencing platform. In this manuscript we present the generation, assembly and annotation of over 325,000 reads from P. coffeae. After assembling these reads, 56,325 contigs and singletons with an average length of 353bp were selected for further analyses. Homology searches revealed that 25% of these sequences had significant matches to the Swiss-prot/trEMBL database and 29% had significant matches in nematode E...

2011-01-01

Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels

Responses to comments received on the draft final report of the Secretary of Energy Advisory Board Task Force on Radioactive Waste Management

BackgroundBiodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production.ResultsNext generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45% of the high quality reads were assembled into 33,307 isotigs with a 31-fold coverage and 376,482 singletons. Assembled sequences and singletons were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and ...

2011-03-14

Pa0148 from Pseudomonas aeruginosa Catalyzes the Deamination of Adenine.

The Task Force solicited comments on its Draft Final Report from a variety of sources. Letters were sent to over 400 individuals who had expressed interest in the interest in the Department`s radioactive waste, management programs, a notice was placed in the Federal Register, the morning session of the January 1993 meeting of the full Secretary of Energy Advisory Board was given over to discussion of the draft, and Task Force members and staff presented the effort at several professional meetings. Altogether 32 written comments were received. They are reproduced here, followed in each case by the Task Force`s response to specific suggestions made to improve the draft. (The panel did not respond to comments that simply reflected policy preferences or that praised the group`s effort.) With one exception, those specific suggestions are highlighted and given a letter designation from {open_quotes}A{close_quotes} to {open_quotes}Z{close_quotes}. The Task Force`s responses, written in the ...

1994-10-01

Definition and means of maintaining the criticality detectors and alarms portion of the PFP safety envelope

Four proteins from NCBI cog1816, previously annotated as adenosine deaminases, have been subjected to structural and functional characterization. Pa0148 (Pseudomonas aeruginosa PAO1), AAur1117 (Arthrobacter aurescens TC1), Sgx9403e, and Sgx9403g have been purified and their substrate profiles determined. Adenosine is not a substrate for any of these enzymes. All of these proteins will deaminate adenine to produce hypoxanthine with k(cat)/K(m) values that exceed 10(5) M(-1) s(-1). These enzymes will also accept 6-chloropurine, 6-methoxypurine, N-6-methyladenine, and 2,6-diaminopurine as alternate substrates. X-ray structures of Pa0148 and AAur1117 have been determined and reveal nearly identical distorted (?/?)(8) barrels with a single zinc ion that is characteristic of members of the amidohydrolase superfamily. Structures of Pa0148 with adenine, 6-chloropurine, and hypoxanthine were also determined, thereby permitting identification of the residues responsible for ...

2011-07-06

Complete genome sequence of Conexibacter woesei type strain (ID131577T)

The purpose of this document is to provide the definition and means of maintaining the Safety Envelope (SE) related to the Criticality Alarm System (CAS). This document provides amplification of the Limiting Condition for Operation (LCO) described in the Plutonium Finishing Plant (PFP) Operational Safety Requirements (OSR), WHC-SD-CP-OSR-010, Rev. 0, 1994, Section 3.1.2, Criticality Detectors and Alarms. This document, with its appendices, provides the following: (1) System functional requirements for determining system operability (Section 3); (2) A list of annotated system block diagrams which indicate the safety envelope boundaries (Appendix C); (3) A list of the Safety Class 1 and 2 Safety Envelope (SC-1/2 SE) equipment for input into the Master Component Index (Appendix B); (4) Functional requirements for individual SC-1/2 SE components, including appropriate setpoints and process parameters (Section 6 and Appendix A); (5) A list of the operational, ...

1997-05-13

Complete genome sequence of Actinosynnema mirum type strain (101T)

The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of des-cent within the class Actinobacteria. Strain ID131577T was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous fla-gella. They may form aggregates after a longer period of growth and, then as a typical charac-teristic, an undulate structure is formed by self-aggregation of flagella with entangled bacteri-al cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.

2010-01-01

Coal liquefaction process streams characterization and evaluation. Volume 2, Participants program final summary evaluation

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA ...

2009-05-20

Assessing the ACGME Competencies in Psychiatry Training programs.

This 4.5-year project consisted of routine analytical support to DOE`s direct liquefaction process development effort (the Base Program), and an extensive effort to develop, demonstate, and apply new analytical methods for the characterization of liquefaction process streams (the Participants Program). The objective of the Base Program was to support the on-going DOE direct coal liquefaction process development program. Feed, process, and product samples were used to assess process operations, product quality, and the effects of process variables, and to direct future testing. The primary objective of the Participants Program was to identify and demonstrate analytical methods for use in support of liquefaction process develpment, and in so doing, provide a bridge between process design, development, and operation and analytical chemistry. To achieve this direct coal liquefaction-derived materials. CONSOL made an evaluation of each analytical technique. During the performance of this ...

1994-05-01

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Tissue culture and micropropagation for forest biomass production

In 2000, the Accreditation Council of Graduate Medical Education (ACGME) laid out a definition of competence that included six specific areas of focus: patient care (including clinical reasoning), medical knowledge, practice-based learning and improvement, interpersonal and communication skills, professionalism, and systems-based practice. The ACGME's intention was to mandate increasingly reliable and valid assessment measures to be used by all training programs over the next decade, with the goal of providing "more credible, accurate, reliable and useful educational outcome data." In this article, the authors will review definitions of competency according to the new ACGME standards and examine the assessment tools currently available, including global evaluations, 360-degree evaluations, checklists, standardized examinations and direct observations. The authors will provide an overview of critical considerations in different assessment methods, including timing, psychometric ...

Selection of melter systems for the DOE/Industrial Center for Waste Vitrification Research

An increase in forest production will be necessary in the future when wood becomes a major renewable source of energy and chemicals along with its traditional role of fibre source. This increase could eventually by achieved be proper selection and breeding of trees. Clonal forestry by vegetative propagation of cuttings is becoming a viable alternative to a seedling-based forestry with many advantages, and cutting could be used to quickly propagate large numbers of clones of control-pollinated seedlings. Most forest trees are propagated sexually and seed orchards were started in the US and Canada in the last 40-50 years for breeding purposes. Forests could ultimately be established with improved seedlings instead of from seed with unknown genetic potential, or by natural regeneration. Micropropagation is the term used to refer to the propagation of plants raised by tissue culture methods rather than from seeds or cuttings. Many clonal plantlets could be regenerated asexually in the ...

1984-09-01

Results of oil-shale investigations in northeastern Nevada

The EPA has designated vitrification as the best developed available technology for immobilization of High-Level Nuclear Waste. In a recent federal facilities compliance agreement between the EPA, the State of Washington, and the DOE, the DOE agreed to vitrify all of the Low Level Radioactive Waste resulting from processing of High Level Radioactive Waste stored at the Hanford Site. This is expected to result in the requirement of 100 ton per day Low Level Radioactive Waste melters. Thus, there is increased need for the rapid adaptation of commercial melter equipment to DOE`s needs. DOE has needed a facility where commercial pilot scale equipment could be operated on surrogate (non-radioactive) simulations of typical DOE waste streams. The DOE/Industry Center for Vitrification Research (Center) was established in 1992 at the Clemson University Department of Environmental Systems Engineering, Clemson, SC, to address that need. This report discusses some of the characteristics of the ...

1993-12-31

Comparing compressed sequences for faster nucleotide BLAST searches.

The major focus of this oil-shale investigation has been on specific localities of oil-shale resource potential. Three main areas of oil-shale occurrence have been studied in detail: the Elko area, Pinon Range area, and Coal Mine Canyon. Geologic mapping, stratigraphic studies, and sampling to delimit the lateral extent of the oil shale deposits were in progress prior to the cooperative agreement with Nevada DOE. These surface geologic studies have been summarized in this report. The results of surface geologic studies conducted near Elko suggested that the Elko area represented the best and most accessible oil-shale deposits; therefore, the Elko area was selected as the site of a shallow exploratory drilling program. Essential to this study was the obtaining of fresh, unweathered oil-shale samples from the Elko area. The samples were obtained from the core-drilling program and tested for oil yield by Fischer assays. The oil yields determined from these samples, together with the ...

1983-01-01

Coal liquefaction process streams characterization and evaluation. Volume 1, Base program activities

Molecular biologists, geneticists, and other life scientists use the BLAST homology search package as their first step for discovery of information about unknown or poorly annotated genomic sequences. There are two main variants of BLAST: BLASTP for searching protein collections and BLASTN for nucleotide collections. Surprisingly, BLASTN has had very little attention; for example, the algorithms it uses do not follow those described in the 1997 BLAST paper and no exact description has been published. It is important that BLASTN is state-of-the-art: Nucleotide collections such as GenBank dwarf the protein collections in size, they double in size almost yearly, and they take many minutes to search on modern general purpose workstations. This paper proposes significant improvements to the BLASTN algorithms. Each of our schemes is based on compressed bytepacked formats that allow queries and collection sequences to be compared four bases at a time, permitting very fast ...