IMGT/HLA Database—a sequence database for the human major histocompatibility complex

The IMGT/HLA Database (www.ebi.ac.uk/imgt/hla/) specialises in sequences of polymorphic genes of the HLA system, the human major histocompatibility complex (MHC). The HLA complex is located within the 6p21.3 region on the short arm of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and these include the 21 highly polymorphic HLA genes, which influence the outcome of clinical transplantation and confer susceptibility to a wide range of non-infectious diseases. The database contains sequences for all HLA alleles officially recognised by the WHO Nomenclature Committee for Factors of the HLA System and provides users with online tools and facilities for their retrieval and analysis. These include allele reports, alignment tools and detailed descriptions of the source cells. The online IMGT/HLA submission tool allows both new and confirmatory sequences to be submitted directly to the WHO Nomenclature Committee. The latest version (release 1.7.0 July 2000) contains 1220 HLA alleles derived from over 2700 component sequences from the EMBL/GenBank/DDBJ databases. The HLA database provides a model which will be extended to provide specialist databases for polymorphic MHC genes of other species.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap’99, Human–Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri­tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins

The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. Analysis has been carried out for different levels of protein similarity, yielding a hierarchical organisation of clusters. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam and ProDom. Links to the InterPro graphical interface allow users to see at a glance whether proteins from the cluster share particular functional sites. CluSTr also provides cross-references to HSSP and PDB. The database is available for querying and browsing at http://www.ebi.ac.uk/clustr.

CKAAPs DB: a conserved key amino acid positions database

The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. The derivation and significance of CKAAPs starting from pairwise structure alignments is described fully in Reddy et al. [Reddy,B.V.B., Li,W.W., Shindyalov,I.N. and Bourne,P.E. (2000) Proteins, in press]. The CKAAPs identified from this theoretical analysis are provided to experimentalists and theoreticians for potential use in protein engineering and modeling. It has been suggested that CKAAPs may be crucial features for protein folding, structural stability and function. Over 170 substructures, as defined by the Combinatorial Extension (CE) database, which are found in approximately 3000 representative polypeptide chains have been analyzed and are available in the CKAAPs DB. CKAAPs DB also provides CKAAPs of the representative set of proteins derived from the CE and FSSP databases. Thus the database contains over 5000 representative poly­peptide chains, covering all known structures in the PDB. A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. Users may query by PDB ID, protein name, function and Enzyme Classification number. Users may also submit protein alignments of their own to obtain CKAAPs. An interface to display CKAAPs on each structure from a web browser is also being implemented. CKAAPs DB is maintained by the San Diego Supercomputer Center and accessible at the URL http://ckaaps.sdsc.edu.

VIDA: a virus database system for the organization of animal virus genome open reading frames

VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on the basis of sequence similarity relationships. Conserved sequence regions of potential functional importance are identified and can be retrieved as sequence alignments. We use a controlled taxonomical and functional classification for all the proteins and protein families in the database. When available, protein structures that are related to the families have also been included. The database is available for online search and sequence information retrieval at http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html.

iProClass: an integrated, comprehensive and annotated protein classification database

The iProClass database is an integrated resource that provides comprehensive family relationships and structural and functional features of proteins, with rich links to various databases. It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs. The iProClass currently consists of more than 200 000 non-redundant PIR and SWISS-PROT proteins organized with more than 28 000 superfamilies, 2600 domains, 1300 motifs, 280 post-translational modification sites and links to more than 30 databases of protein families, structures, functions, genes, genomes, literature and taxonomy. Protein and family summary reports provide rich annotations, including membership information with length, taxonomy and keyword statistics, full family relationships, comprehensive enzyme and PDB cross-references and graphical feature display. The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research. The iProClass is implemented in Oracle 8i object-relational system and available for sequence search and report retrieval at http://pir.georgetow n.edu/iproclass/.

PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data

The Plasmodium falciparum Genome Database (http://PlasmoDB.org) integrates sequence information, automated analyses and annotation data emerging from the P.falciparum genome sequencing consortium. To date, raw sequence coverage is available for >90% of the genome, and two chromosomes have been finished and annotated. Data in PlasmoDB are organized by chromosome (1–14), and can be accessed using a variety of tools for graphical and text-based browsing or downloaded in various file formats. The GUS (Genomics Unified Schema) implementation of PlasmoDB provides a multi-species genomic relational database, incorporating data from human and mouse, as well as P.falciparum. The relational schema uses a highly structured format to accommodate diverse data sets related to genomic sequence and gene expression. Tools have been designed to facilitate complex biological queries, including many that are specific to Plasmodium parasites and malaria as a disease. Additional projects seek to integrate genomic information with the rich data sets now becoming available for RNA transcription, protein expression, metabolic pathways, genetic and physical mapping, antigenic and population diversity, and phylogenetic relationships with other apicomplexan parasites. The overall goal of PlasmoDB is to facilitate Internet- and CD-ROM-based access to both finished and unfinished sequence information by the global malaria research community.

General and specific brain regions involved in encoding and retrieval of events: what, where, and when.

Remembering an event involves not only what happened, but also where and when it occurred. We measured regional cerebral blood flow by positron emission tomography during initial encoding and subsequent retrieval of item, location, and time information. Multivariate image analysis showed that left frontal brain regions were always activated during encoding, and right superior frontal regions were always activated at retrieval. Pairwise image subtraction analyses revealed information-specific activations at (i) encoding, item information in left hippocampal, location information in right parietal, and time information in left fusiform regions; and (ii) retrieval, item in right inferior frontal and temporal, location in left frontal, and time in anterior cingulate cortices. These results point to the existence of general encoding and retrieval networks of episodic memory whose operations are augmented by unique brain areas recruited for processing specific aspects of remembered events.

Casamento de modelos baseado em projeções radiais e circulares invariante a pontos de vista.

Este trabalho aborda o problema de casamento entre duas imagens. Casamento de imagens pode ser do tipo casamento de modelos (template matching) ou casamento de pontos-chaves (keypoint matching). Estes algoritmos localizam uma região da primeira imagem numa segunda imagem. Nosso grupo desenvolveu dois algoritmos de casamento de modelos invariante por rotação, escala e translação denominados Ciratefi (Circula, radial and template matchings filter) e Forapro (Fourier coefficients of radial and circular projection). As características positivas destes algoritmos são a invariância a mudanças de brilho/contraste e robustez a padrões repetitivos. Na primeira parte desta tese, tornamos Ciratefi invariante a transformações afins, obtendo Aciratefi (Affine-ciratefi). Construímos um banco de imagens para comparar este algoritmo com Asift (Affine-scale invariant feature transform) e Aforapro (Affine-forapro). Asift é considerado atualmente o melhor algoritmo de casamento de imagens invariante afim, e Aforapro foi proposto em nossa dissertação de mestrado. Nossos resultados sugerem que Aciratefi supera Asift na presença combinada de padrões repetitivos, mudanças de brilho/contraste e mudanças de pontos de vista. Na segunda parte desta tese, construímos um algoritmo para filtrar casamentos de pontos-chaves, baseado num conceito que denominamos de coerência geométrica. Aplicamos esta filtragem no bem-conhecido algoritmo Sift (scale invariant feature transform), base do Asift. Avaliamos a nossa proposta no banco de imagens de Mikolajczyk. As taxas de erro obtidas são significativamente menores que as do Sift original.

An Introduction to Conservation Easements in the United States: A Simple Concept and a Complicated Mosaic of Law

The idea of a conservation easement – restrictions on the development and use of land designed to protect the land’s conservation or historic values – can be relatively easily understood. More significant and more challenging is the complex body of state and federal laws that shapes the creation, funding, tax treatment, enforcement, modification, and termination of conservation easements. The explosion in the number of conservation easements over the past four decades has made them one of the most popular land protection mechanisms in the United States. The National Conservation Easement Database estimates that the total number of acres encumbered by conservation easements exceeds 40 million.Because conservation easements are both novel and ubiquitous, understanding how they actual work is essential for practicing lawyers, policymakers, land trust professionals, and students of conservation. This article provides a “quick tour” through some of the most important aspects of the developing mosaic of conservation easement law. It gives the reader a sense of the complex inter-jurisdictional dynamics that shape conservation transactions and disputes about conservation easements. Professors of property law, environmental law, tax law, and environmental studies who wish to cover conservation easements in the context of a more general course can use the article to provide their students with a broad but comprehensive overview of the relevant legal and policy issues.

A general proposal to multilingual information access based on syntactic-semantic patterns

In the last few years, there has been a wide development in the research on textual information systems. The goal is to improve these systems in order to allow an easy localization, treatment and access to the information stored in digital format (Digital Databases, Documental Databases, and so on). There are lots of applications focused on information access (for example, Web-search systems like Google or Altavista). However, these applications have problems when they must access to cross-language information, or when they need to show information in a language different from the one of the query. This paper explores the use of syntactic-sematic patterns as a method to access to multilingual information, and revise, in the case of Information Retrieval, where it is possible and useful to employ patterns when it comes to the multilingual and interactive aspects. On the one hand, the multilingual aspects that are going to be studied are the ones related to the access to documents in different languages from the one of the query, as well as the automatic translation of the document, i.e. a machine translation system based on patterns. On the other hand, this paper is going to go deep into the interactive aspects related to the reformulation of a query based on the syntactic-semantic pattern of the request.

Prueba de concepto de expansión de consultas basada en ontologías de dominio financiero

Este trabajo presenta el uso de una ontología en el dominio financiero para la expansión de consultas con el fin de mejorar los resultados de un sistema de recuperación de información (RI) financiera. Este sistema está compuesto por una ontología y un índice de Lucene que permite recuperación de conceptos identificados mediante procesamiento de lenguaje natural. Se ha llevado a cabo una evaluación con un conjunto limitado de consultas y los resultados indican que la ambigüedad sigue siendo un problema al expandir la consulta. En ocasiones, la elección de las entidades adecuadas a la hora de expandir las consultas (filtrando por sector, empresa, etc.) permite resolver esa ambigüedad.

A parallel method for impulsive image noise removal on hybrid CPU/GPU systems

A parallel algorithm for image noise removal is proposed. The algorithm is based on peer group concept and uses a fuzzy metric. An optimization study on the use of the CUDA platform to remove impulsive noise using this algorithm is presented. Moreover, an implementation of the algorithm on multi-core platforms using OpenMP is presented. Performance is evaluated in terms of execution time and a comparison of the implementation parallelised in multi-core, GPUs and the combination of both is conducted. A performance analysis with large images is conducted in order to identify the amount of pixels to allocate in the CPU and GPU. The observed time shows that both devices must have work to do, leaving the most to the GPU. Results show that parallel implementations of denoising filters on GPUs and multi-cores are very advisable, and they open the door to use such algorithms for real-time processing.

Image Noise Removal on Heterogeneous CPU-GPU Configurations

A parallel algorithm to remove impulsive noise in digital images using heterogeneous CPU/GPU computing is proposed. The parallel denoising algorithm is based on the peer group concept and uses an Euclidean metric. In order to identify the amount of pixels to be allocated in multi-core and GPUs, a performance analysis using large images is presented. A comparison of the parallel implementation in multi-core, GPUs and a combination of both is performed. Performance has been evaluated in terms of execution time and Megapixels/second. We present several optimization strategies especially effective for the multi-core environment, and demonstrate significant performance improvements. The main advantage of the proposed noise removal methodology is its computational speed, which enables efficient filtering of color images in real-time applications.

Novel image processing approach to detect malaria

In this paper we present a novel image processing algorithm providing good preliminary capabilities for in vitro detection of malaria. The proposed concept is based upon analysis of the temporal variation of each pixel. Changes in dark pixels mean that inter cellular activity happened, indicating the presence of the malaria parasite inside the cell. Preliminary experimental results involving analysis of red blood cells being either healthy or infected with malaria parasites, validated the potential benefit of the proposed numerical approach.