The COG database: new developments in phylogenetic classification of proteins from complete genomes

The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www.ncbi.nlm.nih.gov/COG). In addition, a supplement to the COGs is available, in which proteins encoded in the genomes of two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and shared with bacteria and/or archaea were included. The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis.

A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages

Coccidiosis of the domestic fowl is a worldwide disease caused by seven species of protozoan parasites of the genus Eimeria. The genome of the model species, Eimeria tenella, presents a complexity of 55-60 MB distributed in 14 chromosomes. Relatively few studies have been undertaken to unravel the complexity of the transcriptome of Eimeria parasites. We report here the generation of more than 45,000 open reading frame expressed sequence tag (ORESTES) cDNA reads of E. tenella, Eimeria maxima and Eimeria acervulina, covering several developmental stages: unsporulated oocysts, sporoblastic oocysts, sporulated oocysts, sporozoites and second generation merozoites. All reads were assembled to constitute gene indices and submitted to a comprehensive functional annotation pipeline. In the case of E. tenella, we also incorporated publicly available ESTs to generate an integrated body of information. Orthology analyses have identified genes conserved across different apicomplexan parasites, as well as genes restricted to the genus Eimeria. Digital expression profiles obtained from ORESTES/EST countings, submitted to clustering analyses, revealed a high conservation pattern across the three Eimeria spp. Distance trees showed that unsporulated and sporoblastic oocysts constitute a distinct clade in all species, with sporulated oocysts forming a more external branch. This latter stage also shows a close relationship with sporozoites, whereas first and second generation merozoites are more closely related to each other than to sporozoites. The profiles were unambiguously associated with the distinct developmental stages and strongly correlated with the order of the stages in the parasite life cycle. Finally, we present The Eimeria Transcript Database (http://www.coccidia.icb.usp.br/eimeriatdb), a website that provides open access to all sequencing data, annotation and comparative analysis. We expect this repository to represent a useful resource to the Eimeria scientific community, helping to define potential candidates for the development of new strategies to control coccidiosis of the domestic fowl. (C) 2011 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

A database ATP simulated waveforms of shunt reactor switching cases with vacuum breakers on motor circuits

This paper presents a database ATP (Alternative Transient Program) simulated waveforms for shunt reactor switching cases with vacuum breakers in motor circuits following interruption of the starting current. The targeted objective is to provide multiple reignition simulated data for diagnostic and prognostic algorithms development, but also to help ATP users with practical study cases and component data compilation for shunt reactor switching. This method can be easily applied with different data for the different dielectric curves of circuit-breakers and networks. This paper presents design details, discusses some of the available cases and the advantages of such simulated data.

Report : analysis of maintenance database inputs

In the previous phase of this project, 2002-059-B Case-Based Reasoning in Construction and Infrastructure Projects, demonstration software was developed using a case-base reasoning engine to access a number of sources of information on lifetime of metallic building components. One source of information was data from the Queensland Department of Public Housing relating to maintenance operations over a number of years. Maintenance information is seen as being a particularly useful source of data about service life of building components as it relates to actual performance of materials in the working environment. If a building is constructed in 1984 and the maintenance records indicate that the guttering was replaced in 2006, then the service life of the gutters was 22 years in that environment. This phase of the project aims to look more deeply at the Department of Housing data, as an example of maintenance records, and formulate methods for using this data to inform the knowledge of service lifetimes.

United States still no closer to database legislation

Last year European Intellectual Property Review published an article comparing the latest version of the proposed US database legislation, the Collections of Information Antipiracy Bill with the UK's Copyright and Rights in Database Regulations 1997. Subsequently a new US Bill, the Consumer and Investor Access to Information Act has emerged, the Antipiracy Bill has been amended and much debate has occurred, but the US seems no closer to enacting database legislation. This article briefly outlines the background to the US legislative efforts, examines the two Bills and draws some comparisons with the UK Regulations. A study of the US Bills clearly demonstrates the starkly divided opinion on database protection held by the Bills' proponents and the principal lobby groups driving the legislative efforts: the Antipiracy Bill is very protective of database producers' interests, whereas the Access Bill is heavily user-oriented. If the US experience is any indication there will be a long horizon involved in achieving any consensus on international harmonisation of this difficult area.

Recognising audio-visual speech in vehicles using the AVICAR database

Interacting with technology within a vehicle environment using a voice interface can greatly reduce the effects of driver distraction. Most current approaches to this problem only utilise the audio signal, making them susceptible to acoustic noise. An obvious approach to circumvent this is to use the visual modality in addition. However, capturing, storing and distributing audio-visual data in a vehicle environment is very costly and difficult. One current dataset available for such research is the AVICAR [1] database. Unfortunately this database is largely unusable due to timing mismatch between the two streams and in addition, no protocol is available. We have overcome this problem by re-synchronising the streams on the phone-number portion of the dataset and established a protocol for further research. This paper presents the first audio-visual results on this dataset for speaker-independent speech recognition. We hope this will serve as a catalyst for future research in this area.

Face authentication test on the BANCA database

This work details the results of a face authentication test (FAT2004) (http://www.ee.surrey.ac.uk/banca/icpr2004) held in conjunction with the 17th International Conference on Pattern Recognition. The contest was held on the publicly available BANCA database (http://www.ee.surrey.ac.uk/banca) according to a defined protocol (E. Bailly-Bailliere et al., June 2003). The competition also had a sequestered part in which institutions had to submit their algorithms for independent testing. 13 different verification algorithms from 10 institutions submitted results. Also, a standard set of face recognition software packages from the Internet (http://www.cs.colostate.edu/evalfacerec) were used to provide a baseline performance measure.

Improving web database search incorporating users query information

The growing importance and need of data processing for information extraction is vital for Web databases. Due to the sheer size and volume of databases, retrieval of relevant information as needed by users has become a cumbersome process. Information seekers are faced by information overloading - too many result sets are returned for their queries. Moreover, too few or no results are returned if a specific query is asked. This paper proposes a ranking algorithm that gives higher preference to a user’s current search and also utilizes profile information in order to obtain the relevant results for a user’s query.

The scalability and the strategy for EMR database encryption techniques

EMR (Electronic Medical Record) is an emerging technology that is highly-blended between non-IT and IT area. One methodology is to link the non-IT and IT area is to construct databases. Nowadays, it supports before and after-treatment for patients and should satisfy all stakeholders such as practitioners, nurses, researchers, administrators and financial departments and so on. In accordance with the database maintenance, DAS (Data as Service) model is one solution for outsourcing. However, there are some scalability and strategy issues when we need to plan to use DAS model properly. We constructed three kinds of databases such as plan-text, MS built-in encryption which is in-house model and custom AES (Advanced Encryption Standard) - DAS model scaling from 5K to 2560K records. To perform custom AES-DAS better, we also devised Bucket Index using Bloom Filter. The simulation showed the response times arithmetically increased in the beginning but after a certain threshold, exponentially increased in the end. In conclusion, if the database model is close to in-house model, then vendor technology is a good way to perform and get query response times in a consistent manner. If the model is DAS model, it is easy to outsource the database, however, some techniques like Bucket Index enhances its utilization. To get faster query response times, designing database such as consideration of the field type is also important. This study suggests cloud computing would be a next DAS model to satisfy the scalability and the security issues.

The proposal on the effective query mechanism for the encrypted database

In the recent past, there are some social issues when personal sensitive data in medical database were exposed. The personal sensitive data should be protected and access must be accounted for. Protecting the sensitive information is possible by encrypting such information. The challenge is querying the encrypted information when making the decision. Encrypted query is practically somewhat tedious task. So we present the more effective method using bucket index and bloom filter technology. We find that our proposed method shows low memory and fast efficiency comparatively. Simulation approaches on data encryption techniques to improve health care decision making processes are presented in this paper as a case scenario.