471313
Dependence network modeling for biomarker identification
MOTIVATION
Our purpose is to develop a statistical modeling approach for cancer biomarker discovery and provide new insights into early cancer detection. We propose the concept of dependence network, apply it for identifying cancer biomarkers, and study the difference between the protein or gene samples from cancer and non-cancer subjects based on mass-spectrometry (MS) and microarray data.


RESULTS
Three MS and two gene microarray datasets are studied. Clear differences are observed in the dependence networks for cancer and non-cancer samples. Protein/gene features are examined three at one time through an exhaustive search. Dependence networks are constructed by binding triples identified by the eigenvalue pattern of the dependence model, and are further compared to identify cancer biomarkers. Such dependence-network-based biomarkers show much greater consistency under 10-fold cross-validation than the classification-performance-based biomarkers. Furthermore, the biological relevance of the dependence-network-based biomarkers using microarray data is discussed. The proposed scheme is shown promising for cancer diagnosis and prediction.


AVAILABILITY
See supplements: http://dsplab.eng.umd.edu/~genomics/dependencenetwork/
7472466
A Protein Class Database Organized with ProSite Protein Groups and PIR Superfamilies
A protein class (ProClass) database is developed as a "value-added" "second-generation" database organized according to family relationships. The database collects non-redundant protein sequence entries from SwissProt and PIR databases, and classifies them in families defined collectively by the ProSite protein groups and PIR superfamilies. The major objectives of the database are to maximize family information retrieval, to provide speedy family identification, and to help organizing existing protein sequence databases. The database has two sub-databases: PCFam (ProClass Family) to define protein families and provide links to ProSite patterns and PIR superfamilies, and PCSeq (ProClass Sequence) to describe sequence entries and provide links to PCFam, SwissProt, PIR, and ProSite databases. The current ProClass release has a total of 85,165 sequence entries, about half of which are classified in 3072 ProClass families; it also contains 10,431 newly established SwissProt-PIR links. The database can help reveal domain structures of related families, define new ProSite and PIR families, and provide family assignments for unclassified sequence entries. New ProSite and PIR family members are readily identified via database cross-reference, including 9437 SwissProt entries and 8522 PIR entries. False negative family members missed by both ProSite and PIR are detected using a neural network family identification system. The newly identified superfamily memberships are being incorporated into the current PIR database releases in a collaborative effort with the PIR. The ProClass database is accessible through anonymous FTP and on-line search on the World Wide Web.
205231250
The Universal Protein Resource (UniProt)
The ability to store and interconnect all available information on proteins is crucial to modern biological research. Accordingly, the Universal Protein Resource (UniProt) plays an increasingly important role by providing a stable, comprehensive, freely accessible central resource on protein sequences and functional annotation. UniProt is produced by the UniProt Consortium, formed in 2002 by the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt web site and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of three major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase and the UniProt Reference Clusters. An additional component consisting of metagenomic and environmental sequences has recently been added to UniProt to ensure availability of such sequences in a timely fashion. UniProt is updated and distributed on a bi-weekly basis and can be accessed online for searches or download at .
21872273
The Protein Information Resource (PIR)
The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Sequence Database (JIPID). The expanded PIR WWW site allows sequence similarity and text searching of the Protein Sequence Database and auxiliary databases. Several new web-based search engines combine searches of sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. New capabilities for searching the PIR sequence databases include annotation-sorted search, domain search, combined global and domain search, and interactive text searches. The PIR-International databases and search tools are accessible on the PIR WWW site at http://pir.georgetown.edu and at the MIPS WWW site at http://www. mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP.
19037242
iProClass: an integrated database of protein family, function and structure information
The iProClass database provides comprehensive, value-added descriptions of proteins and serves as a framework for data integration in a distributed networking environment. The protein information in iProClass includes family relationships as well as structural and functional classifications and features. The current version consists of about 830 000 non-redundant PIR-PSD, SWISS-PROT, and TrEMBL proteins organized with more than 36 000 PIR superfamilies, 145 000 families, 4000 domains, 1300 motifs and 550 000 FASTA similarity clusters. It provides rich links to over 50 database of protein sequences, families, functions and pathways, protein-protein interactions, post-translational modifications, protein expressions, structures and structural classifications, genes and genomes, ontologies, literature and taxonomy. Protein and superfamily summary reports present extensive annotation information and include membership statistics and graphical display of domains and motifs. iProClass employs an open and modular architecture for interoperability and scalability. It is implemented in the Oracle object-relational database system and is updated biweekly. The database is freely accessible from the web site at http://pir.georgetown.edu/iproclass/ and searchable by sequence or text string. The data integration in iProClass supports exploration of protein relationships. Such knowledge is fundamental to the understanding of protein evolution, structure and function and crucial to functional genomic and proteomic research.
7629632
Speech content authentication integrated with CELP speech decoders
A speech content authentication scheme, which is integrated with CELP speech coders to minimize the total computational cost is proposed in this research. Speech features relevant to semantic meaning are extracted, encrypted and attached as the header information. A low cost synchronization algorithm is used to resolve mis-synchronization caused by content preserving operations. Silent and tonal regions in the speech are identified with algorithms of low complexity to enhance the precision of integrity verification. This scheme is not only much faster than traditional cryptographic bitstream integrity algorithms, but also more compatible for a variety of applications. Experimental results are collected by using the GSM-AMR speech coder, and statistical analysis is performed to calculate the false positive rate of tamper detection.
206015400
Genetic-algorithm-based real-time task scheduling with multiple goals
This paper presents and evaluates a new method for real-time task scheduling in multiprocessor systems. Its objectives are to minimize the number of processors required and the total tardiness of tasks. The minimization is carried out through a multiobjective genetic algorithm (GA), because the problem has non-commensurable and competing objectives to be optimized. The experimental results showed that when compared to five methods used previously, such as list-scheduling algorithms and a specific GA, the performance of our algorithm was comparable or better for 178 out of 180 randomly generated task graphs. Also shown is the impact of the sparsity of a task graph on the performance of our algorithm.
26616615
On a Class of Multistage Interconnection Networks
A baseline network and a configuration concept are introduced to evaluate relationships among some proposed multistage interconnection networks. It is proven that the data manipulator (modified version), flip network, omega network, indirect binary n-cube network, and regular SW banyan network (S = F = 2) are topologically equivalent. The configuration concept facilitates developing a homogeneous routing algorithm which allows one-to-one and one- to-many connections from an arbitrary side of a network to the other side. This routing algorithm is extended to full communication which allows connections between terminals on the same side of a network. A conflict resolution scheme is also included. Some practical implications of our results are presented for further research.
1308934
A World-Wide Web server on a multicomputer system
As the number of people browsing the world-wide web increases explosively, the workload of popular web servers also increases rapidly. A multicomputer system that was designed for I/O intensive applications has been found to be quite suitable for serving as a web server. The system is composed of multiple clusters of multiprocessors interconnected by an interconnection network. The interconnection network is an ATM-like cell-based switching network which can be restructured so that the system can be scaled up to meet the increasing demands of web service. It is also found that the multicomputer system can support video streams effectively. Design of the system as well as porting of web servers on to it are discussed in this paper.
29409365
A Parallel Asynchronous Garbage Collection Algorithm for Distributed Systems
The problem of distributed garbage collection is discussed. An algorithm for parallel distributed asynchronous garbage collection is presented. The liveness and safety properties of this method are demonstrated. The algorithm does not require a global clock, complex termination detection methods, or distributed synchronization techniques. A new color code is introduced to distinguish between local cells (black) and those that are exclusively accessible from the remote pointers (gray). The mutator operation is revised to handle a multiple mutator scheme on a given local memory. Simulation results show that the developed distributed and parallel algorithm performs much better than the sequential method as tested on a Balance 8000 computer. >