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PubMed2002

GWFASTA: server for FASTA search in eukaryotic and microbial genomes.

Similarity searches are a powerful method for solving important biological problems such as database scanning, evolutionary studies, gene prediction, and protein structure prediction. FASTA is a widely used sequence comparison tool for rapid database scanning. Here we describe the GWFASTA server that was developed to assist the FASTA user in similarity searches against partially and/or completely sequenced genomes. GWFASTA consists of more than 60 microbial genomes, eight eukaryote genomes, and proteomes of annotatedgenomes. Infact, it provides the maximum number of databases for similarity searching from a single platform. GWFASTA allows the submission of more than one sequence as a single query for a FASTA search. It also provides integrated post-processing of FASTA output, including compositional analysis of proteins, multiple sequences alignment, and phylogenetic analysis. Furthermore, it summarizes the search results organism-wise for prokaryotes and chromosome-wise for eukaryotes. Thus, the integration of different tools for sequence analyses makes GWFASTA a powerful toolfor biologists.

Computer Systems↗
PubMedDate not supplied

XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density.

Xfit is a model-building and map viewing program in XtalView that is used by the structural biology community including researchers in the fields of crystallography, molecular modeling, and electron microscopy. Among its distinguishing features are built-in fast Fourier transforms that allow users flexibility in map calculations including the creation of OMIT maps and the updating of structure factors to reflect model changes from within the program. Written in C and using the freely available XView toolkit, it is highly portable to almost any X-windows based workstation including Intel-based LINUX systems. Its user interface is designed to aid in facile model-building and contains a semiautomated fitting system that allows the user to interactively and rapidly build chain de novo into an electron density map. The program is highly optimized to allow such features as interactive contour levels and map calculations to be completed within a few seconds. Features in the latest version including phase-combination, solvent-flattening, automated water addition, and small-probe dot contact surfaces, as well as basic design features, are discussed.

Computing Methodologies↗
PubMedDate not supplied

New frontiers in design synthesis.

The Intelligent Synthesis Environment (ISE), which is one of the major strategic technologies under development at NASA centers and the University of Virginia, is described. One of the major objectives of ISE is to significantly enhance the rapid creation of innovative affordable products and missions. ISE uses a synergistic combination of leading-edge technologies, including high performance computing, high capacity communications and networking, human-centered computing, knowledge-based engineering, computational intelligence, virtual product development, and product information management. The environment will link scientists, design teams, manufacturers, suppliers, and consultants who participate in the mission synthesis as well as in the creation and operation of the aerospace system. It will radically advance the process by which complex science missions are synthesized, and high-tech engineering Systems are designed, manufactured and operated. The five major components critical to ISE are human-centered computing, infrastructure for distributed collaboration, rapid synthesis and simulation tools, life cycle integration and validation, and cultural change in both the engineering and science creative process. The five components and their subelements are described. Related U.S. government programs are outlined and the future impact of ISE on engineering research and education is discussed.

Astronauts↗
PubMed2004

A novel featureless approach to mass detection in digital mammograms based on support vector machines.

In this work, we present a novel approach to mass detection in digital mammograms. The great variability of the appearance of masses is the main obstacle to building a mass detection method. It is indeed demanding to characterize all the varieties of masses with a reduced set of features. Hence, in our approach we have chosen not to extract any feature, for the detection of the region of interest; in contrast, we exploit all the information available on the image. A multiresolution overcomplete wavelet representation is performed, in order to codify the image with redundancy of information. The vectors of the very-large space obtained are then provided to a first support vector machine (SVM) classifier. The detection task is considered here as a two-class pattern recognition problem: crops are classified as suspect or not, by using this SVM classifier. False candidates are eliminated with a second cascaded SVM. To further reduce the number of false positives, an ensemble of experts is applied: the final suspect regions are achieved by using a voting strategy. The sensitivity of the presented system is nearly 80% with a false-positive rate of 1.1 marks per image, estimated on images coming from the USF DDSM database.

Algorithms↗
PubMed1998

Medical imaging and registration in computer assisted surgery.

Imaging, sensing, and computing technologies that are being introduced to aid in the planning and execution of surgical procedures are providing orthopaedic surgeons with a powerful new set of tools for improving clinical accuracy, reliability, and patient outcomes while reducing costs and operating times. Current computer assisted surgery systems typically include a measurement process for collecting patient specific medical data, a decision making process for generating a surgical plan, a registration process for aligning the surgical plan to the patient, and an action process for accurately achieving the goals specified in the plan. Some of the key concepts in computer assisted surgery applied to orthopaedics with a focus on the basic framework and underlying technologies is outlined. In addition, technical challenges and future trends in the field are discussed.

Bone and Bones↗
PubMed2002

Design and implementation of a brain-computer interface with high transfer rates.

This paper presents a brain-computer interface (BCI) that can help users to input phone numbers. The system is based on the steady-state visual evoked potential (SSVEP). Twelve buttons illuminated at different rates were displayed on a computer monitor. The buttons constituted a virtual telephone keypad, representing the ten digits 0-9, BACKSPACE, and ENTER. Users could input phone number by gazing at these buttons. The frequency-coded SSVEP was used to judge which button the user desired. Eight of the thirteen subjects succeeded in ringing the mobile phone using the system. The average transfer rate over all subjects was 27.15 bits/min. The attractive features of the system are noninvasive signal recording, little training required for use, and high information transfer rate. Approaches to improve the performance of the system are discussed.

Activities of Daily Living↗
PubMed2003

Cine MPR: interactive multiplanar reformatting of four-dimensional cardiac data using hardware-accelerated texture mapping.

Four-dimensional (4-D) imaging to capture the three-dimensional (3-D) structure and motion of the heart in real time is an emerging trend. We present here our method of interactive multiplanar reformatting (MPR), i.e., the ability to visualize any chosen anatomical cross section of 4-D cardiac images and to change its orientation smoothly while maintaining the original heart motion. Continuous animation to show the time-varying 3-D geometry of the heart and smooth dynamic manipulation of the reformatted planes, as well as large image size (100-300 MB), make MPR challenging. Our solution exploits the hardware acceleration of 3-D texture mapping capability of high-end commercial PC graphics boards. Customization of volume subdivision and caching concepts to periodic cardiac data allows us to use this hardware effectively and efficiently. We are able to visualize and smoothly interact with real-time 3-D ultrasound cardiac images at the desired frame rate (25 Hz). The developed methods are applicable to MPR of one or more 3-D and 4-D medical images, including 4-D cardiac images collected in a gated fashion.

Computing Methodologies↗
PubMed2005

Constructive feedforward neural networks using hermite polynomial activation functions.

In this paper, a constructive one-hidden-layer network is introduced where each hidden unit employs a polynomial function for its activation function that is different from other units. Specifically, both a structure level as well as a function level adaptation methodologies are utilized in constructing the network. The functional level adaptation scheme ensures that the "growing" or constructive network has different activation functions for each neuron such that the network may be able to capture the underlying input-output map more effectively. The activation functions considered consist of orthonormal Hermite polynomials. It is shown through extensive simulations that the proposed network yields improved performance when compared to networks having identical sigmoidal activation functions.

Algorithms↗
PubMed1977

Cerebral monitoring by compressed spectral array.

Application of a frequency analysis technique, the compressed spectral array (CSA), permits the display of cerebral activity recorded by the electroencephalogram (EEG) over long periods of time in a succinct, graphic manner. This report is a description of a system which is being developed to investigate long-term monitoring of the EEGs of critically ill patients. The computer-based methodology which has been used to implement this system is described, with illustrations of CSA-transformed EEGs.

Adult↗
PubMed2006

Quantification of the 3D relative movement of external marker sets vs. bones based on magnetic resonance imaging.

BACKGROUND: Most in vivo knee kinematic analyses are based on external markers attached to the shank and the thigh. Literature data show that markers positioning and soft tissues artifacts affect the kinematic parameters of the bones true movement. Most of the techniques of quantification used were invasive. The aim of the present study was to develop and apply a non-invasive methodology to compute the relative movement between the bones and the markers. METHODS: Magnetic resonance imaging acquisitions were performed on the right knee of eleven volunteers without knee injury. The subjects were equipped with external magnetic resonance imaging-compatible marker sets. A foot drive device allowed the subjects to perform an actively loaded knee extension. The whole volume of the subject's knee was processed for four sequentially held knee flexion positions during the knee movement. The bones and external marker sets geometry were reconstructed from magnetic resonance imaging images. Then a registration algorithm was applied to the bones and the relative movement of the thigh and shank marker sets with respect to their underlying bones was computed. FINDINGS: The protocol resulted in a good geometrical accuracy and reproducibility. Marker sets movement differ from that of the bones with a maximum of 22 mm in translation and 15 degrees in rotation and it affects the knee kinematics. INTERPRETATION: Marker sets relative movement modify the knee movement finite helical axes direction (range 10-35 degrees ) and localization (range 0-40 mm). The methodology developed can evaluate external marker set system to be used for kinematic analysis in a clinical environment.

Adult↗
PubMed2006

Major advances in genetic evaluation techniques.

The past quarter-century in genetic evaluation of dairy cattle has been marked by evolution in methodology and computer capacity, expansion in the array of evaluated traits, and globalization. Animal models replaced sire and sire-maternal grandsire models and, more recently, application of Bayesian theory has become standard. Individual test-day observations have been used more effectively in estimation of lactation yield or directly as input to evaluation models. Computer speed and storage are less limiting in choosing procedures. The increased capabilities have supported evaluation of additional traits that affect the net profitability of dairy cows. The importance of traits other than yield has increased, in a few cases due to an antagonistic relationship with yield. National evaluations combined internationally provide evaluations for bulls from all participating countries on each of the national scales, facilitating choices from among many more bulls. Selection within countries has increased inbreeding and the use of similar genetics across countries reduces the previously available outcross population. Concern about inbreeding has prompted changes in evaluation methodology and mating practices, and has promoted interest in crossbreeding. In just the past decade, distribution of genetic evaluations has gone from mailed paper or computer tapes for a limited audience to publicly accessible, request-driven distribution via the Internet. Among the distributed information is a choice of economic indices that combine an increasing array of traits into numbers reflecting breeding goals under different milk-pricing conditions. Considerable progress in genomics and the mapping of the bovine genome have identified markers for some deleterious recessive genes, but broader benefits of marker-assisted selection are still in the future. A possible exception is the proprietary use of DNA testing by semen producers to select among potential progeny test bulls. The collection and analysis of industry-wide data to evaluate genetic merit will continue to be the most important tool for genetic progress into the foreseeable future.

Animals↗
PubMed2003

MICAS: a fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences.

MICAS is a web server for extracting microsatellite information from completely sequenced prokaryote and viral genomes, or user-submitted sequences. This server provides an integrated platform for MICdb (database of prokaryote and viral microsatellites), W-SSRF (simple sequence repeat finding program) and Autoprimer (primer design software). MICAS, through dynamic HTML page generation, helps in the systematic extraction of microsatellite information from selected genomes hosted on MICdb or from user-submitted sequences. Further, it assists in the design of primers with the help of Autoprimer, for sequences containing selected microsatellite tracts.

Algorithms↗
PubMed1984

Demography of the Juang tribal population of Orissa.

Demographic analysis of genealogical data collected in 1954 for 23 Juang villages was undertaken employing indirect estimation techniques and computer projection methodology. Results indicated that this group did not feature the historically high fertility levels associated with Indian tribal groups, although fertility was higher than previously reported for the Juang. The population did feature a mortality differential, with worse mortality conditions than the Indian national population at this time. Reversed sexual mortality differentials, common in South Asian populations, were also present for the Juang. Computer projection investigation revealed a steadily growing population, in contrast to some Indian tribal groups faced with extinction.

Adolescent↗
PubMed1998

Computational methods for exon detection.

Computer methods for the complete and accurate detection of genes in vertebrate genomic sequences are still a long way to perfection. The intermediate task of identifying the coding moiety of genes (coding exons) is now reasonably well achieved using a combination of methods. After reviewing the intrinsic difficulties in interpreting vertebrate genomic sequences, this article presents the state-of-the-art, with an emphasis on similarity search methods and the resources available through Internet.

Animals↗
PubMed2005

High performance workflow implementation for protein surface characterization using grid technology.

BACKGROUND: This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence to the exposed residues of the protein surface. The implementation of this workflow is based on the Italian Grid.it project infrastructure, that is a network of several computational resources and storage facilities distributed at different grid sites. METHODS: Workflows are very common in Bioinformatics because they allow to process large quantities of data by delegating the management of resources to the information streaming. Grid technology optimizes the computational load during the different workflow steps, dividing the more expensive tasks into a set of small jobs. RESULTS: Grid technology allows efficient database management, a crucial problem for obtaining good results in Bioinformatics applications. The proposed workflow is implemented to integrate huge amounts of data and the results themselves must be stored into a relational database, which results as the added value to the global knowledge. CONCLUSION: A web interface has been developed to make this technology accessible to grid users. Once the workflow has started, by means of the simplified interface, it is possible to follow all the different steps throughout the data processing. Eventually, when the workflow has been terminated, the different features of the protein, like the amino acids exposed on the protein surface, can be compared with the data present in the output database.

Automation↗
PubMed2003

myGrid: personalised bioinformatics on the information grid.

MOTIVATION: The (my)Grid project aims to exploit Grid technology, with an emphasis on the Information Grid, and provide middleware layers that make it appropriate for the needs of bioinformatics. (my)Grid is building high level services for data and application integration such as resource discovery, workflow enactment and distributed query processing. Additional services are provided to support the scientific method and best practice found at the bench but often neglected at the workstation, notably provenance management, change notification and personalisation. RESULTS: We give an overview of these services and their metadata. In particular, semantically rich metadata expressed using ontologies necessary to discover, select and compose services into dynamic workflows.

Computational Biology↗
PubMed2002

Telerehabilitation research: emerging opportunities.

The field of clinical rehabilitation is rooted in the premise that carefully planned and delivered therapeutic intervention enhances patient outcomes. Underlying this statement is a deeper scientific reality: The field exists because biosystems (e.g., tissues, cells, organs, persons) are inherently adaptive and can dynamically change as a function of a sequence of inputs (e.g., exercise, pharmaceuticals). The tools of telerehabilitation help minimize the barrier of distance, both of patients to rehabilitative services and of researchers to subject populations. This enhanced access opens up new possibilities for discovering and implementing optimized intervention strategies across the continuum of care. Telecommunications technologies are reviewed from the perspective of systems models of the telerehabilitation process, with a focus on human-technology interface design and a special emphasis on emerging home and mobile technologies. Approaches for providing clinical rehabilitation services through telerehabilitation are addressed, including innovative consumer-centered approaches. Finally, telerehabilitation is proposed as a tool for reinvigorating the rehabilitative bioengineering research enterprise.

Computing Methodologies↗