Browsing protein families via the 'Rich Family Description' format.
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MOTIVATION: Multiple alignments of protein sequences are the basis of structural and functional analysis of protein families. It is however difficult even for an expert biologist to comprehend an alignment of more than 50 to 100 homologous sequences. RESULTS: This paper presents a browser for the analysis of multiple alignments of large numbers of protein sequences. Phylogenetic trees and consensus sequences are computed and used to summarise the alignments; these data are stored in a structure called Rich Family Description. Summary alignments and trees are displayed in HTML pages and can be developed or reduced by the user. This browser is used to display the ProDom domain families on the Web. Its zooming facilities allow extracting information from alignments of more than 1000 homologous sequences. (+info)
A platform for integrating threading results with protein family analyses.
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We have developed a package for the interactive visualization of results from different threading programs. Additionally, we have integrated relevant information about protein sequence, function, evolution, and structure into the interface. (+info)
WebPHYLIP: a web interface to PHYLIP.
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A web interface to PHYLIP (version 3.57 C) is implemented using CGI/Perl programming. It enables users to do phylogenetic analysis through the Internet. (+info)
Comprehensive gene expression profile of the adult human renal cortex: analysis by cDNA array hybridization.
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BACKGROUND: Profiling of gene expression in healthy and diseased renal tissue is important for elucidating the pathogenesis of renal diseases. Comprehensive information about the genes expressed in renal tissue is unavailable. The recently developed cDNA array hybridization methodology allows simultaneous monitoring of thousands of genes expressed renal tissue. METHODS: Complex [alpha-33P]-labeled cDNA probes were prepared from histopathologically uninvolved remnants of nine renal tissues obtained by nephrectomy. Each probe was hybridized to a high-density array of 18,326 paired target genes. The radioactive hybridization signals by phosphorimager screens were quantitated by special software. Bioinformatics from public genomic databases were used to assign a chromosomal location of each expressed transcript and gene function. Cluster analysis was used to arrange genes according to the similarity in pattern of gene expression. RESULTS: A total of 7563 different gene transcripts was detected in the nine tissue samples. Approximately 870 of these genes were full-length mRNA human transcripts (HT), and the remaining 6693 were expressed sequence tags (ESTs). The full-length transcripts were classified by function of the gene product and were listed with information of their chromosomal positions. To allow a comparison between gene expression in clinical and experimental studies, the mouse genes with known similar function to the human counterpart were included in the bioinformatics analysis. Cluster analysis of 502 full-length genes that are expressed in four or more renal tissues revealed more than 110 genes that are highly expressed in all the renal specimens. CONCLUSIONS: The presented data constitute a comprehensive preliminary transcriptional map of the adult human renal cortex. The information may serve as a resource for speeding up the discovery of genes underlying human renal disease. The integrated listing of the full-length expressed human and mouse genes is available through e-mail ([email protected]). (+info)
Elicited sequential presentation for low vision reading.
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This paper reports on a variant of the rapid serial visual presentation (RSVP) technique for low vision reading called elicited sequential presentation (ESP). In both techniques, words are presented sequentially at a constant screen location, but with ESP, the reader elicits presentation of each new word by means of a button press, rather than (as with RSVP) being presented with it automatically at fixed intervals. An experiment comparing reading speeds using, ESP, RSVP and a conventional closed-circuit television (CCTV) reading aid showed that for 15 slow readers who were customary CCTV users with low vision, ESP is superior to RSVP and yields reading speeds averaging 47% faster than RSVP--about the same as CCTV reading speed. The log of the ratio of ESP to RSVP reading speeds was significantly negatively correlated with the log of RSVP reading speed, showing that slower readers benefit more than faster readers; regression predicted no benefit for readers who read with RSVP at 133 wpm or greater. Finally, word length and word presentation duration chosen by subjects reading with ESP were significantly correlated, suggesting that part of the benefit of ESP is due to reader's ability to allocate time based on word length and difficulty. (+info)
Horizontal-disparity tuning of neurons in the visual forebrain of the behaving barn owl.
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Stereovision plays a major role in depth perception of animals having frontally-oriented eyes, most notably primates, cats, and owls. Neuronal mechanisms of disparity sensitivity have only been investigated in anesthetized owls so far. In the current study, responses of 160 visual Wulst neurons to static random-dot stereograms (RDS) were recorded via radiotelemetry in awake, fixating barn owls. The majority of neurons (76%) discharged significantly as a function of horizontal disparity in RDS. The distribution of preferred disparities mirrored the behaviorally relevant range of horizontal disparities that owls can exploit for depth vision. Most tuning profiles displayed periodic modulation and could well be fitted with a Gabor function as expected if disparity detectors were implemented according to the disparity energy model. Corresponding to this observation, a continuum of tuning profiles was observed rather than discrete categories. To assess a possible clustering of neurons with similar disparity-tuning properties, single units, and multi-unit activity recorded at individual recording sites were compared. Only a minority of neurons were clustered according to their disparity-tuning properties, suggesting that neurons in the visual Wulst are not organized into columns by preferred disparity. To assess whether variable vergence eye movements influenced tuning data, we correlated tuning peak positions on a trial-by-trial basis for units that were recorded simultaneously. The general lack of significant correlation between single-trial peak positions of simultaneously recorded units indicated that vergence, if at all, had only a minor influence on the data. Our study emphasizes the significance of visual Wulst neurons in analyzing stereoscopic depth information and introduces the barn owl as a second model system to study stereopsis in awake, behaving animals. (+info)
Parietal neurons represent surface orientation from the gradient of binocular disparity.
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In order to elucidate the neural mechanisms involved in the perception of the three-dimensional (3D) orientation of a surface, we trained monkeys to discriminate the 3D orientation of a surface from binocular disparity cues using a Go/No-go type delayed-matching-to-sample (DMTS) task and examined the properties of the surface-orientation-selective (SOS) neurons. We recorded 57 SOS neurons from the caudal part of the lateral bank of the intraparietal sulcus (area CIP) of three hemispheres of two Japanese monkeys (Macaca fuscata). We tested 29 of 57 SOS neurons using the square plate of a solid figure stereogram (SFS) and random-dot stereogram (RDS) without perspective cues; almost all of the tested neurons (28/29) showed surface orientation selectivity for the SFS and/or the RDS without perspective cues. Eight of these 28 neurons (28.6%) showed selectivity for both the RDS and SFS, 7 (25.0%) were dominantly selective for the RDS, and 13 (46.4%) were dominantly selective for the SFS. These results suggest that neurons that show surface orientation tuning for the RDS without perspective cues compute surface orientation from the gradient of the binocular disparity given by the random-dot across the surface. On the other hand, neurons that show surface orientation tuning for the SFS without perspective cues may represent surface orientation primarily from the gradient of the binocular disparity along the contours. In conclusion, the SOS neurons in the area CIP are likely to operate higher order processing of disparity signals for surface perception by integrating the input signals from many disparity-sensitive neurons with different disparity tuning. (+info)
Radiologist's clinical information review workstation interfaced with digital dictation system.
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Efficient access to information systems integrated into the radiologist's interpretation workflow will result in a more informed radiologist, with an enhanced capability to render an accurate interpretation. We describe our implementation of radStation, a radiologist's clinical information review workstation that combines a digital dictation station with a clinical information display. radStation uses client software distributed to the radiologist's workstation and central server software, both running Windows NT (Microsoft, Redmond, WA). The client system has integrated digital dictation software. The bar-code microphone (Boomerang, Dictaphone Corp, Stratford, CT) also serves as a computer input device forwarding the procedure's accession number to the server software. This initiates multiple queries to available legacy databases, including the radiology information system (RIS), laboratory information system, clinic notes, hospital discharge, and operative report system. The three-tier architecture then returns the clinical results to the radStation client for display. At the conclusion of the dictation, the digital voice file is transferred to the dictation server and the client notifies the RIS to update the examination status. The system is efficient in its information retrieval, with queries displayed in about 1 second. The radStation client requires less than 5 minutes of radiologist training in its operation, given that its control interface integrates with the well-learned dictation process. The telephone-based dictation system, which this new system replaced, remains available as a back-up system in the event of an unexpected digital dictation system failure. This system is well accepted and valued by the radiologists. The system interface is quickly mastered. The system does not interrupt dictation workflow with the display of all information initiated with examination bar-coding. This system's features could become an accepted model as a standard tool for radiologists. (+info)