PolyA_DB: a database for mammalian mRNA polyadenylation.

Messenger RNA polyadenylation is one of the key post-transcriptional events in eukaryotic cells. A large number of genes in mammalian species can undergo alternative polyadenylation, which leads to mRNAs with variable 3' ends. As the 3' end of mRNAs often contains cis elements important for mRNA stability, mRNA localization and translation, the implications of the regulation of polyadenylation can be multifold. Alternative polyadenylation is controlled by cis elements and trans factors, and is believed to occur in a tissue- or disease-specific manner. Given the availability of many databases devoted to other aspects of mRNA metabolism, such as transcriptional initiation and splicing, systematic information on polyadenylation, including alternative polyadenylation and its regulation, is noticeably lacking. Here, we present a database named polyA_DB, through which we strive to provide several types of information regarding polyadenylation in mammalian species: (i) polyadenylation sites and their locations with respect to the genomic structure of genes; (ii) cis elements surrounding polyadenylation sites; (iii) comparison of polyadenylation configuration between orthologous genes; and (iv) tissue/organ information for alternative polyadenylation sites. Currently, polyA_DB contains 45,565 polyadenylation sites for 25,097 human and mouse genes, representing the most comprehensive polyadenylation database till date. The database is accessible via the website (http://polya.umdnj.edu/polyadb).

EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites.

The availability of a draft human genome sequence and ability to monitor the transcription of thousands of genes with DNA microarrays has necessitated the need for new computational tools that can analyze cis-regulatory elements controlling genes that display similar expression patterns. We have developed a tool designated EZ-Retrieve that can: (i) retrieve any particular region of human genome sequence from the NCBI database and (ii) analyze retrieved sequences for putative transcription factor-binding sites (TFBSs) as they appear on the TRANSFAC database. The tool is web-based, user-friendly and offers both batch sequence retrieval and batch TFBS prediction. A major application of EZ-Retrieve is the analysis of co-expressed genes that are highlighted as expression clusters in DNA microarray experiments.

Allocentric spatial memory in humans with hippocampal lesions.

An immersive virtual reality (IVR) system was used to investigate allocentric spatial memory in a patient (PR) who had selective hippocampal damage, and also in patients who had undergone unilateral temporal lobectomies (17 right TL and 19 left TL), their performance compared against normal control groups. A human analogue of the Olton [Olton (1979). Hippocampus, space, and memory. Behavioural Brain Science, 2, 315] spatial maze was developed, consisting of a virtual room, a central virtual circular table and an array of radially arranged up-turned 'shells.' The participant had to search these shells in turn in order to find a blue 'cube' that would then 'move' to another location and so on, until all the shells had been target locations. Within-search errors could be made when the participants returned to a previously visited location during a search, and between-search errors when they revisited previously successful, but now incorrect locations. PR made significantly more between-search errors than his control group, but showed no increase in within-search errors. The right TL group showed a similar pattern of impairment, but the left TL group showed no impairment. This finding implicates the right hippocampal formation in spatial memory functioning in a scenario in which the visual environment was controlled so as to eliminate extraneous visual cues.

Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer.

BACKGROUND: A major goal of cancer research is to identify discrete biomarkers that specifically characterize a given malignancy. These markers are useful in diagnosis, may identify potential targets for drug development, and can aid in evaluating treatment efficacy and predicting patient outcome. Microarray technology has enabled marker discovery from human cells by permitting measurement of steady-state mRNA levels derived from thousands of genes. However many challenging and unresolved issues regarding the acquisition and analysis of microarray data remain, such as accounting for both experimental and biological noise, transcripts whose expression profiles are not normally distributed, guidelines for statistical assessment of false positive/negative rates and comparing data derived from different research groups. This study addresses these issues using Affymetrix HG-U95A and HG-U133 GeneChip data derived from different research groups. RESULTS: We present here a simple non parametric approach coupled with noise filtering to identify sets of genes differentially expressed between the normal and cancer states in oral, breast, lung, prostate and ovarian tumors. An important feature of this study is the ability to integrate data from different laboratories, improving the analytical power of the individual results. One of the most interesting findings is the down regulation of genes involved in tissue differentiation. CONCLUSIONS: This study presents the development and application of a noise model that suppresses noise, limits false positives in the results, and allows integration of results from individual studies derived from different research groups.

Virtual reality-augmented rehabilitation for patients following stroke.

BACKGROUND AND PURPOSE: Recent evidence indicates that intensive massed practice may be necessary to modify neural organization and effect recovery of motor skills in patients following stroke. Virtual reality (VR) technology has the capability of creating an interactive, motivating environment in which practice intensity and feedback can be manipulated to create individualized treatments to retrain movement. CASE DESCRIPTION: Three patients (ML, LE, and DK), who were in the chronic phase following stroke, participated in a 2-week training program (3 1/2 hours a day) including dexterity tasks on real objects and VR exercises. The VR simulations were targeted for range of motion, movement speed, fractionation, and force production. OUTCOMES: ML's function was the most impaired at the beginning of the intervention, but showed improvement in the thumb and fingers in range of motion and speed of movement. LE improved in fractionation and range of motion of his thumb and fingers. DK made the greatest gains, showing improvement in range of motion and strength of the thumb, velocity of the thumb and fingers, and fractionation. Two of the 3 patients improved on the Jebsen Test of Hand Function. DISCUSSION: The outcomes suggest that VR may be useful to augment rehabilitation of the upper limb in patients in the chronic phase following stroke.