When directly manipulating 3D objects in an immersive environment we cannot normally achieve the accuracy and control that we have in the real world. This reduced accuracy stems from hand instability. We present PRISM, which dynamically adjusts the C/D ratio between the hand and the controlled object to provide increased control when moving slowly and direct, unconstrained interaction when moving rapidly. We describe PRISM object translation and rotation and present user studies demonstrating their effectiveness. In addition, we describe a PRISMenhanced version of ray casting which is shown to increase the speed and accuracy of object selection.

BackgroundNucleic acids containing guanine tracts can form quadruplex structures via non-Watson-Crick base pairing. Formation of G-quadruplexes is associated with the regulation of important biological functions such as transcription, genetic instability, DNA repair, DNA replication, epigenetic mechanisms, regulation of translation, and alternative splicing. G-quadruplexes play important roles in human diseases and are being considered as targets for a variety of therapies. Identification of functional G-quadruplexes and the study of their overall distribution in genomes and transcriptomes is an important pursuit. Traditional computational methods map sequence motifs capable of forming G-quadruplexes but have difficulty in distinguishing motifs that occur by chance from ones which fold into G-quadruplexes.ResultsWe present Quadruplex forming ‘G’-rich sequences (QGRS)-Conserve, a computational method for calculating motif conservation across exomes and supports filtering to provide researchers with more precise methods of studying G-quadruplex distribution patterns. Our method quantitatively evaluates conservation between quadruplexes found in homologous nucleotide sequences based on several motif structural characteristics. QGRS-Conserve also efficiently manages overlapping G-quadruplex sequences such that the resulting datasets can be analyzed effectively.ConclusionsWe have applied QGRS-Conserve to identify a large number of G-quadruplex motifs in the human exome conserved across several mammalian and non-mammalian species. We have successfully identified multiple homologs of many previously published G-quadruplexes that play post-transcriptional regulatory roles in human genes. Preliminary large-scale analysis identified many homologous G-quadruplexes in the 5′- and 3′-untranslated regions of mammalian species. An expectedly smaller set of G-quadruplex motifs was found to be conserved across larger phylogenetic distances. QGRS-Conserve provides means to build datasets that can be filtered and categorized in a variety of biological dimensions for more targeted studies in order to better understand the roles that G-quadruplexes play.

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Naturally occurring G-quadruplex structural motifs, formed by guanine-rich nucleic acids, have been reported in telomeric, promoter and transcribed regions of mammalian genomes. G-quadruplex structures have received significant attention because of growing evidence for their role in important biological processes, human disease and as therapeutic targets. Lately, there has been much interest in the potential roles of RNA G-quadruplexes as cis-regulatory elements of post-transcriptional gene expression. Large-scale computational genomics studies on G-quadruplexes have difficulty validating their predictions without laborious testing in ‘wet’ labs. We have developed a bioinformatics tool, QGRS-H Predictor that can map and analyze conserved putative Quadruplex forming 'G'-Rich Sequences (QGRS) in mRNAs, ncRNAs and other nucleotide sequences, e.g. promoter, telomeric and gene flanking regions. Identifying conserved regulatory motifs helps validate computations and enhances accuracy of predictions. The QGRS-H Predictor is particularly useful for mapping homologous G-quadruplex forming sequences as cis-regulatory elements in the context of 5′- and 3′-untranslated regions, and CDS sections of aligned mRNA sequences. QGRS-H Predictor features highly interactive graphic representation of the data. It is a unique and user-friendly application that provides many options for defining and studying G-quadruplexes. The QGRS-H Predictor can be freely accessed at: http://quadruplex.ramapo.edu/qgrs/app/start.

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Object selection and manipulation in 3D immersive environments generally suffers from a lack of precision, primarily due to hand instability and tracking noise. Typically the lack of precision is exacerbated as the user begins to use techniques that allow distant interaction, such as Ray Casting, HOMER, and Go-Go. This problem can be addressed using velocity-based hand scaling such as PRISM, which has been applied to Ray Casting and HOMER previously. We present a study of the combination of Go-Go and PRISM. In our research, we have found that Go-Go + PRISM yields a nearly 2:1 improvement in precision over traditional Go-Go interaction when attempting to align two objects at a distance under time constraints

Groupware applications such as AOL's Instant Messenger and Microsoft's NetMeeting have been growing in popularity in the general public for many years, starting with students on college campuses and more recently gaining acceptance in the business world as effective tools to aid in communication and productivity. Although many of these technologies were first popularized on college campuses, their use has yet to be integrated into the student/instructor teaching relationship, remaining more widely used between students for social purposes. In this paper we present the Cimel Collaborative Tools, a set of integrated groupware applications designed to improve communication between students and instructors and promote an active learning environment for students. In addition to the standard contact list and text messaging functionality, the Cimel Collaborative Tools provide a desktop sharing tool and a course-specific frequently asked questions (FAQ) database.

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