3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions

BACKGROUND:Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a given nucleic acid sequence and reliably identifies clusters of short CAC-containing motifs required for mRNA localization in Xenopus oocytes.DESCRIPTION:In order to facilitate the identification of genes possessing clusters of repeats that regulate post-transcriptional aspects of gene expression in mammalian genes, we used REPFIND to create a database of all repeated motifs in the 3' untranslated regions (UTR) of genes from the Mammalian Gene Collection (MGC). The MGC database includes seven vertebrate species: human, cow, rat, mouse and three non-mammalian vertebrate species. A web-based application was developed to search this database of repeated motifs to generate species-specific lists of genes containing specific classes of repeats in their 3'-UTRs. This computational tool is called 3'-UTR SIRF (Short Interspersed Repeat Finder), and it reveals that hundreds of human genes contain an abundance of short CAC-rich and CAG-rich repeats in their 3'-UTRs that are similar to those found in mRNAs localized to the neurites of neurons. We tested four candidate mRNAs for localization in rat hippocampal neurons by in situ hybridization. Our results show that two candidate CAC-rich (Syntaxin 1B and Tubulin beta4) and two candidate CAG-rich (Sec61alpha and Syntaxin 1A) mRNAs are localized to distal neurites, whereas two control mRNAs lacking repeated motifs in their 3'-UTR remain primarily in the cell body.CONCLUSION:Computational data generated with 3'-UTR SIRF indicate that hundreds of mammalian genes have an abundance of short CA-containing motifs that may direct mRNA localization in neurons. In situ hybridization shows that four candidate mRNAs are localized to distal neurites of cultured hippocampal neurons. These data suggest that short CA-containing motifs may be part of a widely utilized genetic code that regulates mRNA localization in vertebrate cells. The use of 3'-UTR SIRF to search for new classes of motifs that regulate other aspects of gene expression should yield important information in future studies addressing cis-regulatory information located in 3'-UTRs.

Camera Canvas: Image Editing Software for People with Disabilities

Poster is based on the following paper: C. Kwan and M. Betke. Camera Canvas: Image editing software for people with disabilities. In Proceedings of the 14th International Conference on Human Computer Interaction (HCI International 2011), Orlando, Florida, July 2011.

Discovering Clusters in Motion Time-Series Data

A new approach is proposed for clustering time-series data. The approach can be used to discover groupings of similar object motions that were observed in a video collection. A finite mixture of hidden Markov models (HMMs) is fitted to the motion data using the expectation-maximization (EM) framework. Previous approaches for HMM-based clustering employ a k-means formulation, where each sequence is assigned to only a single HMM. In contrast, the formulation presented in this paper allows each sequence to belong to more than a single HMM with some probability, and the hard decision about the sequence class membership can be deferred until a later time when such a decision is required. Experiments with simulated data demonstrate the benefit of using this EM-based approach when there is more "overlap" in the processes generating the data. Experiments with real data show the promising potential of HMM-based motion clustering in a number of applications.

Automated Camera Layout to Satisfy Task-Specific and Floorplan-Specific Coverage Requirements

In many multi-camera vision systems the effect of camera locations on the task-specific quality of service is ignored. Researchers in Computational Geometry have proposed elegant solutions for some sensor location problem classes. Unfortunately, these solutions utilize unrealistic assumptions about the cameras' capabilities that make these algorithms unsuitable for many real-world computer vision applications: unlimited field of view, infinite depth of field, and/or infinite servo precision and speed. In this paper, the general camera placement problem is first defined with assumptions that are more consistent with the capabilities of real-world cameras. The region to be observed by cameras may be volumetric, static or dynamic, and may include holes that are caused, for instance, by columns or furniture in a room that can occlude potential camera views. A subclass of this general problem can be formulated in terms of planar regions that are typical of building floorplans. Given a floorplan to be observed, the problem is then to efficiently compute a camera layout such that certain task-specific constraints are met. A solution to this problem is obtained via binary optimization over a discrete problem space. In experiments the performance of the resulting system is demonstrated with different real floorplans.

An Appearance-Based Framework for 3D Hand Shape Classification and Camera Viewpoint Estimation

An appearance-based framework for 3D hand shape classification and simultaneous camera viewpoint estimation is presented. Given an input image of a segmented hand, the most similar matches from a large database of synthetic hand images are retrieved. The ground truth labels of those matches, containing hand shape and camera viewpoint information, are returned by the system as estimates for the input image. Database retrieval is done hierarchically, by first quickly rejecting the vast majority of all database views, and then ranking the remaining candidates in order of similarity to the input. Four different similarity measures are employed, based on edge location, edge orientation, finger location and geometric moments.

Camera Canvas: Image Editor for People with Severe Disabilities

Camera Canvas is an image editing software package for users with severe disabilities that limit their mobility. It is specially designed for Camera Mouse, a camera-based mouse-substitute input system. Users can manipulate images through various head movements, tracked by Camera Mouse. The system is also fully usable with traditional mouse or touch-pad input. Designing the system, we studied the requirements and solutions for image editing and content creation using Camera Mouse. Experiments with 20 subjects, each testing Camera Canvas with Camera Mouse as the input mechanism, showed that users found the software easy to understand and operate. User feedback was taken into account to make the software more usable and the interface more intuitive. We suggest that the Camera Canvas software makes important progress in providing a new medium of utility and creativity in computing for users with severe disabilities.

Camera-Based Interfaces and Assistive Software for People with Sever Motion Impairments

Intelligent assistive technology can greatly improve the daily lives of people with severe paralysis, who have limited communication abilities. People with motion impairments often prefer camera-based communication interfaces, because these are customizable, comfortable, and do not require user-borne accessories that could draw attention to their disability. We present an overview of assistive software that we specifically designed for camera-based interfaces such as the Camera Mouse, which serves as a mouse-replacement input system. The applications include software for text-entry, web browsing, image editing, animation, and music therapy. Using this software, people with severe motion impairments can communicate with friends and family and have a medium to explore their creativity.

Music Maker – A Camera-based Music Making Tool for Physical Rehabilitation

The therapeutic effects of playing music are being recognized increasingly in the field of rehabilitation medicine. People with physical disabilities, however, often do not have the motor dexterity needed to play an instrument. We developed a camera-based human-computer interface called "Music Maker" to provide such people with a means to make music by performing therapeutic exercises. Music Maker uses computer vision techniques to convert the movements of a patient's body part, for example, a finger, hand, or foot, into musical and visual feedback using the open software platform EyesWeb. It can be adjusted to a patient's particular therapeutic needs and provides quantitative tools for monitoring the recovery process and assessing therapeutic outcomes. We tested the potential of Music Maker as a rehabilitation tool with six subjects who responded to or created music in various movement exercises. In these proof-of-concept experiments, Music Maker has performed reliably and shown its promise as a therapeutic device.

A Customizable Camera-based Human Computer Interaction System Allowing People With Disabilities Autonomous Hands Free Navigation of Multiple Computing Task

Many people suffer from conditions that lead to deterioration of motor control and makes access to the computer using traditional input devices difficult. In particular, they may loose control of hand movement to the extent that the standard mouse cannot be used as a pointing device. Most current alternatives use markers or specialized hardware to track and translate a user's movement to pointer movement. These approaches may be perceived as intrusive, for example, wearable devices. Camera-based assistive systems that use visual tracking of features on the user's body often require cumbersome manual adjustment. This paper introduces an enhanced computer vision based strategy where features, for example on a user's face, viewed through an inexpensive USB camera, are tracked and translated to pointer movement. The main contributions of this paper are (1) enhancing a video based interface with a mechanism for mapping feature movement to pointer movement, which allows users to navigate to all areas of the screen even with very limited physical movement, and (2) providing a customizable, hierarchical navigation framework for human computer interaction (HCI). This framework provides effective use of the vision-based interface system for accessing multiple applications in an autonomous setting. Experiments with several users show the effectiveness of the mapping strategy and its usage within the application framework as a practical tool for desktop users with disabilities.