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.

An Ounce of Prevention is Worth a Pound of Cure: Towards Physically-Correct Specifications of Embedded Real-Time Systems

Predictability — the ability to foretell that an implementation will not violate a set of specified reliability and timeliness requirements - is a crucial, highly desirable property of responsive embedded systems. This paper overviews a development methodology for responsive systems, which enhances predictability by eliminating potential hazards resulting from physically-unsound specifications. The backbone of our methodology is a formalism that restricts expressiveness in a way that allows the specification of only reactive, spontaneous, and causal computation. Unrealistic systems — possessing properties such as clairvoyance, caprice, infinite capacity, or perfect timing — cannot even be specified. We argue that this "ounce of prevention" at the specification level is likely to spare a lot of time and energy in the development cycle of responsive systems - not to mention the elimination of potential hazards that would have gone, otherwise, unnoticed.

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.

Wireless and Physical Security via Embedded Sensor Networks

Wireless Intrusion Detection Systems (WIDS) monitor 802.11 wireless frames (Layer-2) in an attempt to detect misuse. What distinguishes a WIDS from a traditional Network IDS is the ability to utilize the broadcast nature of the medium to reconstruct the physical location of the offending party, as opposed to its possibly spoofed (MAC addresses) identity in cyber space. Traditional Wireless Network Security Systems are still heavily anchored in the digital plane of "cyber space" and hence cannot be used reliably or effectively to derive the physical identity of an intruder in order to prevent further malicious wireless broadcasts, for example by escorting an intruder off the premises based on physical evidence. In this paper, we argue that Embedded Sensor Networks could be used effectively to bridge the gap between digital and physical security planes, and thus could be leveraged to provide reciprocal benefit to surveillance and security tasks on both planes. Toward that end, we present our recent experience integrating wireless networking security services into the SNBENCH (Sensor Network workBench). The SNBENCH provides an extensible framework that enables the rapid development and automated deployment of Sensor Network applications on a shared, embedded sensing and actuation infrastructure. The SNBENCH's extensible architecture allows an engineer to quickly integrate new sensing and response capabilities into the SNBENCH framework, while high-level languages and compilers allow novice SN programmers to compose SN service logic, unaware of the lower-level implementation details of tools on which their services rely. In this paper we convey the simplicity of the service composition through concrete examples that illustrate the power and potential of Wireless Security Services that span both the physical and digital plane.