Unique and conserved MicroRNAs in wheat chromosome 5D revealed by next-generation sequencing

MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat

Pattern based processing of XPath queries

As the popularity of areas including document storage and distributed systems continues to grow, the demand for high performance XML databases is increasingly evident. This has led to a number of research eorts aimed at exploiting the maturity of relational database systems in order to in- crease XML query performance. In our approach, we use an index structure based on a metamodel for XML databases combined with relational database technology to facilitate fast access to XML document elements. The query process involves transforming XPath expressions to SQL which can be executed over our optimised query engine. As there are many dierent types of XPath queries, varying processing logic may be applied to boost performance not only to indi- vidual XPath axes, but across multiple axes simultaneously. This paper describes a pattern based approach to XPath query processing, which permits the execution of a group of XPath location steps in parallel

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.

SummaryThe Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB's integrated MyPDB service.Availability and implementationRCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org)

Augmenting conversations through context-aware multimedia retrieval based on speech recognition

Future’s environments will be sensitive and responsive to the presence of people to support them carrying out their everyday life activities, tasks and rituals, in an easy and natural way. Such interactive spaces will use the information and communication technologies to bring the computation into the physical world, in order to enhance ordinary activities of their users. This paper describes a speech-based spoken multimedia retrieval system that can be used to present relevant video-podcast (vodcast) footage, in response to spontaneous speech and conversations during daily life activities. The proposed system allows users to search the spoken content of multimedia files rather than their associated meta-information and let them navigate to the right portion where queried words are spoken by facilitating within-medium searches of multimedia content through a bag-of-words approach. Finally, we have studied the proposed system on different scenarios by using vodcasts in English from various categories, as the targeted multimedia, and discussed how it would enhance people’s everyday life activities by different scenarios including education, entertainment, marketing, news and workplace

Shared Arrangements: practical inter-query sharing for streaming dataflows

Current systems for data-parallel, incremental processing and view maintenance over high-rate streams isolate the execution of independent queries. This creates unwanted redundancy and overhead in the presence of concurrent incrementally maintained queries: each query must independently maintain the same indexed state over the same input streams, and new queries must build this state from scratch before they can begin to emit their first results. This paper introduces shared arrangements: indexed views of maintained state that allow concurrent queries to reuse the same in-memory state without compromising data-parallel performance and scaling. We implement shared arrangements in a modern stream processor and show order-of-magnitude improvements in query response time and resource consumption for interactive queries against high-throughput streams, while also significantly improving performance in other domains including business analytics, graph processing, and program analysis

Track My Hoist

Construction sites all over the world rely on hoist lifts for transporting material and workers at the job site. Despite being such an integral part of construction projects, there is currently no tool to track the use of this critical and highly necessary piece of equipment at the construction site. The purpose of this project is to design a systemthat would enable the managers and employees of construction companies to efficiently track and manage the hoist lifts at their sites. Efficient tracking and management of the lifts would result in savings of cost, time, and energy for the construction companies. Such improvements would also help boost worker morale, which would consequently boost productivity. Over the course of this project the team has designed an interactive yet intuitive software application that helps effectively track and manage hoist lifts on construction sites

Using SPARQL – the practitioners’ viewpoint

A number of studies have analyzed SPARQL log data to draw conclusions about how SPARQL is being used. To complement this work, a survey of SPARQL users has been undertaken. Whilst confirming some of the conclusions of the previous studies, the current work is able to provide additional insight into how users create SPARQL queries, the difficulties they encounter, and the features they would like to see included in the language. Based on this insight, a number of recommendations are presented to the community. These relate to predicting and avoiding computationally expensive queries; extensions to the language; and extending the search paradigm