QSRlib: a software library for online acquisition of qualitative spatial relations from video

There is increasing interest in using Qualitative Spatial Relations as a formalism to abstract from noisy and large amounts of video data in order to form high level conceptualisations, e.g. of activities present in video. We present a library to support such work. It is compatible with the Robot Operating System (ROS) but can also be used stand alone. A number of QSRs are built in; others can be easily added

Towards Safer Robot Motion: Using a Qualitative Motion Model to Classify Human-Robot Spatial Interaction

For adoption of Autonomous Mobile Robots (AMR) across a breadth of industries, they must navigate around humans in a way which is safe and which humans perceive as safe, but without greatly compromising efficiency. This work aims to classify the Human-Robot Spatial Interaction (HRSI) situation of an interacting human and robot, to be applied in Human-Aware Navigation (HAN) to account for situational context. We develop qualitative probabilistic models of relative human and robot movements in various HRSI situations to classify situations, and explain our plan to develop per-situation probabilistic models of socially legible HRSI to predict human and robot movement. In future work we aim to use these predictions to generate qualitative constraints in the form of metric cost-maps for local robot motion planners, enforcing more efficient and socially legible trajectories which are both physically safe and perceived as safe

Robot deployment in long-term care: a case study of a mobile robot in physical therapy

Background. Healthcare systems in industrialised countries are challenged to provide care for a growing number of older adults. Information technology holds the promise of facilitating this process by providing support for care staff, and improving wellbeing of older adults through a variety of support systems. Goal. Little is known about the challenges that arise from the deployment of technology in care settings; yet, the integration of technology into care is one of the core determinants of successful support. In this paper, we discuss challenges and opportunities associated with technology integration in care using the example of a mobile robot to support physical therapy among older adults with cognitive impairment in the European project STRANDS. Results and discussion. We report on technical challenges along with perspectives of physical therapists, and provide an overview of lessons learned which we hope will help inform the work of researchers and practitioners wishing to integrate robotic aids in the caregiving process

Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii

Toepel J, Albaum S, Arvidsson S, et al. Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii. BMC Genomics. 2011;12(1): 579.ABSTRACT: BACKGROUND: Chlamydomonas reinhardtii is widely accepted as a model organism regarding photosynthesis, circadian rhythm, cell mobility, phototaxis, and biotechnology. The complete annotation of the genome allows transcriptomic studies, however a new microarray platform was needed. Based on the completed annotation of Chlamydomonas reinhardtii a new microarray on an Agilent platform was designed using an extended JGI 3.1 genome data set which included 15000 transcript models. RESULTS: In total 44000 probes were determined (3 independent probes per transcript model) covering 93% of the transcriptome. Alignment studies with the recently published AUGUSTUS 10.2 annotation confirmed 11000 transcript models resulting in a very good coverage of 70% of the transcriptome (17000). Following the estimation of 10000 predicted genes in Chlamydomonas reinhardtii our new microarray, nevertheless, covers the expected genome by 90-95%. CONCLUSIONS: To demonstrate the capabilities of the new microarray, we analyzed transcript levels for cultures grown under nitrogen as well as sulfate limitation, and compared the results with recently published microarray and RNA-seq data. We could thereby confirm previous results derived from data on nutrient-starvation induced gene expression of a group of genes related to protein transport and adaptation of the metabolism as well as genes related to efficient light harvesting, light energy distribution and photosynthetic electron transport

The STRANDS project: long-term autonomy in everyday environments

Thanks to the efforts of the robotics and autonomous systems community, the myriad applications and capacities of robots are ever increasing. There is increasing demand from end users for autonomous service robots that can operate in real environments for extended periods. In the Spatiotemporal Representations and Activities for Cognitive Control in Long-Term Scenarios (STRANDS) project (http://strandsproject.eu), we are tackling this demand head-on by integrating state-of-the-art artificial intelligence and robotics research into mobile service robots and deploying these systems for long-term installations in security and care environments. Our robots have been operational for a combined duration of 104 days over four deployments, autonomously performing end-user-defined tasks and traversing 116 km in the process. In this article, we describe the approach we used to enable long-term autonomous operation in everyday environments and how our robots are able to use their long run times to improve their own performance

The STRANDS project: long-term autonomy in everyday environments

Thanks to the efforts of the robotics and autonomous systems community, the myriad applications and capacities of robots are ever increasing. There is increasing demand from end users for autonomous service robots that can operate in real environments for extended periods. In the Spatiotemporal Representations and Activities for Cognitive Control in Long-Term Scenarios (STRANDS) project (http://strandsproject.eu), we are tackling this demand head-on by integrating state-of-the-art artificial intelligence and robotics research into mobile service robots and deploying these systems for long-term installations in security and care environments. Our robots have been operational for a combined duration of 104 days over four deployments, autonomously performing end-user-defined tasks and traversing 116 km in the process. In this article, we describe the approach we used to enable long-term autonomous operation in everyday environments and how our robots are able to use their long run times to improve their own performance

Identification of genes differentially expressed in a resistant reaction to Mycosphaerella pinodes in pea using microarray technology

<p>Abstract</p> <p>Background</p> <p>Ascochyta blight, caused by <it>Mycosphaerella pinodes </it>is one of the most important pea pathogens. However, little is known about the genes and mechanisms of resistance acting against <it>M. pinodes </it>in pea. Resistance identified so far to this pathogen is incomplete, polygenic and scarce in pea, being most common in <it>Pisum </it>relatives. The identification of the genes underlying resistance would increase our knowledge about <it>M. pinodes-</it>pea interaction and would facilitate the introgression of resistance into pea varieties. In the present study differentially expressed genes in the resistant <it>P. sativum </it>ssp. <it>syriacum </it>accession P665 comparing to the susceptible pea cv. Messire after inoculation with <it>M. pinodes </it>have been identified using a <it>M. truncatula </it>microarray.</p> <p>Results</p> <p>Of the 16,470 sequences analysed, 346 were differentially regulated. Differentially regulated genes belonged to almost all functional categories and included genes involved in defense such as genes involved in cell wall reinforcement, phenylpropanoid and phytoalexins metabolism, pathogenesis- related (PR) proteins and detoxification processes. Genes associated with jasmonic acid (JA) and ethylene signal transduction pathways were induced suggesting that the response to <it>M. pinodes </it>in pea is regulated via JA and ET pathways. Expression levels of ten differentially regulated genes were validated in inoculated and control plants using qRT-PCR showing that the P665 accession shows constitutively an increased expression of the defense related genes as peroxidases, disease resistance response protein 39 (DRR230-b), glutathione S-transferase (GST) and 6a-hydroxymaackiain methyltransferase.</p> <p>Conclusions</p> <p>Through this study a global view of genes expressed during resistance to <it>M. pinodes </it>has been obtained, giving relevant information about the mechanisms and pathways conferring resistance to this important disease. In addition, the <it>M. truncatula </it>microarray represents an efficient tool to identify candidate genes controlling resistance to <it>M. pinodes </it>in pea.</p

Overlapping expression patterns and differential transcript levels of phosphate transporter genes in arbuscular mycorrhizal, Pi-fertilised and phytohormone-treated Medicago truncatula roots

A microarray carrying 5,648 probes of Medicago truncatula root-expressed genes was screened in order to identify those that are specifically regulated by the arbuscular mycorrhizal (AM) fungus Gigaspora rosea, by Pi fertilisation or by the phytohormones abscisic acid and jasmonic acid. Amongst the identified genes, 21% showed a common induction and 31% a common repression between roots fertilised with Pi or inoculated with the AM fungus G. rosea, while there was no obvious overlap in the expression patterns between mycorrhizal and phytohormone-treated roots. Expression patterns were further studied by comparing the results with published data obtained from roots colonised by the AM fungi Glomus mosseae and Glomus intraradices, but only very few genes were identified as being commonly regulated by all three AM fungi. Analysis of Pi concentrations in plants colonised by either of the three AM fungi revealed that this could be due to the higher Pi levels in plants inoculated by G. rosea compared with the other two fungi, explaining that numerous genes are commonly regulated by the interaction with G. rosea and by phosphate. Differential gene expression in roots inoculated with the three AM fungi was further studied by expression analyses of six genes from the phosphate transporter gene family in M. truncatula. While MtPT4 was induced by all three fungi, the other five genes showed different degrees of repression mirroring the functional differences in phosphate nutrition by G. rosea, G. mosseae and G. intraradices

Finding a Needle in the Virus Metagenome Haystack - Micro-Metagenome Analysis Captures a Snapshot of the Diversity of a Bacteriophage Armoire

Viruses are ubiquitous in the oceans and critical components of marine microbial communities, regulating nutrient transfer to higher trophic levels or to the dissolved organic pool through lysis of host cells. Hydrothermal vent systems are oases of biological activity in the deep oceans, for which knowledge of biodiversity and its impact on global ocean biogeochemical cycling is still in its infancy. In order to gain biological insight into viral communities present in hydrothermal vent systems, we developed a method based on deep-sequencing of pulsed field gel electrophoretic bands representing key viral fractions present in seawater within and surrounding a hydrothermal plume derived from Loki's Castle vent field at the Arctic Mid-Ocean Ridge. The reduction in virus community complexity afforded by this novel approach enabled the near-complete reconstruction of a lambda-like phage genome from the virus fraction of the plume. Phylogenetic examination of distinct gene regions in this lambdoid phage genome unveiled diversity at loci encoding superinfection exclusion- and integrase-like proteins. This suggests the importance of fine-tuning lyosgenic conversion as a viral survival strategy, and provides insights into the nature of host-virus and virus-virus interactions, within hydrothermal plumes. By reducing the complexity of the viral community through targeted sequencing of prominent dsDNA viral fractions, this method has selectively mimicked virus dominance approaching that hitherto achieved only through culturing, thus enabling bioinformatic analysis to locate a lambdoid viral “needle" within the greater viral community “haystack". Such targeted analyses have great potential for accelerating the extraction of biological knowledge from diverse and poorly understood environmental viral communities