Perceptions and Responsiveness to Intimacy with Robots; A User Evaluation

In human-robot interactions research it is significant to question what measures humans will take to contest the challenges and what will become of them. Levy hypothesizes that robots will stimulate human senses with their many capabilities and humans will accept them as intimate companions because the human perception of intimacy will transform to accommodate various nuances. However, the question remains, how much humans understand and accept intimacies with robots. We argue that perceptions of human-robot interactions (HRI) and intimate interactions with robots have a certain impact on how individuals comprehend intimacies with robots. Long term contact with robots, in terms of robotic technology and conversations, will change our views and practices regarding intimacy with robots. Our study revealed that lack of awareness of the potentials of future AI robots has created a fear; fear of losing both tangible, intangible, and the sense of dominance. Yet, our participants’ intimate interactions with robots produced varying degree of responses that, we believe are revealing another scope of human-robot interactions

A Preliminary survey of domiciliary cockroaches and their oothecal parasites in Sri Lanka

A survey of domiciliary cockroaches and their oothecal parasites was carriedout in 17 districts. The study was based on empty and live cockroach oothecaecollected from dwelling houses. Five species of cockroaches; Periplanetaamericana (L.) Neostylopyga rhombifolia (Stoll) Periplaneta australasiae (F.)Supella longfpalpa (F.) and Blatella germanica (L.) were found frequentinghouses. Of them, P. american a was the most abundant and widely distributedspecies, while B. germanlca was the least abundant species. P. americana andN. rhombifolia were present in all but one district, while P. australaslae and S.longipalpa were confined to 12 and 08 districts respectively. Mannar districtwas peculiar in that only one domiciliary species, N. rhombifolia was recordedfrom there. Only two species of oothecal parasites, Tetrastlchus hagenowli(Ratz.) and Evania appendlgaster (L.) were encountered during the study. Eachof these parasite species was characterized by the size of the emergence hole theymade in cockroach oothecae. Thus on the basis of the emergence hole alone itwas possible to categorize the empty oothecae as being parasitized. Of theoothecae, those of P. americana and P. australiasae were parasitized by bothspecies of parasites, while oothecae of N. rhombifolla was parasitized by T.hagenowii only. Oothecae of S. longipalpa and B. germanica were not parasitiizedat all. There appears to be a great paucity in the oothecal parasite fauna ofSri Lanka, compared to India where eight species of hymenopterans are known toparasitize oothecae of domiciliary cockroaches. The possibility of controllinghousehold cockroaches using local and introduced parasites remains to be explored.The shortcomings in this preliminary survey are also reported

Automated reconstruction and comparison of metabolic models for diverse fungal genomes

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Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium.

We report here the 4.9-Mb genome sequence of a quinoline-degrading bacterium, Rhodococcus sp. strain ATCC 49988. The draft genome data will enable the identification of genes and future genetic modification to enhance traits relevant to heteroaromatic compound degradation

Novel antibiotic-loaded particles conferring eradication of deep tissue bacterial reservoirs for the treatment of chronic urinary tract infection

A significant proportion of urinary tract infection (UTI) patients experience recurrent episodes, due to deep tissue infection and treatment-resistant bacterial reservoirs. Direct bladder instillation of antibiotics has proved disappointing in treating UTI, likely due to the failure of infused antibiotics to penetrate the bladder epithelium and accumulate to high enough levels to kill intracellular bacteria. This work investigates the use of nitrofurantoin loaded poly(lactic-co-glycolic acid) (PLGA) particles to improve delivery to intracellular targets for the treatment of chronic UTI. Using electrohydrodynamic atomisation, we produced particles with an average diameter of 2.8 μm. In broth culture experiments, the biodegradable particles were effective against a number of UTI-relevant bacterial strains. Dye-loaded particles demonstrated that intracellular delivery was achieved in all cells in 2D cultures of a human bladder epithelial progenitor cell line in a dose-dependent manner, achieving far higher efficiency and concentration than equivalent quantities of free drug. Time-lapse video microscopy confirmed that delivery occurred within 30 min of administration, to 100% of cells. Moreover, the particles were able to deliver the drug to cells through multiple layers of a 3D human bladder organoid model causing minimal cell toxicity, displaying superior killing of bacterial reservoirs harboured within bladder cells compared with unencapsulated drug. The particles were also able to kill bacterial biofilms more effectively than the free drug. These results illustrate the potential for using antibiotic-loaded microparticles to effectively treat chronic UTIs. Such a delivery method could be extrapolated to other clinical indications where robust intracellular delivery is required, such as oncology and gene therapy

Evolution of substrate specificity in a retained enzyme driven by gene loss.

The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes

Computing and applying atomic regulons to understand gene expression and regulation

The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb.2016.01819/full#supplementary-materialUnderstanding gene function and regulation is essential for the interpretation prediction and ultimate design of cell responses to changes in the environment. An important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. These gene sets Atomic Regulons ARs represent fundamental units of function within a cell and could be used to associate genes of unknown function with cellular processes and to enable rational genetic engineering of cellular systems. Here we describe an approach for inferring ARs that leverages large-scale expression data sets gene context and functional relationships among genes. We computed ARs for Escherichia coli based on 907 gene expression experiments and compared our results with gene clusters produced by two prevalent data-driven methods: hierarchical clustering and k-means clustering. We compared ARs and purely data-driven gene clusters to the curated set of regulatory interactions for E. coli found in RegulonDB showing that ARs are more consistent with gold standard regulons than are data-driven gene clusters. We further examined the consistency of ARs and data-driven gene clusters in the context of gene interactions predicted by Context Likelihood of Relatedness CLR analysis finding that the ARs show better agreement with CLR predicted interactions. We determined the impact of increasing amounts of expression data on AR construction and find that while more data improve ARs it is not necessary to use the full set of gene expression experiments available for E. coli to produce high quality ARs. In order to explore the conservation of co-regulated gene sets across different organisms we computed ARs for Shewanella oneidensis Pseudomonas aeruginosa Thermus thermophilus and Staphylococcus aureus each of which represents increasing degrees of phylogenetic distance from E. coli. Comparison of the organism-specific ARs showed that the consistency of AR gene membership correlates with phylogenetic distance but there is clear variability in the regulatory networks of closely related organisms. As large scale expression data sets become increasingly common for model and non-model organisms comparative analyses of atomic regulons will provide valuable insights into fundamental regulatory modules used across the bacterial domain.JF acknowledges funding from [SFRH/BD/70824/2010] of the FCT (Portuguese Foundation for Science and Technology) PhD program. CH and PW were supported by the National Science Foundation under grant number EFRI-MIKS-1137089. RT was supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), U.S. Department of Energy(DOE),and his work is a contribution of the Pacific North west National Laboratory (PNNL) Foundational Scientific Focus Area. This work was partially supported by an award from the National Science Foundation to MD, AB, NT, and RO (NSFABI-0850546). This work was also supported by the United States National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Service [Contract No. HHSN272201400027C]

Improving automated model reconstruction across phylogenetically diverse genome-scale metabolic models

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Automated pathway curation and improving metabolic model reconstruction based on phylogenetic analysis of pathway conservation

ICSB 2017 - 18th International Conference on Systems BiologyMetabolic models generated by automated reconstruction pipelines are widely used for high-throughput prediction of microbial phenotypes. However, the generation of accurate in-silico phenotype predictions based solely on genomic data continues to be a challenge as metabolic models often require extensive gapfilling in order to produce biomass. As a result, the true physiological profile of an organism can be altered by the addition of non-native biochemical pathways or reactions during the gapfilling process. In this study, we constructed draft genome-scale metabolic models for ~1000 diverse set of reference microbial genomes currently available in GenBank, and we decomposed these models into a set of classical biochemical pathways. We then determine the extent to which each pathway is either consistently present or absent in each region of the phylogenetic tree, and we study the degree of conservation in the specific steps where gaps exist in each pathway across a phylogenetic neighborhood. Based on this analysis, we improved the reliability of our gapfilling algorithms, which in turn, improved the reliability of our models in predicting auxotrophy. This also resulted in improvements to the genome annotations underlying our models. We validated our improved auxotrophy predictions using growth condition data collected for a diverse set of organisms. Our improved gapfilling algorithm will be available for use within the DOE Knowledgebase (KBase) platform (https://kbase.us).info:eu-repo/semantics/publishedVersio

Bird communities and feeding guilds in Monaragala, an isolated hill in the eastern intermediate zone of Sri Lanka

The bird communities and foraging guilds were studied in the entire forest of Monaragala hill, by recording species and their abundances, in 33 plots (each 100x20 m), in four transects laid along its altitudinal gradient. Bird calls and sightings were noted for 30 minutes between 7.00-9.30 am, twice each month from 2004-2008.The communities were determined, by cluster and ordination analyses of data in all plots. For each community, relative abundance (RA) and frequency (RF) were calculated. Species were assigned to bird guilds based on their habitats, main food types and feeding strategies, from published informationWithin and outside the plots sampled, 112 bird species (23% of Sri Lanka‟s avifauna, including eight endemics) in 84 genera, 44 families and 13 orders, were recorded. Three communities were identified: i. a low/mid-elevation disturbed forest community (LDFC), inhabited by 40 species (including seven endemics). The Crimson-Fronted Barbet, Black Crested Bulbul and Tickell‟s Blue Flycatcher co-dominated it. ii. a ridge/upper-elevation undisturbed forest community (RUFC) of 45 species that included eight endemics, nine restricted species, the wet zone Sri Lanka Yellow Fronted Barbet and Sri Lanka Wood Pigeon. The Black Bulbul and Sri Lanka Yellow Fronted Barbet were its dominants. Thirty three species were common to both forest communities. iii. a grassland community, with only 10 non-endemic species, dominated by the Crested Tree Swift and Indian Swiftlet. Three grassland species were also seen in the forest communities.In each forest community ten bird guilds were present. The arboreal frugivore and gleaning insectivore guilds ranked highest in them, followed by the hawking/hovering insectivore guild in the LDFC, and the omnivore gleaning guild in the RUFC. The grassland community had only three guilds. Based on RA the sweeping insectivore guild and on RF the aerial carnivore and the sweeping insectivore guilds were co-dominant. The arboreal granivore guild was restricted to the grasslandThe study revealed that this intermediate zone, 43 km2 isolated hill (1,100 m amsl) harbors a rich avifauna, including some typical wet zone species, and rich populations of the rare Sri Lanka Spur fowl and the Sri Lanka Wood pigeon, justifying its high conservation value