Constructing abstract maps from spatial descriptions for goal-directed exploration

This paper describes ongoing work on a system using spatial descriptions to construct abstract maps that can be used for goal-directed exploration in an unfamiliar office environment. Abstract maps contain membership, connectivity, and spatial layout information extracted from symbolic spatial information. In goal-directed exploration, the robot would then link this information with observed symbolic information and its grounded world representation. We demonstrate the ability of the system to extract and represent membership, connectivity, and spatial layout information from spatial descriptions of an office environment. In the planned study, the robot will navigate to the goal location using the abstract map to inform the best direction to explore in.

Finding within-organisation spatial information on the web

Information available on company websites can help people navigate to the offices of groups and individuals within the company. Automatically retrieving this within-organisation spatial information is a challenging AI problem This paper introduces a novel unsupervised pattern-based method to extract within-organisation spatial information by taking advantage of HTML structure patterns, together with a novel Conditional Random Fields (CRF) based method to identify different categories of within-organisation spatial information. The results show that the proposed method can achieve a high performance in terms of F-Score, indicating that this purely syntactic method based on web search and an analysis of HTML structure is well-suited for retrieving within-organisation spatial information.

Automated topometric graph generation from floor plan analysis

The world is rich with information such as signage and maps to assist humans to navigate. We present a method to extract topological spatial information from a generic bitmap floor plan and build a topometric graph that can be used by a mobile robot for tasks such as path planning and guided exploration. The algorithm first detects and extracts text in an image of the floor plan. Using the locations of the extracted text, flood fill is used to find the rooms and hallways. Doors are found by matching SURF features and these form the connections between rooms, which are the edges of the topological graph. Our system is able to automatically detect doors and differentiate between hallways and rooms, which is important for effective navigation. We show that our method can extract a topometric graph from a floor plan and is robust against ambiguous cases most commonly seen in floor plans including elevators and stairwells.

Infant product-related injuries: comparing specialised injury surveillance and routine emergency department data

- Objective To explore the potential for using a basic text search of routine emergency department data to identify product-related injury in infants and to compare the patterns from routine ED data and specialised injury surveillance data. - Methods Data was sourced from the Emergency Department Information System (EDIS) and the Queensland Injury Surveillance Unit (QISU) for all injured infants between 2009 and 2011. A basic text search was developed to identify the top five infant products in QISU. Sensitivity, specificity, and positive predictive value were calculated and a refined search was used with EDIS. Results were manually reviewed to assess validity. Descriptive analysis was conducted to examine patterns between datasets. - Results The basic text search for all products showed high sensitivity and specificity, and most searches showed high positive predictive value. EDIS patterns were similar to QISU patterns with strikingly similar month-of-age injury peaks, admission proportions and types of injuries. - Conclusions This study demonstrated a capacity to identify a sample of valid cases of product-related injuries for specified products using simple text searching of routine ED data. - Implications As the capacity for large datasets grows and the capability to reliably mine text improves, opportunities for expanded sources of injury surveillance data increase. This will ultimately assist stakeholders such as consumer product safety regulators and child safety advocates to appropriately target prevention initiatives.

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same region.

A large-scale analysis of genetic variants within putative miRNA binding sites in prostate cancer

Prostate cancer is the second most common malignancy among men worldwide. Genome-wide association studies have identified 100 risk variants for prostate cancer, which can explain approximately 33% of the familial risk of the disease. We hypothesized that a comprehensive analysis of genetic variations found within the 3' untranslated region of genes predicted to affect miRNA binding (miRSNP) can identify additional prostate cancer risk variants. We investigated the association between 2,169 miRSNPs and prostate cancer risk in a large-scale analysis of 22,301 cases and 22,320 controls of European ancestry from 23 participating studies. Twenty-two miRSNPs were associated (P<2.3×10(-5)) with risk of prostate cancer, 10 of which were within 7 genes previously not mapped by GWAS studies. Further, using miRNA mimics and reporter gene assays, we showed that miR-3162-5p has specific affinity for the KLK3 rs1058205 miRSNP T-allele, whereas miR-370 has greater affinity for the VAMP8 rs1010 miRSNP A-allele, validating their functional role. SIGNIFICANCE Findings from this large association study suggest that a focus on miRSNPs, including functional evaluation, can identify candidate risk loci below currently accepted statistical levels of genome-wide significance. Studies of miRNAs and their interactions with SNPs could provide further insights into the mechanisms of prostate cancer risk.

Kallikrein-related peptidases in prostate cancer: From molecular function to clinical application

Prostate cancer is a leading contributor to male cancer-related deaths worldwide. Kallikrein-related peptidases (KLKs) are serine proteases that exhibit deregulated expression in prostate cancer, with KLK3, or prostate specific antigen (PSA), being the widely-employed clinical biomarker for prostate cancer. Other KLKs, such as KLK2, show promise as prostate cancer biomarkers and, additionally, their altered expression has been utilised for the design of KLK-targeted therapies. There is also a large body of in vitro and in vivo evidence supporting their role in cancer-related processes. Here, we review the literature on studies to date investigating the potential of other KLKs, in addition to PSA, as biomarkers and in therapeutic options, as well as their current known functional roles in cancer progression. Increased knowledge of these KLK-mediated functions, including degradation of the extracellular matrix, local invasion, cancer cell proliferation, interactions with fibroblasts, angiogenesis, migration, bone metastasis and tumour growth in vivo, may help define new roles as prognostic biomarkers and novel therapeutic targets for this cancer.

Structural determination of the K14 capsular polysaccharide from an ST25 Acinetobacter baumannii isolate, D46

The structure of the capsular polysaccharide (CPS) recovered from D46, an extensively antibiotic resistant ST25 Acinetobacter baumannii clinical isolate, was elucidated. The structure was resolved on the basis of NMR spectroscopy and chemical analyses, and was found to contain a branched neutral pentasaccharide with a backbone composed of GalpNAc and Galp residues, all d configured, and a d-Glcp side group. The KL14 gene cluster found in the D46 genome includes genes for four glycosyltransferases but no modules for synthesis of complex sugars, and this is consistent with the structure of K14. The K14 structure and KL14 sequence clarify the relationship between the structure and K locus sequence for A. nosocomialis isolate LUH5541. The identity of the first sugar of the K14 repeat unit (K unit), and the functions of the four encoded glycosyltransferases and Wzy polymerase were predicted.

Isolation and expression analysis of multiple isoforms of putative farnesoic acid O-methyltransferase in several crustacean species

Farnesoic acid O-methyltransferase (FaMeT) is the enzyme responsible for the conversion of farnesoic acid (FA) to methyl farnesoate (MF) in the final step of MF synthesis. Multiple isoforms of putative FaMeT were isolated from six crustacean species belonging to the families Portunidae, Penaeidae, Scyllaridae and Parastacidae. The portunid crabs Portunus pelagicus and Scylla serrata code for three forms: short, intermediate and long. Two isoforms (short and long) were isolated from the penaeid prawns Penaeus monodon and Fenneropenaeus merguiensis. Two isoforms were also identified in the scyllarid Thenus orientalis and parastacid Cherax quadricarinatus. Putative FaMeT sequences were also amplified from the genomic DNA of P. pelagicus and compared to the putative FaMeT transcripts expressed. Each putative FaMeT cDNA isoform was represented in the genomic DNA, indicative of a multi-gene family. Various tissues from P. pelagicus were individually screened for putative FaMeT expression using PCR and fragment analysis. Each tissue type expressed all three isoforms of putative FaMeT irrespective of sex or moult stage. Protein domain analysis revealed the presence of a deduced casein kinase II phosphorylation site present only in the long isoform of putative FaMeT.

Gene expression profiling of cuticular proteins across the moult cycle of the crab Portunus pelagicus

Background: Crustaceans represent an attractive model to study biomineralization and cuticle matrix formation, as these events are precisely timed to occur at certain stages of the moult cycle. Moulting, the process by which crustaceans shed their exoskeleton, involves the partial breakdown of the old exoskeleton and the synthesis of a new cuticle. This cuticle is subdivided into layers, some of which become calcified while others remain uncalcified. The cuticle matrix consists of many different proteins that confer the physical properties, such as pliability, of the exoskeleton. Results: We have used a custom cDNA microarray chip, developed for the blue swimmer crab Portunus pelagicus, to generate expression profiles of genes involved in exoskeletal formation across the moult cycle. A total of 21 distinct moult-cycle related differentially expressed transcripts representing crustacean cuticular proteins were isolated. Of these, 13 contained copies of the cuticle_1 domain previously isolated from calcified regions of the crustacean exoskeleton, four transcripts contained a chitin_bind_4 domain (RR consensus sequence) associated with both the calcified and un-calcified cuticle of crustaceans, and four transcripts contained an unannotated domain (PfamB_109992) previously isolated from C. pagurus. Additionally, cryptocyanin, a hemolymph protein involved in cuticle synthesis and structural integrity, also displays differential expression related to the moult cycle. Moult stage-specific expression analysis of these transcripts revealed that differential gene expression occurs both among transcripts containing the same domain and among transcripts containing different domains. Conclusion: The large variety of genes associated with cuticle formation, and their differential expression across the crustacean moult cycle, point to the complexity of the processes associated with cuticle formation and hardening. This study provides a molecular entry path into the investigation of the gene networks associated with cuticle formation.

Structure of the K12 capsule containing 5,7-di-N-acetylacinetaminic acid from Acinetobacter baumannii isolate D36

The repeat unit of the K12 capsular polysaccharide isolated from the Acinetobacter baumannii global clone 1 clinical isolate, D36, was elucidated by means of chemical and spectroscopical methods. The structure was shown to contain N-acetyl-D-galactosamine (D-GalpNAc), N-acetyl-D-fucosamine and N-acetyl-L-fucosamine linked together in the main chain, with the novel sugar, 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-L-altro-non-2-ulosonic acid (5,7-di-N-acetylacinetaminic acid or Aci5Ac7Ac), attached to D-GalpNAc as a side branch. This matched the sugar composition of the K12 capsule and the genetic content of the KL12 capsule gene cluster reported previously. D-FucpNAc was predicted to be the substrate for the initiating transferase, ItrB3, with the Wzy polymerase making a α-D-FucpNAc-(1 → 3)-D-GalpNAc linkage between the repeat units. The three glycosyltransferases encoded by KL12 are all retaining glycosyltransferases and were predicted to form specific linkages between the sugars in the K12 repeat unit.

Structure of the K6 capsular polysaccharide from Acinetobacter baumannii isolate RBH4

The structure of the capsular polysaccharide (CPS) from an Acinetobacter baumannii global clone 2 (GC2) clinical isolate RBH4 that carries the KL6 gene cluster was elucidated by means of chemical and spectroscopical methods. The repeating unit of K6 CPS is linear and contains N-acetyl-d-galactosamine (d-GalpNAc), two d-galactose (d-Galp) residues and 5,7-di-N-acetylpseudaminic acid (Pse5Ac7Ac). The synthesis of these sugars could be attributed to genes in the KL6 capsule biosynthesis gene cluster, and the formation of the linkages between the sugars were assigned to glycosyltransferases or the Wzy polymerase encoded in KL6.

Analysis of governance for sustainability planning in the Cairns Region

The relationship between governance arrangements and sustainability planning outcomes in complex governance systems remains poorly understood, despite significant discussions of governance in the environmental management literature emerging in the last decade. In order to analyse and examine the relationship between the health of sustainability planning governance and decision-making outcomes, this paper applies the Governance Systems Analysis framework (GSA) in the Cairns region. This paper analyses the sustainability planning governance arrangements in the Cairns region by exploring the capacity, connectivity and knowledge use of institutions in the region to deliver desired sustainability planning outcomes. The paper finds that the planning for sustainability in the Cairns region is on a knife’s edge, and could fail or succeed to deliver its intended decision-making outcomes. The paper concludes with recommendations for governance reform for sustainability in the Cairns region.

Structure and ultrastructure of the silk glands and spinneret of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae)

This study provides comprehensive documentation of silk production in the pest moth Helicoverpa armigera from gland secretion to extrusion of silk thread. The structure of the silk glands, accessory structures and extrusion apparatus are reported. The general schema of the paired silk glands follows that found for Lepidoptera. Morphology of the duct, silk press, muscle attachments and spigot are presented as a three-dimensional reconstruction and the cuticular crescent-shaped profile of the silk press is demonstrated in both open and closed forms with attendant muscle blocks, allowing advances in our knowledge of how the silk press functions to regulate the extrusion of silk. Growth of the spigot across instars is documented showing a distinctive developmental pattern for this extrusion device. Its shape and structure are related to use and load-bearing activity.

Reasoning about natural language phrases for semantic goal driven exploration

This paper presents a symbolic navigation system that uses spatial language descriptions to inform goal-directed exploration in unfamiliar office environments. An abstract map is created from a collection of natural language phrases describing the spatial layout of the environment. The spatial representation in the abstract map is controlled by a constraint based interpretation of each natural language phrase. In goal-directed exploration of an unseen office environment, the robot links the information in the abstract map to observed symbolic information and its grounded world representation. This paper demonstrates the ability of the system, in both simulated and real-world trials, to efficiently find target rooms in environments that it has never been to previously. In three unexplored environments, it is shown that on average the system travels only 8.42% further than the optimal path when using only natural language phrases to complete navigation tasks.