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Purkait P.,University of Adelaide | Chin T.-J.,University of Adelaide | Sadri A.,RMIT University | Suter D.,Australian Research Council ARC
IEEE Transactions on Pattern Analysis and Machine Intelligence | Year: 2016

The extension of conventional clustering to hypergraph clustering, which involves higher order similarities instead of pairwise similarities, is increasingly gaining attention in computer vision. This is due to the fact that many clustering problems require an affinity measure that must involve a subset of data of size more than two. In the context of hypergraph clustering, the calculation of such higher order similarities on data subsets gives rise to hyperedges. Almost all previous work on hypergraph clustering in computer vision, however, has considered the smallest possible hyperedge size, due to a lack of study into the potential benefits of large hyperedges and effective algorithms to generate them. In this paper, we show that large hyperedges are better from both a theoretical and an empirical standpoint. We then propose a novel guided sampling strategy for large hyperedges, based on the concept of random cluster models. Our method can generate large pure hyperedges that significantly improve grouping accuracy without exponential increases in sampling costs. We demonstrate the efficacy of our technique on various higher-order grouping problems. In particular, we show that our approach improves the accuracy and efficiency of motion segmentation from dense, long-term, trajectories. © 2016 IEEE.


Baez S.,University of Buenos Aires | Baez S.,CONICET | Baez S.,Pontifical Catholic University of Argentina | Baez S.,Diego Portales University | And 17 more authors.
Frontiers in Aging Neuroscience | Year: 2013

Cockayne syndrome (CS) is an autosomal recessive disease associated with premature aging, progressive multiorgan degeneration, and nervous system abnormalities including cerebral and cerebellar atrophy, brain calcifications, and white matter abnormalities. Although several clinical descriptions of CS patients have reported developmental delay and cognitive impairment with relative preservation of social skills, no previous studies have carried out a comprehensive neuropsychological and social cognition assessment. Furthermore, no previous research in individuals with CS has examined the relationship between brain atrophy and performance on neuropsychological and social cognition tests. This study describes the case of an atypical late-onset type III CS patient who exceeds the mean life expectancy of individuals with this pathology. The patient and a group of healthy controls underwent a comprehensive assessment that included multiple neuropsychological and social cognition (emotion recognition, theory of mind, and empathy) tasks. In addition, we compared the pattern of atrophy in the patient to controls and to its concordance with ERCC8 gene expression in a healthy brain. The results showed memory, language, and executive deficits that contrast with the relative preservation of social cognition skills. The cognitive profile of the patient was consistent with his pattern of global cerebral and cerebellar loss of gray matter volume (frontal structures, bilateral cerebellum, basal ganglia, temporal lobe, and occipito-temporal/occipito-parietal regions), which in turn was anatomically consistent with the ERCC8 gene expression level in a healthy donor's brain. The study of exceptional cases, such as the one described here, is fundamental to elucidating the processes that affect the brain in premature aging diseases, and such studies provide an important source of information for understanding the problems associated with normal and pathological aging. © 2013 Baez, Couto, Herrera, Bocanegra, Trujillo-Orrego, Madrigal-Zapata, Cardona, Manes, Ibanez and Villegas.


Hellweger F.L.,Northeastern University | Van Sebille E.,Australian Research Council ARC | Fredrick N.D.,Northeastern University
Science | Year: 2014

A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection.


Kim J.,University of New South Wales | Kim J.,Australian Research Council ARC | Tran M.T.T.,University of New South Wales
i-Perception | Year: 2016

We considered whether optic flow generated by 3D relief of a foreground surface might influence visually-mediated self-motion perception (vection). We generated background motion consistent with self-rotation, and a foreground object with bumpy relief was either rotated with the observer (ego-centric) or fixed in world coordinates (world-centric).We found that vection strength ratings were greater in conditions with world-centric retinal motion of the foreground object, despite generating flow that was opposite to background motion. This effect was explained by observer judgments of the axis self-rotation in depth; whereas ego-centric flow generated experiences of more on-axis self-rotation, world-centric flow generated experiences of centrifugal rotation around the foreground object. These data suggest that foreground object motion can increase the perception of self-motion generated by optic flow, even when they reduce net retinal motion coherence and promote conditions for multisensory conflict. This finding supports the view that self-motion perception depends on mid-level representations of whole-scene motion. © The Author(s) 2016.


Buerger P.,Australian Institute of Marine Science | Buerger P.,James Cook University | Buerger P.,Australian Research Council ARC | Alvarez-Roa C.,James Cook University | And 4 more authors.
PeerJ | Year: 2016

Black band disease (BBD) is a common disease of reef-building corals with a worldwide distribution that causes tissue loss at a rate of up to 3 cm/day. Critical for a mechanistic understanding of the disease's aetiology is the cultivation of its proposed pathogen, filamentous cyanobacteria (genus Roseofilum). Here, we optimise existing protocols for the isolation and cultivation of Roseofilum cyanobacteria using a new strain from the central Great Barrier Reef. We demonstrate that the isolation of this bacterium via inoculation onto agar plates was highly effective with a low percentage agar of 0.6% and that growth monitoring was most sensitive with fluorescence measurements of chlorophyll-a (440/685 nm). Cell growth curves in liquid and solid media were generated for the first time for this cyanobacterium and showed best growth rates for the previously untested L1-medium (growth rate k = 0.214 biomass/day; doubling time tgen = 4.67 days). Our results suggest that the trace metals contained in L1-medium maximise biomass increase over time for this cyanobacterium. Since the newly isolated Roseofilum strain is genetically closest to Pseudoscillatoria coralii, but in terms of pigmentation and cell size closer to Roseofilum reptotaenium, we formally merge the two species into a single taxon by providing an emended species description, Roseofilum reptotaenium (Rasoulouniriana) Casamatta emend. Following this optimized protocol is recommended for fast isolation and cultivation of Roseofilum cyanobacteria, for growth curve generation in strain comparisons and for maximisation of biomass in genetic studies. © 2016 Buerger et al.


Wang C.,Australian Research Council ARC | Wang C.,University of Sydney | Deakin J.E.,Australian Research Council ARC | Deakin J.E.,Australian National University | And 8 more authors.
BMC Genomics | Year: 2011

Background: The limited (2X) coverage of the tammar wallaby (Macropus eugenii) genome sequence dataset currently presents a challenge for assembly and anchoring onto chromosomes. To provide a framework for this assembly, it would be a great advantage to have a dense map of the tammar wallaby genome. However, only limited mapping data are available for this non-model species, comprising a physical map and a linkage map.Results: We combined all available tammar wallaby mapping data to create a tammar wallaby integrated map, using the Location DataBase (LDB) strategy. This first-generation integrated map combines all available information from the second-generation tammar wallaby linkage map with 148 loci, and extensive FISH mapping data for 492 loci, especially for genes likely to be located at the ends of wallaby chromosomes or at evolutionary breakpoints inferred from comparative information. For loci whose positions are only approximately known, their location in the integrated map was refined on the basis of comparative information from opossum (Monodelphis domestica) and human. Interpolation of segments from the opossum and human assemblies into the integrated map enabled the subsequent construction of a tammar wallaby first-generation virtual genome map, which comprises 14336 markers, including 13783 genes recruited from opossum and human assemblies. Both maps are freely available at http://compldb.angis.org.au.Conclusions: The first-generation integrated map and the first-generation virtual genome map provide a backbone for the chromosome assembly of the tammar wallaby genome sequence. For example, 78% of the 10257 gene-scaffolds in the Ensembl annotation of the tammar wallaby genome sequence (including 10522 protein-coding genes) can now be given a chromosome location in the tammar wallaby virtual genome map. © 2011 Wang et al; licensee BioMed Central Ltd.


Xiong Y.,University of Queensland | Xiong Y.,Australian Research Council ARC | Zhang M.-X.,University of Queensland | Zhang M.-X.,Australian Research Council ARC
Surface and Coatings Technology | Year: 2014

Although many previous studies have confirmed that cold sprayed Al+xAl2O3 (x=0-75vol.%) composite coatings on magnesium alloys can effectively improve wear and corrosion resistance, the effect of such coatings on tensile and fatigue properties is still unclear. The present work aims to evaluate the tensile properties and fatigue resistance of an AZ91D alloy with cold sprayed Al+xAl2O3 (x=0, 30, 50vol.%) coatings. The experimental results showed that although the cold spray coating leads to an increase in yield strength and fatigue limit, the tensile strength is reduced. In-situ examination of the macro-morphology of surfaces of the coated specimens during tensile testing was carried out through video recording. It indicated that once the tensile specimens have yielded, horizontal cracks that were perpendicular to the tensile axis formed on the surface of the specimens. Fractographic analysis of the fracture surfaces of the tensile specimens in a scanning electron microscope revealed that all the cracks within the cold sprayed coatings were suspended at the coating/substrate interface. Based on these experimental observations, it is considered that the improved yield strength is attributed to the constraint effect of the cold sprayed composite coatings on the magnesium substrate. The enhanced fatigue limit is a result of the higher yield strength and the coating/substrate interface barrier to crack propagation. The decrease in tensile strength is attributed to the brittle fracture of the cold sprayed coatings when yielding of the specimens. © 2014 Elsevier B.V.

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