https://ogma.newcastle.edu.au/vital/access/ /manager/Index ${session.getAttribute("locale")} 5 Strategies for enhancing communication between students, academics and researchers participating in large-scale undergraduate research projects https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:20372 Wed 11 Apr 2018 16:58:08 AEST ]]> A new combinatorial optimization approach for integrated feature selection using different datasets: a prostate cancer transcriptomic study https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:24445 Wed 11 Apr 2018 16:51:11 AEST ]]> GPU-FS-kNN: a software tool for fast and scalable kNN computation using GPUs https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:15138 Wed 11 Apr 2018 16:14:13 AEST ]]> Alzheimer's disease patient groups derived from a multivariate analysis of cognitive test outcomes in the coalition against major diseases dataset https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:25160 Wed 11 Apr 2018 16:09:03 AEST ]]> (N-1) contingency planning in radial distribution networks using genetic algorithms https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:11601 k, where k is the number of switches. Because of the exponential complexity, exact methods are prohibitively time-consuming. This work presents a genetic algorithm that provides a rapid answer to network managers in terms of a switching strategy to reconnect the affected area. The method takes into account the radial topology of the power flow and the operational limits of voltage and cable load. Computational tests were conducted on a real network with 96 buses and 16 switches, located within the operational area of Energy Australia. This paper describes the genetic algorithm in detail, presents thorough computational tests, and a complete contingency plan for the test network.]]> Wed 11 Apr 2018 15:01:42 AEST ]]> An information theoretic clustering approach for unveiling authorship affinities in Shakespearean era plays and poems https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:16800 Wed 11 Apr 2018 14:17:27 AEST ]]> Computer face-matching technology using two-dimensional photographs accurately matches the facial gestalt of unrelated individuals with the same syndromic form of intellectual disability https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:31227 Wed 11 Apr 2018 14:09:18 AEST ]]> A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:9503 Wed 11 Apr 2018 13:47:54 AEST ]]> Iteratively refining breast cancer intrinsic subtypes in the METABRIC dataset https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:23687 Wed 11 Apr 2018 13:07:25 AEST ]]> Basal-like breast cancer: molecular profiles, clinical features and survival outcomes https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:30824 Wed 11 Apr 2018 12:30:47 AEST ]]> Identification of differentially expressed genes through integrated study of alzheimer's disease affected brain regions https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:30004 Wed 11 Apr 2018 12:27:04 AEST ]]> The Gene Interaction Miner: a new tool for data mining contextual information for protein-protein interaction analysis https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:9256 Wed 11 Apr 2018 09:30:32 AEST ]]> Evaluation of different normalization and analysis procedures for Illumina gene expression microarray data involving small changes https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:28613 Wed 11 Apr 2018 09:21:51 AEST ]]> The discovery of novel biomarkers improves breast cancer intrinsic subtype prediction and reconciles the labels in the METABRIC data set https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:25143 Tue 27 Mar 2018 15:15:35 AEDT ]]> Electronic health literacy among magnetic resonance imaging and computed tomography medical imaging outpatients: cluster analysis https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:36905 Thu 16 Jul 2020 12:19:42 AEST ]]> The multiple sclerosis whole blood mRNA transcriptome and genetic associations indicate dysregulation of specific T cell pathways in pathogenesis https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:9594 Sat 24 Mar 2018 08:39:37 AEDT ]]> Switch and tap-changer reconfiguration of distribution networks using evolutionary algorithms. https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:12821 Sat 24 Mar 2018 08:17:17 AEDT ]]> Sifting the wheat from the chaff: prioritizing GWAS results by identifying consistency across analytical methods https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:12709 Sat 24 Mar 2018 08:16:20 AEDT ]]> Computing large-scale distance matrices on GPU https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:16197 Sat 24 Mar 2018 08:03:05 AEDT ]]> kNN-MST-Agglomerative: a fast and scalable graph-based data clustering approach on GPU https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:16196 Sat 24 Mar 2018 08:03:04 AEDT ]]> Entropy-based high performance computation of Boolean SNP-SNP interactions using GPUs https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:20383 Sat 24 Mar 2018 07:58:08 AEDT ]]> Changes in brain transcripts related to Alzheimer's disease in a model of HFE hemochromatosis are not consistent with increased Alzheimer's disease risk https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:20882 -/- mice, a model of hemochromatosis, relative to age- and gender-matched wildtype controls. Classification by functional pathway analysis revealed transcript changes for various genes important in AD. There were decreases of up to 9-fold in transcripts for amyloid-β protein precursor, tau, apolipoprotein E, presenilin 1, and various other γ-secretase components, as well as Notch signaling pathway molecules. This included decreased transcripts for 'hairy and enhancer of split' Hes1 and Hes5, downstream targets of Notch canonical signaling. The reductions in Hes1 and Hes5 transcripts provide evidence that the changes in levels of transcripts for γ-secretase components and Notch signaling genes have functional consequences. The effects appeared relatively specific for AD in that few genes pertaining to other important neurodegenerative diseases, notably Parkinson's disease and Huntington's disease, or to inflammation, oxidative stress, or apoptosis, showed altered transcript levels. The observed effects on AD-related gene transcripts do not appear to be consistent with increased AD risk in HFE hemochromatosis and might, if anything, be predicted to protect against AD to some extent. As Hfe-/- mice did not have higher brain iron levels than wildtype controls, these studies highlight the need for further research in models of more severe hemochromatosis with brain iron loading.]]> Sat 24 Mar 2018 07:57:56 AEDT ]]> Beyond statistics: a new combinatorial approach to identifying biomarker panels for the early detection and diagnosis of Alzheimer's Disease https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:17878 Sat 24 Mar 2018 07:56:13 AEDT ]]> kNN-Borůvka-GPU: a fast and scalable MST construction from <i>k</i>NN graphs on GPU https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:21225 k-nearest neighbor (kNN) structure can provide an efficient solution to this problem. Only a few attempts were found in the literature that focus on solving the problem using the kNNs. This paper briefs the state-of-the-art strategies for the MST problem and a fast and scalable solution combining the classical Borůvka’s MST algorithm and the kNN graph structure. The proposed algorithm is implemented for CUDA enabled GPUs (kNN-Borůvka-GPU), but the basic approach is simple and adaptable to other available architectures. Speed-ups of 30-40 times compared with CPU implementation was observed for several large-scale synthetic and real world data sets.]]> Sat 24 Mar 2018 07:53:01 AEDT ]]> Brain transcriptome perturbations in the Hfe<sup>-/-</sup> mouse model of genetic iron loading https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:21833 HFE gene. There is evidence from both human and animal studies that HFE gene variants may affect brain function and modify risks of brain disease. To investigate how disruption of HFE influences brain transcript levels, we used microarray and real-time reverse transcription polymerase chain reaction to assess the brain transcriptome in Hfe−/− mice relative to wildtype AKR controls (age 10 weeks, n ≥ 4/group). The Hfe−/− mouse brain showed numerous significant changes in transcript levels (p < 0.05) although few of these related to proteins directly involved in iron homeostasis. There were robust changes of at least 2-fold in levels of transcripts for prominent genes relating to transcriptional regulation (FBJ osteosarcoma oncogene Fos, early growth response genes), neurotransmission (glutamate NMDA receptor Grin1, GABA receptor Gabbr1) and synaptic plasticity and memory (calcium/calmodulin-dependent protein kinase IIα Camk2a). As previously reported for dietary iron-supplemented mice, there were altered levels of transcripts for genes linked to neuronal ceroid lipofuscinosis, a disease characterized by excessive lipofuscin deposition. Labile iron is known to enhance lipofuscin generation which may accelerate brain aging. The findings provide evidence that iron loading disorders can considerably perturb levels of transcripts for genes essential for normal brain function and may help explain some of the neurologic signs and symptoms reported in hemochromatosis patients.]]> Sat 24 Mar 2018 07:52:17 AEDT ]]> The MST-kNN with paracliques https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:27314 Sat 24 Mar 2018 07:38:37 AEDT ]]> GPU acceleration of an entroy-based model to quantify epistatic interactions between SNPs https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:26041 Sat 24 Mar 2018 07:26:27 AEDT ]]> Blood metabolite markers of preclinical Alzheimer's disease in two longitudinally followed cohorts of older individuals https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:25518 Sat 24 Mar 2018 07:26:01 AEDT ]]> Parallel hybrid heuristics for the permutation flow shop problem https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:22173 max. In the permutational scenario, the sequence of jobs has to remain the same in all machines. The Flowshop Problem (FSP) is known to be NP-hard when more than three machines are considered. Thus, for medium and large scale instances, high-quality heuristics are needed to find good solutions in reasonable time. We propose and analyse parallel hybrid search methods that fully use the computational power of current multi-core machines. The parallel methods combine a memetic algorithm (MA) and several iterated greedy algorithms (IG) running concurrently. Two test scenarios were included, with short and long CPU times. The tests were conducted on the set of benchmark instances introduced by Taillard (Eur. J. Oper. Res. 64:278–285, 1993), commonly used to assess the performance of new methods. Results indicate that the use of the MA to manage a pool of solutions is highly effective, allowing the improvement of the best known upper bound for one of the instances.]]> Sat 24 Mar 2018 07:14:59 AEDT ]]> Identification of genome-wide SNP-SNP and SNP-clinical Boolean interactions in age-related macular degeneration https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:21967 Sat 24 Mar 2018 07:14:33 AEDT ]]> Extensive transcriptomic and genomic analysis provides new insights about luminal breast cancers https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:25008 Mon 11 Mar 2019 12:12:36 AEDT ]]> Identifying factors associated with sedentary time after stroke. Secondary analysis of pooled data from nine primary studies. https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:35820 30 and >60 min (p = 0.001 and p = 0.004, respectively). Regression models explained 11-19% of the variance in total sedentary time and time in prolonged sedentary bouts. Conclusion: We found that variability in sedentary time of people with stroke was largely unaccounted for by demographic and stroke-related variables. Behavioral and environmental factors are likely to play an important role in sedentary behavior after stroke. Further work is required to develop and test effective interventions to address sedentary behavior after stroke.]]> Mon 09 Dec 2019 16:11:23 AEDT ]]>