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Showing results for: [ Medical and Health Sciences ]
This collection contains raw data files (pClamp format) relating to the measurement of the kinetics of drug binding to hERG channels at ambient temperatures. Data was acquired on behalf of the Ion Cha... morennel Working Group of CiPA, funded by the Safety Pharmacology Society.
A description of methods and implementation is published in the manuscript: Measuring Potency and Kinetics of hERG block for CiPA in Journal of Pharmacological and Toxicological methods.
The Comprehensive in vitro Proarrhythmic assay (CiPA) aims to update current cardiac safety testing to better evaluate arrhythmic risk. A central theme of CiPA is the use of in silico approaches to risk prediction incorporating models of drug binding to hERG. To parameterize these models, accurate in vitro measurement of potency and kinetics of block is required. The Ion Channel Working Group was tasked with: i) selecting a protocol that could measure kinetics of block and was easily implementable on automated platforms for future rollout in industry and ii) acquiring a reference dataset using the standardized protocol. Potency, kinetics and trapping characteristics of hERG block for the CiPA training panel of twelve drugs were measured. Timecourse of block and trapping characteristics could be reliably measured if the time constant for onset of block was between ~500 ms and ~15 sec. Seven drugs, however had time courses of block faster than this cut-off. The dataset from this study is being used by the In Silico Working Group to develop models of drug binding for risk prediction and is being made here freely available as a ‘gold standard’ ambient temperature dataset to evaluate variability across high throughput platforms. less
Acquired - Measuring interactions of drugs with ion channels - Published 06 Feb 2017
This collection contains data for the Plos One paper entitled
"Surface-based fMRI-driven diffusion tractography in the presence of significant brain pathology: A study linking struct... moreure and function in cerebral palsy" by Lee B Reid, Ross Cunnington, Roslyn N Boyd, and Stephen E Rose.
Each participant-dataset is in a separate directory. Datasets contain:
* The skullstripped T1
* Hand-drawn 2D masks, in diffusion space, for the corpus callosum (cc.nii.gz), Posterior Limb of the Internal Capsule (plic.nii.gz) and thalamus (thalamus.nii.gz)
* FA and MD diffusion images
* A track-density image (view in MRTrix viewer MRView for best visualisation)
* Tractography seeds (from fMRI), tracks, and coherency scores for surface-based fMRI using track clustering ("surfaceBasedTractography-ClusterTracks/") and ROI-only approaches ("surfaceBasedTractography-ROIs/"), as well as the SPM voxelwise approach ("voxelwiseBasedTractography"). This tractography is broke up by side of the brain ("left"/"right") and then by anatomy (corticospinal: "motor"; thalamocortical: "sensory")
As described in the paper, not all datasets successfully completed processing. Missing data here reflects a failure for data to process correctly or adequately, and is noted with text files. Explanations for these are contained in the text.less
UQ Analysis of CP MRI data NHMRC JV - Analysis - Published 15 Jul 2016
We describe two versions of COBRA-seq: First, Genome-Wide COBRA (GW-COBRA) that uses PCR to exponentially amplify the sequencing library fragments after linker ligation. Second, Linear Amplification C... moreOBRA (LA-COBRA) that relies on T7 RNA polymerase-mediated transcription yielding many RNA transcripts of the library fragments generated in a linear manner which are subsequently converted to cDNA. The COBRA-seq library protocol is largely adapted to provide robust coverage of the human genome, however, all of the steps are applicable to both model and non-model organisms.
SIEF: Nutritional Genomics - COBRA-seq: Sensitive and Quantitative Methylome Profiling - Published 29 Sep 2015
LipiD-QuanT is novel label-free lipid droplet quantification technique to monitor lipid dynamics, based on automated image analysis of phase contrast microscopy images.
SIEF: Nutritional Genomics - LipiD-QuanT Image Analysis Tool - Published 14 Sep 2015
The Hungry Microbiome is an exciting biomedical animation that takes the audience on a journey through the digestive tract to reveal the world of the human gut microbiome. The video explores how inter... moreactions between a human and their gut microbiota plays a key role in colorectal cancer risk. The dataset comprises a 4 minute mp4 video and a thumbnail.
TCP03 VIZBI Visualising Biological Data - Visualisations - Published 15 Dec 2014
A documented, extendable software library for developing kinetic analysis applications which are used to examine dynamic Positron Emission Tomography (PET) and Magnetic Resonance Imaging (MRI) images.... more
In addition, a multithreaded, application (koala) which supports multiple kinetic models is supplied, along with Matlab(TM) wrappers for various functions such as simulating time activity curves and optimising kinetic model parameters.less
1057.2 FDOPA Imaging-Cancer CouncilQldIK - Analysis and modelling of large dynamic medical images - Published 09 Sep 2014