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Miscellaneous videos of eMouseAtlas models
No full textA collection of video sequences as published on the eMouseAtlas site. These include movies of embryos and embryonic structure developing through time
Videos of eMouseAtlas Models: Theiler Stage 14 (8.5-9.75 dpc)
No full textA number of videos for each of the eMouseAtlas 3D mouse embryo models to show the overall form and in some cases selected anatomy. Each video is identified by the unique EMA ID with annotation if required. The videos labelled as "watermovies" are captured using the OPT system with the embryo spun on a longitudinal axis with no tissue clearing
Videos of eMouseAtlas Models: Theiler Stage 12 (7.5-8.75 dpc)
No full textA number of videos for each of the eMouseAtlas 3D mouse embryo models to show the overall form and in some cases selected anatomy. Each video is identified by the unique EMA ID with annotation if required. The videos labelled as "watermovies" are captured using the OPT system with the embryo spun on a longitudinal axis with no tissue clearing
Videos of eMouseAtlas Models: Theiler Stage 18 (10.5-11.75 dpc)
No full textA number of videos for each of the eMouseAtlas 3D mouse embryo models to show the overall form and in some cases selected anatomy. Each video is identified by the unique EMA ID with annotation if required. The videos labelled as "watermovies" are captured using the OPT system with the embryo spun on a longitudinal axis with no tissue clearing
SV2A is expressed in subpopulations of mouse and human synapses
No full textSynapse pathology is a feature of most brain diseases and there is a pressing need to monitor the onset and progression of this pathology using brain imaging in living patients. A major step toward this goal has been the development of small-molecule radiotracers that bind to synaptic vesicle glycoprotein 2A (SV2A) for use in positron emission tomography (PET). Changes in SV2A radiotracer binding in PET are widely interpreted to report differences in the density of all synapses throughout brain regions.
Here, we analyse the expression of SV2A at single-synapse resolution across regions of adult mouse and human brain. We find that SV2A is expressed in fewer than 50% of excitatory and inhibitory synapses and that the density of SV2A-positive synapses differs between brain regions. Furthermore, individual synapses differ in their amounts of SV2A. These findings have important implications for the interpretation of PET imaging studies in a clinical setting and point to the need for a detailed understanding of SV2A synaptome architecture in both healthy brain and disease cases where PET imaging is being applied
SUPERSEDED: 3D-printable phantoms for quantitative dynamic contrast-enhanced MRI
No full textThis dataset contains the experimental data and code required to reproduce results and figures in the article "3D-printable phantoms for quantitative dynamic contrast-enhanced MRI".
Abstract
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Purpose: A novel 3D-printed phantom design and methodology is proposed, addressing important requirements for technical validation, quality assurance and multi-site harmonisation of quantitative dynamic contrast-enhanced (DCE-) MRI measurements.
Methods: Phantoms were produced by 3D-printing gels incorporating channels and pores as proxies for blood vessels and extravascular extracellular space, respectively. A flow circuit was designed to reproduce clinically relevant arterial input functions (AIF). Using nine gels with variable porosity and channel size we evaluated the effect of 3D-printing parameters on DCE-MRI parameters obtained using the extended Tofts (ET) model. Physical gel and fitted model parameters were correlated by multiple linear regression.
Results: All phantoms generated realistic AIFs and tissue-like signal enhancement curves were accurately modelled by the ET model. As hypothesised, vp was positively associated with vchan (B = 0.86, p < 0.001) and showed a weaker, negative association with vpore (B = -0.18, p = 0.006); PS was positively associated with both vchan (B = 0.13 min-1, p < 0.001) and vpore (B = 0.051 min-1, p < 0.001). ve was positively associated with vpore (B = 0.89, p < 0.001) but not vchan. Fitted parameters were repeatable (coefficient of variation 2.1 - 3.2 %).
Conclusions: Tailorable 3D printed porous gel phantoms generating tissue-mimicking DCE-MRI signals have the potential to support validation, quality assurance and multi-site harmonisation of quantitative DCE-MRI.Refer to readme.txt file
3D scanning electron microscope movie of human neocortex
No full textThis movie is from serial block face scanning electron microscopy of neocortex from a post-mortem tissue donation of a person who died with Alzheimer's disease (UK Brain bank number BBN001.36378). Brain samples were obtained with ethical approval via the University of Edinburgh Sudden Death Brain Bank and the Alzheimer Scotland Brain and Tissue Bank. This study was reviewed and approved by the Edinburgh Brain Bank ethics committee and the Academic and Clinical Central Office for Research and Development, a joint office of the University of Edinburgh and NHS Lothian (approval number 15-HV-016). The Edinburgh Brain Bank is a Medical Research Council funded facility with research ethics committee (REC) approval (16/ES/0084)
Explainable Autonomous Vehicle Intelligence
No full textHEADD is a dataset of natural language explanations elicited from online participants via Prolific with corresponding annotations for each explanation similarly given by online (but different) participants. The data is about driving scenarios in which the behaviour and driving decisions of a single blue agent need to be explained, while the scenarios contain various other agents and environmental elements that influence the behaviour of the blue agent. The dataset contains 14 unique scenarios with qualitatively distinct and interesting driving scenarios including simulated video recordings, ASAM OpenDrive maps, and ASAM OpenScenario descriptions. In addition, HEADD includes 1347 explanations in natural language with 4 explanatory modes (descriptive, teleological, mechanistic, counterfactual) from 54 participants in each of the 14 scenarios, of which 947 non-descriptive explanations are annotated with at least 5 unique annotations regarding the causal content and trustworthiness of the explanations under the various circumstances in the scenarios
Porous plates at incidence: Dataset
No full textThis dataset corresponds to the manuscript - porous plates at incidence. This paper investigates the effect of permeability on two-dimensional rectangular plates at incidences. The flow topology is investigated for Reynolds number () values between 30 and 90, and the forces on the plate are discussed for , where the wake is found to be steady for any value of the Darcy number () and the flow incidence (). At , for a plate normal to the stream and vanishing , the wake shows a vortex dipole with a stagnation point on the plate surface. With increasing , the separation between the vortex dipole and the plate increases; the vortex dipole shortens and is eventually annihilated at a critical . For any value of below the critical one, the vortex dipole disappears with decreasing . However, at low , the two saddle-node pairs merge at the same , annihilating the dipole; while at high , they merge at different , resulting in a single recirculating region for intermediate incidences. The magnitudes of lift, drag, and torque decrease with . Nevertheless, there exists a range of and , where the magnitude of the plate-wise force component increases with , driven by the shear on the plate's pressure side. Finally, the analysis of the fluid impulse suggests that the lift and drag reduction with are associated with the weakening of the leading and trailing edge shear layer, respectively. The present findings will be directly beneficial in understanding the role of permeability on small permeable bodies
Patient derived cancer-associated fibroblasts from non-small cell lung cancer undergo phenotypic drift in culture
No full textNanostring nCounter targeted RNA Seq. data of fibroblast cells isolated from human non-cancerous lung tissue and non-small cell lung cancer tumour tissue as well as fibroblasts maintained for three passages in culture from both origins as shown in Mathieson et al. (submission) "Patient derived cancer-associated fibroblasts from non-small cell lung cancer undergo phenotypic drift in culture".
Cancer-associated fibroblasts (CAFs) are the predominant cell type in the stroma of many solid organ malignancies, including non-small cell lung cancer (NSCLC). They are widely studied and represent a diverse population of cells presenting with different phenotypes and functions. CAF research often relies on propagation and culture in vitro for functional assay and co-culture experimentation. In this study we investigated the phenotype of CAFs from NSCLC patients compared to non-cancerous lung fibroblasts by tracking changes in CAF subset marker expression levels by flow cytometry. We demonstrate that CAFs from NSCLC undergo phenotypic drift in culture, and that of the previously defined subsets there is a convergence to a phenotype predominantly upregulated in non-cancerous lung when CAFs are maintained in standard culture conditions. Together we show the phenotype, transcriptome and function of fibroblasts converge between CAFs and fibroblasts from non-cancerous lung, suggesting that standard culture conditions promote this phenotype. We highlight the need to understand and monitor the culture phenotype during functional studies with CAFs, as the heterogeneity found in the tumour microenvironment is rapidly lost in cultured cells