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  • Several recent studies in larval zebrafish have found evidence for the existence of a dedicated prey-detection system present in the ventrotemporal retina at the earliest layers of visual processing. Functional data from photoreceptors and bipolar cells indicates that this circuitry is strongly UV-dependent (1, 2), while anatomical evidence points to the ‘strike zone’ as being a structurally-defined feature of both retinal and pretectal circuits (3, 4, 5). However, little is known about how retinal ganglion cells, the eye’s sole information output channels, are structurally and functionally tuned to process prey-like features of the visual environment, and how these features might differ between RGCs in the strike zone and those surveying other parts of the visual field. Using a combination of photoactivation-labeling of single RGCs and in vivo 2-photon imaging, we compared the structure and function of RGCs in different parts of the eye. Strike zone RGCs tended to feature more diffuse dendritic structures with numerous large synaptic densities widely distributed across the IPL, and a predominance of UV-ON circuits likely driven by the presence of UV-bright prey in the upper-frontal visual field. In contrast, nasal RGCs tended to feature more narrowly-stratified dendrites, as well as a more diverse array of chromatic and color-opponent channels. Thus, numerous region-specific specializations exist within these two RGC populations which may be linked to the differential visual content of the zebrafish’s underwater habitat and behavioral demands.
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  • This infographic highlights the positive difference medical research charities are making with healthcare technology in the UK. The report was originally published on the AMRC website on 29 November 2017. Data sources can be found here.
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  • Background Independent component analysis (ICA) allows decomposing heterogeneous transcriptomics data and extracting relevant transcriptional signals that correspond either to relevant biological processes or to technical biases. Using independent components as features for downstream analysis requires high reproducibility of decomposition. Here we investigated the number of independent components influence on reproducibility and quality of data analysis. Method We applied the developed parallel consensus Independent Component Analysis algorithm (https://gitlab.com/biomodlih/consica) to TCGA RNA-seq gene expression data on patients with glioblastoma (GMB) and low-grade gliomas (LGG), skin cutaneous melanoma (SKCM), pancreatic adenocarcinoma (PAAD) and non-small cell lung cancers: squamous cell carcinoma (LUSC) and adenocarcinoma (LUAD). Two predicting models were used to classify the patients based on ICA results: random forest and xgboost from corresponding R packages. We also carried out survival prediction with Cox regression (R package survival) on the weights of independent components and examined the dependence between prediction quality and the number of components. Jaccard indexes, coefficients of determination and cosine similarities between identified metagenes were used to assess the stability of deconvolution. Results We estimated the boundary values for the number of components for reproducible transcriptomic data analysis in case of small patient cohorts. Using ICA as a feature engineering method before cancer type classification we estimated effect of the number of components increasing on the quality of lung cancer type classification (LUSC/LUAD) and patients survival prediction. Also, we validated the optimal number of components that allow detecting biologically relevant signals in smaller patient cohorts.
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  • The need for better sanitation in the developing world is clear. 40% of the world’s population - 2.5 billion people - still practice unsafe sanitation or lack access to adequate sanitation facilities. Building upon the hypothesis that malodor makes toilets undesirable and might reduce toilet usage, the Bill and Melinda Gates Foundation has partnered with Firmenich to develop a unique malodor counteractant technology. The technology aims to improve user experience and thus, contribute to Sustainable Development Goal #6.2 by encouraging people to adopt safer behaviors and move up the sanitation ladder, from open defecation to community toilets and eventually to individual toilets. In this context, the Bill and Melinda Gates Foundation asked Firmenich and Archipel&Co to run 10 case studies in low -income settlements across 4 countries to gain further insights on this topic. This research explores the specific role played by malodor among all the factors that influence sanitation decisions in low-income urban settlements. To what extent can the use of malodor counteractant technology encourage people to adopt safer sanitation practices and move up the sanitation ladder? This report presents key results from the 2 case studies in South Africa.
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  • In the vertebrate retina, distinct types of RGCs extract specific features of the visual scene for transmission to the brain. Here, we sought to determine the functional output channels of the zebrafish retina to chart what the fish’s eye tells the fish’s brain. We generated a novel transgenic line in which the calcium reporter GCaMP6f is tagged to the membrane of zebrafish RGCs under the Islet2b promoter (Islet2b:mGCaMP6f) which allowed recording from both RGC dendrites and somata. For this, we used two-photon population imaging of light-evoked calcium activity of RGCs in the in vivo zebrafish larval eye in response to spectrally defined full-field stimuli. We then assigned responses to functional clusters, and for each cluster, computed the anatomical distribution across the eye and IPL depth. Our data suggest a mixed code of colour and time differentially serves distinct regions in visual space, mirroring our earlier finding in bipolar cells that different parts of the eye harbour strongly different functional circuits (Zimmermann, Nevala, Yoshimatsu et al 2018, Curr Biol.). Key observations at odds with the textbook view: Half of all output channels are colour opponent Striking mix of time- and spectral information throughout the eye Near complete absence of blue-On channels or general slowness of the blue-Off channel Complex distribution of diverse UV-responses throughout the eye Taken together, our findings strongly suggest that the achromatic responses of RGCs are dominated by the red-green system. In comparison, UV responses are very region specific, with a notable specialization in the zebrafish’s acute zone (“strike zone”), which is used for prey capture (see Cluster 1). We further speculate that the sluggish Boff channel could provide a useful subtraction signal against which both RG and UV-circuits could compute.
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  • This infographic report outlines key facts and figures about AMRC member charities in the UK and the research they funded in 2018. It was originally published on the AMRC website on 12 June 2019 and the accompanying data sources can be found here: https://www.amrc.org.uk/our-sectors-footprint.
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  • This infographic highlights the ways in which medical research charities are working towards preventing disease and promoting health in the UK’s ageing society. The report was originally published on the AMRC website on 25 July 2018. Data sources can be found here.
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