Bessel beam illumination reduces random and systematic errors in quantitative functional studies using light-sheet microscopy

Light-sheet microscopy (LSM), in combination with intrinsically transparent zebrafish larvae, is a choice method to observe brain function with high frame rates at cellular resolution. Inherently to LSM, however, residual opaque objects cause stripe artifacts, which obscure features of interest and, during functional imaging, modulate fluorescence variations related to neuronal activity. Here, we report how Bessel beams reduce streaking artifacts and produce high-fidelity quantitative data demonstrating a fivefold increase in sensitivity to calcium transients and a 20 fold increase in accuracy in the detection of activity correlations in functional imaging. Furthermore, using principal component analysis, we show that measurements obtained with Bessel beams are clean enough to reveal in one-shot experiments correlations that can not be averaged over trials after stimuli as is the case when studying spontaneous activity. Our results not only demonstrate the contamination of data by systematic and random errors through conventional Gaussian illumination and but,furthermore, quantify the increase in fidelity of such data when using Bessel beams

Roman portraiture and biometric identification

This project utilised three-dimensional scanning technology in the study of ancient Roman art and archaeology: Roman representations of faces executed in marble. In the cultural heritage sector, three-dimensional (3D) scanning finds its primary application in documenting and reconstructing objects and structures mostly of simple geometry: bones, pottery, architecture or the imprint of whole archaeological sites (Adolf 2011). In forensic science, the face is interesting from investigative and probative perspectives, including both recognition and identification. Biometric methods of facial recognition have been part of a plethora of computer science-based applications used in the verification of identity (Davy et al. 2005, Goodwin, Evison and Schofield 2010). The aim of this initial project is to provide objective relevant measurements of key facial features from the two ancient Roman portrait statue three-dimensional scans, which will allow the delineation of relationships between individual portraits including formal and stylistics aspects. The work described in this paper proposal is truly multidisciplinary, it touches on many fields including : Classical archaeologies (specifically ancient art history in the period of the Roman Empire 31BC - AD400), Forensic Anthropology (specifically physical anthropology and human osteology, Facial Biometrics (specifically uniquely recognising humans based upon their intrinsic physical traits and features) and Computer Science and Statistics (specifically the analysis of large complex multi-dimensional data sets)

Roman portraiture and biometric identification

This project utilised three-dimensional scanning technology in the study of ancient Roman art and archaeology: Roman representations of faces executed in marble. In the cultural heritage sector, three-dimensional (3D) scanning finds its primary application in documenting and reconstructing objects and structures mostly of simple geometry: bones, pottery, architecture or the imprint of whole archaeological sites (Adolf 2011). In forensic science, the face is interesting from investigative and probative perspectives, including both recognition and identification. Biometric methods of facial recognition have been part of a plethora of computer science-based applications used in the verification of identity (Davy et al. 2005, Goodwin, Evison and Schofield 2010). The aim of this initial project is to provide objective relevant measurements of key facial features from the two ancient Roman portrait statue three-dimensional scans, which will allow the delineation of relationships between individual portraits including formal and stylistics aspects. The work described in this paper proposal is truly multidisciplinary, it touches on many fields including : Classical archaeologies (specifically ancient art history in the period of the Roman Empire 31BC - AD400), Forensic Anthropology (specifically physical anthropology and human osteology, Facial Biometrics (specifically uniquely recognising humans based upon their intrinsic physical traits and features) and Computer Science and Statistics (specifically the analysis of large complex multi-dimensional data sets)

Reliability of multi-site UK Biobank MRI brain phenotypes for the assessment of neuropsychiatric complications of SARS-CoV-2 infection: The COVID-CNS travelling heads study.

Funder: National Institute for Health Research (NIHR)INTRODUCTION: Magnetic resonance imaging (MRI) of the brain could be a key diagnostic and research tool for understanding the neuropsychiatric complications of COVID-19. For maximum impact, multi-modal MRI protocols will be needed to measure the effects of SARS-CoV-2 infection on the brain by diverse potentially pathogenic mechanisms, and with high reliability across multiple sites and scanner manufacturers. Here we describe the development of such a protocol, based upon the UK Biobank, and its validation with a travelling heads study. A multi-modal brain MRI protocol comprising sequences for T1-weighted MRI, T2-FLAIR, diffusion MRI (dMRI), resting-state functional MRI (fMRI), susceptibility-weighted imaging (swMRI), and arterial spin labelling (ASL), was defined in close approximation to prior UK Biobank (UKB) and C-MORE protocols for Siemens 3T systems. We iteratively defined a comparable set of sequences for General Electric (GE) 3T systems. To assess multi-site feasibility and between-site variability of this protocol, N = 8 healthy participants were each scanned at 4 UK sites: 3 using Siemens PRISMA scanners (Cambridge, Liverpool, Oxford) and 1 using a GE scanner (King's College London). Over 2,000 Imaging Derived Phenotypes (IDPs), measuring both data quality and regional image properties of interest, were automatically estimated by customised UKB image processing pipelines (S2 File). Components of variance and intra-class correlations (ICCs) were estimated for each IDP by linear mixed effects models and benchmarked by comparison to repeated measurements of the same IDPs from UKB participants. Intra-class correlations for many IDPs indicated good-to-excellent between-site reliability. Considering only data from the Siemens sites, between-site reliability generally matched the high levels of test-retest reliability of the same IDPs estimated in repeated, within-site, within-subject scans from UK Biobank. Inclusion of the GE site resulted in good-to-excellent reliability for many IDPs, although there were significant between-site differences in mean and scaling, and reduced ICCs, for some classes of IDP, especially T1 contrast and some dMRI-derived measures. We also identified high reliability of quantitative susceptibility mapping (QSM) IDPs derived from swMRI images, multi-network ICA-based IDPs from resting-state fMRI, and olfactory bulb structure IDPs from T1, T2-FLAIR and dMRI data. CONCLUSION: These results give confidence that large, multi-site MRI datasets can be collected reliably at different sites across the diverse range of MRI modalities and IDPs that could be mechanistically informative in COVID brain research. We discuss limitations of the study and strategies for further harmonisation of data collected from sites using scanners supplied by different manufacturers. These acquisition and analysis protocols are now in use for MRI assessments of post-COVID patients (N = 700) as part of the ongoing COVID-CNS study

Evolution of the eyes of vipers with and without infrared-sensing pit organs

We examined lens and brille transmittance, photoreceptors, visual pigments, and visual opsin gene sequences of viperid snakes with and without infrared-sensing pit organs. Ocular media transmittance is high in both groups. Contrary to previous reports, small as well as large single cones occur in pit vipers. Non-pit vipers differ from pit vipers in having a twotiered retina, but few taxa have been examined for this poorly understood feature. All vipers sampled express rh1, sws1 and lws visual opsin genes. Opsin spectral tuning varies but not in accordance with the presence/absence of pit organs, and not always as predicted from gene sequences. The visual opsin genes were generally under purifying selection, with positive selection at spectral tuning amino acids in RH1 and SWS1 opsins, and at retinal pocket stabilization sites in RH1 or LWS (and without substantial differences between pit and nonpit vipers). Lack of evidence for sensory trade-off between viperid eyes (in the aspects examined) and pit organs might be explained by the high degree of neural integration of vision and infrared detection; the latter representing an elaboration of an existing sense with addition of a novel sense organ, rather than involving the evolution of a wholly novel sensory system

Bodily attractiveness and egalitarianism are negatively related in males.

Ancestrally, relatively attractive individuals and relatively formidable males may have had reduced incentives to be egalitarian (i.e., to act in accordance with norms promoting social equality). If selection calibrated one's egalitarianism to one's attractiveness/formidability, then such people may exhibit reduced egalitarianism ("observed egalitarianism") and be perceived by others as less egalitarian ("perceived egalitarianism") in modern environments. To investigate, we created 3D body models of 125 participants to use both as a source of anthropometric measurements and as stimuli to obtain ratings of bodily attractiveness and perceived egalitarianism. We also measured observed egalitarianism (via an economic "dictator" game) and indices of political egalitarianism (preference for socialism over capitalism) and "equity sensitivity." Results indicated higher egalitarianism levels in women than in men, and moderate-to-strong negative relationships between (a) attractiveness and observed egalitarianism among men, (b) attractiveness and perceived egalitarianism among both sexes, and (c) formidability and perceived egalitarianism among men. We did not find support for two previously-reported findings: that observed egalitarianism and formidability are negatively related in men, and that wealth and formidability interact to explain variance in male egalitarianism. However, this lack of support may have been due to differences in variable measurement between our study and previous studies

Video tracking of dairy cows for assessing mobility scores

Lameness afflicts a large proportion of dairy herds, but could be considerably reduced by automated monitoring by CCTV. Key to this is reliable, robust detection and tracking of individual cows in crowded video sequences. We introduce a novel detection and tracking method, based on the Viola-Jones detector. We show that animals can be tracked and their overall gait patterns and speed automatically extracted from video sequences. Preliminary work on identification of individual animals through principal component analysis and SIFT feature matching is also described