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Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpression, and sequence evolution. Frogs provide an excellent, yet understudied, system for visual evolution research due to their diversity of ecologies (including biphasic aquatic-terrestrial life cycles) that we hypothesize imposed different selective pressures leading to adaptive evolution of the visual system, notably the opsins that encode the protein component of the visual pigments responsible for the first step in visual perception. Here, we analyze the diversity and evolution of visual opsin genes from 93 new eye transcriptomes plus published data for a combined dataset spanning 122 frog species and 34 families. We find that most species express the four visual opsins previously identified in frogs but show evidence for gene loss in two lineages. Further, we present evidence of positive selection in three opsins and shifts in selective pressures associated with differences in habitat and life history, but not activity pattern. We identify substantial novel variation in the visual opsins and, using microspectrophotometry, find highly variable spectral sensitivities, expanding known ranges for all frog visual pigments. Mutations at spectral-tuning sites only partially account for this variation, suggesting that frogs have used tuning pathways that are unique among vertebrates. These results support the hypothesis of adaptive evolution in photoreceptor physiology across the frog tree of life in response to varying environmental and ecological factors and further our growing understanding of vertebrate visual evolution.

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BACKGROUND: Children and young people's (CYP) involvement is an increasing priority in UK healthcare and in heath research, alongside recognition that involving CYP in research requires different considerations to involving adults. Underpinned by children's rights and a co-production ethos this paper, co-authored with young evaluators, explores the learning from a co-produced evaluation of eyeYPAG, a young persons' research advisory group (YPAG) for eye and vision research based at Moorfields Eye Hospital, London, UK. METHODS: A team of young evaluators, supported by the eyeYPAG facilitator, conducted focus groups and online surveys with YPAG members, their parents and carers, researchers, group facilitators and funders. Qualitative data was analysed using a collaborative reflexive thematic analysis approach. Quantitative data, limited by the small number of participants, was analysed in Excel and reported as descriptive data. RESULTS: CYP valued the social and creative aspects of the group as well as learning about research and developing skills and confidence. Learning was a two-way process, with both researchers and facilitators reflecting on how much they had learnt from working with the YPAG. All participants talked about the importance of impact, feeling that CYP are making a difference to research, as well as CYP's right to be involved. Effective planning and facilitation were key to the success of the group, in relation to accessibility and the development and delivery of sessions both online and in-person. Resourcing and administration were key challenges to this, as was engaging researchers who were not already converted to the public involvement cause. As the nature of a YPAG is that it primarily focuses on advising researcher-led projects, co-production was identified as something that the group was 'working towards', including through this evaluation. Co-producing with CYP involves building up knowledge, confidence and acknowledging power dynamics. CONCLUSIONS: Co-producing an evaluation enabled us to learn about the benefits and challenges of involving CYP in research, as well as how to involve them in the development of that evidence. An ethos of co-production and children's rights helped to shift the balance of power and develop more engaging and inclusive ways of working.

Children and young people (CYP) have a right to be involved in things that affect them, including research. There is growing interest in children and young people's involvement in health research in the United Kingdom (UK), as well as understanding that what works for CYP is often different to what works for adults. This paper presents an evaluation of the Young Person's Advisory Group (YPAG) at Moorfields Eye Hospital in London. Evaluation uses research methods to find out how well a service or project is working and meeting the needs of those who use it, and how to improve things that could be better. A group of young evaluators, supported by adult researchers, designed and ran the evaluation; three of the young evaluators also helped write this paper. In our evaluation we used focus (discussion) groups and online surveys with young group members, their parents and carers, researchers who had worked with the group, the group's facilitators (adults who help manage the group) and funders. We found that group members valued the social and creative aspects of the group as well as learning about research and developing skills and confidence. Learning was a two-way process, with both researchers and facilitators talking about how much they had learnt from working with the YPAG. All participants talked about the importance of feeling that CYP are making a difference to research, as well as of CYP's right to be involved. Planning and support were important to the group working well, but we found that having the money and time to do this well was not always easy. And, while lots of researchers were keen to work with the group, and talked about how this had helped their research, we need to do more to engage researchers who have yet to be convinced. We also found that, while we wanted to 'co-produce' the group and share power for all big decisions, this was something we had to work towards, especially when group members were young and/or new to research and involvement. Co-producing an evaluation helped us to learn about the benefits and challenges of involving CYP in research, as well as how to involve them in evaluating that involvement.

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Magnetic resonance imaging (MRI) scanners at ultra-high magnetic fields have become available to use in humans, thus enabling researchers to investigate the human brain in detail. By increasing the spatial resolution, ultra-high field MR allows both structural and functional characterization of cortical layers. Techniques that can differentiate cortical layers, such as histological studies and electrode-based measurements have made critical contributions to the understanding of brain function, but these techniques are invasive and thus mainly available in animal models. There are likely to be differences in the organization of circuits between humans and even our closest evolutionary neighbors. Thus research on the human brain is essential. Ultra-high field MRI can observe differences between cortical layers, but is non-invasive and can be used in humans. Extensive previous literature has shown that neuronal connections between brain areas that transmit feedback and feedforward information terminate in different layers of the cortex. Layer-specific functional MRI (fMRI) allows the identification of layer-specific hemodynamic responses, distinguishing feedback and feedforward pathways. This capability has been particularly important for understanding visual processing, as it has allowed researchers to test hypotheses concerning feedback and feedforward information in visual cortical areas. In this review, we provide a general overview of successful ultra-high field MRI applications in vision research as examples of future research.

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The quantification of vision impairments dates to the mid-nineteenth century with standardization of visual acuity and visual field measures in the eye clinic. Attempts to quantify the impact of vision impairments on patients' lives did not receive clinical attention until the close of the twentieth century. Although formal psychometric theories and measurement instruments were well developed and commonplace in educational testing, as well as in various areas in psychology and rehabilitation medicine, the late start applying them to clinical vision research created a vacuum that invited poorly developed and poorly functioning instruments and analytic methods. Although this research is still burdened with legacy instruments, mandates by regulatory agencies to include the patients' perspectives and preferences in the evaluation of clinical outcomes have stimulated the development and validation of self-report instruments grounded in modern psychometric theory and methods. Here I review the progress and accomplishments of applying modern psychometrics to clinical vision research.

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BACKGROUND: The paired-domain transcription factor paired box gene 6 (PAX6) causes a wide spectrum of ocular developmental anomalies, including congenital aniridia, Peters anomaly and microphthalmia. Here, we aimed to functionally assess the involvement of seven potentially non-canonical splicing variants on missplicing of exon 6, which represents the main hotspot region for loss-of-function PAX6 variants. METHODS: By locus-specific analysis of PAX6 using Sanger and/or targeted next-generation sequencing, we screened a Spanish cohort of 106 patients with PAX6-related diseases. Functional splicing assays were performed by in vitro minigene approaches or directly in RNA from patient-derived lymphocytes cell line, when available. RESULTS: Five out seven variants, including three synonymous changes, one small exonic deletion and one non-canonical splice variant, showed anomalous splicing patterns yielding partial exon skipping and/or elongation. CONCLUSION: We describe new spliceogenic mechanisms for PAX6 variants mediated by creating or strengthening five different cryptic donor sites at exon 6. Our work revealed that the activation of cryptic PAX6 splicing sites seems to be a recurrent and underestimated cause of aniridia. Our findings pointed out the importance of functional assessment of apparently silent PAX6 variants to uncover hidden genetic alterations and to improve variant interpretation for genetic counselling in aniridia.

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The human pupil behavior has gained increased attention due to the discovery of the intrinsically photosensitive retinal ganglion cells and the afferent pupil control path's role as a biomarker for cognitive processes. Diameter changes in the range of 10-2 mm are of interest, requiring reliable and characterized measurement equipment to accurately detect neurocognitive effects on the pupil. Mostly commercial solutions are used as measurement devices in pupillometry which is associated with high investments. Moreover, commercial systems rely on closed software, restricting conclusions about the used pupil-tracking algorithms. Here, we developed an open-source pupillometry platform consisting of hardware and software competitive with high-end commercial stereo eye-tracking systems. Our goal was to make a professional remote pupil measurement pipeline for laboratory conditions accessible for everyone. This work's core outcome is an integrated cross-platform (macOS, Windows and Linux) pupillometry software called PupilEXT, featuring a user-friendly graphical interface covering the relevant requirements of professional pupil response research. We offer a selection of six state-of-the-art open-source pupil detection algorithms (Starburst, Swirski, ExCuSe, ElSe, PuRe and PuReST) to perform the pupil measurement. A developed 120-fps pupillometry demo system was able to achieve a calibration accuracy of 0.003 mm and an averaged temporal pupil measurement detection accuracy of 0.0059 mm in stereo mode. The PupilEXT software has extended features in pupil detection, measurement validation, image acquisition, data acquisition, offline pupil measurement, camera calibration, stereo vision, data visualization and system independence, all combined in a single open-source interface, available at https://github.com/openPupil/Open-PupilEXT.

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The increasing employment of eye-tracking technology in different application areas and in vision research has led to an increased need to measure fast eye-movement events. Whereas the cost of commercial high-speed eye trackers (above 300 Hz) is usually in the tens of thousands of EUR, to date, only a small number of studies have proposed low-cost solutions. Existing low-cost solutions however, focus solely on lower frame rates (up to 120 Hz) that might suffice for basic eye tracking, leaving a gap when it comes to the investigation of high-speed saccadic eye movements. In this paper, we present and evaluate a system designed to track such high-speed eye movements, achieving operating frequencies well beyond 500 Hz. This includes methods to effectively and robustly detect and track glints and pupils in the context of high-speed remote eye tracking, which, paired with a geometric eye model, achieved an average gaze estimation error below 1 degree and average precision of 0.38 degrees. Moreover, average undetection rate was only 0.33%. At a total investment of less than 600 EUR, the proposed system represents a competitive and suitable alternative to commercial systems at a tiny fraction of the cost, with the additional advantage that it can be freely tuned by investigators to fit their requirements independent of eye-tracker vendors.

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BACKGROUND: Retinitis pigmentosa (RP) shows substantial genetic heterogeneity. It has been estimated that in approximately 60%-80% of RP cases, the genetic diagnosis can be found using whole exome sequencing (WES). In this study, the purpose was to identify causative variants in individuals with genetically unexplained retinal disease, which included one consanguineous family with two affected siblings and one case with RP. METHODS: To identify the genetic defect, WES was performed in both probands, and clinical analysis was performed. To obtain insight into the function of KIAA1549 in photoreceptors, mRNA expression, knockdown and protein localisation studies were performed. RESULTS: Through analysis of WES data, based on population allele frequencies, and in silico prediction tools, we identified a homozygous missense variant and a homozygous frameshift variant in KIAA1549 that segregate in two unrelated families. Kiaa1549 was found to localise at the connecting cilium of the photoreceptor cells and the synapses of the mouse retina. Both variants affect the long transcript of KIAA1549, which encodes a 1950 amino acid protein and shows prominent brain expression. The shorter transcript encodes a 734 amino acid protein with a high retinal expression and is affected by the identified missense variant. Strikingly, knockdown of the long transcript also leads to decreased expression of the short transcript likely explaining the non-syndromic retinal phenotype caused by the two variants targeting different transcripts. CONCLUSION: In conclusion, our results underscore the causality of segregating variants in KIAA1549 for autosomal recessive RP. Moreover, our data indicate that KIAA1549 plays a role in photoreceptor function.

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Because they were used for decades to present visual stimuli in psychophysical and psychophysiological studies, cathode ray tubes (CRTs) used to be the gold standard for stimulus presentation in vision research. Recently, as CRTs have become increasingly rare in the market, researchers have started using various types of liquid-crystal display (LCD) monitors as a replacement for CRTs. However, LCDs are typically not cost-effective when used in vision research and often cannot reach the full capacity of a high refresh rate. In this study we measured the temporal and spatial characteristics of a consumer-grade LCD, and the results suggested that a consumer-grade LCD can successfully meet all the technical demands in vision research. The tested LCD, working in a flash style like that of CRTs, demonstrated perfect consistency for initial latencies across locations, yet showed poor spatial uniformity and sluggishness in reaching the requested luminance within the first frame. After these drawbacks were addressed through software corrections, the candidate monitor showed performance comparable or superior to that of CRTs in terms of both spatial and temporal homogeneity. The proposed solution can be used as a replacement for CRTs in vision research.

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The multiple object tracking (MOT) paradigm has proven its value in targeting a number of aspects of visual cognition. This study used MOT to investigate the effect of object-based grouping, both in children with and without autism spectrum disorder (ASD). A modified MOT task was administered to both groups, who had to track and distinguish four targets that moved randomly amongst four distracters, irrespective of the grouping condition. No group difference was revealed between children with and without ASD: both showed adequate MOT abilities and a similar amount of grouping interference. Implications of the current result are considered for previous MOT studies, the developmental trajectory of perceptual grouping, and the idea of heightened sensitivity to task characteristics in ASD.

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Previous research suggested that adolescents with autism spectrum disorder are better than typically developing children in detecting local, non-social details within complex visual scenes. To better understand these differences, we used the image database by Sareen et al., containing the size and on-screen location information of all changes in the images, in a change blindness paradigm. In this task, an original and a modified real-world scene, separated by a gray blank, alternate repeatedly until observers detect the change. Our results indicated that participants with and without autism spectrum disorder performed similarly when scenes were presented upright, but that only the performance of the typically developing adolescents became worse in the inverted scene condition. In this condition, the correlation between performance and both image difficulty and change predictability was significantly weaker in autism spectrum disorder than in typically developing participants. We suggest that these findings result from a more locally biased search strategy in people with autism spectrum disorder, compared to typically developing participants, in tasks in which the rapid processing of global information does not help to improve change detection performance. Finally, although we found change location, change size, and age to influence participant performance, none of these was directly linked to the observed group-level differences.

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Adolescents with and without autism spectrum disorder (ASD) performed two priming experiments in which they implicitly processed a prime stimulus, containing high and/or low spatial frequency information, and then explicitly categorized a target face either as male/female (gender task) or as positive/negative (Valence task). Adolescents with ASD made more categorization errors than typically developing adolescents. They also showed an age-dependent improvement in categorization speed and had more difficulties with categorizing facial expressions than gender. However, in neither of the categorization tasks, we found group differences in the processing of coarse versus fine prime information. This contradicted our expectations, and indicated that the perceptual differences between adolescents with and without ASD critically depended on the processing time available for the primes.

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Noninvasive live imaging has been used extensively for ocular phenotyping in mouse vision research. Bright-field imaging and optical coherence tomography (OCT) are two methods that are particularly useful for assessing the posterior mouse eye (fundus), including the retina, retinal pigment epithelium, and choroid, and are widely applied due to the commercial availability of sophisticated instruments and software. Here, we provide a guide to using these approaches with an emphasis on post-acquisition image processing using Fiji, a bundled version of the Java-based public domain software ImageJ. A bright-field fundus imaging protocol is described for acquisition of multi-frame videos, followed by image registration to reduce motion artifacts, averaging to reduce noise, shading correction to compensate for uneven illumination, filtering to improve image detail, and rotation to adjust orientation. An OCT imaging protocol is described for acquiring replicate volume scans, with subsequent registration and averaging to yield three-dimensional datasets that show reduced motion artifacts and enhanced detail. The Fiji algorithms used in these protocols are designed for batch processing and are freely available. The image acquisition and processing approaches described here may facilitate quantitative phenotyping of the mouse eye in drug discovery, mutagenesis screening, and the functional cataloging of mouse genes by individual laboratories and large-scale projects, such as the Knockout Mouse Phenotyping Project and International Mouse Phenotyping Consortium.

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BACKGROUND: Inherited retinal degenerations (IRDs) are a common cause of visual disturbance with a high clinical and genetic heterogeneity. Recent sequencing techniques such as whole exome sequencing (WES) contribute to the discovery of novel genes. The aim of the current study was to use WES data to identify large deletions that include at least one exon in known IRD genes. METHODS: Patients diagnosed with IRDs underwent a comprehensive ophthalmic evaluation. WES was performed using the NimbleGen V2 paired-end kit and HiSeq 2000. An analysis of exon coverage data was performed on 60 WES samples. Exonic deletions were verified by 'PCR walking' analysis. RESULTS: We analysed data obtained from 60 WES samples of index patients with IRDs. By calculating the average coverage for all exons in the human genome, we were able to identify homozygous and hemizygous deletions of at least one exon in six families (10%), including a single-exon deletion in EYS, deletions of three consecutive exons in MYO7A and NPHP4, deletions of four and eight consecutive exons in RPGR and a multigene deletion on the X-chromosome, including CHM. By using PCR-walking analysis, we were able to identify the borders of five of the deletions and to screen our set of patients for these deletions. CONCLUSIONS: We performed here a comprehensive analysis of WES data as a tool for identifying large genomic deletions in patients with IRDs. Our analysis indicates that large deletions are relatively frequent (about 10% of our WES cohort) and should be screened when analysing WES data.

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In comparison to typically developing (TD) individuals, people with autism spectrum disorder (ASD) appear to be worse in the fast extraction of the global meaning of a situation or picture. Ultra-rapid categorization [paradigm developed by Thorpe et al. (Nature 381:520-522, 1996)] involves such global information processing. We therefore tested a group of adults with and without ASD, without intellectual disability, on a set of ultra-rapid categorization tasks. Individuals with ASD performed equally well as TD individuals except when the task required the categorization of social interactions. These results argue against a general deficit in ultra-rapid gist perception in people with ASD, while suggesting a more specific problem with the fast processing of information about social relations.

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From the late nineteenth century onwards, the phenomena of vision and the anatomy and physiology of the eye of marine animals induced many zoologists, ethologists, physiologists, anatomists, biochemists, and ophthalmologists to travel to the Zoological Station in Naples. Initially, their preferred research objects were fish, but it soon became evident that cephalopods have features which make them particularly suited to research. After the first studies, which outlined the anatomical structure of cephalopods' eyes and optic nerves, the research rapidly shifted to the electrophysiology and biochemistry of vision. In the twentieth century these results were integrated with behavioral tests and training techniques. Between 1909 and 1913 also the well-known debate on color vision between ophthalmologist Carl von Hess and zoologist Karl von Frisch took place in Naples. Largely unknown is that the debate also concerned cephalopods. A comparative historical analysis of these studies shows how different experimental devices, theoretical frameworks, and personal factors gave rise to two diametrically opposing views.

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Numerous findings indicate that spatial phase bears an important cognitive information. Distortion of phase affects topology of edge structures and makes images unrecognizable. In turn, appropriately phase-structured patterns give rise to various illusions of virtual image content and apparent motion. Despite a large body of phenomenological evidence not much is known yet about the role of phase information in neural mechanisms of visual perception and cognition. Here, we are concerned with analysis of the role of spatial phase in computational and biological vision, emergence of visual illusions and pattern recognition. We hypothesize that fundamental importance of phase information for invariant retrieval of structural image features and motion detection promoted development of phase-based mechanisms of neural image processing in course of evolution of biological vision. Using an extension of Fourier phase correlation technique, we show that the core functions of visual system such as motion detection and pattern recognition can be facilitated by the same basic mechanism. Our analysis suggests that emergence of visual illusions can be attributed to presence of coherently phase-shifted repetitive patterns as well as the effects of acuity compensation by saccadic eye movements. We speculate that biological vision relies on perceptual mechanisms effectively similar to phase correlation, and predict neural features of visual pattern (dis)similarity that can be used for experimental validation of our hypothesis of "cognition by phase correlation."

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Many proteins depend on post-translational prenylation for a correct subcellular localisation and membrane anchoring. This involves the covalent attachment of farnesyl or geranylgeranyl residues to cysteines residing in consensus motifs at the C-terminal parts of proteins. Retinal photoreceptor cells are highly compartmentalised and membranous structures, and therefore it can be expected that the proper function of many retinal proteins depends on prenylation, which has been proven for several proteins that are absent or defective in different inherited retinal diseases (IRDs). These include proteins involved in the phototransduction cascade, such as GRK1, the phosphodiesterase 6 subunits and the transducin γ subunit, or proteins involved in transport processes, such as RAB28 and retinitis pigmentosa GTPase regulator (RPGR). In addition, there is another class of general prenylation defects due to mutations in proteins such as AIPL1, PDE6D and rab escort protein-1 (REP-1), which can act as chaperones for subsets of prenylated retinal proteins that are associated with IRDs. REP-1 also is a key accessory protein of geranylgeranyltransferase II, an enzyme involved in the geranylgeranylation of almost all members of a large family of Rab GTPases. Finally, mutations in the mevalonate kinase (MVK) gene, which were known to be principally associated with mevalonic aciduria, were recently associated with non-syndromic retinitis pigmentosa. We hypothesise that MVK deficiency results in a depletion of prenyl moieties that affects the prenylation of many proteins synthesised specifically in the retina, including Rabs. In this review, we discuss the entire spectrum of prenylation defects underlying progressive degeneration of photoreceptors, the retinal pigment epithelium and the choroid.

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BACKGROUND: Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are inherited retinal diseases that cause early onset severe visual impairment. An accurate molecular diagnosis can refine the clinical diagnosis and allow gene specific treatments. METHODS: We developed a capture panel that enriches the exonic DNA of 163 known retinal disease genes. Using this panel, we performed targeted next generation sequencing (NGS) for a large cohort of 179 unrelated and prescreened patients with the clinical diagnosis of LCA or juvenile RP. Systematic NGS data analysis, Sanger sequencing validation, and segregation analysis were utilised to identify the pathogenic mutations. Patients were revisited to examine the potential phenotypic ambiguity at the time of initial diagnosis. RESULTS: Pathogenic mutations for 72 patients (40%) were identified, including 45 novel mutations. Of these 72 patients, 58 carried mutations in known LCA or juvenile RP genes and exhibited corresponding phenotypes, while 14 carried mutations in retinal disease genes that were not consistent with their initial clinical diagnosis. We revisited patients in the latter case and found that homozygous mutations in PRPH2 can cause LCA/juvenile RP. Guided by the molecular diagnosis, we reclassified the clinical diagnosis in two patients. CONCLUSIONS: We have identified a novel gene and a large number of novel mutations that are associated with LCA/juvenile RP. Our results highlight the importance of molecular diagnosis as an integral part of clinical diagnosis.

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