Publications by authors named "Matt Dunn"

22 Publications

  • Page 1 of 1

Eye tracking: empirical foundations for a minimal reporting guideline.

Behav Res Methods 2022 Apr 6. Epub 2022 Apr 6.

Institute of Psychology, University of Kiel, Kiel, Germany.

In this paper, we present a review of how the various aspects of any study using an eye tracker (such as the instrument, methodology, environment, participant, etc.) affect the quality of the recorded eye-tracking data and the obtained eye-movement and gaze measures. We take this review to represent the empirical foundation for reporting guidelines of any study involving an eye tracker. We compare this empirical foundation to five existing reporting guidelines and to a database of 207 published eye-tracking studies. We find that reporting guidelines vary substantially and do not match with actual reporting practices. We end by deriving a minimal, flexible reporting guideline based on empirical research (Section "An empirically based minimal reporting guideline").
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http://dx.doi.org/10.3758/s13428-021-01762-8DOI Listing
April 2022

Neural modeling of antisaccade performance of healthy controls and early Huntington's disease patients.

Chaos 2021 Jan;31(1):013121

School of Optometry and Vision Sciences, Cardiff University, Cardiff CF24 4HQ, United Kingdom.

Huntington's disease (HD), a genetically determined neurodegenerative disease, is positively correlated with eye movement abnormalities in decision making. The antisaccade conflict paradigm has been widely used to study response inhibition in eye movements, and reliable performance deficits in HD subjects have been observed, including a greater number and timing of direction errors. We recorded the error rates and response latencies of early HD patients and healthy age-matched controls performing the mirror antisaccade task. HD participants displayed slower and more variable antisaccade latencies and increased error rates relative to healthy controls. A competitive accumulator-to-threshold neural model was then employed to quantitatively simulate the controls' and patients' reaction latencies and error rates and uncover the mechanisms giving rise to the observed HD antisaccade deficits. Our simulations showed that (1) a more gradual and noisy rate of accumulation of evidence by HD patients is responsible for the observed prolonged and more variable antisaccade latencies in early HD; (2) the confidence level of early HD patients making a decision is unaffected by the disease; and (3) the antisaccade performance of healthy controls and early HD patients is the end product of a neural lateral competition (inhibition) between a correct and an erroneous decision process, and not the end product of a third top-down stop signal suppressing the erroneous decision process as many have speculated.
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http://dx.doi.org/10.1063/5.0021584DOI Listing
January 2021

Beyond Visual Acuity: Development of a Simple Test of the Slow-To-See Phenomenon in Children with Infantile Nystagmus Syndrome.

Curr Eye Res 2021 02 13;46(2):263-270. Epub 2020 Jul 13.

Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton , Southampton, UK.

Purpose: Conventional static visual acuity testing profoundly underestimates the impact of infantile nystagmus on functional vision. The slow-to-see phenomenon explains why many patients with nystagmus perform well in non-time restricted acuity tests but experience difficulty in certain situations. This is often observed by parents when their child struggles to recognise familiar faces in crowded scenes. A test measuring more than visual acuity could permit a more real-world assessment of visual impact and provide a robust outcome measure for clinical trials.

Methods: Children with nystagmus and, age and acuity matched controls attending Southampton General Hospital were recruited for two tasks. In the first, eye-tracking measured the time participants spent looking at an image of their mother when alongside a stranger, this was then repeated with a sine grating and a homogenous grey box. Next, a tablet-based app was developed where participants had to find and press either their mother or a target face from up to 16 faces. Here, the response time was measured. The tablet task was refined over multiple iterations.

Results: In the eye-tracking task, controls spent significantly longer looking at their mother and the grating ( < .05). Interestingly, children with nystagmus looked significantly longer at the grating ( < .05) but not their mother ( > .05). This confirmed a facial target was key to further development. The tablet-based task demonstrated that children with nystagmus take significantly longer to identify the target; this was most pronounced using a 3-min test with 12-face displays.

Conclusion: This study has shown a facial target is key to identifying the time-to-see deficit in infantile nystagmus and provides the basis for an outcome measure for use in clinical treatment trials.
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http://dx.doi.org/10.1080/02713683.2020.1784438DOI Listing
February 2021

An automated segmentation approach to calibrating infantile nystagmus waveforms.

Behav Res Methods 2019 10;51(5):2074-2084

School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.

Infantile nystagmus (IN) describes a regular, repetitive movement of the eyes. A characteristic feature of each cycle of the IN eye movement waveform is a period in which the eyes are moving at minimal velocity. This so-called "foveation" period has long been considered the basis for the best vision in individuals with IN. In recent years, the technology for measuring eye movements has improved considerably, but there remains the challenge of calibrating the direction of gaze in tracking systems when the eyes are continuously moving. Identifying portions of the nystagmus waveform suitable for calibration typically involves time-consuming manual selection of the foveation periods from the eye trace. Without an accurate calibration, the exact parameters of the waveform cannot be determined. In this study, we present an automated method for segmenting IN waveforms with the purpose of determining the foveation positions to be used for calibration of an eye tracker. On average, the "point of regard" was found to be within 0.21° of that determined by hand-marking by an expert observer. This method enables rapid clinical quantification of waveforms and the possibility of gaze-contingent research paradigms being performed with this patient group.
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http://dx.doi.org/10.3758/s13428-018-1178-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6797654PMC
October 2019

An augmented reality sign-reading assistant for users with reduced vision.

PLoS One 2019 16;14(1):e0210630. Epub 2019 Jan 16.

Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire, United States of America.

People typically rely heavily on visual information when finding their way to unfamiliar locations. For individuals with reduced vision, there are a variety of navigational tools available to assist with this task if needed. However, for wayfinding in unfamiliar indoor environments the applicability of existing tools is limited. One potential approach to assist with this task is to enhance visual information about the location and content of existing signage in the environment. With this aim, we developed a prototype software application, which runs on a consumer head-mounted augmented reality (AR) device, to assist visually impaired users with sign-reading. The sign-reading assistant identifies real-world text (e.g., signs and room numbers) on command, highlights the text location, converts it to high contrast AR lettering, and optionally reads the content aloud via text-to-speech. We assessed the usability of this application in a behavioral experiment. Participants with simulated visual impairment were asked to locate a particular office within a hallway, either with or without AR assistance (referred to as the AR group and control group, respectively). Subjective assessments indicated that participants in the AR group found the application helpful for this task, and an analysis of walking paths indicated that these participants took more direct routes compared to the control group. However, participants in the AR group also walked more slowly and took more time to complete the task than the control group. The results point to several specific future goals for usability and system performance in AR-based assistive tools.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210630PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334915PMC
October 2019

The role of Peripheral Vision in the Flashed Face Distortion Effect.

Perception 2019 Jan 19;48(1):93-101. Epub 2018 Dec 19.

School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.

The flashed face distortion effect is a phenomenon whereby images of faces, presented at 4-5 Hz in the visual periphery, appear distorted. It has been hypothesized that the effect is driven by cortical, rather than retinal, components. Here, we investigated the role of peripheral viewing on the effect. Normally sighted participants viewed the stimulus peripherally, centrally, and centrally with a blurring lens (to match visual acuity in the peripheral location). Participants rated the level of distortion using a Visual Analogue Scale. Although optical defocus did have a significant effect on distortion ratings, peripheral viewing had a much greater effect, despite matched visual acuity. We suggest three potential mechanisms for this finding: increased positional uncertainty in the periphery, reduced deployment of attention to the visual periphery, or the visual crowding effect.
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http://dx.doi.org/10.1177/0301006618817419DOI Listing
January 2019

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

Nat Genet 2018 11 1;50(11):1574-1583. Epub 2018 Oct 1.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development.
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http://dx.doi.org/10.1038/s41588-018-0223-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205630PMC
November 2018

Infantile nystagmus: an optometrist's perspective.

Clin Optom (Auckl) 2017 25;9:123-131. Epub 2017 Sep 25.

Research Unit for Nystagmus, School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK,

Infantile nystagmus (IN), previously known as congenital nystagmus, is an involuntary to-and-fro movement of the eyes that persists throughout life. IN is one of three types of early-onset nystagmus that begin in infancy, alongside fusion maldevelopment nystagmus syndrome and spasmus nutans syndrome. Optometrists may also encounter patients with acquired nystagmus. The features of IN overlap largely with those of fusion maldevelopment nystagmus syndrome, spasmus nutans syndrome, and acquired nystagmus, yet the management for each subtype is different. Therefore, the optometrist's role is to accurately discern IN from other forms of nystagmus and to manage accordingly. As IN is a lifelong condition, its presence not only affects the visual function of the individual but also their quality of life, both socially and psychologically. In this report, we focus on the approaches that involve optometrists in the investigation and management of patients with IN. Management includes the prescription of optical treatments, low-vision rehabilitation, and other interventions such as encouraging the use of the null zone and referral to support groups. Other treatments available via ophthalmologists are also briefly discussed in the article.
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http://dx.doi.org/10.2147/OPTO.S126214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6118861PMC
September 2017

Lateral visual occlusion does not change walking trajectories.

J Vis 2018 09;18(9):11

School of Psychology, Cardiff University, Cardiff, UK.

Difficulties with walking are often reported following brain damage that causes a lateralized loss of awareness on one side. Whether lateralized loss of awareness has a direct causal impact on walking is unknown. A review of the literature on visually guided walking suggests several reasons why a lateralized loss of visual awareness might be expected to lead to difficulties walking. Here, we isolated and examined the effect of lateralized vision loss on walking behavior in real and virtual environments. Healthy young participants walked to a target placed within a real room, in a virtual corridor, or on a virtual ground plane. In the ground-plane condition, the scene either was empty or contained three obstacles. We reduced vision on one side by occluding one eye (Experiment 1 and 2) or removing one hemifield, defined relative to either the head or trunk (Experiment 2), through use of eye patching (Experiment 1) and a virtual-reality system (Experiment 2). Visual-field restrictions did not induce significant deviations in walking paths in any of the occlusion conditions or any of the environments. The results provide further insight into the visual information that guides walking in humans, and suggest that lateralized vision loss on its own is not the primary cause of walking difficulties.
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http://dx.doi.org/10.1167/18.9.11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6141229PMC
September 2018

Low-Level Nighttime Light Therapy for Age-Related Macular Degeneration: A Randomized Clinical Trial.

Invest Ophthalmol Vis Sci 2018 09;59(11):4531-4541

Division of Optometry and Visual Science, School of Health Sciences, City, University of London, United Kingdom.

Purpose: To investigate the safety, acceptability, and effectiveness of light therapy on the progression of AMD over 12 months.

Methods: This was a phase I/IIa, prospective, proof-of-concept, single-center, unmasked randomized controlled trial. Sixty participants (55 to 88 years) with early AMD in the study eye and neovascular AMD (nAMD) in the fellow eye were recruited from a hospital nAMD clinic. Eligible participants were randomized (ratio 1:1) to receive light therapy or to an untreated control group. Light therapy was delivered via a light-emitting mask (peak 505 nm, 23 scotopic Td), which was worn each night for 12 months. Co-primary outcome measures were disease progression (onset of nAMD or increased drusen volume beyond test-retest limits) and change in time constant of cone dark adaptation. Other main outcomes included adverse events, compliance, and subjective sleep quality data.

Results: Disease progression over 12 months was seen in 38.1% (18.1%-61.6% confidence interval [CI]) of intervention participants and 48.3% (29.4%-67.5% CI) of controls (Mantel-Haenszel test, common odds ratio = 0.763, P = 0.495). A significantly larger delay in cone adaptation was observed in the intervention group (1.66 ± 0.61 minutes) than in the control group (0.66 ± 0.49 minutes) over the follow-up period. No reported adverse events were deemed to be associated with the intervention.

Conclusions: Although acceptable to the patients, light therapy did not have a substantial effect on the progression of early AMD over 12 months. Further investigation is necessary to discover the permanency and cause of the adverse effect of light therapy on dark adaptation.
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http://dx.doi.org/10.1167/iovs.18-24284DOI Listing
September 2018

Using an Augmented Reality Device as a Distance-based Vision Aid-Promise and Limitations.

Optom Vis Sci 2018 09;95(9):727-737

Department of Psychological & Brain Sciences, Dartmouth College, Hanover, New Hampshire.

Significance: For people with limited vision, wearable displays hold the potential to digitally enhance visual function. As these display technologies advance, it is important to understand their promise and limitations as vision aids.

Purpose: The aim of this study was to test the potential of a consumer augmented reality (AR) device for improving the functional vision of people with near-complete vision loss.

Methods: An AR application that translates spatial information into high-contrast visual patterns was developed. Two experiments assessed the efficacy of the application to improve vision: an exploratory study with four visually impaired participants and a main controlled study with participants with simulated vision loss (n = 48). In both studies, performance was tested on a range of visual tasks (identifying the location, pose and gesture of a person, identifying objects, and moving around in an unfamiliar space). Participants' accuracy and confidence were compared on these tasks with and without augmented vision, as well as their subjective responses about ease of mobility.

Results: In the main study, the AR application was associated with substantially improved accuracy and confidence in object recognition (all P < .001) and to a lesser degree in gesture recognition (P < .05). There was no significant change in performance on identifying body poses or in subjective assessments of mobility, as compared with a control group.

Conclusions: Consumer AR devices may soon be able to support applications that improve the functional vision of users for some tasks. In our study, both artificially impaired participants and participants with near-complete vision loss performed tasks that they could not do without the AR system. Current limitations in system performance and form factor, as well as the risk of overconfidence, will need to be overcome.
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http://dx.doi.org/10.1097/OPX.0000000000001232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6133229PMC
September 2018

The Effect of Gaze Angle on Visual Acuity in Infantile Nystagmus.

Invest Ophthalmol Vis Sci 2017 01;58(1):642-650

School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom.

Purpose: Most individuals with infantile nystagmus (IN) have an idiosyncratic gaze angle at which their nystagmus intensity is minimized. Some adopt an abnormal head posture to use this "null zone," and it has therefore long been assumed that this provides people with nystagmus with improved visual acuity (VA). However, recent studies suggest that improving the nystagmus waveform could have little, if any, influence on VA; that is, VA is fundamentally limited in IN. Here, we examined the impact of the null zone on VA.

Methods: Visual acuity was measured in eight adults with IN using a psychophysical staircase procedure with reversals at three horizontal gaze angles, including the null zone.

Results: As expected, changes in gaze angle affected nystagmus amplitude, frequency, foveation duration, and variability of intercycle foveation position. Across participants, each parameter (except frequency) was significantly correlated with VA. Within any given individual, there was a small but significant improvement in VA (0.08 logMAR) at the null zone as compared with the other gaze angles tested. Despite this, no change in any of the nystagmus waveform parameters was significantly associated with changes in VA within individuals.

Conclusions: A strong relationship between VA and nystagmus characteristics exists between individuals with IN. Although significant, the improvement in VA observed within individuals at the null zone is much smaller than might be expected from the occasionally large variations in intensity and foveation dynamics (and anecdotal patient reports of improved vision), suggesting that improvement of other aspects of visual performance may also encourage use of the null zone.
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http://dx.doi.org/10.1167/iovs.16-20370DOI Listing
January 2017

The pig X and Y Chromosomes: structure, sequence, and evolution.

Genome Res 2016 Jan 11;26(1):130-9. Epub 2015 Nov 11.

Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;

We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.
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http://dx.doi.org/10.1101/gr.188839.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691746PMC
January 2016

Visual Processing in Infantile Nystagmus Is Not Slow.

Invest Ophthalmol Vis Sci 2015 Aug;56(9):5094-101

Purpose: Treatments for infantile nystagmus (IN) sometimes elicit subjective reports of improved visual function, yet quantifiable improvements in visual acuity, if any, are often negligible. One possibility is that these subjective "improvements" may relate to temporal, rather than spatial, visual function. This study aimed to ascertain the extent to which "time to see" might be increased in nystagmats, as compared to normally sighted controls. By assessing both eye movement and response time data, it was possible to determine whether delays in "time to see" were due solely to the eye movements, or to an underlying deficit in visual processing.

Methods: The time taken to respond to the orientation of centrally and peripherally presented gratings was measured in subjects with IN and normally sighted controls (both groups: n = 11). For each vertically displaced grating, the time until the target-acquiring saccade was determined, as was the time from the saccade until the subject's response.

Results: Nystagmats took approximately 60 ms longer than controls to execute target-acquiring saccades to vertically displaced targets (P = 0.010). However, the time from the end of the saccade until subjects responded was not significantly different between groups (P = 0.37). Despite this, nystagmats took longer to respond to gratings presented at fixation.

Conclusions: Individuals with IN took longer to direct their gaze toward objects of interest. However, once a target was foveated, the time taken to process visual information and respond did not appear to differ from that of control subjects. Therefore, conscious visual processing in IN is not slow.
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http://dx.doi.org/10.1167/iovs.15-16977DOI Listing
August 2015

Clostridium sordellii genome analysis reveals plasmid localized toxin genes encoded within pathogenicity loci.

BMC Genomics 2015 May 16;16:392. Epub 2015 May 16.

Department of Life Sciences, Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.

Background: Clostridium sordellii can cause severe infections in animals and humans, the latter associated with trauma, toxic shock and often-fatal gynaecological infections. Strains can produce two large clostridial cytotoxins (LCCs), TcsL and TcsH, related to those produced by Clostridium difficile, Clostridium novyi and Clostridium perfringens, but the genetic basis of toxin production remains uncharacterised.

Results: Phylogenetic analysis of the genome sequences of 44 strains isolated from human and animal infections in the UK, US and Australia placed the species into four clades. Although all strains originated from animal or clinical disease, only 5 strains contained LCC genes: 4 strains contain tcsL alone and one strain contains tcsL and tcsH. Four toxin-positive strains were found within one clade. Where present, tcsL and tcsH were localised in a pathogenicity locus, similar to but distinct from that present in C. difficile. In contrast to C. difficile, where the LCCs are chromosomally localised, the C. sordellii tcsL and tcsH genes are localised on plasmids. Our data suggest gain and loss of entire toxigenic plasmids in addition to horizontal transfer of the pathogenicity locus. A high quality, annotated sequence of ATCC9714 reveals many putative virulence factors including neuraminidase, phospholipase C and the cholesterol-dependent cytolysin sordellilysin that are highly conserved between all strains studied.

Conclusions: Genome analysis of C. sordellii reveals that the LCCs, the major virulence factors, are localised on plasmids. Many strains do not contain the LCC genes; it is probable that in several of these cases the plasmid has been lost upon laboratory subculture. Our data are consistent with LCCs being the primary virulence factors in the majority of infections, but LCC-negative strains may precipitate certain categories of infection. A high quality genome sequence reveals putative virulence factors whose role in virulence can be investigated.
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http://dx.doi.org/10.1186/s12864-015-1613-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4434542PMC
May 2015

Quick phases of infantile nystagmus show the saccadic inhibition effect.

Invest Ophthalmol Vis Sci 2015 Feb 10;56(3):1594-600. Epub 2015 Feb 10.

School of Psychology, Cardiff University, Cardiff, United Kingdom.

Purpose: Infantile nystagmus (IN) is a pathological, involuntary oscillation of the eyes consisting of slow, drifting eye movements interspersed with rapid reorienting quick phases. The extent to which quick phases of IN are programmed similarly to saccadic eye movements remains unknown. We investigated whether IN quick phases exhibit 'saccadic inhibition,' a phenomenon typically related to normal targeting saccades, in which the initiation of the eye movement is systematically delayed by task-irrelevant visual distractors.

Methods: We recorded eye position from 10 observers with early-onset idiopathic nystagmus while task-irrelevant distractor stimuli were flashed along the top and bottom of a large screen at ±10° eccentricity. The latency distributions of quick phases were measured with respect to these distractor flashes. Two additional participants, one with possible albinism and one with fusion maldevelopment nystagmus syndrome, were also tested.

Results: All observers showed that a distractor flash delayed the execution of quick phases that would otherwise have occurred approximately 100 ms later, exactly as in the standard saccadic inhibition effect. The delay did not appear to differ between the two main nystagmus types under investigation (idiopathic IN with unidirectional and bidirectional jerk).

Conclusions: The presence of the saccadic inhibition effect in IN quick phases is consistent with the idea that quick phases and saccades share a common programming pathway. This could allow quick phases to take on flexible, goal-directed behavior, at odds with the view that IN quick phases are stereotyped, involuntary eye movements.
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http://dx.doi.org/10.1167/iovs.14-15655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351650PMC
February 2015

Author response: Grating visual acuity in infantile nystagmus in the absence of image motion.

Invest Ophthalmol Vis Sci 2014 Aug 8;55(8):4955-7. Epub 2014 Aug 8.

School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom; and the.

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http://dx.doi.org/10.1167/iovs.14-15070DOI Listing
August 2014

Genomic analysis of the causative agents of coccidiosis in domestic chickens.

Genome Res 2014 Oct 11;24(10):1676-85. Epub 2014 Jul 11.

Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.
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http://dx.doi.org/10.1101/gr.168955.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199364PMC
October 2014

Grating visual acuity in infantile nystagmus in the absence of image motion.

Invest Ophthalmol Vis Sci 2014 Apr 25;55(4):2682-6. Epub 2014 Apr 25.

School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom.

Purpose: Infantile nystagmus (IN) consists of largely horizontal oscillations of the eyes that usually begin shortly after birth. The condition is almost always associated with lower-than-normal visual acuity (VA). This is assumed to be at least partially due to motion blur induced by the eye movements. Here, we investigated the effect of image motion on VA.

Methods: Grating stimuli were presented, illuminated by either multiple tachistoscopic flashes (0.76 ms) to circumvent retinal image motion, or under constant illumination, to subjects with horizontal idiopathic IN and controls. A staircase procedure was used to estimate VA (by judging direction of tilt) under each condition. Orientation-specific effects were investigated by testing gratings oriented about both the horizontal and vertical axes.

Results: Nystagmats had poorer VA than controls under both constant and tachistoscopic illumination. Neither group showed a significant difference in VA between illumination conditions. Nystagmats performed worse for vertically oriented gratings, even under tachistoscopic conditions (P < 0.01), but there was no significant effect of orientation in controls.

Conclusions: The fact that VA was not significantly affected by either illumination condition strongly suggests that the eye movements themselves do not significantly degrade VA in adults with IN. Treatments and therapies that seek to modify and/or reduce eye movements may therefore be fundamentally limited in any improvement that can be achieved with respect to VA.
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http://dx.doi.org/10.1167/iovs.13-13455DOI Listing
April 2014

Radical cystectomy with extended lymphadenectomy: evaluating separate package versus en bloc submission for node positive bladder cancer.

J Urol 2007 Mar;177(3):876-81; discussion 881-2

Department of Urology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California 90089, USA.

Purpose: To provide future mapping analysis of lymph node positive disease we modified our lymphadenectomy at radical cystectomy for bladder cancer from an en bloc packet to 13 separate nodal packets. We evaluated the clinical and pathological findings resulting from this modification.

Materials And Methods: A total of 1,359 patients underwent en bloc radical cystectomy and extended lymphadenectomy for bladder cancer. They were compared to 262 patients who underwent radical cystectomy and extended lymphadenectomy with lymph nodes submitted in 13 distinct nodal packets. Overall 317 patients (23%) of the en bloc group (group 1) and 66 of the 262 (25%) in the separately packaged group (group 2) had node positive disease. Clinical and pathological findings were analyzed to compare these 2 groups of patients.

Results: Although the incidence of lymph node positivity was not different, the median number of total lymph nodes removed in group 2 was significantly higher than that in group 1 (68, range 14 to 132 vs 31, range 1 to 96, p<0.001). A trend toward more lymph nodes involved was observed in group 2 compared to group 1 (3, range 1 to 91 vs 2, range 1 to 63, p=0.062). These findings significantly lowered median lymph node density in group 2 compared to that in group 1 (6% vs 9%, p=0.006).

Conclusions: Although the overall incidence of lymph node positive disease was not different, the submission of 13 separate nodal packets at radical cystectomy significantly increased the total number of lymph nodes removed/analyzed and identified a slightly higher number of positive lymph nodes compared to en bloc submission.
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http://dx.doi.org/10.1016/j.juro.2006.10.043DOI Listing
March 2007

Fully human, HLA-DR-specific monoclonal antibodies efficiently induce programmed death of malignant lymphoid cells.

Nat Med 2002 Aug 8;8(8):801-7. Epub 2002 Jul 8.

GPC Biotech AG, Martinsried/Munich, Germany.

The Human Combinatorial Antibody Library (HuCAL) was screened for antibodies specific to human leukocyte antigen-DR (HLA-DR) that induce programmed death of lymphoma/leukemia cells expressing the target antigen. The active Fab fragments were affinity-matured, and engineered to IgG(4) antibodies of sub-nanomolar affinity. The antibodies exhibited potent in vitro tumoricidal activity on several lymphoma and leukemia cell lines and on chronic lymphocytic leukemia patient samples. They were also active in vivo in xenograft models of non-Hodgkin lymphoma. Cell death occurred rapidly, without the need for exogenous immunological effector mechanisms, and was selective to activated/tumor-transformed cells. Although the expression of HLA-DR on normal hematopoietic cells is a potential safety concern, the antibodies caused no long-lasting hematological toxicity in primates, in vivo. Such monoclonal antibodies offer the potential for a novel therapeutic approach to lymphoid malignancies.
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http://dx.doi.org/10.1038/nm736DOI Listing
August 2002
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