Biology subjects

Cavanagh, P.

Publications and source records attributed to Cavanagh, P..

15 recordsLinked to original sources

bioRxiv2026

Seeing at Will: Shared Neural Representations of Motion Perception and Intention

Volitional intention can bias perception in cases where two or more interpretations of a stimulus are available to us. The neural mechanisms whereby such an intention influences perception are poorly understood. Here we investigated whether intending to see horizontal versus vertical motion in a subsequently presented instantaneous position shift of a quartet apparent motion stimulus establishes decodable sensory representations prior to both the position shift and the perception of motion. Twelve participants underwent fMRI scanning under three conditions: (1) while passively viewing either continuously or (2) discretely moving quartet stimuli, or (3) while actively intending to see a subsequent single-shot apparent motion as either a vertical or horizontal motion. Multivariate decoding analyses revealed that activity patterns during the intention period of (3) generalized to patterns evoked by both (1) physical and (2) ambiguous motion perception. Cross-decoding was strongest within dorsal/lateral visual regions, including hMT+, V3AB, and the intraparietal sulcus (IPS), but was largely absent from ventral visual cortex. Widespread overlap was also observed between intention-related and perceptual motion representations throughout the dorsal/lateral visual cortex. Our findings suggest that volitional intention establishes prospective sensory representations before perceptual experience emerges and that these representations closely resemble those associated with illusory motion perception. The predominance of intention-related representations within dorsal/lateral visual regions is consistent with top-down influences from attentional control systems. More broadly, the results demonstrate that internally generated cognitive states can shape sensory representations, constraining subsequent perceptual experience.

neuroscience↗

bioRxiv2025

Staphylococcus haemolyticus Population Genomics Provides Insights into Pathogenicity and Commensalism

Staphylococcus haemolyticus is a common commensal bacterium but also an opportunistic pathogen, frequently implicated in bacteraemia and sepsis in preterm neonates and immunocompromised patients. Despite its clinical relevance, relatively little is known about the population structure of S. haemolyticus and how this relates to its ability to colonise humans or cause disease. In this study, we analysed commensal and clinical strains isolated from neonates and adults from 20 countries between 1957 - 2022. Whole genome sequencing of these isolates, combined with publicly available data, generated a comprehensive dataset of 986 genomes. This enabled us to characterise the species population structure and track the distribution of antimicrobial resistance (AMR) and virulence determinants. Our analysis revealed a highly diverse genome structure, with multiple phylogenetic groups showing distinct associations with commensalism or pathogenicity. We observed extensive variation in mobile genetic elements, prophages, and AMR genes, alongside increased carriage of plasmids and AMR genes over time. Furthermore, genes lined to metal homeostasis, detoxification, and oxidative stress tolerance were differently abundant between commensal and clinical isolates. This work provides the most detailed view to date of S. haemolyticus diversity, its evolutionary dynamics, and the genetic factors that may underpin the transition from commensal to pathogen.

genetics↗

bioRxiv2025

Frame Effects Across Space and Time

When two probes are flashed at different times within a moving frame they can be perceived as dramatically separated from each other even though they are at the same location in the display. This effect suggests that we perceive object position relative to the surrounding frame even when it is moving (Ozkan et al., 2021). Here, 8 experiments reveal new properties of this frame effect. First, the influence of the frame on the perceived probe positions extends beyond its bounding contours by several degrees of visual angle, both in the direction of the frames motion and orthogonal to it. It is also undiminished when the probes and the frame are in different depth planes. However, the influence of the frames motion shows no extension in time - there is no effect on probes presented after the frame is removed and none retroactively before the frame appears either. The frame effect is also driven primarily by the displacement of the frame, not by its motion signals: the effect is stronger for moving bounded frames compared to moving, unbounded random-dot textures. When the bounded region has an internal texture that moves with or against the frames motion or remains static, it is the displacement of the frame that produces the perceived position shifts of the probes, while the effect of the internal motion is mostly suppressed. The frames influence is unaffected by whether the motion is self-initiated or not and does not reduce in strength across 2 hours of testing.

neuroscience↗

bioRxiv2023

Assessing perceptual chromatic equiluminance using a reflexive pupillary response

Equiluminant stimuli help assess the integrity of colour perception and the relationship of colour to other visual features. As a result of individual variation, it is necessary to calibrate experimental visual stimuli to suit each individuals unique equiluminant ratio. Most traditional methods rely on training observers to report their subjective equiluminance point. Such paradigms cannot easily be implemented on pre-verbal or non-verbal observers. Here, we present a novel Pupil Frequency-Tagging Method (PFTM) for detecting a participants unique equiluminance point without verbal instruction and with minimal training. PFTM analyses reflexive pupil oscillations induced by slow (< 2 Hz) temporal alternations between coloured stimuli. Two equiluminant stimuli will induce a similar pupil dilation response regardless of colour; therefore, an observers equiluminant point can be identified as the luminance ratio between two colours for which the oscillatory amplitude of the pupil at the tagged frequency is minimal. We compared pupillometry-based equiluminance ratios to those obtained with two established techniques in humans: minimum flicker and minimum motion. In addition, we estimated the equiluminance point in non-human primates, demonstrating that this new technique can be successfully employed in non-verbal subjects. Key PointsO_LIMeasuring equiluminance is challenging in non-verbal subjects. C_LIO_LIThe pupil diameter varies as perceived brightness changes. C_LIO_LIUtilising oscillatory pupillometry, PFTM provides a way to measure equiluminance points without training or the need for a subjective report. C_LI

neuroscience↗

bioRxiv2023

The double-drift illusion biases the marmoset oculomotor system

The double-drift illusion has two unique characteristics: the error between the perceived and physical position of the stimulus grows over time, and saccades to the moving target land much closer to the physical than the perceived location. These results suggest that the perceptual and saccade targeting systems integrate visual information over different timescales. Functional imaging studies in humans have revealed several potential cortical areas of interest, including the prefrontal cortex. However, we currently lack an animal model to study the neural mechanisms of location perception that underlie the double-drift illusion. To fill this gap, we trained two marmoset monkeys to fixate and then saccade to the double drift stimulus. In line with human observers for radial double-drift trajectories, we find that saccade endpoints do show a significant bias that is, as it is in humans, smaller than that seen in perception. This bias is modulated by changes in the external and internal speeds of the stimulus. These results demonstrate that the saccade targeting system of the marmoset monkey is influenced by the double-drift illusion.

animal behavior and cognition↗

bioRxiv2022

Different integration of conflicting motion signals in perception and eye movements during object tracking

The ability to accurately perceive and track moving objects is crucial for many everyday activities. In this study, we use a "double-drift stimulus" Lisi and Cavanagh (2015); Shapiro et al. (2010); Tse and Hsieh (2006) to explore the processing of visual motion signals that underlie perception, pursuit, and saccade responses to a moving object. Participants were presented with peripheral moving apertures filled with noise that either drifted orthogonally to the apertures direction or had no net motion. Participants were asked to saccade to and track these targets with their gaze as soon as they appeared, and then to report their direction. In the trials with internal motion, the target disappeared at saccade onset so that the first 100 ms of the post-saccadic pursuit response was driven uniquely by peripheral information gathered before saccade onset. This provided independent measures of perceptual, pursuit, and saccadic responses to the double-drift stimulus on a trial-by-trial basis. Our analysis revealed systematic differences between saccadic responses on one hand and perceptual and pursuit responses on the other. These differences are unlikely to be caused by differences in the processing of motion signals because saccade and pursuit appear to use a common motion processing mechanism (e.g., Erkelens, 2006; Fleuriet and Goffart, 2012). We conclude that our results are instead due to a difference in how the processing mechanisms underlying perception, pursuit, and saccades combine motor signals with target position. These findings advance our understanding of the mechanisms underlying dissociation in visual processing between perception and eye movements.

neuroscience↗

bioRxiv2022

Exploring the frame effect

Probes flashed within a moving frame are dramatically displaced (Ozkan et al, 2021; Wong &Mack, 1981). The effect is much larger than that seen on static or moving probes (induced motion, Duncker, 1929; Wallach et al, 1978). These flashed probes are often perceived with the separation they have in frame coordinates -- a 100% effect. Here we explore this frame effect on flashed tests with several versions of the standard stimulus. We find that the frame effect holds for smoothly or abruptly displacing frames, even when the frame changed shape or orientation between the endpoints of its travel. The path could be non-linear, even circular. The effect was driven by perceived not physical motion. When there were competing overlapping frames, the effect was determined by which frame was attended. There were a number of constraints that limited the effect. A static anchor near the flashes suppressed the effect but an extended static texture did not. If the probes were continuous rather than flashed, the effect was abolished. The observational reports of 30 online participants suggest that the frame effect is robust to many variations in its shape and path and leads to a perception of flashed tests in their locations relative to the frame as if the frame were stationary. Our results highlight the role of frame continuity and of the grouping of the flashes with the frame in generating the frame effect.

neuroscience↗

bioRxiv2021

The perceived position of a moving object is reset by temporal, not spatial limits

When the internal texture of a Gabor patch drifts orthogonally to its physical path, its perceived motion deviates dramatically from its physical path. The local position shifts accumulate to such an extent that a 45{degrees} oblique physical path appears to be vertical. However, at some point, a limit is reached and the path resets back to its veridical location, whereupon a new accumulation starts, making the new perceived path segment appear parallel to the pre-reset segment, but offset horizontally from it. Here, we tested whether spontaneous resets of this motion-induced position shift depend on the time or the distance over which position errors accrue, or both. We introduced a temporal gap in the middle of the path that forced the illusory path to reset back to its veridical physical position. This gap-triggered reset allowed us to measure the magnitude of the illusory offset up to that point. We found that perceived offset was less than expected for the angle of illusory drift, indicating that spontaneous resets had occurred prior to the gap-induced reset. The position offset decreased when the pre-gap duration increased but approximately doubled when the path length doubled. This pattern of perceived offsets is best accounted for by spontaneous resets that occur randomly over time at a constant rate, independently of the distance traveled. Our results suggest a temporal, not spatial, limit for the accumulation of position errors that underlies this illusion.

neuroscience↗

bioRxiv2021

Measuring the double-drift illusion with hand tracking

If a gabor pattern drifts in one direction while its internal texture drifts in the orthogonal direction, its perceived position deviates further and further away from its true path. We first evaluated the illusion using manual tracking. Participants followed the gabor with a stylus on a drawing tablet that coincided optically with the horizontal monitor surface. Their hand and the stylus were not visible during the tracking. The magnitude of the tracking illusion corresponded closely to previous perceptual and pointing measures indicating that manual tracking is a valid measure for the illusion. This allowed us to use it in a second experiment to capture the behavior of the illusion as it eventually degrades and breaks down in single trials. Specifically, the deviation of the gabor stops accumulating at some point and either stays at a fixed offset or resets toward the veridical position. To report the perceived trajectory of the gabor, participants drew it after the gabor was removed from the monitor. Resets were detected and analyzed and their distribution matches neither a temporal nor a spatial limit, but rather a broad gamma distribution over time. This suggests that resets are triggered randomly, about once per 1.3 s, possible by extraneous distractions or eye movements.

neuroscience↗

bioRxiv2021

Paradoxical stabilization of relative position in moving frames

To capture where things are and what they are doing, the visual system may extract the position and motion of each object relative to its surrounding frame of referencee.g., 1,2. Here we report a particularly powerful example where a paradoxical stabilization is produced by a moving frame. We first take a frame that moves left and right and we flash its right edge before, and its left edge after, the frames motion. For all frame displacements tested, the two edges are perceived as stabilized, with the left edge on the left and right edge on the right, separated by the frames width as if the frame were not moving. This illusory stabilization holds even when the frame travels farther than its width, reversing the actual spatial order of the two flashes. Despite this stabilization, the motion of the frame is still seen, albeit much reduced, and this hides the paradoxical standstill of relative positions. In a second experiment, two probes are flashed inside the frame at the same physical location before and after the frame moves. Despite being physically superimposed, the probes are perceived widely separated, again as if they were seen in the frames coordinates and the frame were stationary. This illusory separation is set by the distance of the frames travel, independently of its speed. This paradoxical stabilization suggests a link to visual constancy across eye movements where the displacement of the entire visual scene may act as a frame to stabilize the perception of relative locations.

neuroscience↗

bioRxiv2019

Neural correlates of conscious visual perception lie outside the visual system: evidence from the double-drift illusion

When perception differs from the physical stimulus, as it does for visual illusions and binocular rivalry, the opportunity arises to localize where perception emerges in the visual processing hierarchy. Representations prior to that stage differ from the eventual conscious percept even though they provide input to it. Here we investigate where and how a remarkable misperception of position emerges in the brain. This \"double-drift\" illusion causes a dramatic mismatch between retinal and perceived location, producing a perceived path that can differ from its physical path by 45{degrees} or more [1]. The deviations in the perceived trajectory can accumulate over at least a second [1] whereas other motion-induced position shifts accumulate over only 80 to 100 ms before saturating [2]. Using fMRI and multivariate pattern analysis, we find that the illusory path does not share activity patterns with a matched physical path in any early visual areas. In contrast, a whole-brain searchlight analysis reveals a shared representation in more anterior regions of the brain. These higher-order areas would have the longer time constants required to accumulate the small moment-to-moment position offsets that presumably originate in early visual cortices, and then transform these sensory inputs into a final conscious percept. The dissociation between perception and the activity in early sensory cortex suggests that perceived position does not emerge in what is traditionally regarded as the visual system but emerges instead at a much higher level.

neuroscience↗

bioRxiv2019

Still moving: The double-drift illusion survives smooth pursuit.

If a gabor pattern drifts in one direction while its internal texture drifts in the orthogonal direction, observers see a remarkable shift in its perceived direction when it is viewed in the periphery. The reported direction of the double-drift stimulus (also known as the infinite regress and curveball illusions) is some combination of the actual external motion of the gabor envelope and the internal motion of its texture (Tse & Hsieh, 2006). Here we find that if the observers track a fixation point that moves in tandem with the gabor, the illusion is undiminished. The pursuit of the moving fixation spot keeps the gabor roughly fixed at one location on the retina, cancelling its external motion, leaving only the internal motion. The gabor is seen to move in the world at roughly its actual speed as the motion of the eye is discounted at some point to recover velocities in world coordinates (e.g. Wallach, 1959). Our finding indicates that the combination of internal and external motion that produces the double drift illusion must happen after the eye movement signals have been factored into stimulus motions. We also test the double drift effect at various path lengths, durations, and speeds, with both mid-grey and black backgrounds, all with a static fixation. These results confirm that a simple vector combination of the two speeds alone accounts for virtually all the direction shifts on the grey background. On the black background, the illusion is eliminated. These results place constraints on where perceived spatial coordinates arise in the visual processing hierarchy to locations at or beyond where compensation for pursuit eye movements arise, specifically V3A, V6, MSTd, and VIP (e.g., Nau et al, 2018).

neuroscience↗

bioRxiv2019

Effects of a demand optimization intervention on laboratory test utilization in primary care

There is evidence of increasing use of laboratory tests with substantial variation between clinical teams which is difficult to justify on clinical grounds. The aim of this project was to assess the effect of a demand optimisation intervention project on laboratory test requesting by general practitioners (GPs) in an area of Northern Ireland supported by the Clinical Chemistry Laboratory service of Western Health and Social Care Trust (WHSCT). The intervention package was developed in conjunction with the Western Local Commissioning Group and consisted of educational initiatives, feedback to 55 individual practices on test request rates with ranking relative to other practices, and a small financial incentive for practices to reflect on their test requesting activity. Overall test utilization rates of profile tests, HbA1c, and PSA one year before, during, and one year after the intervention were measured using laboratory databases of the Altnagelvin Area Hospital, Tyrone County Hospital, and the Erne (South West Acute Hospital. The intervention was associated with mixed effects. First, we observed a reduction of 5.1% in the median profile test request rates and a decrease in their between practice variability. The overall downward trend in variability of profile test request rates was found statistically significant (p = 0.03). Second, we found a significant increase in both the volume (p < 0.0001) and between practice variability (p = 0.0001) of HbA1c requests per patient with diabetes. The increase in HbA1c requests may reflect a more appropriate rate of diabetes monitoring and also the adoption of HbA1c as a diagnostic test. Yet, the subsequent 600% increase in between practice variability of HbA1c ordering rates may imply an inconsistent implementation of recommended guidelines by GPs. Finally, there was a 29.3% increase in the median and 35% increase in between practice variability of request rates for PSA, the reasons for which are unclear.

pathology↗

bioRxiv2018

Idiosyncratic, retinotopic bias in face identification modulated by familiarity

The perception of gender and age of unfamiliar faces is reported to vary idiosyncratically across retinal locations such that, for example, the same androgynous face may appear to be male at one location but female at another. Here we test spatial heterogeneity for the recognition of the identity of personally familiar faces in human participants. We found idiosyncratic biases that were stable within participants and that varied more across locations for low as compared to high familiar faces. These data suggest that like face gender and age, face identity is processed, in part, by independent populations of neurons monitoring restricted spatial regions and that the recognition responses vary for the same face across these different locations. Moreover, repeated and varied social interactions appear to lead to adjustments of these independent face recognition neurons so that the same familiar face is eventually more likely to elicit the same recognition response across widely separated visual field locations. We provide a mechanistic account of this reduced retinotopic bias based on computational simulations.\n\nSignificance statementIn this work we tested spatial heterogeneity for the recognition of personally familiar faces. We found retinotopic biases that varied more across locations for low as compared to highly familiar faces. The retinotopic biases were idiosyncratic and stable within participants. Our data suggest that, like face gender and age, face identity is processed by independent populations of neurons monitoring restricted spatial regions and that recognition may vary for the same face at these different locations. Unlike previous findings, our data and computational simulation address the effects of learning and show how increased familiarity modifies the representation of face identity in face-responsive cortical areas. This new perspective has broader implications for understanding how learning optimizes visual processes for socially salient stimuli.

neuroscience↗

bioRxiv2018

A laboratory demand optimisation project in primary care

BackgroundThere is evidence of increasing use of laboratory tests with substantial variation between clinical teams which is difficult to justify on clinical grounds. The aim of this project was to assess the effect of a demand optimisation intervention on laboratory test requesting in primary care.\n\nMethodsThe intervention comprised educational initiatives, feedback to 55 individual practices on test request rates with ranking relative to other practices, and a small financial incentive for practices to engage and reflect on their test requesting activity. Data on test request numbers were collected from the laboratory databases for consecutive 12 month periods; pre-intervention 2011-12, intervention 2012-13, 2013-14, 2014-15, and post-intervention 2015-16.\n\nResultsThe intervention was associated with a 3.6% reduction in the mean number of profile test requests between baseline and 2015-16, although this was seen only in rural practices. In both rural and urban practices, there was a significant reduction in-between practice variability in request rates. The mean number of HbA1c requests increased from 1.9 to 3.0 per practice patient with diabetes. Variability in HbA1c request rates increased from 23.8% to 36.6%. At all considered time points, test request rates and variability were higher in rural than in urban areas.\n\nConclusionsThe intervention was associated with a reduction in both the volume and between practice variability of profile test requests, with differences noted between rural and urban practices. The increase in HbA1c requests may reflect a more appropriate rate of diabetes monitoring and also the adoption of HbA1c as a diagnostic test.\n\nStrengths & limitations of the studyO_LIWe assessed the effect of a laboratory demand optimisation intervention both on the value and between GP practice variability in laboratory test requesting.\nC_LIO_LIThe changes in laboratory test requesting were separately evaluated for rural and urban GP practices.\nC_LIO_LIOther factors (GP practice organisation, characteristics of general practitioners) potentially affecting between practice differences in laboratory test ordering were not taken into account due to data unavailability.\nC_LIO_LIThe demand management initiative was not accompanied by the cost-effectiveness analysis.\nC_LIO_LIThe demand optimisation intervention was conducted in a Northern Ireland (NI) Western Health and Social Care Trust and the findings have not been independently replicated in any other NI trusts.\nC_LI

pathology↗