Biology subjects

van den Hurk, J.

Publications and source records attributed to van den Hurk, J..

6 recordsLinked to original sources

bioRxiv2024

Visual and auditory object representations in ventral visual cortex after restoring sight in humans

Visual category-selective representations in human ventral occipital temporal cortex (VOTC) seem to emerge early in infancy. Surprisingly, the VOTC of congenitally blind humans features category-selectivity for auditory and haptic objects. Yet it has been unknown whether VOTC would show category-selective visual responses if sight were restored in congenitally blind humans. Assuming competition for synaptic space during development, cross-modal activation of VOTC as a consequence of congenital blindness might interfere with visual processing in sight-recovery individuals. To test this hypothesis, we investigated adults who had suffered a transient phase of congenital blindness due to bilateral dense cataracts before their sight was restored by cataract-removal surgery. In a functional magnetic resonance imaging (fMRI) study, participants watched movies of faces, scenes, body parts and other objects in the visual condition, while in the auditory condition they listened to the corresponding sounds. The most prominent group difference was the reduced face-selectivity in individuals with reversed congenital cataracts compared to age- and sex-matched normally-sighted individuals. In addition, a double dissociation was found: only sight-recovery individuals demonstrated significant decoding accuracy of visual categories based on auditory category representations in VOTC, while only normally-sighted individuals VOTC decoded auditory categories based on visual category representations. The present results uncovered the neural mechanisms of previously observed face processing impairments in individuals with reversed congenital blindness. We suggest that lower face-selectivity in the sight recovery group might arise from selective deficits in the cortical representation of the central visual field in lower-tier visual areas. Additionally, we speculate that in higher-order visual areas cross-modal activity might facilitate - rather than interfere - with visual functional recovery after congenital blindness.

neuroscience↗

bioRxiv2020

LAYNII: A software suite for layer-fMRI

High-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these high-resolution data make it possible to address novel questions of directional information flow within and across brain circuits, the corresponding data analyses are challenged by MRI artifacts, including image blurring, image distortions, low SNR, and restricted coverage. These challenges often result in insufficient spatial accuracy of conventional analysis pipelines. Here we introduce a new software suite that is specifically designed for layer-specific functional MRI: LayNii. This toolbox is a collection of command-line executable programs written in C/C++ and is distributed open-source and as pre-compiled binaries for Linux, Windows, and macOS. LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints and thus cannot be straightforwardly analyzed in alternative software packages. Some of the most popular programs of LayNii contain layerification and columnarization in the native voxel space of functional data as well as many other layer-fMRI specific analysis tasks: layer-specific smoothing, model-based vein mitigation of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data. HighlightsO_LIA new software toolbox is introduced for layer-specific functional MRI: LayNii. C_LIO_LILayNii is a suite of command-line executable C++ programs for Linux, Windows, and macOS. C_LIO_LILayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints. C_LIO_LILayNii performs layerification in the native voxel space of functional data. C_LIO_LILayNii performs layer-smoothing, GE-BOLD deveining, QA, and VASO analysis. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/148080v3_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@e12e9org.highwire.dtl.DTLVardef@1fbb564org.highwire.dtl.DTLVardef@41da13org.highwire.dtl.DTLVardef@1545106_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

neuroscience↗

bioRxiv2020

Extensive individual differences of category information in ventral temporal cortex in the congenitally blind

Human ventral temporal cortex (VTC) is a cortical expanse that performs different functions and computations, but is especially critical for visual categorization. Nevertheless, accumulating evidence shows that category-selective regions persist in VTC in the absence of visual experience - for example, in congenitally blind (CB) participants. Despite this evidence, a large body of previous work comparing functional representations in VTC between sighted and CB participants performed univariate analyses at the group level, which assume a homogeneous population - an assumption that has not been formally tested until the present study. Specifically, using fMRI in CB and sighted participants (male and female), we empirically show that at the group level, distributed category representations in VTC are more reliable in the sighted (when viewing visual stimuli) compared to the CB (when hearing auditorily-substituted visual stimuli). Despite these group differences, there is extensive heterogeneity in VTC category representations in the CB to the point that VTC category representations in a subset of CB participants (some who were born without eyes, but not all) are more similar to sighted individuals compared to other CB participants. Together, our findings support a novel idea that driving factors contributing to the formation of VTC category representations in the blind are subject-specific, which complements factors that may generalize across group members. More broadly, the present findings caution conclusions of homogeneity across subjects within a group when performing group neuroimaging analyses without explicitly quantifying individual differences.

neuroscience↗

bioRxiv2020

A probabilistic functional parcellation of human occipito-temporal cortex

Human visual cortex contains many retinotopic and category-specific regions. These brain regions have been the focus of a large body of functional MRI research, significantly expanding our understanding of visual processing. As studying these regions requires accurate localization of their cortical location, researchers perform functional localizer scans to identify these regions in each individual. However, it not always possible to conduct these localizer scans. Here, we developed and validated a functional region of interest atlas of early visual and category-selective regions in human ventral and lateral occipito-temporal cortex. Results show that for the majority of fROIs, cortex-based alignment results in lower between-subject variability compared to nonlinear volumetric alignment. Furthermore, we demonstrate that (1) the atlas accurately predicts the location of an independent dataset of ventral temporal cortex ROIs and other atlases of place-selectivity, motion-selectivity, and retinotopy. Next, (2) we show that the majority of voxel within our atlas are responding mostly to the labelled category in a left-out subject cross-validation, demonstrating the utility of this atlas. The functional atlas is publicly available (download.brainvoyager.com/data/visfAtlas.zip) and can help identify the location of these regions in healthy subjects as well as populations (e.g. blind people, infants) in which functional localizers cannot be run.

neuroscience↗

bioRxiv2019

Generalization asymmetry in multivariate cross-classification: When representation A generalizes better to representation B than B to A

In recent years, the use of multivariate cross-classification (MVCC) has grown in popularity as a way to test for the consistency of information in neural patterns of activation across cognitive states. In this approach, a classification algorithm is trained on dataset A and then tested on a different dataset B in order to test for commonalities in the information representation in both datasets. Interestingly, several papers report an asymmetry in the generalization direction: training on A and testing on B returns significantly better decoding results than training on B and testing on A. Whereas several neurocognitive hypotheses have been put forward as an explanation for this phenomenon, none of them has been demonstrated directly. Through simple simulations, we show that asymmetry can arise as soon as two datasets with identical ground truths have a different signal-to-noise ratio (SNR) - generalization is best from the lower SNR to the higher SNR dataset. The extent of the asymmetry is further modulated by the overlap in informative voxels and whether the two datasets have an equal number of informative voxels. These findings demonstrate that the observation of decoding direction asymmetry in MVCC can be explained by simple SNR differences and not necessarily implies complex neurocognitive mechanisms.

neuroscience↗

bioRxiv2018

Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesis fauna assembled over the last 15 Myr. Here, we test the hypothesis that recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of the its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric data sets derived from Sulawesis three largest mammals: the Babirusa, Anoa, and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Myr ago to 2-3 Myr ago), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that recent emergence of land on Sulawesi (~1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicates that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.

evolutionary biology↗