Biology subjects

O'Reilly, C.

Publications and source records attributed to O'Reilly, C..

15 recordsLinked to original sources

bioRxiv2026

The Q1K Integrated EEG and Eye-Tracking Experimental Test Battery for Open Autism Science

The Quebec 1000 Families (Q1K) platform has been designed to recruit, phenotype, and collect biospecimens from a large cohort of families with at least one member with autism spectrum disorder or a related neurodevelopmental condition. As part of the Q1K protocol, an experimental test battery was developed and validated using simultaneous high-density electroencephalography (EEG) and eye tracking (ET). We report on the general approach and design principles, multimodal EEG/ET integration, the tasks, and their validation, providing a blueprint for implement such a project. It also describes the cohort and its methods as a reference for future studies using this dataset. By releasing openly this experimental test battery, we aim to support task standardization and multi-project data pooling in autism and related neurodevelopmental disorders.

neuroscience↗

bioRxiv2026

Neural representation of hedonic valence during narrative listening

Hedonic valence, the intrinsic pleasantness or unpleasantness of an experience, is fundamental to human psychological functioning. Yet, how valence is represented in the brain remains an open question. Functional MRI studies have demonstrated that the brain encodes both positive and negative valence, but this evidence largely stems from experiments using simplified, controlled stimuli, such as images, sounds, or words. As a result, it remains unclear how valence is processed during rich, naturalistic experiences that more closely reflect real life. In addition, most studies adopt a single statistical model, raising concerns about the robustness of their findings. This study used a formal voxel-wise Bayesian model selection approach to test alternative statistical models supporting Bipolarity, Valence-General, and Bivalence hypotheses to identify the most optimal model of valence representation during narrative listening. Our results provide evidence for the Bipolar model. We identified distributed brain regions that selectively encode valence as a bipolar continuum (negative to positive) during narrative comprehension, including classical emotion-related hubs such as ventromedial prefrontal cortex, as well as regions not traditionally associated with emotion processing, such as inferior occipital cortex, supramarginal cortex, inferior frontal cortex, and middle cingulate. Regions selectively encoding arousal and those broadly responsive to both valence and arousal were also identified. These findings highlight the importance of using formal model comparison and naturalistic paradigms in affective neuroscience, advancing our understanding of how valence is represented in the brain during real-world experiences.

neuroscience↗

bioRxiv2025

From Chewing to Chirping: The Misophonia Audiovisual Trigger Archive (MATA)

Misophonia is an emerging condition in which everyday sounds, such as chewing, sniffing, or tapping, evoke disproportionately intense emotional and physiological responses. Despite growing recognition of its clinical significance, progress in understanding misophonia has been hindered by the limited availability of standardized and ecologically valid stimulus sets. Here, we present a large, open-access archive of 1,300 five-second audiovisual clips spanning 12 empirically validated categories of misophonic triggers. This resource extends beyond orofacial movement-related sounds to include a diverse array of real-world triggers, and its audiovisual format enables systematic investigation of how visual context shapes responses to misophonic sounds. The archive lowers the barrier for laboratories to study misophonia, promotes reproducibility across sites, and offers applications ranging from crowdsourced assessments of population-level sensitivities to machine learning approaches for automated trigger detection. By providing the largest and most diverse audiovisual misophonia stimulus repository to date, this resource is designed to accelerate mechanistic, clinical, and translational research on misophonia and related sensory-emotional phenomena.

neuroscience↗

bioRxiv2024

Embracing naturalistic paradigms: substituting GPT predictions for human judgments

Naturalistic paradigms can assure ecological validity and yield novel insights in psychology and neuroscience. However, using behavioral experiments to obtain the human ratings necessary to analyze data collected with these paradigms is usually costly and time-consuming. Large language models like GPT have great potential for predicting human-like behavioral judgments. The current study evaluates the performance of GPT as a substitute for human judgments for affective dynamics in narratives. Our results revealed that GPTs inference of hedonic valence dynamics is highly correlated with human affective perception. Moreover, the inferred neural activity based on GPT-derived valence ratings is similar to inferred neural activity based on human judgments, suggesting the potential of using GPTs prediction as a reliable substitute for human judgments.

neuroscience↗

bioRxiv2024

Deep learning and eye-tracking for accurate EOG rejection

The electroencephalogram (EEG) directly measures the electrical activity generated by the brain. Unfortunately, it is often contaminated by various artifacts, notably those caused by eye movements and blinks (EOG artifacts). Such artifacts are usually removed using an independent component analysis (ICA) or other blind source separation techniques. However, it is difficult to assess whether subtracting EOG components estimated through ICA removes some neurogenic activity. It is crucial to address this question to avoid biasing EEG analyses. Toward that objective, we developed a deep learning model for EOG artifact removal that exploits information about eye movements available through eye-tracking (ET). Using a multimodal EEG and ET open-access dataset, we trained within-subject a long short-term memory (LSTM) model to predict the component of EEG signals predictable from ET data. We further used this ET-informed evaluation of EOG artifacts to investigate the sensitivity and specificity of ICA. Our analysis indicates that although ICA is very sensitive to EOG, it has a comparatively low specificity. These results motivate further research on EEG artifact removal to develop approaches with higher EOG rejection specificity.

neuroscience↗

bioRxiv2024

Eye-movement artifact correction in infant EEG

BackgroundIndependent Component Analysis (ICA) is a well-established approach to clean EEG and remove the impact of signals of non-neural origin, such as those from muscular activity and eye movements. However, evidence suggests that ICA removes artifacts less effectively in infants than in adults. This study systematically compares ICA and Artifact Blocking (AB), an alternative approach proposed to improve eye-movement artifact correction in infant EEG. MethodsWe analyzed EEG collected from 50 infants between 6 and 18 months of age as part of the International Infant EEG Data Integration Platform (EEG-IP), a longitudinal multi-study dataset. EEG was recorded while infants sat on their caregivers laps and watched videos. We used ICA and AB to correct for eye-movement artifacts in the EEG and calculated the proportion of effectively corrected segments, signal-to-noise ratio (SNR), power-spectral density (PSD), and multiscale entropy (MSE) in manually selected EEG segments with and without eye-movement artifacts. ResultsOn the one hand, the proportion of effectively corrected segments indicated that ICA corrected eye-movement artifacts (sensitivity) better than AB. SNR and PSD indicated that both AB and ICA correct eye-movement artifacts with equal sensitivity. MSE gave mixed results. On the other hand, AB caused less distortion to the clean segments (specificity) for SNR, PSD, and MSE. ConclusionsOur results suggest that ICA is more sensitive (i.e., it better removes artifacts) but less specific (it distorts clean signals) than AB for correcting eye-movement artifacts in infant EEG.

neuroscience↗

bioRxiv2024

PyLossless: A non-destructive EEG processing pipeline

EEG recordings are typically long and contain large amounts of data, making manual cleaning a time-consuming and error-prone task. Automated pre-processing pipelines can facilitate the efficient and objective extraction of artifacts, enabling standardized and reproducible analyses. However, automated pre-processing pipelines typically remove data considered artifact, and return a subset of irreversibly transformed signals. This approach obfuscates pre-processing decisions, and often makes it impossible to recover the original data or modify the pre-processing steps. Further, it complicates collaboration between research teams working on a common dataset, because different analyses may require specific pre-processing routines. Given the large amount of resources that are devoted to collecting EEG, tools that can help efficiently and transparently pre-process data are greatly needed. PyLossless addresses this need by creating a non-destructive, automated pre-processing pipeline that maintains the continuous EEG structure. It offers a user-friendly API, it is well documented, tested through continuous integration, easily deployable, and integrates with the popular MNE-Python environment. The pipeline further provides a browser-based quality control review (QCR) dashboard that allows researchers to visualize and edit the automated artifact annotations on sensors, time-periods, and independent components. The end product of PyLossless is a lossless annotated data state that can be shared and used with analysis-specific artifact rejection policies, allowing for an optimal balance between flexibility and standardization.

neuroscience↗

bioRxiv2023

DNA barcoding reveals an increased diversity within the genus Culex (Diptera: Culicidae) in Ireland

Arthropod populations are changing globally due to the combined impacts of climate change, land-use transformation, globalisation and trade. Changes in arthropod populations can potentially result in the decline and extinction of some native and/or endemic species, while other species that potentially pose threats may increase. Such dynamics lead to weakened ecosystem resilience, which can facilitate the establishment and spread of species with vector capabilities, such as mosquitoes. While many of the mosquito species present in Ireland possess vector capabilities, populations have not been nationally surveyed since 1991. At that time, species identification relied on morphological examination, a method that was even then recognised as inadequate for differentiating certain species within complexes. In this study, we present the first DNA barcoding investigation of Irish mosquito populations and reveal species and hidden diversity not previously recognised in Ireland. These include two potential new species/ecotypes, Culex torrentium and Culex pipiens form pipiens, which were recorded for the first time in Ireland. We demonstrate that barcoding with Cytochrome C Oxidase Subunit 1 (COI) based primers is suitable for the majority of species-level identifications. However, additional primer sets targeting the Internal Transcribed Spacer regions 1 and 2 (ITS1 and ITS2) were necessary to differentiate species within the Culex pipiens complex. The multi-locus approach employed in this study can enhance national surveillance efforts, especially in monitoring mosquitoes that may transmit vector-borne diseases, and in recognising increased species diversity from a biodiversity perspective.

ecology↗

bioRxiv2023

A high-content screen identified ingenol-3-angelate as an enhancer of B7-H3-CAR T cell activity by increasing B7-H3 protein expression on the target cell surface via protein kinase C alpha activation

CAR T cell therapy is a promising approach to improve outcomes and decrease toxicities for patients with cancer. While extraordinary success has been achieved using CAR T cells to treat patients with CD19-positive malignancies, multiple obstacles have so far limited the benefit of CAR T cell therapy for patients with solid tumors. Novel manufacturing and engineering approaches show great promise to enhance CAR T cell function against solid tumors. However, similar to single agent chemotherapy approaches, CAR T cell monotherapy may be unable to achieve high cure rates for patients with difficult to treat solid tumors. Thus, combinatorial drug plus CAR T cell approaches may ultimately be required to achieve widespread clinical success. In this regard, we developed a novel high-content and high-throughput screen to evaluate 1114 FDA approved drugs to increase expression of the solid tumor antigen B7-H3 in metastatic osteosarcoma cells. In this proof-of-principle screen, we demonstrate that ingenol-3-angelate increased B7-H3 (CD276) mRNA, total protein, and cell surface expression. Mechanistically, ingenol-3-angelate increased B7-H3 expression via protein kinase C alpha activation. Functionally, ingenol-3-angelate induced B7-H3 expression enhanced B7-H3-CAR T cell function, highlighting utility of the approach, and paving the way for expanding this high-throughput and high-content technique to study other tumor and CAR T cell combinations.

cancer biology↗

bioRxiv2022

Invasive genetic rescue: Dispersal following repeated culling reinforces the genetic diversity of an invasive mammal

Since its introduction from the United States in 1876 the invasive North American Eastern grey squirrel (Sciurus carolinensis) has contributed to the decline of the native Eurasian red squirrel (Sciurus vulgaris) in Britain. Consequently, grey squirrel populations are often subjected to extensive control efforts in order to reduce local abundance and prevent spread, particularly within habitats containing red squirrels. Grey squirrel removal from the island of Anglesey off the coast of north Wales began in 1998 and was completed in 2013. A parallel successful red squirrel reinforcement translocation project also took place. The narrow sea-channel, road and rail bridge connection has meant that the adjacent mainland grey squirrel population has been controlled in subsequent years to reduce the probability of re-invasion. The aim of this study was to assess the overall impact of repeated culling efforts carried out between 2011 and 2020 on the genetic diversity of the grey squirrel population in north Wales to inform future adaptive management plans. Using a combination of mitochondrial DNA (mtDNA) and microsatellite DNA analysis, we found high genetic diversity in both marker types, with six diverse mtDNA haplotypes found and relatively high levels of nuclear genetic diversity, even after repeated culling efforts. Our results suggest that ongoing culling efforts may not adequately reduce genetic diversity to a level where it contributes to a long-term population decline.

ecology↗

bioRxiv2022

Reconstruction and simulation of thalamoreticular microcircuitry

Thalamoreticular circuitry is known to play a key role in attention, cognition and the generation of sleep spindles, and is implicated in numerous brain disorders, but the cellular and synaptic mechanisms remain intractable. Therefore, we developed the first detailed computational model of mouse thalamus and thalamic reticular nucleus microcircuitry that captures morphological and biophysical properties of [~]14,000 neurons connected via [~]6M synapses, and recreates biological synaptic and gap junction connectivity. Simulations recapitulate multiple independent network-level experimental findings across different brain states, providing a novel unifying cellular and synaptic account of spontaneous and evoked activity in both wakefulness and sleep. Furthermore, we found that: 1.) inhibitory rebound produces frequency-selective enhancement of thalamic responses during wakefulness, in addition to its role in spindle generation; 2.) thalamic interactions generate the characteristic waxing and waning of spindle oscillations; and 3.) changes in thalamic excitability (e.g. due to neuromodulation) control spindle frequency and occurrence. The model is openly available and provides a new tool to interpret spindle oscillations and test hypotheses of thalamoreticular circuit function and dysfunction across different network states in health and disease.

neuroscience↗

bioRxiv2021

In-phase and in-antiphase connectivity in EEG

Zero-lag synchrony is generally discarded from functional connectivity studies to eliminate the confounding effect of volume conduction. Demonstrating genuine and significant unlagged synchronization between distant brain regions would indicate that most electroencephalography (EEG) connectivity studies neglect an important mechanism for neuronal communication. We previously demonstrated that local field potentials recorded intracranially tend to synchronize with no lag between homotopic brain regions. This synchrony occurs most frequently in antiphase, potentially supporting corpus callosal inhibition and interhemispheric rivalry. We are now extending our investigation to EEG. By comparing the coherency in a recorded and a surrogate dataset, we confirm the presence of a significant proportion of genuine zero-lag synchrony unlikely to be due to volume conduction or to recording reference artifacts. These results stress the necessity for integrating zero-lag synchrony in our understanding of neural communication and for disentangling volume conduction and zero-lag synchrony when estimating EEG sources and their functional connectivity.

neuroscience↗

bioRxiv2020

Structural templates for imaging EEG cortical sources in infants

Electroencephalographic (EEG) source reconstruction is a powerful approach that helps to unmix scalp signals, mitigates volume conduction issues, and allows anatomical localization of brain activity. Algorithms used to estimate cortical sources require an anatomical model of the head and the brain, generally reconstructed using magnetic resonance imaging (MRI). When such scans are unavailable, a population average can be used for adults, but no average surface template is available for cortical source imaging in infants. To address this issue, this paper introduces a new series of 12 anatomical models for subjects between zero and 24 months of age. These templates are built from MRI averages and volumetric boundary element method segmentation of head tissues available as part of the Neurodevelopmental MRI Database. Surfaces separating the pia mater, the gray matter, and the white matter were estimated using the Infant FreeSurfer pipeline. The surface of the skin as well as the outer and inner skull surfaces were extracted using a cube marching algorithm followed by Laplacian smoothing and mesh decimation. We post-processed these meshes to correct topological errors and ensure watertight meshes. The use of these templates for source reconstruction is demonstrated and validated using 100 high-density EEG recordings in 7-month-old infants. Hopefully, these templates will support future studies based on EEG source reconstruction and functional connectivity in healthy infants as well as in clinical pediatric populations. Particularly, they should make EEG-based neuroimaging more feasible in longitudinal neurodevelopmental studies where it may not be possible to scan infants at multiple time points. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/162131v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@8d705dorg.highwire.dtl.DTLVardef@1cc0ac7org.highwire.dtl.DTLVardef@d791caorg.highwire.dtl.DTLVardef@a4707d_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITwelve surface templates for infants in the 0-2 years old range are proposed C_LIO_LIThese templates can be used for EEG source reconstruction using existing toolboxes C_LIO_LIA relatively modest impact of age differences was found in this age range C_LIO_LICorrelation analysis confirms increasing source differences with age differences C_LIO_LISources reconstructed with infants versus adult templates significantly differ C_LI

neuroscience↗

bioRxiv2020

Intracranial recordings reveal ubiquitous in-phase and in-antiphase functional connectivity between homologous brain regions in humans

Whether neuronal populations exhibit zero-lag (in-phase or in-antiphase) functional connectivity is a fundamental question when conceptualizing communication between cell assemblies. It also has profound implications on how we assess such interactions. Given that the brain is a delayed network due to the finite conduction velocity of the electrical impulses traveling across its fibers, the existence of long-distance zero-lag functional connectivity may be considered improbable. However, in this study, using human intracranial recordings we demonstrate that most interhemispheric connectivity between homotopic cerebral regions is zero-lagged and that this type of connectivity is ubiquitous. Volume conduction can be safely discarded as a confounding factor since it is known to drop almost completely within short inter-electrode distances (< 20 mm) in intracranial recordings. This finding should guide future electrophysiological connectivity studies and highlight the importance of considering the role of zero-lag connectivity in our understanding of communication between cell assemblies. Significance statementBy analysing the functional connectivity between pairs of intracranial electrodes, we demonstrate that corresponding regions from the two cerebral hemispheres show oscillatory activity synchronized without any delay. Most often, these synchronized oscillations have an inverted amplitude, suggesting that the hemispheres inhibit one another in alternance. The existence of such synchronous activity between homotopic brain regions has important implications on how we understand communication between brain regions and on how we assess neuronal functional connectivity. Our results show that controlling the confounding effect of volume conduction by discarding instantaneous synchrony may result in missing important brain dynamics. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY Graphical abstract textOffset PLI and standard PLI (sensitive and insensitive to zero-lag connectivity, respectively) for pairs of electrodes separated by more than 105 mm, plotted against their homotopic distance. Significant connectivity (dots above the red dashed line) is found only between homotopic regions and mostly for zero-lag connectivity (offset-PLI).

neuroscience↗

bioRxiv2019

Experimentally-constrained biophysical models of tonic and burst firing modes in thalamocortical neurons

Somatosensory thalamocortical (TC) neurons from the ventrobasal (VB) thalamus are central components in the flow of sensory information between the periphery and the cerebral cortex, and participate in the dynamic regulation of thalamocortical states including wakefulness and sleep. This property is reflected at the cellular level by the ability to generate action potentials in two distinct firing modes, called tonic firing and low-threshold bursting. Although the general properties of TC neurons are known, we still lack a detailed characterization of their morphological and electrical properties in the VB thalamus. The aim of this study was to build biophysically-detailed models of VB TC neurons explicitly constrained with experimental data from rats. We recorded the electrical activity of VB neurons (N = 49) and reconstructed morphologies in 3D (N = 50) by applying standardized protocols. After identifying distinct electrical types, we used a multi-objective optimization to fit single neuron electrical models (e-models), which yielded multiple solutions consistent with the experimental data. The models were tested for generalization using electrical stimuli and neuron morphologies not used during fitting. A local sensitivity analysis revealed that the e-models are robust to small parameter changes and that all the parameters were constrained by one or more features. The e-models, when tested in combination with different morphologies, showed that the electrical behavior is substantially preserved when changing dendritic structure and that the e-models were not overfit to a specific morphology. The models and their analysis show that automatic parameter search can be applied to capture complex firing behavior, such as co-existence of tonic firing and low-threshold bursting over a wide range of parameter sets and in combination with different neuron morphologies.\n\nAuthor summaryThalamocortical neurons are one of the main components of the thalamocortical system, which are implicated in key functions including sensory transmission and the transition between brain states. These functions are reflected at the cellular level by the ability to generate action potentials in two distinct modes, called burst and tonic firing. Biophysically-detailed computational modeling of these cells can provide a tool to understand the role of these neurons within thalamocortical circuitry. We started by collecting single cell experimental data by applying standardized experimental procedures in brain slices of the rat. Prior work has demonstrated that biological constraints can be integrated using multi-objective optimization to build biologically realistic models of neuron. Here, we employ similar techniques as those previously employed, but extend them to capture the multiple firing modes of thalamic neurons. We compared the model results with additional experimental data test their generalization and quantitatively reject those that deviated significantly from the experimental variability. These models can be readily integrated in a data-driven pipeline to reconstruct and simulate circuit activity in the thalamocortical system.

neuroscience↗