Biology subjects

Serre, T.

Publications and source records attributed to Serre, T..

6 recordsLinked to original sources

bioRxiv2024

An active electronic bidirectional interface for high resolution interrogation of the spinal cord

ObjectiveEpidural electrical stimulation (EES) has shown promise as both a clinical therapy and research tool for studying nervous system function. However, available clinical EES paddles are limited to using a small number of contacts due to the burden of wires necessary to connect each contact to the therapeutic delivery device, limiting the treatment area or density of epidural electrode arrays. We aimed to eliminate this burden using advanced on-paddle electronics. ApproachWe developed a smart EES paddle with a 60-electrode programmable array, addressable using an active electronic multiplexer embedded within the electrode paddle body. The electronics are sealed in novel, ultra-low profile hermetic packaging. We conducted extensive reliability testing on the novel array, including a battery of ISO 10993-1 biocompatibility tests and determination of the hermetic package leak rate. We then evaluated the EES device in vivo, placed on the epidural surface of the ovine lumbosacral spinal cord for 15 months. Main resultsThe active paddle array performed nominally when implanted in sheep for over 15 months and no device-related malfunctions were observed. The onboard multiplexer enabled bespoke electrode arrangements across, and within, experimental sessions. We identified stereotyped responses to stimulation in lower extremity musculature, and examined local field potential responses to EES using high-density recording bipoles. Finally, spatial electrode encoding enabled machine learning models to accurately perform EES parameter inference for unseen stimulation electrodes, reducing the need for extensive training data in future deep models. SignificanceWe report the development and chronic large animal in vivo evaluation of a high-density EES paddle array containing active electronics. Our results provide a foundation for more advanced computation and processing to be integrated directly into devices implanted at the neural interface, opening new avenues for the study of nervous system function and new therapies to treat neural injury and dysfunction.

bioengineering↗

bioRxiv2024

Monkeys engage in visual simulation to solve complex problems

Visual simulation -- i.e., using internal reconstructions of the world to experience potential future versions of events that are not currently happening -- is among the most sophisticated capacities of the human mind. But is this ability in fact uniquely human? To answer this question, we tested monkeys on a series of experiments involving the Planko game, which we have previously used to evoke visual simulation in human participants. We found that monkeys were able to successfully play the game using a simulation strategy, predicting the trajectory of a ball through a field of planks while demonstrating a level of accuracy and behavioral signatures comparable to humans. Computational analyses further revealed that the monkeys strategy while playing Planko aligned with a recurrent neural network (RNN) that approached the task using a spontaneously learned simulation strategy. Finally, we carried out awake functional magnetic resonance imaging while monkeys played Planko. We found activity in motion-sensitive regions of the monkey brain during hypothesized simulation periods, even without any perceived visual motion cues. This neural result closely mirrors previous findings from human research, suggesting a shared mechanism of visual simulation across species. In all, these findings challenge traditional views of animal cognition, proposing that nonhuman primates possess a complex cognitive landscape, capable of invoking imaginative and predictive mental experiences to solve complex everyday problems.

neuroscience↗

bioRxiv2022

Deceptive learning in histopathology

Deep learning holds immense potential for histopathology, automating tasks that are simple for expert pathologists, and revealing novel biology for tasks that were previously considered difficult or impossible to solve by eye alone. However, the extent to which the visual strategies learned by deep learning models in histopathological analysis are trustworthy or not has yet to be systematically analyzed. In this work, we address this problem and discover new limits on the histopathological tasks for which deep learning models learn trustworthy versus deceptive solutions. While tasks that have been extensively studied in the field like tumor detection are reliable and trustworthy, recent advances demonstrating the ability to learn molecular profiling from hematoxylin and eosin (H&E) stained slides do not hold up to closer scrutiny. Our analysis framework represents a new approach in understanding the capabilities of deep learning models, which should be incorporated into the computational pathologists toolkit.

pathology↗

bioRxiv2020

Super-human cell death detection with biomarker-optimized neural networks

Cell death is an essential process in biology that must be accounted for in live microscopy experiments. Nevertheless, cell death is difficult to detect without perturbing experiments with stains, dyes or biosensors that can bias experimental outcomes, lead to inconsistent results, and reduce the number of processes that can be simultaneously labelled. These additional steps also make live microscopy difficult to scale for high-throughput screening because of the cost, labor, and analysis they entail. We address this fundamental limitation of live microscopy with biomarker-optimized convolutional neural networks (BO-CNN): computer vision models trained with a ground truth biosensor that detect live cells with superhuman, 96% accuracy more than 100 times faster than previous methods. Our models learn to identify important morphological characteristics associated with cell vitality without human input or additional perturbations, and to generalize to other imaging modalities and cell types for which they have no specialized training. We demonstrate that we can interpret decisions from BO-CNN models to gain biological insight into the patterns they use to achieve superhuman accuracy. The BO-CNN approach is broadly useful for live microscopy, and affords a powerful new paradigm for advancing the state of high-throughput imaging in a variety of contexts.

cell biology↗

bioRxiv2020

Discriminating between sleep and exercise-induced fatigue using computer vision and behavioral genetics

Following prolonged swimming, Caenorhabditis elegans cycle between active swimming bouts and inactive quiescent bouts. Swimming is exercise for C. elegans and here we suggest that inactive bouts are a recovery state akin to fatigue. Previously, analysis of exercise-induced quiescent (EIQ) bouts relied on laborious manual observation, as existing automated analysis methods for C. elegans swimming either cannot analyze EIQ bouts or fail to accurately track animal posture during these bouts. It is known that cGMP-dependent kinase (PKG) activity plays a conserved role in sleep, rest, and arousal. Using C. elegans EGL-4 PKG, we first validate a novel learning-based computer vision approach to automatically analyze C. elegans locomotory behavior and distinguish between activity and inactivity during swimming for long periods of time. We find that C. elegans EGL-4 PKG function predicts EIQ first bout timing, fractional quiescence, bout number, and bout duration, suggesting that previously described pathways are engaged during EIQ bouts. However, EIQ bouts are likely not sleep as animals are feeding during the majority of EIQ bouts. We find that genetic perturbation of neurons required for other C. elegans sleep states also does not alter EIQ dynamics. Additionally, we find that EIQ onset is sensitive to age and DAF-16 FOXO function. In summary, we have validated a new behavioral analysis software that enabled a quantitative and detailed assessment of swimming behavior, including EIQ. We found novel EIQ defects in aged animals and animals with mutations in a gene involved in stress tolerance. We anticipate that further use of this software will facilitate the analysis of genes and pathways critical for fatigue and other C. elegans behaviors.

animal behavior and cognition↗

bioRxiv2019

Differential involvement of EEG oscillatory components in sameness vs. spatial-relation visual reasoning tasks

The development of deep convolutional networks (DCNs) has recently led to great successes in computer vision and have become de facto computational models of vision. However, a growing body of work suggests that they exhibit critical limitations beyond image categorization. Here, we study a fundamental limitation of DCNs for judging whether two items are the same or different (SD) compared to a baseline assessment of their spatial relationship (SR). We test the prediction that SD tasks recruit additional cortical mechanisms which underlie critical aspects of visual cognition that are not explained by current computational models. We thus recorded EEG signals from 14 participants engaged in the same tasks as the computational models. Importantly, the two tasks were matched in terms of difficulty by an adaptive psychometric procedure: yet, on top of a modulation of evoked potentials, our results revealed higher activity in the low beta (13-20Hz) band in the SD compared to the SR conditions, which we surmise as reflecting the crucial involvement of recurrent mechanisms sustaining working memory and attention. Author SummaryDespite the impressive progress of deep convolutional networks (DCNs) in object recognition, recent studies demonstrated that state-of-the-art vision algorithms encounter severe limitations when performing certain visual reasoning tasks: for instance, convolutional networks can easily solve problems involving spatial relations, but fail in identifying whether two items are identical or different (same-different task). This conclusion led us to test the hypothesis that different computational mechanisms are needed to successfully perform these tasks also in the visual system. First, we confirmed in our simulations that DCNs can successfully perform spatial relationship tasks but struggle with same-different ones. Then, we tested 14 participants on the same experimental design while recording their EEG signals. Remarkably, our results revealed a significant difference between the tasks in the occipital brain regions both in evoked potentials and in the oscillatory dynamics. Specifically, an increase of activity was found when performing the SD over the SR condition. We interpret these results as reflecting the fundamental involvement of recurrent mechanisms implementing cognitive functions such as working memory and attention.

neuroscience↗