A Framework for Modeling the Growth and Development of Neurons and Networks

The development of neural tissue is a complex organizing process, in which it is difficult to grasp how the various localized interactions between dividing cells leads relentlessly to global network organization. Simulation is a useful tool for exploring such complex processes because it permits rigorous analysis of observed global behavior in terms of the mechanistic axioms declared in the simulated model. We describe a novel simulation tool, CX3D, for modeling the development of large realistic neural networks such as the neocortex, in a physical 3D space. In CX3D, as in biology, neurons arise by the replication and migration of precursors, which mature into cells able to extend axons and dendrites. Individual neurons are discretized into spherical (for the soma) and cylindrical (for neurites) elements that have appropriate mechanical properties. The growth functions of each neuron are encapsulated in set of pre-defined modules that are automatically distributed across its segments during growth. The extracellular space is also discretized, and allows for the diffusion of extracellular signaling molecules, as well as the physical interactions of the many developing neurons. We demonstrate the utility of CX3D by simulating three interesting developmental processes: neocortical lamination based on mechanical properties of tissues; a growth model of a neocortical pyramidal cell based on layer-specific guidance cues; and the formation of a neural network in vitro by employing neurite fasciculation. We also provide some examples in which previous models from the literature are re-implemented in CX3D. Our results suggest that CX3D is a powerful tool for understanding neural development

Deep learning for EEG-based prognostication after cardiac arrest: from current research to future clinical applications.

Outcome prognostication in comatose patients after cardiac arrest (CA) remains to date a challenge. The major determinant of clinical outcome is the post-hypoxic/ischemic encephalopathy. Electroencephalography (EEG) is routinely used to assess neural functions in comatose patients. Currently, EEG-based outcome prognosis relies on visual evaluation by medical experts, which is time consuming, prone to subjectivity, and oblivious to complex patterns. The field of deep learning has given rise to powerful algorithms for detecting patterns in large amounts of data. Analyzing EEG signals of coma patients with deep neural networks with the goal of assisting in outcome prognosis is therefore a natural application of these algorithms. Here, we provide the first narrative literature review on the use of deep learning for prognostication after CA. Existing studies show overall high performance in predicting outcome, relying either on spontaneous or on auditory evoked EEG signals. Moreover, the literature is concerned with algorithmic interpretability, and has shown that largely, deep neural networks base their decisions on clinically or neurophysiologically meaningful features. We conclude this review by discussing considerations that the fields of artificial intelligence and neurology will need to jointly address in the future, in order for deep learning algorithms to break the publication barrier, and to be integrated in clinical practice

Developmental Origin of Patchy Axonal Connectivity in the Neocortex: A Computational Model

Injections of neural tracers into many mammalian neocortical areas reveal a common patchy motif of clustered axonal projections. We studied in simulation a mathematical model for neuronal development in order to investigate how this patchy connectivity could arise in layer II/III of the neocortex. In our model, individual neurons of this layer expressed the activator-inhibitor components of a Gierer-Meinhardt reaction-diffusion system. The resultant steady-state reaction-diffusion pattern across the neuronal population was approximately hexagonal. Growth cones at the tips of extending axons used the various morphogens secreted by intrapatch neurons as guidance cues to direct their growth and invoke axonal arborization, so yielding a patchy distribution of arborization across the entire layer II/III. We found that adjustment of a single parameter yields the intriguing linear relationship between average patch diameter and interpatch spacing that has been observed experimentally over many cortical areas and species. We conclude that a simple Gierer-Meinhardt system expressed by the neurons of the developing neocortex is sufficient to explain the patterns of clustered connectivity observed experimentall

EEG-based outcome prediction after cardiac arrest with convolutional neural networks: Performance and visualization of discriminative features.

Prognostication for comatose patients after cardiac arrest is a difficult but essential task. Currently, visual interpretation of electroencephalogram (EEG) is one of the main modality used in outcome prediction. There is a growing interest in computer-assisted EEG interpretation, either to overcome the possible subjectivity of visual interpretation, or to identify complex features of the EEG signal. We used a one-dimensional convolutional neural network (CNN) to predict functional outcome based on 19-channel-EEG recorded from 267 adult comatose patients during targeted temperature management after CA. The area under the receiver operating characteristic curve (AUC) on the test set was 0.885. Interestingly, model architecture and fine-tuning only played a marginal role in classification performance. We then used gradient-weighted class activation mapping (Grad-CAM) as visualization technique to identify which EEG features were used by the network to classify an EEG epoch as favorable or unfavorable outcome, and also to understand failures of the network. Grad-CAM showed that the network relied on similar features than classical visual analysis for predicting unfavorable outcome (suppressed background, epileptiform transients). This study confirms that CNNs are promising models for EEG-based prognostication in comatose patients, and that Grad-CAM can provide explanation for the models' decision-making, which is of utmost importance for future use of deep learning models in a clinical setting

An Instruction Language for Self-Construction in the Context of Neural Networks

Biological systems are based on an entirely different concept of construction than human artifacts. They construct themselves by a process of self-organization that is a systematic spatio-temporal generation of, and interaction between, various specialized cell types. We propose a framework for designing gene-like codes for guiding the self-construction of neural networks. The description of neural development is formalized by defining a set of primitive actions taken locally by neural precursors during corticogenesis. These primitives can be combined into networks of instructions similar to biochemical pathways, capable of reproducing complex developmental sequences in a biologically plausible way. Moreover, the conditional activation and deactivation of these instruction networks can also be controlled by these primitives, allowing for the design of a “genetic code” containing both coding and regulating elements. We demonstrate in a simulation of physical cell development how this code can be incorporated into a single progenitor, which then by replication and differentiation, reproduces important aspects of corticogenesis

Topography of MR lesions correlates with standardized EEG pattern in early comatose survivors after cardiac arrest.

AIM Multimodal prognostication in comatose patients after cardiac arrest (CA) is complicated by the fact that different modalities are usually not independent. Here we set out to systematically correlate early EEG and MRI findings. METHODS 89 adult patients from a prospective register who underwent at least one EEG and one MRI in the acute phase after CA were included. The EEGs were characterized using pre-existent standardized categories (highly malignant, malignant, benign). For MRIs, the apparent diffusion coefficient (ADC) was computed in pre-defined regions. We then introduced a novel classification based on the topography of ADC reduction (MR-lesion pattern (MLP) 1: no lesion; MLP 2: purely cortical lesions; MLP 3: involvement of the basal ganglia; MLP 4 involvement of other deep grey matter regions). RESULTS EEG background reactivity and EEG background continuity were strongly associated with a higher MLP value (p < 0.001 and p = 0.003 respectively). The EEG categories highly malignant, malignant and benign were strongly correlated with the MLP values (rho = 0.46, p < 0.001). CONCLUSION The MRI lesions are highly correlated with the EEG pattern. Our results suggest that performing MRI in comatose patients after CA with either highly malignant or with a benign EEG pattern is unlikely to yield additional useful information for prognostication, and should therefore be performed in priority in patients with intermediate EEG patterns ("malignant pattern")

Alterations of the alpha rhythm in visual snow syndrome: a case-control study.

BACKGROUND Visual snow syndrome is a disorder characterized by the combination of typical perceptual disturbances. The clinical picture suggests an impairment of visual filtering mechanisms and might involve primary and secondary visual brain areas, as well as higher-order attentional networks. On the level of cortical oscillations, the alpha rhythm is a prominent EEG pattern that is involved in the prioritisation of visual information. It can be regarded as a correlate of inhibitory modulation within the visual network. METHODS Twenty-one patients with visual snow syndrome were compared to 21 controls matched for age, sex, and migraine. We analysed the resting-state alpha rhythm by identifying the individual alpha peak frequency using a Fast Fourier Transform and then calculating the power spectral density around the individual alpha peak (+/- 1 Hz). We anticipated a reduced power spectral density in the alpha band over the primary visual cortex in participants with visual snow syndrome. RESULTS There were no significant differences in the power spectral density in the alpha band over the occipital electrodes (O1 and O2), leading to the rejection of our primary hypothesis. However, the power spectral density in the alpha band was significantly reduced over temporal and parietal electrodes. There was also a trend towards increased individual alpha peak frequency in the subgroup of participants without comorbid migraine. CONCLUSIONS Our main finding was a decreased power spectral density in the alpha band over parietal and temporal brain regions corresponding to areas of the secondary visual cortex. These findings complement previous functional and structural imaging data at a electrophysiological level. They underscore the involvement of higher-order visual brain areas, and potentially reflect a disturbance in inhibitory top-down modulation. The alpha rhythm alterations might represent a novel target for specific neuromodulation. TRIAL REGISTRATION we preregistered the study before preprocessing and data analysis on the platform osf.org (DOI: https://doi.org/10.17605/OSF.IO/XPQHF , date of registration: November 19th 2022)