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Human brain neuron activities are incredibly significant nowadays. Neuronal behavior is assessed by analyzing signal data such as electroencephalography (EEG), which can offer scientists valuable information about diseases and…
The critical brain hypothesis posits that neural systems operate near a phase transition, optimizing the processing of information. While scale invariance and non-Gaussian dynamics--hallmarks of criticality--have been observed in brain…
A fundamental challenge in calcium imaging has been to infer the timing of action potentials from the measured noisy calcium fluorescence traces. We systematically evaluate a range of spike inference algorithms on a large benchmark dataset…
The complex dynamics of intracellular calcium regulates cellular responses to information encoded in extracellular signals. Here, we study the encoding of these external signals in the context of the Li-Rinzel model. We show that by control…
Calcium scoring, a process in which arterial calcifications are detected and quantified in CT, is valuable in estimating the risk of cardiovascular disease events. Especially when used to quantify the extent of calcification in the coronary…
Partial synchronization plays a crucial role in the functioning of neuronal networks: selective, coordinated activation of neurons enables information processing that flexibly adapts to a changing computational context. Since the structure…
The aim of this paper is to give an introductory review of the cryoelectron microscopy as a complex data source for the most of the system biology branches, including the most perspective non-local approaches known as "localomics" and…
At tripartite synapses, astrocytes are in close contact with neurons and contribute to various functions, from synaptic transmission, maintenance of ion homeostasis and glutamate uptake to metabolism. However, disentangling the precise…
We investigate calcium signaling feedback through calcium-activated potassium channels of a dendritic spine by applying the immersed boundary method with electrodiffusion. We simulate the stochastic gating of such ion channels and the…
NMDA receptors (NMDA-R) typically contribute to excitatory synaptic transmission in the central nervous system. While calcium influx through NMDA-R plays a critical role in synaptic plasticity, experimental evidence indicates that…
In vitro neuronal culture is an important research platform in cellular and network neuroscience. However, neurons cultured on a homogeneous scaffold form dense, randomly connected networks and display excessively synchronized activity;…
Network control theory (NCT) has recently been utilized in neuroscience to facilitate our understanding of brain stimulation effects. A particularly useful branch of NCT is optimal control, which focuses on applying theoretical and…
Neural systems can be modeled as networks of functionally connected neural elements. The resulting network can be analyzed using mathematical tools from network science and graph theory to quantify the system's topological organization and…
The activity of an isolated and auto-connected neuron is studied using Hodgkin--Huxley and Integrate-and-Fire frameworks. Main ingredients of the modeling are the auto-stimulating autaptic current observed in experiments, with a spontaneous…
Since the earliest electroencephalography experiments, large scale oscillations have been observed in the mammalian brain. More recently, episodes of oscillation and bursting have been identified not only in the cerebral cortex and…
Mechanical properties of the cell are important biomarkers for probing its architectural changes caused by cellular processes and/or pathologies. The development of microfluidic technologies have enabled measuring cell mechanics at…
Neurons are spatially extended cells; different parts of a neuron have specific voltage dynamics. Important types of neurons even generate different spikes in different parts of the cell. Neurons' inputs are also often spatially…
Deep learning has received extensive research interest in developing new medical image processing algorithms, and deep learning based models have been remarkably successful in a variety of medical imaging tasks to support disease detection…
As a vital cognitive function of animals, the navigation skill is first built on the accurate perception of the directional heading in the environment. Head direction cells (HDCs), found in the limbic system of animals, are proven to play…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…