Neuronal Models Research Articles

Overview of Spiking Neural Network Learning Approaches and Their Computational Complexities

Spiking neural networks (SNNs) are subjects of a topic that is gaining more and more interest nowadays. They more closely resemble actual neural networks in the brain than their second-generation counterparts, artificial neural networks (ANNs). SNNs have the potential to be more energy efficient than ANNs on event-driven neuromorphic hardware. This can yield drastic maintenance cost reduction for neural network models, as the energy consumption would be much lower in comparison to regular deep learning models hosted in the cloud today. However, such hardware is still not yet widely available. On standard computer architectures consisting mainly of central processing units (CPUs) and graphics processing units (GPUs) ANNs, due to simpler models of neurons and simpler models of connections between neurons, have the upper hand in terms of execution speed. In general, they also win in terms of learning algorithms, as SNNs do not reach the same levels of performance as their second-generation counterparts in typical machine learning benchmark tasks, such as classification. In this paper, we review existing learning algorithms for spiking neural networks, divide them into categories by type, and assess their computational complexity.

Profiling the Hsp70 Chaperone Network in Heat-Induced Proteotoxic Stress Models of Human Neurons.

Heat stroke is among the most hazardous hyperthermia-related illnesses and an emerging threat to humans from climate change. Acute brain injury and long-lasting brain damage are the hallmarks of this condition. Hyperthermic neurological manifestations are remarkable for their damage correlation with stress amplitude and long-term persistence. Hyperthermia-induced protein unfolding, and nonspecific aggregation accumulation have neurotoxic effects and contribute to the pathogenesis of brain damage in heat stroke. Therefore, we generated heat-induced, dose-responsive extreme and mild proteotoxic stress models in medulloblastoma [Daoy] and neuroblastoma [SH-SY5Y] and differentiated SH-SY5Y neuronal cells. We show that heat-induced protein aggregation is associated with reduced cell proliferation and viability. Higher protein aggregation in differentiated neurons than in neuroblastoma precursors suggests a differential neuronal vulnerability to heat. We characterized the neuronal heat shock response through RT-PCR array analysis of eighty-four genes involved in protein folding and protein quality control (PQC). We identify seventeen significantly expressed genes, five of which are Hsp70 chaperones, and four of their known complementing function proteins. Protein expression analysis determined the individual differential contribution of the five Hsp70 chaperones to the proteotoxic stress response and the significance of only two members under mild conditions. The co-expression analysis reveals significantly high co-expression between the Hsp70 chaperones and their interacting partners. The findings of this study lend support to the hypothesis that hyperthermia-induced proteotoxicity may underlie the brain injury of heat stroke. Additionally, this study presents a comprehensive map of the Hsp70 network in these models with potential clinical and translational implications.

Use of in vitro derived human neuronal models to study host-parasite interactions of Toxoplasma gondii in neurons and neuropathogenesis of chronic toxoplasmosis.

Toxoplasma gondii infects approximately one-third of the world's population resulting in a chronic infection with the parasite located in cysts in neurons in the brain. In most immunocompetent hosts the chronic infection is asymptomatic, but several studies have found correlations between Toxoplasma seropositivity and neuropsychiatric disorders, including Schizophrenia, and some other neurological disorders. Host-parasite interactions of bradyzoites in cysts in neurons is not well understood due in part to the lack of suitable in vitro human neuronal models. The advent of stem cell technologies in which human neurons can be derived in vitro from human induced pluripotent stem cells (hiPSCs) or direct conversion of somatic cells generating induced neurons (iNs), affords the opportunity to develop in vitro human neuronal culture systems to advance the understanding of T. gondii in human neurons. Human neurons derived from hiPSCs or iNs, generate pure human neuron monolayers that express differentiated neuronal characteristics. hiPSCs also generate 3D neuronal models that better recapitulate the cytoarchitecture of the human brain. In this review, an overview of iPSC-derived neurons and iN protocols leading to 2D human neuron cultures and hiPSC-derived 3D cerebral organoids will be given. The potential applications of these 2D and 3D human neuronal models to address questions about host-parasite interactions of T. gondii in neurons and the parasite in the CNS, will be discussed. These human neuronal in vitro models hold the promise to advance the understanding of T. gondii in human neurons and to improve the understanding of neuropathogenesis of chronic toxoplasmosis.

Downregulation of mitochondrial calcium uptake family 3 attenuates secondary brain injury after intracerebral hemorrhage in rats.

Intracerebral hemorrhage (ICH) is one type of stroke with a high incidence and mortality. Mitochondria provide energy for various life processes and regulate calcium-mediated signaling pathways by taking up calcium ions from cytoplasm. Mitochondrial calcium uptake family 3 (MICU3) is a tissue-specific enhancer of mitochondrial calcium uptake. The effects and mechanisms of MICU3 in ICH are unknown. In this study, we aimed to explore the role of MICU3 in ICH in rats and neuronal models. First, we constructed ICH model both in vivo and in vitro and observed increased expression of MICU3. Then lentivirus was transduced to knock down MICU3. We observed that knockdown of MICU3 significantly reduced mitochondrial uptake of calcium in primary neurons. Moreover, the downregulation of MICU3 attenuated cell apoptosis and decreased the accumulation of reactive oxygen species (ROS). Recovery of neurobehavioral and cognitive function also benefited from downregulation of MICU3. The findings demonstrated that MICU3 played an important role in cell apoptosis, oxidative stress, and maintenance of mitochondrial structure and function, and promoted rehabilitation of neurobehavior. In conclusion, MICU3 is expected to be a molecular marker and a potential therapeutic target for ICH.

Histone lysine methyltransferase-related neurodevelopmental disorders: current knowledge and saRNA future therapies.

Neurodevelopmental disorders encompass a group of debilitating diseases presenting with motor and cognitive dysfunction, with variable age of onset and disease severity. Advances in genetic diagnostic tools have facilitated the identification of several monogenic chromatin remodeling diseases that cause Neurodevelopmental disorders. Chromatin remodelers play a key role in the neuro-epigenetic landscape and regulation of brain development; it is therefore not surprising that mutations, leading to loss of protein function, result in aberrant neurodevelopment. Heterozygous, usually de novo mutations in histone lysine methyltransferases have been described in patients leading to haploinsufficiency, dysregulated protein levels and impaired protein function. Studies in animal models and patient-derived cell lines, have highlighted the role of histone lysine methyltransferases in the regulation of cell self-renewal, cell fate specification and apoptosis. To date, in depth studies of histone lysine methyltransferases in oncology have provided strong evidence of histone lysine methyltransferase dysregulation as a determinant of cancer progression and drug resistance. As a result, histone lysine methyltransferases have become an important therapeutic target for the treatment of different cancer forms. Despite recent advances, we still lack knowledge about the role of histone lysine methyltransferases in neuronal development. This has hampered both the study and development of precision therapies for histone lysine methyltransferases-related Neurodevelopmental disorders. In this review, we will discuss the current knowledge of the role of histone lysine methyltransferases in neuronal development and disease progression. We will also discuss how RNA-based technologies using small-activating RNAs could potentially provide a novel therapeutic approach for the future treatment of histone lysine methyltransferase haploinsufficiency in these Neurodevelopmental disorders, and how they could be first tested in state-of-the-art patient-derived neuronal models.

Bifurcation analysis of motoneuronal excitability mechanisms under normal and ALS conditions.

Bifurcation analysis allows the examination of steady-state, non-linear dynamics of neurons and their effects on cell firing, yet its usage in neuroscience is limited to single-compartment models of highly reduced states. This is primarily due to the difficulty in developing high-fidelity neuronal models with 3D anatomy and multiple ion channels in XPPAUT, the primary bifurcation analysis software in neuroscience. To facilitate bifurcation analysis of high-fidelity neuronal models under normal and disease conditions, we developed a multi-compartment model of a spinal motoneuron (MN) in XPPAUT and verified its firing accuracy against its original experimental data and against an anatomically detailed cell model that incorporates known MN non-linear firing mechanisms. We used the new model in XPPAUT to study the effects of somatic and dendritic ion channels on the MN bifurcation diagram under normal conditions and after amyotrophic lateral sclerosis (ALS) cellular changes. Our results show that somatic small-conductance Ca2+-activated K (SK) channels and dendritic L-type Ca2+ channels have the strongest effects on the bifurcation diagram of MNs under normal conditions. Specifically, somatic SK channels extend the limit cycles and generate a subcritical Hopf bifurcation node in the V-I bifurcation diagram of the MN to replace a supercritical node Hopf node, whereas L-type Ca2+ channels shift the limit cycles to negative currents. In ALS, our results show that dendritic enlargement has opposing effects on MN excitability, has a greater overall impact than somatic enlargement, and dendritic overbranching offsets the dendritic enlargement hyperexcitability effects. Together, the new multi-compartment model developed in XPPAUT facilitates studying neuronal excitability in health and disease using bifurcation analysis.

Dynamics and synchronization control of fractional conformable neuron system.

Dynamic analysis, electrical coupling and synchronization control of the conformable FitzHugh-Nagumo neuronal models have been presented in this work. Firstly, equations of the Adomian-Decomposition-Method and conformable neuron model have been introduced. The Adomian-Decomposition-Method has been employed for the numerical simulation analysis, since it converges fast and provides serial solutions. Fractional order and external current stimulus have been considered as bifurcation parameters and their effects on neuron model dynamics have been examined in detail. Then, the electrical coupling of the two conformable neuronal models without any controller has been revealed and the significance of the coupling strength parameter has been evaluated. To eliminate impact of the coupling strength parameter on synchronization status of neurons, Lyapunov control method has been employed for synchronization control. In the last step, the numerical simulation studies have been experimentally verified using the Texas Instrument Delfino digital signal processor board. Numerical simulation results together with experimental validation have showed that the types of dynamics of the related neuron model are not affected from the change of the fractional order of conformable derivative, but the frequency of the dynamic response of the neuronal model is changed from the alteration of the fractional order. The frequency of response of the neuron model increases with decreasing values of the fractional order. On the other hand, if there is no synchronization control method, the coupled neuron models exhibit response ranging from synchronous to asynchronous depending on the sign and value of the coupling parameter. Additionally, decreasing values of the fractional order may allow the coupled neurons to enter the synchronous state more quickly due to increasing frequency of response of the neuronal model. Finally, the coupled neuron models could exhibit synchronous behavior, that is determined by calculating the standard deviation results, regardless of the value of the coupling parameter by using the Lyapunov control method.

In Vitro Neurotrophic Properties and Structural Characterization of a New Polysaccharide LTC-1 from Pyrola corbieri Levl (Luticao).

Pyrola corbieri Levl has been used to strengthen bones and nourish the kidney (the kidney governs the bone and is beneficial to the brain) by the local Miao people in China. However, the functional components and neurotrophic activity have not been reported. A new acidic homogeneous heteropolysaccharide named LTC-1 was obtained and characterized by periodate oxidation, Smith degradation, partial acid hydrolysis, GC-MS spectrometry, methylation analysis, and Fourier transform infrared spectroscopy, and its molecular weight was 3239 Da. The content of mannuronic acid (Man A) in LTC-1 was 46%, and the neutral sugar was composed of L-rhamnose (L-Rha), L-arabinose (L-Ara), D-xylose (D-Xyl), D-mannose (D-Man), D-glucose (D-Glc) and D-galactose (D-Gal) with a molar ratio of 1.00:3.63:0.86:1.30:6.97:1.30. The main chain of LTC-1 was composed of Glc, Gal, Man, Man A and the branched chain Ara, Glc, Gal. The terminal residues were composed of Glc and Gal. The main chain and branched chains were linked by (1→5)-linked-Ara, (1→3)-linked-Glc, (1→4)-linked-Glc, (1→6)-linked-Glc, (1→3)-linked-Gal, (1→6)-linked-Gal, (1→3, 6)-linked-Man and ManA. Meanwhile, neurotrophic activity was evaluated through PC12 and primary hippocampal neuronal cell models. LTC-1 exhibited neurotrophic activity in a concentration-dependent manner, which significantly induced the differentiation of PC12 cells, promoted the neurite outgrowth of PC12 cells, enhanced the formation of the web architecture of dendrites, and increased the density of dendritic spines in hippocampal neurons and the expression of PSD-95. These results displayed significant neurotrophic factor-like activity of LTC-1, which suggests that LTC-1 is a potential treatment option for neurodegenerative diseases.

Improving focality and consistency in micromagnetic stimulation.

The novel micromagnetic stimulation (μMS) technology aims to provide high resolution on neuronal targets. However, consistency of neural activation could be compromised by a lack of surgical accuracy, biological variation, and human errors in operation. We have recently modeled the activation of an unmyelinated axon by a circular micro-coil. Although the coil could activate the axon, its performance sometimes lacked focality and consistency. The site of axonal activation could shift by several experimental factors, including the reversal of the coil current, displacement of the coil, and changes in the intensity of the stimulation. Current clinical practice with transcranial magnetic stimulation (TMS) has suggested that figure-eight coils could provide better performance in magnetic stimulation than circular coils. Here, we estimate the performance of μMS by a figure-eight micro-coil, by exploring the impact of the same experimental factors on its focality and consistency in axonal activation. We derived the analytical expression of the electric field and activating function generated by the figure-eight micro-coil, and estimated the location of axonal activation. Using NEURON modeling of an unmyelinated axon, we found two different types (A and B) of axon activation by the figure-eight micro-coil, mediated by coil currents of reversed direction. Type A activation is triggered by membrane hyperpolarization followed by depolarization; Type B activation is triggered by direct membrane depolarization. Consequently, the two types of stimulation are governed by distinct ion channel mechanisms. In comparison to the circular micro-coil, the figure-eight micro-coil requires significantly less current for axonal activation. Under figure-eight micro-coil stimulation, the site of axonal activation does not change with the reversal of the coil current, displacement of the coil, or changes in the intensity of the stimulation. Ultimately, the figure-eight micro-coil provides a more efficient and consistent site of activation than the circular micro-coil in μMS.

IPSC-derived neuronal models from sibling pairs with Gaucher disease discordant for Parkinson disease

iPSC-derived neuronal models from sibling pairs with Gaucher disease discordant for Parkinson disease

Spiking Neuron Mathematical Models: A Compact Overview

The features of the main models of spiking neurons are discussed in this review. We focus on the dynamical behaviors of five paradigmatic spiking neuron models and present recent literature studies on the topic, classifying the contributions based on the most-studied items. The aim of this review is to provide the reader with fundamental details related to spiking neurons from a dynamical systems point-of-view.

LYST deficiency impairs autophagic lysosome reformation in neurons and alters lysosome number and size.

Chediak-Higashi syndrome (CHS) is a rare, autosomal recessive disorder caused by biallelic mutations in the lysosomal trafficking regulator (LYST) gene. Even though enlarged lysosomes and/or lysosome-related organelles (LROs) are the typical cellular hallmarks of CHS, they have not been investigated in human neuronal models. Moreover, how and why the loss of LYST function causes a lysosome phenotype in cells has not been elucidated. We report that the LYST-deficient human neuronal model exhibits lysosome depletion accompanied by hyperelongated tubules extruding from enlarged autolysosomes. These results have also been recapitulated in neurons differentiated from CHS patients' induced pluripotent stem cells (iPSCs), validating our model system. We propose that LYST ensures the correct fission/scission of the autolysosome tubules during autophagic lysosome reformation (ALR), a crucial process to restore the number of free lysosomes after autophagy. We further demonstrate that LYST is recruited to the lysosome membrane, likely to facilitate the fission of autolysosome tubules. Together, our results highlight the key role of LYST in maintaining lysosomal homeostasis following autophagy and suggest that ALR dysregulation is likely associated with the neurodegenerative CHS phenotype.

Synchronization of coupled memristive Hindmarsh–Rose maps under different coupling conditions

The importance of the synchronization emergence in neuronal networks has motivated many researchers to study this phenomenon. However, dealing with the systems in the discrete-time domain is more straightforward and underemphasized. Therefore, neuronal maps have recently been widely used in investigating different collective behaviors of the interacting neurons, including synchronization. Besides, the study of the memristors in neuronal models or as a synaptic function in neuronal networks is another prominent subject of interest nowadays. In fact, the magnetic induction impact on the membrane potential can be considered by the memristors in neuronal models or networks. Hence, in this paper, we investigated the synchronization of the recently proposed memristive Hindmarsh–Rose neuron maps under different coupling conditions: electrical synapses, chemical synapses, inner linking functions, and hybrid synapses. In each case, we analyzed the stability of the synchronous solution using the master stability functions. Also, we calculated the time-averaged synchronization error as a numerical verification. We found that memristive Hindmarsh–Rose neurons synchronize when they are coupled through electrical and hybrid synapses, while through chemical synapses, they cannot reach a synchronous solution. Also, we showed that a slightly lower coupling value is needed to synchronize the neurons interacting through inner linking functions than the electrical synapses.

Simulations of cortical networks using spatially extended conductance-based neuronal models.

The Hodgkin-Huxley model of action potential generation and propagation, published in the Journal of Physiology in 1952, initiated the field of biophysically detailed computational modelling in neuroscience, which has expanded to encompass a variety of species and components of the nervous system. Here we review the developments in this area with a focus on efforts in the community towards modelling the mammalian neocortex using spatially extended conductance-based neuronal models. The Hodgkin-Huxley formalism and related foundational contributions, such as Rall's cable theory, remain widely used in these efforts to the current day. We argue that at present the field is undergoing a qualitative change due to new very rich datasets describing the composition, connectivity and functional activity of cortical circuits, which are being integrated systematically into large-scale network models. This trend, combined with the accelerating development of convenient software tools supporting such complex modelling projects, is giving rise to highly detailed models of the cortex that are extensively constrained by the data, enabling computational investigation of a multitude of questions about cortical structure and function.

Pyrazole Ureas as Low Dose, CNS Penetrant Glucosylceramide Synthase Inhibitors for the Treatment of Parkinson's Disease.

Parkinson's disease is the second most prevalent progressive neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra. Loss-of-function mutations in GBA, the gene that encodes for the lysosomal enzyme glucosylcerebrosidase, are a major genetic risk factor for the development of Parkinson's disease potentially through the accumulation of glucosylceramide and glucosylsphingosine in the CNS. A therapeutic strategy to reduce glycosphingolipid accumulation in the CNS would entail inhibition of the enzyme responsible for their synthesis, glucosylceramide synthase (GCS). Herein, we report the optimization of a bicyclic pyrazole amide GCS inhibitor discovered through HTS to low dose, oral, CNS penetrant, bicyclic pyrazole urea GCSi's with in vivo activity in mouse models and ex vivo activity in iPSC neuronal models of synucleinopathy and lysosomal dysfunction. This was accomplished through the judicious use of parallel medicinal chemistry, direct-to-biology screening, physics-based rationalization of transporter profiles, pharmacophore modeling, and use a novel metric: volume ligand efficiency.

Functional Connectivity Analysis of Neuronal Interactions

Advancements in Computational Neuroscience have resulted in the construction of physiologically realistic and computationally efficient neuronal networks. The developments of diverse neuronal models at various implementation scales have caused an affirmative leap in understanding the numerous causes of brain disorders and anomalies, yet the treatment of the brain is regarded as complicated. Observing the responses of a network of realistic neurons constructed using compartmental modelling makes it possible to overcome the shortcomings of descriptive models, such as their inability to highlight synaptic behaviour and their lack of biological realism in spiking behaviour, which in fact play a crucial role in understanding various cognitive mechanisms via the computational unit called neurons. Henceforth, the dynamics of a microscopic level of interacting neurons coupled hierarchically via feedback and feed forward connections are examined in this article. A tiny network of two and four coupled Hodgkin Huxley (HH) neurons integrated into Freeman KIII set topology have been built using the Spike Timing Dependent plasticity(STDP) algorithm. The entire network has been modelled in Neuron modelling environment using Python as the programming interface, and the functional connectivity between the layers has been analysed.

Modeling and Designing of an All-Digital Resonate-and-Fire Neuron Circuit

Integrate-and-fire (IAF) and leaky integrate-and-fire (LIF) models are the popular models for spiking neurons and spiking neuron networks (SNN). They lack the dynamic properties of the ordinary differential equations (ODEs) model but are simpler. More than half of all neuron implementations were digital circuits. The majority of them were IAF and LIF models. The resonate-and-fire (RAF) model proposed by Izhikevich has both simplicity and dynamic properties. However, the RAF model does not have general structures for hardware implementation. Most realizations of the RAF neuron models were analog designs. In this study, we developed and simulated the model’s equations with digital pulses. Based on this analysis, we proposed block models of digital and all-digital RAF neurons to turn the models into digital hardware. We verified the properties of the proposed models by implementing an all-digital RAF neuron on a Intel 28 nm Cyclone V Field-programmable gate array (FPGA) device. The register-transfer level (RTL) structure of the implementation consumed fewer resources, with just 23 D flip-flops, without floating-point operations or multipliers.

Pharmacological rescue of developmental and synaptic phenotypes in human SHANK3 deficient stem cell-derived neuronal models

Pharmacological rescue of developmental and synaptic phenotypes in human SHANK3 deficient stem cell-derived neuronal models

Urine-derived cells from the aged donor for the 2D/3D modeling of neural cells via iPSCs

Human neural cell models derived from induced pluripotent stem cells (iPSCs) have been widely accepted to model various neurodegenerative diseases such as Alzheimer’s disease (AD) in vitro. Although the most common sources of iPSCs are fibroblasts and peripheral blood mononuclear cells, the collection of these cells is invasive. To reduce the donor’s burden, we propose the use of urine-derived cells (UDCs), which can be obtained non-invasively from a urine sample. However, the collection of UDCs from elderly donors suffering from age-related diseases such as AD has not been reported, and it is unknown whether these UDCs from the donor aged over 80 years old can be converted into iPSCs and differentiated into neural cells. In this study, we reported a case of using the UDCs from the urine sample of an 89-year-old AD patient, and the UDCs were successfully reprogrammed into iPSCs and differentiated into neural cells in four different ways: (i) the dual SMAD inhibition with small-molecules via the neural progenitor precursor stage, (ii) the rapid induction method using transient expression of Ngn2 and microRNAs without going through the neural progenitor stage, (iii) the cortical brain organoids for 3D culture, and (iv) the human astrocytes. The accumulation of phosphorylated Tau proteins, which is a pathological hallmark of AD, was examined in the neuronal models generated from the UDCs of the aged donor. The application of this cell source will broaden the target population for disease modeling using iPS technology.

Human LUHMES and NES cells as models for studying primary cilia in neurons.

Primary cilia are antenna-like organelles emanating from the cell surface. They are involved in cell-to-cell communication and bidirectional signal transduction to/from the extracellular environment. During brain formation, cilia critically aid in neurogenesis and maturation of neuronal structures such as axons, dendrites and synapses. Aberrations in cilia function can induce neuron differentiation defects and pathological consequences of varying severity, resulting in ciliopathies and likely a number of neurodevelopmental disorders. Despite the documented relevance of cilia for proper brain development, human neuronal models to recognize and study cilia biology are still scarce. We have established two types of cell models, Lund Human Mesencephalic (LUHMES) cells and neuroepithelial stem (NES) cells derived from induced pluripotent stem cells (iPSC), to investigate cilia biology in both proliferating neuronal progenitors/precursors and during the entire neuron differentiation and maturation process. We employ improved immunocytochemistry assays able to specifically detect cilia by confocal and super-resolution microscopy. We provide straightforward and robust methods to easily maintain cells in culture, for immunostaining and characterization of cilia orientation, anatomy and shape in human neurons across all stages of differentiation.