scholarly journals COALIA: a computational model of human EEG for consciousness research

2019 ◽  
Author(s):  
Siouar Bensaid ◽  
Julien Modolo ◽  
Isabelle Merlet ◽  
Fabrice Wendling ◽  
Pascal Benquet
Keyword(s):  
Computational Model ◽  
Long Range ◽  
Information Integration ◽  
Computational Models ◽  
Pyramidal Neurons ◽  
Clinical Results ◽  
Neuronal Dynamics ◽  
Human Cortex ◽  
Physiological Processes ◽  
States Of Consciousness

AbstractUnderstanding the origin of the main physiological processes involved in consciousness is a major challenge of contemporary neuroscience, with crucial implications for the study of Disorders of Consciousness (DOC). The difficulties in achieving this task include the considerable quantity of experimental data in this field, along with the non-intuitive, nonlinear nature of neuronal dynamics. One possibility of integrating the main results from the experimental literature into a cohesive framework, while accounting for nonlinear brain dynamics, is the use of physiologically-inspired computational models. In this study, we present a physiologically-grounded computational model, attempting to account for the main micro-circuits identified in the human cortex, while including the specificities of each neuronal type. More specifically, the model accounts for thalamo-cortical (vertical) regulation of cortico-cortical (horizontal) connectivity, which is a central mechanism for brain information integration and processing. The distinct neuronal assemblies communicate through feedforward and feedback excitatory and inhibitory synaptic connections implemented in a template brain accounting for long-range connectome. The EEG generated by this physiologically-based simulated brain is validated through comparison with brain rhythms recorded in humans in two states of consciousness (wakefulness, sleep). Using the model, it is possible to reproduce the local disynaptic disinhibition of basket cells (fast GABAergic inhibition) and glutamatergic pyramidal neurons through long-range activation of VIP interneurons that induced inhibition of SST interneurons. The model (COALIA) predicts that the strength and dynamics of the thalamic output on the cortex control the local and long-range cortical processing of information. Furthermore, the model reproduces and explains clinical results regarding the complexity of transcranial magnetic stimulation TMS-evoked EEG responses in DOC patients and healthy volunteers, through a modulation of thalamo-cortical connectivity that governs the level of cortico-cortical communication. This new model provides a quantitative framework to accelerate the study of the physiological mechanisms involved in the emergence, maintenance and disruption (sleep, anesthesia, DOC) of consciousness.

CSBPI_Site：Multi-Information Sources of Features to RNA Binding Sites Prediction

2021 ◽  
Vol 15 ◽  
Author(s):  
Lichao Zhang ◽  
Zihong Huang ◽  
Liang Kong
Keyword(s):  
Computational Model ◽  
Binding Sites ◽  
Noncoding Rna ◽  
Computational Models ◽  
Information Sources ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Gradient Boosting ◽  
Position Information ◽  
Rna Binding Sites

Background: RNA-binding proteins establish posttranscriptional gene regulation by coordinating the maturation, editing, transport, stability, and translation of cellular RNAs. The immunoprecipitation experiments could identify interaction between RNA and proteins, but they are limited due to the experimental environment and material. Therefore, it is essential to construct computational models to identify the function sites. Objective: Although some computational methods have been proposed to predict RNA binding sites, the accuracy could be further improved. Moreover, it is necessary to construct a dataset with more samples to design a reliable model. Here we present a computational model based on multi-information sources to identify RNA binding sites. Method: We construct an accurate computational model named CSBPI_Site, based on xtreme gradient boosting. The specifically designed 15-dimensional feature vector captures four types of information (chemical shift, chemical bond, chemical properties and position information). Results: The satisfied accuracy of 0.86 and AUC of 0.89 were obtained by leave-one-out cross validation. Meanwhile, the accuracies were slightly different (range from 0.83 to 0.85) among three classifiers algorithm, which showed the novel features are stable and fit to multiple classifiers. These results showed that the proposed method is effective and robust for noncoding RNA binding sites identification. Conclusion: Our method based on multi-information sources is effective to represent the binding sites information among ncRNAs. The satisfied prediction results of Diels-Alder riboz-yme based on CSBPI_Site indicates that our model is valuable to identify the function site.

scholarly journals Understanding sex differences in long-term blood pressure regulation: insights from experimental studies and computational modeling

2019 ◽  
Vol 316 (5) ◽  
pp. H1113-H1123 ◽  
Author(s):  
Sameed Ahmed ◽  
Rui Hu ◽  
Jessica Leete ◽  
Anita T. Layton
Keyword(s):  
Blood Pressure ◽  
Sex Differences ◽  
Computational Models ◽  
Experimental Studies ◽  
Pressure Control ◽  
Blood Pressure Regulation ◽  
Pressure Regulation ◽  
Physiological Processes ◽  
Key Players

Sex differences in blood pressure and the prevalence of hypertension are found in humans and animal models. Moreover, there has been a recent explosion of data concerning sex differences in nitric oxide, the renin-angiotensin-aldosterone system, inflammation, and kidney function. These data have the potential to reveal the mechanisms underlying male-female differences in blood pressure control. To elucidate the interactions among the multitude of physiological processes involved, one may apply computational models. In this review, we describe published computational models that represent key players in blood pressure regulation, and highlight sex-specific models and their findings.

scholarly journals Numerical and Experimental Investigations on Vocal Fold Approximation in Healthy and Simulated Unilateral Vocal Fold Paralysis

2021 ◽  
Vol 11 (4) ◽  
pp. 1817
Author(s):  
Zheng Li ◽  
Azure Wilson ◽  
Lea Sayce ◽  
Amit Avhad ◽  
Bernard Rousseau ◽  
...  
Keyword(s):  
Computational Model ◽  
Vocal Fold ◽  
High Speed ◽  
Computational Models ◽  
Ex Vivo ◽  
Vocal Fold Paralysis ◽  
Future Application ◽  
Experimental Investigations ◽  
Type I ◽  
Mri Scans

We have developed a novel surgical/computational model for the investigation of unilat-eral vocal fold paralysis (UVFP) which will be used to inform future in silico approaches to improve surgical outcomes in type I thyroplasty. Healthy phonation (HP) was achieved using cricothyroid suture approximation on both sides of the larynx to generate symmetrical vocal fold closure. Following high-speed videoendoscopy (HSV) capture, sutures on the right side of the larynx were removed, partially releasing tension unilaterally and generating asymmetric vocal fold closure characteristic of UVFP (sUVFP condition). HSV revealed symmetric vibration in HP, while in sUVFP the sutured side demonstrated a higher frequency (10–11%). For the computational model, ex vivo magnetic resonance imaging (MRI) scans were captured at three configurations: non-approximated (NA), HP, and sUVFP. A finite-element method (FEM) model was built, in which cartilage displacements from the MRI images were used to prescribe the adduction, and the vocal fold deformation was simulated before the eigenmode calculation. The results showed that the frequency comparison between the two sides was consistent with observations from HSV. This alignment between the surgical and computational models supports the future application of these methods for the investigation of treatment for UVFP.

scholarly journals Loss of Calretinin in L5a impairs the formation of the barrel cortex leading to abnormal whisker-mediated behaviors

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Mingzhao Su ◽  
Junhua Liu ◽  
Baocong Yu ◽  
Kaixing Zhou ◽  
Congli Sun ◽  
...  
Keyword(s):  
Information Integration ◽  
Pyramidal Neurons ◽  
Barrel Cortex ◽  
Sensory Information ◽  
Membrane Excitability ◽  
Novelty Preference ◽  
Layer 4 ◽  
Dendritic Complexity ◽  
Cortex System

AbstractThe rodent whisker-barrel cortex system has been established as an ideal model for studying sensory information integration. The barrel cortex consists of barrel and septa columns that receive information input from the lemniscal and paralemniscal pathways, respectively. Layer 5a is involved in both barrel and septa circuits and play a key role in information integration. However, the role of layer 5a in the development of the barrel cortex remains unclear. Previously, we found that calretinin is dynamically expressed in layer 5a. In this study, we analyzed calretinin KO mice and found that the dendritic complexity and length of layer 5a pyramidal neurons were significantly decreased after calretinin ablation. The membrane excitability and excitatory synaptic transmission of layer 5a neurons were increased. Consequently, the organization of the barrels was impaired. Moreover, layer 4 spiny stellate cells were not able to properly gather, leading to abnormal formation of barrel walls as the ratio of barrel/septum size obviously decreased. Calretinin KO mice exhibited deficits in exploratory and whisker-associated tactile behaviors as well as social novelty preference. Our study expands our knowledge of layer 5a pyramidal neurons in the formation of barrel walls and deepens the understanding of the development of the whisker-barrel cortex system.

scholarly journals Loss of Calretinin in L5a Impairs the Formation of the Barrel Cortex Leading to Abnormal Behaviors

2021 ◽  
Author(s):  
Mingzhao Su ◽  
Junhua Liu ◽  
Baocong Yu ◽  
Kaixing Zhou ◽  
Congli Sun ◽  
...  
Keyword(s):  
Information Integration ◽  
Pyramidal Neurons ◽  
Barrel Cortex ◽  
Sensory Information ◽  
Membrane Excitability ◽  
Novelty Preference ◽  
Abnormal Behaviors ◽  
Dendritic Complexity ◽  
Cortex System

Abstract The rodent whisker-barrel cortex system has been established as an ideal model for studying sensory information integration. The barrel cortex consists of barrel and septa columns that receive information input from the lemniscal and paralemniscal pathways, respectively. L5a is involved in both barrel and septa circuits and play a key role in information integration. However, the role of L5a in the development of the barrel cortex remains unclear. Previously, we found that Calretinin is dynamically expressed in L5a. In this study, we analyzed Cr KO mice and found that the dendritic complexity and length of L5a pyramidal neurons were significantly decreased after Cr ablation. The membrane excitability and excitatory synaptic transmission of L5a neurons were increased. Consequently, the organization of the barrels was impaired. Moreover, L4 spiny stellate cells were not able to properly gather, leading to abnormal formation of barrel walls as the ratio of barrel/septum size obviously decreased. Cr KO mice exhibited deficits in exploratory and whisker-associated tactile behaviors as well as social novelty preference. Our study expands our knowledge of L5a pyramidal neurons in the formation of barrel walls and deepens the understanding of the development of the whisker-barrel cortex system.

scholarly journals The Exponential-Weight Mean-Variance Model: A novel computational model for the Balloon Analogue Risk Task

2019 ◽  
Author(s):  
Harhim Park ◽  
Jaeyeong Yang ◽  
Jasmin Vassileva ◽  
Woo-Young Ahn
Keyword(s):  
Computational Model ◽  
Computational Models ◽  
Model Comparison ◽  
Exponential Weight ◽  
Multiple Model ◽  
Variance Model ◽  
Balloon Analogue Risk Task ◽  
Parameter Recovery ◽  
Post Hoc ◽  
Mean Variance

The Balloon Analogue Risk Task (BART) is a popular task used to measure risk-taking behavior. To identify cognitive processes associated with choice behavior on the BART, a few computational models have been proposed. However, the extant models are either too simplistic or fail to show good parameter recovery performance. Here, we propose a novel computational model, the exponential-weight mean-variance (EWMV) model, which addresses the limitations of existing models. By using multiple model comparison methods, including post hoc model fits criterion and parameter recovery, we showed that the EWMV model outperforms the existing models. In addition, we applied the EWMV model to BART data from healthy controls and substance-using populations (patients with past opiate and stimulant dependence). The results suggest that (1) the EWMV model addresses the limitations of existing models and (2) heroin-dependent individuals show reduced risk preference than other groups in the BART.

scholarly journals Representational ‘touch’ and modulatory ‘retouch’—two necessary neurobiological processes in thalamocortical interaction for conscious experience

2021 ◽  
Vol 2021 (2) ◽  
Author(s):  
Talis Bachmann
Keyword(s):  
Pyramidal Neurons ◽  
Conscious Experience ◽  
General Purpose ◽  
Cortical Layer ◽  
Integration Theory ◽  
Conscious Perception ◽  
Dendritic Integration ◽  
States Of Consciousness ◽  
Historical Origins

Abstract Theories of consciousness using neurobiological data or being influenced by these data have been focused either on states of consciousness or contents of consciousness. These theories have occasionally used evidence from psychophysical phenomena where conscious experience is a dependent experimental variable. However, systematic catalog of many such relevant phenomena has not been offered in terms of these theories. In the perceptual retouch theory of thalamocortical interaction, recently developed to become a blend with the dendritic integration theory, consciousness states and contents of consciousness are explained by the same mechanism. This general-purpose mechanism has modulation of the cortical layer-5 pyramidal neurons that represent contents of consciousness as its core. As a surplus, many experimental psychophysical phenomena of conscious perception can be explained by the workings of this mechanism. Historical origins and current views inherent in this theory are presented and reviewed.

A Mechanistic Motor-Clutch Model That Explains Cell Shape Dynamics to Cyclic Stretch

2022 ◽  
Author(s):  
Benjamin W. Scandling ◽  
Jia Gou ◽  
Jessica Thomas ◽  
Jacqueline Xuan ◽  
Chuan Xue ◽  
...  
Keyword(s):  
Computational Model ◽  
Computational Models ◽  
The Body ◽  
Cyclic Stretch ◽  
Substrate Stiffness ◽  
Cell Alignment ◽  
Cellular Mechanisms ◽  
Actin Bundles ◽  
The Impact

Many cells in the body experience cyclic mechanical loading, which can impact cellular processes and morphology. In vitro studies often report that cells reorient in response to cyclic stretch of their substrate. To explore cellular mechanisms involved in this reorientation, a computational model was developed by utilizing the previous computational models of the actin-myosin-integrin motor-clutch system developed by others. The computational model predicts that under most conditions, actin bundles align perpendicular to the direction of applied cyclic stretch, but under specific conditions, such as low substrate stiffness, actin bundles align parallel to the direction of stretch. The model also predicts that stretch frequency impacts the rate of reorientation, and that proper myosin function is critical in the reorientation response. These computational predictions are consistent with reports from the literature and new experimental results presented here. The model suggests that the impact of different stretching conditions (stretch type, amplitude, frequency, substrate stiffness, etc.) on the direction of cell alignment can largely be understood by considering their impact on cell-substrate detachment events, specifically whether detachment occurs during stretching or relaxing of the substrate.

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