Computing the Optimally Fitted Spike Train for a Synapse

2001 ◽  
Vol 13 (11) ◽  
pp. 2477-2494 ◽  
Author(s):  
Thomas Natschläger ◽  
Wolfgang Maass
Keyword(s):  
Experimental Data ◽  
Spike Train ◽  
Computational Methods ◽  
Temporal Pattern ◽  
Neural Circuits ◽  
Spike Trains ◽  
Functional Explanation ◽  
Synaptic Dynamics ◽  
Synaptic Parameters

Experimental data have shown that synapses are heterogeneous: different synapses respond with different sequences of amplitudes of postsynaptic responses to the same spike train. Neither the role of synaptic dynamics itself nor the role of the heterogeneity of synaptic dynamics for computations in neural circuits is well understood. We present in this article two computational methods that make it feasible to compute for a given synapse with known synaptic parameters the spike train that is optimally fitted to the synapse in a certain sense. With the help of these methods, one can compute, for example, the temporal pattern of a spike train (with a given number of spikes) that produces the largest sum of postsynaptic responses for a specific synapse. Several other applications are also discussed. To our surprise, we find that most of these optimally fitted spike trains match common firing patterns of specific types of neurons that are discussed in the literature. Hence, our analysis provides a possible functional explanation for the experimentally observed regularity in the combination of specific types of synapses with specific types of neurons in neural circuits.

What Determines the Frequency of Fast Network Oscillations With Irregular Neural Discharges? I. Synaptic Dynamics and Excitation-Inhibition Balance

2003 ◽  
Vol 90 (1) ◽  
pp. 415-430 ◽  
Author(s):  
Nicolas Brunel ◽  
Xiao-Jing Wang
Keyword(s):  
Local Field ◽  
Oscillation Frequency ◽  
Field Potential ◽  
Spike Trains ◽  
Feedback Mechanism ◽  
Time Constants ◽  
Gamma Range ◽  
Fast Network ◽  
Synaptic Dynamics ◽  
Synaptic Parameters

When the local field potential of a cortical network displays coherent fast oscillations (∼40-Hz gamma or ∼200-Hz sharp-wave ripples), the spike trains of constituent neurons are typically irregular and sparse. The dichotomy between rhythmic local field and stochastic spike trains presents a challenge to the theory of brain rhythms in the framework of coupled oscillators. Previous studies have shown that when noise is large and recurrent inhibition is strong, a coherent network rhythm can be generated while single neurons fire intermittently at low rates compared to the frequency of the oscillation. However, these studies used too simplified synaptic kinetics to allow quantitative predictions of the population rhythmic frequency. Here we show how to derive quantitatively the coherent oscillation frequency for a randomly connected network of leaky integrate-and-fire neurons with realistic synaptic parameters. In a noise-dominated interneuronal network, the oscillation frequency depends much more on the shortest synaptic time constants (delay and rise time) than on the longer synaptic decay time, and ∼200-Hz frequency can be realized with synaptic time constants taken from slice data. In a network composed of both interneurons and excitatory cells, the rhythmogenesis is a compromise between two scenarios: the fast purely interneuronal mechanism, and the slower feedback mechanism (relying on the excitatory-inhibitory loop). The properties of the rhythm are determined essentially by the ratio of time scales of excitatory and inhibitory currents and by the balance between the mean recurrent excitation and inhibition. Faster excitation than inhibition, or a higher excitation/inhibition ratio, favors the feedback loop and a much slower oscillation (typically in the gamma range).

scholarly journals Comparison of Different Spike Train Synchrony Measures Regarding Their Robustness to Erroneous Data From Bicuculline-Induced Epileptiform Activity

2020 ◽  
Vol 32 (5) ◽  
pp. 887-911
Author(s):  
Manuel Ciba ◽  
Robert Bestel ◽  
Christoph Nick ◽  
Guilherme Ferraz de Arruda ◽  
Thomas Peron ◽  
...  
Keyword(s):  
Experimental Data ◽  
Spike Train ◽  
False Positive ◽  
In Silico ◽  
Epileptiform Activity ◽  
False Negative ◽  
Spike Trains ◽  
Spike Detection ◽  
Brain Functions ◽  
Spike Train Data

As synchronized activity is associated with basic brain functions and pathological states, spike train synchrony has become an important measure to analyze experimental neuronal data. Many measures of spike train synchrony have been proposed, but there is no gold standard allowing for comparison of results from different experiments. This work aims to provide guidance on which synchrony measure is best suited to quantify the effect of epileptiform-inducing substances (e.g., bicuculline, BIC) in in vitro neuronal spike train data. Spike train data from recordings are likely to suffer from erroneous spike detection, such as missed spikes (false negative) or noise (false positive). Therefore, different timescale-dependent (cross-correlation, mutual information, spike time tiling coefficient) and timescale-independent (Spike-contrast, phase synchronization (PS), A-SPIKE-synchronization, A-ISI-distance, ARI-SPIKE-distance) synchrony measures were compared in terms of their robustness to erroneous spike trains. For this purpose, erroneous spike trains were generated by randomly adding (false positive) or deleting (false negative) spikes (in silico manipulated data) from experimental data. In addition, experimental data were analyzed using different spike detection threshold factors in order to confirm the robustness of the synchrony measures. All experimental data were recorded from cortical neuronal networks on microelectrode array chips, which show epileptiform activity induced by the substance BIC. As a result of the in silico manipulated data, Spike-contrast was the only measure that was robust to false-negative as well as false-positive spikes. Analyzing the experimental data set revealed that all measures were able to capture the effect of BIC in a statistically significant way, with Spike-contrast showing the highest statistical significance even at low spike detection thresholds. In summary, we suggest using Spike-contrast to complement established synchrony measures because it is timescale independent and robust to erroneous spike trains.

scholarly journals Fano Factor: A Potentially Useful Information

2020 ◽  
Vol 14 ◽  
Author(s):  
Kamil Rajdl ◽  
Petr Lansky ◽  
Lubomir Kostal
Keyword(s):  
Experimental Data ◽  
Spike Train ◽  
Time Window ◽  
Fano Factor ◽  
Spike Trains ◽  
Renewal Processes ◽  
Neuronal Spike ◽  
Markov Renewal Processes ◽  
Neuronal Spike Trains ◽  
Operational Time

The Fano factor, defined as the variance-to-mean ratio of spike counts in a time window, is often used to measure the variability of neuronal spike trains. However, despite its transparent definition, careless use of the Fano factor can easily lead to distorted or even wrong results. One of the problems is the unclear dependence of the Fano factor on the spiking rate, which is often neglected or handled insufficiently. In this paper we aim to explore this problem in more detail and to study the possible solution, which is to evaluate the Fano factor in the operational time. We use equilibrium renewal and Markov renewal processes as spike train models to describe the method in detail, and we provide an illustration on experimental data.

РОЛЬ ФИЗИЧЕСКОЙ РАЗМИНКИ В ПОДГОТОВКЕ К ТРЕНИРОВОЧНЫМ ЗАНЯТИЯМ И СОРЕВНОВАНИЯМ ШАХМАТИСТОВ БГУ

2019 ◽  
pp. 63-65
Author(s):  
Судоргин Е.П. ◽  
Карсакова И.Н.
Keyword(s):  
Experimental Data ◽  
Sport Performance ◽  
Warm Up ◽  
Physical Exercises ◽  
Methods Of Evaluation ◽  
Mental Fitness ◽  
Physical Preparation ◽  
Tools And Methods

Аннотация: О роли разминки перед тренировкой и соревнованиями написано много научных статьей и диссертаций. Ещё больше о значимости физической подготовки спортсменов, в том числе и шахматистов. В то же время авторы считают, что вопросу физической подготовки шахматистов и в частности разминке в научной и научно-методической литературе уделяется недостаточно внимания. В своей статье авторы приводят собственные экспериментальные данные о влиянии физических упражнений (разминки) на умственную работоспособность студентов-шахматистов БГУ и как следствие на спортивные результаты команды. Ключевые слова: Шахматы, разминка, умственная работоспособность, средства и методы разминки, методы оценки результатов. Аннотация: Машыгуунун жана мелдештердин алдында даярдоонун ролу жөнүндө көптөгөн илимий макала жана диссертация жазылган. Ошондой эле илимий жана илимий-методикалык адабияттарда шахматка даярдоого көп көңүл бурулбай жатат. Макаланын авторлору шахмат ойногон студенттерге физикалык көнүгүүлөрдүн тийгизген таасири жөнүндө өздөрүнүн эксперименталдык маалыматтарын көргөзүштү. Түйүндүү сөздөр: Шахмат, акыл-дарамет, курулуштар жана ыкмалар, баа берүү жыйынтыгы боюнча кабыл алынат. Abstract: on the role of warm-up before training and competitions written many scientific articles and theses. More about the significance of the physical preparation of athletes, including players. At the same time, the authors believe that the issue of fit- ness players and in particular workout in scientific and scientific-methodical literature neglected. In his article the authors cite their own experimental data on the influence of physical exercises (warm-up) on the mental fitness of students-BSU players and as a result the sport performance team. Keywords: chess, warm-up, mental fitness, workout tools and methods, methods of evaluation results.

scholarly journals Corticostriatal control of defense behavior in mice induced by auditory looming cues

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhong Li ◽  
Jin-Xing Wei ◽  
Guang-Wei Zhang ◽  
Junxiang J. Huang ◽  
Brian Zingg ◽  
...  
Keyword(s):  
Essential Role ◽  
Neural Circuits ◽  
Temporal Dynamics ◽  
Defense Behavior ◽  
Innate Defense ◽  
Sensory Inputs ◽  
Corticostriatal Projections ◽  
Behavioral Transition ◽  
Auditory Looming

AbstractAnimals exhibit innate defense behaviors in response to approaching threats cued by the dynamics of sensory inputs of various modalities. The underlying neural circuits have been mostly studied in the visual system, but remain unclear for other modalities. Here, by utilizing sounds with increasing (vs. decreasing) loudness to mimic looming (vs. receding) objects, we find that looming sounds elicit stereotypical sequential defensive reactions: freezing followed by flight. Both behaviors require the activity of auditory cortex, in particular the sustained type of responses, but are differentially mediated by corticostriatal projections primarily innervating D2 neurons in the tail of the striatum and corticocollicular projections to the superior colliculus, respectively. The behavioral transition from freezing to flight can be attributed to the differential temporal dynamics of the striatal and collicular neurons in their responses to looming sound stimuli. Our results reveal an essential role of the striatum in the innate defense control.

scholarly journals Oxidation of Terpenoids to Achieve High-Value Flavor and Fragrances—Questioning Microalgae Oxidative Capabilities in the Biotransformation of the Sesquiterpene Valencene and of Selected Natural Apocarotenoids

Chemistry ◽  
2021 ◽  
Vol 3 (3) ◽  
pp. 821-830
Author(s):  
Davide De Simeis ◽  
Stefano Serra ◽  
Alessandro Di Fonzo ◽  
Francesco Secundo
Keyword(s):  
Experimental Data ◽  
Natural Products ◽  
Aqueous Medium ◽  
Photochemical Reaction ◽  
Substrate Oxidation ◽  
Market Size ◽  
Chlorella Sp ◽  
General Opinion ◽  
Natural Way

Natural flavor and fragrance market size is expected to grow steadily due to the rising consumer demand of natural ingredients. This market request is guided by the general opinion that the production of natural compounds leads to a reduction of pollution, with inherent advantages for the environment and people’s health. The biotransformation reactions have gained high relevance in the production of natural products. In this context, few pieces of research have described the role of microalgae in the oxidation of terpenoids. In this present study, we questioned the role of microalgal based oxidation in the synthesis of high-value flavors and fragrances. This study investigated the role of three different microalgae strains, Chlorella sp. (211.8b and 211.8p) and Chlorococcum sp. (JB3), in the oxidation of different terpenoid substrates: α-ionone, β-ionone, theaspirane and valencene. Unfortunately, the experimental data showed that the microalgal strains used are not responsible for the substrate oxidation. In fact, our experiments demonstrate that the transformation of the four starting compounds is a photochemical reaction that involves the oxygen as oxidant. Even though these findings cast a shadow on the use of these microorganisms for an industrial purpose, they open a new possible strategy to easily obtain nootkatone in a natural way by just using an aqueous medium, oxygen and light.

scholarly journals Three-Dimensional Structures of Carbohydrates and Where to Find Them

2020 ◽  
Vol 21 (20) ◽  
pp. 7702 ◽  
Author(s):  
Sofya I. Scherbinina ◽  
Philip V. Toukach
Keyword(s):  
Experimental Data ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Structural Features ◽  
Data Validation ◽  
Data Generation ◽  
Efficient Treatment

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

scholarly journals Development of a rabies virus-based retrograde tracer with high trans-monosynaptic efficiency by reshuffling glycoprotein

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Fan Jia ◽  
Li Li ◽  
Haizhou Liu ◽  
Pei Lv ◽  
Xiangwei Shi ◽  
...  
Keyword(s):  
Experimental Data ◽  
Rabies Virus ◽  
Oncolytic Virus ◽  
Neural Circuits ◽  
Bioinformatic Analysis ◽  
Cell Engineering ◽  
Bias Score ◽  
Codon Pair Bias ◽  
Codon Pair

AbstractRabies virus (RV) is the most widely used vector for mapping neural circuits. Previous studies have shown that the RV glycoprotein can be a target to improve the retrograde transsynaptic tracing efficiency. However, the current versions still label only a small portion of all presynaptic neurons. Here, we reshuffled the oG sequence, a chimeric glycoprotein, with positive codon pair bias score (CPBS) based on bioinformatic analysis of mouse codon pair bias, generating ooG, a further optimized glycoprotein. Our experimental data reveal that the ooG has a higher expression level than the oG in vivo, which significantly increases the tracing efficiency by up to 12.6 and 62.1-fold compared to oG and B19G, respectively. The new tool can be used for labeling neural circuits Therefore, the approach reported here provides a convenient, efficient and universal strategy to improve protein expression for various application scenarios such as trans-synaptic tracing efficiency, cell engineering, and vaccine and oncolytic virus designs.

scholarly journals Elucidating the Complex Interactions between Stress and Epileptogenic Pathways

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Aaron R. Friedman ◽  
Luisa P. Cacheaux ◽  
Sebastian Ivens ◽  
Daniela Kaufer
Keyword(s):  
Experimental Data ◽  
Blood Brain Barrier ◽  
Inflammatory Cytokine ◽  
Stress Hormones ◽  
Brain Barrier ◽  
Barrier Dysfunction ◽  
Complex Interactions ◽  
Narrow Focus ◽  
Analytical Tools

Clinical and experimental data suggest that stress contributes to the pathology of epilepsy. We review mechanisms by which stress, primarily via stress hormones, may exacerbate epilepsy, focusing on the intersection between stress-induced pathways and the progression of pathological events that occur before, during, and after the onset of epileptogenesis. In addition to this temporal nuance, we discuss other complexities in stress-epilepsy interactions, including the role of blood-brain barrier dysfunction, neuron-glia interactions, and inflammatory/cytokine pathways that may be protective or damaging depending on context. We advocate the use of global analytical tools, such as microarray, in support of a shift away from a narrow focus on seizures and towards profiling the complex, early process of epileptogenesis, in which multiple pathways may interact to dictate the ultimate onset of chronic, recurring seizures.

scholarly journals A study of computational methods for wake structure and base pressure prediction of a generic SUV model with fixed and rotating wheels

2017 ◽  
Vol 231 (9) ◽  
pp. 1222-1238 ◽  
Author(s):  
David Forbes ◽  
Gary Page ◽  
Martin Passmore ◽  
Adrian Gaylard
Keyword(s):  
Experimental Data ◽  
Computational Methods ◽  
Large Scale ◽  
Ground Plane ◽  
Computational Cost ◽  
Rear Wheel ◽  
Base Pressure ◽  
Detached Eddy Simulation ◽  
Wake Structure ◽  
Wake Interactions

This study is an evaluation of the computational methods in reproducing experimental data for a generic sports utility vehicle (SUV) geometry and an assessment on the influence of fixed and rotating wheels for this geometry. Initially, comparisons are made in the wake structure and base pressures between several CFD codes and experimental data. It was shown that steady-state RANS methods are unsuitable for this geometry due to a large scale unsteadiness in the wake caused by separation at the sharp trailing edge and rear wheel wake interactions. unsteady RANS (URANS) offered no improvements in wake prediction despite a significant increase in computational cost. The detached-eddy simulation (DES) and Lattice–Boltzmann methods showed the best agreement with the experimental results in both the wake structure and base pressure, with LBM running in approximately a fifth of the time for DES. The study then continues by analysing the influence of rotating wheels and a moving ground plane over a fixed wheel and ground plane arrangement. The introduction of wheel rotation and a moving ground was shown to increase the base pressure and reduce the drag acting on the vehicle when compared to the fixed case. However, when compared to the experimental standoff case, variations in drag and lift coefficients were minimal but misleading, as significant variations to the surface pressures were present.

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