Comparison between single signed integral pulse frequency and sine wave crossing modulation techniques

The single signed integral pulse frequency modulation (SS-IPFM) is used in modeling neural communication processes. The reference signal crossing and in particular sine wave crossings (SWC) are used to describe physiological processes like vision. Under some restrictions upon the input signal it is possible to define SS-IPFM and SWC systems with identical output for the same modulation input. These restrictions and the exact compositions of the encoders are examined by comparison of both SS-IPFM and SWC to general form of Pulse Position Modulation (PPM) technique.     

基于熵准则的鲁棒的RBF谷胱甘肽发酵建模

在谷胱甘肽的发酵过程建模中, 当试验数据含有噪音时, 往往会导致模型预测精度和泛化能力的下降。针对该问题, 提出了一种新的基于熵准则的RBF神经网络建模方法。与传统的基于MSE准则函数的建模方法相比, 新方法能从训练样本的整体分布结构来进行模型参数学习, 有效地避免了传统的基于MSE准则的RBF网络的过学习和泛化能力差的缺陷。将该模型应用到实际的谷胱甘肽发酵过程建模中, 实验结果表明: 该方法具有较高的预测精度、泛化能力和良好的鲁棒性, 从而对谷胱甘肽的发酵建模有潜在的应用价值。     

基于熵准则的鲁棒的RBF谷胱甘肽发酵建模

在谷胱甘肽的发酵过程建模中, 当试验数据含有噪音时, 往往会导致模型预测精度和泛化能力的下降。针对该问题, 提出了一种新的基于熵准则的RBF神经网络建模方法。与传统的基于MSE准则函数的建模方法相比, 新方法能从训练样本的整体分布结构来进行模型参数学习, 有效地避免了传统的基于MSE准则的RBF网络的过学习和泛化能力差的缺陷。将该模型应用到实际的谷胱甘肽发酵过程建模中, 实验结果表明: 该方法具有较高的预测精度、泛化能力和良好的鲁棒性, 从而对谷胱甘肽的发酵建模有潜在的应用价值。     

A Neural Infrastructure for Rhythmic Motor Patterns

It is possible to work out the neural circuity of many invertebrate central pattern generators (CPGs) thereby providing a basis for linking cellular processes to actual behaviors. This review summarizes the infrastructure of the two CPGs in the lobster stomatogastric ganglion in terms of circuitry, ionic conductances and chemical modulation by amines and peptides. Analysis of the circuit using modeling techniques including the use of electronic neurons closes the chapter.     

Attention modulates earliest responses in the primary auditory and visual cortices

A fundamental question about the neural correlates of attention concerns the earliest sensory processing stage that it can affect. We addressed this issue by recording magnetoencephalography (MEG) signals while subjects performed detection tasks, which required employment of spatial or nonspatial attention, in auditory or visual modality. Using distributed source analysis of MEG signals, we found that, contrary to previous studies that used equivalent current dipole (ECD) analysis, spatial attention enhanced the initial feedforward response in the primary visual cortex (V1) at 55-90 ms. We also found attentional modulation of the putative primary auditory cortex (A1) activity at 30-50 ms. Furthermore, we reproduced our findings using ECD modeling guided by the results of distributed source analysis and suggest a reason why earlier studies using ECD analysis failed to identify the modulation of earliest V1 activity.     

Modeling the Afferent Dynamics of the Baroreflex Control System

In this study we develop a modeling framework for predicting baroreceptor firing rate as a function of blood pressure. We test models within this framework both quantitatively and qualitatively using data from rats. The models describe three components: arterial wall deformation, stimulation of mechanoreceptors located in the BR nerve-endings, and modulation of the action potential frequency. The three sub-systems are modeled individually following well-established biological principles. The first submodel, predicting arterial wall deformation, uses blood pressure as an input and outputs circumferential strain. The mechanoreceptor stimulation model, uses circumferential strain as an input, predicting receptor deformation as an output. Finally, the neural model takes receptor deformation as an input predicting the BR firing rate as an output. Our results show that nonlinear dependence of firing rate on pressure can be accounted for by taking into account the nonlinear elastic properties of the artery wall. This was observed when testing the models using multiple experiments with a single set of parameters. We find that to model the response to a square pressure stimulus, giving rise to post-excitatory depression, it is necessary to include an integrate-and-fire model, which allows the firing rate to cease when the stimulus falls below a given threshold. We show that our modeling framework in combination with sensitivity analysis and parameter estimation can be used to test and compare models. Finally, we demonstrate that our preferred model can exhibit all known dynamics and that it is advantageous to combine qualitative and quantitative analysis methods.     

Deep template-based protein structure prediction

MotivationProtein structure prediction has been greatly improved by deep learning, but most efforts are devoted to template-free modeling. But very few deep learning methods are developed for TBM (template-based modeling), a popular technique for protein structure prediction. TBM has been studied extensively in the past, but its accuracy is not satisfactory when highly similar templates are not available.ResultsThis paper presents a new method NDThreader (New Deep-learning Threader) to address the challenges of TBM. NDThreader first employs DRNF (deep convolutional residual neural fields), which is an integration of deep ResNet (convolutional residue neural networks) and CRF (conditional random fields), to align a query protein to templates without using any distance information. Then NDThreader uses ADMM (alternating direction method of multipliers) and DRNF to further improve sequence-template alignments by making use of predicted distance potential. Finally, NDThreader builds 3D models from a sequence-template alignment by feeding it and sequence coevolution information into a deep ResNet to predict inter-atom distance distribution, which is then fed into PyRosetta for 3D model construction. Our experimental results show that NDThreader greatly outperforms existing methods such as CNFpred, HHpred, DeepThreader and CEthreader. NDThreader was blindly tested in CASP14 as a part of RaptorX server, which obtained the best average GDT score among all CASP14 servers on the 58 TBM targets.     

Studying modulation on simultaneously activated SSVEP neural networks by a cognitive task

Since the discovery of steady-state visually evoked potential (SSVEP), it has been used in many fields. Numerous studies suggest that there exist three SSVEP neural networks in different frequency bands. An obvious phenomenon has been observed, that the amplitude and phase of SSVEP can be modulated by a cognitive task. Previous works have studied this modulation on separately activated SSVEP neural networks by a cognitive task. If two or more SSVEP neural networks are activated simultaneously in the process of a cognitive task, is the modulation on different SSVEP neural networks the same? In this study, two different SSVEP neural networks were activated simultaneously by two different frequency flickers, with a working memory task irrelevant to the flickers being conducted at the same time. The modulated SSVEP waves were compared with each other and to those only under one flicker in previous studies. The comparison results show that the cognitive task can modulate different SSVEP neural networks with a similar style.     

Mechanism of enhancement of the responses of the frog glossopharyngeal nerve to electrolytes by enhancers

In frogs, the responses of the glossopharyngeal nerve (GL) to NaCl are enhanced after treatment of the tongue with 8-anilino-1-naphthalene-sulfonic acid (ANS), a hydrophobic probe for biological membranes. The enhancement by ANS treatment has been explained by removal of Ca2+ from the receptor membrane treated with ANS. To explore the mechanism of enhancement by ANS treatment, we recorded neural responses from the frog GL. After ANS treatment, treatment with 10 mM CaCl2 prior to stimulation of NaCl did not affect the enhanced responses to 100 mM NaCl. The response to a relatively high concentration of CaCl2 (50 mM) was enhanced after ANS treatment. It is difficult to interpret these neural events in terms of modulation of the responses by membrane-bound calcium. The presence of NiCl2 in stimulating solution is known as an enhancer. Neural events after ANS treatment were similar to those caused by NiCl2. Our previous studies have demonstrated that enhancement of the responses to electrolytes by NiCl2 is due to modulation of the responses of water fibers in the GL. Water fibers are characterized by sensitivity to water or CaCl2, and they also respond to relatively high concentrations of electrolytes such as NaCl and choline Cl. Using a suction electrode method, we recorded unitary impulses from single water fibers. The ANS treatment led greatly enhanced responses to NaCl or choline Cl in water fibers, suggesting that enhancement by the ANS treatment is due to modulation of the responses of water fibers as well as enhancement by NiCl2. It appears that distinct receptors for each separate cation responsible for the neural responses in water fibers interact with a membrane element that is affected by ANS or Ni2+.     

N-cadherin and Cx43alpha1 gap junctions modulates mouse neural crest cell motility via distinct pathways

Our previous studies showed an essential role for connexin 43 or alpha1 connexin (Cx43alpha1) gap junctions in the modulation of neural crest cell motility. Cx43alpha1 gap junctions and N-cadherin containing adherens junctions are expressed in migrating cardiac neural crest cells. Analysis of the N-cadherin knockout (KO) mouse model revealed that N-cadherin is essential for gap junction mediated dye coupling but not for expression of Cx43alpha1 gap junctions in neural crest cells. Time lapse videomicroscopy and motion analysis showed that the motility of N-cadherin KO neural crest cells were altered, but the motility changes differed compared to Cx43alpha1 KO neural crest cells. These observations suggest that the role of N-cadherin in cell motility is not simply mediated via the modulation of Cx43alpha1 mediated cell-cell communication. This was confirmed by a parallel analysis of wnt-1 deficient neural crest cells, which also showed a reduction in dye coupling, and yet no change in cell motility. Analysis of p120 catenin (p120ctn), an Amardillo family protein known to play a role in cell motility, showed that it is colocalized with N-cadherin and Cx43alpha1 in migrating neural crest cells. This subcellular distribution was altered in the N-cadherin and Cx43alpha1 KO neural crest cells. Given these results, we propose that N-cadherin and Cx43alpha1 may modulate neural crest cell motility by engaging in a dynamic cross-talk with the cell's locomotory apparatus through p120ctn signaling.     

Responsive neuromodulators based on artificial neural networks used to control seizure-like events in a computational model of epilepsy

Deep brain stimulation (DBS) has been noted for its potential to suppress epileptic seizures. To date, DBS has achieved mixed results as a therapeutic approach to seizure control. Using a computational model, we demonstrate that high-complexity, biologically-inspired responsive neuromodulation is superior to periodic forms of neuromodulation (responsive and non-responsive) such as those implemented in DBS, as well as neuromodulation using random and random repetitive-interval stimulation. We configured radial basis function (RBF) networks to generate outputs modeling interictal time series recorded from rodent hippocampal slices that were perfused with low Mg2?/high K? solution. We then compared the performance of RBF-based interictal modulation, periodic biphasic-pulse modulation, random modulation and random repetitive modulation on a cognitive rhythm generator (CRG) model of spontaneous seizure-like events (SLEs), testing efficacy of SLE control. A statistically significant improvement in SLE mitigation for the RBF interictal modulation case versus the periodic and random cases was observed, suggesting that the use of biologically-inspired neuromodulators may achieve better results for the purpose of electrical control of seizures in a clinical setting.     

EZ spheres: A stable and expandable culture system for the generation of pre-rosette multipotent stem cells from human ESCs and iPSCs

We have developed a simple method to generate and expand multipotent, self-renewing pre-rosette neural stem cells from both human embryonic stem cells (hESCs) and human induced pluripotent stem cells (iPSCs) without utilizing embryoid body formation, manual selection techniques, or complex combinations of small molecules. Human ESC and iPSC colonies were lifted and placed in a neural stem cell medium containing high concentrations of EGF and FGF-2. Cell aggregates (termed EZ spheres) could be expanded for long periods using a chopping method that maintained cell–cell contact. Early passage EZ spheres rapidly down-regulated OCT4 and up-regulated SOX2 and nestin expression. They retained the potential to form neural rosettes and consistently differentiated into a range of central and peripheral neural lineages. Thus, they represent a very early neural stem cell with greater differentiation flexibility than other previously described methods. As such, they will be useful for the rapidly expanding field of neurological development and disease modeling, high-content screening, and regenerative therapies based on pluripotent stem cell technology.     

Contributions of Subsurface Cortical Modulations to Discrimination of Executed and Imagined Grasp Forces through Stereoelectroencephalography

Stereoelectroencephalographic (SEEG) depth electrodes have the potential to record neural activity from deep brain structures not easily reached with other intracranial recording technologies. SEEG electrodes were placed through deep cortical structures including central sulcus and insular cortex. In order to observe changes in frequency band modulation, participants performed force matching trials at three distinct force levels using two different grasp configurations: a power grasp and a lateral pinch. Signals from these deeper structures were found to contain information useful for distinguishing force from rest trials as well as different force levels in some participants. High frequency components along with alpha and beta bands recorded from electrodes located near the primary motor cortex wall of central sulcus and electrodes passing through sensory cortex were found to be the most useful for classification of force versus rest although one participant did have significant modulation in the insular cortex. This study electrophysiologically corroborates with previous imaging studies that show force-related modulation occurs inside of central sulcus and insular cortex. The results of this work suggest that depth electrodes could be useful tools for investigating the functions of deeper brain structures as well as showing that central sulcus and insular cortex may contain neural signals that could be used for control of a grasp force BMI.     

A test of a dual central pattern generator hypothesis for subcortical control of locomotion.

This study was designed to examine the nature of neural circuits involved in subcortical inter-limb coordination and reflex modulation mechanisms of locomotion. These circuits, called central pattern generators (CPGs), are believed to receive tonic input and generate rhythmically alternating sets of commands. Although CPGs have been theorized to exist in humans, their potential dual role in inter-limb coordination and reflex modulation is unclear. In the present study, nine participants walked on a treadmill, timing their heel-strikes to a metronome which varied the phase lag from 0.5 to 1.0 pi radians (0.1 pi intervals). A stimulus was delivered to the sural nerve and reflexes were measured in the ipsilateral and contralateral lower extremities through electromyography. The similarity between phase lag conditions for both temporal coordination (i.e., relative timing aspects between muscles and/or limbs) and reflex intensities suggested that they may be controlled by the same subcortical circuitry. Two plausible explanations exist: (1) a single CPG coordinates muscular contractions and phasically alters proprioceptive reflex modulation, as well as cutaneous input, using feed-forward control; (2) two separate circuits are strongly entrained, producing synchronous outputs for inter-limb coordination and reflex modulation. The out-of-phase task used in this study was limited in discerning such a difference, if it exists.     

N-Cadherin and Cx43α1 Gap Junctions Modulates Mouse Neural Crest Cell Motility via Distinct Pathways

Our previous studies showed an essential role for connexin 43 or α₁ connexin (Cx43α1) gap junctions in the modulation of neural crest cell motility. Cx43α1 gap junctions and N-cadherin containing adherens junctions are expressed in migrating cardiac neural crest cells. Analysis of the N-cadherin knockout (KO) mouse model revealed that N-cadherin is essential for gap junction mediated dye coupling but not for expression of Cx43α1 gap junctions in neural crest cells. Time lapse videomicroscopy and motion analysis showed that the motility of N-cadherin KO neural crest cells were altered, but the motility changes differed compared to Cx43α1 KO neural crest cells. These observations suggest that the role of N-cadherin in cell motility is not simply mediated via the modulation of Cx43α1 mediated cell-cell communication. This was confirmed by a parallel analysis of wnt-1 deficient neural crest cells, which also showed a reduction in dye coupling, and yet no change in cell motility. Analysis of p 120 catenin (p 120ctn), an Amardillo family protein known to play a role in cell motility, showed that it is colocalized with N-cadherin and Cx43α1 in migrating neural crest cells. This subcellular distribution was altered in the N-cadherin and Cx43α1 KO neural crest cells. Given these results, we propose that N-cadherin and Cx43α1 may modulate neural crest cell motility by engaging in a dynamic cross-talk with the cell's locomotory apparatus through p120ctn signaling.     

Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons

The modulation of the sensitivity, or gain, of neural responses to input is an important component of neural computation. It has been shown that divisive gain modulation of neural responses can result from a stochastic shunting from balanced (mixed excitation and inhibition) background activity. This gain control scheme was developed and explored with static inputs, where the membrane and spike train statistics were stationary in time. However, input statistics, such as the firing rates of pre-synaptic neurons, are often dynamic, varying on timescales comparable to typical membrane time constants. Using a population density approach for integrate-and-fire neurons with dynamic and temporally rich inputs, we find that the same fluctuation-induced divisive gain modulation is operative for dynamic inputs driving nonequilibrium responses. Moreover, the degree of divisive scaling of the dynamic response is quantitatively the same as the steady-state responses—thus, gain modulation via balanced conductance fluctuations generalizes in a straight-forward way to a dynamic setting.     

Modeling neurodevelopment in a dish with pluripotent stem cells

Pluripotent stem cells (PSCs) can differentiate into all cell types in the body, and their differentiation procedures recapitulate the developmental processes of embryogenesis. Focusing on neurodevelopment, we describe here the application of knowledge gained from embryology to the neural induction of PSCs. Furthermore, PSC‐based neural modeling provides novel insights into neurodevelopmental processes. In particular, human PSC cultures are a powerful tool for the study of human‐specific neurodevelopmental processes and could even enable the elucidation of the mechanisms of human brain evolution. We also discuss challenges and potential future directions in further improving PSC‐based neural modeling.