摘要：
Iterative methods are used to simulate the in vitro feedforward neural networks in physiological experiments. Emissivity can be propagated to a minimum of ten groups. However, the discharge activity of each group will be more synchronized. The feedforward neural networks have a wide range of applications in machine learning, and the weight of synapses considerably influences the propagation of weak signals. Herein, we investigated the effect of Gaussian colored noise and electromagnetic radiation on the propagation of the subthreshold excitatory postsynaptic current signals in the input layer of the multilayer Izhikevich neural feedforward networks. In the absence of electromagnetic radiation, the excitatory postsynaptic current signal is stably propagated and amplified in multilayer feedforward neural networks under the optimal Gaussian colored noise strength or correlation time in the output layer of the network. Compared with the case in which there is no electromagnetic radiation, the presence of electromagnetic radiation slightly reduces the propagation of weak signals. Further, the time required to propagate the excitatory postsynaptic current signal to the output layer increases with the increasing feedback gain. The feedforward neural network considered in this study is a considerably simple model. More complex structures, such as backward connection and delayed feedback, can be observed in real biological systems. Hence, the next step will be to study more complex neural models with neuron models based on the physiological experimental data and compare them with real biological systems. Furthermore, the study of neural networks can be combined with an experimental study about the auditory nervous system of bats to understand the biological mechanism associated with the auditory system function of bats from two perspectives.
作者机构：
[Jia, Ya; Lu, Lulu; Ge, Mengyan; Wang, Guowei; Zhao, Yunjie] Cent China Normal Univ, Inst Biophys, Wuhan 430079, Peoples R China.;[Jia, Ya; Lu, Lulu; Ge, Mengyan; Wang, Guowei; Zhao, Yunjie] Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.
通讯机构：
[Zhao, Yunjie] C;Cent China Normal Univ, Inst Biophys, Wuhan 430079, Peoples R China.;Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.
关键词：
Signal propagation;Fidelity;Noise;Feed-forward hybrid neural network;Electromagnetic radiation
摘要：
The hybrid neural model provides a computationally effective and biophysics-based neuron behavior model, which maintains its simplicity by incorporating the dynamics characteristics of ion channels in two fast ion channels. In view of the issue of signal propagation in multilayer network composed of hybrid neurons is still unclear and the role of neural network is mainly used to generate biological consciousness and help creatures to think and act, it is necessary to explore neural network with more perfect function and better transmission efficiency. Considering a feed-forward neural network (FFN) which is composed of hybrid neurons in the presence of electromagnetic radiation, the effects of the Gaussian white noise, the strength of synaptic weight and inter-layer connection probability on subthreshold excitatory postsynaptic current (EPSC) propagation are investigated. In order to clarify the mechanism of signal transmission more clearly, the dot raster plot of spike and the corresponding post-spike time histogram of each layer are explored. Particularly, the propagation efficiency and fidelity of subthreshold EPSC signal in the FFN are investigated by calculating the power norm and the spike timing precision. Our results indicate that both the power norm and the spike timing precision fluctuate with the increase in the inter-layer connection probability, and the multi-periods bursting discharge mode can be detected in both the transmission layers and the output layer. Besides, there exists an optimal noise intensity to guarantee the best temporal coding and maximum transmission efficiency of subthreshold EPSC signal. Moreover, the optimal noise intensity makes the fidelity of the FFN the highest, which ensures that the weak signal and the excitation caused by noise can be distinguished. The conclusions obtained in this paper have potential value for discussing the encoding, decoding and propagation mechanism of information in real neural networks.
作者机构：
[Jia, Ya; Yang, Yumei; Xu, Ying] Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.;[Ma, Jun] Lanzhou Univ Technol, Dept Phys, Lanzhou 730050, Peoples R China.;[Ma, Jun] Chongqing Univ Posts & Telecommun, Sch Sci, Chongqing 430065, Peoples R China.
通讯机构：
[Jia, Ya] C;Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.
关键词：
Izhikevich neuronal model;Electromagnetic induction;Mixed mode;Hamiltonian energy
摘要：
Energy supply plays a key role in metabolism and signal transmission of biological individuals, neurons in a complex electromagnetic environment must be accompanied by the absorption and release of energy. In this paper, the discharge mode and the Hamiltonian energy are investigated within the Izhikevich neuronal model driven by external signals in the presence of electromagnetic induction. It is found that multiple electrical activity modes can be observed by changing external stimulus, and the Hamiltonian energy is more dependent on the discharge mode. In particular, there is a distinct shift and transition in the Hamiltonian energy when the discharge mode is switched quickly. Furthermore, the amplitude of periodic stimulus signal has a greater effect on the neuronal energy compared to the angular frequency, and the average Hamiltonian energy decreases when the discharge rhythm becomes higher. Based on the principle of energy minimization, the system should choose the minimum Hamiltonian energy when maintaining various trigger states to reduce the metabolic energy of signal processing in biological systems. Therefore, our results give the possible clues for predicting and selecting appropriate parameters, and help to understand the sudden and paroxysmal mechanisms of epilepsy symptoms.
作者机构：
[Jia, Ya; Lu, Lulu; Ge, Mengyan; Li, Anbang; Xu, Ying] Cent China Normal Univ, Inst Biophys, Wuhan 430079, Peoples R China.;[Jia, Ya; Lu, Lulu; Ge, Mengyan; Li, Anbang; Xu, Ying] Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.
通讯机构：
[Jia, Ya] C;Cent China Normal Univ, Inst Biophys, Wuhan 430079, Peoples R China.;Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.
作者机构：
[Jia, Ya; Lu, Lulu; Wang, Huiwen; Ge, Mengyan; Xu, Ying; Zhao, Yunjie] Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China.;[Jia, Ya; Lu, Lulu; Wang, Huiwen; Ge, Mengyan; Xu, Ying; Zhao, Yunjie] Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China.
通讯机构：
[Jia, Ya] C;Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China.;Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China.
关键词：
Izhikevich neural network;Excitatory postsynaptic current;Weak signal propagation
作者机构：
[Yang, Lijian] Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.;Cent China Normal Univ, Inst Biophys, Wuhan 430079, Peoples R China.
通讯机构：
[Jia, Ya] C;Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.
关键词：
Statistical and Nonlinear Physics
摘要：
Both time delay and coupling form are the most important factors in neural networks. The properties of firing rate oscillation and cluster synchronization induced by time delay are studied in random network of different coupling neurons. In previous work, the firing rate oscillation of cortical network was observed at the presence of three factors (time delay, weak sinusoidal signal, and noise). Here, we found that the firing rate oscillation can be induced only by the time delay, and the spike train can be propagated at a certain interval time, which is consistent with the value of delay time. Furthermore, the phenomenon of cluster synchronization occurs in random network, which may originates from network structure, and this connection between the neurons trigger spikes within a time-restricted window, resulting in cluster synchronization between corresponding neurons. These numerical results provide a potential theoretical basis for certain pathological brain rhythms associated with epileptic seizures.
作者机构：
[Jia, Ya; Guan, Zeyu; Wang, Huiwen; Zeng, Chen; Qiu, Jiadi; Zhao, Yunjie] Cent China Normal Univ, Inst Biophys, Dept Phys, Wuhan 430079, Peoples R China.;[Zeng, Chen] George Washington Univ, Dept Phys, Washington, DC 20052 USA.
通讯机构：
[Zhao, Yunjie] C;Cent China Normal Univ, Inst Biophys, Dept Phys, Wuhan 430079, Peoples R China.
摘要：
Kinase proteins have been intensively investigated as drug targets for decades because of their crucial involvement in many biological pathways. Most kinase drugs target the catalytic ATP pocket, which is highly conserved across the kinome, and as such often leads to potential side effects. It is thus highly desirable to develop non-ATP-competitive drugs that inhibit kinase activity via allosteric interactions. However, to elucidate the complex allosteric mechanism, it is essential to build a novel method to characterize a comprehensive non-catalytic pocket for the structurally well-covered human kinome. In this work, we developed a hybrid approach of sequence, structure and network analysis on 168 representative kinases to identify group-specific non-catalytic pockets. The geometric analysis was performed to cluster these pockets and to identify group-specific non-catalytic pockets based on their shape and location characteristics. Subsequent sequence evolutionary analysis reveals the crucial residues of each pocket that will likely interact with inhibitors binding to the pocket. These residues thus serve as potential biomarkers of each pocket for inhibitor design. Moreover, the residue-residue interaction network analysis was performed to elucidate the complex allosteric mechanism of these non-catalytic pockets. The final list of 14 group-specific non-catalytic pockets and their characterized structural, sequence and network features can be an enabling dataset for drug design effort at the human kinome level. The developed hybrid approach is able to identify group-specific non-catalytic pockets and will benefit the research related to human kinome drug design.
期刊：
PHYSICAL CHEMISTRY CHEMICAL PHYSICS,2020年22(44):25474-25482 ISSN：1463-9076
通讯作者：
Zhao, Yunjie
作者机构：
[Jia, Ya; Wang, Huiwen; Zhou, Ting; Song, Linlu; Zhao, Yunjie] Cent China Normal Univ, Inst Biophys, Wuhan 430079, Peoples R China.;[Jia, Ya; Wang, Huiwen; Zhou, Ting; Song, Linlu; Zhao, Yunjie] Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.;[Zeng, Chen] George Washington Univ, Dept Phys, Washington, DC 20052 USA.
通讯机构：
[Zhao, Yunjie] C;Cent China Normal Univ, Inst Biophys, Wuhan 430079, Peoples R China.;Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China.
摘要：
HIV is a virus that attacks the T cells. HIV may either actively replicate or become latent within host cells for years. Since HIV uses its own protein Tat to hijack the host CDK9-Cyclin complex for transcription, Tat is implicated in transcription-dependent HIV latency. To quantify the impact of Tat binding, we propose a computational framework to probe the dynamics of the CDK9-Cyclin interface and the ATP pocket reorganization upon binding by different Tat mutants. Specifically, we focus on mutations at three Tat residues P10, W11, and N12 that are known to interact directly with CDK9 based on the crystal structure of the Tat-CDK9-Cyclin complex. Our molecular dynamics simulations show that the CDK9-Cyclin interface becomes slightly weaker for P10S and W11R mutants but tighter for the K12N mutant. Furthermore, the side chain orientation of residue K48 in the ATP pocket of CDK9 is similar to the inactive state in P10S and W11R simulations, but similar to the active state in K12N simulations. These are consistent with some existing but puzzling observations of latency for these mutants. This framework may hence help gain a better understanding of the role of Tat in the transcription-dependent HIV latency establishment.
摘要：
In this paper, an modified FitzHugh-Nagumo (FHN) neural model was employed to investigate the vibrational resonance (VR) phenomenon, the collective behaviors, and the transmission of weak low-frequency (LF) signal driven by high-frequency (HF) stimulus under the action of different electromagnetic induction in single FHN neuron and feed-forward feedback network (FFN) system, respectively. For the single FHN system, by increasing the amplitude of HF stimulus, the phenomena of vibrational mono-/bi-resonance are observed, and the input weak signal and output of system are synchronized, and the information of the weak LF signal is amplified. For the FFN system, the phenomena of vibrational mono-/bi-resonances are also occurred, both frequency and amplitude of the HF stimulus play an important role in the vibrational bi-resonances and transmission of weak LF signal in the FHN neural FFN. (C) 2020 Elsevier Ltd. All rights reserved.
作者机构：
[Jia, Ya; Liu, Ying; Xu, Ying] Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China;[Jia, Ya; Liu, Ying; Xu, Ying] Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China;[Ma, Jun] Lanzhou Univ Technol, Dept Phys, Lanzhou 730050, Gansu, Peoples R China;[Ma, Jun] Chongqing Univ Posts & Telecommun, Sch Sci, Chongqing 430065, Peoples R China;[Ma, Jun] King Abdulaziz Univ, Fac Sci, Dept Math, NAAM Res Grp, POB 80203, Jeddah 21589, Saudi Arabia
通讯机构：
[Jia, Ya] C;Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China. Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China.
关键词：
Hybrid neuronal model;electrical activity mode;external signal stimulus;electromagnetic radiation;bifurcation and chaos analysis
摘要：
Based on a hybrid neuronal model of the Hindmarsh-Rose (HR) model (the slow negative feedback dynamics) with the Wilson model (the fast variable dynamics), the discharge modes of neurons are studied by using bifurcation analysis. When the hybrid neuronal model is driven by external stimulus current, the hybrid neuronal model is capable of simulating an extensive range of bursting patterns with different systemic parameters. With the increase of external stimulus, the multiple discharge patterns of neurons arise, and the electrical modes of the neurons appear for successive transitions. When the hybrid neuronal model is driven by electromagnetic induction, the electrical activities of the neurons have different responses to the variations in the amplitude and the angular frequency of high and low frequency electromagnetic radiations. It is found that the neuronal discharge activity is transformed from chaotic state to periodic state by increasing the angular frequency, and the firing pattern of neuron can be shifted from the bursting state to chaotic state by increasing the amplitude of the low frequency signal.
作者机构：
[Jia, Ya; Liu, Ying; Wang, Huiwen; Xu, Ying; Wang, Ping; Zhao, Yunjie] Cent China Normal Univ, Sch Phys, Wuhan 430079, Hubei, Peoples R China.;[Jia, Ya; Liu, Ying; Wang, Huiwen; Xu, Ying; Wang, Ping; Zhao, Yunjie] Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China.
通讯机构：
[Jia, Ya] C;Cent China Normal Univ, Sch Phys, Wuhan 430079, Hubei, Peoples R China.;Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China.
摘要：
The distribution of electromagnetic field in both intracellular and extracellular environments can be changed by fluctuations in the membrane potential, and the effects of electromagnetic induction should be considered in dealing with neuronal electrical activities, wherein field coupling plays a very important role in signal exchange between neurons. In this paper, basing on an improved electromagnetic induction model, a chain network is designed to investigate the responses of the neural system to channel noise under field coupling. Both the synchronization factor and coefficient of variation are numerically simulated, and it is found that (i) the weak field coupling strength is conducive to the regularity of discharge patterns in the neuronal network; (ii) the synchronization of neural spikes can be enhanced by selecting a suitable coupling intensity; and (iii) in the presence of the weak noise intensity, the discharge mode of neuron is easily affected by the inducing coefficient. Our results show that the regularity of discharge patterns in a stochastic neural network depends on the field coupling intensity, which reflects the importance of field coupling in the selection of neural discharge modes.
作者机构：
[Yang, Lijian] Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China.;Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China.
通讯机构：
[Jia, Ya] C;Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China.
摘要：
The feed-forward neural networks are the basis and have been widely applied on modern deep learning models, wherein connection strength between neurons plays a critical role in weak signal propagation and neural synchronization. In this paper, a four-variable Hindmarsh–Rose (HR) neural model is presented by introducing an additive variable as magnetic flow which changes the membrane potential via a memristor. The improved HR neurons in the feed-forward multilayer (four and eight layers) networks are investigated. The effects of electromagnetic radiation, synaptic weight and noise intensity on the propagation of the subthreshold excitatory postsynaptic current (EPSC) signal and the neural synchronization are discussed. It is found that when the system is in a weak magnetic field, the subthreshold EPSC signal can be successfully transmitted to the post-layers. Moreover, the neural synchronization of each layer is affected by electromagnetic radiation in the network, and with the help of noise the constant input current will transmit to the post-layers in a stable periodic synchronous form. Our findings provide a possible mechanism for enhancing the subthreshold signal propagation and triggering the neural synchronization in the nervous system.
作者机构：
[Jia, Ya; Ma, Huishu; He, Peng; Yang, Lijian; Billy, Kirunda John] Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China.;[Jia, Ya; Ma, Huishu; He, Peng; Yang, Lijian; Billy, Kirunda John] Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China.
通讯机构：
[Yang, Lijian] C;Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China.;Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China.
摘要：
E2F is a key transcription factor in the cell cycle network that regulates cell transition from G1 to S phase. MiR-17-92 plays an important role in the expression of E2F and regulates the progression of the cell cycle. Based on the Rb-E2F-MiR cell cycle network, we found that introduction of miR-17-92 in the network prolongs the cell cycle transition from G1 to S phase effectively and also maintains the robustness of the network against fluctuations. The dynamics of E2F are highly nonlinear, and by analysis of the bifurcation diagrams, we found that depending on the strength of interaction between E2F, microRNA and Myc, the expression level of E2F and miR-17-92 established is forward or antiphase synchronization. Moreover, through qualitative dynamic analysis and the quantitative Pearson coefficient, ‘miRNA-target avoidance,’ i.e., the relationship between miR-17-92 and E2F has been discovered in the noisy system. These results may help in further scrutiny and understanding the dual nonlinear role of miR-17-92 in many other vital biology processes.
摘要：
BACKGROUND: The kinase pocket structural information is important for drug discovery targeting cancer or other diseases. Although some kinase sequence, structure or drug databases have been developed, the databases cannot be directly used in the kinase drug study. Therefore, a comprehensive database of human kinase protein pockets is urgently needed to be developed. RESULTS: Here, we have developed HKPocket, a comprehensive Human Kinase Pocket database. This database provides sequence, structure, hydrophilic-hydrophobic, critical interactions, and druggability information including 1717 pockets from 255 kinases. We further divided these pockets into 91 pocket clusters using structural and position features in each kinase group. The pocket structural information would be useful for preliminary drug screening. Then, the potential drugs can be further selected and optimized by analyzing the sequence conservation, critical interactions, and hydrophobicity of identified drug pockets. HKPocket also provides online visualization and pse files of all identified pockets. CONCLUSION: The HKPocket database would be helpful for drug screening and optimization. Besides, drugs targeting the non-catalytic pockets would cause fewer side effects. HKPocket is available at http://zhaoserver.com.cn/HKPocket/HKPocket.html.
作者机构：
[Yang, Lijian; Zhang, Zhaokang; Zhan, Xuan; Billy, Kirunda John; Yang, LJ; Zhou, Yannan; Zhao, Yunjie] Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China.;[Yang, Lijian; Zhang, Zhaokang; Zhan, Xuan; Billy, Kirunda John; Yang, LJ; Zhou, Yannan; Zhao, Yunjie] Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China.;[Fan, Haitao] Beijing Polytech, Coll Bioengn, Beijing 100029, Peoples R China.
通讯机构：
[Yang, LJ; Jia, Y] C;Cent China Normal Univ, Inst Biophys, Wuhan 430079, Hubei, Peoples R China.;Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China.
摘要：
<jats:p>As the global population ages, searching for drugs and functional foods which can slow down the aging process has attracted a number of researchers. In this paper, the Lycium barbarum polysaccharides (LBP) extracted from Lycium barbarum was characterized and the effects of LBP on the aging and health of <jats:italic>C. elegans</jats:italic> were studied. Results showed that LBP can prolong the lifespan, improve the abilities to withstand environmental stress, enhance reproductive potentials, and maintain muscle integrity of <jats:italic>C. elegans</jats:italic>. By using genetically mutated <jats:italic>C. elegans</jats:italic> strains, RNAi gene silencing, and measuring the mRNA expression level, it was demonstrated that the lifespan of <jats:italic>C. elegans</jats:italic> was extended by LBP mainly through <jats:italic>sir-2.1</jats:italic>, <jats:italic>daf-12</jats:italic>, and <jats:italic>daf-16</jats:italic>. The present study might provide a basis for further study of LBP as a food or drug to interfere with aging and reduce the incidence of age-related diseases.</jats:p>
作者机构：
[Jia, Ya; Lu, Lulu; Ge, Mengyan; Xu, Ying] Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China.
通讯机构：
[Jia, Ya] C;Cent China Normal Univ, Dept Phys, Wuhan 430079, Hubei, Peoples R China.
关键词：
Statistical and Nonlinear Physics
摘要：
Chimera state in neuronal network means the coexistence of coherent and incoherent firing patterns. In this paper, the FitzHugh-Nagumo (FHN) neuronal model is employed to investigate the coherent resonance chimeras induced by temporally correlated noises. We show that the oscillation state of neuronal system is influenced by the correlation time of noise, the reduction of correlation time can result in a smaller amplitude noise sufficient to maximize the coherent resonance. However, the coherent resonance chimeras can be observed by changing both noise intensity and correlation time in the nonlocally coupled FHN neural network. By virtue of statistical synchronization factor and coherence measurement, it is found that the region of noise intensity threshold for generating coherent resonance chimeras is increased with the increasing of correlation time. The collective behavior of the system is particularly sensitive to the variation of noise intensity when correlation time is greater than 0.1. Furthermore, we demonstrate that the variation of noise intensity or correlation time can cause coherent resonance multi-chimeras in the neural network.
