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Challenges and limitations in computational prediction of protein misfolding in neurodegenerative diseases 计算预测神经退行性疾病中蛋白质错误折叠的挑战和局限性
IF 3.2 4区 医学 Q2 Neuroscience Pub Date : 2024-01-05 DOI: 10.3389/fncom.2023.1323182
Marios G. Krokidis, Georgios N. Dimitrakopoulos, Aristidis G. Vrahatis, T. Exarchos, Vlamos
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引用次数: 0
Positional multi-length and mutual-attention network for epileptic seizure classification 用于癫痫发作分类的位置多长和相互关注网络
IF 3.2 4区 医学 Q2 Neuroscience Pub Date : 2024-01-05 DOI: 10.3389/fncom.2024.1358780
Guokai Zhang, Aiming Zhang, Huan Liu, Jihao Luo, Jianqing Chen

The automatic classification of epilepsy electroencephalogram (EEG) signals plays a crucial role in diagnosing neurological diseases. Although promising results have been achieved by deep learning methods in this task, capturing the minute abnormal characteristics, contextual information, and long dependencies of EEG signals remains a challenge. To address this challenge, a positional multi-length and mutual-attention (PMM) network is proposed for the automatic classification of epilepsy EEG signals. The PMM network incorporates a positional feature encoding process that extracts minute abnormal characteristics from the EEG signal and utilizes a multi-length feature learning process with a hierarchy residual dilated LSTM (RDLSTM) to capture long contextual dependencies. Furthermore, a mutual-attention feature reinforcement process is employed to learn the global and relative feature dependencies and enhance the discriminative abilities of the network. To validate the effectiveness PMM network, we conduct extensive experiments on the public dataset and the experimental results demonstrate the superior performance of the PMM network compared to state-of-the-art methods.

癫痫脑电图(EEG)信号的自动分类在诊断神经系统疾病方面发挥着至关重要的作用。虽然深度学习方法在这一任务中取得了可喜的成果,但捕捉脑电信号的微小异常特征、上下文信息和长期依赖关系仍是一项挑战。为了应对这一挑战,我们提出了一种位置多长和相互关注(PMM)网络,用于癫痫脑电信号的自动分类。PMM 网络包含一个位置特征编码过程,可从脑电信号中提取微小的异常特征,并利用分层残差扩张 LSTM(RDLSTM)的多长度特征学习过程来捕捉长上下文相关性。此外,还采用了相互关注特征强化过程来学习全局和相对特征依赖关系,从而增强网络的分辨能力。为了验证 PMM 网络的有效性,我们在公共数据集上进行了大量实验,实验结果表明 PMM 网络的性能优于最先进的方法。
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引用次数: 0
Editorial: Advances in Shannon-based communications and computations approaches to understanding information processing in the brain 社论:基于香农的通信和计算方法在理解大脑信息处理方面的进展
IF 3.2 4区 医学 Q2 Neuroscience Pub Date : 2024-01-04 DOI: 10.3389/fncom.2023.1352772
James Tee, Giorgio M. Vitetta
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引用次数: 0
Identifying distinctive brain regions related to consumer choice behaviors on branded foods using activation likelihood estimation and machine learning 利用激活似然估计和机器学习识别与消费者品牌食品选择行为相关的独特脑区
IF 3.2 4区 医学 Q2 Neuroscience Pub Date : 2024-01-04 DOI: 10.3389/fncom.2024.1310013
Shinya Watanuki
Introduction

Brand equity plays a crucial role in a brand’s commercial success; however, research on the brain regions associated with brand equity has had mixed results. This study aimed to investigate key brain regions associated with the decision-making of branded and unbranded foods using quantitative neuroimaging meta-analysis and machine learning.

Methods

Quantitative neuroimaging meta-analysis was performed using the activation likelihood method. Activation of the ventral medial prefrontal cortex (VMPFC) overlapped between branded and unbranded foods. The lingual and parahippocampal gyri (PHG) were activated in the case of branded foods, whereas no brain regions were characteristically activated in response to unbranded foods. We proposed a novel predictive method based on the reported foci data, referencing the multi-voxel pattern analysis (MVPA) results. This approach is referred to as the multi-coordinate pattern analysis (MCPA). We conducted the MCPA, adopting the sparse partial least squares discriminant analysis (sPLS-DA) to detect unique brain regions associated with branded and unbranded foods based on coordinate data. The sPLS-DA is an extended PLS method that enables the processing of categorical data as outcome variables.

Results

We found that the lingual gyrus is a distinct brain region in branded foods. Thus, the VMPFC might be a core brain region in food categories in consumer behavior, regardless of whether they are branded foods. Moreover, the connection between the PHG and lingual gyrus might be a unique neural mechanism in branded foods.

Discussion

As this mechanism engages in imaging the feature-self based on emotionally subjective contextual associative memories, brand managers should create future-oriented relevancies between brands and consumers to build valuable brands.

引言品牌资产对品牌的商业成功起着至关重要的作用;然而,对与品牌资产相关的大脑区域的研究结果却不尽相同。本研究旨在利用定量神经影像荟萃分析和机器学习研究与品牌食品和非品牌食品决策相关的关键脑区。结果表明,品牌食品和非品牌食品的腹内侧前额叶皮层(VMPFC)的激活存在重叠。品牌食品会激活舌回和海马旁回(PHG),而无品牌食品则不会激活任何脑区。我们根据报告的病灶数据,参考多体素模式分析(MVPA)结果,提出了一种新的预测方法。这种方法被称为多坐标模式分析(MCPA)。我们采用稀疏偏最小二乘判别分析(sPLS-DA)进行多坐标模式分析,根据坐标数据检测与品牌食品和非品牌食品相关的独特脑区。结果我们发现,舌回是品牌食品的一个独特脑区。因此,在消费行为中,无论是否为品牌食品,VMPFC 都可能是食品类别的核心脑区。讨论由于这一机制是基于情感主观情境联想记忆对特征自我进行成像,因此品牌管理者应在品牌与消费者之间建立面向未来的关联,以打造有价值的品牌。
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引用次数: 0
Retraction: Cerebral microbleed detection via convolutional neural network and extreme learning machine. 撤回:通过卷积神经网络和极端学习机进行脑微出血检测
IF 3.2 4区 医学 Q2 Neuroscience Pub Date : 2023-12-28 eCollection Date: 2023-01-01 DOI: 10.3389/fncom.2023.1358283

[This retracts the article DOI: 10.3389/fncom.2021.738885.].

[本文撤消文章 DOI:10.3389/fncom.2021.738885.]。
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引用次数: 0
Exploring gene-drug interactions for personalized treatment of post-traumatic stress disorder 探索基因与药物的相互作用,实现创伤后应激障碍的个性化治疗
IF 3.2 4区 医学 Q2 Neuroscience Pub Date : 2023-12-21 DOI: 10.3389/fncom.2023.1307523
Konstantina Skolariki, Panagiotis Vlamos
Introduction

Post-Traumatic Stress Disorder (PTSD) is a mental disorder that can develop after experiencing traumatic events. The aim of this work is to explore the role of genes and genetic variations in the development and progression of PTSD.

Methods

Through three methodological approaches, 122 genes and 184 Single Nucleotide Polymorphisms (SNPs) associated with PTSD were compiled into a single gene repository for PTSD. Using PharmGKB and DrugTargetor, 323 drug candidates were identified to target these 122 genes. The top 17 drug candidates were selected based on the statistical significance of the genetic associations, and their promiscuity (number of associated genestargets) and were further assessed for their suitability in terms of bioavailability and drug-like characteristics. Through functional analysis, insights were gained into the biological processes, cellular components, and molecular functions involved in PTSD. This formed the foundation for the next aspect of this study which was to propose an efficient treatment for PTSD by exploring drug repurposing methods.

Results

The main aim was to identify the drugs with the most favorable profile that can be used as a pharmacological approach for PTSD treatment. More in particular, according to the genetic variations present in each individual, the relevant biological pathway can be identified, and the drug candidate proposed will specifically target said pathway, accounting for the personalized aspect of this work. The results showed that the drugs used as off-label treatment for PTSD have favorable pharmacokinetic profiles and the potential drug candidates that arose from DrugTargetor were not very promising. Clozapine showed a promising pharmacokinetic profile and has been linked with decreased psychiatric symptoms. Ambrucin also showed a promising pharmacokinetic profile but has been mostly linked with cancer treatment.

导言创伤后应激障碍(PTSD)是一种可在经历创伤事件后发生的精神障碍。方法通过三种方法,将与创伤后应激障碍相关的122个基因和184个单核苷酸多态性(SNPs)编入创伤后应激障碍的单一基因库。通过使用 PharmGKB 和 DrugTargetor,确定了 323 种候选药物来靶向这 122 个基因。根据基因关联的统计学意义及其杂合性(关联基因靶点的数量),选出了前 17 种候选药物,并进一步评估了它们在生物利用度和类似药物特性方面的适用性。通过功能分析,我们深入了解了创伤后应激障碍所涉及的生物过程、细胞成分和分子功能。这为本研究的下一步工作奠定了基础,即通过探索药物再利用方法,提出治疗创伤后应激障碍的有效方法。更具体地说,根据每个人的基因变异,可以确定相关的生物通路,所提出的候选药物将专门针对所述通路,从而实现这项工作的个性化。研究结果表明,用于创伤后应激障碍标示外治疗的药物具有良好的药代动力学特征,而从 DrugTargetor 中产生的潜在候选药物并不十分理想。氯氮平显示出良好的药代动力学特征,并与精神症状的减少有关。安布鲁新也显示出良好的药代动力学特征,但主要与癌症治疗有关。
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引用次数: 0
Neuro-environmental interactions: a time sensitive matter 神经与环境的相互作用:时间敏感问题
IF 3.2 4区 医学 Q2 Neuroscience Pub Date : 2023-12-19 DOI: 10.3389/fncom.2023.1302010
Azzurra Invernizzi, Stefano Renzetti, Elza Rechtman, Claudia Ambrosi, Lorella Mascaro, Daniele Corbo, Roberto Gasparotti, Cheuk Y. Tang, Donald R. Smith, Roberto G. Lucchini, Robert O. Wright, Donatella Placidi, Megan K. Horton, Paul Curtin
Introduction

The assessment of resting state (rs) neurophysiological dynamics relies on the control of sensory, perceptual, and behavioral environments to minimize variability and rule-out confounding sources of activation during testing conditions. Here, we investigated how temporally-distal environmental inputs, specifically metal exposures experienced up to several months prior to scanning, affect functional dynamics measured using rs functional magnetic resonance imaging (rs-fMRI).

Methods

We implemented an interpretable XGBoost-shapley additive explanation (SHAP) model that integrated information from multiple exposure biomarkers to predict rs dynamics in typically developing adolescents. In 124 participants (53% females, ages, 13–25 years) enrolled in the public health impact of metals exposure (PHIME) study, we measured concentrations of six metals (manganese, lead, chromium, copper, nickel, and zinc) in biological matrices (saliva, hair, fingernails, toenails, blood, and urine) and acquired rs-fMRI scans. Using graph theory metrics, we computed global efficiency (GE) in 111 brain areas (Harvard Oxford atlas). We used a predictive model based on ensemble gradient boosting to predict GE from metal biomarkers, adjusting for age and biological sex.

Results

Model performance was evaluated by comparing predicted versus measured GE. SHAP scores were used to evaluate feature importance. Measured versus predicted rs dynamics from our model utilizing chemical exposures as inputs were significantly correlated (p < 0.001, r = 0.36). Lead, chromium, and copper contributed most to the prediction of GE metrics.

Discussion

Our results indicate that a significant component of rs dynamics, comprising approximately 13% of observed variability in GE, is driven by recent metal exposures. These findings emphasize the need to estimate and control for the influence of past and current chemical exposures in the assessment and analysis of rs functional connectivity.

引言静息状态(rs)神经生理学动态评估依赖于对感觉、知觉和行为环境的控制,以最大限度地减少变异性并排除测试条件下激活的混杂源。在此,我们研究了时间差环境输入(特别是扫描前几个月的金属暴露)如何影响使用 Rs 功能磁共振成像(rs-fMRI)测量的功能动态。方法我们实施了一个可解释的 XGBoost-shapley加法解释(SHAP)模型,该模型整合了来自多种暴露生物标记物的信息,以预测典型发育青少年的 Rs 动态。在参加金属暴露对公共健康影响(PHIME)研究的 124 名参与者(53% 为女性,年龄在 13-25 岁之间)中,我们测量了生物基质(唾液、头发、指甲、脚趾甲、血液和尿液)中六种金属(锰、铅、铬、铜、镍和锌)的浓度,并获得了 rs-fMRI 扫描。利用图论指标,我们计算了 111 个脑区(哈佛牛津地图集)的全局效率(GE)。我们使用了一个基于集合梯度提升的预测模型来预测金属生物标记物的全局效率,并对年龄和生理性别进行了调整。SHAP 评分用于评估特征的重要性。我们利用化学暴露作为输入的模型所测出的 rs 动态与预测的 rs 动态具有显著的相关性(p < 0.001,r = 0.36)。讨论我们的研究结果表明,rs 动态的一个重要组成部分(约占观察到的 GE 变异的 13%)是由最近的金属暴露驱动的。这些发现强调,在评估和分析 rs 功能连接性时,需要估计和控制过去和当前化学暴露的影响。
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引用次数: 0
A lightweight mixup-based short texts clustering for contrastive learning 基于混合的轻量级短文聚类,用于对比学习
IF 3.2 4区 医学 Q2 Neuroscience Pub Date : 2023-12-18 DOI: 10.3389/fncom.2023.1334748
Qiang Xu, HaiBo Zan, ShengWei Ji

Traditional text clustering based on distance struggles to distinguish between overlapping representations in medical data. By incorporating contrastive learning, the feature space can be optimized and applies mixup implicitly during the data augmentation phase to reduce computational burden. Medical case text is prevalent in everyday life, and clustering is a fundamental method of identifying major categories of conditions within vast amounts of unlabeled text. Learning meaningful clustering scores in data relating to rare diseases is difficult due to their unique sparsity. To address this issue, we propose a contrastive clustering method based on mixup, which involves selecting a small batch of data to simulate the experimental environment of rare diseases. The contrastive learning module optimizes the feature space based on the fact that positive pairs share negative samples, and clustering is employed to group data with comparable semantic features. The module mitigates the issue of overlap in data, whilst mixup generates cost-effective virtual features, resulting in superior experiment scores even when using small batch data and reducing resource usage and time overhead. Our suggested technique has acquired cutting-edge outcomes and embodies a favorable strategy for unmonitored text clustering.

传统的基于距离的文本聚类难以区分医疗数据中的重叠表征。通过结合对比学习,可以优化特征空间,并在数据增强阶段隐式地应用混合,从而减轻计算负担。医疗病例文本在日常生活中非常普遍,而聚类是在大量无标记文本中识别主要病症类别的基本方法。由于罕见疾病的独特稀疏性,在与罕见疾病相关的数据中学习有意义的聚类分数非常困难。为了解决这个问题,我们提出了一种基于混合的对比聚类方法,即选择一小批数据来模拟罕见疾病的实验环境。对比学习模块根据阳性样本对共享阴性样本这一事实优化特征空间,并采用聚类方法将具有可比语义特征的数据分组。该模块缓解了数据重叠的问题,同时混合生成了具有成本效益的虚拟特征,即使使用小批量数据也能获得出色的实验得分,并减少了资源使用和时间开销。我们所建议的技术已取得了尖端成果,并体现了无监控文本聚类的有利策略。
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引用次数: 0
Monitoring time domain characteristics of Parkinson’s disease using 3D memristive neuromorphic system 利用三维记忆神经形态系统监测帕金森病的时域特征
IF 3.2 4区 医学 Q2 Neuroscience Pub Date : 2023-12-15 DOI: 10.3389/fncom.2023.1274575
Md Abu Bakr Siddique, Yan Zhang, Hongyu An
IntroductionParkinson’s disease (PD) is a neurodegenerative disorder affecting millions of patients. Closed-Loop Deep Brain Stimulation (CL-DBS) is a therapy that can alleviate the symptoms of PD. The CL-DBS system consists of an electrode sending electrical stimulation signals to a specific region of the brain and a battery-powered stimulator implanted in the chest. The electrical stimuli in CL-DBS systems need to be adjusted in real-time in accordance with the state of PD symptoms. Therefore, fast and precise monitoring of PD symptoms is a critical function for CL-DBS systems. However, the current CL-DBS techniques suffer from high computational demands for real-time PD symptom monitoring, which are not feasible for implanted and wearable medical devices.MethodsIn this paper, we present an energy-efficient neuromorphic PD symptom detector using memristive three-dimensional integrated circuits (3D-ICs). The excessive oscillation at beta frequencies (13–35 Hz) at the subthalamic nucleus (STN) is used as a biomarker of PD symptoms.ResultsSimulation results demonstrate that our neuromorphic PD detector, implemented with an 8-layer spiking Long Short-Term Memory (S-LSTM), excels in recognizing PD symptoms, achieving a training accuracy of 99.74% and a validation accuracy of 99.52% for a 75%–25% data split. Furthermore, we evaluated the improvement of our neuromorphic CL-DBS detector using NeuroSIM. The chip area, latency, energy, and power consumption of our CL-DBS detector were reduced by 47.4%, 66.63%, 65.6%, and 67.5%, respectively, for monolithic 3D-ICs. Similarly, for heterogeneous 3D-ICs, employing memristive synapses to replace traditional Static Random Access Memory (SRAM) resulted in reductions of 44.8%, 64.75%, 65.28%, and 67.7% in chip area, latency, and power usage.DiscussionThis study introduces a novel approach for PD symptom evaluation by directly utilizing spiking signals from neural activities in the time domain. This method significantly reduces the time and energy required for signal conversion compared to traditional frequency domain approaches. The study pioneers the use of neuromorphic computing and memristors in designing CL-DBS systems, surpassing SRAM-based designs in chip design area, latency, and energy efficiency. Lastly, the proposed neuromorphic PD detector demonstrates high resilience to timing variations in brain neural signals, as confirmed by robustness analysis.
导言帕金森病(PD)是一种影响数百万患者的神经退行性疾病。闭环深部脑刺激(CL-DBS)是一种可以缓解帕金森病症状的疗法。CL-DBS系统由向大脑特定区域发送电刺激信号的电极和植入胸部的电池供电刺激器组成。CL-DBS系统中的电刺激需要根据帕金森病症状的状态进行实时调整。因此,快速、精确地监测帕金森病症状是 CL-DBS 系统的关键功能。然而,目前的CL-DBS技术对实时PD症状监测的计算量要求很高,这对于植入式和可穿戴式医疗设备来说是不可行的。结果仿真结果表明,我们的神经形态 PD 检测器采用 8 层尖峰长短时记忆 (S-LSTM) 实现,在识别 PD 症状方面表现出色,在 75%-25% 的数据分割下,训练准确率达到 99.74%,验证准确率达到 99.52%。此外,我们还利用 NeuroSIM 评估了神经形态 CL-DBS 检测器的改进情况。对于单片三维集成电路,我们的 CL-DBS 检测器的芯片面积、延迟、能耗和功耗分别减少了 47.4%、66.63%、65.6% 和 67.5%。同样,对于异构三维集成电路,采用记忆性突触取代传统的静态随机存取存储器(SRAM),可使芯片面积、延迟和功耗分别减少 44.8%、64.75%、65.28% 和 67.7%。 讨论本研究通过直接利用时域中神经活动的尖峰信号,为帕金森病症状评估引入了一种新方法。与传统的频域方法相比,这种方法大大减少了信号转换所需的时间和能量。该研究开创性地将神经形态计算和忆阻器用于设计CL-DBS系统,在芯片设计面积、延迟和能效方面超越了基于SRAM的设计。最后,经鲁棒性分析证实,所提出的神经形态 PD 检测器对大脑神经信号的时序变化具有很强的适应能力。
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引用次数: 0
Cortical field maps across human sensory cortex 横跨人类感觉皮层的皮层场图
IF 3.2 4区 医学 Q2 Neuroscience Pub Date : 2023-12-15 DOI: 10.3389/fncom.2023.1232005
Alyssa A. Brewer, Brian Barton
Cortical processing pathways for sensory information in the mammalian brain tend to be organized into topographical representations that encode various fundamental sensory dimensions. Numerous laboratories have now shown how these representations are organized into numerous cortical field maps (CMFs) across visual and auditory cortex, with each CFM supporting a specialized computation or set of computations that underlie the associated perceptual behaviors. An individual CFM is defined by two orthogonal topographical gradients that reflect two essential aspects of feature space for that sense. Multiple adjacent CFMs are then organized across visual and auditory cortex into macrostructural patterns termed cloverleaf clusters. CFMs within cloverleaf clusters are thought to share properties such as receptive field distribution, cortical magnification, and processing specialization. Recent measurements point to the likely existence of CFMs in the other senses, as well, with topographical representations of at least one sensory dimension demonstrated in somatosensory, gustatory, and possibly olfactory cortical pathways. Here we discuss the evidence for CFM and cloverleaf cluster organization across human sensory cortex as well as approaches used to identify such organizational patterns. Knowledge of how these topographical representations are organized across cortex provides us with insight into how our conscious perceptions are created from our basic sensory inputs. In addition, studying how these representations change during development, trauma, and disease serves as an important tool for developing improvements in clinical therapies and rehabilitation for sensory deficits.
哺乳动物大脑皮层的感官信息处理路径往往被组织成地形表征,这些表征编码各种基本的感官维度。目前,许多实验室已经证明了这些表征是如何在整个视觉和听觉皮层中组织成无数皮层场图(CMF)的,每个皮层场图都支持一种或一系列专门的计算,这些计算是相关知觉行为的基础。单个 CFM 由两个正交的地形梯度定义,这两个梯度反映了该感官特征空间的两个基本方面。然后,多个相邻的 CFM 在视觉和听觉皮层中被组织成宏观结构模式,称为苜蓿叶簇。苜蓿叶簇内的CFM被认为具有共同的特性,如感受野分布、皮层放大和处理特化。最近的测量结果表明,在其他感官中也可能存在CFM,在躯体感觉、味觉和可能的嗅觉皮层通路中至少有一个感官维度的地形表征。在此,我们将讨论人类感觉皮层中 CFM 和四叶草簇组织的证据,以及用于识别此类组织模式的方法。通过了解这些地形表征是如何在大脑皮层中组织起来的,我们可以深入了解我们的意识知觉是如何从我们的基本感觉输入中产生的。此外,研究这些表征如何在发育、创伤和疾病过程中发生变化,也是开发改善感官缺陷的临床疗法和康复的重要工具。
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Frontiers in Computational Neuroscience
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