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WS-BiTM: Integrating White Shark Optimization with Bi-LSTM for enhanced autism spectrum disorder diagnosis WS-BiTM:将白鲨优化与 Bi-LSTM 相结合,增强自闭症谱系障碍诊断。
IF 2.7 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-08 DOI: 10.1016/j.jneumeth.2024.110319
Kainat Khan, Rahul Katarya
Autism Spectrum Disorder (ASD) is a multifaceted neurodevelopmental condition marked by challenges in social communication, sensory processing, and behavioral regulation. The delayed diagnosis of ASD significantly impedes timely interventions, which can exacerbate symptom severity. With approximately 62 million individuals affected worldwide, the demand for efficient diagnostic tools is critical. This study introduces a novel framework that combines a White Shark Optimization (WSO)-based feature selection method with a Bidirectional Long Short-Term Memory (Bi-LSTM) classifier for enhanced autism classification. Utilizing the WSO technique, we identify key features from autism screening datasets, which markedly improves the model's predictive capabilities. The optimized feature set is then processed by the Bi-LSTM classifier, enhancing its efficiency in handling sequential data. We comprehensively address methodological challenges, including overfitting, generalization, interpretability, and computational efficiency. Furthermore, we conduct a comparative analysis against baseline algorithms such as Neural Networks, Convolutional Neural Networks (CNN), and Long Short-Term Memory (LSTM) networks, while also employing Particle Swarm Optimization (PSO) for feature selection validation. We evaluate performance metrics, including accuracy, F1-score, specificity, precision, and sensitivity across three ASD datasets: Toddlers, Adults, and Children. Our results demonstrate that the WS-BiTM model significantly outperforms baseline methods, achieving accuracies of 97.6 %, 96.2 %, and 96.4 % on the respective datasets. Additionally, we implemented leave-one-dataset cross-validation and confirmed the statistical significance of our findings through a paired t-test, supplemented by an ablation study to detail the contributions of individual model components. These findings highlight the potential of the WS-BiTM model as a robust tool for ASD classification.
自闭症谱系障碍(ASD)是一种多方面的神经发育疾病,主要表现为社交沟通、感官处理和行为调节方面的障碍。ASD 的延迟诊断严重阻碍了及时干预,可能会加重症状的严重程度。全球约有 6200 万人受到影响,因此对高效诊断工具的需求至关重要。本研究介绍了一种新颖的框架,它将基于白鲨优化(WSO)的特征选择方法与双向长短期记忆(Bi-LSTM)分类器相结合,以增强自闭症分类能力。利用 WSO 技术,我们从自闭症筛查数据集中识别出关键特征,从而显著提高了模型的预测能力。然后,Bi-LSTM 分类器对优化后的特征集进行处理,从而提高其处理连续数据的效率。我们全面应对了方法学上的挑战,包括过拟合、泛化、可解释性和计算效率。此外,我们还与神经网络、卷积神经网络(CNN)和长短期记忆(LSTM)网络等基准算法进行了比较分析,同时还采用了粒子群优化(PSO)进行特征选择验证。我们评估了三个 ASD 数据集的性能指标,包括准确率、F1 分数、特异性、精确度和灵敏度:幼儿、成人和儿童。结果表明,WS-BiTM 模型明显优于基线方法,在各个数据集上的准确率分别达到了 97.6%、96.2% 和 96.4%。此外,我们还实施了 "留一数据集交叉验证",并通过配对 t 检验确认了研究结果的统计意义,同时还进行了消减研究,以详细了解各个模型组件的贡献。这些发现凸显了 WS-BiTM 模型作为 ASD 分类的可靠工具的潜力。
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引用次数: 0
Cognition enhances cognition: A comprehensive analysis on cognitive stimulation protocols and their effects on cognitive functions in animal models 认知增强认知:全面分析认知刺激方案及其对动物模型认知功能的影响。
IF 2.7 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-07 DOI: 10.1016/j.jneumeth.2024.110316
Eugenia Landolfo , Erica Berretta , Francesca Balsamo , Laura Petrosini , Francesca Gelfo
Brain plasticity is involved in the regulation of neural differentiation as well as in functional processes related to memory consolidation, learning, and cognition during healthy life and brain pathology. Modifications in lifestyle, like poor diet, insufficient physical exercise and cognitive stimulation are associated with an increased risk of neurodegeneration; however, there is a paucity of research regarding the impact of individual factors on dementia risk or progression. Cognitive stimulation is a group of techniques and strategies, including cognitive enrichment (CE) and cognitive training (CT), aimed to maintain or improve the functionality of cognitive abilities, such as memory, learning, cognitive flexibility, and attention. The present scoping review focuses on cognitive stimulation by investigating its neuroprotective and therapeutic role on these cognitive functions in rodents. A methodical bibliographic search of experimental studies on rats and mice was conducted on PubMed and Scopus databases up to June 3, 2024. A pool of 29 original research articles was considered as relevant to the topic of the present work. Evidence shows that CE but above all CT influence cognitive performance and brain structure in rodents with specific differences with respect to the quality and quantity of stimulation. There would appear to be greater effects in restoring damage than in preserving or improving a functioning condition. These results provide a theoretical basis to be considered in the therapeutic setting, although further systematic studies would be necessary to identify and characterize the cognitive stimulation protocols which hold the greatest and task-transferable impact on cognitive functioning and maintenance.
大脑的可塑性参与神经分化的调控,以及与健康生活和大脑病变期间的记忆巩固、学习和认知相关的功能过程。生活方式的改变,如不良饮食习惯、体育锻炼不足和认知刺激,与神经变性风险的增加有关;然而,有关个体因素对痴呆症风险或进展的影响的研究却很少。认知刺激是一组技术和策略,包括认知强化(CE)和认知训练(CT),旨在维持或改善认知能力的功能,如记忆、学习、认知灵活性和注意力。本范围综述侧重于认知刺激,研究其对啮齿类动物这些认知功能的神经保护和治疗作用。截至 2024 年 6 月 3 日,我们在 PubMed 和 Scopus 数据库中对有关大鼠和小鼠的实验研究进行了有条不紊的文献检索。29篇原创研究文章被认为与本次研究的主题相关。有证据表明,CE(尤其是 CT)会影响啮齿类动物的认知能力和大脑结构,而刺激的质和量则存在具体差异。恢复损伤的效果似乎比保持或改善功能状态的效果更大。这些结果为治疗提供了理论依据,尽管还需要进一步的系统研究,以确定和描述对认知功能和维持具有最大影响且可进行任务转移的认知刺激方案。
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引用次数: 0
Positive reinforcement-based magnet training permits social housing in catheterized squirrel monkeys 基于正强化的磁铁训练能让导管松鼠猴适应社会生活
IF 2.7 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-30 DOI: 10.1016/j.jneumeth.2024.110313
Alexandra N. Johansen , Hector M. Figueroa , Jacquelin C. Hecker , Jazmyne Z. Taylor , Evan T. Shukan , Hank P. Jedema , Charles W. Bradberry

Background

Non-human primates play a critical role in neuroscience research. Though they are social animals, laboratory study requirements can sometimes require single housing and thereby prevent social housing.

New Method

To eliminate single housing and promote well-being within our squirrel monkey colony, we used positive reinforcement training in combination with magnetic/mechanical clasps and custom jackets to permit pair housing of catheterized squirrel monkeys used in behavioral studies.

Results

Adult Saimiri boliviensis boliviensis monkeys (n = 7) readily progressed through a six-stage training procedure for cooperative handling and transport from the home cage to the experimental testing rooms.
Comparison with existing methods and conclusions: Given the evidence of isolation induced stress and neurobiological consequences in multiple species, and consistent with an increased regulatory emphasis on social housing of non-human primates, the methods presented herein provide a method for handling squirrel monkeys in behavioral studies that is compatible with social housing.
背景:非人灵长类动物在神经科学研究中发挥着至关重要的作用。虽然它们是社会性动物,但实验室研究要求有时会要求单人饲养,从而阻碍了社会性饲养:新方法:为了在松鼠猴群中消除单只饲养并促进其福利,我们使用正强化训练,结合磁性/机械扣和定制夹克,使用于行为研究的导管松鼠猴能够配对饲养:结果:成年 Saimiri boliviensis boliviensis 猴(n = 7 只)很容易通过六个阶段的训练程序取得进步,从而能够合作处理并从家庭笼子运送到实验测试室:与现有方法的比较:鉴于有证据表明在多个物种中隔离会诱发压力和神经生物学后果,并且随着监管部门越来越重视非人灵长类动物的社会化饲养,本文介绍的方法为行为研究中处理松鼠猴提供了一种与社会化饲养相适应的方法。
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引用次数: 0
Pupillometry is sensitive to speech masking during story listening: A commentary on the critical role of modeling temporal trends 瞳孔测量法对听故事时的语音掩蔽很敏感:对时间趋势建模的关键作用的评论。
IF 2.7 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-19 DOI: 10.1016/j.jneumeth.2024.110299
Andreas Widmann , Björn Herrmann , Florian Scharf
An increase in pupil size is an important index of listening effort, for example, when listening to speech masked by noise. Specifically, the pupil dilates as the signal-to-noise ratio decreases. A growing body of work aims to assess listening effort under naturalistic conditions using continuous speech, such as spoken stories. However, a recent study found that pupil size was sensitive to speech masking only when listening to sentences but not under naturalistic conditions when listening to stories. The pupil typically constricts with increasing time on task during an experimental block or session, and it may be necessary to account for this temporal trend in experimental design and data analysis in paradigms using longer, continuous stimuli. In the current work, we re-analyze the previously published pupil data, taking into account a problematic constraint of randomization and time-on-task, and use the data to outline methodological solutions for accounting for temporal trends in physiological data using linear mixed models. The results show that, in contrast to the previous work, pupil size is indeed sensitive to speech masking even during continuous story listening. Furthermore, accounting for the temporal trend allowed modeling the dynamic changes in the speech masking effect on pupil size over time as the continuous story unfolded. After demonstrating the importance of accounting for temporal trends in the analysis of empirical data, we provide simulations, methodological considerations, and user recommendations for the analysis of temporal trends in experimental data using linear mixed models.
瞳孔增大是听力强度的一个重要指标,例如在听被噪声掩盖的语音时。具体来说,瞳孔会随着信噪比的降低而放大。越来越多的研究旨在使用连续语音(如口语故事)评估自然条件下的听力强度。然而,最近的一项研究发现,只有在听句子时,瞳孔大小才会对语音掩蔽敏感,而在自然条件下听故事时,瞳孔大小则不会。瞳孔通常会随着实验块或实验环节中任务时间的增加而缩小,在使用较长的连续刺激的范式中,可能有必要在实验设计和数据分析中考虑这一时间趋势。在当前的研究中,我们重新分析了之前发表的瞳孔数据,考虑到随机化和任务时间的限制,并利用这些数据概述了使用线性混合模型考虑生理数据时间趋势的方法论解决方案。结果表明,与之前的研究不同,即使在连续听故事的过程中,瞳孔大小确实对语音掩蔽很敏感。此外,考虑时间趋势还能进一步模拟语音掩蔽对瞳孔大小的影响随着连续故事的展开而发生的动态变化。在证明了在分析经验数据时考虑时间趋势的重要性之后,我们提供了使用线性混合模型分析实验数据中时间趋势的模拟、方法考虑和用户建议。
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引用次数: 0
Quantifying population-level neural tuning functions using Ricker wavelets and the Bayesian bootstrap 利用里克小波和贝叶斯引导法量化种群级神经调节函数
IF 2.7 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-19 DOI: 10.1016/j.jneumeth.2024.110303
Laura Ahumada , Christian Panitz , Caitlin M. Traiser , Faith E. Gilbert , Mingzhou Ding , Andreas Keil

Background

Experience changes visuo-cortical tuning. In humans, re-tuning has been studied during aversive generalization learning, in which the similarity of generalization stimuli (GSs) with a conditioned threat cue (CS+) is used to quantify tuning functions. Previous work utilized pre-defined tuning shapes (generalization and sharpening patterns). This approach may constrain the ways in which re-tuning can be characterized since the tuning patterns may not match the prototypical functions.

New method

The present study proposes a flexible and data-driven method for precisely quantifying changes in tuning based on the Ricker wavelet function and the Bayesian bootstrap. This method was applied to EEG and psychophysics data from an aversive generalization learning paradigm.

Results

The Ricker wavelet model fitted the steady-state visual event potentials (ssVEP), alpha-band power, and detection accuracy data well. A Morlet wavelet function was used for comparison and fit the data better in some situations, but was more challenging to interpret. The pattern of re-tuning in the EEG data, predicted by the Ricker model, resembled the shapes of the best fitting a-priori patterns.

Comparison with existing methods

Although the re-tuning shape modeled by the Ricker function resembled the pre-defined shapes, the Ricker approach led to greater Bayes factors and more interpretable results compared to a-priori models. The Ricker approach was more easily fit and led to more interpretable results than a Morlet wavelet model.

Conclusion

This work highlights the promise of the current method for capturing the precise nature of visuo-cortical tuning, unconstrained by the implementation of a-priori models.
背景:经验会改变视觉皮层的调谐。在人类的厌恶泛化学习过程中,对重新调谐进行了研究,其中泛化刺激(GSs)与条件威胁线索(CS+)的相似性被用来量化调谐功能。以前的研究利用了预先确定的调谐形状(泛化和锐化模式)。这种方法可能会限制重新调谐的表征方式,因为调谐模式可能与原型功能不匹配:本研究基于 Ricker 小波函数和贝叶斯引导法,提出了一种灵活的数据驱动方法,用于精确量化调谐变化。该方法被应用于来自厌恶泛化学习范式的脑电图和心理物理学数据:结果:Ricker小波模型很好地拟合了稳态视觉事件电位(ssVEP)、α波段功率和检测准确率数据。莫氏小波函数用于比较,在某些情况下更适合数据,但解释起来更具挑战性。由 Ricker 模型预测的脑电图数据中的再调谐模式与最佳拟合先验模式的形状相似:与现有方法的比较:虽然 Ricker 函数模拟的再调谐形状与预定义的形状相似,但与先验模型相比,Ricker 方法得出的贝叶斯系数更大,结果更易解释。与莫莱特小波模型相比,Ricker 方法更容易拟合,得出的结果也更容易解释:这项工作突出了当前方法在不受先验模型实施限制的情况下捕捉视觉皮层调谐精确性质的前景。
{"title":"Quantifying population-level neural tuning functions using Ricker wavelets and the Bayesian bootstrap","authors":"Laura Ahumada ,&nbsp;Christian Panitz ,&nbsp;Caitlin M. Traiser ,&nbsp;Faith E. Gilbert ,&nbsp;Mingzhou Ding ,&nbsp;Andreas Keil","doi":"10.1016/j.jneumeth.2024.110303","DOIUrl":"10.1016/j.jneumeth.2024.110303","url":null,"abstract":"<div><h3>Background</h3><div>Experience changes visuo-cortical tuning. In humans, re-tuning has been studied during aversive generalization learning, in which the similarity of generalization stimuli (GSs) with a conditioned threat cue (CS+) is used to quantify tuning functions. Previous work utilized pre-defined tuning shapes (generalization and sharpening patterns). This approach may constrain the ways in which re-tuning can be characterized since the tuning patterns may not match the prototypical functions.</div></div><div><h3>New method</h3><div>The present study proposes a flexible and data-driven method for precisely quantifying changes in tuning based on the Ricker wavelet function and the Bayesian bootstrap. This method was applied to EEG and psychophysics data from an aversive generalization learning paradigm.</div></div><div><h3>Results</h3><div>The Ricker wavelet model fitted the steady-state visual event potentials (ssVEP), alpha-band power, and detection accuracy data well. A Morlet wavelet function was used for comparison and fit the data better in some situations, but was more challenging to interpret. The pattern of re-tuning in the EEG data, predicted by the Ricker model, resembled the shapes of the best fitting a-priori patterns.</div></div><div><h3>Comparison with existing methods</h3><div>Although the re-tuning shape modeled by the Ricker function resembled the pre-defined shapes, the Ricker approach led to greater Bayes factors and more interpretable results compared to a-priori models. The Ricker approach was more easily fit and led to more interpretable results than a Morlet wavelet model.</div></div><div><h3>Conclusion</h3><div>This work highlights the promise of the current method for capturing the precise nature of visuo-cortical tuning, unconstrained by the implementation of a-priori models.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"413 ","pages":"Article 110303"},"PeriodicalIF":2.7,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142467907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
T1- and T2-weighted MRI signal and histology findings in suboptimally fixed human brains 亚最佳固定人脑的 T1 和 T2 加权磁共振成像信号和组织学发现。
IF 2.7 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-16 DOI: 10.1016/j.jneumeth.2024.110301
Eve-Marie Frigon , Philippe Pharand , Amy Gérin-Lajoie , Liana Guerra Sanches , Denis Boire , Mahsa Dadar , Josefina Maranzano
Neuroscientific research that requires brain tissue depends on brain banks that provide very small tissue samples fixed by immersion in neutral-buffered formalin (NBF), while anatomy laboratories could provide full brain specimens. However, these brains are generally fixed by perfusion of the full body with solutions other than NBF generally used by brain banks, such as an alcohol-formaldehyde solution (AFS) that is typically used for dissection and teaching. Therefore, fixation quality of these brains needs to be assessed to determine their usefulness in post-mortem investigations through magnetic resonance imaging (MRI) and histology, two common neuroimaging modalities. Here, we report the characteristics of five brains fixed by full body perfusion of an AFS from our Anatomy Laboratory suspected of being poorly fixed, given the altered signal seen on T1w MRI scans in situ. We describe 1- the characteristics of the donors; 2- the fixation procedures applied for each case; 3- the tissue contrast characteristics of the T1w and T2w images; 4- the macroscopic tissue quality after extraction of the brains; 5- the macroscopic arterial characteristics and presence or absence of blood clots; and 6- four histological stains of the areas that we suspected were poorly fixed. We conclude that multiple factors can affect the fixation quality of the brain. Nevertheless, cases in which brain fixation is suboptimal, consequently altering the T1w signal, still have T2w of adequate gray-matter to white-matter contrast and may also be used for histology stains with sufficient quality.
需要脑组织的神经科学研究依赖于脑库提供的浸泡在中性缓冲福尔马林(NBF)中固定的非常小的组织样本,而解剖实验室可以提供完整的大脑标本。不过,这些大脑通常是用脑库常用的 NBF 以外的溶液(如通常用于解剖和教学的酒精-甲醛溶液 (AFS))进行全身灌注固定的。因此,需要对这些大脑的固定质量进行评估,以确定它们在通过磁共振成像(MRI)和组织学这两种常见的神经成像模式进行尸检时是否有用。在此,我们报告了解剖实验室通过全身灌注 AFS 固定的五个大脑的特征,由于在原位 T1w 核磁共振成像扫描中看到的信号改变,我们怀疑这些大脑的固定质量不佳。我们描述了 1- 供体的特征;2- 每个病例采用的固定程序;3- T1w 和 T2w 图像的组织对比度特征;4- 取出大脑后的宏观组织质量;5- 动脉的宏观特征和有无血凝块;以及 6- 我们怀疑固定不良区域的四种组织学染色。我们的结论是,多种因素都会影响大脑的固定质量。尽管如此,如果脑部固定不理想,从而改变了 T1w 信号,但 T2w 仍有足够的灰质与白质对比度,也可用于质量足够高的组织学染色。
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引用次数: 0
Enhancing non-invasive pre-surgical evaluation through functional connectivity and graph theory in drug-resistant focal epilepsy 通过功能连接性和图论加强耐药性局灶性癫痫的非侵入性术前评估
IF 2.7 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-16 DOI: 10.1016/j.jneumeth.2024.110300
Silvana Pelle , Anna Scarabello , Lorenzo Ferri , Giulia Ricci , Francesca Bisulli , Mauro Ursino

Background

Epilepsy, characterized as a network disorder, involves widely distributed areas following seizure propagation from a limited onset zone. Accurate delineation of the epileptogenic zone (EZ) is crucial for successful surgery in drug-resistant focal epilepsy. While visual analysis of scalp electroencephalogram (EEG) primarily elucidates seizure spreading patterns, we employed brain connectivity techniques and graph theory principles during the pre-ictal to ictal transition to define the epileptogenic network.

Method

Cortical sources were reconstructed from 40-channel scalp EEG in five patients during pre-surgical evaluation for focal drug-resistant epilepsy. Temporal Granger connectivity was estimated ten seconds before seizure and at seizure onset. Results have been analyzed using some centrality indices taken from Graph theory (Outdegree, Hubness). A new lateralization index is proposed by taking into account the sum of the most relevant hubness values across left and right regions of interest.

Results

In three patients with positive surgical outcomes, analysis of the most relevant Hubness regions closely aligned with clinical hypotheses, demonstrating consistency in EZ lateralization and location. In one patient, the method provides unreliable results due to the abundant movement artifacts preceding the seizure. In a fifth patient with poor surgical outcome, the proposed method suggests a wider epileptic network compared with the clinically suspected EZ, providing intriguing new indications beyond those obtained with traditional electro-clinical analysis.

Conclusions

The proposed method could serve as an additional tool during pre-surgical non-invasive evaluation, complementing data obtained from EEG visual inspection. It represents a first step toward a more sophisticated analysis of seizure onset based on connectivity imbalances, electrical propagation, and graph theory principles.
背景:癫痫是一种网络障碍性疾病,其发作从有限的起始区传播到广泛分布的区域。准确划分致痫区(EZ)对于耐药性局灶性癫痫的成功手术至关重要。头皮脑电图(EEG)的视觉分析主要阐明癫痫发作的扩散模式,而我们则利用脑连接技术和图论原理,在发作前到发作过渡期间界定致痫网络:方法:在对局灶性耐药性癫痫进行手术前评估时,我们从五名患者的 40 通道头皮脑电图中重建了皮层源。在癫痫发作前十秒和发作开始时估算了时间格兰杰连通性。使用图论中的一些中心性指数(Outdegree、Hubness)对结果进行了分析。考虑到左右相关区域最相关的枢纽度值之和,提出了一种新的侧向化指数:结果:在三名手术效果良好的患者中,对最相关枢纽区域的分析与临床假设密切吻合,证明了 EZ 侧化和位置的一致性。在一名患者中,由于癫痫发作前的大量运动伪影,该方法提供的结果并不可靠。在第五位手术效果不佳的患者中,与临床上怀疑的 EZ 相比,所提出的方法提示了一个更广泛的癫痫网络,提供了传统的电-临床分析所无法获得的令人感兴趣的新指示:结论:所提出的方法可作为手术前非侵入性评估的额外工具,补充脑电图视觉检查所获得的数据。它是基于连接失衡、电传播和图论原理对癫痫发作进行更复杂分析的第一步。
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引用次数: 0
Modified rat pup cerebrospinal fluid collection method 改良大鼠幼崽脑脊液采集法
IF 2.7 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-15 DOI: 10.1016/j.jneumeth.2024.110302
Jiaojiao Wang, Zhifang Dong, Xiuyu Shi

Background

Cerebrospinal fluid (CSF) reflects biochemical changes in the brain due to its direct contact with brain interstitial fluid, making it a valuable tool for diagnosing and monitoring disease progression and therapeutic effectiveness in clinical practice. However, collecting CSF in animal studies, particularly from small animals like rat pups or mice, poses significant challenges.

New method

After attempting various reported protocols, we encountered difficulties in consistently obtaining sufficient CSF from rat pups (P7-P42). Consequently, we modified these methods and developed a protocol with controllable and precise parameters for each step, enhancing reproducibility across different researchers.

Results

The newly developed method enables rapid, single-operator, and reproducible CSF extraction while ensuring high-quality (the absorbance of the “quality control solution” at 415 nm < 0.05 AU, an indicator of oxyhemoglobin contamination for the collected CSF samples) and high-yield samples (33 ± 2.128 μL for P7 pups, 34.10 ± 2.747 μL for P8 pups, 36.67 ± 3.997 μL for P9 pups, 36.90 ± 1.946 μL for P10 pups, 35.11 ± 3.285 μL for P10 hypoxic-ischemic brain damage (HIBD) pups and 51.70 ± 5.256 μL for P42 pups, respectively).

Comparison with existing methods

Unlike existing methods of CSF extraction in rat pups, our protocol has reproducible capillary pipette pulling parameters, controllable CSF quality indexes, and can be operated by a single person with high yield in a short time.

Conclusions

This paper provides a step-by-step comparison and discussion of the CSF collection process, establishing a method that enables a single operator to collect CSF rapidly, consistently, sufficiently, and with controlled quality.
背景脑脊液(CSF)由于与脑间质直接接触,能反映大脑的生化变化,因此是临床上诊断和监测疾病进展及治疗效果的重要工具。新方法在尝试了各种已报道的方案后,我们在从幼鼠(P7-P42)中持续获得足够的 CSF 方面遇到了困难。因此,我们对这些方法进行了修改,并开发了一种每一步都具有可控和精确参数的方案,从而提高了不同研究人员之间的可重复性。结果新开发的方法实现了快速、单人操作和可重复性 CSF 提取,同时确保了高质量(415 nm 处 "质量控制溶液 "的吸光度为 0.05 AU,这是采集的 CSF 样品氧合血红蛋白污染的指标)和高产样品(P7 幼犬为 33 ± 2.128 μL,P8 幼犬为 34.10 ± 2.747 μL,P9 幼犬为 36.67 ± 3.997 μL,P10 幼犬为 36.90 ± 1.946 μL,P12 幼犬为 35.11 ± 3.285 μL,P13 幼犬为 36.90 ± 1.946 μL,P14 幼犬为 36.90 ± 1.946 μL)。与现有方法的比较与现有的大鼠幼崽 CSF 提取方法不同,我们的方案具有可重复的毛细管移液管拉管参数、可控的 CSF 质量指标,且单人操作即可在短时间内获得高产量。结论 本文对 CSF 采集过程进行了逐步比较和讨论,建立了一种单人操作即可快速、一致、充分且质量可控地采集 CSF 的方法。
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引用次数: 0
Localization of neurons from extracellular footprints 从细胞外足迹定位神经元
IF 2.7 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-09 DOI: 10.1016/j.jneumeth.2024.110297
Mélina Scopin , Giulia L.B. Spampinato , Olivier Marre , Samuel Garcia , Pierre Yger

Background:

High density microelectrode arrays (HD-MEAs) are now widely used for both in-vitro and in-vivo recordings, as they allow spikes from hundreds of neurons to be recorded simultaneously. Since extracellular recordings do not allow visualization of the recorded neurons, algorithms are needed to estimate their physical positions, especially to track their movements when the are drifting away from recording devices.

New Method:

The objective of this study was to evaluate the performance of multiple algorithms for neuron localization solely from extracellular traces (MEA recordings), either artificial or obtained from mouse retina. The algorithms compared included center-of-mass, monopolar, and grid-based algorithms. The first method is a barycenter calculation. The second algorithm infers the position of the cell using triangulation with the assumption that the neuron behaves as a monopole. Finally, grid-based methods rely on comparing the recorded spike with a projection of spikes of hypothetical neurons with different positions.

Results:

The Grid-Based algorithm yielded the most satisfactory outcomes. The center-of-mass exhibited a minimal computational cost, yet its average localization was suboptimal. Monopolar algorithms gave cell localizations with an average error of less than 10μm, but they had considerable variability and a high computational cost. For the grid-based method, the variability was smaller, with satisfactory performance and low computational cost.

Comparison with Existing Method(s):

The accuracy of the different localization methods benchmarked in this article had not been properly tested with ground-truth recordings before.

Conclusion:

The objective of this article is to provide guidance to researchers on the selection of optimal methods for localizing neurons based on MEA recordings.
背景:高密度微电极阵列(HD-MEAs)可同时记录数百个神经元的尖峰脉冲,因此目前被广泛用于体外和体内记录。由于细胞外记录无法观察到记录的神经元,因此需要算法来估计它们的物理位置,特别是当它们远离记录设备时跟踪它们的运动:本研究的目的是评估多种算法的性能,以评估仅通过细胞外痕迹(MEA 记录)(人工或从小鼠视网膜获得)进行神经元定位的性能。比较的算法包括质量中心算法、单极算法和基于网格的算法。第一种方法是计算质心。第二种算法使用三角测量法推断细胞的位置,假设神经元表现为单极。最后,基于网格的方法依赖于将记录的尖峰与具有不同位置的假定神经元的尖峰投影进行比较:基于网格的算法取得了最令人满意的结果。质量中心算法的计算成本最低,但其平均定位效果并不理想。单极算法的细胞定位平均误差小于 10μm,但它们具有相当大的变异性和较高的计算成本。与现有方法的比较:与现有方法的比较:本文基准测试的不同定位方法的准确性以前没有用地面实况记录进行过适当的测试:本文旨在为研究人员选择基于 MEA 记录的神经元定位最佳方法提供指导。
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引用次数: 0
Optogenetic estimation of synaptic connections in brain slices 脑片突触连接的光遗传估算。
IF 2.7 4区 医学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-02 DOI: 10.1016/j.jneumeth.2024.110298
Tetsuhiko Kashima , Takuya Sasaki , Yuji Ikegaya

Background

Detection of synaptic connections is essential for understanding neural circuits. By using optogenetics, current injection, and glutamate uncaging to activate presynaptic cells and simultaneously recording the subsequent response of postsynaptic cells, the presence of synaptic connections can be confirmed. However, these methods present throughput challenges, such as the need for simultaneous multicellular patch-clamp recording and two-photon microscopy. These challenges lead to a trade-off between sacrificing resolution and experimental throughput.

New method

We adopted the laser, typically used for local field ablation, and combined this with post hoc analysis. We successfully approximated the synaptic connection probabilities using only an epi-fluorescence microscope and single-cell recordings.

Results

We sequentially stimulated the channelrhodopsin 2-expressing cells surrounding the recorded cell and approximated the synaptic connection probabilities. This probability value was comparable to that obtained from simultaneous multi-cell patch-clamp recordings, which included more than 600 pairs.

Comparison with existing methods

Our setup allows us to estimate connection probabilities within 100 s, outperforming existing methods. We successfully estimated synaptic connection probabilities using only the optical path typically used by an epi-fluorescence microscope and single-cell recordings. It may also be suitable for dendritic ablation experiments.

Conclusions

The proposed method simplifies the estimation of connection probabilities, which is expected to advance the study of neural circuits in conditions such as autism and schizophrenia where connection probabilities vary. Furthermore, this approach is applicable not only to local circuits but also to long-range connections, thus increasing experimental throughput.
背景:检测突触连接对于了解神经回路至关重要。通过使用光遗传学、电流注入和谷氨酸释放来激活突触前细胞,并同时记录突触后细胞的后续反应,可以确认突触连接的存在。然而,这些方法都面临着通量方面的挑战,例如需要同时进行多细胞膜片钳记录和双光子显微镜检查。这些挑战导致了牺牲分辨率和实验通量之间的权衡:新方法:我们采用了通常用于局部场消融的激光,并将其与事后分析相结合。新方法:我们采用了通常用于局部场消融的激光,并将其与事后分析相结合。我们仅使用了外显荧光显微镜和单细胞记录,就成功逼近了突触连接概率:结果:我们依次刺激了记录细胞周围的通道荧光素 2 表达细胞,并估算出了突触连接概率。该概率值与同时进行多细胞贴片钳记录(包括 600 多对细胞)获得的概率值相当:与现有方法的比较:我们的设置使我们能在 100 秒内估算出连接概率,优于现有方法。我们仅使用外显荧光显微镜和单细胞记录通常使用的光路,就成功估算出了突触连接概率。该方法也适用于树突消融实验:结论:所提出的方法简化了连接概率的估算,有望推动对自闭症和精神分裂症等神经回路的研究。此外,这种方法不仅适用于局部回路,也适用于长程连接,从而提高了实验吞吐量。
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引用次数: 0
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Journal of Neuroscience Methods
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