Journal of Neuroscience Methods最新文献

Background

Speech sounds are processed in the human brain through intricate and interconnected cortical and subcortical structures. Two neural signatures, one largely from cortical sources (mismatch response, MMR) and one largely from subcortical sources (frequency-following response, FFR) are critical for assessing speech processing as they both show sensitivity to high-level linguistic information. However, there are distinct prerequisites for recording MMR and FFR, making them difficult to acquire simultaneously

New method

Using a new paradigm, our study aims to concurrently capture both signals and test them against the following criteria: (1) replicating the effect that the MMR to a native speech contrast significantly differs from the MMR to a nonnative speech contrast, and (2) demonstrating that FFRs to three speech sounds can be reliably differentiated.

Results

Using EEG from 18 adults, we observed a decoding accuracy of 72.2 % between the MMR to native vs. nonnative speech contrasts. A significantly larger native MMR was shown in the expected time window. Similarly, a significant decoding accuracy of 79.6 % was found for FFR. A high stimulus-to-response cross-correlation with a 9 ms lag suggested that FFR closely tracks speech sounds.

Comparison with existing method(s)

These findings demonstrate that our paradigm reliably captures both MMR and FFR concurrently, replicating and extending past research with much fewer trials (MMR: 50 trials; FFR: 200 trials) and shorter experiment time (12 minutes).

Conclusions

This study paves the way to understanding cortical-subcortical interactions for speech and language processing, with the ultimate goal of developing an assessment tool specific to early development.

Background:

There is growing interest in understanding the dynamic functional connectivity (DFC) between distributed brain regions. However, it remains challenging to reliably estimate the temporal dynamics from resting-state functional magnetic resonance imaging (rs-fMRI) due to the limitations of current methods.

New methods:

We propose a new model called HDP-HSMM-BPCA for sparse DFC analysis of high-dimensional rs-fMRI data, which is a temporal extension of probabilistic principal component analysis using Bayesian nonparametric hidden semi-Markov model (HSMM). Specifically, we utilize a hierarchical Dirichlet process (HDP) prior to remove the parametric assumption of the HMM framework, overcoming the limitations of the standard HMM. An attractive superiority is its ability to automatically infer the state-specific latent space dimensionality within the Bayesian formulation.

Results:

The experiment results of synthetic data show that our model outperforms the competitive models with relatively higher estimation accuracy. In addition, the proposed framework is applied to real rs-fMRI data to explore sparse DFC patterns. The findings indicate that there is a time-varying underlying structure and sparse DFC patterns in high-dimensional rs-fMRI data.

Comparison with existing methods:

Compared with the existing DFC approaches based on HMM, our method overcomes the limitations of standard HMM. The observation model of HDP-HSMM-BPCA can discover the underlying temporal structure of rs-fMRI data. Furthermore, the relevant sparse DFC construction algorithm provides a scheme for estimating sparse DFC.

Conclusion:

We describe a new computational framework for sparse DFC analysis to discover the underlying temporal structure of rs-fMRI data, which will facilitate the study of brain functional connectivity.

Background:

Emotion is an important area in neuroscience. Cross-subject emotion recognition based on electroencephalogram (EEG) data is challenging due to physiological differences between subjects. Domain gap, which refers to the different distributions of EEG data at different subjects, has attracted great attention for cross-subject emotion recognition.

Comparison with existing methods:

This study focuses on narrowing the domain gap between subjects through the emotional frequency bands and the relationship information between EEG channels. Emotional frequency band features represent the energy distribution of EEG data in different frequency ranges, while relationship information between EEG channels provides spatial distribution information about EEG data.

New method:

To achieve this, this paper proposes a model called the Frequency Band Attention Graph convolutional Adversarial neural Network (FBAGAN). This model includes three components: a feature extractor, a classifier, and a discriminator. The feature extractor consists of a layer with a frequency band attention mechanism and a graph convolutional neural network. The mechanism effectively extracts frequency band information by assigning weights and Graph Convolutional Networks can extract relationship information between EEG channels by modeling the graph structure. The discriminator then helps minimize the gap in the frequency information and relationship information between the source and target domains, improving the model’s ability to generalize.

Results:

The FBAGAN model is extensively tested on the SEED, SEED-IV, and DEAP datasets. The accuracy and standard deviation scores are 88.17% and 4.88, respectively, on the SEED dataset, and 77.35% and 3.72 on the SEED-IV dataset. On the DEAP dataset, the model achieves 69.64% for Arousal and 65.18% for Valence. These results outperform most existing models.

Conclusions:

The experiments indicate that FBAGAN effectively addresses the challenges of transferring EEG channel domain and frequency band domain, leading to improved performance.

Background

Image reconstruction is a critical task in brain decoding research, primarily utilizing functional magnetic resonance imaging (fMRI) data. However, due to challenges such as limited samples in fMRI data, the quality of reconstruction results often remains poor.

New method

We proposed a three-stage multi-level deep fusion model (TS-ML-DFM). The model employed a three-stage training process, encompassing components such as image encoders, generators, discriminators, and fMRI encoders. In this method, we incorporated distinct supplementary features derived separately from depth images and original images. Additionally, the method integrated several components, including a random shift module, dual attention module, and multi-level feature fusion module.

Results

In both qualitative and quantitative comparisons on the Horikawa17 and VanGerven10 datasets, our method exhibited excellent performance.

Comparison with existing methods: For example, on the primary Horikawa17 dataset, our method was compared with other leading methods based on metrics the average hash value, histogram similarity, mutual information, structural similarity accuracy, AlexNet(2), AlexNet(5), and pairwise human perceptual similarity accuracy. Compared to the second-ranked results in each metric, the proposed method achieved improvements of 0.99 %, 3.62 %, 3.73 %, 2.45 %, 3.51 %, 0.62 %, and 1.03 %, respectively. In terms of the SwAV top-level semantic metric, a substantial improvement of 10.53 % was achieved compared to the second-ranked result in the pixel-level reconstruction methods.

Conclusions

The TS-ML-DFM method proposed in this study, when applied to decoding brain visual patterns using fMRI data, has outperformed previous algorithms, thereby facilitating further advancements in research within this field.

Background

Reaching and grasping (R&G) in rats is commonly used as an outcome measure to investigate the effectiveness of rehabilitation or treatment strategies to recover forelimb function post spinal cord injury. Kinematic analysis has been limited to the wrist and digit movements. Kinematic profiles of the more proximal body segments that play an equally crucial role in successfully executing the task remain unexplored. Additionally, understanding of different forelimb muscle activity, their interactions, and their correlation with the kinematics of R&G movement is scarce.

New method

In this work, novel methodologies to comprehensively assess and quantify the 3D kinematics of the proximal and distal forelimb joints along with associated muscle activity during R&G movements in adult rats are developed and discussed.

Results

Our data show that different phases of R&G identified using the novel kinematic and EMG-based approach correlate with the well-established descriptors of R&G stages derived from the Whishaw scoring system. Additionally, the developed methodology allows describing the temporal activity of individual muscles and associated mechanical and physiological properties during different phases of the motor task.

Comparison with existing method(s)

R&G phases and their sub-components are identified and quantified using the developed kinematic and EMG-based approach. Importantly, the identified R&G phases closely match the well-established qualitative descriptors of the R&G task proposed by Whishaw and colleagues.

Conclusions

The present work provides an in-depth objective analysis of kinematics and EMG activity of R&G behavior, paving the way to a standardized approach to assessing this critical rodent motor function in future studies.

Background

The development of Raspberry Pi-based recording devices for video analyses of drug self-administration studies has been shown to be promising in terms of affordability, customizability, and capacity to extract in-depth behavioral patterns. Yet, most video recording systems are limited to a few cameras making them incompatible with large-scale studies.

New method

We expanded the PiRATeMC (Pi-based Remote Acquisition Technology for Motion Capture) recording system by increasing its scale, modifying its code, and adding equipment to accommodate large-scale video acquisition, accompanied by data on throughput capabilities, video fidelity, synchronicity of devices, and comparisons between Raspberry Pi 3B+ and 4B models.

Results

Using PiRATeMC default recording parameters resulted in minimal storage (∼350MB/h), high throughput (< ∼120 seconds/Pi), high video fidelity, and synchronicity within ∼0.02 seconds, affording the ability to simultaneously record 60 animals in individual self-administration chambers for various session lengths at a fraction of commercial costs. No consequential differences were found between Raspberry Pi models.

Comparison with existing method(s)

This system allows greater acquisition of video data simultaneously than other video recording systems by an order of magnitude with less storage needs and lower costs. Additionally, we report in-depth quantitative assessments of throughput, fidelity, and synchronicity, displaying real-time system capabilities.

Conclusions

The system presented is able to be fully installed in a month’s time by a single technician and provides a scalable, low cost, and quality-assured procedure with a high-degree of customization and synchronicity between recording devices, capable of recording a large number of subjects and timeframes with high turnover in a variety of species and settings.

Background

Stereotaxic surgery is a cornerstone in brain research for the precise positioning of electrodes and probes, but its application is limited to species with available brain atlases and tailored stereotaxic frames. Addressing this limitation, we introduce an alternative technique for small animal brain surgery that requires neither an aligned brain atlas nor a stereotaxic frame.

New method

The new method requires an ex-vivo high-contrast MRI brain scan of one specimen and access to a micro-CT scanner. The process involves attaching miniature markers to the skull, followed by CT scanning of the head. Subsequently, MRI and CT images are co-registered using standard image processing software and the targets for brain recordings are marked in the MRI image. During surgery, the animal's head is stabilized in any convenient orientation, and the probe’s 3D position and angle are tracked using a multi-camera system. We have developed a software that utilizes the on-skull markers as fiducial points to align the CT/MRI 3D model with the surgical positioning system, and in turn instructs the surgeon how to move the probe to reach the targets within the brain.

Results

Our technique allows the execution of insertion tracks connecting two points in the brain. We successfully applied this method for neuropixels probe positioning in owls, quails, and mice, demonstrating its versatility.

Comparison with existing methods

We present an alternative to traditional stereotaxic brain surgeries that does not require established stereotaxic tools. Thus, this method is especially of advantage for research in non-standard and novel animal models.

Background

The segmentation of cells and neurites in microscopy images of neuronal networks provides valuable quantitative information about neuron growth and neuronal differentiation, including the number of cells, neurites, neurite length and neurite orientation. This information is essential for assessing the development of neuronal networks in response to extracellular stimuli, which is useful for studying neuronal structures, for example, the study of neurodegenerative diseases and pharmaceuticals.

New method

We have developed NeuroQuantify, an open-source software that uses deep learning to efficiently and quickly segment cells and neurites in phase contrast microscopy images.

Results

NeuroQuantify offers several key features: (i) automatic detection of cells and neurites; (ii) post-processing of the images for the quantitative neurite length measurement based on segmentation of phase contrast microscopy images, and (iii) identification of neurite orientations.

Comparison with existing methods

NeuroQuantify overcomes some of the limitations of existing methods in the automatic and accurate analysis of neuronal structures. It has been developed for phase contrast images rather than fluorescence images. In addition to typical functionality of cell counting, NeuroQuantify also detects and counts neurites, measures the neurite lengths, and produces the neurite orientation distribution.

Conclusions

We offer a valuable tool to assess network development rapidly and effectively. The user-friendly NeuroQuantify software can be installed and freely downloaded from GitHub at https://github.com/StanleyZ0528/neural-image-segmentation.

Background

Delivering optogenetic genes to the peripheral sensory nervous system provides an efficient approach to study and treat neurological disorders and offers the potential to reintroduce sensory feedback to prostheses users and those who have incurred other neuropathies. Adeno-associated viral (AAV) vectors are a common method of gene delivery due to efficiency of gene transfer and minimal toxicity. AAVs are capable of being designed to target specific tissues, with transduction efficacy determined through the combination of serotype and genetic promoter selection, as well as location of vector administration. The dorsal root ganglia (DRGs) are collections of cell bodies of sensory neurons which project from the periphery to the central nervous system (CNS). The anatomical make-up of DRGs make them an ideal injection location to target the somatosensory neurons in the peripheral nervous system (PNS).

Comparison to existing methods

Previous studies have detailed methods of direct DRG injection in rats and dorsal horn injection in mice, however, due to the size and anatomical differences between rats and strains of mice, there is only one other published method for AAV injection into murine DRGs for transduction of peripheral sensory neurons using a different methodology.

New Method/Results

Here, we detail the necessary materials and methods required to inject AAVs into the L3 and L4 DRGs of mice, as well as how to harvest the sciatic nerve and L3/L4 DRGs for analysis. This methodology results in optogenetic expression in both the L3/L4 DRGs and sciatic nerve and can be adapted to inject any DRG.