Journal of Neuroscience Methods

Brain disorders, encompassing a wide spectrum of neurological and psychiatric conditions, present a formidable challenge in modern medicine. Despite decades of research, the intricate complexity of the human brain still eludes comprehensive understanding, impeding the development of effective treatments. Recent advancements in microfluidics and tissue engineering have led to the development of innovative platforms known as "Brain-on-a-Chip" (BoC) i.e., advanced in vitro systems that aim to replicate the microenvironment of the brain with the highest possible fidelity...

BACKGROUND: Motor-Imagery-based Brain-Computer Interface (MI-BCI) is a promising technology to assist communication, movement, and neurological rehabilitation for motor-impaired individuals. Electroencephalography (EEG) decoding techniques using deep learning (DL) possess noteworthy advantages due to automatic feature extraction and end-to-end learning. However, the DL-based EEG decoding models tend to show large variations due to intersubject variability of EEG, which results from inconsistencies of different subjects' optimal hyperparameters...

BACKGROUND: Single-pulse electrical stimulation (SPES) is an established technique used to map functional effective connectivity networks in treatment-refractory epilepsy patients undergoing intracranial-electroencephalography monitoring. While the connectivity path between stimulation and recording sites has been explored through the integration of structural connectivity, there are substantial gaps, such that new modeling approaches may advance our understanding of connectivity derived from SPES studies...

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BACKGROUND: Preclinical models are essential for identifying changes occurring after neurologic injury and assessing therapeutic interventions. Yucatan miniature pigs (minipigs) have brain and spinal cord dimensions like humans and are useful for laboratory-to-clinic studies. Yet, little work has been done to map spinal sensorimotor distributions and identify similarities and differences between the porcine and human spinal cords. NEW METHODS: To characterize efferent and afferent signaling, we implanted a conventional 32-contact, four-column array into the dorsal epidural space over the lumbosacral spinal cord, spanning the L5-L6 vertebrae, in two Yucatan minipigs...

BACKGROUND: In this study, we examined the utility of simultaneous scalp and stereotactic intracranial electroencephalography (SSIEEG) in epilepsy patients. Although SSIEEG offers valuable insights into epilepsy and cognitive function, its routine use is uncommon. Challenges include interpreting post-craniotomy scalp EEG due to surgically implanted electrodes. NEW METHOD: We describe our methodology for conducting SSIEEG recordings. To simulate the potential impact on EEG interpretation, we computed the leadfield of scalp electrodes with and without burrholes using Finite Element Analysis to compare the resulting sensitivity volume and waveforms of simulated intracranial signals between skulls with and without burrholes...

Cell reprogramming holds enormous potential to revolutionize our understanding of neurological and neurodevelopmental disorders, as well as enhance drug discovery and regenerative medicine. We have developed a direct cell reprogramming technology that allows us to generate lineage-specific neural cells. To extend our technology, we have investigated the incorporation of directly reprogrammed human lateral ganglionic eminence precursor cells (hiLGEPs) in a 3-dimensional (3D) matrix. Hydrogels are one of the most promising bio-scaffolds for 3D cell culture, providing cells with a supportive environment to adhere, proliferate, and differentiate...

BACKGROUND: In the realm of neuro-disorders, precise diagnosis and treatment rely heavily on objective imaging-based biomarker identification. This study employs a sparsity approach on resting-state fMRI to discern relevant brain region connectivity for predicting Autism. NEW METHOD: The proposed methodology involves four key steps: (1) Utilizing three probabilistic brain atlases to extract functionally homogeneous brain regions from fMRI data. (2) Employing a hybrid approach of Graphical Lasso and Akaike Information Criteria to optimize sparse inverse covariance matrices for representing the brain functional connectivity...

BACKGROUND: Brainstem mapping with electrical stimulation allows functional identification of neural structures during resection of deep lesions. Single pulses or train of pulses are delivered to map cranial nerves and corticospinal tracts, respectively. NEW METHOD: We introduce a hybrid stimulation technique for mapping the brainstem. The stimulus consists of an electrical single pulse followed by a short train of 3-5 pulses at 500Hz, at an interval of 50-75 ms...

BACKGROUND: Cortico-muscular coherence (CMC) between the cerebral cortex and muscle activity is an effective tool for studying neural communication in the motor control system. To accurately evaluate the coherence between electroencephalogram (EEG) and electromyogram (EMG) signals, it is necessary to accurately calculate the time delay between physiological signals to ensure signal synchronization. NEW METHOD: We proposed a new delay estimation method, named wavelet coherence time lag (WCTL) and the significant increase areas (SIA) index as a measure of the specific region enhancement effect of the magnitude squared coherence (MSC) image...

BACKGROUND: Escape is one of the most essential behaviors for an animal's survival because it could be a matter of life and death. Much of our current understanding of the neural mechanisms underlying escape is derived from the looming paradigm, which mimics a diving aerial predator. Yet, the idea of the looming paradigm does not account for all types of threats like lions hunting antelopes or cats stalking mice. Escape responses to such terrestrial threats may require different strategies and neural mechanisms...

BACKGROUND: Two-photon calcium imaging is widely used to study the odor-evoked glomerular activity in the dorsal olfactory bulb of macrosmatic animals. The nonstationary character of activated patterns sets a limit on the use of a traditional image processing approaches. NEW METHOD: The developed method makes it possible to automatically map cancer biomarkers-activated glomeruli in the rat dorsal olfactory bulb. We interpolated fluorescence intensity of calcium dynamics based on the Gaussian RBF network and synthesized the physiological fluorescence model of the receptive glomerular field...

BACKGROUND: The retinotopic map property of the superior colliculus (SC) is a reliable indicator of visual functional changes in rodents. Electrophysiological mapping of the SC using a single electrode has been employed for measuring visual function in rat and mouse disease models. Single electrode mapping is highly laborious requiring long-term exposure to the SC surface and prolonged anesthetic conditions that can adversely affect the mapping data. NEW METHOD: To avoid the above-mentioned issues, we fabricated a fifty-six (56) electrode multi-electrode array (MEA) for rapid and reliable visual functional mapping of the SC...

The EQIPD Quality System (QS) was conseptiolized and established by an international consortium consisting of academic and industrial partners to ensure that non-regulated biomedical research will be conducted according to Good Research Practice expectations. The QS supports researchers to reflect on and improve internal practices by providing a systematic framework and guidance for implementing the EQIPD QS in a time and cost effective manner. This report describes the content of the EQIPD QS with its key features and 18 Core Requirements (CR) in more detail...

Reaching back more than a century, suspension cultures have provided major insights into processes of histogenesis; e.g., cell communication, distinction of self/nonself, cell sorting and cell adhesion. Besides studies on lower animals, the vertebrate retina served as excellent reaggregate model to analyze 3D reconstruction of a complex neural laminar tissue. Methodologically, keeping cells under suspension is essential to achieve tissue organisation in vitro; thereby, the environmental conditions direct the emergent histotypic particulars...

BACKGROUND: Immunohistochemistry (IHC) is an important technique in understanding the expression of neurochemical molecules in the developing human brain. Despite its routine application in the research and clinical setup, the IHC protocol specific for soft fragile fetal brains that are fixed using the non-perfusion method is still limited in studying the whole brain. NEW METHOD: This study shows that the IHC protocols, using a chromogenic detection system, used in animals and adult humans are not optimal in the fetal brains...

BACKGROUND: To develop a 3D tumor slice model, replicating the individual tumor microenvironment and for individual pharmaceutical testing in vestibular schwannomas with and without relation to NF2. METHODS: Tissue samples from 16 VS patients (14 sporadic, 2 NF2-related) were prospectively analyzed. Slices of 350µm thickness were cultured in vitro, and the 3D tumor slice model underwent thorough evaluation for culturing time, microenvironment characteristics, morphology, apoptosis, and proliferation rates...

BACKGROUND: Existing methods identify only ≈10 Aδ-fibers in human sensory nerves per recording. This study examines methods to increase the detection of Aδ-fibers. NEW METHOD: Two to 20 averages of 500 replicate responses to epidermal nerve stimulation are obtained. Pairs of different averages are constructed. Each pair is analyzed with algorithms applied to amplitude and frequency to detect replication of responses to stimulation as "simultaneous similarities in two averages" (SS2AVs) at ≥99...

BACKGROUND: The thalamic reuniens (Re) and rhomboid (Rh) nuclei are bidirectionally connected with the medial prefrontal cortex (mPFC) and the hippocampus (Hip). Fiber-sparing N-methyl-D-aspartate lesions of the ReRh disrupt cognitive functions, including persistence of certain memories. Because such lesions irremediably damage neurons interconnecting the ReRh with the mPFC and the Hip, it is impossible to know if one or both pathways contribute to memory persistence. Addressing such an issue requires selective, pathway-restricted and direction-specific disconnections...

BACKGROUND: Whole brain delineation (WBD) is utilized in neuroimaging analysis for data preprocessing and deriving whole brain image metrics. Current automated WBD techniques for analysis of preclinical brain MRI data show limited accuracy when images present with significant neuropathology and anatomical deformations, such as that resulting from organophosphate intoxication (OPI) and Alzheimer's Disease (AD), and inadequate generalizability. METHODS: A modified 2D U-Net framework was employed for WBD of MRI rodent brains, consisting of 27 convolutional layers, batch normalization, two dropout layers and data augmentation, after training parameter optimization...