PubMed Journal Database | Journal of neuroscience methods 
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Showing PubMed Articles 1–25 of 354 from Journal of neuroscience methods
Next generation neural interfaces aspire to achieve real-time multi-channel systems by integrating spike sorting on chip to overcome limitations in communication channel capacity. The feasibility of this approach relies on developing highly efficient algorithms for feature extraction and clustering with the potential of low-power hardware implementation. We are proposing a feature extraction method, not requiring any calibration, based on first and second derivative features of the spike waveform. The accur...
New disposable forehead electrode set with excellent signal quality and imaging compatibility.
The use of emergency electroencephalography (EEG) in clinical practice is limited in part due to the lack of commercially available EEG monitoring sets that are suitable for rapid and simple use. The aim of this study was to develop a rapid and simple-to-use disposable forehead EEG electrode set for routine use that is also suitable for long-term monitoring. The EEG set we developed consists of 12 hydrogel-coated electrodes (10 recording electrodes, plus a reference and ground electrode) attached to a solid...
An FPGA-based platform for accelerated offline spike sorting.
There is a push in electrophysiology experiments to record simultaneously from many channels (upwards of 64) over long time periods (many hours). Given the relatively high sampling rates (10-40kHz) and resolutions (12-24bits per sample), these experiments accumulate exorbitantly large amounts of data (e.g. 100GB per experiment), which can be very time-consuming to process. Here, we present an FPGA-based spike-sorting platform that can increase the speed of offline spike sorting by at least 25 times, effecti...
Intravital microscopy such as in vivo imaging of brain dynamics is often performed with custom-built microscope setups controlled by custom-written software to meet specific requirements. Continuous technological advancement in the field has created a need for new control software that is flexible enough to support the biological researcher with innovative imaging techniques and provide the developer with a solid platform for quickly and easily implementing new extensions. Here, we introduce HelioScan, a so...
Three-dimensional (3D) relationships between head muscles and cranial nerves innervating them are complicated. Existing sources present these relationships in illustrations, radiologic scans, or autopsy photographs, which are limited for learning and use. Developed electronic atlases are limited in content, quality, functionality, and/or presentation. We create a truly 3D interactive, stereotactic and high quality atlas, which provides spatial relationships among head muscles, glands and cranial nerves, and...
Research into therapeutics for neuropsychiatric disorders is increasingly focusing on drugs with new mechanisms of action, and such agents are often assessed in preclinical studies using nonhuman primates. However, researchers lack a standardised method to compare different drugs for common adverse effects on the nervous system. We have developed a new scale for this purpose, named "Drug Effects on the Nervous System" (DENS), and tested its utility in an analysis of the second-generation antipsychotic rispe...
Multivariate temporal dictionary learning for EEG.
This article addresses the issue of representing electroencephalographic (EEG) signals in an efficient way. While classical approaches use a fixed Gabor dictionary to analyze EEG signals, this article proposes a data-driven method to obtain an adapted dictionary. To reach an efficient dictionary learning, appropriate spatial and temporal modeling is required. Inter-channels links are taken into account in the spatial multivariate model, and shift-invariance is used for the temporal model. Multivariate learn...
A dual compartment diffusion chamber for studying axonal chemotaxis in 3D collagen.
During nervous system development growing axons are often guided by diffusible chemical gradients. An important contribution to our understanding of the mechanisms involved in this process has been made by in vitro assays. However, an inexpensive and simple assay which allows the establishment of stable and reproducible gradients in a 3D collagen environment has been lacking. Here we present a simple two-compartment diffusion chamber for this purpose. We show that gradient steepnesses of up to 2% are achiev...
Cell-therapy was proposed to be a promising tool in case of death or impairment of specific cell types. Correct identification of implanted cells became crucial when evaluating the success of transplantation therapy. Various methods of cell labeling have been employed in previously published studies. The use of intrinsic signaling of green fluorescent protein (GFP) has led to a well known controversy in the field of cardiovascular research. We encountered similar methodological pitfalls after transplantatio...
Diagnosing synaesthesia with online colour pickers: Maximising sensitivity and specificity.
The most commonly used method for formally assessing grapheme-colour synaesthesia (i.e., experiencing colours in response to letter and/or number stimuli) involves selecting colours from a large colour palette on several occasions and measuring consistency of the colours selected. However, the ability to diagnose synaesthesia using this method depends on several factors that have not been directly contrasted. These include the type of colour space used (e.g., RGB, HSV, CIELUV, CIELAB) and different measures...
Implantable microelectrodes provide a measure to electrically stimulate neurons in the brain and spinal cord and record their electrophysiological activity. A material with a high charge capacity such as activated or sputter-deposited iridium oxide film (AIROF or SIROF) is used as an interface. The Utah electrode array (UEA) uses SIROF for its interface material with neural tissue and oxygen plasma etching (OPE) with an aluminium foil mask to expose the active area, where the interface between the electrode...
Structural and quantitative neuroimaging of the common marmoset monkey using a clinical MRI system.
Purpose was to adapt structural and quantitative magnetic resonance imaging (MRI) from humans to common marmoset monkeys on a clinical 3T scanner and to demonstrate the value for translational research. Three-dimensional T1- and T2-weighted MRI and gradient echo-based multi-parameter mapping was performed on nine adult animals using a wrist coil. Structural MRI was applied in a model of targeted experimental autoimmune encephalomyelitis (EAE). Magnetization transfer (MT) and T1 parameter maps were used to d...
Microwave processing of gustatory tissues for immunohistochemistry.
We use immunohistochemistry to study taste cell structure and function as a means to elucidate how taste receptor cells communicate with nerve fibers and adjacent taste cells. This conventional method, however, is time consuming. In the present study we used taste buds from rat circumvallate papillae to compare conventional immunohistochemical tissue processing with microwave processing for the colocalization of several biochemical pathway markers (PLCβ2, syntaxin-1, IP3R3, α-gustducin) and the nuclear st...
Applications such as 3D cultures and tissue modelling require cell tracking with non-invasive methods. In this work, the suitability of two fluorescent probes, CellTracker, CT, and long chain carbocyanine dye, DiD, was investigated for long-term culturing of labeled human pluripotent stem cell-derived neural cells. We found that these dyes did not affect the cell viability. However, proliferation was decreased in DiD labeled cell population. With both dyes the labeling was stable up to 4 weeks. CT and DiD l...
Brain activity often consists of interactions between internal-or on-going-and external-or sensory-activity streams, resulting in complex, distributed patterns of neural activity. Investigation of such interactions could benefit from closed-loop experimental protocols in which one stream can be controlled depending on the state of the other. We describe here methods to present rapid and precisely timed visual stimuli to awake animals, conditional on features of the animal's on-going brain state; those featu...
Amperometric sensors for oxygen and glucose allow for real time recording from the brain in freely-moving animals. These sensors have been used to detect activity- and drug-induced changes in metabolism in a number of brain regions but little attention has been given over to the hippocampus despite its importance in cognition and disease. Sensors for oxygen and glucose were co-implanted into the hippocampus and allowed to record for several days. Baseline recordings show that basal concentrations of hippoca...
Gaussian Mixture Model-based noise reduction in resting state fMRI data.
Neuroimaging the default mode network (DMN) in resting state has been of significant interest for investigating pathological conditions as resting state data are less affected by the variability in the subject's performance and movement-related artefacts in the electromagnetic field which are often issues in event-related activation experiments. An issue to be considered with resting state data is the very low amplitude of the activation patterns which are not induced by any stimulation or stimulus paradigm...
In this study, we demonstrate capabilities to selectively manipulate dissociated co-cultures of neurons plated in dual-compartment devices. Synaptic receptor antagonists and tetrodotoxin solutions were used to selectively control and study the network-wide burst propagation and cell firing in cortical-cortical and cortical-thalamic co-culture systems. The results show that in cortical-thalamic dissociated co-cultures, burst events initiate in the cortical region and propagate to the thalamic region and the...
Compensation for the intrinsic dynamics of the InMotion2 robot.
The InMotion2 and other similarly designed robots, are commonly used for rehabilitation of neurological injuries and motor adaptation studies. These robots are used to simulate haptic environments; however, anisotropy in end-point impedance due to the intrinsic robot dynamics can compromise these experiments. The goal was to decrease the magnitude and anisotropy of the robot impedance using a dynamic compensation algorithm that reduces the forces normally felt by the user during rapid movements. We tested t...
Delayed repair of the peripheral nerve: A novel model in the rat sciatic nerve.
Peripheral nerve reconstruction is seldom done in the acute phase of nerve injury due to concomitant injuries and the uncertainty of the extent of nerve damage. A proper model that mimics true clinical scenarios is critical but lacking. The aim of this study is to develop a standardized, delayed sciatic nerve repair model in rats and validate the feasibility of direct secondary neurrorraphy after various delay intervals. Immediately or 1, 4, 6, 8 and 12 weeks after sciatic nerve transection, nerve repair wa...
Simple generation of neurons from human embryonic stem cells using agarose multiwell dishes.
Human embryonic stem cells (hESC) are potentially an unlimited source of neurons for study and therapy for human disease. Directed differentiation of hESC has been performed using many different methods, often via neural precursor intermediates generated from aggregates of hESC. We describe here a protocol based on commercially available reusable silicone micromolds and two small molecule growth factor inhibitors to simply and reproducibly generate human neurons from hESC. Hundreds of neurospheres were gene...
Intravenous recording of intracranial, broadband EEG.
The most direct evaluation of human brain activity has been obtained from intracranial electrodes placed either on the surface of the brain or inserted into the brain to record from deep brain structures. Currently, the placement of intracranial electrodes implies transcranial surgery, either through a burr hole or a craniotomy, but the high degree of invasiveness and potential for morbidity of such major surgical procedures limits the applicability of intracranial recording. The vascular system provides a...
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson's disease. LRRK2 kinase activity is required for toxicity in neuronal cell cultures suggesting that selective kinase inhibitors may prevent neurodegeneration in patients. Directly monitoring LRRK2 activity in cells would be advantageous for the development of small molecule LRRK2 inhibitors. Here, we demonstrate that a monoclonal anti-LRRK2 antibody directed against the activation segment binds less efficiently...
FRET excited ratiometric oxygen sensing in living tissue.
Dynamic analysis of oxygen (O(2)) has been limited by the lack of a real-time, quantitative, and biocompatible sensor. To address these demands, we designed a ratiometric optode matrix consisting of the phosphorescence quenching dye platinum (II) octaethylporphine ketone (PtOEPK) and nanocystal quantum dots (NQDs), which when embedded within an inert polymer matrix allows long-term pre-designed excitation through fluorescence resonance energy transfer (FRET). Depositing this matrix on various glass substrat...
Quantifying changes following spinal cord injury with velocity dependent locomotor measures.
Many locomotor measures commonly used to assess functional deficits following neurological injury are velocity dependent. This makes the comparison of faster pre-injury walking to slower post-injury walking a challenging process. In lieu of calculating mean values at specific velocities, we have employed the use of nonlinear regression techniques to quantify locomotor measures across all velocities. This enables us to assess more accurately the locomotor recovery of rats after a cervical spinal cord injury....
