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Journal of Neuroscience Methods

Eduard Bakštein, Tomáš Sieger, Jiří Wild, Daniel Nova'k, Jakub Schneider, Pavel Vostatek, Dušan Urgošík, Robert Jech
BACKGROUND: Extracellular microelectrode recording (MER) is a prominent technique for studies of extracellular single-unit neuronal activity. In order to achieve robust results in more complex analysis pipelines, it is necessary to have high quality input data with a low amount of artifacts. We show that noise (mainly electromagnetic interference and motion artifacts) may affect more than 25% of the recording length in a clinical MER database. NEW METHOD: We present several methods for automatic detection of noise in MER signals, based on i) unsupervised detection of stationary segments, ii) large peaks in the power spectral density, and iii) a classifier based on multiple time- and frequency-domain features...
July 20, 2017: Journal of Neuroscience Methods
Robert E Kelly, George S Alexopoulos, Faith M Gunning, Matthew J Hoptman
Griffanti et al. (in press) provide a rich set of expert-consensus guidelines for how to label components derived from ICA as either belonging to signal of interest or noise to be filtered from fMRI data. These general hypotheses concerning procedures for "hand" classification of components are a good starting point that with further detail would improve reproduction of experiments and facilitate comparisons of alternative hypotheses/procedures. Empirical validation could help to resolve questions by supporting or disconfirming the proposed guidelines...
July 19, 2017: Journal of Neuroscience Methods
Lei Wang, Xi Long, Johan B A M Arends, Ronald M Aarts
BACKGROUND: The traditional EEG features in the time and frequency domain show limited seizure detection performance in the epileptic population with intellectual disability (ID). In addition, the influence of EEG seizure patterns on detection performance was less studied. NEW METHOD: A single-channel EEG signal can be mapped into visibility graphs (VGS), including basic visibility graph (VG), horizontal VG (HVG), and difference VG (DVG). These graphs were used to characterize different EEG seizure patterns...
July 19, 2017: Journal of Neuroscience Methods
A Giovannucci, E A Pnevmatikakis, B Deverett, T Pereira, J Fondriest, M J Brady, S S-H Wang, W Abbas, P Parés, D Masip
BACKGROUND: The preparation consisting of a head-fixed mouse on a spherical or cylindrical treadmill offers unique advantages in a variety of experimental contexts. Head fixation provides the mechanical stability necessary for optical and electrophysiological recordings and stimulation. Additionally, it can be combined with virtual environments such as T-mazes, enabling these types of recording during diverse behaviors. NEW METHOD: In this paper we present a low-cost, easy-to-build acquisition system, along with scalable computational methods to quantitatively measure behavior (locomotion and paws, whiskers, and tail motion patterns) in head-fixed mice locomoting on cylindrical or spherical treadmills...
July 17, 2017: Journal of Neuroscience Methods
Julia C Basso, Joan I Morrell
BACKGROUND: Though voluntary wheel running (VWR) has been used extensively to induce changes in both behavior and biology, little attention has been given to the way in which different variables influence VWR. This lack of understanding has led to an inability to utilize this behavior to its full potential, possibly blunting its effects on the endpoints of interest. NEW METHOD: We tested how running experience, sex, gonadal hormones, and wheel apparatus influence VWR in a range of wheel access "doses"...
July 15, 2017: Journal of Neuroscience Methods
Saeed M Bakhshmand, Ali R Khan, Sandrine de Ribaupierre, Roy Eagleson
BACKGROUND: Construction of brain functional and structural networks by neuroimaging methods facilitates inter-modal studies. These type of studies often demand exploration tools to carry out functional-structural discoveries and answer questions regarding the anatomical basis of brain networks. NEW METHOD: This paper describes the design and development of a software module for interactive visualization and exploration of dual-modal brain networks. Our objective was to equip the user with a research tool to investigate brain connectivity matrices while visualizing relevant anatomical landmarks within a 3D volumetric view...
July 13, 2017: Journal of Neuroscience Methods
Raymond M Klein, Tariq Hassan, Graham Wilson, Yoko Ishigami, Jonathan Mulle
BACKGROUND: Recognizing that attention is not a unitary system, the Attention Network Test (ANT) and its variants were developed to measure the efficacy of the multiple components of attention. One potential weakness of these tests (ANTs) is that they are unengaging. This poses a problem when particular groups are tested (e.g., young children), when more stable measures of performance are desirable (and can only be achieved in longer testing sessions) and when repeated testing is necessary...
July 12, 2017: Journal of Neuroscience Methods
Annika H Runegaard, Kathrine Louise Jensen, Ditte Dencker, Gitta Wörtwein, Ulrik Gether
BACKGROUND: The potential of abused drugs to induce addiction and compulsive drug-related behavior is associated with their ability to alter dopamine signaling. Dopamine plays a key role in reward signaling and it has been of great interest to investigate how various drugs of abuse alter reward-related behavior. COMPARISON WITH EXISTING METHODS: In rodents, the rewarding effects of drugs have often been assessed in self-administration or place preference paradigms; both involving repeated drug exposure and weeks of training and testing...
July 12, 2017: Journal of Neuroscience Methods
Shailesh Appukuttan, Keith L Brain, Rohit Manchanda
BACKGROUND: Computational modeling of biological cells usually ignores their extracellular fields, assuming them to be inconsequential. Though such an assumption might be justified in certain cases, it is debatable for networks of tightly packed cells, such as in the central nervous system and the syncytial tissues of cardiac and smooth muscle. NEW METHOD: In the present work, we demonstrate a technique to couple the extracellular fields of individual cells within the NEURON simulation environment...
July 10, 2017: Journal of Neuroscience Methods
Yohei Bamba, Yonehiro Kanemura, Hideyuki Okano, Mami Yamasaki
BACKGROUND: Neuronal migration is considered a key process in human brain development. However, direct observation of migrating human cortical neurons in the fetal brain is accompanied by ethical concerns and is a major obstacle in investigating human cortical neuronal migration. NEW METHOD: We established a novel system that enables direct visualization of migrating cortical neurons generated from human induced pluripotent stem cells (hiPSCs). RESULTS: We observed the migration of cortical neurons generated from hiPSCs derived from a control and from a patient with lissencephaly...
July 8, 2017: Journal of Neuroscience Methods
Géraldine Pastor, María Jiménez-González, Sandra Plaza-García, Marta Beraza, Daniel Padro, Pedro Ramos-Cabrer, Torsten Reese
BACKGROUND: Differences in the cerebro-vasculature among strains as well as individual animals might explain variability in animal models and thus, a non-invasive method tailored to image cerebral vessel of interest with high signal to noise ratio is required. NEW METHOD: Experimentally, we describe a new general protocol of three-dimensional time-of-flight magnetic resonance angiography to visualize non-invasively the cerebral vasculature in 6 different rat strains...
July 8, 2017: Journal of Neuroscience Methods
Elsa Siggiridou, Vasilios K Kimiskidis, Dimitris Kugiumtzis
BACKGROUND: The mainstream in the estimation of effective brain connectivity relies on Granger causality measures in the frequency domain. If the measure is meant to capture direct causal effects accounting for the presence of other observed variables, as in multi-channel electroencephalograms (EEG), typically the fit of a vector autoregressive (VAR) model on the multivariate time series is required. For short time series of many variables, the estimation of VAR may not be stable requiring dimension reduction resulting in restricted or sparse VAR models...
July 4, 2017: Journal of Neuroscience Methods
Zhifeng Liang, Yuncong Ma, Glenn D R Watson, Nanyin Zhang
BACKGROUND: Understanding the relationship between neural and vascular signals is essential for interpretation of functional MRI (fMRI) results with respect to underlying neuronal activity. Simultaneously measuring neural activity using electrophysiology with fMRI has been highly valuable in elucidating the neural basis of the blood oxygenation-level dependent (BOLD) signal. However, this approach is also technically challenging due to the electromagnetic interference that is observed in electrophysiological recordings during MRI scanning...
July 4, 2017: Journal of Neuroscience Methods
Andrew R Mitz, Ramon Bartolo, Richard C Saunders, Philip G Browning, Thomas Talbot, Bruno B Averbeck
BACKGROUND: Single unit recording in behaving nonhuman primates is widely used to study the primate central nervous system. However, certain questions cannot be addressed without recording large numbers of neurons simultaneously. Multiple 96-electrode probes can be implanted at one time, but certain problems must be overcome to make this approach practical. NEW METHOD: We describe a series of innovations and practical guidance for implanting and recording from 8 arrays of 96 electrodes (768 electrodes) in the frontal cortex of Macaca mulatta...
July 4, 2017: Journal of Neuroscience Methods
Wen-Tung Wang, Benjamin Xu, John A Butman
BACKGROUND: Transcranial magnetic stimulation (TMS) is a noninvasive brain stimulation tool extensively used in clinical and cognitive neuroscience research. TMS has been applied during functional magnetic resonance imaging (i.e., concurrent/interleaved TMS-fMRI) to understand neural mechanisms underlying cognitive functions. However, no advanced commercial multi-channel whole-brain array MR coils can fit the large TMS coil. We developed a low-cost and easy-to-configure setup that takes advantage of the superior signal-to-noise ratio (SNR) performance of commercially available flexible body array coils that can accommodate the TMS coil...
June 30, 2017: Journal of Neuroscience Methods
Simone Gross, Ninja Kolb, Marco Rosati, Kaspar Matiasek
BACKGROUND: Immunohistochemical staining of entire nerve fibres allows for studying the molecular composition of functional fibre subunits and may add to the diagnostic value of nerve fibre teasing. NEW METHOD: In this study, we established a sealed-slide method for reproducible immunostaining of deep axoplasmic proteins in permanently straightened nerve fibres. RESULTS: Immunostaining of teased nerve fibres very much is facilitated by tip-fixation with biocompatible glass adhesives...
June 28, 2017: Journal of Neuroscience Methods
Matthew H Higgs, Charles J Wilson
BACKGROUND: The phase resetting curve (PRC) is a primary measure of a rhythmically firing neuron's responses to synaptic input, quantifying the change in phase of the firing oscillation as a function of the input phase. PRCs provide information about whether neurons will synchronize due to synaptic coupling or shared input. However, PRC estimation has been limited to in vitro preparations where stable intracellular recordings can be obtained and background activity is minimal, and new methods are required for in vivo applications...
June 28, 2017: Journal of Neuroscience Methods
Ankit Parekh, Ivan W Selesnick, Ricardo S Osorio, Andrew W Varga, David M Rapoport, Indu Ayappa
BACKGROUND: Automated single-channel spindle detectors, for human sleep EEG, are blind to the presence of spindles in other recorded channels unlike visual annotation by a human expert. NEW METHOD: We propose a multichannel spindle detection method that aims to detect global and local spindle activity in human sleep EEG. Using a non-linear signal model, which assumes the input EEG to be the sum of a transient and an oscillatory component, we propose a multichannel transient separation algorithm...
June 25, 2017: Journal of Neuroscience Methods
Kevin Q Shan, Evgueniy V Lubenov, Athanassios G Siapas
BACKGROUND: Chronic extracellular recordings are a powerful tool for systems neuroscience, but spike sorting remains a challenge. A common approach is to fit a generative model, such as a mixture of Gaussians, to the observed spike data. Even if non-parametric methods are used for spike sorting, such generative models provide a quantitative measure of unit isolation quality, which is crucial for subsequent interpretation of the sorted spike trains. NEW METHOD: We present a spike sorting strategy that models the data as a mixture of drifting t-distributions...
June 23, 2017: Journal of Neuroscience Methods
Stephan Meesters, Pauly Ossenblok, Louis Wagner, Olaf Schijns, Paul Boon, Luc Florack, Anna Vilanova, Remco Duits
BACKGROUND: An accurate delineation of the optic radiation (OR) using diffusion MR tractography may reduce the risk of a visual field deficit after temporal lobe resection. However, tractography is prone to generate spurious streamlines, which deviate strongly from neighboring streamlines and hinder a reliable distance measurement between the temporal pole and the Meyer's loop (ML-TP distance). NEW METHOD: Stability metrics are introduced for the automated removal of spurious streamlines near the Meyer's loop...
June 23, 2017: Journal of Neuroscience Methods
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