Blind fMRI Source Unmixing via Higher-Order Tensor Decompositions
ConclusionsThe simulation results demonstrate the effectiveness of BTD and BTD2 for challenging scenarios (presence of noise, spatial overlap among activation regions and inter-subject variability in the Haemodynamic Response Function (HRF)). (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - December 14, 2018 Category: Neuroscience Source Type: research

Ground truth construction and parameter tuning for the detection of sleep spindle timing in rodents
ConclusionsWe present a general ground truth based approach for the tuning and validation of spindle extraction algorithms and suggest that algorithms aimed at extracting precise spindle timing in rats should use a systematic approach for parameter tuning. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - December 8, 2018 Category: Neuroscience Source Type: research

Selective Middle Cerebral Artery Occlusion In The Rabbit: Technique And Characterization With Pathologic Findings and Multimodal MRI
ConclusionsWe demonstrate the feasibility of a rabbit model of embolic MCA occlusion with angiographic documentation. Serial MR imaging demonstrated changes comparable to those observed in human ischemic stroke, confirmed histopathologically. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - December 8, 2018 Category: Neuroscience Source Type: research

Characterization of Neurite Dystrophy After Trauma by High Speed Structured Illumination Microscopy and Lattice Light Sheet Microscopy
ConclusionsThese methods can be used to investigate genetic factors and therapeutic interventions that modulate the course of neurite dystrophy after trauma. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - December 7, 2018 Category: Neuroscience Source Type: research

A Robust and Subject-Specific Sequential Forward Search Method for Effective Channel Selection In Brain Computer Interfaces
ConclusionsFeatures extracted by Hilbert transform and sum derivative methods were effectively classified by support vector machine. In conclusion, the results obtained proved that the RSS-SFSM shows great potential for determining effective channel(s). (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - December 7, 2018 Category: Neuroscience Source Type: research

A deep learning based method for large-scale classification, registration, and clustering of in-situ hybridization experiments in the mouse olfactory bulb
ConclusionThe atlas we have complied allows for intra- and inter-laminar comparisons of gene expression patterns in the OB across thousands of genes, as well identification of canonical expression profiles through clustering. We anticipate that this will be a useful resource for investigators studying the bulb’s development and functional topography. Our methods are publicly available for those interested in extending them to other brain areas. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - December 6, 2018 Category: Neuroscience Source Type: research

A new automated device for quantifying mechanical nociceptive responses
ConclusionsThis study demonstrates a new automated, temporally specific method for quantifying nociceptive responses to facilitate rodent pain studies. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - December 4, 2018 Category: Neuroscience Source Type: research

MRI Guidance Technology Development in a Large Animal Model for Hyperlocal Analgesics Delivery to the Epidural Space and Dorsal Root Ganglion
This study provides methods for MRI-guided drug delivery to the periganglionic epidural space and the dorsal root ganglion (DRG) in the Yucatan swine.ResultsPhantom studies showed artifact-corrected needle localization with frequency encoding parallel to the needle shaft, while maximizing bandwidth (125 KHz) minimized needle artifact. A custom constructed 8-12 element surface coil (phased array) wrapped over the spine in conjunction with lateral recumbent positioning achieved diagnostic quality signal to noise ratio at the depth of the DRG and afforded transforaminal access via anterolateral or posterolateral vectors, as w...
Source: Journal of Neuroscience Methods - December 2, 2018 Category: Neuroscience Source Type: research

An automated behavioral apparatus to combine parameterized reaching and grasping movements in 3D space
ConclusionsThe apparatus provides a valuable platform to study upper limb functions in behavioral and neurophysiological studies, and may facilitate simultaneous reconstruction of reaching and grasping movements in brain-machine interfaces (BMIs). (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 29, 2018 Category: Neuroscience Source Type: research

Total Spiking Probability Edges: A Cross-Correlation based Method for Effective Connectivity Estimation of Cortical Spiking Neurons
ConclusionsThe results show that the accuracy of functional connectivity estimation of large scale neuronal networks has been enhanced by TSPE compared to state of the art methods. Furthermore, TSPE enables the classification of excitatory and inhibitory synaptic effects. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 28, 2018 Category: Neuroscience Source Type: research

Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons
ConclusionsThese results demonstrate the modification and isolation of functional SVs using cultured neurons and viral transduction. The ability to readily obtain SVs from genetically engineered neurons will permit linking in situ studies to in vitro experiments in a variety of genetic contexts. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 27, 2018 Category: Neuroscience Source Type: research

Bayesian multi-dipole modelling in the frequency domain
ConclusionsThe Bayesian method described in this paper represents a reliable approach for localization of multiple dipoles in the frequency domain.Graphical abstract (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 25, 2018 Category: Neuroscience Source Type: research

Low Ca2+ levels in the culture media support the heterologous expression of insect odorant receptor proteins in HEK cells
Conclusionsreducing the extracellular Ca2+ level of HEK293 cell culture media after transfection increases the success of functional insect OR expression. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 24, 2018 Category: Neuroscience Source Type: research

Editorial Board
Publication date: 1 January 2019Source: Journal of Neuroscience Methods, Volume 311Author(s): (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 24, 2018 Category: Neuroscience Source Type: research

Direct transdifferentiation of human Wharton’s Jelly mesenchymal stromal cells into Cholinergic-like neurons
ConclusionsThe fastest method to obtain ChLNs from hWJ-MSCs takes only four days using the one-step incubation medium Cholinergic-N-Run.Graphical abstrcat (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 23, 2018 Category: Neuroscience Source Type: research

Denoising High Angular Resolution Diffusion Imaging Data by Combining Singular Value Decomposition and Non-Local Means Filter
ConclusionThe proposed SVD-NLM method can improve HARDI quantitative computations, such as MRI brain tissue segmentation and diffusion profile estimation, that rely on the quality of imaging data. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 23, 2018 Category: Neuroscience Source Type: research

A Feature Extraction Technique based on Tunable Q-Factor Wavelet Transform for Brain Signal Classification
ConclusionThe outcomes of the proposed technique can assist doctors and other health experts to identify diversified EEG categories. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 21, 2018 Category: Neuroscience Source Type: research

Open-source hardware designs for MRI of mice, rats, and marmosets: integrated animal holders and radiofrequency coils
ConclusionsThe confluence of design between the animal holder and RF coil provides a pragmatic solution for routine imaging of small animals. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 21, 2018 Category: Neuroscience Source Type: research

Mass synaptometry: High-dimensional multi parametric assay for single synapses
ConclusionWe applied Mass Synaptometry to analyze 34 parameters simultaneously on more than 390,000 synaptosomes from 13 human brain samples. This new approach revealed regional and disease-specific changes in synaptic phenotypes, including validation of this method with the expected changes in the molecular composition of striatal dopaminergic synapses in Lewy body disease and Alzheimer’s disease. Mass synaptometry enables highly parallel molecular profiling of individual synaptic terminals. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 21, 2018 Category: Neuroscience Source Type: research

Validation of a new data-driven automated algorithm for muscular activity detection in REM sleep behavior disorder
ConclusionsThe results show that i) the proposed method has higher performances than the previous ones in distinguishing C, RBD and PLMD patients, ii) removal of apnea and arousal-related movements is not required, and iii) RBD patients can be better identified when both REM and NREM muscular activities are considered. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 21, 2018 Category: Neuroscience Source Type: research

Editorial Board
Publication date: 1 December 2018Source: Journal of Neuroscience Methods, Volume 310Author(s): (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 21, 2018 Category: Neuroscience Source Type: research

Mediterranean Neuroscience Methods 2017
Publication date: 1 December 2018Source: Journal of Neuroscience Methods, Volume 310Author(s): Liana Fattore, Marc Landry, Giuseppe Di Giovanni (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 21, 2018 Category: Neuroscience Source Type: research

Inter- and Intra-Rater Reliability of Computer-Assisted Planimetry in Experimental Stroke Research
ConclusionComputer-assisted planimetry can be an appropriate method to determine hemispheric or ischemic lesion volume in rodents but requires a sufficiently long learning period of approximately two months. Even an experienced investigator can generate data with serious variation. Inter- and intra-rater-dependent bias should be considered during the design and performance of respective studies. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 19, 2018 Category: Neuroscience Source Type: research

Multifractal detrended fluctuation analysis of continuous neural time series in primate visual cortex
In this study, we provide an analysis of extracellular field potential time series using the sophisticated nonlinear Multi-Fractal Detrended Fluctuation Analysis (MF-DFA). Using the MF-DFA, we demonstrate that the integral of the singularity spectrum is a powerful new method to measure the response tuning of spikes in the continuous field potential channel.ResultsResults show that the spikes in the continuous channel at frequency ranges above the LFP component signals were consistently tuned similar to those in the spike channel. Our results also show that using a low-pass filter (
Source: Journal of Neuroscience Methods - November 17, 2018 Category: Neuroscience Source Type: research

Stimulating the sleeping brain: current approaches to modulating memory-related sleep physiology
ConclusionsAlthough the results are encouraging, suggesting that in general the sleeping brain may be optimized for better memory performance, the road to bring these techniques in free-living conditions is paved with unanswered questions and technical challenges that need to be carefully addressed. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 17, 2018 Category: Neuroscience Source Type: research

An EEG-EMG Correlation-based Brain-Computer Interface for Hand Orthosis Supported Neuro-Rehabilitation
In this study, we have introduced a new corticomuscular feature extraction method based on the correlation between band-limited power time-courses (CBPT) associated with EEG and EMG. 16 healthy individuals and 8 hemiplegic patients participated in a BCI-based hand orthosis triggering task, to test the performance of the CBPT method. The healthy population was equally divided into two groups; one experimental group for CBPT-based BCI experiment and another control group for EEG-EMG coherence based BCI experiment.ResultsThe classification accuracy of the CBPT-based BCI system was found to be 92.81± 2.09 % fo...
Source: Journal of Neuroscience Methods - November 17, 2018 Category: Neuroscience Source Type: research

Bayesian Multi-Dipole Modeling in the Frequency Domain
ConclusionsThe Bayesian method described in this paper represents a reliable approach for localization of multiple dipoles in the frequency domain.Graphical abstract (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 17, 2018 Category: Neuroscience Source Type: research

Pore-former enabled seeding of tau in rats: alleviation by memantine and lithium chloride
ConclusionsThese data validate a novel model of locally infused recombinant human Tau as an inducer of tauopathy in rats and holds the potential for development of novel therapies. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 16, 2018 Category: Neuroscience Source Type: research

Assessing Recurrent Interactions in Cortical Networks: Modeling EEG Response to Transcranial Magnetic Stimulation
ConclusionThe new method strongly suggests that effective feedback connections between cortical regions are required to produce the TMS/EEG in wakefulness. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 14, 2018 Category: Neuroscience Source Type: research

In vivo cell type-specific CRISPR gene editing for sleep research
Publication date: Available online 12 November 2018Source: Journal of Neuroscience MethodsAuthor(s): Hiroshi Yamaguchi, Luis de LeceaAbstractSleep is an innate behavior conserved in all animals and, in vertebrates, is regulated by neuronal circuits in the brain. The conventional techniques of forward and reverse genetics have enabled researchers to investigate the molecular mechanisms that regulate sleep and arousal. However, functional interrogation of genes in specific cell subtypes in the brain remains a challenge. Here, we review the background of newly developed gene-editing technologies using engineered CRISPR/Cas9 s...
Source: Journal of Neuroscience Methods - November 12, 2018 Category: Neuroscience Source Type: research

Variability and uncertainty in the rodent controlled cortical impact model of traumatic brain injury
ConclusionsTogether these data can inform future work to design modifications to commonly used CCI devices that produce TBI with less variability in severity and lesion size. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 11, 2018 Category: Neuroscience Source Type: research

A non-human primate model for stable chronic Parkinson’s disease induced by MPTP administration based on individual behavioral quantification
ConclusionsThis novel strategy of MPTP administration based on global activity evaluations provides an important conceptual advance for the development of chronic NHP Parkinsonian models. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 11, 2018 Category: Neuroscience Source Type: research

Functional assessments through novel proteomics approaches: Application to insulin/IGF signaling in neurodegenerative disease
ConclusionsProteomics analyses have revolutionized the discovery phase of biomedical research but are conventionally limited in scope. The creative use of fractionation prior to proteomic discovery is likely to provide important insights into AD and related disorders. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 7, 2018 Category: Neuroscience Source Type: research

A new polymer-based approach for in vivo transfection in postnatal brain
ConclusionsThis safe and easy system opens perspectives for non viral gene delivery in the rat brain with perspectives to study brain function in vivo. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 6, 2018 Category: Neuroscience Source Type: research

In vitro assessment of radiobiology of meningioma: a pilot study
ConclusionsOur method of cells culture appears suitable for radiosensitivity studies on meningioma. We can confirm that the response to radiotherapy depends not only on irradiation features, but also on tumor radiosensitivity. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 6, 2018 Category: Neuroscience Source Type: research

Cross-subject network investigation of the EEG microstructure: a sleep spindles study
ConclusionWe conclude that the proposed methodology can serve as an observatory tool for the EEG connectivity patterns across subjects, providing a supplementary analysis of the existing topography techniques. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 6, 2018 Category: Neuroscience Source Type: research

Reprint of “Animal models of early-stage Parkinson's disease and acute dopamine deficiency to study compensatory neurodegenerative mechanisms”
Publication date: Available online 2 November 2018Source: Journal of Neuroscience MethodsAuthor(s): Laura Clara Grandi, Giuseppe Di Giovanni, Salvatore GalatiAbstractParkinson’s disease is a common neurodegenerative disease characterized by a widely variety of motor and non-motor symptoms. While the motor deficits are only visible following a severe dopamine depletion, neurodegenerative process and some non-motor symptoms are manifested years before the motor deficits. Importantly, chronic degeneration of dopaminergic neurons leads to the development of compensatory mechanisms that play roles in the progression of th...
Source: Journal of Neuroscience Methods - November 3, 2018 Category: Neuroscience Source Type: research

A non-human primate model for stable chronic Parkinson's disease induced by MPTP administration based on individual behavioral quantification
ConclusionsThis novel strategy of MPTP administration based on global activity evaluations provides an important conceptual advance for the development of chronic NHP Parkinsonian models. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 3, 2018 Category: Neuroscience Source Type: research

Post mortem high resolution diffusion MRI for large specimen imaging at 11.7 T with 3D segmented echo-planar imaging
Conclusions: Our study demonstrated the feasibility of analysing anatomical connectivity using diffusion imaging of a post mortem macaque brain with a 3D-DW seg-EPI sequence acquired at ultra-high field. The combination of high angular and spatial resolution DWI with Gd-soaking and denoising provided data allowing us to perform diffusion tractography with results very similar to those obtained with a 3D-DW SE acquisition (with shorter acquisition times: 222 h versus 37 h for 3D-DW seg-EPI). (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 3, 2018 Category: Neuroscience Source Type: research

Reciprocal Nerve Staining (RNS) for the concurrent detection of Choline Acetyltransferase and Myelin Basic Protein on paraffin-embedded sections
ConclusionsRoutine combination of choline acetyltransferase and myelin basic protein immunostaining provides a highly specific, highly contrasted paraffin-embedded sections where optical differentiation of myelinated motor fibers is easy and straightforward. This method will likely simplify and speed-up the routine histological study of nerve regeneration and will contribute a better identification of the nerve motor component. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - November 2, 2018 Category: Neuroscience Source Type: research

A novel simplistic fabrication technique for cranial epidural electrodes for chronic recording and stimulation in rats
ConclusionWe developed a chronic implantable electrode capable of being fabricated in all wet-labs, are robust, versatile and electrically sensitive enough for long-term chronic use. The simple and versatile electrode design provides scientific, economical and ethical benefits. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - October 31, 2018 Category: Neuroscience Source Type: research

Semantic-hierarchical model improves classification of spoken-word evoked electrocorticography
In this study, we propose a semantic-hierarchical structure for classifying spoken word-evoked cortical responses. The proposed structure decodes the semantic grouping of the words first (e.g., a body part vs. a number) and then decodes which exact word was heard. The proposed classifier structure exhibited a consistent ~10% improvement of classification accuracy when compared with a non-hierarchical structure. Our result provides a tool for investigating the neural representation of semantic hierarchy and the acoustic properties of spoken words in human brains. Our results suggest an improved algorithm for BCIs operated b...
Source: Journal of Neuroscience Methods - October 31, 2018 Category: Neuroscience Source Type: research

Spinal Cord Injury in Zebrafish Induced by Near-Infrared Femtosecond Laser Pulses
ConclusionsWe present a precise and robust method for inducing SCI in zebrafish with single-cell resolution using femtosecond near-infrared laser pulses. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - October 31, 2018 Category: Neuroscience Source Type: research

Direct targeting of the mouse optic nerve for therapeutic delivery
ConclusionsWe successfully targeted the murine optic nerve intraorbitally, through the optic foramen, and transcranially. Of all methods, the injection through the optic foramen is likely the most innovative and fastest. These methods offer additional approaches for therapeutic intervention to be used by those studying white matter damage and axonal regeneration in the CNS. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - October 31, 2018 Category: Neuroscience Source Type: research

A Method to Compare the Discriminatory Power of Data-driven Methods: Application to ICA and IVA
ConclusionsThese results demonstrate that GDMs are an effective way to compare the performances of different factorization-based methods as well as regression-based analyses. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - October 30, 2018 Category: Neuroscience Source Type: research

A principled multivariate intersubject analysis of Generalized Partial Directed Coherence with Dirichlet Regression: application to healthy aging in areas exhibiting cortical thinning
ConclusionsDirichlet Regression allows the study of continuous or discrete variables as predictors for the analysis of GPDC, enabling a wider adoption of this measure of connectivity.Graphical Abstract (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - October 29, 2018 Category: Neuroscience Source Type: research

Baby Faces: Development and psychometric study of a stimuli set based on babies’ emotions
ConclusionsThe findings reinforced the Differential Emotion Theory regarding the expression of basic emotions in infants and evidenced the effect of education level on emotion recognition to the detriment of other sociocultural characteristics (sex and race). This set is freely accessible by email request. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - October 27, 2018 Category: Neuroscience Source Type: research

Development of a Motor and Somatosensory Evoked Potentials-guided Spinal Cord Injury Model in Non-Human Primates
ConclusionsThis method to induce complete SCI in NHP is well tolerated, reproducible and ethically acceptable: these are valuable attributes in a preclinical model that will hopefully help advance testing of new regenerative therapies in SCI. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - October 26, 2018 Category: Neuroscience Source Type: research

High resolution approaches for the identification of amyloid fragments in brain
ConclusionsUsing novel and highly specific antibodies in combination with electron microscopy may reveal important information about the timing of aberrant protein accumulation, as well as the progression of abnormalities in the endolysosomal systems that sort and clear these peptides. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - October 26, 2018 Category: Neuroscience Source Type: research

A Flexible Likelihood Approach for Predicting Neural Spiking Activity from Oscillatory Phase
ConclusionsThis method advances the way spike-phase relationships are visualized and quantified, and captures multimodal spike-phase relationships, including relationships with multiple nested rhythms. Overall, our method is a powerful a tool for revealing a wide range of neural circuit interactions. (Source: Journal of Neuroscience Methods)
Source: Journal of Neuroscience Methods - October 26, 2018 Category: Neuroscience Source Type: research