scholarly journals How do spike collisions affect spike sorting performance?

2021 ◽  
Author(s):  
Samuel Garcia ◽  
Alessio Buccino ◽  
Pierre Yger
Keyword(s):  
Template Matching ◽  
Ground Truth ◽  
Spatial Density ◽  
Neuron Activity ◽  
Spike Sorting ◽  
Extracellular Signals ◽  
New Generation ◽  
Single Neuron Activity

Recently, a new generation of devices have been developed to record neural activity simultaneously from hundreds of electrodes with a very high spatial density, both for in vitro and in vivo applications. While these advances enable to record from many more cells, they also dramatically increase the amount overlapping "synchronous" spikes (colliding in space and/or in time), challenging the already complicated process of spike sorting (i.e. extracting isolated single-neuron activity from extracellular signals). In this work, we used synthetic ground-truth recordings to quantitatively benchmark the performance of state-of-the-art spike sorters focusing specifically on spike collisions. Our results show that while modern template-matching based algorithms are more accurate than density-based approaches, all methods, to some extent, failed to detect synchronous spike events of neurons with similar extracellular signals. Interestingly, the performance of the sorters is not largely affected by the the spiking activity in the recordings, with respect to average firing rates and spike-train correlation levels.

scholarly journals Fast and accurate spike sorting in vitro and in vivo for up to thousands of electrodes

2016 ◽  
Author(s):  
Pierre Yger ◽  
Giulia L.B. Spampinato ◽  
Elric Esposito ◽  
Baptiste Lefebvre ◽  
Stéphane Deny ◽  
...  
Keyword(s):  
Template Matching ◽  
Large Scale ◽  
Ground Truth ◽  
Spike Sorting ◽  
Electrode Arrays ◽  
Ground Truth Data ◽  
Sorting Problem ◽  
Large Populations

AbstractUnderstanding how assemblies of neurons encode information requires recording large populations of cells in the brain. In recent years, multi-electrode arrays and large silicon probes have been developed to record simultaneously from hundreds or thousands of electrodes packed with a high density. However, these new devices challenge the classical way to do spike sorting. Here we developed a new method to solve these issues, based on a highly automated algorithm to extract spikes from extracellular data, and show that this algorithm reached near optimal performance both in vitro and in vivo. The algorithm is composed of two main steps: 1) a “template-finding” phase to extract the cell templates, i.e. the pattern of activity evoked over many electrodes when one neuron fires an action potential; 2) a “template-matching” phase where the templates were matched to the raw data to find the location of the spikes. The manual intervention by the user was reduced to the minimal, and the time spent on manual curation did not scale with the number of electrodes. We tested our algorithm with large-scale data from in vitro and in vivo recordings, from 32 to 4225 electrodes. We performed simultaneous extracellular and patch recordings to obtain “ground truth” data, i.e. cases where the solution to the sorting problem is at least partially known. The performance of our algorithm was always close to the best expected performance. We thus provide a general solution to sort spikes from large-scale extracellular recordings.

scholarly journals MEArec: A Fast and Customizable Testbench Simulator for Ground-truth Extracellular Spiking Activity

2020 ◽  
Vol 19 (1) ◽  
pp. 185-204 ◽  
Author(s):  
Alessio Paolo Buccino ◽  
Gaute Tomas Einevoll
Keyword(s):  
Ground Truth ◽  
Spike Sorting ◽  
Ground Truth Data ◽  
Extracellular Signals ◽  
Software Packages ◽  
Processing Step ◽  
Important Processing ◽  
Spatio Temporal

AbstractWhen recording neural activity from extracellular electrodes, both in vivo and in vitro, spike sorting is a required and very important processing step that allows for identification of single neurons’ activity. Spike sorting is a complex algorithmic procedure, and in recent years many groups have attempted to tackle this problem, resulting in numerous methods and software packages. However, validation of spike sorting techniques is complicated. It is an inherently unsupervised problem and it is hard to find universal metrics to evaluate performance. Simultaneous recordings that combine extracellular and patch-clamp or juxtacellular techniques can provide ground-truth data to evaluate spike sorting methods. However, their utility is limited by the fact that only a few cells can be measured at the same time. Simulated ground-truth recordings can provide a powerful alternative mean to rank the performance of spike sorters. We present here , a Python-based software which permits flexible and fast simulation of extracellular recordings. allows users to generate extracellular signals on various customizable electrode designs and can replicate various problematic aspects for spike sorting, such as bursting, spatio-temporal overlapping events, and drifts. We expect will provide a common testbench for spike sorting development and evaluation, in which spike sorting developers can rapidly generate and evaluate the performance of their algorithms.

scholarly journals MEArec: a fast and customizable testbench simulator for ground-truth extracellular spiking activity

2019 ◽  
Author(s):  
Alessio P. Buccino ◽  
Gaute T. Einevoll
Keyword(s):  
Ground Truth ◽  
Spike Sorting ◽  
Ground Truth Data ◽  
Extracellular Signals ◽  
Software Packages ◽  
Processing Step ◽  
Important Processing ◽  
Spatio Temporal

AbstractWhen recording neural activity from extracellular electrodes, both in vivo and in vitro, spike sorting is a required and very important processing step that allows for identification of single neurons’ activity. Spike sorting is a complex algorithmic procedure, and in recent years many groups have attempted to tackle this problem, resulting in numerous methods and software packages. However, validation of spike sorting techniques is complicated. It is an inherently unsupervised problem and it is hard to find universal metrics to evaluate performance. Simultaneous recordings that combine extracellular and patch-clamp or juxtacellular techniques can provide ground-truth data to evaluate spike sorting methods. However, their utility is limited by the fact that only a few cells can be measured at the same time. Simulated ground-truth recordings can provide a powerful alternative mean to rank the performance of spike sorters. We present here MEArec, a Python-based software which permits flexible and fast simulation of extracellular recordings. MEArec allows users to generate extracellular signals on various customizable electrode designs and can replicate various problematic aspects for spike sorting, such as bursting, spatio-temporal overlapping events, and drifts. We expect MEArec will provide a common testbench for spike sorting development and evaluation, in which spike sorting developers can rapidly generate and evaluate the performance of their algorithms.

scholarly journals Spike sorting of synchronous spikes from local neuron ensembles

2015 ◽  
Vol 114 (4) ◽  
pp. 2535-2549 ◽  
Author(s):  
Felix Franke ◽  
Robert Pröpper ◽  
Henrik Alle ◽  
Philipp Meier ◽  
Jörg R. P. Geiger ◽  
...  
Keyword(s):  
Cortical Neurons ◽  
Template Matching ◽  
Spatial Information ◽  
Simulated Data ◽  
Error Rates ◽  
Dimensional Structure ◽  
Spike Sorting ◽  
Spike Discharge

Synchronous spike discharge of cortical neurons is thought to be a fingerprint of neuronal cooperativity. Because neighboring neurons are more densely connected to one another than neurons that are located further apart, near-synchronous spike discharge can be expected to be prevalent and it might provide an important basis for cortical computations. Using microelectrodes to record local groups of neurons does not allow for the reliable separation of synchronous spikes from different cells, because available spike sorting algorithms cannot correctly resolve the temporally overlapping waveforms. We show that high spike sorting performance of in vivo recordings, including overlapping spikes, can be achieved with a recently developed filter-based template matching procedure. Using tetrodes with a three-dimensional structure, we demonstrate with simulated data and ground truth in vitro data, obtained by dual intracellular recording of two neurons located next to a tetrode, that the spike sorting of synchronous spikes can be as successful as the spike sorting of nonoverlapping spikes and that the spatial information provided by multielectrodes greatly reduces the error rates. We apply the method to tetrode recordings from the prefrontal cortex of behaving primates, and we show that overlapping spikes can be identified and assigned to individual neurons to study synchronous activity in local groups of neurons.

scholarly journals Author response: A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo

2018 ◽  
Author(s):  
Pierre Yger ◽  
Giulia LB Spampinato ◽  
Elric Esposito ◽  
Baptiste Lefebvre ◽  
Stéphane Deny ◽  
...  
Keyword(s):  
Ground Truth ◽  
Author Response ◽  
Spike Sorting

Flavonoids as P-gp Inhibitors: A Systematic Review of SARs

2019 ◽  
Vol 26 (25) ◽  
pp. 4799-4831 ◽  
Author(s):  
Jiahua Cui ◽  
Xiaoyang Liu ◽  
Larry M.C. Chow
Keyword(s):  
Molecular Mechanisms ◽  
Metastatic Cancer ◽  
Drug Candidates ◽  
Chemical Structures ◽  
Transporter Family ◽  
Promising Area ◽  
New Generation ◽  
Nontoxic Inhibitors

P-glycoprotein, also known as ABCB1 in the ABC transporter family, confers the simultaneous resistance of metastatic cancer cells towards various anticancer drugs with different targets and diverse chemical structures. The exploration of safe and specific inhibitors of this pump has always been the pursuit of scientists for the past four decades. Naturally occurring flavonoids as benzopyrone derivatives were recognized as a class of nontoxic inhibitors of P-gp. The recent advent of synthetic flavonoid dimer FD18, as a potent P-gp modulator in reversing multidrug resistance both in vitro and in vivo, specifically targeted the pseudodimeric structure of the drug transporter and represented a new generation of inhibitors with high transporter binding affinity and low toxicity. This review concerned the recent updates on the structure-activity relationships of flavonoids as P-gp inhibitors, the molecular mechanisms of their action and their ability to overcome P-gp-mediated MDR in preclinical studies. It had crucial implications on the discovery of new drug candidates that modulated the efflux of ABC transporters and also provided some clues for the future development in this promising area.

scholarly journals Targeting of p38 Mitogen-Activated Protein Kinases to MEF2 Transcription Factors

1999 ◽  
Vol 19 (6) ◽  
pp. 4028-4038 ◽  
Author(s):  
Shen-Hsi Yang ◽  
Alex Galanis ◽  
Andrew D. Sharrocks
Keyword(s):  
Transcription Factors ◽  
Transcriptional Activation ◽  
Cellular Response ◽  
Map Kinases ◽  
Biological Response ◽  
Extracellular Signals ◽  
Extracellular Signal ◽  
Mitogen Activated Protein

ABSTRACT Mitogen-activated protein (MAP) kinase-mediated signalling to the nucleus is an important event in the conversion of extracellular signals into a cellular response. However, the existence of multiple MAP kinases which phosphorylate similar phosphoacceptor motifs poses a problem in maintaining substrate specificity and hence the correct biological response. Both the extracellular signal-regulated kinase (ERK) and c-Jun NH2-terminal kinase (JNK) subfamilies of MAP kinases use a second specificity determinant and require docking to their transcription factor substrates to achieve maximal substrate activation. In this study, we demonstrate that among the different MAP kinases, the MADS-box transcription factors MEF2A and MEF2C are preferentially phosphorylated and activated by the p38 subfamily members p38α and p38β2. The efficiency of phosphorylation in vitro and transcriptional activation in vivo of MEF2A and MEF2C by these p38 subtypes requires the presence of a kinase docking domain (D-domain). Furthermore, the D-domain from MEF2A is sufficient to confer p38 responsiveness on different transcription factors, and reciprocal effects are observed upon the introduction of alternative D-domains into MEF2A. These results therefore contribute to our understanding of signalling to MEF2 transcription factors and demonstrate that the requirement for substrate binding by MAP kinases is an important facet of three different subclasses of MAP kinases (ERK, JNK, and p38).

scholarly journals 1395. Defining the Magnitude of AUC:MIC Driver for Efficacy of the β-Lactamase Inhibitor VNRX-5133 When Combined with Cefepime Against KPC- and VIM/NDM-Producing Enterobacteriaceae and P. aeruginosa

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S429-S429 ◽  
Author(s):  
Denis Daigle ◽  
Salvador Vernacchio ◽  
Luigi Xerri ◽  
Daniel Pevear
Keyword(s):  
In Vitro Studies ◽  
Dose Fractionation ◽  
Infection Model ◽  
Type Model ◽  
E Coli ◽  
Dose Ranging ◽  
New Generation ◽  
Lactamase Inhibitor

Abstract Background VNRX-5133 is a cyclic boronate β-lactamase inhibitor (BLI) in clinical development with cefepime for treatment of infections caused by ESBL- and carbapenemase producing Enterobacteriaceae and P. aeruginosa. It is a new generation broad-spectrum BLI with direct inhibitory activity against serine-active site and emerging metallo-β-lactamases (e.g., VIM/NDM). In previous in vivo and in vitro studies, the PK-PD driver of efficacy of VNRX-5133 was defined as AUC:MIC. Described herein are in vitro studies to assess the magnitude of VNRX-5133 exposure (AUC:MIC) required to restore efficacy of cefepime against a broad collection of KPC- and VIM/NDM-producing Enterobacteriaceae (ENT) and P. aeruginosa (PSA) clinical isolates. Methods Dose-fractionation studies, consisting of four VNRX-5133 exposures fractionated into regimens administered every 4, 8, 12 and 24 hours, were performed in an in vitro infection model with simulated 2 g q8h dosing of cefepime against NDM-1 producing E. coli. A Hill-type model described the relationship between change in log10 CFU at 24 hours and VNRX-5133 exposure (AUC:MIC), where cefepime MIC was determined with 4 µg/mL VNRX-5133. To evaluate variability of efficacy enabled by VNRX-5133 between isolates as well as between Serine-BL and Metallo-BL producers, dose-ranging studies were completed for eight isolates (seven ENT and one PSA) producing KPC or VIM/NDM metallo-β-lactamases. Results The PK-PD exposure parameter AUC:MIC accurately described the efficacy of VNRX-5133 in rescuing cefepime activity against KPC and VIM/NDM carbapenemase-producing isolates of ENT and PSA. The AUC:MIC ratios associated with net bacterial stasis, 1-, and 2-log10 reductions in bacterial burden from baseline were 6.1, 18.4 and 45, respectively, for a collection of five VIM/NDM- and three KPC-producing isolates with cefepime MICs ranging from 4–8 µg/mL with no significant differences observed between Ser-BL and MBL producers. Conclusion These data confirm the equivalent in vitro activity of cefepime/VNRX-5133 against organisms producing serine- and metallo-β-lactamases and provides an initial PK-PD target for VNRX-5133 efficacy when used in combination with cefepime for the treatment of ESBL- and carbapenemase-producing ENT and PSA infections. Disclosures D. Daigle, VenatoRx Pharmaceuticals Inc.: Employee and Shareholder, Salary. S. Vernacchio, VenatoRx Pharmaceuticals Inc.: Employee and Shareholder, Salary. L. Xerri, VenatoRx Pharmaceuticals Inc.: Employee and Shareholder, Salary. D. Pevear, VenatoRx Pharmaceuticals Inc.: Employee, Salary.

scholarly journals In vitro assessment of the cytotoxic, genotoxic and oxidative stress effects of the synthetic cannabinoid JWH-018 in human SH-SY5Y neuronal cells

2020 ◽  
Vol 9 (6) ◽  
pp. 734-740
Author(s):  
Yigit Sezer ◽  
Ayse Tarbin Jannuzzi ◽  
Marilyn A Huestis ◽  
Buket Alpertunga
Keyword(s):  
Oxidative Stress ◽  
Neuronal Cells ◽  
Underlying Mechanism ◽  
Synthetic Cannabinoid ◽  
Stress Effects ◽  
Legal High ◽  
New Generation ◽  
And Oxidative Stress

Abstract Background: JWH-018 was the first synthetic cannabinoid introduced as a legal high and the first of the new generation of novel psychoactive substances that flooded worldwide drug markets. JWH-018 was marketed as “spice,” “herbal incense,” or “herbal blend,” as a popular and legal (at the time) alternative to cannabis (marijuana). JWH-018 is a potent synthetic cannabinoid with considerable toxicity associated with its use. JWH-018 has qualitatively similar but quantitatively greater pharmacological effects than cannabis, leading to intoxications and even deaths. The mechanisms of action of the drug’s toxicity require research, and thus, the aim of the present study was to investigate the toxicological profile of JWH-018 in human SH-SY5Y neuronal cells. Methods: SH-SY5Y neuronal cells were exposed to increasing concentrations from 5 to 150 μM JWH-018 over 24 h. Cytotoxicity, DNA damage, the apoptotic/necrotic rate, and oxidative stress were assessed following SH-SY5Y exposure. Results: JWH-018 did not produce a significant decrease in SH-SY5Y cell viability, did not alter apoptotic/necrotic rate, and did not cause genotoxicity in SH-SY5Y cells with 24-h exposure. Glutathione reductase and catalase activities were significantly reduced; however, there was no significant change in glutathione peroxidase activity. Also, JWH-018 treatment significantly decreased glutathione concentrations, significantly increased protein carbonylation, and significantly increased malondialdehyde (MDA) concentrations. For significance, all P < 0.05. Discussion/Conclusion: JWH-018 produced oxidative stress in SH-SY5Y cells that could be an underlying mechanism of JWH-018 neurotoxicity. Additional in vivo animal and human-based studies are needed to confirm our findings.

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