Decoding Neural Spike Trains: Calculating the Probability That a Spike Train and an External Signal Are Related

2002 ◽  
Vol 87 (3) ◽  
pp. 1659-1663 ◽  
Author(s):  
Terence D. Sanger
Keyword(s):  
Spike Train ◽  
Cell Activity ◽  
Simulated Data ◽  
External Signal ◽  
Time Varying ◽  
Neural Firing ◽  
Sensory Stimuli ◽  
Correlation Methods ◽  
A Cell ◽  
Recursive Calculation

Experimental and clinical applications of extracellular recordings of spiking cell activity frequently are used to relate the activity of a cell to externally measurable signals such as surface potentials, sensory stimuli, or movement measurements. When the external signal is time-varying, correlation methods have traditionally been used to quantify the degree of relation with the neural firing. However, in some circumstances correlation methods can give misleading results. A new algorithm is described that estimates the extent to which a spike train is related to a continuous time-varying signal. The technique calculates the probability of generating a spike train with Poisson statistics if the time-varying signal determines the Poisson rate. This is accomplished by successive division of the signal and the spike train into halves and recursive calculation of the probability of each half-signal. The performance of the new algorithm is compared with the performance of correlation methods on simulated data.

scholarly journals Detecting long-range interactions between migrating cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
C. Metzner ◽  
F. Hörsch ◽  
C. Mark ◽  
T. Czerwinski ◽  
A. Winterl ◽  
...  
Keyword(s):  
Nk Cells ◽  
Tumor Cells ◽  
Long Range ◽  
Cooperative Behavior ◽  
Simulated Data ◽  
Movement Direction ◽  
Repulsive Interaction ◽  
Collagen Gels ◽  
Long Range Interactions ◽  
A Cell

AbstractChemotaxis enables cells to systematically approach distant targets that emit a diffusible guiding substance. However, the visual observation of an encounter between a cell and a target does not necessarily indicate the presence of a chemotactic approach mechanism, as even a blindly migrating cell can come across a target by chance. To distinguish between the chemotactic approach and blind migration, we present an objective method that is based on the analysis of time-lapse recorded cell migration trajectories: For each movement step of a cell relative to the position of a potential target, we compute a p value that quantifies the likelihood of the movement direction under the null-hypothesis of blind migration. The resulting distribution of p values, pooled over all recorded cell trajectories, is then compared to an ensemble of reference distributions in which the positions of targets are randomized. First, we validate our method with simulated data, demonstrating that it reliably detects the presence or absence of remote cell-cell interactions. In a second step, we apply the method to data from three-dimensional collagen gels, interspersed with highly migratory natural killer (NK) cells that were derived from two different human donors. We find for one of the donors an attractive interaction between the NK cells, pointing to a cooperative behavior of these immune cells. When adding nearly stationary K562 tumor cells to the system, we find a repulsive interaction between K562 and NK cells for one of the donors. By contrast, we find attractive interactions between NK cells and an IL-15-secreting variant of K562 tumor cells. We therefore speculate that NK cells find wild-type tumor cells only by chance, but are programmed to leave a target quickly after a close encounter. We provide a freely available Python implementation of our p value method that can serve as a general tool for detecting long-range interactions in collective systems of self-driven agents.

scholarly journals EMeth: An EM algorithm for cell type decomposition based on DNA methylation data

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hanyu Zhang ◽  
Ruoyi Cai ◽  
James Dai ◽  
Wei Sun
Keyword(s):  
Dna Methylation ◽  
Tumor Cells ◽  
T Regulatory Cells ◽  
Simulated Data ◽  
Cell Types ◽  
Computational Method ◽  
Methylation Data ◽  
Cell Type ◽  
A Cell ◽  
Type Decomposition

AbstractWe introduce a new computational method named EMeth to estimate cell type proportions using DNA methylation data. EMeth is a reference-based method that requires cell type-specific DNA methylation data from relevant cell types. EMeth improves on the existing reference-based methods by detecting the CpGs whose DNA methylation are inconsistent with the deconvolution model and reducing their contributions to cell type decomposition. Another novel feature of EMeth is that it allows a cell type with known proportions but unknown reference and estimates its methylation. This is motivated by the case of studying methylation in tumor cells while bulk tumor samples include tumor cells as well as other cell types such as infiltrating immune cells, and tumor cell proportion can be estimated by copy number data. We demonstrate that EMeth delivers more accurate estimates of cell type proportions than several other methods using simulated data and in silico mixtures. Applications in cancer studies show that the proportions of T regulatory cells estimated by DNA methylation have expected associations with mutation load and survival time, while the estimates from gene expression miss such associations.

Messages of Oscillatory Correlograms: A Spike Train Model

2008 ◽  
Vol 20 (5) ◽  
pp. 1211-1238 ◽  
Author(s):  
Gaby Schneider
Keyword(s):  
Spike Train ◽  
Null Model ◽  
Simulated Data ◽  
Joint Analysis ◽  
Data Set ◽  
Proposed Model ◽  
Peak Asymmetry ◽  
Millisecond Range ◽  
Temporal Interactions ◽  
Underlying Processes

Oscillatory correlograms are widely used to study neuronal activity that shows a joint periodic rhythm. In most cases, the statistical analysis of cross-correlation histograms (CCH) features is based on the null model of independent processes, and the resulting conclusions about the underlying processes remain qualitative. Therefore, we propose a spike train model for synchronous oscillatory firing activity that directly links characteristics of the CCH to parameters of the underlying processes. The model focuses particularly on asymmetric central peaks, which differ in slope and width on the two sides. Asymmetric peaks can be associated with phase offsets in the (sub-) millisecond range. These spatiotemporal firing patterns can be highly consistent across units yet invisible in the underlying processes. The proposed model includes a single temporal parameter that accounts for this peak asymmetry. The model provides approaches for the analysis of oscillatory correlograms, taking into account dependencies and nonstationarities in the underlying processes. In particular, the auto- and the cross-correlogram can be investigated in a joint analysis because they depend on the same spike train parameters. Particular temporal interactions such as the degree to which different units synchronize in a common oscillatory rhythm can also be investigated. The analysis is demonstrated by application to a simulated data set.

scholarly journals The Downlink Performance for Cell-Free Massive MIMO with Instantaneous CSI in Slowly Time-Varying Channels

Entropy ◽  
2021 ◽  
Vol 23 (11) ◽  
pp. 1552
Author(s):  
Tongzhou Han ◽  
Danfeng Zhao
Keyword(s):  
Power Control ◽  
Massive Mimo ◽  
Mimo Systems ◽  
Mimo System ◽  
Multiple Input Multiple Output ◽  
Time Varying ◽  
Input Multiple Output ◽  
Efficiency Performance ◽  
A Cell ◽  
Time Varying Channel

In centralized massive multiple-input multiple-output (MIMO) systems, the channel hardening phenomenon can occur, in which the channel behaves as almost fully deterministic as the number of antennas increases. Nevertheless, in a cell-free massive MIMO system, the channel is less deterministic. In this paper, we propose using instantaneous channel state information (CSI) instead of statistical CSI to obtain the power control coefficient in cell-free massive MIMO. Access points (APs) and user equipment (UE) have sufficient time to obtain instantaneous CSI in a slowly time-varying channel environment. We derive the achievable downlink rate under instantaneous CSI for frequency division duplex (FDD) cell-free massive MIMO systems and apply the results to the power control coefficients. For FDD systems, quantized channel coefficients are proposed to reduce feedback overhead. The simulation results show that the spectral efficiency performance when using instantaneous CSI is approximately three times higher than that achieved using statistical CSI.

scholarly journals Multiscale 2D-SPR Biosensing for Cell Chips

2007 ◽  
Vol 19 (5) ◽  
pp. 519-523 ◽  
Author(s):  
Masayasu Suzuki ◽  
◽  
Toyohiro Ohshima ◽  
Shintaro Hane ◽  
Yasunori Iribe ◽  
...  
Keyword(s):  
Protein A ◽  
Cell Activity ◽  
Ccd Camera ◽  
Pdms Film ◽  
Sensor Film ◽  
Spr Imaging ◽  
Measurement Protocol ◽  
A Cell ◽  
Cooled Ccd ◽  
Imaging Sensor

Evaluating cell activity and functions in different-sized cell chambers requires multiscale sensing. We have been developing multiscale biosensing applied from 10 µm to 1 mm. We measured mouse IgG in micro wells using a high-resolution two-dimensional surface plasmon resonance (SPR) imaging affinity sensor. This sensor uses high refractive optics, a 1X to 7X microscopic lens, and a cooled CCD camera. The micro-well array was prepared with a PDMS film on gold sensor film. Protein A immobilized on sensor film was used for IgG recognition. SPR sensitivity was dramatically decreased with 10 and 8.5 µm microwells. To improve sensor sensitivity, we optimized the sensor’s measurement angle and exposure time, enabling mouse IgG to be detected in wells of 1 mm, 30 µm, and 10 µm using the same 2D-SPR imaging sensor and measurement protocol. These results show the feasibility of multiscale biosensing use in antibody production in a micro well or a cell chamber.

scholarly journals A New Multineuron Spike Train Metric

2008 ◽  
Vol 20 (6) ◽  
pp. 1495-1511 ◽  
Author(s):  
Conor Houghton ◽  
Kamal Sen
Keyword(s):  
Spike Train ◽  
Simulated Data ◽  
Spike Trains ◽  
The Other

The Victor-Purpura spike train metric has recently been extended to a family of multineuron metrics and used to analyze spike trains recorded simultaneously from pairs of proximate neurons. The metric is one of the two metrics commonly used for quantifying the distance between two spike trains; the other is the van Rossum metric. Here, we suggest an extension of the van Rossum metric to a multineuron metric. We believe this gives a metric that is both natural and easy to calculate. Both types of multineuron metric are applied to simulated data and are compared.

Privacy Protection in Vehicular Ad-Hoc Networks

2014 ◽  
pp. 295-332
Author(s):  
Gongjun Yan ◽  
Danda B. Rawat ◽  
Bhed Bahadur Bista ◽  
Wu He ◽  
Awny Alnusair
Keyword(s):  
Privacy Protection ◽  
Capacity Planning ◽  
Vehicular Networks ◽  
Vehicular Ad Hoc Networks ◽  
Ad Hoc ◽  
Geographic Area ◽  
Time Varying ◽  
Detailed Simulation ◽  
A Cell ◽  
Hoc Networks

The first main contribution of this chapter is to take a non-trivial step towards providing a robust and scalable solution to privacy protection in vehicular networks. To promote scalability and robustness the authors employ two strategies. First, they view vehicular networks as consisting of non-overlapping subnetworks, each local to a geographic area referred to as a cell. Each cell has a server that maintains a list of pseudonyms that are valid for use in the cell. Each pseudonym has two components: the cell’s ID and a random number as host ID. Instead of issuing pseudonyms to vehicles proactively (as virtually all existing schemes do) the authors issue pseudonyms only to those vehicles that request them. This strategy is suggested by the fact that, in a typical scenario, only a fraction of the vehicles in an area will engage in communication with other vehicles and/or with the infrastructure and, therefore, do not need pseudonyms. The second main contribution is to model analytically the time-varying request for pseudonyms in a given cell. This is important for capacity planning purposes since it allows system managers to predict, by taking into account the time-varying attributes of the traffic, the probability that a given number of pseudonyms will be required at a certain time as well as the expected number of pseudonyms in use in a cell at a certain time. Empirical results obtained by detailed simulation confirm the accuracy of the authors’ analytical predictions.

scholarly journals Cell structure and cell activity

1930 ◽  
Vol 107 (749) ◽  
pp. 168-181 ◽  
Keyword(s):  
Cell Structure ◽  
Succinic Dehydrogenase ◽  
Cell Activity ◽  
Lactic Dehydrogenase ◽  
Surface Structures ◽  
Catechol Oxidase ◽  
Phosphate Solution ◽  
Pronounced Change ◽  
A Cell ◽  
Alkaline Phosphate

The work of Batelli and Stern and of of Warburg has made clear the importance of surface structures in tissue oxidations, and a survey of oxidation systems as a whole show that there must be a considerable grading in complexity and stability of such structures. Agents such as those which oxidise the purine bases or aldehydes, are extractable from the cell; others have not yet been dissociated from the tissues. So many enzymes can be extracted from the cell only by means which must inevitably affect its structure that its is surprising to find that cell activity (or activity of its catalysts) is at all dependent upon cell structure. Disintegration of a cell, the breaking down of cell membranes, will certainly bring about as A. V. Hill (1928) has pointed out, a biochemical chaos and a medley of reactions. Catalysts will be brought into contact with substrates previously held remote from them. The cell end products will change in type and quantity. But if by activity of a cell is meant the activity of its catalysts, mechanical disintegration of the cell will not, in itself, be expressed to bring about any pronounced change. Muscle ground with sand exhibits a very good oxygen uptake in presence of para-phenylenediamine (Keilin, 1929). A number of de-hydrogenases may be extracted from tissues by shaking or maceration in saline or alkaline phosphate solution. Succinic dehydrogenase can be obtained from muscle and lactic dehydrogenase from yeast in this way. Oxidases of compounds of the aromatic type, e. g. , catechol oxidase or tyrosinase appear to act independently of the cell as a whole; so do peroxidase and the hydrolytic ferments. Failure to extract any enzyme would seem to be due to ignorance of a suitable method of elution from the tissue.

Human hematopoietic stem cells stimulated to proliferate in vitro lose engraftment potential during their S/G2/M transit and do not reenter G0

Blood ◽  
2000 ◽  
Vol 96 (13) ◽  
pp. 4185-4193 ◽  
Author(s):  
Hanno Glimm ◽  
IL-Hoan Oh ◽  
Connie J. Eaves
Keyword(s):  
Cell Cycle ◽  
Stem Cells ◽  
Stem Cell ◽  
Hematopoietic Stem Cells ◽  
Transforming Growth Factor ◽  
Ex Vivo ◽  
Cell Activity ◽  
Human Cord Blood ◽  
Hematopoietic Stem ◽  
A Cell

Abstract An understanding of mechanisms regulating hematopoietic stem cell engraftment is of pivotal importance to the clinical use of cultured and genetically modified transplants. Human cord blood (CB) cells with lymphomyeloid repopulating activity in NOD/SCID mice were recently shown to undergo multiple self-renewal divisions within 6 days in serum-free cultures containing Flt3-ligand, Steel factor, interleukin 3 (IL-3), IL-6, and granulocyte colony-stimulating factor. The present study shows that, on the fifth day, the transplantable stem cell activity is restricted to the G1fraction, even though both colony-forming cells (CFCs) and long-term culture-initiating cells (LTC-ICs) in the same cultures are approximately equally distributed between G0/G1and S/G2/M. Interestingly, the G0 cells defined by their low levels of Hoechst 33342 and Pyronin Y staining, and reduced Ki67 and cyclin D expression (representing 21% of the cultured CB population) include some mature erythroid CFCs but very few primitive CFCs, LTC-ICs, or repopulating cells. Although these findings suggest a cell cycle–associated change in in vivo stem cell homing, the cultured G0/G1 and S/G2/M CD34+ CB cells exhibited no differences in levels of expression of VLA-4, VLA-5, or CXCR-4. Moreover, further incubation of these cells for 1 day in the presence of a concentration of transforming growth factor β1 that increased the G0/G1 fraction did not enhance detection of repopulating cells. The demonstration of a cell cycle–associated mechanism that selectively silences the transplantability of proliferating human hematopoietic stem cells poses both challenges and opportunities for the future improvement of ex vivo–manipulated grafts.

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