296 research outputs found
Estimating the contribution of assembly activity to cortical dynamics from spike and population measures
The hypothesis that cortical networks employ the coordinated activity of groups of neurons, termed assemblies, to process information is debated. Results from multiple single-unit recordings are not conclusive because of the dramatic undersampling of the system. However, the local field potential (LFP) is a mesoscopic signal reflecting synchronized network activity. This raises the question whether the LFP can be employed to overcome the problem of undersampling. In a recent study in the motor cortex of the awake behaving monkey based on the locking of coincidences to the LFP we determined a lower bound for the fraction of spike coincidences originating from assembly activation. This quantity together with the locking of single spikes leads to a lower bound for the fraction of spikes originating from any assembly activity. Here we derive a statistical method to estimate the fraction of spike synchrony caused by assemblies—not its lower bound—from the spike data alone. A joint spike and LFP surrogate data model demonstrates consistency of results and the sensitivity of the method. Combining spike and LFP signals, we obtain an estimate of the fraction of spikes resulting from assemblies in the experimental data
Dynamical density functional theory for interacting Brownian particles: stochastic or deterministic?
We aim to clarify confusions in the literature as to whether or not dynamical
density functional theories for the one-body density of a classical Brownian
fluid should contain a stochastic noise term. We point out that a stochastic as
well as a deterministic equation of motion for the density distribution can be
justified, depending on how the fluid one-body density is defined -- i.e.
whether it is an ensemble averaged density distribution or a spatially and/or
temporally coarse grained density distribution.Comment: 10 pages, 1 figure, to be submitted to Journal of Physics A:
Mathematical and Genera
Deciphering the regulatory landscapte of fetal and adult γδ T-cell development at single-cell resolution
γδ T cells with distinct properties develop in the embryonic and adult thymus and have been identified as critical players in a broad range of infections, antitumor surveillance, autoimmune diseases, and tissue homeostasis. Despite their potential value for immunotherapy, differentiation of γδ T cells in the thymus is incompletely understood. Here, we establish a high‐resolution map of γδ T‐cell differentiation from the fetal and adult thymus using single‐cell RNA sequencing. We reveal novel sub‐types of immature and mature γδ T cells and identify an unpolarized thymic population which is expanded in the blood and lymph nodes. Our detailed comparative analysis reveals remarkable similarities between the gene networks active during fetal and adult γδ T‐cell differentiation. By performing a combined single‐cell analysis of Sox13, Maf, and Rorc knockout mice, we demonstrate sequential activation of these factors during IL ‐17‐producing γδ T‐cell (γδT17) differentiation. These findings substantially expand our understanding of γδ T‐cell ontogeny in fetal and adult life. Our experimental and computational strategy provides a blueprint for comparing immune cell differentiation across developmental stages
Activity of comets: Gas Transport in the Near-Surface Porous Layers of a Cometary Nucleus
The gas transport through non-volatile random porous media is investigated
numerically. We extend our previous research of the transport of molecules
inside the uppermost layer of a cometary surface (Skorov and Rickmann, 1995;
Skorov et al. 2001). We assess the validity of the simplified capillary model
and its assumptions to simulate the gas flux trough the porous dust mantle as
it has been applied in cometary physics. A new microphysical computational
model for molecular transport in random porous media formed by packed spheres
is presented. The main transport characteristics such as the mean free path
distribution and the permeability are calculated for a wide range of model
parameters and compared with those obtained by more idealized models. The focus
in this comparison is on limitations inherent in the capillary model. Finally a
practical way is suggested to adjust the algebraic Clausing formula taking into
consideration the nonlinear dependence of permeability on layer porosity. The
retrieved dependence allows us to accurately calculate the permeability of
layers whose thickness and porosity vary in the range of values expected for
the near-surface regions of a cometary nucleus.Comment: 25 pages, 9 figure
Organics in comet 67P – a first comparative analysis of mass spectra from ROSINA–DFMS, COSAC and Ptolemy
The ESA Rosetta spacecraft followed comet 67P at a close distance for more than 2 yr. In addition, it deployed the lander Philae on to the surface of the comet. The (surface) composition of the comet is of great interest to understand the origin and evolution of comets. By combining measurements made on the comet itself and in the coma, we probe the nature of this surface material and compare it to remote sensing observations. We compare data from the double focusing mass spectrometer (DFMS) of the ROSINA experiment on ESA's Rosetta mission and previously published data from the two mass spectrometers COSAC (COmetary Sampling And Composition) and Ptolemy on the lander. The mass spectra of all three instruments show very similar patterns of mainly CHO-bearing molecules that sublimate at temperatures of 275 K. The DFMS data also show a great variety of CH-, CHN-, CHS-, CHO2- and CHNO-bearing saturated and unsaturated species. Methyl isocyanate, propanal and glycol aldehyde suggested by the earlier analysis of the measured COSAC spectrum could not be confirmed. The presence of polyoxymethylene in the Ptolemy spectrum was found to be unlikely. However, the signature of the aromatic compound toluene was identified in DFMS and Ptolemy data. Comparison with remote sensing instruments confirms the complex nature of the organics on the surface of 67P, which is much more diverse than anticipated
Deep generative modeling for single-cell transcriptomics.
Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in downstream analyses. Here we introduce single-cell variational inference (scVI), a ready-to-use scalable framework for the probabilistic representation and analysis of gene expression in single cells ( https://github.com/YosefLab/scVI ). scVI uses stochastic optimization and deep neural networks to aggregate information across similar cells and genes and to approximate the distributions that underlie observed expression values, while accounting for batch effects and limited sensitivity. We used scVI for a range of fundamental analysis tasks including batch correction, visualization, clustering, and differential expression, and achieved high accuracy for each task
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