Channel based generating function approach to the stochastic Hodgkin-Huxley neuronal system.
Ontology highlight
ABSTRACT:
SUBMITTER: Ling A
PROVIDER: S-EPMC4778126 | biostudies-other | 2016 Mar
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Peripheral nerve injury usually impairs neurological functions. The excessive oxidative stress and disrupted bioelectrical conduction gives rise to a hostile microenvironment and impedes nerve regeneration. Therefore, it is of urgent need to develop tissue engineering products which help alleviate the oxidative insults and restore bioelectrical signals. Melatonin (MLT) is an important endogenous hormone that diminishes the accumulation of reactive oxygen species. Reduced graphene oxide (RGO) possesses the excellent electrical conductivity and biocompatibility. In this study, a multilayered MLT/RGO/Polycaprolactone (PCL) composite scaffold was fabricated with beaded nanostructures to improve cell attachment and proliferation. It also exhibited stable mechanical properties by high elastic modulus and guaranteed structural integrity for nerve regeneration. The live/dead cell staining and cell counting kit assay were performed to evaluate the toxicity of the scaffold. JC-1 staining was carried out to assess the mitochondrial potential. The composite scaffold provided a biocompatible interface for cell viability and improved ATP production for energy supply. The scaffold improved the sensory and locomotor function recovery by walking track analysis and electrophysiological evaluation, reduced Schwann cell apoptosis and increased its proliferation. It further stimulated myelination and axonal outgrowth by enhancing S100β, myelin basic protein, β3-tubulin, and GAP43 levels. The findings demonstrated functional and morphological recovery by this biomimetic scaffold and indicated its potential for translational application.
| S-EPMC8841887 | biostudies-literature
Project description:Calcium puffs are local transient Ca(2+) releases from internal Ca(2+) stores such as the endoplasmic reticulum or the sarcoplasmic reticulum. Such release occurs through a cluster of inositol 1,4,5-trisphosphate receptors (IP3Rs). Based on the IP3R model (which is determined by fitting to stationary single-channel data) and nonstationary single-channel data, we construct a new IP3R model that includes time-dependent rates of mode switches. A point-source model of Ca(2+) puffs is then constructed based on the new IP3R model and is solved by a hybrid Gillespie method with adaptive timing. Model results show that a relatively slow recovery of an IP3R from Ca(2+) inhibition is necessary to reproduce most of the experimental outcomes, especially the nonexponential interpuff interval distributions. The number of receptors in a cluster could be severely underestimated when the recovery is sufficiently slow. Furthermore, we find that, as the number of IP3Rs increases, the average duration of puffs initially increases but then becomes saturated, whereas the average decay time keeps increasing linearly. This gives rise to the observed asymmetric puff shape.
| S-EPMC3852038 | biostudies-literature
Project description:The structure of microbiomes is often classified into discrete or semi-discrete types potentially differing in community-scale functional profiles. Elucidating the mechanisms that generate such "alternative states" of microbiome compositions has been one of the major challenges in ecology and microbiology. In a time-series analysis of experimental microbiomes, we here show that both deterministic and stochastic ecological processes drive divergence of alternative microbiome states. We introduced species-rich soil-derived microbiomes into eight types of culture media with 48 replicates, monitoring shifts in community compositions at six time points (8 media × 48 replicates × 6 time points = 2304 community samples). We then confirmed that microbial community structure diverged into a few state types in each of the eight medium conditions as predicted in the presence of both deterministic and stochastic community processes. In other words, microbiome structure was differentiated into a small number of reproducible compositions under the same environment. This fact indicates not only the presence of selective forces leading to specific equilibria of community-scale resource use but also the influence of demographic drift (fluctuations) on the microbiome assembly. A reference-genome-based analysis further suggested that the observed alternative states differed in ecosystem-level functions. These findings will help us examine how microbiome structure and functions can be controlled by changing the "stability landscapes" of ecological community compositions.
| S-EPMC10897905 | biostudies-literature
Project description:This article presents a new modeling strategy in functional data analysis. We consider the problem of estimating an unknown smooth function given functional data with noise. The unknown function is treated as the realization of a stochastic process, which is incorporated into a diffusion model. The method of smoothing spline estimation is connected to a special case of this approach. The resulting models offer great flexibility to capture the dynamic features of functional data, and allow straightforward and meaningful interpretation. The likelihood of the models is derived with Euler approximation and data augmentation. A unified Bayesian inference method is carried out via a Markov chain Monte Carlo algorithm including a simulation smoother. The proposed models and methods are illustrated on some prostate-specific antigen data, where we also show how the models can be used for forecasting.
| S-EPMC3128649 | biostudies-literature
Project description:In neurons, intracellular calcium signals have crucial roles in activating neurotransmitter release and in triggering alterations in neuronal function. Calmodulin has been widely studied as a Ca(2+) sensor that has several defined roles in neuronal Ca(2+) signalling, but members of the neuronal calcium sensor protein family have also begun to emerge as key components in a number of regulatory pathways and have increased the diversity of neuronal Ca(2+) signalling pathways. The differing properties of these proteins allow them to have discrete, non-redundant functions.
| S-EPMC1887812 | biostudies-literature
Project description:A 3-methoxythiophene-based indophenine reaction with N-(2-hexyldecyl)isatin in the presence of concentrated sulfuric acid produces an indophenine cis-trans isomeric dynamic equilibrium system, which is dominated by the (Z,E,Z) configuration with a trace of the (Z,Z,Z) configuration.
| S-EPMC10061653 | biostudies-literature
Project description:In this work, a high-resolution atomic force acoustic microscopy imaging technique is developed in order to obtain the local indentation modulus at the nanoscale level. The technique uses a model that gives a qualitative relationship between a set of contact resonance frequencies and the indentation modulus. It is based on white-noise excitation of the tip-sample interaction and uses system theory for the extraction of the resonance modes. During conventional scanning, for each pixel, the tip-sample interaction is excited with a white-noise signal. Then, a fast Fourier transform is applied to the deflection signal that comes from the photodiodes of the atomic force microscopy (AFM) equipment. This approach allows for the measurement of several vibrational modes in a single step with high frequency resolution, with less computational cost and at a faster speed than other similar techniques. This technique is referred to as stochastic atomic force acoustic microscopy (S-AFAM), and the frequency shifts of the free resonance frequencies of an AFM cantilever are used to determine the mechanical properties of a material. S-AFAM is implemented and compared with a conventional technique (resonance tracking-atomic force acoustic microscopy, RT-AFAM). A sample of a graphite film on a glass substrate is analyzed. S-AFAM can be implemented in any AFM system due to its reduced instrumentation requirements compared to conventional techniques.
| S-EPMC7214876 | biostudies-literature
Project description:Previous studies have shown that biological noise may drive dynamic phenotypic mosaicism in isogenic unicellular organisms. However, there is no evidence for a similar mechanism operating in metazoans. Here we show that the endothelial-restricted gene, von Willebrand factor (VWF), is expressed in a mosaic pattern in the capillaries of many vascular beds and in the aorta. In capillaries, the mosaicism is dynamically regulated, with VWF switching between ON and OFF states during the lifetime of the animal. Clonal analysis of cultured endothelial cells reveals that dynamic mosaic heterogeneity is controlled by a low-barrier, noise-sensitive bistable switch that involves random transitions in the DNA methylation status of the VWF promoter. Finally, the hearts of VWF-null mice demonstrate an abnormal endothelial phenotype as well as cardiac dysfunction. Together, these findings suggest a novel stochastic phenotype switching strategy for adaptive homoeostasis in the adult vasculature.
| S-EPMC5154372 | biostudies-literature
Project description:Multiparameter optimization (MPO) scoring functions are popular tools for providing guidance on how to design desired molecules in medicinal chemistry. The utility of a new probabilistic MPO (pMPO) scoring function method and its application as a scoring function for CNS drugs are described in this letter. In this new approach, a minimal number of statistically determined empirical boundaries is combined with the probability distribution of the desired molecules to define desirability functions. This approach attempts to minimize the number of parameters that define MPO scores while maintaining a high level of predictive power. Results obtained from a test-set of orally approved drugs show that the pMPO approach described here can be used to separate desired molecules from undesired ones with accuracy comparable to a Bayesian model with the advantage of better human interpretability. The application of this pMPO approach for blood-brain barrier penetrant drugs is also described.
| S-EPMC4716604 | biostudies-literature
Project description:Mass spectrometry is used to investigate global changes in protein abundance in cell lysates. Increasingly powerful methods of data collection have emerged over the past decade, but this has left researchers with the task of sifting through mountains of data for biologically significant results. Often, the end result is a list of proteins with no obvious quantitative relationships to define the larger context of changes in cell behavior. Researchers are often forced to perform a manual analysis from this list or to fall back on a range of disparate tools, which can hinder the communication of results and their reproducibility. To address these methodological problems, we developed Annotator, an application that filters validated mass spectrometry data and applies a battery of standardized heuristic and statistical tests to determine significance. To address systems-level interpretations, we incorporated UniProt and Gene Ontology keywords as statistical units of analysis, yielding quantitative information about changes in abundance for an entire functional category. This provides a consistent and quantitative method for formulating conclusions about cellular behavior, independent of network models or standard enrichment analyses. Annotator allows for "bottom-up" annotations that are based on experimental data and not inferred by comparison to external or hypothetical models. Annotator was developed as an independent postprocessing platform that runs on all common operating systems, thereby providing a useful tool for establishing the inherently dynamic nature of functional annotations, which depend on results from ongoing proteomic experiments. Annotator is available for download at http://people.cs.uchicago.edu/?tyler/annotator/annotator_desktop_0.1.tar.gz .
| S-EPMC3292622 | biostudies-literature