scholarly journals QPot: An R Package for Stochastic Differential Equation Quasi-Potential Analysis

2015 ◽  
Author(s):  
Christopher M. Moore ◽  
Christopher R. Stieha ◽  
Ben C. Nolting ◽  
Maria K. Cameron ◽  
Karen C. Abbott
Keyword(s):  
Stochastic Systems ◽  
Alternative Stable States ◽  
Worked Examples ◽  
R Package ◽  
Two Dimensional ◽  
Stable States ◽  
Potential Analysis ◽  
Relative Stabilities ◽  
Wide Range ◽  
Key Features

QPot is an R package for analyzing two-dimensional systems of stochastic differential equations. It provides users with a wide range of tools to simulate, analyze, and visualize the dynamics of these systems. One of QPot's key features is the computation of the quasi-potential, an important tool for studying stochastic systems. Quasi-potentials are particularly useful for comparing the relative stabilities of equilibria in systems with alternative stable states. This paper describes QPot's primary functions, and explains how quasi-potentials can yield insights about the dynamics of stochastic systems. Three worked examples guide users through the application of QPot's functions.

scholarly journals Serotonergic Axons as Fractional Brownian Motion Paths: Insights into the Self-organization of Regional Densities

2019 ◽  
Author(s):  
Skirmantas Janušonis ◽  
Nils Detering ◽  
Ralf Metzler ◽  
Thomas Vojta
Keyword(s):  
Brownian Motion ◽  
Fractional Brownian Motion ◽  
Adult Brain ◽  
The Self ◽  
Self Organization ◽  
Dense Matrix ◽  
Two Dimensional ◽  
Wide Range ◽  
Motion Paths ◽  
Key Features

ABSTRACTAll vertebrate brains contain a dense matrix of thin fibers that release serotonin (5-hydroxytryptamine), a neurotransmitter that modulates a wide range of neural, glial, and vascular processes. Perturbations in the density of this matrix have been associated with a number of mental disorders, including autism and depression, but its self-organization and plasticity remain poorly understood. We introduce a model based on reflected Fractional Brownian Motion (FBM), a rigorously defined stochastic process, and show that it recapitulates some key features of regional serotonergic fiber densities. Specifically, we use supercomputing simulations to model fibers as FBM-paths in two-dimensional brain-like domains and demonstrate that the resultant steady state distributions approximate the fiber distributions in physical brain sections immunostained for the serotonin transporter (a marker for serotonergic axons in the adult brain). We suggest that this framework can support predictive descriptions and manipulations of the serotonergic matrix and that it can be further extended to incorporate the detailed physical properties of the fibers and their environment.

scholarly journals Many shades of green: the dynamic tropical forest–savannah transition zones

2016 ◽  
Vol 371 (1703) ◽  
pp. 20150308 ◽  
Author(s):  
Immaculada Oliveras ◽  
Yadvinder Malhi
Keyword(s):  
Fire Suppression ◽  
Alternative Stable States ◽  
Terrestrial Ecosystems ◽  
Fire Regimes ◽  
Stable States ◽  
Ecological Processes ◽  
Wide Range ◽  
History Of ◽  
Tropical Areas ◽  
Global And Local

The forest–savannah transition is the most widespread ecotone in tropical areas, separating two of the most productive terrestrial ecosystems. Here, we review current understanding of the factors that shape this transition, and how it may change under various drivers of local or global change. At broadest scales, the location of the transition is shaped by water availability, mediated strongly at local scales by fire regimes, herbivory pressure and spatial variation in soil properties. The frequently dynamic nature of this transition suggests that forest and savannah can exist as alternative stable states, maintained and separated by fire–grass feedbacks and tree shade–fire suppression feedback. However, this theory is still contested and the relative contributions of the main biotic and abiotic drivers and their interactions are yet not fully understood. These drivers interplay with a wide range of ecological processes and attributes at the global, continental, regional and local scales. The evolutionary history of the biotic and abiotic drivers and processes plays an important role in the current distributions of these transitions as well as in their species composition and ecosystem functioning. This ecotone can be sensitive to shifts in climate and other driving factors, but is also potentially stabilized by negative feedback processes. There is abundant evidence that these transitions are shifting under contemporary global and local changes, but the direction of shift varies according to region. However, it still remains uncertain how these transitions will respond to rapid and multi-faceted ongoing current changes, and how increasing human influence will interact with these shifts. This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’.

A Guide to the Bayesian Analysis of Consumer Behavior Experiments With BANOVA Using Worked Examples

2021 ◽  
pp. 183933492110341
Author(s):  
Michel Wedel ◽  
Anna Kopyakova
Keyword(s):  
Bayesian Analysis ◽  
Three Dimensional ◽  
Worked Examples ◽  
R Package ◽  
Mental Simulation ◽  
Three Dimensional Objects ◽  
Continuous Covariates ◽  
Wide Range ◽  
Within Subjects ◽  
Psychological Mechanism

This article provides a step-by-step guide for the analysis of experiments using Bayesian methods, using the BANOVA R package. We provide two worked examples. First, we reanalyze data from research by Romano and Balliet, which examined reciprocity and conformity as alternative mechanisms for cooperation between partners. The study has a between-subjects design and Poisson dependent variable, and we use Bayesian floodlight analysis to explore the interaction between reciprocity/conformity and two continuous covariates. Second, we reanalyze data from a study by Perfecto, Donnelly, and Critcher, who investigated whether mental simulation could be the psychological mechanism that explains how people make volume judgments of three-dimensional objects. The study has a mixed between- and within-subjects design with a Normal dependent variable, and we use Bayesian simple effects to explore the interactions between mental simulation and the shape and orientation of cups. The applications demonstrate the versatility of BANOVA (Bayesian Analysis of Variance) in analyzing a wide range of experimental designs and reveal that the results of the Bayesian analyses differ to some degree from those of the original studies.

scholarly journals Alternative stable states in the intestinal ecosystem: proof of concept in a rat model and a perspective of therapeutic implications

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Maarten Van de Guchte ◽  
Sebastian D. Burz ◽  
Julie Cadiou ◽  
Jiangbo Wu ◽  
Stanislas Mondot ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Alternative Stable States ◽  
Therapeutic Strategies ◽  
Proof Of Concept ◽  
Alternative States ◽  
Stable States ◽  
Inflammatory Conditions ◽  
Inflammatory Status ◽  
Immune Mediated ◽  
Wide Range

Abstract Background Chronic immune-mediated diseases are rapidly expanding and notoriously difficult to cure. Altered relatively stable intestinal microbiota configurations are associated with several of these diseases, and with a possible pre-disease condition (more susceptible to disease development) of the host-microbiota ecosystem. These observations are reminiscent of the behavior of an ecosystem with alternative stable states (different stable configurations that can exist under identical external conditions), and we recently postulated that health, pre-disease and disease represent such alternative states. Here, our aim was to examine if alternative stable states indeed exist in the intestinal ecosystem. Results Rats were exposed to varying concentrations of DSS in order to create a wide range of mildly inflammatory conditions, in a context of diet-induced low microbiota diversity. The consequences for the intestinal microbiota were traced by 16S rRNA gene profiling over time, and inflammation of the distal colon was evaluated at sacrifice, 45 days after the last DSS treatment. The results provide the first formal experimental proof for the existence of alternative stable states in the rat intestinal ecosystem, taking both microbiota and host inflammatory status into consideration. The alternative states are host-microbiota ecosystem states rather than independent and dissociated microbiota and host states, and inflammation can prompt stable state-transition. Based on these results, we propose a conceptual model providing new insights in the interplay between host inflammatory status and microbiota status. These new insights call for innovative therapeutic strategies to cure (pre-)disease. Conclusions We provide proof of concept showing the existence of alternative stable states in the rat intestinal ecosystem. We further propose a model which, if validated in humans, will support innovative diagnosis, therapeutic strategy, and monitoring in the treatment of chronic inflammatory conditions. This model provides a strong rationale for the application of combinatorial therapeutic strategies, targeting host and microbiota rather than only one of the two in chronic immune-mediated diseases.

Fire Feedbacks with Vegetation and Alternative Stable States

2009 ◽  
Vol 18 (1) ◽  
pp. 159-173 ◽  
Author(s):  
Brian Beckage ◽  
Chris Ellingwood ◽  
Keyword(s):  
Alternative Stable States ◽  
Stable States ◽  
Fire Feedbacks

Aromatic Volatile Composition of Celery and Celeriac Cultivars

HortScience ◽  
1990 ◽  
Vol 25 (5) ◽  
pp. 556-559 ◽  
Author(s):  
Fredy Van Wassenhove ◽  
Patrick Dirinck ◽  
Georges Vulsteke ◽  
Niceas Schamp
Keyword(s):  
Volatile Compounds ◽  
Chromatographic Method ◽  
Apium Graveolens ◽  
Volatile Components ◽  
Two Dimensional ◽  
Qualitative Composition ◽  
Volatile Composition ◽  
Wide Range ◽  
Gas Chromatographic Method ◽  
Identification And Quantification

A two-dimensional capillary gas chromatographic method was developed to separate and quantify aromatic volatiles of celery in one analysis. The isolation, identification, and quantification of the volatile compounds of four cultivars of blanching celery (Apium graveolens L. var. dulce) and six cultivars of celeriac (Apium graveolens L. var. rapaceum) are described. The qualitative composition of Likens-Nickerson extracts of both cultivars is similar. The concentration of terpenes and phthalides, the key volatile components, found in various cultivars of both celery and celeriac varied over a wide range.

scholarly journals BloodGen3Module: Blood transcriptional module repertoire analysis and visualization using R

2021 ◽  
Author(s):  
Darawan Rinchai ◽  
Jessica Roelands ◽  
Mohammed Toufiq ◽  
Wouter Hendrickx ◽  
Matthew C Altman ◽  
...  
Keyword(s):  
Transcript Abundance ◽  
R Package ◽  
Supplementary Information ◽  
Illustrative Case ◽  
Bioinformatic Tools ◽  
Transcriptional Module ◽  
Wide Range ◽  
Downstream Analysis ◽  
Computing Module ◽  
Parallel Workflow

Abstract Motivation We previously described the construction and characterization of generic and reusable blood transcriptional module repertoires. More recently we released a third iteration (“BloodGen3” module repertoire) that comprises 382 functionally annotated gene sets (modules) and encompasses 14,168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires. Results We have developed and describe here a R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states. Availability The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Towards explicit regulating-ion-transport: nanochannels with only function-elements at outer-surface

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qun Ma ◽  
Yu Li ◽  
Rongsheng Wang ◽  
Hongquan Xu ◽  
Qiujiao Du ◽  
...  
Keyword(s):  
Ion Transport ◽  
Numerical Simulations ◽  
Power Density ◽  
Outer Surface ◽  
Internal Resistance ◽  
Porous Membranes ◽  
Two Dimensional ◽  
Ionic Selectivity ◽  
Key Features ◽  
Energy Conversion Devices

AbstractFunction elements (FE) are vital components of nanochannel-systems for artificially regulating ion transport. Conventionally, the FE at inner wall (FEIW) of nanochannel−systems are of concern owing to their recognized effect on the compression of ionic passageways. However, their properties are inexplicit or generally presumed from the properties of the FE at outer surface (FEOS), which will bring potential errors. Here, we show that the FEOS independently regulate ion transport in a nanochannel−system without FEIW. The numerical simulations, assigned the measured parameters of FEOS to the Poisson and Nernst-Planck (PNP) equations, are well fitted with the experiments, indicating the generally explicit regulating-ion-transport accomplished by FEOS without FEIW. Meanwhile, the FEOS fulfill the key features of the pervious nanochannel systems on regulating-ion-transport in osmotic energy conversion devices and biosensors, and show advantages to (1) promote power density through concentrating FE at outer surface, bringing increase of ionic selectivity but no obvious change in internal resistance; (2) accommodate probes or targets with size beyond the diameter of nanochannels. Nanochannel-systems with only FEOS of explicit properties provide a quantitative platform for studying substrate transport phenomena through nanoconfined space, including nanopores, nanochannels, nanopipettes, porous membranes and two-dimensional channels.

scholarly journals Prediction of Wide Range Two-Dimensional Refractivity Using an IDW Interpolation Method from High-Altitude Refractivity Data of Multiple Meteorological Observatories

2021 ◽  
Vol 11 (4) ◽  
pp. 1431
Author(s):  
Sungsik Wang ◽  
Tae Heung Lim ◽  
Kyoungsoo Oh ◽  
Chulhun Seo ◽  
Hosung Choo
Keyword(s):  
High Altitude ◽  
Korean Peninsula ◽  
Interpolation Method ◽  
Atmospheric Condition ◽  
Propagation Path ◽  
Two Dimensional ◽  
Data Set ◽  
Wide Range ◽  
Atmospheric Data ◽  
Terrain Surface

This article proposes a method for the prediction of wide range two-dimensional refractivity for synthetic aperture radar (SAR) applications, using an inverse distance weighted (IDW) interpolation of high-altitude radio refractivity data from multiple meteorological observatories. The radio refractivity is extracted from an atmospheric data set of twenty meteorological observatories around the Korean Peninsula along a given altitude. Then, from the sparse refractive data, the two-dimensional regional radio refractivity of the entire Korean Peninsula is derived using the IDW interpolation, in consideration of the curvature of the Earth. The refractivities of the four seasons in 2019 are derived at the locations of seven meteorological observatories within the Korean Peninsula, using the refractivity data from the other nineteen observatories. The atmospheric refractivities on 15 February 2019 are then evaluated across the entire Korean Peninsula, using the atmospheric data collected from the twenty meteorological observatories. We found that the proposed IDW interpolation has the lowest average, the lowest average root-mean-square error (RMSE) of ∇M (gradient of M), and more continuous results than other methods. To compare the resulting IDW refractivity interpolation for airborne SAR applications, all the propagation path losses across Pohang and Heuksando are obtained using the standard atmospheric condition of ∇M = 118 and the observation-based interpolated atmospheric conditions on 15 February 2019. On the terrain surface ranging from 90 km to 190 km, the average path losses in the standard and derived conditions are 179.7 dB and 182.1 dB, respectively. Finally, based on the air-to-ground scenario in the SAR application, two-dimensional illuminated field intensities on the terrain surface are illustrated.

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