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Stochastic modeling

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https://www.readbyqxmd.com/read/28543271/characterization-of-cellular-adhesion-reinforcement-by-multiple-bond-force-spectroscopy-in-alveolar-epithelial-cells
#1
Nguyen Ngoc-Minh, Angely Christelle, Andre Dias Sofia, Planus Emmanuelle, Filoche Marcel, Pelle Gabriel, Louis Bruno, Isabey Daniel
BACKGROUND: Integrin-mediated adhesion is a key process by which cells physically connect their environment, express sensitivity and adaptation through mechanotransduction. A critical step of cell adhesion is the formation of the first bonds which individually generate weak contacts (∼tens pN) but can sustain thousand times higher forces (∼tens nN) when associated. RESULTS: We propose an experimental validation by multiple bond force spectroscopy (MFS) of a stochastic model predicting adhesion reinforcement permitted by non cooperative, multiple bonds on which force is homogeneously distributed (called parallel bond configuration)...
May 24, 2017: Biology of the Cell
https://www.readbyqxmd.com/read/28542717/calibration-of-a-land-subsidence-model-using-insar-data-via-the-ensemble-kalman-filter
#2
Liangping Li, Meijing Zhang, Kurt Katzenstein
The application of interferometric synthetic aperture radar (InSAR) has been increasingly used to improve capabilities to model land subsidence in hydrogeologic studies. A number of investigations over the last decade show how spatially detailed time-lapse images of ground displacements could be utilized to advance our understanding for better predictions. In this work, we use simulated land subsidences as observed measurements, mimicking InSAR data to inversely infer inelastic specific storage in a stochastic framework...
May 23, 2017: Ground Water
https://www.readbyqxmd.com/read/28542620/elevated-catalase-expression-in-a-fungal-pathogen-is-a-double-edged-sword-of-iron
#3
Arnab Pradhan, Carmen Herrero-de-Dios, Rodrigo Belmonte, Susan Budge, Angela Lopez Garcia, Aljona Kolmogorova, Keunsook K Lee, Brennan D Martin, Antonio Ribeiro, Attila Bebes, Raif Yuecel, Neil A R Gow, Carol A Munro, Donna M MacCallum, Janet Quinn, Alistair J P Brown
Most fungal pathogens of humans display robust protective oxidative stress responses that contribute to their pathogenicity. The induction of enzymes that detoxify reactive oxygen species (ROS) is an essential component of these responses. We showed previously that ectopic expression of the heme-containing catalase enzyme in Candida albicans enhances resistance to oxidative stress, combinatorial oxidative plus cationic stress, and phagocytic killing. Clearly ectopic catalase expression confers fitness advantages in the presence of stress, and therefore in this study we tested whether it enhances fitness in the absence of stress...
May 22, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28542484/simulating-within-vector-generation-of-the-malaria-parasite-diversity
#4
Lauren M Childs, Olivia F Prosper
Plasmodium falciparum, the most virulent human malaria parasite, undergoes asexual reproduction within the human host, but reproduces sexually within its vector host, the Anopheles mosquito. Consequently, the mosquito stage of the parasite life cycle provides an opportunity to create genetically novel parasites in multiply-infected mosquitoes, potentially increasing parasite population diversity. Despite the important implications for disease transmission and malaria control, a quantitative mapping of how parasite diversity entering a mosquito relates to diversity of the parasite exiting, has not been undertaken...
2017: PloS One
https://www.readbyqxmd.com/read/28542396/using-stochastic-language-models-slm-to-map-lexical-syntactic-and-phonological-information-processing-in-the-brain
#5
Alessandro Lopopolo, Stefan L Frank, Antal van den Bosch, Roel M Willems
Language comprehension involves the simultaneous processing of information at the phonological, syntactic, and lexical level. We track these three distinct streams of information in the brain by using stochastic measures derived from computational language models to detect neural correlates of phoneme, part-of-speech, and word processing in an fMRI experiment. Probabilistic language models have proven to be useful tools for studying how language is processed as a sequence of symbols unfolding in time. Conditional probabilities between sequences of words are at the basis of probabilistic measures such as surprisal and perplexity which have been successfully used as predictors of several behavioural and neural correlates of sentence processing...
2017: PloS One
https://www.readbyqxmd.com/read/28541916/variance-constrained-state-estimation-for-complex-networks-with-randomly-varying-topologies
#6
Hongli Dong, Nan Hou, Zidong Wang, Weijian Ren
This paper investigates the variance-constrained H∞ state estimation problem for a class of nonlinear time-varying complex networks with randomly varying topologies, stochastic inner coupling, and measurement quantization. A Kronecker delta function and Markovian jumping parameters are utilized to describe the random changes of network topologies. A Gaussian random variable is introduced to model the stochastic disturbances in the inner coupling of complex networks. As a kind of incomplete measurements, measurement quantization is taken into consideration so as to account for the signal distortion phenomenon in the transmission process...
May 23, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28539753/maximum-principle-for-a-stochastic-delayed-system-involving-terminal-state-constraints
#7
Jiaqiang Wen, Yufeng Shi
We investigate a stochastic optimal control problem where the controlled system is depicted as a stochastic differential delayed equation; however, at the terminal time, the state is constrained in a convex set. We firstly introduce an equivalent backward delayed system depicted as a time-delayed backward stochastic differential equation. Then a stochastic maximum principle is obtained by virtue of Ekeland's variational principle. Finally, applications to a state constrained stochastic delayed linear-quadratic control model and a production-consumption choice problem are studied to illustrate the main obtained result...
2017: Journal of Inequalities and Applications
https://www.readbyqxmd.com/read/28539514/wind-conditions-and-geography-shape-the-first-outbound-migration-of-juvenile-honey-buzzards-and-their-distribution-across-sub-saharan-africa
#8
W M G Vansteelant, J Kekkonen, P Byholm
Contemporary tracking studies reveal that low migratory connectivity between breeding and non-breeding ranges is common in migrant landbirds. It is unclear, however, how internal factors and early-life experiences of individual migrants shape the development of their migration routes and concomitant population-level non-breeding distributions. Stochastic wind conditions and geography may determine whether and where migrants end up by the end of their journey. We tested this hypothesis by satellite-tagging 31 fledgling honey buzzards Pernis apivorus from southern Finland and used a global atmospheric reanalysis model to estimate the wind conditions they encountered on their first outbound migration...
May 31, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28539481/inferring-stratified-parasitoid-dispersal-mechanisms-and-parameters-from-coarse-data-using-mathematical-and-bayesian-methods
#9
Christopher Strickland, Nadiah P Kristensen, Laura Miller
Biological invasions have movement at the core of their success. However, due to difficulties in collecting data, medium- and long-distance dispersal of small insects has long been poorly understood and likely to be underestimated. The agricultural release of parasitic hymenoptera, a group of wasps that are critical for biological pest control, represents a rare opportunity to study the spread of insects on multiple spatial scales. As these insects are typically less than 1 mm in size and are challenging to track individually, a first-time biocontrol release will provide a known spatial position and time of initial release for all individuals that are subsequently collected...
May 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28538335/bigaussian-wavefront-model-for-normal-and-keratoconic-eyes
#10
Jos J Rozema, Pablo Rodríguez, Rafael Navarro, Carina Koppen
PURPOSE: To report bigaussian multivariate wavefront models capable of stochastically generating an unlimited amount of plausible wavefront data for either normal or keratoconic eyes. METHODS: The models use centroid wavefront data measured previously with an iTrace in 330 healthy right eyes and 122 keratoconic right eyes. These centroids were fitted to an 11th-order Zernike series, followed by principal component analysis to reduce dimensionality and remove correlations...
June 2017: Optometry and Vision Science: Official Publication of the American Academy of Optometry
https://www.readbyqxmd.com/read/28538151/mapping-interpuff-interval-distribution-to-the-properties-of-inositol-trisphosphate-receptors
#11
Pengxing Cao, Martin Falcke, James Sneyd
Tightly clustered inositol trisphosphate receptors (IP3Rs) control localized Ca(2+) liberation from the endoplasmic reticulum to generate repetitive Ca(2+) puffs. Distributions of the interpuff interval (IPI), i.e., the waiting time between successive puffs, are found to be well characterized by a probability density function involving only two parameters, λ and ξ, which represent the basal rate of puff generation and the recovery rate from refractoriness, respectively. However, how the two parameters depend on the kinetic parameters of single IP3Rs in a cluster is still unclear...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28536035/seasonality-can-induce-coexistence-of-multiple-bet-hedging-strategies-in-dictyostelium-discoideum-via-storage-effect
#12
Ricardo Martínez-García, Corina E Tarnita
The social amoeba Dictyostelium discoideum has been recently suggested as an example of bet-hedging in microbes. In the presence of resources, amoebae reproduce as unicellular organisms. Resource depletion, however, leads to a starvation phase in which the population splits between aggregators, which form a fruiting body made of a stalk and resistant spores, and non-aggregators, which remain as vegetative cells. Spores are favored when starvation periods are long, but vegetative cells can exploit resources in environments where food replenishes quickly...
May 20, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28535715/two-part-models-with-stochastic-processes-for-modelling-longitudinal-semicontinuous-data-computationally-efficient-inference-and-modelling-the-overall-marginal-mean
#13
Sean Yiu, Brian Dm Tom
Several researchers have described two-part models with patient-specific stochastic processes for analysing longitudinal semicontinuous data. In theory, such models can offer greater flexibility than the standard two-part model with patient-specific random effects. However, in practice, the high dimensional integrations involved in the marginal likelihood (i.e. integrated over the stochastic processes) significantly complicates model fitting. Thus, non-standard computationally intensive procedures based on simulating the marginal likelihood have so far only been proposed...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28535148/stochastic-gene-expression-conditioned-on-large-deviations
#14
Jordan M Horowitz, Rahul V Kulkarni
The intrinsic stochasticity of gene expression can give rise to large fluctuations and rare events that drive phenotypic variation in a population of genetically identical cells. Characterizing the fluctuations that give rise to such rare events motivates the analysis of large deviations in stochastic models of gene expression. Recent developments in non-equilibrium statistical mechanics have led to a framework for analyzing Markovian processes conditioned on rare events and for representing such processes by conditioning-free driven Markovian processes...
May 23, 2017: Physical Biology
https://www.readbyqxmd.com/read/28533955/among-site-variability-in-the-stochastic-dynamics-of-east-african-coral-reefs
#15
Katherine A Allen, John F Bruno, Fiona Chong, Damian Clancy, Tim R McClanahan, Matthew Spencer, Kamila Żychaluk
Coral reefs are dynamic systems whose composition is highly influenced by unpredictable biotic and abiotic factors. Understanding the spatial scale at which long-term predictions of reef composition can be made will be crucial for guiding conservation efforts. Using a 22-year time series of benthic composition data from 20 reefs on the Kenyan and Tanzanian coast, we developed Bayesian vector autoregressive state-space models for reef dynamics, incorporating among-site variability, and quantified their long-term behaviour...
2017: PeerJ
https://www.readbyqxmd.com/read/28533237/antimicrobial-resistance-risks-of-cholera-prophylaxis-for-united-nations-peacekeepers
#16
Amber Kunkel, Joseph A Lewnard, Virginia E Pitzer, Ted Cohen
More than five years after a United Nations peacekeeping battalion introduced cholera to Haiti, over 150,000 peacekeepers continue to be deployed annually from cholera endemic countries. The United Nations has thus far declined to provide antimicrobial chemoprophylaxis to peacekeepers, a policy based largely on concerns that the risks of drug resistance generation and spread would outweigh the potential benefits of preventing future cholera importations. In this study, we sought to better understand the relative benefits and risks of cholera chemoprophylaxis for peacekeepers in terms of antibiotic resistance...
May 22, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28530664/flexible-information-routing-by-transient-synchrony
#17
Agostina Palmigiano, Theo Geisel, Fred Wolf, Demian Battaglia
Perception, cognition and behavior rely on flexible communication between microcircuits in distinct cortical regions. The mechanisms underlying rapid information rerouting between such microcircuits are still unknown. It has been proposed that changing patterns of coherence between local gamma rhythms support flexible information rerouting. The stochastic and transient nature of gamma oscillations in vivo, however, is hard to reconcile with such a function. Here we show that models of cortical circuits near the onset of oscillatory synchrony selectively route input signals despite the short duration of gamma bursts and the irregularity of neuronal firing...
May 22, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28530655/a-quantitative-and-multiplexed-approach-to-uncover-the-fitness-landscape-of-tumor-suppression-in-vivo
#18
Zoë N Rogers, Christopher D McFarland, Ian P Winters, Santiago Naranjo, Chen-Hua Chuang, Dmitri Petrov, Monte M Winslow
Cancer growth is a multistage, stochastic evolutionary process. While cancer genome sequencing has been instrumental in identifying the genomic alterations that occur in human tumors, the consequences of these alterations on tumor growth remain largely unexplored. Conventional genetically engineered mouse models enable the study of tumor growth in vivo, but they are neither readily scalable nor sufficiently quantitative to unravel the magnitude and mode of action of many tumor-suppressor genes. Here, we present a method that integrates tumor barcoding with ultradeep barcode sequencing (Tuba-seq) to interrogate tumor-suppressor function in mouse models of human cancer...
May 22, 2017: Nature Methods
https://www.readbyqxmd.com/read/28530167/biofilm-community-succession-a-neutral-perspective
#19
Stephen Woodcock, William T Sloan
Although biofilms represent one of the dominant forms of life in aqueous environments, our understanding of the assembly and development of their microbial communities remains relatively poor. In recent years, several studies have addressed this and have extended the concepts of succession theory in classical ecology into microbial systems. From these datasets, niche-based conceptual models have been developed explaining observed biodiversity patterns and their dynamics. These models have not, however, been formulated mathematically and so remain untested...
May 22, 2017: Microbiology
https://www.readbyqxmd.com/read/28529938/senescence-inflammatory-regulation-of-reparative-cellular-reprogramming-in-aging-and-cancer
#20
Javier A Menendez, Tomás Alarcón
The inability of adult tissues to transitorily generate cells with functional stem cell-like properties is a major obstacle to tissue self-repair. Nuclear reprogramming-like phenomena that induce a transient acquisition of epigenetic plasticity and phenotype malleability may constitute a reparative route through which human tissues respond to injury, stress, and disease. However, tissue rejuvenation should involve not only the transient epigenetic reprogramming of differentiated cells, but also the committed re-acquisition of the original or alternative committed cell fate...
2017: Frontiers in Cell and Developmental Biology
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