Stochastic modeling

UNLABELLED: The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions...

BACKGROUND: Dengue is the most prevalent mosquito-borne viral disease and a major public health problem worldwide. Most primary infections with the four dengue virus serotypes (DENV1-4) are inapparent; nevertheless, prior research has primarily focused on symptomatic infections, which has limited our understanding of the epidemiological burden and spectrum of disease of each DENV serotype. Our study addresses this bottleneck in dengue research by providing a new method and a detailed examination of primary inapparent infections...

In this work we propose a modified Chord Length Sampling (CLS) algorithm, endowed with two layers of "memory effects," aimed at solving particle transport problems in one-dimensional spatially nonhomogeneous Markov media. CLS algorithms are a family of Monte Carlo methods which account for the stochastic nature of the media by sampling on-the-fly the random interfaces between material phases during the particle propagation. The possibility for the particles to remember the last crossed interfaces increases the accuracy of these models with respect to reference solutions obtained by solving the Boltzmann equation on a large number of realizations of the Markov media...

The motivation for the proposed work is drawn from the attachment-detachment observed in biological and physical transport processes that entail finite resources. We investigate the influence of limited particle availability on particle dynamics within two parallel totally asymmetric simple exclusion lanes, with one lane incorporating only particle detachment and the other considering particle attachment. We establish a theoretical framework by employing vertical mean-field theory in conjunction with singular perturbation technique...

We study a nonequilibrium ferromagnetic mean-field spin model exhibiting a phase with spontaneous temporal oscillations of the magnetization, on top of the usual paramagnetic and ferromagnetic phases. This behavior is obtained by introducing dynamic field variables coupled to the spins through nonreciprocal couplings. We determine a nonequilibrium generalization of the Landau free energy in terms of the large deviation function of the magnetization and of an appropriately defined smoothed stochastic time derivative of the magnetization...

Resetting is a renewal mechanism in which a process is intermittently repeated after a random or fixed time. This simple act of stop and repeat profoundly influences the behavior of a system as exemplified by the emergence of nonequilibrium properties and expedition of search processes. Herein we explore the ramifications of stochastic resetting in the context of a single-file system called random average process (RAP) in one dimension. In particular, we focus on the dynamics of tracer particles and analytically compute the variance, equal time correlation, autocorrelation, and unequal time correlation between the positions of different tracer particles...

The statistics of the diffusive motion of particles often serve as an experimental proxy for their interaction with the environment. However, inferring the physical properties from the observed trajectories is challenging. Inspired by a recent experiment, here we analyze the problem of particles undergoing two-dimensional Brownian motion with transient tethering to the surface. We model the problem as a hidden Markov model where the physical position is observed and the tethering state is hidden. We develop an alternating maximization algorithm to infer the hidden state of the particle and estimate the physical parameters of the system...

The synapse is a key element circuit in any memristor-based neuromorphic computing system. A memristor is a two-terminal analog memory device. Memristive synapses suffer from various challenges including high voltage, SET or RESET failure, and READ margin issues that can degrade the distinguishability of stored weights. Enhancing READ resolution is very important to improving the reliability of memristive synapses. Usually, the READ resolution is very small for a memristive synapse with a 4-bit data precision...

In this study, we investigate the communication networks of urban, suburban, and rural communities from three US Midwest counties through a stochastic model that simulates the diffusion of information over time in disaster and in normal situations. To understand information diffusion in communities, we investigate the interplay of information that individuals get from online social networks, local news, government sources, mainstream media, and print media. We utilize survey data collected from target communities and create graphs of each community to quantify node-to-node and source-to-node interactions, as well as trust patterns...

BACKGROUND: The international flight network creates multiple routes by which pathogens can quickly spread across the globe. In the early stages of infectious disease outbreaks, analyses using flight passenger data to identify countries at risk of importing the pathogen are common and can help inform disease control efforts. A challenge faced in this modelling is that the latest aviation statistics (referred to as contemporary data) are typically not immediately available. Therefore, flight patterns from a previous year are often used (referred to as historical data)...

BACKGROUND: Virtually all cases of hepatitis C virus (HCV) infection in children in the United States occur through vertical transmission, but it is unknown how many children are infected. Cases of maternal HCV infection have increased in the United States, which may increase the number of children vertically infected with HCV. Infection has long-term consequences for a child's health, but treatment options are now available for children ≥3 years old. Reducing HCV infections in adults could decrease HCV infections in children...

The efficient coding hypothesis posits that early sensory neurons transmit maximal information about sensory stimuli, given internal constraints. A central prediction of this theory is that neurons should preferentially encode stimuli that are most surprising. Previous studies suggest this may be the case in early visual areas, where many neurons respond strongly to rare or surprising stimuli. For example, previous research showed that when presented with a rhythmic sequence of full-field flashes, many retinal ganglion cells (RGCs) respond strongly at the instance the flash sequence stops, and when another flash would be expected...

Sub-Saharan Africa (SSA) is seeing exceptional urbanization and economic expansion rates. Therefore, the STIRPAT (Stochastic Impacts by Regression on Population, Affluence, and Technology) parameters and the spatial econometric framework are used in this work to examine the influence of economic growth and urbanization on SSA's CO2 emissions. Likewise, to determine the spatial effect and understand how factors influence the spatial dependence of carbon emissions, the study builds a spatial Durbin model (SDM)...

First-principles-based modelings have been extremely successful in providing crucial insights and predictions for complex biological functions and phenomena. However, they can be hard to build and expensive to simulate for complex living systems. On the other hand, modern data-driven methods thrive at modeling many types of high-dimensional and noisy data. Still, the training and interpretation of these data-driven models remain challenging. Here, we combine the two types of methods to model stochastic neuronal network oscillations...

BACKGROUND AND AIM: New nomenclature of steatotic liver disease (SLD) including metabolic dysfunction-associated SLD (MASLD), MASLD and increased alcohol intake (MetALD), and alcohol-associated liver disease (ALD) has recently been proposed. We investigated clustering analyses to decipher the complex landscape of SLD pathologies including the former nomenclature of nonalcoholic fatty liver disease (NAFLD) and metabolic dysfunction-associated fatty liver disease (MAFLD). METHODS: Japanese individuals who received annual health checkups including abdominal ultrasonography (n = 15 788, men/women: 10 250/5538, mean age: 49 years) were recruited...

We use the particle-based stochastic multi-particle collision dynamics (N-MPCD) algorithm to simulate confined nematic liquid crystals in regular two-dimensional polygons such as squares, pentagons and hexagons. We consider a range of values of the nematicities, U , and simulation domain sizes, R , that canvass nano-sized polygons to micron-sized polygons. We use closure arguments to define mappings between the N-MPCD parameters and the parameters in the continuum deterministic Landau-de Gennes framework. The averaged N-MPCD configurations agree with those predicted by Landau-de Gennes theory, at least for large polygons...

Wireless sensor networks (WSNs) encounter a significant challenge in ensuring network security due to their operational constraints. This challenge stems from the potential infiltration of malware into WSNs, where a single infected node can rapidly propagate worms to neighboring nodes. To address this issue, this research introduces a stochastic <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>S</mml:mi> <mml:mi>E</mml:mi> <mml:mi>I</mml:mi> <mml:mi>R</mml:mi> <mml:mi>S</mml:mi></mml:mrow> </mml:math> model to characterize worm spread in WSNs...

The sum score on a psychological test is, and should continue to be, a tool central in psychometric practice. This position runs counter to several psychometricians' belief that the sum score represents a pre-scientific conception that must be abandoned from psychometrics in favor of latent variables. First, we reiterate that the sum score stochastically orders the latent variable in a wide variety of much-used item response models. In fact, item response theory provides a mathematically based justification for the ordinal use of the sum score...

The microtubule cytoskeleton is responsible for sustained, long-range intracellular transport of mRNAs, proteins, and organelles in neurons. Neuronal microtubules must be stable enough to ensure reliable transport, but they also undergo dynamic instability, as their plus and minus ends continuously switch between growth and shrinking. This process allows for continuous rebuilding of the cytoskeleton and for flexibility in injury settings. Motivated by in vivo experimental data on microtubule behavior in Drosophila neurons, we propose a mathematical model of dendritic microtubule dynamics, with a focus on understanding microtubule length, velocity, and state-duration distributions...

As an essential material basis and power source for economic and social development, Western China's low energy use efficiency has hindered its sustainable economic development. This study aims to evaluate the total factor energy efficiency of the region and identify its influencing factors. A three-stage DEA model was used to measure the efficiency of 11 provinces from 2006 to 2021, and the Tobit model was employed to investigate internal factors. The findings show that (i) external environmental factors and stochastic perturbations have a significant impact on TFEE in the western region, overestimating integrated efficiency and scale efficiency and underestimating pure technical efficiency...