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Transient crosslinking kinetics optimize gene cluster interactions

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arXiv 2018年

作者： Walker, Benjamin Taylor, Dane Lawrimore, Josh Hult, Caitlin Adalsteinsson, David Bloom, Kerry Gregory Forest, M. Department of Mathematics University of North Carolina at Chapel Hill Department of Mathematics University at Buffalo State University of New York Computational and Data Enabled Science and Engineering University at Buffalo State University of New York Department of Microbiology and Immunology University of Michigan Medical School Department of Chemical Engineering University of Michigan Departments of Applied Physical Sciences and Biomedical Engineering University of North Carolina at Chapel Hill Department of Biology University of North Carolina at Chapel Hill

Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics. Major protein contributors to chromosome structure and dynamics are condensin and cohesin that stochastically generate loops within and between chains, and entrap proximal strands of sister chromatids. In this paper, we explore the ability of transient, protein-mediated, gene-gene crosslinks to induce clusters of genes, thereby dynamic architecture, within the highly repeated ribosomal DNA that comprises the nucleolus of budding yeast. We implement three approaches: live cell microscopy;computational modeling of the full genome during G1 in budding yeast, exploring four decades of timescales for transient crosslinks between 5kbp domains (genes) in the nucleolus on Chromosome XII;and, temporal network models with automated community (cluster) detection algorithms applied to the full range of 4D modeling datasets. The data analysis tools detect and track gene clusters, their size, number, persistence time, and their plasticity (deformation). Of biological significance, our analysis reveals an optimal mean crosslink lifetime that promotes pairwise and cluster gene interactions through "flexible" clustering. In this state, large gene clusters self-assemble yet frequently interact (merge and separate), marked by gene exchanges between clusters, which in turn maximizes global gene interactions in the nucleolus. This regime stands between two limiting cases each with far less global gene interactions: with shorter crosslink lifetimes, "rigid" clustering emerges with clusters that interact infrequently;with longer crosslink lifetimes, there is a dissolution of clusters. These observations are compared with imaging experiments on a normal yeast strain and two condensin-modified mutant cell strains. We apply the same image analysis pipeline to the experimental and simulated datasets, providing support for the modeling pred

关键词： Genes

Temporal networks provide a unifying understanding of the evolution of cooperation

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arXiv 2023年

作者： Li, Aming Meng, Yao Zhou, Lei Masuda, Naoki Wang, Long Center for Systems and Control College of Engineering Peking University Beijing100871 China Center for Multi-Agent Research Institute for Artificial Intelligence Peking University Beijing100871 China School of Automation Beijing Institute of Technology Beijing100081 China Department of Mathematics State University of New York at Buffalo BuffaloNY14260 United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260 United States

Understanding the evolution of cooperation in structured populations represented by networks is a problem of long research interest, and a most fundamental and widespread property of social networks related to cooperation phenomena is that the node’s degree (i.e., number of edges connected to the node) is heterogeneously distributed. Previous results indicate that static heterogeneous (i.e., degree-heterogeneous) networks promote cooperation in stationarity compared to static regular (i.e., degree-homogeneous) networks if equilibrium dynamics starting from many cooperators and defectors is employed. However, the above conclusion reverses if we employ non-equilibrium stochastic processes to measure the fixation probability for cooperation, i.e., the probability that a single cooperator successfully invades a population. Here we resolve this conundrum by analyzing the fixation of cooperation on temporal (i.e., time-varying) networks. We theoretically prove and numerically confirm that on both synthetic and empirical networks, contrary to the case of static networks, temporal heterogeneous networks can promote cooperation more than temporal regular networks in terms of the fixation probability of cooperation. Given that the same conclusion is known for the equilibrium fraction of cooperators on temporal networks, the present results provide a unified understanding of the effect of temporal degree heterogeneity on promoting cooperation across two main analytical frameworks, i.e., equilibrium and non-equilibrium ones. Copyright © 2023, The Authors. All rights reserved.

关键词： Heterogeneous networks

Modeling of Measurement Error in Financial Returns data

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arXiv 2024年

作者： Jasra, Ajay Maama, Mohamed Mijatović, Aleksandar School of Data Science The Chinese University of Hong Kong Shenzhen China Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Statistics University of Warwick United Kingdom

In this paper we consider the modeling of measurement error for fund returns data. In particular, given access to a time-series of discretely observed log-returns and the associated maximum over the observation period, we develop a stochastic model which models the true log-returns and maximum via a Lévy process and the data as a measurement error there-of. The main technical difficulty of trying to infer this model, for instance Bayesian parameter estimation, is that the joint transition density of the return and maximum is seldom known, nor can it be simulated exactly. Based upon the novel stick breaking representation of [12] we provide an approximation of the model. We develop a Markov chain Monte Carlo (MCMC) algorithm to sample from the Bayesian posterior of the approximated posterior and then extend this to a multilevel MCMC method which can reduce the computational cost to approximate posterior expectations, relative to ordinary MCMC. We implement our methodology on several applications including for real data. Copyright © 2024, The Authors. All rights reserved.

关键词： Markov chains

Epileptic seizure detection

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Epileptic seizure detection

作者： Schuyler, Ronald White, Andrew Staley, Kevin Cios, Krzysztof J. Computational Bioscience Ph.D. Program UCDHSC United States University of Colorado United States American Epilepsy Society Society for Neuroscience United States Department of Neurology Massachusetts General Hospital Harvard Medical School United States Staley Lab. United States University of Colorado at Denver Health Sciences Center United States University of Colorado Bioenergetics Institute United States Data Mining and Bioinformatics Laboratory Turkey Polish Academy of Arts and Sciences Poland Dept. of Computer Science and Engineering University of Colorado at Denver Health Sciences Center P.O. Box 173364 Denver CO 80217-3364 United States

No abstract available

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Linkages of the 2022 Unprecedented Global Heatwave Events to Triple-Dip La Niña

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Linkages of the 2022 Unprecedented Global Heatwave Events to...

IEEE International Symposium on Geoscience and Remote Sensing (IGARSS)

作者： Sachi Perera Joshua B. Fisher Mohamed Allali Hesham El-Askary Computational and Data Sciences Graduate Program Schmid College of Science and Technology Chapman University Orange CA USA Earth Systems Science and Data Solution Lab Chapman University Orange CA USA Schmid College of Science and Technology Chapman University Orange CA USA Fowler School of Engineering Chapman University Orange CA USA Department of Environmental Sciences Faculty of Science Alexandria University Alexandria Egypt

ISBN: (数字)9798350360325

ISBN: (纸本)9798350360332

Heatwaves are influenced significantly by El Niño-Southern Oscillation (ENSO), which alters temperature and precipitation patterns throughout the world. Since 2020, we have witnessed a "triple dip" La Niña conditions persisting for three consecutive years resulting in severe weather and climate driven events globally. In this study, we identified the dominant frequency of Niño 3.4 Sea Surface Temperature (SST) signals and correlated them with regions experiencing unprecedented heat waves in 2022, namely, the Indian Ocean, the North Atlantic around England and Spain, and the Mediterranean Sea. The signal's power spectrum and its three highest power components are determined based on the signal's Singular Spectrum Analysis (SSA) for each region. Furthermore, the power spectrum coherence (PSC) of Niño 3.4 and other study regions is obtained to determine whether ENSO and heatwaves are linked. We find that Niño 3.4 and the Indian Ocean have the same dominant frequency for the highest power received, indicating ENSO's influence on the Indian heat wave. Additionally, we discovered that in March 2022, the Jet stream is essential in bringing warm Arctic waves southward, passing through Niño 3.4 and India. Furthermore, we found that no other region shared the dominant frequency of the Niño 3.4 region.

关键词： Heating systems Couplings Sea surface Precipitation Surface waves Indian Ocean Geoscience and remote sensing

Forecasting Vegetation Health in the MENA Region by Predicting Vegetation Indicators with Machine Learning Models

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Forecasting Vegetation Health in the MENA Region by Predicti...

IEEE International Symposium on Geoscience and Remote Sensing (IGARSS)

作者： Sachi Perera Wenzhao Li Erik Linstead Hesham El-Askary Computational and Data Sciences Graduate Program Schmid College of Science and Technology Chapman University Orange CA USA Schmid College of Science and Technology Chapman University Orange CA USA Fowler School of Engineering Chapman University Orange CA USA Faculty of Science Alexandria University Alexandria Egypt

ISBN: (数字)9781728163741

ISBN: (纸本)9781728163758

Machine learning (ML) techniques can be applied to predict and monitor drought conditions due to climate change. Predicting future vegetation health indicators (such as EVI, NDVI, and LAI) is one approach to forecast drought events for hotspots (e.g. Middle East and North Africa (MENA) regions). Recently, ML models were implemented to predict EVI values using parameters such as land types, time series, historical vegetation indices, land surface temperature, soil moisture, evapotranspiration etc. In this work, we collected the MODIS atmospherically corrected surface spectral reflectance imagery with multiple vegetation related indices for modeling and evaluation of drought conditions in the MENA region. These models are built by a total of 4556 and 519 normalized samples for training and testing purposes, respectively and with 51820 samples used for model evaluation. Models such as multilinear regression, penalized regression models, support vector regression (SVR), neural network, instance-based learning K-nearest neighbor (KNN) and partial least squares were implemented to predict future values of EVI. The models show effective performance in predicting EVI values (R 2 > 0.95) in the testing and (R 2 > 0.93) in the evaluation process.

关键词： Vegetation mapping MODIS Atmospheric modeling Remote sensing Predictive models Training Support vector machines

Stability of Inverse Transport Equation in Diffusion Scaling And Fokker-Planck Limit

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arXiv 2017年

作者： Chen, Ke LI, Qin Wang, Li Mathematics Department University of Wisconsin-Madison 480 Lincoln Dr. MadisonWI53705 United States Mathematics Department and Wisconsin Institute of Discovery University of Wisconsin-Madison 480 Lincoln Dr. MadisonWI53705 United States Department of Mathematics Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo 244 Mathematics Building BuffaloNY14206 United States

We consider the inverse problem of reconstructing the scattering and absorption coefficients using boundary measurements for a time dependent radiative transfer equation (RTE). As the measurement is mostly polluted by errors, both experimental and computational, an important question is to quantify how the error is amplified in the process of reconstruction. In the forward setting, the solution to the RTE behaves differently in different regimes, and the stability of the inverse problem vary accordingly. In particular, we consider two scalings in this paper. The first one concerns with a diffusive scaling whose macroscopic limit is a diffusion equation. In this case, we showed, following the similar approach as in [Chen, Li and Wang, arXiv:1703.00097], that the stability degrades when the limit is taken. The second one considers a highly forward peaked scattering, wherein the scattering operator is approximated by a Fokker-Planck operator as a limit. In this case, we showed that a fully recover of the scattering coefficient is less possible in the limit, whereas obtaining a rescaled version of the scattering coefficient becomes more practice friendly. Copyright © 2017, The Authors. All rights reserved.

关键词： Inverse problems

Enhancing Sustainable Development Goals Through Future Vapor Pressure Deficit Analysis In The Nile River Basin

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Enhancing Sustainable Development Goals Through Future Vapor...

IEEE International Symposium on Geoscience and Remote Sensing (IGARSS)

作者： Surendra Maharjan Wenzhao Li Shahryar Fazli Hani Sewilam Hesham El-Askary Computational and Data Sciences Graduate Program Schmid College of Science and Technology Chapman University Orange CA USA Earth Systems Science and Data Solutions Lab Chapman University Orange CA USA The Center for Applied Research on the Environment and Sustainability The American University in Cairo Cairo Egypt Department of Engineering Hydrology RWTH Aachen University Aachen Germany Department of Environmental Sciences Faculty of Science Alexandria University Alexandria Egypt

ISBN: (数字)9798350360325

ISBN: (纸本)9798350360332

Vapor Pressure Deficit (VPD) is crucial in meteorology and agriculture for understanding plant-environment interactions. Its application as an indicator in agricultural practices notably advances Sustainable Development Goals such as Zero Hunger (SDG 2) and Climate Action (SDG 13). This research focuses on the impact of climate change on agricultural productivity and food security in the Nile River Basin (NRB), emphasizing the role of VPD, temperature, and precipitation. Utilizing Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets from NEX-GDDP-CMIP6, the study analyzes key climatic variables that influence agricultural conditions. The study applies the Mann-Kendall test to evaluate VPD trends from 2000 to 2060 under two Shared Socioeconomic Pathways (SSPs), SSP2-4.5 and SSP5-8.5. The study's findings on the implications of rising VPD levels in the Nile River Basin (NRB), particularly under the SSP 5-8.5 scenario, highlight a critical challenge for the region's agricultural productivity and food security. The increased VPD, indicative of drier conditions, leads to a moisture deficit for crops, potentially reducing agricultural yields. This scenario poses a significant threat to food security, as lower crop yields can result in food shortages and higher food prices, adversely affecting vulnerable populations. The study underscores the necessity of integrating VPD insights into agricultural and water resource management strategies to uphold food security against climatic variations in support of the SDGs.

关键词： Productivity Climate change Precipitation Food security Agriculture Rivers Sustainable development

Multilevel Monte Carlo for a class of Partially Observed Processes in Neuroscience

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arXiv 2023年

作者： Maama, Mohamed Jasra, Ajay Kamatani, Kengo Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia School of Data Science The Chinese University of Hong Kong CN Shenzhen China Institute of Statistical Mathematics Tokyo190-0014 Japan

In this paper we consider Bayesian parameter inference associated to a class of partially observed stochastic differential equations (SDE) driven by jump processes. Such type of models can be routinely found in applications, of which we focus upon the case of neuroscience. The data are assumed to be observed regularly in time and driven by the SDE model with unknown parameters. In practice the SDE may not have an analytically tractable solution and this leads naturally to a time-discretization. We adapt the multilevel Markov chain Monte Carlo method of [15], which works with a hierarchy of time discretizations and show empirically and theoretically that this is preferable to using one single time discretization. The improvement is in terms of the computational cost needed to obtain a pre-specified numerical error. Our approach is illustrated on models applied to examples of Bayesian inference problems using both simulated and real observed data from neuroscience. Copyright © 2023, The Authors. All rights reserved.

关键词： Stochastic systems