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Spatio-temporal modeling

Matthieu Barbier, James R Watson
Predators of all kinds, be they lions hunting in the Serengeti or fishermen searching for their catch, display various collective strategies. A common strategy is to share information about the location of prey. However, depending on the spatial characteristics and mobility of predators and prey, information sharing can either improve or hinder individual success. Here, our goal is to investigate the interacting effects of space and information sharing on predation efficiency, represented by the expected rate at which prey are found and consumed...
October 2016: PLoS Computational Biology
Nirod Kumar Sarangi, K G Ayappa, Sandhya S Visweswariah, Jaydeep Kumar Basu
Cell membranes are believed to be highly complex dynamical systems having compositional heterogeneity involving several types of lipids and proteins as the major constituents. This dynamical and compositional heterogeneity is suggested to be critical to the maintenance of active functionality and response to chemical, mechanical, electrical and thermal stresses. However, delineating the various factors responsible for the spatio-temporal response of actual cell membranes to stresses can be quite challenging...
October 20, 2016: Physical Chemistry Chemical Physics: PCCP
Debasish Sen, Stephen M Jones, Erin M Oswald, Henry Pinkard, Kaitlin Corbin, Matthew F Krummel
Myeloid-derived cells such as monocytes, dendritic cells (DCs), and macrophages are at the heart of the immune effector function in an inflammatory response. But because of the lack of an efficient imaging system to trace these cells live during their migration and maturation in their native environment at sub-cellular resolution, our knowledge is limited to data available from specific time-points analyzed by flow cytometry, histology, genomics and other immunological methods. Here, we have developed a ratiometric imaging method for measuring monocyte maturation in inflamed mouse lungs in situ using real-time using 2-photon imaging and complementary methods...
2016: PloS One
Isabella Bertani, Cara E Steger, Daniel R Obenour, Gary L Fahnenstiel, Thomas B Bridgeman, Thomas H Johengen, Michael J Sayers, Robert A Shuchman, Donald Scavia
Cyanobacteria blooms are a major environmental issue worldwide. Our understanding of the biophysical processes driving cyanobacterial proliferation and the ability to develop predictive models that inform resource managers and policy makers rely upon the accurate characterization of bloom dynamics. Models quantifying relationships between bloom severity and environmental drivers are often calibrated to an individual set of bloom observations, and few studies have assessed whether differences among observing platforms could lead to contrasting results in terms of relevant bloom predictors and their estimated influence on bloom severity...
October 12, 2016: Science of the Total Environment
Jimmy Garnier, Mark A Lewis
Range expansion and range shifts are crucial population responses to climate change. Genetic consequences are not well understood but are clearly coupled to ecological dynamics that, in turn, are driven by shifting climate conditions. We model a population with a deterministic reaction-diffusion model coupled to a heterogeneous environment that develops in time due to climate change. We decompose the resulting travelling wave solution into neutral genetic components to analyse the spatio-temporal dynamics of its genetic structure...
October 14, 2016: Bulletin of Mathematical Biology
Georgios Lolas, Lasse Jensen, George C Bourantas, Vasiliki Tsikourkitoudi, Konstantinos Syrigos
With the exception of a limited number of sites in the body, primary tumors infrequently lead to the demise of cancer patients. Instead, mortality and a significant degree of morbidity result from the growth of secondary tumors in distant organs. Tumor survival, growth and dissemination are associated with the formation of both new blood vessels (angiogenesis) and new lymph vessels (lymphagenesis or lymphangiogenesis). Although intensive research in tumor angiogenesis has been going on for the past four decades, experimental results in tumor lymphangiogenesis began to appear only in the last 10 years...
2016: Advances in Experimental Medicine and Biology
Ricardo Siqueira da Silva, Lalit Kumar, Farzin Shabani, Ezio Marques da Silva, Tarcisio Visintin da Silva Galdino, Marcelo Coutinho Picanço
Seasonal variations are important components in understanding the ecology of insect population of crops. Ecological studies through modeling may be a useful tool for enhancing knowledge of seasonal patterns of insects on field crops as well as seasonal patterns of favorable climatic conditions for species. Recently CLIMEX, a semi-mechanistic niche model, was upgraded and enhanced to consider spatio-temporal dynamics of climate suitability through time. In this study, attempts were made to determine monthly variations of climate suitability for Neoleucinodes elegantalis (Guenée) (Lepidoptera: Crambidae) in five commercial tomato crop localities through the latest version of CLIMEX...
October 13, 2016: International Journal of Biometeorology
Javier Cervera, Salvador Meseguer, Salvador Mafe
The single cell-centred approach emphasises ion channels as specific proteins that determine individual properties, disregarding their contribution to multicellular outcomes. We simulate the interplay between genetic and bioelectrical signals in non-excitable cells from the local single-cell level to the long range multicellular ensemble. The single-cell genetic regulation is based on mean-field kinetic equations involving the mRNA and protein concentrations. The transcription rate factor is assumed to depend on the absolute value of the cell potential, which is dictated by the voltage-gated cell ion channels and the intercellular gap junctions...
October 12, 2016: Scientific Reports
Ewan J Hemingway, Prashant Mishra, M Cristina Marchetti, Suzanne M Fielding
We examine the scaling with activity of the emergent length scales that control the nonequilibrium dynamics of an active nematic liquid crystal, using two popular hydrodynamic models that have been employed in previous studies. In both models we find that the chaotic spatio-temporal dynamics in the regime of fully developed active turbulence is controlled by a single active scale determined by the balance of active and elastic stresses, regardless of whether the active stress is extensile or contractile in nature...
September 28, 2016: Soft Matter
Ricci P H Yue, Harry F Lee, Connor Y H Wu
Infectious diseases have become a rising challenge to mankind in a globalizing world. Yet, little is known about the inland transmission of infectious diseases in history. In this study, we based on the spatio-temporal information of 5559 plague (Yersinia pestis) outbreaks in Europe and its neighboring regions in AD1347-1760 to statistically examine the connection between navigable rivers and plague outbreak. Our results showed that 95.5% of plague happened within 10 km proximity of navigable rivers. Besides, the count of plague outbreak was positively correlated with the width of river and negatively correlated with the distance between city and river...
October 10, 2016: Scientific Reports
P Gonzalez-Navarro, M Moghadamfalahi, M Akcakaya, D Erdogmus
Multichannel electroencephalography (EEG) is widely used in non-invasive brain computer interfaces (BCIs) for user intent inference. EEG can be assumed to be a Gaussian process with unknown mean and autocovariance, and the estimation of parameters is required for BCI inference. However, the relatively high dimensionality of the EEG feature vectors with respect to the number of labeled observations lead to rank deficient covariance matrix estimates. In this manuscript, to overcome ill-conditioned covariance estimation, we propose a structure for the covariance matrices of the multichannel EEG signals...
February 2017: Signal Processing
James T Thorson, Anna Rindorf, Jin Gao, Dana H Hanselman, Henning Winker
The spatial distribution of marine fishes can change for many reasons, including density-dependent distributional shifts. Previous studies show mixed support for either the proportional-density model (PDM; no relationship between abundance and area occupied, supported by ideal-free distribution theory) or the basin model (BM; positive abundance-area relationship, supported by density-dependent habitat selection theory). The BM implies that fishes move towards preferred habitat as the population declines. We estimate the average relationship using bottom trawl data for 92 fish species from six marine regions, to determine whether the BM or PDM provides a better description for sea-bottom-associated fishes...
October 12, 2016: Proceedings. Biological Sciences
Sina David, Johannes Funken, Wolfgang Potthast, Alexander Blanke
Insects show a remarkable diversity of muscle configurations, yet the factors leading to this functional diversity are poorly understood. Here, we use musculoskeletal modelling to understand the spatio-temporal activity of an insect muscle in several dragonfly species and to reveal potential mechanical factors leading to a particular muscle configuration. Bite characteristics potentially show systematic signal, but absolute bite force is not correlated with size. Muscle configuration and inverse dynamics show that the wider relative area of muscle attachment and the higher activity of subapical muscle groups are responsible for this high bite force...
October 2016: Journal of the Royal Society, Interface
Soham Ghosh, Altug Ozcelikkale, J Craig Dutton, Bumsoo Han
Freezing of biomaterials is important in a wide variety of biomedical applications, including cryopreservation and cryosurgeries. For the success of these applications to various biomaterials, biophysical mechanisms, which determine freezing-induced changes in cells and tissues, need to be well understood. Specifically, the significance of the intracellular mechanics during freezing is not well understood. Thus, we hypothesize that cells interact during freezing with the surroundings such as suspension media and the extracellular matrix (ECM) via two distinct but related mechanisms-water transport and cytoskeletal mechanics...
October 2016: Journal of the Royal Society, Interface
Neha Khetan, Chaitanya A Athale
Asters nucleated by Microtubule (MT) organizing centers (MTOCs) converge on chromosomes during spindle assembly in mouse oocytes undergoing meiosis I. Time-lapse imaging suggests that this centripetal motion is driven by a biased 'search-and-capture' mechanism. Here, we develop a model of a random walk in a drift field to test the nature of the bias and the spatio-temporal dynamics of the search process. The model is used to optimize the spatial field of drift in simulations, by comparison to experimental motility statistics...
October 2016: PLoS Computational Biology
Mahdi Nabil, Paolo Zunino
The application of hyperthermia to cancer treatment is studied using a novel model arising from the fundamental principles of flow, mass and heat transport in biological tissues. The model is defined at the scale of the tumour microenvironment and an advanced computational scheme called the embedded multiscale method is adopted to solve the governing equations. More precisely, this approach involves modelling capillaries as one-dimensional channels carrying flow, and special mathematical operators are used to model their interaction with the surrounding tissue...
September 2016: Royal Society Open Science
Margarita Pons-Salort, Natalie A Molodecky, Kathleen M O'Reilly, Mufti Zubair Wadood, Rana M Safdar, Andrew Etsano, Rui Gama Vaz, Hamid Jafari, Nicholas C Grassly, Isobel M Blake
BACKGROUND: Global withdrawal of serotype-2 oral poliovirus vaccine (OPV2) took place in April 2016. This marked a milestone in global polio eradication and was a public health intervention of unprecedented scale, affecting 155 countries. Achieving high levels of serotype-2 population immunity before OPV2 withdrawal was critical to avoid subsequent outbreaks of serotype-2 vaccine-derived polioviruses (VDPV2s). METHODS AND FINDINGS: In August 2015, we estimated vaccine-induced population immunity against serotype-2 poliomyelitis for 1 January 2004-30 June 2015 and produced forecasts for April 2016 by district in Nigeria and Pakistan...
October 2016: PLoS Medicine
Andrew C Muller, Diana L Muller, Arianna Muller
The nature of emerging patterns concerning water quality stressors and the evolution of hypoxia within sub-estuaries of the Chesapeake Bay has been an important unresolved question among the Chesapeake Bay community. Elucidation of the nature of hypoxia in the tributaries of the Chesapeake Bay has important ramifications to the successful restoration of the Bay, since much of Bay states population lives within the watersheds of the tributaries. Very little to date, is known about the small sub-estuaries of the Chesapeake Bay due to limited resources and the difficulties in resolving both space and time dimensions on scales that are adequate to resolve this question...
September 2016: Heliyon
S Kashif Sadiq
Retrovirus particle (virion) infectivity requires diffusion and clustering of multiple transmembrane envelope proteins (Env3) on the virion exterior, yet is triggered by protease-dependent degradation of a partially occluding, membrane-bound Gag polyprotein lattice on the virion interior. The physical mechanism underlying such coupling is unclear and only indirectly accessible via experiment. Modelling stands to provide insight but the required spatio-temporal range far exceeds current accessibility by all-atom or even coarse-grained molecular dynamics simulations...
November 13, 2016: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Qianzheng Zhu, Altaf A Wani
Nucleotide excision repair (NER) eliminates a broad variety of helix-distorting DNA lesions that can otherwise cause genomic instability. NER comprises two distinct sub-pathways: global genomic NER (GG-NER) operating throughout the genome, and transcription-coupled NER (TC-NER) preferentially removing DNA lesions from transcribing DNA strands of transcriptionally active genes. Several NER factors undergo post-translational modifications, including ubiquitination, occurring swiftly and reversibly at DNA lesion sites...
October 1, 2016: Photochemistry and Photobiology
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