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Spatio-temporal modeling

Xufeng Fei, Wanzhen Chen, Shuqing Zhang, Qingmin Liu, Zhonghao Zhang, Qing Pei
BACKGROUND: Incidences of thyroid cancer (TC) have been increasing worldwide in recent decades. In this research, we aimed to analyze the spatiotemporal pattern of TC and explore relevant environmental risk factors in Hangzhou (HZ), which is rapidly urbanizing and home to the highest TC incidence in China. METHODS: Spatial scan statistic was employed to analyze the spatiotemporal pattern of TC in HZ from 2008 to 2012. The geographically weighted regression model (GWR) was implemented to explore environmental risk factors...
March 3, 2018: Science of the Total Environment
Karine Pinel, Coralie Genevois, Christelle Debeissat, Franck Couillaud
RNA interference (RNAi)-based gene therapy has great potential in cancer and infectious disease treatment to correct abnormal up-regulation of gene expression. We show a new original method uses synthetic microRNAs combined with a thermo-inducible promoter to reduce specific gene expression. The targeted gene is the luciferase firefly reporter gene overexpressed in a subcutaneous tumor which allows the RNAi monitoring by bioluminescence imaging (BLI). The inducible inhibition was first demonstrated in vitro using genetically modified cells lines and then in vivo using the corresponding xenograft model in mice...
March 16, 2018: Scientific Reports
Arran Hamlet, Kévin Jean, William Perea, Sergio Yactayo, Joseph Biey, Maria Van Kerkhove, Neil Ferguson, Tini Garske
BACKGROUND: Yellow fever virus (YFV) is a vector-borne flavivirus endemic to Africa and Latin America. Ninety per cent of the global burden occurs in Africa where it is primarily transmitted by Aedes spp, with Aedes aegypti the main vector for urban yellow fever (YF). Mosquito life cycle and viral replication in the mosquito are heavily dependent on climate, particularly temperature and rainfall. We aimed to assess whether seasonal variations in climatic factors are associated with the seasonality of YF reports...
March 2018: PLoS Neglected Tropical Diseases
Antonella Succurro, Oliver Ebenhöh
Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial 'who is there?' QUESTION: An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment...
March 14, 2018: Biochemical Society Transactions
Thais Roque, Laurent Risser, Veerle Kersemans, Sean Smart, Danny Allen, Paul Kinchesh, Stuart Gilchrist, Ana L Gomes, Julia A Schnabel, Michael A Chappell
Predicting tumor growth and its response to therapy remains a major challenge in cancer research and strongly relies on tumor growth models. In this paper, we introduce, calibrate, and verify a novel image-driven reaction-diffusion model of avascular tumor growth. The model allows for proliferation, death and spread of tumor cells, and accounts for nutrient distribution and hypoxia. It is constrained by longitudinal time series of dynamic contrast-enhancement-MRI images. Tumor specific parameters are estimated from two early time points and used to predict the spatio-temporal evolution of the tumor volume and cell densities at later time points...
March 2018: IEEE Transactions on Medical Imaging
Ruth Bowness, Mark A J Chaplain, Gibin G Powathil, Stephen H Gillespie
If improvements are to be made in tuberculosis (TB) treatment, an increased understanding of disease in the lung is needed. Studies have shown that bacteria in a less metabolically active state, associated with the presence of lipid bodies, are less susceptible to antibiotics, and recent results have highlighted the disparity in concentration of different compounds into lesions. Treatment success therefore depends critically on the responses of the individual bacteria that constitute the infection. We propose a hybrid, individual-based approach that analyses spatio-temporal dynamics at the cellular level, linking the behaviour of individual bacteria and host cells with the macroscopic behaviour of the microenvironment...
March 7, 2018: Journal of Theoretical Biology
Jingcong Li, Zhu Liang Yu, Zhenghui Gu, Wei Wu, Yuanqing Li, Lianwen Jin
Detecting and Please provide the correct one analyzing the event-related potential (ERP) remains an important problem in neuroscience. Due to the low signal-to-noise ratio and complex spatio-temporal patterns of ERP signals, conventional methods usually rely on ensemble averaging technique for reliable detection, which may obliterate subtle but important information in each trial of ERP signals. Inspired by deep learning methods, we propose a novel hybrid network termed ERP-NET. With hybrid deep structure, the proposed network is able to learn complex spatial and temporal patterns from single-trial ERP signals...
March 2018: IEEE Transactions on Neural Systems and Rehabilitation Engineering
Diba Khana, Lauren M Rossen, Holly Hedegaard, Margaret Warner
Hierarchical Bayes models have been used in disease mapping to examine small scale geographic variation. State level geographic variation for less common causes of mortality outcomes have been reported however county level variation is rarely examined. Due to concerns about statistical reliability and confidentiality, county-level mortality rates based on fewer than 20 deaths are suppressed based on Division of Vital Statistics, National Center for Health Statistics (NCHS) statistical reliability criteria, precluding an examination of spatio-temporal variation in less common causes of mortality outcomes such as suicide rates (SRs) at the county level using direct estimates...
January 2018: Journal of Data Science: JDS
Maria Papadogiorgaki, Panagiotis Koliou, Michalis E Zervakis
Glioma brain tumors exhibit considerably aggressive behavior leading to high mortality rates. Mathematical modeling of tumor growth aims to explore the interactions between glioma cells and tissue microenvironment, which affect tumor evolution. Leveraging this concept, we present a three-dimensional model of glioma spatio-temporal evolution based on existing continuum approaches, yet incorporating novel factors of the phenomenon. The proposed model involves the interactions between different tumor cell phenotypes and their microenvironment, investigating how tumor growth is affected by complex biological exchanges...
March 8, 2018: Medical & Biological Engineering & Computing
B Souley Kouato, E Thys, V Renault, E Abatih, H Marichatou, S Issa, C Saegerman
Foot-and-mouth disease (FMD) is endemic in Niger, with outbreaks occurring every year. Recently, there was an increasing interest from veterinary authorities to implement preventive and control measures against FMD. However, for an efficient control, improving the current knowledge on the disease dynamics and factors related to FMD occurrence is a prerequisite. The objective of this study was therefore to obtain insights into the incidence and the spatio-temporal patterns of transmission of FMD outbreaks in Niger based on the retrospective analysis of 9-year outbreak data...
March 5, 2018: Transboundary and Emerging Diseases
Yuan-Hao Chen, Tung-Tai Kuo, Jen-Hsin Kao, Eagle Yi-Kung Huang, Tsung-Hsun Hsieh, Yu-Ching Chou, Barry J Hoffer
To determine the influences of exercise on motor deficits and dopaminergic transmission in a hemiparkinson animal model, we measured the effects of exercise on the ambulatory system by estimating spatio-temporal parameters during walking, striatal dopamine (DA) release and reuptake and synaptic plasticity in the corticostriatal pathway after unilateral 6-OHDA lesions. 6-OHDA lesioned hemiparkinsonian rats were exercised on a fixed speed treadmill for 30 minutes per day. Controls received the same lesion but no exercise...
March 5, 2018: Scientific Reports
Alinune N Kabaghe, Michael G Chipeta, Steve Gowelo, Monicah Mburu, Zinenani Truwah, Robert S McCann, Michèle van Vugt, Martin P Grobusch, Kamija S Phiri
BACKGROUND: Spatio-temporal variations in malaria burden are currently complex and costly to measure, but are important for decision-making. We measured the spatio-temporal variation of clinical malaria incidence at a fine scale in a cohort of children under five in an endemic area in rural Chikhwawa, Malawi, determined associated factors, and monitored adult mosquito abundance. METHODS: We followed-up 285 children aged 6-48 months with recorded geolocations, who were sampled in a rolling malaria indicator survey, for one year (2015-2016)...
March 5, 2018: Parasites & Vectors
Joanna Badach, Paulina Kolasińska, Małgorzata Paciorek, Wojciech Wojnowski, Tomasz Dymerski, Jacek Gębicki, Małgorzata Dymnicka, Jacek Namieśnik
Odour nuisance poses a serious problem in many urban areas, yet its evaluation and mitigation is often omitted in the urban planning process. By identifying its range and spatio-temporal variations, it could be taken into consideration by planners in urban development strategies and land use decisions. The aim of the study was to present the application of odour evaluation techniques in the improvement of the quality of life in the built environment. The problem of odours is discussed in regard to human health, social aspects and current practices in the management of spatial development...
March 2, 2018: Journal of Environmental Management
Arran Hodgkinson, Mark A J Chaplain, Pia Domschke, Dumitru Trucu
Spatio-temporal models have long been used to describe biological systems of cancer, but it has not been until very recently that increased attention has been paid to structural dynamics of the interaction between cancer populations and the molecular mechanisms associated with local invasion. One system that is of particular interest is that of the urokinase plasminogen activator (uPA) wherein uPA binds uPA receptors on the cancer cell surface, allowing plasminogen to be cleaved into plasmin, which degrades the extracellular matrix and this way leads to enhanced cancer cell migration...
March 2, 2018: Bulletin of Mathematical Biology
M Cóndor, T Rüberg, C Borau, J Piles, J M García-Aznar
Advances in microfabrication have allowed the development and popularization of microfluidic devices, which are powerful tools to recreate three-dimensional (3-D) biologically relevant in vitro models. These microenvironments are usually generated by using hydrogels and induced chemical gradients. Going further, computational models enable, after validation, the simulation of such conditions without the necessity of real experiments, thus saving costs and time. In this work we present a web-based application that allows, based on a previous numerical model, the assessment of different chemical gradients induced within a 3-D extracellular matrix...
February 6, 2018: Computers in Biology and Medicine
Ishanu Chattopadhyay, Emre Kiciman, Joshua W Elliott, Jeffrey L Shaman, Andrey Rzhetsky
Using several longitudinal datasets describing putative factors affecting influenza incidence and clinical data on the disease and health status of over 150 million human subjects observed over a decade, we investigated the source and the mechanistic triggers of influenza epidemics. We conclude that the initiation of a pan-continental influenza wave emerges from the simultaneous realization of a complex set of conditions. The strongest predictor groups are as follows, ranked by importance: (1) the host population's socio- and ethno-demographic properties; (2) weather variables pertaining to specific humidity, temperature, and solar radiation; (3) the virus' antigenic drift over time; (4) the host populations land-based travel habits, and; (5) recent spatio-temporal dynamics, as reflected in the influenza wave auto-correlation...
February 27, 2018: ELife
Masayuki Kano, Aitaro Kato, Ryosuke Ando, Kazushige Obara
Deep low frequency tremors are indicators of slow slip transients in the brittle-ductile transition zone along subducting plates. Investigation of comprehensive tremor activities is therefore an important issue for understanding the seismic/aseismic characteristics in transition zones. Here, we focus on the radiated energy from tremors to reveal the along-strike heterogeneity in the strength of tremor patches. Based on a tremor catalog that more accurately evaluates radiated energy, we examine the spatio-temporal activity of tremors accompanied by slow slip events (SSEs) in western Shikoku, southwestern Japan...
February 26, 2018: Scientific Reports
Florian Barthélémy, Aurélia Defour, Nicolas Lévy, Martin Krahn, Marc Bartoli
Skeletal muscle undergoes many micro-membrane lesions at physiological state. Based on their sizes and magnitude these lesions are repaired via different complexes on a specific spatio-temporal manner. One of the major repair complex is a dysferlin-dependent mechanism. Accordingly, mutations in the DYSF gene encoding dysferlin results in the development of several muscle pathologies called dysferlinopathies, where abnormalities of the membrane repair process have been characterized in patients and animal models...
2018: Journal of Neuromuscular Diseases
Jongrae Kim, Mathias Foo, Declan G Bates
Measurement techniques in biology are now able to provide data on the trajectories of multiple individual molecules simultaneously, motivating the development of techniques for the stochastic spatio-temporal modelling of biomolecular networks. However, standard approaches based on solving stochastic reaction-diffusion equations are computationally intractable for large-scale networks. We present a novel method for modeling stochastic and spatial dynamics in biomolecular networks using a simple form of the Langevin equation with noisy kinetic constants...
February 22, 2018: Scientific Reports
Angela M Cadavid Restrepo, Yu Rong Yang, Donald P McManus, Darren J Gray, Tamsin S Barnes, Gail M Williams, Ricardo J Soares Magalhães, Nicholas A S Hamm, Archie C A Clements
BACKGROUND: Human cystic (CE) and alveolar (AE) echinococcoses are zoonotic parasitic diseases that can be influenced by environmental variability and change through effects on the parasites, animal intermediate and definitive hosts, and human populations. We aimed to assess and quantify the spatiotemporal patterns of human echinococcoses in Ningxia Hui Autonomous Region (NHAR), China between January 1994 and December 2013, and examine associations between these infections and indicators of environmental variability and change, including large-scale landscape regeneration undertaken by the Chinese authorities...
February 22, 2018: Parasites & Vectors
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