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Spatial dependence analysis

Subrata Dev, Sakuntala Chatterjee
In response to a concentration gradient of chemoattractant, E. coli bacterium modulates the rotational bias of flagellar motors which control its run-and-tumble motion, to migrate towards regions of high chemoattractant concentration. Presence of stochastic noise in the biochemical pathway of the cell has important consequences on the switching mechanism of motor bias, which in turn affects the runs and tumbles of the cell in a significant way. We model the intracellular reaction network in terms of coupled time evolution of three stochastic variables-kinase activity, methylation level, and CheY-P protein level-and study the effect of methylation noise on the chemotactic performance of the cell...
March 2018: Physical Review. E
Projesh Kumar Roy, Markus Heyde, Andreas Heuer
The recent experimental discovery of a semi two-dimensional silica glass has offered a realistic description of the random network theory of a silica glass structure, initially discussed by Zachariasen. To study the structure formation of silica in two dimensions, we introduce a two-body force field, based on a soft core Yukawa potential. The different configurations, sampled via Molecular dynamics simulations, can be directly compared with the experimental structures, which have been provided in the literature...
May 18, 2018: Physical Chemistry Chemical Physics: PCCP
Rosa Bonaventura, Francesca Zito, Marco Chiaramonte, Caterina Costa, Roberta Russo
Many industrial activities release Nickel (Ni) in the environment with harmful effects for terrestrial and marine organisms. Despite many studies on the mechanisms of Ni toxicity are available, the understanding about its toxic effects on marine organisms is more limited. We used Paracentrotus lividus as a model to analyze the effects on the stress pathways in embryos continuously exposed to different Ni doses, ranging from 0.03 to 0.5 mM. We deeply examined the altered embryonic morphologies at 24 and 48 h after Ni exposure...
May 4, 2018: Marine Environmental Research
Eun Jin Han, Kiyeon Kang, So Young Sohn
Governments and also local councils create and enforce their own regional public health care plans for the problem of overweight and obesity in the population. Public sports facilities can help these plans. In this paper, we investigated the contribution of public sports facilities to the reduction of the obesity of local residents. We used the data obtained from the Fifth Korea National Health and Nutrition Examination Surveys; and measured the degree of obesity using body mass index (BMI). We conducted various spatial regression analyses including the global Moran's I test and local indicators of spatial autocorrelation analysis finding that there exists spatial dependence in the error term of spatial regression model for BMI...
May 7, 2018: Geospatial Health
Giovanni Marinaro, Gobind Das, Andrea Giugni, Marco Allione, Bruno Torre, Patrizio Candeloro, Jurgen Kosel, Enzo Di Fabrizio
In this paper, we propose the use of a standing nanowires array, constituted by plasmonic active gold wires grown on iron disks, and partially immersed in a supporting alumina matrix, for surface-enhanced Raman spectroscopy applications. The galvanic process was used to fabricate nanowires in pores of anodized alumina template, making this device cost-effective. This fabrication method allows for the selection of size, diameter, and spatial arrangement of nanowires. The proposed device, thanks to a detailed design analysis, demonstrates a broadband plasmonic enhancement effect useful for many standard excitation wavelengths in the visible and NIR...
May 17, 2018: Materials
Ranjan Muthukrishnan, Adam S Davis, Nicholas R Jordan, James D Forester
Invasion potential should be part of the evaluation of candidate species for any species introduction. However, estimating invasion risks remains a challenging problem, particularly in complex landscapes. Certain plant traits are generally considered to increase invasive potential and there is an understanding that landscapes influence invasions dynamics, but little research has been done to explore how those drivers of invasions interact. We evaluate the relative roles of, and potential interactions between, plant invasiveness traits and landscape characteristics on invasions with a case study using a model parameterized for the potentially invasive biomass crop, Miscanthus × giganteus...
2018: PloS One
Volmar Morais Fontoura, Iolanda Graepp-Fontoura, Floriacy Stabnow Santos, Marcelino Santos Neto, Hanari Santos de Almeida Tavares, Maria Onice Lopes Bezerra, Marcela de Oliveira Feitosa, Adriano Figuerêdo Neves, Jesuane Cavalcante Melo de Morais, Luiz Fernando Costa Nascimento
BACKGROUND: Diarrhea is a waterborne disease that affects children, especially those under 5 years of age. The objective of this study was to identify the spatial patterns of distribution of diarrheal disease in under 5-year-old children in the State of Tocantins, Brazil, from 2008 to 2013. METHODS: Geoprocessing tools were used to carry out an epidemiological study, to prepare thematic maps in the TerraView 4.2.2 software based on secondary data. General indicators of the disease, presence of spatial dependence through the Global Moran's Index (I) and the Spatial Association Index (LISA) were described...
2018: PloS One
Nataliya Rybnikova, Boris A Portnov
Several population-level studies revealed a positive association between breast cancer (BC) incidence and artificial light at night (ALAN) exposure. However, the effect of short-wavelength illumination, implicated by laboratory research and small-scale cohort studies as the main driving force behind BC-ALAN association, has not been supported by any population-level study carried out to date. We investigated a possible link between BC and ALAN of different subspectra using a multi-spectral year-2011 satellite image, taken from the International Space Station, and superimposing it with year-2013 BC incidence data available for the Great Haifa Metropolitan Area in Israel...
May 16, 2018: Chronobiology International
C Hindocha, T P Freeman, M Grabski, H Crudgington, A C Davies, J B Stroud, R K Das, W Lawn, C J A Morgan, H V Curran
Acute nicotine abstinence in cigarette smokers results in deficits in performance on specific cognitive processes, including working memory and impulsivity which are important in relapse. Cannabidiol (CBD), the non-intoxicating cannabinoid found in cannabis, has shown pro-cognitive effects and preliminary evidence has indicated it can reduce the number of cigarettes smoked in dependent smokers. However, the effects of CBD on cognition have never been tested during acute nicotine withdrawal. The present study therefore aimed to investigate if CBD can improve memory and reduce impulsivity during acute tobacco abstinence...
May 15, 2018: Scientific Reports
Arthur Poitout, Amandine Crabos, Ivan Petřík, Ondřej Novák, Gabriel Krouk, Benoît Lacombe, Sandrine Ruffel
Plants face temporal and spatial variation in nitrogen (N) availability. This includes heterogeneity in soil nitrate (NO3-) content. To overcome these constraints, plants modify their gene expression and physiological processes to optimize N acquisition. This plasticity relies on a complex long-distance root-shoot-root signaling network that remains poorly understood. We previously showed that cytokinin (CK) biosynthesis is required to trigger systemic N signaling. Here, we performed split-root experiments and used a combination of CK-related mutant analyses, hormone profiling, transcriptomic analysis, NO3- uptake assays, and root growth measurements to gain insight into systemic N signaling in Arabidopsis thaliana...
May 15, 2018: Plant Cell
Raktim Dasgupta, Markus S Miettinen, Nico Fricke, Reinhard Lipowsky, Rumiana Dimova
The ganglioside GM1 is present in neuronal membranes at elevated concentrations with an asymmetric spatial distribution. It is known to generate curvature and can be expected to strongly influence the neuron morphology. To elucidate these effects, we prepared giant vesicles with GM1 predominantly present in one leaflet of the membrane, mimicking the asymmetric GM1 distribution in neuronal membranes. Based on pulling inward and outward tubes, we developed a technique that allowed the direct measurement of the membrane spontaneous curvature...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
S A Carvalho, M L Martins
Microorganisms and plants very commonly release toxic secondary chemical compounds (allelochemicals) that inhibit or kill sensitive strains or individuals from their own or other species. In this work we study a model that describes two species interacting through allelopathic suppression and competing for resources. Employing linear stability analysis, the conditions for coexistence or extinction of species in spatially homogeneous systems were determined. We found that the borders between the regimes of bistability, coexistence, and the extinction of the weaker by the stronger competitor, are altered by allelopathic interactions...
April 2018: Physical Review. E
Guido Cervone, Carolynne Hultquist
A methodology is presented to calibrate contributed Safecast dose rate measurements acquired between 2011 and 2016 in the Fukushima prefecture of Japan. The Safecast data are calibrated using observations acquired by the U.S. Department of Energy at the time of the 2011 Fukushima Daiichi power plant nuclear accident. The methodology performs a series of interpolations between the U.S. government and contributed datasets at specific temporal windows and at corresponding spatial locations. The coefficients found for all the different temporal windows are aggregated and interpolated using quadratic regressions to generate a time dependent calibration function...
May 8, 2018: Journal of Environmental Radioactivity
Omer F Gulban, Federico De Martino, An T Vu, Essa Yacoub, Kamil Uğurbil, Christophe Lenglet
Diffusion MRI of the cortical gray matter is challenging because the micro-environment probed by water molecules is much more complex than within the white matter. High spatial and angular resolutions are therefore necessary to uncover anisotropic diffusion patterns and laminar structures, which provide complementary (e.g. to anatomical and functional MRI) microstructural information about the cortex architectonic. Several ex-vivo and in-vivo MRI studies have recently addressed this question, however predominantly with an emphasis on specific cortical areas...
May 9, 2018: NeuroImage
Kwabena Asubonteng, Karin Pfeffer, Mirjam Ros-Tonen, Jan Verbesselt, Isa Baud
Tree crops such as cocoa and oil palm are important to smallholders' livelihoods and national economies of tropical producer countries. Governments seek to expand tree-crop acreages and improve yields. Existing literature has analyzed socioeconomic and environmental effects of tree-crop expansion, but its spatial effects on the landscape are yet to be explored. This study aims to assess the effects of tree-crop farming on the composition and the extent of land-cover transitions in a mixed cocoa/oil palm landscape in Ghana...
May 11, 2018: Environmental Management
Sixtine Passot, Beatriz Moreno-Ortega, Daniel Moukouanga, Crispulo Balsera, Soazig Guyomarc'h, Mikael Lucas, Guillaume Lobet, Laurent Laplaze, Bertrand Muller, Yann Guédon
Recent progress in root phenotyping has focused mainly on increasing throughput for genetic studies while identifying root developmental patterns has been comparatively underexplored. We introduce a new phenotyping pipeline for producing high-quality spatio-temporal root system development data and identifying developmental patterns within these data. The SmartRoot image analysis system and temporal and spatial statistical models were applied to two cereals, pearl millet (Pennisetum glaucum) and maize (Zea mays)...
May 11, 2018: Plant Physiology
Nikolai Lebedev, Igor Griva, Anders Blom, Leonard M Tender
Protein molecular conductance has attracted attention from researchers for the possibility of constructing innovative flexible biocompatible nanoscale electronic devices and smart hybrid materials. Due to protein complexity, most evaluations of protein conductivity are based on the simple estimation of protein's molecular orbital energy levels and spatial distributions without analysing its protein interaction with electrodes and the calculation of the rates of electron transfer (ET). In the present work, we included in our density functional theory (DFT) analysis an approach based on the non-equilibrium Green's function (NEGF) allowing for calculation from the first principles the molecular interaction with electrodes and thus the role of electrode materials, Fermi level, the thermal distribution of electronic energy levels, and the coupling efficiency between the molecule and the electrodes...
May 11, 2018: Physical Chemistry Chemical Physics: PCCP
Dengming Ming, Rui Chen, He Huang
Optimizing amino-acid mutations in enzyme design has been a very challenging task in modern bio-industrial applications. It is well known that many successful designs often hinge on extensive correlations among mutations at different sites within the enzyme, however, the underpinning mechanism for these correlations is far from clear. Here, we present a topology-based model to quantitively characterize non-additive effects between mutations. The method is based on the molecular dynamic simulations and the amino-acid network clique analysis...
May 10, 2018: International Journal of Molecular Sciences
J O Andrews, W Conway, W -K Cho, A Narayanan, J -H Spille, N Jayanth, T Inoue, S Mullen, J Thaler, I I Cissé
We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle...
May 9, 2018: Scientific Reports
Kevin J Boyd, Nathan N Alder, Eric R May
The mitochondrial lipid cardiolipin (CL) contributes to the spatial protein organization and morphological character of the inner mitochondrial membrane. Monolysocardiolipin (MLCL), an intermediate species in the CL remodeling pathway, is enriched in the multisystem disease Barth syndrome. Despite the medical relevance of MLCL, a detailed molecular description that elucidates the structural and dynamic differences between CL and MLCL has not been conducted. To this end, we performed comparative atomistic molecular dynamics studies on bilayers consisting of pure CL or MLCL to elucidate similarities and differences in their molecular and bulk bilayer properties...
May 8, 2018: Biophysical Journal
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