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Spatial modeling

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https://www.readbyqxmd.com/read/29334417/combining-allele-frequency-and-tree-based-approaches-improves-phylogeographic-inference-from-natural-history-collections
#1
M Ruffley, M L Smith, A Espíndola, B C Carstens, J Sullivan, D C Tank
Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set, and determine what proportion of the total support the top-ranked model garners, we conduct model selection using two analytical approaches -allele frequency-based, implemented in fastsimcoal2, and gene tree-based, implemented in PHRAPL...
January 15, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29333917/role-of-cortical-microbleeds-in-cognitive-impairment-in%C3%A2-vivo-behavioral-and-imaging-characterization-of-a-novel-murine-model
#2
Sandrine Bergeron, Yaohua Chen, Florent Auger, Julie Deguil, Nicolas Durieux, Emilie Skrobala, Romain Barus, Camille Potey, Charlotte Cordonnier, Florence Pasquier, Laura Ravasi, Régis Bordet, Sophie Gautier
Cerebral microbleeds (CMBs) could contribute to cognitive impairment in the general population and in patients with dementia. We designed a study to (i) develop a murine model of CMBs, (ii) assess whether CMBs affect cognition in this model and (iii) assess whether this model is sensitive to pharmacological modulation. Male C57Bl6/J mice were stereotactically administered collagenase to induce cortical lesion analysed by MRI at 24 h. CMB-mice were assessed at six weeks post-lesion for cognitive performances (Barnes maze and Touchscreen automated paired-associated learning (PAL) task) and for cerebral metabolism (in vivo PET/CT with fluorodeoxyglucose (FDG))...
January 1, 2018: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/29333748/near-infrared-light-sensitive-polyvinyl-alcohol-hydrogel-photoresist-for-spatiotemporal-control-of-cell-instructive-3d-microenvironments
#3
Xiao-Hua Qin, Xiaopu Wang, Markus Rottmar, Bradley J Nelson, Katharina Maniura-Weber
Advanced hydrogel systems that allow precise control of cells and their 3D microenvironments are needed in tissue engineering, disease modeling, and drug screening. Multiphoton lithography (MPL) allows true 3D microfabrication of complex objects, but its biological application requires a cell-compatible hydrogel resist that is sufficiently photosensitive, cell-degradable, and permissive to support 3D cell growth. Here, an extremely photosensitive cell-responsive hydrogel composed of peptide-crosslinked polyvinyl alcohol (PVA) is designed to expand the biological applications of MPL...
January 15, 2018: Advanced Materials
https://www.readbyqxmd.com/read/29333692/measuring-spatial-and-temporal-trends-of-nicotine-and-alcohol-consumption-in-australia-using-wastewater-based-epidemiology
#4
Foon Yin Lai, Coral Gartner, Wayne Hall, Steve Carter, Jake O'Brien, Benjamin J Tscharke, Frederic Been, Cobus Gerber, Jason White, Phong Thai, Raimondo Bruno, Jeremy Prichard, K Paul Kirkbride, Jochen F Mueller
BACKGROUND AND AIMS: Tobacco and alcohol consumption remain priority public health issues worldwide. As participation in population-based surveys has fallen, it is increasingly challenging to estimate accurately the prevalence of alcohol and tobacco use. Wastewater-based epidemiology (WBE) is an alternative approach for estimating substance use at the population level that does not rely on survey participation. This study examined spatio-temporal patterns in nicotine (a proxy for tobacco) and alcohol consumption in the Australian population via WBE...
January 14, 2018: Addiction
https://www.readbyqxmd.com/read/29333592/3d-models-of-female-pelvis-structures-reconstructed-and-represented-in-combination-with-anatomical-and-radiological-sections
#5
L Asensio Romero, M Asensio Gómez, A Prats-Galino, J A Juanes Méndez
We present a computer program designed to visualize and interact with three-dimensional models of the main anatomical structures of the female pelvis. They are reconstructed from serial sections of corpse, from the Visible Human project of the Medical Library of the United States and from serial sections of high-resolution magnetic resonance. It is possible to represent these three-dimensional structures in any spatial orientation, together with sectional images of corpse and magnetic resonance imaging, in the three planes of space (axial, coronal and sagittal) that facilitates the anatomical understanding and the identification of the set of visceral structures of this body region...
January 15, 2018: Journal of Medical Systems
https://www.readbyqxmd.com/read/29333542/acceleration-of-bursty-multiprotein-target-search-kinetics-on-dna-by-colocalisation
#6
Prathitha Kar, Andrey G Cherstvy, Ralf Metzler
Proteins are capable of locating specific targets on DNA by employing a facilitated diffusion process with intermittent 1D and 3D search steps. Gene colocalisation and coregulation-i.e. the spatial proximity of two communicating genes-is one factor capable of accelerating the target search process along the DNA. We perform Monte Carlo computer simulations and demonstrate the benefits of gene colocalisation for minimising the search time in a model DNA-protein system. We use a simple diffusion model to mimic the search for targets by proteins, produced initially in bursts of multiple proteins and performing the first-passage search on the DNA chain...
January 15, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29333080/comparisons-of-traffic-related-ultrafine-particle-number-concentrations-measured-in-two-urban-areas-by-central-residential-and-mobile-monitoring
#7
Matthew C Simon, Neelakshi Hudda, Elena N Naumova, Jonathan I Levy, Doug Brugge, John L Durant
Traffic-related ultrafine particles (UFP; <100 nanometers diameter) are ubiquitous in urban air. While studies have shown that UFP are toxic, epidemiological evidence of health effects, which is needed to inform risk assessment at the population scale, is limited due to challenges of accurately estimating UFP exposures. Epidemiologic studies often use empirical models to estimate UFP exposures; however, the monitoring strategies upon which the models are based have varied between studies. Our study compares particle number concentrations (PNC; a proxy for UFP) measured by three different monitoring approaches (central-site, short-term residential-site, and mobile on-road monitoring) in two study areas in metropolitan Boston (MA, USA)...
November 2017: Atmospheric Environment
https://www.readbyqxmd.com/read/29332946/optimal-groundwater-extraction-under-uncertainty-and-a-spatial-stock-externality
#8
Nathaniel H Merrill, Todd Guilfoos
We introduce a model that incorporates two important elements to estimating welfare gains from groundwater management: stochasticity and a spatial stock externality. We estimate welfare gains resulting from optimal management under uncertainty as well as a gradual stock externality that produces the dynamics of a large aquifer being slowly exhausted. This groundwater model imposes an important aspect of a depletable natural resource without the extreme assumption of complete exhaustion that is necessary in a traditional single cell (bathtub) model of groundwater extraction...
January 1, 2018: American Journal of Agricultural Economics
https://www.readbyqxmd.com/read/29332615/hiv-epidemic-heterogeneity-in-zimbabwe-evidence-from-successive-demographic-and-health-surveys
#9
Zainab Oseni, Farah Seedat, Ngianga-Bakwin Kandala
Zimbabwe has one of the worst HIV epidemics in the world. This study investigated data from two successive Zimbabwe Demographic and Health Surveys (ZDHS) conducted in 2005-06 and 2010-11. A random representative sample of 30,000 men aged 15-59 and women aged 15-49 was selected from the two surveys. The HIV prevalence was mapped with a flexible, coherent regression framework using a geo-additive semi-parametric mixed model. HIV indicator prevalence maps were constructed at the regional level, and at the administrative level relevant for policy design, planning and decision-making...
January 15, 2018: Journal of Biosocial Science
https://www.readbyqxmd.com/read/29332565/beyond-the-lock-and-key-paradigm-targeting-lipid-rafts-to-induce-the-selective-apoptosis-of-cancer-cells
#10
Anna Carolina Schneider Alves, Reinaldo Antonio Dias, Luciano Porto Kagami, Gustavo Machado das Neves, Fernando Cidade Torres, Vera Lucia Eifler-Lima, Ivone Carvalho, Carolina de Miranda Silva, Daniel Fabio Kawano
For more than 40 years, the fluid mosaic model of cellular membranes have supported our vision of an inert lipid bilayer containing membrane protein receptors that are randomly hit by extracellular molecules to trigger intracellular signaling events. However, the notion that compartmentalized cholesterol- and sphingomyelin-rich membrane microdomains (known as lipid rafts) spatially arrange receptors and effectors to promote kinetically favorable interactions necessary for the signal transduction sounds much more realistic...
January 10, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29332384/structure-of-lipid-nanoparticles-containing-sirna-or-mrna-by-dynamic-nuclear-polarization-enhanced-nmr-spectroscopy
#11
Jasmine Viger-Gravel, Anna Schantz, Arthur C Pinon, Aaron J Rossini, Staffan Schantz, Lyndon Emsley
Here we show how dynamic nuclear polarization (DNP) nuclear magnetic resonance (NMR) spectroscopy experiments permit the atomic level structural characterization of loaded and empty lipid nanoparticles (LNPs). The LNPs used here were synthesized by microfluidic mixing technique and are composed of ionizable cationic lipid (DLin-MC3-DMA), a phospholipid (DSPC), cholesterol and PEG (DMPE-PEG 2000), as well as encapsulated cargoes which are either phosphorothioated-siRNA (50 or 100%) or mRNA. We show that LNPs form physically stable complexes with bioactive drug siRNA for a period of 94 days...
January 14, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29332297/integrodifference-equations-in-the-presence-of-climate-change-persistence-criterion-travelling-waves-and-inside-dynamics
#12
Mark A Lewis, Nathan G Marculis, Zhongwei Shen
To understand the effects that the climate change has on the evolution of species as well as the genetic consequences, we analyze an integrodifference equation (IDE) models for a reproducing and dispersing population in a spatio-temporal heterogeneous environment described by a shifting climate envelope. Our analysis on the IDE focuses on the persistence criterion, travelling wave solutions, and the inside dynamics. First, the persistence criterion, characterizing the global dynamics of the IDE, is established in terms of the basic reproduction number...
January 13, 2018: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/29332124/optimal-audiovisual-integration-in-the-ventriloquism-effect-but-pervasive-deficits-in-unisensory-spatial-localization-in-amblyopia
#13
Michael D Richards, Herbert C Goltz, Agnes M F Wong
Purpose: Classically understood as a deficit in spatial vision, amblyopia is increasingly recognized to also impair audiovisual multisensory processing. Studies to date, however, have not determined whether the audiovisual abnormalities reflect a failure of multisensory integration, or an optimal strategy in the face of unisensory impairment. We use the ventriloquism effect and the maximum-likelihood estimation (MLE) model of optimal integration to investigate integration of audiovisual spatial information in amblyopia...
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29331720/temporal-spatial-gait-parameter-models-of-very-slow-walking
#14
Andrew J J Smith, Edward D Lemaire
This study assessed the relationship between walking speed and common temporal-spatial stride-parameters to determine if a change in gait strategy occurs at extremely slow walking speeds. Stride-parameter models that represent slow walking can act as a reference for lower extremity exoskeleton and powered orthosis controls since these devices typically operate at walking speeds less than 0.4 m/s. Full-body motion capture data were collected from 30 health adults while walking on a self-paced treadmill, within a CAREN-Extended virtual reality environment...
January 6, 2018: Gait & Posture
https://www.readbyqxmd.com/read/29331690/effect-of-depressive-symptoms-on-the-evolution-of-neuropsychological-functions-over-the-course-of-adolescence
#15
Mohammad H Afzali, Maeve Oleary-Barrett, Jean R Séguin, Patricia Conrod
INTRODUCTION: Comprehensive understanding of the association between depression and neuropsychological functioning over the course of adolescence requires developmentally sensitive assessment through longitudinal data. The aim of current study is to examine the concurrent and subsequent effects of depressive symptoms on the initial level and evolution of four neuropsychological functioning domains (i.e., spatial working memory, delayed recall memory, perceptual reasoning, and inhibitory control)...
December 22, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/29331677/identification-of-potential-mr-derived-biomarkers-for-tumor-tissue-response-to-177lu-octreotate-therapy-in-an-animal-model-of-small-intestine-neuroendocrine-tumor
#16
Mikael Montelius, Johan Spetz, Oscar Jalnefjord, Evelin Berger, Ola Nilsson, Maria Ljungberg, Eva Forssell-Aronsson
Magnetic resonance (MR) methods enable noninvasive, regional tumor therapy response assessment, but associations between MR parameters, underlying biology, and therapeutic effects must be investigated. The aim of this study was to investigate response assessment efficacy and biological associations of MR parameters in a neuroendocrine tumor (NET) model subjected to radionuclide treatment. Twenty-one mice with NETs received 177Lu-octreotate at day 0. MR experiments (day -1, 1, 3, 8, and 13) included T2-weighted, dynamic contrast-enhanced (DCE) and diffusion-weighted imaging (DWI) and relaxation measurements (T1/T2*)...
January 10, 2018: Translational Oncology
https://www.readbyqxmd.com/read/29331450/mapping-stimulus-feature-selectivity-in-macaque-v1-by-two-photon-ca2-imaging-encoding-model-analysis-of-fluorescence-responses-to-natural-movies
#17
REVIEW
Koji Ikezoe, Mahya Amano, Shinji Nishimoto, Ichiro Fujita
In vivo calcium (Ca2+) imaging using two-photon microscopy allows activity to be monitored simultaneously from hundreds of individual neurons within a local population. While this allows us to gain important insights into how cortical neurons represent sensory information, factors such as photo-bleaching of the Ca2+ indicator limit imaging duration (and thus the numbers of stimuli that can be tested), which in turn hampers the full characterization of neuronal response properties. Here, we demonstrate that using an encoding model combined with presentation of natural movies results in detailed characterization of receptive field (RF) properties despite the relatively short time for data collection...
January 10, 2018: NeuroImage
https://www.readbyqxmd.com/read/29331283/the-influx-of-marine-debris-from-the-great-japan-tsunami-of-2011-to-north-american-shorelines
#18
Cathryn Clarke Murray, Nikolai Maximenko, Sherry Lippiatt
Marine debris is one of the leading threats to the ocean and the Great East Japan Earthquake and tsunami on March 11, 2011 washed away an estimated 5million tons of debris in a single, tragic event. Here we used shoreline surveys, disaster debris reports and ocean drift models to investigate the temporal and spatial trends in the arrival of tsunami marine debris. The increase in debris influx to surveyed North American and Hawaiian shorelines was substantial and significant, representing a 10 time increase over the baseline in northern Washington State where a long term dataset was available...
January 10, 2018: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/29331121/diffusion-of-a-particle-in-the-spatially-correlated-exponential-random-energy-landscape-transition-from-normal-to-anomalous-diffusion
#19
S V Novikov
Diffusive transport of a particle in a spatially correlated random energy landscape having exponential density of states has been considered. We exactly calculate the diffusivity in the nondispersive quasi-equilibrium transport regime for the 1D transport model and found that for slow decaying correlation functions the diffusivity becomes singular at some particular temperature higher than the temperature of the transition to the true non-equilibrium dispersive transport regime. It means that the diffusion becomes anomalous and does not follow the usual ∝ t1/2 law...
January 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29330677/evaluating-efficacy-of-landsat-derived-environmental-covariates-for-predicting-malaria-distribution-in-rural-villages-of-vhembe-district-south-africa
#20
Oupa E Malahlela, Jane M Olwoch, Clement Adjorlolo
Malaria in South Africa is still a problem despite existing efforts to eradicate the disease. In the Vhembe District Municipality, malaria prevalence is still high, with a mean incidence rate of 328.2 per 100,0000 persons/year. This study aimed at evaluating environmental covariates, such as vegetation moisture and vegetation greenness, associated with malaria vector distribution for better predictability towards rapid and efficient disease management and control. The 2005 malaria incidence data combined with Landsat 5 ETM were used in this study...
January 12, 2018: EcoHealth
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