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Spatial dependence analysis

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https://www.readbyqxmd.com/read/28820921/analysis-of-cone-mosaic-reflectance-properties-in-healthy-eyes-and-in-eyes-with-nonproliferative-diabetic-retinopathy-over-time
#1
Letizia Mariotti, Nicholas Devaney, Giuseppe Lombardo, Marco Lombardo
Purpose: We investigate the reflectance properties of the cone mosaic in adaptive optics (AO) images of healthy subjects and subjects with nonproliferative diabetic retinopathy (NPDR) over time. Methods: We acquired images of the parafoveal cone mosaic over 5 years in 12 healthy subjects and in six patients with mild NPDR. We analyzed the parameters of the cone intensity histogram distribution (mean, SD, and skewness), two metrics of the cone mosaic texture (sharpness and entropy), and two novel metrics (cone/intercone intensity and slope of the variogram)...
August 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28820904/parametric-studies-of-metabolic-cooperativity-in-escherichia-coli-colonies-strain-and-geometric-confinement-effects
#2
Joseph R Peterson, John A Cole, Zaida Luthey-Schulten
Characterizing the complex spatial and temporal interactions among cells in a biological system (i.e. bacterial colony, microbiome, tissue, etc.) remains a challenge. Metabolic cooperativity in these systems can arise due to the subtle interplay between microenvironmental conditions and the cells' regulatory machinery, often involving cascades of intra- and extracellular signalling molecules. In the simplest of cases, as demonstrated in a recent study of the model organism Escherichia coli, metabolic cross-feeding can arise in monoclonal colonies of bacteria driven merely by spatial heterogeneity in the availability of growth substrates; namely, acetate, glucose and oxygen...
2017: PloS One
https://www.readbyqxmd.com/read/28817289/how-to-drive-a-flashing-electron-ratchet-to-maximize-current
#3
Ofer Kedem, Bryan Lau, Emily A Weiss
Biological systems utilize a combination of asymmetry, noise, and chemical energy to produce motion in the highly damped environment of the cell with molecular motors, many of which are "ratchets", non-equilibrium devices for producing directed transport using non-directional perturbations, without a net bias. The underlying ratchet principle has been implemented in man-made micro- and nano-devices, to transport charged particles by oscillating an electric potential with repeating asymmetric features. In this experimental study, the ratcheting of electrons in an organic semiconductor is optimized by tuning the temporal modulation of the oscillating potential, applied using nanostructured electrodes...
August 17, 2017: Nano Letters
https://www.readbyqxmd.com/read/28813680/antibiotics-disrupt-coordination-between-transcriptional-and-phenotypic-stress-responses-in-pathogenic-bacteria
#4
Paul A Jensen, Zeyu Zhu, Tim van Opijnen
Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28812230/simulation-of-left-ventricular-dynamics-using-a-low-order-mathematical-model
#5
Michael J Moulton, Brian D Hong, Timothy W Secomb
The eventual goal of this study is to develop methods for estimating dynamic stresses in the left ventricle (LV) that could be used on-line in clinical settings, based on routinely available measurements. Toward this goal, a low-order theoretical model is presented, in which LV shape is represented using a small number of parameters, allowing rapid computational simulations of LV dynamics. The LV is represented as a thick-walled prolate spheroid containing helical muscle fibers with nonlinear passive and time-dependent active contractile properties...
August 15, 2017: Cardiovascular Engineering and Technology
https://www.readbyqxmd.com/read/28808033/multiplex-quantitative-cellular-analysis-in-large-tissue-volumes-with-clearing-enhanced-3d-microscopy-ce3d
#6
Weizhe Li, Ronald N Germain, Michael Y Gerner
Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (Ce3D), which generates excellent tissue transparency for most organs, preserves cellular morphology and protein fluorescence, and is robustly compatible with antibody-based immunolabeling...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28805936/characterizing-hypoxia-in-human-glioma-a-simultaneous-multimodal-mri-and-pet-study
#7
Christine Preibisch, Kuangyu Shi, Anne Kluge, Mathias Lukas, Benedikt Wiestler, Jens Göttler, Jens Gempt, Florian Ringel, Mohamed Al Jaberi, Jürgen Schlegel, Bernhard Meyer, Claus Zimmer, Thomas Pyka, Stefan Förster
Hypoxia plays an important role for the prognosis and therapy response of cancer. Thus, hypoxia imaging would be a valuable tool for pre-therapeutic assessment of tumor malignancy. However, there is no standard validated technique for clinical application available yet. Therefore, we performed a study in 12 patients with high-grade glioma, where we directly compared the two currently most promising techniques, namely the MR-based relative oxygen extraction fraction (MR-rOEF) and the PET hypoxia marker H-1-(3-[(18) F]-fluoro-2-hydroxypropyl)-2-nitroimidazole ([(18) F]-FMISO)...
August 14, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28805850/dispersible-oxygen-microsensors-map-oxygen-gradients-in-three-dimensional-cell-cultures
#8
Sasha Cai Lesher-Pérez, Ge-Ah Kim, Chuan-Hsien Kuo, Brendan M Leung, Sanda Mong, Taisuke Kojima, Christopher Moraes, M D Thouless, Gary D Luker, Shuichi Takayama
Phase fluorimetry, unlike the more commonly used intensity-based measurement, is not affected by differences in light paths from culture vessels or by optical attenuation through dense 3D cell cultures and hydrogels thereby minimizing dependence on signal intensity for accurate measurements. This work describes the use of phase fluorimetry on oxygen-sensor microbeads to perform oxygen measurements in different microtissue culture environments. In one example, cell spheroids were observed to deplete oxygen from the cell-culture medium filling the bottom of conventional microwells within minutes, whereas oxygen concentrations remained close to ambient levels for several days in hanging-drop cultures...
August 14, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28802145/ensemble-of-expert-deep-neural-networks-for-spatio-temporal-denoising-of-contrast-enhanced-mri-sequences
#9
A Benou, R Veksler, A Friedman, T Riklin Raviv
Dynamic contrast-enhanced MRI (DCE-MRI) is an imaging protocol where MRI scans are acquired repetitively throughout the injection of a contrast agent. The analysis of dynamic scans is widely used for the detection and quantification of blood-brain barrier (BBB) permeability. Extraction of the pharmacokinetic (PK) parameters from the DCE-MRI concentration curves allows quantitative assessment of the integrity of the BBB functionality. However, curve fitting required for the analysis of DCE-MRI data is error-prone as the dynamic scans are subject to non-white, spatially-dependent and anisotropic noise...
August 2, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28801951/modeling-ion-recombination-in-liquid-ionization-chambers-improvement-and-analysis-of-the-two-dose-rate-method
#10
Jonas Andersson, Heikki Tölli
PURPOSE: The use of liquid ionization chambers can provide useful information to endeavors with radiation dosimetry for highly modulated beams. Liquid ionization chambers may be particularly suitable for computed tomography applications where conventional ionization chambers do not present a high enough sensitivity for the spatial resolution required to characterize common X-ray beams. Due to the sensitivity, which leads to high charge densities, liquid ionization chambers can suffer from large recombination losses leading to degradation in signal to dose rate linearity...
August 12, 2017: Medical Physics
https://www.readbyqxmd.com/read/28801608/broadband-surface-plasmon-lasing-in-one-dimensional-metallic-gratings-on-semiconductor
#11
Seung-Hyun Kim, Won Seok Han, Tae-Young Jeong, Hyang-Rok Lee, H Jeong, D Lee, Seung-Bo Shim, Dai-Sik Kim, Kwang Jun Ahn, Ki-Ju Yee
We report surface plasmon (SP) lasing in metal/semiconductor nanostructures, where one-dimensional periodic silver slit gratings are placed on top of an InGaAsP layer. The SP nature of the lasing is confirmed from the emission wavelength governed by the grating period, polarization analysis, spatial coherence, and comparison with the linear transmission. The excellent performance of the device as an SP source is demonstrated by its tunable emission in the 400-nm-wide telecom wavelength band at room temperature...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28799646/-birds-of-a-feather-fail-together-exploring-the-nature-of-dependency-in-sme-defaults
#12
Raffaella Calabrese, Galina Andreeva, Jake Ansell
This article studies the effects of incorporating the interdependence among London small business defaults into a risk analysis framework using the data just before the financial crisis. We propose an extension from standard scoring models to take into account the spatial dimensions and the demographic characteristics of small and medium-sized enterprises (SMEs), such as legal form, industry sector, and number of employees. We estimate spatial probit models using different distance matrices based only on the spatial location or on an interaction between spatial locations and demographic characteristics...
August 11, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/28793046/influence-of-the-tilt-angle-of-percutaneous-aortic-prosthesis-on-velocity-and-shear-stress-fields
#13
Bruno Alvares de Azevedo Gomes, Gabriel Cordeiro Camargo, Jorge Roberto Lopes Dos Santos, Luis Fernando Alzuguir Azevedo, Ângela Ourivio Nieckele, Aristarco Gonçalves Siqueira-Filho, Glaucia Maria Moraes de Oliveira
Background: Due to the nature of the percutaneous prosthesis deployment process, a variation in its final position is expected. Prosthetic valve placement will define the spatial location of its effective orifice in relation to the aortic annulus. The blood flow pattern in the ascending aorta is related to the aortic remodeling process, and depends on the spatial location of the effective orifice. The hemodynamic effect of small variations in the angle of inclination of the effective orifice has not been studied in detail...
August 7, 2017: Arquivos Brasileiros de Cardiologia
https://www.readbyqxmd.com/read/28792468/real-time-external-respiratory-motion-measuring-technique-using-an-rgb-d-camera-and-principal-component-analysis
#14
Udaya Wijenayake, Soon-Yong Park
Accurate tracking and modeling of internal and external respiratory motion in the thoracic and abdominal regions of a human body is a highly discussed topic in external beam radiotherapy treatment. Errors in target/normal tissue delineation and dose calculation and the increment of the healthy tissues being exposed to high radiation doses are some of the unsolicited problems caused due to inaccurate tracking of the respiratory motion. Many related works have been introduced for respiratory motion modeling, but a majority of them highly depend on radiography/fluoroscopy imaging, wearable markers or surgical node implanting techniques...
August 9, 2017: Sensors
https://www.readbyqxmd.com/read/28790931/microtissues-enhance-smooth-muscle-differentiation-and-cell-viability-of-hadscs-for-three-dimensional-bioprinting
#15
Jin Yipeng, Xu Yongde, Wu Yuanyi, Sun Jilei, Guo Jiaxiang, Gao Jiangping, Yang Yong
Smooth muscle differentiated human adipose derived stem cells (hADSCs) provide a crucial stem cell source for urinary tissue engineering, but the induction of hADSCs for smooth muscle differentiation still has several issues to overcome, including a relatively long induction time and equipment dependence, which limits access to abundant stem cells within a short period of time for further application. Three-dimensional (3D) bioprinting holds great promise in regenerative medicine due to its controllable construction of a designed 3D structure...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28789993/functional-overestimation-due-to-spatial-smoothing-of-fmri-data
#16
Peng Liu, Vince Calhoun, Zikuan Chen
BACKGROUND: Pearson correlation (simply correlation) is a basic technique for neuroimage function analysis. It has been observed that the spatial smoothing may cause functional overestimation, which however remains a lack of complete understanding. Herein, we present a theoretical explanation from the perspective of correlation scale invariance. NEW METHODS: For a task-evoked spatiotemporal functional dataset, we can extract the functional spatial map by calculating the temporal correlations (tcorr) of voxel timecourses against the task timecourse...
August 5, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/28783913/sea-level-anomaly-in-the-north-atlantic-and-seas-around-europe-long-term-variability-and-response-to-north-atlantic-teleconnection-patterns
#17
Isabel Iglesias, M Nieves Lorenzo, Clara Lázaro, M Joana Fernandes, Luísa Bastos
Sea level anomaly (SLA), provided globally by satellite altimetry, is considered a valuable proxy for detecting long-term changes of the global ocean, as well as short-term and annual variations. In this manuscript, monthly sea level anomaly grids for the period 1993-2013 are used to characterise the North Atlantic Ocean variability at inter-annual timescales and its response to the North Atlantic main patterns of atmospheric circulation variability (North Atlantic Oscillation, Eastern Atlantic, Eastern Atlantic/Western Russia, Scandinavian and Polar/Eurasia) and main driven factors as sea level pressure, sea surface temperature and wind fields...
August 1, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28783537/investigation-of-the-hd-semg-probability-density-function-shapes-with-varying-muscle-force-using-data-fusion-and-shape-descriptors
#18
Mariam Al Harrach, Sofiane Boudaoud, Vincent Carriou, Jeremy Laforet, Adrien J Letocart, Jean-François Grosset, Frédéric Marin
This work presents an evaluation of the High Density surface Electromyogram (HD-sEMG) Probability Density Function (PDF) shape variation according to contraction level. On that account, using PDF shape descriptors: High Order Statistics (HOS) and Shape Distances (SD), we try to address the absence of a consensus for the sEMG non-Gaussianity evolution with force variation. This is motivated by the fact that PDF shape information are relevant in physiological assessment of the muscle architecture and function, such as contraction level classification, in complement to classical amplitude parameters...
August 1, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28782681/a-bayesian-spatial-model-for-neuroimaging-data-based-on-biologically-informed-basis-functions
#19
Ismael Huertas, Marianne Oldehinkel, Erik S B van Oort, David Garcia-Solis, Pablo Mir, Christian F Beckmann, Andre F Marquand
The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data is characterized as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state...
August 4, 2017: NeuroImage
https://www.readbyqxmd.com/read/28782543/the-active-construction-of-the-visual-world
#20
REVIEW
Thomas Parr, Karl J Friston
What we see is fundamentally dependent on where we look. Despite this seemingly obvious statement, many accounts of the neurobiology underpinning visual perception fail to consider the active nature of how we sample our sensory world. This review offers an overview of the neurobiology of visual perception, which begins with the control of saccadic eye movements. Starting from here, we can follow the anatomy backwards, to try to understand the functional architecture of neuronal networks that support the interrogation of a visual scene...
August 3, 2017: Neuropsychologia
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