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Spatial dependence analysis

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https://www.readbyqxmd.com/read/28212083/aliasing-detection-and-reduction-scheme-on-angularly-undersampled-light-fields
#1
Zhaolin Xiao, Qing Wang, Guoqing Zhou, Jingyi Yu
When using plenoptic camera for digital refocusing, angular undersampling can cause severe (angular) aliasing artifacts. Previous approaches have focused on avoiding aliasing by pre-processing the acquired light field via prefiltering, demosaicing, reparameterization, etc. In this paper, we present a different solution that first detects and then removes angular aliasing at the light field refocusing stage. Different from previous frequency domain aliasing analysis, we carry out a spatial domain analysis to reveal whether the angular aliasing would occur and uncover where in the image it would occur...
February 13, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28208207/-spatial-distribution-of-type-2-diabetes-mellitus-in-berlin-application-of-a-geographically-weighted-regression-analysis-to-identify-location-specific-risk-groups
#2
Boris Kauhl, Jonas Pieper, Jürgen Schweikart, Andrea Keste, Marita Moskwyn
Understanding which population groups in which locations are at higher risk for type 2 diabetes mellitus (T2DM) allows efficient and cost-effective interventions targeting these risk-populations in great need in specific locations. The goal of this study was to analyze the spatial distribution of T2DM and to identify the location-specific, population-based risk factors using global and local spatial regression models. To display the spatial heterogeneity of T2DM, bivariate kernel density estimation was applied...
February 16, 2017: Das Gesundheitswesen
https://www.readbyqxmd.com/read/28207000/spatial-transcriptomic-analysis-of-cryosectioned-tissue-samples-with-geo-seq
#3
Jun Chen, Shengbao Suo, Patrick Pl Tam, Jing-Dong J Han, Guangdun Peng, Naihe Jing
Conventional gene expression studies analyze multiple cells simultaneously or single cells, for which the exact in vivo or in situ position is unknown. Although cellular heterogeneity can be discerned when analyzing single cells, any spatially defined attributes that underpin the heterogeneous nature of the cells cannot be identified. Here, we describe how to use Geo-seq, a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology. The combination of these two methods enables the elucidation of cellular heterogeneity and spatial variance simultaneously...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28205341/spatiotemporal-microstructural-white-matter-changes-in-diffusion-tensor-imaging-after-transient-focal-ischemic-stroke-in-rats
#4
Won-Beom Jung, Yong Hee Han, Julius Juhyun Chung, Sun Young Chae, Sung Hoon Lee, Geun Ho Im, JiHoon Cha, Jung Hee Lee
Structural reorganization in white matter (WM) after stroke is a potential contributor to substitute or to newly establish the functional field on the injured brain in nature. Diffusion tensor imaging (DTI) is an imaging modality that can be used to evaluate damage and recovery within the brain. This method of imaging allows for in vivo assessment of the restricted movements of water molecules in WM and provides a detailed look at structural connectivity in the brain. For longitudinal DTI studies after a stroke, the conventional region of interest method and voxel-based analysis are highly dependent on the user-hypothesis and parameter settings for implementation...
February 16, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28202765/the-lateral-organization-of-influenza-virus-proteins-in-the-budozone-region-of-the-plasma-membrane
#5
George P Leser, Robert A Lamb
Influenza virus assembles and buds at the plasma membrane of virus-infected cells. The viral proteins assemble at the same site on the plasma membrane for budding to occur. This involves a complex web of interactions among viral proteins. Some, like HA, NA, and M2 are integral membrane proteins. M1 is peripherally membrane associated, whereas NP associates with the viral RNA to form an RNP complex that associates with the cytoplasmic face of the plasma membrane. Furthermore, HA and NP have been shown to be concentrated in cholesterol-rich membrane raft domains whereas M2, although containing a cholesterol binding motif, is not raft associated...
February 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28194128/disrupted-resting-state-default-mode-network-in-betel-quid-dependent-individuals
#6
Xueling Zhu, Qiuling Zhu, Canhua Jiang, Huaizhen Shen, Furong Wang, Weihua Liao, Fulai Yuan
Recent studies have shown that substance dependence (addiction) is accompanied with altered activity patterns of the default mode network (DMN). However, the neural correlates of the resting-state DMN and betel quid dependence (BQD)-related physiopathological characteristics still remain unclear. Resting-state functional magnetic resonance imaging images were obtained from 26 BQD individuals and 28 matched healthy control subjects. Group independent component analysis was performed to analyze the resting state images into spatially independent components...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28192677/prevalence-of-antibiotic-resistance-genes-in-bacterial-communities-associated-with-i-cladophora-glomerata-i-mats-along-the-nearshore-of-lake-ontario
#7
Michael Ibsen, Dinesh Fernando, Ayush Kumar, Andrea Kirkwood
The alga <i>Cladophora glomerata</i> can erupt in nuisance blooms throughout the lower Great Lakes. Since bacterial abundance increases with the emergence and decay of <i>Cladophora</i>, we investigated the prevalence of antibiotic resistance (ABR) in <i>Cladophora</i>-associated bacterial communities up-gradient and down-gradient from a large sewage treatment plant (STP) on Lake Ontario. Although STPs are well-known sources of ABR, we also expected detectable ABR from up-gradient wetland communities since they receive surface run-off from urban and agricultural sources...
February 13, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28192457/time-varying-spectral-power-of-resting-state-fmri-networks-reveal-cross-frequency-dependence-in-dynamic-connectivity
#8
Maziar Yaesoubi, Robyn L Miller, Vince D Calhoun
Brain oscillations and synchronicity among brain regions (brain connectivity) have been studied in resting-state (RS) and task-induced settings. RS-connectivity which captures brain functional integration during an unconstrained state is shown to vary with the frequency of oscillations. Indeed, high temporal resolution modalities have demonstrated both between and cross-frequency connectivity spanning across frequency bands such as theta and gamma. Despite high spatial resolution, functional magnetic resonance imaging (fMRI) suffers from low temporal resolution due to modulation with slow-varying hemodynamic response function (HRF) and also relatively low sampling rate...
2017: PloS One
https://www.readbyqxmd.com/read/28190837/analysis-of-distribution-and-intraparticle-diffusion-of-a-fluorescent-dye-in-mesoporous-silica-gel-by-confocal-fluorescence-microspectroscopy
#9
Tatsumi Sato, Kiyoharu Nakatani
A micrometer-sized spherical silica gel microparticle (pore diameter, ∼7 nm) was injected into an aqueous rhodamine 6G solution using microcapillary manipulation-injection technique, and the dye distribution in the single microparticle was measured as the fluorescence depth profile by confocal fluorescence microspectroscopy. The fluorescence depth profile was simulated by the convolution and deconvolution methods to correct the contribution of the spatial resolution of the experimental system. The dye homogeneously or heterogeneously distributed in the microparticle at the adsorption equilibrium, dependent on the type of silica gel...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/28179124/comparative-analysis-of-2d-and-3d-distance-measurements-to-study-spatial-genome-organization
#10
Elizabeth H Finn, Gianluca Pegoraro, Sigal Shachar, Tom Misteli
The spatial organization of eukaryotic genomes is non-random, cell-type specific, and has been linked to cellular function. The investigation of spatial organization has traditionally relied extensively on fluorescence microscopy. The validity of the imaging methods used to probe spatial genome organization often depends on the accuracy and precision of distance measurements. Imaging-based measurements may either use 2 dimensional datasets or 3D datasets including the z-axis information in image stacks. Here we compare the suitability of 2D versus 3D distance measurements in the analysis of various features of spatial genome organization...
February 4, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28177782/vertical-and-horizontal-distribution-of-sediment-nitrite-dependent-methane-oxidizing-organisms-in-a-mesotrophic-freshwater-reservoir
#11
Yan Long, Changbao Liu, Hengliang Lin, Ningning Li, Qingwei Guo, Shuguang Xie
The present study was to investigate the spatial change of sediment n-damo organisms in mesotrophic freshwater Gaozhou Reservoir (six different sampling locations and two sediment depths (0-5 cm, 5-10 cm)), one of the largest drinking water reservoirs in China. The abundance of sediment n-damo bacteria was quantified using quantitative PCR assay, while the richness, diversity and composition of n-damo pmoA gene sequences were characterized using clone library analysis. The vertical and horizontal changes of sediment n-damo bacterial abundance occurred in Gaozhou Reservoir, with 1...
January 31, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28173613/illumina-sequencing-based-analysis-of-sediment-bacteria-community-in-different-trophic-status-freshwater-lakes
#12
Yu Wan, Xiaohong Ruan, Yaping Zhang, Rongfu Li
Sediment bacterial community is the main driving force for nutrient cycling and energy transfer in aquatic ecosystem. A thorough understanding of the community's spatiotemporal variation is critical for us to understand the mechanisms of cycling and transfer. Here, we investigated the sediment bacterial community structures and their relations with environmental factors, using Lake Taihu as a model system to explore the dependence of biodiversity upon trophic level and seasonality. To combat the limitations of conventional techniques, we employed Illumina MiSeq Sequencing and LeFSe cladogram to obtain a more comprehensive view of the bacterial taxonomy and their variations of spatiotemporal distribution...
February 7, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28167048/biochemical-fractionation-of-time-resolved-drosophila-embryos-reveals-similar-transcriptomic-alterations-in-replication-checkpoint-and-histone-mrna-processing-mutants
#13
Fabio Alexis Lefebvre, Louis Philip Benoit Bouvrette, Julie Bergalet, Eric Lécuyer
In higher eukaryotes, maternally provided gene products drive the initial stages of embryogenesis until the zygotic transcriptional program takes over, a developmental process called the midblastula transition (MBT). In addition to zygotic genome activation, the MBT involves alterations in cell-cycle length and the implementation of DNA damage/replication checkpoints that serve to monitor genome integrity. Previous work has shown that mutations affecting histone mRNA metabolism or DNA replication checkpoint factors severely impact developmental progression through the MBT, prompting us to characterize and contrast the transcriptomic impact of these genetic perturbations...
February 3, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28164343/size-matters-point-pattern-analysis-biases-the-estimation-of-spatial-properties-of-stomata-distribution
#14
Paulette I Naulin, Gerardo Valenzuela, Sergio A Estay
Stomata distribution is an example of biological patterning. Formal methods used to study stomata patterning are generally based on point-pattern analysis, which assumes that stomata are points and ignores the constraints imposed by size on the placement of neighbors. The inclusion of size in the analysis requires the use of a null model based on finite-size object geometry. In this study, we compare the results obtained by analyzing samples from several species using point and disc null models. The results show that depending on the null model used, there was a 20% reduction in the number of samples classified as uniform; these results suggest that stomata patterning is not as general as currently reported...
March 2017: New Phytologist
https://www.readbyqxmd.com/read/28163143/on-the-detection-of-high-frequency-correlations-in-resting-state-fmri
#15
Cameron Trapp, Kishore Vakamudi, Stefan Posse
Current studies of resting-state connectivity rely on coherent signal fluctuations at frequencies below 0.1 Hz, however, recent studies using high-speed fMRI have shown that fluctuations above 0.5 Hz may exist. This study replicates the feasibility of measuring high frequency (HF) correlations in six healthy controls and a patient with a brain tumor while analyzing non-physiological signal sources via simulation. Resting-state data were acquired using a high-speed multi-slab echo-volumar imaging pulse sequence with 136 ms temporal resolution...
February 3, 2017: NeuroImage
https://www.readbyqxmd.com/read/28163122/comparison-of-bold-diffusion-weighted-fmri-and-adc-fmri-for-stimulation-of-the-primary-visual-system-with-a-block-paradigm
#16
R Nicolas, H Gros-Dagnac, F Aubry, P Celsis
The blood oxygen level-dependent (BOLD) effect is extensively used for functional MRI (fMRI) but presents some limitations. Diffusion-weighted fMRI (DfMRI) has been proposed as a method more tightly linked to neuronal activity. This work proposes a protocol of DfMRI acquired for several b-values and diffusion directions that is compared to gradient-echo BOLD (GE-BOLD) and to repeated spin-echo BOLD (SE-BOLD, acquisitions performed with b=0s/mm(2)), which was also used to ensure the reproducibility of the response...
February 2, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28159858/transcriptomic-alterations-in-the-brain-of-painted-turtles-chrysemys-picta-developmentally-exposed-to-bisphenol-a-or-ethinyl-estradiol
#17
Lindsey K Manshack, Caroline M Conard, Sara J Bryan, Sharon L Deem, Dawn K Holliday, Nathan J Bivens, Scott A Givan, Cheryl Susan Rosenfeld
Developmental exposure of turtles and other reptiles to endocrine disrupting chemicals (EDCs), including bisphenol A (BPA) and ethinyl estradiol (EE), can stimulate partial to full gonadal sex-reversal in males. We have also recently shown that in ovo exposure to either EDC can induce similar sex-dependent behavioral changes typified by improved spatial learning and memory or possibly feminized brain responses. Observed behavioral changes are presumed to be due to BPA- and EE-induced brain transcriptomic alterations during development...
February 3, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28158178/dynamic-maternal-gradients-control-timing-and-shift-rates-for-drosophila-gap-gene-expression
#18
Berta Verd, Anton Crombach, Johannes Jaeger
Pattern formation during development is a highly dynamic process. In spite of this, few experimental and modelling approaches take into account the explicit time-dependence of the rules governing regulatory systems. We address this problem by studying dynamic morphogen interpretation by the gap gene network in Drosophila melanogaster. Gap genes are involved in segment determination during early embryogenesis. They are activated by maternal morphogen gradients encoded by bicoid (bcd) and caudal (cad). These gradients decay at the same time-scale as the establishment of the antero-posterior gap gene pattern...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28157554/running-induced-memory-enhancement-correlates-with-the-preservation-of-thin-spines-in-the-hippocampal-area-ca1-of-old-c57bl-6-mice
#19
Benke Xu, Anbang Sun, Yun He, Feng Qian, Lian Liu, Yuncai Chen, Huanmin Luo
The effects of prolonged physical training on memory performance and underlying synaptic mechanisms were investigated in old C57BL/6 mice. Training via voluntary running wheels was initiated at 16 months of age and continued for 5 months (1 hour per day and 5 days per week), followed by learning and memory test and spine/synapse analysis. Trained old mice were compared with their age-matched sedentary controls and aged adult controls. This training improved hippocampal-dependent spatial learning and memory function in old mice, and enhanced cognition was accompanied by increased density of spines on CA1 pyramidal cells in the hippocampus...
January 11, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28156212/changes-in-the-hippocampal-proteome-associated-with-spatial-memory-impairment-after-exposure-to-low-20-cgy-doses-of-1-gev-n-56-fe-radiation
#20
Richard A Britten, Jessica S Jewell, Leslie K Davis, Vania D Miller, Melissa M Hadley, O John Semmes, György Lonart, Sucharita M Dutta
Exposure to low (∼20 cGy) doses of high-energy charged(HZE) particles, such as 1 GeV/n (56)Fe, results in impaired hippocampal-dependent learning and memory (e.g., novel object recognition and spatial memory) in rodents. While these findings raise the possibility that astronauts on deep-space missions may develop cognitive deficits, not all rats develop HZE-induced cognitive impairments, even after exposure to high (200 cGy) HZE doses. The reasons for this differential sensitivity in some animals that develop HZE-induced cognitive failure remain speculative...
February 3, 2017: Radiation Research
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