SEARCH · PubMed Health

Results for “spatial dependency”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 379 records · Page 21Linked to original sources

PubMedDate not supplied

Spatial variability of nitrous oxide emissions and their soil-related determining factors in an agricultural field.

To evaluate spatial variability of nitrous oxide (N2O) emissions and to elucidate their determining factors on a field-scale basis, N2O fluxes and various soil properties were evaluated in a 100- x 100-m onion (Allium cepa L.) field. Nitrous oxide fluxes were determined by a closed chamber method from the one-hundred 10- x 10-m plots. Physical (e.g., bulk density and water content), chemical (e.g., total N and pH), and biological (e.g., microbial biomass C and N) properties were determined from surface soil samples (0-0.1 m) of each plot. Geostatistical analysis was performed to examine spatial variability of both N2O fluxes and soil properties. Multivariate analysis was also conducted to elucidate relationships between soil properties and observed fluxes. Nitrous oxide fluxes were highly variable (average 331 microg N m(-2) h(-1), CV 217%) and were log-normally distributed. Log-transformed N2O fluxes had moderate spatial dependence with a range of >75 m. High N2O fluxes were observed at sites with relatively low elevation. Multivariate analysis indicated that an organic matter factor and a pH factor of the principal component analysis were the main soil-related determining factors of log-transformed N2O fluxes. By combining multivariate analysis with geostatistics, a map of predicted N2O fluxes closely matched the spatial pattern of measured fluxes. The regression equation based on the soil properties explained 56% of the spatially structured variation of the log-transformed N2O fluxes. Site-specific management to regulate organic matter content and water status of a soil could be a promising means of reducing N2O emissions from agricultural fields.

Air Pollutants↗

PubMed2005

Physically based reflectance model utilizing polarization measurement.

A surface bidirectional reflectance distribution function (BRDF) depends on both the optical properties of the material and the microstructure of the surface and appears as combination of these factors. We propose a method for modeling the BRDF based on a separate optical-property (refractive-index) estimation by polarization measurement. Because the BRDF and the refractive index for precisely the same place can be determined, errors cased by individual difference or spatial dependence can be eliminated. Our BRDF model treats the surface as an aggregation of microfacets, and the diffractive effect is negligible because of randomness. An example model of a painted aluminum plate is presented.

Journal Article↗

PubMed2005

Geostatistical analysis of disease data: estimation of cancer mortality risk from empirical frequencies using Poisson kriging.

BACKGROUND: Cancer mortality maps are used by public health officials to identify areas of excess and to guide surveillance and control activities. Quality of decision-making thus relies on an accurate quantification of risks from observed rates which can be very unreliable when computed from sparsely populated geographical units or recorded for minority populations. This paper presents a geostatistical methodology that accounts for spatially varying population sizes and spatial patterns in the processing of cancer mortality data. Simulation studies are conducted to compare the performances of Poisson kriging to a few simple smoothers (i.e. population-weighted estimators and empirical Bayes smoothers) under different scenarios for the disease frequency, the population size, and the spatial pattern of risk. A public-domain executable with example datasets is provided. RESULTS: The analysis of age-adjusted mortality rates for breast and cervix cancers illustrated some key features of commonly used smoothing techniques. Because of the small weight assigned to the rate observed over the entity being smoothed (kernel weight), the population-weighted average leads to risk maps that show little variability. Other techniques assign larger and similar kernel weights but they use a different piece of auxiliary information in the prediction: global or local means for global or local empirical Bayes smoothers, and spatial combination of surrounding rates for the geostatistical estimator. Simulation studies indicated that Poisson kriging outperforms other approaches for most scenarios, with a clear benefit when the risk values are spatially correlated. Global empirical Bayes smoothers provide more accurate predictions under the least frequent scenario of spatially random risk. CONCLUSION: The approach presented in this paper enables researchers to incorporate the pattern of spatial dependence of mortality rates into the mapping of risk values and the quantification of the associated uncertainty, while being easier to implement than a full Bayesian model. The availability of a public-domain executable makes the geostatistical analysis of health data, and its comparison to traditional smoothers, more accessible to common users. In future papers this methodology will be generalized to the simulation of the spatial distribution of risk values and the propagation of the uncertainty attached to predicted risks in local cluster analysis.

Journal Article↗

PubMed2004

Spatial regimes in the dynamics of polyolefins: self-motion.

Molecular dynamics simulations are used to investigate the spatial dependence of dynamics in a series of polyolefins. The dynamic indicator used is the self-intermediate scattering function, which parallels the observable in an incoherent quasielastic neutron scattering experiment such as time of flight or backscattering. As with neutron time of flight experiments, two processes are evident. The fast process is a single exponential, and has relaxation times that scale as q(-2), where q is the momentum transfer. The slow process is the stretched exponential decay usually associated with the motion underlying the glass transition. The stretching exponent is a function of spatial scale, with the minimum values occurring near the spatial scale of interchain packing. Relaxation times for the slow process scale as q(-2/beta) for all materials investigated. The relative contribution of the two processes is a function of spatial scale, with the crossover from fast to slow dynamics at the location of closest possible interchain contacts, which is approximately three times the cage size. These observations apply equally well to the four materials considered. We consider the relative ordering of relaxation times of the series in light of their local chain architecture. This ordering varies depending on the observable calculated..

Journal Article↗

PubMed1999

Stimulation of aggrecan synthesis in cartilage explants by cyclic loading is localized to regions of high interstitial fluid flow.

Chondrogenesis in cartilage development and repair and cartilage degeneration in arthritis can be regulated by mechanical-load-induced physical factors such as tissue deformation, interstitial fluid flow and pressure, and electrical fields or streaming potentials. Previous animal and tissue explant studies have shown that time-varying dynamic tissue loading can increase the synthesis and deposition of matrix molecules in an amplitude-, frequency-, and spatially dependent manner. To provide information on the cell-level physical factors which may stimulate chondrocytes to increase production and export of aggrecan, the main proteoglycan component of the cartilage matrix, we characterized local changes in aggrecan synthesis within cyclically loaded tissue explant disks and compared those changes to values of predicted local physical factors. Aggrecan synthesis following a 23-h compression/radiolabel protocol was measured with a spatial resolution of approximately 0.1 mm across the 1.5-mm radius of explanted disks using a quantitative autoradiography method. A uniform stimulation of aggrecan synthesis was observed at an intermediate frequency of 0.01 Hz, while, at a higher frequency of 0.1 Hz, stimulation was only seen at peripheral radial positions. Profiles of radial solid matrix deformation and interstitial fluid pressure and velocity predicted to be occurring across the radius of the disk during sinusoidal loading were estimated using a composite poroelastic model. Tissue regions experiencing high interstitial fluid velocities corresponded to those displaying increased aggrecan synthesis. These results reinforce the role of load-induced flow of interstitial fluid in the stimulation of aggrecan production during dynamic loading of cartilage.

Aggrecans↗

PubMedDate not supplied

Exploratory spatial analysis of birth defect rates in an urban population.

Are birth defect rates unusually high in particular urban localities? The answer requires that the birth defect rate for which 'significance' is claimed be adjusted for the variable population sizes of each area for which the rate is computed and for the spatial dependence of rates based on shared observations between neighboring areas. By address-matching birth and birth defect records to a digital road map, we are able to compute local birth defect rates at regular grid locations by dividing the number of birth defects that occurred in the geographical vicinity of a grid location by the total number of births in the same vicinity. We test for significance, at regular spatial intervals, against the null hypothesis that the observed rate at any locality could reasonably have arisen by chance alone, given the underlying geographical variation in births. Significance is determined by using Monte Carlo simulations, where each birth location has an identical probability of being a defect. From 1000 simulations, a statistical distribution of the birth defect rate for each grid location is determined. The proportion of the simulated birth defect rates that are less than the observed rate at any grid location is the probability that the observed rate is significant. These probabilities, portrayed as isarithmic maps, show areas that have significantly high birth defect rates. Our results show birth defect rates for the period 1983 to 1990 in Des Moines, Iowa, U.S.A.

Cluster Analysis↗

PubMed2006

Bacterial activity, community structure, and centimeter-scale spatial heterogeneity in contaminated soil.

In an anthropogenically disturbed soil (88% sand, 8% silt, 4% clay), 150-mg samples were studied to examine the fine-scale relationship of bacterial activity and community structure to heavy metal contaminants. The soils had been contaminated for over 40 years with aromatic solvents, Pb, and Cr. Samples from distances of <1, 5, 15, and 50 cm over a depth range of 40-90 cm underwent a sequential analysis to determine metabolic potential (from 14C glucose mineralization), bacterial community structure [using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)], and total extractable Pb and Cr levels. Metabolic potential varied by as much as 10,000-fold in samples <1 cm apart; log-log plots of metal concentration and microbial metabolic potential showed no correlation with each other. Overall, metal concentrations ranged from 9 to 29,000 mg kg(-1) for Pb and from 3 to 8500 mg kg(-1) for Cr with small zones of high contamination present. All regions exhibited variable metal concentrations, with some soil samples having 30-fold differences in metal concentration in sites <1 cm apart. Geostatistical analysis revealed a strong spatial dependence for all three parameters tested (metabolic activity, Pb, and Cr levels) with a range up to 30 cm. Kriging maps showed that in zones of high metal, the corresponding metabolic activity was low suggesting that metals negatively impacted the microbial community. PCR-DGGE analysis revealed that diverse communities were present in the soils with a random distribution of phylotypes throughout the sampling zones. These results suggest the presence of spatially isolated microbial communities within the soil profile.

Bacteria↗

PubMed2005

Tissue plasminogen activator and plasminogen mediate stress-induced decline of neuronal and cognitive functions in the mouse hippocampus.

Repeated stress can impair function in the hippocampus, a brain structure essential for learning and memory. Although behavioral evidence suggests that severe stress triggers cognitive impairment, as seen in major depression or posttraumatic stress disorder, little is known about the molecular mediators of these functional deficits in the hippocampus. We report here both pre- and postsynaptic effects of chronic stress, manifested as a reduction in the number of NMDA receptors, dendritic spines, and expression of growth-associated protein-43 in the cornu ammonis 1 region. Strikingly, the stress-induced decrease in NMDA receptors coincides spatially with sites of plasminogen activation, thereby predicting a role for tissue plasminogen activator (tPA) in this form of stress-induced plasticity. Consistent with this possibility, tPA-/- and plasminogen-/- mice are protected from stress-induced decrease in NMDA receptors and reduction in dendritic spines. At the behavioral level, these synaptic and molecular signatures of stress-induced plasticity are accompanied by impaired acquisition, but not retrieval, of hippocampal-dependent spatial learning, a deficit that is not exhibited by the tPA-/- and plasminogen-/- mice. These findings establish the tPA/plasmin system as an important mediator of the debilitating effects of prolonged stress on hippocampal function at multiple levels of neural organization.

Analysis of Variance↗

PubMed2006

Allosteric enhancement of metabotropic glutamate receptor 5 function promotes spatial memory.

Group I metabotropic glutamate receptors (mGluRs) have been implicated in learning and memory formation. Recent findings indicate an important function of the group I mGluR subtype 5. Here, we used the Y-maze spatial alternation task and examined whether enhancement of intrinsic mGluR5 activity immediately after learning, i.e. during a critical period for memory consolidation, would have any consequences on long-term memory retention in rats. Intracerebroventricular application of the allosteric mGluR5 potentiator DFB (3,3'-difluorobenzaldazine) resulted in a marked improvement in spatial alternation retention when it was tested 24 h after training. The promnesic effect increased with the difficulty of the task and was apparently due to a substantial enhancement of consolidation. The applied dose of DFB did not cause behavioral changes in the open field, and was devoid of structural side-effects as evaluated by immunohistochemical examination. Our results suggest an important function of post-training mGluR5 activation in some types of hippocampus-dependent spatial learning.

Allosteric Regulation↗

PubMed1996

Development of methods for dynamic radiation therapy with specified dose distributions.

Several methods for dose deposition of a given isodose distribution were developed by implementation of different techniques of accelerator use. Common to all of these methods is the time-dependent change of certain accelerator parameters during radiation treatment. The accelerators for which these methods can be used are equipped with independent collimator jaws, however, not with any kind of multileaf collimation. This method was designed to deposit a certain group of dose distributions that are restricted by a small number of constraints. The developed methods were implemented into a digitally controlled medical linear accelerator and the dosimetric results of such treatments were evaluated. Dose distributions with spatial dependencies in one and in two dimensions were deposited by movement of one X-ray jaw pair. Furthermore, a method for generation of a two-dimensional rotationally symmetric dose distribution was developed.

Algorithms↗

PubMed2004

Beta-sheet breaker peptide prevents Abeta-induced spatial memory impairments with partial reduction of amyloid deposits.

Current evidence supports the notion that beta-amyloid deposits or Abeta intermediates may be responsible for the pathogenesis in Alzheimer's disease (AD) patients. In the present work, we have assessed the neuroprotective effect of the chronic intraperitoneal administration of a five-amino-acid beta-sheet breaker peptide (iAbeta5p) on the rat behavioral deficit induced by the intrahippocampal Abeta-fibrils injection. At 1 month after the injection, animals showed a partial reduction of the amyloid deposits formed and a decreased astrocytic response around the injection site. More importantly, we report that following the iAbeta5p treatment, hippocampal-dependent spatial learning paradigms, including the standard Morris water maze and a working memory analysis, showed a significant prevention from impairments induced by Abeta deposits in the dorsal hippocampus. Thus, it is possible that a noninvasive treatment such as the one presented here with beta-sheet breaker peptides may be used as a potential therapy for AD patients.

Alzheimer Disease↗

PubMed2003

Impairment of radial maze delayed nonmatching after lesions of anterior thalamus and parahippocampal cortex.

This study compared the effects of lesions damaging hippocampus-related pathways in anterior thalamus (AT) and parahippocampal (PH) cortex on allocentric spatial memory. Rats were trained to perform radial maze delayed nonmatching (DNM) with random selection of arms to prevent egocentric solutions. After experimental treatment (control, excitotoxic AT, radiofrequency PH, or combined AT-PH lesions), rats were retrained for 30 sessions from 2 to 8 weeks after surgery. Results showed comparable impairments for AT and PH lesions that added without interaction in the combined AT-PH group. During chronic recovery, the AT-PH group exhibited delay-dependent deficits comparable to previous results for hippocampal lesions. Thus, AT and PH lesions appear to have separate effects that together disrupt hippocampus-dependent spatial memory.

Animals↗

PubMed2005

Modeling and suppression of respiration-related physiological noise in echo-planar functional magnetic resonance imaging using global and one-dimensional navigator echo correction.

A major source of noise in functional magnetic resonance imaging (fMRI) arises from modulations in the local magnetic field in the head due to motion of the subject's chest through the respiratory cycle, and this physiologic noise can nullify the gains in statistical power expected by the use of higher magnetic fields for fMRI. In particular, fMRI data acquired using echo-planar imaging (EPI) are very sensitive to these spatially and temporally varying respiration-induced frequency offsets. In this study, accurate 3D magnetic field maps in the head were measured and used to determine the frequency offsets at the two extremes of the respiratory cycle. From these maps, spatially dependent frequency variations from about -1.0 Hz to +1.5 Hz were measured in the brain through the respiratory cycle. Simulations of a typical axial EPI fMRI experiment acquired in the presence of this measured field variation were performed, demonstrating regional image intensity variations between 1 and 5% in single pixel time series. The inadequacy of either global or 1D navigator echo corrections to measure and suppress respiratory-induced noise in fMRI time series is demonstrated. The nature of the spatial variations observed suggests that 2D approaches should be considered.

Brain Mapping↗

PubMed2005

A role for adult neurogenesis in spatial long-term memory.

Adult hippocampal neurogenesis has been linked to learning but details of the relationship between neuronal production and memory formation remain unknown. Using low dose irradiation to inhibit adult hippocampal neurogenesis we show that new neurons aged 4-28 days old at the time of training are required for long-term memory in a spatial version of the water maze. This effect of irradiation was specific since long-term memory for a visibly cued platform remained intact. Furthermore, irradiation just before or after water maze training had no effect on learning or long-term memory. Relationships between learning and new neuron survival, as well as proliferation, were investigated but found non-significant. These results suggest a new role for adult neurogenesis in the formation and/or consolidation of long-term, hippocampus-dependent, spatial memories.

Animals↗

PubMed1996

Textural parameters based on the Spatial Gray Level Dependence Method applied to melanocytic nevi.

The purpose of this study is to evaluate the Spatial Gray Level Dependence Method (SGLDM) of texture analysis with respect to its ability to discriminate between melanocytic nevi and normal skin. Thirteen textural features based on the SGLDM were evaluated with respect to their relative sensitivities to both texture and tone. Ten features were found to be more sensitive to texture than tone and were selected for further study. Twenty-four digitized images of benign melanocytic nevi were obtained from six volunteers. Ten textural features were analyzed for each nevus and for surrounding sections of normal skin. Of these 10 features, 8 features can distinguish between textural properties of melanocytic nevi and surrounding skin.

Humans↗

PubMedDate not supplied

Modelling spatial disease rates using maximum likelihood.

This paper concerns maximum likelihood estimation for a generalized linear mixed model (GLMM) useful for modelling spatial disease rates. The model allows for log-linear covariate adjustment and local smoothing of rates through estimation of spatially correlated random effects. The covariance structure of the random effects is based on a recently proposed model which parameterizes spatial dependence through the inverse covariance matrix. A Markov chain Monte Carlo algorithm for performing maximum likelihood estimation for this model is described. Results of a computer simulation study that compared maximum likelihood (ML) and penalized quasi-likelihood (PQL) estimators are presented. Compared with PQL, ML produced less biased estimates of the intercept but the ML estimates were slightly more variable. Estimates of the other regression coefficients were unbiased and nearly identical for the two methods. ML estimators of the random effects standard deviation and spatial correlation were more biased than the corresponding PQL estimators. The conclusion is that ML estimators for GLMMs cannot be expected to perform better than PQL for small samples.

Algorithms↗

PubMedDate not supplied

Neonatal exposure to novel environment enhances hippocampal-dependent memory function during infancy and adulthood.

Early life experience affects behavior and brain mechanisms. Handling rats during the first three weeks in life can slow age-related cognitive decline (as measured by a hippocampal-dependent spatial learning task) and reduce age-related hippocampal neuron loss. It is not clear, however, whether this early environmental influence on learning is selective for old age or is more general, affecting cognitive development during infancy and young adulthood as well. We briefly exposed neonatal rats to a novel non-home environment for 3 min daily during the first three weeks of life (as a component of the handling method). We found that this brief early environmental manipulation resulted in enhanced hippocampal-dependent learning immediately after weaning and that this learning enhancement persisted into adulthood. These results suggest that subtle early life events can affect cognitive development in all developmental stages and that changes in neural mechanisms other than neuron number are likely to mediate the learning enhancement at multiple developmental stages.

Animals↗

PubMed2026

A host-encoded prophage targets a Candidate Phyla Radiation bacterium and shapes episymbiotic interactions.

The Patescibacteriota, also known as the Candidate Phyla Radiation (CPR), represent a large lineage of ultrasmall bacteria with highly reduced genomes and obligate dependence on bacterial hosts. Although genomic analyses have revealed CRISPR-Cas and restriction-modification systems in many CPR genomes, no cognate bacteriophages (phages) have been isolated, leaving CPR-phage interactions unexplored. Nanosynbacter lyticus TM7x, the first cultivated CPR bacterium, grows episymbiotically on its host, Schaalia odontolytica XH001, in the human oral microbiome. Here, we identify Xhp1, an inducible prophage of XH001 that is preferentially activated during episymbiosis with TM7x. Released Xhp1 particles infect prophage-free XH001 via distinct strategies determined by host growth mode, establishing lysogeny under planktonic conditions but driving lytic infection during surface-associated growth. Xhp1 also binds efficiently to TM7x and exhibits limited infection under the conditions tested, indicating direct phage-CPR interactions. Importantly, TM7x modulates Xhp1 availability in a spatially dependent manner. In planktonic culture, free-floating TM7x reduces lysogenic conversion of XH001ΔXhp1, consistent with TM7x acting as a phage sink that lowers effective phage concentration. In contrast, during surface-associated growth, TM7x increases XH001ΔXhp1 susceptibility to lytic infection, likely by locally concentrating phage particles within a constrained niche. These results demonstrate that CPR bacteria can regulate viral encounter rates through spatial organization. In spatially structured environments such as oral biofilms, such modulation may shape infection dynamics and community structure. Together, this work characterizes the first CPR-targeting phage and reveals a an important role for phages in CPR-host bacteria interactions.

Prophages↗