PubMed Health⌕ Search

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 217 records · Page 12Linked to original sources
PubMed2005

Timing precision in circle drawing does not depend on spatial precision of the timing target.

The authors manipulated the width of a timing target in continuous circle drawing to determine whether a more stringent spatial-timing criterion would produce an increase in participants' (N = 30) temporal variability. They also examined the effect of the computational method of determining cycle duration. There was no effect of spatial precision on temporal variability in circle drawing, and tapping and circle drawing were found to use the same criterion. Those findings lend strong support to the earlier view of R. B. Ivry, R. M. Spencer, H. N. Zelaznik, and J. Diedrichsen (2002), who argued that continuous tasks such as circle drawing are timed differently from discrete-like tasks such as tapping. Therefore, the results of the present study provide support for the event and emergent timing frameworks.

Humans↗
PubMed2026

transFusion: a novel comprehensive platform for integration analysis of single-cell and spatial transcriptomics.

MOTIVATION: Understanding spatial organization, intercellular interactions, and regulatory networks within the spatial context of tissues is crucial for uncovering complex biological processes and disease mechanisms. Spatial transcriptomics technologies have revolutionized this field by enabling the spatially resolved profiling of gene expression. 10× Visium has emerged as the predominant spatial technology, but its low resolution and the complexity of integrating multimodal datasets present significant analytical challenges, particularly for researchers with limited computational and statistical expertise. Current spatial transcriptomics analysis platforms generally fall short of effectively integrating multimodal data and maximizing the utility of spatial information-such as uncovering complex cellular spatial dependencies, multimodal gradient patterns, and spatial coexpression of ligand-receptor pairs and regulatory networks related to disease or biological states-thereby limiting their ability to provide comprehensive end-to-end analytical workflows when analyzing 10× Visium data. RESULTS: To address these limitations, we developed transFusion, a novel, advanced web-based platform specializing in the most comprehensive and effective integration analysis of scRNA-seq and 10× Visium spatial transcriptomics data. transFusion offers 12 key functions, from basic visualization to advanced analyses, including intercellular dependency analysis, ligand-receptor coexpression identification and visualization, and spatial multimodal gradient variation patterns. Two case studies were used to demonstrate transFusion's capabilities in exploring tissue architecture, intercellular communication, dependency networks, and multimodal gradient variation patterns with minimal computational skills and statistical expertise. transFusion provides a flexible and powerful framework for multimodal data integration analysis. AVAILABILITY AND IMPLEMENTATION: transFusion is freely available at https://github.com/WQLin8/transFusion.

Spatial Transcriptomics↗
PubMedDate not supplied

Spatial learning in the 5-HT1B receptor knockout mouse: selective facilitation/impairment depending on the cognitive demand.

Age-related memory decline is associated with a combined dysfunction of the cholinergic and serotonergic systems in the hippocampus and frontal cortex, in particular. The 5-HT1B receptor occupies strategic cellular and subcellular locations in these structures, where it plays a role in the modulation of ACh release. In an attempt to characterize the contribution of this receptor to memory functions, 5-HT1B receptor knockout (KO) mice were submitted to various behavioral paradigms carried out in the same experimental context (water maze), which were aimed at exposing mice to various levels of memory demand. 5-HT1BKO mice exhibited a facilitation in the acquisition of a hippocampal-dependent spatial reference memory task in the Morris water maze. This facilitation was selective of task difficulty, showing thus that the genetic inactivation of the 5-HT1B receptor is associated with facilitation when the complexity of the task is increased, and reveals a protective effect on age-related hippocampal-dependent memory decline. Young-adult and aged KO and wild-type (WT) mice were equally able to learn a delayed spatial matching-to-sample working memory task in a radial-arm water maze with short (0 or 5 min) delays. However, 5-HT1BKO mice, only, exhibited a selective memory impairment at intermediate and long (15, 30, and 60 min) delays. Treatment by scopolamine induced the same pattern of performance in wild type as did the mutation for short (5 min, no impairment) and long (60 min, impairment) delays. Taken together, these studies revealed a beneficial effect of the mutation on the acquisition of a spatial reference memory task, but a deleterious effect on a working memory task for long delays. This 5-HT1BKO mouse story highlights the problem of the potential existence of "global memory enhancers."

Animals↗
PubMed2005

Differential expression of PSD proteins in age-related spatial learning impairments.

Deficits in hippocampus-dependent spatial learning that are typical for a subpopulation of aged rats are not associated with loss of neurons or excitatory synapses but accompanied by significant reduction of postsynaptic density (PSD) area in perforated synapses. Here, we examined whether structural alterations in aged learning-impaired rats correlate with altered content of PSD proteins which are critically involved in normal synaptic function. Spatial memory tasks were used to separate male rats into young, aged learning-unimpaired and impaired groups. Semi-quantitative immunohistochemistry revealed significant alterations in the content of the AMPA receptor GluR1 subunit, PSD-95 and synGAP in the hippocampal formation of aged-learning impaired compared to aged-unimpaired and young rats. While synGAP expression was reduced, GluR1 and PSD95 levels were selectively increased in aged-learning-impaired subjects. These findings suggest that age-induced changes of the PSD protein expression levels are more pronounced in learning-impaired rats compared to unimpaired subjects and that the alterations in synaptic protein content may result in reduced synaptic function, potentially underlying the individual differences in mnemonic functions during aging.

Aging↗
PubMed2006

Testing the core/shell model of nanoconfined water in reverse micelles using linear and nonlinear IR spectroscopy.

A core/shell model has often been used to describe water confined to the interior of reverse micelles. The validity of this model for water encapsulated in AOT/isooctane reverse micelles ranging in diameter from 1.7 to 28 nm (w0 = 2-60) and bulk water is investigated using four experimental observables: the hydroxyl stretch absorption spectra, vibrational population relaxation times, orientational relaxation rates, and spectral diffusion dynamics. The time dependent observables are measured with ultrafast infrared spectrally resolved pump-probe and vibrational echo spectroscopies. Major progressive changes appear in all observables as the system moves from bulk water to the smallest water nanopool, w0 = 2. The dynamics are readily distinguishable for reverse micelle sizes smaller than 7 nm in diameter (w0 = 20) compared to the response of bulk water. The results also demonstrate that the size dependent absorption spectra and population relaxation times can be quantitatively predicted using a core-shell model in which the properties of the core (interior of the nanopool) are taken to be those of bulk water and the properties of the shell (water associated with the headgroups) are taken to be those of w0 = 2. A weighted sum of the core and shell components reproduces the size dependent spectra and the nonexponential population relaxation dynamics. However, the same model does not reproduce the spectral diffusion and the orientational relaxation experiments. It is proposed that, when hydrogen bond structural rearrangement is involved (orientational relaxation and spectral diffusion), dynamical coupling between the shell and the core cause the water nanopool to display more homogeneous dynamics. Therefore, the absorption spectra and vibrational lifetime decays can discern different hydrogen bonding environments whereas orientational and spectral diffusion correlation functions predict that the dynamics are size dependent but not as strongly spatially dependent within a reverse micelle.

Journal Article↗
PubMed2004

Quantitative SPECT leads to improved performance in discrimination tasks related to prodromal Alzheimer's disease.

UNLABELLED: We investigated the impact of the quantitation and reconstruction protocol on clinical tasks. The performance of standard clinical reconstruction procedures in discrimination tasks related to the diagnosis of prodromal Alzheimer's disease (AD) was compared with the performance of a quantitative approach incorporating improved corrections for scatter, attenuation, intrinsic spatial resolution, and distance-dependent spatial resolution. METHODS: Seventeen normal controls (normal group), 56 subjects who did not have dementia, who did have memory problems, but who did not develop AD within 5 y of follow-up (questionable group), and 27 subjects who did not have dementia, who did have memory problems, and who did develop AD over the follow-up period (converter group) were considered in this study. (99m)Tc-hexamethylpropyleneamine oxime SPECT and MRI studies were performed for each subject at baseline. The standard quantitation protocol (STD), routinely used in our clinic, consisted of Compton window scatter correction followed by filtered backprojection with attenuation correction using a uniform attenuation map. In the improved quantitative approach (QUAN), projections were corrected for scatter by use of a general spectral method and reconstructed by use of ordered-subset(s) expectation maximization, incorporating corrections for collimator response and attenuation using both a uniform attenuation map (QUANunif) and a nonuniform attenuation map (QUANnonunif). Mean SPECT activity concentration and MRI volume were estimated for 7 structures: rostral anterior cingulate gyrus, caudal anterior cingulate gyrus, posterior cingulate gyrus, hippocampus, basal forebrain, amygdala, and the banks of the superior temporal sulcus. Data were analyzed by pairwise discriminant analysis, and performance in binary group discrimination was measured by correlated receiver-operating-characteristic analysis. RESULTS: The use of QUANnonunif yielded a small but systematic improvement in discrimination accuracy for normal versus converter groups (accuracy or area under the receiver-operating-characteristic curve [Az], 0.965), normal versus questionable groups (Az, 0.973), and questionable versus converter groups (Az, 0.881) compared with the results obtained with QUANunif (Az, 0.955, 0.962, and 0.866, respectively). Discrimination performance was significantly lower (P < 0.05) with STD than with QUAN in all 3 tasks (Az with STD, 0.906, 0.878, and 0.768, respectively). MRI volume estimation led to a lower overall performance in all 3 tasks than did QUANnonunif (Az with MRI, 0.947, 0.917, and 0.872, respectively). CONCLUSION: Improved quantitative image reconstruction with accurate compensation for scatter, attenuation, and variable collimator response led to significantly better performance in discrimination tasks related to the diagnosis of prodromal AD than did standard clinical reconstruction procedures. The use of a nonuniform brain attenuation map yields a small improvement in discrimination accuracy.

Aged↗
PubMed2003

The importance of hippocampus-dependent non-spatial tasks in analyses of homology and homoplasy.

The hippocampus or a homologous region plays a role in spatial tasks in a large number of vertebrate species. This result, in combination with recent findings of adaptive specializations of the hippocampus for spatial demands, has led to the conclusion that the prominent selective force behind hippocampal evolution was a need for spatial abilities. However, a review of non-spatial hippocampus-dependent tasks shows that many vertebrate species also share non-spatial functions of the hippocampus. Placed in the appropriate phylogenetic context, it becomes clear that non-spatial facets of hippocampal function were just as likely to be present in our vertebrate ancestors as spatial ones. In addition, the absence of spatial strategy use in three lineages suggests divergence of this feature. Divergence in this character and other characteristics of hippocampal function are meaningful indicators of lineage specific functions. Studies of the evolution of the hippocampus must include examination of spatial and non-spatial functions of the hippocampus and consider both conserved, as well as derived, features.

Animals↗
PubMed1999

Dissociation of human caudate nucleus activity in spatial and nonspatial working memory: an event-related fMRI study.

We employed a novel event-related fMRI design and analysis technique to explore caudate nucleus contributions to spatial and nonspatial working memory. The spatial condition of a delayed-response task revealed greater mnemonic activation in four of six subjects when the delay period preceded immediately a probe stimulus requiring an overt motor response, as contrasted with a probe requiring no response. This effect was not seen in frontal or parietal cortical areas, and was seen in the caudate nucleus in a formally identical object condition in just one of six subjects. We hypothesized that this pattern of activity represented spatially dependent motor preparation. A second experiment confirmed this hypothesis: delay-period activity of the caudate nucleus showed greater time dependence in a task that featured spatial and motoric memory demands than in a comparable nonspatial task that featured the same response contingencies. These results suggest an important subcortical locus of the dissociation between spatial and nonspatial working memory, and a role for the human caudate nucleus in the integration of spatially coded mnemonic information with motor preparation to guide behavior.

Adult↗
PubMed2002

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.

There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation. A constant adjustment is often used to force the distribution of the intensity log ratios to have a median of zero for each slide. However, such global normalization approaches are not adequate in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. This article proposes normalization methods that are based on robust local regression and account for intensity and spatial dependence in dye biases for different types of cDNA microarray experiments. The selection of appropriate controls for normalization is discussed and a novel set of controls (microarray sample pool, MSP) is introduced to aid in intensity-dependent normalization. Lastly, to allow for comparisons of expression levels across slides, a robust method based on maximum likelihood estimation is proposed to adjust for scale differences among slides.

Animals↗
PubMed2006

A dynamic conditional random field model for foreground and shadow segmentation.

This paper proposes a dynamic conditional random field (DCRF) model for foreground object and moving shadow segmentation in indoor video scenes. Given an image sequence, temporal dependencies of consecutive segmentation fields and spatial dependencies within each segmentation field are unified by a dynamic probabilistic framework based on the conditional random field (CRF). An efficient approximate filtering algorithm is derived for the DCRF model to recursively estimate the segmentation field from the history of observed images. The foreground and shadow segmentation method integrates both intensity and gradient features. Moreover, models of background, shadow, and gradient information are updated adaptively for nonstationary background processes. Experimental results show that the proposed approach can accurately detect moving objects and their cast shadows even in monocular grayscale video sequences.

Algorithms↗
PubMed1997

Decrease in highly polysialylated neuronal cell adhesion molecules and in spatial learning during ageing are not correlated.

Age-dependent spatial memory impairments have been related to a decline in hippocampal plasticity. Highly polysialylated neuronal cell adhesion molecules (PSA-NCAM) show a strong expression during adulthood within regions associated with neuroplastic events. Furthermore, NCAM molecules have been proposed to mediate neuronal plasticity during learning and memory. The aim of the present study was to examine the effect of ageing on the expression of PSA-NCAM within the hippocampus. To investigate whether age-dependent changes in expression of PSA-NCAM were accentuated in aged rats with learning impairment, animals were in a first step assessed for their cognitive abilities using a Morris water maze. Seven-month-old and 24-month-old-rats were tested for their performance in the Morris water maze. The animals were sacrificed and brain sections were processed for PSA-NCAM immunohistochemistry. Ageing was accompanied by an overall decrease in PSA-NCAM-immunoreactivity (-IR) within the forebrain, presenting a important decrease of the number of PSA-NCAM-IR perikarya within the hippocampus. These results were confirmed by Western blot analysis. No difference in PSA-NCAM immunoreactivity was observed in aged rats with or without spatial learning impairment. It is concluded that although changes in PSA-NCAM accompanied the decrease in cognitive abilities, our data did not evidence a causal relationship between these two parameters.

Aging↗
PubMed1996

Genetic variation in the morphology of the septo-hippocampal cholinergic and GABAergic systems in mice: II. Morpho-behavioral correlations.

We investigated the contribution of the septo-hippocampal cholinergic and GABAergic system to spatial and nonspatial aspects of learning and memory that had previously been found to correlate with the extent of the hippocampal intra- and infrapyramidal mossy fiber projection in different inbred mouse strains. The following cholinergic and GABAergic markers were measured in the septi and hippocampi of male mice: the number of cholinergic and parvalbumin-containing neurons in the medial septum/vertical limb of the diagonal band of Broca (MS/vDB), the number of septo-hippocampal cholinergic and GABAergic projection neurons, the density of cholinergic fibers in different hippocampal subfields, and the density of muscarinic receptors (predominantly M1 and M2) in the hippocampus. In addition, animals were behaviorally tested for spatially dependent and activity-dependent variables in a water maze and spatial and nonspatial working and reference memory in different experimental set-ups in an eight-arm radial maze. Using only those variables for which significant strain differences were obtained, we looked for covariations between behavior and neuroanatomy. The density of cholinergic fibers in the dentate gyrus was significantly correlated with activity-dependent learning in the water maze, whereas the number of septo-hippocampal cholinergic projection neurons correlated with spatial and, to a lesser extent, also with nonspatial aspects of radial maze learning. Only weak correlations were found between receptor densities and behavioral traits. From these data we conclude that variations in the septo-hippocampal cholinergic system, like variations in the mossy fiber projection, entail functional consequences for different types of maze learning in mice.

Acetylcholinesterase↗
PubMed2003

Patterns of brain acetylcholine release predict individual differences in preferred learning strategies in rats.

Acetylcholine release was measured simultaneously in the hippocampus and dorsal striatum of rats before and during training on a maze that could be learned using either a hippocampus-dependent spatial strategy or a dorsal striatum-dependent turning strategy. A probe trial administered after rats reached a criterion of 9/10 correct responses revealed that about half of the rats used a spatial strategy and half a turning strategy to solve the task. Acetylcholine release in the hippocampus, as well as the ratio of acetylcholine release in the hippocampus vs. the dorsal striatum, measured either before or during training, predicted these individual differences in strategy selection during learning. These findings suggest that differences in release of acetylcholine across brain areas may provide a neurobiological marker of individual differences in selection of the strategies rats use to solve a learning task.

Acetylcholine↗
PubMed2000

Spatial summation of blue-on-yellow light increments and decrements in human vision.

In the primate retina, blue-OFF cells are less numerous than blue-ON cells but no psychophysical equivalent of this asymmetry has been found so far. The hypothesis put forward in the present study is that the ON-OFF asymmetry should manifest itself in the size and effectiveness of spatial summation of S-cone signals of opposite polarity. To test this hypothesis upon selective stimulation of the S-cones in man, a 3 cd/m(2) blue light was superimposed on a 300 cd/m(2) yellow background and the test stimulus consisted in a luminance increment or decrement of the blue light from its steady level over a circular area of variable size. The test stimuli were presented at 12.5 degrees retinal eccentricity. Within the test-stimulus spectral band, sensitivity was that of Stiles' pi(1) mechanism. Increasing stimulus area reduced more the decrement threshold than the increment threshold, and Ricco's area was larger for luminance decrements (0.8-2 degrees ) than for increments (0.6-0.9 degrees ). Experiments with red-on-red stimuli confirmed that the large summation area and stimulus-polarity-dependent spatial summation are specific for the isolated S-cone signals. The sign-dependency of spatial summation is probably a psychophysical correlate of the asymmetry of the ON- and OFF- visual pathways receiving S-cone input.

Adult↗
PubMed2006

A completely automated CAD system for mass detection in a large mammographic database.

Mass localization plays a crucial role in computer-aided detection (CAD) systems for the classification of suspicious regions in mammograms. In this article we present a completely automated classification system for the detection of masses in digitized mammographic images. The tool system we discuss consists in three processing levels: (a) Image segmentation for the localization of regions of interest (ROIs). This step relies on an iterative dynamical threshold algorithm able to select iso-intensity closed contours around gray level maxima of the mammogram. (b) ROI characterization by means of textural features computed from the gray tone spatial dependence matrix (GTSDM), containing second-order spatial statistics information on the pixel gray level intensity. As the images under study were recorded in different centers and with different machine settings, eight GTSDM features were selected so as to be invariant under monotonic transformation. In this way, the images do not need to be normalized, as the adopted features depend on the texture only, rather than on the gray tone levels, too. (c) ROI classification by means of a neural network, with supervision provided by the radiologist's diagnosis. The CAD system was evaluated on a large database of 3369 mammographic images [2307 negative, 1062 pathological (or positive), containing at least one confirmed mass, as diagnosed by an expert radiologist]. To assess the performance of the system, receiver operating characteristic (ROC) and free-response ROC analysis were employed. The area under the ROC curve was found to be Az = 0.783 +/- 0.008 for the ROI-based classification. When evaluating the accuracy of the CAD against the radiologist-drawn boundaries, 4.23 false positives per image are found at 80% of mass sensitivity.

Algorithms↗
PubMed2000

Dynamics of prey moving through a predator field: a model of migrating juvenile salmon.

The migration of a patch of prey through a field of relatively stationary predators is a situation that occurs frequently in nature. Making quantitative predictions concerning such phenomena may be difficult, however, because factors such as the number of the prey in the patch, the spatial length and velocity of the patch, and the feeding rate and satiation of the predators all interact in a complex way. However, such problems are of great practical importance in many management situations; e.g., calculating the mortality of juvenile salmon (smolts) swimming down a river or reservoir containing many predators. Salmon smolts often move downstream in patches short compared with the length of the reservoir. To take into account the spatial dependence of the interaction, we used a spatially-explicit, individual-based modeling approach. We found that the mortality of prey depends strongly on the number of prey in the patch, the downstream velocity of prey in the patch, and the dispersion or spread of the patch in size through time. Some counterintuitive phenomena are predicted, such as predators downstream capturing more prey per predator than those upstream, even though the number of prey may be greatly depleted by the time the prey patch reaches the downstream predators. Individual-based models may be necessary for complex spatial situations, such as salmonid migration, where processes such as schooling occur at fine scales and affect system predictions. We compare some results to predictions from other salmonid models.

Animals↗
PubMed1987

Intracellular topography of rhodopsin bleaching.

In a vertebrate eye, the photoreceptor cells are aligned so that most of the light passes through them lengthwise. At the light-transducing outer segment region of the photoreceptor, photons are absorbed in a time-varying, spatially dependent fashion. Because the transduction event is spatially localized around the site of photon absorption, the spatiotemporal patterns of light absorption in outer segments are an important receiver input characteristic. This aspect of receptor biophysics has now been measured; the results were consistent with a theoretical model proposed for bleaching of a pigment in an unstirred layer.

Animals↗