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PubMed2002

Spatial characteristics of fine particulate matter: identifying representative monitoring locations in Seattle, Washington.

This study investigates how PM2.5 varies spatially and how these spatial characteristics can be used to identify potential monitoring sites that are most representative of the overall ambient exposures to PM2.5 among susceptible populations in the Seattle, WA, area. Data collected at outdoor sites at the homes of participants of a large exposure assessment study were used in this study. Harvard impactors (HIs) were used at 40 outdoor sites throughout the Seattle metropolitan area. Up to six sites at a time were monitored for 10 consecutive 24-hr average periods. A fixed-effect analysis of variance (ANOVA) model that included date and location effects was used to analyze the spatial variability of outdoor PM2.5 concentrations. Both date and location effects were shown to be highly significant, explaining 92% of the variability in outdoor PM2.5 measurements. The day-to-day variability was 10 times higher than the spatial variability between sites. The site mean square was more than twice the error mean square, showing that differences between sites, while modest, are potentially an important contribution to measurement error. Variances of the model residuals and site effects were examined against spatial characteristics of the monitoring sites. The spatial characteristics included elevation, distance from arterials, and distance from major PM2.5 point sources. Results showed that the most representative PM2.5 sites were located at elevations of 80-120 m above sea level, and at distances of 100-300 m from the nearest arterial road. Location relative to industrial PM2.5 sources is not a significant predictor of residential outdoor PM2.5 measurements. Additionally, for sites to be representative of the average population exposures to PM2.5 among those highly susceptible to the health effects of PM2.5, areas of high elderly population density were considered. These representative spatial characteristics were used as multiple, overlapping criteria in a Geographic Information System (GIS) analysis to determine where the most representative sites are located.

Air Pollutants↗
PubMed1994

Towards a clarification of spatial processing.

Three experiments that adopt an interference paradigm to investigate characteristics of a type of movement causing interference with spatial processing are reported. Experiment 1 illustrates the importance of distinguishing between movement and attention to movement when investigating the movement characteristics of spatial processing. The technique of passive movement is used to minimize attention in the subsequent experiments. Experiment 2 confirms earlier experiments showing that passive movement causes interference in spatial processing. However, it extends the previous findings by demonstrating that passive movement is detrimental to spatial processing only when the movement is to a sequence of locations known in advance by the subjects. Experiment 3 demonstrates that the movement interference cannot be interpreted as a general interference effect but that it is selective for spatial processing. The results of these experiments permit a more precise delineation of the disruptive effects of movement in spatial processing and allow an explicit definition of spatial processing to be put forward.

Attention↗
PubMed1997

Working memory constraints on linear reasoning with spatial and temporal contents.

The present article reports two experiments testing the use of working memory components during reasoning with temporal and spatial relations in four-term series problems. In the first experiment four groups of subjects performed reasoning tasks with temporal and with spatial contents either without (control) or with a secondary task (articulatory suppression, visuo-spatial suppression or central executive suppression). The second experiment tested the secondary task effects in a within-subjects design either on problems with a spatial content or on problems with a temporal content, and within each content domain either under conditions of self-paced or of fixed presentation of the premises. Both experiments found effects of all three secondary tasks on reasoning accuracy. This supports the hypothesis that the subjects construct spatial representations of the premise information with the support of visuo-spatial resources of working memory. The second experiment also showed that during premise intake, only visuo-spatial and central executive secondary tasks had an effect. The implications of the data for the working memory requirements of reasoning and for theories of linear reasoning are discussed.

Adult↗
PubMed2004

The spatial and temporal characteristics of the apparent-diffusion-coefficient-dependent fMRI signal changes during visual stimulation.

The blood oxygenation level dependent (BOLD) contrast has been commonly used to detect fMRI signal. The majority of the BOLD signals are believed to arise from the venous and capillary networks. However, only those from the capillaries are spatially close to the neuronal activities, while the signals from large veins could be distant, rendering the overall localization inaccurate. In recent years, an alternative contrast using arterial spin labeled (ASL) perfusion imaging techniques has been proposed for predominant capillary sensitivity. Such acquisition methods, however, are intrinsically limited in temporal resolution and spatial coverage. Another contrast mechanism, free of such constraints, is based on the apparent diffusion coefficient (ADC) changes during brain activation using isotropic diffusion weighting. It has been shown that these changes are synchronized with brain activation and that they, as a whole, temporally precede BOLD activation, suggesting significant upstream arterial contribution. Moreover, the spatial overlaps between the upstream ADC and downstream BOLD activations are shown to be more localized in the capillaries, which are the temporal and spatial middle ground. In this paper, we sought to further investigate the temporal and spatial characteristics of ADC contrast with additional arterial signal suppression. Also, a pixel-based evaluation was performed in conjunction with the averaged global assessment. It was found that in addition to the known spatial discrepancy and global timing advance compared to the BOLD signal, the ADC activation endured significant temporal heterogeneities. Such fine spatial and temporal assessment could help characterize the exact signal sources of ADC contrast, and ultimately achieve exclusive capillary sensitivity.

Brain↗
PubMed2025

Enhancing and accelerating cell type deconvolution of large-scale spatial transcriptomics slices with dual network model.

MOTIVATION: Cell type deconvolution deciphers spatial distribution of mRNA transcripts at single cell level by integrating single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics data to infer mixture of cell types of spots in slices. Current algorithms are criticized for neglecting connection between scRNA-seq and spatial transcriptomics data, as well as time-consuming, hampering their application to large-scale datasets. RESULTS: In this study, we propose a joint learning nonnegative matrix factorization algorithm for fast cell type deconvolution (aka jMF2D), which integrates scRNA-seq and spatial transcriptomics data with network models. To bridge scRNA-seq and spatial transcriptomics data, jMF2D jointly learns cell type similarity network to enhance quality of signatures of cell types, thereby promoting accuracy and efficiency of deconvolution. Experiments demonstrate that jMF2D outperforms state-of-the-art baselines in terms of accuracy by saving about 90% running time on various datasets generated by different platforms. Furthermore, it can also facilitates the identification of spatial domains and bio-marker genes, providing an efficient and effective model for analyzing spatial transcriptomics data. AVAILABILITY AND IMPLEMENTATION: The software is coded using python, and is free available for academic https://github.com/xkmaxidian/jMF2D.

Algorithms↗
PubMed2025

BISON: bi-clustering of spatial omics data with feature selection.

MOTIVATION: The advent of next-generation sequencing-based spatially resolved transcriptomics (SRT) techniques has reshaped genomic studies by enabling high-throughput gene expression profiling while preserving spatial and morphological context. Understanding gene functions and interactions in different spatial domains is crucial, as it can enhance our comprehension of biological mechanisms, such as cancer-immune interactions and cell differentiation in various regions. It is necessary to cluster tissue regions into distinct spatial domains and identify discriminating genes (DGs) that elucidate the clustering result, referred to as spatial domain-specific DGs. Existing methods for identifying these genes typically rely on a two-stage approach, which can lead to the phenomenon known as double-dipping. RESULTS: To address the challenge, we propose a unified Bayesian latent block model that simultaneously detects a list of DGs contributing to spatial domain identification while clustering these DGs and spatial locations. The efficacy of our proposed method is validated through a series of simulation experiments, and its capability to identify DGs is demonstrated through applications to benchmark SRT datasets. AVAILABILITY AND IMPLEMENTATION: The R/C++ implementation of BISON is available at https://github.com/new-zbc/BISON.

Software↗
PubMed2006

Disease mapping and spatial regression with count data.

In this paper, we provide critical reviews of methods suggested for the analysis of aggregate count data in the context of disease mapping and spatial regression. We introduce a new method for picking prior distributions, and propose a number of refinements of previously used models. We also consider ecological bias, mutual standardization, and choice of both spatial model and prior specification. We analyze male lip cancer incidence data collected in Scotland over the period 1975-1980, and outline a number of problems with previous analyses of these data. In disease mapping studies, hierarchical models can provide robust estimation of area-level risk parameters, though care is required in the choice of covariate model, and it is important to assess the sensitivity of estimates to the spatial model chosen, and to the prior specifications on the variance parameters. Spatial ecological regression is a far more hazardous enterprise for two reasons. First, there is always the possibility of ecological bias, and this can only be alleviated by the inclusion of individual-level data. For the Scottish data, we show that the previously used mean model has limited interpretation from an individual perspective. Second, when residual spatial dependence is modeled, and if the exposure has spatial structure, then estimates of exposure association parameters will change when compared with those obtained from the independence across space model, and the data alone cannot choose the form and extent of spatial correlation that is appropriate.

Epidemiologic Methods↗
PubMed2005

Spatial neglect--a vestibular disorder?

The phenomenon of spatial neglect after right brain damage greatly helps our understanding of the normal mechanisms of directing and maintaining spatial attention, of spatial orientation, and the characteristics of neural representation of space. The intriguing symptom is a spontaneous orientation bias towards the right leading to neglect of objects or persons on the left. Interestingly, we observe similar symptoms namely a spontaneous bias of eyes and head along the horizontal dimension of space in patients with unilateral vestibular dysfunction. Further similarities concern anatomical findings. Both spatial neglect and vestibular processing at cortical level show dominance in the right hemisphere and involve common brain areas. Lesion studies in human and monkey, electrical and transcranial magnetic stimulation, as well as functional imaging results have revealed the superior temporal cortex, insula and the temporo-parietal junction to be substantial parts of the multisensory (vestibular) system as well as to be affected in spatial neglect. We argue that these structures are not strictly 'vestibular' but rather have a multimodal character representing a significant site for the neural transformation of converging vestibular, auditory, neck proprioceptive and visual input into higher order spatial representations. Neurons of these regions provide us with redundant information about the position and motion of our body in space. They seem to play an essential role in adjusting body position relative to external space. This view may initiate further development of those strategies to treat spatial neglect that use routes to rehabilitation based on specific manipulations of sensory input feeding into this system.

Animals↗
PubMed2000

Lesions affecting the parahippocampal cortex yield spatial memory deficits in humans.

Anatomical studies in monkeys, and functional imaging and lesion studies in humans, suggest that, within the primate medial temporal neocortex, the parahippocampal cortex (PHC) is particularly involved in spatial tasks. However, evidence for a functional specialization of the PHC regarding its spatial memory functions has so far been lacking. Here, we investigated spatial memory functions of the human perirhinal cortex (PRC) and PHC. Patients with lesions affecting the PRC but sparing the PHC, and patients with lesions affecting both PRC and PHC, performed an oculomotor delayed response task with unpredictably varied memory delays of up to 30 s. Compared to controls, patients with PRC+PHC lesions showed a significant delay-dependent inaccuracy of memory-guided eye movements contralateral to the lesion side, whereas patients with PRC lesions showed no significant inaccuracy. Our results show that the PHC is a critical component for spatial memory in humans and suggest that (i) extrahippocampal spatial memory functions of the medial temporal lobe may not be equally distributed in the medial temporal neocortex, but may be largely confined to the PHC, and (ii) damage to connections between cortices involved in spatial cognition and rostral regions of the temporal lobe is unlikely to account for the observed spatial memory deficits with PHC lesions.

Adult↗
PubMed2001

Structure--function spatial covariance in the human visual cortex.

The value of sulcal landmarks for predicting functional areas was quantitatively examined. Medial occipital sulci were identified using anatomical magnetic resonance images to create individual cortical-surface models. Functional visual areas were identified using retinotopically organized visual stimuli, and positron emission tomography subtraction imaging with intra-subject averaging. Functional areas were assigned labels by placement along the cortical surface from V1. Structure-function spatial covariances between sulci and functional areas, and spatial covariances among functional areas, were determined by projecting sulcal landmarks and functional areas into a standardized stereotaxic space and computing the 'r' statistics. A functional area was considered to spatially covary with a sulcus or another functional area if their geometric centers correlated significantly (P < 0.05) in two or more axes. Statistically significant spatial covariances were found for some, but not all comparisons. The finding of significant spatial covariances within a standardized stereotaxic space indicates that nine-parameter spatial normalization does not account for all the predictive value of structural or functional locations, and may be improved upon by using selected sulcal and functional landmarks. The present findings quantify for the first time the strength of structure--function spatial covariance and comment directly on developmental theories addressing the etiology of structure--function correspondence.

Adolescent↗
PubMed2005

Visuo-spatial consciousness and parieto-occipital areas: a high-resolution EEG study.

Conscious and unconscious visuo-spatial processes are mainly related to parieto-occipital cortical activation. In this study, the working hypothesis was that a specific pattern of parieto-occipital activation is induced by conscious, as opposed to unconscious, visuo-spatial processes. Electroencephalographic data (128 channels) were recorded in 12 normal adults during a visuo-spatial task. A cue stimulus appeared on the right or the left (equal probability) monitor side for a 'threshold time' inducing approximately 50% of correct recognitions. It was followed (after 2 s) by visual go stimuli at spatially congruent or incongruent positions with reference to the cue location. The left (right) mouse button was clicked if the go stimulus appeared on the left (right) monitor side. Subjects were required to say 'seen' if they had detected the cue stimulus or 'not seen' if they missed it (self-report). 'Seen' and 'not seen' electroencephalographic trials were averaged separately to form visual evoked potentials. Sources of these potentials were estimated by LORETA software. Reaction time to go stimuli was shorter during spatially congruent than incongruent 'seen' trials, possibly due to covert attention on cue for self-report. It was also shorter during spatially congruent than incongruent 'not seen' trials, as an objective sign of unconscious processes. Cue stimulus evoked parieto-occipital potentials which has the same peak latencies in the 'seen' and 'not seen' cases. Sources of these potentials were located in occipital area 19 and parietal area 7. Source strength was significantly stronger in 'seen' than 'not seen' cases at approximately +300 ms post-stimulus. These results may unveil features of parieto-occipital activation accompanying visuo-spatial consciousness.

Adult↗
PubMed2005

Characterization of the spatial dispersion of corn root injury by corn rootworms (Coleoptera: Chrysomelidae).

The dispersion of root injury to Zea mays L. by corn rootworm, Diabrotica spp., larvae was characterized using geostatistics to determine the appropriate sampling distance to obtain independent estimates of root injury. We also investigated the effect of the root injury levels on the spatial dependence of root injury at three different spatial scales: large-scale study with 25-m sampling distance in three, 8-ha fields; moderate-scale study with 0.2-m sampling distance in six, 2-ha fields; and small-scale study with exhaustive sampling in eight, 12-m(2) plots within cornfields. In the large-scale study, a nugget model best fit the semivariograms, indicating the dispersion of root injury exhibited a random pattern. In the moderate-scale study, all the semivariograms were best fit with an exponential model, and 68 to 96% of the variability was explained by spatial dependence, suggesting a high degree of spatial aggregation of corn root larval injury. The ranges of semivariograms fell within < 4 m, except one field that had the range of 14.7 m. In the small-scale study, the Gaussian, exponential, or spherical models fit the semivariograms best and 50 to 89% of the variability was explained by spatial dependence, suggesting spatial aggregation of root injury. The ranges of semivariograms were from 0.35 to 1.04 m. In the small-scale study, the degree of spatial dependence increased significantly (P < 0.05) as the average root injury increased within the range of root injury observed in the study. These results suggest that the minimum distance between root samples in small-plot insecticide trials should be > 1 m within a row to obtain unbiased estimates of root injury.

Animals↗
PubMed2003

A comparison of manual and automated systems for soil CO2 flux measurements: trade-offs between spatial and temporal resolution.

Soil respiration is affected by distributions of roots and soil carbon substrates and by temperature and soil water content, all of which vary spatially and temporally. The objective of this paper was to compare a manual system for measuring soil respiration in a temperate forest, which had a greater spatial distribution of measurements (n=12), but poorer temporal resolution (once per week), with an automated system which had poorer spatial distribution (n=3) but superior temporal frequency of measurements (hourly). Soil respiration was measured between 18 June and 21 August, 2002, at the Harvard Forest in central Massachusetts, USA. The fluxes measured within 1 h of each other by these systems were not significantly different. However, extrapolations of the mid-morning manual measurements to daily flux values were consistently lower (averaging 13% lower) than the daily estimates obtained from summing the 24 hourly measurements of the automated system. On the other hand, seasonal flux estimates obtained by interpolating between weekly manual sampling dates or by summing the hourly automated measurements were nearly identical. Underestimates by interpolated weekly manual measurements during some periods were cancelled by overestimates during other periods. Hence, a weekly sampling schedule may be sufficient to capture the most important variation of seasonal efflux of CO(2) from the soil. The larger number of chambers that could be measured with the manual system (larger n) resulted in a smaller 95% confidence interval for characterizing spatial variability within the study area on most dates. However, the greater sampling frequency of the automated system revealed rapid responses of soil respiration to wetting events, which permitted better empirical modelling of the effects of soil temperature and moisture on soil respiration than could have been achieved with the manual sampling system. Most of the positive residuals of a function that predicts soil respiration based on temperature were from fluxes measured within 12 h of a rain event, and the residuals were positively correlated with water content of the O horizon. The automated system also demonstrated that Q(10) values calculated for diel variation in soil temperature over a few days were not significantly different than Q(10) values for the entire 3 month summer sampling period. In summary, a manual system of numerous, spatially well-distributed flux chambers measured on a weekly basis may be adequate for measuring seasonal fluxes and may maximize confidence in the characterization of spatial variance. The high temporal frequency of measurements afforded by automation greatly improves the ability to measure and model the effects of rapidly varying water content and temperature. When the two approaches can be combined, the temporal representativeness of the manual measurements can be tested with the automated measurements and the spatial representativeness of the automated measurements can be tested by the manual measurements.

Carbon Dioxide↗
PubMed2001

Event-related TMS over the right posterior parietal cortex induces ipsilateral visuo-spatial interference.

The right posterior parietal cortex (PPC) is implicated in visuo-spatial processing, as illustrated by patients with visuo-spatial neglect, but the precise time-course of its contribution is still an open question. In the present study we assessed whether single-pulse transcranial magnetic stimulation (TMS) can interfere with the performance of normal subjects in a standard visuo-spatial task. Participants had to perform a landmark task while TMS was applied over the right PPC, the homologue region in the left hemisphere or the right primary motor cortex. Stimulation was time-locked to the stimulus presentation with a stimulus onset asynchrony (SOA) varying between 50 and 200 ms. Our results indicate that TMS interfered mainly with the visuo-spatial task when applied over the right PPC at an early stage (50 ms post-stimulus). The interference effect of single-pulse TMS in the present visuo-spatial processing is revealed by a processing cost for ipsilateral targets. These results are in agreement with neuropsychological and brain imaging studies showing a right hemispheric dominance in visuo-spatial processing but add crucial information about the time-course of visuo-spatial processing within the right PPC.

Adult↗
PubMed2001

Localizing acute stroke-related EEG changes: assessing the effects of spatial undersampling.

Because of its sensitivity to metabolic and ionic disturbances related to ischemia, the EEG can be a potentially useful tool for acute stroke detection and for monitoring affected tissue. However, the clinical use of the EEG in detecting stroke is determined in part by how accurately the spatial information is characterized. The purpose of the current study was to determine the effects of spatial undersampling on the distribution and interpretation of the stroke-related topographic EEG. Using a 128-channel sensor montage, EEG was recorded from six stroke patients acutely (between 8 and 36 hours) after symptom onset. The EEG was submitted to a spectral analysis and was compared with patient symptoms and MRI and computed tomographic findings. To determine loss of spatial and clinical information resulting from spatial undersampling, the average-referenced data from the original 128-channel recording montage were subsampled into 64-, 32-, and 19-channel arrays. Furthermore, the analytical findings were compared with a board-certified electroencephalographer's review of the raw EEG using a conventional clinical montage. As predicted, the results showed that accurate description of stroke-related topographic EEG changes is dependent on adequate spatial sampling density. Accurate description of the spatial distribution of the stroke-related EEG was achieved only with the 64- and 128-channel EEG. As the recording density decreases to 32 channels, the distribution of the scalp EEG spectra is distorted, potentially resulting in mislocalization of the affected region. Results of the clinical review by an expert electroencephalographer corroborated the quantitative analyses, and the results also demonstrated the shortcomings of the conventional 10-20 recording density for capturing focal EEG abnormalities in several cases. The EEG provides useful information about the localization of acute cerebral ischemia, but recording densities of 64 channels or higher are required for accurate spatial characterization of focal stroke-related EEG changes.

Adult↗
PubMed2003

Correction of tibial malunion and nonunion with six-axis analysis deformity correction using the Taylor Spatial Frame.

OBJECTIVE: To determine the effectiveness of six-axis analysis deformity correction using the Taylor Spatial Frame for the treatment of posttraumatic tibial malunions and nonunions. DESIGN: Retrospectively reviewed, consecutive series. Mean duration of follow-up was 3.2 years (range 2-4.2 years). SETTING: Tertiary referral center for deformity correction. PATIENTS/PARTICIPANTS: Eighteen patients were included in the study (11 malunions and 7 nonunions). All deformities were posttraumatic in nature. The mean number of operations before the application of the spatial frame was 2.6 (range 1-6 operations). All patients completed the study. INTERVENTION: Six-axis analysis deformity correction using the Taylor Spatial Frame (Smith & Nephew, Memphis, TN) was used for correction of posttraumatic tibial malunion or nonunion. Nine patients had bone grafting at the time of frame application. One patient with a tibial plafond fracture simultaneously had deformity correction and an ankle fusion for a mobile atrophic nonunion. Two patients had infected tibial nonunions that were treated with multiple débridements, antibiotic beads, and bone grafting at the time of spatial frame application. A rotational gastrocnemius flap was used to cover a proximal third tibial defect in one patient. The average length of time the spatial frame was worn, time to healing, was 18.5 weeks (range 12-32 weeks). MAIN OUTCOME MEASUREMENTS: Assessment of deformity correction in six axes, knee and ankle range of motion, incidence of infection, and return to preinjury activities. RESULTS: Of the 18 patients treated with the Taylor Spatial Frame, with adjunctive bone graft as necessary, 17 achieved union and significant correction of their deformities in six axes (ie, coronal angulation and translation, sagittal angulation and translation, rotation, and shortening). Fifteen patients returned to their preinjury activities at last follow-up. CONCLUSION: Six-axis analysis deformity correction using the Taylor Spatial Frame is an effective technique to treat posttraumatic malunions and nonunions of the tibia, with several advantages over previously used devices.

Adolescent↗
PubMed2006

Neuroprotective effects of behavioural training and nicotine on age-related deficits in spatial learning.

Studies in humans and animals show a clear decline in spatial memory with age and several approaches have been adopted to alleviate this impairment. The purpose of our review is to assess the studies that have suggested the possible neuroprotective actions of behavioural training and nicotine-applied both independently and in conjunction-on age-related deficits in spatial learning. Both spatial pretraining and nonspatial experiences influence an animal's performance in spatial tasks. In aged rats, the experience of training in the water maze task increases the number of newly generated neurons in the hippocampus. The neuroprotective effects of nicotine have been demonstrated in both in-vitro and in-vivo models, although the molecular mechanisms underlying these actions are not yet fully understood. It had been concluded in different studies that nicotine can improve, impair or have no effect on performance in the water maze. Neurobiological data also suggest an interaction between nicotine and prior experience in complex tasks, although few studies have raised the question of whether nicotine treatment and training in spatial tasks may contribute in an interactive manner to alleviate spatial cognition impairment associated with the ageing process. Different findings suggest that past experience could be a confounding variable in longitudinal studies that aim to evaluate the neuroprotective effects of nicotine on age-related deficits in spatial learning.

Aging↗
PubMed2006

Differential influences of negative emotion on spatial and verbal working memory: Evidence from event-related potential and source current density analysis.

We used the event-related potential technique to assess the influences of negative emotion on spatial and verbal working memory with a modified n-back task. In both spatial and verbal tasks, the anterior late positive component and the posterior P300 were affected by negative emotion. These effects were, however, greater in spatial tasks than in verbal ones. Especially, the parietal P300 was reduced by negative emotion in spatial tasks, but not in verbal tasks. Current density analysis revealed high current density in the frontal-parietal cortex, but only in the spatial tasks. The results suggest differential effects of negative emotion on spatial and verbal working memory and that the frontal-parietal cortex may be the area where negative emotion and spatial working memory interact.

Adult↗