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PubMed2004

Mixed models for the analysis of replicated spatial point patterns.

The statistical methodology for the analysis of replicated spatial point patterns in complex designs such as those including replications is fairly undeveloped. A mixed model is developed in conjunction with maximum pseudolikelihood and generalized linear mixed modeling by extending Baddeley and Turner's (2000, Australian and New Zealand Journal of Statistics 42, 283-322) work on pseudolikelihood for single patterns. A simulation experiment is performed on parameter estimation. Fixed- and mixed-effect models are compared, and in some respects the mixed model is found to be superior. An example using the Strauss process for modeling neuron locations in post-mortem brain slices is shown.

Brain↗

PubMed1997

GATA-5: a transcriptional activator expressed in a novel temporally and spatially-restricted pattern during embryonic development.

Members of the GATA family of zinc finger transcription factors regulate critical steps of cellular differentiation during vertebrate development. In the studies described in this report, we have isolated and functionally characterized the murine GATA-5 cDNA and protein and defined the temporal and spatial pattern of GATA-5 gene expression during mammalian development. The amino terminus of the mouse GATA-5 protein shares high level amino acid sequence identity with the murine GATA-4 and -6 proteins, but not with other members of the GATA family. GATA-5 binds to the functionally important CEF-1 nuclear protein binding site in the cardiac-specific slow/cardiac troponin C (cTnC) transcriptional enhancer and overexpression of GATA-5 transactivates the cTnC enhancer in noncardiac muscle cell lines. During embryonic and postnatal development, the pattern of GATA-5 gene expression differs significantly from that of other GATA family members. In the primitive streak embryo, GATA-5 mRNA is detectable in the precardiac mesoderm. Within the embryonic heart, the GATA-5 gene is expressed within the atrial and ventricular chambers (ED 9.5), becomes restricted to the atrial endocardium (ED 12.5), and is subsequently not expressed in the heart during late fetal and postnatal development. Moreover, coincident with the earliest steps in lung development, only the GATA-5 gene is expressed within the pulmonary mesenchyme. Finally, the GATA-5 gene is expressed in tissue-restricted subsets of smooth muscle cells (SMCs), including bronchial SMCs and SMCs in the bladder wall. These data are consistent with a model in which GATA-5 performs a unique temporally and spatially restricted function in the embryonic heart and lung. Moreover, these data suggest that GATA-5 may play an important role in the transcriptional program(s) that underlies smooth muscle cell diversity.

3T3 Cells↗

PubMed2003

Oscillations and patterns in spatially discrete models for developmental intercellular signalling.

We extend previous models for nearest neighbour ligand-receptor binding to include both lateral induction and inhibition of ligand and receptor production, and different geometries (strings of cells and hexagonal arrays, in addition to square arrays). We demonstrate the possibility of lateral inhibition giving patterns with a characteristic length scale of many cell diameters, when receptor production is included. In contrast, lateral induction combined with inhibition of receptor synthesis cannot give rise to a patterning instability under any circumstances. Interesting new dynamics include the analytical prediction and consequent numerical observation of spatiotemporal oscillations, this depends crucially on the production terms and on the relationship between the decay rates of ligand and free receptor. Our approach allows for a detailed comparison with the model for Delta-Notch interactions of Collier et al. [4], and we find that a formal reduction may be made only when the ligand receptor binding kinetics are very slow. Without such very slow receptor kinetics, spatial pattern formation via lateral inhibition in hexagonal cellular arrays requires significant activation of receptor production, a feature that is not apparent from previous analyses.

Algorithms↗

PubMed1995

Spatio-temporal decomposition of the EEG: a general approach to the isolation and localization of sources.

The principal-component method of source localization for the background EEG is generalized to arbitrary spatio-temporal decompositions. It is shown that as long as the spatial patterns of the decomposition span the same signal space as the principal spatial components, the computational process of attempting to localize the sources is the same. Decompositions other than the principal components are shown to be superior for the EEG in that they appear to enable individual sources to be better isolated. An example is given using the common spatial pattern decomposition and using a raw varimax rotation of a subset of the common spatial patterns. The results show that the principal component decomposition is almost ineffective for isolating spike and sharp wave activity in an EEG from a patient with epilepsy, that the common spatial pattern decomposition is significantly better and that the varimax rotation is better yet. That the varimax rotation is best is demonstrated by attempting to locate dipole sources inside the brain which account for the spike and sharp wave activity on the scalp. The question which remains is whether there exists some oblique rotation of the basis vectors of the EEG signal space which is optimal for isolating individual sources.

Adult↗

PubMed2006

Localization of latent epileptic activities using spatio-temporal independent component analysis of FMRI data.

Localizing interictal epileptic activities is a difficult problem in clinical practice. We report a novel noninvasive technique, resting functional magnetic resonance imaging (fMRI) with spatio-temporal independent component analysis (ICA), for localizing interictal epileptic activities. First, the fMRI data is separated into independent spatial patterns by spatial-ICA, and the patterns with Z-values larger than a threshold are selected as the potential spatial patterns of the epileptic activities. Second, the temporal series of the active points in the selected patterns are separated by temporal-ICA, and the component with the biggest Gaussian deviation (kurtosis) is selected as the representative of the epileptic discharge activity in a sub-region. Finally, those spatial sub-regions, which have distinct epileptic discharge activities confirmed by temporal-ICA are considered as the epileptic foci. This method was applied to fMRI data of six epileptic patients, and the results are consistent with the clinical assessment. Though more studies are required to validate this technique, the above preliminary results demonstrate the potential of using the resting fMRI with spatio-temporal ICA to detect and localize latent epileptic activities.

Adult↗

PubMed2001

Temporal and spatial expression patterns of TUB9, a beta-tubulin gene of Arabidopsis thaliana.

Transgenic plants carrying chimeric genes composed of segments of the 5'-flanking region of the Arabidopsis 9-tubulin gene (TUB9) fused to the coding region of the beta-glucuronidase (GUS) gene of Escherichia coli were used to investigate the temporal and spatial patterns of TUB9 expression. Chimeric genes that contained at least 800 bp of TUB9 5'-flanking DNA were expressed primarily in floral tissues, with high levels of expression observed in pollen, elongating pollen tubes and ovules. The expression of the reporter genes in ovules ceased at the time of fertilization. In situ hybridization was used to verify that the reporter gene expression in pollen of transgenic plants is representative of the patterns of expression of the endogenous TUB9 gene. In situ hybridization also provided new insight into TUB9 transcript accumulation in ovules. The possible role of TUB9 and the functional implication of the largely non-overlapping expression patterns of tubulin genes are discussed.

Arabidopsis↗

PubMed2006

Interactions between pattern formation and domain growth.

In this paper we develop a theoretical framework for investigating pattern formation in biological systems for which the tissue on which the spatial pattern resides is growing at a rate which is itself regulated by the diffusible chemicals that establish the spatial pattern. We present numerical simulations for two cases of interest, namely exponential domain growth and chemically controlled growth. Our analysis reveals that for domains undergoing rapid exponential growth dilution effects associated with domain growth influence both the spatial patterns that emerge and the concentration of chemicals present in the domain. In the latter case, there is complex interplay between the effects of the chemicals on the domain size and the influence of the domain size on the formation of patterns. The nature of these interactions is revealed by a weakly nonlinear analysis of the full system. This yields a pair of nonlinear equations for the amplitude of the spatial pattern and the domain size. The domain is found to grow (or shrink) at a rate that depends quadratically on the pattern amplitude, the particular functional forms used to model the local tissue growth rate and the kinetics of the two diffusible species dictating the resulting behaviour.

Body Patterning↗

PubMed2026

Spatial inheritance patterns across maize ears are associated with alleles that reduce pollen fitness.

Often, more pollen grains land on recipient flowers than there are ovules to fertilize. Consequently, the haploid male gametophyte engages in post-pollination competition, one way that pollen genotype can influence inheritance. The maize (Zea mays subsp. mays L.) inflorescence (ear), with its elongated stigma and style structures (silks), has a conspicuous spatial heterogeneity, with longer silks at the base of the ear than at the apex. To evaluate the hypothesis that alleles with reduced pollen fitness influence the spatial distribution of progeny genotypes along the ear, we developed an updated phenotyping platform that maps fluorescently marked mutant (Ds-GFP) kernel phenotypes on the ear via an implementation of the Faster R-CNN machine vision model (EarVision.v2) and a statistical pipeline that evaluates the relationship between kernel position and transmission ratio (EarScape). Our dataset (1384 ears) represents 58 Ds-GFP insertion alleles. None of the 48 alleles with Mendelian inheritance showed any significant spatial trend. In contrast, 50% of alleles with a pollen-specific transmission defect (5/10) exhibited significant spatial effects. An insertional mutant of the gene encoding a putative actin-binding protein, base-to-apex gradient1* (bag1*), is associated with decreased mutant transmission at the ear base relative to the apex. Surprisingly, a mutant allele of another pollen-expressed gene (Zm00001eb236740) generates the opposite trend, decreased mutant transmission toward the ear apex; and two mutant alleles of the sperm cell attachment factor gamete expressed2 (gex2) can produce ears with transmission highest at both base and apex. We conclude that pollen fitness mutants cause unexpectedly diverse spatial patterns of progeny genotypes.

Zea mays↗

PubMed1992

Temporal and spatial expression patterns of the small heat shock (hsp16) genes in transgenic Caenorhabditis elegans.

The expression of the hsp16 gene family in Caenorhabditis elegans has been examined by introducing hsp16-lacZ fusions into the nematode by transformation. Transcription of the hsp16-lacZ transgenes was totally heat-shock dependent and resulted in the rapid synthesis of detectable levels of beta-galactosidase. Although the two hsp16 gene pairs of C. elegans are highly similar within both their coding and noncoding sequences, quantitative and qualitative differences in the spatial pattern of expression between gene pairs were observed. The hsp16-48 promoter was shown to direct greater expression of beta-galactosidase in muscle and hypodermis, whereas the hsp16-41 promoter was more efficient in intestine and pharyngeal tissue. Transgenes that eliminated one promoter from a gene pair were expressed at reduced levels, particularly in postembryonic stages, suggesting that the heat shock elements in the intergenic region of an hsp16 gene pair may act cooperatively to achieve high levels of expression of both genes. Although the hsp16 gene pairs are never constitutively expressed, their heat inducibility is developmentally restricted; they are not heat inducible during gametogenesis or early embryogenesis. The hsp16 genes represent the first fully inducible system in C. elegans to be characterized in detail at the molecular level, and the promoters of these genes should find wide applicability in studies of tissue- and developmentally regulated genes in this experimental organism.

Animals↗

PubMed1991

The temporal and spatial distribution pattern of maternal exuperantia protein: evidence for a role in establishment but not maintenance of bicoid mRNA localization.

The exuperantia (exu) gene of Drosophila melanogaster plays a fundamental role in the establishment of polarity of the oocyte and early embryo by ensuring the proper localization of the mRNA of the bicoid (bcd) gene to anterior regions of the oocyte. We have isolated and sequenced the exu gene, sequenced its female-specific transcript and a mutant allele of exu that affects primarily exu's female germline function, and determined the temporal and spatial pattern of exu protein expression during oogenesis. The exu protein is basic, with at least one basic residue being identified as necessary for exu function in the female germline, and is present transiently during oogenesis. Our results suggest that exu is not required for the maintenance of bcd mRNA localization during late stages of oogenesis and early embryogenesis, but rather for the establishment of bcd mRNA localization in the developing oocyte. We propose that the exu protein may serve to modify a component that binds bcd mRNA or to modify the bcd message itself, or may perform a role in docking the bcd mRNA at its site of localization in the developing oocyte.

Amino Acid Sequence↗

PubMed2006

Urban air pollution patterns, land use, and thermal landscape: an examination of the linkage using GIS.

This article investigates the relationship of local air pollution pattern with urban land use and with urban thermal landscape using a GIS approach. Ambient air quality measurements for sulfur dioxide, nitrogen oxide, carbon monoxide, total suspended particles, and dust level were obtained for Guangzhou City in South China between 1981 and 2000. Landsat TM images and aerial photo derived maps were used to examine city's land use and land cover at different times and changes. Landsat thermal infrared data were employed to compute land surface temperatures and to assess urban thermal patterns. Relationships among the spatial patterns of air pollution, land use, and thermal landscape were sought through GIS and correlation analyses. Results show that the spatial patterns of air pollutants probed were positively correlated with urban built-up density, and with satellite derived land surface temperature values, particularly with measurements taken during the summer. It is suggested that further studies investigate the mechanisms of this linkage, and that remote sensing of air pollution delves into how the energy interacts with the atmosphere and the environment and how sensors see pollutants. Thermal infrared imagery could play a unique role in monitoring and modeling atmospheric pollution.

Air Pollution↗

PubMed1998

Noise-induced regularity of spatial wave patterns in subalpine abies forests

In subalpine forests dominated by Abies species in Japan and northeastern United States, trees show traveling wave of regeneration with many striped zones of tree dieback, moving downwind at a constant rate. Previous theoretical studies have demonstrated that a very simple model can generate wave-like spatio-temporal patterns of tree regeneration in a lattice-structured habitat with each site occupied by a cohort of trees. A cohort taller than the average height of its windward neighbor experiences stand-level dieback in the next time step and the height becomes zero. Otherwise the cohort increases its height at a constant rate. Starting from a random initial pattern, this simple deterministic model can generate a saw-toothed pattern that moves downwind at a constant rate, but the distance between adjacent dieback zones has a large variance. In this paper, we study the effects of "noises" in tree dieback rules in two forms which help to generate more regular patterns: (1) additional random disturbances at a low rate, which change the size of "clusters" (defined as a group of cohorts between adjacent dieback zones) by splitting a large cluster into two or by merging a small one with a neighbor, and (2) the stochastic rule of tree dieback, represented by the probability of dieback in unit time being a sigmoidal function of the difference in the tree height between the site and the windward neighbors. These noises are effective both for one-dimensional and two-dimensional models, but spatial patterns are much more regular in the two-dimensional model than in the one-dimensional model. Copyright 1998 Academic Press

Journal Article↗

PubMed1995

Principal-component localization of the sources of the background EEG.

A method, based on principal components for localizing the sources of the background EEG, is presented which overcomes the previous limitations of this approach. The spatiotemporal source model of the EEG is assumed to apply, and the method involves attempting to fit the spatial aspects of this general model with an optimal rotation of a subset of the principal components of a particular EEG. The method is shown to be equivalent to the subspace scanning method, a special case of the MUSIC algorithm, which enables multiple sources to be localized individually rather than all at once. The novel aspect of the new method is that it offers a way of selecting the relevant principal components for the localization problem. The relevant principal components are chosen by decomposing the EEG using spatial patterns common with a control EEG. These spatial patterns have the property that they account for maximally different proportions of the combined variances in the two EEG's. An example is given using a particular EEG from a neurologic patient. Components containing spike and sharp wave potentials are extracted, with respect to a standard EEG derived from 15 normal volunteers. Spike and sharp wave potentials are identified visually using the common spatial patterns decomposition and an EEG reconstructed from these components. Four dipole sources are fitted to the principal components of the reconstructed EEG and these source account for over 88% of the temporal variance present in that EEG.

Action Potentials↗

PubMed1994

Temporal-specific and spatial-specific patterns of neurotensin gene expression in the small bowel.

Expression of the neurotensin/neuromedin N (NT/N) gene is developmentally regulated in a temporal- and spatial-specific pattern in the small bowel. The purpose of our study was to determine 1) whether the temporal expression of NT/N could be altered by ectopic placement of small bowel and 2) whether the spatial-specific expression of NT/N could be altered by different diets. We found that the relative temporal pattern of NT/N expression was unchanged in rat jejunal and ileal xenografts implanted into the flanks of athymic nude mice. To determine whether the spatial-specific pattern of NT/N expression could be altered by different luminal nutrients, 28-day-old rats were randomized to receive chow or chemically defined liquid diets for 60 days at which time the jejunoileum was divided into eight equal segments, and NT/N expression was analyzed. The normal pattern of increasing levels of NT/N mRNA along the jejunum-to-ileum axis was not altered by any of the liquid diets. In contrast to NT/N, we found that expression of sucrase-isomaltase varied greatly depending on both location and type of luminal nutrients. We conclude that the strict temporal- and spatial-specific pattern of NT/N expression is not affected by either location or luminal contents, thus suggesting an intrinsic program of NT/N gene expression. Furthermore, we speculate that the NT/N gene may provide a useful endocrine paradigm to investigate the factors regulating the establishment and maintenance of certain cell lineage-specific patterns along the cephalocaudal axis of the gut.

Aging↗

PubMed2003

Spatial expression patterns of activin and its signaling system in the zebrafish ovarian follicle: evidence for paracrine action of activin on the oocytes.

We have previously demonstrated that activin is likely an ovarian mediator of pituitary gonadotropin(s) and local epidermal growth factor in their stimulating oocyte maturation and maturational competence in the zebrafish. However, the downstream events controlled by activin remain unknown. One possible mechanism is that activin may directly work on the oocytes to promote the development of oocyte maturational competence. To substantiate this hypothesis, we performed the present study to demonstrate the expression of the activin system in different compartments of zebrafish follicles, namely, the follicle cells and oocytes. The proteins examined include activin subunits (betaA and betaB), activin-binding protein (follistatin), activin type II receptors (type IIA and IIB), the type I activin receptor-like kinases (ALK1-like, ALK2-like, and ALK4-like), and the intracellular activin signaling molecules (Smad2, Smad3, Smad4, and Smad7). The results showed that the entire activin signaling system is expressed by the full-grown immature zebrafish oocytes ( approximately 0.65 mm in diameter), including ALK4-like (ActRIB), ALK2-like (ActRIA), ActRIIA, ActRIIB, Smad2, Smad3, Smad4, and Smad7, therefore supporting our hypothesis that the oocytes are one of the direct targets of activin actions in the zebrafish ovary. In contrast, activin itself (betaA and betaB) and ALK1-like type I receptor are predominantly expressed in the follicle cells surrounding the oocytes. Interestingly, although follistatin is expressed in both the follicle cells and oocytes, its level of expression is significantly higher in the oocytes than the follicle cells, implying that follistatin may serve as a signal from the oocytes to modulate the activity of activin produced by the follicle cells. Taken together, the present study provides convincing evidence that although all members of the activin system are expressed in the whole follicle, they exhibit distinct spatial patterns of expression among different compartments of the follicle. It is likely that activin works directly on the oocytes in a paracrine manner to promote oocyte maturation and maturational competence. On the other hand, instead of being controlled passively by the follicle cells, the oocytes may actively participate in the regulation of follicle development by releasing various modulating molecules such as follistatin.

Activin Receptors↗

PubMed2005

Spatio-temporal variability of richness estimators: coastal marine fish communities as examples.

We assessed the performance of two estimators of species richness, the Chao2 and the Coleman 'random placement curve'. Using a dataset of intertidal fish from the Norwegian Skagerrak coast, we found that Chao2 was effective for low sampling intensity, often reaching asymptotic values for few samples, but for higher sampling intensity the performance deteriorated. For large samples, the Coleman random placement curve was more effective than the Chao2 estimates when comparing spatio-temporal patterns of species richness. Spatial patterns were clearly and consistently identified by both methods, whereas the coastal fish communities displayed too much variability in the early summer for any sensible measure of temporal patterns of fish-species richness to be made. To control for spurious results due to systematic differences in mean abundance of the samples the analyses were performed also on data standardised by the number of individuals in the samples, without any significant change in the results. We conclude that modest sampling effort is sufficient to characterise spatial patterns of coastal fish-species richness, while a detailed and high-precision description of seasonal patterns could not be obtained with any reasonable sampling effort.

Analysis of Variance↗

PubMed2005

Ndn, volume transmission, and self-organization in brain dynamics.

Fields of neural activity are seen in synchronized oscillations that are detected at mesoscopic scales in syntheses of multicellular recordings of action potentials and electroencephalograms (EEGs) over broad areas of cerebral cortex. The waves often have large-scale, highly textured spatial patterns of cortical activity, formed in the context of associative learning under classical and operant conditioning in rabbits. The patterns show spatial amplitude modulation of shared oscillations of carrier waves in the beta and gamma ranges of the EEG, with recurrence at frame rates in the alpha and theta ranges. The frames also show spatial phase modulation that is inconsistent with driving of the oscillations by focal pacemakers. The hypothesis is developed that the synchronization manifests continuous distributions of activity in cortical neuropil that modulate firings of selected neural networks embedded in the neuropil. Five interactive agencies have been postulated to explain the mechanism for the field synchrony: electric fields; magnetic fields; electromagnetic fields (radio waves); diffusion chemical gradients; and order parameters that control self-organization of large populations of neurons by widespread synaptic interaction constituting negative and positive feedback. Only the last interactive agency fits the data. The points are emphasized that these field patterns in frames require interactive neural dynamics that is modulated in respect to global operations mediating arousal, attention, selective emotional stance, wake, sleep, learn, habituate, dishabituate, etc., and that these operations require differing but complementary fields that form by massive parallel feed-forward architectures of brainstem neuromodulatory nuclei. An example is given using histamine of the neural discharges of brainstem nuclei that do not require fine spatiotemporal texturing of their firing; they operate by nonsynaptic release of neuromodulators that effect changes in background state, such that textured patterns of cortical activity can form and update in flexible adaptations of brains to their environments. These systems instantiate volume transmission by nonsynaptic diffusion transmission, in concert with the self-organization of the textured neural activity that supports cognition.

Animals↗

PubMed2005

Correlating velocity patterns with spatial dynamics in glioma cell migration.

Highly malignant neuroepithelial tumors are known for their extensive tissue invasion. Investigating the relationship between their spatial behavior and temporal patterns by employing detrended fluctuation analysis (DFA), we report here that faster glioma cell motility is accompanied by both greater predictability of the cells' migration velocity and concomitantly, more directionality in the cells' migration paths. Implications of this finding for both experimental and clinical cancer research are discussed.

Acceleration↗