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At least 1,243 records · Page 69Linked to original sources
PubMed2026

Integrative transcriptomic, spatial and functional-genomic analysis identifies a UFMylation-related vascular-stromal program and prioritizes WWTR1 in glioblastoma.

Glioblastoma (GBM) contains spatially organized stress-adaptive and vascular niches. Because transcript abundance does not measure UFM1 conjugation, we asked whether a UFMylation-related transcriptional axis identifies a reproducible tissue program and alters candidate prioritization. In 518 unique primary TCGA-GBM tumors profiled on the Affymetrix HT Human Genome U133A array, weighted gene co-expression network analysis of 8,000 variable genes yielded 12 modules. The 278-gene green module ranked first across nine prespecified traits (mean |r|=0.637). Direct overlap comprised 1/3 measurable UFMylation-core, 5/19 ER-stress/UPR, and 2/15 proteostasis genes; after excluding overlapping genes, correlations with the green eigengene remained significant (r = 0.373, 0.831, 0.639, and 0.699 for UFMylation-core, ER-stress/UPR, proteostasis, and composite scores, respectively). The green score was associated with overall survival per standard-deviation increase (HR 1.17, 95% CI 1.07-1.28), although clinical adjustment attenuated the estimate. In a 10-sample single-cell dataset, sample-level scores were higher in pericytes and endothelial cells than in malignant cells. Donor-aware IvyGAP analysis supported regional organization, whereas one Visium section showed stronger concordance with ER-stress/UPR and mesenchymal scores than with the UFMylation-core score. CellChat indicated pathway-selective rather than global remodeling of inferred vascular communication. Layer ablation moved WWTR1 from rank 48 using WGCNA alone to rank 4 overall and rank 1 among non-common-essential genes after cross-platform integration. These findings define an ER-stress/mesenchymal-weighted, UFMylation-related vascular-stromal transcriptional association and nominate WWTR1 for experimental testing.

Humans↗
PubMed1986

Occupational and spatial mobility of temporary Mexican migrants to the U.S.: a comparative analysis.

"U.S. job and spatial mobility are compared here for recent returnee migrants from two Mexican areas--Rio Grande, Zacatecas, in the interior; and Nueva Rosita-Muzquiz, Coahuila, near the U.S. border. Results suggest that the interior migrants fit a hierarchical migrant model: they move up the urban hierarchy from U.S. rural areas to towns and cities, experiencing substantial job mobility at first, but little after reaching the urban sector. Border migrants fit a shuttle migrant model: they return to the same job and place year after year, experiencing little or no spatial and occupational mobility, although they tend to hold somewhat higher status jobs."

Americas↗
PubMed1989

[EEG factor analysis in the treatment with antidepressants].

Spatial EEG factor analysis was performed in patients under gamonil and damilen treatment. Groups of EEG-factors were discovered that describe the peculiarities of the brain electrical processes spatial reorganization under pharmacotherapy. Major groups comprised the EEG factors: 1. characterizing the proper action of the drug; 2. connected to the syndromal peculiarities of depression or the course of mental state changes; 3. those depending on the efficiency of the therapy.

Action Potentials↗
PubMed2005

Localizing human visual gamma-band activity in frequency, time and space.

Neuronal gamma-band (30-100 Hz) synchronization subserves fundamental functions in neuronal processing. However, different experimental approaches differ widely in their success in finding gamma-band activity. We aimed at linking animal and human studies of gamma-band activity and at preparing optimized methods for an in-depth investigation of the mechanisms and functions of gamma-band activity and gamma-band coherence in humans. In the first step described here, we maximized the signal-to-noise ratio with which we can observe visually induced gamma-band activity in human magnetoencephalographic recordings. We used a stimulus and task design that evoked strong gamma-band activity in animals and combined it with multi-taper methods for spectral analysis and adaptive spatial filtering for source analysis. With this approach, we found human visual gamma-band activity very reliably across subjects and across multiple recording sessions of a given subject. While increases in gamma-band activity are typically accompanied by decreases in alpha- and beta-band activity, the gamma-band enhancement was often the spectral component with the highest signal-to-noise ratio. Furthermore, some subjects demonstrated two clearly separate visually induced gamma bands, one around 40 Hz and another between 70 and 80 Hz. Gamma-band activity was sustained for the entire stimulation period, which was up to 3 s. The sources of gamma-band activity were in the calcarine sulcus in all subjects. The results localize human visual gamma-band activity in frequency, time and space and the described methods allow its further investigation with great sensitivity.

Adolescent↗
PubMed1999

Adaptive spatial sampling of contaminated soil.

Suppose that a residential neighborhood may have been contaminated by a nearby abandoned hazardous waste site. The suspected contamination consists of elevated soil concentrations of chemicals that are also found in the absence of site-related contamination. How should a risk manager decide which residential properties to sample and which ones to clean? This paper introduces an adaptive spatial sampling approach which uses initial observations to guide subsequent search. Unlike some recent model-based spatial data analysis methods, it does not require any specific statistical model for the spatial distribution of hazards, but instead constructs an increasingly accurate nonparametric approximation to it as sampling proceeds. Possible cost-effective sampling and cleanup decision rules are described by decision parameters such as the number of randomly selected locations used to initialize the process, the number of highest-concentration locations searched around, the number of samples taken at each location, a stopping rule, and a remediation action threshold. These decision parameters are optimized by simulating the performance of each decision rule. The simulation is performed using the data collected so far to imput multiple probable values of unknown soil concentration distributions during each simulation run. This optimized adaptive spatial sampling technique has been applied to real data using error probabilities for wrongly cleaning or wrongly failing to clean each location (compared to the action that would be taken if perfect information were available) as evaluation criteria. It provides a practical approach for quantifying trade-offs between these different types of errors and expected cost. It also identifies strategies that are undominated with respect to all of these criteria.

Hazardous Waste↗
PubMed2004

Perceptual functions in prosopagnosia.

Some patients with prosopagnosia may have an apperceptive basis to their recognition defect. Perceptual abnormalities have been reported in single cases or small series, but the causal link of such deficits to prosopagnosia is unclear. Our goal was to identify candidate perceptual processes that might contribute to prosopagnosia, by subjecting several prosopagnosic patients to a battery of functions that may be necessary for accurate facial perception. We tested seven prosopagnosic patients. Three had unilateral right occipitotemporal lesions, two had bilateral posterior occipitotemporal lesions, and one had right anterior-to-occipital temporal damage along with a small left temporal lesion. These lesions all included the fusiform face area, in contrast to one patient with bilateral anterior temporal lesions. Most patients had impaired performance on face-matching tests and difficulty with subcategory judgments for non-face objects. The most consistent deficits in patients with lesions involving the fusiform face area were impaired perception of spatial relations in dot patterns and reduced contrast sensitivity in the 4 to 8 cycles deg(-1) range. Patients with bilateral lesions were impaired in saturation discrimination. Luminance discrimination was normal in all but two patients, and spatial resolution was uniformly spared. Curvature and line-orientation discrimination were impaired in only one patient, who also had the most difficulty with more basic-level object recognition. We conclude that deficits in luminance, spatial resolution, curvature, line orientation, and contrast at low spatial frequencies are unlikely to contribute to apperceptive prosopagnosia. More relevant may be contrast sensitivity at higher spatial frequencies and the analysis of object spatial structure. Deficits in these functions may impair perception of subtle variations in object shape, and may be one mechanism by which the recognition defect in prosopagnosia can extend to other classes of object subcategorization.

Adult↗
PubMedDate not supplied

[Spatial structure of myelopeptides: I. Conformational analysis of MP-1, MP-2, and MP-3].

Theoretical conformational analysis was used to study the spatial structure and conformational properties of myelopeptides, bone-marrow peptide mediators. The low-energy conformations of three hexapeptides MP-1 (Phe-Leu-Gly-Phe-Pro-Thr), MP-2 (Leu-Val-Val-Tyr-Pro-Trp), and MP-3 (Leu-Val-Cys-Tyr-Pro-Gln) were found, the values of dihedral angles of the backbone and side chains of the amino acid residues constituting these peptides were determined, and the energies of intra- and interresidual interactions were estimated.

Amino Acid Sequence↗
PubMed2004

A ghost of retrieval past: a functional network of alpha EEG related to source memory in elderly humans.

The electrophysiological data from a study of source memory in young and older adults were analyzed in the frequency domain in order to find functional networks of alpha band activity related to source memory performance and cortical reorganization with age. Participants were instructed to remember noun pairs embedded in sentences, with sentences grouped into two temporally distinct lists. At test, in response to noun probes, participants made old/new, followed by source (i.e., list) judgments. Lower band alpha electroencephalography (EEG) recorded during recognition and source retrieval epochs was analyzed using spatial covariance analysis [Hum. Brain Mapp. 2 (1994) 79; J.R. Moeller, C. Ghez, A. Antonini, M.F. Ghilardi, V. Dhawan, K. Kazumata, D. Eidelberg, Brain networks of motor behavior assessed by principal component analysis, in: R.E. Carson, M.E. Daube-Witherspoon, P. Herscovitch (Eds.), Quantitative Functional Brain Imaging with Positron Emission Tomography, Academic, San Diego, 1998]: significant activation patterns were found in source retrieval epochs. For young subjects, the regional covariance pattern involved coactivation of right anterior and left posterior electrode sites. Source retrieval performance was predicted by the subject difference in pattern expression between epochs involving correct and incorrect source attribution. The older adults also exhibited significant coactivation of the right anterior and left posterior electrode sites. However, no compensatory activation sites were identified for these elders who performed near chance in source retrieval. In this regard, we replicated the main functional difference between good and poor performing elders reported in a recent O-15 PET study of source retrieval in young and older subjects [Neuroimage 17 (2002) 1394]. These alpha band and O-15 PET findings complement the age group differences found in the time-domain (ERP) analysis of our EEG data [Psychol. Aging 14 (1999) 390]. We suggest that spatial covariance analyses of spectral EEG and MEG data will reveal new information about functional brain activity relevant to normal aging.

Adult↗
PubMed1986

The genetic structure of a tribal population, the Yanomama Indians. XV. Patterns inferred by autocorrelation analysis.

Fifteen allele frequencies have previously been determined for 50 villages of the Yanomama, an Amerindian tribe from southern Venezuela and northern Brazil. These frequencies were subjected to spatial autocorrelation analysis to investigate their population structure. There are significant spatial patterns for most allele frequencies. Clinical patterns, investigated by one-dimensional and directional spatial correlograms, were relatively few in number and were moderate in strength. Overall, however, there is a marked decline in genetic similarity with geographic distance. The results are compatible with a hierarchic population structure superimposed on the geography, and generated by a stochastic fission-fusion model of village propagation, followed by localized gene flow. Strong temporal autocorrelations of allele frequencies based on linguistic-historical distances representing time since divergence were also found. There appears to be a stronger relation between geography and linguistic-historical hierarchic subdivisions than between either feature and genetic distances. These findings confirm by different approaches the results of earlier analyses concerning the important roles of both stochastic and social factors in determining village allele frequencies and the occurrence within this tribe of some allele frequency clines most likely due to the operation of chance historical processes.

Alleles↗
PubMed1989

Capillary spatial pattern and muscle fiber geometry in three hamster striated muscles.

The primary goal of this project was to elucidate the spatial pattern of capillaries in three hamster striated muscles according to statistical techniques of pattern analysis. The spatial pattern of capillaries and traditional measures of capillarity are important to understanding the supply and distribution of oxygen and nutrients in a tissue. Statistical tests based on the distance between nearest neighbor capillaries are the most sensitive for detecting regularity in a pattern. A mathematical model was created to simulate the observed muscle fields. The same statistical tests that were performed on the empirical data were performed on the modelled data. The results of the analysis of the modelled data agree sufficiently with those of the empirical data to justify overall confidence in the assumptions. Conclusions that may be drawn from this investigation are (1) the spatial pattern of capillaries tends to be more regular than random and never was there evidence for aggregation using the test statistics; (2) as many as 60-75% of capillaries are located at the corners of muscle fibers indicating that there is some preferential placement for capillaries, and (3) the model developed is a good first approximation to the real situation.

Animals↗
PubMed2003

The relationship between hodological and cytoarchitectonic organization in the vestibular complex of the 11-day chicken embryo.

To understand the relationship between structure and function in specific brain regions, it is necessary to ascertain which anatomical features are physiologically relevant. Physiological studies of brain function traditionally have been set in the context of anatomical features based on cytoarchitectonics and myeloarchitectonics, but the relationship between structure and function in this context can be complex. Alternative schemes of anatomical organization, such as that based on hodology (the mapping of projections) may provide greater insight. Here, we make a direct comparison of the hodological and the cytoarchitectonic organization of the vestibular complex in the mid-term chicken embryo, using retrograde tracing and three-dimensional reconstruction. In one set of experiments, vestibulospinal and vestibulo-ocular neuron groups were selectively labeled with biotin dextran-amines and aligned with the cytoarchitectonically defined vestibular nuclei in alternating sections that were then combined into intercalated three-dimensional models. This allowed a semiquantitative analysis of the apportionment of individual hodological groups among cytoarchitectonic nuclei. In another set of experiments, vestibulospinal and vestibulo-ocular neuron groups were labeled differentially with fluorescent dextran-amines, three-dimensionally reconstructed, and subjected to a quantitative analysis of spatial overlap. Our results provide the first three-dimensional representation and quantitative analysis of the hodological compartmentalization of the vestibular complex (the "hodological mosaic"). They also show directly how each hodologically defined neuron group relates to the conventional vestibular nuclei, underscoring the fact that the units of the hodological mosaic do not bear a one-to-one correspondence to the cytoarchitectonic nuclear divisions. Some hodologically defined groups are localized to restricted portions of a nucleus, whereas others overlap multiple nuclei. Thus, hodology and cytoarchitectonic features appear to be separately regulated in the vestibular complex of the chicken embryo, possibly through different sets of positional specification mechanisms. The three-dimensional representations we present here provide a foundation for integrating anatomical, physiological, developmental, and evolutionary studies of the vestibular system.

Animals↗
PubMed2000

Dissociable cognitive impairments in problem drinkers.

Patients in a treatment programme for severe alcohol dependence were tested on a battery of tests designed to examine organizational and visuo-spatial abilities. Analysis using a case-study approach indicated independent organizational and visuo-spatial impairments. An understanding of aetiological factors underlying these cognitive deficits and implications for treatment are discussed.

Adult↗
PubMed2004

Transfer to intermediate forms following concept discrimination by pigeons: chimeras and morphs.

Two experiments examined pigeons' generalization to intermediate forms following training of concept discriminations. In Experiment 1, the training stimuli were sets of images of dogs and cats, and the transfer stimuli were head/body chimeras, which humans tend to categorize more readily in terms of the head part rather than the body part. In Experiment 2, the training stimuli were sets of images of heads of dogs and cats, and the intermediate stimuli were computer-generated morphs. In both experiments, pigeons learned the concept discrimination quickly and generalized with some decrement to novel instances of the categories. In both experiments, transfer tests were carried out with intermediate forms generated from both familiar and novel exemplars of the training sets. In Experiment 1, the pigeons' transfer performance, unlike that of human infants exposed to similar stimuli, was best predicted by the body part of the stimulus when the chimeras were formed from familiar exemplars. Spatial frequency analysis of the stimuli showed that the body parts were richer in high spatial frequencies than the head parts, so these data are consistent with the hypothesis that categorization is more dependent on local stimulus features in pigeons than in humans. There was no corresponding trend when the chimeras were formed from novel exemplars. In Experiment 2, when morphs of training stimuli were used, response rates declined smoothly as the proportion of the morph contributed by the positive stimulus fell, although results with morphs of novel stimuli were again less orderly.

Animals↗
PubMed1998

Spatial genetic structure of human populations in Japan.

We studied spatial patterns for 24 allele frequencies representing 15 systems (blood antigens, enzymes, serum proteins, color blindness, and cerumen) in Japan. The total number of samples over all systems and localities is 1125. We investigated patterns of genetic variation graphically as interpolated allele frequency surfaces, as one-dimensional and directional correlograms, and by testing for the direction of maximal genetic autocorrelation. We examined the allele frequency surfaces by various techniques of spatial autocorrelation analysis and found 13 allele frequency surfaces from 9 genetic systems exhibiting significant spatial patterns. Several surfaces have clinal patterns along the major axis of the Japanese archipelago; others tend toward a maximum or minimum in south-central Honshu. Yet other allele frequencies show long-distance differentiation or patchiness. We discovered seven areas of rapid genetic change by using the wombling method. These areas largely reflect maritime and montane barriers, and some are associated with dialectal boundaries in these populations. The observed patterns support the hybridization or dual structure hypothesis for the peopling of Japan.

Alleles↗
PubMed2001

Spatial and temporal independent component analysis of functional MRI data containing a pair of task-related waveforms.

Independent component analysis (ICA) is a technique that attempts to separate data into maximally independent groups. Achieving maximal independence in space or time yields two varieties of ICA meaningful for functional MRI (fMRI) applications: spatial ICA (SICA) and temporal ICA (TICA). SICA has so far dominated the application of ICA to fMRI. The objective of these experiments was to study ICA with two predictable components present and evaluate the importance of the underlying independence assumption in the application of ICA. Four novel visual activation paradigms were designed, each consisting of two spatiotemporal components that were either spatially dependent, temporally dependent, both spatially and temporally dependent, or spatially and temporally uncorrelated, respectively. Simulated data were generated and fMRI data from six subjects were acquired using these paradigms. Data from each paradigm were analyzed with regression analysis in order to determine if the signal was occurring as expected. Spatial and temporal ICA were then applied to these data, with the general result that ICA found components only where expected, e.g., S(T)ICA "failed" (i.e., yielded independent components unrelated to the "self-evident" components) for paradigms that were spatially (temporally) dependent, and "worked" otherwise. Regression analysis proved a useful "check" for these data, however strong hypotheses will not always be available, and a strength of ICA is that it can characterize data without making specific modeling assumptions. We report a careful examination of some of the assumptions behind ICA methodologies, provide examples of when applying ICA would provide difficult-to-interpret results, and offer suggestions for applying ICA to fMRI data especially when more than one task-related component is present in the data.

Algorithms↗
PubMed1996

[Optimal protocol for 99mTc-tetrofosmin myocardial SPECT imaging with exercise or dipyridamole stress test and the characteristics of bullseye normal file].

To determine optimal protocol for 99mTc-tetrofosmin SPECT imaging, 30 normal volunteers underwent treadmill or dipyridamole stress test with 770 MBq of tetrofosmin injection. Anterior planar images were acquired every 10-15 minutes for calculating heart/liver ratio. SPECT images were also obtained every 30 minutes for generating Bullseye normal files. In analysis of spatial tracer distribution among normal files, myocardium in Bullseye plot was divided in 9 areas, where mean values of % tracer uptake were calculated and compared by analysis of variance (ANOVA). In those 9 areas, mean values of SD (SD mean) were also compared for predicting artificial blackout in the Bullseye plot among 3 standard normal files: dipyridamole-201Tl, dipyridamole-tetrofosmin (60 min post-injection), and treadmill-tetrofosmin (30 min post-injection). In planar image analysis, high initial uptake in the liver and its acceptable clearance were noted in dipyridamole stress test. Adequate heart/liver ratio was accomplished immediately after treadmill, but 40 minutes later after dipyridamole stress test. ANOVA analysis showed no statistical difference in the spatial % tracer uptake among normal files, irrespective of time after acquisition, data collection time, or difference of tracer. However, SD means in inferior and lateral area of treadmill-tetrofosmin file were significantly small compared to that of dipyridamole-201Tl normal file (p < 0.02 by ANOVA). Thus, we conclude that optimal timing for tetrofosmin SPECT imaging is immediately after treadmill, but at least 40 minutes after dipyridamole stress test. In addition, we should also keep in mind that unexpected blackout may appear in inferior and lateral area, when applying our normal files for reference.

Analysis of Variance↗
PubMed2006

Use of the spatial scan statistic to identify geographic variations in late stage colorectal cancer in California (United States).

OBJECTIVES: To identify geographic variations in colorectal cancer by stage at diagnosis in California using a descriptive analysis coupled with a spatial analysis and to discuss methodological considerations concerning the spatial statistical method. METHODS: We analyzed 59,076 colorectal cancer cases diagnosed in California from 1996 to 2000 by logistic regression and by a spatial scan statistic to identify areas with a higher and lower relative risk of late-stage colorectal cancer. RESULTS: In California, 57% of overall cases of colorectal cancer were diagnosed at a late stage. Californians diagnosed with late-stage colorectal cancer were more likely to be Hispanic and living in areas of lower socioeconomic status. The spatial scan identified two areas where the observed number of late-stage cancer was different than the number expected from the distribution in the rest of the state. CONCLUSIONS: Spatial scan analyses can complement descriptive statistics, but results must be interpreted with consideration of factors that affect the ability to detect meaningful differences such as the number of events observed, accuracy in geocoding rural versus urban addresses, and the difficulty of adjusting for covariates.

Aged↗
PubMed1997

[Digital storage phosphor mammography in a magnification technic: experimental studies for spatial resolution and for detection of microcalcifications].

PURPOSE: Since the routine use of storage phosphor systems for mammography has been limited by its inadequate spatial resolution of 5 linepairs/mm, a combination of a magnification mammography technique with storage phosphor plates was investigated to detect microcalcifications. MATERIAL AND METHODS: A new mammography system with a microfocus tube using an anode of 0.05-0.12 mm allowed to obtain survey views of the breast with 1.7x magnification (m), and spot views with 4x magnification. The digital image receptor comprised a high resolution storage phosphor plate. To determine spatial resolution, contrast transfer curves were obtained, and the detection of microcalcifications was investigated by ROC (receiver operating characteristic) analysis. RESULTS: Spatial resolution for digital survey views (m = 1.7) was 8 linepairs/mm and for spot views (m = 4) was 18 linepairs/mm. ROC analysis demonstrated a significantly higher performance of the digital magnification technique compared to the conventional screen-film mammography technique. CONCLUSIONS: The limitations of digital mammography with respect to spatial resolution can be overcome by using a high magnification technique.

Breast Diseases↗