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At least 1,783 records · Page 99Linked to original sources
PubMed2005

Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo.

Dorsal is a sequence-specific transcription factor that is distributed in a broad nuclear gradient across the dorsal-ventral (DV) axis of the early Drosophila embryo. It initiates gastrulation by regulating at least 30-50 target genes in a concentration-dependent fashion. Previous studies identified 18 enhancers that are directly regulated by different concentrations of Dorsal. Here, we employ computational methods to determine the basis for these distinct transcriptional outputs. Orthologous enhancers were identified in a variety of divergent Drosophila species, and their comparison revealed several conserved sequence features responsible for DV patterning. In particular, the quality of Dorsal and Twist recognition sequences correlates with the DV coordinates of gene expression relative to the Dorsal gradient. These findings are entirely consistent with a gradient threshold model for DV patterning, whereby the quality of individual Dorsal binding sites determines in vivo occupancy of target enhancers by the Dorsal gradient. Linked Dorsal and Twist binding sites constitute a conserved composite element in certain "type 2" Dorsal target enhancers, which direct gene expression in ventral regions of the neurogenic ectoderm in response to intermediate levels of the Dorsal gradient. Similar motif arrangements were identified in orthologous loci in the distant mosquito genome, Anopheles gambiae. We discuss how Dorsal and Twist work either additively or synergistically to activate different target enhancers.

Animals↗
PubMed2004

Population vector analysis of primate prefrontal activity during spatial working memory.

Population vectors were used to examine information represented by a population of prefrontal activity and its temporal change during spatial working memory processes while monkeys performed ODR and R-ODR tasks. In the ODR task, monkeys made a saccade to the cue location after the delay, whereas in the R-ODR task, they made a saccade 90 degrees clockwise from the cue location. We first constructed population vectors using cue- and response-period activity. The directions of population vectors were similar to the cue directions and the saccade target directions, respectively, indicating that population vectors correctly represented information regarding directions of visual cues and saccade targets. We then calculated population vectors during a 250 ms time-window from the cue presentation to the end of the response period. In the ODR task, all population vectors were directed toward the cue direction. However, in the R-ODR task, the population vector gradually rotated during the delay period from the cue direction to the saccade direction. These results indicate that spatial information represented by a population of prefrontal activity can be shown as the direction of the population vector and that its temporal change during spatial working memory tasks can be depicted as the temporal change of the vector's direction.

Animals↗
PubMed1998

The geographical spread of influenza.

How infectious diseases spread in space within one cycle of an epidemic is an important question that has received considerable theoretical attention. There are, however, few empirical studies to support theoretical approaches, because data are scarce. Weekly reports obtained since 1984 from a network of general practitioners spanning the entire French territory allows the analysis of the spatio-temporal dynamics of influenza over a fine spatial scale. This analysis indicates that diffusion over long distances, possibly due to global transportation systems, is so quick that homogeneous global mixing occurs before the epidemic builds up within infected patches. A simple model in which the total number of cases is given by the empirical time-series and cases are randomly assigned to patches according to the population weight of the patches exhibits the same spatio-temporal properties as real epidemic cycles: homogeneous mixing models constitute appropriate descriptions, except in the vicinity of the epidemic's peak, where geographic heterogeneities play a role.

Epidemiologic Studies↗
PubMed2003

A new algorithm for computational image analysis of deformable motion at high spatial and temporal resolution applied to root growth. Roughly uniform elongation in the meristem and also, after an abrupt acceleration, in the elongation zone.

A requirement for understanding morphogenesis is being able to quantify expansion at the cellular scale. Here, we present new software (RootflowRT) for measuring the expansion profile of a growing root at high spatial and temporal resolution. The software implements an image processing algorithm using a novel combination of optical flow methods for deformable motion. The algorithm operates on a stack of nine images with a given time interval between each (usually 10 s) and quantifies velocity confidently at most pixels of the image. The root does not need to be marked. The software calculates components of motion parallel and perpendicular to the local tangent of the root's midline. A variation of the software has been developed that reports the overall root growth rate versus time. Using this software, we find that the growth zone of the root can be divided into two distinct regions, an apical region where the rate of motion, i.e. velocity, rises gradually with position and a subapical region where velocity rises steeply with position. In both zones, velocity increases almost linearly with position, and the transition between zones is abrupt. We observed this pattern for roots of Arabidopsis, tomato (Lycopersicon lycopersicum), lettuce (Lactuca sativa), alyssum (Aurinia saxatilis), and timothy (Phleum pratense). These velocity profiles imply that relative elongation rate is regulated in a step-wise fashion, being low but roughly uniform within the meristem and then becoming high, but again roughly uniform, within the zone of elongation. The executable code for RootflowRT is available from the corresponding author on request.

Algorithms↗
PubMed2002

Suppressive and facilitatory spatial interactions in peripheral vision: peripheral crowding is neither size invariant nor simple contrast masking.

Peripheral vision is characterized by reduced spatial resolution and inhibitory spatial interactions that extend over long distances. This work had three goals. (1) We considered whether the extensive crowding in peripheral vision is a consequence of a shift in the spatial scale of analysis. To test this, using a large range of target sizes and spatial frequencies, we measured the extent of crowding for targets that were limited in their spatial frequency content. (2) We considered whether crowding in peripheral vision can be explained on the basis of contrast masking by remote flanks. To test this hypothesis, we measured and compared crowding in a direction-identification experiment with masking by remote flanks in a detection experiment. In each of the experiments, our targets and flanks were composed of Gabor features, thus allowing us to control the feature contrast, spatial frequency, and orientation. (3) We examined the relationship between the suppressive and facilitatory interactions in peripheral contrast detection and crowding. Our results show that unlike the normal fovea (Levi, Klein, & Hariharan, 2002), peripheral crowding is not scale invariant nor is it attributable to simple contrast masking. Rather, our results suggest that inhibitory spatial interactions in peripheral crowding extend over larger distances than in the fovea for targets of the same size. In peripheral vision, the critical distance for crowding is approximately 0.1 times the target eccentricity. Observers can easily detect the features that compose our targets (Gabor patches) under conditions where crowding is strong. Thus, we speculate that peripheral crowding occurs because the target and flanks are combined or pooled at a second stage, following the stage of feature extraction. In peripheral vision, this pooling takes place over a large distance.

Contrast Sensitivity↗
PubMed2005

The local and global processing of chromatic Glass patterns.

Glass patterns are a valuable tool to study the cortical stages of form perception. We use circular Glass patterns (cGP) to study the relation between form and color vision. The detection of Glass patterns is thought to be carried out in at least two stages. In the first stage, the local orientation information from the pairs of dots is analyzed. A later stage integrates this local orientation information to yield the global percept of form. Previous work (K. S. Cardinal & D. C. Kiper, 2003) has shown that the second stage is chromatically selective, with a broad tuning in color space. Here we completed our characterization of the integration stage by measuring the size of the spatial integration area. We find that the integration area is similar to the size of V4 receptive fields. Furthermore, we measured the chromatic selectivity and spatial resolution of the first stage mechanisms. First stage mechanisms are more selective for color than the integration stage. Their spatial resolution is consistent with the idea that V1/V2 neurons perform the analysis of the dot pairs' orientation. Our results are consistent with the idea that V1/V2 neurons perform the local analysis, and that spatial integration is achieved at the level of V4.

Color Perception↗
PubMed2001

Geographic information system-aided analysis of factors associated with the spatial distribution of Echinococcus multilocularis infections of foxes.

To investigate the influence of environmental factors on the spatial epidemiology of infections with Echinococcus multilocularis, foxes were sampled in a focal endemic region in the Northwest of Brandenburg, Germany, and examined for infection by the parasite. The locations where foxes were obtained were recorded in a geographic information system database. Positions of infected and uninfected foxes were analyzed on the background of geographic vector data of water, settlements, streets, forests, crop, and pasture. Fox positions were allocated to different land-use classes by use of a Landsat Thematic Mapper (TM) satellite image. Infected foxes were more frequently shot near water, in areas of high soil humidity, and on pastures, suggesting that dryness may limit the tenacity of E. multilocularis oncospheres. Thus open landscapes with humid soil seem to be favorable for the life cycle of the parasite. In contrast, infected foxes were significantly underrepresented in forest areas.

Animals↗
PubMed2006

Spatial, environmental and entomological risk factors analysis on a rural dengue outbreak in Lundu District in Sarawak, Malaysia.

The objective of this study was to elucidate the association of various risk factors with dengue cases reported in Lundu district, Sarawak, by analyzing the interaction between environmental, entomological, socio-demographic factors. Besides conventional entomological, serological and house surveys, this study also used GIS technology to generate geographic and environmental data on Aedes albopictus and dengue transmission. Seven villages were chosen based on the high number of dengue cases reported. A total of 551 households were surveyed. An overall description of the socio-demographic background and basic facilities was presented together with entomological and geographical profiles. For serological and ovitrap studies, systematic random sampling was used. Serological tests indicated that 23.7% of the 215 samples had a history of dengue, either recent or previous infections. Two samples (0.9%) were confirmed by IgM ELISA and 49 samples (22.8%) had IgG responses. A total of 32,838 Aedes albopictus eggs were collected in 56 days of trapping. Cluster sampling was also done to determine whether any of the risk factors (entomological or geographical) were influenced by geographical location. These clusters were defined as border villages with East Kalimantan and roadside villages along Lundu/Biawas trunk road. The data collected were analyzed using SPSS version 10.01. Descriptive analysis using frequency, means, and median were used. To determine the association between variables and dengue cases reported, and to describe the differences between the two clusters of villages, two-sample t-test, and Pearson's Chi-Square were used. Accurate maps were produced with overlay and density function, which facilitates the map visualization and report generating phases. This study also highlights the use of differential Global Positioning System in mapping sites of 1m accuracy. Analysis of the data revealed there are significant differences in clusters of villages attributable to container density, house density, distance of the house from the main road, and number of Ae. albopictus eggs from ovitraps set indoor, outdoor and in dumping sites (Person's Chi-Square = 6.111, df = 1, p < 0.01). Further analysis using t-test showed that house density, container density, indoor mosquitoes egg count, outdoor mosquitoes egg count, and dumping sites mosquitoes egg count were higher at the roadside villages compared to border villages. A number of potential risk factors including those generated from GIS were investigated. None of the factors investigated in this study were associated with the dengue cases reported.

Aedes↗
PubMed1990

Acoustic analysis of experimental prosthetic apparatus on spatial distribution formants.

This study concerns the effects of various prosthetic apparatus on speech perception. In this study we analyzed not only the first and second formant frequencies (as have often been studied previously) but also the third formant frequencies, and the three formant frequencies en masse. Our study demonstrated that of the six kinds of prosthetic apparatus we examined, the least effective apparatus was the L.S. type, while the most effective was the M.P. type.

Adult↗
PubMed1977

[Use of methods of spectral-correlation analysis for studying the temporal and spatial organization of tissues].

Tissues within the organism represent multidimensional systems organized in time and space and having statistical dispersion in each parameter. Changes in its state may have a character of a monotonous trend and be periodical (the matter of chronobiology). The methods for detection of latent periodicities, developed in chronobiology, are applied for estimation of not only temporary but also spacial characteristics of the object. One of such methods is the calculation of the power spectrum of the autocorrelative function. Examples of its application are given.

Histological Techniques↗
PubMed2005

A time course analysis of cyclooxygenase-2 suggests a role in spatial memory retrieval in rats.

We previously showed a role for COX-2 in spatial memory retention. In that study we investigated the effects of post-training intrahippocampal infusion of celecoxib as a COX-2-specific inhibitor on spatial memory retention. Those infusions impaired spatial memory retention in the Morris water maze. In the present study a time course analysis of role of COX-2 in spatial memory was conducted. Here stereotaxic surgery was employed for the bilateral implantation of guide cannulas into the CA1 region of the hippocampus. Training trials were started after recovery of the animals. Immediately after last trial of training on third day, the celecoxib (0.1M) was infused bilaterally and testing trials, were performed 1, 2, 3, and 7 days after celecoxib infusions. Significant alterations were observed in escape latency and traveled distance 2 and 3 days after celecoxib infusions. The maximum impairment was obtained 72 h after the infusions. The data suggests that the effect of celecoxib is transient and that its effect on performance is likely caused by a problem in memory retrieval. Quantification analyses of the immunostaining of COX-2-containing neurons in the dorsal hippocampus show that celecoxib infusions significantly reduced (P<0.05) COX-2 immunoreactivity for the animals that were tested 3 days after the drug infusion. Results from the behavioral study along with the findings from immunohistochemical analyses suggest that COX-2 has significant role in spatial memory retrieval. Moreover, the memory deficits induced by the infusions continuously persists for 3 days.

Animals↗
PubMed2005

Development of SOVAT: a numerical-spatial decision support system for community health assessment research.

INTRODUCTION: The development of numerical-spatial routines is frequently required to solve complex community health problems. Community health assessment (CHA) professionals who use information technology need a complete system that is capable of supporting the development of numerical-spatial routines. BACKGROUND: Currently, there is no decision support system (DSS) that is effectively able to accomplish this task as the majority of public health geospatial information systems (GIS) are based on traditional (relational) database architecture. On-Line Analytical Processing (OLAP) is a multidimensional data warehouse technique that is commonly used as a decision support system in standard industry. OLAP alone is not sufficient for solving numerical-spatial problems that frequently occur in CHA research. Coupling it with GIS technology offers the potential for a very powerful and useful system. METHODOLOGY: A community health OLAP cube was created by integrating health and population data from various sources. OLAP and GIS technologies were then combined to develop the Spatial OLAP Visualization and Analysis Tool (SOVAT). RESULTS: The synergy of numerical and spatial environments within SOVAT is shown through an elaborate and easy-to-use drag and drop and direct manipulation graphical user interface (GUI). Community health problem-solving examples (routines) using SOVAT are shown through a series of screen shots. DISCUSSION: The impact of the difference between SOVAT and existing GIS public health applications can be seen by considering the numerical-spatial problem-solving examples. These examples are facilitated using OLAP-GIS functions. These functions can be mimicked in existing GIS public applications, but their performance and system response would be significantly worse since GIS is based on traditional (relational) backend. CONCLUSION: OLAP-GIS system offer great potential for powerful numerical-spatial decision support in community health analysis. The functionality of an OLAP-GIS system has been shown through a series of example community health numerical-spatial problems. Efforts are now focused on determining its usability during human-computer interaction (HCI). Later work will focus on performing summative evaluations comparing SOVAT to existing decision support tools used during community health assessment research.

Decision Support Systems, Management↗
PubMedDate not supplied

Evaluation of the spatial resolution of a CT scanner by direct analysis of the edge response function.

A new approach to the measurement of the spatial resolution of a computed tomography (CT) scanner system is presented. The method is based on a direct least-squares fit of an analytical expression to a set of data obtained from a CT image of the interface between two materials. The implementation of the method in connection with the G.E.RTPLAN computer configuration is described. The method has been applied in determining the resolution of an EMI-7070 scanner and it is shown that the assumption of uniformity of the system resolution across the CT image is fulfilled within the accuracy of the present method. The reproducibility of the method has been estimated from a series of spatial resolution determinations performed on ten images taken with identical scan parameters. The standard deviation of this series was 3.2%.

Evaluation Studies as Topic↗
PubMed2003

Development of Dynamic Spatial Video Camera (DSVC) for 4D observation, analysis and modeling of human body locomotion.

We have developed an imaging system for free and quantitative observation of human locomotion in a time-spatial domain by way of real time imaging. The system is equipped with 60 computer controlled video cameras to film human locomotion from all angles simultaneously. Images are installed into the main graphic workstation and translated into a 2D image matrix. Observation of the subject from optional directions is able to be performed by selecting the view point from the optimum image sequence in this image matrix. This system also possesses a function to reconstruct 4D models of the subject's moving human body by using 60 images taken from all directions at one particular time. And this system also has the capability to visualize inner structures such as the skeletal or muscular systems of the subject by compositing computer graphics reconstructed from the MRI data set. We are planning to apply this imaging system to clinical observation in the area of orthopedics, rehabilitation and sports science.

Human Body↗
PubMed2005

Epidemiologic evaluation of diarrhea in dogs in an animal shelter.

OBJECTIVES: To determine associations among infectious pathogens and diarrheal disease in dogs in an animal shelter and demonstrate the use of geographic information systems (GISs) for tracking spatial distributions of diarrheal disease within shelters. SAMPLE POPULATION: Feces from 120 dogs. PROCEDURE: Fresh fecal specimens were screened for bacteria and bacterial toxins via bacteriologic culture and ELISA, parvovirus via ELISA, canine coronavirus via nested polymerase chain reaction assay, protozoal cysts and oocysts via a direct fluorescent antibody technique, and parasite ova and larvae via microscopic examination of direct wet mounts and zinc sulfate centrifugation flotation. RESULTS: Salmonella enterica and Brachyspira spp were not common, whereas other pathogens such as canine coronavirus and Helicobacter spp were common among the dogs that were surveyed. Only intestinal parasites and Campylobacterjejuni infection were significant risk factors for diarrhea by univariate odds ratio analysis. Giardia lamblia was significantly underestimated by fecal flotation, compared with a direct fluorescent antibody technique. Spatial analysis of case specimens by use of GIS indicated that diarrhea was widespread throughout the entire shelter, and spatial statistical analysis revealed no evidence of spatial clustering of case specimens. CONCLUSIONS AND CLINICAL RELEVANCE: This study provided an epidemiologic overview of diarrhea and interacting diarrhea-associated pathogens in a densely housed, highly predisposed shelter population of dogs. Several of the approaches used in this study, such as use of a spatial representation of case specimens and considering multiple etiologies simultaneously, were novel and illustrate an integrated approach to epidemiologic investigations in shelter populations.

Animals↗
PubMed1994

Residues responsible for distinct biological functions are characterized by different statistical features of sequential and spatial neighborhoods: a thermolysin example.

An investigation of the functional topography of thermolysin was carried out using frequency analysis of its primary and tertiary structures. The statistical validity of this approach was estimated for the enzyme active site, the substrate-binding pocket, the inter-domain interface and calcium-binding sites' predictions. We showed that frequency analysis of primary structure could be employed to predict the localization of contiguous parts of the inter-domain interface. The same approach appears to be unsuitable to a search for conformation-dependent enzyme active sites and substrate-binding pockets. In contrast, frequency analysis of the spatial neighborhood is not effective for predicting the inter-domain interface as distinct from the active site, substrate-binding pocket and calcium-binding sites. These differences should be taken into account when investigating and understanding protein structure-function relationships.

Amino Acid Sequence↗