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PubMed1997

Allelopathy in Spatially Distributed Populations

In a homogeneously mixing population of E. coli, colicin-producing and colicin-sensitive strategies both may be evolutionarily stable for certain parameter ranges, with the outcome of competition determined by initial conditions. In contrast, in a spatially-structured population, there is a unique ESS for any given set of parameters; the outcome is determined by how effective allelopathy is in relation to its costs. Furthermore, in a spatially-structured environment, a dynamic equilibrium may be sustained among a colicin-sensitive type, a high colicin-producing type, and a "cheater" that expends less on colicin production but is resistant. Copyright 1997 Academic Press Limited

Journal Article↗

PubMed2001

Evidence for velocity-tuned motion-sensitive descending neurons in the honeybee.

Behavioural experiments suggest the existence of two functionally distinct movement-sensitive pathways in honeybees: one mediates optomotor behaviour, consisting of reflexive turning responses preventing deviations from course, and the other controls flight speed. The first consists of direction-selective neurons responding optimally to a particular temporal frequency of motion, regardless of the pattern's spatial structure. The temporal frequency dependence matches the temporal tuning of the optomotor output. Behavioural experiments suggest the second pathway contains velocity-tuned cells, which generate equal-sized responses for any given image velocity, for patterns with a range of spatial structures. Here, recordings were made from direction-selective neurons in the honeybee's ventral nerve cord. Neurons were tested for responses to motion at velocities of 40-1000 deg s(-1) using four gratings with spatial periods of 11-76 degrees. In addition to temporal frequency-dependent optomotor neurons, direction-selective cells were found that had the same shaped velocity-response functions for all four patterns. The velocity-tuning properties of these cells suggest a possible role in monitoring flight speed because their velocity tuning matches the image velocities encountered during free flight and landing behaviour.

Animals↗

PubMed1984

Human primary visual cortex topography imaged via positron tomography.

The visuotopic structure of primary visual cortex was studied in a group of 7 human volunteers using positron emission transaxial tomography (PETT) and 18F-labeled 2-deoxy-2-fluoro-D-glucose ( [18F]DG). A computer animation was constructed with a spatial structure which was matched to estimates of human cortical magnification factor and to striate cortex stimulus preferences. A lateralized cortical 'checker-board' pattern of [18F]DG was stimulated in primary visual cortex by having subjects view this computer animation following i.v. injection of [18F]DG. The spatial structure of the stimulus was designed to produce an easily recognizable 'signature' in a series of 9 serial PETT scans obtained from each of a group of 7 volunteers. The predicted lateralized topographic 'signature' was observed in 6 of 7 subjects. Applications of this method for further PETT studies of human visual cortex are discussed.

Deoxyglucose↗

PubMed1994

Fractal analysis of pulmonary arteries: the fractal dimension is lower in pulmonary hypertension.

We analyzed the spatial structure of contact radiographs of barium-filled pulmonary arteries of rats raised in room air and in two environments that induce pulmonary arterial hypertension (PAH)--hypoxia and hyperoxia. We found that the spatial structure of the pulmonary arteries was fractal in both the control and the hypertensive lungs. The fractal dimension of the pulmonary arteries of the control lungs was 1.62 +/- 0.01 (mean +/- SEM), which is greater than that of both the hypoxic lungs 1.50 +/- 0.03 (p < 0.01) and the hyperoxic lungs 1.44 +/- 0.01 (p < 0.01). There was no significant difference between the hypoxic and hyperoxic lungs. The fractal dimension may be a useful clinical index to quantify pathologic changes in the pulmonary arterial tree.

Animals↗

PubMed2006

Multiple testing methods for ChIP-Chip high density oligonucleotide array data.

Cawley et al. (2004) have recently mapped the locations of binding sites for three transcription factors along human chromosomes 21 and 22 using ChIP-Chip experiments. ChIP-Chip experiments are a new approach to the genomewide identification of transcription factor binding sites and consist of chromatin (Ch) immunoprecipitation (IP) of transcription factor-bound genomic DNA followed by high density oligonucleotide hybridization (Chip) of the IP-enriched DNA. We investigate the ChIP-Chip data structure and propose methods for inferring the location of transcription factor binding sites from these data. The proposed methods involve testing for each probe whether it is part of a bound sequence using a scan statistic that takes into account the spatial structure of the data. Different multiple testing procedures are considered for controlling the familywise error rate and false discovery rate. A nested-Bonferroni adjustment, which is more powerful than the traditional Bonferroni adjustment when the test statistics are dependent, is discussed. Simulation studies show that taking into account the spatial structure of the data substantially improves the sensitivity of the multiple testing procedures. Application of the proposed methods to ChIP-Chip data for transcription factor p53 identified many potential target binding regions along human chromosomes 21 and 22. Among these identified regions, 18% fall within a 3 kb vicinity of the 5'UTR of a known gene or CpG island and 31% fall between the codon start site and the codon end site of a known gene but not inside an exon. More than half of these potential target sequences contain the p53 consensus binding site or very close matches to it. Moreover, these target segments include the 13 experimentally verified p53 binding regions of Cawley et al. (2004), as well as 49 additional regions that show higher hybridization signal than these 13 experimentally verified regions.

5' Untranslated Regions↗

PubMed2005

Viral infection in internally structured hosts. I. Conditions for persistent infection.

For a virus population within its host, two important levels of structure can be considered: multiple cell types which can be infected, and tissue types or body compartments which may be coupled via movement. We develop a model with both types of structure. Migration between compartments can create "sources" and "sinks" within the virus population, where realized viral growth rate and abundance is lowered in some compartments compared to what would be observed in isolation. Using both analytical and numerical methods, we investigate how this within-host spatial structure affects the conditions for persistent viral infection. We find that migration between compartments makes the establishment of infection more difficult than it would be in the absence of migration, implying that within-host spatial structure combined with viral movement decreases the likelihood of viral establishment. If migration is symmetrical and compartments are heterogeneous, an increase in migration rates between compartments generally makes establishment less likely. This may help to explain the tissue specificity observed for many viruses. There are, however, important exceptions to this result. These include circumstances where the virus initially invades a compartment that is unfavorable to population growth and migration is necessary to infect other parts of the host body. Stochastic aspects of viral establishment may also favor increased migration as it tends to dampen the amplitude of fluctuations in population size during the initial transient phase of establishment.

Animals↗

PubMedDate not supplied

Color shifts induced by S-cone patterns are mediated by a neural representation driven by multiple cone types.

This study investigated chromatic induction from inhomogeneous background patterns. Previous work showed that a background pattern detected by only S cones induced strong color shifts in a nearby test area (Monnier & Shevell, 2003). In that work, the S-cone patterns were composed with constant L- and M-cone stimulation over the entire background; in terms of L and M cones, therefore, the background was uniform. S-cone stimulation was varied over space to produce S-cone-isolated background patterns. These S-cone patterns, however, established spatial structure (the pattern) at both the receptoral level (S-cone stimulation) and the postreceptoral level (S/(L+M)). Here, these two levels of pattern representation were unconfounded to determine whether color shifts induced by S-cone patterns were due to spatial structure within an S-cone-specific neural pathway versus a pathway that combines responses from S cones and other cone types (e.g. S/(L+M)). The results showed that the induced color shifts were mediated by signals within a pathway that combines responses from multiple cone types. These results are consistent with a +s/-s spatially antagonistic neural receptive field, which is found in some neurons in V1 and V2.

Color↗

PubMedDate not supplied

["External chromophores" and intensive bands in circular dichroism spectra of liquid-crystalline microphases of nucleic acids].

From the analysis of CD-spectra of liquid crystalline microphases formed from DNA molecules in complexes with "external chromophores" requirements are formulated for the compounds to be used in revealing peculiarities of spatial structure of nucleic acids liquid crystalline microphases. These requirements satisfied it is possible to record the CD-spectra having intensive bands in the regions of chromophores absorption. These bands prove the helical pattern of the spatial structure of nucleic acid liquid crystalline microphase.

Chemical Phenomena↗

PubMed2003

Spatial characteristics of Kalpha x-ray emission from relativistic femtosecond laser plasmas.

The spatial structure of the Kalpha emission from Ti targets irradiated with a high intensity femtosecond laser has been studied using a two-dimensional monochromatic imaging technique. For laser intensities I<5 x 10(17) W/cm(2), the observed spatial structure of the Kalpha emission can be explained by the scattering of the hot electrons inside the solid with the help of a hybrid particle-in-cell/Monte Carlo model. By contrast, at the maximum laser intensity I=7 x 10(18) W/cm(2) the half-width of the Kalpha emission was 70 microm compared to a laser-focus half-width of 3 microm. Moreover, the main Kalpha peak was surrounded by a halo of weak Kalpha emission with a diameter of 400 microm and the Kalpha intensity at the source center did not increase with increasing laser intensity. These three features point to the existence of strong self-induced fields, which redirect the hot electrons over the target surface.

Journal Article↗

PubMed2005

A suite of methods for representing activity space in a healthcare accessibility study.

BACKGROUND: "Activity space" has been used to examine how people's habitual movements interact with their environment, and can be used to examine accessibility to healthcare opportunities. Traditionally, the standard deviational ellipse (SDE), a Euclidean measure, has been used to represent activity space. We describe the construction and application of the SDE at one and two standard deviations, and three additional network-based measures of activity space using common tools in GIS: the road network buffer (RNB), the 30-minute standard travel time polygon (STT), and the relative travel time polygon (RTT). We compare the theoretical and methodological assumptions of each measure, and evaluate the measures by examining access to primary care services, using data from western North Carolina. RESULTS: Individual accessibility is defined as the availability of healthcare opportunities within that individual's activity space. Access is influenced by the shape and area of an individual's activity space, the spatial distribution of opportunities, and by the spatial structures that constrain and direct movement through space; the shape and area of the activity space is partly a product of how it is conceptualized and measured. Network-derived measures improve upon the SDE by incorporating the spatial structures (roads) that channel movement. The area of the STT is primarily influenced by the location of a respondent's residence within the road network hierarchy, with residents living near primary roads having the largest activity spaces. The RNB was most descriptive of actual opportunities and can be used to examine bypassing. The area of the RTT had the strongest correlation with a healthcare destination being located inside the activity space. CONCLUSION: The availability of geospatial technologies and data create multiple options for representing and operationalizing the construct of activity space. Each approach has its strengths and limitations, and presents a different view of accessibility. While the choice of method ultimately lies in the research question, interpretation of results must consider the interrelated issues of method, representation, and application. Triangulation aids this interpretation and provides a more complete and nuanced understanding of accessibility.

Journal Article↗

PubMed2007

Biological structure and health implications from tooth size at Mission San Luis de Apalachee.

This study analyzes dental metric variation to examine the biological structure of the native population at Mission San Luis de Apalachee, a late 17th century mission located in the Apalachee Province of Spanish colonial Florida. Three topics are addressed: (1) comparison of tooth sizes among adult and subadults, (2) analysis of the bio-spatial structure of skeletons within the church area, and (3) comparison of phenotypic profiles of individuals interred within coffins in the ritual nucleus of the church: the altar region. Analyses indicate that subadults had smaller average tooth sizes than adults for the posterior dentition that was particularly evident in mandibular nonpolar molars and premolars. This disparity, also documented in two other mission populations, likely represents ontogenetic stress and resulting increased mortality among those most at risk for early death. Analysis of the spatial structure of graves failed to document biological structuring by side of the aisle or by burial row, although some gross differences were evident when front, middle, and rear church burials were compared. Individuals buried in coffins within the same row were phenotypically similar to one another. However, inter-row comparisons indicated lack of phenotypic similarity among all coffin interments. These analyses suggest maintenance of kin-structured burial for elites alone within the San Luis community.

Age Factors↗

PubMedDate not supplied

A comparison of two stochastic inverse methods in a field-scale application.

Inverse modeling is a useful tool in ground water flow modeling studies. The most frequent difficulties encountered when using this technique are the lack of conditioning information (e.g., heads and transmissivities), the uncertainty in available data, and the nonuniqueness of the solution. These problems can be addressed and quantified through a stochastic Monte Carlo approach. The aim of this work was to compare the applicability of two stochastic inverse modeling approaches in a field-scale application. The multi-scaling (MS) approach uses a downscaling parameterization procedure that is not based on geostatistics. The pilot point (PP) approach uses geostatistical random fields as initial transmissivity values and an experimental variogram to condition the calibration. The studied area (375 km2) is part of a regional aquifer, northwest of Montreal in the St. Lawrence lowlands (southern Québec). It is located in limestone, dolomite, and sandstone formations, and is mostly a fractured porous medium. The MS approach generated small errors on heads, but the calibrated transmissivity fields did not reproduce the variogram of observed transmissivities. The PP approach generated larger errors on heads but better reproduced the spatial structure of observed transmissivities. The PP approach was also less sensitive to uncertainty in head measurements. If reliable heads are available but no transmissivities are measured, the MS approach provides useful results. If reliable transmissivities with a well inferred spatial structure are available, then the PP approach is a better alternative. This approach however must be used with caution if measured transmissivities are not reliable.

Calibration↗

PubMedDate not supplied

[Theoretical conformational analysis of methylamide of N-acetyl-L-lysine].

The spatial structure of the methylamide of N-acetyl-L-lysine has been analysed taking into account non-bonded and electrostatic interactions, torsional energy, bond angles distortion and hydrogen bonding. Conformational capacities of the backbone and mutual dependence of spatial structures of the backbone and the side chain was described by conformational maps obtained by energy minimisation, the dihedral angles and the bond angles of the side chain being varied for every phi, psi point. Every possible combination for phi, psi, x1-x5-angles was used corresponding to the stable form of the backbone and to torsion potential minima of the initial approximations in the calculation of preferred conformations of the molecule. Comparisons are made between stable forms of the methylamide of N-acetyl-L-lysine and Lys residues in proteins with known structure.

Amides↗

PubMed2006

Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru.

BACKGROUND AND AIMS: Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. METHODS: Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. KEY RESULTS: Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. CONCLUSIONS: These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.

Cacao↗

PubMedDate not supplied

[A mechanism of development of spatial-temporal orderliness in bacterial systems].

Peculiarities of the mechanism of intercellular regulation capable of initiating nonhomogeneous spatial structures in different experimental bacterial systems are analysed. A model of band formation of bacterial density in agar-stabilized bacterial system with opposite gradients of the substrate and oxygen is suggested. It is shown that for the appearance of spatial structures in the bacterial systems a time delay in the cell response to the external signal is of principal importance, as well as the hysteresis of transitions between differentiated bacterial states.

Bacteria↗

PubMed1978

1H nuclear-magnetic-resonance studies of the molecular conformation of monomeric glucagon in aqueous solution.

Dilute aqueous solutions of glucagon were investigated by high-resolution 1H nuclear magnetic resonance at 360 MHZ. Monomeric glucagon was found to adopt predominantly an extended flexible conformation which contains, however, a local non-random spatial structure involving the fragment--Phe-22--Val-23--Gln-24--Trp-25--. This local conformation is preserved in the partial sequence 22--26 and could thus be characterized in detail. Two interesting conclusions resulted from these experiments. One is that the local spatial structure in the fragment 22--25 of glucagon is identical to that observed in the fragment 20--23 of the human parathyroid hormone. Secondly, the backbone conformation in the C-terminal fragment of glucagon in solution must be different from the alpha-helical structure observed in single crystals of glucagon. These new structural data are analyzed with regard to relationships with glucagon binding to the target cells.

Glucagon↗

PubMed2006

Geographic structure of pollinator communities, reproductive assurance, and the evolution of self-pollination.

Reproductive assurance is often invoked as an explanation for the evolution of self-fertilization in plants. However, key aspects of this hypothesis have received little empirical support. In this study, I use geographic surveys of pollinator communities along with functional studies of floral trait variation to examine the role of pollination ecology in mating system differentiation among populations and subspecies of the annual plant Clarkia xantiana. A greenhouse experiment involving 30 populations from throughout the species' range indicated that variation in two floral traits, herkogamy and protandry, was closely related to levels of autofertility and that trait variation was partitioned mainly among populations. Emasculation experiments in the field showed that autonomous selfing confers reproductive assurance by elevating fruit and seed production. Surveys of pollinator communities across the geographic range of the species revealed that bee pollinator abundance and community composition differed dramatically between populations of the outcrossing subspecies xantiana and the selfing subspecies parviflora despite their close proximity. Specialist bee pollinators of Clarkia were absent from selfing populations, but they were the most frequent visitors to outcrossing populations. Moreover, within the outcrossing subspecies xantiana, there was a close correspondence between specialist abundance and population differentiation in herkogamy, a key mating system trait. This spatial covariation arose, in part, because geographically peripheral populations had reduced herkogamy, higher autofertility, and lower pollinator abundance compared to central populations of xantiana. Finally, I detected strong spatial structure to bee communities both across the range of the species and within the outcrossing subspecies. In both cases, spatial structure was stronger for specialist bees compared to generalist bees, and pollinator communities varied in parallel with population variation in herkogamy. These results provide evidence that mating system differentiation parallels spatial variation in pollinator abundance and community composition at both broad and more restricted spatial scales, consistent with the hypothesis that pollinator abundance and reproductive assurance are important drivers of plant mating system evolution.

Adaptation, Biological↗

PubMed2003

A comparative analysis of structure and spatial distribution of decorin in human leiomyoma and normal myometrium.

Leiomyoma is a benign smooth muscle tumor of the uterus that affects many women in active reproductive life. It is composed by bundles of smooth muscle cells surrounded by extracellular matrix. We have recently shown that the glycosylation of extracellular matrix proteoglycans is modified in leiomyoma: increased amounts of galactosaminoglycans with structural modifications are present. The data here presented show that decorin is present in both normal myometrium and leiomyoma but tumoral decorin is glycosylated with longer galactosaminoglycan side chains. Furthermore, these chains contain a higher ratio D-glucuronate/L-iduronate, as compared to normal tissue. To determine if these changes in proteoglycan glycosylation correlates with modifications in the extracellular matrix organization, we compared the general structural architecture of leiomyoma to normal myometrium. By histochemical and immunofluorescence methods, we found a reorganization of muscle fibers and extracellular matrix, with changes in the distribution of glycoproteins, proteoglycans, and collagen. Thin reticular fibers, possibly composed by types I and III collagen, were replaced by thick fibers, possibly richer in type I collagen. Type I collagen colocalized with decorin both in leiomyoma and normal myometrium, in contrast to type IV collagen that did not. The relative amount of decorin was increased and the distribution of decorin and collagen was totally modified in the tumor, as compared to the normal myometrium. These findings reveal that not only decorin structure is modified in leiomyoma but also the tissue architecture changed, especially concerning extracellular matrix.

Adult↗