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At least 829 records · Page 46Linked to original sources

PubMed2004

An agent-based model of sleeping sickness: simulation trials of a forest focus in southern Cameroon.

An agent-based model (AMB) used to simulate the spread of Human African Trypanosomiasis is presented together with the results of simulations of a focus of the disease. This model is a completely spatialized approach taking into account a series of often overlooked parameters such as human behaviour (activity-related movements), the density and mobility of the disease vectors--tsetse flies (Glossina spp.)--and the influence of other tsetse feeding hosts (livestock and wild animal populations). The agents that represent humans and tsetse flies move in a spatially structured environment managed by specialized location agents. Existing compartmental mathematical models governed by differential equations fail to incorporate the spatial dimension of the disease transmission. Furthermore, on a small scale, transmission is unrealistically represented by entities less than one. This ABM was tested with data from one village of the Bipindi sleeping sickness focus (southern Cameroon) and with obtained realistic simulations of stable transmission involving an animal reservoir. In varying different spatial configurations, we observe that the stability of spread is linked to the spatial complexity (number of heterogeneous locations). The prevalence is very sensitive to the human densities and to the number of tsetse flies initially infected in a given location. A relatively low and durable prevalence is obtained with shortening the phase I. In addition, we discuss some upgrading possibilities, in particular the linkage to a Geographical Information System (GIS). The agent-based approach offers new ways to understanding the spread of the disease and a tool to evaluate risk and test control strategies.

Cameroon↗

PubMed2007

Local-scale genetic structure in the peatmoss Sphagnum fuscum.

Sphagnum (peatmoss) dominates huge areas of the Northern Hemisphere and acts as a significant carbon sink on a global scale, yet little is known about the genetic structure of Sphagnum populations. We investigated genetic structure within a population of the common peatmoss Sphagnum fuscum, to assess local patterns of genetic diversity and the spatial extent of clones. One hundred seventeen shoots were sampled from five transects in Fuglmyra, central Norway, and sequenced for three anonymous DNA regions. Five neighbourhood patches were marked along each transect, and from each patch, five stems were sampled for molecular analyses. Seventeen haplotypes could be distinguished and two major groups of haplotypes differed by 12 mutational steps. The two major haplotype groups differed significantly in microhabitat association along the distance to groundwater table and the pH gradients, indicating microhabitat differentiation. The haplotypes within these groups were all genetically similar, differing by one or two mutations. The most common haplotype occurred in four transects separated by 250-m distance. Most of the molecular variation in the population was found among transects, and within patches. Large dominating clones within each transect resulted in low variation explained by the among-patch-within-transect component of spatial structure. Mutation appears to account for a larger proportion of the population variation than recombination. Within the population, vegetative growth and asexual reproduction from gametophyte fragments dominate as the main reproductive mode.

Analysis of Variance↗

PubMed2004

[Research advances in dynamic mechanism and its simulation of eco-hydrological process in forest catchment].

Hydrological process is the key link between climatic fluctuations and ecologic dynamics of forests at spatial and temporal scales. To some extent, global climate change and large-scale human's activities will impact the spatial-temporal changes of eco-hydrological process in forest catchments in the future. Therefore, researches on the dynamic mechanism of eco-hydrological processes in forest catchments play a crucial role in understanding and controlling the rational use of ecological resources, resuming regional ecology, and sustainable development in economy. This paper described the interception, evapotranspiration and rainfall-runoff of forest ecological system and their effects on hydrological process. The spatial structure of soil moisture and its evolution with time were also the cause and consequence of forest. The spatial-temporal interaction between hydrologic and ecologic dynamics, the application of distributed hydrological model, and the eco-hydrological dynamics and cybernetics of forest would be the most exciting frontiers of the relative researches in the future.

Climate↗

PubMed2004

The influence of space in genetic-environmental relationships when environmental heterogeneity and seed dispersal occur at similar scale.

We tested the importance of microenvironmental topographic parameters as predictors of emmer wheat genetic variation using three classes of single-locus (or at most several-loci) genetic markers (allozymes, glutenins, and qualitative traits) and two classes of markers of polygenic inheritance (phenological and morphological traits). Canonical correspondence analysis (CCA) and redundancy analysis (RDA) detected a significant effect of spatially structured environmental variation on genetic differences between plants for allozymes, glutenins, and quantitative morphological and phenological traits. However, after removing a spatial component of variation in partial CCA and partial RDA, the relationship of the remaining environmental variation with these genetic markers could be explained by chance alone, allowing us to rule out microniche topographic specialization in emmer wheat. Topographic autocorrelation exhibited a certain degree of similarity with genetic marker autocorrelation, indicating similar scales of environmental heterogeneity and seed flow. The detected population genetic structure agrees with one expected under isolation by distance as a result of limited gene flow. A negative relationship of genetic similarity with the logarithm of distance between plants was detected for both molecular markers and quantitative traits, which differed in the strength but not the pattern of association.

Alleles↗

PubMed1989

Structure and supramolecular architecture of membrane channel-forming peptides.

Peptides gathering together to induce channels in lipid bilayers may be classified in several categories according to the spatial structures involved. For example, gramicidin A forms intramolecular tubes, alamethicin, bundles of helical rods with intermolecular pores, porins (being proteins, properly speaking) are rich in beta-sheets that may form barrels, whereas cyclic peptides might stack together resulting in the formation of pores. The chemical structure of these compounds is now well characterized. The transmembrane electrical signals that they transmit are also typical of the particular supramolecular configurations (or architecture). Investigations in this field are thus relevant to structure-function relationship studies due to the availability of natural or synthetic analogues allowing the measurement of the influence of physico-chemical parameters upon the energy profiles of the pores. Consequently, questions such as the existence and probabilities of conductance substrates, their voltage-dependence and their ion or molecular selectivity can be tackled. Today, the loosest aspect of these studies lies in the actual molecular conformations and architecture in the membranes of the peptide aggregates, the knowledge of which remains imprecise, even 'at rest' in the best-studied cases. This review attempts to point out still unresolved questions and to propose some plausible approaches concerning, for example: 1) the configurations of the molecular aggregates responsible for ion transfer; 2) the mechanisms for channel-opening and closing (gating); 3) the eventual cooperative phenomena between channels, via the bilayer or interfacial components. Possible applications of these structures will be tentatively outlined.

Alamethicin↗

PubMed2003

Speciation along environmental gradients.

Traditional discussions of speciation are based on geographical patterns of species ranges. In allopatric speciation, long-term geographical isolation generates reproductively isolated and spatially segregated descendant species. In the absence of geographical barriers, diversification is hindered by gene flow. Yet a growing body of phylogenetic and experimental data suggests that closely related species often occur in sympatry or have adjacent ranges in regions over which environmental changes are gradual and do not prevent gene flow. Theory has identified a variety of evolutionary processes that can result in speciation under sympatric conditions, with some recent advances concentrating on the phenomenon of evolutionary branching. Here we establish a link between geographical patterns and ecological processes of speciation by studying evolutionary branching in spatially structured populations. We show that along an environmental gradient, evolutionary branching can occur much more easily than in non-spatial models. This facilitation is most pronounced for gradients of intermediate slope. Moreover, spatial evolutionary branching readily generates patterns of spatial segregation and abutment between the emerging species. Our results highlight the importance of local processes of adaptive divergence for geographical patterns of speciation, and caution against pitfalls of inferring past speciation processes from present biogeographical patterns.

Animals↗

PubMed1984

[Contribution of NMR spectroscopy to the study of structure-function relations of proteins and peptides].

NMR spectroscopy provides a unique means to study molecular conformation, mechanisms of action and structure-function relationships for peptides and proteins in solution under conditions approaching those of their physiological environment. Development of NMR techniques, especially directed to the peptide and protein conformational analysis, is considered under the topics of two-level signal assignment and structural significance of homo- and heteronuclear spin-spin couplings. The results of NMR conformational analysis are presented for solution spatial structure of valinomy cin and gramicidin A antibiotics, honey-bee neurotoxin apamin, scorpion insectotoxin I5A and snake venom neurotoxins of "short" and "long" types. The structure-function relationships are discussed for these biologically active molecules.

Amino Acid Sequence↗

PubMed1998

Objective malignancy grading: a review emphasizing unbiased stereology applied to breast tumors.

Low reproducibility reduces the clinical value of morphologic grading of malignant tumors, and the replacement of subjective classification by objective quantification has been suggested. Simple mitosis counting has been employed for objective malignancy grading most frequently and has proved its prognostic significance in, e.g., sarcomas and carcinomas of the breast and ovary. These and other measurements of morphometry are, however, obtained in two dimensions only, introducing bias due to ignorance of the fact that biologic structures are three-dimensional. Stereologic estimators are, to that end, well-suited, because they enable the assessment of spatial structure from sections. Studies addressing the impact of stereology in tumor pathology are the subject of the current review. Details of estimation are provided of stereologic variables of tumor size, numbers and densities of cancer cell nuclei and mitoses, mean size and size variability of cancer cell nuclei and variables of tissue architecture. Besides a description of their practical estimation the influence on variables of sampling method, tissue processing and observer variability is assessed, and estimator efficiency and measuring equipment is evaluated. Exemplifying the clinical importance of objective grading, results are summarized of prognostic studies of quantitative histopathology in women with breast cancer. It has been shown that many stereologic estimators are applicable to ordinary histologic sections processed under routine conditions. If a systematic random scheme of sampling is employed then the efficiency of estimation is usually high, and reproducible, accurate and representative results are ensured. For objective malignancy grading of breast cancer especially the volume-weighted mean nuclear size, vv (nuc), seems valuable, and the variable usually provides independent information to that of staging parameters. The prognostic value of vv (nuc) seems greatest in lymph node positive subsets, whereas the importance in lymph node negative patients should be further investigated. The clinical significance of some stereologic variables may be restricted due to relatively time consuming measurement procedures. However, the unbiased technique may provide precise measures of basic parameters like "tumor burden" and tumor growth pattern, and thereby be highly useful in experimental oncology. In conclusion, stereology is of great value for quantifying tumor elements. For objective malignancy grading especially assessment of the three-dimensional mean nuclear size seems useful. Prognostic significance of this variable has been demonstrated in, e.g., malignant melanoma and carcinomas of the breast, lung, bladder, prostate and uterine cervix. To determine the real clinical value of the measurements, further evaluation in a routine setting is necessary. In case such prospective studies confirm previous findings, the future replacement of subjective grading techniques by reproducible, objective variables seems feasible.

Breast Neoplasms↗

PubMed2005

The two cysteine-rich head domains of minicollagen from Hydra nematocysts differ in their cystine framework and overall fold despite an identical cysteine sequence pattern.

Synthetic replicates of naturally occurring cysteine-rich peptides such as hormones, neurotransmitters, growth factors, enzyme inhibitors, defensins and toxins often can be oxidatively folded in high yields to their native structure in simple redox buffers. Thereby, identical cysteine patterns in the sequence were found to generate identical disulfide connectivities and homologous spatial structures despite significant variability in the non-cysteine positions. Minicollagen-1 from the nematocysts of Hydra is a trimeric protein that contains cysteine-rich domains at the N and C termini, which are involved in the assembly of an intermolecular disulfide network. Determination of the three-dimensional structures of peptides corresponding to the N-terminal and C-terminal domains by NMR spectroscopy revealed a remarkable exception from the general rule. Despite an identical cysteine pattern, the two domains of minicollagen-1 form different disulfide bridges and exhibit distinctly different folds, both of which are not found in the current structural databases. To our knowledge, this is the first case where two relatively short peptides with the abundant cysteine residues in identical sequence positions fold uniquely and with high yields into defined, but differing, structures. Therefore, the cysteine-rich domains of minicollagen constitute ideal model systems for studies of the interplay between folding and oxidation in proteins.

Amino Acid Sequence↗

PubMed1995

Investigation of the configurational and conformational influences on the hormonal activity of 1,2-bis(2,6-dichloro-4-hydroxyphenyl)ethylenediamines and of their platinum(II) complexes. 1. Synthesis, estradiol receptor affinity, and estrogenic activity of diastereomeric [N-alkyl- and N,N'-dialkyl-1,2- bis(2,6-dichloro-4-hydroxyphenyl)ethylenediamine]dichloroplatinum(II) complexes.

N-Monoalkylated (Et) and N,N'-dialkylated (Me and Et) 1,2-bis(2,6-dichloro-4-hydroxyphenyl)-ethylenediamines and their dichloroplatinum(II) complexes were synthesized, and their configuration and conformational behavior were 1H-NMR spectroscopically clarified. The latter was brought in relation to their relative binding affinity (RBA) to the estrogen receptor as well as to their estrogenic potency. In contrast to the RR/SS-configurated diamines, the R/S-configurated ones showed marked estrogenic properties which correlate with the RBA's. In the related R/S-configurated complexes the estrogenic activity is determined by the same structural requirements as in the diamine series. However, a correlation between RBA's and estrogenic potencies is missing. The connection between spatial structure and activity is discussed by use of a drug-receptor model recently proposed by Höltje and Dall.

Animals↗

PubMed2005

Population structure and coil dimorphism in a tropical land snail.

Tree snails of the subgenus Amphidromus s. str. are unusual because of the chiral dimorphism that exists in many species, with clockwise (dextrally) and counter-clockwise (sinistrally) coiled individuals co-occurring in the same population. Given that mating in snails is normally impeded when the two partners have opposite coil, positive frequency-dependent selection should prevent such dimorphism from persisting. We test the hypothesis that a strong population structure with little movement between tree-based demes may result in the fixation of coiling morphs at a very small spatial scale, but apparent dimorphism at all larger scales. To do so, we describe the spatial structure in a Malaysian population of A. inversus (Müller, 1774) with 36% dextrals. We marked almost 700 juvenile and adult snails in a piece of forest consisting of 92 separate trees, and recorded dispersal and the proportions of dextrals and sinistrals in all trees over a 7-day period. We observed frequent movement between trees (155 events), and found that no trees had snail populations with proportions of dextrals and sinistrals that were significantly different from random. Upon recapture 1 year later, almost two-thirds of the snails had moved away from their original tree. We conclude that population structure alone cannot stabilise the coil dimorphism in Amphidromus.

Animal Structures↗

PubMed2006

Long-term persistence of the spatial organization of temperature fluctuation lifetime in turbulent air avalanches.

It has been recently proposed that some natural phenomena, such as sunspot occurrence, can be represented by a modulated Markov jitter, which is a high-frequency Markov signal multiplied by a long-term component. The two parameters of this model can be estimated using a nonlinear method based on absolute derivatives. This analysis is applied here to a different physical system: the temperature time series measured during air avalanches in the vertical access pit of an underground quarry. The thermal fluctuations associated with these turbulent flows, driven by the external temperature forcing, actually appear as another practical realization of a modulated Markov jitter. One parameter of the model provides the lifetime of the temperature fluctuations, which can be estimated as a function of time and position. The obtained lifetime is of the order of 10 to 25 min , and is remarkably constant in time for each sensor, independently of the amplitude of the forcing. Furthermore, a significant and persistent spatial structure is observed, revealing a long-term intrinsic organization of the turbulent air flows in the pit. Such a stable spatial organization may reflect a general feature of turbulent phenomena.

Journal Article↗

PubMed2006

Spatio-temporal dynamics of alternative male phenotypes in coho salmon populations in response to ocean environment.

1. The coexistence of alternative reproductive phenotypes will probably be shaped by spatial and temporal variability in the environment. However, the effects of such variability on coexistence and the scale at which it operates are seldom understood. 2. To quantify such effects, we examined spatial and temporal dynamics in the abundance and frequency of alternative phenotypes of male coho salmon, Oncorhynchus kisutch Walbaum, which mature as either large fighters (age-3 'hooknoses') or small sneakers (age-2 'jacks'). Using over 20 years of data on coded-wire tagged fish released from nine Oregon hatcheries, we tested for the effects of ocean environment independent of those due to freshwater rearing. 3. Annual fluctuations of the abundance of jack and hooknose males within populations were correlated strongly by brood year (cohort) but not by return year (breeding group). This occurred independently of significant effects of release practice (i.e. the number of fish released, body size at release and date of release), indicating that a synchronized fluctuation in mortality during the first year at sea was the predominant cause. As a result, the annual frequency of the alternative phenotypes at breeding varied considerably within populations. 4. Spatial patterns in the annual fluctuations of the two phenotypes were similar (i.e. synchronous among populations), except that jacks showed local spatial structure (decreased synchrony with distance) not evident among hooknoses. This suggests that oceanic processes affecting the two phenotypes operate at different spatial scales. Despite effects on salmon abundance, the ocean environment had little influence through its effects on salmon growth on the relative frequencies of the alternative phenotypes within and among populations. 5. The results provide insight into the evolutionary dynamics of alternative phenotypes, including an intragenerational time lag that increases annual variability in phenotype frequencies at breeding (return years) and the significance of local freshwater processes, rather than oceanic processes, on phenotype expression. Freshwater processes, such as juvenile growth, timing of migration and breeding competition, operating at evolutionary and intragenerational time-scales, are probably the predominant forces affecting phenotype frequency.

Aging↗

PubMed2005

SA1 and RA afferent responses to static and vibrating gratings.

SA1 and RA afferent fibers differ both in their ability to convey information about the fine spatial structure of tactile stimuli and in their frequency sensitivity profiles. In the present study, we investigated the extent to which the spatial resolution of the signal conveyed by SA1 and RA fibers depends on the temporal properties of the stimulus. To that end, we recorded the responses evoked in SA1 and RA fibers of macaques by static and vibrating gratings that varied in spatial period, vibratory frequency, and amplitude. Gratings were oriented either parallel to the long axis of the finger (vertical) or perpendicular to it (horizontal). We examined the degree to which afferent responses were dependent on the spatial period, vibratory frequency, amplitude, and orientation of the gratings. We found that the spatial modulation of the afferent responses increased as the spatial period of the gratings increased; the spatial modulation was the same for static and vibrating gratings, despite large differences in evoked spike rates; the spatial modulation in SA1 responses was independent of stimulus amplitude over the range of amplitudes tested, whereas RA modulation decreased slightly as the stimulus amplitude increased; vertical gratings evoked stronger and more highly modulated responses than horizontal gratings; the modulation in SA1 responses was higher than that in RA responses at all frequencies and amplitudes. The behavioral consequences of these neurophysiological findings are examined in a companion paper.

Action Potentials↗

PubMed1991

Spatiotemporal mechanisms in receptive fields of visual cortical simple cells: a model.

1. Simple cells in the visual cortex have been subdivided into nondirection-selective (NDS), direction asymmetric (DA), and direction-selective (DS) cells. DA cells reverse their preferred direction with reversal of the stimulus contrast; DS2 cells respond with the same preferred direction for light and dark stimuli, whereas DS1 cells respond only to one (light or dark) contrast. Also, four velocity response groups have been distinguished: velocity broadband, low-pass, high-pass, and -tuned cells. This study describes an analytic model of feed-forward spatiotemporal interactions within a receptive field that reproduces these basic features of cortical simple cell behavior in the cat. 2. The spatial structure of the receptive fields is simulated with Gabor functions. Two neurobiologically plausible mechanisms, temporal low-pass filtering and intracortical spatial distribution of activity, are modeled. The central feature of the study is the implementation of both mechanisms in a spatially continuous way. The model is analytic, but an equivalent neural network diagram was drawn and is used to explain the features of the model. 3. First-order temporal low-pass filtering is performed both after convolving the stimulus light-intensity function with the Gabor type receptive field and also at the final output step of the model. In the circuit diagram this would correspond to low-pass filtering in lateral geniculate nucleus (LGN) and cortical cells. Filtering was adjusted to have a -3-dB drop-off frequency of 2-3 Hz, corresponding to the drop-off frequencies observed in response to temporal modulation of sine-wave gratings. 4. The mechanism that we call intracortical distribution of activity is implemented along the axis of stimulus motion. A response elicited from the part of the receptive field that is stimulated at a given time will spread out in the receptive field, influencing regions that have not been stimulated. It is equivalent to spreading of activity on the cortical surface. This mechanism extends the existing ideas of discrete interactions between subfields to a continuous scheme throughout the whole receptive field. It is based on findings that intracortical interactions exist even within single subfields. The impact of distributing the activity is assumed to decrease exponentially with the Euclidian distance between the stimulated region and the region under consideration. 5. Thresholds are implemented only at the level of the cortex. Both the activity distributing mechanism and the output of the cell being studied are thresholded.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed2006

Hyperspace geography: visualizing fitness landscapes beyond 4D.

Human perception is finely tuned to extract structure about the 4D world of time and space as well as properties such as color and texture. Developing intuitions about spatial structure beyond 4D requires exploiting other perceptual and cognitive abilities. One of the most natural ways to explore complex spaces is for a user to actively navigate through them, using local explorations and global summaries to develop intuitions about structure, and then testing the developing ideas by further exploration. This article provides a brief overview of a technique for visualizing surfaces defined over moderate-dimensional binary spaces, by recursively unfolding them onto a 2D hypergraph. We briefly summarize the uses of a freely available Web-based visualization tool, Hyperspace Graph Paper (HSGP), for exploring fitness landscapes and search algorithms in evolutionary computation. HSGP provides a way for a user to actively explore a landscape, from simple tasks such as mapping the neighborhood structure of different points, to seeing global properties such as the size and distribution of basins of attraction or how different search algorithms interact with landscape structure. It has been most useful for exploring recursive and repetitive landscapes, and its strength is that it allows intuitions to be developed through active navigation by the user, and exploits the visual system's ability to detect pattern and texture. The technique is most effective when applied to continuous functions over Boolean variables using 4 to 16 dimensions.

Algorithms↗

PubMed1987

The Roepke Lecture in Economic Geography: urban restructuring from a demographic perspective.

"The central argument of this paper is that recent research has overemphasized the notions of urban restructuring and undervalued the role of spatial demographics in understanding urban and [regional] spatial patterns. The paper examines the notions embedded in urban restructuring and suggests that a focus on several elements of demographic processes is an equally important component of understanding urban and [regional] spatial structure. A specific discussion of the Los Angeles region indicates that there is a high level of complexity in social-spatial change. Social-spatial change is not simply explained by reference to an unspecified urban restructuring."

Americas↗

PubMedDate not supplied

[Structural analysis of the complex of phenoxazone antibiotic actinocyl-bis-(2-deoxytetranucleotide 5'-d(TpGpCpA) by the methods of two dimensional 1H-NMR-spectroscopy and molecular mechanics].

The spatial structures of intercalated complexes of synthetic phenoxazone antibiotic actinocyl-bis-(2-dimethylaminoethyl) amide with self-complementary deoxytetranucleotide 5'-d(TpGpCpA) have been investigated. Analysis has been made using two-dimensional NMR (2D-NOESY) data in aqueous solution and molecular mechanics simulation. Distinctive features of the conformation of drug-DNA complexes have been determined at two possible orientations of the chromophore of phenoxazone antibiotic at the intercalation site.

Anti-Bacterial Agents↗