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Airborne lidar point clouds of vegetation capture the 3-D distribution of its scattering elements, including leaves, branches, and ground features. Assessing the contribution from vegetation to the lidar point clouds requires an understanding of the physical interactions between the emitted laser pulses and their targets. Most of the current methods to estimate the gap probability ( P gap ) or leaf area index (LAI) from small-footprint airborne laser scan (ALS) point clouds rely on either point-number-based (PNB) or intensity-based (IB) approaches, with additional empirical correlations with field measurements. However, site-specific parameterizations can limit the application of certain methods to other landscapes. The universality evaluation of these methods requires a physically based radiative transfer model that accounts for various lidar instrument specifications and environmental conditions. We conducted an extensive study to compare these approaches for various 3-D forest scenes using a point-cloud simulator developed for the latest version of the discrete anisotropic radiative transfer (DART) model. We investigated a range of variables for possible lidar point intensity, including radiometric quantities derived from Gaussian Decomposition (GD), such as the peak amplitude, standard deviation, integral of Gaussian profiles, and reflectance. The results disclosed that the PNB methods fail to capture the exact P gap as footprint size increases. By contrast, we verified that physical methods using lidar point intensity defined by either the distance-weighted integral of Gaussian profiles or reflectance can estimate P gap and LAI with higher accuracy and reliability. Additionally, the removal of certain additional empirical correlation coefficients is feasible. Routine use of small-footprint point-cloud radiometric measures to estimate P gap and the LAI potentially confirms a departure from previous empirical studies, but this depends on additional parameters from lidar instrument vendors.

Particulate matter air pollution has considerably increased during the last decades; vanadium is a transition element adhered to this particulate matter, and the combustion of fossil fuels is the main source in the atmosphere. It has been reported that air pollution and specifically vanadium exposure increases the probability of suffering arrhythmias; however the biological mechanism of such a relationship remains unknown. It has been established that a diminished presence of NCadherin alters the Connexin-43 arrangement, and the consequent altered presence of these proteins predisposes to ventricular heart rate problems. We analyzed myocardial histology and the expression of N-Cadherin and Connexin-43 by immunohistochemistry in mouse that inhaled vanadium. Our results showed a significant and progressive reduction in both N-Cadherin and Connexin-43, as well as the presence of meganucleus; myofibrils disruption, and clumping in the exposed groups were also observed. Our findings add more information about a possible explanation for the arrythmogenic effect observed in dwellers of cities with high particulate matter atmospheric pollution.

This study presents an improved theoretical formulation of the gap probability (Pgap) model, typically applied to indirectly estimate LAI in woody ecosystems. Specifically, we present the woody element projection function (GW), which characterises the angular contribution of non-leaf facets in woody ecosystems, and explain how it may be used to improve the accuracy of indirect LAI retrieval via the application of the Pgap model. GW enables separate treatment of the leaf and wood projection functions in the theoretical model, important in the typical case when Pgap includes the influence of both leaf and wood canopy elements. This study then validates the improved theoretical model using experimental data. Here, Pgap was calculated from a 3D scattering model, parameterised with highly-detailed 3D explicit tree models reconstructed from empirical data of a sampled forest stand. The experimental data was then used to quantify additional effects of view zenith angle (VZA), leaf angle distribution (LAD), and the influence of woody components on the indirect estimation of LAI and within-crown clumping via application of the Pgap model. Additionally, we quantify within-crown clumping of reconstructed tree models for leaf and woody elements both together and separately for the first time. LAI errors up to 25% at zenith were found when ignoring GW and were shown to be a function of VZA. Conversely, at the approximate 57.3° (1 radian) VZA, results show that there was no effect of GW due to the wood projection function converging with leaf projection functions. Within-crown clumping factors for the modelled dataset were as low as 0.35. Consequently, making a common assumption of a random distribution of canopy elements at the crown scale would lead to an LAI error of up to 65% for the 3D forest stand. We also conclude that when estimating LAI via the Pgap model, separate treatment of canopy material projection ‘G’ functions are required at VZA’s other than 1 radian. The findings of this study and the extended physical formulation presented here impact upon indirect Pgap LAI retrieval methods from sensors of all platforms in clumped canopy environments or canopies with woody (non-leaf) elements contributing to the extinction of light.

Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis in mammals. Brucella strains containing the O-polysaccharide in their cell wall structure exhibit a smooth phenotype whereas the strains devoid of the polysaccharide show rough phenotype. B. abortus strain RB51 is a stable rough attenuated mutant which is used as a licensed live vaccine for bovine brucellosis. Previous studies have shown that the wboA gene, which encodes a glycosyltransferase required for the synthesis of O-polysaccharide, is disrupted in B. abortus RB51 by an 1711 element. Although complementation of strain RB51 with a functional wboA gene results in O-polysaccharide synthesis in the cytoplasm, it does not result in smooth phenotype. The aim of this study was to determine if overexpression of Brucella WbkA or WbkE, two additional putative glycosyltransferases essential for O-polysaccharide synthesis, in strain RB51 would result in the O-polysaccharide synthesis and smooth phenotype. Our results demonstrate that overexpression of wbkA or wbkE gene in RB51 does not result in O-polysaccharide expression as shown by Western blotting with specific antibodies. However, wbkA, but not wbkE, overexpression leads to the development of a clumping phenotype and the production of exopolysaccharide(s) containing mannose, galactose, N-acetylglucosamine, and N-acetylgalactosamine. Moreover, we found that the clumping recombinant strain displays increased adhesion to polystyrene plates. The recombinant strain was similar to strain RB51 in its attenuation characteristic and in its ability to induce protective immunity against virulent B. abortus challenge in mice. Public Health Service grant from National Institute of Allergy and Infectious Diseases [AI065667-01A2] This work was supported by Public Health Service grant AI065667-01A2 from the National Institute of Allergy and Infectious Diseases.

Negative density dependence (NDD) of recruitment is pervasive in tropical tree species. We tested the hypotheses that seed dispersal is NDD, due to intraspecific competition for dispersers, and that this contributes to NDD of recruitment. We compared dispersal in the palm Attalea butyracea across a wide range of population density on Barro Colorado Island in Panama and assessed its consequences for seed distributions. We found that frugivore visitation, seed removal and dispersal distance all declined with population density of A. butyracea, demonstrating NDD of seed dispersal due to competition for dispersers. Furthermore, as population density increased, the distances of seeds from the nearest adult decreased, conspecific seed crowding increased and seedling recruitment success decreased, all patterns expected under poorer dispersal. Unexpectedly, however, our analyses showed that NDD of dispersal did not contribute substantially to these changes in the quality of the seed distribution; patterns with population density were dominated by effects due solely to increasing adult and seed density.

Mycorrhizal associations of important tree species were investigated within the research area of the Tropenbos Cameroon Programme (TCP), situated on the western portion of the Atlantic Biafrean forest of south Cameroon. Ninety-seven tree species of economic, social, and ecological importance, and three lianas were selected in three sites that differed in altitude, soil clay content, and soil pH. In each site plots were laid out in undisturbed forest. In each plot, seedlings, saplings, juvenile, and mature trees were identified to species level and counted; girth at breast height measured and basal area calculated; root samples were taken and examined for mycorrhizal type and extent of mycorrhizal colonization. All 100 species investigated were mycorrhizal. Tree of 74 species formed exclusively arbuscular mycorrhizas (AM); 23 trees and three Gnetum species formed ectomycorrhizas (ECM). Five of these ECM plants also harbored AM structures. Extent of mycorrhizal root colonization showed large differences for various AM trees; however, colonization of more than half of these trees was less than 25%. Colonization of ECM trees was often higher than 75%. The contribution of ECM trees to basal area varied between 19 and 35%. ECM trees often occurred in small to large clumps. In sustainable forest management plans, existing ECM forest clumps should be given special conservation value. # 2001 Elsevier Science B.V. All rights reserved.

– The objective of the present study was to determine the best concentration of urea solution and rinsing time to remove adhesiveness of African catfish eggs. Four different concentrations of rinse solution were used in this experiment comprising of 2 g, 4 g, 6 g and 8 g of urea diluted in 4 g NaCl/L of water producing a concentration of 0.486 mM, 0.973 mM, 1.458 mM, and 1.946 mM of urea concentration respectively, while 4 g NaCl/L of water without urea were used as control. The fish eggs were rinsed with the solutions at different durations namely; 1, 5 and 10 minutes. Each rinsing solution concentration and rinsing time were conducted in three replicates. The fertilization and hatching rates increased and peaked from the control (0 mM of urea) to 0.466 mN urea and decreased when concentration of urea was increased to 0.973 mM urea and 1.458 mM urea, then increased again at 1.946 mM urea, but these values were lower than at 0.486 mM urea. Thus, the best concentration for fertilization and hatching rates were 0.486 urea of urea. However 0.973 mM of urea was optimum in reducing clumping of eggs. Keywords : Clumping; Fertilization; Hatching; Brood fish

Rapid, reliable and meaningful estimates of forest canopies are essential to the characterization of forest ecosystems. The aim of the research was to conduct a thorough technical appraisal of existing available digital photographic methods for forest canopy estimation. The more traditionally used digital hemispherical photography (DHP), which measures the gap fraction at multiple zenith angles, was compared with methods that measure the gap fraction at a single zenith angle, namely 57° photography and cover photography (DCP). DCP is a more recent canopy photographic method, which measures gap fraction at the zenith (0°). These methods were applied in deciduous forests of beech, chestnut and Turkey oak. All photographic methods provided good indirect estimates of canopy properties, as compared with reference direct methods obtained by littertraps and AccuPAR ceptometers. However, all methods showed different advantages and disadvantages, which were discussed and addressed. Among the methods, DCP showed high potential as a means to quickly obtain inexpensive estimates of forest canopy over large areas, being therefore highly suitable for routine, research and monitoring of forest canopy attributes. The method also appeared particularly suitable for calibrating nadir remotely-sensed canopy estimates, on account of its high vertical resolution imagery. Comparison of logarithm gap fraction averaging procedures implied in DHP allowed defining a protocol for effective leaf area index and apparent clumping index extraction from non segmented analysis of gap fraction, which can be applied to both DHP and LAI-2000 PCA. The results have important implications for the evaluation of satellite-based leaf area index product of airborne laser scanning (LiDAR). Comparisons of compact (point-and-shoot) cameras with digital single lens reflex cameras allowed defining standardized field protocol for image acquisition and software analysis. The outcome can greatly assist canopy photographic methods to achieve the standards of an ideal device. The study also provided a suite of several variables of interest such as light extinction coefficient and crown porosity, which can provide insights towards the characterization of deciduous forests, and which can be further applied for further canopy studies in deciduous stands. L’obiettivo della tesi è di fornire una analisi tecnica approfondita delle metodologie esistenti per la caratterizzazione e la stima degli attributi della copertura forestale basate sull’utilizzo della fotografia digitale. La fotografia emisferica (DHP), tecnica tradizionalmente impiegata in campo forestale, basata su misure multiple simultanee della trasmittanza a diversi angoli zenithali, viene comparata con metodi basati su singole misure della trasmittanza, registrate rispettivamente a 57° gradi e allo zenith (0°); quest’ultima metodologia, detta fotografia cover (DCP), rappresenta la tecnica fotografica di più recente introduzione, basata su singole misure verticali della trasmittanza ottenute tramite l’utilizzo di una focale di 70 mm (focale equivalente 35 mm) orientata allo zenith. Queste metodologie sono state testate in foreste decidue di faggio, castagno e cerro. Tutti le tecniche fotografiche sono risultate accurate per la stima degli attributi forestali della copertura, a partire dal confronto con metodologie dirette di riferimento. Tuttavia, ciascun metodo ha mostrato differenti vantaggi e svantaggi, che vengono analizzati e discussi in dettaglio. Tra le tecniche, la più recente DCP offre notevoli vantaggi in termini di semplicità, rapidità e basso costo, essendo pertanto altamente indicata per l’utilizzo in protocolli di monitoraggio e di ricerca di lungo termine. L’analisi degli algoritmi utilizzati per la stima degli attributi della copertura in DHP ha permesso di definire un protocollo standard per la stima dell’indice di area fogliare effettiva e per la caratterizzazione della eterogeneità spaziale della copertura a differenti scale. Viene infine valutata l’accuratezza delle fotocamere compatte e delle più recenti reflex digitali. L’analisi ha permesso di definire un protocollo per la acquisizione e il processamento delle immagini, che può essere considerato come riferimento per il raggiungimento di alti livelli di accuratezza nell’utilizzo della tecnica fotografica digitale. Dottorato di ricerca in Ecologia forestale

P. falciparum causes the majority of severe malarial infections. The pathophysiological mechanisms underlying cerebral malaria (CM) are not fully understood and several hypotheses have been put forward, including mechanical obstruction of microvessels by P. falciparum-parasitized red blood cells (pRBC). Indeed, during the intra-erythrocytic stage of its life cycle, P. falciparum has the unique ability to modify the surface of the infected erythrocyte by exporting surface antigens with varying adhesive properties onto the RBC membrane. This allows the sequestration of pRBC in multiple tissues and organs by adhesion to endothelial cells lining the microvasculature of post-capillary venules (1). By doing so, the mature forms of the parasite avoid splenic clearance of the deformed infected erythrocytes (2) and restrict their environment to a more favorable low oxygen pressure (3). As a consequence of this sequestration, it is only immature asexual parasites and gametocytes that can be detected in peripheral blood. Cytoadherence and sequestration of mature pRBC to the numerous host receptors expressed on microvascular beds occurs in severe and uncomplicated disease. However, several lines of evidence suggest that only specific adhesive phenotypes are likely to be associated with severe pathological outcomes of malaria. One example of such specific host-parasite interactions has been demonstrated in vitro, where the ability of intercellular adhesion molecule-1 to support binding of pRBC with particular adhesive properties has been linked to development of cerebral malaria (4,5). The placenta has also been recognized as a site of preferential pRBC accumulation in malaria-infected pregnant women, with chondrotin sulphate A expressed on syncytiotrophoblasts that line the placental intervillous space as the main receptor (6). Rosetting of pRBC to uninfected erythrocytes via the complement receptor 1 (CD35)(7,8) has also been associated with severe disease (9). One of the most recently described P. falciparum cytoadherence phenotypes is the ability of the pRBC to form platelet-mediated clumps in vitro. The formation of such pRBC clumps requires CD36, a glycoprotein expressed on the surface of platelets. Another human receptor, gC1qR/HABP1/p32, expressed on diverse cell types including endothelial cells and platelets, has also been shown to facilitate pRBC adhesion on platelets to form clumps (10). Whether clumping occurs in vivo remains unclear, but it may account for the significant accumulation of platelets described in brain microvasculature of Malawian children who died from CM (11). In addition, the ability of clinical isolate cultures to clump in vitro was directly linked to the severity of disease in Malawian (12) and Mozambican patients (13), (although not in Malian (14)). With several aspects of the pRBC clumping phenotype poorly characterized, current studies on this subject have not followed a standardized procedure. This is an important issue because of the known high variability inherent in the assay (15). Here, we present a method for in vitro platelet-mediated clumping of P. falciparum with hopes that it will provide a platform for a consistent method for other groups and raise awareness of the limitations in investigating this phenotype in future studies. Being based in Malawi, we provide a protocol specifically designed for a limited resource setting, with the advantage that freshly collected clinical isolates can be examined for phenotype without need for cryopreservation.

Title: Radiation in stellar winds. Resonance line formation in inhomogeneous hot star winds Author: M.Sc. Brankica Šurlan Department: Astronomical Institute of the Academy of Sciences of the Czech Republic Supervisor: RNDr. Jiří Kubát, CSc., Astronomical Institute of the Academy of Sciences of the Czech Republic Abstract: To incorporate the three-dimensional (3-D) nature of stellar wind clump- ing into radiative transfer calculations, in this thesis a newly developed full 3-D Monte Carlo radiative transfer code for inhomogeneous expanding stellar winds is presented and used to investigate how different model parameters influence reso- nance line formation. Realistic 3-D models that describe the dense as well as the rarefied wind components are used to model the formation of resonance lines in a clumped stellar wind. Non-monotonic velocity fields are accounted for as well. It is shown that the 3-D density and velocity wind inhomogeneities have very strong impact on the resonance line formation. The models show that the line opacity is lower for a larger clump separation and shallower velocity gradients within the clumps. They also demonstrate that to obtain empirically correct mass-loss rates from UV resonance lines, wind clumping and its 3-D nature must be taken into account. 1

Empirical relations are frequently used to derive leaf area index (LAI). Such relations often make assumptions that make it hard to link the derived LAI to realistic trees and forest canopies. In previous work we developed a set of analytical expressions to describe LiDAR waveforms with only a limited number of assumptions based on radiative transfer. These expressions were a function of crown macro-structure and LAI. The expressions were successfully tested when applied on crown archetypes, but showed significant error when applied to more realistic crowns. In this study, we analyse the effect of clumping on inferring LAI from realistic trees. Despite the potential of the expressions to detect subtle changes in LAI, absolute inferred LAI values can be significantly off. However, the strong correlation between true and inferred LAI (R2 > 0.97) for the two test cases in this study, allows for calibration of the inferred LAI values.

International audience; Cell enumeration and diagnosis using peripheral blood smears are routine tasks in many biological and pathological examinations. Not every area in the smear is appropriate for such tasks due to severe cell clumping or sparsity. Manual working area selection is slow, subjective, inconsistent and statistically biased. Automatic working area classification can reproducibly identify appropriate working smear areas. However, very little research has been reported in the literature. With the aim of providing a preprocessing step for further detailed cell enumeration and diagnosis for high throughput screening, we propose an integrated algorithm for area classification and quantify both cell spreading and cell clumping in terms of individual clumps and the occurrence probabilities of the group of clumps over the image. Comprehensive comparisons are presented to compare the effect of these quantifications and their combinations. Our experiments using images of Giemsa-stained blood smears show that the method is efficient, accurate (above 88.9% hit rates for all areas in the validation set of 140 images) and robust (above 78.1% hit rates for a test set of 4878 images). This lays a good foundation for fast working area selection in high throughput screening.

International audience; Sun-shade models proved to be simple, fast and reliable tools for estimating the fraction of absorbed PAR (fAPAR) and the photosynthesis of low and simple canopies (e.g. wheat). Applications on tall canopies, or non-ideal canopies (e.g. row-planting, azimuthal heterogeneity, clumping, non-spherical leaf angle distribution, large proportion of non-green elements) were limited so far. We attempted to apply the Sun-shade model proposed by de Pury and Farquhar [de Pury, D.G.G., Farquhar, G.D., 1997. Simple scaling of photosynthesis from leaves to canopies without the errors of big-leaf models. Plant Cell Environ. 20, 537–557] at the scale of the non-ideal canopy of adult coconut palms. The gap fractions of the whole cover, fraction of intercepted PAR (fIPAR), clumping index and leaf orientation derived from LAI-2000 (PCA) were closely matching the simulations of a reference 3D architectural model (3DM) used for cross-validation. Moreover, 3DM supplied a relationship for down-scaling the gap-fractions from the whole cover to green elements of the canopy. The derived Sun-shade simulations of fAPAR by green leaves agreed within 5% with 3DM, on a half-hourly time-step and for 1 year, confirming combined PCA and Sun-shade methods as a fast and reliable tool, even for tall or complex canopies. fIPAR and plant area index (PAI) were compared with the coconut literature and an empirical model was proposed for estimating fIPAR from age and planting density. The coefficient of extinction, K, was adjusted to 0.33 for the regular range of planting density.

Inverting radiative transfer (R-T) models against remote sensing observations to retrieve key biogeophysical parameters such as leaf area index (LAI) is a common approach. Even if new inversion techniques allow the use of three-dimensional (3D) models for that purpose, onedimensional (1D) models are still widely used because of their ease of implementation and computational efficiency. Nevertheless, they assume a random distribution of foliage elements whereas most canopies show a clumped organization. Due to that crude simplification in the representation of the canopy structure, sizeable discrepancies can occur between 1D simulations and real canopy reflectance, which may further lead to false LAI values. The present investigation aims to appraise to which extent the incorporation of a clumping index (noted l) into 1D R-T model could improve the simulations of Bidirectional Reflectance Distribution Function (BRDF). Canopy BRDF is simulated here for three growth stages of a maize crop with the Discrete Anisotropic Radiative Transfer (DART) model in the visible and near infrared spectral bands, for two contrasted soil types (dark and bright) and different levels of heterogeneity to represent the canopy structure. 3D numerical scenes are based on in-situ structural measurements and associated BRDF simulations are thus considered as references. 1D scenarios assume either that leaves are randomly distributed (l = 1) or clumped (l < 1). If BRDF simulations seem globally reliable under the assumption of a random distribution in near infrared, it can also lead to relative errors on the total BRDF up to 30% in the red spectral band. It comes out that the use of a clumping index in a 1D reflectance model generally improves BRDF simulations in the red considering a bright soil, which seems relatively independent of LAI. In the near infrared, best results are usually obtained with homogeneous canopies, except with the dark soil. Clearly, influent factors are mainly the LAI and the spectral contrast between soil and leaves.

The spatial pattern was characterized in five experimental plots of 0.5 ha established in Scots pine stands located in the Central Mountain Range of Spain with different ecological conditions and in which different silvicultural practises are employed. A new method is proposed to asses the spatial pattern from hemispherical photographs, based on the variance between the gap fractions in sky sectors, which was calculated as a function of the angular distance. The results were compared with the spatial pattern analysis based on the second moment measure, and with the analysis of the structure of the tree number semivariogram. The three methods give a very similar scale of the pattern for most of the plots. The mature plot with more intensive silviculture showed a regular pattern at scales below 6 m. The mature plot in which the silviculture was less intensive showed a cluster pattern at scales around 10 m, and clustering at similar scales was detected during regeneration. Cluster patterns at scales around 5 m were found at the upper limit of the altitudinal range of Scots pine as well as at the lower limit, where Pyrenean oak stands merge with the pinewood. The method proposed allows the scale of the pattern of the canopy to be determined from hemispherical photographs, and can be easily implemented in forest inventories. © 2007 Elsevier B.V. All rights reserved.

* Simple models of light interception are useful to identify the key structural parameters involved in light capture. We developed such models for isolated trees and tested them with virtual experiments. Light interception was decomposed into the projection of the crown envelope and the crown porosity. The latter was related to tree structure parameters. * Virtual experiments were conducted with three-dimensional (3-D) digitized apple trees grown in Lebanon and Switzerland, with different cultivars and training. The digitized trees allowed actual values of canopy structure (total leaf area, crown volume, foliage inclination angle, variance of leaf area density) and light interception properties (projected leaf area, silhouette to total area ratio, porosity, dispersion parameters) to be computed, and relationships between structure and interception variables to be derived. * The projected envelope area was related to crown volume with a power function of exponent 2/3. Crown porosity was a negative exponential function of mean optical density, that is, the ratio between total leaf area and the projected envelope area. The leaf dispersion parameter was a negative linear function of the relative variance of leaf area density in the crown volume. * The resulting models were expressed as two single equations. After calibration, model outputs were very close to values computed from the 3-D digitized databases.

International audience; Light models for vegetation canopies based on the turbid medium analogy are usually limited by the basic assumption of random foliage dispersion in the canopy space. The objective of this paper was to assess the effect of three possible sources of non-randomness in tree canopies on light interception properties. For this purpose, four three-dimensional (3-D) digitized trees and four theoretical canopies – one random and three built from fractal rules – were used to compute canopy structure parameters and light interception, namely the sky-vault averaged STAR (Silhouette to Total Area Ratio). STAR values were computed from (1) images of the 3-D plants, and (2) from a 3-D turbid medium model using space discretization at different scales. For all trees, departure from randomness was mainly due to the spatial variations in leaf area density within the canopy volume. Indeed STAR estimations, based on turbid medium assumption, using the finest space discretization were very close to STAR values computed from the plant images. At this finest scale, foliage dispersion was slightly clumped, except one theoretical fractal canopy, which showed a marked regular dispersion. Taking into account a non-infinitely small leaf size, whose effect is theoretically to shorten self-shading, had a minor effect on STAR computations. STAR values computed from the 3-D turbid medium were very sensitive to plant lacunarity, a parameter introduced in the context of fractal studies to characterize the distribution of gaps in porous media at different scales. This study shows that 3-D turbid medium models based on space discretization are able to give correct estimation of light interception by 3-D isolated trees, provided that the 3-D grid is properly defined, that is, discretization maximizes plant lacunarity.

Although a significant number of behavioral studies of desert tenebrionids have been done, almost nothing is recorded of Trichoton sordidum (LeConte) (Coleoptera: Tenebrionidae), an inhabitant of the sunny, sparsely vegetated US/Mexican borderlands. For this small, flightless beetle successful predator evasion and adaptation to a desert environment has required development of complicated, quickly utilizable behavioral mechanisms for regulating exposure to extremes of heat, light, humidity, and habitat structure. In this study, T. sordidum was exposed to sudden changes in temperature, illumination, and habitat complexity, and some patterns representing its normal aggregation were recorded. Minimum Risk Distribution models (Floater 2001) predict changes in spatial distribution patterns of groups of individuals as they are exposed to environmental change. A successful species must have a large percentage of individuals adhering to changes with a set pattern of behaviors. All groups of T. sordidum tested demonstrated both rapid and cohesive dispersal patterns. They normally showed little tendency toward clustering, except clear adhesive aggregation patterns in cases of limited resources in a fragmented environment. Under conditions of extreme heat or light, aggregations in the form of clumping did occur. The formation of clumps from simple two-stacks to groups of up to ten is documented here. The sophistication, consistency of use, and rapid initiation of clumps suggest clumping might well be a highly evolved and successful mechanism for group threat evasion. The morphology of T. sordidum shows how clumping is achieved. An examination of the conditions leading to clumping gives clues to why clumps are formed. Abbreviation: MRD: Minimum Risk Distribution: A model of spatial distribution of individuals that results in the minimum number of premature deaths in a population, and leads to maximized population growth (Floater 2001). C-value: A statistical measurement used in this study to quantify relative clump sizes for Trichoton sordidum rather than total number of individuals in a clump. Homogeneous environment: Environment composed only of uniform, similar features with no irregular detail. In this experiment, open areas of sand, cloth, or fine debris were used. Habitat complexity: Structural interference in a habitat which leads to spatial variability. The result is predicted to be a change in the spatial distribution of individuals within the habitat. In this study pebbles were added to the homogeneous environment to break up a uniform surface area.

A typical feature of the long time behavior of continuous super-Brownian motion in a stable catalytic medium is the development of large mass clumps (or clusters) at spatially rare sites. We describe this phenomenon by means of a functional limit theorem under renormalization. The limiting process is a Poisson point field of mass clumps with no spatial motion component and with infinite variance. The mass of each cluster evolves independently according to a non-Markovian continuous process trapped at mass zero, which we describe explicitly by means of a Brownian snake construction in a random medium. We also determine the survival probability and asymptotic size of the clumps.

The Chen-Stein method of Poisson approximation has been used to establish theorems about comparison of two DNA or protein sequences. The most useful result for sequence alignment applies to alignment scoring with no gaps. However, there has not been a valid method to assign statistical significance to alignment scores with gaps. In this paper we extend Poisson approximation techniques using the Aldous clumping heuristic to a practical method of estimating statistical significance.

For critical spatially homogeneous branching processes of finite intensity the following dichotomy is well-known: convergence to non-trivial steady states, or local extinction. In the latter case the underlying phenomenon is the growth of large clumps at spatially rare sites. For this situation a precise description is given in terms of a scaling limit theorem provided that the dimension of the ambient space is small enough. In fact, a space-time-mass scaling limit exists and is a critical measure-valued branching process without a motion component. The clumps are located at Poissonian points and their sizes evolve according to critical continuous-state Galton-Watson processes. The spatial irregularities (intermittency) will grow in the sense that clumps will disappear as time increases in spite of the fact that the overall density remains constant in time.