Spatial patterns or trees in the Picinguara coastal sandy forest (state of Sao-Paulo, Brazil)

The species of the sandy plains forests (forests of the ''restingas'') have not yet had their spatial patterns studied as aids to the understanding of the diversity found in the different physiognomies along the Brazilian coast. In this paper a 10 x 10 m quadrat framework laid in a hectare of a tree dominant forest in the sandy plains of the Picinguaba area of the Serra do Mar State Park (municipality of Ubatuba, state of São Paulo, Brazil) was used to assess the spatial pattern of distribution for the ten most important species : Pera glabrata, Euterpe edulis, Eugenia brasiliensis, Alchornea triplinervea, Guatteria australis, Myrcia racemosa, Jacaranda semiserrata, Guarea macrophylla, Euplassa cantareirae and Nectandra oppositifolia. The spatial patterns were inferred through the calculations of their T-Square Index (C) and Dispersal Distance Index (I). P. glabrata shows a random pattern, E. edulis aggregate, E. brasiliensis, A. triplinervia, G. australis, E. cantareirae and N. oppositifolia with a tendency between aggregate and uniform and, M. racemosa, J. semiserrata and G. macrophylla between aggregate and random. Although the indexes are dependent of the sample size and of the technique adjustments, the relationship of the pattern with the environmental factors is shown by clustering methods. The results give confirmation of how the spatial patterns bring associations between populations and shape of the vegetation physiognomy.

Functional and phylogenetic diversity of scattered trees in an agricultural landscape: Implications for conservation

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Automatic Design of Boolean Networks for Modelling Differentiation Trees

Real living cell is a complex system governed by many process which are not yet fully understood: the process of cell differentiation is one of these. In this thesis work we make use of a cell differentiation model to develop gene regulatory networks (Boolean networks) with desired differentiation dynamics. To accomplish this task we have introduced techniques of automatic design and we have performed experiments using various differentiation trees. The results obtained have shown that the developed algorithms, except the Random algorithm, are able to generate Boolean networks with interesting differentiation dynamics. Moreover, we have presented some possible future applications and developments of the cell differentiation model in robotics and in medical research. Understanding the mechanisms involved in biological cells can gives us the possibility to explain some not yet understood dangerous disease, i.e the cancer. Le cellula è un sistema complesso governato da molti processi ancora non pienamente compresi: il differenziamento cellulare è uno di questi. In questa tesi utilizziamo un modello di differenziamento cellulare per sviluppare reti di regolazione genica (reti Booleane) con dinamiche di differenziamento desiderate. Per svolgere questo compito abbiamo introdotto tecniche di progettazione automatica e abbiamo eseguito esperimenti utilizzando vari alberi di differenziamento. I risultati ottenuti hanno mostrato che gli algoritmi sviluppati, eccetto l'algoritmo Random, sono in grado di poter generare reti Booleane con dinamiche di differenziamento interessanti. Inoltre, abbiamo presentato alcune possibili applicazioni e sviluppi futuri del modello di differenziamento in robotica e nella ricerca medica. Capire i meccanismi alla base del funzionamento cellulare può fornirci la possibilità di spiegare patologie ancora oggi non comprese, come il cancro.

Inputs to parasol ganglion cells in the primate retina

Retinal ganglion cells carry signals from the eye to the brain. One of the most common types of ganglion cells is parasol cells. They have larger dendritic trees, somas and axons than other ganglion cells. While much was known about parasol cell light responses, little was known about how these responses are formed. One possibility is that they receive input from a unique set of local circuit neurons that have similar responses. The goal was to identify these presynaptic neurons and study their synaptic connectivity.^ Ganglion cells receive input from bipolar and amacrine cells, but there are numerous subtypes of each. To determine which of these were most likely to provide input to parasol cells, the parasol cells were intracellularly-injected and then various bipolar and amacrine cells were immunolabeled and the tissue analyzed using a confocal microscope. DB3 bipolar cells labeled with antibodies to calbindin made extensive contacts with OFF parasol cells. Antibodies to recover in labeled flat midget bipolar cells (FMB). They made only random contacts with OFF parasol cells, and they are not expected to provide significant input. Type DB2 bipolar cells and FMB cells labeled with antibodies to excitatory amino acid transporter-2 made extensive contacts with OFF parasol cells. This suggests that DB2 bipolar cells are likely to provide input to parasol cells.^ Two types of amacrine cells were labeled in material containing injected parasol cells. Cholinergic amacrine cells were labeled with antibodies to choline acetyltransferase, and they made extensive contacts with ON parasol cells. The large amacrine cells labeled with antibodies to a precursor of cholecystokinin were among the amacrine cells that are tracer-coupled to parasol cells.^ From electron microscopic (EM) analysis, most of the synapses made by DB3 axons were found on varicosities. Some postsynaptic and presynaptic amacrine cells resembled AII amacrine cells. Others were relatively electron-lucent and may be cholinergic amacrine cells or cholecystokinin-containing amacrine cells. Gap junctions were found between neighboring DB3 axons. They occurred whenever two axons contacted each other, and the junctions were as large as the area of contact. In double-label EM experiments, DB3 axons made synapses onto OFF parasol cells. ^

Effect of nonnormal random components on level and power in group-randomized trials

The use of group-randomized trials is particularly widespread in the evaluation of health care, educational, and screening strategies. Group-randomized trials represent a subset of a larger class of designs often labeled nested, hierarchical, or multilevel and are characterized by the randomization of intact social units or groups, rather than individuals. The application of random effects models to group-randomized trials requires the specification of fixed and random components of the model. The underlying assumption is usually that these random components are normally distributed. This research is intended to determine if the Type I error rate and power are affected when the assumption of normality for the random component representing the group effect is violated. ^ In this study, simulated data are used to examine the Type I error rate, power, bias and mean squared error of the estimates of the fixed effect and the observed intraclass correlation coefficient (ICC) when the random component representing the group effect possess distributions with non-normal characteristics, such as heavy tails or severe skewness. The simulated data are generated with various characteristics (e.g. number of schools per condition, number of students per school, and several within school ICCs) observed in most small, school-based, group-randomized trials. The analysis is carried out using SAS PROC MIXED, Version 6.12, with random effects specified in a random statement and restricted maximum likelihood (REML) estimation specified. The results from the non-normally distributed data are compared to the results obtained from the analysis of data with similar design characteristics but normally distributed random effects. ^ The results suggest that the violation of the normality assumption for the group component by a skewed or heavy-tailed distribution does not appear to influence the estimation of the fixed effect, Type I error, and power. Negative biases were detected when estimating the sample ICC and dramatically increased in magnitude as the true ICC increased. These biases were not as pronounced when the true ICC was within the range observed in most group-randomized trials (i.e. 0.00 to 0.05). The normally distributed group effect also resulted in bias ICC estimates when the true ICC was greater than 0.05. However, this may be a result of higher correlation within the data. ^

Drought avoidance and the effect of local topography on trees in the understorey of Bornean lowland rain forest

The water relations of two tree species in the Euphorbiaceae were compared to test in part a hypothesis that the forest understorey plays an integral role in drought response. At Danum, Sabah, the relatively common species Dimorphocalyx muricatus is associated with ridges whilst another species, Mallotus wrayi, occurs widely both on ridges and lower slopes. Sets of subplots within two 4 -ha permanent plots in this lowland dipterocarp rain forest, were positioned on ridges and lower slopes. Soil water potentials were recorded in 1995-1997, and leaf water potentials were measured on six occasions. Soil water potentials on the ridges (-0.047 MPa) were significantly lower than on the lower slopes (-0.012 MPa), but during the driest period in May 1997 they fell to similarly low levels on both sites (-0.53 MPa). A weighted 40-day accumulated rainfall index was developed to model the soil water potentials. At dry times, D. muricatus (ridge) had significantly higher pre-dawn (-0.21 v. -0.57 MPa) and mid-day (-0.59 v. -1.77 MPa) leaf water potentials than M. wrayi (mean of ridge and lower slope). Leaf osmotic potentials of M. wrayi on the ridges were lower (-1.63 MPa) than on lower slopes (-1.09 MPa), with those for D. muricatus being intermediate (-1.29 MPa): both species adjusted osmotically between wet and dry times. D. muricatus trees were more deeply rooted than M. wrayi trees (97 v. 70 cm). M. wrayi trees had greater lateral root cross-sectional areas than D. muricatus trees although a greater proportion of this sectional area for D. muricatus was further down the soil profile. D. muricatus appeared to maintain relatively high water potentials during dry periods because of its access to deeper water supplies and thus it largely avoided drought effects, but M. wrayi seemed to be more affected yet tolerant of drought and was more plastic in its response. The interaction between water availability and topography determines these species' distributions and provides insights into how rain forests can withstand occasional strong droughts.

Matchings and phylogenetic trees

This paper presents a natural coordinate system for phylogenetic trees using a correspondence with the set of perfect matchings in the complete graph. This correspondence produces a distance between phylogenetic trees, and a way of enumerating all trees in a minimal step order. It is useful in randomized algorithms because it enables moves on the space of trees that make random optimization strategies “mix” quickly. It also promises a generalization to intermediary trees when data are not decisive as to their choice of tree, and a new way of constructing Bayesian priors on tree space.

Shape anisotropy of a single random-walk polymer

Random walks have been used to describe a wide variety of systems ranging from cell colonies to polymers. Sixty-five years ago, Kuhn [Kuhn, W. (1934) Kolloid-Z. 68, 2–11] made the prediction, backed later by computer simulations, that the overall shape of a random-walk polymer is aspherical, yet no experimental work has directly tested Kuhn's general idea and subsequent computer simulations. By using fluorescence microscopy, we monitored the conformation of individual, long, random-walk polymers (fluorescently labeled DNA molecules) at equilibrium. We found that a polymer most frequently adopts highly extended, nonfractal structures with a strongly anisotropic shape. The ensemble-average ratio of the lengths of the long and short axes of the best-fit ellipse of the polymer was much larger than unity.

Applying network analysis to the conservation of habitat trees in urban environments: a case study from Brisbane, Australia

In Australia more than 300 vertebrates, including 43 insectivorous bat species, depend on hollows in habitat trees for shelter, with many species using a network of multiple trees as roosts, We used roost-switching data on white-striped freetail bats (Tadarida australis; Microchiroptera: Molossidae) to construct a network representation of day roosts in suburban Brisbane, Australia. Bats were caught from a communal roost tree with a roosting group of several hundred individuals and released with transmitters. Each roost used by the bats represented a node in the network, and the movements of bats between roosts formed the links between nodes. Despite differences in gender and reproductive stages, the bats exhibited the same behavior throughout three radiotelemetry periods and over 500 bat days of radio tracking: each roosted in separate roosts, switched roosts very infrequently, and associated with other bats only at the communal roost This network resembled a scale-free network in which the distribution of the number of links from each roost followed a power law. Despite being spread over a large geographic area (> 200 km(2)), each roost was connected to others by less than three links. One roost (the hub or communal roost) defined the architecture of the network because it had the most links. That the network showed scale-free properties has profound implications for the management of the habitat trees of this roosting group. Scale-free networks provide high tolerance against stochastic events such as random roost removals but are susceptible to the selective removal of hub nodes. Network analysis is a useful tool for understanding the structural organization of habitat tree usage and allows the informed judgment of the relative importance of individual trees and hence the derivation of appropriate management decisions, Conservation planners and managers should emphasize the differential importance of habitat trees and think of them as being analogous to vital service centers in human societies.

Irreducibility of Random Hilbert Schemes

We prove that a random Hilbert scheme that parametrizes the closed subschemes with a fixed Hilbert polynomial in some projective space is irreducible and nonsingular with probability greater than $0.5$. To consider the set of nonempty Hilbert schemes as a probability space, we transform this set into a disjoint union of infinite binary trees, reinterpreting Macaulay's classification of admissible Hilbert polynomials. Choosing discrete probability distributions with infinite support on the trees establishes our notion of random Hilbert schemes. To bound the probability that random Hilbert schemes are irreducible and nonsingular, we show that at least half of the vertices in the binary trees correspond to Hilbert schemes with unique Borel-fixed points.

Biased Random-key Genetic Algorithms For The Winner Determination Problem In Combinatorial Auctions.

Abstract In this paper, we address the problem of picking a subset of bids in a general combinatorial auction so as to maximize the overall profit using the first-price model. This winner determination problem assumes that a single bidding round is held to determine both the winners and prices to be paid. We introduce six variants of biased random-key genetic algorithms for this problem. Three of them use a novel initialization technique that makes use of solutions of intermediate linear programming relaxations of an exact mixed integer-linear programming model as initial chromosomes of the population. An experimental evaluation compares the effectiveness of the proposed algorithms with the standard mixed linear integer programming formulation, a specialized exact algorithm, and the best-performing heuristics proposed for this problem. The proposed algorithms are competitive and offer strong results, mainly for large-scale auctions.

Fisionomia e organização da vegetação do carrasco no planalto da Ibiapaba, estado do Ceará

Is the carrasco on the Ibiapaba plateau a unique plant formation? To answer this question the vertical height (except of climbers) and the stem basal diameter (from 3cm on) of woody plants were measured, and soil extracts (0-50 and 50-100cm depth) were taken from 100 random plots (10x10m) at Jaburuna (3º54'34S and 40º59'24W, altitudes near 830m), municipality of Ubajara, Ceará State. Data on climate, soil, diameter height, density, basal area, and physiognomy were compared with those surveyed by other researchers from the carrasco, caatinga, and cerrado in Northeastern Brazil. The carrasco occurs under an annual rainfall of between 668 and 1,289mm and temperatures from 22 to 24ºC, on alic Quartz Sand soils, at altitudes between 700 and 900m: it has a larger density and a smaller basal area than the caatinga and the cerrado, small and similar diameters, and an average vertical height between 3,7 and 5,4m. It differs from the caatinga, cerrado (and cerradão) and secondary forest in many items of lhe ecotope, organization and physiognomy, thus being a unique plain formation, which can be characterized as a deciduous, high, closed, and unistratified shrubland intermingled by lianas, with an irregular canopy and sparse, emergent trees.

Allometric models for estimating the phytomass of a secondary Atlantic Forest area of southeastern Brazil

The purpose of this study was to develop and validate equations to estimate the aboveground phytomass of a 30 years old plot of Atlantic Forest. In two plots of 100 m², a total of 82 trees were cut down at ground level. For each tree, height and diameter were measured. Leaves and woody material were separated in order to determine their fresh weights in field conditions. Samples of each fraction were oven dried at 80 °C to constant weight to determine their dry weight. Tree data were divided into two random samples. One sample was used for the development of the regression equations, and the other for validation. The models were developed using single linear regression analysis, where the dependent variable was the dry mass, and the independent variables were height (h), diameter (d) and d²h. The validation was carried out using Pearson correlation coefficient, paired t-Student test and standard error of estimation. The best equations to estimate aboveground phytomass were: lnDW = -3.068+2.522lnd (r² = 0.91; s y/x = 0.67) and lnDW = -3.676+0.951ln d²h (r² = 0.94; s y/x = 0.56).

Synthesis and structural characterization of block and random low molecular weight copolymers composed of L-lactic acid and isosorbide succinate moieties

Isosorbide succinate moieties were incorporated into poly(L-lactide) (PLLA) backbone in order to obtain a new class of biodegradable polymer with enhanced properties. This paper describes the synthesis and characterization of four types of low molecular weight copolymers. Copolymer I was obtained from monomer mixtures of L-lactide, isosorbide, and succinic anhydride; II from oligo(L-lactide) (PLLA), isosorbide, and succinic anhydride; III from oligo(isosorbide succinate) (PIS) and L-lactide; and IV from transesterification reactions between PLLA and PIS. MALDI-TOFMS and 13C-NMR analyses gave evidence that co-oligomerization was successfully attained in all cases. The data suggested that the product I is a random co-oligomer and the products II-IV are block co-oligomers.

WOOD DENSITY VARIATION AND TREE RING DEMARCATION IN Gmelina arborea TREES USING X-RAY DENSITOMETRY

Due to its relationship with other properties, wood density is the main wood quality parameter. Modern, accurate methods - such as X-ray densitometry - are applied to determine the spatial distribution of density in wood sections and to evaluate wood quality. The objectives of this study were to determinate the influence of growing conditions on wood density variation and tree ring demarcation of gmelina trees from fast growing plantations in Costa Rica. The wood density was determined by X-ray densitometry method. Wood samples were cut from gmelina trees and were exposed to low X-rays. The radiographic films were developed and scanned using a 256 gray scale with 1000 dpi resolution and the wood density was determined by CRAD and CERD software. The results showed tree-ring boundaries were distinctly delimited in trees growing in site with rainfall lower than 25 10 mm/year. It was demonstrated that tree age, climatic conditions and management of plantation affects wood density and its variability. The specific effect of variables on wood density was quantified by for multiple regression method. It was determined that tree year explained 25.8% of the total variation of density and 19.9% were caused by climatic condition where the tree growing. Wood density was less affected by the intensity of forest management with 5.9% of total variation.