The importance of plant life form on spatial associations along a subtropical coastal dune gradient

Questions Does the spatial association between isolated adult trees and understorey plants change along a gradient of sand dunes? Does this association depend on the life form of the understorey plant? Location Coastal sand dunes, southeast Brazil. Methods We recorded the occurrence of understorey plant species in 100 paired 0.25 m2 plots under adult trees and in adjacent treeless sites along an environmental gradient from beach to inland. Occurrence probabilities were modelled as a function of the fixed variables of the presence of a neighbour, distance from the seashore and life form, and a random variable, the block (i.e. the pair of plots). Generalized linear mixed models (GLMM) were fitted in a backward step-wise procedure using Akaike's information criterion (AIC) for model selection. Results The occurrence of understorey plants was affected by the presence of an adult tree neighbour, but the effect varied with the life form of the understorey species. Positive spatial association was found between isolated adult neighbour and young trees, whereas a negative association was found for shrubs. Moreover, a neutral association was found for lianas, whereas for herbs the effect of the presence of an adult neighbour ranged from neutral to negative, depended on the subgroup considered. The strength of the negative association with forbs increased with distance from the seashore. However, for the other life forms, the associational pattern with adult trees did not change along the gradient. Conclusions For most of the understorey life forms there is no evidence that the spatial association between isolated adult trees and understorey plants changes with the distance from the seashore, as predicted by the stress gradient hypothesis, a common hypothesis in the literature about facilitation in plant communities. Furthermore, the positive spatial association between isolated adult trees and young trees identified along the entire gradient studied indicates a positive feedback that explains the transition from open vegetation to forest in subtropical coastal dune environments.

Gaussian deconvolution: a useful method for a form-free modeling of scattering data from mono- and multilayered planar systems

A new method for analysis of scattering data from lamellar bilayer systems is presented. The method employs a form-free description of the cross-section structure of the bilayer and the fit is performed directly to the scattering data, introducing also a structure factor when required. The cross-section structure (electron density profile in the case of X-ray scattering) is described by a set of Gaussian functions and the technique is termed Gaussian deconvolution. The coefficients of the Gaussians are optimized using a constrained least-squares routine that induces smoothness of the electron density profile. The optimization is coupled with the point-of-inflection method for determining the optimal weight of the smoothness. With the new approach, it is possible to optimize simultaneously the form factor, structure factor and several other parameters in the model. The applicability of this method is demonstrated by using it in a study of a multilamellar system composed of lecithin bilayers, where the form factor and structure factor are obtained simultaneously, and the obtained results provided new insight into this very well known system.

The Tomato (Solanum Lycopersicum cv. Micro-Tom) Natural Genetic Variation Rg1 and the DELLA Mutant Procera Control the Competence Necessary to Form Adventitious Roots and Shoots

Despite the wide use of plant regeneration for biotechnological purposes, the signals that allow cells to become competent to assume different fates remain largely unknown. Here, it is demonstrated that the Regeneration1 (Rg1) allele, a natural genetic variation from the tomato wild relative Solanum peruvianum, increases the capacity to form both roots and shoots in vitro; and that the gibberellin constitutive mutant procera (pro) presented the opposite phenotype, reducing organogenesis on either root-inducing medium (RIM) or shoot-inducing medium (SIM). Mutants showing alterations in the formation of specific organs in vitro were the auxin low-sensitivity diageotropica (dgt), the lateral suppresser (ls), and the KNOX-overexpressing Mouse ears (Me). dgt failed to form roots on RIM, Me increased shoot formation on SIM, and the high capacity for in vitro shoot formation of ls contrasted with its recalcitrance to form axillary meristems. Interestingly, Rg1 rescued the in vitro organ formation capacity in proRg1 and dgtRg1 double mutants and the ex vitro low lateral shoot formation in pro and ls. Such epistatic interactions were also confirmed in gene expression and histological analyses conducted in the single and double mutants. Although Me phenocopied the high shoot formation of Rg1 on SIM, it failed to increase rooting on RIM and to rescue the non-branching phenotype of ls. Taken together, these results suggest REGENERATION1 and the DELLA mutant PROCERA as controlling a common competence to assume distinct cell fates, rather than the specific induction of adventitious roots or shoots, which is controlled by DIAGEOTROPICA and MOUSE EARS, respectively.

Correlation between maxillary central incisor crown morphology and mandibular dental arch form in normal occlusion subjects

The aim of this study was to evaluate the correlation between the morphology of the mandibular dental arch and the maxillary central incisor crown. Cast models from 51 Caucasian individuals, older than 15 years, with optimal occlusion, no previous orthodontic treatment, featuring 4 of the 6 keys to normal occlusion by Andrews (the first being mandatory) were observed. The models were digitalized using a 3D scanner, and images of the maxillary central incisor and mandibular dental arch were obtained. These were printed and placed in an album below pre-set models of arches and dental crowns, and distributed to 12 dental surgeons, who were asked to choose which shape was most in accordance with the models and crown presented. The Kappa test was performed to evaluate the concordance among evaluators while the chi-square test was used to verify the association between the dental arch and central incisor morphology, at a 5% significance level. The Kappa test showed moderate agreement among evaluators for both variables of this study, and the chi-square test showed no significant association between tooth shape and mandibular dental arch morphology. It may be concluded that the use of arch morphology as a diagnostic method to determine the shape of the maxillary central incisor is not appropriate. Further research is necessary to assess tooth shape using a stricter scientific basis.

Cross-cultural adaptation of the Safety Attitudes Questionnaire - Short Form 2006 for Brazil

The objective of this study was to perform a cross-cultural adaptation of the Safety Attitudes Questionnaire - Short Form 2006 for Brazil. The instrument was applied in six hospitals in three regions of Brazil. Content, face, and construct validity was performed. Analysis of the instrument's reliability was performed by verifying the items' internal consistency through Cronbach's alpha. The sample was composed of 1301 professionals working in clinical and surgical wards of six hospitals. Confirmatory analysis showed that the model including 41 items was satisfactory. The Portuguese version presented an alpha of 0.89. The item-total correlations among the domains were moderate to strong, except for the domain Stress Recognition. We concluded that the instrument's version adapted to Portuguese and applied in our sample is valid and reliable.

Reliability-based design optimization strategies based on FORM: a review

In deterministic optimization, the uncertainties of the structural system (i.e. dimension, model, material, loads, etc) are not explicitly taken into account. Hence, resulting optimal solutions may lead to reduced reliability levels. The objective of reliability based design optimization (RBDO) is to optimize structures guaranteeing that a minimum level of reliability, chosen a priori by the designer, is maintained. Since reliability analysis using the First Order Reliability Method (FORM) is an optimization procedure itself, RBDO (in its classical version) is a double-loop strategy: the reliability analysis (inner loop) and the structural optimization (outer loop). The coupling of these two loops leads to very high computational costs. To reduce the computational burden of RBDO based on FORM, several authors propose decoupling the structural optimization and the reliability analysis. These procedures may be divided in two groups: (i) serial single loop methods and (ii) unilevel methods. The basic idea of serial single loop methods is to decouple the two loops and solve them sequentially, until some convergence criterion is achieved. On the other hand, uni-level methods employ different strategies to obtain a single loop of optimization to solve the RBDO problem. This paper presents a review of such RBDO strategies. A comparison of the performance (computational cost) of the main strategies is presented for several variants of two benchmark problems from the literature and for a structure modeled using the finite element method.

Matrix-vector multiplication and triangular linear solver using GPGPU for symmetric positive definite matrices derived from elliptic equations

The modern GPUs are well suited for intensive computational tasks and massive parallel computation. Sparse matrix multiplication and linear triangular solver are the most important and heavily used kernels in scientific computation, and several challenges in developing a high performance kernel with the two modules is investigated. The main interest it to solve linear systems derived from the elliptic equations with triangular elements. The resulting linear system has a symmetric positive definite matrix. The sparse matrix is stored in the compressed sparse row (CSR) format. It is proposed a CUDA algorithm to execute the matrix vector multiplication using directly the CSR format. A dependence tree algorithm is used to determine which variables the linear triangular solver can determine in parallel. To increase the number of the parallel threads, a coloring graph algorithm is implemented to reorder the mesh numbering in a pre-processing phase. The proposed method is compared with parallel and serial available libraries. The results show that the proposed method improves the computation cost of the matrix vector multiplication. The pre-processing associated with the triangular solver needs to be executed just once in the proposed method. The conjugate gradient method was implemented and showed similar convergence rate for all the compared methods. The proposed method showed significant smaller execution time.

Evolution of signal form

Visual signals, used for communication both within and between species, vary immensely in the forms that they take. How is it that all this splendour has evolved in nature? Since it is the receiver’s preferences that cause selective pressures on signals, elucidating the mechanism behind the response of the signal receiver is vital to gain a closer understanding of the evolutionary process. In my thesis I have therefore investigated how receivers, represented by chickens, Gallus gallus domesticus, respond to different stimuli displayed on a peck-sensitive computer screen. According to the receiver bias hypothesis, animals and humans often express biases when responding to certain stimuli. These biases develop as by-products of how the recognition mechanism categorises and discriminates between stimuli. Since biases are generated from general stimulus processing mechanisms, they occur irrespective of species and type of signal, and it is often possible to predict the direction and intensity of the biases. One of the results from the experiments in my thesis demonstrates that similar experience in different species may generate similar biases. By giving chickens at least some of the experience of human faces as humans presumably have, the chickens subsequently expressed preferences for the same faces as a group of human subjects. Another kind of experience generated a bias for symmetry. This bias developed in the context of training chickens to recognise two mirror images of an asymmetrical stimulus. Untrained chickens and chickens trained on only one of the mirror images expressed no symmetry preferences. The bias produced by the training regime was for a specific symmetrical stimulus which had a strong resemblance to the familiar asymmetrical exemplar, rather than a general preference for symmetry. A further kind of experience, training chickens to respond to some stimuli but not to others, generated a receiver bias for exaggerated stimuli, whereas chickens trained on reversed stimuli developed a bias for less exaggerated stimuli. To investigate the potential of this bias to drive the evolution of signals towards exaggerated forms, a simplified evolutionary process was mimicked. The stimuli variants rejected by the chickens were eliminated, whereas the selected forms were kept and evolved prior to the subsequent display. As a result, signals evolved into exaggerated forms in all tested stimulus dimensions: length, intensity and area, despite the inclusion of a cost to the sender for using increasingly exaggerated signals. The bias was especially strong and persistent for stimuli varying along the intensity dimension where it remained despite extensive training. All the results in my thesis may be predicted by the receiver bias hypothesis. This implies that biases, developed due to stimuli experience, may be significant mechanisms driving the evolution of signal form.

Transposable elements: structure and dynamic of the autonomous retrotransposon R2 in Arthropoda with non-canonical reproduction

Eukaryotic ribosomal DNA constitutes a multi gene family organized in a cluster called nucleolar organizer region (NOR); this region is composed usually by hundreds to thousands of tandemly repeated units. Ribosomal genes, being repeated sequences, evolve following the typical pattern of concerted evolution. The autonomous retroelement R2 inserts in the ribosomal gene 28S, leading to defective 28S rDNA genes. R2 element, being a retrotransposon, performs its activity in the genome multiplying its copy number through a “copy and paste” mechanism called target primed reverse transcription. It consists in the retrotranscription of the element’s mRNA into DNA, then the DNA is integrated in the target site. Since the retrotranscription can be interrupted, but the integration will be carried out anyway, truncated copies of the element will also be present in the genome. The study of these truncated variants is a tool to examine the activity of the element. R2 phylogeny appears, in general, not consistent with that of its hosts, except some cases (e.g. Drosophila spp. and Reticulitermes spp.); moreover R2 is absent in some species (Fugu rubripes, human, mouse, etc.), while other species have more R2 lineages in their genome (the turtle Mauremys reevesii, the Japanese beetle Popilia japonica, etc). R2 elements here presented are isolated in 4 species of notostracan branchiopods and in two species of stick insects, whose reproductive strategies range from strict gonochorism to unisexuality. From sequencing data emerges that in Triops cancriformis (Spanish gonochoric population), in Lepidurus arcticus (two putatively unisexual populations from Iceland) and in Bacillus rossius (gonochoric population from Capalbio) the R2 elements are complete and encode functional proteins, reflecting the general features of this family of transposable elements. On the other hand, R2 from Italian and Austrian populations of T. cancriformis (respectively unisexual and hermaphroditic), Lepidurus lubbocki (two elements within the same Italian population, gonochoric but with unfunctional males) and Bacillus grandii grandii (gonochoric population from Ponte Manghisi) have sequences that encode incomplete or non-functional proteins in which it is possible to recognize only part of the characteristic domains. In Lepidurus couesii (Italian gonochoric populations) different elements were found as in L. lubbocki, and the sequencing is still in progress. Two hypothesis are given to explain the inconsistency of R2/host phylogeny: vertical inheritance of the element followed by extinction/diversification or horizontal transmission. My data support previous study that state the vertical transmission as the most likely explanation; nevertheless horizontal transfer events can’t be excluded. I also studied the element’s activity in Spanish populations of T. cancriformis, in L. lubbocki, in L. arcticus and in gonochoric and parthenogenetic populations of B. rossius. In gonochoric populations of T. cancriformis and B. rossius I found that each individual has its own private set of truncated variants. The situation is the opposite for the remaining hermaphroditic/parthenogenetic species and populations, all individuals sharing – in the so far analyzed samples - the majority of variants. This situation is very interesting, because it isn’t concordant with the Muller’s ratchet theory that hypothesizes the parthenogenetic populations being either devoided of transposable elements or TEs overloaded. My data suggest a possible epigenetic mechanism that can block the retrotransposon activity, and in this way deleterious mutations don’t accumulate.

Theoretical investigation of the interaction of a polymer film with a nanoparticle

The fundamental aim in our investigation of the interaction of a polymer film with a nanoparticle is the extraction of information on the dynamics of the liquid using a single tracking particle. In this work two theoretical methods were used: one passive, where the motion of the particle measures the dynamics of the liquid, one active, where perturbations in the system are introduced through the particle. In the first part of this investigation a thin polymeric film on a substrate is studied using molecular dynamics simulations. The polymer is modeled via a 'bead spring' model. The particle is spheric and non structured and is able to interact with the monomers via a Lennard Jones potential. The system is micro-canonical and simulations were performed for average temperatures between the glass transition temperature of the film and its dewetting temperature. It is shown that the stability of the nanoparticle on the polymer film in the absence of gravity depends strongly on the form of the chosen interaction potential between nanoparticle and polymer. The relative position of the tracking particle to the liquid vapor interface of the polymer film shows the glass transition of the latter. The velocity correlation function and the mean square displacement of the particle has shown that it is caged when the temperature is close to the glass transition temperature. The analysis of the dynamics at long times shows the coupling of the nanoparticle to the center of mass of the polymer chains. The use of the Stokes-Einstein formula, which relates the diffusion coefficient to the viscosity, permits to use the nanoparticle as a probe for the determination of the bulk viscosity of the melt, the so called 'microrheology'. It is shown that for low frequencies the result obtained using microrheology coincides with the results of the Rouse model applied to the polymer dynamics. In the second part of this investigation the equations of Linear Hydrodynamics are solved for a nanoparticle oscillating above the film. It is shown that compressible liquids have mechanical response to external perturbations induced with the nanoparticle. These solutions show strong velocity and pressure profiles of the liquid near the interface, as well as a mechanical response of the liquid-vapor interface. The results obtained with this calculations can be employed for the interpretation of experimental results of non contact AFM microscopy

Charakterisierung von apoFNR, einer weiteren Form des Sauerstoffsensors FNR aus Escherichia coli und von NreB, einem potentiellen Sauerstoffsensor aus Staphylococcus carnosus

FNR (Fumarat Nitratreduktase Regulator) ist der Sauerstoffsensor aus Escherichia coli. Bisher waren zwei Formen von FNR bekannt, der aktive Zustand, ein Dimer mit je einem [4Fe4S]-Zentrum und ein inaktiver Zustand, in dem FNR als Monomer mit je einem [2Fe2S]-Zentrum vorliegt. Die Untersuchungen dieser Arbeit geben nun Hinweise, dass es mit apoFNR eine dritte physiologische Form von FNR gibt. Es wurde die Entstehung von apoFNR aus [4Fe4S]•FNR untersucht und die biochemischen Eigenschaften von apoFNR charakterisiert. ApoFNR konnte in vitro zu [4Fe4S]•FNR rekonstituiert werden, hierbei konnte die Lagphase der Rekonstitution durch Zusatz von Glutaredoxinen zum Rekonstitutionsansatz verkürzt werden. FNR, dessen Cysteinreste in vivo unter aeroben bzw. anaeroben Bedingungen mit 4-Acetamido-4´-Maleimidylstilbene-2,2´Disulfonsäure markiert wurden, zeigt auf SDS-Gelen einen Shift zu einer höheren Masse im Vergleich zu unmarkiertem FNR. Allerdings trat in aeroben Zellen eine zusätzliche Bande bei einer niedrigeren Masse auf. Es waren hier also weniger Cysteinreste markierbar. Weiterhin wurde mit NreB ein potentieller Sauerstoffsensor aus Staphylococcus carnosus untersucht. Es wurden Hinweise auf ein Eisen-Schwefel-Zentrum vom FNR-Typ als Cofaktor gefunden. Der Einbau dieses Cofaktors war abhängig von der Anwesenheit der Cysteinreste in NreB, von der Cysteindesulfurase NifSAV und von Eisenionen. Der Cofaktor war sauerstoffempfindlich und beeinflusste die Autophosphorylierung von NreB.

Theoretical and implementation aspects in the mechanization of the metatheory of programming languages

Interactive theorem provers are tools designed for the certification of formal proofs developed by means of man-machine collaboration. Formal proofs obtained in this way cover a large variety of logical theories, ranging from the branches of mainstream mathematics, to the field of software verification. The border between these two worlds is marked by results in theoretical computer science and proofs related to the metatheory of programming languages. This last field, which is an obvious application of interactive theorem proving, poses nonetheless a serious challenge to the users of such tools, due both to the particularly structured way in which these proofs are constructed, and to difficulties related to the management of notions typical of programming languages like variable binding. This thesis is composed of two parts, discussing our experience in the development of the Matita interactive theorem prover and its use in the mechanization of the metatheory of programming languages. More specifically, part I covers: - the results of our effort in providing a better framework for the development of tactics for Matita, in order to make their implementation and debugging easier, also resulting in a much clearer code; - a discussion of the implementation of two tactics, providing infrastructure for the unification of constructor forms and the inversion of inductive predicates; we point out interactions between induction and inversion and provide an advancement over the state of the art. In the second part of the thesis, we focus on aspects related to the formalization of programming languages. We describe two works of ours: - a discussion of basic issues we encountered in our formalizations of part 1A of the Poplmark challenge, where we apply the extended inversion principles we implemented for Matita; - a formalization of an algebraic logical framework, posing more complex challenges, including multiple binding and a form of hereditary substitution; this work adopts, for the encoding of binding, an extension of Masahiko Sato's canonical locally named representation we designed during our visit to the Laboratory for Foundations of Computer Science at the University of Edinburgh, under the supervision of Randy Pollack.

Measurement of the K + - pi + pi - e + - (-) v e form factors and of the pi pi scattering length a 0 0

The quark condensate is a fundamental free parameter of Chiral Perturbation Theory ($chi PT$), since it determines the relative size of the mass and momentum terms in the power expansion. In order to confirm or contradict the assumption of a large quark condensate, on which $chi PT$ is based, experimental tests are needed. In particular, the $S$-wave $pipi$ scattering lengths $a_0^0$ and $a_0^2$ can be predicted precisely within $chi PT$ as a function of this parameter and can be measured very cleanly in the decay $K^{pm} to pi^{+} pi^{-} e^{pm} stackrel{mbox{tiny(---)}}{nu_e}$ ($K_{e4}$). About one third of the data collected in 2003 and 2004 by the NA48/2 experiment were analysed and 342,859 $K_{e4}$ candidates were selected. The background contamination in the sample could be reduced down to 0.3% and it could be estimated directly from the data, by selecting events with the same signature as $K_{e4}$, but requiring for the electron the opposite charge with respect to the kaon, the so-called ``wrong sign'' events. This is a clean background sample, since the kaon decay with $Delta S=-Delta Q$, that would be the only source of signal, can only take place through two weak decays and is therefore strongly suppressed. The Cabibbo-Maksymowicz variables, used to describe the kinematics of the decay, were computed under the assumption of a fixed kaon momentum of 60 GeV/$c$ along the $z$ axis, so that the neutrino momentum could be obtained without ambiguity. The measurement of the form factors and of the $pipi$ scattering length $a_0^0$ was performed in a single step by comparing the five-dimensional distributions of data and MC in the kinematic variables. The MC distributions were corrected in order to properly take into account the trigger and selection efficiencies of the data and the background contamination. The following parameter values were obtained from a binned maximum likelihood fit, where $a_0^2$ was expressed as a function of $a_0^0$ according to the prediction of chiral perturbation theory: f'_s/f_s = 0.133+- 0.013(stat)+- 0.026(syst) f''_s/f_s = -0.041+- 0.013(stat)+- 0.020(syst) f_e/f_s = 0.221+- 0.051(stat)+- 0.105(syst) f'_e/f_s = -0.459+- 0.170(stat)+- 0.316(syst) tilde{f_p}/f_s = -0.112+- 0.013(stat)+- 0.023(syst) g_p/f_s = 0.892+- 0.012(stat)+- 0.025(syst) g'_p/f_s = 0.114+- 0.015(stat)+- 0.022(syst) h_p/f_s = -0.380+- 0.028(stat)+- 0.050(syst) a_0^0 = 0.246+- 0.009(stat)+- 0.012(syst)}+- 0.002(theor), where the statistical uncertainty only includes the effect of the data statistics and the theoretical uncertainty is due to the width of the allowed band for $a_0^2$.