Crystallization and preliminary X-ray diffraction analysis of three myotoxic phospholipases A2 from Bothrops brazili venom

Two myotoxic and noncatalytic Lys49-phospholipases A2 (braziliantoxin-II and MT-II) and a myotoxic and catalytic phospholipase A2 (braziliantoxin-III) from the venom of the Amazonian snake Bothrops brazili were crystallized. The crystals diffracted to resolutions in the range 2.562.05 angstrom and belonged to space groups P3121 (braziliantoxin-II), P6522 (braziliantoxin-III) and P21 (MT-II). The structures were solved by molecular-replacement techniques. Both of the Lys49-phospholipases A2 (braziliantoxin-II and MT-II) contained a dimer in the asymmetric unit, while the Asp49-phospholipase A2 braziliantoxin-III contained a monomer in its asymmetric unit. Analysis of the quaternary assemblies of the braziliantoxin-II and MT-II structures using the PISA program indicated that both models have a dimeric conformation in solution. The same analysis of the braziliantoxin-III structure indicated that this protein does not dimerize in solution and probably acts as a monomer in vivo, similar to other snake-venom Asp49-phospholipases A2.

Simcluster: clustering enumeration gene expression data on the simplex space

Abstract Background Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these measurements constitute compositional data exhibiting properties particular to the simplex space where the summation of the components is constrained. These properties are not present on regular Euclidean spaces, on which hybridization-based microarray data is often modeled. Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this space. Results Here we present a software tool, Simcluster, designed to perform clustering analysis for data on the simplex space. We present Simcluster as a stand-alone command-line C package and as a user-friendly on-line tool. Both versions are available at: http://xerad.systemsbiology.net/simcluster. Conclusion Simcluster is designed in accordance with a well-established mathematical framework for compositional data analysis, which provides principled procedures for dealing with the simplex space, and is thus applicable in a number of contexts, including enumeration-based gene expression data.

SEM analysis and push-out bond strength of fiberglass posts luted with different cements of glass-ionomer in humid environment: pilot test

The objective of this study was to evaluate the push-out bond strength of fiberglass resin reinforced bonded with five ionomer cements. Also, the interface between cement and dentin was inspected by means of SEM. Fifty human canines were chose after rigorous scrutiny process, endodontically treated and divided randomly into five groups (n = 3) according to cement tested: Group I – Ionoseal (VOCO), Group II – Fugi I (GC), Group III – Fugi II Improved (GC), Group IV – Rely X Luting 2 (3M ESPE), Group V – Ketac Cem (3M ESPE). The post-space was prepared to receive a fiberglass post, which was tried before cementation process. No dentin or post surface pretreatment was carried out. After post bonding, all roots were cross-sectioned to acquire 3 thin-slices (1 mm) from three specific regions of tooth (cervical, medium and apical). A Universal test machine was used to carry out the push-out test with cross-head speed set to 0.5mm/mim. All failed specimens were observed under optical microscope to identify the failure mode. Representative specimens from each group was inspected under SEM. The data were analyzed by Kolmogorov-Smirnov and Levene’s tests and by two-way ANOVA, and Tukey’s port hoc test at a significance level of 5%. It was compared the images obtained for determination of types of failures more occurred in different levels. SEM inspection displayed that all cements filled the space between post and dentin, however, some imperfections such bubles and voids were noticed in all groups in some degree of extension. The push-out bond strength showed that cement Ketac Cem presented significant higher results when compared to the Ionoseal (P = 0.02). There were no statistical significant differences among other cements.

Aesthetic analysis of an implant-supported denture at the cleft area

Objective: To evaluate the aesthetics of an implant-supported denture at the cleft area, comparing the peri-implant tissues and prosthetic crown with the contralateral tooth. Settings: Hospital for Rehabilitation of Craniofacial Anomalies, Bauru, São Paolo, Brazil. Patients: A total of 39 individuals of both genders, with complete unilateral cleft lip and palate, who received secondary alveolar bone graft and were rehabilitated with single implant-supported dentures at the area of the missing maxillary lateral incisor after completion of orthodontic treatment. Interventions: The following parameters were analyzed in follow-up sessions: length and width of prosthetic crown and contralateral tooth, characteristics of implants, filling of interproximal space by the papilla, and smile height of the patients. Results: The implant-supported prosthetic crowns were longer than the contralateral tooth (p < .001). Among the 78 papillae analyzed, 29 (37.17%) received a score of 3; 32 (41.02%) papillae had a score of 2; and 17 (21.79%) received a score of 1. Concerning the smile height, among the 39 patients analyzed, 23 (56.41%) had a medium smile, 15 (38.46%) had a high smile, and two (5.12%) presented a low smile. Conclusion: The use of dental implants to rehabilitate the edentulous cleft area is an excellent option. However, adequate evaluation of the bone quantity and quality, positioning and shape of adjacent teeth, smile height, and patient expectations should be considered to achieve success and avoid aesthetic deformities such as elongated teeth and absence of gingival papillae.

Morphometric analysis of the placenta in the New World mouse Necromys lasiurus (Rodentia, Cricetidae): a comparison of placental development in cricetids and murids

Background: Stereology is an established method to extrapolate three-dimensional quantities from two-dimensional images. It was applied to placentation in the mouse, but not yet for other rodents. Herein, we provide the first study on quantitative placental development in a sigmodontine rodent species with relatively similar gestational time. Placental structure was also compared to the mouse, in order to evaluate similarities and differences in developmental patterns at the end of gestation. Methods: Fetal and placental tissues of Necromys lasiurus were collected and weighed at 3 different stages of gestation (early, mid and late gestation) for placental stereology. The total and relative volumes of placenta and of its main layers were investigated. Volume fractions of labyrinth components were quantified by the One Stop method in 31 placentae collected from different individuals, using the Mercator® software. Data generated at the end of gestation from N. lasiurus placentae were compared to those of Mus musculus domesticus obtained at the same stage. Results: A significant increase in the total absolute volumes of the placenta and its main layers occurred from early to mid-gestation, followed by a reduction near term, with the labyrinth layer becoming the most prominent area. Moreover, at the end of gestation, the total volume of the mouse placenta was significantly increased compared to that of N. lasiurus although the proportions of the labyrinth layer and junctional zones were similar. Analysis of the volume fractions of the components in the labyrinth indicated a significant increase in fetal vessels and sinusoidal giant cells, a decrease in labyrinthine trophoblast whereas the proportion of maternal blood space remained stable in the course of gestation. On the other hand, in the mouse, volume fractions of fetal vessels and sinusoidal giant cells decreased whereas the volume fraction of labyrinthine trophoblast increased compared to N. lasiurus placenta. Conclusions: Placental development differed between N. lasiurus and M. musculus domesticus. In particular, the low placental efficiency in N. lasiurus seemed to induce morphological optimization of fetomaternal exchanges. In conclusion, despite similar structural aspects of placentation in these species, the quantitative dynamics showed important differences.

Spontaneous combined rupture of a pelvicalyceal cyst into the collector system and retroperitoneal space during the acquisition of computed tomography scan images: a case report

Abstract Introduction Pelvicalyceal cysts are common findings in autopsies and can manifest with a variety of patterns. These cystic lesions are usually a benign entity with no clinical significance unless they enlarge enough to cause compression of the adjacent collecting system and consequently obstructive uropathy. Few cases of the spontaneous rupture of pelvicalyceal renal cysts have been published and to the best of our knowledge there is no report of a combined rupture to collector system and retroperitoneal space documented during a multiphase computed tomography. Case presentation We report a case of a ‘real-time’ spontaneous rupture of a pelvicalyceal cyst into the collecting system with fistulization into the retroperitoneum. The patient was a 78-year-old Caucasian man with a previous history of renal stones and a large pelvicalyceal renal cyst who was admitted to our Emergency department with acute right flank pain. A multiphase computed tomography was performed and the pre-contrast images demonstrated a right pelvicalyceal renal cyst measuring 12.0 × 6.1cm in the lower pole causing moderate dilation of the upper right renal collection system. In addition, a partially obstructive stone on the left distal ureter with mild left hydronephrosis was noted. The nephrographic phase did not add any new information. The excretory phase (10-minute delay) demonstrated a spontaneous rupture of the cyst into the pelvicalyceal system with posterior fistulization into the retroperitoneal space. Conclusion In this case study we present time-related changes of a rare pelvicalyceal cyst complication, which to the best of our knowledge has fortunately not been previously documented. Analysis of the sequential images and comparison with an earlier scan allowed us to better understand the physiopathological process of the rupture, the clinical presentation and to elaborate hypotheses for its etiopathogenesis.

Relationship between space distribution of the benthic macroinvertebrates community and trophic state in a Neotropical reservoir (Itupararanga, Brazil)

The purpose of this work was to verify the benthic macroinvertebrates community responses through environmental factors along a headwater tropical reservoir. Samplings were taken with a Van-Veen grab along the reservoir in littoral and profundal regions and in the headwater, next to the dam and the middle of the reservoir. Samples were taken during both wet and dry seasons. Dissolved oxygen concentrations, electric conductivity, temperature and pH near the sediment have been performed in situ, at every sampling station by using a multiprobe and Secchi disc. Total water phosphorus and chlorophyll a concentrations were analyzed to determine the trophic state index. Sediment's organic matter, total phosphorus, nitrogen concentrations and granulometric composition were measured. In order to verify which environmental variables would have more influence over the benthic macroinvertebrates community, a canonical correspondence analysis (CCA) was performed. The total number of recorded taxa was 28. Among them, the family Chironomidae (Diptera) was the richest group (19 taxa). It can be proposed that the benthic macroinvertebrates community may be influenced by environmental conditions such as nutrient and organic matter availability, as well as dissolved oxygen concentration. Macroinvertebrates are adequate bioindicators of water quality due to their sensibility to environmental changes mentioned before. Chironomus sp, Limnodrilus hoffmeisteri and Branchiura sowerbyi comprises a group that can be considered bio-indicators of eutrophic conditions. A second group can be considered as indicator of mesotrophic conditions. The presence of two or more members from that group which comprises Tanytarsini spp, Fissimentum sp, Pelomus sp and Goeldichironomus sp, like predominant taxa, may indicates mesotrophic conditions.

Shear force and torsion in reinforced concrete beam elements: theoretical analysis based on Brazilian Standard Code ABNT NBR 6118:2007

Reinforced concrete beam elements are submitted to applicable loads along their life cycle that cause shear and torsion. These elements may be subject to only shear, pure torsion or both, torsion and shear combined. The Brazilian Standard Code ABNT NBR 6118:2007 [1] fixes conditions to calculate the transverse reinforcement area in beam reinforced concrete elements, using two design models, based on the strut and tie analogy model, first studied by Mörsch [2]. The strut angle θ (theta) can be considered constant and equal to 45º (Model I), or varying between 30º and 45º (Model II). In the case of transversal ties (stirrups), the variation of angle α (alpha) is between 45º and 90º. When the equilibrium torsion is required, a resistant model based on space truss with hollow section is considered. The space truss admits an inclination angle θ between 30º and 45º, in accordance with beam elements subjected to shear. This paper presents a theoretical study of models I and II for combined shear and torsion, in which ranges the geometry and intensity of action in reinforced concrete beams, aimed to verify the consumption of transverse reinforcement in accordance with the calculation model adopted As the strut angle on model II ranges from 30º to 45º, transverse reinforcement area (Asw) decreases, and total reinforcement area, which includes longitudinal torsion reinforcement (Asℓ), increases. It appears that, when considering model II with strut angle above 40º, under shear only, transverse reinforcement area increases 22% compared to values obtained using model I.

Space-temporal dynamics of limnological variables in a floodplain wetland located at Ribeira do Iguape Valley (São Paulo, Brazil) at different hydrological periods

AIM: The main goal of this research was to investigate the influence of the hydrological pulses on the space-temporal dynamics of physical and chemical variables in a wetland adjacent to Jacupiranguinha River (São Paulo, Brazil); METHODS: Eleven sampling points were distributed among the wetland, a tributary by its left side and the adjacent river. Four samplings were carried out, covering the rainy and the dry periods. Measures of pH, dissolved oxygen, electrical conductivity and redox potential were taken in regular intervals of the water column using a multiparametric probe. Water samples were collected for the nitrogen and total phosphorus analysis, as well as their dissolved fractions (dissolved inorganic phosphorus, total dissolved phosphorus, ammoniacal nitrogen and nitrate). Total alkalinity and suspended solids were also quantified; RESULTS: The Multivariate Analysis of Variance showed the influence of the seasonality on the variability of the investigated variables, while the Principal Component Analysis gave rise in two statistical significant axes, which delimited two groups representative of the rainy and dry periods. Hydrological pulses from Jacupiranguinha River, besides contributing to the inputs of nutrients and sediments during the period of connectivity, accounted for the decrease in spatial gradients in the wetland. This "homogenization effect" was evidenced by the Cluster Analysis. The research also showed an industrial raw effluent as the main point source of phosphorus to the Jacupiranguinha River and, indirectly, to the wetland; CONCLUSIONS: Therefore, considering the scarcity of information about the wetlands in the study area, this research, besides contributing to the understanding of the influence of hydrological pulses on the investigated environmental variables, showed the need for adoption of conservation policies of these ecosystems face the increase anthropic pressures that they have been submitted, which may result in lack of their ecological, social and economic functions.

A scale-space aproach to nonlocal optical flow calculations

[EN] This paper presents an interpretation of a classic optical flow method by Nagel and Enkelmann as a tensor-driven anisotropic diffusion approach in digital image analysis. We introduce an improvement into the model formulation, and we establish well-posedness results for the resulting system of parabolic partial differential equations. Our method avoids linearizations in the optical flow constraint, and it can recover displacement fields which are far beyond the typical one-pixel limits that are characteristic for many differential methods for optical flow recovery. A robust numerical scheme is presented in detail. We avoid convergence to irrelevant local minima by embedding our method into a linear scale-space framework and using a focusing strategy from coarse to fine scales. The high accuracy of the proposed method is demonstrated by means of a synthetic and a real-world image sequence.

Non-Markovian stochastic processes and their applications: from anomalous diffusion to time series analysis

This work provides a forward step in the study and comprehension of the relationships between stochastic processes and a certain class of integral-partial differential equation, which can be used in order to model anomalous diffusion and transport in statistical physics. In the first part, we brought the reader through the fundamental notions of probability and stochastic processes, stochastic integration and stochastic differential equations as well. In particular, within the study of H-sssi processes, we focused on fractional Brownian motion (fBm) and its discrete-time increment process, the fractional Gaussian noise (fGn), which provide examples of non-Markovian Gaussian processes. The fGn, together with stationary FARIMA processes, is widely used in the modeling and estimation of long-memory, or long-range dependence (LRD). Time series manifesting long-range dependence, are often observed in nature especially in physics, meteorology, climatology, but also in hydrology, geophysics, economy and many others. We deepely studied LRD, giving many real data examples, providing statistical analysis and introducing parametric methods of estimation. Then, we introduced the theory of fractional integrals and derivatives, which indeed turns out to be very appropriate for studying and modeling systems with long-memory properties. After having introduced the basics concepts, we provided many examples and applications. For instance, we investigated the relaxation equation with distributed order time-fractional derivatives, which describes models characterized by a strong memory component and can be used to model relaxation in complex systems, which deviates from the classical exponential Debye pattern. Then, we focused in the study of generalizations of the standard diffusion equation, by passing through the preliminary study of the fractional forward drift equation. Such generalizations have been obtained by using fractional integrals and derivatives of distributed orders. In order to find a connection between the anomalous diffusion described by these equations and the long-range dependence, we introduced and studied the generalized grey Brownian motion (ggBm), which is actually a parametric class of H-sssi processes, which have indeed marginal probability density function evolving in time according to a partial integro-differential equation of fractional type. The ggBm is of course Non-Markovian. All around the work, we have remarked many times that, starting from a master equation of a probability density function f(x,t), it is always possible to define an equivalence class of stochastic processes with the same marginal density function f(x,t). All these processes provide suitable stochastic models for the starting equation. Studying the ggBm, we just focused on a subclass made up of processes with stationary increments. The ggBm has been defined canonically in the so called grey noise space. However, we have been able to provide a characterization notwithstanding the underline probability space. We also pointed out that that the generalized grey Brownian motion is a direct generalization of a Gaussian process and in particular it generalizes Brownain motion and fractional Brownain motion as well. Finally, we introduced and analyzed a more general class of diffusion type equations related to certain non-Markovian stochastic processes. We started from the forward drift equation, which have been made non-local in time by the introduction of a suitable chosen memory kernel K(t). The resulting non-Markovian equation has been interpreted in a natural way as the evolution equation of the marginal density function of a random time process l(t). We then consider the subordinated process Y(t)=X(l(t)) where X(t) is a Markovian diffusion. The corresponding time-evolution of the marginal density function of Y(t) is governed by a non-Markovian Fokker-Planck equation which involves the same memory kernel K(t). We developed several applications and derived the exact solutions. Moreover, we considered different stochastic models for the given equations, providing path simulations.

Pattern recognition analysis on heavy ion reaction data

One of the problems in the analysis of nucleus-nucleus collisions is to get information on the value of the impact parameter b. This work consists in the application of pattern recognition techniques aimed at associating values of b to groups of events. To this end, a support vec- tor machine (SVM) classifier is adopted to analyze multifragmentation reactions. This method allows to backtracing the values of b through a particular multidimensional analysis. The SVM classification con- sists of two main phase. In the first one, known as training phase, the classifier learns to discriminate the events that are generated by two different model:Classical Molecular Dynamics (CMD) and Heavy- Ion Phase-Space Exploration (HIPSE) for the reaction: 58Ni +48 Ca at 25 AMeV. To check the classification of events in the second one, known as test phase, what has been learned is tested on new events generated by the same models. These new results have been com- pared to the ones obtained through others techniques of backtracing the impact parameter. Our tests show that, following this approach, the central collisions and peripheral collisions, for the CMD events, are always better classified with respect to the classification by the others techniques of backtracing. We have finally performed the SVM classification on the experimental data measured by NUCL-EX col- laboration with CHIMERA apparatus for the previous reaction.

Topological analysis of singularity loci for serial and parallel manipulators

Singularities of robot manipulators have been intensely studied in the last decades by researchers of many fields. Serial singularities produce some local loss of dexterity of the manipulator, therefore it might be desirable to search for singularityfree trajectories in the jointspace. On the other hand, parallel singularities are very dangerous for parallel manipulators, for they may provoke the local loss of platform control, and jeopardize the structural integrity of links or actuators. It is therefore utterly important to avoid parallel singularities, while operating a parallel machine. Furthermore, there might be some configurations of a parallel manipulators that are allowed by the constraints, but nevertheless are unreachable by any feasible path. The present work proposes a numerical procedure based upon Morse theory, an important branch of differential topology. Such procedure counts and identify the singularity-free regions that are cut by the singularity locus out of the configuration space, and the disjoint regions composing the configuration space of a parallel manipulator. Moreover, given any two configurations of a manipulator, a feasible or a singularity-free path connecting them can always be found, or it can be proved that none exists. Examples of applications to 3R and 6R serial manipulators, to 3UPS and 3UPU parallel wrists, to 3UPU parallel translational manipulators, and to 3RRR planar manipulators are reported in the work.

BEM-FEM coupling model for the dynamic analysis of piles and pile groups

[EN] This paper shows a BEM-FEM coupling model for the time harmonic dynamic analysis of piles and pile groups embeddes in an elastic half-space. Piles are modelled using Finite Elements (FEM) as a beam according to the Bernoulli hypothesis, while the soil modelled using  Boundary Elements (BEM) as a continuum, semi-infinite, isotropic, homogeneous or zoned homogeneous, linear, viscoelastic medium.

Mesh Generation for Isogeometric Analysis with T-spline

[EN]The application of the Isogeometric Analysis (IA) with T-splines [1] demands a partition of the parametric space, C, in a tiling containing T-junctions denominated T-mesh. The T-splines are used both for the geometric modelization of the physical domain, D, and the basis of the numerical approximation. They have the advantage over the NURBS of allowing local refinement. In this work we propose a procedure to construct T-spline representations of complex domains in order to be applied to the resolution of elliptic PDE with IA. In precedent works [2, 3] we accomplished this task by using a tetrahedral parametrization…