Template-based quadrilateral mesh generation from imaging data

This paper describes a novel template-based meshing approach for generating good quality quadrilateral meshes from 2D digital images. This approach builds upon an existing image-based mesh generation technique called Imeshp, which enables us to create a segmented triangle mesh from an image without the need for an image segmentation step. Our approach generates a quadrilateral mesh using an indirect scheme, which converts the segmented triangle mesh created by the initial steps of the Imesh technique into a quadrilateral one. The triangle-to-quadrilateral conversion makes use of template meshes of triangles. To ensure good element quality, the conversion step is followed by a smoothing step, which is based on a new optimization-based procedure. We show several examples of meshes generated by our approach, and present a thorough experimental evaluation of the quality of the meshes given as examples.     

Reconstruction of cellular biological structures from optical microscopy data

Developments in optical microscopy imaging have generated large high-resolution data sets that have spurred medical researchers to conduct investigations into mechanisms of disease, including cancer at cellular and subcellular levels. The work reported here demonstrates that a suitable methodology can be conceived that isolates modality-dependent effects from the larger segmentation task and that 3D reconstructions can be cognizant of shapes as evident in the available 2D planar images. In the current realization, a method based on active geodesic contours is first deployed to counter the ambiguity that exists in separating overlapping cells on the image plane. Later, another segmentation effort based on a variant of Voronoi tessellations improves the delineation of the cell boundaries using a Bayesian formulation. In the next stage, the cells are interpolated across the third dimension thereby mitigating the poor structural correlation that exists in that dimension. We deploy our methods on three separate data sets obtained from light, confocal, and phase-contrast microscopy and validate the results appropriately.     

Arity and alternation: a proper hierarchy in higher order logics

We study the effect of simultaneously bounding the maximal-arity of the higher-order variables and the alternation of quantifiers in higher-order logics, as to their expressive power on finite structures (or relational databases). Let $\mathit{AA}^i(r,m)$ be the class of (i?+?1)-th order logic formulae where all quantifiers are grouped together at the beginning of the formulae, forming m alternating blocks of consecutive existential and universal quantifiers, and such that the maximal-arity (a generalization of the concept of arity, not just the maximal of the arities of the quantified variables) of the higher-order variables is bounded by r. Note that, the order of the quantifiers in the prefix may be mixed. We show that, for every i?≥?1, the resulting $\mathit{AA}^i(r,m)$ hierarchy of formulae of (i?+?1)-th order logic is proper. This extends a result by Makowsky and Pnueli who proved that the same hierarchy in second-order logic is proper. In both cases the strategy used to prove the results consists in considering formulae which, represented as finite structures, satisfy themselves. As the well known diagonalization argument applies here, this gives rise, for each order i and each level of the $\mathit{AA}^i(r,m)$ hierarchy of arity and alternation, to a class of formulae which is not definable in that level, but which is definable in a higher level of the same hierarchy. We then use a similar argument to prove that the classes of $\Sigma^i_m \cup \Pi^i_m$ formulae in which the higher-order variables of all orders up to i?+?1 have maximal-arity at most r, also induce a proper hierarchy in each higher-order logic of order i?≥?3. It is not known whether the correspondent hierarchy in second-order logic is proper. Using the concept of finite model truth definitions introduced by M. Mostowski, we give a sufficient condition for that to be the case.     

Development of an Autonomous Robot for Gas Storage Spheres Inspection

Inspection for corrosion of gas storage spheres at the welding seam lines must be done periodically. Until now this inspection is being done manually and has a high cost associated to it and a high risk of inspection personel injuries. The Brazilian Petroleum Company, Petrobras, is seeking cost reduction and personel safety by the use of autonomous robot technology. This paper presents the development of a robot capable of autonomously follow a welding line and transporting corrosion measurement sensors. The robot uses a pair of sensors each composed of a laser source and a video camera that allows the estimation of the center of the welding line. The mechanical robot uses four magnetic wheels to adhere to the sphere’s surface and was constructed in a way that always three wheels are in contact with the sphere’s metallic surface which guarantees enough magnetic atraction to hold the robot in the sphere’s surface all the time. Additionally, an independently actuated table for attaching the corrosion inspection sensors was included for small position corrections. Tests were conducted at the laboratory and in a real sphere showing the validity of the proposed approach and implementation.     

To lock, or not to lock: That is the question

Mechanisms to control concurrent access over project artefacts are needed to execute the software development process in an organized way. These mechanisms are implemented by concurrency control policies in version control systems that may inhibit (i.e. ‘to lock’) or allow (i.e., ‘not to lock’) parallel development. This work presents a novel approach named Orion that analyzes the project's historical changes and suggests the most appropriate concurrency control policy for each software element. This suggestion aims at minimizing conflict situations and thus improving the productivity of the development team. In addition, it identifies critical elements that do not work well with any of these policies and are candidates to refactoring. We evaluated Orion through two experimental studies and the results, which indicated it was effective, led us to a prototype implementation. Apart from the Orion approach this paper also presents the planning, execution, and analysis stages of the evaluation, and details of prototype internals.     

From a Conceptual Framework for Agents and Objects to a Multi-Agent System Modeling Language

In this paper we propose a multi-agent system modeling language (MAS-ML) that extends UML (Unified Modeling Language) based on structural and dynamic properties presented in a conceptual framework (metamodel) called Taming Agents and Objects (TAO). Our focus is the adaptation according to TAO concepts of the static Class diagram and the interaction Sequence diagram proposed by UML. These two diagrams have been chosen because they are the most commonly used and because it is possible to use them to illustrate both the structural and dynamic aspects of TAO metamodel. We propose a conservative extension of the UML metamodel, which includes agent-related notions that are part of the TAO conceptual framework while preserving all object-related concepts, which constitute the UML metamodel. The main difference between our approach and the others presented in the literature is the clear definition and representation of the elements that compose MASs and their corresponding behavior. In order to extend UML with TAO non-object concepts, it is not possible to use only the three basic extensions mechanisms provided by UML and new metaclasses and stereotypes have been created and associated with the UML metamodel.     

Oligomerization-Dependent Beta-Structure Formation in SARS-CoV-2 Envelope Protein

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. In SARS-CoV-2, the channel-forming envelope (E) protein is almost identical to the E protein in SARS-CoV, and both share an identical α-helical channel-forming domain. Structures for the latter are available in both detergent and lipid membranes. However, models of the extramembrane domains have only been obtained from solution NMR in detergents, and show no β-strands, in contrast to secondary-structure predictions. Herein, we have studied the conformation of purified SARS-CoV-2 E protein in lipid bilayers that mimic the composition of ER–Golgi intermediate compartment (ERGIC) membranes. The full-length E protein at high protein-to-lipid ratios produced a clear shoulder at 1635 cm⁻¹, consistent with the β-structure, but this was absent when the E protein was diluted, which instead showed a band at around 1688 cm⁻¹, usually assigned to β-turns. The results were similar with a mixture of POPC:POPG (2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine/3-glycerol) and also when using an E-truncated form (residues 8–65). However, the latter only showed β-structure formation at the highest concentration tested, while having a weaker oligomerization tendency in detergents than in full-length E protein. Therefore, we conclude that E monomer–monomer interaction triggers formation of the β-structure from an undefined structure (possibly β-turns) in at least about 15 residues located at the C-terminal extramembrane domain. Due to its proximity to the channel, this β-structure domain could modulate channel activity or modify membrane structure at the time of virion formation inside the cell.     

Biological Solubilisation of Leather Industry Waste in Anaerobic Conditions: Effect of Chromium (III) Presence,Pre-Treatments and Temperature Strategies

Collagen-based polymers and their blends have attracted considerable interest for new materials development due to their unique combination of biocompatibility, physical and mechanical properties and durability. Leather, a modified natural biopolymer made from animal rawhide and the first synthetic collagen-based polymer known since the dawn of civilization, combines all these features. Rawhide is transformed into leather by tanning, a process in which the collagen is cross-linked with different agents to make it stronger and more durable and to prevent its decay. Research on the development of environmentally friendly procedures and sustainable materials with higher efficiency and lower costs is a rapidly growing field, and leather industry is not an exemption. Chrome-tanned and vegetable-tanned (chromium-free) shavings from the leather industry present a high content of organic matter, yet they are considered recalcitrant waste to be degraded by microbiological processes like anaerobic digestion (AD), a solid technology to treat organic waste in a circular economy framework. In this technology however, the solubilisation of organic solid substrates is a significant challenge to improving the efficiency of the process. In this context, we have investigated the process of microbial decomposition of leather wastes from the tannery industry to search for the conditions that produce optimal solubilisation of organic matter. Chrome-tanned and chromium-free leather shavings were pre-treated and anaerobically digested under different temperature ranges (thermophilic–55 °C-, intermediate–42 °C- and mesophilic–35 °C) to evaluate the effect on the solubilisation of the organic matter of the wastes. The results showed that the presence of chromium significantly inhibited the solubilization (up to 60%) in the mesophilic and intermediate ranges; this is the fastest and most efficient solubilization reached under thermophilic conditions using the chromium-free leather shaving as substrates. The most suitable temperature for the solubilization was the thermophilic regime (55 °C) for both chromium-free and chrome-tanned shavings. No significant differences were observed in the thermophilic anaerobic digestion of chromium-free shavings when a pre-treatment was applied, since the solubilisation was already high without pre-treatment. However, the pre-treatments significantly improved the solubilisation in the mesophilic and intermediate configurations; the former pre-treatment was better suited in terms of performance and cost-effectiveness compared to the thermophilic range. Thus, the solubilisation of chromium-free tannery solid wastes can be significantly improved by applying appropriate pre-treatments at lower temperature ranges; this is of utter importance when optimizing anaerobic processes of recalcitrant organic wastes, with the added benefit of substantial energy savings in the scaling up of the process in an optimised circular economy scenario.     

Roles of Calcium Signaling in Gene Expression and Photosynthetic Acclimatization of Solanum lycopersicum Micro-Tom (MT) after Mechanical Damage

A momentary increase in cytoplasmic Ca²⁺ generates an oscillation responsible for the activation of proteins, such as calmodulin and kinases, which interact with reactive oxygen species (ROS) for the transmission of a stress signal. This study investigated the influence of variations in calcium concentrations on plant defense signaling and photosynthetic acclimatization after mechanical damage. Solanum lycopersicum Micro-Tom was grown with 0, 2 and 4 mM Ca²⁺, with and without mechanical damage. The expression of stress genes was evaluated, along with levels of antioxidant enzymes, hydrogen peroxide, lipid peroxidation, histochemistry, photosynthesis and dry mass of organs. The ROS production generated by mechanical damage was further enhanced by calcium-free conditions due to the inactivation of the oxygen evolution complex, contributing to an increase in reactive species. The results indicated that ROS affected mechanical damage signaling because calcium-free plants exhibited high levels of H₂O₂ and enhanced expression of kinase and RBOH1 genes, necessary conditions for an efficient response to stress. We conclude that the plants without calcium supply recognized mechanical damage but did not survive. The highest expression of the RBOH1 gene and the accumulation of H₂O₂ in these plants signaled cell death. Plants grown in the presence of calcium showed higher expression of SlCaM2 and control of H₂O₂ concentration, thus overcoming the stress caused by mechanical damage, with photosynthetic acclimatization and without damage to dry mass production.