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Marine Pollution Bulletin, 2021

The deposition of remaining nanoparticles in the Caribbean Sea generates the formation of potenti... more The deposition of remaining nanoparticles in the Caribbean Sea generates the formation of potentially dangerous elements, which influence at the imbalance of ecosystems. The detection of nanoparticles is not simple and the use of conventional methods is difficult application, which is why we highlight the immediacy and importance of this research for the areas of marine biology, urbanism, engineering and geosciences, applied in the Caribbean Sea. The general objective of this study is to evaluate the use of advanced methods for the determination of toxic nanoparticles, which can directly affect the development of marine organisms in the aquatic ecosystem in waters of the Caribbean Sea, favoring the construction of future international public policies with the elaboration of projects capable of mitigating these levels of contamination. The morphology and structure of nanoparticles were analyzed by emission scanning electron microscope with a high-resolution electron microscope. The nanoparticles smaller than 97 nm were identified in different proportions. The morphological analyses indicated nanoparticles' presence in the form of nanotubes, nanospheres, and nanofibers, which were shown in an agglomerated form. The presence of potentially hazardous elements, such as As, Cd, Pb, Mg, Ni and V were verified. In addition, the presence of asbestos in the form of minerals was confirmed, and that of titanium dioxide was found in large quantities. The results provide new data and emphasize the possible consequences to the in the Caribbean Sea, with the identification of dangerous elements (As, Cb, Pb, Hg, Ni and V), harmful to the marine ecosystem. Therefore, there is a need for strict control to reduce contamination of the Caribbean Sea and avoid risks to the ecosystem and public health, through suggestions of international public policies, through constant monitoring and the application of environmental recovery projects in this marine estuary.

2014 IEEE Symposium on Swarm Intelligence, 2014

In Particle Swarm Optimizers (PSO), the way particles communicate plays an important role on thei... more In Particle Swarm Optimizers (PSO), the way particles communicate plays an important role on their search behavior influencing the trade-off between exploration and exploitation. The interactions boundaries defined by the swarm topology is an example of this influence. For instance, a swarm with the ring topology tends to explore the environment more than with the fully connected global topology. On the other hand, more connected topologies tend to present a higher exploitation capability. We propose that the analysis of the particles interactions can be used to assess the swarm search mode, without the need for any particles properties (e.g. the particle's position, the particle's velocity, etc.). We define the weighted swarm influence graph I tw t that keeps track of the interactions from the last tw iterations before a given iteration t. We show that the search mode of the swarm does have a signature on this graph based on the analysis of its components and the distribution of the node strengths.

Science of The Total Environment, 2012

The extraction of sulphur produces a hematite-rich waste, known as roasted pyrite ash, which cont... more The extraction of sulphur produces a hematite-rich waste, known as roasted pyrite ash, which contains significant amounts of environmentally sensitive elements in variable concentrations and modes of occurrence. Whilst the mineralogy of roasted pyrite ash associated with iron or copper mining has been studied, as this is the main source of sulphur worldwide, the mineralogy, and more importantly, the characterization of nanoparticles, in coal-derived roasted pyrite ash remain to be resolved. In this work we provide essential data on the chemical composition and nanomineralogical assemblage of roasted pyrite ash. XRD, HR-TEM and FE-SEM were used to identify a large variety of minerals of anthropogenic origin. These phases result from highly complex chemical reactions occurring during the processing of coal pyrite of southern Brazil for sulphur extraction and further manufacture of sulphuric acid. Iron-rich nanoparticles within the ash may contain high proportions of toxic elements such as As, Se, U, among others. A number of elements, such as As,

Proceedings of the National Academy of Sciences, 1992

X-ray diffraction data were collected from human rhinovirus 14 crystals a few minutes after expos... more X-ray diffraction data were collected from human rhinovirus 14 crystals a few minutes after exposure to acid vapor and prior to excessive crystalline disorder. Conformational changes occurred (i) in the GH loop of viral protein (VP) 1, (ii) at the ion binding site on the outer surface of the pentamer center, and (iii) in VP3 and VP4 on the virion's interior in the vicinity of the fivefold axis. Amino acid substitutions in mutants resistant to low pH, or to drugs that inhibit uncoating, were concentrated in the vicinity of the GH loop. It is proposed that the acid-induced changes reflect processes that trigger uncoating.

Proceedings of the National Academy of Sciences, 1988

The binding to human rhinovirus 14 of a series of eight antiviral agents that inhibit picornavira... more The binding to human rhinovirus 14 of a series of eight antiviral agents that inhibit picornaviral uncoating after entry into host cells has been characterized crystallographically. All of these bind into the same hydrophobic pocket within the viral protein VP1 beta-barrel structure, although the orientation and position of each compound within the pocket was found to differ. The compounds cause the protein shell to be less flexible, thereby inhibiting disassembly. Although the antiviral potency of these compounds varies by 120-fold, they all induce the same conformational changes on the virion. The interactions of these compounds with the viral capsid are consistent with their observed antiviral activities against human rhinovirus 14 drug-resistant mutants and other rhinovirus serotypes. Crystallographic studies of one of these mutants confirm the partial sequencing data and support the finding that this is a single mutation that occurs within the binding pocket.

Structure, 1997

Background: Rhinoviruses belong to the picornavirus family and are small, icosahedral, non-envelo... more Background: Rhinoviruses belong to the picornavirus family and are small, icosahedral, non-enveloped viruses containing one positive RNA strand. Human rhinovirus 16 (HRV16) belongs to the major receptor group of rhinoviruses, for which the cellular receptor is intercellular adhesion molecule-1 (ICAM-1). In many rhinoviruses, one of the viral coat proteins (VP1) contains a hydrophobic pocket which is occupied by a fatty acid-like molecule, or so-called 'pocket factor'. Antiviral agents have been shown to bind to the hydrophobic pocket in VP1, replacing the pocket factor. The presence of the antiviral compound blocks uncoating of the virus and in some cases inhibits receptor attachment. A refined, high-resolution structure would be expected to provide further information on the nature of the pocket factor and other features previously not clearly identified. Results: The structure of native HRV16 has been refined to a resolution of 2.15 Å. The hydrophobic pocket in VP1 is observed in two alternative conformations. In one of these, the pocket is filled by a pocket factor and the protein structure is similar to virus-antiviral compound complexes. In the other conformation, the hydrophobic pocket is collapsed and empty. RNA bases stack against both a tryptophan and a phenylalanine residue on the internal surface of the viral capsid. Site-directed mutagenesis of the tryptophan, which is conserved across the picornaviruses, to nonconservative residues results in non-viable virus. Five symmetry-related N termini of coat protein VP4 form a ten-stranded, antiparallel ␤ barrel around the base of the icosahedral fivefold axis. The N termini of VP1 are amphipathic ␣ helices, which stack on the outside of this ␤ barrel. The N termini of VP1 and VP4 have not been observed previously in rhinovirus structures. Conclusions: The observation of a partially occupied hydrophobic pocket in HRV16 forms a missing link between HRV14, which is always observed with no pocket factor in the native form, and rhinovirus 1A and other picornaviruses (e.g. poliovirus, coxsackievirus) which contain pocket factors. The pocket factor molecules probably regulate viral entry, uncoating and assembly. Picornavirus assembly is known to proceed via pentamers, therefore, the interaction of RNA with the conserved tryptophan residues across twofold axes between pentamers may play a role in picornavirus assembly. The positioning of a cation on the icosahedral fivefold axes and the structure of the N termini of VP4 and VP1 around these axes suggest a mechanism for the uncoating of rhinoviruses.

Lecture Notes in Computer Science, 2016

Since they were introduced, Particle Swarm Optimizers have suffered from early stagnation due to ... more Since they were introduced, Particle Swarm Optimizers have suffered from early stagnation due to premature convergence. Assessing swarm spatial diversity might help to mitigate early stagnation but swarm spatial diversity itself emerges from the main property that essentially drives swarm optimizers towards convergence and distinctively distinguishes PSO from other optimization techniques: the social interaction between the particles. The swarm influence graph captures the structure of particle interactions by monitoring the information exchanges during the search process; such graph has been shown to provide a rich overall structure of the swarm information flow. In this paper, we define swarm communication diversity based on the component analysis of the swarm influence graph. We show how communication diversity relates to other measures of swarm spatial diversity as well as how each swarm topology leads to different communication signatures. Moreover, we argue that swarm communication diversity might potentially be a better way to understand early stagnation since it takes into account the (social) interactions between the particles instead of properties associated with individual particles.

Marine Pollution Bulletin, 2021

The deposition of remaining nanoparticles in the Caribbean Sea generates the formation of potenti... more The deposition of remaining nanoparticles in the Caribbean Sea generates the formation of potentially dangerous elements, which influence at the imbalance of ecosystems. The detection of nanoparticles is not simple and the use of conventional methods is difficult application, which is why we highlight the immediacy and importance of this research for the areas of marine biology, urbanism, engineering and geosciences, applied in the Caribbean Sea. The general objective of this study is to evaluate the use of advanced methods for the determination of toxic nanoparticles, which can directly affect the development of marine organisms in the aquatic ecosystem in waters of the Caribbean Sea, favoring the construction of future international public policies with the elaboration of projects capable of mitigating these levels of contamination. The morphology and structure of nanoparticles were analyzed by emission scanning electron microscope with a high-resolution electron microscope. The nanoparticles smaller than 97 nm were identified in different proportions. The morphological analyses indicated nanoparticles' presence in the form of nanotubes, nanospheres, and nanofibers, which were shown in an agglomerated form. The presence of potentially hazardous elements, such as As, Cd, Pb, Mg, Ni and V were verified. In addition, the presence of asbestos in the form of minerals was confirmed, and that of titanium dioxide was found in large quantities. The results provide new data and emphasize the possible consequences to the in the Caribbean Sea, with the identification of dangerous elements (As, Cb, Pb, Hg, Ni and V), harmful to the marine ecosystem. Therefore, there is a need for strict control to reduce contamination of the Caribbean Sea and avoid risks to the ecosystem and public health, through suggestions of international public policies, through constant monitoring and the application of environmental recovery projects in this marine estuary.

2014 IEEE Symposium on Swarm Intelligence, 2014

In Particle Swarm Optimizers (PSO), the way particles communicate plays an important role on thei... more In Particle Swarm Optimizers (PSO), the way particles communicate plays an important role on their search behavior influencing the trade-off between exploration and exploitation. The interactions boundaries defined by the swarm topology is an example of this influence. For instance, a swarm with the ring topology tends to explore the environment more than with the fully connected global topology. On the other hand, more connected topologies tend to present a higher exploitation capability. We propose that the analysis of the particles interactions can be used to assess the swarm search mode, without the need for any particles properties (e.g. the particle's position, the particle's velocity, etc.). We define the weighted swarm influence graph I tw t that keeps track of the interactions from the last tw iterations before a given iteration t. We show that the search mode of the swarm does have a signature on this graph based on the analysis of its components and the distribution of the node strengths.

Science of The Total Environment, 2012

The extraction of sulphur produces a hematite-rich waste, known as roasted pyrite ash, which cont... more The extraction of sulphur produces a hematite-rich waste, known as roasted pyrite ash, which contains significant amounts of environmentally sensitive elements in variable concentrations and modes of occurrence. Whilst the mineralogy of roasted pyrite ash associated with iron or copper mining has been studied, as this is the main source of sulphur worldwide, the mineralogy, and more importantly, the characterization of nanoparticles, in coal-derived roasted pyrite ash remain to be resolved. In this work we provide essential data on the chemical composition and nanomineralogical assemblage of roasted pyrite ash. XRD, HR-TEM and FE-SEM were used to identify a large variety of minerals of anthropogenic origin. These phases result from highly complex chemical reactions occurring during the processing of coal pyrite of southern Brazil for sulphur extraction and further manufacture of sulphuric acid. Iron-rich nanoparticles within the ash may contain high proportions of toxic elements such as As, Se, U, among others. A number of elements, such as As,

Proceedings of the National Academy of Sciences, 1992

X-ray diffraction data were collected from human rhinovirus 14 crystals a few minutes after expos... more X-ray diffraction data were collected from human rhinovirus 14 crystals a few minutes after exposure to acid vapor and prior to excessive crystalline disorder. Conformational changes occurred (i) in the GH loop of viral protein (VP) 1, (ii) at the ion binding site on the outer surface of the pentamer center, and (iii) in VP3 and VP4 on the virion's interior in the vicinity of the fivefold axis. Amino acid substitutions in mutants resistant to low pH, or to drugs that inhibit uncoating, were concentrated in the vicinity of the GH loop. It is proposed that the acid-induced changes reflect processes that trigger uncoating.

Proceedings of the National Academy of Sciences, 1988

The binding to human rhinovirus 14 of a series of eight antiviral agents that inhibit picornavira... more The binding to human rhinovirus 14 of a series of eight antiviral agents that inhibit picornaviral uncoating after entry into host cells has been characterized crystallographically. All of these bind into the same hydrophobic pocket within the viral protein VP1 beta-barrel structure, although the orientation and position of each compound within the pocket was found to differ. The compounds cause the protein shell to be less flexible, thereby inhibiting disassembly. Although the antiviral potency of these compounds varies by 120-fold, they all induce the same conformational changes on the virion. The interactions of these compounds with the viral capsid are consistent with their observed antiviral activities against human rhinovirus 14 drug-resistant mutants and other rhinovirus serotypes. Crystallographic studies of one of these mutants confirm the partial sequencing data and support the finding that this is a single mutation that occurs within the binding pocket.

Structure, 1997

Background: Rhinoviruses belong to the picornavirus family and are small, icosahedral, non-envelo... more Background: Rhinoviruses belong to the picornavirus family and are small, icosahedral, non-enveloped viruses containing one positive RNA strand. Human rhinovirus 16 (HRV16) belongs to the major receptor group of rhinoviruses, for which the cellular receptor is intercellular adhesion molecule-1 (ICAM-1). In many rhinoviruses, one of the viral coat proteins (VP1) contains a hydrophobic pocket which is occupied by a fatty acid-like molecule, or so-called 'pocket factor'. Antiviral agents have been shown to bind to the hydrophobic pocket in VP1, replacing the pocket factor. The presence of the antiviral compound blocks uncoating of the virus and in some cases inhibits receptor attachment. A refined, high-resolution structure would be expected to provide further information on the nature of the pocket factor and other features previously not clearly identified. Results: The structure of native HRV16 has been refined to a resolution of 2.15 Å. The hydrophobic pocket in VP1 is observed in two alternative conformations. In one of these, the pocket is filled by a pocket factor and the protein structure is similar to virus-antiviral compound complexes. In the other conformation, the hydrophobic pocket is collapsed and empty. RNA bases stack against both a tryptophan and a phenylalanine residue on the internal surface of the viral capsid. Site-directed mutagenesis of the tryptophan, which is conserved across the picornaviruses, to nonconservative residues results in non-viable virus. Five symmetry-related N termini of coat protein VP4 form a ten-stranded, antiparallel ␤ barrel around the base of the icosahedral fivefold axis. The N termini of VP1 are amphipathic ␣ helices, which stack on the outside of this ␤ barrel. The N termini of VP1 and VP4 have not been observed previously in rhinovirus structures. Conclusions: The observation of a partially occupied hydrophobic pocket in HRV16 forms a missing link between HRV14, which is always observed with no pocket factor in the native form, and rhinovirus 1A and other picornaviruses (e.g. poliovirus, coxsackievirus) which contain pocket factors. The pocket factor molecules probably regulate viral entry, uncoating and assembly. Picornavirus assembly is known to proceed via pentamers, therefore, the interaction of RNA with the conserved tryptophan residues across twofold axes between pentamers may play a role in picornavirus assembly. The positioning of a cation on the icosahedral fivefold axes and the structure of the N termini of VP4 and VP1 around these axes suggest a mechanism for the uncoating of rhinoviruses.

Lecture Notes in Computer Science, 2016

Since they were introduced, Particle Swarm Optimizers have suffered from early stagnation due to ... more Since they were introduced, Particle Swarm Optimizers have suffered from early stagnation due to premature convergence. Assessing swarm spatial diversity might help to mitigate early stagnation but swarm spatial diversity itself emerges from the main property that essentially drives swarm optimizers towards convergence and distinctively distinguishes PSO from other optimization techniques: the social interaction between the particles. The swarm influence graph captures the structure of particle interactions by monitoring the information exchanges during the search process; such graph has been shown to provide a rich overall structure of the swarm information flow. In this paper, we define swarm communication diversity based on the component analysis of the swarm influence graph. We show how communication diversity relates to other measures of swarm spatial diversity as well as how each swarm topology leads to different communication signatures. Moreover, we argue that swarm communication diversity might potentially be a better way to understand early stagnation since it takes into account the (social) interactions between the particles instead of properties associated with individual particles.