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Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638

Dom, 20/05/2018 - 19:00
Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638 In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain. 2018-05-21T00:00:00Z

Fission-fusion dynamics as a temporally and spatially flexible behavioral strategy in spider monkeys

Dom, 31/12/2017 - 18:00
Fission-fusion dynamics as a temporally and spatially flexible behavioral strategy in spider monkeys Fission-fusion dynamics (FFD) encompass a behavioral strategy present in many animal species that reduces the costs and increases the benefits of group living. In this case study, we investigated how group characteristics (size and composition) and fission rates in spider monkeys varied in space and time with rainfall, fruit availability, and fruit variability in two sites, each presenting different characteristics regarding the distribution and size of food patches and rainfall. Habitat characteristics strongly influenced FFD in spider monkeys, particularly subgroup size and fission rate. Subgroup size varied with fruit availability and its variability, while fission rates varied with rainfall and fruit variability. However, both subgroup size and fission rate varied in opposite ways, depending upon habitat type. Subgroups tended to present stable mixed-sex composition regardless of fruit availability. We conclude that for spider monkeys, FFD are part of a flexible behavioral strategy to cope with a locally fluctuating environment and with different environments within the geographic range of the species.

Choreographies in the n-vortex Problem

Dom, 31/12/2017 - 18:00
Choreographies in the n-vortex Problem We consider the equations of motion of n vortices of equal circulation in the plane, in a disk and on a sphere. The vortices form a polygonal equilibrium in a rotating frame of reference. We use numerical continuation in a boundary value setting to determine the Lyapunov families of periodic orbits that arise from the polygonal relative equilibrium. When the frequency of a Lyapunov orbit and the frequency of the rotating frame have a rational relationship, the orbit is also periodic in the inertial frame. A dense set of Lyapunov orbits, with frequencies satisfying a Diophantine equation, corresponds to choreographies of n vortices. We include numerical results for all cases, for various values of n, and we provide key details on the computational approach.

Grounding 4E Cognition in Mexico: introduction to special issue on spotlight on 4E Cognition research in Mexico

Dom, 31/12/2017 - 18:00
Grounding 4E Cognition in Mexico: introduction to special issue on spotlight on 4E Cognition research in Mexico Embodied, embedded, extended and enactive (4EC) perspectives on cognition have gained epistemic legitimacy during the last 25 years in the international arena. They have encouraged new ways to understand the mind. Mexico has not been an exception; rather, it has the potential to provide a fertile ground for the development of 4EC perspectives, as shown by the variety of contributions in this special issue. In this editorial introduction, we discuss recent concerns about a lack of coherence in the inter-relations between these perspectives, and we propose that it is more appropriate to view 4EC as an emerging pluralistic research tradition that shares crucial commitments. Furthermore, we show that this pluralistic tradition has been gaining ground in the specific research context of Mexico, because of the country's distinctive historical, scientific and philosophical development. We finish by describing the promising research potential of the current heterogeneous explanations as evidenced by the papers in this issue.

Entraining chaotic dynamics: A novel movement sonification paradigm could promote generalization

Dom, 31/12/2017 - 18:00
Entraining chaotic dynamics: A novel movement sonification paradigm could promote generalization C Tasks encountered in daily living may have instabilities and more dimensions than are sampled by the senses such as when carrying a cup of coffee and only the surface motion and overall momentum are sensed, not the fluid dynamics. Anticipating non-periodic dynamics is difficult but not impossible because mutual coordination allows for chaotic processes to synchronize to each other and become periodic. A chaotic oscillator with random period and amplitude affords being stabilized onto a periodic trajectory by a weak input if the driver incorporates information about the oscillator. We studied synchronization with predictable and unpredictable stimuli where the unpredictable stimuli could be non-interactive or interactive. The latter condition required learning to control a chaotic system. We expected better overall performance with the predictable but more learning and generalization with unpredictable interactive stimuli. Participants practiced an auditory-motor synchronization task by matching their sonified hand movements to sonified tutors: the Non-Interactive Predictable tutor (NI-P) was a sinusoid, the Non-Interactive Unpredictable (NI-U) was a chaotic system, the Interactive Unpredictable (I-U) was the same chaotic system with an added weak input from the participant's movement. Different pre/post-practice stimuli evaluated generalization. Quick improvement was seen in NIP. Synchronization, dynamic similarity, and causal interaction increased with practice in I-U but not in NI-U. Generalization was seen for few pre-post stimuli in NI-P, none in NI-U, and most stimuli in I-U. Synchronization with novel chaotic dynamics is challenging but mutual interaction enables the behavioral control of such dynamics and the practice of complex motor skills.

MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle.

Dom, 22/10/2017 - 19:00
MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. The increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging. We describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare, and infer complex metabolic pathways in large "omic" datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github. com/eead-csic-compbio/metagenome Pfam score. To demonstrate its use, we modeled the sulfur cycle by exhaustively curating the molecular and ecological elements involved (compounds, genes, metabolic pathways, and microbial taxa). This information was reduced to a collection of 112 characteristic Pfam protein domains and a list of complete-sequenced sulfur genomes. Using the mathematical framework of relative entropy (H'), we quantitatively measured the enrichment of these domains among sulfur genomes. The entropy of each domain was used both to build up a final score that indicates whether a (meta) genomic sample contains the metabolic machinery of interest and to propose marker domains in metagenomic sequences such as DsrC (PF04358). MEBS was benchmarked with a dataset of 2107 non-redundant microbial genomes from RefSeq and 935 metagenomes from MG-RAST. Its performance, reproducibility, and robustness were evaluated using several approaches, including random sampling, linear regression models, receiver operator characteristic plots, and the area under the curve metric (AUC). Our results support the broad applicability of this algorithm to accurately classify (AUC = 0.985) hard-to-culture genomes (e.g., Candidatus Desulforudis audaxviator), previously characterized ones, and metagenomic environments such as hydrothermal vents, or deep-sea sediment. Our benchmark indicates that an entropy-based score can capture the metabolic machinery of interest and can be used to efficiently classify large genomic and metagenomic datasets, including uncultivated/unexplored taxa. 2017-10-23T00:00:00Z

Localization of sound sources in robotics: A review

Vie, 04/08/2017 - 19:00
Localization of sound sources in robotics: A review Sound source localization (SSL) in a robotic platform has been essential in the overall scheme of robot audition. It allows a robot to locate a sound source by sound alone. It has an important impact on other robot audition modules, such as source separation, and it enriches human robot interaction by complementing the robot's perceptual capabilities. The main objective of this review is to thoroughly map the current state of the SSL field for the reader and provide a starting point to SSL in robotics. To this effect, we present: the evolution and historical context of SSL in robotics; an extensive review and classification of SSL techniques and popular tracking methodologies; different facets of SSL as well as its state-of-the-art; evaluation methodologies used for SSL; and a set of challenges and research motivations. 2017-08-05T00:00:00Z

Combining the ADMM and mathematical homogenization for atmospherical pollutant dispersion modeling

Sáb, 22/07/2017 - 19:00
Combining the ADMM and mathematical homogenization for atmospherical pollutant dispersion modeling O método multicamadas de advecção-difusão (ADMM) produz soluções semianalíticas precisas dos problemas devalores de contorno/iniciais para equações de advecção-difusão com coeficientes variáveis que modelam a dispersão depoluentes na atmosfera, e apresenta o menor custo computacional quando comparado com outros métodos baseados emtransformadas integrais. Contudo, em situações operativas tais como desastres naturais/industriais que resultam na fugade poluentes na atmosfera, é necessário aferir rapidamente e com exatidão a distribuição da concentração dos poluentesno nível do solo para minimizar o impacto na saúde e na economia. Aqui, para acelerar a disponibilidade de resultadoscom mínima perda de precisão, o ADMM é combinado com homogeneização matemática, cujo emprego na modelagemde dispersão de poluentes parece ser novidade. A abordagem proposta é comparada com a aplicação direta do ADMM eàs observações do experimento de Hanford para avaliar a exatidão das estimativas, assim como sua eficiênciacomputacional, considerando condições atmosféricas estáveis e a influência da velocidade de deposição. Os resultadosmostram que a combinação do ADMM com a homogeneização matemática apresenta uma redução significativa nocusto computacional com pouca perda de precisão. 2017-07-23T00:00:00Z

A game-theory modeling approach to utility and strength of interactions dynamics in biomedical research social networks

Lun, 15/05/2017 - 19:00
A game-theory modeling approach to utility and strength of interactions dynamics in biomedical research social networks Collaboration has become a cornerstone in biomedical research today. In contrast to physics which has a long history and experience in collaborative projects, biology is only recently becoming an evermore collaborative discipline. In this article we explore the effect of a collaboration network on the distribution of players having access to certain amount of resources from other players in the network and the distribution of the strength of interactions among them. We are interested in how they affect each other in the context of a network of scientific collaboration under the idea that while researchers are interested in maximizing their utilities, they also know that it is important to invest in building collaborative relationships. 2017-05-16T00:00:00Z

A game-theory modeling approach to utility and strength of interactions dynamics in biomedical research social networks

Lun, 15/05/2017 - 19:00
A game-theory modeling approach to utility and strength of interactions dynamics in biomedical research social networks Collaboration has become a cornerstone in biomedical research today. In contrast to physics which has a long history and experience in collaborative projects, biology is only recently becoming an evermore collaborative discipline. In this article we explore the effect of a collaboration network on the distribution of players having access to certain amount of resources from other players in the network and the distribution of the strength of interactions among them. We are interested in how they affect each other in the context of a network of scientific collaboration under the idea that while researchers are interested in maximizing their utilities, they also know that it is important to invest in building collaborative relationships. 2017-05-16T00:00:00Z

Where There Is Life There Is Mind: In Support of a Strong Life-Mind Continuity Thesis

Jue, 13/04/2017 - 19:00
Where There Is Life There Is Mind: In Support of a Strong Life-Mind Continuity Thesis This paper considers questions about continuity and discontinuity between life and mind. It begins by examining such questions from the perspective of the free energy principle (FEP). The FEP is becoming increasingly influential in neuroscience and cognitive science. It says that organisms act to maintain themselves in their expected biological and cognitive states, and that they can do so only by minimizing their free energy given that the long-term average of free energy is entropy. The paper then argues that there is no singular interpretation of the FEP for thinking about the relation between life and mind. Some FEP formulations express what we call an independence view of life and mind. One independence view is a cognitivist view of the FEP. It turns on information processing with semantic content, thus restricting the range of systems capable of exhibiting mentality. Other independence views exemplify what we call an overly generous non-cognitivist view of the FEP, and these appear to go in the opposite direction. That is, they imply that mentality is nearly everywhere. The paper proceeds to argue that non-cognitivist FEP, and its implications for thinking about the relation between life and mind, can be usefully constrained by key ideas in recent enactive approaches to cognitive science. We conclude that the most compelling account of the relationship between life and mind treats them as strongly continuous, and that this continuity is based on particular concepts of life (autopoiesis and adaptivity) and mind (basic and non-semantic). 2017-04-14T00:00:00Z

A Package for Measuring emergence, Self-organization, and Complexity Based on Shannon entropy

Lun, 27/03/2017 - 18:00
A Package for Measuring emergence, Self-organization, and Complexity Based on Shannon entropy We present a set of Matlab/Octave functions to compute measures of emergence, self-organization, and complexity applied to discrete and continuous data. These measures are based on Shannon’s information and differential entropy. Examples from different datasets and probability distributions are provided to show how to use our proposed code. 2017-03-28T00:00:00Z

A Package for Measuring emergence, Self-organization, and Complexity Based on Shannon entropy

Lun, 27/03/2017 - 18:00
A Package for Measuring emergence, Self-organization, and Complexity Based on Shannon entropy We present a set of Matlab/Octave functions to compute measures of emergence, self-organization, and complexity applied to discrete and continuous data. These measures are based on Shannon’s information and differential entropy. Examples from different datasets and probability distributions are provided to show how to use our proposed code.

Towards the complete proteinaceous regulome of Acinetobacter baumannii

Mié, 22/03/2017 - 18:00
Towards the complete proteinaceous regulome of Acinetobacter baumannii The emergence ofAcinetobacter baumanniistrains, with broad multidrug-resistance phenotypes and novel virulence factorsunique to hypervirulent strains, presents a major threat to human health worldwide. Although a number of studies havedescribed virulence-affecting entities for this organism, very few have identified regulatory elements controlling theirexpression. Previously, our group has documented the global identification and curation of regulatory RNAs inA. baumannii.As such, in the present study, we detail an extension of this work, the performance of an extensive bioinformatic analysis toidentify regulatory proteins in the recently annotated genome of the highly virulent AB5075 strain. In so doing, 243transcription factors, 14 two-component systems (TCSs), 2 orphan response regulators, 1 hybrid TCS and 5sfactors werefound. A comparison of these elements between AB5075 and other clinical isolates, as well as a laboratory strain, led to theidentification of several conserved regulatory elements, whilst at the same time uncovering regulators unique tohypervirulent strains. Lastly, by comparing regulatory elements compiled in this study to genes shown to be essential forAB5075 infection, we were able to highlight elements with a specific importance for pathogenic behaviour. Collectively, ourwork offers a unique insight into the regulatory network ofA. baumanniistrains, and provides insight into the evolution ofhypervirulent lineages 2017-03-23T00:00:00Z

Towards the complete proteinaceous regulome of Acinetobacter baumannii

Mié, 22/03/2017 - 18:00
Towards the complete proteinaceous regulome of Acinetobacter baumannii The emergence ofAcinetobacter baumanniistrains, with broad multidrug-resistance phenotypes and novel virulence factorsunique to hypervirulent strains, presents a major threat to human health worldwide. Although a number of studies havedescribed virulence-affecting entities for this organism, very few have identified regulatory elements controlling theirexpression. Previously, our group has documented the global identification and curation of regulatory RNAs inA. baumannii.As such, in the present study, we detail an extension of this work, the performance of an extensive bioinformatic analysis toidentify regulatory proteins in the recently annotated genome of the highly virulent AB5075 strain. In so doing, 243transcription factors, 14 two-component systems (TCSs), 2 orphan response regulators, 1 hybrid TCS and 5sfactors werefound. A comparison of these elements between AB5075 and other clinical isolates, as well as a laboratory strain, led to theidentification of several conserved regulatory elements, whilst at the same time uncovering regulators unique tohypervirulent strains. Lastly, by comparing regulatory elements compiled in this study to genes shown to be essential forAB5075 infection, we were able to highlight elements with a specific importance for pathogenic behaviour. Collectively, ourwork offers a unique insight into the regulatory network ofA. baumanniistrains, and provides insight into the evolution ofhypervirulent lineages

The combination of the functionalities of feedback circuits is determinant for the attractors’ number and size in pathway-like Boolean networks

Jue, 09/02/2017 - 18:00
The combination of the functionalities of feedback circuits is determinant for the attractors’ number and size in pathway-like Boolean networks Molecular regulation was initially assumed to follow both a unidirectional and a hierarchical organization forming pathways. Regulatory processes, however, form highly interlinked networks with non-hierarchical and non-unidirectional structures that contain statistically overrepresented circuits or motifs. Here, we analyze the behavior of pathways containing non-unidirectional (i.e. bidirectional) and non-hierarchical interactions that create motifs. In comparison with unidirectional and hierarchical pathways, our pathways have a high diversity of behaviors, characterized by the size and number of attractors. Motifs have been studied individually showing that feedback circuit motifs regulate the number and size of attractors. It is less clear what happens in molecular networks that usually contain multiple feedbacks. Here, we find that the way feedback circuits couple to each other (i.e., the combination of the functionalities of feedback circuits) regulate both the number and size of the attractors. We show that the different expected results of epistasis analysis (a method to infer regulatory interactions) are produced by many non-hierarchical and non-unidirectional structures. Thus, these structures cannot be correctly inferred by epistasis analysis. Finally, we show that the combinations of functionalities, combined with other network properties, allow for a better characterization of regulatory structures 2017-02-10T00:00:00Z

The combination of the functionalities of feedback circuits is determinant for the attractors’ number and size in pathway-like Boolean networks

Jue, 09/02/2017 - 18:00
The combination of the functionalities of feedback circuits is determinant for the attractors’ number and size in pathway-like Boolean networks Molecular regulation was initially assumed to follow both a unidirectional and a hierarchical organization forming pathways. Regulatory processes, however, form highly interlinked networks with non-hierarchical and non-unidirectional structures that contain statistically overrepresented circuits or motifs. Here, we analyze the behavior of pathways containing non-unidirectional (i.e. bidirectional) and non-hierarchical interactions that create motifs. In comparison with unidirectional and hierarchical pathways, our pathways have a high diversity of behaviors, characterized by the size and number of attractors. Motifs have been studied individually showing that feedback circuit motifs regulate the number and size of attractors. It is less clear what happens in molecular networks that usually contain multiple feedbacks. Here, we find that the way feedback circuits couple to each other (i.e., the combination of the functionalities of feedback circuits) regulate both the number and size of the attractors. We show that the different expected results of epistasis analysis (a method to infer regulatory interactions) are produced by many non-hierarchical and non-unidirectional structures. Thus, these structures cannot be correctly inferred by epistasis analysis. Finally, we show that the combinations of functionalities, combined with other network properties, allow for a better characterization of regulatory structures

FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems

Dom, 22/01/2017 - 18:00
FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems A particular challenge to water safety in populous intertropical regions is the lack of reliable faecal indicators to detect microbiological contamination of water, while the numerical relationships of specific viral indicators remain largely unexplored. The aim of this study was to investigate the numerical relationships of FRNA-bacteriophage genotypes, adenovirus 41, and human adenoviruses (HADV) in Mexican surface water systems to assess sewage contamination. We studied the presence of HADV, HADV41 and FRNA bacteriophage genotypes in water samples and quantified by qPCR and RT-qPCR. Virus and water quality indicator variances, as analyzed by principal component analysis and partial least squared regression, followed along the major percentiles of water faecal enterococci. FRNA bacteriophages adequately deciphered viral and point source water contamination. The strongest correlation for HADV was with FRNA bacteriophage type II, in water samples higher than the 50th percentiles of faecal enterococci, thus indicating urban pollution. FRNA bacteriophage genotypes I and III virus indicator performances were assisted by their associations with electrical conductivity and faecal enterococci. In combination, our methods are useful for inferring water quality degradation caused by sewage contamination. The methods used have potential for determining source contamination in water and, specifically, the presence of enteric viruses where clean and contaminated water have mixed. 2017-01-23T00:00:00Z

FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems

Dom, 22/01/2017 - 18:00
FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems A particular challenge to water safety in populous intertropical regions is the lack of reliable faecal indicators to detect microbiological contamination of water, while the numerical relationships of specific viral indicators remain largely unexplored. The aim of this study was to investigate the numerical relationships of FRNA-bacteriophage genotypes, adenovirus 41, and human adenoviruses (HADV) in Mexican surface water systems to assess sewage contamination. We studied the presence of HADV, HADV41 and FRNA bacteriophage genotypes in water samples and quantified by qPCR and RT-qPCR. Virus and water quality indicator variances, as analyzed by principal component analysis and partial least squared regression, followed along the major percentiles of water faecal enterococci. FRNA bacteriophages adequately deciphered viral and point source water contamination. The strongest correlation for HADV was with FRNA bacteriophage type II, in water samples higher than the 50th percentiles of faecal enterococci, thus indicating urban pollution. FRNA bacteriophage genotypes I and III virus indicator performances were assisted by their associations with electrical conductivity and faecal enterococci. In combination, our methods are useful for inferring water quality degradation caused by sewage contamination. The methods used have potential for determining source contamination in water and, specifically, the presence of enteric viruses where clean and contaminated water have mixed.

Design of a Fuzzy Networked Control Systems. Priority Exchange Scheduling Algorithm

Jue, 31/03/2016 - 18:00
Design of a Fuzzy Networked Control Systems. Priority Exchange Scheduling Algorithm This work presents a supervisory control strategy for Networked Control Systems (NCSs). This shows the identification and control of the plant using fuzzy theory. The fuzzy model incorporates the delay dynamics within the fuzzy rules based upon a real-time hierarchical scheduling strategy. A hierarchical scheduling Priority Exchange algorithm is used based upon codesign strategy following mutual correlation among control and network algorithms in order to bounded time delays. A system of magnetic levitation is presented as a case study. 2016-04-01T00:00:00Z

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