Transcriptome of the deep-sea black scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae) : tissue-specific expression patterns and candidate genes associated to depth adaptation

Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotations were performed by Newbler and InterPro/Pfam analyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against the NCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities between A. carbo and other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fish A. carbo first transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes.Publisher PDFPeer reviewe

Design of a Virtual Assistant to Improve Interaction Between the Audience and the Presenter

This article presents a novel design of a Virtual Assistant as part of a human-machine interaction system to improve communication between the presenter and the audience that can be used in education or general presentations for improving interaction during the presentations (e.g., auditoriums with 200 people). The main goal of the proposed model is the design of a framework of interaction to increase the level of attention of the public in key aspects of the presentation. In this manner, the collaboration between the presenter and Virtual Assistant could improve the level of learning among the public. The design of the Virtual Assistant relies on non-anthropomorphic forms with ‘live’ characteristics generating an intuitive and self-explainable interface. A set of intuitive and useful virtual interactions to support the presenter was designed. This design was validated from various types of the public with a psychological study based on a discrete emotions’ questionnaire confirming the adequacy of the proposed solution. The human-machine interaction system supporting the Virtual Assistant should automatically recognize the attention level of the audience from audiovisual resources and synchronize the Virtual Assistant with the presentation. The system involves a complex artificial intelligence architecture embracing perception of high-level features from audio and video, knowledge representation, and reasoning for pervasive and affective computing and reinforcement learning to teach the intelligent agent to decide on the best strategy to increase the level of attention of the audience

Complete breakdown of the Debye model of rotational relaxation near the isotropic-nematic phase boundary: Effects of intermolecular correlations in orientational dynamics

The Debye-Stokes-Einstein (DSE) model of rotational diffusion predicts that the rotational correlation times $\tau_{l}$ vary as $[l(l+1)]^{-1}$, where $l$ is the rank of the orientational correlation function (given in terms of the Legendre polynomial of rank $l$). One often finds significant deviation from this prediction, in either direction. In supercooled molecular liquids where the ratio $\tau_{1}/\tau_{2}$ falls considerably below three (the Debye limit), one usually invokes a jump diffusion model to explain the approach of the ratio $\tau_{1}/\tau_{2}$ to unity. Here we show in a computer simulation study of a standard model system for thermotropic liquid crystals that this ratio becomes much less than unity as the isotropic-nematic phase boundary is approached from the isotropic side. Simultaneously, the ratio $\tau_2/\eta$ (where $\eta$ is the shear viscosity of the liquid) becomes {\it much larger} than hydrodynamic value near the I-N transition. We have also analyzed the break down of the Debye model of rotational diffusion in ratios of higher order rotational correlation times. We show that the break down of the DSE model is due to the growth of orientational pair correlation and provide a mode coupling theory analysis to explain the results.Comment: Submitted to Physical Review

Discretization-related issues in the KPZ equation: Consistency, Galilean-invariance violation, and fluctuation--dissipation relation

In order to perform numerical simulations of the KPZ equation, in any dimensionality, a spatial discretization scheme must be prescribed. The known fact that the KPZ equation can be obtained as a result of a Hopf--Cole transformation applied to a diffusion equation (with \emph{multiplicative} noise) is shown here to strongly restrict the arbitrariness in the choice of spatial discretization schemes. On one hand, the discretization prescriptions for the Laplacian and the nonlinear (KPZ) term cannot be independently chosen. On the other hand, since the discretization is an operation performed on \emph{space} and the Hopf--Cole transformation is \emph{local} both in space and time, the former should be the same regardless of the field to which it is applied. It is shown that whereas some discretization schemes pass both consistency tests, known examples in the literature do not. The requirement of consistency for the discretization of Lyapunov functionals is argued to be a natural and safe starting point in choosing spatial discretization schemes. We also analyze the relation between real-space and pseudo-spectral discrete representations. In addition we discuss the relevance of the Galilean invariance violation in these consistent discretization schemes, and the alleged conflict of standard discretization with the fluctuation--dissipation theorem, peculiar of 1D.Comment: RevTex, 23pgs, 2 figures, submitted to Phys. Rev.

Self-isospectrality, mirror symmetry, and exotic nonlinear supersymmetry

We study supersymmetry of a self-isospectral one-gap Poschl-Teller system in the light of a mirror symmetry that is based on spatial and shift reflections. The revealed exotic, partially broken nonlinear supersymmetry admits seven alternatives for a grading operator. One of its local, first order supercharges may be identified as a Hamiltonian of an associated one-gap, non-periodic Bogoliubov-de Gennes system. The latter possesses a nonlinear supersymmetric structure, in which any of the three non-local generators of a Clifford algebra may be chosen as the grading operator. We find that the supersymmetry generators for the both systems are the Darboux-dressed integrals of a free spin-1/2 particle in the Schrodinger picture, or of a free massive Dirac particle. Nonlocal Foldy- Wouthuysen transformations are shown to be involved in the supersymmetric structure.Comment: 20 pages, comment added. Published versio

Enterprise information portals: potential for evaluating research for knowledge management and human capital assets using social network analysis

Paper presented at the ECKM 2010 – 11th European Conference on Knowledge Management, 2-3 September, 2010, Famalicão, Portugal. URL: http://www.academic-conferences.org/eckm/eckm2010/eckm10-home.htmEnterprise Information Portals (EIP) are being increasingly referred in the literature as one interesting technological solution to support organizations in their knowledge management initiatives. This paper seeks to explore the hidden potential of enterprise information portals to support knowledge management initiatives through the usage of social network analysis on research results and co-authorship/co-work relationships that may suggest ways to more effectively utilize knowledge capital and other organizational resources. For that purpose in this paper we will present field research results on evaluating knowledge management and human capital assets based on EIP data repositories using social network analysis. This evaluation will be made through the use of social network analysis techniques applied to authorship data from papers published in international journals with refereeing covering the last twenty years of research activities from a Portuguese leading research institution in the field of telecommunications - Instituto de Telecomunicações (IT)

Heat exchange between two interacting nanoparticles beyond the fluctuation-dissipation regime

We show that the observed non-monotonic behavior of the thermal conductance between two nanoparticles when they are brought into contact is originated by an intricate phase space dynamics. Here it is assumed that this dynamics results from the thermally activated jumping through a rough energy landscape. A hierarchy of relaxation times plays the key role in the description of this complex phase space behaviour. Our theory enables us to analyze the heat transfer just before and at the moment of contact.Comment: 4 pages, 1 figure, approved for publication in Physical Review Letter

Kosterlitz-Thouless transition in three-state mixed Potts ferro-antiferromagnets

We study three-state Potts spins on a square lattice, in which all bonds are ferromagnetic along one of the lattice directions, and antiferromagnetic along the other. Numerical transfer-matrix are used, on infinite strips of width $L$ sites, $4 \leq L \leq 14$. Based on the analysis of the ratio of scaled mass gaps (inverse correlation lengths) and scaled domain-wall free energies, we provide strong evidence that a critical (Kosterlitz-Thouless) phase is present, whose upper limit is, in our best estimate, $T_c=0.29 \pm 0.01$. From analysis of the (extremely anisotropic) nature of excitations below $T_c$, we argue that the critical phase extends all the way down to T=0. While domain walls parallel to the ferromagnetic direction are soft for the whole extent of the critical phase, those along the antiferromagnetic direction seem to undergo a softening transition at a finite temperature. Assuming a bulk correlation length varying, for $T>T_c$, as $\xi (T) =a_\xi \exp [ b_\xi (T-T_c)^{-\sigma}]$, $\sigma \simeq 1/2$, we attempt finite-size scaling plots of our finite-width correlation lengths. Our best results are for $T_c=0.50 \pm 0.01$. We propose a scenario in which such inconsistency is attributed to the extreme narrowness of the critical region.Comment: 11 pages, 6 .eps figures, LaTeX with IoP macros, to be published in J Phys

Avaliação termoanalítica de óleos essenciais de Eucalyptus spp suscetíveis e resistentes ao psilideo-de-concha.

O Glycaspis brimblecombei é uma praga florestal que ataca diversas espécies de eucalipto. Os terpenos e monoterpenos são os principais constituintes dos óleos essenciais do eucalipto. Amostras de óleos essenciais foram extraídas de folhas trituradas de eucaliptos resistentes e suscetíveis a este inseto. Os óleos foram analisados pelas técnicas termoanalíticas e observados comportamentos diferentes para os extraídos de eucaliptos resistentes e suscetíveis. Mais estudos são necessários para determinar as composições.Edição dos Anais do 7º Simpósio de Análise Térmica, 2015, Bauru

La-images: A Software For Elemental Distribution Bioimaging Using La-icp-ms Data

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)The spatial distribution of chemical elements in different types of samples is an important field in several research areas such as biology, paleontology or biomedicine, among others. Elemental distribution imaging by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is an effective technique for qualitative and quantitative imaging due to its high spatial resolution and sensitivity. By applying this technique, vast amounts of raw data are generated to obtain high-quality images, essentially making the use of specific LA-ICP-MS imaging software that can process such data absolutely mandatory. Since existing solutions are usually commercial or hard-to-use for average users, this work introduces LA-iMageS, an open-source, free-to-use multiplatform application for fast and automatic generation of high-quality elemental distribution bioimages from LA-ICP-MS data in the PerkinElmer Elan XL format, whose results can be directly exported to external applications for further analysis. A key strength of LA-iMageS is its substantial added value for users, with particular regard to the customization of the elemental distribution bioimages, which allows, among other features, the ability to change color maps, increase image resolution or toggle between 2D and 3D visualizations.8Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP, Sao Paulo, Brazil)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq, Brasilia, Brazil)Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES, Brasilia, Brazil)Provincial Council of Ourense [INOU-16-05]national funds from FCT/MEC [UID/QUI/50006/2013, UID/Multi/04378/2013]ERDF under the PT2020 Partnership Agreement [POCI-01-0145-FEDER-007265, POCI-01-0145-FEDER-007728]Unidade de Ciencias Biomoleculares Aplicadas-UCIBIOXunta de GaliciaFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES