Tokamak TCABR: Acquisition system, data analysis, and remote participation using MDSplus

Each plasma physics laboratory has a proprietary scheme to control and data acquisition system. Usually, it is different from one laboratory to another. It means that each laboratory has its own way to control the experiment and retrieving data from the database. Fusion research relies to a great extent on international collaboration and this private system makes it difficult to follow the work remotely. The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The choice of MDSplus (Model Driven System plus) is proved by the fact that it is widely utilized, and the scientists from different institutions may use the same system in different experiments in different tokamaks without the need to know how each system treats its acquisition system and data analysis. Another important point is the fact that the MDSplus has a library system that allows communication between different types of language (JAVA, Fortran, C, C++, Python) and programs such as MATLAB, IDL, OCTAVE. In the case of tokamak TCABR interfaces (object of this paper) between the system already in use and MDSplus were developed, instead of using the MDSplus at all stages, from the control, and data acquisition to the data analysis. This was done in the way to preserve a complex system already in operation and otherwise it would take a long time to migrate. This implementation also allows add new components using the MDSplus fully at all stages. (c) 2012 Elsevier B.V. All rights reserved.

BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

Calculation of parameter ranges for robust gain tuning of power system controllers

This work proposes a computational tool to assist power system engineers in the field tuning of power system stabilizers (PSSs) and Automatic Voltage Regulators (AVRs). The outcome of this tool is a range of gain values for theses controllers within which there is a theoretical guarantee of stability for the closed-loop system. This range is given as a set of limit values for the static gains of the controllers of interest, in such a way that the engineer responsible for the field tuning of PSSs and/or AVRs can be confident with respect to system stability when adjusting the corresponding static gains within this range. This feature of the proposed tool is highly desirable from a practical viewpoint, since the PSS and AVR commissioning stage always involve some readjustment of the controller gains to account for the differences between the nominal model and the actual behavior of the system. By capturing these differences as uncertainties in the model, this computational tool is able to guarantee stability for the whole uncertain model using an approach based on linear matrix inequalities. It is also important to remark that the tool proposed in this paper can also be applied to other types of parameters of either PSSs or Power Oscillation Dampers, as well as other types of controllers (such as speed governors, for example). To show its effectiveness, applications of the proposed tool to two benchmarks for small signal stability studies are presented at the end of this paper.

Facoemulsificação versus extração extracapsular no sistema público de saúde: análise de custos para o hospital, para o governo e para a sociedade

OBJETIVO: Comparar custos da cirurgia de catarata em larga escala para um hospital público, para o governo e para a sociedade, pelas técnicas de facoemulsificação (FACO) e extração extracapsular (EECP). MÉTODOS: Foi realizada revisão baseada principalmente em diversos estudos clínicos realizados entre 2002 e 2010, no Centro Cirúrgico Ambulatorial do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo. RESULTADOS: Os gastos estimados com os insumos utilizados para as cirurgias foram de R$ 468,92 no grupo FACO e R$ 259,96 no grupo EECP. As despesas hospitalares com o acompanhamento pós-operatório foram em média de R$ 16,40 (42%) menores no grupo FACO. Com relação ao gasto estimado para a Previdência Social, o grupo EECP custou em média, US$ 44,58 por paciente a mais que o grupo FACO. CONCLUSÃO: O incentivo e o investimento governamental para a realização da FACO no SUS são socialmente justificados, deve-se considerar também a economia dos pacientes e do sistema empresarial, bem como as vantagens clínicas para os pacientes e vantagens econômicas para os hospitais.

Dynamics of cell and tissue genesis in the male reproductive system of ticks (Acari: Ixodidae) Amblyomma cajennense (Fabricius, 1787) and Amblyomma aureolatum (Pallas, 1772): a comparative analysis

Ticks are classified into three families: Argasidae, Ixodidae, and Nutalliellidae. The taxonomy and phylogeny within Ixodidae are still discussed by the specialists, thus requiring further studies. Amblyomma cajennese and Amblyomma aureolatum (Brazil) belong to two species complexes known as “cajennese” and “ovale”, respectively, and are directly related to the transmission of the Brazilian spotted fever. This confirms the medical and veterinary significance of these species, as well as the need for further morphological studies that will bring a better understanding of their taxonomy, phylogeny, and control. In this context, the present study aimed to characterize the morphology of the male reproductive system of A. cajennese and A. aureolatum when unfed and after 4 days of feeding, thereby seeking to: (a) distinguish the two species or “complexes”, and (b) study an internal system which has the potential to be targeted by acaricides. Therefore, males from both species (unfed and after 4 days of feeding) were cold-anesthetized, dissected, and had their reproductive systems removed for histological analysis. The results showed that the morphology of the male reproductive system is generally similar between both species, like in other Ixodidae ticks, exhibiting a multilobed accessory gland complex related to seminal fluid secretion, a pair of vasa deferentia and a pair of testes housing germ cells (spermatocytes) in different stages. The main differences were found in the development of the accessory gland complex cells and germ cells, showing that the maturation of the male reproductive system starts later in A. aureolatum, when compared to A. cajennese. However, during the blood meal, A. aureolatum development is increased, thus making germ cell maturation and gland complex activity higher than in A. cajennese. This study shows the differences in the development of the male reproductive systems of both species, while providing information that can assist in the establishment of new control methods.

ANALYSIS OF MANGROVE FOREST SUCCESSION, USING SEDIMENT CORES: A CASE STUDY IN THE CANANEIA-IGUAPE COASTAL SYSTEM, SAO PAULO-BRAZIL

Sediment cores are an essential tool for the analysis of the dynamics of mangrove succession. Coring was used to correlate changes in depositional environments and lateral sedimentary facies with discrete stages of forest succession at the Cananeia-Iguape Coastal System in southeastern Brazil. A local level successional pattern was examined based on four core series T1) a sediment bank; T2) a smooth cordgrass Spartina alterniflora bank; T3) an active mangrove progradation fringe dominated by Laguncularia racemosa, and; T4) a mature mangrove forest dominated by Avicennia schaueriana. Cores were macroscopically described in terms of color, texture, sedimentary structure and organic components. The base of all cores exhibited a similar pattern suggesting common vertical progressive changes in depositional conditions and subsequent successional colonization pattern throughout the forest. The progradation zone is an exposed bank, colonized by S. alterniflora. L. racemosa, replaces S. alterniflora as progradation takes place. As the substrate consolidates A. schaueriana replaces L. racemosa and attains the greatest structural development in the mature forest. Cores collected within the A. schaueriana dominated stand contained S. alterniflora fragments near the base, confirming that a smooth cordgrass habitat characterized the establishment and early seral stages. Cores provide a reliable approach to describe local-level successional sequences in dynamic settings subject to drivers operating on multiple temporal and spatial scales where spatial heterogeneity can lead to multiple equilibria and where similar successional end-points may be reached through convergent paths.

Paleoenvironmental reconstruction of a Late Quaternary lagoon system in southern Brazil (Jaguaruna region, Santa Catarina state) based on multi-proxy analysis

This paper provides a paleoenvironmental reconstruction of a Late Quaternary lagoon system in the Jaguaruna region of Santa Catarina state, southern Brazil. Integrated results of bulk sedimentary organic matter characterization (delta C-13, delta N-15 and C/N), microfossil (pollen and diatom) and grain-size analysis from three shallow cores (similar to 2.5m depth) allowed us to propose an evolving paleogeographic scenario in this coastal region for the last ca. 5500 cal a BP. The lagoonal system in this area was more extensive during the mid-Holocene than today, with a gradual and continuous lagoon-sea disconnection until the present. We add to the debate regarding relative sea-level (RSL) variations for the Brazilian coast during the Holocene and discuss the importance of sedimentary dynamics for interpreting changes in coastal ecosystems. The multi-proxy analysis suggests that changes in coastal ecosystems could be directly related to local sedimentary processes, which are not necessarily linked to RSL fluctuations and/or to climatic variations. Copyright (c) 2011 John Wiley & Sons, Ltd.

A new analysis of the GJ581 extrasolar planetary system

We have done a new analysis of the available observations of the GJ581 exoplanetary system. Today this system is controversial due to choices that can be done in the orbital determination. The main ones are the occurrence of aliases and the additional bodies-the planets f and g-announced in Vogt et al. (Astrophys J 723:954-965, 2010). Any dynamical study of exoplanets requires the good knowledge of the orbital elements and the investigations involving the planet g are particularly interesting, since this body would lie in the habitable zone (HZ) of the star GJ581. This region, for this system, is very attractive of the dynamical point of view due to several resonances of two and three bodies present there. In this work, we investigate the conditions under which the planet g may exist. We stress the fact that the planet g is intimately related with the orbital elements of the planet d; more precisely, we conclude that it is not possible to disconnect its existence from the determination of the eccentricity of the planet d. Concerning the planet f, we have found one solution with period a parts per thousand 450 days, but we are judicious about any affirmation concerning this body because its signal is in the threshold of detection and the high period is in a spectral region where the occurrence of aliases is very common. Besides, we outline some dynamical features of the HZ with the dynamical map and point out the role played by some resonances laying there.

Combinatorial-topological framework for the analysis of global dynamics

We discuss an algorithmic framework based on efficient graph algorithms and algebraic-topological computational tools. The framework is aimed at automatic computation of a database of global dynamics of a given m-parameter semidynamical system with discrete time on a bounded subset of the n-dimensional phase space. We introduce the mathematical background, which is based upon Conley's topological approach to dynamics, describe the algorithms for the analysis of the dynamics using rectangular grids both in phase space and parameter space, and show two sample applications. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4767672]

An in-depth analysis of the HIV-1/AIDS dynamics by comprehensive mathematical modeling

This work presents major results from a novel dynamic model intended to deterministically represent the complex relation between HIV-1 and the human immune system. The novel structure of the model extends previous work by representing different host anatomic compartments under a more in-depth cellular and molecular immunological phenomenology. Recently identified mechanisms related to HIV-1 infection as well as other well known relevant mechanisms typically ignored in mathematical models of HIV-1 pathogenesis and immunology, such as cell-cell transmission, are also addressed. (C) 2011 Elsevier Ltd. All rights reserved.

Bifurcation analysis of an aeroelastic system with concentrated nonlinearities

Analytical and numerical analyses of the nonlinear response of a three-degree-of-freedom nonlinear aeroelastic system are performed. Particularly, the effects of concentrated structural nonlinearities on the different motions are determined. The concentrated nonlinearities are introduced in the pitch, plunge, and flap springs by adding cubic stiffness in each of them. Quasi-steady approximation and the Duhamel formulation are used to model the aerodynamic loads. Using the quasi-steady approach, we derive the normal form of the Hopf bifurcation associated with the system's instability. Using the nonlinear form, three configurations including supercritical and subcritical aeroelastic systems are defined and analyzed numerically. The characteristics of these different configurations in terms of stability and motions are evaluated. The usefulness of the two aerodynamic formulations in the prediction of the different motions beyond the bifurcation is discussed.

Analysis of nonlinear dynamics of vocal folds using high-speed video observation and biomechanical modeling

Primary voice production occurs in the larynx through vibrational movements carried out by vocal folds. However, many problems can affect this complex system resulting in voice disorders. In this context, time-frequency-shape analysis based on embedding phase space plots and nonlinear dynamics methods have been used to evaluate the vocal fold dynamics during phonation. For this purpose, the present work used high-speed video to record the vocal fold movements of three subjects and extract the glottal area time series using an image segmentation algorithm. This signal is used for an optimization method which combines genetic algorithms and a quasi-Newton method to optimize the parameters of a biomechanical model of vocal folds based on lumped elements (masses, springs and dampers). After optimization, this model is capable of simulating the dynamics of recorded vocal folds and their glottal pulse. Bifurcation diagrams and phase space analysis were used to evaluate the behavior of this deterministic system in different circumstances. The results showed that this methodology can be used to extract some physiological parameters of vocal folds and reproduce some complex behaviors of these structures contributing to the scientific and clinical evaluation of voice production. (C) 2010 Elsevier Inc. All rights reserved.