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.

Evaluation of physiologic complexity in time series using generalized sample entropy and surrogate data analysis

Complexity in time series is an intriguing feature of living dynamical systems, with potential use for identification of system state. Although various methods have been proposed for measuring physiologic complexity, uncorrelated time series are often assigned high values of complexity, errouneously classifying them as a complex physiological signals. Here, we propose and discuss a method for complex system analysis based on generalized statistical formalism and surrogate time series. Sample entropy (SampEn) was rewritten inspired in Tsallis generalized entropy, as function of q parameter (qSampEn). qSDiff curves were calculated, which consist of differences between original and surrogate series qSampEn. We evaluated qSDiff for 125 real heart rate variability (HRV) dynamics, divided into groups of 70 healthy, 44 congestive heart failure (CHF), and 11 atrial fibrillation (AF) subjects, and for simulated series of stochastic and chaotic process. The evaluations showed that, for nonperiodic signals, qSDiff curves have a maximum point (qSDiff(max)) for q not equal 1. Values of q where the maximum point occurs and where qSDiff is zero were also evaluated. Only qSDiff(max) values were capable of distinguish HRV groups (p-values 5.10 x 10(-3); 1.11 x 10(-7), and 5.50 x 10(-7) for healthy vs. CHF, healthy vs. AF, and CHF vs. AF, respectively), consistently with the concept of physiologic complexity, and suggests a potential use for chaotic system analysis. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4758815]

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.

Falhas de mercado e redes em políticas públicas: desafios e possibilidades ao Sistema Único de Saúde

Os princípios e as diretrizes do Sistema Único de Saúde (SUS) impõem uma estrutura de assistência baseada em redes de políticas públicas que, combinada ao modelo de financiamento adotado, conduz a falhas de mercado. Isso impõe barreiras à gestão do sistema público de saúde e à concretização dos objetivos do SUS. As características institucionais e a heterogeneidade dos atores, aliadas à existência de diferentes redes de atenção à saúde, geram complexidade analítica no estudo da dinâmica global da rede do SUS. Há limitações ao emprego de métodos quantitativos baseados em análise estática com dados retrospectivos do sistema público de saúde. Assim, propõe-se a abordagem do SUS como sistema complexo, a partir da utilização de metodologia quantitativa inovadora baseada em simulação computacional. O presente artigo buscou analisar desafios e potencialidades na utilização de modelagem com autômatos celulares combinada com modelagem baseada em agentes para simulação da evolução da rede de serviços do SUS. Tal abordagem deve permitir melhor compreensão da organização, heterogeneidade e dinâmica estrutural da rede de serviços do SUS e possibilitar minimização dos efeitos das falhas de mercado no sistema de saúde brasileiro.

Anthropogenic influences in a lagoonal environment: a multiproxy approach at the valo grande mouth, Cananéia-Iguape system (SE Brazil)

The Cananeia-Iguape system, SE Brazil, consists of a complex of lagoonal channels, located in a United Nations Educational, Scientific and Cultural Organization (UNESCO) Biosphere Reserve. Nevertheless, important environmental changes have occurred in approximately the last 150 yrs due to the opening of an artificial channel, the Valo Grande, connecting the Ribeira de Iguape River to the lagoonal system. Our objective is to assess the historical record of the uppermost layers of the sedimentary column of the lagoonal system in order to determine the history of environmental changes caused by the opening of the artificial channel. In this sense, an integrated geochemical-faunal approach is used. The environmental changes led significant modifications in salinity, in changes of the depositional patterns of sediments and foraminiferal assemblages (including periods of defaunation), and, more drastically, in the input of heavy metals to the coastal environment. The concentrations Pb in the core analyzed here were up to two times higher than the values measured in contaminated sediments from the Santos estuary, the most industrialized coastal zone in Brazil.

Semantic information extraction from images of complex documents

Even though the digital processing of documents is increasingly widespread in industry, printed documents are still largely in use. In order to process electronically the contents of printed documents, information must be extracted from digital images of documents. When dealing with complex documents, in which the contents of different regions and fields can be highly heterogeneous with respect to layout, printing quality and the utilization of fonts and typing standards, the reconstruction of the contents of documents from digital images can be a difficult problem. In the present article we present an efficient solution for this problem, in which the semantic contents of fields in a complex document are extracted from a digital image.

Relative abundance and population biology of the non-indigenous crab Charybdis hellerii (Crustacea: Brachyura: Portunidae) in a southwestern Atlantic estuary-bay complex

Invasive species are potential threats to biodiversity, especially if they become established and outnumber native species. In this study, a population of the non-indigenous crab Charybdis hellerii was analyzed in an estuary-bay complex on the southeastern Brazilian coast, with respect to its abundance relative to sympatric native brachyuran species, as well as the size structure, sexual maturity, sex ratio, frequency of mutilation, reproductive period, and development of the reproductive system. Crabs were sampled monthly both in the intertidal zone of rocky shores and on sublittoral soft-bottom. Nine species were recorded on the rocky shores, where C. hellerii was the second most abundant species; only three individuals of C. hellerii were collected in the sublittoral samples. This population of C. hellerii showed a unimodal size structure composed mainly of mature individuals; males were larger than females, and the sex ratio was skewed toward males (3.1:1). About 46.9% of the individuals (75 of 160 crabs) had mutilated or regenerating appendages, more frequent in males (56.8%) than in females (28.2%), which may reflect both inter- and intraspecific agonistic interactions. A continuous reproductive pattern is suggested for this population, although ovigerous females occurred unevenly during the year, with 58.82% of them being collected in winter. There was evidence of multiple spawning, since the ovigerous females with an initial egg mass showed mature ovaries as well as seminal receptacles filled with sperm. C. hellerii is well established in the estuary-bay complex, but is concentrated in intertidal and shallow subtidal rocky shores, where it may compete with and replace other species such as the portunid Cronius ruber. This study also highlights the importance of systematic monitoring studies to evaluate the effects of the introduction of non-indigenous species on ecologically similar natives.

Modulation of Maternal Immune System During Pregnancy in the Cow

There is a molecular crosstalk between the trophoblast and maternal immune cells of bovine endometrium. The uterine cells are able to secrete cytokine/chemokines to either induce a suppressive environment for establishment of the pregnancy or to recruit immune cells to the endometrium to fight infections. Despite morphological differences between women and cows, mechanisms for immune tolerance during pregnancy seem to be conserved. Mechanisms for uterine immunesuppression in the cow include: reduced expression of major histocompatability proteins by the trophoblast; recruitment of macrophages to the pregnant endometrium; and modulation of immune-related genes in response to the presence of the conceptus. Recently, an eGFP transgenic cloned embryo model developed by our group showed that there is modulation of foetal proteins expressed at the site of syncytium formation, suggesting that foetal cell can regulate not only by the secretion of specific factors such as interferon-tau, but also by regulating their own protein expression to avoid excessive maternal recognition by the local immune system. Furthermore, foetal DNA can be detected in the maternal circulation; this may reflect the occurrence of an invasion of trophoblast cells and/or their fragment beyond the uterine basement membrane in the cow. In fact, the newly description of exosome release by the trophoblast cell suggests that could be a new fashion of maternal-foetal communication at the placental barrier. Additionally, recent global transcriptome studies on bovine endometrium suggested that the immune system is aware, from an immunological point of view, of the presence of the foetus in the cow during early pregnancy.

Toward the Optimization of an e-Tongue System Using Information Visualization: A Case Study with Perylene Tetracarboxylic Derivative Films in the Sensing Units

The wide variety of molecular architectures used in sensors and biosensors and the large amount of data generated with some principles of detection have motivated the use of computational methods, such as information visualization techniques, not only to handle the data but also to optimize sensing performance. In this study, we combine projection techniques with micro-Raman scattering and atomic force microscopy (AFM) to address critical issues related to practical applications of electronic tongues (e-tongues) based on impedance spectroscopy. Experimentally, we used sensing units made with thin films of a perylene derivative (AzoPTCD acronym), coating Pt interdigitated electrodes, to detect CuCl(2) (Cu(2+)), methylene blue (MB), and saccharose in aqueous solutions, which were selected due to their distinct molecular sizes and ionic character in solution. The AzoPTCD films were deposited from monolayers to 120 nm via Langmuir-Blodgett (LB) and physical vapor deposition (PVD) techniques. Because the main aspects investigated were how the interdigitated electrodes are coated by thin films (architecture on e-tongue) and the film thickness, we decided to employ the same material for all sensing units. The capacitance data were projected into a 2D plot using the force scheme method, from which we could infer that at low analyte concentrations the electrical response of the units was determined by the film thickness. Concentrations at 10 mu M or higher could be distinguished with thinner films tens of nanometers at most-which could withstand the impedance measurements, and without causing significant changes in the Raman signal for the AzoPTCD film-forming molecules. The sensitivity to the analytes appears to be related to adsorption on the film surface, as inferred from Raman spectroscopy data using MB as analyte and from the multidimensional projections. The analysis of the results presented may serve as a new route to select materials and molecular architectures for novel sensors and biosensors, in addition to suggesting ways to unravel the mechanisms behind the high sensitivity obtained in various sensors.

The IgA1 immune complex-mediated activation of the MAPK/ERK kinase pathway in mesangial cells is associated with glomerular damage in IgA nephropathy

IgA nephropathy (IgAN), the most common primary glomerulonephritis worldwide, has significant morbidity and mortality as 20-40% of patients progress to end-stage renal disease within 20 years of onset. In order to gain insight into the molecular mechanisms involved in the progression of IgAN, we systematically evaluated renal biopsies from such patients. This showed that the MAPK/ERK signaling pathway was activated in the mesangium of patients presenting with over 1 g/day proteinuria and elevated blood pressure, but absent in biopsy specimens of patients with IgAN and modest proteinuria (<1 g/day). ERK activation was not associated with elevated galactose-deficient IgA1 or IgG specific for galactose-deficient IgA1 in the serum. In human mesangial cells in vitro, ERK activation through mesangial IgA1 receptor (CD71) controlled pro-inflammatory cytokine secretion and was induced by large-molecular-mass IgA1-containing circulating immune complexes purified from patient sera. Moreover, IgA1-dependent ERK activation required renin-angiotensin system as its blockade was efficient in reducing proteinuria in those patients exhibiting substantial mesangial activation of ERK. Thus, ERK activation alters mesangial cell-podocyte crosstalk, leading to renal dysfunction in IgAN. Assessment of MAPK/ERK activation in diagnostic renal biopsies may predict the therapeutic efficacy of renin-angiotensin system blockers in IgAN. Kidney International (2012) 82, 1284-1296; doi:10.1038/ki.2012.192; published online 5 September 2012

Robust and optimal adjustment of Power System Stabilizers through Linear Matrix Inequalities

This work presents the application of Linear Matrix Inequalities to the robust and optimal adjustment of Power System Stabilizers with pre-defined structure. Results of some tests show that gain and zeros adjustments are sufficient to guarantee robust stability and performance with respect to various operating points. Making use of the flexible structure of LMI's, we propose an algorithm that minimizes the norm of the controllers gain matrix while it guarantees the damping factor specified for the closed loop system, always using a controller with flexible structure. The technique used here is the pole placement, whose objective is to place the poles of the closed loop system in a specific region of the complex plane. Results of tests with a nine-machine system are presented and discussed, in order to validate the algorithm proposed. (C) 2012 Elsevier Ltd. All rights reserved.

Unveiling the relationship between complex networks metrics and word senses

The automatic disambiguation of word senses (i.e., the identification of which of the meanings is used in a given context for a word that has multiple meanings) is essential for such applications as machine translation and information retrieval, and represents a key step for developing the so-called Semantic Web. Humans disambiguate words in a straightforward fashion, but this does not apply to computers. In this paper we address the problem of Word Sense Disambiguation (WSD) by treating texts as complex networks, and show that word senses can be distinguished upon characterizing the local structure around ambiguous words. Our goal was not to obtain the best possible disambiguation system, but we nevertheless found that in half of the cases our approach outperforms traditional shallow methods. We show that the hierarchical connectivity and clustering of words are usually the most relevant features for WSD. The results reported here shed light on the relationship between semantic and structural parameters of complex networks. They also indicate that when combined with traditional techniques the complex network approach may be useful to enhance the discrimination of senses in large texts. Copyright (C) EPLA, 2012

The role of wax and resin in the nestmate recognition system of a stingless bee, Tetragonisca angustula

Recent research has shown that entrance guards of the stingless bee Tetragonisca angustula make less errors in distinguishing nestmates from non-nestmates than all other bee species studied to date, but how they achieve this is unknown. We performed four experiments to investigate nestmate recognition by entrance guards in T. angustula. We first investigated the effect of colony odours on acceptance. Nestmates that acquired odour from non-nestmate workers were 63% more likely to be rejected while the acceptance rate of non-nestmates treated with nestmate odour increased by only 7%. We further hypothesised that guards standing on the wax entrance tube might use the tube as an odour referent. However, our findings showed that there was no difference in the acceptance of non-nestmates by guards standing on their own colony's entrance tube versus the non-nestmate's entrance tube. Moreover, treatment of bees with nestmate and non-nestmate resin or wax had a negative effect on acceptance rates of up to 65%, regardless of the origin of the wax or resin. The role of resin as a source of recognition cues was further investigated by unidirectionally transferring resin stores between colonies. Acceptance rates of nestmates declined by 37% for hives that donated resin, contrasting with resin donor hives where acceptance of non-nestmates increased by 21%. Overall, our results confirm the accuracy of nestmate recognition in T. angustula and reject the hypothesis that this high level of accuracy is due to the use of the wax entrance tubes as a referent for colony odour. Our findings also suggest that odours directly acquired from resin serve no primary function as nestmate recognition cues. The lack of consistency among colonies plus the complex results of the third and fourth experiments highlight the need for further research on the role of nest materials and cuticular profiles in understanding nestmate recognition in T. angustula.

On Site Stripping Voltammetric Determination of Zn(II), Cd(II) and Pb(II) in Water Samples of the Cananeia-Iguape Estuarine-Lagoon Complex in Sao Paulo State, Brazil

Estuarine systems play an important role in the retention of toxic trace elements owing to the affinity of these elements with particles dissolved in water. This work presents the use of a voltammetric sensor to monitor heavy metal (Zn (II), Cd(II) and Pb (II)) concentrations in the Cananeia-Iguape Estuarine-Lagoon region (Sao Paulo State, Brazil). Lower concentrations were found in the Southern estuarine system (Cananeia City) and increased concentrations observed in the Northern sector (Iguape City) were promoted by anthropogenic activities, with particular influence from the historical introduction of mining wastes and inputs from agricultural, industrial and domestic effluents. The proposed method is reliable, inexpensive and fast, can simultaneously provide information on the concentration of these metallic ions and can be easily used for field measurements aboard oceanographic ships.

Amazon Rainforest Exchange of Carbon and Subcanopy Air Flow: Manaus LBA Site-A Complex Terrain Condition

On the moderately complex terrain covered by dense tropical Amazon Rainforest (Reserva Biologica do Cuieiras-ZF2-02 degrees 36'17.1 '' S, 60 degrees 12'24.4 '' W), subcanopy horizontal and vertical gradients of the air temperature, CO2 concentration and wind field were measured for the dry and wet periods in 2006. We tested the hypothesis that horizontal drainage flow over this study area is significant and can affect the interpretation of the high carbon uptake rates reported by previous works at this site. A similar experimental design as the one by Tota et al. (2008) was used with a network of wind, air temperature, and CO2 sensors above and below the forest canopy. A persistent and systematic subcanopy nighttime upslope (positive buoyancy) and daytime downslope (negative buoyancy) flow pattern on a moderately inclined slope (12%) was observed. The microcirculations observed above the canopy (38 m) over the sloping area during nighttime presents a downward motion indicating vertical convergence and correspondent horizontal divergence toward the valley area. During the daytime an inverse pattern was observed. The microcirculations above the canopy were driven mainly by buoyancy balancing the pressure gradient forces. In the subcanopy space the microcirculations were also driven by the same physical mechanisms but probably with the stress forcing contribution. The results also indicated that the horizontal and vertical scalar gradients (e. g., CO2) were modulated by these micro-circulations above and below the canopy, suggesting that estimates of advection using previous experimental approaches are not appropriate due to the tridimensional nature of the vertical and horizontal transport locally. This work also indicates that carbon budget from tower-based measurement is not enough to close the system, and one needs to include horizontal and vertical advection transport of CO2 into those estimates.