Epstein-Barr Virus (EBV) detection and typing by PCR: a contribution to diagnostic screening of EBV-positive Burkitt's lymphoma

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Establishing Standards for the Integrated Recommendation and Diagnosis System (DRIS) for Irrigated Bean Crops

This article addresses the establishment of integrated diagnostics and recommendation system (DRIS) standards for irrigated bean crops (Phaseolus vulgaris) and compares leaf concentrations and productivity in low- and high-productivity populations. The work was carried out in Santa Fe de Goias, Goias State, Brazil, in the agricultural years 1999/2000 and 2000/2001. For the nutritional diagnosis, leaf samples were collected, and leaf concentrations of nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sulfur (S), boron (B), copper (Cu), iron (Fe), manganese (Mn), and zinc (Zn) were established in 100 commercial bean crops. A database was set up listing the leaf nutrient content and the respective productivities, subdivided into two subpopulations, high and low productivity, using a bean yield value of 3000 kg ha-1 to separate these subpopulations. Sufficiency values found in the high-productivity population matched only for the micronutrients B and Zn. The nutritional balance among the populations studied was coherent and was lower in the high-productivity population. The DRIS standards proposed for irrigated bean farming were efficient in evaluating the nutritional status of the crop areas studied. Calcium, Cu, and S were found to be the least available nutrients, indicating high response potential for the fertilizing using these nutrients.

Conservation and use of palm trees in Brazil's landscaping

Palm trees belong to the Arecaceae family and are widely utilized in landscaping of tropical countries. Although there are many species, just a few are used in Brazil's landscaping, the majority coming from other countries. So, this study had the objective to characterize the plants in the collection of palm trees at UNESP/FCAV, Campus of Jaboticabal, Sao Paulo State, Brazil. The germination of seeds was also studied to increase the production of seedlings for use in landscaping, as this is the biggest difficulty for spreading new species. The introduction of new species in the collection was accomplished. It was also made a survey of major pests and diseases that occur in the collection. The most common pests found were: Brassolis sophorae, Parisoschoenus obesulus, Rhynchophorus palmarum and Coraliomela sp., and the most common disease causing fungi: Colletrotrichum sp., Curvularia sp., Bipolaris sp., Helminthosporium sp., Alternaria sp., Phyllosticta sp., Pestalotia sp., Exosporium palmivorum and Ceratocystis pardoxa.

Lidar observation campaign of sugar cane fires and industrial emissions in the State of São Paulo, Brazil

Brazil has an important role in the biomass burning, with the detection of approximately 100,000 burning spots in a single year (2007). Most of these spots occur in the southern part of the Amazon basin during the dry season (from August to november) and these emissions reach the southeast of the country, a highly populated region and with serious urban air pollution problems. With the growing demand on biofuels, sugarcane is considerably expanding in the state of São Paulo, being a strong contributor to the bad air quality in this region. In the state of São Paulo, the main land use are pasture and sugarcane crop, that covers around 50% and 10% of the total area, respectively. Despite the aerosol from sugarcane burning having reduced atmospheric residence time, from a few days to some weeks, they might get together with those aerosol which spread over long distances (hundreds to thousands of kilometers). In the period of June through February 2010 a LIDAR observation campaign was carried in the state of São Paulo, Brazil, in order to observe and characterize optically the aerosols from two distinct sources, namely, sugar cane biomass burning and industrial emissions. For this purpose 2 LIDAR systems were available, one mobile and the other placed in a laboratory, both working in the visible (532 nm) and additionally the mobile system had a Raman channel available (607 nm). Also this campaign counted with a SODAR, a meteorological RADAR specially set up to detect aerosol echoes and gas-particle analyzers. To guarantee a good regional coverage 4 distinct sites were available to deploy the instruments, 2 in the near field of biomass burning activities (Rio Claro and Bauru), one for industrial emissions (Cubatão) and others from urban sources (São Paulo). The whole campaign provide the equivalent of 30 days of measurements which allowed us to get aerosol optical properties such as backscattering/extinction coefficients, scatter and LIDAR ratios, those were used to correlate with air quality and meteorological indicators and quantities. In this paper we should focus on the preliminary results of the Raman LIDAR system and its derived aerosol optical quantities. © 2010 Copyright SPIE - The International Society for Optical Engineering.

Delay time detection and accommodation for a networked DC motor control

This paper presents a control method that is effective to reduce the degenerative effects of delay time caused by a treacherous network. In present application a controlled DC motor is part of an inverted pendulum and provides the equilibrium of this system. The control of DC motor is accomplished at the distance through a treacherous network, which causes delay time in the control signal. A predictive technique is used so that it turns the system free of delay. A robust digital sliding mode controller is proposed to control the free-delay system. Due to the random conditions of the network operation, a delay time detection and accommodation strategy is also proposed. A computer simulation is shown to illustrate the design procedures and the effectiveness of the proposed method. © 2011 IEEE.

Water availability determines the richness and density of fig trees within Brazilian semideciduous forest landscapes

The success of fig trees in tropical ecosystems is evidenced by the great diversity (+750 species) and wide geographic distribution of the genus. We assessed the contribution of environmental variables on the species richness and density of fig trees in fragments of seasonal semideciduous forest (SSF) in Brazil. We assessed 20 forest fragments in three regions in Sao Paulo State, Brazil. Fig tree richness and density was estimated in rectangular plots, comprising 31.4 ha sampled. Both richness and fig tree density were linearly modeled as function of variables representing (1) fragment metrics, (2) forest structure, and (3) landscape metrics expressing water drainage in the fragments. Model selection was performed by comparing the AIC values (Akaike Information Criterion) and the relative weight of each model (wAIC). Both species richness and fig tree density were better explained by the water availability in the fragment (meter of streams/ha): wAICrichness = 0.45, wAICdensity = 0.96. The remaining variables related to anthropic perturbation and forest structure were of little weight in the models. The rainfall seasonality in SSF seems to select for both establishment strategies and morphological adaptations in the hemiepiphytic fig tree species. In the studied SSF, hemiepiphytes established at lower heights in their host trees than reported for fig trees in evergreen rainforests. Some hemiepiphytic fig species evolved superficial roots extending up to 100 m from their trunks, resulting in hectare-scale root zones that allow them to efficiently forage water and soil nutrients. The community of fig trees was robust to variation in forest structure and conservation level of SSF fragments, making this group of plants an important element for the functioning of seasonal tropical forests. © 2013 Elsevier Masson SAS. All rights reserved.

Utilização de modelos de falhas e observadores de estado em estruturas reticuladas

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Diagnose de falhas via observadores de estado em sistemas mecânicos com absorvedores dinâmicos de vibrações tipo lâmina vibrante

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Diagnóstico de falhas via observadores de estado com excitações desconhecidas, identificadas via funções ortogonais

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Incorporating Varying Test Costs and Fault Severities into Test Case Prioritization

Test case prioritization techniques schedule test cases for regression testing in an order that increases their ability to meet some performance goal. One performance goal, rate offault detection, measures how quickly faults are detected within the testing process. In previous work we provided a metric, APFD, for measuring rate of fault detection, and techniques for prioritizing test cases to improve APFD, and reported the results of experiments using those techniques. This metric and these techniques, however, applied only in cases in which test costs and fault severity are uniform. In this paper, we present a new metric for assessing the rate of fault detection of prioritized test cases, that incorporates varying test case and fault costs. We present the results of a case study illustrating the application of the metric. This study raises several practical questions that might arise in applying test case prioritization; we discuss how practitioners could go about answering these questions.

Plasmodium vivax: Reverse transcriptase real-time PCR for gametocyte detection and quantitation in clinical samples

The proportion of Plasmodium vivax-infected subjects that carry mature gametocytes, and thus are potentially infectious, remains poorly characterized in endemic settings. Here, we describe a quantitative reverse transcriptase (RI) real-time PCR (qRT-PCR) that targets transcripts of the mature gametocyte-specific pvs25 gene. We found mature gametocytes in 42 of 44 (95.4%) P. vivax infections diagnosed during an ongoing cohort study in northwestern Brazil. SYBR green qRT-PCR was more sensitive than a conventional RT-PCR that targets the same gene. Molecular detection of gametocytes failed, however, when dried bloodspots were used for RNA isolation and complementary DNA synthesis. Estimating the number of pvs25 gene transcripts allowed for examining the potential infectiousness of gametocyte carriers in a quantitative way. We found that most (61.9%) gametocyte carriers were either asymptomatic or had subpatent parasitemias and would have been missed by routine malaria control strategies. However, potentially undiagnosed gametocyte carriers usually had low-density infections and contributed a small fraction (up to 4%) to the overall gametocyte burden in the community. Further studies are required to determine the relative contribution to malaria transmission of long-lasting but low-density gametocytemias in asymptomatic carriers that are left undiagnosed and untreated. (C) 2012 Elsevier Inc. All rights reserved.

A low complexity system based on multiple weighted decision trees for indoor localization

[EN] Indoor position estimation has become an attractive research topic due to growing interest in location-aware services. Nevertheless, satisfying solutions have not been found with the considerations of both accuracy and system complexity. From the perspective of lightweight mobile devices, they are extremely important characteristics, because both the processor power and energy availability are limited. Hence, an indoor localization system with high computational complexity can cause complete battery drain within a few hours. In our research, we use a data mining technique named boosting to develop a localization system based on multiple weighted decision trees to predict the device location, since it has high accuracy and low computational complexity.

Detection and localization of GLUTs in spermatozoa from different domestic species

Sperm cells need hexoses as a substrate for their function, for both the maintenance of membrane homeostasis and the movement of the tail. These cells have a peculiar metabolism that has not yet been fully understood, but it is clear that they obtain energy from hexoses through glycolisis and/or oxidative phosphorylation. Spermatozoa are in contact with different external environments, beginning from the testicular and epididymal fluid, passing to the seminal plasma and finally to the female genital tract fluids; in addition, with the spread of reproductive biotechnologies, sperm cells are diluted and stored in various media, containing different energetic substrates. To utilize these energetic sources, sperm cells, as other eukaryotic cells, have a well-constructed protein system, that is mainly represented by the GLUT family proteins. These transporters have a membrane-spanning α-helix structure and work as an enzymatic pump that permit a fast gradient dependent passage of sugar molecules through the lipidic bilayer of sperm membrane. Many GLUTs have been studied in man, bull and rat spermatozoa; the presence of some GLUTs has been also demonstrated in boar and dog spermatozoa. The aims of the present study were - to determine the presence of GLUTs 1, 2, 3, 4 and 5 in boar, horse, dog and donkey spermatozoa and to describe their localization; - to study eventual changes in GLUTs location after capacitation and acrosome reaction in boar, stallion and dog spermatozoa; - to determine possible changes in GLUTs localization after capacitation induced by insulin and IGF stimulation in boar spermatozoa; - to evaluate changes in GLUTs localization after flow-cytometric sex sorting in boar sperm cells. GLUTs 1, 2, 3 and 5 presence and localization have been demonstrated in boar, stallion, dog and donkey spermatozoa by western blotting and immunofluorescence analysis; a relocation in GLUTs after capacitation has been observed only in dog sperm cells, while no changes have been observed in the other species examined. As for boar, the stimulation of the capacitation with insulin and IGF didn’t cause any change in GLUTs localization, as well as for the flow cytometric sorting procedure. In conclusion, this study confirms the presence of GLUTs 1, 2 ,3 and 5 in boar, dog, stallion and donkey spermatozoa, while GLUT 4 seems to be absent, as a confirmation of other studies. Only in dog sperm cells capacitating conditions induce a change in GLUTs distribution, even if the physiological role of these changes should be deepened.

Lesion detection and classification in breast cancer: evaluation of approaches based on morphological features, tracer kinetic modelling and semi-quantitative parameters in MR functional imaging (DCE-MRI)

The diagnosis, grading and classification of tumours has benefited considerably from the development of DCE-MRI which is now essential to the adequate clinical management of many tumour types due to its capability in detecting active angiogenesis. Several strategies have been proposed for DCE-MRI evaluation. Visual inspection of contrast agent concentration curves vs time is a very simple yet operator dependent procedure, therefore more objective approaches have been developed in order to facilitate comparison between studies. In so called model free approaches, descriptive or heuristic information extracted from time series raw data have been used for tissue classification. The main issue concerning these schemes is that they have not a direct interpretation in terms of physiological properties of the tissues. On the other hand, model based investigations typically involve compartmental tracer kinetic modelling and pixel-by-pixel estimation of kinetic parameters via non-linear regression applied on region of interests opportunely selected by the physician. This approach has the advantage to provide parameters directly related to the pathophysiological properties of the tissue such as vessel permeability, local regional blood flow, extraction fraction, concentration gradient between plasma and extravascular-extracellular space. Anyway, nonlinear modelling is computational demanding and the accuracy of the estimates can be affected by the signal-to-noise ratio and by the initial solutions. The principal aim of this thesis is investigate the use of semi-quantitative and quantitative parameters for segmentation and classification of breast lesion. The objectives can be subdivided as follow: describe the principal techniques to evaluate time intensity curve in DCE-MRI with focus on kinetic model proposed in literature; to evaluate the influence in parametrization choice for a classic bi-compartmental kinetic models; to evaluate the performance of a method for simultaneous tracer kinetic modelling and pixel classification; to evaluate performance of machine learning techniques training for segmentation and classification of breast lesion.

Implications of regional fault distribution and kinematics for the uplift of rift flanks around the Rwenzori Mountains, Southwestern Uganda

Das Ziel dieser Arbeit bestand in der Untersuchung der Störungsverteilung und der Störungskinematik im Zusammenhang mit der Hebung der Riftschultern des Rwenzori Gebirges.rnDas Rwenzori Gebirge befindet sich im NNE-SSWbis N-S verlaufenden Albertine Rift, des nördlichsten Segments des westlichen Armes des Ostafrikanischen Grabensystems. Das Albertine Rift besteht aus Becken unterschiedlicher Höhe, die den Lake Albert, Lake Edward, Lake George und Lake Kivu enthalten. Der Rwenzori horst trennt die Becken des Lake Albert und des Lake Edward. Es erstreckt sich 120km in N-S Richtung, sowie 40-50km in E-W Richtung, der h¨ochste Punkt befindet sich 5111 ü. NN. Diese Studie untersucht einen Abschnitt des Rifts zwischen etwa 1°N und 0°30'S Breite sowie 29°30' und 30°30' östlicher Länge ersteckt. Auch die Feldarbeit konzentrierte sich auf dieses Gebiet.rnrnHauptzweck dieser Studie bestand darin, die folgende These auf ihre Richtigkeit zu überprüfen: ’Wenn es im Verlauf der Zeit tatsächlich zu wesentlichen Änderungen in der Störungskinematik kam, dann ist die starke Hebung der Riftflanken im Bereich der Rwenzoris nicht einfach durch Bewegung entlang der Graben-Hauptst¨orungen zu erklären. Vielmehr ist sie ein Resultat des Zusammenspiels mehrerer tektonische Prozesse, die das Spannungsfeld beeinflussen und dadurch Änderungen in der Kinematik hervorrufen.’ Dadurch konzentrierte sich die Studie in erster Linie auf die Störungsanalyse.rnrnDie Kenntnis regionaler Änderungen der Extensionsrichtung ist entscheidend für das Verständnis komplexer Riftsysteme wie dem Ostafrikanischen Graben. Daher bestand der Kern der Untersuchung in der Kartierung von Störungen und der Untersuchung der Störungskinematik. Die Aufnahme strukturgeologischer Daten konzentrierte sich auf die Ugandische Seite des Rifts, und Pal¨aospannungen wurden mit Hilfe von St¨orungsdaten durch Spannungsinversion rekonstruiert.rnDie unterschiedliche Orientierung spr¨oder Strukturen im Gelände, die geometrische Analyse der geologischen Strukturen sowie die Ergebnisse von Mikrostrukturen im Dünnschliff (Kapitel 4) weisen auf verschiedene Spannungsfelder hin, die auf mögliche Änderungen der Extensionsrichtung hinweisen. Die Resultate der Spannungsinversion sprechen für Ab-, Über- und Blattverschiebungen sowie für Schrägüberschiebungen (Kapitel 5). Aus der Orientierung der Abschiebungen gehen zwei verschiedene Extensionsrichtungen hervor: im Wesentlichen NW-SE Extension in fast allen Gebieten, sowie NNE-SSW Extension im östlichen Zentralbereich.rnAus der Analyse von Blattverschiebungen ergaben sich drei unterschiedliche Spannungszustände. Zum Einen NNW-SSE bis N-S Kompression in Verbindung mit ENE-WSW bzw E-W Extension wurde für die nördlichen und die zentralen Ruwenzoris ausgemacht. Ein zweiter Spannungszustand mit WNW-ESE Kompression/NNE-SSW Extension betraf die Zentralen Rwenzoris. Ein dritter Spannungszustand mit NNW-SSE Extension betraf den östlichen Zentralteil der Rwenzoris. Schrägüberschiebungen sind durch dazu schräge Achsen charakterisiert, die für N-S bis NNW-SSE Kompression sprechen und ausschließlich im östlichen Zentralabschnitt auftreten. Überschiebungen, die hauptsächlich in den zentralen und den östlichen Rwenzoris auftreten, sprechen für NE-SW orientierten σ2-Achsen und NW-SE Extension.rnrnEs konnten drei unterschiedliche Spannungseinflüsse identifiziert werden: auf die kollisionsbedingte Bildung eines Überschiebungssystem folgte intra-kratonische Kompression und schließlich extensionskontrollierte Riftbildung. Der Übergang zwischen den beiden letztgenannten Spannungszuständen erfolgte Schrittweise und erzeugte vermutlich lokal begrenzte Transpression und Transtension. Gegenw¨artig wird die Störungskinematik der Region durch ein tensiles Spannungsregime in NW-SE bis N-S Richtung bestimmt.rnrnLokale Spannungsvariationen werden dabei hauptsächlich durch die Interferenzrndes regionalen Spannungsfeldes mit lokalen Hauptst¨orungen verursacht. Weitere Faktoren die zu lokalen Veränderungen des Spannungsfeldes führen können sind unterschiedliche Hebungsgeschwindigkeiten, Blockrotation oder die Interaktion von Riftsegmenten. Um den Einfluß präexistenter Strukturen und anderer Bedingungen auf die Hebung der Rwenzoris zu ermitteln, wurde der Riftprozeß mit Hilfe eines analogen ’Sandbox’-Modells rekonstruiert (Kapitel 6). Da sich die Moho-Diskontinuität im Bereich des Arbeitsgebietes in einer Tiefe von 25 km befindet, aktive Störungen aber nur bis zu einer Tiefe von etwa 20 km beobachtet werden können (Koehn et al. 2008), wurden nur die oberen 25 km im Modell nachbebildet. Untersucht und mit Geländebeobachtungen verglichen wurden sowohl die Reihenfolge, in der Riftsegmente entstehen, als auch die Muster, die sich im Verlauf der Nukleierung und des Wachstums dieser Riftsegmente ausbilden. Das Hauptaugenmerk wurde auf die Entwicklung der beiden Subsegmente gelegt auf denen sich der Lake Albert bzw. der Lake Edward und der Lake George befinden, sowie auf das dazwischenliegende Rwenzori Gebirge. Das Ziel der Untersuchung bestand darin herauszufinden, in welcher Weise das südwärts propagierende Lake Albert-Subsegment mit dem sinistral versetzten nordwärts propagierenden Lake Edward/Lake George-Subsegment interagiert.rnrnVon besonderem Interesse war es, in welcherWeise die Strukturen innerhalb und außerhalb der Rwenzoris durch die Interaktion dieser Riftsegmente beeinflußt wurden. rnrnDrei verschiedene Versuchsreihen mit unterschiedlichen Randbedingungen wurden miteinander verglichen. Abhängig vom vorherrschenden Deformationstyp der Transferzone wurden die Reihen als ’Scherungs-dominiert’, ’Extensions-dominiert’ und als ’Rotations-dominiert’ charakterisiert. Die Beobachtung der 3-dimensionalen strukturellen Entwicklung der Riftsegmente wurde durch die Kombination von Modell-Aufsichten mit Profilschnitten ermöglicht. Von den drei genannten Versuchsreihen entwickelte die ’Rotationsdominierten’ Reihe einen rautenförmiger Block im Tranferbereich der beiden Riftsegmente, der sich um 5−20° im Uhrzeigersinn drehte. DieserWinkel liegt im Bereich des vermuteten Rotationswinkel des Rwenzori-Blocks (5°). Zusammengefasst untersuchen die Sandbox-Versuche den Einfluss präexistenter Strukturen und der Überlappung bzw. Überschneidung zweier interagierender Riftsegmente auf die Entwicklung des Riftsystems. Sie befassen sich darüber hinaus mit der Frage, welchen Einfluss Blockbildung und -rotation auf das lokale Stressfeld haben.