sMapReduce: a programming pattern for wireless sensor networks

Wireless Sensor Networks (WSNs) are increasingly used in various application domains like home-automation, agriculture, industries and infrastructure monitoring. As applications tend to leverage larger geographical deployments of sensor networks, the availability of an intuitive and user friendly programming abstraction becomes a crucial factor in enabling faster and more efficient development, and reprogramming of applications. We propose a programming pattern named sMapReduce, inspired by the Google MapReduce framework, for mapping application behaviors on to a sensor network and enabling complex data aggregation. The proposed pattern requires a user to create a network-level application in two functions: sMap and Reduce, in order to abstract away from the low-level details without sacrificing the control to develop complex logic. Such a two-fold division of programming logic is a natural-fit to typical sensor networking operation which makes sensing and topological modalities accessible to the user.

In-situ X-ray diffraction studies during growth of Ni-Ti shape memory alloy films and their complementary ex-situ characterization

Shape Memory Alloy (SMA) Ni-Ti films have attracted much interest as functional and smart materials due to their unique properties. However, there are still important issues unresolved like formation of film texture and its control as well as substrate effects. Thus, the main challenge is not only the control of the microstructure, including stoichiometry and precipitates, but also the identification and control of the preferential orientation since it is a crucial factor in determining the shape memory behaviour. The aim of this PhD thesis is to study the optimisation of the deposition conditions of films of Ni-Ti in order to obtain the material fully crystallized at the end of the deposition, and to establish a clear relationship between the substrates and texture development. In order to achieve this objective, a two-magnetron sputter deposition chamber has been used allowing to heat and to apply a bias voltage to the substrate. It can be mounted into the six-circle diffractometer of the Rossendorf Beamline (ROBL) at the European Synchrotron Radiation Facility (ESRF), Grenoble, France, enabling an in-situ characterization by X-ray diffraction(XRD) of the films during their growth and annealing. The in-situ studies enable us to identify the different steps of the structural evolution during deposition with a set of parameters as well as to evaluate the effect of changing parameters on the structural characteristics of the deposited film. Besides the in-situ studies, other complementary ex-situ characterization techniques such as XRD at a laboratory source, Rutherford backscattering spectroscopy(RBS), Auger electron spectroscopy (AES), cross-sectional transmission electron microscopy (X-TEM), scanning electron microscopy (SEM), and electrical resistivity (ER) measurements during temperature cycling have been used for a fine structural characterization. In this study, mainly naturally and thermally oxidized Si(100) substrates, TiN buffer layers with different thicknesses (i.e. the TiN topmost layer crystallographic orientation is thickness dependent) and MgO(100) single crystals were used as substrates. The chosen experimental procedure led to a controlled composition and preferential orientation of the films. The type of substrate plays an important role for the texture of the sputtered Ni-Ti films and according to the ER results, the distinct crystallographic orientations of the Ni-Ti films influence their phase transformation characteristics.

Fractional central pattern generators for bipedal locomotion

Locomotion has been a major research issue in the last few years. Many models for the locomotion rhythms of quadrupeds, hexapods, bipeds and other animals have been proposed. This study has also been extended to the control of rhythmic movements of adaptive legged robots. In this paper, we consider a fractional version of a central pattern generator (CPG) model for locomotion in bipeds. A fractional derivative D α f(x), with α non-integer, is a generalization of the concept of an integer derivative, where α=1. The integer CPG model has been proposed by Golubitsky, Stewart, Buono and Collins, and studied later by Pinto and Golubitsky. It is a network of four coupled identical oscillators which has dihedral symmetry. We study parameter regions where periodic solutions, identified with legs’ rhythms in bipeds, occur, for 0<α≤1. We find that the amplitude and the period of the periodic solutions, identified with biped rhythms, increase as α varies from near 0 to values close to unity.

Increase in cases of malaria in Mozambique, 2014: epidemic or new endemic pattern?

ABSTRACT OBJECTIVE To describe the increase in cases of malaria in Mozambique. METHODS Cross-sectional study conducted in 2014, in Mozambique with national weekly epidemiological bulletin data. I analyzed the number of recorded cases in the 2009-2013 period, which led to the creation of an endemic channel using the quartile and C-Sum methods. Monthly incidence rates were calculated for the first half of 2014, making it possible to determine the pattern of endemicity. Months in which the incidence rates exceeded the third quartile or line C-sum were declared as epidemic months. RESULTS The provinces of Nampula, Zambezia, Sofala, and Inhambane accounted for 52.7% of all cases in the first half of 2014. Also during this period, the provinces of Nampula, Sofala and Tete were responsible for 54.9% of the deaths from malaria. The incidence rates of malaria in children, and in all ages, have showed patterns in the epidemic zone. For all ages, the incidence rate has peaked in April (2,573 cases/100,000 inhabitants). CONCLUSIONS The results suggest the occurrence of an epidemic pattern of malaria in the first half of 2014 in Mozambique. It is strategic to have a more accurate surveillance at all levels (central, provincial and district) to target prevention and control interventions in a timely manner.

A pattern language for parallelizing irregular algorithms

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Informática

Dynamic Analysis and Pattern Visualization of Forest Fires

This paper analyses forest fires in the perspective of dynamical systems. Forest fires exhibit complex correlations in size, space and time, revealing features often present in complex systems, such as the absence of a characteristic length-scale, or the emergence of long range correlations and persistent memory. This study addresses a public domain forest fires catalogue, containing information of events for Portugal, during the period from 1980 up to 2012. The data is analysed in an annual basis, modelling the occurrences as sequences of Dirac impulses with amplitude proportional to the burnt area. First, we consider mutual information to correlate annual patterns. We use visualization trees, generated by hierarchical clustering algorithms, in order to compare and to extract relationships among the data. Second, we adopt the Multidimensional Scaling (MDS) visualization tool. MDS generates maps where each object corresponds to a point. Objects that are perceived to be similar to each other are placed on the map forming clusters. The results are analysed in order to extract relationships among the data and to identify forest fire patterns.

Magma flow pattern in dykes of the Azores revealed by ansiotropy of magnetic susceptibility

The localization of magma melting areas at the lithosphere bottom in extensional volcanic domains is poorly understood. Large polygenetic volcanoes of long duration and their associated magma chambers suggest that melting at depth may be focused at specific points within the mantle. To validate the hypothesis that the magma feeding a mafic crust, comes from permanent localized crustal reservoirs, it is necessary to map the fossilized magma flow within the crustal planar intrusions. Using the AMS, we obtain magmatic flow vectors from 34 alkaline basaltic dykes from São Jorge, São Miguel and Santa Maria islands in the Azores Archipelago, a hot-spot related triple junction. The dykes contain titanomagnetite showing a wide spectrum of solid solution ranging from Ti-rich to Ti-poor compositions with vestiges of maghemitization. Most of the dykes exhibit a normal magnetic fabric. The orientation of the magnetic lineation k1 axis is more variable than that of the k3 axis, which is generally well grouped. The dykes of São Jorge and São Miguel show a predominance of subhorizontal magmatic flows. In Santa Maria the deduced flow pattern is less systematic changing from subhorizontal in the southern part of the island to oblique in north. These results suggest that the ascent of magma beneath the islands of Azores is predominantly over localized melting sources and then collected within shallow magma chambers. According to this concept, dykes in the upper levels of the crust propagate laterally away from these magma chambers thus feeding the lava flows observed at the surface.

Pattern of mycobacterial antigen detection in leprosy

Immunohistochemistry reaction (Peroxidase anti-peroxidase - PAP) was carried out on fifty-two skin biopsies from leprosy patients with the purpose to identify the antigenic pattern in mycobacteria and to study the sensitivity of this method. Five different patterns were found: bacillar, granular, vesicular, cytoplasmatic and deposits, classified according to the antigenic material characteristics. Deposits (thinely particulate material) appeared more frequently, confirming the immunohistochemistry sensitivity to detect small amounts of antigens even when this material is not detected by histochemical stainings.

Dynamic Analysis and Pattern Visualization of Forest Fires

This paper analyses forest fires in the perspective of dynamical systems. Forest fires exhibit complex correlations in size, space and time, revealing features often present in complex systems, such as the absence of a characteristic length-scale, or the emergence of long range correlations and persistent memory. This study addresses a public domain forest fires catalogue, containing information of events for Portugal, during the period from 1980 up to 2012. The data is analysed in an annual basis, modelling the occurrences as sequences of Dirac impulses with amplitude proportional to the burnt area. First, we consider mutual information to correlate annual patterns. We use visualization trees, generated by hierarchical clustering algorithms, in order to compare and to extract relationships among the data. Second, we adopt the Multidimensional Scaling (MDS) visualization tool. MDS generates maps where each object corresponds to a point. Objects that are perceived to be similar to each other are placed on the map forming clusters. The results are analysed in order to extract relationships among the data and to identify forest fire patterns.

p53 immunostaining pattern in Brazilian patients with hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is an important type of cancer etiologically related to some viruses, chemical carcinogens and other host or environmental factors associated to chronic liver injury in humans. The tumor suppressor gene p53 is mutated in highly variable levels (0-52%) of HCC in different countries. OBJECTIVE: The objective of the present study was to compare the frequency of aberrant immunohistochemical expression of p53 in HCC occurring in cirrhotic or in non-cirrhotic patients as well as in liver cell dysplasia and in adenomatous hyperplasia. We studied 84 patients with HCC or cirrhosis. RESULTS: We detected p53 altered immuno-expression in 58.3% of patients in Grade III-IV contrasting to 22.2% of patients in Grade I-II (p = 0.02). Nontumorous areas either in the vicinity of HCC or in the 30 purely cirrhotic cases showed no nuclear p53 altered expression, even in foci of dysplasia or adenomatous hyperplasia. No significant difference was found among cases related to HBV, HCV or alcohol. CONCLUSION: The high frequency of p53 immunoexpression in this population is closer to those reported in China and Africa, demanding further studies to explain the differences with European and North American reports.

Cobalt-, zinc- and iron-bound forms of adenylate kinase (AK) from the sulfate-reducing bacterium Desulfovibrio gigas: purification, crystallization and preliminary X-ray diffraction analysis

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Sep 1;65(Pt 9):926-9

Purification, crystallization and preliminary X-ray diffraction analysis of adenosine triphosphate sulfurylase (ATPS) from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Jul 1;64(Pt 7):593-5

The pattern of immune cell infiltration in chromoblastomycosis: involvement of macrophage inflammatory protein-1 alpha/CCL3 and fungi persistence

Chromoblastomycosis (CR) is a subcutaneous chronic mycosis characterized by a granulomatous inflammatory response. However, little is known regarding the pattern of leukocyte subsets in CR and the pathways involved in their recruitment. The objective of this study was to assess the cellular subsets, chemokine, chemokine receptors and enzymes in CR. The inflammatory infiltrate was characterized by immunohistochemistry using antibodies against macrophages (CD68), Langerhans'cells (S100), lymphocytes (CD3, CD4, CD8, CD45RO, CD20 and CD56) and neutrophils (CD15). The expression of MIP-1alpha (Macrophage inflammatory protein-1alpha), chemokine receptors (CXCR3 and CCR1) and enzymes (superoxide dismutase-SOD and nitric oxide synthase-iNOS) was also evaluated by the same method. We observed an increase in all populations evaluated when compared with the controls. Numbers of CD15+ and CD56+ were significantly lower than CD3+, CD4+, CD20+ and CD68+ cells. Statistical analysis revealed an association of fungi numbers with CD3, CD45RO and iNOS-positive cells. Furthermore, MIP-1alpha expression was associated with CD45RO, CD68, iNOS and CXCR3. Our results suggest a possible role of MIP-1alpha and fungi persistence in the cell infiltration in CR sites.

Syncope and Intermittent Brugada ECG Pattern

A síndrome de Brugada é uma síndrome rara, com uma prevalência aproximada na Europa de 1-5/10 000 habitantes, mas cuja apresentação clínica inicial pode ser morte súbita. Embora com um padrão eletrocardiográfico típico, este é por vezes intermitente. Os autores apresentam o caso clínico de um doente de sexo masculino, de 32 anos, sem fatores de risco pessoais conhecidos e história familiar de morte súbita, que recorre ao Serviço de Urgência por síncope sem pródromos. O primeiro eletrocardiograma (ECG) em ritmo sinusal documenta a presença de uma elevação isolada e inespecífica do segmento ST em V2. Da restante investigação diagnóstica realizada, salienta-se a repetição do ECG, que revelou a presença de padrão de Brugada tipo 1. Este mesmo padrão é exacerbado posteriormente numa situação de infeção respiratória. O doente foi submetido a estudo eletrofisiológico, seguido de implantação de cardiodesfibrilhador (CDI), tendo tido um episódio de fibrilhação ventricular convertido com choque via CDI 2 meses após a implantação.

AN UPWARD TREND IN DNA P16INK4A METHYLATION PATTERN AND HIGH RISK HPV INFECTION ACCORDING TO THE SEVERITY OF THE CERVICAL LESION

SUMMARY High-risk human papillomavirus (hr-HPV) infection is necessary but not sufficient for cervical cancer development. Recently, P16INK4A gene silencing through hypermethylation has been proposed as an important cofactor in cervical carcinogenesis due to its tumor suppressor function. We aimed to investigate P16INK4A methylation status in normal and neoplastic epithelia and evaluate an association with HPV infection and genotype. This cross-sectional study was performed with 141 cervical samples from patients attending Hospital Moncorvo Filho, Rio de Janeiro. HPV detection and genotyping were performed through PCR and P16INK4A methylation by nested-methylation specific PCR (MSP). HPV frequency was 62.4% (88/141). The most common HPV were HPV16 (37%), HPV18 (16.3%) and HPV33/45(15.2%). An upward trend was observed concerning P16INK4A methylation and lesion degree: normal epithelia (10.7%), low grade lesions (22.9%), high grade (57.1%) and carcinoma (93.1%) (p < 0.0001). A multivariate analysis was performed to evaluate an association between methylation, age, tobacco exposure, HPV infection and genotyping. A correlation was found concerning methylation with HPV infection (p < 0.0001), hr-HPV (p = 0.01), HSIL (p < 0.0007) and malignant lesions (p < 0.0001). Since viral infection and epigenetic alterations are related to cervical carcinoma, we suggest that P16INK4A methylation profile maybe thoroughly investigated as a biomarker to identify patients at risk of cancer.