Detection of EBV-DNA in serum samples of an immunosuppressed child during a three years follow-up: association of clinical and PCR data with active infection

Twenty-four whole blood and serum samples were drawn from an eight year-old heart transplant child during a 36 months follow-up. EBV serology was positive for VCA-IgM and IgG, and negative for EBNA-IgG at the age of five years old when the child presented with signs and symptoms suggestive of acute infectious mononucleosis. After 14 months, serological parameters were: positive VCA-IgG, EBNA-IgG and negative VCA-IgM. This serological pattern has been maintained since then even during episodes suggestive of EBV reactivation. PCR amplified a specific DNA fragment from the EBV gp220 (detection limit of 100 viral copies). All twenty-four whole blood samples yielded positive results by PCR, while 12 out of 24 serum samples were positive. We aimed at analyzing whether detection of EBV-DNA in serum samples by PCR was associated with overt disease as stated by the need of antiviral treatment and hospitalization. Statistical analysis showed agreement between the two parameters evidenced by the Kappa test (value 0.750; p < 0.001). We concluded that detection of EBV-DNA in serum samples of immunosuppressed patients might be used as a laboratory marker of active EBV disease when a Real-Time PCR or another quantitative method is not available.

On the analysis of data emerging in non-linear and complex systemscomparison of two X-Ray prony spectra

New arguments proving that successive (repeated) measurements have a memory and actually remember each other are presented. The recognition of this peculiarity can change essentially the existing paradigm associated with conventional observation in behavior of different complex systems and lead towards the application of an intermediate model (IM). This IM can provide a very accurate fit of the measured data in terms of the Prony's decomposition. This decomposition, in turn, contains a small set of the fitting parameters relatively to the number of initial data points and allows comparing the measured data in cases where the “best fit” model based on some specific physical principles is absent. As an example, we consider two X-ray diffractometers (defined in paper as A- (“cheap”) and B- (“expensive”) that are used after their proper calibration for the measuring of the same substance (corundum a-Al2O3). The amplitude-frequency response (AFR) obtained in the frame of the Prony's decomposition can be used for comparison of the spectra recorded from (A) and (B) - X-ray diffractometers (XRDs) for calibration and other practical purposes. We prove also that the Fourier decomposition can be adapted to “ideal” experiment without memory while the Prony's decomposition corresponds to real measurement and can be fitted in the frame of the IM in this case. New statistical parameters describing the properties of experimental equipment (irrespective to their internal “filling”) are found. The suggested approach is rather general and can be used for calibration and comparison of different complex dynamical systems in practical purposes.

Landslide susceptibility assessment in Karanganyar regency - Indonesia - Comparison of knowledge-based and Data-driven Models

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Fractures in Children and Adolescents with Spina Bifida: The Experience of a Portuguese Tertiary-Care Hospital

AIM: The morbidity associated with osteoporosis and fractures in children and adolescents with spina bifida highlights the importance of osteoporosis prevention and treatment in these patients. The aim of this study was to examine the occurrence and pattern of bone fractures in paediatric patients with spina bifida. METHOD: We reviewed the data of all paediatric patients with spina bifida who were treated in our centre between 1999 and 2008. RESULTS: One hundred and thirteen patients were included in the study (63 females, 50 males; mean age 10y 8mo, SD 4y 10mo, range 6mo-18y). The motor levels were thoracic in six, upper lumbar in 22, lower lumbar in 42, and sacral in 43 patients. Of the 113 patients, 58 (51.3%) had shunted hydrocephalus. Thirty-six (31.8%) were non-ambulatory (wheelchair-dependent [unable to self-propel wheelchair] n=3, wheelchair-independent [able to self-propel wheelchair] n=33), 13 were partial ambulators, 61 were full ambulators, and three were below the age of walking. Forty-five fractures were reported in 25 patients. The distal femur was the most common fracture site. Statistical analyses showed that patients with higher levels of involvement and in wheelchairs had a significantly increased risk of having a [corrected] fracture (p<0.001). Spontaneous fractures were the principal mechanism of injury, and an association was identified between fracture mechanism, type of ambulation, and lesion level: the fractures of patients with higher levels of motor functioning and those in wheelchairs were mainly pathological (p=0.01). We identified an association between risk of a second fracture, higher motor level lesion, and non-ambulation. There was an increased risk of having a second fracture after a previous spontaneous fracture (p=0.004). INTERPRETATION: Data in this study indicate a high prevalence of fractures in patients with spina bifida.

Spatial Patterns and Irregularities of the electoral data: general elections in Canada

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

SDAR: a package for plotting and analyzing stratigraphy data in R

Stratigraphic Columns (SC) are the most useful and common ways to represent the eld descriptions (e.g., grain size, thickness of rock packages, and fossil and lithological components) of rock sequences and well logs. In these representations the width of SC vary according to the grain size (i.e., the wider the strata, the coarser the rocks (Miall 1990; Tucker 2011)), and the thickness of each layer is represented at the vertical axis of the diagram. Typically these representations are drawn 'manually' using vector graphic editors (e.g., Adobe Illustrator®, CorelDRAW®, Inskape). Nowadays there are various software which automatically plot SCs, but there are not versatile open-source tools and it is very di cult to both store and analyse stratigraphic information. This document presents Stratigraphic Data Analysis in R (SDAR), an analytical package1 designed for both plotting and facilitate the analysis of Stratigraphic Data in R (R Core Team 2014). SDAR, uses simple stratigraphic data and takes advantage of the exible plotting tools available in R to produce detailed SCs. The main bene ts of SDAR are: (i) used to generate accurate and complete SC plot including multiple features (e.g., sedimentary structures, samples, fossil content, color, structural data, contacts between beds), (ii) developed in a free software environment for statistical computing and graphics, (iii) run on a wide variety of platforms (i.e., UNIX, Windows, and MacOS), (iv) both plotting and analysing functions can be executed directly on R's command-line interface (CLI), consequently this feature enables users to integrate SDAR's functions with several others add-on packages available for R from The Comprehensive R Archive Network (CRAN).

The role of qualitative data and systems thinking in addressing service decline in market towns

Retail services are a main contributor to municipal budget and are an activity that affects perceived quality-of-life, especially for those with mobility difficulties (e.g. the elderly, low income citizens). However, there is evidence of a decline in some of the services market towns provide to their citizens. In market towns, this decline has been reported all over the western world, from North America to Australia. The aim of this research was to understand retail decline and enlighten on some ways of addressing this decline, using a case study, Thornbury, a small town in the Southwest of England. Data collected came from two participatory approaches: photo-surveys and multicriteria mapping. The interpretation of data came from using participants as analysts, but also, using systems thinking (systems diagramming and social trap theory) for theory building. This research moves away from mainstream economic and town planning perspectives by making use of different methods and concepts used in anthropology and visual sociology (photo-surveys), decision-making and ecological economics (multicriteria mapping and social trap theory). In sum, this research has experimented with different methods, out of their context, to analyse retail decline in a small town. This research developed a conceptual model for retail decline and identified the existence of conflicting goals and interests and their implications for retail decline, as well as causes for these. Most of the potential causes have had little attention in the literature. This research also identified that some of the measures commonly used for dealing with retail decline may be contributing to the causes of retail decline itself. Additionally, this research reviewed some of the measures that can be used to deal with retail decline, implications for policy-making and reflected on the use of the data collection and analysis methods in the context of small to medium towns.

How can clusters help in the product type choice? The case of a specialized retail store

This work project (WP) is a study about a clustering strategy for Sport Zone. The general cluster study’s objective is to create groups such that within each group the individuals are similar to each other, but should be different among groups. The clusters creation is a mix of common sense, trial and error and some statistical supporting techniques. Our particular objective is to support category managers to better define the product type to be displayed in the stores’ shelves by doing store clusters. This research was carried out for Sport Zone, and comprises an objective definition, a literature review, the clustering activity itself, some factor analysis and a discriminant analysis to better frame our work. Together with this quantitative part, a survey addressed to category managers to better understand their key drivers, for choosing the type of product of each store, was carried out. Based in a non-random sample of 65 stores with data referring to 2013, the final result was the choice of 6 store clusters (Figure 1) which were individually characterized as the main outcome of this work. In what relates to our selected variables, all were important for the distinction between clusters, which proves the adequacy of their choice. The interpretation of the results gives category managers a tool to understand which products best fit the clustered stores. Furthermore, as a side finding thanks to the clusterization, a STP (Segmentation, Targeting and Positioning) was initiated, being this WP the first steps of a continuous process.

Interpretation of the presence of IgM and IgG antibodies in a rapid test for dengue: analysis of dengue antibody prevalence in Fortaleza City in the 20th year of the epidemic

INTRODUCTION: The diagnosis of dengue and the differentiation between primary and secondary infections are important for monitoring the spread of the epidemic and identifying the risk of severe forms of the disease. The detection of immunoglobulin (Ig)M and IgG antibodies is the main technique for the laboratory diagnosis of dengue. The present study assessed the application of a rapid test for dengue concerning detection of new cases, reinfection recognition, and estimation of the epidemic attack rate. METHODS: This was a retrospective, cross-sectional, descriptive study on dengue using the Fortaleza Health Municipal Department database. The results from 1,530 tested samples, from 2005-2006, were compared with data from epidemiological studies of dengue outbreaks in 1996, 2003, and 2010. RESULTS: The rapid test confirmed 52% recent infections in the tested patients with clinical suspicion of dengue: 40% detected using IgM and 12% of new cases using IgG in the non-reactive IgM results. The positive IgM plus negative IgG (IgM+ plus IgG-) results showed that 38% of those patients had a recent primary dengue infection, while the positive IgG plus either positive or negative IgM (IgG+ plus IgM+/-) results indicated that 62% had dengue for at least a second time (recent secondary infections). This proportion of reinfections permitted us to estimate the attack rate as >62% of the population sample. CONCLUSIONS: The rapid test for dengue has enhanced our ability to detect new infections and to characterize them into primary and secondary infections, permitting the estimation of the minimal attack rate for a population during an outbreak.

Pressure sores among malnourished necropsied adults - preliminary data

Pressure sores are common among bedridden, elderly, or malnourished patients, and may occur in terminal ill patients because of impaired mobility, fecal or urinary incontinence, and decreased healing capacity. The aim of this study was to compare frequency of pressure sores between malnourished and non-malnourished necropsied adults. METHOD: All (n = 201) adults (age ³ 18 years) autopsied between 1986 and 1996 at the Teaching Hospital of Triangulo Mineiro Medical School (Uberaba) were eligible for the study. Gender, race, weight, height and main diagnoses were recorded. Ninety-six cases were excluded because of probable body water retention (congestive heart failure, hepatic insufficiency, nephrotic syndrome) or pressure sores secondary to peripheral vascular ischemia. Body mass index (BMI) was used to define malnourished (BMI < 18.5 kg/m²) and non-malnourished (BMI > 18.5kg/m²) groups. RESULTS: Except for weight (42.5kg; range: 28-57 vs. 60; 36-134.5kg) and BMI (16.9; range: 12.4-18.5 vs. 22.7; range: 18.5-54.6kg/m²), respectively, there were no statistical differences among 43 malnourished and 62 non-malnourished cases in relation to age (54.9 ± 20.4 vs. 52.9 ± 17.9 years), percentage of white persons (74.4 vs. 64.5%), male gender (76.7 vs. 69.3%) and main diagnoses. Five malnourished (11.6%) and 7 (11.5%) non-malnourished cases had pressure sores (p=0.89). CONCLUSION: Pressure sores were equally common findings in necropsied persons with protein-energy malnutrition, as assessed by body mass index.

Reclamações dos utentes : estudo dos resultados e medidas correctivas no contexto dos Agrupamentos de Centros de Saúde de Lisboa e Vale do Tejo

RESUMO - A qualidade dos cuidados de saúde, evolui ao longo dos tempos e é agora considerada um direito e um pilar fundamental nos serviços de saúde. As reclamações dos utentes podem revelar informação acerca das experiências entre os utentes e as organizações de saúde. Desta forma as reclamações podem ser consideradas como indicadores de qualidade que permitem identificar áreas e/ou oportunidades de melhoria, e de grande representatividade no processo da melhoria contínua da qualidade na saúde. Sendo fundamental dar voz aos utentes do SNS e possibilitar a sua participação activa no processo de melhoria da prestação dos cuidados de saúde, com este trabalho pretendeu-se estudar a forma como as reclamações dos utentes nos ACES na Região de Saúde de Lisboa e Vale do Tejo, contribuem para a melhoria da qualidade nos referidos serviços de saúde. Foram reconhecidas e analisadas as principais causas de reclamação, as correspondentes medidas correctivas e as necessidades e/ou dificuldades no seu processo de implementação, bem como a respectiva avaliação dos resultados obtidos e identificação das recomendações dos Coordenadores dos Gabinetes do Utente no âmbito dos ACES da Região de Saúde de LVT. Efectuou-se a análise de revisão bibliográfica e a consulta dos dados, desagregados, das causas mais mencionadas nas reclamações no âmbito do estudo e foram realizados contactos informais com a estrutura regional e nacional do Sistema SIM-Cidadão. Foram aplicados 15 questionários aos Coordenadores Locais dos Gabinetes do Cidadão dos ACES da ARSLVT, apresentando a investigação um carácter exploratório e qualitativo. Os questionários, foram enviados e recebidos anonimamente através da plataforma para estudos estatísticos Survey Monkey. A sua análise e interpretação, foi efectuada de forma a organizar os seus dados de uma forma sistematizada e permitir categorizar a informação para permitir a sua análise. Os resultados evidenciaram que as reclamações dos utentes apresentadas nos Gabinetes do Cidadão, de certa forma, foram um contributo para o processo da melhoria da qualidade nos ACES da Região de Saúde de Lisboa e Vale do Tejo através do adopção de medidas e acções correctivas, ultrapassando algumas limitações devida à criação de estratégias locais. No entanto foi evidente que algumas limitações não foram passiveis de ser ultrapassadas, pois envolvem decisões do âmbito externo aos ACES. Os resultados alcançados e as recomendações dos Coordenadores, podem evidenciar algumas mudanças organizacionais, mas transparecem a ideia de que existe ainda um longo caminho a percorrer.

Premature thelarche: identification of clinical and laboratory data for the diagnosis of precocious puberty

PURPOSE: Two groups of girls with premature breast development were studied retrospectively. We tried to identify clinical, radiological, and hormonal parameters that could distinguish between a benign, nonprogressive premature thelarche and a true precocious puberty. METHODS: The clinical outcome of 88 girls with breast enlargement before 6.1 years of age was analyzed. Taking into account the progression of their sexual maturation, we allocated the children into 2 groups: "Isolated Premature Thelarche" (n = 63) and "Precocious Puberty" (n = 25) groups. Chronological and bone ages, height and growth velocity centiles, computerized tomography of hypothalamus-pituitary area, pelvic ultrasonography, gonadotropin response to luteinizing hormone-releasing hormone stimulation as well as basal levels of luteinizing hormone, follicle-stimulating hormone, estradiol, and prolactin were studied in both groups. Statistical analysis were performed using the Student t test to compare the sample means. Fisher's exact test and chi² test were used to analyze the nonparametric variables. RESULTS: Isolated premature thelarche most frequently affected girls younger than 2 years who presented exaggerated follicle-stimulating hormone response to luteinizing hormone-releasing hormone stimulation test. The precocious puberty group had higher initial stature, accelerated growth rate and bone age, increased uterine and ovarian volumes, high spontaneous luteinizing hormone levels by immunofluorimetric assay, as well as a high luteinizing hormone response and peak luteinizing hormone/follicle-stimulating hormone ratio after luteinizing hormone-releasing hormone stimulation. CONCLUSION: At initial presentation, girls who undergo true precocious puberty present advanced bone age, increased uterine and ovarian volumes in addition to breast enlargement, as well as an luteinizing hormone-predominant response after a luteinizing hormone-releasing hormone stimulation test.

Uma abordagem à organização e tratamento de dados baseada na resolução de problemas

Relatório de estágio de mestrado em Ensino do 1.º e 2.º Ciclo do Ensino Básico

Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

Integrating data from heterogeneous DNA microarray platforms

DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus.