A framework for supporting knowledge representation – an ontological based approach

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores

Sectorization: measures and an electromagnetism based approach

Sectorization means dividing a set of basic units into sectors or parts, a procedure that occurs in several contexts, such as political, health and school districting, social networks and sales territory or airspace assignment, to achieve some goal or to facilitate an activity. This presentation will focus on three main issues: Measures, a new approach to sectorization problems and an application in waste collection. When designing or comparing sectors different characteristics are usually taken into account. Some are commonly used, and they are related to the concepts of contiguity, equilibrium and compactness. These fundamental characteristics will be addressed, by defining new generic measures and by proposing a new measure, desirability, connected with the idea of preference. A new approach to sectorization inspired in Coulomb’s Law, which establishes a relation of force between electrically charged points, will be proposed. A charged point represents a small region with specific characteristics/values creating relations of attraction/repulsion with the others (two by two), proportional to the charges and inversely proportional to their distance. Finally, a real case about sectorization and vehicle routing in solid waste collection will be mentioned.

Electromagnetism based approach to Sector design in Waste Collection

For efficient planning of waste collection routing, large municipalities may be partitioned into convenient sectors. The real case under consideration is the municipality of Monção, in Portugal. Waste collection involves more than 1600 containers over an area of 220 km2 and a population of around 20,000 inhabitants. This is mostly a rural area where the population is distributed in small villages around the 33 boroughs centres (freguesia) that constitute the municipality. In most freguesias, waste collection is usually conducted 3 times a week. However, there are situations in which the same collection is done every day. The case reveals some general and specific characteristics which are not rare, but are not widely addressed in the literature. Furthermore, new methods and models to deal with sectorization and routing are introduced, which can be extended to other applications. Sectorization and routing are tackled following a three-phase approach. The first phase, which is the main concern of the presentation, introduces a new method for sectorization inspired by Electromagnetism and Coulomb’s Law. The matter is not only about territorial division, but also the frequency of waste collection, which is a critical issue in these types of applications. Special characteristics related to the number and type of deposition points were also a motivation for this work. The second phase addresses the routing problems in each sector: new Mixed Capacitated Arc Routing with Limited Multi-Landfills models will be presented. The last phase integrates Sectoring and Routing. Computational results confirm the effectiveness of the entire novel approach.

Rapid HIV diagnostic test in undocumented pregnant women applied at an inner-city teaching hospital

A significant number of Brazilian gestational-age women are still not tested for HIV, representing a high risk of transmission to their newborns. The current study sought to identify the number of pregnant women with no previous testing or undocumented for HIV referred to the Gynecology and Obstetrics Department of a Regional Teaching Hospital and included diagnosis of HIV infection determined by a rapid test and perinatal transmission in pregnancy. Medical records of all pregnant women admitted to hospital from January 2001 to December 2005 were reviewed. Pregnant women without HIV results were submitted to a rapid HIV test. Those who tested positive were further tested by ELISA and confirmed by indirect immunofluorescence assay (IIA) or Western blot (WB). The viral load from babies born to HIV-infected mothers was assessed by bDNA. Of the 16,424 pregnant women analyzed (6.6%), 1,089 were undocumented for HIV. Eleven women were positive in rapid testing and 10 were confirmed by ELISA, IIA or WB, with 0.9% seropositivity. Mother/infant pairs received zidovudine monotherapy prophylaxis and infant viral load was lower than 50 copies/mL. A higher number of pregnant women previously tested for HIV during antenatal care was verified, compared to that obtained nationwide.

Serology using rROP2 antigen in the diagnostic of toxoplasmosis in pregnant women

Toxoplasma gondii causes severe fetal disease during acute infection in pregnant women, thus demanding early diagnosis for effective treatment and fetus preservation. Fetal tests are inefficient and risky, and diagnosis is based on maternal IgM serology, which had weak screening ability due to increased sensitivity, with alternative IgG avidity tests. Here, we performed ELISA and avidity assays using a recombinant T. gondii antigen, rROP2, in samples from 160 pregnant women screened from a large public hospital who were referred due to positive IgM assays. IgG serology and avidity assays were compared using whole T. gondii extract or rROP2. ELISA IgG detection with rROP2 showed good agreement with assays performed with T. gondii extract, but rROP2 IgG avidity assays were unrelated to whole extract antigen IgG avidity, regardless of the chaotrope used. These data show that avidity maturation is specific to individual antigen prevalence and immune response during infection. ELISA rROP2 IgG assays may be an alternative serological test for the diagnosis of toxoplasmosis during pregnancy, although our data do not support their use in avidity assays.

High diagnostic efficiency of IgM-ELISA with the use of multiple antigen peptides (MAP1) from T. gondii ESA (SAG-1, GRA-1 and GRA-7), in acute toxoplasmosis

The main serological marker for the diagnosis of recent toxoplasmosis is the specific IgM antibody, along with IgG antibodies of low avidity. However, in some patients these antibodies may persist long after the acute/recent phase, contributing to misdiagnosis in suspected cases of toxoplasmosis. In the present study, the diagnostic efficiency of ELISA was evaluated, with the use of peptides derived from T. gondii ESA antigens, named SAG-1, GRA-1 and GRA-7. In the assay referred to, we studied each of these peptides individually, as well as in four different combinations, as Multiple Antigen Peptides (MAP), aiming to establish a reliable profile for the acute/recent toxoplasmosis with only one patient serum sample. The diagnostic performance of the assay using MAP1, with the combination of SAG-1, GRA-1 and GRA-7 peptides, demonstrated better discrimination of the acute/recent phase from non acute/recent phase of toxoplasmosis. Our results show that IgM antibodies to MAP1 may be useful as a serological marker, enhancing the diagnostic efficiency of the assay for acute/recent phase of toxoplasmosis.

Towards Human-like Bimanual Movements in Anthropomorphic Robots: A Nonlinear Optimization Approach

Previously we have presented a model for generating human-like arm and hand movements on an unimanual anthropomorphic robot involved in human-robot collaboration tasks. The present paper aims to extend our model in order to address the generation of human-like bimanual movement sequences which are challenged by scenarios cluttered with obstacles. Movement planning involves large scale nonlinear constrained optimization problems which are solved using the IPOPT solver. Simulation studies show that the model generates feasible and realistic hand trajectories for action sequences involving the two hands. The computational costs involved in the planning allow for real-time human robot-interaction. A qualitative analysis reveals that the movements of the robot exhibit basic characteristics of human movements.

Organizational culture in cooperatives: an exploratory approach

In recent years, organizational culture has become one of the common themes of interest of scientific and academic research. Each organization has its own unique cultural identity. Based on the recognition that organizational culture is considered important to an organization’s results, and social economy organizations are concerned with improving managerial practices and results, our objective is to study organizational culture in cooperatives: identifying their organizational culture as a specific type of organization of the social economy, recognized as increasingly important economic agents; and in doing so, explore the usage of a widely known model, the Competing Values Framework (Quinn & Rohrbaugh 1983). Three cooperatives were studied. Their presidents were interviewed, and a questionnaire was applied to cooperative members to obtain demographic and organizational culture data. Differences between the cooperatives’ cultural profiles seem to be consistent with both the circumstances of Portuguese social economy organizations (SEOs), and to the organizations’ uniqueness regarding their trade, focuses, and history. International firm trends were compared with this study’s results, and also appear to be explained by the SEO’s management practices evolution standpoint: lack of structured way of working, and the need to improvise and innovate in order to get things done. The importance of our research is held in the fact that social economy, and the cooperative movement in particular, has a developing importance in the expansion of many economies, the lack of literature on culture in SEOs, and the exploratory usage of a well-known model of management literature in cooperatives.

An organizational culture approach to performance in information technology micro-firms

This study aims to analyze and compare micro-firms’ organizational culture related to organizational performance. A case study methodology was used based on four firms, competitors among themselves in the Information Technology business, focusing on the years between 2008-2013. Findings pointed out many similarities to larger firms, but some specificities of micro-firms were found and propositions were defined: clan culture predominance is related to best performing micro-firms; the configuration of several culture types seemed to be the most suitable for obtaining good organizational results, provided that they do not focus only on hierarchy and market types of culture; the market culture predominance perception by employees is associated with low job satisfaction; and, after a certain time in business, micro-firms, as do larger companies, seek to standardize and control processes. Recognizing that organizational culture is considered important to firms’ results, this study sheds some light on that important factor for micro-firms.

On an acute case of Chagas disease in a region under vector control in the state of São Paulo, Brazil

No vector transmitted cases of Chagas disease had been notified in the state of São Paulo since the 1970s. However, in March, 2006, the death of a six-year-old boy from the municipality of Itaporanga was notified to the Center for Epidemiological Survey of the São Paulo State Health Secretariat: an autochthonous case of acute Chagas disease. The postmortem histopathological examination performed in the Hospital das Clínicas of the Botucatu School of Medicine confirmed the diagnosis. Reference to hospital records, consultation with the health professionals involved in the case and interviews with members of the patient's family supplied the basis for this study. We investigated parasite route of transmission, probable local reservoirs and vectors. No further human cases of acute Chagas disease were diagnosed. No locally captured vectors or reservoirs were found infected with Trypanosoma cruzi. Alternative transmission hypotheses - such as the possible ingestion of foods contaminated with vector excreta - are discussed, as well as the need to keep previously endemic regions and infested houses under close surveillance. Clinicians should give due attention to such signs as uni- or bilateral palpebral edema, cardiac failure, myocarditis, pericarditis, anasarca and atypical signs of nephrotic syndrome or nephritis and consider the diagnostic hypothesis of Chagas disease.

Attachment, Physiological and Familial Vulnerability in Childhood Obesity: an Interactive Multisystem Approach

The aims of the present study were to test the association between insecure attachment and basal cortisol and catecholamines levels in a sample of obese children. The role of familial vulnerability and gender was also investigated. Methods: Cortisol and catecholamines levels of 8- to 13-year olds obese children were measured. Self-report questionnaires were used to assess attachment pattern and current anxiety and depression, and parent-report questionnaires were used to assess attachment, current anxiety and depression and familial vulnerability. Linear regression analyses were performed for individuals that scored low versus high on parental internalizing problems, and for boys and girls, separately. Results: In the group with high parental internalizing problems, insecure attachment was significantly associated with reduced basal levels of cortisol, in boys (p=0.007, b= -0.861, R2= 73.0%). In the group with low parental internalizing problems, the association between insecure attachment and cortisol was not significant in either boys or girls, and it was negative in boys (p=0.075, b= -0.606, R2= 36.7%) and positive in girls (p=0.677, b= 0.176, R2= 3.1%) . Conclusions: Apparently, physiological risk factors for psicopathology in obesity are more evident in individuals with a high familial vulnerability. In addition, patterns of physiological risk for psicopathology in obesity are different in boys and girls. Therefore, it is important to take into account familial vulnerability and gender when investigating physiological risk factors for psycopathology in obesity. Insecure attachment in childhood may be a risk factor for obesity. Interventions to increase children's attachment security should examine the effects on children's weight.

Biological predictors of survival in limphoma and mechanisms underlying follicular lymphoma transformaion into diffuse large B cell lymphoma (vol I e II)

RESUMO: Os biomarcadores tumorais permitem identificar os doentes com maior risco de recorrência da doença, predizer a resposta tumoral à terapêutica e, finalmente, definir candidatos a novos alvos terapêuticos. Novos biomarcadores são especialmente necessários na abordagem clínica dos linfomas. Actualmente, esses tumores são diagnosticados através de uma combinação de características morfológicas, fenotípicas e moleculares, mas o prognóstico e o planeamento terapêutico estão quase exclusivamente dependentes de características clínicas. Estes factores clínicos são, na maioria dos linfomas, insuficientes numa proporção significativa dos doentes, em particular, aqueles com pior prognóstico. O linfoma folicular (LF) é, globalmente, o segundo subtipo mais comum de linfoma. É tipicamente uma doença indolente com uma sobrevida média entre os 8 e 12 anos, mas é geralmente fatal quando se transforma num linfoma agressivo de alto grau, habitualmente o linfoma difuso de grandes células B (LDGCB). Morfologicamente e funcionalmente, as células do LF recapitulam as células normais do centro germinativo na sua dependência de sobrevivência do microambiente não-tumoral, especialmente das células do sistema imunológico. Biomarcadores preditivos de transformação não existem pelo que um melhor conhecimento da biologia intrínseca de progressão do LF poderá revelar novos candidatos. Nesta tese descrevo duas abordagens distintas para a descoberta de novos biomarcadores. A primeira, o estudo da expressão global de genes ('genomics') obtidos por técnicas de alto rendimento que analisam todo o genoma humano sequenciado, permitindo identificar novas anomalias genéticas que possam representar mecanismos biológicos importantes de transformação. São descritos novos genes e alterações genómicas associados à transformação do LF, sendo especialmente relevantes as relacionadas com os eventos iniciais de transformação em LDGCB. A segunda, baseou-se em várias hipóteses centradas no microambiente do LF, rico em vários tipos de células nãomalignas. Os estudos imunoarquitectural de macrófagos, células T regulatórias e densidade de microvasos efectuado em biopsias de diagnóstico de doentes com LF tratados uniformemente correlacionaram-se significativamente, e independentemente dos critérios clínicos, com a evolução clínica e, mais importante, com o risco de transformação em LDGCB. Nesta tese, foram preferencialmente utilizadas (e optimizadas) técnicas que permitam o uso de amostras fixadas em parafina e formalina (FFPET). Estas são facilmente acessíveis a partir das biopsias de diagnóstico de rotina presentes nos arquivos de todos os departamentos de patologia, facilitando uma transição rápida dos novos marcadores para a prática clínica. Embora o FL fosse o tema principal da tese, os novos achados permitiram estender facilmente hipóteses semelhantes a outros subtipos de linfoma. Assim, são propostos e validados vários biomarcadores promissores e relacionados com o microambiente não tumoral, sobretudo dependentes das células do sistema imunológico, como contribuintes importantes para a biologia dos linfomas. Estes sugerem novas opções para a abordagem clínica destas doenças e, eventualmente, novos alvos terapêuticos.------------- ABSTRACT: Cancer biomarkers provide an opportunity to identify those patients most at risk for disease recurrence, predict which tumours will respond to different therapeutic approaches and ultimately define candidate biomarkers that may serve as targets for personalized therapy. New biomarkers are especially needed in the management of lymphoid cancers. At present, these tumours are diagnosed using a combination of morphologic, phenotypic and molecular features but prognosis and overall survival are mostly dependent on clinical characteristics. In most lymphoma types, these imprecisely assess a significant proportion of patients, in particular, those with very poor outcomes. Follicular lymphoma (FL) is the second most common lymphoma subtype worldwide. It is typically an indolent disease with current median survivals in the range of 8-12 years, but is usually fatal when it transforms into an aggressive high-grade lymphoma, characteristically Diffuse Large B Cell Lymphoma (DLBCL). Morphologically and functionally it recapitulates the normal cells of the germinal center with its survival dependency on non-malignant immune and immunerelated cells. Informative markers of transformation related to the intrinsic biology of FL progression are needed. Within this thesis two separate approaches to biomarker discovery were employed. The first was to study the global expression of genes (‘genomics’) obtained using high-throughput, wholegenome-wide approaches that offered the possibility for discovery of new genetic abnormalities that might represent the important biological mechanisms of transformation. Gene signatures associated with early events of transformation were found. Another approach relied on hypothesis-driven concepts focusing upon the microenvironment, rich in several non-malignant cell types. The immunoarchitectural studies of macrophages, regulatory T cells and microvessel density on diagnostic biopsies of uniformly treated FL patients significantly predicted clinical outcome and, importantly, also informed on the risk of transformation. Techniques that enabled the use of routine formalin fixed paraffin embedded diagnostic specimens from the pathology department archives were preferentially used in this thesis with the goal of fulfilling a rapid bench-to-beside” translation for these new findings. Although FL was the main subject of the thesis the new findings and hypotheses allowed easy transition into other lymphoma types. Several promising biomarkers were proposed and validated including the implication of several non-neoplastic immune cells as important contributors to lymphoma biology, opening new options for better treatment planning and eventually new therapeutic targets and candidate therapeutics.

Analysis of Synaptic Proteins in the Cerebrospinal Fluid as a New Tool in the Study of Inborn Errors of Neurotransmission

Abstract In a few rare diseases, specialised studies in cerebrospinal fluid (CSF) are required to identify the underlying metabolic disorder. We aimed to explore the possibility of detecting key synaptic proteins in the CSF, in particular dopaminergic and gabaergic, as new procedures that could be useful for both pathophysiological and diagnostic purposes in investigation of inherited disorders of neurotransmission. Dopamine receptor type 2 (D2R), dopamine transporter (DAT) and vesicular monoamine transporter type 2 (VMAT2) were analysed in CSF samplesfrom 30 healthy controls (11 days to 17 years) by western blot analysis. Because VMAT2 was the only protein with intracellular localisation, and in order to compare results, GABA vesicular transporter, which is another intracellular protein, was also studied. Spearman’s correlation and Student’s t tests were applied to compare optical density signals between different proteins. All these synaptic proteins could be easily detected and quantified in the CSF. DAT, D2R and GABA VT expression decrease with age, particularly in the first months of life, reflecting the expected intense synaptic activity and neuronal circuitry formation. A statistically significant relationship was found between D2R and DAT expression, reinforcing the previous evidence of DAT regulation by D2R. To our knowledge, there are no previous studies on human CSF reporting a reliable analysis of these proteins. These kinds of studies could help elucidate new causes of disturbed dopaminergic and gabaergic transmission as well as understanding different responses to L-dopa in inherited disorders affecting dopamine metabolism. Moreover, this approach to synaptic activity in vivo can be extended to different groups of proteins and diseases.