A solution for estimates in software development projects

The Corporate world is becoming more and more competitive. This leads organisations to adapt to this reality, by adopting more efficient processes, which result in a decrease in cost as well as an increase of product quality. One of these processes consists in making proposals to clients, which necessarily include a cost estimation of the project. This estimation is the main focus of this project. In particular, one of the goals is to evaluate which estimation models fit the Altran Portugal software factory the most, the organization where the fieldwork of this thesis will be carried out. There is no broad agreement about which is the type of estimation model more suitable to be used in software projects. Concerning contexts where there is plenty of objective information available to be used as input to an estimation model, model-based methods usually yield better results than the expert judgment. However, what happens more frequently is not having this volume and quality of information, which has a negative impact in the model-based methods performance, favouring the usage of expert judgement. In practice, most organisations use expert judgment, making themselves dependent on the expert. A common problem found is that the performance of the expert’s estimation depends on his previous experience with identical projects. This means that when new types of projects arrive, the estimation will have an unpredictable accuracy. Moreover, different experts will make different estimates, based on their individual experience. As a result, the company will not directly attain a continuous growing knowledge about how the estimate should be carried. Estimation models depend on the input information collected from previous projects, the size of the project database and the resources available. Altran currently does not store the input information from previous projects in a systematic way. It has a small project database and a team of experts. Our work is targeted to companies that operate in similar contexts. We start by gathering information from the organisation in order to identify which estimation approaches can be applied considering the organization’s context. A gap analysis is used to understand what type of information the company would have to collect so that other approaches would become available. Based on our assessment, in our opinion, expert judgment is the most adequate approach for Altran Portugal, in the current context. We analysed past development and evolution projects from Altran Portugal and assessed their estimates. This resulted in the identification of common estimation deviations, errors, and patterns, which lead to the proposal of metrics to help estimators produce estimates leveraging past projects quantitative and qualitative information in a convenient way. This dissertation aims to contribute to more realistic estimates, by identifying shortcomings in the current estimation process and supporting the self-improvement of the process, by gathering as much relevant information as possible from each finished project.

Comparison of in vitro activity of five antifungal agents against dermatophytes, using the agar dilution and broth microdilution methods

The purpose of this study was to compare the agar dilution and broth microdilution methods for determining the minimum inhibitory concentration (MIC) of fluconazole, itraconazole, ketoconazole, griseofulvin and terbinafine for 60 dermatophyte samples belonging to the species Trichophyton rubrum, Trichophyton mentagrophytes and Microsporum canis. The percentage agreement between the two methods, for all the isolates with < 2 dilutions that were tested was 91.6% for ketoconazole and griseofulvin, 88.3% for itraconazole, 81.6% for terbinafine and 73.3% for fluconazole. One hundred percent agreement was obtained for Trichophyton mentagrophytes isolates evaluated with ketoconazole and griseofulvin. Thus, until a reference method for testing the in vitro susceptibility of dermatophytes is standardized, the similarity of the results between the two methods means that the agar dilution method may be useful for susceptibility testing on these filamentous fungi.

Novo Software para análise do epitélio nasal humano

A discinesia ciliar primária (DCP) resulta de disfunção ciliar no ser humano, estando associada a um conjunto de sintomas muito diversificados. É uma doença respiratória rara caracterizada por infecções respiratórias, situs inversus, infertilidade e hidrocefalia. Em Portugal não existe nenhum centro de diagnóstico da doença. Mas a inten-ção de criar um surgiu, seguindo o método de centros de diagnóstico para DCP utilizado noutros países. Este diagnóstico consiste em recolher amostras dos cílios do nariz, através do método de escovagem nasal e obter a gravação do batimento das células ciliadas por uma câmara de alta velocidade acoplada a um microscópio com objectivas de alta resolução. É possível estudar a DCP através da análise do comportamento físico dos cílios, e, para uma melhor abordagem, foi desenvolvido um programa executável, em C#, para análise destas amostras. Este, após a escolha de uma zona de interesse da sequência de imagens pelo utilizador (ROI), detecta as frequências do bati-mento ciliar, indicando uma lista com as percentagens das frequências obtidas e cria um mapa de frequências do ROI. A ferramenta permite ainda calcular o comprimento do cílio e realizar um estudo do movimento do mesmo, algo que ainda não foi abordado por outros programas. O código desenvolvido permitirá, assim, obter um diagnóstico de DCP em Por-tugal, rápido e nalguns casos com um melhor desempenho do que a inspecção visual seguida noutros centros de diagnóstico.

Evaluation of the histopathological hepatic lesions and opportunistic agents in Brazilian HIV patients

INTRODUCTION: to evaluated the type histopathological hepatic lesions and opportunistic agents in Brazilian HIV-infected patients. METHODS: we examined 52 percutaneous liver biopsies of 50 HIV-infected patients who had at least two of the following conditions: fever of unknown origin, unexplained severe emaciation, hepatomegaly or abnormal liver chemistry. The specimens were cultured for mycobacteria and fungi and stained by standard procedures. RESULTS: reactive patterns, granulomatous hepatitis and chronic active hepatitis were verified in 28 (54%), 11 (21%) and 8 (15%) of the patients respectively. Opportunistic infections were diagnosed in 18 (36%) patients: mycobacteria in 12 (24%), Cryptococcus neoformans in 5 (10%) patients and mycobacteria and yeast was isolated from the same liver fragment in one patient. CONCLUSIONS: mycobacteriosis was the most common opportunistic infection and liver tissue culture is an important method to detect opportunistic agents, even in the absence of histological lesions.

Plataforma online de partilha e comparação de software para análise de imagens da retina

Nesta Tese foi desenvolvida uma plataforma online multiutilizador, que tem como objetivo principal comparar algoritmos de análise de imagens para de-terminar o seu grau de eficácia. Um exemplo de aplicação é a comparação de algoritmos de análise de imagens da retina para deteção de drusas. A compa-ração é feita considerando um dos algoritmos como referência padrão e sobre o este são avaliados os restantes. O funcionamento da plataforma é semelhante à de um fórum, onde é possível a um utilizador criar tópicos publicando imagens e seu descritivo. Após a cria-ção do tópico qualquer utilizador pode visualizar o mesmo, dando a hipótese de comentar ou de acrescentar imagens processadas com os seus próprios al-goritmos de análise. Com o aumento de imagens processadas, obtém-se uma base de dados de algoritmos de análise de imagens sobre a qual é possível avaliar o seu grau de eficácia. A plataforma pretende também criar comunidades onde os utilizadores pos-sam interagir uns com os outros comentando sobre os tópicos, contribuindo assim para o melhoramento dos algoritmos. Deste modo, além de uma base de dados que qualquer utilizador pode usar, obtém-se uma fonte de informação disponibilizada por outros profissionais da área.

Injuries and envenoming by aquatic animals in fishermen of Coxim and Corumbá municipalities, state of Mato Grosso do Sul, Brazil: identification of the causative agents, clinical aspects and first aid measures

INTRODUCTION: The fishes of continental Brazil have socioeconomic importance due to their potential for sport fishing and commercial and subsistence uses, as seen in the Upper Paraguay River Basin, particularly in the municipalities of the Pantanal region, where it is the second largest economic activity. Injuries caused in professional fishermen are common and poorly studied, as in other regions of the country. METHODS: Data were obtained from questionnaires and interviews with 100 professional fishermen, 50 in each municipality, between December 2008 and October 2009. RESULTS: All the fishermen reported some kind of injury caused by fish stings (78% of injuries) and fish, alligator and snake bites (22%) on the hands (46% of cases) and feet (35% of cases). Most of the patients had mild symptoms. The most severe cases were associated with secondary bacterial infections and required specific treatment and prolonged recovery associated with social and economic losses. CONCLUSIONS: The results of this study indicate that the stressful work conditions, inattention to basic preventive measures and carelessness were factors that contributed to accidents and that the toxicity and ability to inflict mechanical trauma of some aquatic species, plus the ineffective use of first aid and hospital treatment, contributed to the high morbidity and complications in many cases. Data from this study are relevant to the fishing communities of the Pantanal region, since they reveal high rates of accidents, lack of knowledge concerning first aid, initial treatment, injury prevention and lack of medical follow-up of the population.

O uso do software de edição áudio Audacity 2.0.5: aprendizagens decorrentes da sua utilização

Contém CD com áudio como anexo

Aptamers binding to Bradykinin

Bradykinin is a peptide of the kinin group, involved in a number of receptor-mediated physiological actions, including inflammation and vasodilation, as well as neuromodulation, neuroprotection and promotion of neurogenesis. Bradykinin is the main ligand of the B2 receptor- the main kinin receptor- which is involved in the cardiac and renal protective effects of kinins in diseases. Antibodies have been considered for a long time as promising therapeutic agents in various fields, especially cancer-related ones. Aptamers, on the other hand, have proven to be an excellent alterative, since they have similar properties to those of monoclonal antibodies, such a high-specificity of recognition and high-affinity binding. Plus, they are developed using in vitro selection procedures and can be reproduced by enzymatic reactions. SELEX is a powerful tool for the development of both DNA and RNA aptamers. The main goal of this project was to design a method to select aptamers against bradykinin using capillary electrophoresis alongside the SELEX technique. The selection was done by comparing the aptamers’ (ssDNA-target complex) electrophoretic mobility with that of the ssDNA and the target, which allowed us to define an appropriate collection window that took into consideration the analytes’ detection time, thus enabling the collection of the desired oligonucleotides. After two selection rounds, the collected pool was sequenced, the affinity was measured and the aptamers’ secondary structure was predicted. We concluded that with only two selection cycles, the original DNA library’s bulk affinity grew around 0.4%. The structural characterization of the aptamers, performed with the aid of the Mfold software, revealed that there are many repetitive motifs amongst them, indicating that the selection process was successful. We have obtained 16 sequences of candidate aptamers as bradykinin ligands of similar sequences and secondary structures whose biological activity should be analyzed after synthesis; mainly in regard to their role as bradykinin inhibitors.

Performance of the Vitek 2 system software version 5.03 in the bacterial identification and antimicrobial susceptibility test: evaluation study of clinical and reference strains of Gram-positive cocci

Introduction. The genera Enterococcus, Staphylococcus and Streptococcus are recognized as important Gram-positive human pathogens. The aim of this study was to evaluate the performance of Vitek 2 in identifying Gram-positive cocci and their antimicrobial susceptibilities. Methods. One hundred four isolates were analyzed to determine the accuracy of the automated system for identifying the bacteria and their susceptibility to oxacillin and vancomycin. Results. The system correctly identified 77.9% and 97.1% of the isolates at the species and genus levels, respectively. Additionally, 81.8% of the Vitek 2 results agreed with the known antimicrobial susceptibility profiles. Conclusion. Vitek 2 correctly identified the commonly isolated strains; however, the limitations of the method may lead to ambiguous findings.

Colistin and anti-Gram-positive bacterial agents against Acinetobacter baumannii

Introduction Acinetobacter baumannii has attained an alarming level of resistance to antibacterial drugs. Clinicians are now considering the use of older agents or unorthodox combinations of licensed drugs against multidrug-resistant strains to bridge the current treatment gap. We investigated the in vitro activities of combination treatments that included colistin with vancomycin, norvancomycin or linezolid against multidrug-resistant Acinetobacter baumannii. Methods The fractional inhibitory concentration index and time-kill assays were used to explore the combined effects of colistin with vancomycin, norvancomycin or linezolid against 40 clinical isolates of multidrug-resistant Acinetobacter baumannii. Transmission electron microscopy was performed to evaluate the interactions in response to the combination of colistin and vancomycin. Results The minimum inhibitory concentrations (MICs) of vancomycin and norvancomycin for half of the isolates decreased below the susceptibility break point, and the MIC of linezolid for one isolate was decreased to the blood and epithelial lining fluid concentration using the current dosing regimen. When vancomycin or norvancomycin was combined with subinhibitory doses of colistin, the multidrug-resistant Acinetobacter baumannii test samples were eradicated. Transmission electron microscopy revealed that subinhibitory doses of colistin were able to disrupt the outer membrane, facilitating a disruption of the cell wall and leading to cell lysis. Conclusions Subinhibitory doses of colistin significantly enhanced the antibacterial activity of vancomycin, norvancomycin, and linezolid against multidrug-resistant Acinetobacter baumannii.

Phlebotominae sand flies (Diptera: Psychodidae): potential vectors of American cutaneous leishmaniasis agents in the area associated with the Santo Antônio Hydroelectric System in Western Amazonian Brazil

INTRODUCTION: An entomological study was conducted as part of a vector-monitoring program in the area associated with the Santo Antônio hydroelectric system in State of Rondônia, Western Amazonian Brazil. METHODS: Fourteen sampling sites were surveyed to obtain data on the potential vectors of Leishmania spp. in the area. Sand flies were collected from 2011 to 2014 during the months of January/February (rainy season), May/June (dry season), and September/October (intermediary season) using light traps arranged in three vertical strata (0.5, 1, and 20m). RESULTS : A total of 7,575 individuals belonging to 62 species/subspecies were collected. The five most frequently collected sand flies were Psychodopygus davisi (Root) (36.67%), Trichophoromyia ubiquitalis (Mangabeira) (8.51%), Nyssomyia umbratilis (Ward & Fraiha) (6.14%), Bichromomyia flaviscutellata (Mangabeira) (5.74%), and Psychodopygus complexus (Mangabeira) (5.25%). These species have been implicated in the transmission of American cutaneous leishmaniasis agents in the Brazilian Amazon region and described as potential vectors of this disease in the study area. CONCLUSIONS: Additional surveillance is needed, especially in areas where these five species of sand fly are found.

User-centric product derivation in software product lines

Software Product Line (SPL) engineering aims at achieving efficient development of software products in a specific domain. New products are obtained via a process which entails creating a new configuration specifying the desired product’s features. This configuration must necessarily conform to a variability model, that describes the scope of the SPL, or else it is not viable. To ensure this, configuration tools are used that do not allow invalid configurations to be expressed. A different concern, however, is making sure that a product addresses the stakeholders’ needs as best as possible. The stakeholders may not be experts on the domain, so they may have unrealistic expectations. Also, the scope of the SPL is determined not only by the domain but also by limitations of the development platforms. It is therefore possible that the desired set of features goes beyond what is possible to currently create with the SPL. This means that configuration tools should provide support not only for creating valid products, but also for improving satisfaction of user concerns. We address this goal by providing a user-centric configuration process that offers suggestions during the configuration process, based on the use of soft constraints, and identifying and explaining potential conflicts that may arise. Suggestions help mitigating stakeholder uncertainty and poor domain knowledge, by helping them address well known and desirable domain-related concerns. On the other hand, automated conflict identification and explanation helps the stakeholders to understand the trade-offs required for realizing their vision, allowing informed resolution of conflicts. Additionally, we propose a prototype-based approach to configuration, that addresses the order-dependency issues by allowing the complete (or partial) specification of the features in a single step. A subsequent resolution process will then identify possible repairs, or trade-offs, that may be required for viabilization.

Phage display as a tool for generation of bio-therapeutic agents for breast cancer

Notch is a conserved signalling pathway, which plays a crucial role in a multiple cellular processes such as stem cell self-renewal, cell division, proliferation and apoptosis. In mammalian, four Notch receptors and five ligands are described, where interaction is achieved through their extracellular domains, leading to a transcription activation of different target genes. Increased expression of Notch ligands has been detected in several types of cancer, including breast cancer suggesting that these proteins represent possible therapeutic targets. The goal of this work was to generate quality protein targets and, by phage display technology, select function-blocking antibodies specific for Notch ligands. Phage display is a powerful technique that allows the generation of highly specific antibodies to be used for therapeutics, and it has also proved to be a reliable approach in identifying and validating new cancer-related targets. Also, we aimed at solving the tri-dimensional structure of the Notch ligands alone and in complex with selected antibodies. In this work, the initial phase focused on the optimization of the expression and purification of a human Delta-like 1 ligand mutant construct (hDLL1-DE3), by refolding from E. coli inclusion bodies. To confirm the biological activity of the produced recombinant protein cellular functional studies were performed, revealing that treatment with hDLL1-DE3 protein led to a modulation of Notch target genes. In a second stage of this study, Antibody fragments (Fabs) specific for hDLL1-DE3 were generated by phage display, using the produced protein as target, in which one good Fab candidate was selected to determine the best expression conditions. In parallel, multiple crystallization conditions were tested with hDLL1-DE3, but so far none led to positive results.