Multi-dimensional scaling applied to histogram-based DNA analysis

This paper aims to study the relationships between chromosomal DNA sequences of twenty species. We propose a methodology combining DNA-based word frequency histograms, correlation methods, and an MDS technique to visualize structural information underlying chromosomes (CRs) and species. Four statistical measures are tested (Minkowski, Cosine, Pearson product-moment, and Kendall τ rank correlations) to analyze the information content of 421 nuclear CRs from twenty species. The proposed methodology is built on mathematical tools and allows the analysis and visualization of very large amounts of stream data, like DNA sequences, with almost no assumptions other than the predefined DNA “word length.” This methodology is able to produce comprehensible three-dimensional visualizations of CR clustering and related spatial and structural patterns. The results of the four test correlation scenarios show that the high-level information clusterings produced by the MDS tool are qualitatively similar, with small variations due to each correlation method characteristics, and that the clusterings are a consequence of the input data and not method’s artifacts.

The predominance of M2-polarized macrophages in the stroma of low-hypoxic bladder tumors is associated with BCG immunotherapy failure

OBJECTIVE: Bacillus Calmette-Guérin (BCG) immunotherapy is the gold standard treatment for superficial bladder tumors with intermediate/high risk of recurrence or progression. However, approximately 30% of patients fail to respond to the treatment. Effective BCG therapy needs precise activation of the type 1 helper cells immune pathway. Tumor-associated macrophages (TAMs) often assume an immunoregulatory M2 phenotype and may directly interfere with the BCG-induced antitumor immune response. Thus, we aim to clarify the influence of TAMs, in particular of the M2 phenotype in stroma and tumor areas, in BCG treatment outcome. PATIENTS AND METHODS: The study included 99 patients with bladder cancer treated with BCG. Tumors resected before treatment were evaluated using immunohistochemistry for CD68 and CD163 antigens, which identify a lineage macrophage marker and a M2-polarized specific cell surface receptor, respectively. CD68+ and CD163+ macrophages were evaluated within the stroma and tumor areas, and high density of infiltrating cells spots were selected for counting. Hypoxia, an event known to modulate macrophage phenotype, was also assessed through hypoxia induced factor (HIF)-1α expression. RESULTS: Patients in whom BCG failed had high stroma-predominant CD163+ macrophage counts (high stroma but low tumor CD163+ macrophages counts) when compared with the ones with a successful treatment (71% vs. 47%, P = 0.017). Furthermore, patients presenting this phenotype showed decreased recurrence-free survival (log rank, P = 0.008) and a clear 2-fold increased risk of BCG treatment failure was observed in univariate analysis (hazard ratio = 2.343; 95% CI: 1.197-4.587; P = 0.013). Even when adjusted for potential confounders, such as age and therapeutic scheme, multivariate analysis revealed 2.6-fold increased risk of recurrence (hazard ratio = 2.627; 95% CI: 1.340-5.150; P = 0.005). High stroma-predominant CD163+ macrophage counts were also associated with low expression of HIF-1α in tumor areas, whereas high counts of CD163+ in the tumor presented high expression of HIF-1α in tumor nests. CONCLUSIONS: TAMs evaluation using CD163 is a good indicator of BCG treatment failure. Moreover, elevated infiltration of CD163+ macrophages, predominantly in stroma areas but not in the tumor, may be a useful indicator of BCG treatment outcome, possibly owing to its immunosuppressive phenotype.

An uncertainty and sensitivity analysis applied to the prioritisation of pharmaceuticals as surface water contaminants from wastewater treatment plant direct emissions

In this study, the concentration probability distributions of 82 pharmaceutical compounds detected in the effluents of 179 European wastewater treatment plants were computed and inserted into a multimedia fate model. The comparative ecotoxicological impact of the direct emission of these compounds from wastewater treatment plants on freshwater ecosystems, based on a potentially affected fraction (PAF) of species approach, was assessed to rank compounds based on priority. As many pharmaceuticals are acids or bases, the multimedia fate model accounts for regressions to estimate pH-dependent fate parameters. An uncertainty analysis was performed by means of Monte Carlo analysis, which included the uncertainty of fate and ecotoxicity model input variables, as well as the spatial variability of landscape characteristics on the European continental scale. Several pharmaceutical compounds were identified as being of greatest concern, including 7 analgesics/anti-inflammatories, 3 β-blockers, 3 psychiatric drugs, and 1 each of 6 other therapeutic classes. The fate and impact modelling relied extensively on estimated data, given that most of these compounds have little or no experimental fate or ecotoxicity data available, as well as a limited reported occurrence in effluents. The contribution of estimated model input variables to the variance of freshwater ecotoxicity impact, as well as the lack of experimental abiotic degradation data for most compounds, helped in establishing priorities for further testing. Generally, the effluent concentration and the ecotoxicity effect factor were the model input variables with the most significant effect on the uncertainty of output results.

A Random Access Protocol incorporating Multi-Packet Reception, Retransmission Diversity and Successive Interference Cancellation

8th International Workshop on Multiple Access Communications (MACOM2015), Helsinki, Finland.

Dimensionar a logística interna da fábrica Toyota Ovar para a produção de nova viatura

O projeto foi realizado na Toyota (divisão fabril de Ovar), no ano letivo 2014/2015, teve por base um estágio extracurricular que foi realizado para que desta forma tomasse contacto com uma realidade concreta e absoluta no contexto empresarial. O estágio serviu, principalmente, como uma experiência na compreensão do funcionamento de uma indústria de automóveis. Este projeto desenvolve-se no âmbito do 2ºano do Mestrado de Logística e apresenta os contributos desenvolvidos no departamento de logística para a reorganização da mesma para a produção de um novo modelo automóvel. Atualmente, a Toyota, para os modelos de automóveis que produz, recebe os componentes em CKD (Completed Knocked Down) provenientes do Japão em lotes de cinco unidades. Estes lotes são armazenados no armazém, de onde só saem quando for dada ordem para serem produzidos. Cada lote tem várias caixas, que são colocadas à vez numa zona comum de abertura. São retidos os componentes das caixas CKD e colocados nos transportadores próprios dos postos correspondentes (supermercado de linha). Isto significa que sempre que é solicitado uma viatura de um determinado lote, são obrigados a produzir as cinco unidades. Isto significa que as restantes unidades do lote terão que ficar em parque aberto a aguardar venda futura, para além de ter um stock desnecessário, estas unidades ficam vulneráveis e sofrem desgaste, pois estão expostas à intempérie, causando graves problemas de qualidade e respetivos custos associados. Recentemente, foi decidida a produção do modelo Land Cruiser 70 na unidade industrial de Ovar, Portugal, o que obrigou a uma reorganização da produção e processos logísticos para a sua produção. Os objetivos que a empresa pretende com a entrada de um novo projeto Land Cruiser 70, são os seguintes: Alterar o sistema de abastecimento, implementando o abastecimento unitário em toda a fábrica para o novo modelo, garantindo o “one by one production”; Definir o funcionamento do processo logístico desde a chegada dos componentes até ficarem disponíveis no supermercado de linha. Para isso será necessário dimensionar armazém e zona de abertura, definir layouts e quantidade de stocks, bem como definir sistemas de comunicação entre abertura e supermercado; Verificar as peças que vão fazer parte do chassi por posto e contabilizar os dolly´s1 necessários; Fazer o layout de abastecimento da linha do chassi; Calcular o tempo de abertura, de abastecimento e de picking do chassi e de triming. Este projeto tem em conta a política de melhoria contínua de forma a conseguir satisfazer o cliente (ser eficaz) utilizando cada vez menos recursos quer físicos quer humanos (ser eficiente, detetar e eliminar os desperdícios). O presente projeto foi inserido na equipa de melhoria contínua da logística, maioritariamente no chassi. Em termos globais, os objetivos propostos neste estágio foram atingidos com êxito.

Building Smarter Cities through Social Entrepreneurship

The objective of the present study is to examine the extent to which social ventures are able to increase the smartness of the cities. To achieve this goal, we adopt a qualitative approach, based on the case study method to obtain valuable insights about different characteristics and strategies of Cais (a non-profit association dedicated to help disadvantaged people in urban areas). By focusing on the analysis of the Cais activities, we assess whether its social intervention match the dimensions proposed by Giffinger et al. (2007) to rank smart cities’ performance, namely if it has smart: (i) economy; (ii) people; (iii) governance; (iv) mobility; (v) environment; and (vi) living. The research shows that the action pursued comprises elements from all the above mentioned dimensions. Further, the analysis reveals that Cais reinforces the smartness of the city where it acts (attributes such as living, economy, people, and environment).