Efficient Haplotype Inference with Pseudo-Boolean Optimization

Abstract. Haplotype inference from genotype data is a key computational problem in bioinformatics, since retrieving directly haplotype information from DNA samples is not feasible using existing technology. One of the methods for solving this problem uses the pure parsimony criterion, an approach known as Haplotype Inference by Pure Parsimony (HIPP). Initial work in this area was based on a number of different Integer Linear Programming (ILP) models and branch and bound algorithms. Recent work has shown that the utilization of a Boolean Satisfiability (SAT) formulation and state of the art SAT solvers represents the most efficient approach for solving the HIPP problem. Motivated by the promising results obtained using SAT techniques, this paper investigates the utilization of modern Pseudo-Boolean Optimization (PBO) algorithms for solving the HIPP problem. The paper starts by applying PBO to existing ILP models. The results are promising, and motivate the development of a new PBO model (RPoly) for the HIPP problem, which has a compact representation and eliminates key symmetries. Experimental results indicate that RPoly outperforms the SAT-based approach on most problem instances, being, in general, significantly more efficient

Gender Performativities: Discourses and Representations of a Group of Catholic Nuns

O presente documento analisa as performatividades de género de irmãs religiosas católicas portuguesas. A partir de um estudo qualitativo procurou perceber-se se as performativida-des de género de um grupo de irmãs religiosas são constrangidas pelos discursos e represen-tações oficiais da Igreja Católica. Procurou-se também analisar de que modo estas mulheres caracterizam as relações sociais de género e se posicionam face às noções de feminilidade e masculinidade tradicionalmente propagadas pela ordem de género (Connell, 2009) e, mais concretamente, pelo regime de género da Igreja Católica. Para tal realizaram-se 7 entrevis-tas individuais semiestruturadas a irmãs religiosas católicas residentes em instituições da região do Grande Porto. Os dados recolhidos foram tratados através de uma análise de con-teúdo. Concluiu-se que as irmãs religiosas são efetivamente constrangidas pelos discursos e representações da Igreja Católica, performatizando o género por via da reprodução e reite-ração de conceções tradicionais de feminilidade e masculinidade. O género é por elas mate-rializado nas ações quotidianas, tendo por base prescrições institucionais e sociais altamen-te conservadoras.This paper explores the gender performativities of Portuguese Catholic religious nuns. Based on a qualitative study, we intended to understand if gender performativities of a group of religious nuns are constrained by the official discourses and representations of the Catholic Church. We also intended to analyze these women’s perspectives about gender social relations and their positions towards femininity and masculinity conceptions tradi-tionally propagated by the gender order (Connell, 2009) and, concretely, by the Catholic Church gender regime. For that purpose 7 individual semi-structured interviews were con-ducted with nuns living in institutions located in Oporto Metropolitan area. Data was ana-lyzed through a content analysis. It was concluded that nuns are, in fact, constrained by the discourses and representations of Catholic Church, performing gender through repro-ductions and reiteration of traditional conceptions of femininity and masculinity. Gender is materialized by them through daily actions, based on institutional and social prescriptions highly conservative

Prescription patterns of pharmaceuticals

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Economics from the NOVA – School of Business and EconomicsIn May 2011, Portugal signed the Memorandum of Understanding in which it guarantees a reduction in the public spending on pharmaceuticals. The aim of this research work is to analyse the possibility of hospital cost reductions in HIV, oncology and rheumatism related pharmaceutical drugs, by better practice of medical physicians. The patterns of drug prescriptions were modelled using a relative distribution, stochastic dominance analysis and an ordered probit model. It was found that there is great divergence in expenditure levels of pharmaceutical products across hospitals and medical specialties. Outlier physicians tend to maintain their prescribing behaviour, even after the introduction of feedback. Therefore, there is room to reduce hospital costs of pharmaceutical products, by better practice

Molecular modelling of ABC transporters: from ATP hydrolysis to substrate transport

Dissertação para a obtenção de grau de doutor em Bioquímica pelo Instituto de Tecnologia Química e Biológica da Universidade Nova de LisboaDespite the great advances that have been made in the past decades in the ABC transporters field, the molecular mechanisms involved in transport across membranes remains largely an enigma. To date, questions regarding the molecular mechanism of transport, nucleotide hydrolysis and inorganic phosphate exit from the binding sites are still unanswered. In this thesis the dynamic behavior of several ABC transporters during the ATP-hydrolytic cycle is investigated using molecular modeling methods. The content of this thesis is compiled in three main scientific publications [1-3], corresponding to sections 3, 4 and 5, respectively. Although these three works are performed in prokaryotic family ABC transporters, it is likely that eukaryotic ones use similar mechanisms for nucleotide hydrolysis, inter-domain communication and allocrite translocation.(...)Esta tese teve o apoio financeiro da FCT e do FSE no âmbito do Quadro Comunitário de Apoio, BD nº SFRH/BD/21433/200

The effect of government budget on Portuguese stock market

Government budget reflects a prevision of future expenses and revenues which will predict the economic and financial situation of the country. This paper studies the effect of the publication, approval and actions inside the Portuguese government budget on the stock market performance of Portuguese companies. Additionally, the effects of presidential and legislative elections are also tested in the stock prices. The 46 companies represented in this study are listed on the Portuguese Stock Index between 1998 and 2013. I realize that a publication of government budget to the Parliament leads to a positive and significant return on the full sample results, basic materials and consumer services sector. The same sectors react in a positive way to periods of presidential elections. This study also provides a comparison between sectors. The consumer services sector reveals to be the more volatile sector before changes in the resources invested in each ministry. The consumer services sector is predominantly affected, in a negative way, by not rational expenses in the Ministry of Health. The financial sector has negative reactions on stock returns when the investment in the Ministry of Finance is reduced by the State

Changing Practices, Changing Identities: A Study with Students at Risk of Educational Exclusion

This study discusses how students at risk of educational exclusion can restore their identity and improve learning and scientific literacy. This qualitative research adopts an interpretative orientation. Twenty-eight secondary school students, aged 16 to 20 participated. Data was collected of the interactions between students in lessons, focus group interview and written documents. Data analysis was inductive, consistent with a naturalistic research paradigm, and consisted of uncovering salient patterns, singularities, and themes associated with research aims. Several students, at risk of educational exclusion, value this kind of practice. By changing practice, the learning social context varied, as well as students’ identities and their relationships with knowledge, teachers and school

The effect of Brand Experience on Consumer Satisfaction, Brand Trust and Brand Loyalty - In the Portuguese Skincare Industry

Dissertation presented as the partial requirement for obtaining a Master's degree in Information Management, specialization in Marketing IntelligenceThis study intends to understand and examine the direct and indirect effects that brand experience may have on consumer satisfaction, brand trust and brand loyalty, and ultimately to determine whether Portuguese women have brand loyalty when it comes to skincare products in the cosmetic sector and what can be done to improve that loyalty. The main factors that may affect the purchase of this type of products were also analyzed in order to determine which factors exert higher influence on Portuguese women when it comes to the purchase of skincare products. With this in mind, the results provided by this study will contribute to the existing knowledge in this subject with meaningful data that has clear practical application, since it can help either existing or new domestic and international companies to better understand the Portuguese market and consequently, develop their marketing strategies. A total of 255 responses were collected through an online questionnaire that targeted Portuguese women with ages between 18 and 65. The findings of this study revealed that brand experience has a significantly and positive effect on consumer satisfaction, brand trust and brand loyalty. In addition, a mediation analysis showed that consumer experience and brand trust significantly mediate the relationship between brand experience and brand loyalty. The findings also demonstrate that country of origin (preference for Portuguese products), price and social influence have a significative influence on brand loyalty, while the organic nature of skincare products and the use of harmful ingredients in these products don’t affect brand loyalty in a significative way

Student Perceptions of Secondary Science Teachers’ Practices Following Curricular Change

Inquiry-based teaching has emerged as a highly valued strategy in science education. In Portugal, the science curriculum has been redesigned in order to promote such teaching. This implies substantial change in teacher practice. It is therefore important to understand students’ perceptions of teacher practice. Aim: In this study, we describe student perception of teacher practices and look for associations between the perceptions and student motivation. Method: Three low-achieving, secondary-level science classes were studied. Motivation was measured by two scales (Intrinsic and Extrinsic); Perceptions were measured in four dimensions. Results: Significant associations (p < .05) were observed between intrinsic motivation and (a) Perception of the use of Laboratory Work; (b) Perception of Science-Technology-Society and (c) Perceived Student Autonomy. No association was noted between intrinsic motivation and the Perception of Teacher as Facilitator. Conclusions: Results are generally consistent with previous literature. Teacher professional development lags behind curricular change. Teachers require new conceptions of assessment.Projeto financiado pelo CIEFCU