Supporting Scientific Research Through Machine and Deep Learning: Fluorescence Microscopy and Operational Intelligence Use Cases

Although the debate of what data science is has a long history and has not reached a complete consensus yet, Data Science can be summarized as the process of learning from data. Guided by the above vision, this thesis presents two independent data science projects developed in the scope of multidisciplinary applied research. The first part analyzes fluorescence microscopy images typically produced in life science experiments, where the objective is to count how many marked neuronal cells are present in each image. Aiming to automate the task for supporting research in the area, we propose a neural network architecture tuned specifically for this use case, cell ResUnet (c-ResUnet), and discuss the impact of alternative training strategies in overcoming particular challenges of our data. The approach provides good results in terms of both detection and counting, showing performance comparable to the interpretation of human operators. As a meaningful addition, we release the pre-trained model and the Fluorescent Neuronal Cells dataset collecting pixel-level annotations of where neuronal cells are located. In this way, we hope to help future research in the area and foster innovative methodologies for tackling similar problems. The second part deals with the problem of distributed data management in the context of LHC experiments, with a focus on supporting ATLAS operations concerning data transfer failures. In particular, we analyze error messages produced by failed transfers and propose a Machine Learning pipeline that leverages the word2vec language model and K-means clustering. This provides groups of similar errors that are presented to human operators as suggestions of potential issues to investigate. The approach is demonstrated on one full day of data, showing promising ability in understanding the message content and providing meaningful groupings, in line with previously reported incidents by human operators.

The need for adequate ethical guidelines for qualitative health research

O artigo discute a adequação de aplicar a Resolução 196/961 do Conselho Nacional de Saúde - CNS, às pesquisas qualitativas em saúde, que se baseiam em paradigmas não positivistas. Nestas pesquisas, freqüentemente as decisões sobre a pesquisa são tomadas conjuntamente com a comunidade em estudo. Há a preocupação de favorecer a justiça e a mudança social. E, uma vez que a subjetividade pode ser considerada seu instrumento privilegiado, busca-se o balanço entre objetividade e subjetividade, e discute-se como superar a visão do pesquisador. Estudamos o âmbito de aplicação e a concepção de pesquisa presentes nas diretrizes éticas internacionais e brasileiras. Verificamos que elas adotam uma concepção positivista de pesquisa, que prevê: teste de hipótese, definição prévia de todos os procedimentos pelo pesquisador e neutralidade do pesquisador e do conhecimento produzido. Serão apresentadas algumas características das pesquisas qualitativas, as implicações éticas da maneira como a pesquisa qualitativa é concebida nos paradigmas não positivistas e um breve histórico dos documentos sobre ética em pesquisa. Concluímos que não é adequado analisar estas pesquisas com base nestes documentos e sugerimos a elaboração de diretrizes específicas

Investigando o passado para planear o futuro: uma análise bibliométrica das publicações dos Açores em revistas do SCI entre 1974-2012

Jornadas "Ciência nos Açores – que futuro? Tema Ciências Naturais e Ambiente", Ponta Delgada, 7-8 de Junho de 2013.

Robots and humans as co-workers? The human-centred perspective of work with autonomous systems

The design of work organisation systems with automated equipment is facing new challenges and the emergence of new concepts. The social aspects that are related with new concepts on the complex work environments (CWE) are becoming more relevant for that design. The work with autonomous systems implies options in the design of workplaces. Especially that happens in such complex environments. The concepts of “agents”, “co-working” or “human-centred technical systems” reveal new dimensions related to human-computer interaction (HCI). With an increase in the number and complexity of those human-technology interfaces, the capacities of human intervention can become limited, originating further problems. The case of robotics is used to exemplify the issues related with automation in working environments and the emergence of new HCI approaches that would include social implications. We conclude that studies on technology assessment of industrial robotics and autonomous agents on manufacturing environment should also focus on the human involvement strategies in organisations. A needed participatory strategy implies a new approach to workplaces design. This means that the research focus must be on the relation between technology and social dimensions not as separate entities, but integrated in the design of an interaction system.

Clearing the cloudy crystal balls: Hybrid modelling for energy and climate change mitigation scenarios – A case study for Portugal

Dissertação para obtenção do Grau de Doutor em Ambiente

The Portuguese programme one laptop per child: political, educational and social impact

In 2008, the XVII Portuguese Constitutional Government launched the ‘e.escolinha’ programme, within the Technological Plan for Education, which set out the distribution of a computer, called ‘Magalhães’, designed for chil-dren attending the 1st cycle of basic education. Suspended in 2011 by the XIX Government, this programme has allowed, however, almost 500 000 children to have access to a personal computer. It was expected that this political measure would “revolutionise” the national education system by bringing changes to the pedagogical practices of teachers and the learning processes of children and by achieving educational success, in general. Based on documental analysis and on a set of interviews with key decision-makers in conceiving, implementing and monitoring this governmental initiative, the fi rst part of this chapter presents and analyses the ‘e.escolinha’ initiative and the policies be-hind that governmental programme, seeking to disassemble those objectives and provide some insights into the relationship between discourses, rhetoric, and reality. After that, the chapter focuses on children’s uses and practices with the ‘Magalhães’ laptop, at school and at home. Based on the results of questionnaires fi lled in by approximately 1500 children from 32 First Cycle public schools of the municipality of Braga (north of Portugal) and also from questionnaires applied to their parents and teachers, this chapter intends to analyse the real impact of this initiative for children, family and school. It also seeks to discuss the contribution of this educational policy to children’s digital literacy and also to their own and their families’ social and digital inclusion. To understand if it represented an added value to teachers’ pedagogical practice is another of its aims. The fi ndings point out a major focus on technology and access rather than on uses and competences or even on social, educational and cultural change. In fact, a major conclusion is the existence of a strong gap between the policy and the practices, typical of a top-down policy design. This study is an integrant part of a research project titled “Navigating with ‘Magalhães’: Study on the Impact of Digital Media in Schoolchildren” conducted at the University of Minho, Portugal, financed by the Portuguese Foundation for Science and Technology [PTDC/CCI-COM/101381/2008] and co-funded by the European Regional Development Fund [COMPETE: FCOMP-01-0124-FEDER-009056].

IPH response to the HIQA consultation on the National Demographic Dataset and Guidance for use in health and social care settings in Ireland

The remit of the Institute of Public Health in Ireland (IPH) is to promote cooperation for public health between Northern Ireland and the Republic of Ireland in the areas of research and information, capacity building and policy advice. Our approach is to support Departments of Health and their agencies in both jurisdictions, and maximise the benefits of all-island cooperation to achieve practical benefits for people in Northern Ireland and the Republic of Ireland. IPH have previously responded to consultations to the Department of Health’s Discussion Paper on the Proposed Health Information Bill (June 2008), the Health Information and Quality Authority on their Corporate Plan (Oct 2007), and the Road Safety Authority of Ireland Road Safety Strategy (Jul 2012). IPH supports the development of a national standard demographic dataset for use within the health and social care services. Provided necessary safeguards are put in place (such as ethics and data protection) and the purpose of collecting the information is fully explained to subjects, mandatory provision of a minimum demographic dataset is usually the best way to achieve the necessary coverage and data quality. Demographic information is needed in several forms to support the public health function: Detailed aggregated information for comparison to population counts in order to assess equity of access to healthcare as well as examining population patterns and trends in morbidity and mortality Accurate demographic information for the surveillance of infectious disease outbreaks, monitoring vaccination programmes, setting priorities for public health interventions Linked to other data outside of health and social care such as population data, survey data, and longitudinal studies for research and analysis purposes.   Identify and address public health issues to tackle health inequalities, and to monitor the success of such efforts to tackle them.

OER in Portugal as agent of curriculum innovation and technological change. Inducing practices of "new" teaching standards

This research project aimed the following goal: promote the creation, use and disclosure of OER in a Group of Schools, involving schools and teachers from different learning levels, expecting to test and validate the use of OER, in a learning-teaching model towards curricular innovation. Defining as a starting point different subjects and teachers from distinct academic areas, we have implemented a set of activities leading to the creation of OER supported, when possible, in FLOSS tools. We adopted an action research methodology with a dual purpose: to act within a community of teachers and students, while increasing at the same time their knowledge, as well as the researcher's. The activity was developed cooperatively in order to process a certain reality of the teaching-learning process, through practical/reflective action towards it and inducing its implementation by others in the Portuguese School System, based on the production and sharing OER.

Assisted reproductive technology and obstetric outcome in couples when the male partner has a chronic viral disease.

BACKGROUND Assisted reproductive technology (ART) with washed semen can achieve pregnancy with minimal risk of horizontal and vertical transmission of chronic viral diseases (CVD) such as human immunodeficiency virus (HIV), hepati- tis C virus (HCV) and hepatitis B virus (HBV) among serodiscordant couples. How- ever, few studies have been made of the use made by these couples of ARTs or of the obstetric results achieved. MATERIALS AND METHODS In this retrospective study, 93 men who were seropositive for HIV, HCV or HBV and who underwent assisted reproduction treatment at our centre (Hospital Universitario Virgen de las Nieves, Granada, Spain) were included. Washed semen was tested to detect viral particles. Non-infected women were tested before and after each treatment, as were the neonates at birth and after three months. RESULTS A total of 62 sperm samples were washed, and none were positive for the detec- tion of viral molecules. Semen samples from 34 HBV positive males were not washed since the female partner had immunity to hepatitis B. In total, 38 clinical pregnancies were achieved (22% per cycle and 40.9% per couple) out of 173 cycles initiated, and 28 births were achieved (16.2% per cycle and 30.1% per couple), producing 34 live births. The rate of multiple pregnancies was 21.4%. Obstetric and neonatal results were similar in the groups of couples studied. At follow-up, no seroconversion was detected in the women or neonates. CONCLUSION Sperm washing and intracytoplasmic sperm injection are shown to be a safe and effective option for reducing the risk of transmission or super infection in serodiscordant or concordant couples who wish to have a child. Pregnancies ob- tained by ART in couples when the male is CVD infected achieve good obstetric and neonatal results.

Policy attitudes, ideological values and social representations

This article reviews research on policy attitudes and ideological values from the perspective of social representations theory. In the first part of the paper, key features of lay political thinking are presented, its pragmatic imperative, its focus on communication and the social functions of shared knowledge. Objectification transforms abstract and group-neutral ideological values into concrete and socially useful knowledge, in particular stereotypes of value-conforming and value-violating groups. Such shared understandings of intergroup relations provide citizens with common reference knowledge which provides the cognitive and cultural basis of policy attitudes. Social representations theory further suggests that lay knowledge reflects the social context in which it has been elaborated (anchoring), an aspect which allows conceptualising aggregate-level differences in policy attitudes. In the second part of the paper, a model of lay conceptions of social order is outlined which organises four shared conceptions of social order, along with the stereotype-based thinking associated with each conception: Moral order, Free Market, Social diversity and Structural inequality. We conclude by arguing that policy attitudes are symbolic devices expressed to justify or to challenge existing social arrangements.

A study of the effects of PVAC on works of art on paper and wood: pH and colour change

This paper presents the preliminary findings of pH and colour measurements carried out on artworks on paperand on wood that had been treated with a poly(vinyl acetate) (PVAC) based adhesive in the 1980s. In both cases, areas treated with PVAC proved to be less acidic than untreated areas. Contrary to expectations, the conservation treatments have not, as yet, increased acidity levels in the objects under study. Colour measurements of the works on paper showed that those that had been backed with a cotton fabric using a mixture of methylcellulose and PVAC were less yellow than those from the same print run that had not been backed. This finding suggests that the backing somehow prevented the natural degradation of the support. In view of these preliminary results, further research is clearly needed. This study forms part of a broader ongoing project to assess the role of PVAC in the conservation of a range of cultural assets.

Supporting interdisciplinary case studies: development and implementation of a joint learning environment for students in forensic science and criminal law

Scientific reporting and communication is a challenging topic for which traditional study programs do not offer structured learning activities on a regular basis. This paper reports on the development and implementation of a web application and associated learning activities that intend to raise the awareness of reporting and communication issues among students in forensic science and law. The project covers interdisciplinary case studies based on a library of written reports about forensic examinations. Special features of the web framework, in particular a report annotation tool, support the design of various individual and group learning activities that focus on the development of knowledge and competence in dealing with reporting and communication challenges in the students' future areas of professional activity.

Estimating slope and level change in N=1 designs

The current study proposes a new procedure for separately estimating slope change and level change between two adjacent phases in single-case designs. The procedure eliminates baseline trend from the whole data series prior to assessing treatment effectiveness. The steps necessary to obtain the estimates are presented in detail, explained, and illustrated. A simulation study is carried out to explore the bias and precision of the estimators and compare them to an analytical procedure matching the data simulation model. The experimental conditions include two data generation models, several degrees of serial dependence, trend, level and/or slope change. The results suggest that the level and slope change estimates provided by the procedure are unbiased for all levels of serial dependence tested and trend is effectively controlled for. The efficiency of the slope change estimator is acceptable, whereas the variance of the level change estimator may be problematic for highly negatively autocorrelated data series.

A study of the effects of PVAC on works of art on paper and wood: pH and colour change

This paper presents the preliminary findings of pH and colour measurements carried out on artworks on paperand on wood that had been treated with a poly(vinyl acetate) (PVAC) based adhesive in the 1980s. In both cases, areas treated with PVAC proved to be less acidic than untreated areas. Contrary to expectations, the conservation treatments have not, as yet, increased acidity levels in the objects under study. Colour measurements of the works on paper showed that those that had been backed with a cotton fabric using a mixture of methylcellulose and PVAC were less yellow than those from the same print run that had not been backed. This finding suggests that the backing somehow prevented the natural degradation of the support. In view of these preliminary results, further research is clearly needed. This study forms part of a broader ongoing project to assess the role of PVAC in the conservation of a range of cultural assets.

A study of the effects of PVAC on works of art on paper and wood: pH and colour change

This paper presents the preliminary findings of pH and colour measurements carried out on artworks on paperand on wood that had been treated with a poly(vinyl acetate) (PVAC) based adhesive in the 1980s. In both cases, areas treated with PVAC proved to be less acidic than untreated areas. Contrary to expectations, the conservation treatments have not, as yet, increased acidity levels in the objects under study. Colour measurements of the works on paper showed that those that had been backed with a cotton fabric using a mixture of methylcellulose and PVAC were less yellow than those from the same print run that had not been backed. This finding suggests that the backing somehow prevented the natural degradation of the support. In view of these preliminary results, further research is clearly needed. This study forms part of a broader ongoing project to assess the role of PVAC in the conservation of a range of cultural assets.