Artur Rocha

• Senior Researcher/Centre Coordinator at Institute for Systems and Computer Engineering, Technology and Science (INESC TEC)

Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were im...

Background: A European research infrastructure – RECAP Preterm – federating observational cohorts permits research about the aetiology, prognosis and care of very preterm (VPT) birth, but randomised controlled trials (RCT) are key for propelling advances; however, increasing feasibility constraints mean their numbers are decreasing. Long-term follo...

Background Preterm birth is a global health concern. Its adverse consequences may persist throughout the life course, exerting a potentially heavy burden on families, health systems, and societies. In high-income countries, the first children who benefited from improved care are now adults entering middle age. However, there is a clear gap in the k...

Background Internet-based interventions can be effective in the treatment of depression. However, internet-based interventions for older adults with depression are scarce, and little is known about their feasibility and effectiveness. Objective To present the design of 2 studies aiming to assess the feasibility of internet-based cognitive behavior...

Optimizing research on the developmental origins of health and disease (DOHaD) involves implementing initiatives maximizing the use of the available cohort study data; achieving sufficient statistical power to support subgroup analysis; and using participant data presenting adequate follow-up and exposure heterogeneity. It also involves being able...

BACKGROUND Internet-based interventions can be effective in the treatment of depression. However, internet-based interventions for older adults with depression are scarce and little is known about their feasibility and effectiveness. OBJECTIVE To present the design of two studies aiming to assess the feasibility of internet-based cognitive behavio...

BACKGROUND Preterm birth is a global health concern. Its adverse consequences may persist throughout the life course, exerting a potentially heavy burden on families, health systems, and societies. In high-income countries, the first children who benefited from improved care are now adults entering middle age. However, there is a clear gap in the k...

Background The small sample sizes available within many very preterm (VPT) longitudinal birth cohort studies mean that it is often necessary to combine and harmonise data from individual studies to increase statistical power, especially for studying rare outcomes. Curating and mapping data is a vital first step in the process of data harmonisation....

Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. So far, widespread adoption of AIR...

iReceptor Plus will enable researchers around the world to share and analyse huge immunological distributed datasets, from multiple countries, containing sequencing data pertaining to both healthy and sick individuals. Most of the Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) data is currently stored and curated by individual labs, usin...

Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. To date, widespread adoption of AI...

Background Internet-based cognitive-behavioral therapy (iCBT) is more effective when it is guided by human support than when it is unguided. This may be attributable to higher adherence rates that result from a positive effect of the accompanying support on motivation and on engagement with the intervention. This protocol presents the design of a p...

The Adaptive Immune Receptor Repertoire (AIRR) Community is a research-driven group that is establishing a clear set of community-accepted data and metadata standards; standards-based reference implementation tools; and policies and practices for infrastructure to support the deposit, curation, storage, and use of high-throughput sequencing data fr...

Background Self-reported client assessments during online treatments enable the development of statistical models for the prediction of client improvement and symptom development. Evaluation of these models is mandatory to ensure their validity. Methods For this purpose, we suggest besides a model evaluation based on study data the use of a simulat...

Background: Blended treatments, combining digital components with face-to-face (FTF) therapy, are starting to find their way into mental health care. Knowledge on how blended treatments should be set up is, however, still limited. To further explore and optimize blended treatment protocols, it is important to obtain a full picture of what actually...

Open access to high quality data on marine ecosystems’ structure and functioning is determinant in driving research and promoting better advice and policy making. The SeaBioData platform was developed to accommodate different types of data, including data on human impacts, with the aim to implement tools (added-value services) to integrate and anal...

Introduction Clinical trials of blended Internet-based treatments deliver a wealth of data from various sources, such as self-report questionnaires, diagnostic interviews, treatment platform log files and Ecological Momentary Assessments (EMA). Mining these complex data for clinically relevant patterns is a daunting task for which no definitive bes...

Technology driven interventions provide us with an increasing amount of fine-grained data about the patient. This data includes regular ecological momentary assessments (EMA) but also response times to EMA questions by a user. When observing this data, we see a huge variation between the patterns exhibited by different patients. Some are more stabl...

In this paper we introduce a new Android library, called ULTEMAT, for the delivery of ecological momentary assessments (EMAs) on mobile devices and we present its use in the MoodBuster app developed in the H2020 E-COMPARED project. We discuss context-aware, or event-based, triggers for the presentation of EMAs and discuss the potential they have to...

Current mobile devices allow the execution of sophisticated applications with the capacity for identifying the user situation, which can be helpful in treatments of mental disorders. In this paper, we present SituMan, a solution that provides situation awareness to MoodBuster, an ecological momentary assessment and intervention mobile application u...

Weather and sea-related forecasts provide crucial insights for the practice of nautical sports such as surf and kite surf, and mobile devices are appropriate interfaces for the visualization of meteorology and operational oceanography data. Data are collected and processed by several agencies and are often obtained from forecast models. Their use r...

Effective metadata handling is determinant for successful data discovery among the organizations and in the context of a Distributed Oceanographic Observatory. However, in any distributed system, the harvesting of consistent metadata from data services implemented by distinct providers is not without obstacles. In this publication authors will desc...

Abstract for part by MN Kamel Boulos: This presentation will discuss the main ingredients for a successful implementation of game mechanics (gamification) in e-health interventions intended for health-related behaviour and lifestyle modifications (e.g., in obesity [diet and exercise] or for smoking cessation), drawing on the best current research e...

A considerable number of domains deal with large and complex volumes of temporal data. The management of these volumes, from capture, storage, search, transfer, analysis and visualization, still provides interesting challenges. One critical task is the efficient retrieval of data (raw data or intermediate results from analytic tools). Previous work...

Many tasks dealing with temporal data, such as interactive browse through temporal data, require intensive retrieval from the database. Depending on the user's task, the data retrieved may be too large to fit in the local memory. Even if it fits, the time taken to retrieve the data may compromise user interaction. This work proposes a method, Trave...

The development of a distributed and scalable architecture for the Portuguese solid Earth community will be discussed. This work is a prelude to developing and deploying an e-Infrastructure for the solid Earth community, in articulation with the efforts occurring in projects such as EPOS. This work describes a high-level architecture proposal which...

Depression is expected to be the disorder with the highest disease burden in high-income countries by the year 2030. ICT4Depression (ICT4D) is a European FP7 project, which aims to contribute to the alleviation of this burden by making use of depression treatment and ICT innovations. In this project we developed an ICT-based system for use in prima...

One of the main goals of RAIA Project is to incorporate the requirements defined by the European Directive INSPIRE, which establishes an infrastructure for spatial information in Europe to support Community environmental policies and activities, in order to ensure that the spatial data infrastructures collected by the oceanographic observatory for...

FP7 ICT4Depression project aims at providing a set of tools to further improve both patient outcome and increase of access to treatment of the patients suffering from major depression. This article describes the Information Systems (IS) architecture used in the project. ICT4Depression uses a service oriented architecture as means of bringing togeth...

Purpose: This paper describes proposed health care services innovations, provided by a system called CAALYX (Complete Ambient Assisted Living eXperiment). CAALYX aimed to provide healthcare innovation by extending the state-of-the-art in tele-healthcare, by focusing on increasing the confidence of elderly people living autonomously, by building on...

In this paper we discuss the development and clinical evaluation of a wireless platform for health signs sensing. The sensors measure physical activity, ECG, blood oxygen saturation, temperature and respiratory rate. An important aspect of the approach is that the sensors are integrated into one waist-worn device. A mobile phone collects data from...

Recent advances in mobile positioning systems and telecommunications are providing the technology needed for the development of location-aware tele-care applications. This paper introduces CAALYX--Complete Ambient Assisted Living Experiment, an EU-funded project that aims at increasing older people's autonomy and self-confidence by developing a wea...

In this article we focus on interoperable geographic information (GI) services from the crisis management perspective. Based on Open Geospatial Consortium [10] standards and initiatives, we present the building blocks of the interoperable solution for supporting crisis management that is proposed as a result of the EU sponsored project, MEDSI [1]....

Resumo: Este artigo descreve uma aproximação à inclusão de suporte para lógica espaço-temporal em Web Feature Services (WFS). Este tipo de Web Services permite a interrogação de fontes heterogéneas de informação geográfica, num ambiente distribuído, retornando o resultado em formato Geography Markup Language (GML). No entanto, não é possível obter,...

This paper describes an architecture which can be used to access geographic information from mobile devices with limited display and processing characteristics, such as Personal Digital Assistants (PDA) or Mobile Phones. The information may come from different sources leading to an interoperable solution. M-GIS obtains geographic information from s...

SINUP consists of a geographical information system whose purpose is to store, in a coherent manner, data resulting from key activities of Oporto local authority, allowing to better structure the knowledge about the urban reality. In the possession of such knowledge, and with the revision of Oporto’s Municipal Master Plan taking place soon, the mun...

Geographical information is of strategic importance, when comes to land use management decision-making and GIS are essential resources for the production of land use management instruments, commonly known as plans (e.g. master plans). To build them, local authorities require multi-disciplinary teams with different competences and responsibilities....

Resumo Este artigo descreve uma forma de acesso interoperável a um sistema de informação geográfica através de dispositivos móveis de características limitadas (e.g. telemóveis ou Per-sonal Digital Assistants). O sistema M-GIS segue uma arquitectura cliente-servidor tendo por base informação geográfica no formato GML que é transformada, através de...