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Publications

Publications by Artur Rocha

2003

An interoperable GIS solution for the public administration

Authors
Rocha, A; Lopes, JC; Bartolo, L; Chilro, R;

Publication
ELECTRONIC GOVENMENT, PROCEEDINGS

Abstract
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. Many of these teams are external to the municipality and in the position of sub-contractors. With so many actors involved, the result is often a complex mesh of incoherent spatial data. Overcoming this problem often leads to huge overheads for the public administration. This paper addresses a possible technical solution for this issue, based on international standards (e.g. OpenGIS) and profiting from the current state of technological development.

2023

Using Digital Tools to Study the Health of Adults Born Preterm at a Large Scale: e-Cohort Pilot Study

Authors
Lorthe, E; Santos, C; Ornelas, JP; Doetsch, JN; Marques, SCS; Teixeira, R; Santos, AC; Rodrigues, C; Goncalves, G; Sousa, PF; Lopes, JC; Rocha, A; Barros, H;

Publication
JOURNAL OF MEDICAL INTERNET RESEARCH

Abstract
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 knowledge regarding the long-term outcomes of individuals born preterm. Objective: This study aimed to assess the feasibility of recruiting and following up an e-cohort of adults born preterm worldwide and provide estimations of participation, characteristics of participants, the acceptability of questions, and the quality of data collected. Methods: We implemented a prospective, open, observational, and international e-cohort pilot study (Health of Adult People Born Preterm-an e-Cohort Pilot Study [HAPP-e]). Inclusion criteria were being an adult (aged =18 years), born preterm (<37 weeks of gestation), having internet access and an email address, and understanding at least 1 of the available languages. A large, multifaceted, and multilingual communication strategy was established. Between December 2019 and June 2021, inclusion and repeated data collection were performed using a secured web platform. We provided descriptive statistics regarding participation in the e-cohort, namely, the number of persons who registered on the platform, signed the consent form, initiated and completed the baseline questionnaire, and initiated and completed the follow-up questionnaire. We also described the main characteristics of the HAPP-e participants and provided an assessment of the quality of the data and the acceptability of sensitive questions. Results: As of December 31, 2020, a total of 1004 persons had registered on the platform, leading to 527 accounts with a confirmed email and 333 signed consent forms. A total of 333 participants initiated the baseline questionnaire. All participants were invited to follow-up, and 35.7% (119/333) consented to participate, of whom 97.5% (116/119) initiated the follow-up questionnaire. Completion rates were very high both at baseline (296/333, 88.9%) and at follow-up (112/116, 96.6%). This sample of adults born preterm in 34 countries covered a wide range of sociodemographic and health characteristics. The gestational age at birth ranged from 23+6 to 36+6 weeks (median 32, IQR 29-35 weeks). Only 2.1% (7/333) of the participants had previously participated in a cohort of individuals born preterm. Women (252/333, 75.7%) and highly educated participants (235/327, 71.9%) were also overrepresented. Good quality data were collected thanks to validation controls implemented on the web platform. The acceptability of potentially sensitive questions was excellent, as very few participants chose the I prefer not to say option when available. Conclusions: Although we identified room for improvement in specific procedures, this pilot study confirmed the great potential for recruiting a large and diverse sample of adults born preterm worldwide, thereby advancing research on adults born preterm.

2022

Life course of retrospective harmonization initiatives: key elements to consider

Authors
Fortier, I; Wey, TW; Bergeron, J; de Moira, AP; Nybo Andersen, AM; Bishop, T; Murtagh, MJ; Miocevic, M; Swertz, MA; van Enckevort, E; Marcon, Y; Mayrhofer, MT; Ornelas, JP; Sebert, S; Santos, AC; Rocha, A; Wilson, RC; Griffith, LE; Burton, P;

Publication
JOURNAL OF DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE

Abstract
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 to undertake comparison, cross-validation, or replication across data sets. To answer these requirements, cohort study data need to be findable, accessible, interoperable, and reusable (FAIR), and more particularly, it often needs to be harmonized. Harmonization is required to achieve or improve comparability of the putatively equivalent measures collected by different studies on different individuals. Although the characteristics of the research initiatives generating and using harmonized data vary extensively, all are confronted by similar issues. Having to collate, understand, process, host, and co-analyze data from individual cohort studies is particularly challenging. The scientific success and timely management of projects can be facilitated by an ensemble of factors. The current document provides an overview of the 'life course' of research projects requiring harmonization of existing data and highlights key elements to be considered from the inception to the end of the project.

2024

Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data

Authors
Peres, A; Klein, V; Frankel, B; Lees, W; Polak, P; Meehan, M; Rocha, A; Correia Lopes, J; Yaari, G;

Publication
Briefings in Bioinformatics

Abstract
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 implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains. © 2024 The Author(s). Published by Oxford University Press.

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