10 years of experience

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Robustness Assessment with a Data-Centric Machine Learning Pipeline

Publisher Copyright: AuthorAs long as the COVID-19 pandemic is still active in most countries worldwide, rapid diagnostic continues to be crucial to mitigate the impact of seasonal infection waves. Commercialized rapid antigen self-tests proved they cannot handle the most demanding periods, lacking availability and leading to cost rises. Thus, developing a non-invasive, costless, and more decentralized technology capable of giving people feedback about the COVID-19 infection probability would fill these gaps. This paper explores a sound-based analysis of vocal and respiratory audio data to achieve that objective. This work presents a modular data-centric Machine Learning pipeline for COVID-19 identification from voice and respiratory audio samples. Signals are processed to extract and classify relevant segments that contain informative events, such as coughing or breathing. Temporal, amplitude, spectral, cepstral, and phonetic features are extracted from audio along with available metadata for COVID-19 identification. Audio augmentation and data balancing techniques are used to mitigate class disproportionality. The open-access Coswara and COVID-19 Sounds datasets were used to test the performance of the proposed architecture. Obtained sensitivity scores ranged from 60.00% to 80.00% in Coswara and from 51.43% to 77.14% in COVID-19 Sounds. Although previous works report higher accuracy on COVID-19 detection, this research focused on a data-centric approach by validating the quality of the samples, segmenting the speech events, and exploring interpretable features with physiological meaning. As the pandemic evolves, its lessons must endure, and pipelines such as the proposed one will help prepare new stages where quick and easy disease identification is essential.publishersversionepub_ahead_of_prin

A score methodology to assess concept maps in medical education in the context of pathophysiology teaching

The main objective of pathophysiology teaching is to facilitate the learning of mechanisms of diseases and the understanding of their expressions in patients (symptoms, signs and tests). This objective requires the application of basic biomedical science to explain the abnormalities expressed by the patients. The capacity to integrate this new organization of knowledge is essential to the understanding of pathophysiological mechanisms, which explain expressions of specific diseases. Our group has a longstanding experience in the teaching of pathophysiology to medical students using problem-based learning (PBL) and concept mapping (CM). This semestral discipline has a yearly intake of 190 students, divided into 18 tutorial groups and supported by 14 tutors. The students’ learning progress is evaluated by their performance during the tutorial sessions and the CM methodology has been introduced as an additional tool to visualize the integration of knowledge and how it is displayed in the different pathophysiological mechanisms. Until now, the evaluation of CM has been qualitative and used as an additional assessment tool by the tutors. This study reports how we are changing this approach by training the tutors and developing a scoring methodology, which will be described in detail, together with a preliminary application in selected mapsFonseca, M.; Oliveira, B.; Carreiro-Martins, P.; Neuparth, N.; Rendas, A. (2020). A score methodology to assess concept maps in medical education in the context of pathophysiology teaching. En 6th International Conference on Higher Education Advances (HEAd'20). Editorial Universitat Politècnica de València. (30-05-2020):867-874. https://doi.org/10.4995/HEAd20.2020.11163OCS86787430-05-202

A narrative review

Funding Information: João Gaspar Marques has received research grants from AstraZeneca and honorarium as speaker/consultant from AstraZeneca, Novartis, Sanofi and TEVA. Mafalda van Zeller has received honorarium as speaker/consultant from AstraZeneca, GlaxoSmithKline, Novartis and TEVA. Pedro Carreiro Martins has received research grants from AstraZeneca and honorarium as speaker/consultant from AstraZeneca, GlaxoSmithKline, Novartis and Sanofi. Cláudia Chaves Loureiro has received honorarium as speaker/consultant from AstraZeneca, GlaxoSmithKline, Novartis, Sanofi and TEVA. Publisher Copyright: © 2021 Sociedade Portuguesa de Pneumologia Copyright: Copyright 2021 Elsevier B.V., All rights reserved.Introduction and objectives: Severe asthma management during the coronavirus disease 2019 (COVID-19) pandemic is a challenge and will continue to be, at least in the next few months, as herd immunity is still a mirage. A lot has to be learned about how COVID-19 affects underlying diseases, and severe asthma is no exception. Methods: Narrative review of papers available until February 2021 in PubMed and Google Scholar, relating severe asthma and COVID-19. Four main research topics were reviewed: SARS-CoV-2 infection: immunology and respiratory pathology; interrelationship of severe asthma endotypes and COVID-19 disease mechanisms; severe asthma epidemiology and COVID-19; and biologics for severe asthma in the context of COVID-19. Results: COVID-19 disease mechanisms start with upper respiratory cell infection, and afterwards several immunological facets are activated, contributing to disease severity, namely cell-mediated immunity and antibody production. Although infrequent in the COVID-19 course some patients develop a cytokine storm that causes organ damage and may lead to acute respiratory distress syndrome or multiorgan failure. Regarding severe asthma endotypes, type2-high might have a protective role both in infection risk and disease course. There is conflicting data regarding the epidemiological relationship between COVID-19 among severe asthma patients, with some studies reporting increased risk of infection and disease course, whereas others the other way round. Biologics for severe asthma do not seem to increase the risk of infection and severe COVID-19, although further evidence is needed. Conclusions: Globally, in the era of COVID-19, major respiratory societies recommend continuing the biologic treatment, preferably in a self-home administration program.publishersversionpublishe

A clinical argument or an access constraint?

Funding Information: In the preparation of this article, the authors received collaboration from the medical writer Duarte Oliveira (W4Research) financially supported by Sanofi. Sanofi had no role in the preparation of the manuscript or in the decision to submit the manuscript for publication. All authors declare collaborating and receiving fees from Sanofi and other pharmaceutical companies either through participation in advisory boards or consultancy, congress symposia, conducting clinical trials, investigator-initiated trials or grants. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.proofpublishe

Ventilatory defects and treatable traits in very elderly patients

Funding: The author(s) disclosed receipt of the following financial support for the research, authorship and/or publication of this article: This study was supported by AstraZeneca – Projecto OLDER (CEDOC/2015/59) and Finnee Project (PTDC/CCI-BIO/29702/2017).Though the approach used to classify chronic respiratory diseases is changing to a treatable-traits (TT) approach, data regarding very elderly patients is lacking. The objectives of this study were to assess TT frequency in very elderly patients and to study the link between extrapulmonary TT and ventilatory defects. Individuals (≥75 years) residing in elderly care centres answered a standardised questionnaire, underwent spirometry, atopy and fractional exhaled nitric oxide assessments and had their blood pressure and peripheral pulse oximetry measured. Pulmonary, extrapulmonary and behavioural TT were evaluated. Outcome variables were an airflow limitation (post-bronchodilator z-score FEV1/FVC<-1.64) and a restrictive spirometry pattern (z-score FEV1/FVC ≥ +1.64 and z-score FVC<-1.64). Seventy-two percent of the individuals who took part in the study (n = 234) were women, and the median age of participants was 86 (IQR: 7.4). At least one pulmonary TT was identified in 105 (44.9%) individuals. The most frequent extrapulmonary TTs were: persistent systemic inflammation (47.0%), anaemia (34.4%), depression (32.5%) and obesity (27.4). Airflow limitation was exclusively associated with smoking (OR 5.03; 95% CI 1.56-16.22). A restrictive spirometry pattern was associated with cognitive impairment (OR: 3.89; 95% CI: 1.55-9.79). A high frequency of various TTs was found. The novel association between a restrictive spirometry pattern and cognitive impairment highlights the urgency of clinical research on this vulnerable age group.publishersversionpublishe

A concept map template to be used by medical students for displaying pathophysiological mechanisms within clinical cases

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A scoping review comparing different mapping approaches pointing to the need for standardizing concept maps in medical education: A preliminary analysis

This study aims to analyze how visual tools, labeled as maps, are built, and used in medical education. Based on the educational model of concept maps (CMs), proposed by Novak and Cañas (2008), and adapted to medicine by Daley and Torre (2010), we are currently analyzing the results of a scoping review following the PRISMA extension methodology, specifically for these purposes. Other visual tools, such as knowledge maps (KMs) and mind maps (MMs), used in medical education, were also included. The search was made through the databases EBSCO, PubMed/MEDLINE, PsycINFO, Scopus, and Eric, using the following items: “concept map*”, “knowledge map*”, “mind map*” and “medical education”. Only articles in English were considered and exclusively in medical education, from undergraduate to resident training. The analysis of selected articles included the following features: construction rules (if they followed Novakian instructions), teaching area, student level (undergraduate, postgraduate/residents), and use for assessment. Other features were the capacity to relate basic science knowledge to clinical concepts, the use of maps with other educational methods, such as problem-based learning (PBL), and providing feedback to students. From a quantitative perspective, the use of CMs is dominant in all phases of medical education. A failure to follow Novakian rules was found in around half of the articles labeled as CMs and KMs. As for MMs, which follow different rules for construction and use, they were considered relevant in helping students to summarize and retain information. Simultaneous use with other educational methods was only found with CMs

Food Allergy and Anaphylaxis in Infants and Preschool-Age Children

Food allergy (FA) prevalence data in infants and preschool-age children are sparse, and proposed risk factors lack confirmation. In this study, 19 children’s day care centers (DCC) from 2 main Portuguese cities were selected after stratification and cluster analysis. An ISAAC’s (International Study of Asthma and Allergies in Childhood) derived health questionnaire was applied to a sample of children attending DCCs. Outcomes were FA parental report and anaphylaxis. Logistic regression was used to explore potential risk factors for reported FA. From the 2228 distributed questionnaires, 1217 were included in the analysis (54.6%). Children’s median age was 3.5 years, and 10.8% were described as ever having had FA. Current FA was reported in 5.7%. Three (0.2%) reports compatible with anaphylaxis were identified. Reported parental history of FA, personal history of atopic dermatitis, and preterm birth increased the odds for reported current FA. A high prevalence of parental-perceived FA in preschool-age children was identified. Risk factor identification may enhance better prevention

Reported Drug Allergy among Children Attending Day Care Centers

Introdução: A prevalência de alergia a fármacos na população geral não se encontra devidamente caraterizada, existindo poucos estudos publicados que tenham abordado esta situação em crianças com idades inferior a seis anos de idade. Este estudo tem como objetivo principal estimar a prevalência de alergia a medicamentos reportada pelos pais de crianças de infantários de Lisboa e do Porto. Material e Métodos: No âmbito da Fase II do projeto “ENVIRH – Ambiente e Saúde em Creches e Infantários” foi aplicado um questionário sobre alergia a medicamentos aos pais das crianças, recrutadas por amostragem aleatória estratificada dos infantários. Resultados: Foram analisados 1 169 questionários, 52,5% de rapazes. A idade média foi de 3,5 ± 1,5 anos. A prevalência de alergia a medicamentos reportada foi de 4,1% (IC 95%: 3,0 - 5,2%). Os fármacos mais referidos foram os antibióticos (em 27 reações) e os AINEs (em seis reações). Na análise multivariável, a alergia a medicamentos reportada associou-se diretamente com a idade da criança (OR 1,19; IC 95% 1,01 - 1,41) e com a referência a alergia alimentar (OR 3,19; IC95% 1,41 - 7,19) e inversamente com o nível de escolaridade dos pais (OR 0,25; IC95% 0,10 - 0,59). Discussão: Apesar das limitações do estudo, os resultados encontram-se de acordo com o reportado por outros autores e sugerem que a prevalência reportada de alergia a medicamentos seja elevada no grupo etário estudado. Conclusão: Torna-se necessário que situações de alergia a medicamentos reportadas pelos pais sejam devidamente estudadas, no sentido de evitar evicções desnecessárias que possam condicionar opções terapêuticas em futuras situações de doença