An Artificial Intelligence Method to Describe the Onset and Transition from Stochastic to Coordinated Neural Activity in Danionella Translucida Embryo

Dissertation presented as the partial requirement for obtaining a Master's degree in Data Science and Advanced Analytics, specialization in Data ScienceNos últimos anos, a aprendizagem profunda tem se tornado cada vez mais bem-sucedida quando aplicada para lidar com diferentes questões em diversos campos. Na análise de bioimagem, tem sido usada para extrair informações significativas de imagens microscópicas, onde aplicamos aprendizagem profunda a dados de microscopia de light-sheet para compreender o desenvolvimento inicial do sistema nervoso. Atualmente, sabe-se que o cérebro é responsável pela maioria de nossas ações voluntárias e involuntárias e que regula os processos fisiológicos em todo o corpo. No entanto, as barreiras técnicas deixaram muitas questões em aberto em relação ao desenvolvimento e função dos circuitos neuronais. Imagiologia provou ser uma técnica poderosa para responder a essas perguntas, embora as dificuldades em segmentar e rastrear neurônios individuais tenham retardado o progresso. Danionella translucida foi recentemente introduzida como um poderoso organismo modelo para estudos neurocientíficos devido a ter o menor cérebro de vertebrado conhecido e não desenvolver um crânio completo na idade adulta, tornando-a facilmente acessível para estudos de imagem. No entanto, o surgimento da atividade neural e subsequente montagem de circuitos neurais no desenvolvimento inicial do embrião não foi ainda caracterizado. Esta dissertação pretende fornecer uma descrição inicial de todo o processo de resolução celular, utilizando técnicas avançadas de microscopia e um método de inteligência artificial para segmentar e analisar os dados. Usamos microscopia de fluorescência de light-sheet para obter imagens do início e da coordenação da atividade neuronal da medula espinhal da Danionella translucida com alta resolução temporal e por longos períodos de tempo. Além disso, analisamos os dados com um algoritmo baseado em aprendizagem profunda para detetar, segmentar e rastrear no espaço e no tempo o sinal de cada neurônio. Focamos nossa análise nos picos de intensidade do sinal, ou seja, no momento em que os neurónios estavam a disparar, e encontramos mais atividade na região inferior do embrião, sugerindo uma correspondência com a extensão da cauda. Este trabalho demonstra que a combinação de métodos utilizados foi capaz de gerar imagens e analisar os dados com sucesso. Abre as possibilidades para um estudo mais aprofundado da rede neuronal da Danionella translucida, e para estudar sinais de imagens aglomeradas com resolução de célula única que, de outra forma, seriam muito complexas para serem analisadas

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

Mammals in Portugal: a data set of terrestrial, volant, and marine mammal occurrences in Portugal

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished georeferenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of the Azores and Madeira that includes 105,026 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (43%), sign surveys (35%), camera trapping (16%), bioacoustics surveys (4%) and radiotracking, and inquiries that represent less than 1% of the records. The data set includes 13 types of records: (1) burrows | soil mounds | tunnel, (2) capture, (3) colony, (4) dead animal | hair | skulls | jaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8), observation in shelters, (9) photo trapping | video, (10) predators diet | pellets | pine cones/nuts, (11) scat | track | ditch, (12) telemetry and (13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n =31,573) has the highest number of records followed by Chiroptera (n = 18,857), Carnivora (n = 18,594), Lagomorpha (n = 17,496), Cetartiodactyla (n = 11,568) and Eulipotyphla (n = 7008). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus [n = 12,159], Monachus monachus [n = 1,512], and Lynx pardinus [n = 197]). We believe that this data set may stimulate the publication of other European countries data sets that would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications

Tumor carcinóide do timo - Caso clínico Thymic carcinoid - case report

Os tumores neuroendócrinos primários representam cerca de 4% do total dos tumores do mediastino anterior, incluindo o timo, afectando mais homens que mulheres numa razão de 3:1 e apresentando uma maior incidência entre os 40 e os 60 anos. Antigamente classificados como timomas, desde 1972 são considerados um grupo distinto de neoplasias tímicas, podendo ser biologicamente activos, estando sobretudo associados à síndroma NEM-1 (19 a 25% dos doentes, sendo nestes casos mais agressivos). São descritos como tendo grande progressão local, recorrência e metástases em elevada percentagem de casos, o que determina um mau prognóstico. O estadiamento é o parâmetro mais importante para determinar a sobrevida. Tumores detectados em fase precoce e capsulados associam-se a um excelente prognóstico, enquanto em estádios avançados, localmente invasivos, têm prognóstico relativamente pobre. A remoção cirúrgica completa, para todos os tumores tímicos, é a base da terapêutica e o factor crítico para a sobrevivência a longo prazo, independentemente do tipo histológico. São uma causa de morte importante, nomeadamente os tumores associados a NEM-1 e síndroma de Cushing, e há autores que defendem a realização de timectomia profiláctica nestes doentes.Primary neuroendocrine tumours (carcinoid tumours) account for about 4% of anterior mediastinal tumours concerning thymus localization. They appear to have a male predilection (3:1 ratio) and occur mostly between 40 and 60 years of age. Classified primarily as thymomas, they have been considered a different group of thymic neoplasia since 1972. They can be biologically active, mostly associated with MEN-1 (19-25% of patients and more aggressive in these cases). As a locally invasive disease, with recurrence and metastasis in a high percentage of cases, it correlates with a poor prognosis. Staging is the most important determinant of survival. Encapsulated tumours diagnosed in early stages have an excellent prognosis, while locally invasive tumours in more advanced stages have a relatively poor prognosis as happens with thymomas. Complete surgical removal is the critical factor for long-term survival rates and the basis for treatment of all thymic tumours, independent of histologic type. As an important cause of death, especially in carcinoid tumours associated with MEN-1 and Cushing’s syndrome, some authors advocate the need for profilactic thymectomy in these patients

The National Student Survey: validation in Portuguese medical students

The UK National Student Survey (NSS) is a sound and widely used instrument for assessing students’ academic experiences. We aimed to translate the NSS for Portuguese students and to validate the instrument in a sample of medical undergraduates. The research team translated and adapted the NSS for Portuguese students (NSS-P). The survey was administered on an online platform to 1,256 final-year students at eight Portuguese medical schools. A total of 329 medical students (69.9% female) replied to the NSS-P, a response rate of 26.2%. Confirmatory factor analysis showed that the original six-factor structure had an adequate fit to the data. Adequate internal consistency was observed for all the subscales. Medium to large correlations were found among all the subscale scores and between the subscale scores and the students’ overall satisfaction. Multiple regression showed that the scores on the Teaching, Organization and Management and Personal Development subscales significantly predicted the students’ overall satisfaction. Approximately 64% of the students reported being satisfied with the quality of their courses. Significant differences among the medical schools in their NSS-P scores were found. The NSS-P is a valid and reliable measure for assessing medical students’ perceptions of academic quality

Assessment of calcinosis in Portuguese patients with systemic sclerosis: a multicenter study

© The Author(s), under exclusive licence to International League of Associations for Rheumatology (ILAR) 2023Introduction/objectives: The study aims to define the clinical and subclinical calcinosis prevalence, the sensitivity of radiographed site and clinical method for its diagnosis, and the phenotype of Portuguese systemic sclerosis (SSc) patients with calcinosis. Method: A cross-sectional multicenter study was conducted with SSc patients fulfilling Leroy/Medsger 2001 or ACR/EULAR 2013 classification criteria, registered in the Reuma.pt. Calcinosis was assessed through clinical examination and radiographs of hands, elbows, knees, and feet. Independent parametric or non-parametric tests, multivariate logistic regression, and sensitivity calculation of radiographed site and clinical method for calcinosis detection were performed. Results: We included 226 patients. Clinical calcinosis was described in 63 (28.1%) and radiological calcinosis in 91 (40.3%) patients, of which 37 (40.7%) were subclinical. The most sensitive location to detect calcinosis was the hand (74.7%). Sensitivity of the clinical method was 58.2%. Calcinosis patients were more often female (p = 0.008) and older (p < 0.001) and had more frequently longer disease duration (p < 0.001), limited SSc (p = 0.017), telangiectasia (p = 0.039), digital ulcers (p = 0.001), esophageal (p < 0.001) and intestinal (p = 0.003) involvements, osteoporosis (p = 0.028), and late capillaroscopic pattern (p < 0.001). In multivariate analysis, digital ulcers (OR 2.63, 95% CI 1.02-6.78, p = 0.045) predicted overall calcinosis, esophageal involvement (OR 3.52, 95% CI 1.28-9.67, p = 0.015) and osteoporosis (OR 4.1, 95% CI 1.2-14.2, p = 0.027) predicted hand calcinosis, and late capillaroscopic pattern (OR 7.6, 95% CI 1.7-34.9, p = 0.009) predicted knee calcinosis. Anti-nuclear antibody positivity was associated with less knee calcinosis (OR 0.021, 95% CI 0.001-0477, p = 0.015). Conclusions: Subclinical calcinosis high prevalence suggests that calcinosis is underdiagnosed and radiographic screening might be relevant. Multifactorial pathogenesis may explain calcinosis predictors' variability. Key Points • Prevalence of subclinical calcinosis in SSc patients is substantial. • Hand radiographs are more sensitive to detect calcinosis than other locations or clinical method. • Digital ulcers were associated with overall calcinosis, esophageal involvement and osteoporosis were associated with hand calcinosis, and late sclerodermic pattern in nailfold capillaroscopy was associated with knee calcinosis. • Anti-nuclear antibody positivity may be a protective factor for knee calcinosis.info:eu-repo/semantics/publishedVersio

Characterisation of microbial attack on archaeological bone

As part of an EU funded project to investigate the factors influencing bone preservation in the archaeological record, more than 250 bones from 41 archaeological sites in five countries spanning four climatic regions were studied for diagenetic alteration. Sites were selected to cover a range of environmental conditions and archaeological contexts. Microscopic and physical (mercury intrusion porosimetry) analyses of these bones revealed that the majority (68%) had suffered microbial attack. Furthermore, significant differences were found between animal and human bone in both the state of preservation and the type of microbial attack present. These differences in preservation might result from differences in early taphonomy of the bones. © 2003 Elsevier Science Ltd. All rights reserved

Respiratory support in patients with severe COVID-19 in the International Severe Acute Respiratory and Emerging Infection (ISARIC) COVID-19 study: a prospective, multinational, observational study

Background: Up to 30% of hospitalised patients with COVID-19 require advanced respiratory support, including high-flow nasal cannulas (HFNC), non-invasive mechanical ventilation (NIV), or invasive mechanical ventilation (IMV). We aimed to describe the clinical characteristics, outcomes and risk factors for failing non-invasive respiratory support in patients treated with severe COVID-19 during the first two years of the pandemic in high-income countries (HICs) and low middle-income countries (LMICs). Methods: This is a multinational, multicentre, prospective cohort study embedded in the ISARIC-WHO COVID-19 Clinical Characterisation Protocol. Patients with laboratory-confirmed SARS-CoV-2 infection who required hospital admission were recruited prospectively. Patients treated with HFNC, NIV, or IMV within the first 24 h of hospital admission were included in this study. Descriptive statistics, random forest, and logistic regression analyses were used to describe clinical characteristics and compare clinical outcomes among patients treated with the different types of advanced respiratory support. Results: A total of 66,565 patients were included in this study. Overall, 82.6% of patients were treated in HIC, and 40.6% were admitted to the hospital during the first pandemic wave. During the first 24 h after hospital admission, patients in HICs were more frequently treated with HFNC (48.0%), followed by NIV (38.6%) and IMV (13.4%). In contrast, patients admitted in lower- and middle-income countries (LMICs) were less frequently treated with HFNC (16.1%) and the majority received IMV (59.1%). The failure rate of non-invasive respiratory support (i.e. HFNC or NIV) was 15.5%, of which 71.2% were from HIC and 28.8% from LMIC. The variables most strongly associated with non-invasive ventilation failure, defined as progression to IMV, were high leukocyte counts at hospital admission (OR [95%CI]; 5.86 [4.83-7.10]), treatment in an LMIC (OR [95%CI]; 2.04 [1.97-2.11]), and tachypnoea at hospital admission (OR [95%CI]; 1.16 [1.14-1.18]). Patients who failed HFNC/NIV had a higher 28-day fatality ratio (OR [95%CI]; 1.27 [1.25-1.30]). Conclusions: In the present international cohort, the most frequently used advanced respiratory support was the HFNC. However, IMV was used more often in LMIC. Higher leucocyte count, tachypnoea, and treatment in LMIC were risk factors for HFNC/NIV failure. HFNC/NIV failure was related to worse clinical outcomes, such as 28-day mortality. Trial registration This is a prospective observational study; therefore, no health care interventions were applied to participants, and trial registration is not applicable

Respiratory support in patients with severe COVID-19 in the International Severe Acute Respiratory and Emerging Infection (ISARIC) COVID-19 study: a prospective, multinational, observational study

Background: Up to 30% of hospitalised patients with COVID-19 require advanced respiratory support, including high-flow nasal cannulas (HFNC), non-invasive mechanical ventilation (NIV), or invasive mechanical ventilation (IMV). We aimed to describe the clinical characteristics, outcomes and risk factors for failing non-invasive respiratory support in patients treated with severe COVID-19 during the first two years of the pandemic in high-income countries (HICs) and low middle-income countries (LMICs). Methods: This is a multinational, multicentre, prospective cohort study embedded in the ISARIC-WHO COVID-19 Clinical Characterisation Protocol. Patients with laboratory-confirmed SARS-CoV-2 infection who required hospital admission were recruited prospectively. Patients treated with HFNC, NIV, or IMV within the first 24 h of hospital admission were included in this study. Descriptive statistics, random forest, and logistic regression analyses were used to describe clinical characteristics and compare clinical outcomes among patients treated with the different types of advanced respiratory support. Results: A total of 66,565 patients were included in this study. Overall, 82.6% of patients were treated in HIC, and 40.6% were admitted to the hospital during the first pandemic wave. During the first 24 h after hospital admission, patients in HICs were more frequently treated with HFNC (48.0%), followed by NIV (38.6%) and IMV (13.4%). In contrast, patients admitted in lower- and middle-income countries (LMICs) were less frequently treated with HFNC (16.1%) and the majority received IMV (59.1%). The failure rate of non-invasive respiratory support (i.e. HFNC or NIV) was 15.5%, of which 71.2% were from HIC and 28.8% from LMIC. The variables most strongly associated with non-invasive ventilation failure, defined as progression to IMV, were high leukocyte counts at hospital admission (OR [95%CI]; 5.86 [4.83–7.10]), treatment in an LMIC (OR [95%CI]; 2.04 [1.97–2.11]), and tachypnoea at hospital admission (OR [95%CI]; 1.16 [1.14–1.18]). Patients who failed HFNC/NIV had a higher 28-day fatality ratio (OR [95%CI]; 1.27 [1.25–1.30]). Conclusions: In the present international cohort, the most frequently used advanced respiratory support was the HFNC. However, IMV was used more often in LMIC. Higher leucocyte count, tachypnoea, and treatment in LMIC were risk factors for HFNC/NIV failure. HFNC/NIV failure was related to worse clinical outcomes, such as 28-day mortality. Trial registration This is a prospective observational study; therefore, no health care interventions were applied to participants, and trial registration is not applicable