A Biomedical Entity Extraction Pipeline for Oncology Health Records in Portuguese

Textual health records of cancer patients are usually protracted and highly unstructured, making it very time-consuming for health professionals to get a complete overview of the patient's therapeutic course. As such limitations can lead to suboptimal and/or inefficient treatment procedures, healthcare providers would greatly benefit from a system that effectively summarizes the information of those records. With the advent of deep neural models, this objective has been partially attained for English clinical texts, however, the research community still lacks an effective solution for languages with limited resources. In this paper, we present the approach we developed to extract procedures, drugs, and diseases from oncology health records written in European Portuguese. This project was conducted in collaboration with the Portuguese Institute for Oncology which, besides holding over $10$ years of duly protected medical records, also provided oncologist expertise throughout the development of the project. Since there is no annotated corpus for biomedical entity extraction in Portuguese, we also present the strategy we followed in annotating the corpus for the development of the models. The final models, which combined a neural architecture with entity linking, achieved $F_1$ scores of $88.6$, $95.0$, and $55.8$ per cent in the mention extraction of procedures, drugs, and diseases, respectively

An Unusual Case of Tricuspid Stenosis

Tricuspid stenosis is an uncommon valvular abnormality commonly associated with other valvular lesions. Ebstein's anomaly is a rare congenital heart malformation characterized primarily by abnormalities of the tricuspid valve and right ventricle. Endomyocardial fibrosis is a restrictive cardiomyopathy observed in tropical and subtropical regions. It may cause right ventricular distortion with apparent apical displacement of the tricuspid valve, mimicking Ebstein’s anomaly. Eosinophilia is the most commonly cited aetiological link in endomyocardial fibrosis. Here we report the case of 42-year-old male patient who presented with heart failure and severe tricuspid stenosis where a diagnosis of hypereosinophilic syndrome was also established. This case represented a diagnostic challenge in the search for the definitive cause of the tricuspid stenosis

Size at maturity and length-weight relationships of the blurred lantern shark Etmopterus bigelowi (Squaliformes: Etmopteridae) caught off southeastern Brazil

The blurred lantern shark Etmopterus bigelowi, a deep-water squaloid shark, is globally widespread in temperate and tropical waters, but there is little available information about its biology owing to its relative rarity of capture and taxonomic confusion with its sibling species Etmopterus pusillus. Specimens used in this study were collected from July to December 2004 as by-catch in the commercial deep-water trawl fishery targeting red shrimp Aristaeomorpha foliacea in the southwestern Atlantic. We examined 55 specimens (22 males and 33 females) ranging in total length (TL) from 31.5 to 73 cm and in total weight from 103 to 1600 g. Length-weight relationships were explored for each sex and significant differences were found in the slope coefficients of the male and female regressions. The size at maturity for each sex was evaluated fitting a logistic regression. Females matured at larger sizes than males, with estimated sizes at first maturity of 56.0 cm TL for females and 45.1 cm TL for males. The present study provides important preliminary information about E. bigelowi that can be incorporated in risk assessment and stock assessment models, essential for efficient management practices aimed at avoiding overexploitation of these vulnerable deep-sea sharks.National Council for Scientific and Technological Development (CNPq, Brazil)info:eu-repo/semantics/publishedVersio

Demanda por saneamento básico no Brasil: uma análise com uso do modelo multinomial logit

Basic sanitary services, that include waste disposal, treated water supplies and sewage services, have a strong effect on human health and on the environment. Brazil stands as having a large deficit in these services which results in a decrease in the productivity of labor and losses in GDP. This study aims at estimating an exploratory sanitary service demand model for Brazil. Two complementary approaches are used. The first one is a demand model estimated by a logit type regression where the three sanitary services are jointly analyzed. The second model takes each component individually for analytical purposes. In this sense, a random utility model based on the multinomial logit is used for waste disposal and sewage. In spite of data limitation, in both models it was possible to observe that demand is sensitive to factors such as education, family background, race, location, etc. Also relevant as a determining factor is the effect of household income, being especially true for poorer households

Sequencing CYP2D6 for the detection of poor-metabolizers in post-mortem blood samples with tramadol

Tramadol concentrations and analgesic effect are dependent on the CYP2D6 enzymatic activity. It is well known that some genetic polymorphisms are responsible for the variability in the expression of this enzyme and in the individual drug response. The detection of allelic variants described as non-functional can be useful to explain some circumstances of death in the study of post-mortem cases with tramadol. A Sanger sequencing methodology was developed for the detection of genetic variants that cause absent or reduced CYP2D6 activity, such as *3, *4, *6, *8, *10 and *12 alleles. This methodology, as well as the GC/MS method for the detection and quantification of tramadol and its main metabolites in blood samples was fully validated in accordance with international guidelines. Both methodologies were successfully applied to 100 post-mortem blood samples and the relation between toxicological and genetic results evaluated. Tramadol metabolism, expressed as its metabolites concentration ratio (N-desmethyltramadol/O-desmethyltramadol), has been shown to be correlated with the poor-metabolizer phenotype based on genetic characterization. It was also demonstrated the importance of enzyme inhibitors identification in toxicological analysis. According to our knowledge, this is the first study where a CYP2D6 sequencing methodology is validated and applied to post-mortem samples, in Portugal. The developed methodology allows the data collection of post-mortem cases, which is of primordial importance to enhance the application of these genetic tools to forensic toxicology and pathology.info:eu-repo/semantics/publishedVersio

Learning from Online Voices: A Mixed Methods Approach to Explore Patient Online Reviews of Hospital Care in Portugal

Online patient reviews can offer a rich information source to users of healthcare services, as well as for hospital management and quality monitoring. Whereas in recent years the volume of online patient reviews has been consistently growing, organizations still lack standardized approaches and tools to allow for the systematic monitoring of users’ online comments. Therefore, managers are lagging in the ability to make use of such data from patients’ voices for improving the quality of the services provided. If organizations fail to develop the right capabilities to consider users’ online reviews and feedback, they risk not only to miss important quality failure alerts, as wells as to frustrate their customers’ expectations for service and attention. In this chapter, we present a qualitative analysis of patients’ reviews for healthcare services in Portugal, building on a sample of data extracted from Google for the year of 2019. The chapter reports the major quality management themes addressed by hospital users in their online expressions and offers some guidelines to support a structured analysis and visualization of results from online users’ word of mouth data

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